gebhart/patrepeval huggingface dataset:
Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles (2023)

Abstract Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single molecule or single particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during FRET analysis in the presence of a significant donor-only fraction. To address this problem, we combined particle localization with phasor-based FLIM analysis. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (standard deviation &lt;5% for a 4 ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in sub diffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme (IN) in viral particles, and conclude that eGFP, mTurquoise2 and mScarlet perform best. Finally, for viral particles co-expressing FRET-donor/acceptor labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities. Why it matters Phasor-FLIM is an extraordinarily popular tool for fluorescence lifetime imaging analysis. However, it remains susceptible for low signal intensities, operational challenges and therefore required informed users and a clear analysis understanding. In this work we developed a convenient all-graphical workflow for quantitative phasor-FLIM in heterogenous and low-signal samples and applied it to quantifying absolute FRET efficiencies from protein-protein interactions inside single viral particles. Moreover, containing a well-illustrated theoretical introduction to time-domain phasor-FLIM, our paper helps novice users to correctly implement phasor-FLIM in standard microscopy practice.
A COMPACT PLANAR HEXA-BAND INTERNAL ANTENNA FOR MOBILE PHONE (2010)

A planar hexa-band internal antenna designed for mobile phone applications is presented. The antenna occupying a small area of 45 12 mm 2 is placed on the top no-ground portion of the system circuit board with a ground-plane size of 45 100 mm 2 . The design begins with constructing a meandered monopole. With a parasitic and an impedance-adjustment structure subsequently added, the resulting antenna can be viewed as a printed planar inverted-F antenna with a parasitic resonant element. Two wide impedance bands can be generated by the designed antenna to support GSM 850, GSM 900, DCS, PCS, UMTS, and 2.4-GHz WLAN operations. The measurement was found to agree reasonably well with the simulation. Design procedures and rules along with the design concepts behind are all presented in detail.
Multistress endurance characterization of EPR cable models (2002)

The results of life tests performed on EPR cable models aged by combined thermal-electrical stresses are reported, showing electrical and thermal life lines, intersections of the life surface with the planes at constant stress. The Combined Analysis Method (CAM) is used to obtain more information on the behavior of the tested cable in a wide voltage and temperature range. Parameters useful for insulation characterization and cable design are derived.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Warm starting the projected Gauss-Seidel algorithm for granular matter simulation (2015)

The effect on the convergence of warm starting the projected Gauss-Seidel solver for nonsmooth discrete element simulation of granular matter are investigated. It is found that the computational performance can be increased by a factor 2 to 5.
Isavuconazole (BAL4815) Pharmacodynamic Target Determination in an <i>In Vivo</i> Murine Model of Invasive Pulmonary Aspergillosis against Wild-Type and <i>cyp51</i> Mutant Isolates of Aspergillus fumigatus (2013)

Invasive pulmonary aspergillosis (IPA) continues to rise in concert with increasing numbers of immune suppression techniques to treat other medical conditions and transplantation. Despite these advances, morbidity and mortality rates remain unacceptably high. One strategy used to optimize outcomes is antifungal pharmacodynamic (PD) examination. We explored the pharmacodynamics of a new triazole in development, isavuconazole, in a murine neutropenic IPA model. Ten A. fumigatus isolates were used, including four wild-type isolates and six cyp51 mutants. The MIC range was 0.125 to 8 mg/liter. Following infection, groups of mice were treated orally with the prodrug (BAL8557) at 40 to 640 mg/kg/12 h for 7 days. Efficacy was determined by quantitative PCR of lung homogenates. At the start of therapy, mice had 4.97 log10 conidial equivalents (CE)/ml of lung homogenate, and this increased to 6.82 log10 CE/ml of lung homogenate in untreated animals. The infection model was uniformly lethal in untreated control mice. The PD target endpoints examined included the static-dose AUC/MIC ratio and the 1-log10 killing AUC/MIC ratio. A stasis endpoint was achieved for all isolates with an MIC of ≤1 mg/liter and 1-log10 killing in all isolates with an MIC of ≤0.5 mg/liter, regardless of the presence or absence of the cyp51 mutation. The static-dose range was 65 to 617 mg/kg/12 h. The corresponding median free-drug AUC/MIC ratio was near 5. The 1-log10 killing dose range was 147 to 455 mg/kg/12 h, and the corresponding median free-drug AUC/MIC ratio was 11.1. These values are similar to those previously reported for other triazoles.
Incomplete Extrusion of an Acrylic Punctum Plug in a Case of Severe Dry Eye Syndrome (2005)

The peculiarity of this case is the persistence of clinical efficacy of the soft punctum plug even if partially extruded. The patient experienced relief of symptoms that can be compared to the benefits usually obtained with a successfully implanted silicon plug.
Adhesion Forces and Coaggregation between Vaginal Staphylococci and Lactobacilli (2012)

Urogenital infections are the most common ailments afflicting women. They are treated with dated antimicrobials whose efficacy is diminishing. The process of infection involves pathogen adhesion and displacement of indigenous Lactobacillus crispatus and Lactobacillus jensenii. An alternative therapeutic approach to antimicrobial therapy is to reestablish lactobacilli in this microbiome through probiotic administration. We hypothesized that lactobacilli displaying strong adhesion forces with pathogens would facilitate coaggregation between the two strains, ultimately explaining the elimination of pathogens seen in vivo. Using atomic force microscopy, we found that adhesion forces between lactobacilli and three virulent toxic shock syndrome toxin 1-producing Staphylococcus aureus strains, were significantly stronger (2.2-6.4 nN) than between staphylococcal pairs (2.2-3.4 nN), especially for the probiotic Lactobacillus reuteri RC-14 (4.0-6.4 nN) after 120 s of bond-strengthening. Moreover, stronger adhesion forces resulted in significantly larger coaggregates. Adhesion between the bacteria occurred instantly upon contact and matured within one to two minutes, demonstrating the potential for rapid anti-pathogen effects using a probiotic. Coaggregation is one of the recognized mechanisms through which lactobacilli can exert their probiotic effects to create a hostile micro-environment around a pathogen. With antimicrobial options fading, it therewith becomes increasingly important to identify lactobacilli that bind strongly with pathogens.
Integrative Genomic Analysis Reveals Four Protein Biomarkers for Platelet Traits (2020)

We identified 4 proteins that are causally linked to PLTs. These proteins may also have roles in the pathogenesis of CVD via a platelet/blood coagulation-based mechanism.
Transport Properties of Monolayer MoS<sub>2</sub> Grown by Chemical Vapor Deposition (2014)

Recent success in the growth of monolayer MoS2 via chemical vapor deposition (CVD) has opened up prospects for the implementation of these materials into thin film electronic and optoelectronic devices. Here, we investigate the electronic transport properties of individual crystallites of high quality CVD-grown monolayer MoS2. The devices show low temperature mobilities up to 500 cm(2) V(-1) s(-1) and a clear signature of metallic conduction at high doping densities. These characteristics are comparable to the electronic properties of the best mechanically exfoliated monolayers in literature, verifying the high electronic quality of the CVD-grown materials. We analyze the different scattering mechanisms and show that the short-range scattering plays a dominant role in the highly conducting regime at low temperatures. Additionally, the influence of optical phonons as a limiting factor is discussed.
Investigation of the Interaction of Sprays from Clustered Orifices under Ambient Conditions Relevant for Diesel Engines (2008)

&lt;div class="htmlview paragraph"&gt;The objective of this research is to investigate the behavior of interacting sprays, so-called spray clusters, under typical Diesel combustion conditions. Visualizations and Phase-Doppler Anemometry are employed to characterize the macro- and microscopic spray properties. A significant effect of the cluster geometry on spray formation is noticed. Direct spray-spray interaction is found in all cases, with varying intensity depending on the included angle of the orifices within a cluster. The sprays from all investigated cluster nozzles penetrated significantly slower than those of a comparable conventional nozzle. The stability of the sprays is found to be very sensitive to the orientation of the cluster. Depending on this parameter the sprays from one cluster penetrate very similar or exhibit significant instabilities, especially at lower injection pressures.&lt;/div&gt;
Peripheral Immune Cell Gene Expression Predicts Survival of Patients with Non-Small Cell Lung Cancer (2012)

Prediction of cancer recurrence in patients with non-small cell lung cancer (NSCLC) currently relies on the assessment of clinical characteristics including age, tumor stage, and smoking history. A better prediction of early stage cancer patients with poorer survival and late stage patients with better survival is needed to design patient-tailored treatment protocols. We analyzed gene expression in RNA from peripheral blood mononuclear cells (PBMC) of NSCLC patients to identify signatures predictive of overall patient survival. We find that PBMC gene expression patterns from NSCLC patients, like patterns from tumors, have information predictive of patient outcomes. We identify and validate a 26 gene prognostic panel that is independent of clinical stage. Many additional prognostic genes are specific to myeloid cells and are more highly expressed in patients with shorter survival. We also observe that significant numbers of prognostic genes change expression levels in PBMC collected after tumor resection. These post-surgery gene expression profiles may provide a means to re-evaluate prognosis over time. These studies further suggest that patient outcomes are not solely determined by tumor gene expression profiles but can also be influenced by the immune response as reflected in peripheral immune cells.
Optimizing mix-zone coverage in pervasive wireless networks (2013)

Location privacy is a major concern in pervasive networks where static device identifiers enable malicious eavesdroppers to continuously track users and their movements. In order to prevent such identifier-based tracking, devices could coordinate regular identifier change operations in special areas called mix-zones. Although mix-zones provide spatio-temporal de-correlation between old and new identifiers, depending on the position of the mix-zone, identifier changes can generate a substantial inconvenience (or “cost”) to the users in terms of lost communications and increased energy consumption. In this paper, we address this trade-off between privacy and cost by studying the problem of determining an optimal set of mix-zones such that the degree of mixing in the network is maximized and the overall network-wide mixing cost is minimized. We follow a graph-theoretic approach and model the optimal mixing problem as a generalization of the vertex cover problem, called the Mix Cover (MC) problem. We propose three approximation algorithms for the MC problem and derive a lower bound on the solution quality guaranteed by them. Additionally, we outline two other heuristics for solving the MC problem. These heuristics are simple, but do not provide any guarantees on the solution quality. By means of extensive empirical evaluation using real data, we compare the performance and solution quality of these algorithms. The combinatorics-based approach used in this work enables us to study the feasibility of determining optimal mix-zones regularly and under dynamic network conditions.
RNA structures and dynamics with Å resolution revealed by x-ray free electron lasers (2023)

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free electron laser sources to reveal the formation and ready identification of Å scale features in structured and unstructured RNAs. New structural signatures of RNA secondary and tertiary structures are identified through wide angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base paired intermediate to assume a triple helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. In addition to understanding how RNA triplexes form and thereby function as dynamic signaling elements, this new method can vastly increase the rate of structure determination for these biologically essential, but mostly uncharacterized macromolecules.
The Acid Sphingomyelinase/Ceramide Pathway: Biomedical Significance and Mechanisms of Regulation (2010)

One of the most intriguing enzymes of sphingolipid biology is acid sphingomyelinase (ASMase). In a phospholipase C reaction, ASMase catalyzes the cleavage of the phosphocholine head group of sphingomyelin to generate ceramide. Cumulative efforts of various laboratories over the past 40 years have placed ASMase and its product ceramide at the forefront of lipid research. Activation of the ASMase/ceramide pathway is a shared response to an ever-growing list of receptor and non-receptor mediated forms of cellular stress including: death ligands (TNFalpha, TRAIL, Fas ligand), cytokines (IL-1, IFNgamma), radiation, pathogenic infections, cytotoxic agents and others. The strategic role of ASMase in lipid metabolism and cellular stress response has sparked interest in investigatig the molecular mechanisms underlying ASMase activation. In this article, we review the translational role of the ASMase/ceramide pathway and recent advances on its mechanisms of regulation.
Anomalous activity classification in the distributed camera network (2008)

Unlike existing methods that used the human actions or trajectories to analyze the human activity in overlapping field-of-views, this paper proposes the appearance and travel time-based human activity classification in the camera network of non-overlapping field-of-views. The mixture of Gaussian-based appearance similarity model incorporates the appearance variance between different cameras to address changes in varying lighting conditions. To address the problem of limited labeled training data, we propose the use of semi-supervised expectation-maximization algorithm for activity classification. The human activities observed in a simulated camera network with nine cameras and twenty-five nodes are classified into one normal and three anomalous classes. A similar camera network is built and tested in real-life experiments, in which the proposed approach achieves satisfactory performance.
Multicellular Reservoir Computing (2022)

A bstract The capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However, single cell engineering is limited by the necessary molecular complexity and the accompanying metabolic burden of synthetic circuits. To overcome these limitations, synthetic biologists have begun engineering multicellular systems that combine cells with designed subfunctions. To further advance information processing in synthetic multicellular systems, we introduce the application of reservoir computing. Reservoir computers (RCs) approximate a temporal signal processing task via a fixed-rule dynamic network (the reservoir) with a regression-based readout. Importantly, RCs eliminate the need of network rewiring, as different tasks can be approximated with the same reservoir. Previous work has already demonstrated the capacity of single cells, as well as populations of neurons, to act as reservoirs. In this work, we extend reservoir computing in multicellular populations with the widespread mechanism of diffusion-based cell-cell signaling. As a proof-of-concept, we simulated a reservoir made of a 3D community of cells communicating via diffusible molecules and used it to approximate two benchmark signal processing tasks, computing median and parity functions from binary input signals. We demonstrate that a diffusion-based multicellular reservoir is a feasible synthetic framework for performing complex temporal computing tasks that provides a computational advantage over single cell reservoirs. We also identified a number of biological properties that can affect the computational performance of these processing systems.
Direction-Adaptive Partitioned Block Transform for Color Image Coding (2010)

The direction-adaptive partitioned block transform (DA-PBT) is proposed to exploit the directional features in color images to improve coding performance. Depending on the directionality in an image block, the transform either selects one of the eight directional modes or falls back to the nondirectional mode equivalent to the conventional 2-D DCT. The selection of a directional mode determines the transform direction that provides directional basis functions, the block partitioning that spatially confines the high-frequency energy, the scanning order that arranges the transform coefficients into a 1-D sequence for efficient entropy coding, and the quantization matrix optimized for visual quality. The DA-PBT can be incorporated into image coding using a rate-distortion optimized framework for direction selection, and can therefore be viewed as a generalization of variable blocksize transforms with the inclusion of directional transforms and nonrectangular partitions. As a block transform, it can naturally be combined with block-based intra or inter prediction to exploit the directionality remaining in the residual. Experimental results show that the proposed DA-PBT outperforms the 2-D DCT by more than 2 dB for test images with directional features. It also greatly reduces the ringing and checkerboard artifacts typically observed around directional features in images. The DA-PBT also consistently outperforms a previously proposed directional DCT. When combined with directional prediction, gains are less than additive, as similar signal properties are exploited by the prediction and the transform. For hybrid video coding, significant gains are shown for intra coding, but not for encoding the residual after accurate motion-compensated prediction.
Transient photoconductivity responses in amorphous In-Ga-Zn-O films (2012)

We studied the photoconductivity responses in amorphous In-Ga-Zn-O (a-IGZO) films using a time-resolved microwave photoconductivity decay (μ-PCD) technique. The a-IGZO film characteristics are correlated with three components in the photoconductivity response: the peak value and two decay constants. The peak value originated from the density of the photo-generated free carriers through carrier generation and recombination processes during laser pulse irradiation. Power law characteristics indicated that the peak values are attributed to recombination process related to the exponential distribution of the conduction band tail states. After the laser pulse was turned off, the reflectivity signal decreased rapidly, indicating fast recombination of the photo-generated carriers. This fast decay component is suggested to be related to the recombination processes through the deep level states. Following the fast decay, a slow decay with a decay constant on the order of microseconds appeared. This slow decay was attributed to the reemission of trapped carriers with an activation energy of ∼0.2 eV. In addition, both the fast and slow decays for the wet annealed a-IGZO film were longer than those of the as-deposited a-IGZO film. The decay constants are considered to reflect the density of the subgap states that act as trapping or recombination centers. The μ-PCD method provides a useful estimation of the film quality, such as the density of the defect states, and the physical properties of electronic devices using a-IGZO films.
Embedded DiCAD linear phase shifter for 57&amp;#x2013;65GHz reconfigurable direct frequency modulation in 90nm CMOS (2009)

A digitally controlled artificial dielectric (DiCAD) differential transmission line is designed to perform agile linear phase shift over 100deg with thermometer-coded 16 step control. It also operates with a 16 gain-step VGA to enable re-configurable and direct-frequency modulation at 60 GHz with 256 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> states (1.1deg angular and 0.0007 magnitude resolutions) and -31 dB static EVM for multiple PSK/QAM modulations. The modulator uses 0.33 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> core area in 90 nm CMOS and consumes 10 mA at 1 V.
In situ synthesis of composite nanowires consisting of metal nanoparticles in ion-exchangeable polymer matrix using porous alumina templates (2012)

One-dimensional (1D) superstructures constructing of inorganic nanoparticles have unique and technologically important potential applications in the areas of nanoelectronics, plasmonics, and molecular sensors. Herein, we describe how nanoporous template and in situ synthetic process can be combined for the construction of composite nanowires consisting of silver nanoparticles dispersed in polymer matrices. We show that, by limiting the space where nanoparticles grow, the silver nanoparticles are encapsulated inward within the polymer nanowires. We also demonstrated that the composite microstructure could be controlled by varying the initial precursor structure, pore size of the template and temperature.