gebhart/patrepeval huggingface dataset:
Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022 (2023)

Abstract This article describes the first detections of disease due to natural infection with highly pathogenic avian influenza virus (HPAIv) H5N1 of the Eurasian lineage goose/Guangdong clade 2.3.4.4b in wild terrestrial mammals throughout the United States during 2021-2022. Affected mammalian species include 50 red foxes ( Vulpes vulpes ), 6 striped skunks ( Mephitis mephitis ), 4 raccoons ( Procyon lotor ), 2 bobcats ( Lynx rufus ), 2 Virginia opossums ( Didelphis virginiana ), 1 coyote ( Canis latrans ), 1 fisher ( Pekania pennanti ), and 1 gray fox ( Urocyon cinereoargenteus ). Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.
Microglia changes associated to Alzheimer's disease pathology in aged chimpanzees (2018)

In Alzheimer's disease (AD), the brain's primary immune cells, microglia, become activated and are found in close apposition to amyloid beta (Aβ) protein plaques and neurofibrillary tangles (NFT). The present study evaluated microglia density and morphology in a large group of aged chimpanzees (n = 20, ages 37-62 years) with varying degrees of AD-like pathology. Using immunohistochemical and stereological techniques, we quantified the density of activated microglia and morphological variants (ramified, intermediate, and amoeboid) in postmortem chimpanzee brain samples from prefrontal cortex, middle temporal gyrus, and hippocampus, areas that show a high degree of AD pathology in humans. Microglia measurements were compared to pathological markers of AD in these cases. Activated microglia were consistently present across brain areas. In the hippocampus, CA3 displayed a higher density than CA1. Aβ42 plaque volume was positively correlated with higher microglial activation and with an intermediate morphology in the hippocampus. Aβ42-positive vessel volume was associated with increased hippocampal microglial activation. Activated microglia density and morphology were not associated with age, sex, pretangle density, NFT density, or tau neuritic cluster density. Aged chimpanzees displayed comparable patterns of activated microglia phenotypes as well as an association of increased microglial activation and morphological changes with Aβ deposition similar to AD patients. In contrast to human AD brains, activated microglia density was not significantly correlated with tau lesions. This evidence suggests that the chimpanzee brain may be relatively preserved during normal aging processes but not entirely protected from neurodegeneration as previously assumed.
Antiarrhythmic efficacy, clinical electrophysiology, and pharmacokinetics of 3-methoxy-O-desmethyl encainide (MODE) in patients with inducible ventricular tachycardia or fibrillation. (1989)

In most patients, the clinical effects of therapy with encainide are mediated by the generation of the active metabolites O-desmethyl encainide and 3-methoxy-O-desmethyl encainide (MODE). Data from in vitro and animal studies have indicated that MODE has electrophysiologic and pharmacokinetic features that make its further evaluation desirable; in earlier studies, we found that MODE suppressed chronic high-frequency nonsustained ventricular arrhythmias at plasma concentrations of 50-160 ng/ml. We now report the clinical electrophysiology, antiarrhythmic activity, and pharmacokinetics of MODE in 17 patients with inducible ventricular tachyarrhythmias (VTs) in whom programmed electrical stimulation was performed before drug administration and after one or two sequences of loading and maintenance infusions of MODE. Because the relation between plasma concentration and effect had been incompletely defined, a dose-titration approach was adopted: available pharmacokinetic data were used to construct loading and maintenance infusion regimens that were predicted to attain low plasma concentrations in initial patients while higher infusion rates were evaluated in subsequent patients. MODE prevented VT induction in three of 17 patients and VT cycle length was increased by greater than or equal to 100 msec in a further seven of 17; most responses to MODE occurred at plasma concentrations greater than 556 ng/ml (greater than 1 SD above mean plasma MODE during encainide therapy). Response to MODE did not predict subsequent response to oral therapy with encainide. MODE increased intracardiac conduction times, QT intervals during atrial and ventricular pacing, and right ventricular effective refractory periods (RVERP); changes in RVERP were most prominent at rapid pacing rates, while changes in intracardiac conduction were rate-independent at cycle lengths between 400 and 600 msec. Plasma MODE concentrations measured during electrophysiology study correlated well with those predicted by the pharmacokinetic simulations (r = 0.91, p less than 0.001). Serial plasma sampling after programmed electrical stimulation indicated a minimum MODE elimination half-life of 8.2 +/- 5.4 hours. Side effects were confined to three instances of asymptomatic conduction system depression in subjects with latent conduction system disturbances. We conclude that MODE slows intracardiac conduction, delays repolarization, and can suppress or substantially modify inducible VT. Moreover, it was only with the adoption of the dose-titration strategy that we were able to safely demonstrate that plasma MODE concentrations higher than those routinely observed during encainide therapy were required to substantially alter cardiac electrophysiology.
A role for bacterial urease in gut dysbiosis and Crohn’s disease (2017)

Gut dysbiosis during inflammatory bowel disease involves alterations in the gut microbiota associated with inflammation of the host gut. We used a combination of shotgun metagenomic sequencing and metabolomics to analyze fecal samples from pediatric patients with Crohn's disease and found an association between disease severity, gut dysbiosis, and bacterial production of free amino acids. Nitrogen flux studies using <sup>15</sup>N in mice showed that activity of bacterial urease, an enzyme that releases ammonia by hydrolysis of host urea, led to the transfer of murine host-derived nitrogen to the gut microbiota where it was used for amino acid synthesis. Inoculation of a conventional murine host (pretreated with antibiotics and polyethylene glycol) with commensal <i>Escherichia coli</i> engineered to express urease led to dysbiosis of the gut microbiota, resulting in a predominance of Proteobacteria species. This was associated with a worsening of immune-mediated colitis in these animals. A potential role for altered urease expression and nitrogen flux in the development of gut dysbiosis suggests that bacterial urease may be a potential therapeutic target for inflammatory bowel diseases.
Abstract 17109: Input Impedance Analysis of Pulmonary Hypertension Models Indicates That Monocrotaline and Sugen/hypoxia Induce Mechanically Different Vascular Remodeling (2015)

Introduction: Although complex pulmonary arterial remolding characterizes pulmonary hypertension (PH), the vascular mechanics has been evaluated by the static pressure-flow relationship (resistance, R) ignoring dynamic mechanical properties (compliance, C). We therefore evaluated pulmonary arterial input impedance (Z) capable of identifying not only resistance but also compliance in monocrotaline (MCT) and Sugen/Hypoxia (SuHx) PH models. Methods: In 6 weeks Sprague-Dawley rats, we induced PH by the subcutaneous injection of MCT (60 mg/kg) or Sugen5416 (20 mg/kg) with 3 weeks hypoxia. In anesthetized PH rats, we measured pulmonary artery flow (PAF) and pressure (PAP) at 1000 Hz for 107.52 seconds under irregular pacing. We Fourier transformed both PAF and PAP to derive ensembled power spectra and crosspower spectra and taking their ratio yielded Z. We fitted the 2-element Windkessel model to Z and estimated R and C. Results: MCT and SuHx significantly increased mean PAP (Control: 19.4±2.0, MCT: 31.3±4.0, SuHx: 39.4±6.5 mmHg, p &lt;0.01) and shifted Z upward indicating the increased R (Control: 17.8±3.3, MCT: 71.4±16.3, SuHx: 81.8±18.4 mmHg/ml/sec, p &lt;0.01). MCT and SuHx both decreased C (Control: 2.6±0.4, MCT: 1.5±0.6, SuHx: 0.9±0.2 х10 -3 ml/mmHg, p &lt;0.01). However, the time constant was higher in MCT than in SuHx (Control: 90.7±8.6, MCT: 130.0±21.5, SuHx: 92.6±2.0 msec, p &lt;0.05) (Figure). MCT predominantly remodeled resistance vessels while SuHx remodeled both resistance and compliance vessels. Conclusions: We conclude that the impedance analysis is capable of characterizing how remodeling affects vascular mechanical properties, which are not identifiable if we analyze resistance alone. Hence the impedance analysis is applicable in patients, it may serve as a new tool in functionally analyzing vascular remodeling in PH patients.
Integer programming for optimal reduction of calibration targets (2008)

Abstract Calibration targets are widely used to characterize imaging devices. The question addressed in this article is that of how many surfaces in a calibration target are needed to account for the performance of the whole target. Different to previous research where the problem of reducing calibration charts is addressed independently of the calibration problem; in this article we tackle the reduction question based on the calibration performance. We argue that the outcome of both spectral and colorimetric calibration is dependent on the properties of the cross‐product matrix encompassing the color‐signals. Further, we show that by careful mathematical manipulation it is possible to write the cross‐product matrix as a linear sum of the submatrices corresponding to each individual color signal. This formulation allows us to cast the reduction problem as a quadratic minimization where we ask: given the spectral properties of the available color signals, what is the minimum number of surfaces needed to emulate the global cross‐product matrix. To reduce the number of surfaces we impose an integer constraint on the minimization, where the weight of each surface can only assume a value of 1 or 0. Our results show that around 13 surfaces are sufficient to account of the 24 surfaces of the Macbeth color checker. © 2008 Wiley Periodicals, Inc. Col Res Appl, 33, 212–220, 2008
Automated Podosome Identification and Characterization in Fluorescence Microscopy Images (2013)

Podosomes are cellular adhesion structures involved in matrix degradation and invasion that comprise an actin core and a ring of cytoskeletal adaptor proteins. They are most often identified by staining with phalloidin, which binds F-actin and therefore visualizes the core. However, not only podosomes, but also many other cytoskeletal structures contain actin, which makes podosome segmentation by automated image processing difficult. Here, we have developed a quantitative image analysis algorithm that is optimized to identify podosome cores within a typical sample stained with phalloidin. By sequential local and global thresholding, our analysis identifies up to 76% of podosome cores excluding other F-actin-based structures. Based on the overlap in podosome identifications and quantification of podosome numbers, our algorithm performs equally well compared to three experts. Using our algorithm we show effects of actin polymerization and myosin II inhibition on the actin intensity in both podosome core and associated actin network. Furthermore, by expanding the core segmentations, we reveal a previously unappreciated differential distribution of cytoskeletal adaptor proteins within the podosome ring. These applications illustrate that our algorithm is a valuable tool for rapid and accurate large-scale analysis of podosomes to increase our understanding of these characteristic adhesion structures.
Research on key technologies in multiview video and interactive multiview video streaming (2011)

Emerging video applications are being developed where multiple views of a scene are captured. Two central issues in the deployment of future multiview video (MVV) systems are compression efficiency and interactive video experience, which makes it necessary to develop advanced technologies on multiview video coding (MVC) and interactive multiview video streaming (IMVS). The former aims at efficient compression of all MVV data in a ratedistortion (RD) optimal manner by exploiting both temporal and inter-view redundancy, while the latter offers a viewer the ability to freely interact with MVV data, such that she can periodically request her desired viewpoint as the video is played back. Based on the observation that MVC and IMVS are fundamentally different MVV problems, in this thesis, we focus on developing different algorithms for practical MVC and IMVS designs.The first part of the thesis focuses on our research works on MVC. We first develop projective rectification-based view interpolation and extrapolation methods and apply them to MVC. Experimental results show that these schemes can achieve better RD performance than the current joint multiview video coding (JMVC) standard as well as view interpolation and extrapolation-based MVC schemes without using rectification. To explain the experimental results, we also develop mathematical models for the rectification-based view interpolation and extrapolation, from which we develop an improved theoretical model to compare the performances of various MVC schemes. Simulation results can verify the experimental results very well. In the second part of the thesis, we propose three major technological improvements to existing IMVS works to enhance its interactivity experience and implement it in a realistic network condition. First, in addition to camera-captured views, we make available additional virtual views between each pair of captured views for viewers’ selection, by transmitting both texture and depth maps of neighboring captured views and synthesizing intermediate views at decoder using depth-based image rendering (DIBR). Second, we construct a Markovian view-switching model that more accurately captures viewers’ behaviors. Third, we optimize frame structures and schedule the transmission of frames in a network-delay-cognizant manner, so that viewers can enjoy zero-delay view-switching even over transmission network with non-negligible network delay.
Novel spectral similarity measure for high resolution urban scenes (2012)

Spectral similarity measures can differentiate subtle differences between spectral footprints extracted from remotely sensed images. Prior research on urban scenes examined low-to-medium resolution images where many details of an urban scene are lost. For high spatial resolution imagers, a number of problems arise in the analysis of urban scenes since virtually all objects are resolved. Issues of spatially varying scene illumination and unavailability of surface reflectance data prevent classical spectral similarity measures from being extensively applied. Commonly used measures have limitations from a feature space perspective such as favoring either spectral direction or spectral magnitude. In this paper, a novel spectral similarity measure based on Mahalanobis distance is proposed to take into account the unique properties of high resolution urban scenes. A simplified radiometric transfer model is also incorporated. The results confirm the advantage of the new spectral similarity measure when applied to complex urban images.
Iron Fluoride–Carbon Nanocomposite Nanofibers as Free‐Standing Cathodes for High‐Energy Lithium Batteries (2018)

Abstract The development of low‐cost, high‐energy cathodes from nontoxic, broadly available resources is a big challenge for the next‐generation rechargeable lithium or lithium‐ion batteries. As a promising alternative to traditional intercalation‐type chemistries, conversion‐type metal fluorides offer much higher theoretical capacity and energy density than conventional cathodes. Unfortunately, these still suffer from irreversible structural degradation and rapid capacity fading upon cycling. To address these challenges, here a versatile and effective strategy is harnessed for the development of metal fluoride–carbon (C) nanocomposite nanofibers as flexible, free‐standing cathodes. By taking iron trifluoride (FeF 3 ) as a successful example, assembled FeF 3 –C/Li cells with a high reversible FeF 3 capacity of 550 mAh g −1 at 100 mA g −1 (three times that of traditional cathodes, such as lithium cobalt oxide, lithium nickel cobalt aluminum oxide, and lithium nickel cobalt manganese oxide) and excellent stability (400+ cycles with little‐to‐no degradation) are demonstrated. The promising characteristics can be attributed to the nanoconfinement of FeF 3 nanoparticles, which minimizes the segregation of Fe and LiF upon cycling, the robustness of the electrically conductive C network and the prevention of undesirable reactions between the active material and the liquid electrolyte using the composite design and electrolyte selection.
Carbonic anhydrase membranes for carbon capture and storage (2022)

Carbonic anhydrase (CA) based membranes with unique biological activities have been widely explored for carbon capture and storage (CCS), owing to their high efficiency, easy operation, low energy requirement, and environmental sustainability. However, limitations of CA enzymes, such as low thermal stabilities, narrow optimum pH ranges, and difficulties in recovery from reaction media, hinder its practical applications. Consequently, combining its enzymatic activity with membrane technologies for industrial uses is an attractive strategy. This current review explores a variety of immobilization approaches and summarizes the mechanistic features of enzymatic membranes in CO2 capture. Immobilized enzymes can be recycled to reduce process costs and improve the CO2 permeability and selectivity of the membranes. This makes enzymatic membranes attractive for CCS. The study also summarizes the structure, synthesis, and applications of a variety of CA analogues to demonstrate their advantages compared with natural CA. CA analogues hold promise for industrial and biomimetic applications.
Model-Based Multiscale Gigapixel Image Formation Pipeline on GPU (2016)

We present an efficient and flexible GPU implementation of a highly-parallelizable and scalable image formation pipeline for gigapixel images based on the MapReduce framework. The presented implementation was developed to operate with the AWARE multiscale gigapixel cameras, but it is also able to efficiently form gigapixel images from any source. The AWARE cameras are compact camera arrays that simultaneously collect images that span a wide field-of-view to generate high-resolution and high dynamic range panoramic images and video. The proposed GPU implementation exploits the mutiscale nature of the AWARE image acquisition, not only enabling the fast composition of gigapixel-scale panoramas, but also the rapid formation of images of arbitrary portions of the field-of-view at current display-scale resolutions at video rates.
Compact free-space optical programmable logic array (1988)

To implement a parallel optical digital computer, in addition to the two variables, multiple variable optical logic gates are needed. One way to implement a generalized multiple variable optical logic device is to use an optical programmable logic array. We propose a new method to realize a medium scale, compact, and free-space optical programmable logic array. Using either a 2-D or an array of 1-D optical spatial light modulators inside a lens-based multiple-beam path cavity, an array of optical multiple variable logic product (AND gate) term is generated. This device, together with a programmable multiple variable logic OR matrix, can be used to implement any Boolean combinatorial logic operations. For an optical binary combinatorial logic computation, the proposed methods efficiently use 3-D space and optical elements. Preliminary experimental results obtained using an inexpensive liquid-crystal TV are included.
<title>Evaluation of real-time acoustical holography for breast imaging and biopsy guidance</title> (1999)

Ultrasound is an attractive modality for adjunctive characterization of certain breast lesions, but it is not considered specific for cancer and it is not recommended for screening. An imaging technique remarkably different from pulse-echo ultrasound, termed Optical Sonography<SUP>TM</SUP> (Advanced Diagnostics, Inc.), uses the through-transmission signal. The method was applied to breast examinations in 41 asymptomatic and symptomatic women ranging in age from 18 to 83 years to evaluate this imaging modality for detection and characterization of breast disease and normal tissue. This approach uses coherent sound and coherent light to produce real-time, large field-of-view images with pronounced edge definition in soft tissues of the body. The system patient interface was modified to improve coupling to the breast and bring the chest wall to within 3 cm of the sound beam. System resolution (full width half maximum of the line-spread function) was 0.5 mm for a swept-frequency beam centered at 2.7 MHz. Resolution degrades slightly in the periphery of the very large 15.2-cm field of view. Dynamic range of the reconstructed 'raw' images (no post processing) was 3000:1. Included in the study population were women with dense parenchyma, palpable ductal carcinoma in situ with negative mammography, superficial and deep fibroadenomas, and calcifications. Successful breast imaging was performed in 40 of 41 women. These images were then compared with images generated using conventional X-ray mammography and pulse-echo ultrasound. Margins of lesions and internal textures were particularly well defined and provided substantial contrast to fatty and dense parenchyma. In two malignant lesions, Optical Sonography<SUP>TM</SUP> appeared to approximate more closely tumor extent compared to mammography than pulse-echo sonography. These preliminary studies indicate the method has unique potential for detecting, differentiating, and guiding the biopsy of breast lesions using real-time acoustical holography.
Microfluidic jet injection for delivering macromolecules into cells (2013)

We present a microfluidic based injection system designed to achieve intracellular delivery of macromolecules by directing a picoliter-jet of a solution towards individual cells. After discussing the concept, we present design specification and criteria, elucidate performance and discuss results. The method has the potential to be quantitative and high throughput, overcoming limitations of current intracellular delivery protocols.