gebhart/patrepeval huggingface dataset:
Expression of the histidine-rich protein PfHRP1 by knob-positive Plasmodium falciparum is not sufficient for cytoadherence of infected erythrocytes (1988)

Six culture-adapted knob-positive Plasmodium falciparum parasites, four of which were nonbinding in an in vitro cytoadherence assay, were tested for the presence of the knob-associated histidine-rich protein PfHRP1. Two knob-positive, strongly cytoadherence-positive P. falciparum strains from Aotus monkeys were also examined. All parasites expressed PfHRP1, suggesting that it plays a structural or functional role related to knobs but is not by itself sufficient for cytoadherence of P. falciparum-infected erythrocytes.
A Novel Three-Dimensional Immune Oncology Model for High-Throughput Testing of Tumoricidal Activity (2018)

The latest advancements in oncology research are focused on autologous immune cell therapy. However, the effectiveness of this type of immunotherapy for cancer remediation is not equivalent for all patients or cancer types. This suggests the need for better preclinical screening models that more closely recapitulate <i>in vivo</i> tumor biology. The established method for investigating tumoricidal activity of immunotherapies has been study of two-dimensional (2D) monolayer cultures of immortalized cancer cell lines or primary tumor cells in standard tissue culture vessels. Indeed, a proven means to examine immune cell migration and invasion are 2D chemotaxis assays in permeabilized supports or Boyden chambers. Nevertheless, the more <i>in vivo</i>-like three-dimensional (3D) multicellular tumor spheroids are quickly becoming the favored model to examine immune cell invasion and tumor cell cytotoxicity. Accordingly, we have developed a 3D immune oncology model by combining 96-well permeable support systems and 96-well low-attachment microplates. The use of the permeable support system enables assessment of immune cell migration, which was tested in this study as chemotactic response of natural killer NK-92MI cells to human stromal-cell derived factor-1 (SDF-1α). Immune invasion was assessed by measuring NK-92MI infiltration into lung carcinoma A549 cell spheroids that were formed in low-attachment microplates. The novel pairing of the permeable support system with low-attachment microplates permitted simultaneous investigation of immune cell homing, immune invasion of tumor spheroids, and spheroid cytotoxicity. In effect, the system represents a more comprehensive and <i>in vivo</i>-like immune oncology model that can be utilized for high-throughput study of tumoricidal activity.
Protecting Against Post-influenza Bacterial Pneumonia by Increasing Phagocyte Recruitment and ROS Production (2013)

Seasonal and especially pandemic influenza predispose patients to secondary bacterial pneumonias, which are a major cause of deaths and morbidity. Staphylococcus aureus is a particularly common and deadly form of post-influenza pneumonia, and increasing staphylococcal drug resistance makes the development of new therapies urgent. We explored an innate immune-mediated model of the lung to define novel mechanisms by which the host can be protected against secondary staphylococcal pneumonia after sub-lethal influenza infection. We found that stimulating the innate immunity in the lung by overexpression of GM-CSF will result in resistance to S. aureus pneumonia after sublethal influenza infection. Resistance was mediated by alveolar macrophages and neutrophils, and was associated with increased production of reactive oxygen species (ROS) by alveolar macrophages. Resistance was abrogated by treatment with agents that scavenged ROS. We conclude that stimulating innate immunity in the lung markedly reduces susceptibility to post-influenza staphylococcal pneumonia and that this may represent a novel immunomodulatory strategy for prevention and treatment of secondary bacterial pneumonia after influenza.
Backscatter Based Cooperative Transmission in Wireless-Powered Heterogeneous Networks (2019)

In this paper, we propose backscatter based cooperative transmission for wireless-powered heterogeneous networks (WPHetNets). In WPHetNets, where various kinds of nodes such as high-power base station (e.g., TV tower, macro base station) and small-power access point (e.g., WiFi) coexist, we aim to increase transmission range and support fair communication for battery-free internet-of-things (IoT) devices through user cooperation. For this, we propose long-range bistatic backscatter (BB) based distributed beamforming (DTB) where ambient backscatter (AB) supports short-range information exchange between devices for energy neutral operation, which is termed 'Cooperation mode'. In order to ensure fairness between devices, we formulate common-throughput maximization problem, where an algorithm for optimal time allocation is presented. Comparing with 'Non-Cooperation mode' (i.e., no information exchange via AB) and active RF based cooperation schemes, the proposed scheme is shown to increase both coverage and fairness between IoT devices for low-power wide area network (LP-WAN).
Designing an optimized enterprise windows NT/95/98 client backup solution with intelligent data management (1998)

Recent times have seen a vast increase in the number of PC's deployed on company networks, as well as a significant increase in the drive space attached to those machines. This situation presents a growing problem for those responsible for both maintaining corporate networks and insuring the integrity and safety of corporate data. The increase in the enterprise data set translates to an increase in the amount of data on the wire, as it is sent over the network to be archived, as well as an increase in the amount of tape media that must be used to protect the data. Faced with an ever-increasing amount of data to support, it is becoming necessary to discover a means to identify business critical data, so that only the necessary files are committed to long-term storage. At the same time, the non-critical data must also be tracked, so that machines can be fully recovered in case of machine failure.

In this paper we will discuss the concept behind our system of intelligently managing redundant and unneeded information in the enterprise. Our method employs a rule system that allows us to reduce or eliminate the redundant and useless information that we backup while still providing quick restore times in the event of data loss.
Visual Change Detection Using Multiscale Super Pixel (2017)

The use of autonomous drones in industrial inspection is gaining momentum with improvements in hardware and control. Considering the availability of historical data as drones gather information by regular sorties, a new opportunity for change detection is emerging for inspection and maintenance. In this paper, we propose a visual change detection framework using multi- scale super pixel approach. A framework that can (i) automatically capture appropriate images that match the stored images in the data agnostic drone store, and (ii) perform visual change detection is proposed. The algorithm is tested on a street-view change detection dataset containing images from 152 categories. Image matching step resulted in an accuracy of over 90%. On the street-view dataset, a change detection rate of over 90% is achieved with 60% categories detecting more than 60% of changed region. The proposed approach achieves better performance compared to other state-of-the- art methods that use image descriptors. The capability is implemented on an off-the-shelf drone to demonstrate the utility.
The GID1-Mediated Gibberellin Perception Mechanism Is Conserved in the Lycophyte <i>Selaginella moellendorffii</i> but Not in the Bryophyte <i>Physcomitrella patens</i> (2007)

In rice (Oryza sativa) and Arabidopsis thaliana, gibberellin (GA) signaling is mediated by GIBBERELLIN-INSENSITIVE DWARF1 (GID1) and DELLA proteins in collaboration with a GA-specific F-box protein. To explore when plants evolved the ability to perceive GA by the GID1/DELLA pathway, we examined these GA signaling components in the lycophyte Selaginella moellendorffii and the bryophyte Physcomitrella patens. An in silico search identified several homologs of GID1, DELLA, and GID2, a GA-specific F-box protein in rice, in both species. Sm GID1a and Sm GID1b, GID1 proteins from S. moellendorffii, showed GA binding activity in vitro and interacted with DELLA proteins from S. moellendorffii in a GA-dependent manner in yeast. Introduction of constitutively expressed Sm GID1a, Sm G1D1b, and Sm GID2a transgenes rescued the dwarf phenotype of rice gid1 and gid2 mutants. Furthermore, treatment with GA(4), a major GA in S. moellendorffii, caused downregulation of Sm GID1b, Sm GA20 oxidase, and Sm GA3 oxidase and degradation of the Sm DELLA1 protein. These results demonstrate that the homologs of GID1, DELLA, and GID2 work in a similar manner in S. moellendorffii and in flowering plants. Biochemical studies revealed that Sm GID1s have different GA binding properties from GID1s in flowering plants. No evidence was found for the functional conservation of these genes in P. patens, indicating that GID1/DELLA-mediated GA signaling, if present, differs from that in vascular plants. Our results suggest that GID1/DELLA-mediated GA signaling appeared after the divergence of vascular plants from the moss lineage.
Imaging the femoral cortex: Thickness, density and mass from clinical CT (2012)

There is growing evidence that focal thinning of cortical bone in the proximal femur may predispose a hip to fracture. Detecting such defects in clinical CT is challenging, since cortices may be significantly thinner than the imaging system's point spread function. We recently proposed a model-fitting technique to measure sub-millimetre cortices, an ill-posed problem which was regularized by assuming a specific, fixed value for the cortical density. In this paper, we develop the work further by proposing and evaluating a more rigorous method for estimating the constant cortical density, and extend the paradigm to encompass the mapping of cortical mass (mineral mg/cm(2)) in addition to thickness. Density, thickness and mass estimates are evaluated on sixteen cadaveric femurs, with high resolution measurements from a micro-CT scanner providing the gold standard. The results demonstrate robust, accurate measurement of peak cortical density and cortical mass. Cortical thickness errors are confined to regions of thin cortex and are bounded by the extent to which the local density deviates from the peak, averaging 20% for 0.5mm cortex.
Early Stall Warning Technique for Axial Flow Compressors (2004)

This paper proposes a unique stall warning index based on pressure signals by high response transducers on the casing wall at the rotor leading edge location. The aim of the research is to explore the possibility of reducing current excessive stall margin requirement for compressor design based on the worst case scenario. The index is generated by computing correlation degradation of pressure time histories of current and one revolution before over each blade pitch. Tests conducted on a research compressor exhibits that the correlation diminishes significantly with proximity to stall and the proposed technique might have the capability of generating a stall warning signal sufficiently in advance of spike inception. Extensive experiments on a research compressor show that the degree of the index degradation depends on various factors such as flow coefficient, tip clearance and rotor blade incidence. In order to obtain a reliable stall warning signal in practical use, these effects must be carefully examined.
Non-invasive ultrasonic instrument for counter-terrorism and drug interdiction operations - the acoustic inspection device (AID) (2004)

The Pacific Northwest National Laboratory (PNNL) has developed a portable, battery-operated, handheld ultrasonic device that provides non-invasive container interrogation and material identification capabilities. The technique governing how the acoustic inspection device (AID) functions, involves measurements of ultrasonic pulses (0.1 to 5 MHz) that are launched into a container or material. The return echoes from these pulses are analyzed in terms of time-of-flight and frequency content to extract physical property measurements (the acoustic velocity and attenuation coefficient) of the material under test. The AID performs an automated analysis of the return echoes to identify the material, and detect contraband in the form of submerged packages and concealed compartments in liquid filled containers and solid-form commodities. This device utilizes a database consisting of material property measurements acquired from an automated, ultrasonic fluid characterization system called the Velocity-Attenuation Measurement System (VAMS). Both prototype technologies are discussed here. This manuscript describes the functionality, capabilities and measurement methodology of the technology as it relates to the material property measurements and homeland security applications.
Leptin‐based glycopeptide induces weight loss and simultaneously restores fertility in animal models (2009)

No resistance induction to peptide E1/Aca or toxicity in either obese or healthy rodents was observed, indicating the potential for widespread utility of the peptidomimetic in the treatment of leptin-deficiency disorders. We provide additional proof for the hypothesis that difficulties in current leptin therapies reside at the BBB penetration stage, and we document that by either glycosylation or intranasal peptide administration we can overcome this limitation.
Leveraging Computational Reuse for Cost- and QoS-Efficient Task Scheduling in Clouds (2018)

Cloud-based computing systems could get oversubscribed due to budget constraints of cloud users which causes violation of Quality of Experience(QoE) metrics such as tasks' deadlines. We investigate an approach to achieve robustness against uncertain task arrival and oversubscription through smart reuse of computation while similar tasks are waiting for execution. Our motivation in this study is a cloud-based video streaming engine that processes video streaming tasks in an on-demand manner. We propose a mechanism to identify various types of "mergeable" tasks and determine when it is appropriate to aggregate tasks without affecting QoS of other tasks. Experiment shows that our mechanism can improve robustness of the system and also saves the overall time of using cloud services by more than 14%.
Moxifloxacin and Cholesterol Combined Treatment of Pneumococcal Keratitis (2010)

Treatment with a mixture of moxifloxacin and cholesterol significantly lowers the severity of infection caused by pneumococcal keratitis as compared to treatment with moxifloxacin alone, cholesterol alone, or PBS. This treatment mixture eradicates the bacteria in the cornea, unlike treatment with PBS or cholesterol alone. Using cholesterol with moxifloxacin as a treatment for bacterial keratitis could help lower the clinical severity of the infection.
<title>Fundamental approach for optoelectronic and microfluidic integration for miniaturizing spectroscopic devices</title> (2002)

We have described an approach for miniaturizing spectroscopic devices by using the advantages presented by elastomeric based microfluidics and semiconductor detectors/emitters. Elastomers allow for both absorption and fluorescent spectroscopy in the visible range to be conducted on small volumes of solution and allow for easy integration with existing detectors such as CMOS imagers, CCD imagers, and silicon photodiodes. Results of some basic experiments are presented to demonstrate the effectiveness of the system. In addition, several ideas for emission sources are also discussed with their relevance yet to be determined.
Characterization and optimization of novel surface-enhanced Raman scattering (SERS)-based nanoimaging probes for chemical imaging (2005)

We have developed a novel class of surface-enhanced Raman scattering (SERS)-based nanoimaging probes for chemical imaging with nanometer scale spatial resolution. Using these SERS nanoimaging probes it is possible to differentiate between different chemical components within the sample under analysis. These SERS nanoimaging probes are fabricated from coherent fiber optic imaging bundles composed of 30,000 individual image transmission elements. Using a specially programmed micropipette puller, the individual fiber elements are uniformly heated and pulled, creating a tapered bundle with a flat tip. In order to create the SERS active surface, the tapered end of the fiber bundle is roughened on the "molecular scale" via chemical etching, and is then over-coated with silver in a controlled manner via vapor deposition in a vacuum evaporator. Following etching, six regularly spaced peaks are produced surrounding each of the individual image transmission elements of the bundle, and it is these peaks onto which the metal over-layer is deposited. Due to the high degree of uniformity in the surface of these tapered and etched tips, these SERS nanoimaging probes exhibit significantly greater reproducibility than SERS substrates fabricated through similar silver film over nanostructure fabrication processes. Characterization and optimization of these SERS nanoimaging probes using SERS active chemicals is discussed.
Abstract 135: Reprogramming of Pig Cardiac Fibroblasts to Cardiomyocyte Fate: Implications for Gene Therapy to Treat Myocardial Infarction (2014)

There is an urgent clinical need to develop new therapeutic approaches to treat heart failure, but the biology of cardiovascular regeneration is complex. A new generation of reprogramming technology involves trans-differentiating one adult somatic cell type directly into another. We reported previously that administration of gene transfer vectors encoding Gata4 (G), Mef 2c (M) and Tbx5 (T), reprograms rat cardiac fibroblasts into induced cardiomyocytes (iCMs) in vitro and improves cardiac function in myocardial infarction models. Previous cardiac reprogramming studies were restricted to rodent and human fibroblasts. However studies in large animal models relevant for pre-clinical studies is lacking. The Aim of the present study was to determine the optimal combination of factors necessary for direct reprogramming of porcine fibroblasts towards a cardiomyocyte lineage for the first time. Here we have used human lentiviral system to express various cardiomyocyte enriched transcriptional regulators such as GMT, Hand2, myocardin, and two microRNAs, miR-590 and mir-199, in porcine cardiac fibroblasts. Reprogramming of fibroblasts into iCMs was determined 4 weeks post-virus transduction by FACS analysis for the activation of endogenous cardiac troponin T (cTnT). GMT alone was not sufficient to reprogram porcine fibroblasts although this combination was shown previously to be sufficient to convert rodent fibroblasts into iCMs. Addition of mir-199 to GMT was also not sufficient to promote reprogramming. However, adding miR-590 or Hand2, and myocardin (HM) to GMT resulted in reprogramming, although the efficiency remained low. Together, our results show that combination of 5 distinct transcription regulators (GMTHM) or GMT plus mir-590 is necessary for reprogramming porcine fibroblast. These findings demonstrate that pig fibroblasts can be directly reprogrammed toward the cardiomyocyte lineage, and represent a step toward possible therapeutic application of this reprogramming approach in a pre-clinical setting.
Organometallic vapor deposition of epitaxial ZnSe films on GaAs substrates (1978)

Smooth epitaxial single-crystalline layers of (100) ZnSe on (100) GaAs substrates are grown by a new low-pressure low-temperature organometallic chemical vapor deposition process. The strong band-edge photoluminescence peak and the absence of any substantial luminescence intensity at longer wavelengths indicate an absence of deep trapping centers which is typically not observed in other CVD growth.
The structure–property relationship of four crystal forms of rifaximin (2012)

The crystal structures of four crystal forms of rifaximin, named α, β, δ and ε, have been elucidated by a combination of single crystal and powder diffraction experiments with synchrotron and X-ray sources. The crystal structures of the δ and ε forms have been determined from powder diffraction data alone. Hot stage microscopy has also been of paramount importance in the understanding of the β → α conversion process.
Hypothesis Stitcher for End-to-End Speaker-attributed ASR on Long-form Multi-talker Recordings (2021)

An end-to-end (E2E) speaker-attributed automatic speech recognition (SA-ASR) model was proposed recently to jointly perform speaker counting, speech recognition and speaker identification. The model achieved a low speaker-attributed word error rate (SA-WER) for monaural overlapped speech comprising an unknown number of speakers. However, the E2E modeling approach is susceptible to the mismatch between the training and testing conditions. It has yet to be investigated whether the E2E SA-ASR model works well for recordings that are much longer than samples seen during training. In this work, we first apply a known decoding technique that was developed to perform single-speaker ASR for long-form audio to our E2E SA-ASR task. Then, we propose a novel method using a sequence-to-sequence model, called hypothesis stitcher. The model takes multiple hypotheses obtained from short audio segments that are extracted from the original long-form input, and it then outputs a fused single hypothesis. We propose several architectural variations of the hypothesis stitcher model and compare them with the conventional decoding methods. Experiments using LibriSpeech and LibriCSS corpora show that the proposed method significantly improves SA-WER especially for long-form multi-talker recordings.
Spherical optical surface defects digitizing evaluation system (2018)

This paper introduces a spherical optical surface defects evaluation system (SSDES) based on the dark-field microscopic scattering imaging (DFMSI) method. The specially designed annular illuminant with variable aperture angles ensures the condition of DFMSI for spherical optical components with variable surface shapes and radii of curvature. On account of the small imaging field of view (FOV) of the SSDES relative to the large spherical optical component under test, the scanning path for subaperture images is planned along longitudes and latitudes of the spherical surface to detect the whole surface. Besides, for avoiding the misplaced subaperture images stitching due to the decenter error, a centering system is utilized to perform the alignment of the optical axis of the spherical optics in relation to the reference axis before capturing subaperture images. Then we propose a defect evaluation method, primarily involving the threedimensional (3D) image reconstruction and global coordinate transformation, the projective stitching of 3D subaperture images, and the quantitative evaluation of defects, to process the captured spherical subaperture images. Experiments results are shown in good accordance with the OLYMPUS microscope for the relative error within 5%, and validate the SSDES to the micrometer resolution.