gebhart/patrepeval huggingface dataset:
Role of HMGB1 in the activation of innate immune responses during SARS-CoV-2 infection (2023)

Abstract The ongoing COVID-19 pandemic caused by SARS-CoV-2 has resulted in overwhelming number of deaths worldwide, affecting all age groups. Due to the emergence and rapid spread of SARS-CoV-2 variants and waning immunity in humans to current vaccines, it is imperative that new treatment modalities must continue to be developed for combating this deadly disease. The molecular mechanisms by which SARS-CoV-2 increases risk of serious respiratory disease is largely unknown but exuberant lung inflammatory and immune responses are key. Understanding of the cascades of events that initiate and sustain inflammatory processes contributing to more severe disease is crucial for developing effective therapies for COVID-19. In this study, we found that the release of high-mobility group box 1 (HMGB1), a proinflammatory mediator that alerts the immune system, was increased in the medium of human lung epithelial cells (A549-ACE2 and Calu-3/2B4) in vitro infected with SARS-CoV-2, and in the serum of SARS-CoV-2 infected mice and humans. Our studies showed that SARS-CoV-2 induced acute inflammation by downregulating the retinoic acid inducible gene-I (RIG-I)-dependent interferon (IFN)-mediated innate antiviral immune response and nuclear factor erythroid 2-related factor (NRF2)-dependent antioxidant mechanism. Treatment with rHMGB1 significantly activated the innate antiviral and antioxidant pathways and inhibited the viral replication. Our studies demonstrated an important role of HMGB1 in the regulation of viral replication and cellular protection as well as the activation of innate immune signaling cascades to promote inflammation. Modulation of HMGB1’s proinflammatory signaling may attenuate SARS-CoV-2-induced lung inflammation. This work was supported by COVID-19 and Emerging Respiratory Viruses Research Award from American Lung Association (COVID-920427), COVID-19 Bridging grant from Sealy Institute for Vaccine Sciences (C28455), Young Clinical Scientist Award from the Flight Attendant Medical Research Institute (FAMRI) (grant I.D. number 123385), NIH/NIAID R21 AI35619, Short-Term Provost’s Scholar Award by CTSA Mentored Career Development Award, CTSA KL2 COVID Funds (NIH/NCATS KL2TR001441) to YMH.
Opening of the New Japanese Balloon Base at the Taiki Aerospace Research Field (2010)

The Japanese balloon base was moved from the Sanriku Balloon Center (SBC) to the Taiki Aerospace Research Field (TARF). The SBC was closed in September 2007, and the new base at the TARF became operational in May 2008. In 2008, the first series of balloon flights at the TARF was carried out. By the success of these flights, we verified that the whole system of the new balloon base is well established. From FY 2009, regular balloon operations with science payloads started at the TARF. In May/June 2009, flight operations of three science experiments were carried out successfully. Five more science flights are planned at the TARF in August/September 2009.
Highly Efficient Single Molecule Detection in Different Micro and submicrometer Channels with cw-excitation (2001)

In this article we describe a detailed comparison between single molecule detection in three different types of microchannels. The overall detection efficiencies and the signal-to-noise ratios are compared. A new data evaluation technique that is used is explained in detail. The average number of photons per molecule is calculated from the measurements and the detection properties of each channel with respect to the diffusional characteristics of the dye molecules are investigated. From the detection efficiencies advantages and drawbacks of the individual methods are elucidated as well as possible applications of the techniques are illustrated.
Long Range Outdoor Sound Propagation Model (1995)

In the case of medium and long ranges outdoor sound propagation, refraction due to temperature and wind gradients may increase (or decrease) the sound pressure due to a point source[l,2]. To fulfill the needs of practical outdoor sound propagation studies, it appears to be necessary to develop practical and reliable software for engineering purposes to predict outdoor sound propagation under general meteorological conditions. This paper present the software LORAP developed to reach that goal.
Taxol-based eluting stents from theory to human validation: clinical and intravascular ultrasound observations. (2003)

Treatment with antiproliferative drugs via coated stents appears to be a promising approach to both mechanically remodel target lesions and biologically reduce neointimal hyperplasia. Drug-eluting stents can maximize local drug effects and minimize the potential for systemic toxic effects. The purpose of this review is to describe the effects of a lipophilic microtubular inhibitor, paclitaxel, a strong antiproliferative agent under clinical investigation, and to define the vascular response to taxol-based eluting stents by intravascular ultrasound.
The Performance of Paxos in the Cloud (2014)

This experience report presents the results of an extensive performance evaluation conducted using four open-source implementations of Paxos deployed in Amazon's EC2. Paxos is a fundamental algorithm for building fault-tolerant services, at the core of state-machine replication. Implementations of Paxos are currently used in many prototypes and production systems in both academia and industry. Although all protocols surveyed in the paper implement Paxos, they are optimized in a number of different ways, resulting in very different behavior, as we show in the paper. We have considered a variety of configurations and failure-free and faulty executions. In addition to reporting our findings, we propose and assess additional optimizations to existing implementations.
The long QT syndrome: a transatlantic clinical approach to diagnosis and therapy (2013)

The mind-boggling progress in the understanding of the molecular mechanisms underlying the long QT syndrome (LQTS) has been the subject of many articles and reviews. Still, when it comes to the management of the patients affected by this life-threatening disorder, too many errors still take place, both in the diagnostic process and in the therapeutic choices. The price of these errors is paid by the patients and their families. This review is not directed to the relatively small number of LQTS experts who know what to do. It does not deal with genetics, with epidemiology, or with the well-known clinical manifestations. We have focused solely on the approach to diagnosis and therapy and we have directed this review to the average clinical cardiologist who, in his/her practice, sees occasionally patients affected or suspected to be affected by LQTS; the cardiologist who may know enough to manage them but not enough to be completely confident on his/her most critical choices. We have provided our personal views without making any attempt to blend differences whenever present. On most issues we agree fully but where we do not, we make it clear to the reader by indicating who is thinking what. The result may be unconventional, but it mirrors the challenges, often severe, that we all face in managing and protecting these patients from sudden death while also helping them live and thrive despite their diagnosis. We trust that this unabashed presentation of our clinical approach will be useful for both cardiologists and patients.
Dynamic visualization of graphs with extended labels (2005)

The paper describes a novel technique to visualize graphs with extended node and link labels. The lengths of these labels range from a short phrase to a full sentence to an entire paragraph and beyond. Our solution is different from all the existing approaches that almost always rely on intensive computational effort to optimize the label placement problem. Instead, we share the visualization resources with the graph and present the label information in static, interactive, and dynamic modes without the requirement for tackling the intractability issues. This allows us to reallocate the computational resources for dynamic presentation of real time information. The paper includes a user study to evaluate the effectiveness and efficiency of the visualization technique.
Fibroblast state switching orchestrates dermal maturation and wound healing (2018)

Murine dermis contains functionally and spatially distinct fibroblast lineages that cease to proliferate in early postnatal life. Here, we propose a model in which a negative feedback loop between extracellular matrix (ECM) deposition and fibroblast proliferation determines dermal architecture. Virtual-tissue simulations of our model faithfully recapitulate dermal maturation, predicting a loss of spatial segregation of fibroblast lineages and dictating that fibroblast migration is only required for wound healing. To test this, we performed <i>in vivo</i> live imaging of dermal fibroblasts, which revealed that homeostatic tissue architecture is achieved without active cell migration. In contrast, both fibroblast proliferation and migration are key determinants of tissue repair following wounding. The results show that tissue-scale coordination is driven by the interdependence of cell proliferation and ECM deposition, paving the way for identifying new therapeutic strategies to enhance skin regeneration.
Linux block IO (2013)

The IO performance of storage devices has accelerated from hundreds of IOPS five years ago, to hundreds of thousands of IOPS today, and tens of millions of IOPS projected in five years. This sharp evolution is primarily due to the introduction of NAND-flash devices and their data parallel design. In this work, we demonstrate that the block layer within the operating system, originally designed to handle thousands of IOPS, has become a bottleneck to overall storage system performance, specially on the high NUMA-factor processors systems that are becoming commonplace. We describe the design of a next generation block layer that is capable of handling tens of millions of IOPS on a multi-core system equipped with a single storage device. Our experiments show that our design scales graciously with the number of cores, even on NUMA systems with multiple sockets.
Building Application-Specific Overlays on FPGAs with High-Level Customizable IPs (2020)

Overlays are virtual, re-configurable architectures that overlay on top of physical FPGA fabrics. An overlay that is specialized for an application, or a class of applications, offers both fast reconfiguration and minimized performance penalty. Such an overlay is usually implemented by hardware designers in hardware "assembly" languages at register-transfer level (RTL). This short article proposes an idea for a software programmer, instead of hardware designers, to quickly implement an application-specific overlay using high-level customizable IPs. These IPs are expressed succinctly by a specification language, whose abstraction level is much higher than RTL but can nonetheless expresses many performance-critical loop and data optimizations on FPGAs, and thus would offer competitively high performance at a much lower cost of maintenance and much easier customizations. We propose new language features to easily put the IPs together into an overlay. A compiler automatically implements the specified optimizations to generate an efficient overlay, exposes a multi-tasking programming interface for the overlay, and inserts a runtime scheduler for scheduling tasks to run on the IPs of the overlay, respecting the dependences between the tasks. While an application written in any language can take advantage of the overlay through the programming interface, we show a particular usage scenario, where the application itself is also succinctly specified in the same language. We describe the new language features for expressing overlays, and illustrate the features with an LU decomposer and a convolutional neural network. A system is under construction to implement the language features and workloads.
Regulatory B cells in autoimmune diseases and mucosal immune homeostasis (2010)

B lymphocytes contribute to physiological immunity through organogenesis of secondary lymphoid organs, presentation of antigen to T cells, production of antibodies, and secretion of cytokines. Their role in several autoimmune diseases, mainly as producers of pathogenic antibodies, is also well known. However, certain subsets of B cells are emerging as the important regulatory cell populations in both mouse and human. The regulatory functions of B cells have been demonstrated in a variety of mouse models of autoimmune diseases including collagen-induced arthritis (CIA), experiment autoimmune encephalomyelitis (EAE), anterior chamber-associated immune deviation (ACAID), diabetes, contact hypersensitivity (CHS), and intestinal mucosal inflammation. Accumulating evidence from both mouse and human studies confirms the existence of regulatory B cells, and is beginning to define their mechanisms of action. In this article, we first review the history of B cells with regulatory function in autoimmune diseases, and summarize the current understanding about the characterizations of such B-cell subsets. We then discuss the possible regulatory mechanisms of B cells, and specifically define the role of regulatory B cells in immune homeostasis in the intestine.
MINIMIZING ASCORBIC ACID LOSS DURING AIR DRYING WITH A CONSTRAINT ON ENZYME INACTIVATION FOR A HYPOTHETICAL FOODSTUFF (1983)

The utility of a simulation-optimization approach based on the complex method was demonstrated for a multi-stage drying process. Optimal stage-duration and temperature control were found for minimizing ascorbic acid loss using a literature-derived kinetic model. In addition, enzyme (catalase) inactivation was considered in the staged process. It was desired to control the process so that catalase activity was reduced below a specified level while minimizing ascorbic acid loss. Inequality constraints were also placed on the final retention of moisture and the temperature control range. Due to the large difference in temperature sensitivity at high moisture levels, the optimal configuration maintained the dry- and wet-bulb temperatures very high in a brief first stage to inactivate catalase, followed by milder drying conditions in the final stages to reduce ascorbic acid degradation.
Detection of Human Bocavirus in the Cerebrospinal Fluid of Children With Encephalitis (2012)

We report 4 children with encephalitis associated with human bocavirus (HBoV) 1 or 2. All children were severely underweight, and 2 died; 1 of them had a matching HBoV2 nucleotide sequence isolated from serum and bocavirus like particles in the cerebrospinal fluid that were observed with electron microscopy. No further pathogens were detected in the cerebrospinal fluid of these patients.
Electrochemical photovoltaic cells. Project 65021 final technical progress report, April 15, 1979-April 17, 1980 (1980)

The overall goals of this program have been to experimentally identify semiconductor photoanode/redox couple systems that (a) show promise of meeting acceptable solar efficiencies using polycrystalline materials, and (b) have the potential for use in conjunction with a suitable cathode in which another redox species is available for reduction. Such an overall system allows for the convenient removal, storage, and later discharge of reaction products through the use of porous, flow-through redox electrodes. Increasing solar energy conversion efficiencies and identifying potentially long-life systems were emphasized. Semiconductor/redox couple systems were selected on the basis of the apparent positions of their conduction and valence band energy levels at the interface, together with the semiconductor decomposition potential. Selected redox couples should possess equilibrium potentials that lie negative of the semiconductor decomposition potential and positive of the semiconductor conduction band. Liquid-junction solar cells were characterized using n-MoSe/sub 2/, n-WSe/sub 2/, n-CdSe, and n-GaAs as photoanodes. Results are presented in detail. (WHK)
Techniques for multilayer channel routing (1988)

The techniques described have been implemented in a multilayer channel router called Chameleon. Chameleon consists of two stages: a partitioner and a detailed router. The partitioner divides the problems into two-layer and three-layer subproblems such that global channel area is minimized. The detailed router then implements the connections using generalizations of the algorithms used in YACR2 (see ibid., vol.CAD-4, no.3, p.208-19, 1985). In particular, a three-dimensional maze router is used for the vertical connections; this methodology is effective even when cycle constraints are present. Chameleon has produced optimal results on a wide range of industrial and academic examples for a variety of layer and pitch combinations, and can handle a variety of technology constraints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Temperature monitoring of retinal tissues during laser radiation by speckle variance optical coherence tomography (Conference Presentation) (2018)

Retinal photocoagulation techniques are widely used to treat various retinal diseases such as retinal detachment, diabetic retinopathy and ischemic retinal vein occlusion. The degree of coagulation, which plays important role for optimal surgical outcomes, depends on the tissue temperature achieved and the exposure time. The temperature distribution is affected by indeterminate characteristics, such as the pigmentation of the retinal tissue and the radiative transfer by its structure, in addition to the laser radiation condition. Therefore, an accurate measurement of the tissue temperature offers crucial information that could prevent excessive burning and collateral damage. There have been many researches on temperature monitoring methods using various sensors or imaging systems such as fiber optic sensor, ultrasound imaging, MRI, photoacoustic imaging, and optical coherence tomography (OCT). Among them, the OCT is a promising technique for retina imaging because it is a non-invasive system providing depth resolved images with microscale resolution. One of the OCT technique, speckle variance optical coherence tomography (svOCT), is known to detect moving molecules or coagulation in tissues sensitively by calculating changes of speckle pattern with time. In this paper, we proposed temperature monitoring of retinal tissues by svOCT imaging during photocoagulation since photocoagulation of retinal tissues is closely related to its temperature distribution. An ex-vivo bovine retina was continuously radiated by 10 mW green laser after removal of cornea, lens, and vitreous humor. SvOCT images of the retina was acquired every 1 minutes and analyzed with temperature data measured by thermometer. The results showed that speckle variance signal increases as temperature increases. Based on our result, we expect that svOCT will be an effective method for temperature monitoring to improve and automate laser treatments in ophthalmology.
Far sidelobes measurement of the Atacama Cosmology Telescope (2012)

The Atacama Cosmology Telescope (ACT) is a 6m telescope designed to map the Cosmic Microwave Background (CMB) simultaneously at 145GHz, 220 GHz and 280 GHz. Its off-axis Gregorian design is intended to minimize and control the off-axis sidelobe response, which is critical for scientific purposes. The expected sidelobe level for this kind of design is less than -50 dB and can be challenging to measure. Here we present a measurement of the 145GHz far sidelobes of ACT done on the near-field of the telescope. We used a 1mW microwave source placed 13 meters away from the telescope and a chopper wheel to produce a varying signal that could be detected by the camera for different orientations of the telescope. The source feed was designed to produce a wide beam profile. Given that the coupling is expected to be dominated by diffraction over the telescope shielding structure, when combined with a measurements of the main beam far field response, these measurement can be used to validate elements of optical design and constrain the level of spurious coupling at large angles. Our results show that the diffractive coupling beyond the ground screen is consistently below -75 dB, satisfying the design expectations.
Modification Design Method for an Enveloping Hourglass Worm Gear with Consideration of Machining and Misalignment Errors (2013)

The influences of machining and misalignment errors play a very critical role in the performance of the anti-backlash double-roller enveloping hourglass worm gear(ADEHWG).However,a corresponding efficient method for eliminating or reducing these errors on the tooth profile of the ADEHWG is seldom reported.The gear engagement equation and tooth profile equation for considering six different errors that could arise from the machining and gear misalignment are derived from the theories of differential geometry and gear meshing.Also,the tooth contact analysis(TCA) is used to systematically investigate the influence of the machining and misalignment errors on the contact curves and the tooth profile by means of numerical analysis and three-dimensional solid modeling.The research results show that vertical angular misalignment of the worm wheel(Δβ) has the strongest influences while the tooth angle error(Δα) has the weakest influences on the contact curves and the tooth profile.A novel efficient approach is proposed and used to minimize the effect of the errors in manufacturing by changing the radius of the grinding wheel and the approaching point of contact.The results from the TCA and the experiment demonstrate that this tooth profile design modification method can indeed reduce the machining and misalignment errors.This modification design method is helpful in understanding the manufacturing technology of the ADEHWG.
Chasing Seasonal Influenza — The Need for a Universal Influenza Vaccine (2017)

Chasing Seasonal Influenza As we prepare for a potentially severe influenza season, we must consider whether our current vaccines can be improved and whether longer-term, transformative vaccine approaches are needed to minimize influenza-related morbidity and mortality.
$\varepsilon$-dimension in infinite dimensional hyperbolic cross approximation and application to parametric elliptic PDEs (2017)

In this article, we present a cost-benefit analysis of the approximation in tensor products of Hilbert spaces of Sobolev-analytic type. The Sobolev part is defined on a finite dimensional domain, whereas the analytical space is defined on an infinite dimensional domain. As main mathematical tool, we use the $\varepsilon$-dimension of a subset in a Hilbert space. The $\varepsilon$-dimension gives the lowest number of linear information that is needed to approximate an element from the set in the norm of the Hilbert space up to an accuracy $\varepsilon&gt;0$. From a practical point of view this means that we a priori fix an accuracy and ask for the amount of information to achieve this accuracy. Such an analysis usually requires sharp estimates on the cardinality of certain index sets which are in our case infinite-dimensional hyperbolic crosses. As main result, we obtain sharp bounds of the $\varepsilon$-dimension of the Sobolev-analytic-type function classes which depend only on the smoothness differences in the Sobolev spaces and the dimension of the finite dimensional domain where these spaces are defined. This implies in particular that, up to constants, the costs of the infinite dimensional (analytical) approximation problem is dominated by the finite-variate Sobolev approximation problem. We demonstrate this procedure with an examples of functions spaces stemming from the regularity theory of parametric partial differential equation.