gebhart/patrepeval huggingface dataset:
Pharmacokinetics and biodistribution of near-infrared fluorescence polymeric nanoparticles (2009)

There has been increased interest in the use of polymeric nanoparticles as carriers for near-infrared fluorescence (NIRF) dyes for cancer diagnosis. However, efficient delivery of nanoparticles to the tumors after systemic administration is limited by various biobarriers. In this study, we investigated the pharmacokinetics, biodistribution, and tumor uptake of sub-nanometer sized polymeric nanoparticles (<100 nm in diameter) coated with polyethylene glycol in tumor-bearing mice. To facilitate our studies, these particles were labeled with gamma emitter indium-111. We found that two NIRF nanoparticles having the same size (approximately 20 nm) and chemical composition but different structures (i.e., hydrogel versus core-shell nanolatex), or the same core-shell nanolatex particles with different sizes (20, 30, and 60 nm), had different blood circulation times, biodistribution, and tumor uptake. Interestingly, the tumor uptake of the nanolatex particles correlated well with their blood residence times (R(2) = 0.95), but similar correlations were not found between nanogel and nanolatex particles (R(2) = 0.05). These results suggest that both the blood circulation time and the extent of hydration of the nanoparticles play an important role in the tumor uptake of nanoparticles. Prolonged blood circulation of these NIRF nanoparticles allowed clear visualization of tumors with gamma-scintigraphy and optical imaging after intravenous administration. A better understanding with regard to how the characteristics of nanoparticles influence their in vivo behavior is an important step towards designing NIRF nanoparticles suitable for molecular imaging applications and for efficient tumor delivery.
Encapsulation and Controlled Release of Rapamycin from Polycaprolactone Nanoparticles Prepared by Membrane Micromixing Combined with Antisolvent Precipitation (2016)

Rapamycin-loaded polycaprolactone nanoparticles (RAPA-PCL NPs) with a polydispersity index of 0.006-0.073 were fabricated by antisolvent precipitation combined with micromixing using a ringed stainless steel membrane with 10 μm diameter laser-drilled pores. The organic phase composed of 6 g L<sup>-1</sup> PCL and 0.6-3.0 g L<sup>-1</sup> RAPA in acetone was injected through the membrane at 140 L m<sup>-2</sup> h<sup>-1</sup> into 0.2 wt % aqueous poly(vinyl alcohol) solution stirred at 1300 rpm, resulting in a Z-average mean of 189-218 nm, a drug encapsulation efficiency of 98.8-98.9%, and a drug loading in the NPs of 9-33%. The encapsulation of RAPA was confirmed by UV-vis spectroscopy, XRD, DSC, and ATR-FTIR. The disappearance of sharp characteristic peaks of crystalline RAPA in the XRD pattern of RAPA-PCL NPs revealed that the drug was molecularly dispersed in the polymer matrix or RAPA and PCL were present in individual amorphous domains. The rate of drug release in pure water was negligible due to low aqueous solubility of RAPA. RAPA-PCL NPs released more than 91% of their drug cargo after 2.5 h in the release medium composed of 0.78-1.5 M of the hydrotropic agent N,N-diethylnicotinamide, 10 vol % ethanol, and 2 vol % Tween 20 in phosphate buffered saline. The dissolution of RAPA was slower when the drug was embedded in the PCL matrix of the NPs than dispersed in the form of pure RAPA nanocrystals.
Development and utilization of new diagnostics for dense-phase pneumatic transport (1992)

In 1988, we proposed a program to develop new diagnostics for dense gas-solid suspensions, with particular interest toward the dense pneumatic transport of cohesive solid plugs. This program included three main objectives, as follows: to develop probes for local measurements of (1) local particle volume fraction and (2) individual particle velocities in dense gas-solid flows; and (3) to construct a bench-scale setup for transporting dense cohesive solid plugs and to analyze data from the resulting tests.
Domain modeling of software process models (2002)

The paper presents a novel application involving two important software engineering research areas: process modeling and software reuse. The Spiral Model is a risk-driven process model, which, depending on the specific risks associated with a given project, may be tailored to create a project-specific process model. The software reuse area is that of domain modeling of families of systems, which capture the similarities and variations among the members of the family. The domain modeling approach is used to create a domain model of a Spiral Process Model (SPM), thereby capturing the similarities and variations among a family of process models. The SPM domain model has been extended to capture the key process areas of the Software Engineering Institute's Capability Maturity Model (CMM). The domain model is used to generate project-specific process models. This approach allows managers to configure and reuse process models that manage the risks associated with new software development.
Simple and efficient system for photoconverting light-sensitive proteins in serial crystallography experiments (2017)

Proteins that change their structure in response to light absorption regulate many functional processes in living cells. Moreover, biotechnological approaches like optogenetics and super-resolution fluorescence microscopy recently triggered the generation of new genetically modified photosensitive proteins. Light-induced structural changes in photosensitive proteins can be studied by time-resolved serial femtosecond crystallography (SFX), an X-ray diffraction technique that allows the determination of macromolecular structures at X-ray free-electron lasers from a large number of nano- to micro-sized crystals. This article describes a simple and efficient system for converting photosensitive proteins into light-induced semi-stationary states by inline laser illumination prior to sample injection with a gas-focused liquid jet and subsequent optical pump–X-ray probe exposure. The simple setup of this device makes it suitable for integration into other liquid injectors (like electro-spinning and electro-kinetic injectors) and potentially also in high-viscosity extruders, provided that embedding microcrystals in viscous media does not alter protein photophysical properties. The functioning of the device is demonstrated with an example of a photoswitchable fluorescent protein pre-illuminated (photoactivated) for time-resolved SFX experiments. The device can be easily adapted for the conversion in time-resolved SFX experiments of other microcrystalline proteins, such as photosystems, phytochromes and rhodopsins.
An Area Shading Graphics Display System (1979)

A computer graphics display system for rapidly shading areas on a raster scan screen is described. With the system, the host computer provides the display controller with the parameters of a set of component trapezoids which cover the area to be shaded. The paper gives an algorithm for use in the host to decompose an arbitrary polygon into component trapezoids and it describes a microcomputer based controller to shade the trapezoids.
Two Bitcoins at the Price of One? Double-Spending Attacks on Fast Payments in Bitcoin. (2012)

Bitcoin is a decentralized payment system that is basedonProof-of-Work. Bitcoiniscurrentlygaining popularity as a digital currency; several businesses are starting to accept Bitcoin transactions. An examplecaseofthegrowinguseofBitcoinwasrecently reported in the media; here, Bitcoins were used as a form of fast payment in a local fast-food restaurant. In this paper, we analyze the security of using Bitcoin for fast payments, where the time between the exchange of currency and goods is short (i.e., in the order of few seconds). We focus on doublespending attacks on fast payments and demonstrate that these attacks can be mounted at low cost on currently deployed versions of Bitcoin. We further showthatthemeasuresrecommendedbyBitcoindevelopersfortheuseofBitcoininfasttransactionsare not always effective in resisting double-spending; we show that if those recommendations are integrated in future Bitcoin implementations, double-spending attacks on Bitcoin will still be possible. Finally, we leverage on our findings and propose a lightweight countermeasurethatenablesthedetectionofdoublespending attacks in fast transactions. 1
DIRECT DRIVE SYSTEMS WITH TRANSVERSE FLUX RELUCTANCE MOTORS (2004)

Abstract – The transverse flux motor (TFM), quite a new concept of an electric machine, begins its impetus in the late 80s of the last century. The transverse flux reluctance motor (TFRM) is a variant of TFM with passive rotor and simpler construction. The achievable power TFRMs ’ to total machine weight ratio is smaller than for TFM with permanent magnets on the rotor (PMTFM), but larger than for conventional machines. Since TFRM has a large number of poles the motor is well suited for variable low speed direct drive applications. TFRM actual state-of-art will be presented in the paper with more strength on its construction, design, supply control and applications. Partly being a review of the already published information the paper contains some original developments concerning mainly TFRM design. the start-up difficulties and to obtain continuous rotation [6, 7]. a)
2P047 The structural and thermodynamic analysis of the interaction between ciguatoxin and its Antibody 10C9 Fab(Proteins-structure and structure-function relationship,Poster Presentations) (2007)

11 dDen Un C MDI
Asymptotic theory of time-varying social networks with heterogeneous activity and tie allocation (2016)

The dynamic of social networks is driven by the interplay between diverse mechanisms that still challenge our theoretical and modelling efforts. Amongst them, two are known to play a central role in shaping the networks evolution, namely the heterogeneous propensity of individuals to i) be socially active and ii) establish a new social relationships with their alters. Here, we empirically characterise these two mechanisms in seven real networks describing temporal human interactions in three different settings: scientific collaborations, Twitter mentions, and mobile phone calls. We find that the individuals' social activity and their strategy in choosing ties where to allocate their social interactions can be quantitatively described and encoded in a simple stochastic network modelling framework. The Master Equation of the model can be solved in the asymptotic limit. The analytical solutions provide an explicit description of both the system dynamic and the dynamical scaling laws characterising crucial aspects about the evolution of the networks. The analytical predictions match with accuracy the empirical observations, thus validating the theoretical approach. Our results provide a rigorous dynamical system framework that can be extended to include other processes shaping social dynamics and to generate data driven predictions for the asymptotic behaviour of social networks.
Treatment allocation in patients with early‐stage esophageal adenocarcinoma: Prevalence and predictors of lymph node involvement (2016)

For patients with low-grade Tis or T1 tumors measuring ≤2 cm in size, the incidence of lymph node metastasis appears to be comparable to the mortality rate associated with esophagectomy. For highly selected patients with early esophageal adenocarcinomas, the results of the current study support the recommendation that local endoscopic resection can be considered as an alternative to surgical management when followed by rigorous endoscopic and radiographic surveillance. Cancer 2016;122:2150-7. © 2016 American Cancer Society.
Molecular Insights into Adhesion at a Buried Silica-Filled Silicone/Polyethylene Terephthalate Interface (2020)

Silicone adhesives are widely used in many important applications in aviation, automotive, construction, and electronics industries. The mixture of (3-glycidoxypropyl)trimethoxysilane (γ-GPS) and hydroxy-terminated dimethyl methylvinyl co-siloxanol (DMMVS) has been widely used as an adhesion promoter in silicone elastomers to enhance the adhesion between silicone and other materials including polymers. The interfacial molecular structures of silicone elastomers and the adhesion promotion mechanisms of a γ-GPS-DMMVS mixture in silicone without a filler or an adhesion catalyst (AC) have been extensively investigated using sum frequency generation (SFG) vibrational spectroscopy previously. In this research, SFG was applied to study interfacial structures of silicone elastomeric adhesives in the presence of a silica filler and/or a zirconium(IV) acetylacetonate adhesion catalyst at the silicone/polyethylene terephthalate (PET) interface <i>in situ</i> nondestructively to understand their individual and synergy effects. The interfacial structures obtained from the SFG study were correlated to the adhesion behavior to PET. The interfacial reactions of methoxy and epoxy groups of the adhesion promoter were found to play significant roles in enhancing the interfacial adhesion of the buried interface. This research provides an in-depth molecular-level understanding on the effects of a filler and an adhesion catalyst on the interfacial behavior of the adhesion promotion system for silicone elastomers as well as the related impact on adhesion.
Structural studies of the MMP-3 interaction with triple-helical collagen introduce new roles for the enzyme in tissue remodelling (2019)

Matrix metalloproteinase-3 (MMP-3) participates in normal extracellular matrix turnover during embryonic development, organ morphogenesis and wound healing, and in tissue-destruction associated with aneurysm, cancer, arthritis and heart failure. Despite its inability to cleave triple-helical collagens, MMP-3 can still bind to them, but the mechanism, location and role of binding are not known. We used the Collagen Toolkits, libraries of triple-helical peptides that embrace the entire helical domains of collagens II and III, to map MMP-3 interaction sites. The enzyme recognises five sites on collagen II and three sites on collagen III. They share a glycine-phenylalanine-hydroxyproline/alanine (GFO/A) motif that is recognised by the enzyme in a context-dependent manner. Neither MMP-3 zymogen (proMMP-3) nor the individual catalytic (Cat) and hemopexin (Hpx) domains of MMP-3 interact with the peptides, revealing cooperative binding of both domains to the triple helix. The Toolkit binding data combined with molecular modelling enabled us to deduce the putative collagen-binding mode of MMP-3, where all three collagen chains make contacts with the enzyme in the valley running across both Cat and Hpx domains. The observed binding pattern casts light on how MMP-3 could regulate collagen turnover and compete with various collagen-binding proteins regulating cell adhesion and proliferation.
U1 small nuclear RNA chimeric ribozymes with substrate specificity for the Rev pre-mRNA of human immunodeficiency virus. (1996)

The in vivo effectiveness of ribozymes strongly depends on the correct choice of the vector molecule. High levels of expression, stability, active conformation, and correct cellular localization are the most important features for a ribozyme vector. We have exploited the utilization of the U1 small nuclear RNA (snRNA) as a vector for specifically targeting a ribozyme into the nucleus. The Rev pre-mRNA of human immunodeficiency virus type 1 was chosen as target for testing the activity of the Ul-ribozyme. The catalytic core of the hammerhead motif, plus the recognition sequences, substituted the stem-loop III of the U1 snRNA. The resulting construct displays efficient cleavage activity in vitro. In addition, in the in vivo system of Xenopus laevis oocytes, the Ul-chimeric ribozyme accumulates in large amounts in the nucleus and produces a considerable reduction of Rev pre-mRNA levels. The Rev-specific ribozyme was also inserted in a derivative of the Ul snRNA mutated in the region of pairing with the 5' splice site, such as to match it with the suboptimal splice junction of the Rev precursor. This construct shows more efficient reduction of Rev pre-mRNA in vivo than the wild-type U1 vector.
Preliminary tests using magnetic resonance imaging of two-phase flow patterns and transitions (1993)

This paper presents the results of preliminary tests used to establish the feasibility of using magnetic resonance imaging (MRI) to examine and quantitatively characterize two-phase flow patterns and flow transitions. These tests were performed at the University of California, San Francisco (UCSF) School of Medicine MRI Center as a collaborative research effort with Oregon State University (OSU). Special scanning sequences designed by UCSF for flow imaging were implemented in the tests. UCSF operated the MRI facility, and OSU constructed and operated a cocurrent air-water flow loop consisting of a 1-in.-diam test section capable of producing air superficial velocities j[sub g] ranging from 0.3 to 14 m/s, and water superficial velocities j[sub l] ranging from 0.08 to 1.3 m/s.
Temporary Bonding: Electrostatic (2012)

This chapter contains sections titled: Basic Principles: Electrostatic Forces between Parallel Plates Technological Concept for Manufacture of Mobile Electrostatic Carriers Characterization of Electrostatic Carriers Electrostatic Carriers for Processing of Thin and Flexible Substrates Summary and Outlook References
On the use of the magnetic vector potential in the nodal and edge finite element analysis of 3D magnetostatic problems (1996)

An overview of various finite element techniques based on the magnetic vector potential for the solution of three-dimensional magnetostatic problems is presented. If nodal finite elements are used for the approximation of the vector potential, a lack of gauging results in an ill-conditioned system. The implicit enforcement of the Coulomb gauge dramatically improves the numerical stability, but the normal component of the vector potential must be allowed to be discontinuous on iron/air interfaces. If the vector potential is is interpolated with the aid of edge finite elements and no gauge is enforced, a singular system results. It can be solved efficiently by conjugate gradient methods, provided care is taken to ensure that the current density is divergence free. Finally, if a tree-cotree gauging of the vector potential is introduced, the numerical stability depends on how the tree is selected with no obvious optimal choice available.
MDCT of the Ovarian Vein: Normal Anatomy and Pathology (2008)

Volume-rendered images and curved planar reformatted images can be used to show the ovarian veins. MDCT findings allow the diagnosis of various ovarian vein disorders in patients with abdominal and pelvic pain, pulmonary thromboembolism, and pelvic mass.
Enhancement of phosphorus activation in vacancy engineered thin silicon-on-insulator substrates (2009)

The concentration of vacancy-type defects in a silicon-on-insulator substrate consisting of a 110 nm silicon overlayer and a 200 nm buried oxide has been quantified using variable energy positron annihilation spectroscopy following 300 keV Si+ ion implantation to a dose of 1.5×1015 cm−2 and subsequent annealing at temperatures ranging from 300 to 700 °C. The preferential creation of vacancies (relative to interstitials) in the silicon overlayer leads to a net vacancy-type defect concentration after annealing. Assuming that the defects have a structure close to that of the divacancy we determine the concentration to range from 1.7×1019 to 5×1018 cm−3 for annealing temperatures ranging from 300 to 700 °C. The measured defect concentration is in excellent agreement with that predicted via Monte Carlo simulation. The impact of this net vacancy population on the diffusion and activation of phosphorus introduced by a 2 keV implantation to a dose of 1×1015 cm−2 has been observed. For samples that combine both Si+ and P+ implantations, postimplantation phosphorus diffusion is markedly decreased relative to that for P+ implantation only. Further, a fourfold increase in the electrical activation of phosphorus after postimplantation annealing at 750 °C is observed when both implantations of Si+ and P+ are performed. We ascribe this affect to the reduction in phosphorus-interstitial clusters by the excess vacancy concentration beyond the amorphous/crystalline interface created by the P+ implantation.
Pharmacological inhibition of focal adhesion kinase 1 (FAK1) and anaplastic lymphoma kinase (ALK) identified via kinome profile analysis attenuates lipopolysaccharide-induced endothelial inflammatory activation (2020)

Sepsis is a life-threatening condition often leading to multiple organ failure for which currently no pharmacological treatment is available. Endothelial cells (EC) are among the first cells to respond to pathogens and inflammatory mediators in sepsis and might be a sentinel target to prevent the occurrence of multiple organ failure. Lipopolysaccharide (LPS) is a Gram-negative bacterial component that induces endothelial expression of inflammatory adhesion molecules, cytokines, and chemokines. This expression is regulated by a network of kinases, the result of which in vivo enables leukocytes to transmigrate from the blood into the underlying tissue, causing organ damage. We hypothesised that besides the known kinase pathways, other kinases are involved in the regulation of EC in response to LPS, and that these can be pharmacologically targeted to inhibit cell activation. Using kinome profiling, we identified 58 tyrosine kinases (TKs) that were active in human umbilical vein endothelial cells (HUVEC) at various timepoints after stimulation with LPS. These included AXL tyrosine kinase (Axl), focal adhesion kinase 1 (FAK1), and anaplastic lymphoma kinase (ALK). Using siRNA-based gene knock down, we confirmed that these three TKs mediate LPS-induced endothelial inflammatory activation. Pharmacological inhibition with FAK1 inhibitor FAK14 attenuated LPS-induced endothelial inflammatory activation and leukocyte adhesion partly via blockade of NF-κB activity. Administration of FAK14 after EC exposure to LPS also resulted in inhibition of inflammatory molecule expression. In contrast, inhibition of ALK with FDA-approved inhibitor Ceritinib attenuated LPS-induced endothelial inflammatory activation via a pathway that was independent of NF-κB signalling while it did not affect leukocyte adhesion. Furthermore, Ceritinib administration after start of EC exposure to LPS did not inhibit inflammatory activation. Combined FAK1 and ALK inhibition attenuated LPS-induced endothelial activation in an additive manner, without affecting leukocyte adhesion. Summarising, our findings suggest the involvement of FAK1 and ALK in mediating LPS-induced inflammatory activation of EC. Since pharmacological inhibition of FAK1 attenuated endothelial inflammatory activation after the cells were exposed to LPS, FAK1 represents a promising target for follow up studies.