gebhart/patrepeval huggingface dataset:
Actin-binding proteins differentially regulate endothelial cell stiffness, ICAM-1 function and neutrophil transmigration (2014)

Chronic vascular inflammation is driven by interactions between activated leukocytes and the endothelium. Leukocyte β2-integrins bind to endothelial intercellular adhesion molecule 1 (ICAM-1), which allows leukocyte spreading, crawling and transendothelial migration. Leukocytes scan the vascular endothelium for permissive sites to transmigrate, which suggests that there is apical membrane heterogeneity within the endothelium. However, the molecular basis for this heterogeneity is unknown. Leukocyte adhesion induces ICAM-1 clustering, which promotes its association to the actin-binding proteins filamin B, α-actinin-4 and cortactin. We show that these endothelial proteins differentially control adhesion, spreading and transmigration of neutrophils. Loss of filamin B, α-actinin-4 and cortactin revealed adaptor-specific effects on a nuclear-to-peripheral gradient of endothelial cell stiffness. By contrast, increasing endothelial cell stiffness stimulates ICAM-1 function. We identify endothelial α-actinin-4 as a key regulator of endothelial cell stiffness and of ICAM-1-mediated neutrophil transmigration. Finally, we found that the endothelial lining of human and murine atherosclerotic plaques shows elevated levels of α-actinin-4. These results identify endothelial cell stiffness as an important regulator of endothelial surface heterogeneity and of ICAM-1 function, which in turn controls the adhesion and transmigration of neutrophils.
Novel RF-MEMS capacitive switching structures (2002)

This paper reports on novel RF-MEMS capacitive switching devices implementing an electrically floating metal layer covering the dielectric to ensure intimate contact with the bridge in the down state. This results in an optimal switch down capacitance and allows optimisation of the down/up capacitance ratio all that are not possible with standard characteristics compared to standard RF-MEMS capacitive switches, in the frequency range from 1 to 30 GHz. Down/up capacitance ratios higher than 450 have been measured, an improvement of a factor 34 over standard designs with equal size and using the same materials.
Very efficient speckle contrast reduction realized by moving diffuser device (2010)

Speckle noise reduction is best tested on a precise speckle contrast measurement bench, which should be able to measure 100% contrast in fully developed speckle as well as the smallest contrast (for example, less than 10%) after its reduction. On such a test bench, we have measured very efficient speckle contrast reduction by temporal averaging using a moving diffuser on a tuning fork, which vibrates at 100 Hz over 60 microm in amplitude, a distance that is three times the surface roughness correlation length of the diffuser.
OBSERVABILITY ANALYSIS AND STATE ESTIMATION ON A PERSONAL COMPUTER (1988)

This paper discusses the development of a state estimation package on an IBM PC/AT. The package was designed so that observability analysis and state estimation studies are simplified. The design criteria and the resulting decisions are discussed. The observability determination program uses the symbolic matrix reduction algorithm. The state estimation program uses the decoupled- gain-matrix weighted least squares algorithm.
Identification of Novel Inhibitors of Dietary Lipid Absorption Using Zebrafish (2010)

Pharmacological inhibition of dietary lipid absorption induces favorable changes in serum lipoprotein levels in patients that are at risk for cardiovascular disease and is considered an adjuvant or alternative treatment with HMG-CoA reductase inhibitors (statins). Here we demonstrate the feasibility of identifying novel inhibitors of intestinal lipid absorption using the zebrafish system. A pilot screen of an unbiased chemical library identified novel compounds that inhibited processing of fluorescent lipid analogues in live zebrafish larvae. Secondary assays identified those compounds suitable for testing in mammals and provided insight into mechanism of action, which for several compounds could be distinguished from ezetimibe, a drug used to inhibit cholesterol absorption in humans that broadly inhibited lipid absorption in zebrafish larvae. These findings support the utility of zebrafish screening assays to identify novel compounds that target complex physiological processes.
Solar-thermic sewage sludge treatment in extreme alpine environments (2007)

In the framework of a program for environmental protection conducted by the German mountaineers' club (DAV) problems emerging from residual solids accumulating in on-site wastewater treatment plants of mountain refuges were investigated. To handle these problems in an ecologically and economically reasonable way two devices for solar-supported treatment of sludge and bio-solids have been developed. These units support gravity-filtration and evaporation of liquid sludge as well as thermal acceleration of composting processes. Two solar sludge dryers were installed and operated without external energy supply at alpine refuges treating primary and secondary sludge, respectively. Batch-filling during the season could increase load capacity and a total solids concentration of up to 40% could be achieved before discharge at the beginning of the next season. The promising results from the solar sludge dryer encouraged for the development of a solar composter. The period of temperature levels suitable for composting biosolids in mountain areas can be extended considerably by application of this technology--measured temperature distribution indicated no freezing at all.
The Chemistry of Phenol-Formaldehyde Resin Crosslinking of EPDM as Studied with Low-Molecular-Weight Models: Part II. Formation of Inert Species, Crosslink Precursors and Crosslinks (2000)

Abstract Phenol-formaldehyde resins (resols) are the preferred crosslinking agents for the dynamic vulcanization of blends of polypropylene and ethylene—propylene—diene rubber (PP/EPDM) for the production of thermoplastic vulcanizates (TPVs). The goals of this study were to elucidate in detail the chemical structures formed using low-molecular-weight model compounds and to elaborate on the chemical mechanism of resol cure of EPDM as presented in our previous study. The use of model compounds for EPDM (2-ethylidenenorbornane [ENBH] and 4-methylheptane), but also for resol (2-hydroxymethylphenol [HMP] and 2,6-di(hydroxymethyl)- p -cresol) allowed the characterization of the chemical structures formed with the aid of gas chromatography/mass spectrometry (GC/MS). In combination with derivatization of unreacted hydroxyls a large variety of species could be distinguished with the general structure of R−phenol-[-CH 2 −phenol-] n −R ′ ( n=0 , 1 or 2). R and R′ can be inert end groups resulting from degradation or disproportionation, viz. —H, —CH 3 or —CHO, reactive end groups, viz. —CH 2 OH, and products of addition to ENBH (C 9 H 14 ), viz. —CH 2 —C 9 H 13 . When either R or R′ is —CH 2 —C 9 H 13 a model crosslink precursor is formed, when both are —CH 2 —C 9 H 13 a model crosslink is formed. It has been demonstrated beyond doubt that both chroman and methylene bridged species are produced. It is still unclear what parameters determine the selectivity for chroman versus methylene bridged structures (presence of activators, structure of olefin etc.). The two major model crosslink products of HMP and ENBH have also been characterized with nuclear magnetic resonance, which confirmed the chroman and methylene bridged structures and showed that the addition of the phenol predominantly occurs at the least sterically hindered C-8 of ENBH. The yield of the reaction of resol with ENBH is enhanced by temperature increase and/or the addition of SnCl 2 ·2H 2 O. 4-Methylheptane does not react with HMP. This indicates that in a PP/EPDM based TPV only crosslinking of EPDM via the residual diene unsaturation occurs and that tertiary C-atoms of PP or of the ethylene—propylene rubber (EPM) chain of EPDM are not involved. The high reactivity of ENBH compared with 1-decene or hydrogenated dicyclopentadiene supports a cationic mechanism.
ALL HAIL THE GREAT ABSTRACTION: STAR WARS AND THE POLITICS OF COGNITIVE PSYCHOLOGY (2015)

Form rhizomes and not roots, never plant! Don’t sow, forage!
Be neither a One nor a Many, but multiplicities! Form a line, 
never a point! Speed transforms the point into a line. Be fast, 
even while standing still! Line of chance, line of hips, line of 
flight. Don’t arouse the General in yourself! Make maps, not 
photographs or drawings. Be the Pink Panther, and let your 
loves be like the wasp and the orchid, the cat and the baboon.
Perforin and IFN-γ Are Involved in the Antitumor Effects of Antibody-Targeted Superantigens (1998)

Abstract The bacterial superantigen staphylococcal enterotoxin A (SEA) is a potent inducer of cytokine production and cytotoxic T cell responses. To target a T cell attack against tumor cells we have genetically engineered a fusion protein of SEA and the Fab part of the tumor-reactive mAb C215. Injection of this Fab-SEA fusion protein to mice carrying lung metastases of the poorly immunogenic B16 melanoma transfected with the C215 Ag resulted in infiltration of cytokine-producing T cells, perforin-containing CTL, and a marked tumor elimination. Fab-SEA therapy induced substantial levels of IFN-γ and TNF-α in serum. In the present study we have characterized the molecular mechanisms of the antitumor effect induced by Fab-SEA treatment in vivo. Neutralization of cytokines by specific Abs demonstrated a major role for IFN-γ in the suppression of tumor growth. In addition, a minor contribution of TNF-α was recorded. Injections of Fab-SEA into normal mice induced strong CTL activity but failed to promote cytotoxic function in perforin knockout mice. Also, a markedly reduced therapy was noted in perforin knockout mice, implicating a role for CTL in Fab-SEA-mediated tumor eradication. The data suggest that Fab-SEA-targeted T cells may suppress tumor growth by both perforin-dependent cytotoxicity and local release of cytokines such as IFN-γ. The latter mechanism may have an important role in cytostatic effects against Ag-negative bystander tumor cells.
Depostition of submicron aerosol particles in turbulent and transitional flow (1993)

Abstract Brownian and turbulent diffusive deposition of submicron aerosol particles from pipe flow is studied experimentally and theoretically. A theoretical model for evaluating the turbulent diffusive deposition is presented in which a turbulent flow in a circular pipe is numerically calculated based on the k‐ϵ turbulent flow model and deposition velocities are derived by solving the convection‐diffusion equation. Deposition velocities of monodisperse aerosol particles, 0.01–0.04 μm in diameter, are obtained experimentally by measuring the decrease in the particle number concentration of an aerosol at two cross‐sections of a circular test pipe through which the aerosol is flowing. The deposition velocities obtained when Re is larger than about 3,000 agree well with those predicted by the present analysis which are proportional to the 0.92nd power of Reynolds number and the 0.33rd power of Schmidt number. The particle deposition rates are measured when 1, 000 ≲ Re ≲ 2,000 suggest a transitional state for particle deposition which cannot be explained by the present analysis nor by the laminar pipe flow deposition theory.
Stabilizing the Anaerobic Digestion of Food Waste for Biomethane Production (2017)

Anaerobic digestion (AD) is a viable method for conversion of food waste and other organic materials into methane-rich biogas. However, when used at high organic loading rates, using only food waste can lead to an unstable process. Process instability is indicated by frequent changes in pH, and increase in ammonia and hydrogen sulfide concentration. These uncontrolled changes combined with over-production of organic acids can inhibit biogas production and ultimately lead to digester failure. Therefore, certain co-substrates produced as wastes in the regional food sector were tested as stabilizing agents for food waste digestion with an objective of achieving stable non-manure based digestion. The substrates tested were acid whey, bread, manure, caffeinated drink, paper napkins and apple pomace. The biogas production was increased by 12% in reactors containing bread, by 10% with acid whey, and by 12% when the co-substrate was caffeinated drink. The reactors containing paper and manure showed decreased biogas production by 6% and 12% respectively, but these changes are relatively small and thus not considered inhibitory. Co-digestion with apple pomace was found to be inhibitory and resulted in digester failure. This initial study has demonstrated that the stability of AD systems may be improved by strategically combining available food waste feedstocks.
O4‐04‐01: Microglial Exosomes Propagate Tau Protein from the Entorhinal Cortex to the Hippocampus: An Early Pathophysiology of Alzheimer's Disease (2016)

The neurofibrillary tangle is a pathological hallmark of Alzheimer's disease (AD) and primarily consists of hyper-phosphorylated tau protein (pTau). pTau first appears in the entorhinal cortex in the presymptomatic stage, then gradually disseminates to the hippocampal region around the onset of clinical symptoms of AD. Halting this tau spread in the asympomatic stage is a promising therapeutic approach for AD. The exosome is a small vesicle of 50-100 nm in diameter, enriched in ceramide, and is suggested to contain neuropathogenic proteins, such as prion, a-synuclein, and recently tau proteins. A growing body of evidence suggests that microglia contribute to tauopathy-related pathogenesis in both human and animal models. We hypothesize that microglia transduce tau aggregates into nearby neuronal cells via exosomal secretion, and that inhibition of the exosome synthesis or secretory pathway reduces tau dissemination. Adeno-associated virus serotype 6 expressing FTDP-17-linked mutation of tau protein was stereotaxically injected into the entorhinal cortical region of C57BL/6 mice, and the animals were sacrificed at 7 and 28 days post injection. The brain specimens were examined for tau accumulation in the hippocampal region. The animals were also systemically treated with specific inhibitors of neutral sphingomyelinase-2 to block exosome synthesis, or colony stimulating factor 1 receptor (CSF1R) to deplete microglia. We found that human tau propagate from entorhinal cortical neurons to dentate granular cells after AAV injection, and that this propagation is sensitive to the inhibition of exosome synthesis or microglial depletion. We also found that tau-containing exosomes isolated from microglia efficiently transduce tau protein to neurons in vitro and in vivo. Finally, these results were reproduced in P301S tau mice (PS19) treated with these compounds. These results demonstrate that exosome secretion from microglia play a significant role in propagation of tau protein from entorhinal cortex to hippocampal neurons. Our findings could lead to an entirely novel paradigm for delaying the progression of disease in AD and other tauopathies such as frontotemporal dementia and chronic traumatic encephalopathy.
Location Data Analytics in Wireless Lighting Systems (2015)

Location data analytics refers to the statistical analysis of data pertaining to user location. Such analytics offers useful insights into the interactions among occupants and with their environment. Based on the insights, building facility management may be improved. We consider location data analytics using wireless sensors, which are part of a wireless lighting system, to collect radio received signal strength indicator data resulting from device transmissions from user mobile devices. Zone positioning of users is first performed. Zone position data are then used for analytics to obtain: 1) occupancy density; 2) environment characterization; 3) crowd detection; and 4) occupant connectivity. The approach is evaluated in a simulated open-plan office lighting environment considering simple occupant motion profiles and wireless device transmission models.
Resonances in symmetric Josephson interferometers (1980)

A simple analytical theory is presented which calculates the current due to self-induced resonances in symmetric two-junction Josephson interferometers as a function of voltage, control current, and damping. Experimental measurements of interferometer I-V curves near a resonance and of peak resonance amplitudes as a function of control current were carried out and found to agree with the theory. The existence of a negative-resistance region in the I-V curves of lightly damped, current-biased interferometers is predicted and experimentally verified. The theory allows accurate determination of the resonant voltage and the interferometer damping from experimental I-V curves.
A Single-stranded DNA-binding Protein of Bacteriophage T7 Defective in DNA Annealing (2021)

The annealing of complementary strands of DNA is a vital step during the process of DNA replication, recombination, and repair. In bacteriophage T7-infected cells, the product of viral gene 2.5, a single-stranded DNA-binding protein, performs this function. We have identified a single amino acid residue in gene 2.5 protein, arginine 82, that is critical for its DNA annealing activity. Expression of gene 2.5 harboring this mutation does not complement the growth of a T7 bacteriophage lacking gene 2.5. Purified gene 2.5 protein-R82C binds single-stranded DNA with a greater affinity than the wild-type protein but does not mediate annealing of complementary strands of DNA. A carboxyl-terminal-deleted protein, gene 2.5 protein-Delta26C, binds even more tightly to single-stranded DNA than does gene 2.5 protein-R82C, but it anneals homologous strands of DNA as well as does the wild-type protein. The altered protein forms dimers and interacts with T7 DNA polymerase comparable with the wild-type protein. Gene 2.5 protein-R82C condenses single-stranded M13 DNA in a manner similar to wild-type protein when viewed by electron microscopy.
Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma (2018)

Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole-exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominates in 10/32 samples, while nine show microsatellite instability (MSI) profiles. UV-damage SeC exhibited poorly differentiated, infiltrative histopathology compared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Moreover, UV-damage SeC transcriptomes and anatomic distribution closely resemble those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations per Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquires far fewer mutations without a dominant signature, but show frequent truncations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.
Which public health interventions are effective in reducing morbidity, mortality and health inequalities from infectious diseases amongst children in low-income and middle-income countries (LMICs): protocol for an umbrella review (2019)

CRD42019141673.
Publisher’s Note: Overcoming the Diffraction Limit in Wave Physics using a Time-Reversal Mirror and a Novel Acoustic Sink [Phys. Rev. Lett.89, 124301 (2002)] (2002)

Received 4 September 2002DOI:https://doi.org/10.1103/PhysRevLett.89.219901©2002 American Physical Society
The Role of Cotranscriptional Histone Methylations (2010)

The carboxy-terminal domain (CTD) of the RNA polymerase II subunit Rpb1 undergoes dynamic phosphorylation, with different phosphorylation sites predominating at different stages of transcription. Our laboratory studies show how various mRNA-processing and chromatin-modifying enzymes interact with the phosphorylated CTD to efficiently produce mRNAs. The H3K36 methyltransferase Set2 interacts with CTD carrying phosphorylations characteristic of downstream elongation complexes, and the resulting cotranscriptional H3K36 methylation targets the Rpd3S histone deacetylase to downstream transcribed regions. Although positively correlated with gene activity, this pathway actually inhibits transcription elongation as well as initiation from cryptic promoters within genes. During early elongation, CTD serine 5 phosphorylation helps recruit the H3K4 methyltransferase complex containing Set1. Within 5' transcribed regions, cotranscriptional H3K4 dimethylation (H3K4me2) by Set1 recruits the deacetylase complex Set3C. Finally, H3K4 trimethylation at the most promoter-proximal nucleosomes is thought to stimulate transcription by promoting histone acetylation by complexes containing the ING/Yng PHD finger proteins. Surprisingly, the Rpd3L histone deacetylase complex, normally a transcription repressor, may also recognize H3K4me3. Together, the cotranscriptional histone methylations appear to function primarily to distinguish active promoter regions, which are marked by high levels of acetylation and nucleosome turnover, from the deacetylated, downstream transcribed regions of genes.
Direct observation of point defects in Nb12O29by high-resolution electron microscopy (1973)

Point defects have been observed directly in non-stoichiometric niobium oxides, Nb12O29, by high- resolution electron microscopy at a resolution of 3-4 Å. A proposed model for the point defect is a complex composed of two interstitial metal atoms and two interstitial oxygen atoms. Observations have been made on the annealing out of these defects under electron irradiation. Evidence on the density of these defects offers a semi-quantitative explanation of how the non-stoichiometric oxygen excess in these oxides is accommodated in the matrix structure.
Battery Lifetime Prediction and Degradation Reconstruction based on Probabilistic Convolutional Neural Network (2022)

Capacity degradation of lithium-ion batteries influences their service abilities as energy storage systems. Lifetime prediction, historical degradation curve trajectory, and capacity estimation help prognose the long-term serviceability and timely health status of batteries, which guides early maintenance and intelligent management. This paper proposed a novel method to predict the lifetime, reconstruct the historical degradation curve and estimate the capacity via excavating the information hindered under partially charged capacity and temperature curves. Only partial raw data of temperature and charged capacity are needed for modeling without manual feature engineering. The convolutional neural network is used to build the lifetime prediction and capacity estimation models. In addition, the probabilistic regression is added to the establishment of the capacity estimation model, which could provide the probabilistic estimation results. Finally, transfer learning is adopted to update the model with a few available data of testing batteries. Results show that the predictions are accurate and reliable.
Radiofrequency ablation for the treatment of gastric antral vascular ectasia (2014)

RFA for the treatment of GAVE seems feasible and safe, and significantly reduced the need for RBC transfusion and increased the hemoglobin level in this retrospective case series.