gebhart/patrepeval huggingface dataset:
Summarization assessment methodology for multiple corpora using queries and classification for functional evaluation (2022)

Extractive summarization is an important natural language processing approach used for document compression, improved reading comprehension, key phrase extraction, indexing, query set generation, and other analytics approaches. Extractive summarization has specific advantages over abstractive summarization in that it preserves style, specific text elements, and compound phrases that might be more directly associated with the text. In this article, the relative effectiveness of extractive summarization is considered on two widely different corpora: (1) a set of works of fiction (100 total, mainly novels) available from Project Gutenberg, and (2) a large set of news articles (3000) for which a ground truthed summarization (gold standard) is provided by the authors of the news articles. Both sets were evaluated using 5 different Python Sumy algorithms and compared to randomly-generated summarizations quantitatively. Two functional approaches to assessing the efficacy of summarization using a query set on both the original documents and their summaries, and using document classification on a 12-class set to compare among different summarization approaches, are introduced. The results, unsurprisingly, show considerable differences consistent with the different nature of these two data sets. The LSA and Luhn summarization approaches were most effective on the database of fiction, while all five summarization approaches were similarly effective on the database of articles. Overall, the Luhn approach was deemed the most generally relevant among those tested.
Motexafin gadolinium (Gd-Tex) selectively induces apoptosis in HIV-1 infected CD4+ T helper cells (2002)

Here, we show that motexafin gadolinium (Gd-Tex), a compound that promotes intracellular oxidative stress, selectively induces apoptosis in HIV-1-infected CD4(+) T cells in IL-2-stimulated cultures of peripheral blood mononuclear cells infected in vitro with HIV-1. This selective induction of apoptosis, which we detect by FACS analysis of intracellular HIV/p24 and concomitant surface and apoptosis marker expression, is abrogated by the glutathione precursor, N-acetyl-l-cysteine. Importantly, it occurs at Gd-Tex concentrations that are not cytotoxic to uninfected cells in the culture. These findings suggest that Gd-Tex may have therapeutic utility as an anti-HIV agent capable of selectively targeting and removing HIV-infected cells in an infected host.
Incremental distributed trigger insertion for efficient FPGA debug (2014)

FPGA-based prototyping enables evaluating complex designs directly in hardware, at speeds orders of magnitude faster than simulation. However, this approach suffers from the lack of observability during debugging. To enhance observability, designers insert debug instrumentation; trace buffers are used to record a small subset of data. Since these buffers have limited capacity, trigger circuits are required to start and/or stop recording based on the values of selected signals in the circuit. Although it is possible to insert trigger circuits at compile time, changing the trigger behaviour requires re-compiling the design, increasing the cost of each debug iteration. In this paper, we propose inserting trigger circuits at run-time by distributing trigger logic over spare resources of a fully placed-and-routed design such that its mapping is completely preserved. We also propose CAD optimizations which improve routability of the trigger circuitry, and minimize the impact on circuit delay. We find that using our techniques to implement the trigger logic can be an order of magnitude faster than a full recompilation.
Top-emitting 980-nm vertical-cavity surface-emitting laser diodes with improved optical power (2012)

Top-emitting, oxide-confined, polyimide-planarized 980-nm VCSELs with copper-plated heatsinks were fabricated and characterized. Increasing the plated heatsink radius from 0-μm to 4-μm larger than the mesa diameter for lasers with 8-μm oxide aperture diameter reduced the measured thermal impedance, increased the maximum bias current density, and increased the maximum output optical power achieved by a 29%, 37%, and 73%, respectively. VCSELs with oxide aperture diameter and heatsink overlap of 8-μm and 4-μm, respectively, demonstrated 17°C decrease in the internal device temperature (i.e. active region temperature) at the maximum output optical power. Devices with similar mesa diameters of 26-μm and different heatsink overlaps exhibited a threshold bias current and a total series resistance of (630±4%)μA and ~95Ω, respectively.
Data-driven Assessment of Structural Image Quality (2017)

ABSTRACT Data quality is increasingly recognized as one of the most important confounding factors in brain imaging research. It is particularly important for studies of brain development, where age is systematically related to in-scanner motion and data quality. Prior work has demonstrated that in-scanner head motion biases estimates of structural neuroimaging measures. However, objective measures of data quality are not available for most structural brain images. Here we sought to identify quantitative measures of data quality for T1-weighted volumes, describe how such measures of quality relate to cortical thickness, and delineate how this in turn may bias inference regarding associations with age in youth. Three highly-trained raters provided manual ratings of 1,840 raw T1-weighted volumes. These images included a training set of 1,065 images from Philadelphia Neurodevelopmental Cohort (PNC), a test set of 533 images from the PNC, as well as an external test set of 242 adults acquired on a different scanner. Manual ratings were compared to automated quality measures provided by the Preprocessed Connectomes Project’s Quality Assurance Protocol (QAP), as well as FreeSurfer’s Euler number, which summarizes the topological complexity of the reconstructed cortical surface. Results revealed that the Euler number was consistently correlated with manual ratings across samples. Furthermore, the Euler number could be used to identify images scored “unusable” by human raters with a high degree of accuracy (AUC: 0.98-0.99), and outperformed proxy measures from functional timeseries acquired in the same scanning session. The Euler number also was significantly related to cortical thickness in a regionally heterogeneous pattern that was consistent across datasets and replicated prior results. Finally, data quality both inflated and obscured associations with age during adolescence. Taken together, these results indicate that reliable measures of data quality can be automatically derived from T1-weighted volumes, and that failing to control for data quality can systematically bias the results of studies of brain maturation.
Calcium signals and calcium channels in osteoblastic cells. (1998)

Calcium (Ca2+) channels are present in non-excitable as well as in excitable cells. In bone cells of the osteoblast lineage, Ca2+ channels play fundamental roles in cellular responses to external stimuli including both mechanical forces and hormonal signals. They are also proposed to modulate paracrine signaling between bone-forming osteoblasts and bone-resorbing osteoclasts at local sites of bone remodeling. Calcium signals are characterized by transient increases in intracellular Ca2+ levels that are associated with activation of intracellular signaling pathways that control cell behavior and phenotype, including patterns of gene expression. Development of Ca2+ signals is a tightly regulated cellular process that involves the concerted actions of plasma membrane and intracellular Ca2+ channels, along with Ca2+ pumps and exchangers. This review summarizes the current state of knowledge concerning the structure, function, and role of Ca2+ channels and Ca2+ signals in bone cells, focusing on the osteoblast.
A 30 GHz silicon photonic platform: Multi-project wafer shuttles for next-generation optical systems (2013)

Shared shuttle run services are ideal for rapid and relatively inexpensive prototyping. We present a silicon photonic platform that offers monolithically integrated modulators and photodetectors with 30 GHz bandwidths, available through the OpSIS MPW service.
Energy efficiency of optical grooming of QAM optical transmission channels (2016)

Analysis of the energy use for optical grooming of quadrature amplitude modulated signals in optical transmission systems is used to determine the potential efficiency benefits. An energy model is developed for both optical and electronic grooming and used to study the relative efficiency for three different network scenarios. The energy efficiency is evaluated considering both coherent and direct detection transceivers including power management strategies. Results indicate efficiency improvements up to an order of magnitude may be possible for 100 GBaud rates and 25-30 GBaud is a critical point at which optical grooming becomes the more efficient approach. These results are further shown to apply for the case of projected efficiency improvements in the underlying device technologies.
Presentation &#x201C;Automotive electronics and energy efficiency&#x201D; (2013)

The potential of energy efficiency as an energy source, however, goes significantly beyond this approach. But it can only be developed through consistent application of new as well as already existing technologies. It is important that we think holistically. Approaches are possible at every point along the value chain: 1. Energy production: New technologies - especially the use of semiconductors - are fundamental in enabling renewable energies to be fed into the grid efficiently and thus, to play a central role in the future energy mix. With the right technologies, conventional power plants can also run more efficiently. 2. Energy transmission and distribution: In the future, two developments will be more and more prevalent: For one, energy will be produced less and less at the locations where it is most heavily used (e.g. offshore wind parks and inland industrial plants); for another, it will also be produced in small decentral units, e.g. by households that have their own photovoltaic installations. For this to proceed, grids must be able to transport energy as loss-free as possible over long distances - and more intelligently. 3. Energy consumption: The greatest emphasis must be placed here because the most economic source of energy still remains not using it in the first place. Particularly in regard to energy consumption, semiconductor products can have a great impact without cutting into the prosperity of people.
Concanavalin‐A‐binding Proteins on the Surface of Human Malignant and Normal Lymphocytes (1979)

The concanavalin-A-binding cell surface glycoproteins from normal and certain leukaemic human lymphocytes were radiolabelled and then solubilized with detergent, isolated by affinity chromatography on Con A insolubilized on agarose beads, and subsequently analysed by SDS-polyacrylamide gel electrophoresis. Leukaemic T cells from patients with Sezary syndrome were found to express major concanavalin-A-binding glycoproteins on their outer surface similar to those of normal T lymphocytes. Leukaemic B cells from patients with chronic lymphocytic leukaemia expressed Con-A-binding proteins similar to those of B-cell lines. HLA antigens were predominant among the major Con-A-binding proteins on the surface of the normal and the malignant T cells studied. Human Ia-like antigens, HLA antigens, and the cell surface immunoglobulins IgD and IgM represented the major Con-A-binding proteins on the B cells studied. beta 2-microglobulin was found associated with HLA antigens on both leukaemic and non-leukaemic T and B cells. The presence of additional Con-A-binding proteins expressed on the surface of the different cell types studied is discussed along with some physical characteristics of the human Ia-like antigens isolated.
Effects of strengthening and stretching exercise programmes on kinematics and kinetics of running in older adults: a randomised controlled trial (2016)

The aim of this study was to investigate the effects of strengthening and stretching exercises on running kinematics and kinetics in older runners. One hundred and five runners (55-75 years) were randomly assigned to either a strengthening (n = 36), flexibility (n = 34) or control (n = 35) group. Running kinematics and kinetics were obtained using an eight-camera system and an instrumented treadmill before and after the eight-week exercise protocol. Measures of strength and flexibility were also obtained using a dynamometer and inclinometer/goniometer. A time effect was observed for the excursion angles of the ankle sagittal (P = 0.004, d = 0.17) and thorax/pelvis transverse (P < 0.001, d = 0.20) plane. Similarly, a time effect was observed for knee transverse plane impulse (P = 0.013, d = 0.26) and ground reaction force propulsion (P = 0.042, d = -0.15). A time effect for hip adduction (P = 0.006, d = 0.69), ankle dorsiflexion (P = 0.002, d = 0.47) and hip internal rotation (P = 0.048, d = 0.30) flexibility, and hip extensor (P = 0.001, d = -0.48) and ankle plantar flexor (P = 0.01, d = 0.39) strength were also observed. However, these changes were irrespective of exercise group. The results of the present study indicate that an eight-week stretching or strengthening protocol, compared to controls, was not effective in altering age-related running biomechanics despite changes in ankle and trunk kinematics, knee kinetics and ground reaction forces along with alterations in muscle strength and flexibility were observed over time.
Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning (2014)

Flavin mononucleotide (FMN)-based fluorescent proteins are versatile reporters that can monitor various cellular processes in both aerobic and anaerobic conditions. However, the understanding of the role of individual amino acid residues on the protein function has been limited and has restricted the development of better functional variants. Here we examine the functional amino acid residues of Escherichia coli flavin mononucleotide binding fluorescent protein (EcFbFP) using the application of high-throughput sequencing of functional variants, termed deep mutational scanning. The variants were classified into 329 function-retained (FR) and 259 function-loss (FL) mutations, and further the mutational enrichment in each amino acid residues was weighed to find the functionally important residues of EcFbFP. We show that the crucial amino acid residues of EcFbFP lie among the FMN-binding pocket, turns and loops of the protein where conformation changes occur, and spatially clustered residues near the E56-K97 salt bridges. In addition, the mutational sensitivity of the critical residues was confirmed by site-directed mutagenesis. The deep mutational scanning of EcFbFP has demonstrated important implications for constructing better functioning protein variants.
Luminal disequilibrium pH and ammonia transport in outer medullary collecting duct (1987)

Page F1148: Robert A. Star, Maurice B. Burg, and Mark A. Knepper. “Luminal disequilibrium pH and ammonia transport in outer medullary collecting duct.” We regret that an error was made in the title of this article. The correct title and the article are reprinted in the August 1987 issue of this journal.
<title>Curved-linear 128x7 two-dimensional array for 1.5D ultrasound medical imaging</title> (1997)

The potential of 1.5D ultrasonic imaging is investigated, using an elevation sampling of 7 elements (4 channels). The number of elements has been chosen in accordance with the number of channels that will be available in commercial beamformers in the future. The probe technology has been developed for curved array geometry with no limitation in radius of curvature. The transducer has been designed to introduce no limitation of electroacoustic performances, allowing fair comparison with images obtained with 1D arrays. Possible approaches for the array design are discussed. Achieved performances on prototypes of a 3.5 MHz, 40 mm radius, 128 by 7 elements, 0.5 by 2.4 mm pitch probe are presented. Electroacoustic performances are in the range of state-of-the-art 1D probes. Several figures of merit are defined and analyzed. Theoretical and experimental comparisons with 1D arrays show drastic improvement for various focusing strategies. Prototypes of curved-linear 1.5D probes with high density of elements, exhibiting performances consistent with high end diagnosis equipment, and using fabrication processes suitable for industrial production, are now available. First clinical evaluations have been conducted and confirm very promising capabilities. The results will be used for the definition of an optimized 1.5D probe family.
<title>Investigation of pH and temperature effects on FRET systems for glucose sensing</title> (2002)

Glucose monitoring is of critical importance in the life of Type I and many Type II diabetics. This research furthers work toward a minimally invasive implantable glucose sensor based on fluorescence detection. Current experimental models use heterogeneous fluorescence resonance energy transfer (FRET) systems for sensing; ideally, the response of one fluorophore bound to a large polysaccharide is enhanced greatly in the presence of glucose while the other fluorophore bound to a glucose sensitive protein is diminished or unaffected. Many fluorophores are affected by environmental factors such as pH and temperature. FRET experiments using two fluorophores, tetramethylrodamine isothiocyanate (TRITC) and fluoroscein isothiocyanate (FITC), are performed evaluating the effects of fluctuations over the range of pH 4-8 and temperature 25-45 degree(s)C for various concentrations of glucose in a flow cell. TRITC is bound to the lectin Concanavalin A (Con A), and FITC is bound to dextran molecules of varying sizes.
Markers of Polyfunctional SARS-CoV-2 Antibodies in Convalescent Plasma (2021)

Convalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but the antibody characteristics that contribute to efficacy remain poorly understood. This study analyzed plasma samples from 126 eligible convalescent blood donors in addition to 15 naive individuals, as well as an additional 20 convalescent individuals as a validation cohort. Multiplexed Fc Array binding assays and functional antibody response assays were utilized to evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody composition and activity. Donor convalescent plasma samples contained a range of antibody cell- and complement-mediated effector functions, indicating the diverse antiviral activity of humoral responses observed among recovered individuals. In addition to viral neutralization, convalescent plasma samples contained antibodies capable of mediating such Fc-dependent functions as complement activation, phagocytosis, and antibody-dependent cellular cytotoxicity against SARS-CoV-2. Plasma samples from a fraction of eligible donors exhibited high activity across all activities evaluated. These polyfunctional plasma samples could be identified with high accuracy with even single Fc Array features, whose correlation with polyfunctional activity was confirmed in the validation cohort. Collectively, these results expand understanding of the diversity of antibody-mediated antiviral functions associated with convalescent plasma, and the polyfunctional antiviral functions suggest that it could retain activity even when its neutralizing capacity is reduced by mutations in variant SARS-CoV-2.<b>IMPORTANCE</b> Convalescent plasma has been deployed globally as a treatment for COVID-19, but efficacy has been mixed. Better understanding of the antibody characteristics that may contribute to its antiviral effects is important for this intervention as well as offer insights into correlates of vaccine-mediated protection. Here, a survey of convalescent plasma activities, including antibody neutralization and diverse effector functions, was used to define plasma samples with broad activity profiles. These polyfunctional plasma samples could be reliably identified in multiple cohorts by multiplex assay, presenting a widely deployable screening test for plasma selection and investigation of vaccine-elicited responses.
Models and remodeling: mechanisms and clinical implications. (1999)

Ventricular remodeling is a process by which the size, shape and composition of cardiac chambers as well as the thickness and composition of the walls are altered in response to physical loads and/or receptor activation, whether created by loss or overload of cardiac myocytes, or the effects of external hormonal or chemical factors. Involved in this process are hypertrophy, dilation, myocyte loss whether due to necrosis or apoptosis, and myocyte hyperplasia. The present review discusses the dynamic and plastic structure of the heart in its capacity to respond to loading. The mechanisms by which myocyte growth as well as myocyte loss are mediated offer therapeutic opportunities to alter these events.
On Source Coding with Coded Side Information for a Binary Source with Binary Side Information (2007)

The lossless rate region for the coded side information problem is "solved," but its solution is expressed in terms of an auxiliary random variable. As a result, finding the rate region for any fixed example requires an optimization over a family of allowed auxiliary random variables. While intuitive constructions are easy to come by and optimal solutions are known under some special conditions, proving the optimal solution is surprisingly difficult even for examples as basic as a binary source with binary side information. We derive the optimal auxiliary random variables and corresponding achievable rate regions for a family of problems where both the source and side information are binary. Our solution involves first tightening known bounds on the alphabet size of the auxiliary random variable and then optimizing the auxiliary random variable subject to this constraint. The technique used to tighten the bound on the alphabet size applies to a variety of problems beyond the one studied here.