gebhart/patrepeval huggingface dataset:
Protein sorting by lipid phase-like domains supports emergent signaling function in B lymphocyte plasma membranes (2017)

Diverse cellular signaling events, including B cell receptor (BCR) activation, are hypothesized to be facilitated by domains enriched in specific plasma membrane lipids and proteins that resemble liquid-ordered phase-separated domains in model membranes. This concept remains controversial and lacks direct experimental support in intact cells. Here, we visualize ordered and disordered domains in mouse B lymphoma cell membranes using super-resolution fluorescence localization microscopy, demonstrate that clustered BCR resides within ordered phase-like domains capable of sorting key regulators of BCR activation, and present a minimal, predictive model where clustering receptors leads to their collective activation by stabilizing an extended ordered domain. These results provide evidence for the role of membrane domains in BCR signaling and a plausible mechanism of BCR activation via receptor clustering that could be generalized to other signaling pathways. Overall, these studies demonstrate that lipid mediated forces can bias biochemical networks in ways that broadly impact signal transduction.
A novel class of evolutionarily conserved genes defined by <i>piwi</i> are essential for stem cell self-renewal (1998)

Germ-line stem cells (GSCs) serve as the source for gametogenesis in diverse organisms. We cloned and characterized the Drosophila piwi gene and showed that it is required for the asymmetric division of GSCs to produce and maintain a daughter GSC but is not essential for the further differentiation of the committed daughter cell. Genetic mosaic and RNA in situ analyses suggest that piwi expression in adjacent somatic cells regulates GSC division. piwi encodes a highly basic novel protein, well conserved during evolution. We isolated piwi homologs in Caenorhabditis elegans and humans and also identified Arabidopsis piwi-like genes known to be required for meristem cell maintenance. Decreasing C. elegans piwi expression reduces the proliferation of GSC-equivalent cells. Thus, piwi represents a novel class of genes required for GSC division in diverse organisms.
Queueing network modelling with distributed neural networks for service quality estimation in B-ISDN networks (2000)

We discuss a scheme based on distributed feedforward neural networks (NN), aimed at modelling several queueing systems in cascade fed with bursty traffic. For each queueing system, a neural network is trained to anticipate the average number of waiting packets, the packet loss rate and the coefficient of variation of the packet inter-departure time, given the mean rate, the peak rate and the coefficient of variation of the packet inter-arrival time. The latter serves for the calculation of the coefficient of variation of the cell inter-arrival time of the aggregated traffic which is fed as input to the next NN along the path. The potential of this method was sucessfully illustrated on several single server FIFO queues in Aussem et al. (1999). We now apply this technique to model a small queueing network made up from a combination of queues in tandem and in parallel fed by a superimposition of OnOff sources. Our long-term goal is the design of preventive control strategy in a multiservice communication network.
Sonochemical Preparation of Shape-Selective ZnO Nanostructures (2007)

A simple and facile sonochemical route has been demonstrated for the shape-selective preparation of highly crystalline ZnO nanostructures, such as nanorods, nanocups, nanodisks, nanoflowers, and nanospheres. The concentration of precursor chemicals, the kind of hydroxide anion-generating agents, the ultrasonication time, and the use of a capping agent are key factors in the morphological control of ZnO nanostructures. This method is fast, simple, convenient, economical, and environmentally benign. On the basis of our shape-control of the ZnO nanostructures by the sonochemical technique, growth mechanisms of ZnO nanostructures were also proposed. We believe this technique will be readily adopted in realizing other forms of various nanostructured materials.
Electron spin polarization (CIDEP) studies of the dynamics of geminate free radical reactions (1999)

The variation with viscosity of the fraction of radicals which survive re-encounter within the geminate period of a radical recombination reaction is measured using the relative contributions of the triplet and radical pair mechanisms to the electron spin polarization observed in their electron spin resonance spectra. This fraction differs from the fraction of re-encounters as a result of reaction. From a triplet precursor 2% of the radicals produced in a photolysis flash recombine in the geminate cage in methanol but 15% do in propan-1,2-diol.
Dynamic failure of reinforced concrete plates (1994)

A theoretical study of rectangular plates exposed to air blast load is performed using Lagrange's theory for small deflections of thin plates, von Karman's theory for large deflections of thin plates and Mindlin's theory for (moderately) thick plates. The plate theories are analysed to approximate the walls and roofs of a complex structure. All modelling are done with isotropic material models. Pressure-Impulse diagrams (PI-diagrams) are constructed to predict the flexural damage load. Critical loads, which initiate damage, are determined for rectangular plates as a function of thickness to span ratio. Numerical results of a box structure are presented to check the plate approximation of the wall. Some experimental results are also described.
Biochemical Studies on a Virus Associated with Egg Drop Syndrome 1976 (1978)

SUMMARY A number of hitherto undescribed, serologically identical viruses have been isolated from a syndrome of depressed egg production in broiler breeder flocks (Egg Drop Syndrome 1976). One of these, 127 virus, was purified after growth in chick embryo liver cells. Three particle types B1, B2 and B3 with densities of 1.32, 1.30 and 1.28 g/ml, respectively, were separated in CsCl equilibrium density gradients. B1 and B2 particles possessed infectivity and were labelled with 3H-thymidine. However, they differed morphologically and B2 particles agglutinated chicken erythrocytes whereas B1 particles did not. B3 particles were not infectious, were not labelled with 3H-thymidine but agglutinated chicken erythrocytes. They were penetrated by stain when examined by electron microscopy and probably correspond to empty particles. B1, B2 and B3 particles differed in their polypeptide compositions; seven of the polypeptides in B1 and B2 particles had counterparts in purified fowl adenovirus type 1. The soluble haemagglutinin from 127 virus, which did not sediment under centrifugation conditions sufficient to pellet virus particles, was purified using DEAE cellulose chromatography and gel filtration. Purified soluble haemagglutinin contained two polypeptides (mol. wt. 67000 and 65000), which co-migrated in polyacrylamide gels with two of those present in purified 127 virus particles. The soluble haemagglutinin sedimented heterogeneously (20 to 50S) in sucrose density gradients and had a density of 1.24 g/ml in CsCl. It was inactivated by trypsin, urea and pyridine. Electron microscopy of purified soluble haemagglutinin showed rod-like structures with lengths of 25 to 30 nm, which radiated from a central area measuring approx. 10 nm in diam. It is suggested that 127 virus is an adenovirus.
Migrating enterprise storage applications to the cloud - eScholarship (2011)

Cloud computing has emerged as a model for hosting computing infrastructure and outsourcing management of that infrastructure. It offers the promise of simplified provisioning and management, lower costs, and access to resources that scale up and down with demand. Cloud computing has seen growing use for Web site hosting, large batch processing jobs, and similar tasks. Despite potential advantages, however, cloud computing is not much used for enterprise applications such as backup, shared file systems, and other internal systems. Many challenges need to be overcome to make cloud suitable for these applications, among them cost, performance, security, and interface mismatch. In this dissertation, I investigate how cloud infrastructure can be used for internal services in an organization, with a focus on storage applications. I show how to design systems to address the challenges of using the cloud by building two example systems. The first, Cumulus, implements file system backup to a remote cloud storage provider. With Cumulus I consider the constraints imposed by the interface to cloud storage, and how to work within those constraints to minimize the cost. The second system, BlueSky, is a shared network file server which is backed by cloud storage. BlueSky builds on ideas from Cumulus to reduce system cost. It relies on cloud storage for data durability, but provides good performance by caching data locally. I additionally study how file system maintenance tasks can be offloaded to the cloud while protecting the confidentiality and integrity of file system data. Together, these two systems demonstrate that, despite the challenges, we can bring the benefits of the cloud to enterprise storage applications
Three to Tango: MUC1 as a Ligand for Both E-Selectin and ICAM-1 in the Breast Cancer Metastatic Cascade (2012)

CANCER CELL TETHERING AND ROLLING ON THE VASCULAR WALL IS FACILITATED BY VARIOUS SELECTIN: glycoprotein interactions which lead to eventual extravasation and metastases. The aberrantly underglycosylated mucin MUC1 has been shown to both abundantly express selectin binding moieties (sialyl Lewis x and a) and to consistently expose its core epitope. Flow cytometry was used to determine MUC1 expression on ZR-75-1 and MCF7 cells, while immunofluorescence microscopy was used to confirm the aberrant form of MUC1 and MUC1:ICAM-1 interactions. Each cell line was then perfused through combined E-selectin and ICAM-1 coated microtubes, as a model of the microvascular endothelium. ZR-75-1 and MCF7 were found to express abundant and low levels of underglycosylated MUC1, respectively. The rolling/adhesion profiles showed that ZR-75-1 cells, when compared to MCF7 cells, interact with E-selectin more efficiently resulting in sufficiently slow rolling velocities to form MUC1:ICAM-1 interactions thereby facilitating firm adhesion. The purpose and novelty of this work is the demonstration of the synergistic adhesion capabilities of MUC1 in the metastatic adhesion cascade, where the observed differential adhesion is consistent with the relative metastatic potential of the ZR-75-1 (highly metastatic) and MCF7 (weakly metastatic) cell lines.
Growth of <i>Thiobacillus ferrooxidans</i> on various substrates (1969)

When Thiobacillus ferrooxidans was grown on ferrous iron and chalcopyrite (CuFeS 2 ) in excess of 96% of the bacterial population was associated with the insoluble material. When sulfur was the substrate 77% of the bacteria were so associated. This necessitated consideration of the complete growth system to obtain accurate growth curves. By using total bacterial nitrogen as the measure of growth, it was shown that T. ferrooxidans had a minimum generation time of 6.5 to 10 hours on a ferrous iron substrate, 7 to 8 days on a sulfur substrate, and 14 to 17 hours on a chalcopyrite substrate. The pH range for growth was dependent on the substrate used.
A Game Theoretic Approach to Model Cyber Attack and Defense Strategies (2018)

Most of the cybersecurity research focus on either presenting a specific vulnerability %or hacking technique, or proposing a specific defense algorithm to defend against a well-defined attack scheme. Although such cybersecurity research is important, few have paid attention to the dynamic interactions between attackers and defenders, where both sides are intelligent and will dynamically change their attack or defense strategies in order to gain the upper hand over their opponents. This 'cyberwar' phenomenon exists among most cybersecurity incidents in the real world, which warrants special research and analysis. In this paper, we propose a dynamic game theoretic framework (i.e., hyper defense) to analyze the interactions between the attacker and the defender as a non-cooperative security game. The key idea is to model attackers/defenders to have multiple levels of attack/defense strategies that are different in terms of effectiveness, strategy costs, and attack gains/damages. Each player adjusts his strategy based on the strategy's cost, potential attack gain/damage, and effectiveness in anticipating of the opponent's strategy. We study the achievable Nash equilibrium for the attacker-defender security game where the players employ an efficient strategy according to the obtained equilibrium. Furthermore, we present case studies of three different types of network attacks and put forth how our hyper defense system can successfully model them. Simulation results show that the proposed game theoretical system achieves a better performance compared to two other fixed-strategy defense systems.
A 2GHz 52¿W Wake-Up Receiver with -72dBm Sensitivity Using Uncertain-IF Architecture (2008)

A wake-up receiver (WuRx) is used in wireless sensor networks (WSN) to detect wireless traffic directed to a node's receiver and activate it upon detection, improving network latency and energy dissipation by maximizing data transceiver sleep time. The always-on nature of the WuRx sets a power dissipation floor for the entire system. In realistic WSN scenarios, the adoption of a WuRx leads to energy savings only if it can be realized with about 50muW of power dissipation in Lin, E.Y., et al, (2004), testing the limits of low-power receiver design. While diode detectors provide for the simplest detector structure, such receivers are strongly gain-limited due to the thresholding effect of the nonlinear detector in Pletcher, N., et al, (2007) and adding gain at RF to improve sensitivity only increases power consumption. A more attractive approach is to adopt a heterodyne architecture, where the extra gain needed for robust energy detection can be obtained at an intermediate frequency (IF) with a much lower power cost. However, a survey of previous receiver designs for WSN reveals that the power requirements of the required local oscillator (LO) exceed the total power budget of the WuRx in Otis, B., et al, (2005).
Fully Continuous Flow Synthesis of 3-Chloro-4-oxopentyl Acetate: An Important Intermediate for Vitamin B1 (2021)

A fully continuous flow synthesis of 3-chloro-4-oxopentyl acetate (2), an important intermediate for vitamin B1 (1), was developed. This continuous flow manufacturing included two chemical transformations and an inline extraction step without intermediate purification and solvent exchange. In this work, the traditional synthetic route for batch operation was efficiently simplified via a series of separated screening tests in flows under various conditions. We found that the chlorination reaction can be carried out in only 30 s at room temperature by flow. We also simplified the decarboxylation/acylation step by using a cross-mixer, so that acetic anhydride was no longer required in the acylation reaction. A computational fluid dynamics simulation was carried out to study the improved micromixing of liquid–liquid two-phase streams. Finally, 3-chloro-4-oxopentyl acetate (2) was obtained in a 90% isolated yield with a product purity of 96% and a total residence time of approximately 32 min. This fully continuous process was operated smoothly for 12 h, and approximately 19.1 g of the desired product was generated with a production rate of 1.79 g h–1.
A signaling network stimulated by β <sub>2</sub> integrin promotes the polarization of lytic granules in cytotoxic cells (2014)

Cytotoxic lymphocytes kill target cells through the polarized release of the contents of intracellular perforin-containing granules. In natural killer (NK) cells, the binding of β2 integrin to members of the intercellular adhesion molecule family is sufficient to promote not only the adhesion of NK cells to target cells but also the polarization of intracellular lytic granules toward the target. We used NK cells in an experimental system designed to enable us to study the polarization of lytic granules in the absence of their release through degranulation, as well as β2 integrin signaling independently of inside-out signals from other receptors. Through a proteomics approach, we identified a signaling network centered on an integrin-linked kinase (ILK)-Pyk2-paxillin core that was required for granule and microtubule-organizing center (MTOC) polarization. The conserved Cdc42-Par6 signaling pathway, which controls cell polarity, was also activated by ILK and was required for granule polarization toward the target cell. A subset of the signaling components required for polarization contributed also to the convergence of granules on the MTOC. These results delineate two connected signaling networks that are stimulated upon β2 integrin engagement and control the polarization of the MTOC and associated lytic granules toward the site of contact with target cells to mediate cellular cytotoxicity.
Coordination of Energy Efficiency and Demand Response (2010)

This paper reviews the relationship between energy efficiency and demand response and discusses approaches and barriers to coordinating energy efficiency and demand response. The paper is intended to support the 10 implementation goals of the National Action Plan for Energy Efficiency's Vision to achieve all cost-effective energy efficiency by 2025. Improving energy efficiency in our homes, businesses, schools, governments, and industries - which consume more than 70 percent of the nation's natural gas and electricity - is one of the most constructive, cost-effective ways to address the challenges of high energy prices, energy security and independence, air pollution, and global climate change. While energy efficiency is an increasingly prominent component of efforts to supply affordable, reliable, secure, and clean electric power, demand response is becoming a valuable tool in utility and regional resource plans. The Federal Energy Regulatory Commission (FERC) estimated the contribution from existing U.S. demand response resources at about 41,000 megawatts (MW), about 5.8 percent of 2008 summer peak demand (FERC, 2008). Moreover, FERC recently estimated nationwide achievable demand response potential at 138,000 MW (14 percent of peak demand) by 2019 (FERC, 2009).2 A recent Electric Power Research Institute study estimates that 'the combination of demand response and energy efficiency programs has the potential to reduce non-coincident summer peak demand by 157 GW' by 2030, or 14-20 percent below projected levels (EPRI, 2009a). This paper supports the Action Plan's effort to coordinate energy efficiency and demand response programs to maximize value to customers. For information on the full suite of policy and programmatic options for removing barriers to energy efficiency, see the Vision for 2025 and the various other Action Plan papers and guides available at www.epa.gov/eeactionplan.
Droplet-based photoresist deposition (2006)

Photoresist droplets are ejected onto a wafer surface by an acoustic two-dimensional micromachined ejector array. The spread of single droplets on a silicon wafer surface at varying droplet speeds is studied. Series of photoresist droplets are printed periodically drop on demand on a silicon wafer surface and profiles of a single droplet and two droplets overlapping with varying distances of 25 and 1μm on a silicon wafer are demonstrated. Moreover, 3.4μm thick spinless full coverage of a 4in. wafer with photoresist is demonstrated which indicates a potential for coating wafers in less than a few seconds.
Miniature SAW filters in GHz range (2002)

This paper describes low-loss surface acoustic wave (SAW) filters with center frequencies of 0.8 GHz, 1.9 GHz and 2.4 GHz for wireless applications. The SAW filters are mounted in miniature surface-mount-type ceramic packages, 3.2/spl times/2.5/spl times/0.9 mm/sup 3/ for the 0.8 GHz filter and 2.5/spl times/2.0/spl times/0.9 mm/sup 3/ for the 1.9 GHz and 2.4 GHz filters, using a flip-chip assembly technique for SAW devices. The SAW filters provide a minimum insertion loss of about 2 dB. The flip-chip SAW filters are suitable for miniaturization of wireless applications.
Single point mutations reveal amino acid residues important for Chromobacterium violaceum transaminase activity in the production of unnatural amino acids (2018)

Unnatural amino acids (UAAs) are chiral amines with high application potential in drug discovery and synthesis of other valuable chemicals. Biocatalysis offers the possibility to synthesise novel optically pure UAAs with different physical and chemical properties. While the biocatalytic potential of transaminases in the synthesis of UAAs has been demonstrated, there is still a need to improve the activity with non-native substrates and to understand which amino acids residues are important for activity with these UAAs. Using a rational design approach, six variants of Chromobacterium violaceum DSM30191 transaminase (CV_TA) carrying a single and one variant carrying two substitutions were generated. Among the variants with a single substitution, CV_Y168F showed a 2 to 2.6-fold increased affinity for 2-oxooctanoic acid (2-OOA) and 3-oxobutyric acid (3-OBA) methyl ester used to synthesise an α- and β-UAA. Analysis of the first half of the transaminase reaction showed no change in the activity with the donor (S)-1-phenylethylamine. The combination of W60C and Y168F substitutions improved the CV_TA affinity for 2-OOA 10-fold compared to the wild type. Other substitutions showed no change, or reduced activity with the tested substrates. Our findings provide structural information on CV_TA and demonstrate the potential of rational design for biosynthesis of UAAs.
Macrophage-Membrane-Coated Nanoparticles for Tumor-Targeted Chemotherapy (2018)

Various delivery vectors have been integrated within biologically derived membrane systems to extend their residential time and reduce their reticuloendothelial system (RES) clearance during systemic circulation. However, rational design is still needed to further improve the in situ penetration efficiency of chemo-drug-loaded membrane delivery-system formulations and their release profiles at the tumor site. Here, a macrophage-membrane-coated nanoparticle is developed for tumor-targeted chemotherapy delivery with a controlled release profile in response to tumor microenvironment stimuli. Upon fulfilling its mission of tumor homing and RES evasion, the macrophage-membrane coating can be shed via morphological changes driven by extracellular microenvironment stimuli. The nanoparticles discharged from the outer membrane coating show penetration efficiency enhanced by their size advantage and surface modifications. After internalization by the tumor cells, the loaded drug is quickly released from the nanoparticles in response to the endosome pH. The designed macrophage-membrane-coated nanoparticle (cskc-PPiP/PTX@Ma) exhibits an enhanced therapeutic effect inherited from both membrane-derived tumor homing and step-by-step controlled drug release. Thus, the combination of a biomimetic cell membrane and a cascade-responsive polymeric nanoparticle embodies an effective drug delivery system tailored to the tumor microenvironment.