gebhart/patrepeval huggingface dataset:
Dentipain, a Streptococcus pyogenes IdeS protease homolog, is a novel virulence factor of Treponema denticola (2010)

Treponema denticola is a major pathogen of chronic periodontitis. Analysis of the T. denticola genome revealed a gene orthologous with a cysteine protease-encoding gene from Streptococcus pyogenes (IdeS). IdeS interferes with IgG-dependent opsonophagocytosis by specific cleavage of IgG molecules. Analysis of this gene (termed ideT) revealed it to encode a two-domain protein whose N-terminus is composed of tandem immunoglobulin-like domains followed by a C-terminal IdeS-like protease domain. In this study we show that during secretion the IdeT protein is processed into an N-terminal fragment which remains associated with the cell, and a C-terminal part released into the medium. Although the secreted domain of IdeT, termed dentipain, shows only 25% identity to the IdeS protease, the putative catalytic cysteine and histidine residues are strongly conserved. Recombinant dentipain cleaves the insulin β-chain, an activity which is inhibited by E-64, a diagnostic inhibitor of cysteine proteases. Apart from insulin no cleavage of other protein substrates was detected, suggesting that dentipain has oligopeptidase activity. A mutant strain was constructed expressing a modified IdeT variant, the dentipain domain of which was deleted. This strain was found to be significantly reduced in its abscess-forming activity compared with the parental strain in a murine abscess model, suggesting that dentipain contributes to the virulence of T. denticola.
Antibody targeting of doxorubicin-loaded liposomes suppresses the growth and metastatic spread of established human lung tumor xenografts in severe combined immunodeficient mice. (2000)

Beta1 integrins, expressed on the cell surface of human non-small cell lung carcinomas, are used here as a target for the selective delivery of anti-cancer drug-loaded liposomes. Fab' fragments of a monoclonal antibody specific for human beta1 integrins were conjugated to sterically stabilized liposomes. Confocal microscopy of beta1 integrin-positive lung tumor cells incubated with fluorescently labeled anti-beta1 Fab immunoliposomes revealed a tumor-specific binding and efficient internalization of the liposomes into the tumor cells. The ability of these liposomes to deliver cytotoxic drugs to the tumor and kill these cells was demonstrated in vitro by incubating tumor cells with doxorubicin-loaded anti-beta1 Fab' immunoliposomes. The drug-loaded immunoliposomes were >30-fold more cytotoxic to the tumor cells than drug-loaded liposomes without antibody, nonspecific Fab' control immunoliposomes with drug or immunoliposomes without drug. The therapeutic efficacy of doxorubicin-loaded immunoliposomes was also evaluated in a metastatic human lung tumor xenograft/severe combined immunodeficient (SCID) mouse model. SCID mice that received i.v. injections of human lung tumor cells developed primary tumor nodules in the lung that subsequently metastasized to the liver and adrenal gland. Treatment of SCID mice bearing established lung tumor xenografts with doxorubicin-loaded anti-beta1 Fab immunoliposomes resulted in a significant suppression of tumor growth (monitored periodically by quantifying serum levels of a tumor marker), whereas tumors grew progressively in mice treated with control formulations. In addition to suppressing the growth of the primary lung tumor nodules, the immunoliposomes prevented the metastatic spread of the tumor to the liver and adrenal glands and increased the median survival time of the tumor-bearing mice. We conclude that Fab' immunoliposomes directed to tumor-associated integrins represent a potentially viable approach clinically for the selective delivery of drugs to solid tumors and may be useful in preventing the metastatic spread of lung cancer.
Ion-Selective Lipid Bilayers Tethered to Microcontact Printed Self-Assembled Monolayers Containing Cholesterol Derivatives (1998)

Microcontact printing has been used to prepare patterned self-assembled monolayers (SAMs) of cholesterylpolyethylenoxy thiol. These patterned SAMs were used as supports for the formation of integral supported lipid bilayers. Biofunctionality was confirmed by addition of valinomycin ionophores and gramicidin ion channels. Impedance spectroscopy of the resulting bilayer structures, incorporating valinomycin and the gramicidin, showed the expected ion selectivity.
A Demonstration of Artificial Neural Networks Based Data Mining for Gas Turbine Driven Compressor Stations (2000)

This paper presents a successful demonstration of application of Neural networks to perform various data mining functions on an RB211 gas turbine driven compressor station. Radial Basis Function networks were optimized and were capable of performing the following functions: a) Backup of critical parameters, b) Detection of sensor faults, c) Prediction of complete engine operating health with few variables, and d) Estimation of parameters that cannot be measured. A Kohonen SOM technique has also been applied to recognize the correctness and validity of any data once the network is trained on a good set of data. This was achieved by examining the activation levels of the winning unit on the output layer of the network. Additionally, it would also be possible to determine the suspicious, faulty or corrupted parameter(s) in the cases which are not recognized by the network by simply examining the activation levels of the input neurons.
Nonlinear amplification of side-modes in frequency combs (2013)

We investigate how suppressed modes in frequency combs are modified upon frequency doubling and self-phase modulation. We find, both experimentally and by using a simplified model, that these side-modes are amplified relative to the principal comb modes. Whereas frequency doubling increases their relative strength by 6 dB, the growth due to self-phase modulation can be much stronger and generally increases with nonlinear propagation length. Upper limits for this effect are derived in this work. This behavior has implications for high-precision calibration of spectrographs with frequency combs used for example in astronomy. For this application, Fabry-Pérot filter cavities are used to increase the mode spacing to exceed the resolution of the spectrograph. Frequency conversion and/or spectral broadening after non-perfect filtering reamplify the suppressed modes, which can lead to calibration errors.
Dimensionality reduction and phase plane analysis (2014)

The firing of action potentials has been successfully described by the Hodgkin–Huxley model, originally for the spikes in the giant axon of the squid but also, with appropriate modifications of the model, for other neuron types. The Hodgkin–Huxley model is defined by four nonlinear differential equations. The behavior of high-dimensional systems of nonlinear differential equations is difficult to visualize – and even more difficult to analyze. For an understanding of the firing behavior of the Hodgkin–Huxley model, we therefore need to turn to numerical simulations of the model. In Section 4.1 we show, as an example, some simulation results in search of the firing threshold of the Hodgkin–Huxley model. However, it remains to show whether we can get some deeper insights into the observed behavior of the model.
The OFDM Principle (2005)

In this chapter we introduced the basic OFDM principle: a data stream is split into Nc parallel lower rate data streams that are modulated on separate subcarriers. Practical implementations of OFDM systems use the IDFT operation for this modulation. Although this parallellization already reduces the impact of ISI, it can be completely removed by means of a cyclic prefix. For long, implementing an OFDM scheme was prohibitive complex. Practical interest only appeared in the '90s due to the progress in digital signal processing and microelectronics [8].
A Facile Route toward Structured Hybrid Particles Based on Liquid–Solid Assembly (2014)

Structured hybrid particles with strongly improved colloidal stability are synthesized through a facile fabrication method based on the assembly of miniemulsion droplets containing liquid monomeric precursors onto solid nanoparticles. Classical heterocoagulation experiments between solid particles with similar compositions are performed for comparison and result in coagulated samples. A two-step mechanism is proposed which involves polymerization to fixate the final hybrid particle morphology after electrostatically driven self-assembly. Negatively charged polyacrylonitrile (PAN) nanoparticles with a high degree of semicrystallinity are utilized as solid core and combined with positively charged monomer droplets of varying compositions. A simple adjustment of miniemulsion composition enables the tailored synthesis of raspberry or core–shell structured hybrid particles. While the ζ-potential strongly affects the colloidal stability, adjusting the Tg of the polymer and/or the cross-linking degree after polymerization is an efficient tool to determine the final latex morphology. As-prepared hybrid dispersions can form transparent films with embedded PAN domains with an undisturbed high degree of semicrystallinity and thus show potentials in a wide variety of applications, e.g., for coatings and adhesives with reinforced mechanical properties and improved barrier performance.
Through the membrane &#x00026; along the channel flooding in PEMFCs (2009)

Neutron imaging of a polymer electrolyte membrane fuel cell (PEMFC) revealed distinct patterns of water fronts moving through the gas diffusion layers (GDL) and channels. The PEMFC was operating with dead-ended, straight and almost vertically-oriented anode channels; hence the gravity driven accumulation of liquid water at the end of the channel caused flooding in an upward direction. In order to predict the spatiotemporal evolution of water patterns inside severely-flooded fuel cells, various distributed parameter models of the water transport through the membrane and GDLs to the cathode and anode channels have been developed by the authors and others. In this paper, a zero-dimensional moving front model is presented which captures the location of the water phase transition inside the GDL, instead of using the standard partial differential equation (PDE) approach for modeling liquid water in porous media which is numerically difficult to solve. This model uses three nonlinear states (the anode and cathode GDL front location and the membrane water content) and three inputs (the anode and cathode vapor concentration and the current density) to predict the slowly evolving front locations in both anode and cathode side GDLs during flooding and drying as well as the dynamic changes in membrane water content. The unit cell model is finally formulated with three hybrid modes and their transition laws. The hybrid-state model will be parameterized in the future using experimentally observed front evolutions. This parameterized unit cell model will be used to model the water accumulation along the channel in order to predict and avoid severe flooding conditions.
Figure A1 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial (2023)

Figure A1 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
Ge-on-Si waveguide device for self-referenced fingerprint region absorption spectroscopy (2023)

We present the development of Ge-on-Si waveguide-based devices for low-noise mid-infrared absorption spectroscopy of aqueous solutions, targeting wavelengths between 6 and 10 μm, that are able to reduce the relative intensity noise which is a key roadblock when measuring tiny analyte absorptions masked by a large background matrix absorption. The sensor uses a pair of integrated thermo-optic switches to continuously switch light between a reference waveguide and a sensor waveguide, so that common noise components can be cancelled out, even when the light source and photodetector are not integrated on the same chip.
Self-evolving photonic crystals for ultrafast photonics (2023)

Ultrafast dynamics in nanophotonic materials is attracting increasing attention from the perspective of exploring new physics in fundamental science and expanding functionalities in various photonic devices. In general, such dynamics is induced by external stimuli such as optical pumping or voltage application, which becomes more difficult as the optical power to be controlled becomes larger owing to the increase in the energy required for the external control. Here, we demonstrate a concept of the self-evolving photonic crystal, where the spatial profile of the photonic band is dynamically changed through carrier-photon interactions only by injecting continuous uniform current. Based on this concept, we experimentally demonstrate short-pulse generation with a high peak power of 80 W and a pulse width of <30 ps in a 1-mm-diameter GaAs-based photonic crystal. Our findings on self-evolving carrier-photon dynamics will greatly expand the potential of nanophotonic materials and will open up various scientific and industrial applications.
A Smart Positioning System for Personalized Energy Management in buildings (2016)

Energy consumption in official buildings contributes to 42% of total energy generation in India. The key features in commercial buildings are usage of high energy consuming devices, long duration of usage of electrical equipments, large population density and large equipment density compared with the floor area usage in houses. Hence this problem has motivated to perform research on energy management in official buildings. The individuals in these buildings mostly have unique authority on most of the equipments they handle, and they have their own comfort level requirement based on the context and the equipment availability. Therefore, to devise an effective energy management solution it is required to consider personal requirements with highest priority than the community requirements. Hence in this research work we design and develop systems & solutions needed for Personalized Energy Management (PEM). Our proposed system is developed to capture the spatio-temporal data of context and electrical usage pattern for each individual with bare minimum sensors. To address this challenge, we proposed a smart positioning system (SPS) for personalized energy management. In SPS, we have developed an Real time Smart Positioning System (RSPS) algorithm for integrating electrical map and sensing coverage of electrical appliances inside a building to position the individual in real-time with respect to each of the electrical appliances. Using SPS, the current position of an individual inside the building is determined along with the position of nearby electrical appliances to automate the appliance usage. This is performed using the proposed RSPS algorithm where real-time mapping of electrical map, sensing coverage of nearby equipments, signal strength, and pattern of individual requirements are used to control usage of equipments related to individual's choice. Experimental analysis of the RSPS algorithm on our prototype has been performed and the results showed that it requires a minimum of 2 coverage and it is not required to have 3 coverage as in other localization algorithms. Under the above condition of 2 coverage this algorithm was able to achieve an accuracy of 90%.
Cardiopulmonary function in two human disorders of the hypoxia‐inducible factor (HIF) pathway: von Hippel‐Lindau disease and HIF‐2α gain‐of‐function mutation (2011)

The hypoxia-inducible factors (HIFs; isoforms HIF-1α, HIF-2α, HIF-3α) mediate many responses to hypoxia. Their regulation is principally by oxygen-dependent degradation, which is initiated by hydroxylation of specific proline residues followed by binding of von Hippel-Lindau (VHL) protein. Chuvash polycythemia is a disorder with elevated HIF. It arises through germline homozygosity for hypomorphic VHL alleles and has a phenotype of hematological, cardiopulmonary, and metabolic abnormalities. This study explores the phenotype of two other HIF pathway diseases: classic VHL disease and HIF-2α gain-of-function mutation. No cardiopulmonary abnormalities were detected in classic VHL disease. HIF-2α gain-of-function mutations were associated with pulmonary hypertension, increased cardiac output, increased heart rate, and increased pulmonary ventilation relative to metabolism. Comparison of the HIF-2α gain-of-function responses with data from studies of Chuvash polycythemia suggested that other aspects of the Chuvash phenotype were diminished or absent. In classic VHL disease, patients are germline heterozygous for mutations in VHL, and the present results suggest that a single wild-type allele for VHL is sufficient to maintain normal cardiopulmonary function. The HIF-2α gain-of-function phenotype may be more limited than the Chuvash phenotype either because HIF-1α is not elevated in the former condition, or because other HIF-independent functions of VHL are perturbed in Chuvash polycythemia.
Normal-Stressed Electromagnetic Triaxial Fast Tool Servo for Microcutting (2022)

Short strokes and complicated structures commonly degrade the operating performance of current piezo-actuated triaxial fast tool servos (FTSs). To overcome those deficiencies, we present a novel normal-stressed electromagnetic triaxial FTS for microcutting, which achieves a compact structure and a high resonant frequency with triaxial motions in hundreds of micrometers. The magnetic FTS has a single armature to provide the triaxial decoupled and noncontact driving forces, as well as a symmetric three-DOF corrugated compliant bearing to support and guide the decoupled outputs. With the parameters jointly optimized by an analytical and finite element model, the prototype showed a high degree of agreement with the design target for both static and dynamic performances. A linear active disturbance rejection control is implemented for the triaxial FTS, and an iterative learning scheme is further employed for the triaxial FTS to achieve fast and accurate trajectory tracking. The developed triaxial FTS is comprehensively demonstrated by fabricating a hexagonal spherical microlens array with each lenslet generated within 0.24 s. The practical error for the spatial trajectory tracking was within <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$ \pm$</tex-math></inline-formula> 30 nm, and good surface quality with a form error of 63.66 nm and surface roughness of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Sa</i> = 2.05 nm is achieved.
Presymptomatic diagnosis ofvon Hippel-Lindau disease withflanking DNA markers (1992)

Hippel-Lindau (VHL)disease isa dominantly inherited cancersyndrome characterised bythedevelopment ofreti- nal,cerebellar, andspinalhaemangio- blastomas, renalcellcarcinoma, and phaeochromocytoma. ThegeneforVHL disease hasbeenmappedtochromosome 3p25-p26andflanking markersidenti- fied. We haveinvestigated theusefulness ofcurrently available DNA markersfor thepresymptomatic diagnosis ofVHL disease. Inthefirst partofthisinvestiga- tion, genetic linkage datafromtwopre- viously published studies wereupdated andreanalysed toprovide accurate esti- matesofsexspecific recombination frac- tionsandtoconfirmthatthereisno evidence oflocusheterogeneity. Inthe second partofthisstudy, 14families con- taining 23asymptomatic subjects at50% priorriskofVHL disease wereinvesti- gatedwithclosely linked DNA markers (RAF1,D3S18,D3S732). Seventeen sub- jects wereinformative withoneormore markers, sixofwhom wereinformative at markersflanking theVHL disease gene.Bycombining agerelated andDNA basedriskinformation thecarrier risk for11subjects wasreduced to<2%. (JMedGenet1992;29:902-5)
Functional evaluation of engineered 3d muscle‐tendon constructs (2006)

Our purpose was to evaluate the contractile and structural characteristics of three‐dimensional (3D) skeletal muscle constructs co‐cultured with engineered tendon constructs (ETC), segments of adult (ART), or fetal rat tail (FRT) tendon. The utilization of muscle only (MO) constructs is limited due to the lack of adhesion of the construct to synthetic anchors during force production. We hypothesized that the co‐culture of tendon tissue and muscle would produce constructs with viable muscle‐tendon interfaces that remain intact during force production. Construct diameter (μ M) and maximum isometric force (μ N) were measured and specific force (MPa) was determined on ETC (n=3), ART (n=3), MO (n=3) and FRT (n=5). Following measure of force, constructs were loaded at a constant strain rate until failure and surface strains were recorded optically across the tendon, muscle and the interface and used to determine nominal stress vs. nominal strain. The maximum tangent stiffness was determined by calculating the secondary slope of the stress‐strain response. There were no differences between the groups with respect to diameter, maximum force or specific force. The muscle‐tendon interface was robust and withstood tensile loading. The tendon region was 3x as stiff as the muscle region, therefore the muscle took on most of the strain and little or no strain was seen within the tendon. The majority of the constructs failed in the muscle region. In conclusion, using three sources of tendon tissue, we have successfully engineered 3D muscle‐tendon construct with viable muscle‐tendon interfaces. DARPA AFOSR FA9550‐05‐1‐0015.
The Terms of Scientific Debate and the Issue of its Reception (2014)

The theme of global warming has a special status in the environmental debates that animates political and social life, particularly in France. Our aim during this symposium is to understand the difficulties and deadlocks faced by our country, and others, with respect to the relations between science, technology and society, the role of scientific progress in economic and social development, the way the media and the political sphere tackle this issue, and finally, the democratic dialogue betw...
Liver Iron Content Determination Using a Volumetric Breath‐Hold Gradient‐Echo Sequence With In‐Line R2* Calculation (2020)

1 TECHNICAL EFFICACY STAGE: 2.
Normalization of HE-stained histological images using cycle consistent generative adversarial networks (2021)

CycleGANs have proven to efficiently normalize HE-stained images. The approach compensates for deviations resulting from image acquisition (e.g. different scanning devices) as well as from tissue staining (e.g. different staining protocols), and thus overcomes the staining variations in images from various institutions.The code is publicly available at https://github.com/m4ln/stainTransfer_CycleGAN_pytorch . The data set supporting the solutions is available at https://doi.org/10.11588/data/8LKEZF .
Managerial Decision Making as an Application for Control Science and Engineering (2022)

The principles and methodology of control science and engineering are relevant beyond engineered systems to all dynamical systems. In this paper we discuss how control terminology and concepts can be interpreted in the context of decision-making by human managers, and the benefits that can accrue from the analogy. Examples of managerial decision making are presented in a control systems context. A selected review of earlier literature in the area is included. The connections of some popular business practices with control principles are reviewed. Points of differentiation, especially human-in-the-loop aspects of managerial control, are highlighted. Two examples, on return-on-investment dynamics and short interval control in process plant operation, are discussed. A number of control concepts are mapped to the management domain, revealing what we hope are useful insights for decision makers. This is the main paper for a tutorial session at the 2022 American Control Conference. An appendix is included that contains abstracts of the other papers and presentations in the session.