gebhart/patrepeval huggingface dataset:
Functional and Spatial Analysis of C. elegans SYG-1 and SYG-2, Orthologs of the Neph/Nephrin Cell Adhesion Module Directing Selective Synaptogenesis (2011)

The assembly of specific synaptic connections represents a prime example of cellular recognition. Members of the Ig superfamily are among the most ancient proteins represented in the genomes of both mammalian and invertebrate organisms, where they constitute a trans-synaptic adhesion system. The correct connectivity patterns of the highly conserved immunoglobulin superfamily proteins nephrin and Neph1 are crucial for the assembly of functional neuronal circuits and the formation of the kidney slit diaphragm, a synapse-like structure forming the filtration barrier. Here, we utilize the nematode C. elegans model for studying the requirements of synaptic specificity mediated by nephrin-Neph proteins. In C. elegans, the nephrin/Neph1 orthologs SYG-2 and SYG-1 form intercellular contacts strictly in trans between epithelial guidepost cells and neurons specifying the localization of synapses. We demonstrate a functional conservation between mammalian nephrin and SYG-2. Expression of nephrin effectively compensated loss of syg-2 function in C. elegans and restored defective synaptic connectivity further establishing the C. elegans system as a valuable model for slit diaphragm proteins. Next, we investigated the effect of SYG-1 and SYG-2 trans homodimerization respectively. Strikingly, synapse assembly could be induced by homophilic SYG-1 but not SYG-2 binding indicating a critical role of SYG-1 intracellular signalling for morphogenetic events and pointing toward the dynamic and stochastic nature of extra- and intracellular nephrin-Neph interactions to generate reproducible patterns of synaptic connectivity.
Detection of CEBPA Double Mutants in Acute Myeloid Leukemia Using a Custom Gene Expression Array (2013)

Double (bi-allelic) mutations in the gene encoding the CCAAT/enhancer-binding protein-alpha (CEBPA) transcription factor have a favorable prognostic impact in acute myeloid leukemia (AML). Double mutations in CEBPA can be detected using various techniques, but it is a notoriously difficult gene to sequence due to its high GC-content. Here we developed a two-step gene expression classifier for accurate and standardized detection of CEBPA double mutations. The key feature of the two-step classifier is that it explicitly removes cases with low CEBPA expression, thereby excluding CEBPA hypermethylated cases that have similar gene expression profiles as a CEBPA double mutant, which would result in false-positive predictions. In the second step, we have developed a 55 gene signature to identity the true CEBPA double-mutation cases. This two-step classifier was tested on a cohort of 505 unselected AML cases, including 26 CEBPA double mutants, 12 CEBPA single mutants, and seven CEBPA promoter hypermethylated cases, on which its performance was estimated by a double-loop cross-validation protocol. The two-step classifier achieves a sensitivity of 96.2% (95% confidence interval [CI] 81.1 to 99.3) and specificity of 100.0% (95% CI 99.2 to 100.0). There are no false-positive detections. This two-step CEBPA double-mutation classifier has been incorporated on a microarray platform that can simultaneously detect other relevant molecular biomarkers, which allows for a standardized comprehensive diagnostic assay. In conclusion, gene expression profiling provides a reliable method for CEBPA double-mutation detection in patients with AML for clinical use.
Bagging based plankton image classification (2009)

Plankton image classification plays an important role in ocean biological research. In this paper, we present an approach based on the bagging technique to classify the marine plankton images captured by the shadowed image particle profiling and evaluation recorder. The difficulty of such classification is multifold because the data set is much noisier, and the plankton images are deformable, projection-variant, and often in partial occlusion. In addition, the images in our experiments are binary, thus are lack of pixel-depth information. By random sampling with replacement on the original training set, a number of independent bootstrap replicates are generated. Using these replicates as new training sets, we construct multiple classifiers that are complementary of one another. While such individual classifiers are less effective than a single classifier trained on the whole training set, the fusion of them using majority voting produces an improved tenfold cross-validation accuracy by more than 93%.
Multi-probe measurement technique for echo suppression in near-field measurements (2013)

Multipath propagation between the device under test and the probe antenna leads to an erroneous near-field distribution. Echo suppression techniques can be applied during data post-processing so that these errors are not carried over to the far-field. In this paper, a measurement technique which enhances a subsequent removal of the multipath components is presented. This is achieved by collecting additional near-field data with multiple probe antennas such that more information is obtained about the device under test and the measurement environment. The data so acquired is transformed using a well-adapted plane wave based near-field far-field transformation algorithm with the echo sources integrated by means of auxilliary sources.
Measurement-based simulation model for TCP over ATM (2003)

Cell level analysis of ATM networks by means of simulation requires an accurate model for traffic sources. We present a simple model for TCP over ATM traffic sources in an ATM LAN, which captures the fundamental characteristics of the behaviour of TCP in this environment. The model was developed by extensive statistical analysis of numerous traffic traces recorded in an ATM testbed. Simulated traffic generated by our model has roughly the same properties observed in real traffic, even on the time scale of milliseconds. This makes it suitable for use by the analysis of various scheduling and congestion management algorithms.
Multiphysics Simulation for TEM Objective Lens Evaluation & Design (2022)

Journal Article Multiphysics Simulation for TEM Objective Lens Evaluation & Design Get access Patrick McBean, Patrick McBean School of Physics, Trinity College Dublin, Dublin, IrelandAdvanced Microscopy Laboratory, Centre for Research on Adaptive Nanostructures & Nanodevices (CRANN), Dublin, Ireland Search for other works by this author on: Oxford Academic Google Scholar Zachary Milne, Zachary Milne Center for Integrated Nanotechnologies, Sandia National Laboratories. Albuquerque, NM, United States Search for other works by this author on: Oxford Academic Google Scholar Arjun Kanthawar, Arjun Kanthawar Center for Integrated Nanotechnologies, Sandia National Laboratories. Albuquerque, NM, United States Search for other works by this author on: Oxford Academic Google Scholar Khalid Hattar, Khalid Hattar Center for Integrated Nanotechnologies, Sandia National Laboratories. Albuquerque, NM, United States Search for other works by this author on: Oxford Academic Google Scholar Katherine Jungjohann, Katherine Jungjohann Center for Integrated Nanotechnologies, Sandia National Laboratories. Albuquerque, NM, United States Search for other works by this author on: Oxford Academic Google Scholar Lewys Jones Lewys Jones School of Physics, Trinity College Dublin, Dublin, IrelandAdvanced Microscopy Laboratory, Centre for Research on Adaptive Nanostructures & Nanodevices (CRANN), Dublin, Ireland Corresponding author: lewys.jones@tcd.ie Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 2494–2495, https://doi.org/10.1017/S1431927622009540 Published: 01 August 2022
Paraffin Wax Crystal Coarsening: Effects of Strains and Wax Crystal Shape (2019)

We developed a model of paraffin wax crystal coarsening that well describes our experimental results and allows behavior of the paraffin films to be predicted on the basis of the extracted kinetic parameters. Wax crystalline films were evaporated on different substrates (silicon wafer, glass slide, thin layer of gold on silicon), thermally treated at different temperatures, and investigated by powder X-ray diffraction, high-resolution scanning electron microscopy, and optical confocal imaging of the surfaces. Preferred (110) crystal orientation of all deposited wax films, independently of substrate type, was observed from the start and increased during heat treatment. The change in preferred orientation was accompanied by changes in crystal morphology and shape, resulting in surface nano-roughening. We modeled the process as the coarsening of oriented C36H74 crystal islands driven by the decrease in total surface energy. Coarsening kinetics was controlled by diffusion of single molecular chains along the substrate. Evolution of nano-roughness during annealing time was well described by a surface coarsening law. Two additional factors influenced the evolution rate: strains accumulated in wax crystals during deposition, and divergence of initial crystal shape from the shape at equilibrium. Both factors lowered activation energy and effectively shortened coarsening time.
Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves (2017)

DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
ESE: Efficient Speech Recognition Engine with Sparse LSTM on FPGA (2016)

Long Short-Term Memory (LSTM) is widely used in speech recognition. In order to achieve higher prediction accuracy, machine learning scientists have built larger and larger models. Such large model is both computation intensive and memory intensive. Deploying such bulky model results in high power consumption and leads to high total cost of ownership (TCO) of a data center. In order to speedup the prediction and make it energy efficient, we first propose a load-balance-aware pruning method that can compress the LSTM model size by 20x (10x from pruning and 2x from quantization) with negligible loss of the prediction accuracy. The pruned model is friendly for parallel processing. Next, we propose scheduler that encodes and partitions the compressed model to each PE for parallelism, and schedule the complicated LSTM data flow. Finally, we design the hardware architecture, named Efficient Speech Recognition Engine (ESE) that works directly on the compressed model. Implemented on Xilinx XCKU060 FPGA running at 200MHz, ESE has a performance of 282 GOPS working directly on the compressed LSTM network, corresponding to 2.52 TOPS on the uncompressed one, and processes a full LSTM for speech recognition with a power dissipation of 41 Watts. Evaluated on the LSTM for speech recognition benchmark, ESE is 43x and 3x faster than Core i7 5930k CPU and Pascal Titan X GPU implementations. It achieves 40x and 11.5x higher energy efficiency compared with the CPU and GPU respectively.
Cyclization of Trichloroacetimidates by Olefin Aminopalladation β‐Heteroatom Elimination (2009)

Abstract The cyclization of δ‐acetoxy‐ O ‐allyl‐ and ϵ‐acetoxy‐ O ‐homoallyl‐trichloroacetimidates to 4‐vinyloxazolines and a 4‐vinyldihydrooxazine has been efficiently achieved by olefin aminopalladation–β‐heteroatom elimination. ( Z )‐Allylic imidates bearing a secondary δ‐acetoxy group underwent Pd II ‐catalysed cyclization to give the E isomers of 4‐vinyloxazolines selectively and gave no Overman rearrangement products. Using a chiral substrate, it has been demonstrated that cyclization to 4‐vinyloxazolines occurs with high chirality transfer. Stereoselective E isomer formation and chirality transfer provided a basis from which to discuss the possible reaction mechanism. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Transient Cathodic Method to Measure Oxygen Diffusivity in Concrete (2019)

Abstract Oxygen diffusivity is a key parameter in modeling corrosion rate of steel in concrete. Measuring diffusivity can be a complicated and slow process, in conditions or geometries not always representative of those encountered by rebar in concrete. A method is introduced that eliminates some of those difficulties by using transient cathodic current measurements in reinforced concrete specimens subjected to alternating air/nitrogen mixtures. Kinetic parameters obtained from electrochemical testing were used as input to a physical model. Values of effective oxygen diffusing coefficients were obtained that are in the range of those reported in literature.
Initial Results with an Activated Pyrolytic Carbon Tip Electrode (1983)

The initial results acquired from testing of a new activated pyrocarbon electrode for cardiac pacing are presented. In vitro testing has shown energy efficiency to be higher than for platinum electrodes. Histologic examination of implanted leads in animals has demonstrated a less significant tissue reaction at the tip. Finally, in a clinical trial of 121 patients with these leads, strength-duration curves have low rheobase values. Chronic thresholds are often consistently low. These reports suggest very satisfactory results with this pyrolytic carbon electrode.
Utilization of anonymization techniques to create an external control arm for clinical trial data (2023)

Abstract Background Subject-level real-world data (RWD) collected during daily healthcare practices are increasingly used in medical research to assess questions that cannot be addressed in the context of a randomized controlled trial (RCT). A novel application of RWD arises from the need to create external control arms (ECAs) for single-arm RCTs. In the analysis of ECAs against RCT data, there is an evident need to manage and analyze RCT data and RWD in the same technical environment. In the Nordic countries, legal requirements may require that the original subject-level data be anonymized, i.e., modified so that the risk to identify any individual is minimal. The aim of this study was to investigate and compare how well pseudonymized and anonymized RWD perform in the creation of an ECA for an RCT. Methods This was a hybrid observational cohort study using clinical data from the control arm of the completed randomized phase II clinical trial (PACIFIC-AF) and RWD cohort from Finnish healthcare data sources. The initial pseudonymized RWD were anonymized within the ( k , ε )-anonymity framework (a model for protecting individuals against identification). Propensity score matching and weighting methods were applied to the anonymized and pseudonymized RWD, to balance potential confounders against the RCT data. Descriptive statistics for the potential confounders and overall survival analyses were conducted prior to and after matching and weighting, using both the pseudonymized and anonymized RWD sets. Results Anonymization affected the baseline characteristics of potential confounders only marginally. The greatest difference was in the prevalence of chronic obstructive pulmonary disease (4.6% vs. 5.4% in the pseudonymized compared to the anonymized data, respectively). Moreover, the overall survival changed in anonymization by only 8% (95% CI 4–22%). Both the pseudonymized and anonymized RWD were able to produce matched ECAs for the RCT data. Anonymization after matching impacted overall survival analysis by 22% (95% CI -21–87%). Conclusions Anonymization is a viable technique for cases where flexible data transfer and sharing are required. However, as anonymization necessarily affects some aspects of the original data, careful consideration of anonymization strategy is recommended.
Micellar Hybrid Nanoparticles for Simultaneous Magnetofluorescent Imaging and Drug Delivery (2008)

Multimodale Nanoassoziate aus magnetischen Nanopartikeln, Quantenpunkten und dem Tumortherapeutikum Doxorubicin in einer einzigen PEG-Phospholipid-Micelle wurden hergestellt (siehe Schema; PEG=Polyethylenglycol). Wenn diese Nanostrukturen das Zielpeptid F3 enthielten, ermöglichten sie simultan die gezielte Wirkstofffreigabe und das duale Abbilden von Tumorgewebe durch Nah-IR-Fluoreszenz und NMR-Spektroskopie.
Characterization of multilayer coatings by X-ray reflection (1988)

Methods to deduce the parameters of a multilayer X-ray mirror from its reflectivity curve are reviewed. Inversion methods are successful for coatings with few layers and give the thickness of each layer and the roughness of each interface. A statistical description of the coating is used for coatings with many layers, and simple formulas are given to derive the average thickness error and boundary roughness in a multilayer mirror.
Study of Mach Number Effect on Cruise Efficiency for a Co-Flow Jet General Aviation Airplane (2021)

View Video Presentation: https://doi.org/10.2514/6.2021-1303.vid This paper numerically studies the Mach number effect on cruise performance of a Co-Flow Jet (CFJ) general aviation (GA) airplane at freestream Mach number of 0.15, 0.30, and 0.46 with an aspect ratio of 21.3. An optimized CFJ-NACA-6421 airfoil is used for the CFJ wing. The advantages of using a thick airfoil are two folds: 1) higher cruise lift coefficient; 2) lighter weight. The numerical simulations employ the intensively validated in house FASIP CFD code, which utilizes a 3D RANS solver with Spalart-Allmaras (S-A) turbulence model, 3rd order WENO scheme for the inviscid fluxes, and 2nd order central differencing for the viscous terms. Two constant C_mu of 0.03 and 0.04 are studied to examine the effect on the aircraft cruise performance. The angle of attack (AoA) is held at 5deg corresponding to the optimal aerodynamic and productivity efficiency in the previous study for the wing performance at different Mach number. At C_mu of 0.03, the flow is very well attached for Mach 0.15, which gives the highest pure lift to drag ratio CL/CD, the corrected aerodynamic efficiency with CFJ power coefficient included (CL/CDc), and the productivity efficiency (CL^2/CDc. When the Mach number is increased to 0.46, the lift coefficient is increased by 8.6% from 1.16 to 1.26 due to the compressibility effect, but all the three aerodynamic performance parameters, CL/CD, (CL/CD)c, and (CL^2/CD)c drop substantially. The reason is that the a flow separation at the wing-fuselage junction occurs. The drag coefficient is significantly increased by 67% when the Mach number is increased form 0.15 to 0.46 due to the flow separation, higher skin friction drag, and higher induced drag. When the Cmu is increased to 0.04, the wing-fuselage junction flow separation is removed. The CFJ power coefficient is increased by 33%, but remains at a very low level due to the low energy expenditure feature of the CFJ flow control. The CL/CD, CL/CDc, and CL^2/CDc are significantly increased by 21.3%, 10.7%, and 19.8% respectively. In other words, the CFJ power increased due to Cmu of 0.04 at Mach 0.46 is converted to more system efficiency gain reflected by enhanced CL/CD_c and CL^2/CD)c, which include the CFJ power coefficient. The system efficiency gains are attributed to the increased CL and substantially reduced CD due to the removed flow separation at low CFJ energy expenditure.
Effect of pH on Polymerization of Silicic Acid (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of pH on Polymerization of Silicic AcidKatsumi GotoCite this: J. Phys. Chem. 1956, 60, 7, 1007–1008Publication Date (Print):July 1, 1956Publication History Published online1 May 2002Published inissue 1 July 1956https://pubs.acs.org/doi/10.1021/j150541a046https://doi.org/10.1021/j150541a046research-articleACS PublicationsRequest reuse permissionsArticle Views1091Altmetric-Citations62LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Comparative inhibitory effects of suramin and other selected compounds on the infectivity and replication of human T‐cell lymphotropic virus (HTLV‐III)/lymphadenopathy‐associated virus (LAV) (1986)

Suramin and various other selected compounds were evaluated for their in vitro inhibitory effects on the infectivity and replication of human T-cell lymphotropic virus (HTLV/III)/lymphadenopathy-associated virus (LAV). As parameters for infectivity and replication, respectively, we followed the cytopathic effect of HTLV-III/LAV on ATH 8 cells, a T-cell clone with high susceptibility to HTLV-III/LAV, and the expression of HTLV-III/LAV p24 gag protein in H9 cells infected with HTLV-III/LAV. As the most effective inhibitors of HTLV-III/LAV the following substances emerged (in order of decreasing activity): Evans Blue approximately equal to suramin greater than phosphonoformic acid greater than Direct Yellow 50. Several purine nucleoside analogues including vidarabine, tubercidin, neplanocin A, dihydroxypropyladenine, pyrazofurin and ribavirin were not inhibitory to HTLV-III/LAV. In our test systems, involving a high multiplicity of infection, HPA-23, previously reported to be effective against LAV reverse transcriptase, showed no inhibitory effect on HTLV-III/LAV infectivity for ATH 8 cells and proved only weakly inhibitory to HTLV-III/LAV replication in H9 cells. Thus, among the anionic dyes that are structurally related to suramin, compounds were found which were as active as suramin itself, if not more so.