gebhart/patrepeval huggingface dataset:
Mechanical control of cAMP signaling through integrins is mediated by the heterotrimeric Gαs protein (2009)

Mechanical stresses that are preferentially transmitted across the cell surface via transmembrane integrin receptors activate gene transcription by triggering production of intracellular chemical second messengers, such as cAMP. Here we show that the sensitivity of the cAMP signaling pathway to mechanical stresses transferred across beta1 integrins is mediated by force-dependent activation of the heterotrimeric G protein subunit Galphas within focal adhesions at the site of stress application. Galphas is recruited to focal adhesions that form within minutes following clustering of beta1 integrins induced by cell binding to magnetic microbeads coated with activating integrin ligands, and beta1 integrin and Galphas co-precipitate when analyzed biochemically. Stress application to activated beta1 integrins using magnetic twisting cytometry increases Galphas recruitment and activates these large G proteins within focal adhesions, as measured by binding of biotinylated azido-anilido-GTP, whereas application of similar stresses to inactivated integrins or control histocompatibility antigens has little effect. This response is relevant physiologically as application of mechanical strain to cells bound to flexible extracellular matrix-coated substrates induce translocation of phospho-CREB to the nucleus, which can be attenuated by inhibiting Galphas activity, either using the inhibitor melittin or suppressing its expression using siRNA. Although integrins are not typical G protein-coupled receptors, these results show that integrins focus mechanical stresses locally on heterotrimeric G proteins within focal adhesions at the site of force application, and transduce mechanical stimuli into an intracellular cAMP signaling response by activating Galphas at these membrane signaling sites.
Angular and spatial light modulation by single digital micromirror device for display applications (2020)

A single Digital Micromirror Device with a single illumination source projects multiple, independent patterns into corresponding directions across a nearly-doubled angular extent by time multiplexing and by nanosecond illumination pulse synchronization for a binary patterned programmable blazed grating. The resulting “Angular Spatial Light Modulator” (ASLM) system nearly-doubles the étendue of a DMD-type SLM and creates a multiplication factor for the output pixel count and effective pixel density. We demonstrate an extended FOV display, a light-field projector, and a multi-view display which can be implemented into AR/VR systems. We present an implementation update using the DLP7000 DMD, increasing output pixel count by and effective pixel density orders-of-magnitude beyond traditional SLM systems while achieving an extended field-of-view and/or eye-box size due to the increased étendue.
Production and antibacterial activity of malforming C, a toxic metabolite of Aspergillus niger (1977)

The production of the new mycotoxin malformin C by a solid substrate fermentation is described. Malformin C is highly toxic (mean lethal dose = 0.9 mg/kg) and exerts antibacterial activity against a variety of gram-positive and gram-negative organisms.
TALE-induced cell death executors: an origin outside immunity? (2021)

Phytopathogenic bacteria inject effector proteins into plant host cells to promote disease. Plant resistance (R) genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins mediate the recognition of functionally and structurally diverse microbial effectors, including transcription-activator like effectors (TALEs) from the bacterial genus Xanthomonas. TALEs bind to plant promoters and transcriptionally activate either disease-promoting host susceptibility (S) genes or cell death-inducing executor-type R genes. It is perplexing that plants contain TALE-perceiving executor-type R genes in addition to NLRs that also mediate the recognition of TALE-containing xanthomonads. We present recent findings on the evolvability of TALEs, which suggest that the native function of executors is not in plant immunity, but possibly in the regulation of developmentally controlled programmed cell death (PCD) processes.
Will Kinase Inhibitors Have a Dark Side? (2006)

Small-molecule inhibitors of Akt kinase are being developed as potential therapeutic agents for cancer. However, a recent study suggests that they may promote metastasis in certain settings.
A layer correlation technique for pion energy calibration at the 2004 ATLAS Combined Beam Test (2011)

A new method for calibrating the hadron response of a segmented calorimeter is developed and successfully applied to beam test data. It is based on a principal component analysis of energy deposits in the calorimeter layers, exploiting longitudinal shower development information to improve the measured energy resolution. Corrections for invisible hadronic energy and energy lost in dead material in front of and between the calorimeters of the ATLAS experiment were calculated with simulated Geant4 Monte Carlo events and used to reconstruct the energy of pions impinging on the calorimeters during the 2004 Barrel Combined Beam Test at the CERN H8 area. For pion beams with energies between 20GeV and 180GeV, the particle energy is reconstructed within 3% and the energy resolution is improved by between 11% and 25% compared to the resolution at the electromagnetic scale.
Document Image Compression by Nonlinear Binary Subband Decomposition and Concatenated Arithmetic Coding (2000)

This paper proposes a new subband coding approach to compression of document images, which is based on nonlinear binary subband decomposition followed by the concatenated arith- metic coding. We choose to use the sampling-exclusive OR (XOR) subband decomposition to exploit its beneficial characteristics to conserve the alphabet size of symbols and provide a small region of support while providing the perfect reconstruction property. We propose a concatenated arithmetic coding scheme to alleviate the degradation of predictability caused by subband decomposition, where three high-pass subband coefficients at the same location are concatenated and then encoded by an octave arithmetic coder. The proposed concatenated arithmetic coding is performed based on a conditioning context properly selected by exploiting a nature of the sampling-XOR subband filter bank as well as taking the ad- vantage of noncausal prediction capability of subband coding. We also introduce a unicolor map to efficiently represent large uniform regions frequently appearing in document images. Simulation re- sults show that each of the functional blocks proposed in the paper performs very well, and consequently, the proposed subband coder provides good compression of document images.
Generation of antigen-specific immunity following systemic immunization with DNA vaccine encoding CCL25 chemokine immunoadjuvant (2012)

A significant hurdle in vaccine development for many infectious pathogens is the ability to generate appropriate immune responses at the portal of entry, namely mucosal sites. The development of vaccine approaches resulting in secretory IgA and mucosal cellular immune responses against target pathogens is of great interest and in general, requires live viral infection at mucosal sites. Using HIV-1 and influenza A antigens as models, we report here that a novel systemically administered DNA vaccination strategy utilizing co-delivery of the specific chemokine molecular adjuvant CCL25 (TECK) can produce antigen-specific immune responses at distal sites including the lung and mesenteric lymph nodes in mice. The targeted vaccines induced infiltration of cognate chemokine receptor, CCR9+/CD11c+ immune cells to the site of immunization. Furthermore, data shows enhanced IFN-λ secretion by antigen-specific CD3+/CD8+ and CD3+/CD4+ T cells, as well as elevated HIV-1-specific IgG and IgA responses in secondary lymphoid organs, peripheral blood, and importantly, at mucosal sites. These studies have significance for the development of vaccines and therapeutic strategies requiring mucosal immune responses and represent the first report of the use of plasmid co-delivery of CCL25 as part of the DNA vaccine strategy to boost systemic and mucosal immune responses following intramuscular injection.
Efficacy of the New Neuraminidase Inhibitor CS-8958 against H5N1 Influenza Viruses (2010)

Currently, two neuraminidase (NA) inhibitors, oseltamivir and zanamivir, which must be administrated twice daily for 5 days for maximum therapeutic effect, are licensed for the treatment of influenza. However, oseltamivir-resistant mutants of seasonal H1N1 and highly pathogenic H5N1 avian influenza A viruses have emerged. Therefore, alternative antiviral agents are needed. Recently, a new neuraminidase inhibitor, R-125489, and its prodrug, CS-8958, have been developed. CS-8958 functions as a long-acting NA inhibitor in vivo (mice) and is efficacious against seasonal influenza strains following a single intranasal dose. Here, we tested the efficacy of this compound against H5N1 influenza viruses, which have spread across several continents and caused epidemics with high morbidity and mortality. We demonstrated that R-125489 interferes with the NA activity of H5N1 viruses, including oseltamivir-resistant and different clade strains. A single dose of CS-8958 (1,500 microg/kg) given to mice 2 h post-infection with H5N1 influenza viruses produced a higher survival rate than did continuous five-day administration of oseltamivir (50 mg/kg twice daily). Virus titers in lungs and brain were substantially lower in infected mice treated with a single dose of CS-8958 than in those treated with the five-day course of oseltamivir. CS-8958 was also highly efficacious against highly pathogenic H5N1 influenza virus and oseltamivir-resistant variants. A single dose of CS-8958 given seven days prior to virus infection also protected mice against H5N1 virus lethal infection. To evaluate the improved efficacy of CS-8958 over oseltamivir, the binding stability of R-125489 to various subtypes of influenza virus was assessed and compared with that of other NA inhibitors. We found that R-125489 bound to NA more tightly than did any other NA inhibitor tested. Our results indicate that CS-8958 is highly effective for the treatment and prophylaxis of infection with H5N1 influenza viruses, including oseltamivir-resistant mutants.
Activation of CD147 with Cyclophilin A Induces the Expression of IFITM1 through ERK and PI3K in THP-1 Cells (2010)

CD147, as a receptor for Cyclophilins, is a multifunctional transmembrane glycoprotein. In order to identify genes that are induced by activation of CD147, THP-1 cells were stimulated with Cyclophilin A and differentially expressed genes were detected using PCR-based analysis. Interferon-induced transmembrane 1 (IFITM1) was detected to be induced and it was confirmed by RT-PCR and Western blot analysis. CD147-induced expression of IFITM1 was blocked by inhibitors of ERK, PI3K, or NF-κB, but not by inhibitors of p38, JNK, or PKC. IFITM1 appears to mediate inflammatory activation of THP-1 cells since cross-linking of IFITM1 with specific monoclonal antibody against it induced the expression of proinflammatory mediators such as IL-8 and MMP-9. These data indicate that IFITM1 is one of the pro-inflammatory mediators that are induced by signaling initiated by the activation of CD147 in macrophages and activation of ERK, PI3K, and NF-κB is required for the expression of IFITM1.
Exposing Differences in Monomer Exchange Rates of Multicomponent Supramolecular Polymers in Water (2015)

The formation of multicomponent and bioactive supramolecular polymers is a promising strategy for the formation of biomaterials that match the dynamic and responsive nature of biological systems. In order to fully realize the potential of this strategy, knowledge of the location and behavior of bioactive components within the system is crucial. By employing synthetic strategies to create multifunctional monomers, coupled with FRET and STORM techniques, we have investigated the formation and behavior of a bioactive and multicomponent supramolecular polymer. By creating a peptide-dye-monomer conjugate, we were able to measure high degrees of monomer incorporation and to visualize the equal distribution of monomers within the supramolecular polymer. Furthermore, by tracking the movement of monomers, we uncovered small differences in the dynamics of the bioactive monomers.
Statistical Channel Model with Multi-Frequency and Arbitrary Antenna Beamwidth for Millimeter-Wave Outdoor Communications (2015)

This paper presents a 3-dimensional millimeter- wave statistical channel impulse response model from 28 GHz and 73 GHz ultrawideband propagation measurements. An accurate 3GPP-like channel model that supports arbitrary carrier frequency, RF bandwidth, and antenna beamwidth (for both omnidirectional and arbitrary directional antennas), is provided. Time cluster and spatial lobe model parameters are extracted from empirical distributions from field measurements. A step-by- step modeling procedure for generating channel coefficients is shown to agree with statistics from the field measurements, thus confirming that the statistical channel model faithfully recreates spatial and temporal channel impulse responses for use in millimeter-wave 5G air interface designs.
Reaction properties of NO and CO over an Ir(211) surface (2007)

The adsorption and thermal reactivity of NO and CO over an Ir(211) surface were studied using x-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, and temperature-programed desorption. NO adsorbed on the atop site of the (111) terrace and the bridge site of the (100) step at 273K. In contrast, CO adsorbed only on the atop site at 273K, initially on the (111) terrace and then on the (100) step. Both atop NO and bridge NO decomposed to N2 through the recombination of atomic nitrogen, indicating that the Ir(211) surface provides high NO dissociation activity. When NO and CO were coadsorbed, the preadsorption of atop CO on the terrace sites selectively inhibited the adsorption of atop NO on the terrace sites, while preadsorption of atop CO on the step sites significantly inhibited the adsorption of bridge NO on the step sites. These results indicate that NO may be selectively reduced by CO in the presence of O2 when Ir(211) is used as the catalyst.
NUCLEON Satellite Mission. Status and Plans (2003)

The main objective of the NUCLEON satellite mission is direct measurements of the elemental energy spectra of high-energy (10(exp 11) - 10(exp 15) eV) cosmic rays with Kinematic Lightweight Energy Meter (KLEM) device. The design of the instrument has been corrected to increase geometry factor and improve charge resolution. The special mechanical and electronic systems have been developed for installation of the experimental apparatus in a regular Russian satellite. It is planned to launch the NUCLEON instrument in 2006.
Cytokine Stimulation of MUC4 Expression in Human Female Reproductive Tissue Carcinoma Cell Lines and Endometrial Cancer (2015)

MUC4, a transmembrane glycoprotein, interferes with cell adhesion, and promotes EGFR signaling in cancer. Studies in rat models have demonstrated steroid hormonal regulation of endometrial MUC4 expression. In this study, qRT-PCR screening of mouse tissues determined that Muc4 mRNA also was robustly expressed in mouse uteri. Previous studies from our labs have demonstrated MUC4 mRNA was expressed at levels <1% of MUC1 mRNA in human endometrium and endometriotic tissue. Multiple human endometrial adenocarcinoma cell lines were assayed for MUC4 mRNA expression revealing extremely low basal expression in the Ishikawa, RL-95-2, AN3CA, and KLE lines. Moderate to high expression was observed in HEC50 and HEC-1A cells. MUC4 mRNA expression was not affected by progesterone and/or estrogen treatment, but was greatly stimulated at both mRNA and protein levels by proinflammatory cytokines (IFN-γ and TNF-α), particularly when used in combination. In endometrial tissue, MUC4 mRNA levels did not change significantly between normal or cancerous samples; although, a subset of patients with grade 1 and 2 tumors displayed substantially higher expression. Likewise, immunostaining of human endometrial adenocarcinoma tissues revealed little to no staining in many patients (low MUC4), but strong staining in some patients (high MUC4) independent of cancer grade. In cases where staining was observed, it was heterogeneous with some cells displaying robust MUC4 expression and others displaying little or no staining. Collectively, these observations demonstrate that while MUC4 is highly expressed in the mouse uterus, it is not a major mucin in normal human endometrium. Rather, MUC4 is a potential marker of endometrial adenocarcinoma in a subset of patients.
The synthesis of α‐tert‐butyl‐ω‐[p‐vinylphenyl]‐terminated poly(2‐methylpropene) macromonomers (1993)

Abstract In this communication a novel synthetic route to α‐ tert ‐butyl‐ω‐[ p ‐vinylphenyl]xy1terminated poly(2‐methylpropene) (PIB) macromonomers ( P3 (VB); P5 ) is described: magnified image and magnified image Attempts to synthesize such macromonomers in both one‐ and two‐step syntheses are described. The one‐step method using 4‐chloromethylstyrene/AlR3 as initiating system for the polymerization of 2‐methylpropene did not yield linear macromonomers but rather highly branched products. The alternative two‐step synthesis using 1‐(2‐bromoethyl)‐4‐chloromethylbenzene (BCB) or BCB/AgSbF, as initiator also failed to yield the desired products. Successful syntheticroutes, optimised on the basis of model experiments with low molar mass compounds, are also described for preparing the above macromonomers. Both of these routes involve isopropenylterminated PIB, which is easily assessible by Inifer technique followed by dehydrohalogenation. Friedel‐Crafts alkylation of phenol by the terminal olefin group of PIB, followed by subsequentesterification of the phenolic end‐groups with 4‐vinylbenzoyl chloride, affords the macromonomer P3(VB). Conversion of the terminal olefin group of PIB into a primary alcohol using 9‐bora[3,3, I]‐bicyclononane/H202, followed by esterification, yields the macromonomer P5 .
α‐Glyceryl‐phosphoryl‐ethanolamine protects human hippocampal neurons from ageing‐induced cellular alterations (2022)

Brain ageing has been related to a decrease in cellular metabolism, to an accumulation of misfolded proteins and to an alteration of the lipid membrane composition. These alterations act as contributive aspects of age-related memory decline by reducing membrane excitability and neurotransmitter release. In this sense, precursors of phospholipids (PLs) can restore the physiological composition of cellular membranes and ameliorate the cellular defects associated with brain ageing. In particular, phosphatidylcholine (PC) and phosphatidylethanolamine (PE) have been shown to restore mitochondrial function, reduce the accumulation of amyloid beta (Aβ) and, at the same time, provide the amount of acetylcholine needed to reduce memory deficit. Among PL precursors, alpha-glycerylphosphorylethanolamine (GPE) has shown to protect astrocytes from Aβ injuries and to slow-down ageing of human neural stem cells. GPE has been evaluated in aged human hippocampal neurons, which are implicated in learning and memory, and constitute a good in vitro model to investigate the beneficial properties of GPE. In order to mimic cellular ageing, the cells have been maintained 21 days in vitro and challenged with GPE. Results of the present paper showed GPE ability to increase PE and PC content, glucose uptake and the activity of the chain respiratory complex I and of the GSK-3β pathway. Moreover, the nootropic compound showed an increase in the transcriptional/protein levels of neurotrophic and well-being related genes. Finally, GPE counteracted the accumulation of ageing-related misfolded proteins (a-synuclein and tau). Overall, our data underline promising effects of GPE in counteracting cellular alterations related to brain ageing and cognitive decline.
How accurate channel prediction needs to be for adaptive modulation in Rayleigh MIMO channels? (2004)

Adaptive modulation improves system throughput considerably by matching transmitter parameters to time-varying wireless fading channels. Crucial to adaptive modulation is the quality of channel state information (CSI) at the transmitter. We consider a channel predictor based on pilot symbol assisted modulation (PSAM) for multi-input multi-output (MIMO) Rayleigh fading channels. We analyze the impact of the channel prediction error on the bit error rate (BER) performance of an adaptive system assuming perfect CSI. Our numerical results reveal the critical value of the normalized prediction error, below which the predicted channels can be treated as perfect by the adaptive modulator; otherwise, explicit consideration of the channel imperfection must be accounted for at the transmitter.
An MR-Compatible Haptic Device for fMRI Investigations of Force Control (2007)

An MRI compatible haptic device was built to investigate human motor control. The device allows application of force and motion in one dimension to the index finger with the thumb kept fixed. Finger position and forces applied by the subject are recorded. Initial results of an fMRI study on force control are presented. Subjects had to counter-balance externally applied force fields of different complexity. Compared to the application of a constant force varying force fields resulted in increased activation of supplementary motor area, ipsi- and contralateral primary motor cortex, and the cerebellum.
Efficient Privilege De-Escalation for Ad Libraries in Mobile Apps (2015)

The proliferation of mobile apps is due in part to the advertising ecosystem which enables developers to earn revenue while providing free apps. Ad-supported apps can be developed rapidly with the availability of ad libraries. However, today?s ad libraries essentially have access to the same resources as the parent app, and this has caused signi?cant privacy concerns. In this paper, we explore ef?cient methods to de-escalate privileges for ad libraries where the resource access privileges for ad libraries can be different from that of the app logic. Our system, PEDAL, contains a novel machine classi?er for detecting ad libraries even in the presence of obfuscated code, and techniques for automatically instrumenting bytecode to effect privilege de-escalation even in the presence of privilege inheritance. We evaluate PEDAL on a large set of apps from the Google Play store and demonstrate that it has a 98% accuracy in detecting ad libraries and imposes less than 1% runtime overhead on apps.
Rule extraction from linear support vector machines (2005)

We describe an algorithm for converting linear support vector machines and any other arbitrary hyperplane-based linear classifiers into a set of non-overlapping rules that, unlike the original classifier, can be easily interpreted by humans. Each iteration of the rule extraction algorithm is formulated as a constrained optimization problem that is computationally inexpensive to solve. We discuss various properties of the algorithm and provide proof of convergence for two different optimization criteria We demonstrate the performance and the speed of the algorithm on linear classifiers learned from real-world datasets, including a medical dataset on detection of lung cancer from medical images. The ability to convert SVM's and other "black-box" classifiers into a set of human-understandable rules, is critical not only for physician acceptance, but also to reducing the regulatory barrier for medical-decision support systems based on such classifiers.