gebhart/patrepeval huggingface dataset:
Development of a high-efficiency method for gene marking of Dunning prostate cancer cell lines with the enzyme β-galactosidase (1996)

Although the bacterial enzyme beta-galactosidase has been used as a reporter gene in a variety of mammalian systems; the variability and instability of its expression has limited its use. Transfection of Dunning rat prostatic cell lines with beta-galactosidase expression plasmids resulted in 5-10% of cells expressing the enzyme transiently, and < 5% of G418-resistant clones showing any level of expression. To address this problem, we developed a labeling protocol using a replication defective retrovirus containing a beta-galactosidase expression cassette. Between 30-50% of cells transduced expressed high levels of this enzyme. Homogeneous cell populations were isolated by subsequent fluorescence-activated cell sorting, using a fluorescent beta-galactosidase substrate. Using a modification of standard staining procedures, small metastatic foci of cells expressing beta-galactosidase in mouse lung tissue were detected with high sensitivity. This method has several advantages over standard transfection protocols, including the expedient and efficient transfer of the beta-galactosidase gene and the stability of its expression in a variety of Dunning sublines.
Systemic and local cardiac inflammation after experimental long bone fracture, traumatic brain injury and combined trauma in mice (2021)

Injuries to the head and extremities frequently occur after severe trauma. In our study, we analyzed the effects of closed tibia fracture, isolated TBI, and the combination of both injuries with regard to the development of post-traumatic secondary cardiac injuries.
Secret Key Distillation over Satellite-to-satellite Free-space Optics Channel with Eavesdropper Dynamic Positioning (2020)

The conventional omnipotent eavesdropper assumption in quantum cryptography study can be too strict for some realistic scenarios. In this paper, we study the secret key distillation over a satellite-to-satellite free space optics channel in which we assume that the eavesdropper (Eve) is restricted in her ability of power collection due to the limited size of her aperture but can change the position of her aperture to gain advantages over the communication parties (Alice and Bob) and we determine the achievable key rate lower and upper bounds with respect to different scenarios. We first study the case where Eve is behind Bob and we prove that the optimal eavesdropping strategy for her in long-distance transmission case is to place her aperture on the beam transmission axis and set Bob-to-Eve distance equal to Alice-to-Bob distance. We also show that the achievable key rate would be characterized by a Bessel function integral related to Eve's position in a short-distance transmission case. We then investigate the case where Eve is before Bob and show similar results with Eve's and Bob's roles exchanged.
Peak Power Reduction Method Based on Structure of Parity-Check Matrix for LDPC Coded OFDM Transmission (2007)

In this paper, we propose a peak power reduction method for LDPC coded OFDM system, where transmit data sequence is grouped into several clusters based on structure of a low density parity-check matrix and the phase or each cluster is adjusted so as to minimize PAPR of OFDM signal by multiplying weighting factors (WFs). At the receiver, WFs are estimated with sufficient accuracy by exploiting the decoding property of LDPC code. The proposed method can be applied to not only systematic coded signal but also non-systematic one. Computer simulation results show that, when LDPC code with code-rate of R ap 1/2 is used, PAPR of OFDM signal can be reduced by about 2.4 dB without significant degradation in BLER performance as compared to perfect WF estimation in attenuated 12-path Rayleigh fading condition.
Plasmonic Electrochromism of Metal Oxide Nanocrystals (2013)

This chapter describes a new type of electrochromic phenomenon, plasmonic electrochromism, which enables faster switching times, improved durability and the required spectral selectivity. This new paradigm has been realised thanks to the development of colloidal plasmonic nanocrystals. The chapter discusses the colloidal synthesis of doped metal oxide nanocrystals. Growing colloidal nanocrystals from solution phase is a kinetically controlled process; introducing dopants within the lattice, therefore requires a fine balance of the host nanocrystal growth rate and the dopant incorporation rate. The chapter presents a research on plasmonic electrochromic electrodes based on colloidal Sn-doped In2O3 (ITO) and Al-doped ZnO (AZO) nanocrystals. Design principles for nanocrystal-based plasmonic electrochromics are presented. The chapter describes two types of advanced electrochromic electrodes based on plasmonic nanocrystals: mesoporous NIR-selective nanocrystal assemblies with ordered, tunable pore sizes and enhanced charge capacity and switching kinetics, and dual-band ‘nanocrystal-in-glass’ composites with enhanced optical contrast and durability.
Synthesis of Rhenium(I) Tricarbonyl Complexes with Carbohydrate‐Pendant Tridentate Ligands and Their Cellular Uptake (2011)

Abstract Twelve [Re I L (CO) 3 ] n + complexes with various carbohydrate‐pendant ligands L have been prepared and their uptake into HeLa S3 cells were investigated. The ligand library includes: (i) glucose/galactose as the carbohydrate group; (ii) bis(2‐pyridylmethyl)amine (DPA), bis(2‐quinolylmethyl)amine (DQA), or N ‐(2‐pyridylmethyl)glycine (NPG) as the metal binding component; and (iii) an ethylene chain as a linker between the metal binding site and the O / C ‐glycosides. Microwave induced plasma mass spectroscopy (MIP‐MS) measurements revealed that all complexes were extensively incorporated into the HeLa cells over a 24 h period, and the DQA complexes showed the highest uptake of all the complexes in the series. However, in comparison to the corresponding Re complexes without the pendant carbohydrate functions (prepared with the related ligands L DPA , L DQA , and L NPG ), only the NPG complexes exhibited carbohydrate enhanced cellular uptake. Considering their water solubility and cellular uptake properties, the NPG complexes containing an O ‐glycoside group ( L1 and L′1 ) are the best candidates for enhancing cellular uptake of metal ions. Microscopic analysis with PC‐12 cells in the presence of thefluorescent complex [Re( L′7 )(CO) 3 ]Cl, revealed that the complex stays in the cell cytosol and cannot penetrate into the nucleus.
Narrow electroluminescence in bromide ligand-capped cadmium chalcogenide nanoplatelets (2022)

Colloidal zinc blende II–VI semiconductor nanoplatelets (NPLs) demonstrate as a promising class of materials for optoelectronic devices due to their unique excitonic characteristics, narrow emission linewidth, and quantum well-structure. Adopting heterostructures for these nanocrystals allows tuning of their optical features and enhances their photostability, photoluminescence (PL), quantum yield (QY), and color purity for further device integration. Exchanging of carboxylate capping ligands on top and bottom [001] facets of CdSe NPLs with halide ligands is an alternative to achieve the aims of spectral tunability and improve surface passivation, but to date there have been no reports on integrating the advantages of halide ligand exchanged CdSe NPLs for device fabrication. In this work, we demonstrate green electroluminescence (EL) of bromide ligand-capped CdSe NPLs as active emitters in an electrically driven light emitting diode (LED) with a low turn-on voltage of 3.0 V. We observed EL emission at 533.1 nm with a narrow linewidth of 19.4 nm, a maximum luminance of 1276 cd/m2, and the highest external quantum efficiency (EQE) of 0.803%. These results highlight the ability of halide ligand exchange in tuning the EL properties of CdSe NPL-LEDs and potential of bromide ligand-capped CdSe NPLs in contributing to the green emission region of NPL-LEDs, demonstrating its potential for future device integration and contribution to a high color rendering index of future NPL displays.
Filamentous Bacteriophage Delay Healing of Pseudomonas-Infected Wounds (2020)

Summary We have identified a novel role for filamentous bacteriophage in the delayed healing associated with chronic Pseudomonas aeruginosa (Pa) wound infections. Pf phage delays wound re-epithelialization in the absence of live Pa, indicative that Pf effects on wound healing are independent of Pa pathogenesis. Pf phage directly inhibits autocrine signaling of CXCL1 (KC) to impede keratinocyte migration and wound re-epithelization. In agreement with these studies, a prospective cohort study of 36 human patients with chronic Pa wound infections revealed that wounds infected with Pf positive strains of Pa took longer to heal and were more likely to increase in size compared to wounds infected with Pf negative strains. Together, these data implicate Pf phage in the delayed wound healing associated with Pa infection through direct manipulation of mammalian target cells. We propose that Pf phage may have potential as a biomarker and therapeutic target in delayed wound healing.
Kinesin-1 transport reductions enhance human tau hyperphosphorylation, aggregation and neurodegeneration in animal models of tauopathies (2010)

Neurodegeneration induced by abnormal hyperphosphorylation and aggregation of the microtubule-associated protein tau defines neurodegenerative tauopathies. Destabilization of microtubules by loss of tau function and filament formation by toxic gain of function are two mechanisms suggested for how abnormal tau triggers neuronal loss. Recent experiments in kinesin-1 deficient mice suggested that axonal transport defects can initiate biochemical changes that induce activation of axonal stress kinase pathways leading to abnormal tau hyperphosphorylation. Here we show using Drosophila and mouse models of tauopathies that reductions in axonal transport can exacerbate human tau protein hyperphosphorylation, formation of insoluble aggregates and tau-dependent neurodegeneration. Together with previous work, our results suggest that non-lethal reductions in axonal transport, and perhaps other types of minor axonal stress, are sufficient to induce and/or accelerate abnormal tau behavior characteristic of Alzheimer's disease and other neurodegenerative tauopathies.
Thermoconformable, Flexible Lithium‐Ion Batteries (2022)

Abstract This work introduces a scalable method for fabrication of flexible, thermoconformable lithium‐ion batteries, suitable for the interior of vehicles. Electrodes with a composite structure are fabricated by combining conventional granular slurries with a porous carbon nanotube fabric current collector and a solid gel polymer electrolyte. The composite structure reduces polarization at high current densities, for example, with 50% and 17% higher charge capacity at 1C in LTO/Li half cells than control samples and commercial electrodes, respectively. Introducing a gel‐polymer electrolyte increases cell durability, safety, and thermal stability. Cyclability test at of 1C shows a capacity retention as high as 91% after almost 400 cycles (average capacity fade of 0.025% cycle −1 ). Full cells operate from 0 to 60 °C without any additives. Cells stored for 30 min up to 90 °C suffer minor capacity degradation. The possibility to withstand high temperatures and significant flexural deformation enable subjecting these pouch cells to thermoconformable processes. A roof panel with four 25 cm 2 pouch cells is demonstrated. Flammability test shows that the carbon nanotube fibers (CNTF)‐LFP/CNTF‐LTO cells have a 50% lower peak of heat release rate and a much smaller total heat released than control cells with metallic current collector and liquid electrolyte.
Improving Plate Anchor Design with a Keying Flap (2014)

Suction embedded plate anchors have been increasingly applied in deepwater projects because of their efficiency and limited cost. Current industry practice equips the fluke of the anchor with an outwardly rotating keying flap aiming at a reduction of the loss of embedment during keying. However, recent experimental and numerical research has questioned the efficiency of the keying flap currently used in practice because it has demonstrated that the flap does not open during keying as was intended. This paper presents a two-dimensional plain strain large deformation finite-element analysis by assuming the soil as homogenous to investigate the performance of plate anchors equipped with various keying flap designs. The results of the paper agree with previous centrifuge and finite-element analysis that the outwardly keying flap has no effect on the loss of embedment and results in a reduction of the bearing capacity postkeying. The performance of an alternative keying flap design where the flap is rotating inward is also discussed. The new design effectively reduces the loss of embedment during keying and exhibits a bearing capacity higher than the current design.
Sign Inversion in Photopharmacology: Incorporation of Cyclic Azobenzenes in Photoswitchable Potassium Channel Blockers and Openers (2019)

Photopharmacology relies on ligands that change their pharmacodynamics upon photoisomerization. Many of these ligands are azobenzenes that are thermodynamically more stable in their elongated trans-configuration. Often, they are biologically active in this form and lose activity upon irradiation and photoisomerization to their cis-isomer. Recently, cyclic azobenzenes, so-called diazocines, have emerged, which are thermodynamically more stable in their bent cis-form. Incorporation of these switches into a variety of photopharmaceuticals could convert dark-active ligands into dark-inactive ligands, which is preferred in most biological applications. This "pharmacological sign-inversion" is demonstrated for a photochromic blocker of voltage-gated potassium channels, termed CAL, and a photochromic opener of G protein-coupled inwardly rectifying potassium (GIRK) channels, termed CLOGO.
A remote cancelable palmprint authentication protocol based on multi‐directional two‐dimensional PalmPhasor‐fusion (2013)

ABSTRACT Biometric template security and privacy issues are critical in biometric authentication systems and require special attention. However, remote biometric authentication systems demand wider array of measures for maximum protection. This paper proposes a remote cancelable palmprint authentication protocol based on multi‐directional two‐dimensional PalmPhasor‐fusion. The main contribution is three‐fold. First, with a transposition direction selection mechanism, multi‐directional two‐dimensional PalmPhasor (MTDPP) improves the accuracy performance of two‐dimensional PalmPhasor. Second, we provide the theoretical analysis of the effect of transposition on the accuracy performance of two‐dimensional PalmPhasor, and hence establish an effective transposition direction range for the proposed MTDPP. Third, according to our analysis, the existing remote palmprint authentication system does not satisfy non‐invertibility criterion of secure template protection and is vulnerable to interception. Besides, secret message embedding as a countermeasure for database attacks deteriorates accuracy performance and causes inconvenience in updating authenticator. The proposed protocol uses multi‐directional two‐dimensional PalmPhasor‐fusion, one‐time random number encrypted with asymmetric cryptography and encrypted hash codes of MTDPP to address the problems. Copyright © 2013 John Wiley &amp; Sons, Ltd.
Agrin-Matrix Metalloproteinase-12 axis confers a mechanically competent microenvironment in skin wound healing (2021)

An orchestrated wound healing program drives skin repair via collective epidermal cell proliferation and migration. However, the molecular determinants of the tissue microenvironment supporting wound healing remain poorly understood. Herein we discover that proteoglycan Agrin is enriched within the early wound-microenvironment and is indispensable for efficient healing. Agrin enhances the mechanoperception of keratinocytes by augmenting their stiffness, traction stress and fluidic velocity fields in retaliation to bulk substrate rigidity. Importantly, Agrin overhauls cytoskeletal architecture via enhancing actomyosin cables upon sensing geometric stress and force following an injury. Moreover, we identify Matrix Metalloproteinase-12 (MMP12) as a downstream effector of Agrin's mechanoperception. We also reveal a promising potential of a recombinant Agrin fragment as a bio-additive material that assimilates optimal mechanobiological and pro-angiogenic parameters by engaging MMP12 in accelerated wound healing. Together, we propose that Agrin-MMP12 pathway integrates a broad range of mechanical stimuli to coordinate a competent skin wound healing niche.
Cardiovascular Protection by Angiotensin-Converting Enzyme 2: A New Paradigm (2008)

A novel angiotensin-converting enzyme (ACE) homolog, named ACE2, was recently described. ACE2 degrades Ang II, a peptide with vasoconstrictive and proliferative effects, to generate Ang-(1-7), which, acting through its receptor Mas, exerts vasodilatory and antiproliferative actions. In addition, ACE2 is a multifunctional enzyme and its actions on other vasoactive peptides can also contribute to its vasoactive effects. The discovery of ACE2 corroborates the establishment of two counter-regulatory arms within the renin-angiotensin system. The first arm is formed by the classical pathway involving the ACE-Ang II-AT(1)-receptor axis, and the second arm is constituted by the ACE2-Ang-(1-7)-Mas-receptor axis. Owing to its characteristics, the ACE2-Ang-(1-7)-Mas axis may represent new possibilities for developing novel therapeutic strategies for the treatment of hypertension and cardiovascular diseases. In this review, we will summarize the biochemical and pathophysiological aspects of ACE2 with particular focus on its role in the heart.
A review of the auditory-gut-brain axis (2023)

Hearing loss places a substantial burden on medical resources across the world and impacts quality of life for those affected. Further, it can occur peripherally and/or centrally. With many possible causes of hearing loss, there is scope for investigating the underlying mechanisms involved. Various signaling pathways connecting gut microbes and the brain (the gut-brain axis) have been identified and well established in a variety of diseases and disorders. However, the role of these pathways in providing links to other parts of the body has not been explored in much depth. Therefore, the aim of this review is to explore potential underlying mechanisms that connect the auditory system to the gut-brain axis. Using select keywords in PubMed, and additional hand-searching in google scholar, relevant studies were identified. In this review we summarize the key players in the auditory-gut-brain axis under four subheadings: anatomical, extracellular, immune and dietary. Firstly, we identify important anatomical structures in the auditory-gut-brain axis, particularly highlighting a direct connection provided by the vagus nerve. Leading on from this we discuss several extracellular signaling pathways which might connect the ear, gut and brain. A link is established between inflammatory responses in the ear and gut microbiome-altering interventions, highlighting a contribution of the immune system. Finally, we discuss the contribution of diet to the auditory-gut-brain axis. Based on the reviewed literature, we propose numerous possible key players connecting the auditory system to the gut-brain axis. In the future, a more thorough investigation of these key players in animal models and human research may provide insight and assist in developing effective interventions for treating hearing loss.
Adolescent to young adult longitudinal development of subcortical volumes in two European sites with four waves (2021)

Abstract Adolescent subcortical structural brain development might underlie psychopathological symptoms, which often emerge in adolescence. At the same time, sex differences exist in psychopathology, which might be mirrored in underlying sex differences in structural development. However, previous studies showed inconsistencies in subcortical trajectories and potential sex differences. Therefore, we aimed to investigate the subcortical structural trajectories and their sex differences across adolescence using for the first time a single cohort design, the same quality control procedure, software and a general additive mixed modeling approach. We investigated two large European sites from ages 14 to 24 with 503 participants and 1408 total scans from France and Germany as part of the IMAGEN project including four waves of data acquisition. We found significantly larger volumes in males versus females in both sites and across all seven subcortical regions. Sex differences in age-related trajectories were observed across all regions in both sites. Our findings provide further evidence of sex differences in longitudinal adolescent brain development of subcortical regions and thus might eventually support the relationship of underlying brain development and different adolescent psychopathology in boys and girls.
Analyzing High-Resolution Clouds and Convection using Multi-Channel VAEs (2021)

Understanding the details of small-scale convection and storm formation is crucial to accurately represent the larger-scale planetary dynamics. Presently, atmospheric scientists run high-resolution, storm-resolving simulations to capture these kilometer-scale weather details. However, because they contain abundant information, these simulations can be overwhelming to analyze using conventional approaches. This paper takes a data-driven approach and jointly embeds spatial arrays of vertical wind velocities, temperatures, and water vapor information as three "channels" of a VAE architecture. Our "multi-channel VAE" results in more interpretable and robust latent structures than earlier work analyzing vertical velocities in isolation. Analyzing and clustering the VAE's latent space identifies weather patterns and their geographical manifestations in a fully unsupervised fashion. Our approach shows that VAEs can play essential roles in analyzing high-dimensional simulation data and extracting critical weather and climate characteristics.
Motion Control for Piezoelectric-Actuator-Based Surgical Device Using Neural Network and Extended State Observer (2019)

This paper presents a robust neural network with an extended state observer control methodology for a piezoelectric-actuator-based surgical device. This control methodology is proposed for tracking of desired motion trajectories in the presence of unknown or uncertain system parameters, nonlinearities including friction, hysteresis, and disturbances in the motion system. In particular, the radial basis function neural network, which serves as a function approximator, aims to create a model for an unknown function to find a relationship between input and output data. An extended state observer is utilized to assist in canceling disturbances and uncertainties of the system dynamically. The stability of the control approach is analyzed. The convergence of position and velocity tracking errors is proven theoretically. Experiments are conducted to demonstrate that the performance with an improved accuracy can be attained by the proposed control scheme. With the motion tracking capability, the control methodology helps the novel surgical device achieve higher success rate in operation, which is also suitable for similar piezoelectric ultrasonic actuator applications.