gebhart/patrepeval huggingface dataset:
EGFR and Src are involved in indole-3-carbinol-induced death and cell cycle arrest of human breast cancer cells (2006)

Indole-3-carbinol (I3C), a dietary chemopreventive compound, induced marked reduction in epidermal growth factor receptor (EGFR) prior to cell death in cells representing three breast cancer subtypes. Signalling pathways, linking these events were investigated in detail. I3C modulated tyrosine phosphorylation from 30 min in four cell lines. In MDA-MB-468 and HBL100 cells, it induced Src activation after 5 h. In MDA-MB-468 cells, I3C induced signalling between 4.5 and 7 h, which involved sequential activation of Src, EGFR, STAT-1 and STAT-3, followed by EGFR degradation. It also induced physical association between activated Src and EGFR. In MCF7 and MDA-MB-231 cells, I3C modulated expression of cell cycle-related proteins, p21Cip1, p27Kip1, cyclin E, cyclin D1 and CDK6, with upregulation of p21Cip1 and cyclin E being dependent on Src. Inhibition of EGFR by specific inhibitors PD153035 or ZD1839 increased susceptibility to I3C-induced apoptosis of MCF7, MDA-MB-468 and MDA-MB-231 cells. Inhibition of Src sensitized MDA-MB-468 and MDA-MB-231 cells to I3C, whereas overexpression of c-Src increased resistance to I3C in MDA-MB-468 and HBL100 cells. Modulation of Src in MDA-MB-468 cells influenced the basal level of EGFR expression and cell viability; the latter being positively correlated with EGFR activation levels. Therefore, EGFR and Src activities are essential for I3C-induced cell cycle arrest and death; however, I3C-induced pathways depend on specific features of breast cancer cells. The cancer types, which rely on 'EGFR addiction' or Src deregulation, are likely to be susceptible to I3C.
A new, optical-lever based atomic force microscope (1994)

A new optical-lever based atomic force microscope is described in which the cantilever scans and is accurately tracked by a scanning focused spot. It can operate at forces below one nanoNewton over image areas greater than 100 μ×100 μ. It can be combined with optical microscopes of high numerical aperture and operated with the sample and cantilever in fluids. As examples of its applications, images of living cells in Petri dishes and a 6 in. (15.24 mm) silicon wafer are included.
Excitatory neuronal CHD8 in the regulation of neocortical development and sensory-motor behaviors (2021)

CHD8 (chromodomain helicase DNA-binding protein 8) is a chromatin remodeler associated with autism spectrum disorders. Homozygous Chd8 deletion in mice leads to embryonic lethality, making it difficult to assess whether CHD8 regulates brain development and whether CHD8 haploinsufficiency-related macrocephaly reflects normal CHD8 functions. Here, we report that homozygous conditional knockout of Chd8 restricted to neocortical glutamatergic neurons causes apoptosis-dependent near-complete elimination of neocortical structures. These mice, however, display normal survival and hyperactivity, anxiolytic-like behavior, and increased social interaction. They also show largely normal auditory function and moderately impaired visual and motor functions but enhanced whisker-related somatosensory function. These changes accompany thalamic hyperactivity, revealed by 15.2-Tesla fMRI, and increased intrinsic excitability and decreased inhibitory synaptic transmission in thalamic ventral posterior medial (VPM) neurons involved in somatosensation. These results suggest that excitatory neuronal CHD8 critically regulates neocortical development through anti-apoptotic mechanisms, neocortical elimination distinctly affects cognitive behaviors and sensory-motor functions in mice, and Chd8 haploinsufficiency-related macrocephaly might represent compensatory responses.
Microstructure and strain relief of Ge films grown layer by layer on Si(001) (1990)

We have studied the microstructure of Ge films grown layer by layer on Si(001) surfaces. The growth mode was changed from a Stranski-Krastanov mode (layer by layer for 3 monolayers, followed by islanding) to a layer-by-layer growth mode by passivation of the surface with 1 monolayer of arsenic. This change in growth morphology results in drastic changes in the mechanism of strain relief. Unlike films grown on bare Si, these films remain pseudomorphically strained up to a thickness of about 10 monolayers. At a film thickness of 12 monolayers, we observe the catastrophic formation of strain-induced defects. These consist of several {111} planes tilted perpendicular to the substrate. The defects are ssV-shaped and, consequently, relieve the misfit progressively as the film grows. At a film thickness of 50 monolayers, we observe that the ssV-shaped defects serve as nucleation sites for dislocations that climb down into the Si substrate. These dislocations then glide through the film to relieve the misfit in previously undefected areas. Thus, the misfit is relieved partly by ssV-shaped defects located in the Ge layer and partly by edge dislocations located in the Si substrate. For thick films, we observe that most of the ssV-shaped defects have been covered by Ge oriented epitaxially with the substrate, but they have also generated twins and stacking faults that extend throughout the whole film. This work has fundamental implications for the understanding of strain relief during ``normal'' growth. Indeed, it demonstrates that the so-called critical thickness has to take into account the formation energy of the strain-relieving defects (in general, dislocations), and not only the energy to move the defects, as has generally been done up to now.
Hydrogen‐Free Gas‐Phase Deoxydehydration of 2,3‐Butanediol to Butene on Silica‐Supported Vanadium Catalysts (2017)

Abstract The gas‐phase deoxydehydration of 2,3‐butanediol to butene was investigated in a plug flow reactor over SiO 2 ‐supported vanadium oxide, γ‐alumina, P/ZSM‐5, and MgO catalysts with acid/base sites of varying strengths. 5 wt % vanadium on SiO 2 (i.e., 5V/SiO 2 ) showed the best performance with 100 % conversion and up to 45.2 % butene selectivity. The combination of weak acid sites and polymeric VO x surface species provided the 5V/SiO 2 catalyst with bifunctional capabilities to achieve both dehydration and transfer hydrogenation, which allowed it to catalyze the deoxydehydration of 2,3‐butanediol to butene even in the absence of H 2 . As 2,3‐butanediol is a common yet underutilized biomass product, this reaction may provide a viable route for a biomass‐to‐chemicals application for 2,3‐butanediol.
Interaction of Caveolin-3 and HCN is involved in the pathogenesis of diabetic cystopathy (2016)

Abstract A growing body of research suggests that impaired bladder Cajal-like interstitial cells (ICCs) are a important component in the pathogenesis of diabetes-induced bladder dysfunction, although the molecular mechanisms have not been illustrated completely. The purpose of this study was to examine whether the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in ICCs-DM were responsible for the detrusor weak contractility of Diabetic cystopathy (DCP) and to study the possible mechanism of regulating the expression and function of HCN channels. HCN channels expression were decreased at the mRNA and protein levels. Forskolin (FSK), which can elevate intracellular cAMP levels, increased the density of the hyperpolarization-activated current and intracellular calcium concentration in both normal control (NC) rats and DCP rats, but the sensitivity of FSK on HCN channels was clearly down-regulated in DCP rats. The loss of caveolae and caveolin was in accordance with the decrease in HCN channels. Caveolin-3 co-localizes with and affects the expression and function of HCN. Taken together, these results indicate that the loss of caveolae and HCN channels in ICCs-DM is important in the pathogenesis of DCP. Increasing the number of caveolae to enhance the function of HCN channels may represent a viable target for the pharmacological treatment of DCP.
Electrodeposition of Cumn from a Deep Eutectic Electrolyte (2016)

We demonstrate our recent progress in conducting electrodeposition of CuMn thin film using a deep eutectic solvent, which consists of CHCl and ethyl glycol. The sources for Cu ions and Mn ions are C 10 H 14 CuO 4 and MnCl 2 , respectively. Plating methods such as potentiostatic, galvanostatic, and current pulsing have been explored with relevant electrochemical parameters optimized and discussed. We determine that the current pulsing route enables the formation of CuMn thin film with desirable Mn amount. Material characterizations including Scanning Electron Microscopy, X-ray diffraction, X-ray Photoelectron Spectroscopy, and X-ray Absorption Microscopy have been carried out. Our results indicate that Mn exists in both metallic form and oxide, and after heat treatment, precipitates with excess Mn are found on the surface. In addition, the conductivity of deep eutectic electrolyte is greatly affected by the ambient moisture and consequently, the plating process is kept in a glovebox to minimize unnecessary interference.
Study of direct current characteristics of carbon-doped GaInP/GaAs heterojunction bipolar transistor grown by solid source molecular beam epitaxy (2004)

This article reports the dc characteristics of a GaInP/GaAs heterojunction bipolar transistor (HBT) with carbon-doped GaAs base layer grown by solid source molecular beam epitaxy using carbon tetrabromide (CBr4) as p-type dopant precursor. Hydrofluoric acid (HF) was used to passivate the GaInP/GaAs HBTs. At base bias voltages below 0.9 V in the Gummel plot, the base current of large area devices after HF passivation, was greatly reduced indicating that the extrinsic base surface recombination current was significantly reduced. After HF passivation, detailed dc characterization of the device performance within the temperature range of 300–380 K was carried out, and the carrier transport properties were investigated. The base current and collector current ideality factors at 300 K were 1.12 and 1.01, respectively. This indicates that a space charge region recombination current is insignificant in the base. From the temperature dependent Gummel plot, the activation energies of the collector current and base current were obtained. For the collector current, the activation energy is 1.4 eV, which is close to the band gap of the GaAs base. This indicates that the collector current is determined by the drift-diffusion process. For the base current, the activation energy is also 1.4 eV, indicating that band-to-band recombination plays a dominant role in the base current. No trap-related recombination was observed in the base and collector currents, which further indicates the good base material quality in the HBT structure. The current gain versus collector current characteristics at different temperatures were also investigated and analyzed.
Sparse decomposition light-field microscopy for high speed imaging of neuronal activity (2020)

One of the major challenges in large scale optical imaging of neuronal activity is to simultaneously achieve sufficient temporal and spatial resolution across a large volume. Here, we introduce sparse decomposition light-field microscopy (SDLFM), a computational imaging technique based on light-field microscopy (LFM) that takes algorithmic advantage of the high temporal resolution of LFM and the inherent temporal sparsity of spikes to improve effective spatial resolution and signal-to-noise ratios (SNRs). With increased effective spatial resolution and SNRs, neuronal activity at the single-cell level can be recovered over a large volume. We demonstrate the single-cell imaging capability of SDLFM with in vivo imaging of neuronal activity of whole brains of larval zebrafish with estimated lateral and axial resolutions of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>∼</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>3.5</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mtext>µ</mml:mtext> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">m</mml:mi> </mml:mrow> </mml:mrow> </mml:mrow> </mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>∼</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>7.4</mml:mn> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mtext>µ</mml:mtext> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">m</mml:mi> </mml:mrow> </mml:mrow> </mml:mrow> </mml:math> , respectively, acquired at volumetric imaging rates up to 50 Hz. We also show that SDLFM increases the quality of neural imaging in adult fruit flies.
Content feature based bit rate modelling for scalable video coding using machine learning algorithms (2013)

Rate control mechanisms for scalable video coding are known to be a complex problem, suffering from inaccurate performance due to the layered structure of scalable video. In this study, multiple machine learning methods are evaluated to design rate-complexity-quantization models for efficient rate control. Specifically, the bit rates of SVC multi-layered bit streams are predicted, based on the quantization parameters used for encoding and a number of features describing the complexity of the video content. The results indicate that general regression neural networks can be used as an alternative to the statistical models classically used for rate control. Moreover, this approach is able to capture the influence of video complexity on the bit rate of all layers at once, and offers the possibility of increasing its effectiveness as it gains experience through on-line learning. The constructed models provide a good prediction of the encoded bit rates, with a Pearson correlation well above 0.9 and an average error of about 5%. The resulting predictor can serve as basis for a more elaborate rate control system for scalable video coding.
Wind Patterns over a Heliostat Field (2014)

Heliostats constitute a major portion of the direct costs of a concentrating solar power tower plant. As a result, a significant amount of effort is being focused on designing and developing cheaper heliostats. The optical and structural performance of these new and existing heliostats under dynamic wind loads must be characterized and understood in order to meet both cost and performance objectives. This paper presents the second phase of a U.S. DOE-sponsored program at Sandia National Laboratories' National Solar Thermal Test Facility (NSTTF) that includes dynamic testing and analysis of multiple full-scale heliostats. The objectives of these tests and analyses are to characterize and understand some differences in the impacts of dynamic wind loads on heliostat strain and cyclic fatigue between perimeter and inner-field heliostats. A weather tower with three tri-axial ultrasonic anemometers has been erected just outside the field to measure the approaching boundary winds, while a portable tower was set up to characterize wind velocities and turbulence between subsequent rows within the field. Anemometers have also been mounted to some heliostats to gather close range measurement of turbulence and wind frequencies and to provide a point of comparison for computational fluid dynamics models of wind flow over the field. This paper presents mean wind speeds and wind loads on heliostats as a function of field position. The calculated mean wind loads were used to assess the mean wind-load reduction correlation of Peterka [1].
Relation of Nasal Air Flow to Nasal Cavity Dimensions (2009)

Our study indicates statistically significant associations between nasal cavity dimensions and PNIF. The most important structural determinant for PNIF is the minimal cross-sectional area of the nasal cavity.
INT-path: Towards Optimal Path Planning for In-band Network-Wide Telemetry (2019)

With the ever-increasing complexity of networks, fine-grained network monitoring enables better network reliability and timely feedback control. The In-band Network Telemetry (INT) allows cost-effective network monitoring by encapsulating device-internal states into probe packets. However, INT only specifies an underlying device-level primitive while how to achieve network-wide traffic monitoring remains undefined. In this work, we propose INT-path, a network-wide telemetry framework, by decoupling the system into a routing mechanism and a routing path generation policy. Specifically, we embed source routing into INT probes to allow specifying the route the probe packet takes through the network. Above the mechanism, we develop an Euler trail-based path planning policy to generate non-overlapped INT paths that cover the entire network with a minimum path number. Besides, an exhaustive analysis of algorithm's run-time complexity is also provided. INT-path can “encode” the network-wide traffic status into a series of “bitmap images”, transforming network troubleshooting into pattern recognition problems. INT-path is very suitable for deployment in data center networks thanks to their symmetric network topologies.
A Nonlinear Rheological Model for Active and Passive Skeletal Muscle (2003)

An existing rheological model of skeletal muscle (Forcinito et al., 1998) was modified with a nonlinear Maxwell fluid element to provide a phenomenological model capable of analyzing the strain-stiffening behavior typically found in passive, and occasionally observed in active, skeletal muscle. This new model describes both active and passive muscular behavior as a combination of the behavior of each model component, without requiring prior knowledge of the force-length or force-velocity characteristics of the muscle.
Enhanced Electrochemical Stability of Graphite Anodes via Adsorption of Reductively Polymerizable Dibromothiophene in Lithium Ion Batteries (2014)

This is the first report showing the improvement of electrochemical stability of a graphite (Gt) anode in lithium ion batteries (LIBs) by using 2,5-dibromothiophene (DBT) as a surface-adsorbent. DBT adsorbed onto Gt underwent reductive electro-polymerization during the first discharge (Li+ intercalation) to form a protective cap over catalytically active sites of Gt. Poly-DBT, thus formed, helped the formation of a compact and thin SEI layer during subsequent Li+ ion intercalation, preventing the continuous formation of SEI layers. The cyclic performance of a half-cell with DBT-adsorbed Gt was compared with half-cells composed of various anode materials (i.e., mere Gt, pyrrole-adsorbed Gt, and thiophene-adsorbed Gt). The adsorption of small amounts of DBT on Gt improved the capacity retention of the half-cells by nearly 7.5% and decreased a fading rate to 0.09 mAh·g−1·cycle−1, relative to mere Gt which showed a fading rate of 0.17 mAh·g−1·cycle−1. The dissolution of DBT in electrolyte, however, had detrimental effects on cell performance, suggesting that surface-adsorption of DBT is more beneficial. The formation of a compact and thin SEI layer on DBT-adsorbed Gt was confirmed by surface-composition analysis and impedance spectroscopy.
Modification of Expression of the Malignant Phenotype in Radiation-initiated Cells (1987)

Carcinogenesis is a multistage process consisting minimally of initiation and promotion/progression stages. Radiation and many environmental xenobiotics are potent initiating agents. We have shown that initiation of carcinogenesis in vivo by these agents is a common cellular event. In the irradiated thyroid (5 Gy) at least one in 20 cells is initiated. Initiation by both radiation and chemicals has also been shown to be a common cellular event in the mammary gland. Initiation therefore is most likely not the sole rate-limiting event in the carcinogenic process. The propensity of the initiated cell to express the malignant phenotype is modulated by many factors, including environmental chemicals and physiological and genetic factors. Scopal and abscopal physiological factors can either enhance or suppress the progression of initiated cells to a frank tumour. For example, prolactin enhances the rate of progression of radiation and chemically initiated mammary tumours while glucocorticoids suppress this progression. TSH enhances the progression of radiation-initiated thyroid tumours while a scopal factor associated with unirradiated thyroid cells suppresses progression of this tumour type.
Pharmacokinetics of plasma-derived and recombinant factor IX: using population pharmacokinetics with sparse sampling data needs further study (2013)

The concept of using pharmacokinetics for prophylactic dose tailoring with limited blood sampling in clinical practice has been demonstrated for factor VIII but not for factor IX. The pharmacokinetics of factor IX are more complicated than for factor VIII and also differ between plasma-derived and recombinant factor IX. Therefore, the pharmacokinetics of factor IX need to be further explored in clinical trials including comparative studies of prophylaxis with different factor IX concentrates. These are the main conclusions drawn from two of the last manuscripts written by Professor Sven Björkman and published in Haemophilia. Professor Björkman suddenly and unexpectedly died last summer. Thanks to the academic network created around his skill and through his enthusiasm for the pharmacokinetics of clotting factors and ability to convey his wisdom to others, this work will continue. Sven Björkman opened a new era in hemophilia prophylaxis.
Enhanced Channel Access for Connection State of Bluetooth Low Energy Networks (2017)

According to Bluetooth Low Energy (BLE) specifications, a pair of connected devices (master and slave) should sleep whenever packet transmission is failed twice consecutively, although they still have packets to be sent. However, when BLE devices are densely deployed in a small geographical area, such sleeping can occur frequently, and as a result, the BLE performance can be degraded largely. Moreover, when considering that a message consists of multiple packets in many Internet of things (IoT) applications, the situation gets worse because the master and slave of BLE alternately have the transmission opportunity not in the unit of message but in the unit of packet. In this paper, we suggest two enhancements of data channel access for improving the BLE performance by making up the above-mentioned weaknesses: One is to continue packet transmission by avoiding bad-quality channel via channel hopping instead of sleeping; the other is a message-based alternation of transmission opportunity between master and slave. We formulate a Markov model for analyzing the performance of the proposed scheme and derive a closed-form solution. The numerical results demonstrate that, from the proposed two enhancements, the throughput and delay performances of BLE are remarkably improved with a slight increase of consumed energy.
Linear Position Estimation on Smart Actuators Using a Nonlinear Observer (2019)

This paper focuses on observer design for a dynamic system with non-monotonic nonlinear measurement equations. A Lyapunov-analysis-based observer design method for exponentially stable state estimation and a corresponding LMI for computing the observer design gains are developed. This observer design method is applied to linear position estimation using magnetic fields for smart industrial actuators. The output equations for magnetic field as a function of position are nonlinear and non-monotonic. A single constant gain that can satisfy the observer stability condition over the entire range of operating conditions does not exist, but a constant stabilizing gain does exist in each piecewise monotonic region. A methodology for discretizing the operating range into piecewise regions and using a finite state machine for switching between piecewise regions with stabilizing observer gains is developed. Experimental results are presented on the performance of the observer in accurately estimating linear position.