gebhart/patrepeval huggingface dataset:
Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip (2016)

Neurovascular inflammation is a major contributor to many neurological disorders, but modeling these processes in vitro has proven to be difficult. Here, we microengineered a three-dimensional (3D) model of the human blood-brain barrier (BBB) within a microfluidic chip by creating a cylindrical collagen gel containing a central hollow lumen inside a microchannel, culturing primary human brain microvascular endothelial cells on the gel's inner surface, and flowing medium through the lumen. Studies were carried out with the engineered microvessel containing endothelium in the presence or absence of either primary human brain pericytes beneath the endothelium or primary human brain astrocytes within the surrounding collagen gel to explore the ability of this simplified model to identify distinct contributions of these supporting cells to the neuroinflammatory response. This human 3D BBB-on-a-chip exhibited barrier permeability similar to that observed in other in vitro BBB models created with non-human cells, and when stimulated with the inflammatory trigger, tumor necrosis factor-alpha (TNF-α), different secretion profiles for granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6) were observed depending on the presence of astrocytes or pericytes. Importantly, the levels of these responses detected in the 3D BBB chip were significantly greater than when the same cells were co-cultured in static Transwell plates. Thus, as G-CSF and IL-6 have been reported to play important roles in neuroprotection and neuroactivation in vivo, this 3D BBB chip potentially offers a new method to study human neurovascular function and inflammation in vitro, and to identify physiological contributions of individual cell types.
Proteomic profile of osteoclast membrane proteins: Identification of Na+/H+ exchanger domain containing 2 and its role in osteoclast fusion (2008)

Osteoclast formation and bone resorption are multiple processes that involve the participation of specialized membrane structures and their associated proteins. In this study, we used an MS to analyze the profile of proteins associated with osteoclast membranes and focused on the function of channel proteins in osteoclast differentiation and function. We filtered out with a SEQUEST score greater than 10 and a peptide hit number of more than 2, resulting in the identification of 499 proteins that were commonly found in both macrophages and osteoclasts, 96 proteins selectively found in osteoclasts, and 179 proteins selectively found in macrophages. The proteins that were selectively found in osteoclasts were classified based on their localizations: plasma membrane (17%), ER/Golgi and lysosome/endosome (15%), mitochondrion (18%), nucleus (13%), cytosol (19%), and unknown (18%). Proteins associated with osteoclast function such as v-ATPase, IGF2R, TRAP, and cathepsin K were found in osteoclasts as previously shown. We found several ion channel proteins such as Ank and Nhedc2 and signaling molecules such as Dock5 and RAB-10 in osteoclasts. Inhibition of the Na(+)/H(+) exchanger family by amiloride suppressed RANKL-induced osteoclast fusion and bone resorption. In addition, shRNA for Nhedc2 inhibited osteoclast differentiation. Our results provide a proteomic profile of osteoclast membrane proteins and identify Nhedc2, which is probably associated with proton transport in osteoclasts, as a regulator of osteoclast function.
Antagonistic effects ofc-myc and Epstein-Barr virus latent genes on the phenotype of human B cells (2001)

Epstein-Barr virus (EBV) immortalized cells and Burkitt lymphoma cells have a completely different growth pattern and phenotype. EBV immortalized cells express a set of 11 viral genes to accommodate B cell activation and proliferation, whereas EBV-positive Burkitt lymphoma cells highly express the c-myc oncogene that is activated through translocation into 1 of the immunoglobulin loci and EBNA1 as the only viral protein. We have developed a primary human B cell line conditionally immortalized by Epstein-Barr virus in which the viral gene program responsible for the induction of proliferation can be switched on and off by the addition or withdrawal of estrogen (cell line EREB2-5). Starting from this cell line we have generated 2 daughter cell lines that proliferate in a c-myc dependent fashion, 1 with a highly active exogenous c-myc gene (cell line A1) and 1 with a regulatable c-myc gene that can be switched on by withdrawal and switched off by addition of tetracycline (cell line P493-6). The comparison of the 3 cell lines has allowed us to dissect the contribution of c-myc and EBV genes to the regulation of the growth pattern and expression of cell surface molecules. We show that MYC and EBNA2 (and their respective target genes) have opposing effects on the expression of several surface markers involved in B cell activation. We show that MYC contributes to the phenotype of Burkitt lymphoma cells by upregulating CD10 and CD38 and downregulating activation markers. The phenotype of the cells is determined on one hand by the absence of the viral gene products EBNA2 and LMP1 that mediate the phenotype of activated lymphoblasts and to a lesser extent by an active contribution of the c-myc gene.
Promotion of Phenol Photodecomposition over TiO2 Using Au, Pd, and Au–Pd Nanoparticles (2012)

Noble metal nanoparticles (Au, Pd, Au-Pd alloys) with a narrow size distribution supported on nanocrystalline TiO(2) (M/TiO(2)) have been synthesized via a sol-immobilization route. The effect of metal identity and size on the photocatalytic performance of M/TiO(2) has been systematically investigated using phenol as a probe molecule. A different phenol degradation pathway was observed when using M/TiO(2) catalysts as compared to pristine TiO(2). We propose a mechanism to illustrate how the noble metal nanoparticles enhance the efficiency of phenol decomposition based on photoreduction of p-benzoquinone under anaerobic conditions. Our results suggest that the metal nanoparticles not only play a role in capturing photogenerated electrons, but are strongly involved in the photocatalytic reaction mechanism. The analysis of the reaction intermediates allows us to conclude that on M/TiO(2) undesired redox reactions that consume photogenerated radicals are effectively suppressed. The analysis of the final products shows that the reusability performance of the catalyst is largely dependent on the pretreatment of the catalyst and the identity of the metal nanoparticle. Interestingly, the as-prepared Pd and Au-Pd decorated TiO(2) materials exhibit excellent long-term photoactivity, in which ~90% of the phenol can be fully decomposed to CO(2) in each cycle.
LaWeCo: Active region detection in non-uniformly sampled data using Laplacian-weighted covariance (2016)

Event detection in sparse, non-uniformly sampled multidimensional data eludes traditional signal processing techniques. We propose a method that, within the graph-theoretic framework, successfully addresses the task of localizing and characterizing active regions by leveraging the coherent behavior detection capabilities of the covariance matrix together with the natural definition of graph neighborhood connectivity provided by the Laplacian. We further extend this framework using scale space formulation to detect the extent of active region. Our method exhibits significant improvement in detecting active regions compared to other similar state-of-the art techniques. The method is demonstrated on interferometric synthetic aperture radar (InSAR) data that is both sparse and non-uniformly sampled. Comparison with three widely used event detection methods reveals the efficacy and efficiency of the Laplacian-weighted covariance technique.
Deployment of Private Crowdsourcing System with Quality Control Methods (2015)

Current crowdsourcing platforms such as Amazon Mechanical Turk provide an attractive solution for processing of high-volume tasks at low cost. However, problems of quality control remain a major concern. In the present work, we developed a private crowdsourcing system(PCSS) running in a intranetwork, that allow us to devise for quality control methods. For quality control, we introduce four worker selection methods: preprocessing filtering, real-time filtering, post-processing filtering, and guess processing filtering. In addition to a basic approach involving initial training or the use of gold standard data, these methods include a novel approach, utilizing collaborative filtering techniques. Furthermore, we collected a large amount of vocabulary data for natural language processing, such as voice recognition and text to speech using PCSS. The quality control methods increased accuracy by 32.4% in collecting vocabulary task. Then, we got 138 thousand vocabulary data. We found that PCSS is a practical system to collect data, and used for three years since 2011.
Unexpected Binding Modes of Nitric Oxide Synthase Inhibitors Effective in the Prevention of a Cerebral Palsy Phenotype in an Animal Model (2010)

Selective inhibition of the neuronal isoform of nitric oxide synthase NOS (nNOS) has been shown to prevent brain injury and is important for the treatment of various neurodegenerative disorders. However, given the high active site conservation among all three NOS isoforms, the design of selective inhibitors is an extremely challenging problem. Here we present the structural basis for why novel and potent nNOS inhibitors exhibit the highest level of selectivity over eNOS reported so far (approximately 3,800-fold). By using a combination of crystallography, computational methods, and site-directed mutagenesis, we found that inhibitor chirality and an unanticipated structural change of the target enzyme control both the orientation and selectivity of these novel nNOS inhibitors. A new hot spot generated as a result of enzyme elasticity provides important information for the future fragment-based design of selective NOS inhibitors.
Gastrointestinal bleeding (2013)

Endoscopy Essentials Reviews in the Endoscopy Essentials series cite publications from the past year which, in the authors’ opinion, reflect the state-of-the-art in endoscopy. Alongside a short summary of each paper, authors explain why they consider their selected articles to be of importance.
The SNO+ experiment: status and overview (2013)

SNO+ is a multi-purpose Neutrino Physics experiment, succeeding to the Sudbury Neutrino Observatory by replacing heavy water with liquid scintillator. Its scientific goals are the search for neutrinoless double-beta decay, the study of solar neutrinos and antineutrinos from reactors and the Earth's natural radioactivity, as well as supernovae neutrinos. The experimental advantages of SNO+ are the possibility of loading large quantities of double-beta decaying isotope in the liquid scintillator volume, and the very low backgrounds allowed by the deep underground location and radiopurity of the employed materials. The installation of the detector at SNOLAB is being completed, and commissioning has already started, with a dry run. Filling with water and later, with scintillator, will start next year. This talk will summarize the Physics goals of SNO+, as well as the main detector developments.
Difference of Component Changes in Salt-Fermented Spring and Autumn Anchovy, Engraulis japonicus Sauce during Fermentation (2001)

To investigate difference of component changes in salt-fermented spring (SAS) and autumn (AAS) anchovy, Engraulis japonicus sauce during fermentation, various chemical properties were examined at months intervals during 18 months fermentation, The contents of total and amino nitrogen were higher in SAS than in AAS until 15.7 and 17.4 months fermentation, respectively, but there were no difference after that. The cross point of inosine (HxR) + hypoxanthine (Hx) and uric acid was faster in SAS with 10.6 months fermentation than in AAS with 11.5 months fermentation, After 18 months of fermentation, the SAS was rich in free amino acids, such as glutamic acid, alanine, aspartic acid, valine, lysine in that order, On the other hand, the AAS was rich in free amino acids, such as glutamic acid, leucine, alanine, lysine, isoleucine in that order. Absorbance at 453 nm were higher in SAS than in AAS, and increased gradually during fermentation.
Testosterone in prostate cancer: the Bethesda consensus (2011)

• Understanding the mechanisms of androgen biosynthesis relating to PCa as well as prognostic implications might achieve a consensus regarding the role of ADT for both the androgen-sensitive and -insensitive disease state.
Synthesis and characterization of new soluble polyamides derived from 3,3?,5,5?-tetramethyl-2,2-bis[4-(4-carboxyphenoxy)phenyl]propane (1999)

A series of new soluble polyamides having isopropylidene and methyl-substituted arylene ether moieties in the polymer chain were prepared by the direct polycondensation of 3,3′,5,5′-tetramethyl-2,2-bis[4-(4-carboxyphenoxy)phenyl]propane and various diamines in N-methyl-2-pyrrolidinone (NMP) containing CaCl2 using triphenyl phosphite and pyridine as condensing agents. Polymers were produced with moderate to high inherent viscosities of 0.85–1.47 dL g−1 while the weight-average molecular weight and number-average molecular weight were in the range of 86,700–259,000 and 43,300–119,000, respectively. All the polymers were readily dissolved in polar aprotic solvents such as NMP, N,N-dimethylacetamide, and N,N-dimethylformamide, as well as less polar solvents such as m-cresol and pyridine, and even soluble in tetrahydrofuran. These polymers were solution-cast into transparent, flexible and tough films. All of the polymers were amorphous and the polyamide films had a tensile strength range of 82–122 MPa, an elongation at break range of 6–18%, and a tensile modulus range of 2.0–2.8 GPa. These polyamides had glass transition temperatures between 233–260°C and 10% weight loss temperatures in the range of 450–489 and 459–493°C in nitrogen and air atmosphere, respectively. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1997–2003, 1999
Crystal structure, electronic structure, temperature-dependent optical and scintillation properties of CsCe2Br7 (2015)

The structure–property relationships, thermal quenching, and point defects in CsCe<sub>2</sub>Br<sub>7</sub> single-crystal scintillator were comprehensively studied.
The Maturation of Synthetic Scaffolds for Osteochondral Donor Sites of the Knee (2009)

The Trufit BGS plug demonstrates a predictable pattern of postoperative maturation on MRI images that parallels its biological incorporation. An intermediate postoperative interval can be associated with unfavorable MRI findings. However, the plug appearance significantly improves with greater postoperative duration and has mean T2 relaxation times that approach those of normal articular cartilage.
Isoliquiritigenin and glycyrrhizin inhibit the inflammasome activation in a different manner. (P1246) (2013)

Abstract A soponin glycyrrhizin (GL) and a chalcone isoliquiritigenin(ILG) are representative components of Glycyrrhiza uralensis, which attenuate inflammatory responses mediated by TLR4. We have showed that GL and ILG suppressed different steps of the LPS sensor TLR4/MD-2 complex signaling at the receptor level. GL and ILG attenuated LPS binding to the TLR4/MD-2 complex and LPS-induced TLR4 homodimerization, respectively. In the present study, we examined effects of ILG and GL on IL-1β production in macrophage. When bone marrow-derived macrophages were stimulated with LPS to prime TLR4 signaling pathway followed by ATP to activate NLRP3 inflammasome, significant IL-1β production was observed. However, addition of ILG or GL together with ATP severely impaired the IL-1β production without changing the pro-IL-1β expression levels. We infer from these results that ILG and GL inhibit the NLRP3 inflammasome activation in both priming phase as well as activating phase. We also investigated effects of ILG and GL on the AIM2 inflammasome activation and found that GL but not ILG could suppress its activation, while both ILG and GL could suppress ATP-dependent inflammasome activation.We will discuss molecular mechanisms by which these compounds suppress inflammasome activation.
Experimental investigation of a fiber Bragg grating integrated optical limiting amplifier with high dynamic range (1998)

Shien-Kuei Liaw Sien Chi National Chiao-Tung University Institute of Electro-Optical Engineering Hsin-Chu 300 Taiwan E-mail: u8424802@cc.nctu.edu.tw Abstract. By inserting a bidirectional erbium-doped fiber amplifier (EDFA) in between an optical circulator and a fiber Bragg grating (FBG), we realize an FBG-integrated optical limiting amplifier (OLA) with high dynamic range. The dual-pass OLA has a wide dynamic range of over 40 dB and a saturation signal output power of about 13.0 dBm. The performance of dual-pass OLA has no obvious degradation due to back reflection of the amplified signal. A negligible power penalty of about 0.3 dB is observed when compared with other conventional configurations. The FBG-integrated OLA configuration has potential application in wavelength division multiplexing (WDM) systems where high saturated power is needed for multichannel transmission. © 1998 Society of Photo-Optical Instrumentation Engineers. [S0091-3286(98)02207-7]
Induced well-distributed sets in Riemannian spaces (2003)

The concept of Riemannian geometries is used to construct induced homogeneous point sets on manifolds that are based on well-distributed point sets in unit cubes of an appropriately chosen Euclidean space. These well-distributed point sets in unit cubes are based on standard low-discrepancy sequences. The approach is algorithmic, that is, the methods developed in this article have been implemented and tested. Applications in image processing, graph theory and measurement-based exploration are presented.
Supplementary Table 2, 4 and 3 cont. from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays (2023)

Supplementary Table 2, 4 and 3 cont. from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays
Micromechanical Behavior of Silicate Glass Films on Alumina Substrates (1997)

Abstract In polycrystalline liquid-phase sintered (LPS) alumina ceramics, intergranular phases have proved to have a profound effect on mechanical properties such as strength, toughness, plastic deformation, and high-temperature creep. The presence of such intergranular phases, can also influence the kinetics of many processes including sintering, grain growth, and phase transformations. As a result, the key to optimizing the performance of a ceramic material is frequently related to optimizing the properties of these grain boundary regions. In order to understand the interactions between the glass layer and the crystalline grains at a fundamental level, the amorphous material must be placed in contact with the crystalline ceramic as a thin film in a controlled manner. Preparation of such a glass phase in the thin-film geometry has also prompted the use of nontraditional mechanicaltesting techniques. In the present study, interfaces between silicate glass and single-crystal α-Al2O3 have been studied using AFM and nanoindentation.
900 MHz path loss measurements and prediction techniques for in-building communication system design (2002)

The effects of walls, floors, and building type on path loss in four different buildings are considered. Using a simple d/sup n/ model, average path loss falls off to the n=3.14 power with a standard deviation of 16.3 dB for the entire data set. However, when the effects of building type and number of floors between the transmitter and receiver are considered, standard deviations are reduced to 5 dB about a mean d/sup n/ power law. Average floor attenuation factors which describe the additional path loss caused by floors between the transmitter and receiver are found for as many as four floors in a typical office building. Preliminary evaluation of techniques to predict signal strength based on site-specific geometry are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC) (2019)

Inherited retinal diseases (IRDs) cause visual loss due to dysfunction or progressive degeneration of photoreceptors. These diseases show marked phenotypic and genetic heterogeneity. The Israeli IRD consortium (IIRDC) was established in 2013 with the goal of performing clinical and genetic mapping of the majority of Israeli IRD patients. To date, we recruited 2,420 families including 3,413 individuals with IRDs. On the basis of our estimation, these patients represent approximately 40% of Israeli IRD patients. To the best of our knowledge, this is, by far, the largest reported IRD cohort, and one of the first studies addressing the genetic analysis of IRD patients on a nationwide scale. The most common inheritance pattern in our cohort is autosomal recessive (60% of families). The most common retinal phenotype is retinitis pigmentosa (43%), followed by Stargardt disease and cone/cone-rod dystrophy. We identified the cause of disease in 56% of the families. Overall, 605 distinct mutations were identified, of which 12% represent prevalent founder mutations. The most frequently mutated genes were ABCA4, USH2A, FAM161A, CNGA3, and EYS. The results of this study have important implications for molecular diagnosis, genetic screening, and counseling, as well as for the development of new therapeutic strategies for retinal diseases.
Comparative study on the preparation of C(3)‐hydroxy‐1,3‐dihydro‐2H‐1,4‐benzodiazepin‐2‐ones (1979)

Abstract C (3)‐Hydroxy‐1,4‐benzodiazepin‐2‐ones 1–3 have been prepared in high yields using a new, two step approach. In the first step, the 3‐deoxy‐precursors 4–6 were acetylated at C (3) using the redox‐system lead tetraacetate and iodine, or potassium iodide, in acetic acid. The intermediary acetates 9–11 were quantitatively hydrolyzed into 1–3 in non‐aqueous conditions, i.e. in a methanol‐methylene chloride solvent mixture in the presence of sodium methoxide. Another route to the title compounds has been improved as follows. The yields of C (3)‐bromination of compounds 4–6 has been significantly augmented in relation to the known methods using the strong trifluoroacetic acid in very dilute carbon tetrachloride solutions as a catalyst for NBS mediated bromination. The intermediary C (3)‐bromo derivatives have been acetoxylated in situ , and compounds 9–11 have been isolated in over 80% yield. These compounds were solvolyzed into 1–3 as described above. The third part of this paper describes the search for feasible reaction conditions in the synthesis of 3 according to a known method (Scheme 1.); optimization of the yields in all steps was performed.
Driven-dissipative confined polariton condensate under magnetic field (2014)

We investigate exciton-polariton condensation under magnetic field in a single high-quality semiconductor micropillar cavity. We observe successive polariton condensation of each spin component for two distinct threshold powers. Pronounced and non-monotonous variations of both the Zeeman splitting and the circular polarization of the emission are measured across these two condensation thresholds. This unexpected behavior deeply deviates from the so-called spin Meissner effect predicted for a fully thermalized system. Our measurements can be understood in a kinetic approach taking into account spin-anisotropic interactions within the entire system: the polariton condensate and the cloud of uncondensed excitons.