gebhart/patrepeval huggingface dataset:
Pulse Repetition Interval Modulation Recognition Using Symbolization (2010)

Information on the pulse repetition interval (PRI) modulation of a radar signal plays an important role in detecting and identifying each radar signal in an electronic warfare support (ES) system. In this paper, we present a new method for recognizing the PRI modulation type of a radar signal using symbolization. The proposed method uses three key feature parameters extracted from symbol sequences in order to discriminate each PRI modulation type. The recognition capability of the method presented is verified through extensive simulations.
Detection of Vesicoureteral Reflux Using Electrical Impedance Tomography (2018)

VUR is the most common congenital urinary tract abnormality in children. The condition predisposes children to urinary tract infections and kidney damage. The current gold standard diagnostic test, a voiding cystourethrogram, is invasive and uses ionizing radiation; therefore, there is a need for new tools for identifying VUR in children. This study presents a noninvasive method to detect VUR in animal models, illustrating the potential for EIT as a screening tool in clinical scenarios.
Polymer-encased nanodiscs with improved buffer compatibility (2017)

Styrene-maleic acid copolymers allow for solubilization and reconstitution of membrane proteins into nanodiscs. These polymer-encased nanodiscs are promising platforms for studies of membrane proteins in a near-physiologic environment without the use of detergents. However, current styrene-maleic acid copolymers display severe limitations in terms of buffer compatibility and ensued flexibility for various applications. Here, we present a new family of styrene-maleic acid copolymers that do not aggregate at low pH or in the presence of polyvalent cations, and can be used to solubilize membrane proteins and produce nanodiscs of controlled sizes.
Dynamically Multiplexed Ion Mobility Time-of-Flight Mass Spectrometry (2008)

Ion mobility spectrometry-time-of-flight mass spectrometry (IMS-TOFMS) has been increasingly used in analysis of complex biological samples. A major challenge is to transform IMS-TOFMS to a high-sensitivity, high-throughput platform, for example, for proteomics applications. In this work, we have developed and integrated three advanced technologies, including efficient ion accumulation in an ion funnel trap prior to IMS separation, multiplexing (MP) of ion packet introduction into the IMS drift tube, and signal detection with an analog-to-digital converter, into the IMS-TOFMS system for the high-throughput analysis of highly complex proteolytic digests of, for example, blood plasma. To better address variable sample complexity, we have developed and rigorously evaluated a novel dynamic MP approach that ensures correlation of the analyzer performance with an ion source function and provides the improved dynamic range and sensitivity throughout the experiment. The MP IMS-TOFMS instrument has been shown to reliably detect peptides at a concentration of 1 nM in the presence of a highly complex matrix, as well as to provide a 3 orders of magnitude dynamic range and a mass measurement accuracy of better than 5 ppm. When matched against human blood plasma database, the detected IMS-TOF features were found to yield approximately 700 unique peptide identifications at a false discovery rate (FDR) of approximately 7.5%. Accounting for IMS information gave rise to a projected FDR of approximately 4%. Signal reproducibility was found to be greater than 80%, while the variations in the number of unique peptide identifications were <15%. A single sample analysis was completed in 15 min that constitutes almost 1 order of magnitude improvement compared to a more conventional LC-MS approach.
Isolation, Catalytic Properties, and Competitive Inhibitors of the Zinc-Dependent Murine Glutaminyl Cyclase (2005)

Murine glutaminyl cyclase (mQC) was identified in the insulinoma cell line beta-TC 3 by determination of enzymatic activity and RT-PCR. The cloned cDNA was expressed in the secretory pathway of the methylotrophic yeast Pichia pastoris and purified after fermentation using a new three-step protocol. mQC converted a set of various substrates with very similar specificity to human QC, indicating a virtually identical catalytic competence. Furthermore, mQC was competitively inhibited by imidazole derivatives. A screen of thiol reagents revealed cysteamine as a competitive inhibitor of mQC bearing a Ki value of 42 +/-2 microM. Substitution of the thiol or the amino group resulted in a drastic loss of inhibitory potency. The pH dependence of catalysis and inhibition support that an uncharged nitrogen of the inhibitors and the substrate is necessary in order to bind to the active site of the enzyme. In contrast to imidazole and cysteamine, the heterocyclic chelators 1,10-phenanthroline, 2,6-dipicolinic acid, and 8-hydroxyquinoline inactivated mQC in a time-dependent manner. In addition, citric acid inactivated the enzyme at pH 5.5. Inhibition by citrate was abolished in the presence of zinc ions. A determination of the metal content by total reflection X-ray fluorescence spectrometry and atomic absorption spectroscopy in mQC revealed stoichiometric amounts of zinc bound to the protein. Metal ion depletion appeared to have no significant effect on protein structure as shown by fluorescence spectroscopy, suggesting a catalytic role of zinc. The results demonstrate that mQC and probably all animal QCs are zinc-dependent catalysts. Apparently, during evolution from an ancestral protease, a switch occurred in the catalytic mechanism which is mainly based on a loss of one metal binding site.
108 Gb/s OFDMA-PON With Polarization Multiplexing and Direct Detection (2009)

In this paper, we propose and experimentally demonstrate the first single-¿ 40 Gb/s and 108 Gb/s multiple-input multiple-output orthogonal frequency-division multiple access (OFDMA) passive optical networks (PON) architecture for next-generation PON systems based on OFDM, polarization multiplexing (POLMUX), and direct detection. Superior performance was exhibited after 20 km SSMF transmission and a 1:32 optical split. The novel POLMUX approach greatly simplified receiver-end hardware compared to coherent detectors, while increasing spectral efficiency to enable 40 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> Gb/s data rates. Moreover, the proposed solution achieved the highest single-wavelength downstream transmission reported to date in any PON system. As such, the introduced architecture may be viewed as a highly attractive candidate for next-generation optical access.
Variable frame rate parameter encoding via adaptive frame selection using dynamic programming (2002)

This paper presents a block-coded VFR strategy that removes the familiar "anchor frame" constraint in favor of a generalized delayed decision analysis. This approach is referred to as adaptive frame selection using dynamic programming (AFS/DP). The AFS/DP algorithm determines optimal breakpoint locations using a perceptually-based performance measure, accommodates fixed bit-rate operation, and operates with fixed delay and low complexity. The AFS/DP algorithm has been implemented in the context of the MELP vocoder at 2400 bits/sec, and has demonstrated comparable performance to block VFR methods, with lower coder delay.
Inhibition of Influenza Virus Infection by a Novel Antiviral Peptide That Targets Viral Attachment to Cells (2006)

Influenza A viruses continue to cause widespread morbidity and mortality. There is an added concern that the highly pathogenic H5N1 influenza A viruses, currently found throughout many parts of the world, represent a serious public health threat and may result in a pandemic. Intervention strategies to halt an influenza epidemic or pandemic are a high priority, with an emphasis on vaccines and antiviral drugs. In these studies, we demonstrate that a 20-amino-acid peptide (EB, for entry blocker) derived from the signal sequence of fibroblast growth factor 4 exhibits broad-spectrum antiviral activity against influenza viruses including the H5N1 subtype in vitro. The EB peptide was protective in vivo, even when administered postinfection. Mechanistically, the EB peptide inhibits the attachment to the cellular receptor, preventing infection. Further studies demonstrated that the EB peptide specifically binds to the viral hemagglutinin protein. This novel peptide has potential value as a reagent to study virus attachment and as a future therapeutic.
MRI Tissue Magnetism Quantification through Total Field Inversion with Deep Neural Networks (2019)

Quantitative susceptibility mapping (QSM) utilizes MRI signal phase to infer estimates of local tissue magnetism (magnetic susceptibility), which has been shown useful to provide novel image contrast and as biomarkers of abnormal tissue. QSM requires addressing a challenging post-processing problem: filtering of image phase estimates and inversion of the phase to susceptibility relationship. A wide variety of quantification errors, robustness limitations, and artifacts plague QSM algorithms. To overcome these limitations, a robust deep-learning-based single-step QSM reconstruction approach is proposed and demonstrated. This neural network was trained using magnetostatic physics simulations based on in-vivo data sources. Random perturbations were added to the physics simulations to provide sufficient input-label pairs for the training purposes. The network was quantitatively tested using gold-standard in-silico labeled datasets against established QSM total field inversion approaches. In addition, the algorithm was applied to susceptibility-weighted imaging (SWI) data collected on a cohort of clinical subjects with brain hemmhorage. When quantitatively compared against gold-standard in-silico labels, the proposed algorithm outperformed the existing comparable approaches. High quality QSM were consistently estimated from clinical susceptibility-weighted data on 100 subjects without any noticeable inversion failures. The proposed approach was able to robustly generate high quality QSM with improved accuracy in in-silico gold-standard experiments. QSM produced by the proposed method can be generated in real-time on existing MRI scanner platforms and provide enhanced visualization and quantification of magnetism-based tissue contrasts.
Cell-Permeable Peptide DEPDC1-ZNF224 Interferes with Transcriptional Repression and Oncogenicity in Bladder Cancer Cells (2010)

Abstract Bladder cancer is the second most common genitourinary cancer worldwide, yet its oncogenic origins remain poorly understood. The cancer-testis antigen DEPDC1 was shown recently to contribute to bladder cancer oncogenesis. In this study, we examined the biological functions of DEPDC1 and defined a potential therapeutic strategy to target this molecule. Coimmunoprecipitation and immunocytochemistry revealed that DEPDC1 interacted and colocalized with zinc finger transcription factor ZNF224, a known transcriptional repressor. Inhibiting this interaction with a cell-permeable peptide corresponding to the ZNF224-interacting domain in DEPDC1 induced apoptosis of bladder cancer cells in vitro and in vivo. By inhibiting DEPDC1-ZNF224 complex formation, this peptide triggered transcriptional activation of A20, a potent inhibitor of the NF-κB signaling pathway. Our findings indicate that the DEPDC1-ZNF224 complex is likely to play a critical role in bladder carcinogenesis. Cancer Res; 70(14); 5829–39. ©2010 AACR.
Adaptive Sparse Representations for Video Anomaly Detection (2013)

Video anomaly detection can be used in the transportation domain to identify unusual patterns such as traffic violations, accidents, unsafe driver behavior, street crime, and other suspicious activities. A common class of approaches relies on object tracking and trajectory analysis. Very recently, sparse reconstruction techniques have been employed in video anomaly detection. The fundamental underlying assumption of these methods is that any new feature representation of a normal/anomalous event can be approximately modeled as a (sparse) linear combination prelabeled feature representations (of previously observed events) in a training dictionary. Sparsity can be a powerful prior on model coefficients but challenges remain in the detection of anomalies involving multiple objects and the ability of the linear sparsity model to effectively allow for class separation. The proposed research addresses both these issues. First, we develop a new joint sparsity model for anomaly detection that enables the detection of joint anomalies involving multiple objects. This extension is highly nontrivial since it leads to a new simultaneous sparsity problem that we solve using a greedy pursuit technique. Second, we introduce nonlinearity into, that is, kernelize. The linear sparsity model to enable superior class separability and hence anomaly detection. We extensively test on several real world video datasets involving both single and multiple object anomalies. Results show marked improvements in detection of anomalies in both supervised and unsupervised scenarios when using the proposed sparsity models.
Split luciferase-based assay to detect botulinum neurotoxins using human motor neurons derived from induced pluripotent stem cell. (2021)

Abstract Botulinum neurotoxins (BoNTs) have been widely used clinically as a muscle relaxant. These toxins target motor neurons and cleave proteins essential for neurotransmitter release like Synaptosomal-associated protein of 25 kDa (SNAP-25). Most in vitro assays for BoNT testing use rodent cells or immortalized cell lines, which showed limitations in accuracy and physiological relevance. Here, we report a cell-based assay for detecting SNAP25-cleaving BoNTs by combining human induced Pluripotent Stem Cells (hiPSC)-derived motor neurons and a luminescent detection system based on split nanoluc luciferase. This assay is convenient, rapid, free-of-specialized antibodies, and can discriminate the potency of different BoNTs, with a detection sensitivity of femtomolar concentrations of toxin and can be used to study the different steps of BoNT intoxication. Abreviations: BoNT, Botulinum neurotoxin, SNAP-25, Synaptosomal-associated protein of 25 kDa, hiPSC, human induced Pluripotent Stem Cells, SNARE, soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor, SV2, synaptic vesicle proteins, MLB, mouse lethality bioassay, LD 50 , toxin’s dose lethal for half of the animal injected, CB-assay, cell-based assays, FRET, Förster resonance energy transfer, Concanamycin A, EC50, Half maximal effective concentration, MNs, motor neurons.
Nickel Based Superalloy with Improved Weldability and Oxidation Resistance. Fourth quarterly report for the period July 1999 to October 1999 (1999)

The aim of this project is to determine and provide technical and economic data to a commercial end user of the alloy so that a full-scale alloy qualification program can be defined and implemented. The object of this project is to define the compositional range for a new alloy that is suitable for evaluation and qualification by a commercial enterprise. Alloy properties that will need to be determined include weldability, oxidation resistance, creep strength, resistance to thermo-mechanical fatigue, microstructure stability, and cost. Test results will be used to finalize the compositional range of an alloy that will undergo a rigorous qualification process.
Oncolytic Herpes Simplex Virus Counteracts the Hypoxia-Induced Modulation of Glioblastoma Stem-Like Cells (2012)

Glioblastoma (GBM), a fatal malignant brain tumor, contains abundant hypoxic regions that provide a "niche" to promote both the maintenance and enrichment of glioblastoma stem-like cells (GSCs) and confer resistance to chemo- and radiotherapy. Since GSCs, with an ability to resist conventional therapies, may be responsible for tumor recurrence, targeting GSCs located in such a hypoxic environment may be critical to improving the therapeutic outcome for GBM patients. Oncolytic viral therapies have been tested in the clinic as a promising therapeutic approach for GBM. In this study, we analyzed and compared the therapeutic effects of oncolytic herpes simplex virus (oHSV) type 1 G47Δ (γ34.5(-)ICP6(-)LacZ(+)α47(-)) in patient-derived GSCs under normoxia (21% oxygen) and hypoxia (1% oxygen). GSCs cultured in hypoxia showed an increased ability to form neurospheres and expressed higher levels of the putative stem cell marker CD133 compared with GSCs cultured in normoxia. G47Δ exhibited a comparable ability to infect, replicate, and kill GSCs in normoxia and hypoxia in vitro. Importantly, G47Δ could counteract hypoxia-mediated enhancement of the stem-like properties of GSCs, inhibiting their self-renewal and stem cell marker expression. Using orthotopic human GSC xenografts in mice, we demonstrated that intratumoral injection of G47ΔUs11fluc, a newly developed G47Δ derivative that expresses firefly luciferase driven by a true late viral promoter, led to an equivalent frequency of viral infection and replication in hypoxic and nonhypoxic tumor areas. These findings suggest that oHSV G47Δ represents a promising therapeutic strategy to target and kill GSCs, not only in normoxic areas of GBM but also within the hypoxic niche.
Computerized analysis of multiple-mammographic views: potential usefulness of special view mammograms in computer-aided diagnosis (2001)

Purpose: To investigate the potential usefulness of special view mammograms in the computer-aided diagnosis of mammographic breast lesions. Materials and Methods: Previously, we developed a computerized method for the classification of mammographic mass lesions on standard-view mammograms, i.e., mediolateral oblique (MLO) view and/or cranial caudal (CC) views. In this study, we evaluate the performance of our computerized classification method on an independent database consisting of 70 cases (33 malignant and 37 benign cases), each having CC, MLO, and special view mammograms (spot compression or spot compression magnification views). The mass lesion identified in each of the three mammographic views was analyzed using our previously developed and trained computerized classification method. Performance in the task of distinguishing between malignant and benign lesions was evaluated using receiver operating characteristic analysis. On this independent database, we compared the performance of individual computer-extracted mammographic features, as well as the computer-estimated likelihood of malignancy, for the standard and special views. Results: Computerized analysis of special view mammograms alone in the task of distinguishing between malignant and benign lesions yielded an A/sub z/ of 0.95, which is significantly higher (p < 0.005) than that obtained from the MLO and CC views (A/sub z/ values of 0.78 and 0.75, respectively). Use of only the special views correctly classified 19 of 33 benign cases (a specificity of 58%) at 100% sensitivity, whereas use of the CC and MLO views alone correctly classified 4 and 8 of 33 benign cases (specificities of 12% and 24%, respectively). In addition, we found that the average computer output of the three views (A/sub z/ of 0.95) yielded a significantly better performance than did the maximum computer output from the mammographic views. Conclusions: Computerized analysis of special view mammograms provides an improved prediction of the benign versus malignant status of mammographic mass lesions.
A New Method for Manufacturing Nanostructured Electrodes on Plastic Substrates (2001)

The present paper describes a new method for manufacturing a nanostructured porous layer of a semiconductor material on a conducting plastic substrate for use in an electrochemical or photoelectrochemical cell. The method involves the deposition of a layer of semiconductor particles on conducting plastic and the compression of the particle layer to form a mechanically stable, electrically conducting, porous nanostructured film at room temperature. Photoelectrochemical characteristics of the resulting nanostructured films are presented showing, for example, overall solar to electric conversion efficiencies of up to 4.9% (0.1 sun). The potential use of the new manufacturing method in future applications of nanostructured electrodes is discussed.
Enhanced CO<sub>2</sub> Adsorption in Metal-Organic Frameworks via Occupation of Open-Metal Sites by Coordinated Water Molecules (2009)

CO2 is one of the most important greenhouse gases and its removal from flue gas and natural gas has become increasingly important. We report an interesting discovery in which the CO2 uptake and its selectivity over N2 and CH4 in the metal-organic framework (MOF) Cu-BTC were significantly increased by the presence of water molecules coordinated to open-metal sites in the framework. This was first predicted by molecular simulations and later validated by experiments. A detailed analysis of simulation data revealed that interaction between the quadrupole moment of CO2 and the electric field created by water molecules is responsible for the enhanced CO2 uptake. These findings could open new possibilities for tuning the adsorption behavior of MOFs for CO2 capture and other applications.
BUOYANT DISCHARGES FROM SUBMERGED MULTIPORT DIFFUSERS (1974)

The application of submerged multiport diffusers for the discharge of degradable liquid wastes and of heated cooling water from electric power generation forms an important aspect of coastal zone management. Previous buoyant jet models for submerged diffuser discharge have been developed for the limiting case of discharge in unconfined deep water in the form of rising buoyant jets. These models can be used for sewage diffusers, but are not applicable for diffusers in shallow receiving water with low buoyancy, the type used for thermal discharges ("thermal diffusers"). A multiport diffuser will produce a general three-dimensional flow. Yet the predominantly two dimensional flow which exists in the center portion of the three-dimensional diffuser can be analyzed as a two-dimensional "channel model". Theoretical solutions for diffuser-induced dilutions are derived for the two-dimensional case and verified experimentally. Furthermore, the theory can be applied to the three-dimensional situation by requiring equivalency of far-field effects, that is the frictional resistance governing the diffuser-induced motion at larger distances from the diffuser line.
Non-iterative phase hologram computation for low speckle holographic image projection (2016)

Phase-only spatial light modulators (SLMs) are widely used in holographic display applications, including holographic image projection (HIP). Most phase computer generated hologram (CGH) calculation algorithms have an iterative structure with a high computational load, and also are prone to speckle noise, as a result of the random phase terms applied on the desired images to mitigate the encoding noise. In this paper, we present a non-iterative algorithm, where simple Discrete Fourier Transform (DFT) relations are exploited to compute phase CGHs that exactly control half of the desired image samples (those on even - or odd - indexed rows - or columns) via a single Fast Fourier Transform (FFT) and trivial arithmetic operations. The encoding noise appearing on the uncontrolled half of the image samples is reduced by the application of structured, non-random initial phase terms so that speckle noise is also kept low. High quality reconstructions are obtained under temporal averaging of several SLM frames. Interlaced video within half of the addressable image area is readily deliverable without frame rate division. Our algorithm provides about 6X and 20X reduction in computational cost compared to IFTA and FIDOC algorithms, respectively. Simulations and experiments verify that the algorithm constitutes a promising option for real-time computation of phase CGHs.