gebhart/patrepeval huggingface dataset:
Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook (2022)

Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
Monte Carlo Collision Simulation of Positive-Negative Ion Recombination for a Given Rate Constant (1998)

Here is proposed the Monte Carlo collision simulation method for the positive-negative ion recombination whose rate constant is given as a function of temperature. The method makes it possible to simulate a nonequilibrium state of ions in electric discharges.
Apparatus for contact angle measurements between molten salts and solids and surface tensions of molten salts at high temperatures (1966)

A vacuum-tight apparatus has been constructed for the measurement of contact angles between molten salts and solids by the sessile drop method. This same method permits direct measurement of the surface tension of the molten salts. Contact angles can be measured under different gas atmospheres and as a function of the temperature. An electrode system was adapted permitting the passage of an electric current through the solid-liquid interface.
The peptide HDEF as a new retention signal is necessary and sufficient to direct proteins to the endoplasmic reticulum (1998)

The key feature of tomato RNase LX localised solely outside the vacuole is the C-terminal peptide HDEF which is very similar to known endoplasmic reticulum (ER) retention signals. For functional testing of the ER-targeting ability of HDEF, different constructs including the complete RNase LX, two truncated forms without HDEF and the truncated chitinase FB7-1deltaVTP C-terminally flanked by HDEF, were expressed in Saccharomyces cerevisiae. The majority of RNase and chitinase, both containing HDEF, accumulates within the ER. However, the truncated constructs without the peptide are released into the medium. We provide compelling evidence that peptide HDEF at the C-terminus of secretory plant proteins is a new ER retention signal in yeast and most likely in plants.
Green route synthesis of 4-thiazolidinone analogs of isonicotinic acid hydrazide (2011)

Abstract The broad and potent activity of 4-thiazolidinones has established it as one of the biologically important scaffolds. The synthesis of N-(2-aryl-4-oxothiazolidin-3-yl)isonicotinamide by a novel method of stirring and sonication is described. The conventional method for synthesis of 4-thiazolidinones involves use of a Dean-Stark water separator for the removal of water from the reaction with long reaction times (12–48 h), and the stirring procedure also involves the use of DCC (dicyclohexylcarbodiimide) as a dehydrating agent. We report the synthesis of 4-thiazolidinone analogs of isonicotinic acid hydrazide by novel, green route methods of sonication and stirring using molecular sieves. Results indicate that high yields and shorter reaction times can be achieved by employing novel green route methods of synthesis.
Nonlinear control based on the NARX plant representation (2002)

The paper presents a two-degrees of freedom output feedback controller for nonlinear SISO systems where the plant to be controlled is represented by a discrete-time input-output model (NARX representation). As a difference to conventional internal model control, the approach is based on geometric methods. A modification of the control structure which improves robustness and is suitable for unstable plants is also given.
Temperature Dependent Deformation Mechanisms of a High Nitrogen-Manganese Austenitic Stainless Steel (2009)

The influence of temperature on the deformation behaviour of a Fe-16.5Cr-8Mn-3Ni-2Si-1Cu-0.25N (wt%) austenitic stainless steel alloy was investigated using transmission electron microscopy and X-ray diffraction measurements. Recrystallized samples were deformed under tension at −75°C, 20°C, and 200°C and the microstructures were characterized after 5% strain and after testing to failure. Deformation to failure at −75°C resulted in extensive transformation induced plasticity (TRIP) with over 90% α′-martensite. The sample deformed to 5% strain at −75°C shows that the austenite transformed first to ϵ-martensite which served to nucleate the α′-martensite. Transformation induced martensite prohibits localized necking providing total elongation to failure of over 70%. At room temperature, in addition to some TRIP behaviour, the majority of the deformation is accommodated by dislocation slip in the austenite. Some deformation induced twinning (TWIP) was also observed, although mechanical twinning provides only a small contribution to the total deformation at room temperature. Finally, dislocation slip is the dominant deformation mechanism at 200°C with a corresponding decrease in total elongation to failure. These changes in deformation behaviour are related to the temperature dependence on the relative stability of austenite and martensite as well as the changes in stacking fault energy (SFE) as a function of temperature.
Efficacy of nebulized acetylcysteine for relieving symptoms and reducing usage of expectorants in patients with radiation pneumonitis (2018)

The beneficial effects of nebulized acetylcysteine for patients with radiation pneumonitis included relieving sputum severity and minimizing expectorant use, especially in severe cases. Further investigation is required to clarify and expand on the benefits of nebulized acetylcysteine for patients with radiation pneumonitis.
Firing and Sustaining Discharge Characteristics in Alternating Current Microdischarge Cell With Three Electrodes (2004)

The firing and sustaining characteristics in an AC microdischarge cell with three electrodes are examined based on varying the distances between the three electrodes. In particular, the breakdown voltage and the sustaining voltage are measured as a parameter of the width of the discharge gap between the three electrodes. It is found that the firing and sustaining conditions vary according to the distance between the three electrodes and the discharge characteristics strongly depend on the voltage applied on the three electrode, especially with a wide discharge gap structure.
Siamese CBOW: Optimizing Word Embeddings for Sentence Representations (2016)

We present the Siamese Continuous Bag of Words (Siamese CBOW) model, a neural network for efficient estimation of high-quality sentence embeddings. Averaging the embeddings of words in a sentence has proven to be a surprisingly successful and efficient way of obtaining sentence embeddings. However, word embeddings trained with the methods currently available are not optimized for the task of sentence representation, and, thus, likely to be suboptimal. Siamese CBOW handles this problem by training word embeddings directly for the purpose of being averaged. The underlying neural network learns word embeddings by predicting, from a sentence representation, its surrounding sentences. We show the robustness of the Siamese CBOW model by evaluating it on 20 datasets stemming from a wide variety of sources.
UCN-01 inhibits p53 up-regulation and abrogates gamma-radiation-induced G(2)-M checkpoint independently of p53 by targeting both of the checkpoint kinases, Chk2 and Chk1. (2002)

UCN-01 (7-hydroxystaurosporine) is a cell-cycle checkpoint abrogator that sensitizes cells to ionizing radiation (IR) and chemotherapeutic agents. It has been shown previously that UCN-01 abrogates DNA-damage-induced G(2) checkpoint most selectively in p53-defective cells, by primarily targeting Chk1. Here we show that UCN-01 prevented IR-induced p53 up-regulation and p53 phosphorylation on serine 20, a site previously identified for Chk2 (or/and Chk1) kinase. We found that in human colon carcinoma HCT116 cells, IR treatment enhanced Chk2 kinase activity, whereas Chk1 activity remained unchanged, which suggested that UCN-01 may interrupt IR-induced p53 response by inhibiting Chk2 kinase. This conclusion is supported by in vitro kinase assays, showing that UCN-01 inhibits Chk2 immunoprecipitated from HCT116 cells (IC(50), approximately 10 nM). In addition, UCN-01 efficiently abrogated both the initiation and maintenance of IR-induced G(2) arrest in HCT116 cells and their isogenic p53 (-/-) derivative, indicating that G(2) checkpoint abrogation by UCN-01 is p53 independent. In the p53 (-/-) cells, there was no p21(Waf1/Cip1) induction nor UCN-01-induced apoptosis. Taken together, these observations indicate that UCN-01 can modulate both Chk1 and Chk2 in intact cells and enhance IR-induced apoptosis in p53-deficient, and consequently p21-deficient, cells.
Retained Capsule Endoscopy in a Large Tertiary Care Academic Practice and Radiologic Predictors of Retention (2015)

In a tertiary care population without obstructive symptoms, capsule retention occurred in only 0.3% of cases. Review of surgical history and prior imaging for obstruction or SB anastomoses may help to reduce retention.
Safety, tolerability and pharmacokinetics of oral administration of GW786034 in pts with solid tumors (2005)

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New generations of tools sets that enable FDSOI and 3-D tri-gate technologies (2012)

Today no insurmountable obstacles are foreseen inhibiting scaling logic devices to the 10nm node. Cost effective processes and equipment sets have been developed that allow both 3-D Tri-Gate and Ultra-Thin Body SOI integration schemes to be scaled. This allows the equipment industry to focus on innovations of new material and their integration into cost effective tool sets in time for high volume manufacturing in sub 10nm node technology. In this paper we review various process challenges the equipment industry overcame to enable the 3-D Tri-Gate and Ultra-Thin Body SOI architecture in partnership with integrated device manufactures.
Local and Remote Visualization Tech- niques for Interactive Direct Volume Render- ing in Neuroradiology 1 (2001)

The increasing capabilities of magnetic resonance (MR) imaging and mul-tisection spiral computed tomography (CT) to acquire volumetric datawith near-isotropic voxels make three-dimensional (3D) postprocessing anecessity, especially in studies of complex structures like intracranial ves-sels. Since most modern CT and MR imagers provide limited postpro-cessing capabilities, 3D visualization with interactive direct volume ren-dering requires expensive graphics workstations that are not available atmany institutions. An approach has been developed that combines fastvisualization on a low-cost PC system with high-quality visualization on ahigh-end graphics workstation that is directly accessed and remotely con-trolled from the PC environment via the Internet by using a Java client.For comparison of quality, both techniques were applied to several neuro-radiologic studies: visualization of structures related to the inner ear, intra-cranial aneurysms, and the brainstem and surrounding neurovascularstructures. The results of pure PC-based visualization were comparablewith those of many commercially available volume-rendering systems. Inaddition, the high-end graphics workstation with 3D texture-mappingcapabilities provides visualization results of the highest quality. Combininglocal and remote 3D visualization allows even small radiologic institutionsto achieve low-cost but high-quality 3D visualization of volumetric data.
A CALL FOR CONSISTENCY: OPEN SEAWATER INTAKES, DESALINATION, AND THE CALIFORNIA WATER CODE (2011)

This Comment argues that the federal and state standards for reducing marine life mortality from power-plant intakes should be applied to a statewide policy for new desalination projects in California. Under this framework, open seawater intakes should not be permitted for new desalination plants. Part II of this Comment provides an overview of the history and technology of desalination as well as environmental impacts of open seawater intakes and alternative intake technologies. Part III surveys existing state and federal laws addressing open seawater intakes and suggests a framework for applying these laws to desalination projects. Part IV argues that new desalination plants should not be permitted to use open seawater intakes because doing so would be inconsistent with California law and would undercut other California efforts to protect marine life. Part V presents the Carlsbad Desalination Project as a case study of how existing state law has been improperly applied to grant water permits. Part VI concludes with a summary of why a statewide desalination policy should be implemented consistent with state law.
Coherent integration of photonics on silicon through the growth of nanostructures on GaP/Si (2011)

Selected results obtained in the framework of MBE grown nanostructure for photonics on silicon are repsented in this paper. We present first a comprehensive study of GaAsPN/GaPN quantum wells (QWs) grown onto GaP substrates, in the light of a comparison with their N-free GaAsP/GaP QWs counterpart system. High density of small InGaAs/GaP Quantum Dots are presented next with their PL properties. Finally, RT photoluminescence properties of GaAsPN/GaPN QWs onto Si substrate are presented and discussed in term of carrier injection efficiency. However, for future development, optical properties of the active area must be improved and are tightly bound to the structural perfection of the GaP/Si template layer. To address this point, structural analyses including X-Ray Diffraction (lab setup and synchrotron) and Transmission Electron Microscopy have been performed, with a particular care for typical III-V/Si defect characterisation. First results of Si buffer layer growth are also presented as a perspective for future low defect MBE grown GaP/Si template layers.
Anti-oncogenic effects of tropomyosin: isoform specificity and importance of protein coding sequences. (1996)

Suppression of muscle type isoforms of tropomyosin (TM) is a common biochemical event in malignantly transformed cells. To evaluate the role of TM proteins and isoform specificity in cellular transformation, cDNAs that consist of coding sequences of TM1 (product of beta gene) and TM2 (product of alpha gene), but lacking untranslated regions (UTRs), have been expressed separately in DT (v-Ki-ras transformed NIH3T3) cells, and elevated levels of the corresponding proteins were detected. DT cells which over express TM2 manifest growth in soft agar. Elevated levels of TM1 protein in DT cells resulted in flattened cell morphology and complete abolition of anchorage independent growth. Tumorigenesis in athymic nude mice was observed in the absence of transduced TM1 mRNA. Thus, expression of TM1 protein is sufficient for tumor suppression: the UTRs of TM1 are not required for the tumor suppressive effects. Expression of TM2 protein, on the other hand, has no effect on the transformed phenotype of DT cells. These data indicate that isoforms 1 and 2 of TMs perform distinct physiological roles.
Generation and validation of a formula to calculate hemoglobin loss on a cohort of healthy adults subjected to controlled blood loss (2021)

The resulting formula will allow objective benchmarking of surgical blood loss, enabling informed decision making as to the need for pre-operative type-and-cross only vs. reservation of packed red cell units, depending on a patient's anemia tolerance, and thus contributing to resource management.
Demonstrating a Personalized Secure-by-Default Bring Your Own Device Solution Based on Software Defined Networking. (2016)

Network virtualization is one classical use-case for Software Defined Networks (SDN). By programmatically instantiating virtual networks, traffic from one or more devices can be separated or connectivity can be established as needed. S-BYOD, which is presented in this demonstration, applies the SDN concept to Bring Your Own Device (BYOD) scenarios and offers personalized virtual networks that are set up and extended on demand. This is done once the user authenticates, activates access to additional applications, or as soon as applications scale out and involve more servers. The described proof-of-concept implementation explores, to what degree an agent-less BYOD solution, based only on SDN, can lower the attack surface by explicit user opt-ins for particular services. Further, an assessment of the number of required rules within the flow tables of switches completes this work.
Direct visualization of initial SEI morphology and growth kinetics during lithium deposition by in situ electrochemical transmission electron microscopy (2013)

Deposition of Li is a major safety concern existing in Li-ion secondary batteries. Here we perform the first in situ high spatial resolution measurement coupled with real-time quantitative electrochemistry to characterize SEI formation on gold using a standard battery electrolyte. We demonstrate that a dendritic SEI forms prior to Li deposition and that it remains on the surface after Li electrodissolution.
Coupling between Progressive Mechanical Damage, Temperature and Permeability of Concrete: Experimental and Numerical Study (2006)

International audience
Regiospecific substitution of pyridine by trialkylalkynylborates in the presence of acetyl chloride (1974)

An outline is given of a novel, versatile, and gentle process which involves trialkylalkynylborates and leads specifically to 4-substituted dihydropyridines.
Exploiting System Dynamics for Resource-Efficient Automotive CPS Design (2019)

Automotive embedded systems are safety-critical, while being highly cost-sensitive at the same time. The former requires resource dimensioning that accounts for the worst case, even if such a case occurs infrequently, while this is in conflict with the latter requirement. In order to manage both of these aspects at the same time, one research direction being explored is to dynamically assign a mixture of resources based on needs and priorities of different tasks. Along this direction, in this paper we show that by properly modeling the physical dynamics of the systems that an automotive control software interacts with, it is possible to better save resources while still guaranteeing safety properties. Towards this, we focus on a distributed controller implementation that uses an automotive FlexRay bus. Our approach combines techniques from timing/schedulability analysis and control theory and shows the significance of synergistically combining the cyber component and physical processes in the cyber-physical systems (CPS) design paradigm.
An Investigation of the Effects of Film Cooling in a High-Pressure Aeroengine Turbine Stage (2005)

Cooling is required to enable the turbine components to survive and have acceptable life in the very high gas temperatures occurring in modern engines. The cooling air is bled from the compression system, with typically about 15% of the core flow being diverted in military engines and about 20% in civil turbofans. Cooling benefits engine specific thrust and efficiency by allowing higher cycle temperatures to be employed, but the bleed air imposes cycle penalties and also reduces the aerodynamic efficiency of the turbine blading, typically by 2–4%. Cooling research aims to develop and validate improved design methodologies that give maximum cooling effectiveness for minimum cooling flow. This paper documents external cooling research undertaken in the Isentropic Light Piston Facility at QinetiQ as part of a European collaborative programme on turbine aerodynamics and heat transfer. In Phase I, neither the ngv nor the rotor was cooled; cooling was added to the ngv only for Phase II, and to the rotor and ngv in Phase III. Coolant blowing rates and density ratios were also varied in the experiments. This paper describes the ILPF and summarises the results of this systematic programme, paying particular attention to the variation in aerofoil heat transfer with changing coolant conditions, and the effects coolant ejection has on the aerofoil’s aerodynamic performance.
Steady‐State Composition Profiles in Mixed Molten Salt Electrochemical Devices: I . Lithium/Sulfur Battery Analogs (1978)

During charge or discharge of batteries with a binary molten salt mixture as the electrolyte, composition gradients are produced by the electrode reactions and the differences in mobilities of the electroactive and nonelectroactive ions. The effects of current density, electrode separation, and initial composition of the electrolyte are predicted by an analytical solution of the flux equations derived with transport properties similar to those of mixtures. Numerical solution of the flux equations predicts the composition profiles in lithium sulfur battery analogs with mixtures of differing compositions. Either complete depletion of the electroactive constituent at one electrode, or precipitation of a solid phase at the electrodes, could result from the predicted composition gradients. Changes in electrolyte composition at the electrodes may also affect J‐phase formation at the sulfur electrode during discharge.
DNA condensation in two dimensions (2000)

We have found that divalent electrolyte counterions common in biological cells (Ca(2+), Mg(2+), and Mn(2+) ) can condense anionic DNA molecules confined to two-dimensional cationic surfaces. DNA-condensing agents in vivo include cationic histones and polyamines spermidine and spermine with sufficiently high valence (Z) 3 or larger. In vitro studies show that electrostatic forces between DNA chains in bulk aqueous solution containing divalent counterions remain purely repulsive, and DNA condensation requires counterion valence Z >/= 3. In striking contrast to bulk behavior, synchrotron x-ray diffraction and optical absorption experiments show that above a critical divalent counterion concentration the electrostatic forces between DNA chains adsorbed on surfaces of cationic membranes reverse from repulsive to attractive and lead to a chain collapse transition into a condensed phase of DNA tethered by divalent counterions. This demonstrates the importance of spatial dimensionality to intermolecular interactions where nonspecific counterion-induced electrostatic attractions between the like-charged polyelectrolytes overwhelm the electrostatic repulsions on a surface for Z = 2. This new phase, with a one-dimensional counterion liquid trapped between DNA chains at a density of 0.63 counterions per DNA bp, represents the most compact state of DNA on a surface in vitro and suggests applications in high-density storage of genetic information and organo-metallic materials processing.