gebhart/patrepeval huggingface dataset:
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal to noise fluorescence (2022)

Abstract The expanded application of fluorescence imaging in biomedical and biological research towards more complex systems and geometries requires tools that can analyze a multitude of components at widely varying time- and length-scales. The major challenge in such complex imaging experiments is to cleanly separate multiple fluorescent labels with overlapping spectra from one another and background autofluorescence, without perturbing the sample with high levels of light. Thus, there is a requirement for efficient and robust analysis tools capable of quantitatively separating these signals. In response, we have combined multispectral fluorescence microscopy with hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). Here we demonstrate its capabilities in the dynamic imaging of multiple fluorescent labels in live, developing zebrafish embryos. HyU is more sensitive to low light levels of fluorescence compared to conventional linear unmixing approaches, permitting better multiplexed volumetric imaging over time, with less bleaching. HyU can also simultaneously image both bright exogenous and dim endogenous labels because of its high dynamic range. This allows studies of cellular behaviors, tagged components, and cell metabolism within the same specimen, offering a powerful window into the orchestrated complexity of biological systems.
Dependence of Composite Properties Upon Statistical Variations in Fiber Length (2008)

It is proposed that in high fiber-fraction composites with relatively weak matrices, final fracture and toughness may be more dependent upon architectural details than upon crack behavior in the matrix phase. Specifically, implications of statistical variations in fiber length are considered. A simple analytical model for the stress-strain behavior of a fiber dominated composite is described. Characteristics of the model are discussed with regard to existing experimental data.
Computational overlay metrology with adaptive data analytics (2017)

With photolithography as the fundamental patterning step in the modern nanofabrication process, every wafer within a semiconductor fab will pass through a lithographic apparatus multiple times. With more than 20,000 sensors producing more than 700GB of data per day across multiple subsystems, the combination of a light source and lithographic apparatus provide a massive amount of information for data analytics. This paper outlines how data analysis tools and techniques that extend insight into data that traditionally had been considered unmanageably large, known as adaptive analytics, can be used to show how data collected before the wafer is exposed can be used to detect small process dependent wafer-towafer changes in overlay.
Multivalued mappings in generalized chaos synchronization (2001)

The onset of generalized synchronization of chaos in directionally coupled systems corresponds to the formation of a continuous mapping that enables one to persistently define the state of the response system from the trajectory of the drive system. A recently developed theory of generalized synchronization of chaos deals only with the case where this synchronization mapping is a single-valued function. In this paper, we explore generalized synchronization in a regime where the synchronization mapping can become a multivalued function. Specifically, we study the properties of the multivalued mapping that occurs between the drive and response systems when the systems are synchronized with a frequency ratio other than one-to-one, and address the issues of the existence and continuity of such mappings. The basic theoretical framework underlying the considered synchronization regimes is then developed.
One‐Pot Three‐Component Highly Selective Synthesis of Homoallylboronates by Using Metal‐Free Catalysis (2012)

Metal-free selectivity: The first metal-free one-pot three-component highly chemo- and regioselective catalytic synthesis of homoallylboranes using simple N-heterocyclic carbenes (NHC) and amines is presented. The catalytic reaction between B2(pin)2, α,β-unsaturated aldehydes and 2-(triphenylphosphoranylidene)acetate esters proceeds through a catalytic metal-free β-boration/Wittig cascade sequence (see scheme).
AssemblyNet: A Novel Deep Decision-Making Process for Whole Brain MRI\n Segmentation (2019)

Whole brain segmentation using deep learning (DL) is a very challenging task\nsince the number of anatomical labels is very high compared to the number of\navailable training images. To address this problem, previous DL methods\nproposed to use a global convolution neural network (CNN) or few independent\nCNNs. In this paper, we present a novel ensemble method based on a large number\nof CNNs processing different overlapping brain areas. Inspired by parliamentary\ndecision-making systems, we propose a framework called AssemblyNet, made of two\n"assemblies" of U-Nets. Such a parliamentary system is capable of dealing with\ncomplex decisions and reaching a consensus quickly. AssemblyNet introduces\nsharing of knowledge among neighboring U-Nets, an "amendment" procedure made by\nthe second assembly at higher-resolution to refine the decision taken by the\nfirst one, and a final decision obtained by majority voting. When using the\nsame 45 training images, AssemblyNet outperforms global U-Net by 28% in terms\nof the Dice metric, patch-based joint label fusion by 15% and SLANT-27 by 10%.\nFinally, AssemblyNet demonstrates high capacity to deal with limited training\ndata to achieve whole brain segmentation in practical training and testing\ntimes.\n
Endoscopic Ultrasound–Guided Biopsy for The Diagnosis of Focal Lesions of The Spleen (2003)

EUS-FNA cytodiagnosis in patients with unknown splenic lesions seems feasible, even in very small foci, when CT- or US-guided biopsy fails. Additional material for bacteriology may show benign treatable diseases such as abscesses or tuberculosis.
Pre-sensitized B-cells prevent anti-CD154 mediated cardiac allograft tolerance (102.21) (2007)

Abstract Memory T-cells have been identified to be a significant cause of costimulatory resistant rejection; however, the role of pre-sensitized B cells has yet to be elucidated. We have developed a heart transplant model that specifically generates allospecific memory B-cells without generating allospecific memory T-cells. Pre-sensitized 3.83 B-cells with dual-specificity for H-2Kk and H-2Kb were generated in 3.83 BCR (BALB/c background) knock-in mice that received C3H (H-2Kk) hearts. To test whether pre-sensitized 3.83 B-cells can prevent tolerance induction by α-CD154 treatment, C3H-primed 3.83 recipients (30–90d post-C3H heart transplant) received a second heart and treatment with α-CD154. Second B/6 hearts (H-2Kb), which can be recognized by the pre-sensitized 3-83 B-cells, were acutely rejected within 10–13 days despite α-CD154 therapy. To confirm the importance of the pre-sensitized B cells, we transferred only B-cells or T-cells from C3H-presensitized 3.83 mice into naïve BALB/c recipients treated with α-CD154. Only transferred B-cells, but not T-cells, abrogated the tolerogenic effects of α-CD154. Histological examination of the rejected grafts from pre-sensitized 3-83 recipients treated with α-CD154 revealed significant numbers of infiltrating T cells. Also, B/6-specific IFNγ-producing T cells were detected in the pre-sensitized 3.83 recipients treated with α-CD154, but not in similarly treated naïve 3-83 recipients. We conclude that pre-sensitized B-cells are sufficient to prevent tolerance induction by permitting the CD40-CD40L independent activation of alloreactive T cells. Funding source: NIH Immunology Training Grant.
A Robust and Scalable Harmonic Cancellation Digital Predistortion Technique for HF Transmitters (2020)

High frequency (HF) transmitter implemented with the multioctave broadband power amplifier (PA) enables long-distance communication and has strong survivability. However, it is faced with the problem of harmonics because of the nonlinearity of the PA. We first consider canceling the harmonics using a harmonic cancellation digital predistortion (HC-DPD) technique, instead of lossy and bulky analog filter banks. A uniform complex-valued Hilbert transform-based polynomial (HTBP) function is proposed for the modeling of the harmonics, as well as the fundamental component in the real-valued input and output signals. In order to validate this idea, detailed experiments were performed for carrier frequencies located at 5 and 10 MHz, respectively. After the proposed HC-DPD, the harmonics were all canceled to satisfy the linearization requirements. In particular, the improvement of the second harmonic is more than 40 dB, which is nearly 20 dB better than that of the memoryless polynomial (MLP) model. Furthermore, the experimental results demonstrate that the proposed technique is scalable, in which the model coefficients extracted at a specific power level, signal bandwidth, and carrier frequency can be extended to other scenarios. Both the second and third harmonics were canceled for being below -45 dBc after the HC-DPD.
FedML: A Research Library and Benchmark for Federated Machine Learning (2020)

Federated learning (FL) is a rapidly growing research field in machine learning. However, existing FL libraries cannot adequately support diverse algorithmic development; inconsistent dataset and model usage make fair algorithm comparison challenging. In this work, we introduce FedML, an open research library and benchmark to facilitate FL algorithm development and fair performance comparison. FedML supports three computing paradigms: on-device training for edge devices, distributed computing, and single-machine simulation. FedML also promotes diverse algorithmic research with flexible and generic API design and comprehensive reference baseline implementations (optimizer, models, and datasets). We hope FedML could provide an efficient and reproducible means for developing and evaluating FL algorithms that would benefit the FL research community. We maintain the source code, documents, and user community at https://fedml.ai.
Severe Life-Threatening or Disabling Anaphylaxis in Patients with Systemic Mastocytosis: A Single-Center Experience (2011)

SM may be accompanied by life-threatening mediator-related symptoms. Most of these patients have indolent SM or SSM. In patients with SSM(SY) with uncontrolled symptoms (grade IV), therapy with 2CdA should be considered.
CTR plasma engineering studies. Progress report, 1 September 1975--30 Jun 1976 (1976)

During the past contract period, this research has been concerned with three principal tasks, namely: (1) Fusion-product studies. The primary objective of this work is to study potential effects (e.g. instabilities, changes in heating profile and wall loadings, etc.) caused by high-energy fusion products. A second objective is to establish the operating conditions and measurements required for use of D-/sup 3/He in early experiments such as TFTR to simulate D-T burns. (2) Mirror system studies. The objective of this work is to provide specialized support for the mirror research and development effort at the Lawrence Livermore Laboratory. Three topics are under study: charge-exchange losses during neutral beam injection; the dynamics of plasma build-up during start-up; new approaches to mirror systems such as the ''twin-beam'' mirror. (3) Exploratory studies. Several new studies have been initiated during this period. These include: extension of the mirror neutral-beam injection studies to toroidal geometry and preliminary studies of reversed field configurations. Further details about each of these areas are contained in subsequent sections.
Nitrite reductase from Pseudomonas aeruginosa induces inflammatory cytokines in cultured respiratory cells (1997)

Persistent infection with Pseudomonas aeruginosa increases interleukin-8 (IL-8) levels and causes dense neutrophil infiltrations in the airway of patients with chronic airway diseases. To investigate the role of P. aeruginosa infection in IL-8 production in the airway of these patients, we examined whether cell lysates of P. aeruginosa could cause IL-8 production from human bronchial epithelial cells. Diluted sonicated supernatants of P. aeruginosa (SSPA) with a mucoid or nonmucoid phenotype stimulated human bronchial epithelial (BET-1A) cells to produce IL-8. In this study, we have purified a 59-kDa heat-stable protein with IL-8-inducing activity from the SSPA by sequential ion-exchange chromatography. The N-terminal sequence of this purified protein completely matched a sequence at the N-terminal part of the mature protein of nitrite reductase from P. aeruginosa. In addition, immunoblotting with a polyclonal immunoglobulin G (IgG) against recombinant Pseudomonas nitrite reductase demonstrated a specific binding to the purified protein. Furthermore, the immunoprecipitates of the SSPA with a polyclonal IgG against recombinant nitrite reductase induced a twofold-higher IL-8 production in the BET-1A cell culture than did the immunoprecipitates of the SSPA with a control IgG. These lines of evidence confirmed that Pseudomonas nitrite reductase was responsible for IL-8 production in the BET-1A cells. The purified nitrite reductase induced maximal expression of IL-8 mRNA in the BET-1A cells at 1 to 3 h after stimulation, and the IL-8 mRNA expression declined by 8 h after stimulation. New protein translation was not required for nitrite reductase-mediated IL-8 mRNA expression in the BET-1A cells. Nitrite reductase stimulated the BET-1A cells, as well as human alveolar macrophages, pulmonary fibroblasts, and neutrophils, to produce IL-8. In contrast, nitrite reductase induced significant levels of tumor necrosis factor alpha and IL-1beta protein only in human alveolar macrophages. These data support the notion that nitrite reductase from P. aeruginosa induces the production of inflammatory cytokines by respiratory cells and may contribute to the pathogenesis of chronic airway diseases and persistent P. aeruginosa infection.
Semi-supervised normalized embeddings for land-use classification from multiple view data (2018)

Land-use classification from multiple data sources is an important problem in remote sensing. Data fusion algorithms like Semi-Supervised Manifold Alignment (SSMA) and Manifold Alignment with Schroedinger Eigenmaps (SEMA) use spectral and/or spatial features from multispectral, multimodal imagery to project each data source into a common latent space in which classification can be performed. However, in order for these algorithms to be well-posed, they require an expert user to either directly identify pairwise dissimilarities in the data or to identify class labels for a subset of points from which pairwise dissimilarities can be derived. In this paper, we propose a related data fusion technique, which we refer to as Semi-Supervised Normalized Embeddings (SSNE). SSNE is defined by modifying the SSMA/SEMA objective functions to incorporate an extra normalization term that enables a latent space to be well-defined even when no pairwise-dissimilarities are provided. Using publicly available data from the 2017 IEEE GRSS Data Fusion Contest, we show that SSNE enables similar land-use classification performance to SSMA/SEMA in scenarios where pairwise dissimilarities are available, but that unlike SSMA/SEMA, it also enables land-use classification in other scenarios.
Interferon Messenger RNA: Translation in Heterologous Cells (1972)

A viral inhibitor with the characteristics of mouse interferon is produced by avian and simian cells preincubated with RNA extracted from interferon-producing mouse cells. Similarly, RNA extracted from interferon-producing monkey cells induces a monkey interferon-like substance in avian cells and also in a line of simian cells, VERO, which normally lacks the capacity to produce its own interferon. In both cases, the RNA effect is inhibited by treatment of the receptor cells by cycloheximide, but not by actinomycin D. We conclude that interferon messenger RNA has been translated in the receptor cells. Thus, the production of interferon in heterologous cells can be used as a sensitive assay of interferon messenger RNA.
The ZNF217 gene amplified in breast cancers promotes immortalization of human mammary epithelial cells. (2001)

The functional consequences of overexpression of a candidate oncogene on chromosome 20q13.2, ZNF217, were examined by transducing the gene into finite life span human mammary epithelial cells (HMECs). In four independent experiments, ZNF217-transduced cultures gave rise to immortalized cells. HMECs that overcame senescence initially exhibited heterogeneous growth and continued telomere erosion, followed by increasing telomerase activity, stabilization of telomere length, and resistance to transforming growth factor beta growth inhibition. The incremental changes in telomerase activity and growth that occurred in ZNF217-transduced cultures after they overcame senescence were similar to the conversion pattern we have described previously in rare HMEC lines immortalized after exposure to a chemical carcinogen. Aberrant expression of ZNF217 may be selected for during breast cancer progression because it allows breast cells to overcome senescence and attain immortality.
Circulating Spexin Levels Negatively Correlate With Age, BMI, Fasting Glucose, and Triglycerides in Healthy Adult Women (2018)

Circulating spexin levels decrease with age, suggesting a possible role of this peptide in aging-related functions and disorders. Further investigations are needed to expand the clinical significance of this finding.
Numerical investigation of oil droplet combustion using single particle ignition cell model (2020)

Pre-ignition in internal combustion engines is an abnormal combustion phenomenon which often results in structural damage to the engine. It occurs when an ignition event takes place in the combustion chamber before the designed ignition time. In this work, a numerical study was done to investigate the pre-ignition with potential application to natural gas marine engines. This was done by simulating experiments of lube oil–induced ignition and subsequent combustion in a constant volume combustion chamber using an in-house version of the KIVA4-CFD code. Initial conditions of the chamber gases are obtained from the pre-burn process of a known composition of C 2 H 2 /oxidizer mixture. Natural gas was injected from a single-hole injector at an injection temperature and pressure of 300 K and 10 5 Pa, respectively. A rotating fan was modeled, as is in the experimental setup. Oil droplet of known size and velocity is injected into the constant volume combustion chamber. For accurate prediction of oil droplet ignition, the computational cells that contain the droplets are to be refined. Combustion calculations are then carried out on the refined grid. Ignition delay times of both lube oil and methane/air mixtures were calculated. Parametric studies were also conducted by varying droplet conditions, and their results are also presented.
Recurrent Inference Machines as inverse problem solvers for MR relaxometry (2021)

In this paper, we propose the use of Recurrent Inference Machines (RIMs) to perform T1 and T2 mapping. The RIM is a neural network framework that learns an iterative inference process based on the signal model, similar to conventional statistical methods for quantitative MRI (QMRI), such as the Maximum Likelihood Estimator (MLE). This framework combines the advantages of both data-driven and model-based methods, and, we hypothesize, is a promising tool for QMRI. Previously, RIMs were used to solve linear inverse reconstruction problems. Here, we show that they can also be used to optimize non-linear problems and estimate relaxometry maps with high precision and accuracy. The developed RIM framework is evaluated in terms of accuracy and precision and compared to an MLE method and an implementation of the ResNet. The results show that the RIM improves the quality of estimates compared to the other techniques in Monte Carlo experiments with simulated data, test-retest analysis of a system phantom, and in-vivo scans. Additionally, inference with the RIM is 150 times faster than the MLE, and robustness to (slight) variations of scanning parameters is demonstrated. Hence, the RIM is a promising and flexible method for QMRI. Coupled with an open-source training data generation tool, it presents a compelling alternative to previous methods.
Deliverable 5.1 Preliminary evaluation results and plan for proof-of-concept demonstrations (2022)

This document presents the current status of DAEMON WP5 activities. It presents the validation activities, performance evaluations and functional assessment tests of all the NI-solutions developed in WP3 and WP4 to date. The performance evaluation aims at meeting 9 target KPIs in well-defined scenarios, which are measured and assessed by developing 7 evaluations. Each evaluation relies on a set of technical tools, employed to perform 23 experimental activities. Such activities target different facets of a single evaluation.
Spatial Distribution of Distortion due to Nonlinear Power Amplification in Distributed Massive MIMO (2021)

Due to the nonlinearity of power amplifiers (PAs), the transmit signal is distorted. Previous works have studied the spatial distribution of this distortion for a central massive multiple input multiple output (MIMO) array. In this work, we extend the analysis for distributed massive MIMO in a line-of-sight (LoS) scenario. We show that the distortion is not always uniformly distributed in space. In the single-user case, it coherently combines at the user location. In the few users case, the signals will add up at the user locations plus several others locations. As the number of users increases, it becomes close to uniformly distributed. As a comparison with a central massive MIMO system, having the same total number of antennas, the distortion in distributed massive MIMO is considerably more uniformly distributed in space. Moreover, the potential coherent combining is contained in a zone rather than in generic directions, i.e., in a beamspot. Furthermore, a small-scale fading effect is observed at unintended locations due to the non-coherent combining of the signals. As a result, one can expect that going towards distributed systems allows working closer to saturation, increasing the PA operating efficiency and/or using low-cost PAs.
Expression of Mouse Histone Genes: Transcription into 3′ Intergenic DNA and Cryptic Processing Sites Downstream from the 3′ End of the H3 Gene (1987)

Introduction of the mouse histone H3.1 gene into tk- mouse L cells by cotransfection with the herpesvirus thymidine kinase gene resulted in the production of two mRNAs from the transfected gene, one with a normal 3' end and the other one with a longer 3'-untranslated region, ending at site X, which was poly(A)+. In contrast, the endogenous histone H3.1 gene only produced a single mRNA. The cryptic poly(A)+ site was only used when the histone H3.1 gene was transfected. To localize possible downstream cryptic processing sites, the hairpin loop at the end of the histone gene was deleted and the resulting deletions were introduced into L cells. Two major mRNAs were produced from this gene, one ending at site X and the major one ending at site Y, which was located 150 nucleotides before site X. Transcription extended downstream of site X efficiently in the endogenous gene, as judged by the extent of transcription of downstream sequences in isolated nuclei. Transcription extended downstream of site X in the transfected gene because the placement of a normal histone 3' end downstream of site X resulted in transcripts that ended at site X and longer transcripts that ended with the new histone 3' end. These results indicate that transcription may normally proceed a substantial distance past the hairpin loop (greater than 500 bases). The formation of the different 3' ends in these transfected genes was due to competition between different processing mechanisms.