gebhart/patrepeval huggingface dataset:
Effects of a novel orally administered calpain inhibitor SNJ‐1945 on immunomodulation and neurodegeneration in a murine model of multiple sclerosis (2014)

Multiple sclerosis (MS) pathology is marked by the massive infiltration of myelin-specific T cells into the CNS. Hallmarks of T helper (Th) cells during active disease are pro-inflammatory Th1/Th17 cells that predominate over immunoregulatory Th2/Treg cells. Neurodegeneration, a major factor in progressive MS, is often overlooked when considering drug prescription. Here, we show that oral dosing with SNJ-1945, a novel water-soluble calpain inhibitor, reduces experimental autoimmune encephalomyelitis clinical scores in vivo and has a two pronged effect via anti-inflammation and protection against neurodegeneration. We also show that SNJ-1945 treatment down-regulates Th1/Th17 inflammatory responses, and promotes regulatory T cells (Tregs) and myeloid-derived suppressor cells in vivo, which are known to have the capacity to suppress helper as well as cytotoxic T cell functions. Through analysis of spinal cord samples, we show a reduction in calpain expression, decreased infiltration of inflammatory cells, and signs of inhibition of neurodegeneration. We also show a marked reduction in neuronal cell death in spinal cord (SC) sections. These results suggest that calpain inhibition attenuates experimental autoimmune encephalomyelitis pathology by reducing both inflammation and neurodegeneration, and could be used in clinical settings to augment the efficacy of standard immunomodulatory agents used to treat MS. Multiple sclerosis (MS) pathology is marked by inflammation and infiltration of myelin-specific T cells into the central nervous system. Inflammation leads to neurodegeneration in progressive MS which also leads to epitope spreading, feedback looping to more inflammation. Calpain can play a role in both arms of the disease. Here, oral dosing with SNJ-1945, a novel water-soluble calpain inhibitor, reduces experimental autoimmune encephalomyelitis clinical scores in vivo and has a two-pronged effect via anti-inflammation and protection against neurodegeneration.
Excitatory or Inhibitory: A New Semantic Orientation Extracts Contradiction and Causality from the Web (2012)

We propose a new semantic orientation, Ex-citation, and its automatic acquisition method. Excitation is a semantic property of predicates that classifies them into excitatory, inhibitory and neutral. We show that Excitation is useful for extracting contradiction pairs (e.g., destroy cancer ⊥ develop cancer) and causality pairs (e.g., increase in crime ⇒ heighten anxiety). Our experiments show that with automatically acquired Excitation knowledge we can extract one million contradiction pairs and 500,000 causality pairs with about 70 % precision from a 600 million page Web corpus. Furthermore, by combining these extracted causality and contradiction pairs, we can generate one mil-lion plausible causality hypotheses that are not written in any single sentence in our corpus with reasonable precision. 1
Hybrid MR/near infrared imaging of the murine brain: optimization of optical fiber arrangement and use of a-priori knowledge (2003)

In this work we will present our initial study into the use of hybrid MRI/Near Infrared (NIR) imaging system and the reconstruction algorithm for the murine head. We will show that the arrangement of optical fibers on one side of the head, near the brain, will provide more information about optical changes within the brain. Also, we will show that by the use of a-priori information from MRI and appropriate constraints within our reconstruction algorithm it is possible to improve the quality of image reconstruction.
A selective defect of IFN-gamma- but not of IFN-alpha-induced JAK/STAT pathway in a subset of U937 clones prevents the antiretroviral effect of IFN-gamma against HIV-1. (1999)

IFN-gamma induces transcription of several IFN-stimulated genes (ISGs). Recently, the IFN-gamma-dependent Janus kinase (JAK)/STAT pathway has been shown to mediate the activation of some ISGs, by the sequential phosphorylation of two JAK kinases (JAK1 and JAK2) and of STAT1. Given that the JAK/STAT is the major, but not the only pathway linked to the IFN-gammaR, aim of our work was to investigate the signal-transduction pathway(s) by which IFN-gamma exerts its effects on acute replication of HIV in monocytic cells. To this end, we utilized clones previously derived from the U937 promonocytic cell line, differing for their efficient (plus clones) or inefficient (minus clones) abilities of supporting HIV replication. Unlike IFN-alpha, IFN-gamma did not inhibit HIV replication in plus clones, whereas virus production in minus cells was efficiently inhibited by both types of IFN. Plus clones generated a JAK/STAT signal-transduction pathway in response to IFN-alpha, but not IFN-gamma. In contrast, minus clones responded to either cytokines. The functional defect of plus clones in response to IFN-gamma was correlated to a selective defect of IFN-gammaR2, but not IFN-gammaR1, membrane expression. Surprisingly enough, IFN-gamma stimulation of plus clones induced IFN-stimulated gene factor 3 (ISGF3gamma). These results strongly support the hypothesis that the JAK/STAT pathway is responsible for the antiretroviral effect of IFN-gamma, and further provide evidence for a potential second pathway triggered by IFN-gamma in the absence of IFN-gammaR2 chain cell surface expression and involving ISGF3gamma.
Cyclooxygenase inhibitors impair CD4 T cell immunity and exacerbate Mycobacterium tuberculosis infection in aerosol-challenged mice (2019)

Tuberculosis, caused by infection with <i>Mycobacterium tuberculosis</i> (Mtb), kills over 1.6 million people each year despite availability of antibiotics. The increase in drug resistant Mtb strains is a major public health emergency and host-directed therapy as adjunct to antibiotic treatment has gained increased interest. Cyclooxygenase inhibitors (COXi) are frequently used drugs to alleviate tuberculosis related symptoms. Mouse studies of acute intravenous Mtb infection have suggested a potential benefit of COXi for host-directed therapy. Here we show that COXi treatment (ibuprofen and celecoxib) is detrimental to Mtb control in different mouse models of respiratory infection. This effect links to impairments of the Type-1 helper (Th1) T-cell response as CD4 T-cells in COXi-treated animals have significantly decreased Th1 differentiation, reduced IFNγ expression and decreased protective capacity upon adoptive transfer. If confirmed in clinical trials, these findings could have major impact on global health and question the use of COXi for host-directed therapy.
Laser cooling and confining of atoms (1985)

Using six optical beams (+ and − directions on three orthogonal axes) tuned slightly to the red of resonance it is possible to cool sodium atoms to a few hundred microkelvin. The cooling occurs because the laser radiation pressure creates a damping force which reduces the atomic velocities to a rms value of ~60 cm/s, determined by random scattering. In this optical molasses, the laser beams propagate in all directions and the light acts as a viscous photon fluid which damps the atomic velocity. The resulting motion of the sodium atoms is diffusive until the atoms reach the edge of the laser beams where they escape. The process of atomic confinement by optical molasses can be modeled as a random walk in a viscous medium with a boundary. For a spherical volume of 0.2 cm 3 the resulting confinement time is ~0.1 s for half of the atoms to escape. Direct time-of-flight measurement of the atomic temperature gives ~240 μ K, which agrees with predictions of quantum limited cooling by resonance radiation pressure. With confinement times of 0.1 s and temperatures of ~240 μ K this method provides a source of atoms sufficiently slow for even the highest resolution optical spectroscopy, collision studies, or optical traps.
Role of axonal components during myelination (1998)

Myelination is a multistep ordered process whereby Schwann cells in the peripheral nervous system (PNS) and oligodendrocytes in the central nervous system (CNS), produce and extend membranous processes that envelop axons. Mechanisms that regulate this complex process are not well understood. Advances in deciphering the regulatory components of myelination have been carried out primarily in the PNS and although the mechanisms for triggering and directing myelination are not known, it is well established that myelination does not occur in the absence of axons or axon/neuron-derived factors. This appears to be true both in PNS and CNS. Progress in understanding CNS myelinogenesis has been relatively slow because of the unavailability of a suitable culture system, which, in turn, is partly due to complexity in the cellular organization of the CNS. Though the myelin composition differs between PNS and CNS, the regulation of myelination seems to parallel rather than differ between these two systems. This article reviews the regulatory role of axonal components during myelination. The first half consists of an overview of in vitro and in vivo studies carried out in the nervous system. The second half discusses the use of a cerebellar slice culture system and generation of anti-axolemma monoclonal antibodies to investigate the role of axonal membrane components that participate in myelination. It also describes the characterization of an axonal protein involved in myelination.
Why does adding a poor thermal conductor increase propagation rate in solid propellants? (2019)

Solid propellant additives have a long history of modulating burning rate by introducing materials with high thermal diffusivities to better concentrate and transfer heat to nearby areas. However, recent studies have demonstrated a counterintuitive result in that additives with thermally insulating properties—notably SiO2 particles—can also enhance the propagation rate in solid propellants. In this work, high-speed microscopy and thermometry were performed on 3D printed solid propellant films containing both thermally conducting (graphite) and insulating (SiO2) particles to investigate the role of these additives on film propagation rate. It was found that addition of SiO2 particles increased the effective surface area of the reaction front through inhomogeneous heat transfer in the films, and that such corrugation of the reaction front area on the micrometer scale manifests itself as a global increase in the propagation rate on the macro scale. Graphite additive was observed to have a substantially lower burning surface area and propagation rate, suggesting that the effect of reaction front surface area is larger than the effect of thermal diffusivity for low-weight percent additives in solid propellants.
Au@MoS2@WS2 Core–Shell Architectures: Combining Vapor Phase and Solution-Based Approaches (2020)

Solution preparation provides a versatile platform to extend the applications of transition-metal dichalcogenides (TMDs) beyond those achievable with traditional vapor-based preparation methods. However, existing solution-based synthesis and exfoliation approaches present numerous challenges, including low-crystallinity material and incompatibility with complex geometries, particularly with respect to spatial control over interfacial regions. Perhaps interestingly, these disadvantages align well with some of the advantages of vapor phase synthesis. Here, we introduce a strategy that combines vapor phase deposition and solution chemistry to build TMD core–shell heterostructures housed in aqueous media and reap the benefits of both preparation methods. We report a new TMD core–shell heterostructure, Au@MoS2@WS2, with an Au nanoparticle core and MoS2 and WS2 shells and provide a means of suspending the structure in solution to allow for higher order patterning and ligand-based functionalization. High-resolution electron microscopy and Raman spectroscopy provide a detailed analysis of the structure and interfaces of the core–shell heterostructures. UV–vis, dynamic light scattering, and zeta potential measurements exhibit outstanding natural stability and monodispersity of Au@MoS2@WS2 in solution. As a proof of concept, the aqueous environment is utilized to both functionalize the core–shell heterostructures with electrostatic ligands and pattern them into desired configurations on a target substrate. This work harnesses the advantages of vapor phase preparation of nanomaterials and the functionality possible with aqueous suspension to expand future engineering and application opportunities of TMD heterostructures.
A Visual Similarity Metric for View-based Web Page Retrieval (2008)

We are developing a system for retrieving web browsing history based on visual information such as design and layout. This system's performance would be improved by refining the sketch retrieval results. For this purpose, we have developed “color-layout signature,” a visual similarity metric for web pages. We showed that use of the developed metric improves retrieval performance from 27%(conventional method) to 42%.
A unique bacterial secretion machinery with multiple secretion centers (2022)

The Porphyromonas gingivalis type IX secretion system (T9SS) promotes periodontal disease by secreting gingipains and other virulence factors. By in situ cryoelectron tomography, we report that the P. gingivalis T9SS consists of 18 PorM dimers arranged as a large, caged ring in the periplasm. Near the outer membrane, PorM dimers interact with a PorKN ring complex of ∼52 nm in diameter. PorMKN translocation complexes of a given T9SS adopt distinct conformations energized by the proton motive force, suggestive of different activation states. At the inner membrane, PorM associates with a cytoplasmic complex that exhibits 12-fold symmetry and requires both PorM and PorL for assembly. Activated motors deliver substrates across the outer membrane via one of eight Sov translocons arranged in a ring. The T9SSs are unique among known secretion systems in bacteria and eukaryotes in their assembly as supramolecular machines composed of apparently independently functioning translocation motors and export pores.
Applications of unconditional pseudorandomness in complexity theory (2007)

Pseudorandomness—that is, information that appears even though it is generated using very little true randomness—is a fundamental notion in cryptography and complexity theory. 
This thesis explores the applications of pseudorandomness within complexity theory, with a focus on pseudorandomness that can be constructed unconditionally, that is without relying on any unproven complexity assumptions. Such pseudorandomness only fools restricted classes of algorithms, and yet it can be applied to prove complexity results that concern very general models of computation. For instance, we show the following: (1)  Randomness-Efficient Error Reduction for Parallel Algorithms. Typically, to gain confidence in a randomized algorithm, one repeats the algorithm several times (with independent randomness) and takes the majority vote of the executions. While very effective, this is wasteful in terms of the number of random bits that are used. Randomness-efficient error reduction techniques are known for polynomial-time algorithms, but do not readily apply to parallel algorithms since the techniques seem inherently sequential. We achieve randomness-efficient error reduction for highly-parallel algorithms. Specifically, we can reduce the error of a parallel algorithm to any δ > 0 while paying only O(log(1/δ)) additional random bits, thereby matching the results for polynomial-time. (2) Hardness Amplification within NP. A fundamental question in average-case complexity is whether P ≠ NP implies the existence of functions in NP that are hard on average (over randomly-chosen inputs). While the answer to this question seems far beyond the reach of current techniques, we show that powerful hardness amplification is indeed feasible within NP. In particular, we show that if NP has a mildly hard-on-average function f (i.e., any small circuit for computing f fails on at least a constant fraction of inputs), then NP has a function f' that is extremely hard on average (i.e., any small circuit for computing f' only succeeds with exponentially-small advantage over random guessing). Previous results only obtained functions f' that could not be computed with polynomial advantage over random guessing. Our stronger results are obtained by using derandomization and nondeterminism in constructing f'. 
A common theme in our results is the computational efficiency of pseudorandom generators. Indeed, our results both rely upon, and enable us to construct pseudorandom generators that can be computed very efficiently (in terms of parallel complexity).
Efficient Kernel Principal Component Analysis Algorithm for Large-Scale Data Set (2009)

提出一种大规模数据集求解核主成分的计算方法.首先使用Gram矩阵生成一个Gram-power矩阵,根据线性代数的理论可知,新形成的矩阵和原先的Gram矩阵具有相同的特征向量.因此,可以把Gram矩阵的每一列看成核空间迭代算法的输入样本,这样,无须使用特征分解即可迭代地计算出核主成分.该算法的空间复杂度只有O(m);在大规模数据集的情况下,时间复杂度也降低为O(pkm).实验结果表明了所提出算法的有效性.更为重要的是,在大规模数据集的情况下,当传统的特征分解技术无法使用时,该方法仍然可以提取非线性特征.
Understanding the roles of nanoparticle dispersion and polymer crystallinity in controlling the mechanical properties of HA/PHBV nanocomposites (2008)

Understanding the roles of nanoparticle dispersion and polymer crystallinity in controlling the mechanical properties of HA/PHBV nanocomposites, Wadcharawadee Noohom, Kevin S Jack, Darren Martin, Matt Trau
Photodarkening and photobleaching of an ytterbium-doped silica double-clad LMA fiber (2007)

We studied the temporal evolution of the photodarkening effect in an Yb-doped silica LMA fiber. The absorption spectra exhibit an increase in absorption in the visible and in the near infrared spectral range when the fiber is exposed to pump light around 980 nm. We show the influence of the photodarkening on the cw lasing properties of the fiber, and demonstrate photobleaching of the same fiber by exposure to UV light at 355 nm. The corresponding absorption spectra and lasing performances are shown and are entirely comparable to those of a new fiber.
Treatment of Meningomyelocele in Indigent and Nonindigent Patients (1974)

The records for the years 1964 through 1971 of 38 indigent children with meningomyelocele treated at a municipal hospital and 52 nonindigent children with meningomyelocele treated at a private hospital were reviewed. In those cases not lost to follow-up, there was a 50% mortality in the indigent children compared with a 22% mortality in the nonindigent children. Forty-five percent of indigent patients who had shunt procedures became infected, in contrast to 15% of nonindigent children who had shunt procedures. Possible factors influencing success or failure of treatment are discussed, and methods to decrease morbidity and mortality in indigent patients with meningomyelocele are reviewed.
Top-down pairwise potentials for piecing together multi-class segmentation puzzles (2010)

Top-down class-specific knowledge is crucial for accurate image segmentation, as low-level color and texture cues alone are insufficient to identify true object boundaries. However, existing methods such as conditional random field models (CRFs) generally impose the class-specific knowledge only at the “node” level, evaluating class membership probabilities at the (super)pixels that define the random field graph. We introduce a strategy for pairwise potential functions that capture top-down information, where we prefer to assign the same label to adjacent regions when the entropy reduction that would result from their merging is high. By measuring how the certainty of the object-level classifiers changes when considering the appearance description extracted from adjacent regions, we can “piece together” objects whose heterogenous texture would prevent both the too-local node potentials and conventional bottom-up smoothness terms from recognizing the object. We show how this idea can be used as either an affinity function for agglomerative clustering, or a pairwise potential for a CRF model. Experiments with two datasets show that the proposed entropy-guided affinity function has a clear positive impact on multi-class segmentation.
Anaplastic Large Cell Lymphoma Occurring in Women with Breast Implants (2014)

Breast implant-associated ALCL is a novel manifestation of site- and material-specific lymphoma originating in a specific scar location, presenting a wide array of diverse characteristics and suggesting a multifactorial cause.
Scintillation properties of Eu-doped LiF-CaF<inf>2</inf> eutectic for neutron detectors with different Eu concentration (2013)

Eu <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> -doped LiF/CaF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> eutectic scintillators with different Eu concentrations were fabricated by the simple solidification method. Eu concentrations were 0.005, 0.02, 0.05, 0.1, 0.3, 1, 3, and 5%, and they looked visibly semitransparent. In SEM analysis, fine lamellar structure was observed in Eu low concentration samples. Radioluminescence spectra were collected under X-ray exposure and Eu <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> 5d-4f emission appeared at 435 nm. Finally, thermal neutrons were irradiated to samples and the scintillation light yields monotonically decreased with Eu concentrations.
Training signal design for MIMO OFDM channel estimation in the presence of frequency offsets (2005)

All existing training signal designs for channel estimation in OFDM systems assume no frequency offsets. In practice, frequency offset is unavoidable and seriously degrades the performance of OFDM systems. In this paper, we address the problem of designing optimal training signals for the estimation of frequency-selective channels in MIMO OFDM systems with frequency offsets. The mean square error advantage of our proposed optimal training signals can be quite significant for moderate-to-high values of SNR and frequency offsets.
Direct-Acting Small-Molecule Antivirals for the Treatment of COVID-19 (2021)

Medicinal Chemistry Reviews is an outstanding 965 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
RadioWeaves for efficient connectivity: analysis and impact of constraints in actual deployments (2019)

We present a new type of wireless access infrastructure consisting of a fabric of dispersed electronic circuits and antennas that collectively function as a massive, distributed antenna array. We have chosen to name this new wireless infrastructure "RadioWeaves" and anticipate they can be integrated into indoor and outdoor walls, furniture, and other objects, rendering them a natural part of the environment. Technologically, RadioWeaves will deploy distributed arrays to create both favorable propagation and antenna array interaction. The technology leverages on the ideas of large-scale intelligent surfaces and cell-free wireless access. Offering close to the service connectivity and computing, new grades in energy efficiency, reliability, and low latency can be reached. The new concept moreover can be scaled up easily to offer a very high capacity in specific areas demanding so. In this paper we anticipate how two different demanding use cases can be served well by a dedicated RadioWeaves deployment: a crowd scenario and a highly reflective factory environment. A practical approach towards a RadioWeaves prototype, integrating dispersed electronics invisibly in a room environment, is introduced. We outline the many and diverse R&D challenges that need to be addressed to realize the great potential of the RadioWeaves technology.