gebhart/patrepeval huggingface dataset:
Molecular dynamics simulations of silicon chloride ion incidence during Si etching in Cl-based plasmas (2014)

Classical molecular dynamics (MD) simulations have been performed for SiCl x + ( x = 0–4) ions incident on Si(100) surfaces, using an improved Stillinger–Weber (SW) potential form, to understand the surface reaction kinetics of etch byproduct ion incidence during Si etching in Cl-based plasmas. The ions were normally incident on surfaces with translational energies in the range of E i = 20–500 eV, and the surface reaction kinetics of Cl x + ( x = 1, 2) ion incidence were also simulated for reference. The etch yields and thresholds presently simulated were in agreement with the experimental results previously reported for the respective ion beam incidences on Si. Numerical results indicated that the etch yields y* per halogen (or per constituent Cl atom of incident ions), thresholds, surface coverages of Cl atoms adsorbed, and thicknesses of chlorinated surface layers are almost the same, when compared at the same translational energy per halogen; moreover, the stoichiometries of product species desorbed, stoichiometries of chlorinated surface layers, and their depth profiles are also similar when compared at the same . Thus, it follows that the etching characteristics for SiCl x + as well as Cl x + incidences on Si are determined primarily or scaled universally by , unless the deposition is significant at low E i or for SiCl + and SiCl 2 + .
Magnesium and cardiovascular biology: an important link between cardiovascular risk factors and atherogenesis. (1995)

In this review, a rationale is presented for how hypercholesterolemia, hypertension, diabetes mellitus, end-stage renal disease, renal dialysis, and prolonged stress can all lead to atherosclerosis, ischemic heart disease, and stroke. The data indicate that Mg deficiency caused either by poor diet and/or errors in Mg metabolism may be a missing link between diverse cardiovascular risk factors and atherosclerosis. Data from our laboratories and others indicate that reduction in extracellular and intracellular free Mg ions (Mg2+) can induce an entire array of pathophysiological phenomena known to be important in atherogenesis, that is, vasospasm, increased vascular reactivity, elevation in [Ca2+]i, formation of proinflammatory agents, oxygen radicals, platelet aggegation, reduction in cardiac bioenergetics, cardiac failure, oxidation of lipoproteins, gender-related modulation of endothelial-derived relaxing factor/NO, changes in membrane fatty acid saturation, changes in membrane plasmalogens and N-phospholipids (suggesting changes in intracellular phospholipid signals), and probably transcription factors.
Opportunities to improve health, production efficiency and sustainability through applied gene editing (2017)

Recent advances in gene editing technologies and in the application of these technologies to livestock animals have created a wealth of opportunity for improving animal health and well being and thereby the production and sustainability of animal protein productions. I review two technology examples in porcine and bovine systems that Genus is engaged in advancing through development. In porcine, recent published work has demonstrated that a simple edit producing a loss of function variant for the gene product CD163 can produce full resistance to the devastating pig disease porcine reproductive and respiratory syndrome virus (PRRSv) . In cattle, a more subtle edit, involving an edit of the -5 amino acid before the signal cleavage site of the CD 18 gene product from glutamine to glycine has been shown in cell model systems to confer resistance to the Mannheimia haemolytica leukotoxin , hypothesized to improve resilience to bovine respiratory disease (BRD). Among other challenges, the development and successful commercialization of these types of gene editing technologies will require the creation of multiple, consistent, reproducible edits in commercial founder lines of elite genetics. The practical challenges of deploying these technologies in beef, dairy and pork production systems are considered.
In peripartum cardiomyopathy plasminogen activator inhibitor-1 is a potential new biomarker with controversial roles (2019)

In PPCM patients, circulating and cardiac PAI-1 expression are up-regulated. While circulating PAI-1 may add 16 kDa-PRL to induce vascular impairment via the uPAR/NF-κB/miR-146a pathway, experimental data suggest that cardiac PAI-1 expression seems to protect the PPCM heart from fibrosis. Thus, measuring circulating PAI-1 and miR-146a, together with an uPAR/NF-κB-activity assay could be developed into a specific diagnostic marker assay for PPCM, but unrestricted reduction of PAI-1 for therapy may not be advised.
VOSD: A General-Purpose Virtual Observatory over Semantic Databases (2014)

E-Science relies heavily on manipulating massive amounts of data for research purposes. Researchers should be able to contribute their own data and methods, thus making their results accessible and reproducible by others worldwide. They need an environment which they can use anytime and anywhere to perform data-intensive computations. Virtual observatories serve this purpose. With the advance of the Semantic Web, more and more data is available in Resource Description Framework based databases. It is often desirable to have the ability to link data from local sources to these public data sets. We present a prototype system, which satisfies the requirements of a virtual observatory over semantic databases, such as user roles, data import, query execution, visualization, exporting result, etc. The system has special features which facilitate working with semantic data: visual query editor, use of ontologies, knowledge inference, querying remote endpoints, linking remote data with local data, extracting data from web pages.
Atomistic simulations of cross-slip nucleation at screw dislocation intersections in face-centered cubic nickel (2009)

The Escaig model for thermally activated cross-slip in face-centered cubic (fcc) materials assumes that cross-slip preferentially occurs at obstacles that produce large stress gradients on the Shockley partials of the screw dislocations. However, it is unclear as to the source, identity and concentration of such obstacles in single-phase fcc materials. Embedded atom potential, molecular-statics simulations of screw character dislocation intersections with 120° forest dislocations in fcc Ni are described that illustrate a mechanism for cross-slip nucleation. The simulations show how such intersections readily produce cross-slip nuclei and thus may be preferential sites for cross-slip. The energies of the dislocation intersection cores are estimated and it is shown that a partially cross-slipped configuration for the intersection is the most stable. In addition, simple three-dimensional dislocation dynamics simulations accounting for Shockley partials are shown to qualitatively reproduce the atomistically determined core structures for the same dislocation intersections.
The temporal pattern of intracortical microstimulation pulses elicits distinct temporal and spatial recruitment of cortical neuropil and neurons (2020)

<i>Objective.</i>The temporal spacing or distribution of stimulation pulses in therapeutic neurostimulation waveforms-referred to here as the Temporal Pattern (TP)-has emerged as an important parameter for tuning the response to deep-brain stimulation and intracortical microstimulation (ICMS). While it has long been assumed that modulating the TP of ICMS may be effective by altering the rate coding of the neural response, it is unclear how it alters the neural response at the network level. The present study is designed to elucidate the neural response to TP at the network level.<i>Approach</i>. We use<i>in vivo</i>two-photon imaging of mice expressing the calcium sensor<i>Thy1</i>-GCaMP or the glutamate sensor<i>hSyn</i>-iGluSnFr to examine the layer II/III neural response to ICMS with different TPs. We study the neuronal calcium and glutamate response to TPs with the same average frequency (10 Hz) and same total charge injection, but varying degrees of bursting. We also investigate one control pattern with an average frequency of 100 Hz and 10X the charge injection.<i>Main Results</i>. Stimulation trains with the same average frequency and same total charge injection but distinct TPs recruit distinct sets of neurons. More than half (60% of 309 cells) of neurons prefer one TP over the other. Despite their distinct spatial recruitment patterns, cells exhibit similar ability to follow 30 s trains of both TPs without failing, and they exhibit similar levels of glutamate release during stimulation. Both neuronal calcium and glutamate release entrain to the bursting TP pattern, with a ∼21-fold increase in relative power at the frequency of bursting. Bursting also results in a statistically significant elevation in the correlation between somatic calcium activity and neuropil activity, which we explore as a metric for inhibitory-excitatory tone. Interestingly, soma-neuropil correlation during the bursting pattern is a statistically significant predictor of cell preference for TP, which exposes a key link between TP and inhibitory-excitatory tone. Finally, using mesoscale imaging, we show that both TPs result in distal inhibition during stimulation, which reveals complex spatial and temporal interactions between TP and inhibitory-excitatory tone in ICMS.<i>Significance</i>. Our results may ultimately suggest that TP is a valuable parameter space to modulate inhibitory-excitatory tone and to recruit distinct network activity in ICMS. This presents a broader mechanism of action than rate coding, as previously thought. By implicating these additional mechanisms, TP may have broader utility in the clinic and should be pursued to expand the efficacy of ICMS therapies.
Colloidal aggregates tested via nanoindentation and simultaneous 3D imaging (2011)

The mechanical properties of aggregated colloids depend on the mutual interplay of inter-particle potentials, contact forces, aggregate structure and material properties of the bare particles. Owing to this variety of influences experimental results from macroscopic mechanical testings were mostly compared to time-consuming, microscopic simulations rather than to analytical theories. The aim of the present paper was to relate both macroscopic and microscopic mechanical data with each other and simple analytical models. We investigated dense amorphous aggregates made from monodisperse poly-methyl methacrylate (PMMA) particles (diameter: 1.6μm) via nanoindentation in combination with confocal microscopy. The resulting macroscopic information were complemented by the three dimensional aggregate structure as well as the microscopic strain field. The strain field was in reasonable agreement with the predictions from analytical continuum theories. As a consequence the measured force-depth curves could be analyzed within a theoretical framework that has frequently been used for nanoindentation of atomic matter such as metals, ceramics and polymers. The extracted values for hardness and effective elastic modulus represented average values characteristic of the aggregate. On base of these parameters we discuss the influence of the strength of particle bonds by introducing polystyrene (PS) between the particles.
Identification of miniproteins using cellulose-bound duotope scans (2006)

Protein domains or small molecules that mimic protein-protein contact sites are playing an increasing role in drug discovery, diagnostics and biotechnology. The identification of such protein mimics is based on two different strategies: (1) biologically as well as chemically prepared combinatorial libraries that are utilized for the de novo generation of novel sequences; and (2) approaches that are based on three-dimensional structures of endogenous protein ligands. Reduction of their size by truncation or deletion of amino acids which are not involved in the interaction and subsequent optimization by site-directed mutagenesis may also involve and library techniques. In contrast, this study describes an approach based on the primary structure of a protein ligand. One important technique for the mapping of protein-protein contact sites is the use of scans of overlapping peptides derived from a protein sequence (peptide scan, Fig. 1 left) which are subsequently tested for binding of the respective interaction partner [1]. This technique is the method of choice for the identification of linear binding sites where most of the important residues for the interaction are located within one stretch of the primary structure. In contrast, the key interacting residues of discontinuous binding sites are distributed over two or more binding regions which are separated in the protein sequence and only form the composite high affinty epitope upon protein folding. The mapping of discontinuous binding sites with peptide scans is very difficult, if not impossible, since peptides comprising single binding regions characteristically have very low affinities for the binding partner. Hence, we introduced a novel type of peptide library, called a duotope scan. The rationale of this scan is that a discontinuous binding site can only be mimicked adequately if two or more binding regions are connected in one molecule by a linker moiety resembling their spacing in the three-dimensional structure. Therefore, all possible combinations of two overlapping peptides from a conventional peptide scan are synthesized as one linear molecule i. E. combinatorial chemistry with peptides as second level building blocks (Fig. 1 right). The duotope scans are synthesized on continuous cellulose membranes by SPOT-synthesis [2], a highly parallel positionally addressable synthesis technique.
Strong enhancement of flux pinning in thick NdBa2Cu3O7-δ films grown on ion-beam assisted deposition-MgO templates via three-dimensional self-assembled stacks of BaZrO3 nanodots (2007)

Thick, epitaxial NdBa2Cu3O7-δ (NdBCO) films (up to 2.1 μm) with a high density of nanoscale columnar defects parallel to the c-axis of the film were deposited on ion-beam assisted deposition-MgO templates via pulsed laser deposition. The columnar defects were composed of self-assembled BaZrO3 (BZO) nanodots. A significant enhancement in Jc for H∥c is found for these films. In addition, an overall improvement in the in-field Jc at all field orientations is observed. Compared to pure NdBCO of similar thickness, the in-field Jc at H∥c for 0.7 μm thick NdBCO+BZO film is improved by a factor of 2–4 in the field range of 0.1–4 T and 10–20 at 7–8 T at 77 K. In addition, a smaller α∼0.17 is found in the field regime where Jc∼H−α. Also, a higher maximum pinning force, Fpmax∼14 GN∕m3, is found at 3 T and a larger Hirr over 8 T is found for the NdBCO films with columnar defects.
For Richer, for Poorer, in Sickness or in Health... (2016)

People are amassing large personal information stores. These stores present rich opportunities for analysis and use in matters of wealth, health, living and legacy. But these stores also bring with them new challenges for managing information across long periods of time. Hence personal information management (PIM) research increasingly must address the long term. For the seventh PIM workshop in a successful series started in 2005, we propose taking a look at personal information with exactly this longitudinal perspective. We expect the workshop to attract a range of people doing research related to PIM, HCI, personal digital archiving, aging, and the design of informational spaces for later life. Attendees will discuss issues related to storing information for the long run, how stored information can benefit a person throughout their lifetime (and into old age), and the legacy of a person's personal information.
OFDM systems with differential modulation schemes and turbo decoding techniques (2002)

Orthogonal frequency division multiplexing (OFDM) has some technical advantages compared with single carrier transmission in high data rate applications and multipath fading channels. Differential modulation techniques are used in combination with OFDM to avoid any effort for channel estimation and equalization in the receiver. In this paper, the combination of differential modulation and convolutional channel coding is re-interpreted as a concatenated code in which the differential modulation scheme is the rate R=1 inner code and the convolutional code the outer code. Turbo decoding is applied in this case at the receiver resulting in a signal-to-noise ratio (SNR) gain of more than 3.5 dB compared with classical soft decision Viterbi decoding.
Relasjonslæring i tverrfaglige team : et internt perspektiv i kunnskapsbaserte tjenestebedrifter (2014)

Denne masteroppgaven består av to artikler, og bidrar med ny innsikt om årsaker til og effekter av relasjonslæring i tverrfaglige team internt i kunnskapsbaserte tjenestebedrifter. Markedsorientering, tillit og læringsintensjon er årsaksfaktorene, og er studert i artikkel 1. Innovasjon, ansattes forpliktelse, lagånd og kreativitet i strategi er effektfaktorene, og er studert i artikkel 2. Det ble anvendt et spørreskjema hvor spørsmålene ble tilpasset fra tidligere testet teori. Resultatene i studien er basert på svar fra 210 ansatte i rådgivningsbedrifter, som i oppgaven representerer kunnskapsbaserte tjenestebedrifter. Det ble utviklet en konseptuell modell, og hypotesene ble testet. Studien finner støtte for at bedriftens markedsorientering, tillit blant de ansatte og læringsintensjon har en signifikant positiv sammenheng med relasjonslæring. Videre finner studien at relasjonslæring har en signifikant positiv sammenheng med effekter som innovasjon, ansattes forpliktelse, lagånd og kreativitet i strategi for kunde. Studien begrenser seg til å studere relasjonslæring i tverrfaglige team internt i store kunnskapsbaserte tjenestebedrifter, og de empiriske funnene viser at relasjonslæring som fenomen også finner sted internt i slike bedrifter. Studien understreker viktigheten av at ledere øker bedriftens markedsorientering, har fokus på tillit mellom ansatte, og kommuniserer at samarbeid i tverrfaglige team er en læringsarena bedriften ønsker å benytte. Videre må det oppfordres og legges til rette for åpenhet i tverrfaglige team, der mest mulig kommunikasjon mellom medlemmene foregår “face-to-face”, slik at et mangfold av meninger enklere kommer frem. Dette kan i så fall gi bedriften fordeler i form av 1) innovasjon, 2) mer forpliktede ansatte, 3) bedre lagånd og 4) mer kreative strategier for kunder. Det er, så vidt oss bekjent, første gang det undersøkes empirisk årsaker til og effekter av relasjonslæring i en intern kontekst i kunnskapsbaserte tjenestebedrifter.
Overnight delivery of hypertonic saline by nasal cannula aerosol for cystic fibrosis (2017)

The most likely cause for the failure to accelerate MCC was under-dosing of HS relative to the active transport of salt from the airways.
Design and Implementation of Packet Filtering System for IPv4/IPv6 Tunneling Environment (2006)

As substituting IPv6 network for all IPv4 network in a short time seems unattainable due to high cost and technical limitation, IPv4 and IPv6 are expected to coexist for a certain period of time. Under the co]existing environment of IPv4 and IPv6, interworking brings a number of extra security considerations even if it may have no security problem for each protocol respectively. Thus, the analysis and solutions for those various attacks toward IPv4/IPv6 interworking-related security are inevitably required for the sake of effective transition and settlement to IPv6. In this paper we carried out a proper rule of packet filtering for IPv6-in-IPv4 tunneling interworking environment to protect the IPv4/IPv6 interworking-related security attacks. Design and implementation of the packet filtering system suitable for IPv4/IPv6 tunneling environment in the form of Linux netfilter and ip6tables are also shown. Thru this study, the packet filtering system was found operating correctly ill the tunneling mechanism.
Empirical evidence of transmission over a school-household network for SARS-CoV-2; exploration of transmission pairs stratified by primary and secondary school (2023)

The results provide evidence of transmission on a bipartite school-household network. Schools play an important role in transmission within study years, and households play an important role in transmission between study years and between primary and secondary schools. Spatial distance between infections in a transmission pair reflects the smaller school catchment area of primary schools versus secondary schools. Many of these observed patterns likely hold for other respiratory pathogens.
The heuristic refinement method for deriving solution structures of proteins (1986)

A new method is presented for determining structures of proteins in solution. The method uses constraints inferred from analytic data to successively refine both the locations for parts of the structure and the levels of detail for describing those parts. A computer program, called PROTEAN, which encodes this method, has been partially implemented and was used to derive structures for the lac-repressor headpiece from experimental data.
Biodegradable Polymersomes with Structure Inherent Fluorescence and Targeting Capacity for Enhanced Photo‐Dynamic Therapy (2021)

Biodegradable nanostructures displaying aggregation-induced emission (AIE) are desirable from a biomedical point of view, due to the advantageous features of loading capacity, emission brightness, and fluorescence stability. Herein, biodegradable polymers comprising poly (ethylene glycol)-block-poly(caprolactone-gradient-trimethylene carbonate) (PEG-P(CLgTMC)), with tetraphenylethylene pyridinium-TMC (PAIE) side chains have been developed, which self-assembled into well-defined polymersomes. The resultant AIEgenic polymersomes are intrinsically fluorescent delivery vehicles. The presence of the pyridinium moiety endows the polymersomes with mitochondrial targeting ability, which improves the efficiency of co-encapsulated photosensitizers and improves therapeutic index against cancer cells both in vitro and in vivo. This contribution showcases the ability to engineer AIEgenic polymersomes with structure inherent fluorescence and targeting capacity for enhanced photodynamic therapy.
In vivo volumetric imaging of human retinal circulation with phase-variance optical coherence tomography (2011)

We present in vivo volumetric images of human retinal micro-circulation using Fourier-domain optical coherence tomography (Fd-OCT) with the phase-variance based motion contrast method. Currently fundus fluorescein angiography (FA) is the standard technique in clinical settings for visualizing blood circulation of the retina. High contrast imaging of retinal vasculature is achieved by injection of a fluorescein dye into the systemic circulation. We previously reported phase-variance optical coherence tomography (pvOCT) as an alternative and non-invasive technique to image human retinal capillaries. In contrast to FA, pvOCT allows not only noninvasive visualization of a two-dimensional retinal perfusion map but also volumetric morphology of retinal microvasculature with high sensitivity. In this paper we report high-speed acquisition at 125 kHz A-scans with pvOCT to reduce motion artifacts and increase the scanning area when compared with previous reports. Two scanning schemes with different sampling densities and scanning areas are evaluated to find optimal parameters for high acquisition speed in vivo imaging. In order to evaluate this technique, we compare pvOCT capillary imaging at 3x3 mm(2) and 1.5x1.5 mm(2) with fundus FA for a normal human subject. Additionally, a volumetric view of retinal capillaries and a stitched image acquired with ten 3x3 mm(2) pvOCT sub-volumes are presented. Visualization of retinal vasculature with pvOCT has potential for diagnosis of retinal vascular diseases.