gebhart/patrepeval huggingface dataset:
Methods for Kinetic Modeling of Temporally Resolved Hyperspectral Confocal Fluorescence Images (2009)

Elucidating kinetic information (rate constants) from temporally resolved hyperspectral confocal fluorescence images offers some very important opportunities for the interpretation of spatially resolved hyperspectral confocal fluorescence images but also presents significant challenges, these being (1) the massive amount of data contained in a series of time-resolved spectral images (one time course of spectral data for each pixel) and (2) unknown concentrations of the reactants and products at time = 0, a necessary precondition normally required by traditional kinetic fitting approaches. This paper describes two methods for solving these problems: direct nonlinear (DNL) estimation of all parameters and separable least squares (SLS). The DNL method can be applied to reactions of any rate law, while the SLS method is restricted to first-order reactions. In SLS, the inherently linear and nonlinear parameters of first-order reactions are solved in separate linear and nonlinear steps, respectively. The new methods are demonstrated using simulated data sets and an experimental data set involving photobleaching of several fluorophores. This work demonstrates that both DNL and SLS hard-modeling methods applied to the kinetic modeling of temporally resolved hyperspectral images can outperform traditional soft-modeling and hard/soft-modeling methods which use multivariate curve resolution-alternating least squares (MCRALS) methods. In addition, the SLS method is much faster and is able to analyze much larger data sets than the DNL method.
Parametric UMAP: learning embeddings with deep neural networks for representation and semi-supervised learning (2021)

We propose Parametric UMAP, a parametric variation of the UMAP (Uniform Manifold Approximation and Projection) algorithm. UMAP is a non-parametric graph-based dimensionality reduction algorithm using applied Riemannian geometry and algebraic topology to find low-dimensional embeddings of structured data. The UMAP algorithm consists of two steps: (1) Compute a graphical representation of a dataset (fuzzy simplicial complex), and (2) Through stochastic gradient descent, optimize a low-dimensional embedding of the graph. Here, we replace the second step of UMAP with a deep neural network that learns a parametric relationship between data and embedding. We demonstrate that our method performs similarly to its non-parametric counterpart while conferring the benefit of a learned parametric mapping (e.g. fast online embeddings for new data). We then show that UMAP loss can be extended to arbitrary deep learning applications, for example constraining the latent distribution of autoencoders, and improving classifier accuracy for semi-supervised learning by capturing structure in unlabeled data.
FoxP3 Expression in Papillary Thyroid Carcinoma: A Possible Resistance Biomarker to Iodine 131 Treatment (2013)

The data show an association of FoxP3 expression with features of PTC that seem to have a specific impact on radioiodine sensitivity.
Magnetic suspension system for a laboratory model annular momentum control device (1979)

Feasibility of the annular momentum control device (AMCD) for the control and stabilization of spacecraft is presented. The AMCD is momentum storage equipment consisting of a thin rim, magnetically suspended and rotated by noncontacting electromagnetic actuators. The laboratory model AMCD, the rim, and the magnetic suspension system are described, along with their evaluation tests. Because it utilizes permanent magnet flux biased magnetic bearing elements, the original laboratory model magnetic suspension system produced control limitations, and a new suspension system which used zero flux bias was designed and fabricated. Tests of the improved system show that a medium control loop bandwidth is required to achieve stability at low rim velocities, but at higher rim speed the bandwidth of the control loop interacts with bending modes of the rim and causes instability. Decreasing the bandwidth by changing to a precession control mode is discussed, and the results of such a computer simulation are presented.
Dielectric properties of vegetable oil modified by monodisperse Fe<inf>3</inf>O<inf>4</inf> nanoparticles (2014)

Various nanoparticles have been used to composite insulating oil based nanofluids and to improve electrical breakdown and thermal properties of insulating oils. The insulating nanofluids must meet requirements of both electrical property and dispersion stability of nanoparticles. In the work, monodisperse hydrophobicity Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> nanoparticles were synthesized by the high temperature decomposition method and were used to modify a type of vegetable insulating oil. The preparation and characterization of the vegetable insulating oil based nanofluid were presented. The experimental results show that the monodisperse Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> nanoparticles dissolve well in the vegetable insulating oil and form a stable nanofluid with high shelf life. The monodisperse Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> nanoparticles are capable of enhancing AC breakdown voltages of vegetable insulating oils.
A Study on the Design and Mechanical Adhesion of Polymer Foam-Metal Joints (2008)

The design of metal-polymer foam adhesion and load transfer characteristics is carried out in this research work. The metal inserts are used as the load transfer component, while the foam is used as the structural element of the system. The inserts are embedded in the foam during the foaming process. Flexural testing was conducted on different metal foam configurations to establish the typical interaction trends. The load-deflection response and the mode of failure of the structure were documented. Moduli of elasticity of the system for various geometries and embedded lengths were evaluated, and behavior patterns were gleaned. Rectangular, circular, and triangular (taper-/wedgelike) inserts were used. Results show that simple taper inserts embedded in foam slabs perform better than the other shapes. Finite element analyses of the interaction under different loads were carried out. The modeling results coincided with the experimental ones hence validating the model.
Properties of Human Growth Hormone Polypeptides: Purified from Pituitary Extracts and Synthesized in Monkey Kidney Cells and Bacteria (1982)

Several forms of human GH (hGH) have been elucidated by extraction of human pituitary and recombinant DNA techniques. In the present study we have characterized five of these hGH polypeptides by gel filtration, RIA, and radioreceptor assays. These include extractable pituitary hGH and its naturally occurring 20K variant. Two hGH polypeptides were produced from naturally occurring human genes in simian kidney cells (SV-hGH 1 and 2) and another preparation was produced from a partially synthesized gene in bacteria (E. coli-hGH). As predicted from their known DNA sequences, naturally occurring pituitary hGH, SV-hGH 1, and E. coli-hGH migrated as a single peak on Sephadex G-100 column and had the same immunological and receptor-binding properties. By contrast, SV-hGH 2 (14 dispersed amino acid substitutions) and the 20K variant (amino acid residues 32-46 deleted from hGH) contained more higher molecular weight components and had diminished immunological and receptor-binding potency. SV-hGH 2 differed from the 20K variant by having even lower immunological potency and containing more of the higher molecular weight component. These variant forms of hGH may provide an explanation for the heterogeneity of both pituitary and plasma hGH.
Primary structure of the yeast choline transport gene and regulation of its expression. (1990)

The yeast Saccharomyces cerevisiae possesses a choline transport system encoded by the CTR gene. Incorporated choline is exclusively utilized for the synthesis of phosphatidylcholine. Determination of the complete nucleotide sequence of the CTR gene showed that the deduced primary sequence of the choline transporter comprised 563 amino acid residues with a calculated molecular weight of 62,055. Both the amino- and carboxyl-terminal regions were hydrophilic whereas the rest of the sequence was highly hydrophobic and contained several membrane-spanning regions. There were four potential glycosylation sites in the hydrophilic parts of the sequence. The transporter showed significant sequence similarities to the yeast arginine and histidine transporters. A 2.0-kilobase RNA species was identified as the CTR transcript. Disruption of the CTR locus completely abolished the choline transport activity, indicating that the CTR product is the sole choline transporter in yeast. The regulation of choline transport mRNA was investigated by Northern blot analysis using a CTR probe. The abundance of CTR mRNA significantly decreased on incubation of cells with a combination of choline and myo-inositol. The CTR mRNA level was high in the exponential growth phase but decreased dramatically when cells entered the stationary phase. Similar control had been observed for some enzymes in yeast phospholipid synthesis.
Selection on Glycine β-1,3-Endoglucanase Genes Differentially Inhibited by a Phytophthora Glucanase Inhibitor ProteinSequence data from this article have been deposited with EMBL/GenBank Data Libraries under accession nos. AY461847, AY466133, AY466134, AY466135, AY466136, AY466137, AY466138, AY466139, AY466140, AY466141, AY466142, AY466143, AY466144, AY466145, AY466146, AY466147, AY466148, AY466149, AY466150, AY466151, AY466152, AY466153, AY466154, AY466155, AY466156, AY468381, AY468382, AY468383, AY468384, AY468385, AY468386, AY468387, AY468388, AY468389, AY468390, AY468391, AY468392, AY468393, AY468394, AY468395, AY468396, AY468397, AY468398, AY468399, AY468400, AY468401, AY468402, AY468403, AY468404, AY468405, AY468406, AY468407, and AY628413, AY628414, AY628415. (2004)

Abstract Plant endo-β-1,3-glucanases (EGases) degrade the cell wall polysaccharides of attacking pathogens and release elicitors of additional plant defenses. Isozymes EGaseA and EGaseB of soybean differ in susceptibility to a glucanase inhibitor protein (GIP1) produced by Phytophthora sojae, a major soybean pathogen. EGaseA, the major elicitor-releasing isozyme, is a high-affinity ligand for GIP1, which completely inhibits it, whereas EGaseB is unaffected by GIP1. We tested for departures from neutral evolution on the basis of partial sequences of EGaseA and EGaseB from 20 widespread accessions of Glycine soja (the wild progenitor of soybean), from 4 other Glycine species, and across dicotyledonous plants. G. soja exhibited little intraspecific variation at either locus. Phylogeny-based codon evolution models detected strong evidence of positive selection on Glycine EGaseA and weaker evidence for selection on dicot EGases and Glycine EGaseB. Positively selected peptide sites were identified and located on a structural model of EGase bound to GIP1. Positively selected sites and highly variable sites were found disproportionately within 4.5 Å of bound GIP1. Low variation within G. soja EGases, coupled with positive selection in both Glycine and dicot lineages and the proximity of rapidly evolving sites to GIP1, suggests an arms race involving repeated adaptation to pathogen attack and inhibition.
Platform, position, and purpose: Analyzing the studio recordings and live performances of U2 (2005)

This thesis explores the music of rock band U2, utilizing two perspectives: current research in popular musicology, specifically the work of Albin Zak, Allan Moore, and Lori Burns, and the thoughts of the band members of U2. These two perspectives provide the framework for the discussion that covers several examples from across the bands discography (1980-2000). The role of music in communicating with the listener is discussed from the perspective of the band members of U2. This discussion highlights the desire of the band members to actively participate in the songs' meaning by shaping the musical performance to the themes and ideas discussed within the text. The way that the text shapes the understanding is examined through a discussion of the songs "All Along the Watchtower," and "Playboy Mansion." The bands live performances are also considered, through a discussion of the Elevation Tour. The songs "Sunday Bloody Sunday," and "Bullet the Blue Sky" are discussed in-depth, taking into account the music, text, and performance from their initial studio recordings in the 1980s, to the recent performances in the Elevation Tour. The focus centers on the messages communicated through the bands music, the choices made in shaping their sound, and the importance of the details in fully understanding each performance.
Performance of IPv6 Segment Routing in Linux Kernel (2018)

IPv6 Segment Routing (SRv6) is a promising solution to support advanced services such as Traffic Engineering, Service Function Chaining, Virtual Private Networks, and Load Balancing. The SRv6 data-plane is supported in many different forwarding engines including the Linux kernel. It has been introduced into the 4.10 release of the Linux kernel to support both endhost and router functionalities. The implementation has been updated several times, with every new kernel release, to include new features and also to improve the performance of existing ones. In this paper, we present SRPerf, a performance evaluation framework for software and hardware implementations of SRv6. SRPerf is able to perform different benchmarking tests such as throughput and latency. The architecture of SRPerf can be easily extended to support new benchmarking methodologies as well as different SRv6 implementations. We have used SRPerf to evaluate the performance of the SRv6 implementation in the Linux kernel.
Value Memory Graph: A Graph-Structured World Model for Offline Reinforcement Learning (2022)

Reinforcement Learning (RL) methods are typically applied directly in environments to learn policies. In some complex environments with continuous state-action spaces, sparse rewards, and/or long temporal horizons, learning a good policy in the original environments can be difficult. Focusing on the offline RL setting, we aim to build a simple and discrete world model that abstracts the original environment. RL methods are applied to our world model instead of the environment data for simplified policy learning. Our world model, dubbed Value Memory Graph (VMG), is designed as a directed-graph-based Markov decision process (MDP) of which vertices and directed edges represent graph states and graph actions, separately. As state-action spaces of VMG are finite and relatively small compared to the original environment, we can directly apply the value iteration algorithm on VMG to estimate graph state values and figure out the best graph actions. VMG is trained from and built on the offline RL dataset. Together with an action translator that converts the abstract graph actions in VMG to real actions in the original environment, VMG controls agents to maximize episode returns. Our experiments on the D4RL benchmark show that VMG can outperform state-of-the-art offline RL methods in several goal-oriented tasks, especially when environments have sparse rewards and long temporal horizons. Code is available at https://github.com/TsuTikgiau/ValueMemoryGraph
A Dual-reporter Platform for Screening Tumor-targeted Extracellular Vesicles (2021)

Abstract Extracellular vesicle (EV)-mediated transfer of biomolecules plays an essential role in intercellular communication and may improve targeted drug delivery. In the past decade, various approaches to EV surface modification for targeting specific cells or tissues have been proposed, including genetic engineering of parental cells or postproduction EV engineering. However, due to technical limitations, targeting moieties of engineered EVs have not been thoroughly characterized. Here, we report the bioluminescence resonance energy transfer (BRET) EV reporter, PalmReNL-based dual-reporter platform for characterizing the cellular uptake of tumor homing peptide (THP)-engineered EVs, targeting PDL1, uPAR, or EGFR proteins expressed in MDA-MB-231 breast cancer cells, simultaneously by bioluminescence measurement and fluorescence microscopy. Bioluminescence analysis of cellular EV uptake revealed the highest binding efficiency of uPAR-targeted EVs, whereas PDL1-targeted EVs showed slower cellular uptake. EVs engineered with two known EGFR-binding peptides via lipid nanoprobes did not increase cellular uptake, indicating that designs of EGFR-binding peptide conjugation to the EV surface are critical for functional EV engineering. Fluorescence analysis of cellular EV uptake allowed us to track individual PalmReNL-EVs bearing THPs in recipient cells. These results demonstrate that the PalmReNL-based EV assay platform can be a foundation for high-throughput screening of tumor-targeted EVs.
FGF receptors ubiquitylation: dependence on tyrosine kinase activity and role in downregulation (2002)

A crucial aspect of ligand-mediated receptor activation and shut-down is receptor internalization and degradation. Here we compared the ubiquitylation of either wild type or a K508A 'kinase-dead' mutant of fibroblast growth factor receptor 3 (FGFR3) with that of its naturally occurring overactive mutants, G380R as in achondroplasia, or K650E involved in thanatophoric dysplasia. Fibroblast growth factor receptors ubiquitylation was found to be directly proportional to their intrinsic tyrosine kinase activity, both of which could be blocked using kinase inhibitors. Despite excessive ubiquitylation, both overactive mutants failed to be efficiently degraded, even when challenged with ligand or overexpression of c-Cbl, a putative E3 ligase. We conclude that phosphorylation is essential for FGFR3 ubiquitylation, but is not sufficient to induce downregulation of its internalization resistant mutants.
IL6 Mediates Suppression of T- and NK-cell Function in EMT-associated TKI-resistant EGFR-mutant NSCLC (2023)

These data indicate that IL6 is upregulated in EGFR-mutant NSCLC tumors with acquired EGFR-TKI resistance and suppressed T- and NK-cell function. IL6 blockade enhanced antitumor immunity and efficacy of anti-PD-1 therapy warranting future clinical combinatorial investigations.
Supplementary Data (for Review only) from Functional Genomics Identifies Hepatitis-Induced STAT3–TYRO3–STAT3 Signaling as a Potential Therapeutic Target of Hepatoma (2023)

&lt;p&gt;Supplemental information of Materials and Methods&lt;/p&gt;
Delineation of DNA sequences that are important for in vitro transcription from the adenovirus EIIa late promoter. (1988)

Late in infection, transcription of the EIIa gene is initiated primarily at map unit 72 of the adenovirus genome. A cell-free nuclear extract system was used to determine sequence elements important for the function of this late promoter. In such a system, the transcriptional activity of a circular template was found to be much higher (5- to 10-fold) than that of a linear template. The effect of template topology appeared to be dependent on two distal upstream elements with 5' boundaries located near -265 to -223 and -147 to -133 (in relation to the initiation site), since deletions of these regions reduced transcription of the circular template, in a stepwise fashion, to a level similar to that observed with the linear template. Further deletions revealed an element in the -116 region that appeared to be more important for transcription of the circular template (10-fold reduction) than for transcription of the linear template (3-fold reduction). Lastly, deletion of the TACAAA sequence in the -29 region resulted in further reduction in transcription, indicating that this element functions as a promoter in vitro.
Synthesis and Molecular Structures of the Magnesium and Aluminum Adducts of a Niobium−Oxo Complex. X-ray Crystal Structures of [{NbOCl4(THF)}2Mg(THF)4] and [{NbOCl4(THF)}2AlCl(THF)3] (1997)

The niobium−oxo adducts [{NbOCl4(THF)}2Mg(THF)4] and [{NbOCl4(THF)}2AlCl(THF)3] are synthesized in direct reaction of NbCl5 with MgCl2 or AlCl3 in tetrahydrofuran and structurally characterized by X-ray diffraction.
Synthesis and Hybridization Properties of Modified Oligonucleotides with PNA-DNA Dimer Blocks (1997)

Abstract Different modified PNA-DNA dimer-analogous synthons (I and II) were synthesized as phosphoramidites. These dimer units were assembled by a 5′-modified deoxythymidine and a modified PNA monomer. These synthons were used in the routine coupling procedure for oligonucleotides. Therefore no PNA coupling chemistry is necessary to synthesize PNA-DNA chimeric oligonucleotides. Various deoxyoligonucleotides were synthesized introducing the dimer blocks I and II at different positions in the sequences. Melting temperatures of the modified oligonucleotides with their complementary DNA analogues were determined. Backbone modifications of oligonucleotides are required in the antisense strategy for protection against endonucleolytic cleavage in biological environment. Peptide nucleic acids (PNA fragments) are known to be nuclease resistant analogues, which show stable and discriminating hybridization. For this reason we prepared chimeric PNA-DNA oligomers by incorporation of two different modified PNA-DNA dimer blocks (Scheme A) into oligonucleotides. Melting temperatures of the modified oligonucleotides with their complementary DNA were determined.
Dissection of Drosophila Ovaries (2006)

Here we demonstrate a method of dissecting ovaries in Drosophila. As the method of culturing the different cell types that exist in the Drosophila ovary has yet been defined, this is a rapid method to obtain the Drosophila ovarian tissue. Essentially, we show that dissecting Drosophila ovaries involves a simple two-or three-step procedure. Subsequent treatment of these dissected ovaries depend on the downstream experiments that will be performed.
Plantes transgéniques et biodiversité végétale (2011)

article de vulgarisation. http://www.sfecologie.org/regards/2011/05/10/r17-a-et-b-ogm/
Rapid control of mold temperature during injection molding process: Effect of packing pressure (2015)

A thorough analysis of the effect of operative conditions of injection molding process on the morphology distribution inside the obtained molded is performed, with particular reference to semi- crystalline polymers. In particular, fully characterized injection molding tests are presented using an isotactic polypropylene, previously carefully characterized as far as most of properties of interest. The effects of mold temperature and packing conditions are analyzed. The mold temperature was controlled by a thin heating device, composed by polyimide as insulating layer and polyimide loaded carbon black as electrical conductive layer, that is able to increase temperature on mold surface in few seconds (70°C/s) by joule effect and cool down soon after. The shear layer thickness in the molded is reduced in the samples produced at high mold temperatures, that means high electrical power and long heating time, and this reduction is more significant at lower packing pressures, indeed, at 360bar as packing pressure and 20s as heating time the shear layer disappear. The resulting morphology was analyzed by optical microscope.