gebhart/patrepeval huggingface dataset:
Transgenic Drosophila to Functionally Validate Fall Armyworm ABCC2 Mutations Conferring Bt Resistance (2023)

The fall armyworm (FAW), <i>Spodoptera frugiperda</i> (J.E. Smith; Lepidoptera: Noctuidae) is an invasive agricultural pest with a global distribution, causing major crop losses annually. Its control strategies largely rely on chemical insecticides and transgenic crops expressing <i>Bacillus thuringiensis</i> insecticidal proteins (Cry and Vip toxins); however, the development of high resistance poses a significant issue. The ATP-binding cassette transporter C2 (ABCC2) has been linked to Cry toxin pore formation, acting as a receptor of some Cry toxins. Recently detected mutations in the SfABCC2 gene in extracellular loop 4 (ECL4) have been associated with Bt toxin resistance in FAW. In the present study, we expressed the SfABCC2 gene in <i>Drosophila melanogaster</i>, a species normally unaffected by the Bt toxins. We demonstrate that susceptibility can be introduced by the ectopic and tissue-specific expression of wildtype SfABCC2. Next, we introduced mutations into ECL4-both individually and in combination-that have been recently described in Brazilian FAW and functionally validated by toxicity bioassays against the foliar Bt product Xentari. Our results provide an efficient demonstration of the suitability of transgenic <i>Drosophila</i> for validating FAW ABCC2 resistance mutations in ECL4 against Bt toxins, and potential cross-resistance issues between closely related proteins that use ABCC2.
P1‐377: BIIB092 DOES NOT INTERFERE WITH RADIOLABELED MK6240 BINDING TO NEUROFIBRILLARY TANGLES: RESULTS FROM IN VITRO COMPETITION BINDING STUDY IN ALZHEIMER'S BRAIN TISSUE SECTIONS (2019)

BIIB092 is a humanized monoclonal antibody that binds to the N-terminal region of tau that is currently in a phase 2 clinical trial in patients with mild cognitive impairment (MCI) or mild Alzheimer's disease (AD). [18F]-MK6240, a highly selective positron emission tomography (PET) imaging agent for measuring tau neurofibrillary tangles (NFT) associated with AD, is being leveraged to test the hypothesis that BIIB092-mediated removal of extracellular tau will inhibit the spread of NFT pathology in the brain. In order to confirm that the theraputic antibody (BIIB092) does not compete for the same binding site and thus interfere with [18F]-MK6240 binding to NFT, in vitro competition binding studies were conducted, the results of which are reported here. Autoradiography (ARG) experiments were conducted using both [3H]-MK6240 and [18F]-MK6240. Fresh frozen frontal or temporal gyrus tissue sections from Alzheimer's disease and control individuals (n=3 each for [18F] ARG; n=4 control / 5 AD for [3H] ARG) were employed. NFT pathology was confirmed using immunohistochemistry in all patient tissues. Sections were incubated with a single concentration of [3H]-MK6240 or [18F]-MK6240 and co-incubated with up to 10 mM of BIIB092 or isotype control antibody (negative control) or excess unlabeled MK6240 (positive control). Sections were then opposed to phosphor imager plates. For [18F]-MK6240 ARG, plates were scanned on Typhoon Imager FLA 7500 and analyzed with MCID. Competition of unlabeled agents with [18F]-MK6240 binding was quantified as % inhibition. For [3H]-MK6240 ARG, a tritium standard was included in each plate for quantification. Plates were scanned on Cyclone Storage phosphor system and analyzed with OptiQuant. [3H]-MK6240 binding was quantified as fmol/mg of protein. In the presence of unlabeled MK6240, [3H]-MK6240 and [18F]-MK6240 binding signal were both blocked as expected. Radiolabeled MK6240 binding signal was unaffected in the presence of up to 10 mM BIIB092 or isotype control antibody.
Rho GTPases Modulate Entry of Ebola Virus and Vesicular Stomatitis Virus Pseudotyped Vectors (2009)

To explore mechanisms of entry for Ebola virus (EBOV) glycoprotein (GP) pseudotyped virions, we used comparative gene analysis to identify genes whose expression correlated with viral transduction. Candidate genes were identified by using EBOV GP pseudotyped virions to transduce human tumor cell lines that had previously been characterized by cDNA microarray. Transduction profiles for each of these cell lines were generated, and a significant positive correlation was observed between RhoC expression and permissivity for EBOV vector transduction. This correlation was not specific for EBOV vector alone as RhoC also correlated highly with transduction of vesicular stomatitis virus GP (VSVG) pseudotyped vector. Levels of RhoC protein in EBOV and VSV permissive and nonpermissive cells were consistent with the cDNA gene array findings. Additionally, vector transduction was elevated in cells that expressed high levels of endogenous RhoC but not RhoA. RhoB and RhoC overexpression significantly increased EBOV GP and VSVG pseudotyped vector transduction but had minimal effect on human immunodeficiency virus (HIV) GP pseudotyped HIV or adeno-associated virus 2 vector entry, indicating that not all virus uptake was enhanced by expression of these molecules. RhoB and RhoC overexpression also significantly enhanced VSV infection. Similarly, overexpression of RhoC led to a significant increase in fusion of EBOV virus-like particles. Finally, ectopic expression of RhoC resulted in increased nonspecific endocytosis of fluorescent dextran and in formation of increased actin stress fibers compared to RhoA-transfected cells, suggesting that RhoC is enhancing macropinocytosis. In total, our studies implicate RhoB and RhoC in enhanced productive entry of some pseudovirions and suggest the involvement of actin-mediated macropinocytosis as a mechanism of uptake of EBOV GP and VSVG pseudotyped viral particles.
ONTOGENY OF HUMAN EPIDERMAL LANGERHANS CELLS (1984)

PELLETIER, MLCHELINE; PERREAULT, CLAUDE; LANDRY, DIANE; DAVID, MICHÈLE; MONTPLAISIR, SERGE Author Information
Sputtering process of Aluminum in Ar/He mixtures (2021)

In the frame of fusion research, the interaction of helium with various materials has been widely studied. For instance, it has been proved that He implantation in tungsten at high substrate temperature and low ion kinetic energy leads to the formation of fiberform nanostructures, called fuzz [1]. It has been observed that this nanostructure is formed at a kinetic energy below the atomic displacement threshold, and exhibits high porosity (90 %), which could be of great interest for various applications (light absorption, catalysis etc.). Further investigations have evidenced the formation of various porous structures on molybdenum, nickel, iron or aluminum surfaces [2]. The underlying formation mechanism seems to be related to the very particular behavior of He inside metal lattices [3]. To take advantage of He insertion and release at metal surfaces, several authors have investigated the deposition of metal thin films by magnetron sputtering in helium gas. Various results have been obtained like formation of He filled bubbles in the film thickness and/or apparition of porosity [4,5]. In the present work, we studied Al target sputtering in various He/Ar mixtures in the aim to synthesize nanostructured films for hydrogen production application. The evolution of the magnetron discharge depending on the He percentage in the gas phase was characterized by following the cathode voltage at a fixed current. By comparing with the deposition rate evolution, three sputtering regimes have been evidenced leading to very different depositions conditions at the substrate and thus, to different film morphologies. The nature and energy distribution function of sputtered and backscattered atoms from the target were analysed by performing SRIM simulations. The ion energy distribution function of Al + , Ar + and He + ions was determined using mass spectrometry. Good correlations have been obtained between calculations and experiments for sputtered Al atoms. Nevertheless, unexpected Ar + and He + distribution functions were found at high He % and/or low gas pressure inside the chamber. Moreover, SRIM simulations predict that high energy He + (60 eV) are backscattered at the target, reaching the substrate. Since they are neutralized at the target, they were not detected, although their role on film growth seems tremendous. Therefore, this poster will give us the opportunity to discuss both problems.
Multi-Shell Hybrid Diffusion Imaging (HYDI) at 7 Tesla in TgF344-AD Transgenic Alzheimer Rats (2015)

Diffusion weighted imaging (DWI) is widely used to study microstructural characteristics of the brain. Diffusion tensor imaging (DTI) and high-angular resolution imaging (HARDI) are frequently used in radiology and neuroscience research but can be limited in describing the signal behavior in composite nerve fiber structures. Here, we developed and assessed the benefit of a comprehensive diffusion encoding scheme, known as hybrid diffusion imaging (HYDI), composed of 300 DWI volumes acquired at 7-Tesla with diffusion weightings at b = 1000, 3000, 4000, 8000 and 12000 s/mm2 and applied it in transgenic Alzheimer rats (line TgF344-AD) that model the full clinico-pathological spectrum of the human disease. We studied and visualized the effects of the multiple concentric "shells" when computing three distinct anisotropy maps-fractional anisotropy (FA), generalized fractional anisotropy (GFA) and normalized quantitative anisotropy (NQA). We tested the added value of the multi-shell q-space sampling scheme, when reconstructing neural pathways using mathematical frameworks from DTI and q-ball imaging (QBI). We show a range of properties of HYDI, including lower apparent anisotropy when using high b-value shells in DTI-based reconstructions, and increases in apparent anisotropy in QBI-based reconstructions. Regardless of the reconstruction scheme, HYDI improves FA-, GFA- and NQA-aided tractography. HYDI may be valuable in human connectome projects and clinical research, as well as magnetic resonance research in experimental animals.
Rapid changes in the gut microbiome during human evolution (2014)

Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.
Synthesis of some carbocyclic nucleoside analogues based on a bicyclo[3.1.0]hexane ring system (1994)

H. Gooding, S. M. Roberts and R. Storer, J. Chem. Soc., Perkin Trans. 1, 1994, 1891 DOI: 10.1039/P19940001891
ON THE FEASIBILITY OF STEERING SWALLOWABLE MICROSYSTEM CAPSULES USING COMPUTER-AIDED MAGNETIC LEVITATION (2008)

Swallowable capsule endoscopy is used for non-invasive diagnosis of some gastrointestinal (GI)\norgans. However, control over the position of the capsule is a major unresolved issue. This study presents a\ndesign for steering the capsule based on magnetic levitation. The levitation is stabilized with the aid of a\ncomputer-aided feedback control system and diamagnetism. Peristaltic and gravitational forces to be overcome\nwere calculated. A levitation setup was built to analyze the feasibility of using Hall Effect sensors to locate the in-\nvivo capsule. CAD software Maxwell 3D (Ansoft, Pittsburgh, PA) was used to determine the dimensions of the\nresistive electromagnets required for levitation and the feasibility of building them was examined. Comparison\nbased on design complexity was made between positioning the patient supinely and upright.
Current Status of Solid-State X-Ray Systems (1985)

Solid state x-ray sensing systems have been used for many years in conjunction with scanning and transmission electron microscopes. Such systems conveniently provide users with elemental area maps and quantitative chemical analyses of samples. Improvements on these tools are currently sought in the following areas: sensitivity at longer and shorter x-ray wavelengths and minimization of noise-broadening of spectral lines. In this paper, we review basic limitations and recent advances in each of these areas. Throughout the review, we emphasize the systems nature of the problem. That is. limitations exist not only in the sensor elements but also in the preamplifier/amplifier chain and in the interfaces between these components. Solid state x-ray sensors usually function by way of incident photons creating electron-hole pairs in semiconductor material. This radiation-produced mobile charge is swept into external circuitry by electric fields in the semiconductor bulk.
New Steroidal 4-Aminoquinolines Antagonize Botulinum Neurotoxin Serotype A in Mouse Embryonic Stem Cell Derived Motor Neurons in Postintoxication Model (2018)

The synthesis and inhibitory potencies against botulinum neurotoxin serotype A light chain (BoNT/A LC) using in vitro HPLC based enzymatic assay for various steroidal, benzothiophene, thiophene, and adamantane 4-aminoquinoline derivatives are described. In addition, the compounds were evaluated for the activity against BoNT/A holotoxin in mouse embryonic stem cell derived motor neurons. Steroidal derivative 16 showed remarkable protection (up to 89% of uncleaved SNAP-25) even when administered 30 min postintoxication. This appears to be the first example of LC inhibitors antagonizing BoNT intoxication in mouse embryonic stem cell derived motor neurons (mES-MNs) in a postexposure model. Oral administration of 16 was well tolerated in the mouse up to 600 mg/kg, q.d. Although adequate unbound drug levels were not achieved at this dose, the favorable in vitro ADMET results strongly support further work in this series.
Optical Properties of Three-Band White Light Emitting Diodes (2003)

A phosphor was synthesized using a decomposition method without the use of toxic gas. and ZnCdS:Ag,Cl phosphors were chosen to produce green and red emissions, respectively, under excitation from a blue light emitting diode (LED). A three band white LED was obtained through a combination of nonabsorbed blue emission from a blue LED and green and red emissions from the and ZnCdS:Ag,Cl phosphors. The optical properties of the three band white LED are also discussed. © 2003 The Electrochemical Society. All rights reserved.
Poorly Differentiated Prostate Cancer Treated With Radical Prostatectomy: Long-Term Outcome and Incidence of Pathological Downgrading (2006)

Patients diagnosed with poorly differentiated prostate cancer (Gleason score 8 to 10) on biopsy do not uniformly have a poor prognosis. Of the patients 39% remain free of cancer recurrence 10 years after radical prostatectomy. Of these cancers 45% have a lower Gleason score in the radical prostatectomy specimen and a correspondingly more favorable long-term outcome. Predictors of downgrading are lower clinical stage (cT1c) and Gleason score 8 in the biopsy specimen.
Multiaccurate Proxies for Downstream Fairness (2022)

We study the problem of training a model that must obey demographic fairness conditions when the sensitive features are not available at training time — in other words, how can we train a model to be fair by race when we don’t have data about race? We adopt a fairness pipeline perspective, in which an “upstream” learner that does have access to the sensitive features will learn a proxy model for these features from the other attributes. The goal of the proxy is to allow a general “downstream” learner — with minimal assumptions on their prediction task — to be able to use the proxy to train a model that is fair with respect to the true sensitive features. We show that obeying multiaccuracy constraints with respect to the downstream model class suffices for this purpose, provide sample- and oracle efficient-algorithms and generalization bounds for learning such proxies, and conduct an experimental evaluation. In general, multiaccuracy is much easier to satisfy than classification accuracy, and can be satisfied even when the sensitive features are hard to predict.
Diffusion coefficients of fluorescent organic molecules in inert gases (2013)

We use arrested-flow pulse broadening to measure the diffusion coefficients of four archetype organic semiconductors in two carrier gases, N2 and Ar, with a precision of 5%. The measurements are realized by the injection and transport of pulses of organic molecules in an organic vapor phase deposition chamber, followed by their detection using laser induced fluorescence that dynamically measures the organic concentration in the gas phase. Measurements show that the diffusivity of tris(8-hydroxyquinoline) aluminum (Alq3) in N2 and Ar varies as the square of the temperature and inversely with pressure over a large range of gas conditions. We show that classical Chapman-Enskog theory can be used to approximate the diffusivity with an accuracy that depends on the physical dimensions of the organic molecular species, with the most accurate predictions for spherical and rigid molecules such as Alq3.
Hierarchy-driven Exploration of Multidimensional Data Cubes (2007)

Analysts interact with OLAP data in a predominantly drill-down fashion, i.e. gradually descending from a coarsely grained overview towards the desired level of detail. Analysis tools enable visual exploration as a sequence of navigation steps in the data cubes and their dimensional hierarchies. However, most state-of-the-art solutions are limited either in their capacity to handle complex multidimensional data or in the ability of their visual metaphors to provide an overview+details context. This work proposes an explorative framework for OLAP data based on a simple but powerful approach to analyzing data cubes of virtually arbitrary complexity. The data is queried using an intuitive navigation in which each dimension is represented by its hierarchy schema. Any granularity level can be dragged into the visualization to serve as an disaggregation axis. The results of the iterative exploration are mapped to a specified visualization technique. We favor hierarchical layouts for their natural ability to show step-wise decomposition of aggregate values. The power of the tool to support various application scenarios is demonstrated by presenting use cases from different domains and the visualization techniques suitable for solving specific analysis tasks.
Design, Fabrication, and Characterization of Photonic Devices. (1999)

Future technology and business opportunities in photonics: a view from the Optoelectronics Industry Development Association (OIDA), Oxide-confined vertical-cavity surface-emitting lasers, quantum dots, and the Purcell effect: can scaling the mode size improve laser performance?, Optical nonlinearities in semiconductors, Recent progress of photonic device research, Measurement of mounting-induced strain in high-power laser diode arrays (Invited Paper) Fabrication and characterization of high-power diode lasers, Stimulated emission and pump-probe studies of wide-gap nitrides for UV-blue photonic applications (Invited Paper), Optical properties of InGaN grown by MOCVD on sapphire and on bulk GaN, Comparison of optical properties of GaN and InGaN quantum,well structures, and Low-cost synthesis of ZnCdSe semiconducting thin films for optoelectronic applications.
An arithmetic intersection formula for denominators of Igusa class polynomials (2012)

In this paper we prove an explicit formula for the arithmetic intersection number (CM(K).G1)_{\ell} on the Siegel moduli space of abelian surfaces, generalizing the work of Bruinier-Yang and Yang. These intersection numbers allow one to compute the denominators of Igusa class polynomials, which has important applications to the construction of genus 2 curves for use in cryptography. Bruinier and Yang conjectured a formula for intersection numbers on an arithmetic Hilbert modular surface, and as a consequence obtained a conjectural formula for the intersection number (CM(K).G1)_{\ell} under strong assumptions on the ramification of the primitive quartic CM field K. Yang later proved this conjecture assuming that O_K is freely generated by one element over the ring of integers of the real quadratic subfield. In this paper, we prove a formula for (CM(K).G1)_{\ell} for more general primitive quartic CM fields, and we use a different method of proof than Yang. We prove a tight bound on this intersection number which holds for all primitive quartic CM fields. As a consequence, we obtain a formula for a multiple of the denominators of the Igusa class polynomials for an arbitrary primitive quartic CM field. Our proof entails studying the Embedding Problem posed by Goren and Lauter and counting solutions using our previous article that generalized work of Gross-Zagier and Dorman to arbitrary discriminants.
A novel frequency-dependent-model for electric conductors (2009)

This paper deals with the inclusion of frequency effects (skin effect) in an enhanced transport delay model for electric cables of arbitrary length connected to a PWM-IGBT-Variable Frequency Drive (VFD), to better predict overvoltage peaks in the lin
A Comprehensive Geophysical Case Study at a Former Radioactive Waste Disposal Site in the Columbia River Valley, Southeastern Washington (2005)

As part of a site investigation, sponsored by the United States Department of Energy, at the Hanford superfund site in southeastern Washington, a magnetics, electromagnetics (EM), and resistivity survey was completed. A dense coverage of geo‐referenced EM and magnetics data was simultaneously obtained over the 50‐acre site to delineate the location of buried waste disposal trenches in the Hanford alluvial formation. Radioactive contaminants of concern in the trenches consisted of Uranium, Plutonium, Cesium, Strontium, and Technetium. The EM and magnetics results confirmed suspected trench locations and the location of pipelines used to transport the liquid waste to the trenches. High resolution resistivity (HRR), conducted in a pole‐pole array, was used to image the vertical and lateral distribution of the electrical resistivity beneath a single trench. Five parallel lines of lengths 200m to 300m and spaced approximately 8m apart indicated that the plume has migrated downward from the trench to 30m below ground surface. A hydraulically resistive layer of fine silt has significantly impeded the plume from reaching the water table. An additional line, which bisected several trenches, suggested that the plume is extensive and the contributions from each trench combine to form a single contiguous plume. Remediation strategies are currently being considered.
Room Temperature Deoxyfluorination of Benzaldehydes and α-Ketoesters with Sulfuryl Fluoride and Tetramethylammonium Fluoride (2019)

A method for the room temperature deoxyfluorination of benzaldehydes and α-ketoesters using sulfuryl fluoride and Me<sub>4</sub>NF is described. A large scope of aryl and heteroaryl substrates is demonstrated, and this method compares favorably to other common deoxyfluorination methods for many substrates.