gebhart/patrepeval huggingface dataset:
Analysis of C[sub 60] insertion into single wall carbon nanotube by molecular dynamics simulation (2001)

Classical molecular dynamics is used to simulate the insertion of C60 into a (10, 10) single wall nano tube (SWNT). We propose that the insertion process occurs through the open end of the tube. After insertion, the energy exchange between the C60 and the nanotube causes the kinetic energy of the former to decrease as it moves inside the tube. This kinetic energy loss is due to a “friction force” which we calculated for several insertion conditions. The binding energy of the C60 with the SWNT is due to Van der Waals interaction, and is found to be about 3.5 eV.
Hair cell transducer design based on optical fiber Bragg gratings (2004)

The development of a biomimetic transducer that reproduces the sensing mechanism of a single hair cell is presented. When light from a broadband source is input into an optical fiber terminated by a Bragg grating, the undisturbed grating reflects a fraction of the incident light at the Bragg wavelength, and the corresponding light intensity can be measured by a photodiode. The end of the fiber onto which the grating is written is adhered to two spacers separated by a 1-mm gap, and this assembly is adhered to two plates connected by a hinge, which is located below the gap. One plate is held rigidly and the tip of the other (free) plate experiences transverse vibrations, when ensonified. These vibrations induce longitudinal strains in the length of the fiber situated over the gap. Each unstrained portion of the grating reflects a small amount of light at the Bragg wavelength, resulting in two interfering light signals. The strain modulates the interference signal and produces an ac voltage at the photodiode output. The characteristics and performance of the transducer are presented, and its applications as the building block for underwater vector and tensor sensors are discussed. [Work supported by ONR.]
The interesting case—orphan diseases—double trouble (2019)

With an incidence of 1:20,000-1:30,000, Wilson's disease is regarded as a rare disease. Yet rarer, however, is the co-occurrence of two unrelated orphan diseases in the same patient. By means of two case reports, we would like to illustrate the necessity of an appropriate differential diagnostic evaluation and treatment of these disorders.
Heterogenous expression of antigenic markers on retinoblasts (1987)

Using a large panel of monoclonal antibodies to antigenic determinants specific for photoreceptor outer segments (S-Ag), for cells of neural (Leu-7) bipolar and/or ganglion cell (A2B5), glial/astrocytic (LN-1) or Muller's cell (M.M.) and two polyclonal antibodies to S-Ag and S-100 protein, the authors studied the expression of these antigenic determinants in four newly established retinoblastoma cell cultures and in cells derived from the Y-79 cell line. All four newly established retinoblastoma cell cultures demonstrated antigenic determinants specific for photoreceptors, astrocyte/glial and Muller's cells. The population of cells derived from the Y-79 cell line reacted mainly with the polyclonal antibody to S-100 protein, reflecting the homogeneity of its cell population mainly harboring antigenic determinants specific for astrocyte/glial cells. The heterogeneic staining of the newly established retinoblastoma cell cultures may reflect the multipotential-embryonic origin of these cells demonstrated by their ability to express antigenic determinants specific for the different cellular elements of the mature neuro-retina while the strictly glial staining of the Y-79 may be the result of cloning of this cell line.
Copper(I)‐Mediated Synthesis of Trisubstituted 1,2,3‐Triazoles. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Apelin/APJ signaling system: a potential link between adipose tissue and endothelial angiogenic processes (2008)

Adipose tissue is an active endocrine organ that produces a variety of secretory factors involved in the initiation of angiogenic processes. The bioactive peptide apelin is the endogenous ligand of the G protein-coupled receptor, APJ. Here we investigated the potential role of apelin and its receptor, APJ, in the angiogenic responses of human endothelial cells and the development of a functional vascular network in a model of adipose tissue development in mice. Treatment of human umbilical vein endothelial cells with apelin dose-dependently increased angiogenic responses, including endothelial cell migration, proliferation, and Matrigel(R) capillary tubelike structure formation. These endothelial effects of apelin were due to activation of APJ, because siRNA directed against APJ, which led to long-lasting down-regulation of APJ mRNA, abolished cell migration induced by apelin in contrast to control nonsilencing siRNA. Hypoxia up-regulated the expression of apelin in 3T3F442A adipocytes, and we therefore determined whether apelin could play a role in adipose tissue angiogenesis in vivo. Epididymal white adipose tissue (EWAT) transplantation was performed as a model of adipose tissue angiogenesis. Transplantation led to increased apelin mRNA levels 2 and 5 days after transplantation associated with tissue hypoxia, as evidenced by hydroxyprobe staining on tissue sections. Graft revascularization evolved in parallel, as the first functional vessels in EWAT grafts were observed 2 days after transplantation and a strong angiogenic response was apparent on day 14. This was confirmed by determination of graft hemoglobin levels, which are indicative of functional vascularization and were strongly increased 5 and 14 days after transplantation. The role of apelin in the graft neovascularization was then assessed by local delivery of stable complex apelin-targeting siRNA leading to dramatically reduced apelin mRNA levels and vascularization (quantified by hemogloblin content) in grafted EWAT on day 5 when compared with control siRNA. Taken together, our data provide the first evidence that apelin/APJ signaling pathways play a critical role in the development of the functional vascular network in adipose tissue. In addition, we have shown that adipocyte-derived apelin can be up-regulated by hypoxia. These findings provide novel insights into the complex relationship between adipose tissue and endothelial vascular function and may lead to new therapeutic strategies to modulate angiogenesis.
Combined C−H Functionalization/C−N Bond Formation Route to Carbazoles (2005)

A new method in which a series of substituted carbazoles is efficiently produced by the combination of an amide and an arene is described. The key feature of this method is the palladium-catalyzed tandem directed C-H functionalization and amide arylation. The method tolerates substitution on either ring of the biaryl amide substrates, and the products can be assembled in a simple two-step protocol from readily available reagents. The Pd(0) species generated are reoxidized to Pd(II) in the presence of Cu(OAc)2 and an atmosphere of oxygen.
A High-Resolution Low-Power Incremental $\Sigma\Delta$ ADC With Extended Range for Biosensor Arrays (2010)

A calibration-free, high-resolution analog-to-digital converter designed for a bioluminescence sensor array employs incremental sigma-delta (ΣΔ) modulation to combine the advantages of oversampling with an input multiplexing capability. The resolution of incremental ΣΔ modulators can be improved significantly by means of a technique similar to extended counting. In the approach proposed in this paper, analog-to-digital conversion is accomplished with a two-step process in which the residual error from a second-order incremental ΣΔ modulator is encoded using a successive approximation ADC. By this means it is possible to achieve enhanced resolution and improved static linearity while maintaining a one-to-one mapping between individual input and output samples. An experimental implementation of the proposed modulator has been integrated in a 0.18-μm CMOS technology. Operating from a 1.8-V supply, it achieves a dynamic range of 90.1 dB and a peak signal-to-noise and distortion ratio (SNDR) of 86.3 dB at a conversion rate of 1 MSample/s, with 38.1-mW power consumption.
Effects of Current Density on Elongation of an Electropulsing Treated Zn-Al Based Alloy (2009)

Effects of static electropulsing on microstructure and elongation of the ZA 22 alloy were studied by using scanning electron microscopy and transmission electron microscopy techniques. It was found that the current density of electropulsing treatment (EPT) was one of the factors that influenced microstructural changes and dislocation structure in the EPT alloy. The identity of the microstructure and the dislocation density played an important role in plastic elongation of the EPT alloy. The effects of the current density of electropulsing on elongation of the alloy were discussed from the point of view of microstructural evolution and dislocation dynamics.
A Review of Adaptive Optics Optical Coherence Tomography: Technical Advances, Scientific Applications, and the Future (2016)

Adaptive optics OCT continues to evolve technically and to contribute to our basic and clinical knowledge of the retina. Due to its capacity to reveal cellular and microscopic detail invisible to clinical OCT systems, it is an ideal companion to those instruments and has the demonstrable potential to produce images that can guide the interpretation of clinical findings.
Joint distributions for arbitrary variables (2002)

We compare the methods of Cohen (1971) and of Baraniuk and Jones (see Proc. IEEE ICASSP-93, p.320-323, 1993) for obtaining joint distributions for arbitrary variables. We show that the two methods produce identical results for variables whose associated operators are obtained via a unitary transformation of the time and frequency operators. In addition, we generalize this result and show that all pairs of variables connected by a unitary transformation have joint distributions that are identical in functional form. This result shows how pairs of variables can be grouped into classes whose joint distributions are functionally equivalent and, therefore, share equivalent properties.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Responses to dopamine of isolated human gastroepiploic arteries. (1989)

Responses to dopamine were compared in helical strips of human gastroepiploic arteries (proximal portion) and their epiploic branches (distal portion), partially contracted with prostaglandin F2 alpha. Dopamine produced a dose-related contraction in the proximal arteries, which was reversed to a relaxation by treatment with phentolamine. On the other hand, the distal arteries responded to low concentrations of dopamine with relaxations and to high concentrations with contractions. The relaxant response was selectively suppressed by treatment with droperidol and reversed to a contraction by SCH23390, but was not influenced by domperidone and propranolol. The amine-induced relaxation was not reduced by removal of the endothelium. The distal arteries, in which dopamine elicited a relaxation, responded to norepinephrine with dose-related contractions, which were suppressed by phentolamine but were not reversed to relaxations. It may be concluded that dopamine contracts human gastroepiploic arteries of the proximal portion, due to a predominant activation of alpha-adrenoceptors, and dilates the distal arteries by acting preferentially on dopaminergic DA1-receptors, possibly residing in smooth muscle. In the distal arteries, the ability of norepinephrine to activate alpha-adrenoceptors appears to be evidently higher than that of dopamine.
Monte Carlo studies of mirror fusion reactor neutral beam injection (1976)

The transport of neutral atoms in fusion plasma is investigated computationally using Monte Carlo particle tracking techniques. Studies of energetic neutral-beam heating of near-term mirror devices (the mirror experiment (MX) and the Fusion Engineering Research Facility (FERF)) are discussed here. Important plasma engineering information regarding the trapping of the neutral beam in the target plasma as well as the angular and energy distributions of the charge-transfer-produced neutral particle bombardment of the first wall is obtained in 3-D geometries.
New hybrid organic-inorganic nanocomposites based on functional [Ti 16O16(OEt)24(OEMA)8] nano-fillers (2005)

New hybrid nanocomposites based on a methacrylate functionalized titanium-oxo cluster as nano-cross-linker show improved mechanical properties, optical transparency and photochromic activity.
miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale (2021)

Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
De novo synthesis and salvage pathway coordinately regulate polyamine homeostasis and determine T cell proliferation and function (2020)

Robust and effective T cell-mediated immune responses require proper allocation of metabolic resources through metabolic pathways to sustain the energetically costly immune response. As an essential class of polycationic metabolites ubiquitously present in all living organisms, the polyamine pool is tightly regulated by biosynthesis and salvage pathway. We demonstrated that arginine is a major carbon donor and glutamine is a minor carbon donor for polyamine biosynthesis in T cells. Accordingly, the dependence of T cells can be partially relieved by replenishing the polyamine pool. In response to the blockage of biosynthesis, T cells can rapidly restore the polyamine pool through a compensatory increase in extracellular polyamine uptake, indicating a layer of metabolic plasticity. Simultaneously blocking synthesis and uptake depletes the intracellular polyamine pool, inhibits T cell proliferation, and suppresses T cell inflammation, indicating the potential therapeutic value of targeting the polyamine pool for managing inflammatory and autoimmune diseases.
Synthesis and Investigation of Cobalt Containing Nanoparticles Morphology (2017)

En. Rashid, for the company and assistance during experiments
Model-based clustering and new edge modelling in large computer networks (2016)

Computer networks are complex and the analysis of their structure in search for anomalous behaviour is both a challenging and important task for cyber security. For instance, new edges, i.e. connections from a host or user to a computer that has not been connected to before, provide potentially strong statistical evidence for detecting anomalies. Unusual new edges can sometimes be indicative of both legitimate activity, such as automated update requests permitted by the client, and illegitimate activity, such as denial of service (DoS) attacks to cause service disruption or intruders escalating privileges by traversing through the host network. In both cases, capturing and accumulating evidence of anomalous new edge formation represents an important security application. Computer networks tend to exhibit an underlying cluster structure, where nodes are naturally grouped together based on similar connection patterns. What constitutes anomalous behaviour may strongly differ between clusters, so inferring these peer groups constitutes an important step in modelling the types of new connections a user would make. In this article, we present a two-step Bayesian statistical method aimed at clustering similar users inside the network and simultaneously modelling new edge activity, exploiting both overall-level and cluster-level covariates.
In vitro and in vivo pharmacological profile of RP6503, a novel dual PI3K δ/γ inhibitor, in pulmonary disease systems (2013)

Introduction: Dual PI3Kδ/γ inhibition has been strongly implicated as an effective new treatment in allergic and non-allergic inflammatory pulmonary disorders and autoimmune diseases. The objective of the experiments was to explore the therapeutic potential of RP6503, a novel, small molecule PI3Kδ/γ inhibitor, in airway diseases. Methods: Potency and selectivity of RP6503 for PI3Kδ and γ isoforms and subsequent downstream activity was determined in several enzyme and cell-based assays. Efficacy of inhaled or intra-nasally administered RP6503 was examined in animal models relevant to asthma and COPD. Results: RP6503 had high potency against PI3Kδ (IC 50 =29.3 nM) and γ (IC 50 =28.1 nM) enzymes with selectivity over α (>10,000-fold) and β (>60-fold) isoforms as well as 441 diverse kinases (>50-fold). Cellular potency was confirmed in target-specific assays, namely anti-FceR1-(IC 50 =48.0 nM) or fMLP (IC 50 =52.4 nM)-induced CD63 expression in human basophils. RP6503 potently inhibited several immune cell responses in vitro including neutrophil functions, mast cell degranulation, and cytokine release from macrophages. Nebulization with RP6503 inhibited LPS-induced lung TNFα and neutrophil infiltration in rats (ED 50 =0.1 mg/kg). Intranasal administration of the compound also significantly reduced ovalbumin-induced lung eosinophil infiltration in guinea pigs (ED 50 =0.02 mg/kg), and attenuated cigarette smoke-induced neutrophil infiltration in mice (ED 50 =0.003 mg/kg). Conclusions: Results demonstrate that RP6503 is a potent and selective dual PI3Kδ/γ inhibitor with therapeutic potential in asthma and COPD. RP6503 is currently in preclinical development.
Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells (2017)

This is the first study identifying Giardia ESPs and evaluating their effects on IECs. It highlights the importance of host and parasite ESPs during interactions and reveals the intricate cellular responses that can explain disease mechanisms and attenuated inflammatory responses during giardiasis.
A wildland fire modeling and visualization environment (2011)

We present an overview of a modeling environment, consisting of a coupled atmosphere-wildfire model, utilities for visualization, data processing, and diagnostics, open source software repositories, and a community wiki. The fire model, called SFIRE, is based on a fire-spread model, implemented by the level-set method, and it is coupled with the Weather Research Forecasting (WRF) model. A version with a subset of the features is distributed with WRF 3.3 as WRF-Fire. In each time step, the fire module takes the wind as input and returns the latent and sensible heat fluxes. The software architecture uses WRF parallel infrastructure for massively parallel computing. Recent features of the code include interpolation from an ideal logarithmic wind profile for nonhomogeneous fuels and ignition from a fire perimeter with an atmosphere and fire spin-up. Real runs use online sources for fuel maps, fine-scale topography, and meteorological data, and can run faster than real time. Visualization pathways allow generating images and animations in many packages, including VisTrails, VAPOR, MayaVi, and Paraview, as well as output to Google Earth. The environment is available from openwfm.org. New diagnostic variables were added to the code recently, including a new kind of fireline intensity, which takes into account also the speed of burning, unlike Byram's fireline intensity.
Internal deformation of the human crystalline lens during accommodation (2008)

The model predicted that during accommodation, changes in lens thickness are mainly caused by deformation of the nucleus. In the older, non-accommodating lens, the deformations occur predominantly in the equatorial region and do not affect the central curvatures of the lens.
Control of the Purcell effect of quantum dots embedded in photonic crystal nanocavity by manipulating Q-factor (2012)

Modulation of the Purcell effect by controlling both the Q-factor and detuning in a quantum-dot-nanocavity coupled system was investigated. The Q-factor and detunings are controlled independently by using a nanocavity, a waveguide and a reflector formed in a two-dimensional photonic crystal slab, in combination with a newly developed nitrogen adsorption/desorption technique that enables local control of the refractive index. We investigated analytically and experimentally how the density of states of cavity mode is modulated, and we experimentally clarified how the emission of a quantum dot on resonance with a cavity is modulated. We observed that the emission of a quantum dot via a cavity mode was increased by 3.3 times when the Q-factor was changed from 3,500 to 6,900 while keeping the detuning fixed. The dependence of the Purcell effect on the Q-factor was directly observed.
Surface‐Anisotropic Janus Silicon Quantum Dots via Masking on 2D Silicon Nanosheets (2021)

Surface-anisotropic nanoparticles represent a new class of materials that shows potential in a variety of applications, including self-assembly, microelectronics, and biology. Here, the first synthesis of surface-anisotropic silicon quantum dots (SiQDs), obtained through masking on 2D silicon nanosheets, is presented. SiQDs are deposited on the 2D substrate, thereby exposing only one side of the QDs, which is functionalized through well-established hydrosilylation procedures. The UV-sensitive masking substrate is removed through UV-irradiation, which simultaneously initiates the hydrosilylation of a second substrate, thereby introducing a second functional group to the other side of the now free-standing SiQDs. This renders surface-anisotropic SiQDs that have two different functional groups on either side of the particle. This method can be used to introduce a variety of functional groups including hydrophilic and hydrophobic substrates, while the unique optoelectronic properties of the SiQDs remain unaffected. The anisotropic morphology of the QDs is confirmed through the aggregation behavior of amphiphilic Janus SiQDs at the interface of water and hexane. Additionally, anisotropic SiQDs are used to produce the first controlled (sub)monolayer of SiQDs on a gold wafer.
p‐Phosphonated Calix[n]arene Stabilizes Superparamagnetic Nanoparticles for Nitrate and Phosphate Uptake (2016)

Highly faceted superparamagnetic magnetite nanoparticles roughly 11 nm in diameter are readily accessible in the presence of p-phosphonated calix[n]arenes of different ring sizes (n=4, 5 and 6), through the use of a simple co-precipitation technique. In contrast, the larger calix[8]arene affords spherical particles of comparable size. The maximum magnetization is 70-60 emu g<sup>-1</sup> , which decreases with increasing size of the calixarene macrocycle, and the evidence indicates that the calixarenes bind to the surface of the nanoparticles via the phosphonate head groups rather than the phenolic oxygen centers. The stabilized nanoparticles show dual functionality: they remove up to 62 % of nitrate nitrogen and 48 % of phosphate from an aqueous effluent after 24 hours at concentrations of only 1 g L<sup>-1</sup> of calixarene-coated nanoparticles.