gebhart/patrepeval huggingface dataset:
Dysregulation of autophagy in chronic lymphocytic leukemia with the small-molecule Sirtuin inhibitor Tenovin-6 (2013)

Tenovin-6 (Tnv-6) is a bioactive small molecule with anti-neoplastic activity. Inhibition of the Sirtuin class of protein deacetylases with activation of p53 function is associated with the pro-apoptotic effects of Tnv-6 in many tumors. Here, we demonstrate that in chronic lymphocytic leukemia (CLL) cells, Tnv-6 causes non-genotoxic cytotoxicity, without adversely affecting human clonogenic hematopoietic progenitors in vitro, or murine hematopoiesis. Mechanistically, exposure of CLL cells to Tnv-6 did not induce cellular apoptosis or p53-pathway activity. Transcriptomic profiling identified a gene program influenced by Tnv-6 that included autophagy-lysosomal pathway genes. The dysregulation of autophagy was confirmed by changes in cellular ultrastructure and increases in the autophagy-regulatory proteins LC3 (LC3-II) and p62/Sequestosome. Adding bafilomycin-A1, an autophagy inhibitor to Tnv-6 containing cultures did not cause synergistic accumulation of LC3-II, suggesting inhibition of late-stage autophagy by Tnv-6. Thus, in CLL, the cytotoxic effects of Tnv-6 result from dysregulation of protective autophagy pathways.
Effect of Poly(ethylene glycol) Grafting Density on Methylcellulose Fibril Formation (2018)

We investigate the effect of short-chain poly(ethylene glycol) (PEG) graft density on the formation of methylcellulose (MC) fibrils at elevated temperatures. Thiol–ene click chemistry was used to systematically graft 800 and 2000 g/mol PEG onto the backbone of allylated MC, with a wide range of grafting densities from 0.7% to 33%. As determined from light scattering, grafting leads to an increase in the persistence length of this semiflexible copolymer, by as much as a factor of 10. Upon heating, SAXS and AFM studies show that fibril formation is suppressed at around 10% grafting density for shorter PEG grafts, corresponding to persistence lengths about ∼22 nm. For longer grafts fibril formation is suppressed at 7% grafting density, at around the same ∼22 nm persistence length. The radius of the fibrils increases with the square root of the persistence length of the chains, which is consistent with a theory for the radius of twisted chains. The ability to form networks at 80 °C is highly correlated to the ability to form fibrils, and accordingly the modulus systematically decreases with grafting density. When the fibril formation is suppressed, MC solutions no longer form solid networks. Therefore, grafting modulates the molecular architecture and gelation properties of MC and also provides new insight into the structure of MC fibrils.
Why Ashwagandha for Prevention and Treatment of COVID-19? (2020)

A novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-coronavirus 2; SARS-CoV-2)
emerged in December 2019 in Wuhan, China, and caused fatal Coronavirus disease 2019 (COVID-19). It became
an international pandemic, disrupted all aspects of normal life and called global health emergency. High infected
numbers and deaths world-wide have evoked urgent initiation of new line of drug and vaccine development on one
hand, and repurposing of the existing drugs on the other. Because of the immunity enhancing properties of several
kinds of traditional home medicine, they have been recommended for the prevention and treatment of COVID-19.
Ashwagandha, an Ayurvedic herb that enjoys 5000 years of history was explored for its potential for antiCOVID-19
activity using bioinformatics and experimental technologies. Active with anolides of Ashwagandha (Withaferin-A;
Wi-A and Withanone; Wi-N) were tested for their binding to a highly conserved protein (Mpro, an essential protein
for virus replication and survival) of SARS-CoV-2. Wi-N, but not Wi-A, showed strong binding to Mpro with the
binding energy equivalent to a known Mpro inhibitor (N3) predicting that Wi-N may serve as natural drug for
COVID-19. We also examined potential of Wi-A and Wi-N to bind to a cell membrane protein (TPMRSS2) that
acts as a gate for entry of virus to the host cell. We found that although both Wi-A and Wi-N could bind and stably
interact with TMPRSS2, Wi-N showed stronger interactions. Furthermore, human cells treated with Wi-N showed
low level of expression of TMPRSS2 predicting three-way action of Wi-N to deal with SARS-CoV-2 (blocking its
entry to the host cells by interaction with TMPRSS2, downregulation of TMPRSS2 expression and diminishing the
viral survival through inhibition of viral Mpro protein).
An association of soluble CD40 ligand (CD154) with adverse reactions to platelet transfusions (2006)

These are the first data demonstrating that a PLT-derived mediator, sCD40L, is associated with adverse transfusion events. Existing clinical factors, for example, inflammation or leukopenia, may influence whether infused mediators cause reactions.
Reactions of palm oil‐based mcl‐PHAs with epoxidized natural rubber (2009)

Abstract A palm oil‐based medium‐chain‐length polyhydroxyalkanoate (mcl‐PHA) was allowed to react with epoxidized natural rubber (ENR). There was no noticeable reaction at ambient temperature for short reaction times. However, after 30 min at 170°C, the mcl‐PHA underwent thermal degradation to generate carboxylic terminal groups that attacked the epoxy groups of the ENR. Evidence of the ring‐opening reaction was provided by both FTIR and 1 H‐NMR. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Passivation of Deep Levels at the SiO2/SiC Interface (2010)

The analysis of trapping phenomena in 4H- and 6H-SiC MOS capacitors from C-V and CCDLTS measurements is presented. Three categories of defect levels are distinguished: namely, oxide traps, semiconductor bulk traps, and interface states. NO annealing results in a dramatic decrease of the density of the interface states and the oxide traps in both polytypes, but does not reduce that of the SiC bulk traps.
Regulation of integrin‐mediated adhesion to laminin and collagen in human melanocytes and in non‐metastatic and highly metastatic human melanoma cells (1993)

We compared integrin-mediated adhesion to extracellular matrix (ECM) components of cultured human melanocytes and 6 human melanoma cell lines with different metastatic capacities in nude mice. Cultured melanocytes and most melanoma cell lines adhered strongly to fibronectin (FN), whereas only highly metastatic cell lines adhered to laminin (LM), collagen type I (COI) and type IV (COIV). Adhesion to LM and CO could be blocked by anti-alpha 6 and anti-alpha 2 monoclonal antibodies (MAbs) respectively. This observation is consistent with the finding that expression of LM receptor alpha 6 beta 1 and LM/CO receptor alpha 2 beta 1 was low on melanocytes and non- or poorly metastatic cell lines, whereas these integrins were strongly expressed on highly metastatic cell lines. In addition, immunoprecipitation from [35S]-methionine-labeled cells demonstrated increased synthesis of alpha 6, alpha 2 and beta 1 in highly metastatic cell lines and immunohistochemistry showed expression of alpha 6 beta 1 and alpha 2 beta 1 only in xenograft lesions from highly metastatic cell lines. Furthermore, the observation that adhesion of melanocytes and non- or poorly metastatic cell lines could be stimulated with anti beta 1 MAbs demonstrates that these receptors, on these cells, are expressed in an inactive state. Our results suggest that alpha 2 beta 1 and alpha 6 beta 1 play a role in human melanoma metastasis in nude mice and demonstrate that interactions of these integrins with their ligands can be regulated at the level of surface expression and activation state of the receptor.
Bacillus anthracis lcp Genes Support Vegetative Growth, Envelope Assembly, and Spore Formation (2015)

Products of genes essential for bacterial envelope assembly represent targets for antibiotic development. The LytR-CpsA-Psr (LCP) enzymes tether bactoprenol-linked intermediates of secondary cell wall polymers to the C6 hydroxyl of N-acetylmuramic acid in peptidoglycan; however, the role of LCPs as a target for antibiotic therapy is not defined. We show here that LCP enzymes are essential for the cell cycle, vegetative growth, and spore formation of Bacillus anthracis, the causative agent of anthrax disease. Furthermore, we assign functions for each of the six LCP enzymes, including cell size and shape, vegetative growth and sporulation, and S-layer and S-layer-associated protein assembly.
Phase and Amplitude Imaging from Noisy Intensity Measurements using a Kalman Filter (2010)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. Waller, M. Tsang, S. Ponda, and G. Barbastathis, "Phase and Amplitude Imaging from Noisy Intensity Measurements using a Kalman Filter," in Frontiers in Optics 2010/Laser Science XXVI, OSA Technical Digest (CD) (Optica Publishing Group, 2010), paper FTuK3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Thermally Responsive Pulsating Nanotubules (2012)

The nanotube formed from stacked macrocyclic units undergoes thermally induced swelling and unswelling and mimics the action of a pump.
ChemInform Abstract: Features of Organolanthanoid Complexes (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Karhunen–Loéve expansion of Burgers’ model of turbulence (1988)

Characteristics of the Karhunen–Loéve expansion of a strongly inhomogeneous random process possessing small viscous length scales and a large outer scale have been investigated in relation to the application of the expansion to turbulent flow fields. Monte Carlo simulations of a randomly forced Burgers’ equation with zero velocity boundary conditions generate the random process numerically and the Karhunen–Loéve (KL) eigenfunctions and the eigenvalue spectra are computed for different Reynolds numbers. The eigenfunctions possess thin viscous boundary layers at the walls and are independent of Reynolds number in the core, where the random process is quasihomogeneous. The eigenfunctions and eigenvalues of the outer, large scale motions obey a principle of Reynolds number similarity. Eigenvalue spectra contain much of the energy in the first few modes, but they are as broad as ordinary trigonometric power spectra. The rate at which the expansion converges to within 90% of the total energy decreases with increasing Reynolds numbers and the expansion of the mean plus the fluctuation converges more rapidly than the expansion of the fluctuation alone.
Supplementary Figure 2, Video 1 from Enhancement of Human Cancer Cell Motility and Invasiveness by Anaphylatoxin C5a via Aberrantly Expressed C5a Receptor (CD88) (2023)

&lt;p&gt;AVI file - 13904K, Time-lapse video analysis-C5aR(-)C5a(-)&lt;/p&gt;
CrowdMask: Using Crowds to Preserve Privacy in Crowd-Powered Systems via Progressive Filtering (2017)

Crowd-powered systems leverage human intelligence to go beyond the capabilities of automated systems, but also introduce privacy and security concerns because unknown people must view the data that the system processes. While automated approaches cannot robustly filter private information from these datasets, people have the ability to do so if the risk from them viewing the data can be mitigated. We present a crowd-powered approach to masking private content in data by segmenting and distributing smaller segments to crowd workers so that individual workers can identify potentially private content without being able to fully view it themselves. We introduce a novel pyramid workflow for segmentation that uses segments at multiple levels of granularity to overcome problems with fixed-sized approaches. We implement our approach in CrowdMask, a system that allows images with potentially sensitive content to be masked by appearing in progressively larger, more identifiable segments, and masking portions of the image as soon as a risk is identified. Our experiments with 4134 Mechanical Turk workers show that CrowdMask can effectively mask private content from images without revealing sensitive content to constituent workers, while still enabling future systems to use the filtered result.
Low voltage drop plasma switch for inverter and modulator applications (1993)

A low forward voltage drop plasma switch has been developed for high-efficiency inverter and modulator applications. The switch, called the HOLLOTRON, is based on a grid-controlled, thermionic hollow-cathode discharge. A low forward voltage drop (10–20 V) is achieved by operating the hollow-cathode discharge in a static gas pressure of xenon. The dense plasma generated in the Ba-oxide dispenser hollow cathode is spread over a relatively large control grid area by a diverging magnetic field superimposed on the discharge. Interruption of the discharge current at high current densities (≳4 A/cm2) over the grid area is achieved by biasing the control grid sufficiently negative with respect to the plasma. The HOLLOTRON switch has demonstrated voltage stand-off of up to 20 kV, switching times of ≤0.3 μs, and pulse repetition frequencies of 20 kHz at 50% duty.
A Peptide from Alveolar Macrophages That Releases Neutrophil Enzymes into the Lungs in Patients with the Adult Respiratory Distress Syndrome (1988)

A monoclonal antibody has been made to a peptide that is released by human alveolar macrophages. This enzyme-releasing peptide (ERP) causes neutrophils to secrete azurophilic granule enzymes. Normal subjects, patients with pulmonary fibrosis, and patients with sarcoidosis had similar concentrations of this peptide in their bronchoalveolar lavage fluids. However, patients with the adult respiratory distress syndrome (ARDS) had about 2.7 times higher concentrations in their lavage fluids. The enzyme-releasing activity in the lavage fluids was significantly correlated with 2 indices of the severity of the clinical illness in patients with ARDS, the APACHE score, and the chest radiograph score. The correlation was diminished or ablated by removing the peptide with the monoclonal antibody bound to staphylococcal Sepharose 4B. This peptide accounted for 62.08% (SD = 15.88%) of the enzyme-releasing activity in fluids from lungs of patients with ARDS and 86.39% (SD = 24.46%) of the activity in fluids from lungs of normal control subjects. Therefore, ERP is the major neutrophil enzyme-releasing agent in the bronchoalveolar lavage fluid from patients with ARDS and from normal persons. There was a significant correlation between the neutrophil enzyme-releasing activity and the ERP concentrations in BAL of patients with ARDS. These observations suggest that modulation of neutrophil function by ERP significantly controls the protease and peroxidase loads in the lungs of patients with ARDS.
Experimental and molecular dynamics studies of anthraquinone dyes in a nematic liquid-crystal host: a rationale for observed alignment trends (2016)

Five anthraquinone dyes with bis(4-propylphenyl) substituents, connected via sulfide or amine linking groups at the 1,5-positions or directly at the 2,6-positions, have been studied as guests in the nematic liquid crystal host, E7. Polarized UV-visible absorption spectra of aligned samples were used to obtain experimental dichroic order parameters, which exhibit values in the range 0.51-0.74. Fully atomistic MD simulations of these guest-host systems were carried out, generally using default parameters but using new force constants derived here for the dyes containing flexible phenyl-sulfide and phenyl-amine linking groups. An analysis of the alignment of the dye molecules in these simulations provides calculated molecular order parameters, which are combined with calculated order parameters for the alignment of the transition dipole moments within the dyes, reported previously, to give calculated dichroic order parameters. The trend in the calculated dichroic order parameters between the dyes shows a good match with the trend in the experimental values, enabling the observed variation to be rationalised primarily by changes in the alignment of the calculated transition dipole moments within the dyes; the calculated molecular order parameters show a relatively small variation between the dyes. The results indicate that this computational approach may be used generally to rationalise trends in the alignment of guest molecules in liquid crystal hosts, suggesting that it may also be able to provide a predictive aid in the design of guest dyes.
Optical band gap and ultralow dielectric constant materials prepared by a simple dip coating process (2003)

A simple procedure for producing silica films containing ordered porous silica films, with pore sizes in the range of 40–1000 nm, is described. The precursors were prepared by mixing polystyrene latex (PSL) colloidal spheres and silica nanoparticles. The precursors were dipped vertically onto a silicon wafer or glass substrate and the PSL particles were then completely removed at a temperature of approximately 400 °C. This method permits the pore size to be selected by appropriate adjusting of the size of the PSL particles. The presence of an optical band gap, which is dependent on the dielectric constant periodicity of the material, was clearly observed. A simple medium effective model to calculate the effective refraction index of the film combined with a Bragg diffraction equation exhibit calculation results in agreement with the measured data. The film produced using this procedure has a dielectric constant as low as 1.192, thus confirming that the proposed method has also the potential for producing ultralow dielectric constant materials.
Distinct Biochemical Properties ofArabidopsis thalianaActin Isoforms (2015)

Plants and animals express multiple actin isoforms in a manner that is dependent on tissues, organs and the stage of development. Previous genetic analyses suggested that individual actin isoforms have specific roles in cells, but there is little biochemical evidence to support this hypothesis. In this study, we purified four recombinant Arabidopsis actin isoforms, two major vegetative actin isoforms, ACT2 and ACT7, and two major reproductive isoforms, ACT1 and ACT11, and characterized them biochemically. Phalloidin bound normally to the filaments of the two reproductive actins as well as to the filaments of skeletal muscle actin. However, phalloidin bound only weakly to ACT7 filaments and hardly at all to ACT2 filaments, despite the conserved sequence of the phalloidin-binding site. Polymerization and phosphate release rates among these four actin isoforms were also significantly different. Moreover, interactions with profilin (PRF) were also different among the four Arabidopsis actin isoforms. PRF1 and PRF2 inhibited the polymerization of ACT1, ACT11 and ACT7, while ACT2 was only weakly affected. Plant actin isoforms have different biochemical properties. This result supports the idea that actin isoforms play specific roles to achieve multiple cell functions.
Refractive Index Measurements of BeZnTe and Related Superlattices on InP and Application for Waveguide Analysis of MgZnCdSe/BeZnTe Visible Lasers (2002)

Refractive indices of BeZnTe, ZnCdSe/BeZnTe superlattices (SLs) and MgSe/BeZnTe SLs grown on InP substrates were measured for the first time. The refractive index of BeZnTe with a wide bandgap (Eg) of 3.12 eV was higher than that of ZnCdSe with a narrower Eg of 2.1 eV. This tendency in BeZnTe is unexpected, because for other materials, wider bandgaps may generally give lower indices. The refractive indices of the ZnCdSe/BeZnTe and MgSe/BeZnTe SLs were controlled in the wide range by changing the layer thickness combination. Waveguide analysis is performed for laser structures consisting of ZnCdSe/BeZnTe SL active layer and MgSe/BeZnTe SL p-cladding layer. As a result, optical confinement factors around 5.9% are estimated at a wavelength of 564 nm.
Real-Time In Vivo Assessment of the Nerve Microenvironment with Coherent Anti–Stokes Raman Scattering Microscopy (2009)

The authors conclude that coherent anti-Stokes Raman scattering microscopy has the ability to image the peripheral nerve following demyelinating crush injury. This technology, which permits in vivo, real-time microscopy of nerves at a resolution of 5 mum, could provide invaluable diagnostic and prognostic information regarding intraneural preservation and recovery following injury.
Reduce Computing Complexity of Deep Neural Networks Through Weight Scaling (2022)

Large deep neural network (DNN) models are computation and memory intensive, which limits their deployment especially on edge devices. Therefore, pruning, quantization, data sparsity and data reuse have been applied to DNNs to reduce memory and computation complexity at the expense of some accuracy loss. The reduction in the bit-precision results in loss of information, and the aggressive bit-width reduction could result in noticeable accuracy loss. This paper introduces Scaling-Weight-based Convolution (SWC) technique to reduce the DNN model size and the complexity and number of arithmetic operations. This is achieved by, using a small set of high-precision weights (maximum absolute weight “MAW”) and a large set of low-precision weights (Scaling weights “SWs”). This results in decreasing the model size with minimum loss in accuracy compared to simply reducing the precision. Moreover, a scaling and quantized network-acceleration processor (SQNAP) is proposed based on the SWC method to achieve high-speed and low-power with reduced memory accesses. The proposed SWC eliminate >90% of the multiplications in the network. Moreover, the less important SWs are pruned, which has a small portion of the MAW. Retraining is applied in order to maintain accuracy. Full analysis for MNIST, Fashion MNIST, Cifar 10 and Cifar 100 datasets is presented for image recognition, where different DNN models are used including LeNet, ResNet, AlexNet and VGG 16.
Electroless Copper Deposition with PEG Suppression for All-Copper Flip-Chip Connections (2009)

A fabrication technique using electroless copper deposition has been used to produce all-copper chip-to-substrate connections. This process replaces solder by electrolessly joining copper pillars on a chip and substrate. Previously, solid copper-to-copper bonding was demonstrated using a known electroless copper bath followed by low temperature annealing at for 1 h in a nitrogen environment. Although the process feasibility was demonstrated, it was inherently slow and required excessive process time. In this paper, an acceleration-suppression approach to copper plating was used to achieve a rapid deposition of high quality copper in enclosed regions. Elevated temperature was used for acceleration along with poly(ethylene glycol) (PEG) suppression. High temperature increased the transport of reactants and products in spatially restricted regions, and the addition of PEG provided control of the deposition rate. This allowed a kinetically controlled deposition while still maintaining good quality copper deposits without excessive porosity. Plating rates as high in the spatially restricted region between mated pillars were achieved.