gebhart/patrepeval huggingface dataset:
Fonctionnement et assemblage du complexe de membrane interne du systeme de transport du maltose et des maltodextrines d'escherichia coli (1998)

Les transporteurs a atp binding cassette sont caracterises par une organisation en quatre domaines : deux domaines hydrophobes qui forment un site de reconnaissance de substrat, et deux domaines hydrophiles conserves qui hydrolysent l'atp, source d'energie du transport. Ces transporteurs servent a l'import ou l'export de substrats varies en taille et nature chimique et jouent un role important en sante humaine. Mais la comprehension du mecanisme moleculaire du transport est encore imparfaite. Nous nous sommes interesses au role des interactions proteine-proteine dans le systeme modele du complexe de membrane interne du systeme de transport du maltose d'escherichia coli. Ce transporteur est constitue de quatre polypeptides : malf et malg, les domaines hydrophobes, qui servent a l'accrochage de deux copies de malk, les domaines hydrophiles. Nous avons etudie par mutagenese dirigee le role fonctionnel d'une boucle cytoplasmique conservee de malf et malg, la region eaa. Nous avons montre que cette region sert a l'interaction avec un domaine dit helical de malk. En incubant la proteine malk purifiee avec des vesicules a la topologie inversee contennant malf et malg, nous avons reconstitue un transporteur fonctionnel. En utilisant cette approche nous avons montre que la fixation de l'atp module l'interaction entre malk et malf-malg. La fixation de l'atp induit un changement de conformation de malk, et un site de son domaine helical devient accessible a la proteolyse. Ce site est protege de l'attaque d'une protease par la presence de malf-malg, suggerant de nouveau que ce domaine est implique dans les interactions avec malf-malg. Enfin, nous avons montre que l'insertion dans la membrane de malf surproduite sans malg induit une reponse de stress extracytoplasmique. Une grande boucle periplasmique de malf en est la cause et la presence de malg abolit cette induction, suggerant que l'interaction entre malf et malg joue un role important dans le repliement correct de malf.
How important is spatial phase in texture segmentation and contour integration? (2010)

In a recent study by Huang, Kingdom, and Hess, (VSS 2005) it was suggested that the visual system has only two phase mechanisms, namely +cosine and -cosine. This suggests rather limited access to the rich distribution of receptive field phase that neurophysiologists tell us are represented in the different response profiles of striate simple cells. While that study has suggested that striate receptive field phase is not directly available to perception for the detection/discrimination of localized stimuli, here we investigate whether such information might be utilized in more integrative texture segmentation and contour integration tasks. Specifically, given that simple cells have different local absolute phase response profiles, we ask whether a network of simple cells with similar phase preferences can interact in such a way as to extract textures and/or contours on the basis of phase alone. Accordingly, we designed two novel 4AFC texture segmentation experiments and one 2AFC contour integration experiment both using random-phase fields of log-Gabors with embedded sub-regions of same-phase elements with the intention of providing an answer to the question of how useful is local absolute spatial phase for texture segmentation and contour integration. The results add further support to the proposition that, at the perceptual level, only two phase mechanisms (±cosine) are available, be it for the detection/discrimination of an isolated feature or the segmentation/integration of globally distributed features.
Flexible and Programmable Pulse Shaping MOPA Fiber Laser Platform, Performances and Applications (2013)

Optical fiber amplifiers used in a MOPA architecture open up a lot of possibilities for developing flexible laser sources, thanks to their efficiency, their high single-pass gain, broad spectral gain bandwidth and intrinsic high beam quality and stability. Combining fiber amplifiers with advanced digital electronics, used for synchronizing and modulating high-speed signals for the generation of programmable nanosecond pulse shapes and bursts of picosecond pulses, can make remarkable laser sources offering unprecedented opportunities for the exploration of laser-matter interactions on a wide and fine scale. Those monolithic laser sources show great potential as development tools for speeding up the optimization of laser materials processing as well as sufficient maturity and robustness to be used as single, multi-role laser sources, working in industrial environment and performing multiple tasks requiring wildly varying laser parameters.
Deep Mouse: An End-to-end Auto-context Refinement Framework for Brain Ventricle and Body Segmentation in Embryonic Mice Ultrasound Volumes (2019)

High-frequency ultrasound (HFU) is well suited for imaging embryonic mice due to its noninvasive and real-time characteristics. However, manual segmentation of the brain ventricles (BVs) and body requires substantial time and expertise. This work proposes a novel deep learning based end-to-end auto-context refinement framework, consisting of two stages. The first stage produces a low resolution segmentation of the BV and body simultaneously. The resulting probability map for each object (BV or body) is then used to crop a region of interest (ROI) around the target object in both the original image and the probability map to provide context to the refinement segmentation network. Joint training of the two stages provides significant improvement in Dice Similarity Coefficient (DSC) over using only the first stage (0.818 to 0.906 for the BV, and 0.919 to 0.934 for the body). The proposed method significantly reduces the inference time (102.36 to 0.09 s/volume around 1000x faster) while slightly improves the segmentation accuracy over the previous methods using slide-window approaches.
Grammont’s Idea: The Story of Paul Grammont’s Functional Surgery Concept and the Development of the Reverse Principle (2011)

The development of the modern reverse prosthesis is the result of the intellectual and experimental work conducted by Grammont and his team for 20 years. Knowledge of this history is essential to envision future developments.
Fiber Bundle Based Fluorescence Tomography System for Human Breast Imaging (2009)

Fluorescence diffuse optical tomography (FT) is a promising molecular imaging technique that can spatially resolve both fluorophore concentration and lifetime parameters. In this phantom study, we built a photo-multiplier tube (PMT) based single detection system that uses fiber bundles to collect light. Measurements were acquired both with a 1 mm diameter single fiber and a 6 mm diameter fiber bundle using the very same detection unit for comparison purposes. We demonstratethat the fluorescence concentration and lifetime can be well recovered for 6 mm diameter objects deeply embedded in an 80 mm diameter breast-sized phantom when the fiber bundle is utilized.
Clap Detection and Discrimination for Rhythm Therapy (2006)

An auditory training system relies on determining how well individual users can clap their hands together 'in time' with a prompt. Because the system is intended for a scenario in which an entire class of students is simultaneously engaged in this training, each system must distinguish between the claps of a single user and background claps from other nearby users. Available cues for this discrimination include the absolute energy of the clap sound, its source azimuth (estimated from stereo microphones), and its range as conveyed by the direct-to-reverberant energy balance. We present a set of features to capture these cues, and report our results on detecting and distinguishing 'near-field' and 'far-field' claps in a corpus of 1650 claps recorded in realistic classroom environments. When room and location are matched between training and test data, the classification error rate falls as low as 0.13%; when training data is recorded from a separate room, the error rate is still below 4.8% in the worst case.
Anti-COX-2 autoantibody is a novel biomarker of immune aplastic anemia (2022)

In immune aplastic anemia (IAA), severe pancytopenia results from the immune-mediated destruction of hematopoietic stem cells. Several autoantibodies have been reported, but no clinically applicable autoantibody tests are available for IAA. We screened autoantibodies using a microarray containing >9000 proteins and validated the findings in a large international cohort of IAA patients (n = 405) and controls (n = 815). We identified a novel autoantibody that binds to the C-terminal end of cyclooxygenase 2 (COX-2, aCOX-2 Ab). In total, 37% of all adult IAA patients tested positive for aCOX-2 Ab, while only 1.7% of the controls were aCOX-2 Ab positive. Sporadic non-IAA aCOX-2 Ab positive cases were observed among patients with related bone marrow failure diseases, multiple sclerosis, and type I diabetes, whereas no aCOX-2 Ab seropositivity was detected in the healthy controls, in patients with non-autoinflammatory diseases or rheumatoid arthritis. In IAA, anti-COX-2 Ab positivity correlated with age and the HLA-DRB1*15:01 genotype. 83% of the >40 years old IAA patients with HLA-DRB1*15:01 were anti-COX-2 Ab positive, indicating an excellent sensitivity in this group. aCOX-2 Ab positive IAA patients also presented lower platelet counts. Our results suggest that aCOX-2 Ab defines a distinct subgroup of IAA and may serve as a valuable disease biomarker.
Phase Noise Compensation Using FDM Based Pilot Symbol Assisted EKF for OFDM Based Radio Backhaul Links (2022)

This paper proposes an iterative phase noise compensation (PNC) method using an extended Kalman filter (EKF) that employs pilot symbol assisted (PSA) PNC for computing the initial values in the EKF for orthogonal frequency division multiplexing radio backhaul links. In the PSA PNC stage of the proposed method, the phase noise is estimated and compensated using frequency division multiplexing (FDM) pilot symbols that are multiplexed into the data symbols. Based on the decision symbols after the PSA PNC, the time-varying phase noise estimate and variance in the time domain are tracked and updated using the EKF iteratively. The proposed method achieves a low computational complexity because low-density parity-check (LDPC) decoding is conducted only once after the phase noise in the received signal is suppressed by PSA-EKF PNC. Computer simulation results show that the loss in the required received signal-to-noise power ratio (SNR) satisfying the bit error rate (BER) of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> of the proposed method compared to that without phase noise is suppressed to within approximately 1.2 dB for 256QAM with LDPC coding at the coding rate of 8/9.
Phase Transformation of Doped LiCoPO4 during Galvanostatic Cycling (2020)

In situ X-ray diffraction was employed to investigate the crystal structure changes in Cr/Si co-doped Li(Co,Fe)PO<sub>4</sub> cathode material during a galvanostatic charge/discharge process at a slow rate of C/30. The evolution of the X-ray patterns revealed that the phase transformation between the Cr/Si-Li(Co,Fe)PO<sub>4</sub> and Cr/Si-(Co,Fe)PO<sub>4</sub> is a two-step process, which involves the formation of an intermediate compound of Cr/Si-Li<sub>0.62</sub>(Co,Fe)PO<sub>4</sub> upon the extraction of Li ions from the pristine phase. Different from the previously reported two biphasic transition steps, the phase transformation of the Cr/Si-Li(Co,Fe)PO<sub>4</sub> followed a solid solution and a biphasic reaction pathway at different stages of the delithiation/lithiation process, respectively.
Cyanine dyes: synergistic action of hydrogen, halogen and chalcogen bonds allows discrete I42− anions in crystals (2018)

Discrete tetraiodide dianions (I<sub>4</sub><sup>2−</sup>) are formed in crystals <italic>via</italic> halogen bond coordination of I<sub>2</sub> by iodide anions which are pinned in their positions by a network of hydrogen bonds involving a benzoselenazole cyanine dye.
<title>Accurate sizing of deposited PSL spheres from light scatter measurements</title> (2001)

This paper reviews a light scatter technique used to size particle depositions of polystyrene latex spheres on silicon wafers. The technique has proved to provide accurate (approximately 1% uncertainty) sizing of PSL sphere depositions. Measurements were made of NIST Standard Reference Materials as a means of checking the technique and an uncertainty analysis was performed using the techniques prescribed by NIST. The technique has the advantage that measurements are made of PSL spheres depositions on a substrate, which is the way in which they are used to calibrate defect scanners. In addition to presenting the details of the sizing technique the paper also discusses implications for scanner calibration accuracy.
Smith-Purcell radiation from low-energy electrons (2017)

Recent advances in the fabrication of nanostructures and nanoscale features in metasurfaces offer new prospects for generating visible light emission from low-energy electrons. Here we present the experimental observation of visible light emission from low-energy free electrons interacting with nanoscale periodic surfaces through the Smith–Purcell (SP) effect. We demonstrate SP light emission from nanoscale gratings with periodicity as small as 50 nm, enabling the observation of tunable visible radiation from low-energy electrons (1.5 to 6 keV), an order of magnitude lower in energy than previously reported. We study the emission wavelength and intensity dependence on the grating pitch and electron energy, showing agreement between experiment and theory. Our results open the way to the production of SP-based nanophotonics integrated devices. Built inside electron microscopes, SP sources could enable the development of novel electron–optical correlated spectroscopic techniques and facilitate the observation of new quantum effects in light sources.
Regulating Specific Growth Factor Signaling Using Immobilized Branched Ligands (2012)

VEGF-binding peptide ligands are incorporated into hydrogel microspheres and reduce the amount of growth factor in solution. VEGF binding affinity is enhanced by creating ligands with a dimer structure. The spheres are able to knock down VEGF-mediated HUVEC growth and reduce calcium signaling. The binding interaction is reversible, allowing the spheres to be used as a VEGF delivery vehicle.
Thin-Separator for Low-Melting Point Thermal Battery Electrolytes (2022)

Thermal Batteries have been used extensively as the primary power source for defense applications, with operating temperatures that typically operate above 400 °C. The battery uses a solid electrolyte that is inactive at ambient temperature and can be stored with little to no power loss for long periods (&gt;25 years)[1]. Recent efforts have been done in the implementation of high porosity ceramic felt separators for electrolyte immobilization in thermal batteries [2], which resulted in a higher specific energy density of the thermal cells with ceramic felt compared to the traditional MgO separators, due to the increased ionic conductivity of the separator layer. In this research, a low melting point eutectic electrolyte (CsBr-LiBr-KBr) was immobilized in ceramic felt separators and tested for the LiSi/FeS 2 system. Reducing the melting point of the electrolyte has several advantages such as reducing the activation time and the amount of pyrotechnic material needed to activate the battery, and it also opens the opportunity to lower temperature applications (275-400 °C) such as geothermal instrumentation[3]. Findings of this work will be presented at the meeting. [1] R. A. Guidotti and P. Masset, “Thermally activated (‘thermal’) battery technology. Part I: An overview,” J. Power Sources , vol. 161, no. 2, pp. 1443–1449, 2006, doi: 10.1016/j.jpowsour.2006.06.013. [2] A. Yazdani, M. Sanghadasa, and G. G. Botte, “Integration of ceramic felt as separator / electrolyte in lithium salt thermal batteries and the prospect of rechargeability,” J. Power Sources , vol. 521, no. January, p. 230967, 2022, doi: 10.1016/j.jpowsour.2021.230967. [3] R. A. Guidotti and F. W. Reinhardt, “Guidotti, R. A., &amp; Reinhardt, F. W. Characterization of the LiSi/CsBr-LiBr-KBr/FeS (2) System for Potential Use as a Geothermal Borehole Power Source (1999). Characterization of the LiSi/CsBr-LiBr-KBr/FeS (2) System for Potential Use as a Geothermal Borehole Power Source,” . Sandia National Lab No. SAND99-1702C. United States, 1999.
Symbolic Regression using Mixed-Integer Nonlinear Optimization (2020)

The Symbolic Regression (SR) problem, where the goal is to find a regression function that does not have a pre-specified form but is any function that can be composed of a list of operators, is a hard problem in machine learning, both theoretically and computationally. Genetic programming based methods, that heuristically search over a very large space of functions, are the most commonly used methods to tackle SR problems. An alternative mathematical programming approach, proposed in the last decade, is to express the optimal symbolic expression as the solution of a system of nonlinear equations over continuous and discrete variables that minimizes a certain objective, and to solve this system via a global solver for mixed-integer nonlinear programming problems. Algorithms based on the latter approach are often very slow. We propose a hybrid algorithm that combines mixed-integer nonlinear optimization with explicit enumeration and incorporates constraints from dimensional analysis. We show that our algorithm is competitive, for some synthetic data sets, with a state-of-the-art SR software and a recent physics-inspired method called AI Feynman.
2021 White Paper on Recent Issues in Bioanalysis: TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness (

Part 3

– Recommendations on Gene Therapy, Cell Therapy, Vaccine Assays; Immunogenicity of Biotherapeutics and Novel Modalities; Integrated Summary of Immunogenicity Harmonization) (2022)

The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "Context of Use - COU"); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and, critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 2 (ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry) are published in volume 14 of Bioanalysis, issues 9 and 10 (2022), respectively.
A glycan FRET assay for detection and characterization of catalytic antibodies to the Cryptococcus neoformans capsule (2021)

Classic antibody functions include opsonization, complement activation, and enhancement of cellular antimicrobial function. Antibodies can also have catalytic activity, although the contribution of catalysis to their biological functions has been more difficult to establish. With the ubiquity of catalytic antibodies against glycans virtually unknown, we sought to advance this knowledge. The use of a glycan microarray allowed epitope mapping of several monoclonal antibodies (mAbs) against the capsule of <i>Cryptococcus neoformans</i> From this, we designed and synthesized two glycan-based FRET probes, which we used to discover antibodies with innate glycosidase activity and analyze their enzyme kinetics, including mAb 2H1, the most efficient identified to date. The validity of the FRET assay was confirmed by demonstrating that the mAbs mediate glycosidase activity on intact cryptococcal capsules, as observed by a reduction in capsule diameter. Furthermore, the mAb 18B7, a glycosidase hydrolase, resulted in the appearance of reducing ends in the capsule as labeled by a hydroxylamine-armed fluorescent (HAAF) probe. Finally, we demonstrate that exposing <i>C. neoformans</i> cells to catalytic antibodies results in changes in complement deposition and increased phagocytosis by macrophages, suggesting that the antiphagocytic properties of the capsule have been impaired. Our results raise questions over the ubiquity of antibodies with catalytic activity against glycans and establish the utility of glycan-based FRET and HAAF probes as tools for investigating this activity.
µ-Opioid Receptor Gene (OPRM1) Polymorphism A118G: Lack of Association in Finnish Populations with Alcohol Dependence or Alcohol Consumption (2013)

These results suggest that A118G (Asn40Asp) polymorphism may not have a major effect on the development of alcohol use disorders at least in the Finnish population.
Miniature optical fibre ultrasonic hydrophone usinga Fabry-Perot polymer film interferometer (1997)

An optical fibre hydrophone for the measurement and detection of ultrasound is described. The active sensing element consists of a low finesse Fabry-Perot polymer film interferometer bonded to the tip of an optical fibre, of 50 µm core diameter and 0.25 mm outer diameter. Sensitivity was found to be 114 mV/MPa with an acoustic noise floor of 15 kPa over a 25 MHz bandwidth.
Detecting cardiomyopathies in pregnancy and the postpartum period with an electrocardiogram-based deep learning model (2021)

An ECG-based deep learning model effectively identifies cardiomyopathy during pregnancy and the postpartum period and outperforms natriuretic peptides and traditional clinical parameters with the potential to become a powerful initial screening tool for cardiomyopathy in the obstetric care setting.