gebhart/patrepeval huggingface dataset:
<title>Knowledge-based image retrieval: a new generation design</title> (1994)

A knowledge-based approach to predicting and pre-fetching prior images has been proposed to better meet radiologists' information and performance requirements during primary reading in a totally digitized radiology environment. The knowledge required to accurately predict the related images that a radiologist would wish to review for the diagnosis of a new examination includes classification/subclassification of reason-for-examination (based on examination requisition and patient information), and anatomical-portion/disease/abnormality-dependent cross-modality, cross-anatomical-portion and temporal examination relationships. Developing knowledge-based system to embody and process such knowledge involves a number of challenges. Specifically, because image retrieval knowledge infers many patient, examination and other pertinent data attributes, knowledge representation and processing need to be effective with knowledge and data relationships. Furthermore, because distributed and object- based architecture offer performance and easy-expansion advantages to database systems that house image-retrieval-related multimedia data, the design of a knowledge-based image retrieval system needs to handle distributed object-oriented data and knowledge interactions efficiently. A new generation Image Retrieval Expert System (IRES) has adopted a coupled knowledge-base/database architecture using an object-oriented knowledge and data representation. This paper will depict the architectural design as well as the detailed design/implementation results of IRES in this new generation.
Improving naturalness in text-to-speech synthesis using natural glottal source (1991)

Various methods to improve text-to-speech in its naturalness and its ability to model individual speakers are discussed. Methods using a natural glottal source which is extracted from natural speech by an inverse-filtering technique are described. One method uses a repeating loop. Another method creates a source waveform of the desired pitch by concatenating single pulses. A multisource method which utilizes different types of glottal source by cross-fading techniques is proposed. Perceptual listening tests were performed with synthetic stimuli. The preliminary results show that these methods have the potential to improve the quality of text-to-speech synthesis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Properties of a plasma-based laser-triggered micro-lens (2011)

This paper investigates the characteristic properties of a laser triggered micro-lens for focusing and energy selection of laser generated MeV proton and ion beams. Both experimental and computational studies that have been carried out leading to the understanding of the physical processes driving the micro-lens. After a one side irradiation of a hollow metallic cylinder a radial electric field develops inside the cylinder. Hot electrons generated by the interaction between laser pulse and cylinder wall spread inside the cylinder generating a plasma at the wall. This plasma expands into vacuum and sustains an electric field that acts as a collecting lens for proton or ion beams propagating axially through the cylinder. Various measurements including the reduction of the intrinsic beam divergence, the focusing quality, the energy selection and temporal response were carried out which contribute to the understanding of the lens properties. In addition, proton imaging was employed to study the electron transport inside the cylinder, revealing a transport along the wall surface. Each aspect studied experimentally is interpreted using 2D PIC and ray tracing simulations. A very good consistency between experimental and computational data was found.
Optimization of Heat Treatment Scheduling for Hot Press Forging Using Data-Driven Models (2021)

Scheduling heat treatment jobs in a hot press forging factory involves forming batches of multiple workpieces for the given furnaces, determining the start time of heating each batch, and sorting out the order of cooling the heated workpieces. Among these, forming batches is particularly difficult because of the various constraints that must be satisfied. This paper proposes an optimization method based on an evolutionary algorithm to search for a heat treatment schedule of maximum productivity with minimum energy cost, satisfying various constraints imposed on the batches. Our method encodes a candidate solution as a permutation of heat treatment jobs and decodes it such that the jobs are grouped into batches satisfying all constraints. Each candidate schedule is evaluated by simulating the heating and cooling processes using cost models for processing time and energy consumption, which are learned from historical process data. Simulation experiments reveal that the schedules built using the proposed method achieve higher productivity with lower energy costs than those built by human experts.
Retargeting adenoviruses for therapeutic applications and vaccines (2020)

Adenoviruses (Ads) are robust vectors for therapeutic applications and vaccines, but their use can be limited by differences in their in vitro and in vivo pharmacologies. This review emphasizes that there is not just one Ad, but a whole virome of diverse viruses that can be used as therapeutics. It discusses that true vector targeting involves not only retargeting viruses, but importantly also detargeting the viruses from off-target cells.
A novel therapeutic strategy targeting multiple members of the γc-family cytokines; principles, relevance and potentially broad clinical applications. (2017)

AbstractCytokines play diverse roles in normal and abnormal immunity. Dysregulated production of cytokines underlies a variety of disorders in humans by causing improper immune responses. Intervention to such abnormal cytokine action has been utilized in the clinical field as therapy and proven effective as treatments. However the current anti-cytokine approaches lack effective and safe options for treating human diseases involving more than two cytokines as the pathogenic reason. This is an issue as the list of multi-cytokine diseases is expanding. To address this, a novel technology was developed by generating a novel class of multi-cytokine inhibitors (MCI). In short, cytokine-mimetic peptides were rationally designed each of which contains a motif shared only by the cytokines of the target and tested using specific biological assay. Peptides showing desired antagonistic activity were screened further for target specificity. The lead MCI, BNZ 132-1, specifically inhibits IL-2, -9 and -15 while it does not affect other γc-cytokines (IL-4, -7. and -21) or non-γc cytokines. This design ensures safety of the peptide upon clinical use by limiting off-target effects to the minimum, unlike small-molecule Jak kinase inhibitors which suppress a diverse array of cytokines and cause multiple adverse effects. Currently, we are conducting clinical trials involving BNZ 132-1 and saw expected transient decrease of select subsets of lymphocytes with minimum toxicity. BNZ 132-1 may provide a novel opportunity for treating many diseases such as myelopathy caused by human T-cell leukemia virus-1 (HTLV-1), non-viral human T-cell malignancies, autoimmunity (Alopecia areata, rheumatoid arthritis), graft-versus-host disease (GvH) upon transplant and cytokine release syndromes post microbial infections.
A Prokaryotic Membrane Sculpting BAR Domain Protein (2020)

Abstract Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here we report the first prokaryotic BAR domain protein, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and scaffolding OMEs into a consistent diameter and curvature. Cryogenic transmission electron microscopy reveals a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubes produced by the wild type strain. Overexpression of BdpA promotes OME formation during conditions where they are less common. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli . Based on the ability of BdpA to alter membrane curvature in vivo , we propose that BdpA and its homologs comprise a newly identified class of prokaryotic BAR (P-BAR) domains.
Detection of Chlorinated and Brominated Byproducts of Drinking Water Disinfection Using Electrospray Ionization−High-Field Asymmetric Waveform Ion Mobility Spectrometry−Mass Spectrometry (1999)

The lower limit of detection for low molecular weight polar and ionic analytes using electrospray ionization-mass spectrometry (ESI-MS) is often severely compromised by an intense background that obscures ions of trace components in solution. Recently, a new technique, referred to as high-field asymmetric waveform ion mobility spectrometry (FAIMS), has been shown to separate gas-phase ions at atmospheric pressure and room temperature. A FAIMS instrument is an ion filter that may be tuned, by control of electrical voltages, to continuously transmit selected ions from a complex mixture. This capability offers significant advantages when FAIMS is coupled with ESI, a source that generates a wide variety of ions, including solvent clusters and salt adducts. In this report, the tandem arrangement of ESI-FAIMS-MS is used for the analysis of haloacetic acids, a class of disinfection byproducts regulated by the US EPA. FAIMS is shown to effectively discriminate against background ions resulting from the electrospray of tap water solutions containing the haloacetic acids. Consequently, mass spectra are simplified, the selectivity of the method is improved, and the limits of detection are lowered compared with conventional ESI-MS. The detection limits of ESI-FAIMS-MS for six haloacetic acids ranged between 0.5 and 4 ng/mL in 9:1 methanol/tap water (5 and 40 ng/mL in the original tap water samples) with no preconcentration, derivatization, or chromatographic separation prior to analysis.
A Novel Chimeric Oncolytic Virus Vector for Improved Safety and Efficacy as a Platform for the Treatment of Hepatocellular Carcinoma (2018)

Oncolytic viruses represent an exciting new aspect of the evolving field of cancer immunotherapy. We have engineered a novel hybrid vector comprising vesicular stomatitis virus (VSV) and Newcastle disease virus (NDV), named recombinant VSV-NDV (rVSV-NDV), wherein the VSV backbone is conserved but its glycoprotein has been replaced by the hemagglutinin-neuraminidase (HN) and the modified, hyperfusogenic fusion (F) envelope proteins of recombinant NDV. In comparison to wild-type VSV, which kills cells through a classical cytopathic effect, the recombinant virus is able to induce tumor-specific syncytium formation, allowing efficient cell-to-cell spread of the virus and a rapid onset of immunogenic cell death. Furthermore, the glycoprotein exchange substantially abrogates the off-target effects in brain and liver tissue associated with wild-type VSV, resulting in a markedly enhanced safety profile, even in immune-deficient NOD.CB17-prkdc<sup>scid</sup>/NCrCrl (NOD-SCID) mice, which are highly susceptible to wild-type VSV. Although NDV causes severe pathogenicity in its natural avian hosts, the incorporation of the envelope proteins in the chimeric rVSV-NDV vector is avirulent in embryonated chicken eggs. Finally, systemic administration of rVSV-NDV in orthotopic hepatocellular carcinoma (HCC)-bearing immune-competent mice resulted in significant survival prolongation. This strategy, therefore, combines the beneficial properties of the rapidly replicating VSV platform with the highly efficient spread and immunogenic cell death of a fusogenic virus without risking the safety and environmental threats associated with either parental vector. Taking the data together, rVSV-NDV represents an attractive vector platform for clinical translation as a safe and effective oncolytic virus.<b>IMPORTANCE</b> The therapeutic efficacy of oncolytic viral therapy often comes as a tradeoff with safety, such that potent vectors are often associated with toxicity, while safer viruses tend to have attenuated therapeutic effects. Despite promising preclinical data, the development of VSV as a clinical agent has been substantially hampered by the fact that severe neurotoxicity and hepatotoxicity have been observed in rodents and nonhuman primates in response to treatment with wild-type VSV. Although NDV has been shown to have an attractive safety profile in humans and to have promising oncolytic effects, its further development has been severely restricted due to the environmental risks that it poses. The hybrid rVSV-NDV vector, therefore, represents an extremely promising vector platform in that it has been rationally designed to be safe, with respect to both the recipient and the environment, while being simultaneously effective, both through its direct oncolytic actions and through induction of immunogenic cell death.
Biological Characterization of 3-(2-amino-ethyl)-5-[3-(4-butoxyl-phenyl)-propylidene]-thiazolidine-2,4-dione (K145) as a Selective Sphingosine Kinase-2 Inhibitor and Anticancer Agent (2013)

In our effort to develop selective sphingosine kinase-2 (SphK2) inhibitors as pharmacological tools, a thiazolidine-2,4-dione analogue, 3-(2-amino-ethyl)-5-[3-(4-butoxyl-phenyl)-propylidene]-thiazolidine-2,4-dione (K145), was synthesized and biologically characterized. Biochemical assay results indicate that K145 is a selective SphK2 inhibitor. Molecular modeling studies also support this notion. In vitro studies using human leukemia U937 cells demonstrated that K145 accumulates in U937 cells, suppresses the S1P level, and inhibits SphK2. K145 also exhibited inhibitory effects on the growth of U937 cells as well as apoptotic effects in U937 cells, and that these effects may be through the inhibition of down-stream ERK and Akt signaling pathways. K145 also significantly inhibited the growth of U937 tumors in nude mice by both intraperitoneal and oral administration, thus demonstrating its in vivo efficacy as a potential lead anticancer agent. The antitumor activity of K145 was also confirmed in a syngeneic mouse model by implanting murine breast cancer JC cells in BALB/c mice. Collectively, these results strongly encourage further optimization of K145 as a novel lead compound for development of more potent and selective SphK2 inhibitors.
Optoelectronic information encryption with phase-shifting interferometry (2000)

A technique that combines the high speed and the high security of optical encryption with the advantages of electronic transmission, storage, and decryption is introduced. Digital phase-shifting interferometry is used for efficient recording of phase and amplitude information with an intensity recording device. The encryption is performed by use of two random phase codes, one in the object plane and another in the Fresnel domain, providing high security in the encrypted image and a key with many degrees of freedom. We describe how our technique can be adapted to encrypt either the Fraunhofer or the Fresnel diffraction pattern of the input. Electronic decryption can be performed with a one-step fast Fourier transform reconstruction procedure. Experimental results for both systems including a lensless setup are shown.
A low-temperature IC-compatible process for fabricating surface-micromachined metallic microchannels (1998)

In this paper, a low-temperature integrated-circuit (IC)-compatible process for fabricating metallic microchannels is described. Arrays of 1-100 metallic microchannels have been fabricated on silicon and glass substrates. The process can be extended to many planar substrate materials including polymers and ceramics. The microchannels are formed using microelectro-formed metals. The microchannels demonstrated in this paper use nickel as the structural material and gold as the surface coating on the inside walls of the microchannels. The inner dimensions of the individual microchannels fabricated to date range from 30 /spl mu/m to 1.5 mm in width, 0.5 mm to several centimeters in length, and 5-100 /spl mu/m in thickness. The wall thickness ranges from 5 to 50 /spl mu/m. The microchannel fabrication technology enables the fabrication of surface microchannels with a relatively large cross-sectional area. The metallic microchannels can be fabricated to extend from the substrate edge. Interfacing schemes are given for attaching external pressure feeds.
Automated motion correction using parallel-strip registration for wide-field en face OCT angiogram (2016)

We propose an innovative registration method to correct motion artifacts for wide-field optical coherence tomography angiography (OCTA) acquired by ultrahigh-speed swept-source OCT (>200 kHz A-scan rate). Considering that the number of A-scans along the fast axis is much higher than the number of positions along slow axis in the wide-field OCTA scan, a non-orthogonal scheme is introduced. Two en face angiograms in the vertical priority (2 y-fast) are divided into microsaccade-free parallel strips. A gross registration based on large vessels and a fine registration based on small vessels are sequentially applied to register parallel strips into a composite image. This technique is extended to automatically montage individual registered, motion-free angiograms into an ultrawide-field view.
Automatic control of excitation parameters for switched-reluctance motor drives (2003)

This paper presents a new approach to the automatic control of the turn-on angle used to excite the switched-reluctance motor (SRM). The control algorithm determines the turn-on angle that supports the most efficient operation of the motor drive system, and consists of two pieces. The first piece of the control technique monitors the position of the first peak of the phase current (/spl theta//sub p/) and seeks to align this position with the angle where the inductance begins to increase (/spl theta//sub m/). The second piece of the controller monitors the peak phase current and advances the turn-on angle if the commanded reference current cannot be produced by the controller. The first piece of the controller tends to be active below base speed of the SRM, where phase currents can be built easily by the inverter and /spl theta//sub p/ is relatively independent of /spl theta//sub m/. The second piece of the controller is active above base speed, where the peak of the phase currents tends to naturally occur at /spl theta//sub m/ regardless of the current amplitude. The two pieces of the controller naturally exchange responsibility as a result of a change in command or operating point. The motor, inverter and control system are modeled in Simulink to demonstrate the operation of the system. The control technique is then applied to an experimental SRM system. Experimental operation documents that the technique provides for efficient operation of the drive.
Automatic calibration of stratigraphic forward models for predicting reservoir presence in exploration (2014)

Understanding and predicting reservoir presence and characteristics at regional to basin scales is important for evaluating risk and uncertainty in hydrocarbon exploration. Simulating reservoir distribution within a basin by a stratigraphic forward model enables the integration of available prior information with fundamental geologic processes embedded in the numerical model. Stratigraphic forward model predictions can be significantly improved by calibrating the models to independent constraints, such as thicknesses from seismic or well data. A three-dimensional basin-scale stratigraphic forward-modeling tool is coupled with an inversion algorithm. The inversion algorithm is a modification of the neighborhood algorithm (a type of genetic algorithm), which is designed to sample complex multimodal objective functions and is parallelized on computer clusters to accelerate convergence. The process generates a set of representative geological models that are consistent with prior ranges for uncertain parameters, calibration constraints, and associated tolerance thresholds. The workflow is first demonstrated on two data sets: a synthetic example based on a clastic passive margin and a real hydrocarbon exploration example for slope and basin-floor stratigraphic traps in the Neocomian (Lower Cretaceous) of the West Siberian Basin. The analysis of calibrated models provides constraints on stratigraphic controls, and allows prediction of locations with higher potential to develop stratigraphic traps. These locations are related to complex interactions between paleobathymetry, subsidence, eustatic fluctuations, characteristics of sediment-input sources, and sediment-transport parameters. Results show the potential of stratigraphic forward modeling combined with inverse methods as an additional tool to support conventional play-based exploration and reservoir-presence prediction.
Identification of a Small Molecule That Selectively Inhibits ERG-Positive Cancer Cell Growth (2018)

Oncogenic activation of the ETS-related gene (<i>ERG</i>) by recurrent gene fusions (predominantly TMPRSS2-ERG) is one of the most validated and prevalent genomic alterations present in early stages of prostate cancer. In this study, we screened small-molecule libraries for inhibition of ERG protein in <i>TMPRSS2-ERG</i> harboring VCaP prostate cancer cells using an In-Cell Western Assay with the highly specific ERG-MAb (9FY). Among a subset of promising candidates, 1-[2-Thiazolylazo]-2-naphthol (NSC139021, hereafter ERGi-USU) was identified and further characterized. ERGi-USU selectively inhibited growth of ERG-positive cancer cell lines with minimal effect on normal prostate or endothelial cells or ERG-negative tumor cell lines. Combination of ERGi-USU with enzalutamide showed additive effects in inhibiting growth of VCaP cells. A screen of kinases revealed that ERGi-USU directly bound the ribosomal biogenesis regulator atypical kinase RIOK2 and induced ribosomal stress signature. <i>In vivo</i>, ERGi-USU treatment inhibited growth of ERG-positive VCaP tumor xenografts with no apparent toxicity. Structure-activity-based derivatives of ERGi-USU recapitulated the ERG-selective activity of the parental compound. Taken together, ERGi-USU acts as a highly selective inhibitor for the growth of ERG-positive cancer cells and has potential for further development of ERG-targeted therapy of prostate cancer and other malignancies.<b>Significance:</b> A highly selective small-molecule inhibitor of ERG, a critical driver of early stages of prostate cancer, will be imperative for prostate cancer therapy. <i>Cancer Res; 78(13); 3659-71. ©2018 AACR</i>.
Characterization of higher-order-mode content in large-mode-area fibers (2008)

Higher-order modes propagating in large-mode-area fibers are characterized using spatially-resolved modal interference. The measurements provide the fraction of power contained in multiple higher-order-modes, and allow for mode identification without prior knowledge of the fiber characteristics.