gebhart/patrepeval huggingface dataset:
Timing is everything: cell cycle control of Rad52 (2010)

Regulation of the repair of DNA double-strand breaks by homologous recombination is extremely important for both cell viability and the maintenance of genomic integrity. Modulation of double-strand break repair in the yeast Saccharomyces cerevisiae involves controlling the recruitment of one of the central recombination proteins, Rad52, to sites of DNA lesions. The Rad52 protein, which plays a role in strand exchange and the annealing of single strand DNA, is positively regulated upon entry into S phase, repressed during the intra-S phase checkpoint, and undergoes posttranslational modification events such as phosphorylation and sumoylation. These processes all contribute to the timing of Rad52 recruitment, its stability and function. Here, we summarize the regulatory events affecting the Rad52 protein and discuss how this regulation impacts DNA repair and cell survival.
275. Prostate Targeting Peptides Via the Prostate Specific Membrane Antigen (2004)

Background A genetically modified HSV1, JS1/ICP34.5-/ICP47-, incorporating the hGM-CSF transgene and which selectively replicates and kills tumour cells, is being tested in a Phase I clinical trial in a number of solid tumours. The preliminary results are encouraging and planning for a Phase II clinical trial in combination with chemotherapy in breast cancer is underway. Tumour selectivity is conferred by the deletion of ICP34.5, which is also an anti-apoptotic gene. Deletion of ICP47, which blocks antigen presentation, and the insertion of GM-CSF aims to enhance the immune response to infected malignant cells. The aim of the in vitro work was to assess the effects of combining the virus and paclitaxel in breast cancer cell lines and to study the mechanism of action of the virus, paclitaxel and the combination of the two.
NPBDREG: A Non-parametric Bayesian Deep-Learning Based Approach for Diffeomorphic Brain MRI Registration (2021)

Quantification of uncertainty in deep-neural-networks (DNN) based image registration algorithms plays an important role in the safe deployment of real-world medical applications and research-oriented processing pipelines, and in improving generalization capabilities. Currently available approaches for uncertainty estimation, including the variational encoder-decoder architecture and the inference-time dropout approach, require specific network architectures and assume parametric distribution of the latent space which may result in sub-optimal characterization of the posterior distribution for the predicted deformation-fields. We introduce the NPBDREG, a fully non-parametric Bayesian framework for unsupervised DNN-based deformable image registration by combining an \texttt{Adam} optimizer with stochastic gradient Langevin dynamics (SGLD) to characterize the true posterior distribution through posterior sampling. The NPBDREG provides a principled non-parametric way to characterize the true posterior distribution, thus providing improved uncertainty estimates and confidence measures in a theoretically well-founded and computationally efficient way. We demonstrated the added-value of NPBDREG, compared to the baseline probabilistic \texttt{VoxelMorph} unsupervised model (PrVXM), on brain MRI images registration using $390$ image pairs from four publicly available databases: MGH10, CMUC12, ISBR18 and LPBA40. The NPBDREG shows a slight improvement in the registration accuracy compared to PrVXM (Dice score of $0.73$ vs. $0.68$, $p \ll 0.01$), a better generalization capability for data corrupted by a mixed structure noise (e.g Dice score of $0.729$ vs. $0.686$ for $\alpha=0.2$) and last but foremost, a significantly better correlation of the predicted uncertainty with out-of-distribution data ($r>0.95$ vs. $r<0.5$).
Active vibration control of a simply supported beam using a spatially distributed actuator (1987)

The application of a spatially shaped distributed actuator for the vibration control of a simply supported beam is studied both analytically and experimentally. The actuator consists of a layer of polyvinylidene fluoride (PVF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) bonded to one face of the beam. A summary of the underlying theory is presented, with emphasis on how controllability requirements affect the choice of the film's spatial distribution. The requisite film controller has a linearly varying spatial distribution that facilitates the control of both even- and odd-order vibrational modes. Experimental results are presented for the control of the beam's first three modes, using both the linearly varying as well as a uniform spatial distribution. The linearly varying distribution is shown to be effective in controlling both even- and odd-order modes, serving to increase the modal loss factors by up to a factor of 4.5. In addition, the experimental results are found to corroborate a simplified computer model of the controller.
Outdoor Scene Synthesis in the Infrared Range for Remote Sensing Applications (2002)

International audience
43.1: Invited Paper : UB‐FFS: New Materials for Advanced Mobile Applications (2015)

In the recent years, displays for mobile electronic devices have been revolutionized, mostly driven by smartphones and tablets. Strongest trends are (besides growing sizes) the ever‐increasing resolution, improved contrast, very good viewing angle and color performance. This went hand in hand with a trend to more “refined” display technologies, namely fringe field switching (FFS). Now, as the latest step, Ultra‐Brightness (UB‐) FFS is at the brink to widespread commercialization in mobile and IT displays. It can provide transmittance improvement of more than 15%. The Liquid Crystal (LC) plays a key role here, because UB‐FFS uses LCs with negative dielectric anisotropy — whereas “traditional” FFS uses LCs with positive dielectric anisotropy. There are two key challenges. First is providing LCs with a fast switching speed. Second point is keeping the high reliability level of FFS even though completely different materials with much higher challenges on reliability are used. In this paper the recent progress for both key points will be discussed.
Deep learning for monaural speech separation (2014)

Monaural source separation is useful for many real-world applications though it is a challenging problem. In this paper, we study deep learning for monaural speech separation. We propose the joint optimization of the deep learning models (deep neural networks and recurrent neural networks) with an extra masking layer, which enforces a reconstruction constraint. Moreover, we explore a discriminative training criterion for the neural networks to further enhance the separation performance. We evaluate our approaches using the TIMIT speech corpus for a monaural speech separation task. Our proposed models achieve about 3.8∼4.9 dB SIR gain compared to NMF models, while maintaining better SDRs and SARs.
The Effect of Transcranial Direct Current Stimulation on Jaw Motor Function Is Task Dependent: Speech, Syllable Repetition and Chewing (2018)

Motor cortex transcranial direct current stimulation (tDCS) has been shown to enhance motor learning in healthy adults as well as various neurological conditions. However, there has been limited data on whether tDCS enhances jaw motor performance during different oral behaviors such as speech, maximum syllable repetition, and chewing. Because the effects of anodal and cathodal stimulation are known to be dependent on task demands, we hypothesized that tDCS would have a distinct effect on the jaw motor performance during these disparate oral behaviors. Ten healthy adults completed speech, maximum syllable repetition, and chewing tasks as their jaw movements were recorded using 3D optical motion capture during sham, anodal, and cathodal tDCS. Our findings showed that compared to the sham condition, jaw displacements during speech and syllable repetition were smaller during anodal stimulation, but larger during cathodal stimulation for syllable repetition and chewing indicating improved performance during anodal tDCS. On the other hand, there were no effects of anodal tDCS during chewing. These results confirm our hypotheses that: (1) tDCS induces a significant effect on jaw motor function; (2) its effects are polarity dependent; and (3) its effects are dependent on the task demands on jaw motor function. These findings support future studies exploring the effects of tDCS on persons with oral sensorimotor impairments and the development of therapeutic protocols.
Haemodynamic, pathological, haematological and behavioural changes during endotoxin infusion in equine neonates (1990)

The purpose of this study was to evaluate the effects of experimentally induced sublethal endotoxaemia in equine neonates. Four foals, between two and five days of age, were infused intravenously with 0.5 microgram/kg bodyweight of Salmonella typhimurium endotoxin (LPS) over a 5 h period. A four-day-old and a five-day-old foal, similarly infused with sterile isotonic saline, served as controls. Clinical signs were monitored, blood samples obtained for evaluation of selected haematological and biochemical parameters; and haemodynamic parameters were recorded hourly during the infusion, as well as 6 and 24 h post infusion. Depression, anorexia, increased rectal temperature, leucopenia followed by leucocytosis, hypoglycaemia, increased prothrombin time, partial thromboplastin time (APTT), pulmonary artery pressure, pulmonary artery wedge pressure, right atrial pressure, pulmonary and systemic vascular resistance and mild hypoxaemia were consistent findings in the foals receiving endotoxin. There was marked variation over time in the above parameters, during the infusion. Shock was not induced, and the foals appeared to be healthy shortly after the infusion was discontinued. The return to baseline values of body temperature (3 of 4 foals), APTT (1 of 4 foals) and neutrophil count (2 of 4 foals), during endotoxin infusion, suggests induction of early tolerance. The control foals remained alert and the temperature, prothrombin time and fibrinogen remained stable during the study. Hyperglycaemia, transient increased APTT and variations in selected haemodynamic parameters were recorded in the control foals during the infusion.
Radical prostatectomy for high-risk clinically localized prostate cancer: a prospective single institution series (2011)

Radical prostatectomy is associated with favourable biochemical progression-free, clinical and overall survival in selected men with high-risk localized prostate cancer, and should therefore be considered an option in these patients. Baseline PSA >20 ng/mL is a significant independent predictor of PSA recurrence.
Failure of Spectra® Polyethylene Fiber-Reinforced Composites under Ballistic Impact Loading (1994)

Failure modes of Spectra polyethylene fiber-reinforced composites were examined under ballistic impact loading. Both woven fabric-reinforced laminates and angle-plied unidirectional fiber-reinforced laminates were found to exhibit sequential delamination, cut-out of a plug induced by through-the-thickness shear, and combined modes of shear and tensile failure offibers as obserxed in the cases of glass and graphite fiber composites. At low areal density, both laminates demonstrated similar ballistic limits. However, as areal density increased, differences in ballistic limit became more apparent, with angle-plied composite laminates showing higher values. When subjected to the repeated impact of a constant striking velocity below the ballistic limit, a progressive growth of local delamination was observed until gross failure of composites occurred. The use of lower striking velocity of the projectile led to the increase in cumulative numbers of impacts for full penetration defining an impact fatigue lifetime profile. The results of impact testing indicated that Spectra fiber-reinforced composites with vinyl ester resin matrix have a higher ballistic limit and longer impact fatigue life at a given striking velocity than the polyurethane matrix composites. Less effective absorption of impact energy by flexible polyurethane matrix composites was attributed to much more restrained pattern of delamination growth. Correlated with the results of dynamic mechanical analysis, these trends indicated that the stiffness of resin matrices plays an important role in controlling the ballistic impact resistance of Spectra fiber composites. Damping factor and resultant stress wave attenuation characteristics of materials seem to be less important parameters.
Chemical dynamics of d1-methyldiacetylene (CH3CCCCD; X 1A1) and d1-ethynylallene (H2CCCH(C2D); X 1A′) formation from reaction of C2D(X 2Σ+) with methylacetylene, CH3CCH(X 1A1) (2001)

The crossed beam reaction of the d1-ethynyl radical C2D(X 2Σ+), with methylacetylene, CH3CCH(X 1A1), was investigated at an average collision energy of 39.8 kJ mol−1. Our experimental results were combined with electronic structure calculations. The chemical reaction dynamics are indirect, involve three distinct channels, and are initiated via a barrierless addition of C2D to the acetylenic bond through long lived cis and trans CH3CCH(C2D), 1-ethynylpropen-2-yl, intermediates. The reduced cone of acceptance of the carbon atom holding the methyl group favors a carbon–carbon σ bond formation at the carbon atom adjacent to the acetylenic hydrogen atom. A crossed beam experiment of C2D with partially deuterated methylacetylene, CD3CCH, shows explicitly that the reactive intermediates decompose to form both methyldiacetylene, CD3CCCCD (channel 1, 70%–90%), and to a minor amount ethynylallene, D2CCCH(C2D) (channel 2; 10%–30%), isomers through exit transition states located 7–15 kJ mol−1 above the products. The computed reaction energies to form both isomers are −135 and −107 kJ mol−1, respectively, with respect to the separated reactants. A minor reaction pathway involves a H shift in CH3CCH(C2D) to an 1-ethynylpropen-1-yl radical which fragments to methyldiacetylene via a barrier of 8.8 kJ mol−1 (channel 3). Neither methyl group elimination nor the formation of the CC(CH3)(C2D) carbene was observed in our experiments. The experimentally observed “sideways scattering” and ab initio investigation verify our conclusions of a predominate formation of the methyldiacetylene isomer. These electronic structure calculations depict a hydrogen atom loss in the exit transition state to methyldiacetylene almost parallel to the total angular momentum vector J as found in our center-of-mass angular distribution. Since the title reaction and the corresponding reaction of the C2H radical with CH3CCH both have no entrance barriers, are exothermic, and all the involved transition states are located well below the energy of the separated reactants, the assignment of the ethynyl versus H atom exchange suggests the formation of both isomers under single collision conditions in extraterrestrial environments such as cold, molecular clouds as well as the atmosphere of Saturn’s moon Titan.
Cytokine Genes and Pain Severity in Lung Cancer: Exploring the Influence of TNF-α-308 G/A IL6-174G/C and IL8-251T/A (2007)

In this preliminary analysis, we found evidence of the influence of cytokine genes on pain in White patients with lung cancer. Additional larger studies are needed to validate our findings. The long-term application is to tailored pain therapies.
Phobic Anxiety and Risk of Coronary Heart Disease and Sudden Cardiac Death Among Women (2005)

These prospective data suggest that high levels of phobic anxiety are associated with an increased risk of fatal CHD, particularly from SCD. Some but not all of this risk can be accounted for by CHD risk factors associated with phobic anxiety.
ATTfold: RNA Secondary Structure Prediction With Pseudoknots Based on Attention Mechanism (2020)

Accurate RNA secondary structure information is the cornerstone of gene function research and RNA tertiary structure prediction. However, most traditional RNA secondary structure prediction algorithms are based on the dynamic programming (DP) algorithm, according to the minimum free energy theory, with both hard and soft constraints. The accuracy is particularly dependent on the accuracy of soft constraints (from experimental data like chemical and enzyme detection). With the elongation of the RNA sequence, the time complexity of DP-based algorithms will increase geometrically, as a result, they are not good at coping with relatively long sequences. Furthermore, due to the complexity of the pseudoknots structure, the secondary structure prediction method, based on traditional algorithms, has great defects which cannot predict the secondary structure with pseudoknots well. Therefore, few algorithms have been available for pseudoknots prediction in the past. The ATTfold algorithm proposed in this article is a deep learning algorithm based on an attention mechanism. It analyzes the global information of the RNA sequence via the characteristics of the attention mechanism, focuses on the correlation between paired bases, and solves the problem of long sequence prediction. Moreover, this algorithm also extracts the effective multi-dimensional features from a great number of RNA sequences and structure information, by combining the exclusive hard constraints of RNA secondary structure. Hence, it accurately determines the pairing position of each base, and obtains the real and effective RNA secondary structure, including pseudoknots. Finally, after training the ATTfold algorithm model through tens of thousands of RNA sequences and their real secondary structures, this algorithm was compared with four classic RNA secondary structure prediction algorithms. The results show that our algorithm significantly outperforms others and more accurately showed the secondary structure of RNA. As the data in RNA sequence databases increase, our deep learning-based algorithm will have superior performance. In the future, this kind of algorithm will be more indispensable.
Computational-Fluid-Dynamics- and Computational-Structural-Dynamics-Based Time-Accurate Aeroelasticity of Helicopter Rotor Blades (2010)

A modular capability to compute dynamic aeroelastic characteristics of rotor blades using the Euler/Navier-Stokes flow equations and finite element structural equations is presented. The approach is based on a time-accurate analysis procedure that is suitable for nonlinear fluid-structure interaction problems. Fluids and structural solvers are time-accurately coupled in the C++ environment. Unsteady aerodynamic and aeroelastic results are validated with experimental data for nonrotating and rotating isolated blades.
Densification of Submicron YSZ (Yttria-Stabilized Zirconia) Powders with Alumina and Borate Additives. (1984)

Precipitated yttria (8.0 wt%) stabilized zirconia powders (YSZ) were sintered in the range 1150-1350 using Al203 and B203 as flux additions. A (2:1) Al203:B203 additive mixture at approximately 2 vol% concentration, gave significant densification when sintered at 1200 Cl/1 hr. Washing of the powders to remove residual Cl was necessary to achieve high densification below 1300 C. Samples obtained were optically translucent at 1 mm thickness with average grain size 0.2-0.4 micrometer. Mechanical, thermal and electrical properties were not degraded by the flux additions to YSZ. Densification by liquid phase sintering was determined for both B203 and Al203. Excess Al203 was found to exist as discrete particles in the YSZ matrix. Depletion of yttria from the grain matrix was observed with the flux additions but non-cubic phase transitions were not evident.
Lightweight Directory Access Protocol (LDAP): String Representation of Search Filters (2006)

Lightweight Directory Access Protocol (LDAP) search filters are
transmitted in the LDAP protocol using a binary representation that is
appropriate for use on the network. This document defines a human-
readable string representation of LDAP search filters that is
appropriate for use in LDAP URLs (RFC 4516) and in other applications.
[STANDARDS-TRACK]
Empreinte: New Horizons for Pipelines Integrity Assessment (2013)

Abstract Integrity assessment of pipelines exhibiting defects becomes more and more an issue in the oil and gas industry in particular because of field lifetime extension. Three levels of defects assessments can be distinguished:" Level 1 " assessments are based on very simplified acceptance criteria such as a dent depth. They are very conservative and their main advantage is to allow assessments in very short time period." Level 2 " assessments are based on analytical/empirical models supported by full scale testing. In principle, they cannot be used outside the conditions covered by full scale tests." Level 3 " assessments are based on advanced calculations such as finite elements. They allow reducing conservatisms but they need detailed material data and are, in general, very time consuming. The goal of " Empreinte " is to perform reasonably conservative " level 3 " assessments in a very short time period (typically within 48 hours from defect discovery to assessment). " Empreinte " is basically a pre and post processor to Abaqus finite element calculations. It was originally developed to assess the integrity of pipelines exhibiting severe dents with taking into account that when a dent is discovered, the only available information is, most of the time, the actual pipe geometry (defect profile and remaining wall thickness). The principle of " Empreinte " is to use the final pipe profile to design back a " virtual tool " from which the damaging process is modeled. Then, the burst strength of the damaged pipe is determined from finite element calculations. This actual burst strength is used to derive a safe operating pressure. " Empreinte " validation is supported by full scale tests in various conditions. It includes criteria to capture failure by plastic collapse and by ductile fracture after significant damage development. " Empreinte " has been recently extended to the assessment of dents submitted to cyclic loading conditions using the Dang Van criterion. The enlargement of " Empreinte " validation tests database has to be a continuous effort. Updating materials data requirements for next pipeline projects is also a target. " Empreinte " has already been successfully used. " Empreinte " can be used for design purposes (risk assessments) or for integrity assessments.
Hosting capacity analysis of many distributed photovoltaic systems in future distribution networks (2017)

Installation of photovoltaic (PV) systems need to be accelerated much for the mitigation of climate change. This paper targets on huge penetration of distributed PV systems into feeders, of which the total PV capacity is several or several ten times of the existing load. Three kinds of countermeasures, improvement of conductor sizes, partial boosting voltage, smart invertors, and their combinations were analyzed with the criteria of the PV hosting capacity. Simulation results suggested that, without PV reactive power control, the increase of the hosting capacity for improvement of conductor size and boosting voltage were limited because of voltage rise in low voltage networks. The combination of the three kinds of countermeasures were necessary for the huge penetration of distributed PV systems. In such cases, the voltage needed to drop in the middle voltage networks in order to compensate the voltage rise in low voltage networks.
Temperature Measurement on Micro-Area of Specimen in TEM by Using Thermal Diffuse Scattering Effect (1990)

The intensity of beam current through a specimen film changes as a function of the temperature due to the thermal diffuse scattering. This feature is applied to temperature measurement. The measuring region is restricted to a small area of about 1 μm in diameter by the method of selected area diffraction. As the beam intensity from the center spot in diffraction mode decreases almost in proportion to increase of the temperature, it is expected that the local temperature can be measured from the variation of the beam intensity in a high spatial and temporal resolution although some other parameters affect the beam intensity.