gebhart/patrepeval huggingface dataset:
A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation (2018)

Abstract Bacterial populations that colonize a host can play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. With the use of whole genome sequencing to determine genetic distance between isolates, a common solution to estimate acquisition and clearance rates has been to assume a fixed genetic distance threshold below which isolates are considered to represent the same strain. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we present a fully Bayesian model that provides probabilities of whether two strains should be considered the same, allowing us to determine bacterial clearance and acquisition from genomes sampled over time. Our method explicitly models the within-host variation using population genetic simulation, and the inference is done using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We validate the method with multiple carefully conducted simulations and demonstrate its use in practice by analyzing a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates from a large recently completed longitudinal clinical study. An R-code implementation of the method is freely available at: https://github.com/mjarvenpaa/bacterial-colonization-model.git . Author summary As colonizing bacterial populations are the source for much transmission and a reservoir for infection, they are a major focus of interest clinically and epidemiologically. Understanding the dynamics of colonization depends on being able to confidently identify acquisition and clearance events given intermittent sampling of hosts. To do so, we need a model of within-host bacterial population evolution from acquisition through the time of sampling that enables estimation of whether two samples are derived from the same population. Past efforts have frequently relied on empirical genetic distance thresholds that forgo an underlying model or employ a simple molecular clock model. Here, we present an inferential method that accounts for the timing of sample collection and population diversification, to provide a probabilistic estimate for whether two isolates represent the same colonizing strain. This method has implications for understanding the dynamics of acquisition and clearance of colonizing bacteria, and the impact on these rates by factors such as sensitivity of the sampling method, pathogen genotype, competition with other carriage bacteria, host immune response, and antibiotic exposure.
High Q-Factor All-Dielectric Metasurface Based on Bound States in the Continuum (2019)

We propose a realization of bound states in the continuum (BICs) with metasurfaces. Resonances with theoretically-infinite quality-factors can be achieved in the BIC regime and with up to a few thousand in the near-BIC.
Constrained Geometry Organoactinides as Versatile Catalysts for the Intramolecular Hydroamination/Cyclization of Primary and Secondary Amines Having Diverse Tethered C−C Unsaturation (2007)

A series of "constrained geometry" organoactinide complexes, (CGC)An(NMe)2 (CGC = Me2Si(eta5-Me4C5)(tBuN); An = Th, 1; U, 2), has been prepared via efficient in situ, two-step protodeamination routes in good yields and high purity. Both 1 and 2 are quantitatively converted to the neutrally charged, solvent-free dichlorides (1-Cl2, 2-Cl2) and slightly more soluble diiodides (1-I2, 2-I2) with excess Me3Si-X (X = Cl, I) in non-coordinating solvents. The new complexes were characterized by NMR spectroscopy, elemental analysis, and (for 1 and 2) single-crystal X-ray diffraction, revealing substantially increased metal coordinative unsaturation vs the corresponding Me2SiCp' '2AnR2 (Cp' ' = eta5-Me4C5; An = Th, R = CH2(SiMe3), 3; An = U, R = CH2Ph, 4) and Cp'2AnR2 (Cp' = eta5-Me5C5 ; An = Th, R = CH2(SiMe3), 5; An = U, R = CH2(SiMe3), 6) complexes. Complexes 1-6 exhibit broad applicability for the intramolecular hydroamination of diverse C-C unsaturations, including terminal and internal aminoalkenes (primary and secondary amines), aminoalkynes (primary and secondary amines), aminoallenes, and aminodienes. Large turnover frequencies (Nt up to 3000 h-1) and high regioselectivities (>/=95%) are observed throughout, along with moderate to high diastereoselectivities (up to 90% trans ring closures). With several noteworthy exceptions, reactivity trends track relative 5f ionic radii and ancillary ligand coordinative unsaturation. Reactivity patterns and activation parameters are consistent with a reaction pathway proceeding via turnover-limiting C=C/CC insertion into the An-N sigma-bond.
Analysis of the internal transcribed spacer regions of ribosomal DNA in common airborne allergenic fungi (1997)

Ribosomal DNA internal transcribed spacer (ITS) sequences were investigated in the genera Alternaria, Aspergillus, Cladosporium and Penicillium, to identify regions suitable for the design of genus- and species-specific oligonucleotide probes. The ITS regions of all four genera were quite distinct. However, we discovered that the genera Aspergillus and Penicillium displayed high similarity in most of the ITS2 region. Whilst interspecies similarity within Alternaria and Cladosporium was high in both ITS regions 1 and 2, ITS1 similarity within Aspergillus and Penicillium was lower by comparison. We conclude that: (1) the ITS2 region is highly conserved between Aspergillus and Penicillium, and (2) the ITS1 region will allow for the development of specific probes to distinguish between Aspergillus and Penicillium.
Glidar3DJ: A View-Invariant gait identification via flash lidar data\n correction (2019)

Gait recognition is a leading remote-based identification method, suitable\nfor real-world surveillance and medical applications. Model-based gait\nrecognition methods have been particularly recognized due to their scale and\nview-invariant properties. We present the first model-based gait recognition\nmethodology, $\\mathcal{G}$lidar3DJ using a skeleton model extracted from\nsequences generated by a single flash lidar camera. Existing successful\nmodel-based approaches take advantage of high quality skeleton data collected\nby Kinect and Mocap, for example, are not practicable for applications outside\nthe laboratory. The low resolution and noisy imaging process of lidar\nnegatively affects the performance of state-of-the-art skeleton-based systems,\ngenerating a significant number of outlier skeletons. We propose a rule-based\nfiltering mechanism that adopts robust statistics to correct for skeleton joint\nmeasurements. Quantitative measurements validate the efficacy of the proposed\nmethod in improving gait recognition.\n
Crystallographic, Optical, and Electronic Properties of the Cs2AgBi1–xInxBr6 Double Perovskite: Understanding the Fundamental Photovoltaic Efficiency Challenges (2021)

We present a crystallographic and optoelectronic study of the double perovskite Cs2AgBi1–xInxBr6. From structural characterization we determine that the indium cation shrinks the lattice and shifts the cubic-to-tetragonal phase transition point to lower temperatures. The absorption onset is shifted to shorter wavelengths upon increasing the indium content, leading to wider band gaps, which we rationalize through first-principles band structure calculations. Despite the unfavorable band gap shift, we observe an enhancement in the steady-state photoluminescence intensity, and n-i-p photovoltaic devices present short-circuit current greater than that of neat Cs2AgBiBr6 devices. In order to evaluate the prospects of this material as a solar absorber, we combine accurate absorption measurements with thermodynamic modeling and identify the fundamental limitations of this system. Provided radiative efficiency can be increased and the choice of charge extraction layers are specifically improved, this material could prove to be a useful wide band gap solar absorber.
Using computer‐extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage (2015)

The current results indicate that MRI phenotypes have promise for predicting breast cancer pathologic stage and lymph node status. Cancer 2016;122:748-757. © 2015 American Cancer Society.
A New Gust Generator for a Low Speed Wind Tunnel: Design and Commissioning (2017)

An artificial gust generator system has been developed for the University of Bristol Large low speed Wind Tunnel. This paper covers the design, manufacture, and initial testing. The system comprises two horizontal NACA-0015 gust vanes placed upstream of the working section. Two independent servo-motors are used to simultaneously rotate the vanes causing the airflow to be deflected, resulting in a temporary change in the angle of attack of the free-stream in the working section. The gust vanes are a carbon fibre composite construction, and were designed using FE analysis to place the first natural frequency above the desired maximum operating frequency of 20 Hz. Initial experimental data, collected from a cobra probe, indicates the system is reliably capable of creating gusts with amplitudes up-to 10°. The experimental data is also compared to CFD simulations which were performed as part of the design trade studies. The CFD uses overset meshing methods to accurately model the motion of the gust vanes and the trailing wakes.
High-Resolution Optical Fiber Refractive-Index Tomography using Higher-Order Intensity Derivatives (2013)

A technique that uses higher-order intensity derivatives within partially coherent quantitative phase microscopy is shown to increase the radial resolution of reconstructed optical fiber tomograms to the diffraction limit without introducing additional noise.
A Stiffness Criterion For Cooling Time Estimation (1999)

Abstract The cooling time of an injection molded part directly affects the production cost and efficiency. In order to accurately estimate the cooling time, it is necessary to define the ejection condition. One common criterion for part ejection is when the mean or maximal temperature is equal or less than an estimated ejection temperature, T e [1]. But in industrial practice, the ejection condition is determined by the part's deformation or warpage due to ejection forces and subsequent cooling [2]. This research uses a combination of experimental, analytical, and statistical methods to discuss different ejection criteria and their rationality, thereby developing a more effective criterion based on part stiffness. This stiffness criterion facilitates more accurate estimation of cooling time at early stages of product development. This knowledge will help the designer to improve the design and reduce the cost by increasing the production efficiency while simultaneously ensuring injection molded part quality.
Protein kinase inhibitors flavopiridol and 7-hydroxy-staurosporine down-regulate antiapoptosis proteins in B-cell chronic lymphocytic leukemia (2000)

Compounds that inhibit protein kinases are currently undergoing clinical evaluation for the treatment of a variety of malignancies. The kinase inhibitors flavopiridol and 7 hydroxy-staurosporine (UCN-01) were examined for their effects on B-cell chronic lymphocytic leukemia (B-CLL) cells in vitro (n = 49). Flavopiridol and UCN-01 induced concentration-dependent apoptosis of most B-CLL samples tested, with greater than 50% cell killing occurring at concentrations of less than 1 mcmol/L, and with flavopiridol displaying more potent activity than UCN-01. Flavopiridol (0.1 mcmol/L) and UCN-01 (1 mcmol/L) also induced striking decreases in the levels of the antiapoptosis proteins Mcl-1, X-linked inhibitor of apoptosis (XIAP), and BAG-1 in nearly all cases of B-CLL and of Bcl-2 in approximately half of B-CLL specimens evaluated. In contrast, expression of the proapoptotic proteins Bax and Bak was not significantly influenced by these kinase inhibitors. Flavopiridol-induced decreases in the levels of antiapoptosis proteins Mcl-1 and XIAP preceded apoptosis and were not substantially affected by the addition of caspase inhibitors to cultures. In contrast, UCN-01-stimulated decreases in antiapoptosis proteins were slower, occurred concurrently with apoptosis, and were partially prevented by caspase inhibitors. The findings suggest that flavopiridol and UCN-01 induce apoptosis of B-CLL cells through different mechanisms. The potent apoptotic activities of flavopiridol and UCN-01 against cultured B-CLL cells suggest that they may be effective as single agents in the treatment of B-CLL or for sensitizing B-CLL cells to conventional cytotoxic drugs. (Blood. 2000;96:393-397)
Supplementary Figure 1 from Intratumoral Induction of CD103 Triggers Tumor-Specific CTL Function and CCR5-Dependent T-Cell Retention (2023)

Supplementary Figure 1 from Intratumoral Induction of CD103 Triggers Tumor-Specific CTL Function and CCR5-Dependent T-Cell Retention
Supporting Workplace Detachment and Reattachment with Conversational Intelligence (2018)

Research has shown that productivity is mediated by an individual's ability to detach from their work at the end of the day and reattach with it when they return the next day. In this paper we explore the extent to which structured dialogues, focused on individuals' work-related tasks or emotions, can help them with the detachment and reattachment processes. Our inquiry is driven with SwitchBot, a conversational bot which engages with workers at the start and end of their work day. After preliminarily validating the design of a detachment and reattachment dialogue frame-work with 108 crowdworkers, we study SwitchBot's use in-situ for 14 days with 34 information workers. We find that workers send fewer e-mails after work hours and spend a larger percentage of their first hour at work using productivity applications than they normally would when using SwitchBot. Further, we find that productivity gains were better sustained when conversations focused on work-related emotions. Our results suggest that conversational bots can be effective tools for aiding workplace detachment and reattachment and help people make successful use of their time on and off the job.
Pharmaceutical Nano‐Cocrystals: Sonochemical Synthesis by Solvent Selection and Use of a Surfactant (2010)

Nanopharmaceutics: Sonochemistry and the use of a surfactant (Span-85) was introduced to generate pharmaceutical cocrystals of nanometer-scale dimensions. This method overcomes the inherent solubility difference between the pharmaceutical agent (caffeine in this case) and the cocrystal former (2,4-dihydroxybenzoic acid; see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Pixel2Mesh: 3D Mesh Model Generation via Image Guided Deformation (2020)

In this paper, we propose an end-to-end deep learning architecture that generates 3D triangular meshes from single color images. Restricted by the nature of prevalent deep learning techniques, the majority of previous works represent 3D shapes in volumes or point clouds. However, it is non-trivial to convert these representations to compact and ready-to-use mesh models. Unlike the existing methods, our network represents 3D shapes in meshes, which are essentially graphs and well suited for graph-based convolutional neural networks. Leveraging perceptual features extracted from an input image, our network produces the correct geometry by progressively deforming an ellipsoid. To make the whole deformation procedure stable, we adopt a coarse-to-fine strategy, and define various mesh/surface related losses to capture properties of various aspects, which benefits producing the visually appealing and physically accurate 3D geometry. In addition, our model by nature can be adapted to objects in specific domains, e.g., human faces, and be easily extended to learn per-vertex properties, e.g., color. Extensive experiments show that our method not only qualitatively produces the mesh model with better details, but also achieves the higher 3D shape estimation accuracy compared against the state-of-the-arts.
Determination of intrinsic mid-infrared absorption of a fluoride glass (1991)

The intrinsic mid-infrared optical absorption of a ZrF(4)-BaF(2)-LaF(3)-AlF(3)-NaF (ZBLAN) glass has been determined by combining laser calorimetry and spark-source mass spectrographic analysis. The total optical absorption of four samples of varying purity was measured at 3.9 microm with laser calorimetry. The extrinsic contribution to the total absorption for each glass was calculated from the measured concentration of rare-earth impurity ions and known extinction coefficients. The intrinsic absorption of this glass at 3.9 microm determined from the difference between the total measured absorption and the calculated extrinsic absorption is 6.11 (+/-0.61) x 10(-4) cm(-1).
Principles of magnetic levitation force and motor torque generation by superposition of harmonics in bearingless brushless motors (2009)

In this paper the principles of motor torque and suspension force generation in bearingless brushless motors with high pole numbers are explained, graphically illustrated and analyzed in detail. The necessary harmonic components of the flux density in the air-gap are calculated and it is visualized how these can be generated by superposition of harmonics depending on a specific rotor pole / stator slot ratio. Especially, for bearingless motors with a fractional pole / slot ratio, it is shown how superior suspension performance and high rotational speeds can be achieved. The considerations are exemplified for a 26-pole / 24-slots bearingless brushless motor.
Comparison of planar fluorescence measurements and computational modeling of shock-layer flow (1996)

Planar laser-induced fluorescence is used to image transient and quasisteady flow phenomena associated with an impulsively started supersonic jet incident on a circular cylinder. The transient phenomena observed are consistent with established theoretical work on the development of nozzle flows in a shock tunnel and with well-understood shock reflection processes. The technique is also used to measure the rotational temperature in the jet and in the shock layer on the cylinder after the establishment of quasisteady flow conditions. The inviscid flow between the bow shock and the edge of the boundary layer and the viscous flow within the boundary layer are modeled numerically using an iterative scheme. Good agreement is achieved between the computational and experimental results for most of the imaged field, except for the region near the shock vertex, where flow nonuniformities near the centerline perturb the shock from the shape expected for a uniform incident flow.
Ulnar lengthening in the treatment of Kienböckʼs disease. (1982)

Twenty patients with Kienböck's disease were treated with a modification of the Persson ulnar-lengthening procedure to remove compressive stress from the damaged lunate. After an average follow-up of thirty-seven months, relief of pain was satisfactory in eighteen patients who had returned to work (nine of whom had strenuous occupations), and two patients were dissatisfied because they had persistent pain and were not able to return to their previous occupations. Non-union at the site of the ulnar osteotomy occurred in three patients who were treated early in the series and was the result of inadequate internal fixation or insufficient duration of protective splinting. All three of the patients had satisfactory results after replating and bone-grafting. The procedure appears to help to maintain carpal height, prevent further collapse of the lunate, encourage consolidation of the fragmented lunate, and increase grip strength. Except for ulnar deviation, which the procedure may further diminish, the postoperative motions of the wrist were moderately improved.
HDFx: A Novel Biologic Immuno Modulator for potential Control and Treatment of NK Cell and Macrophage Dysfunction in Drug-Resistant Tuberculosis (2017)

The Madridge Journal of Immunology is an open-access peer-review journal focusing on a qualitative approach to review and publishing papers in all fields of immunology. Readers from underdeveloped economies can even easily access the content without involving monetary issues thus stimulating the research in less privileged regions as well.
Image tiling for a high-resolution helmet-mounted display (2005)

Head-mounted or helmet-mounted displays (HMDs) have long proven invaluable for many military applications. Integrated with head position, orientation, and/or eye-tracking sensors, HMDs can be powerful tools for training. For such training applications as flight simulation, HMDs need to be lightweight and compact with good center-of-gravity characteristics, and must display realistic full-color imagery with eye-limited resolution and large field-of-view (FOV) so that the pilot sees a truly realistic out-the-window scene. Under bright illumination, the resolution of the eye is ~300 &mu;r (1 arc-min), setting the minimum HMD resolution. There are several methods of achieving this resolution, including increasing the number of individual pixels on a CRT or LCD display, thereby increasing the size, weight, and complexity of the HMD; dithering the image to provide an apparent resolution increase at the cost of reduced frame rate; and tiling normal resolution subimages into a single, larger high-resolution image. Physical Optics Corporation (POC) is developing a 5120 × 4096 pixel HMD covering 1500 × 1200 mr with resolution of 300 &mu;r by tiling 20 subimages, each of which has a resolution of 1024 × 1024 pixels, in a 5 × 4 array. We present theory and results of our preliminary development of this HMD, resulting in a 4k × 1k image tiled from 16 subimages, each with resolution 512 × 512, in an 8 × 2 array.
INDIVIDUAL HYDROGEN-BOND LENGTHS IN HYDROGEN-BONDED TRIMERS*** (1988)

A linear trimer such as $Y-(HCN)_{2}$ may be viewed as a composite of the two dimers Y-HCN and HCN-HCN. The trimer formation changes properties of the dimers such as vibrational anplitudes and the center of mass (c.m.) separation r of adjacent monomers. Accurate values for $r_{1}$ and $r_{2}$ are difficult to obtain from the rotational constants of the trimers because the c.m. of the middle monomer is close to the c.m. of the trimer. However, an isotopic substitution method has given us good results in several cases. In linear $(HCN)_{3}$, $r_{1}$ and $r_{2}$ are close to equal, 4.389(10) and 42 401(10) A respectively, both about 0.05 A shorter than the r for the dimer, 4.448 A.2. The overall shrinkage in OC-HCN-HCN is a bit less. 0.083(3) versus 0.106(1) A, but it is highly asymmetric, 0.07(1) A for $r_{1}$ and only 0.010(5) A for $r_{7}$. The figures for N2-HCN-HCN are comparable, an overall shrinkage of 0.075(3) A with 0.065(10) and 0.009(6) A for $r_{1}$ and $r_{2}$ respectively. The results for these and other hydrogen-bonded trimers will be presented and discussed.
Enantiomeric resolution and simulation studies of four enantiomers of 5-bromo-3-ethyl-3-(4-nitrophenyl)-piperidine-2,6-dione on a Chiralpak IA column (2016)

Enantiomeric resolution and simulation studies of four enantiomers of 5-bromo-3-ethyl-3-(4-nitrophenyl)-piperidine-2,6-dione on a Chiralpak IA column were presented.