gebhart/patrepeval huggingface dataset:
Proximity Charge Sensing With Semiconductor Detectors (2009)

Semiconductor radiation detectors are routinely used for the detection, imaging, and spectroscopy of gamma-ray, x-ray, and charged particles. In basic form, a detector is comprised of a semiconductor crystal with two or more electrodes formed on its surfaces. Besides allowing for the application of bias voltage, one or more of the electrodes on a detector also serve as readout electrode. Charge carriers drifting across the detector induce a charge signal on the electrode, which can then be measured by a charge-sensitive amplifier connected to the electrode. Although in general the readout electrodes of a detector are formed on the detector itself, charge can be induced on any electrode, even if the electrode is not physically in contact with the semiconductor. Such proximity charge sensing effects can be utilized to achieve a variety of advantages in applications involving semiconductor detectors. In this paper, we report on the experimental verification of signal readout using proximity electrodes and demonstrate several possible applications of this technique, including the position-sensitive readout of detectors and the sensing of incomplete charge collection in detectors as a means to reduce spectral background.
A<i>Limulus</i>Antilipopolysaccharide Factor-Derived Peptide Exhibits a New Immunological Activity with Potential Applicability in Infectious Diseases (2000)

Previous studies have shown that cyclic peptides corresponding to residues 35 to 52 of the Limulus antilipopolysaccharide (anti-LPS) factor (LALF) bind and neutralize LPS-mediated in vitro and in vivo activities. Therapeutic approaches based on agents which bind and neutralize LPS activities are particularly attractive because these substances directly block the primary stimulus for the entire proinflammatory cytokine cascade. Here we describe new activities of the LALF(31-52) peptide, other than its LPS binding ability. Surprisingly, supernatants from human mononuclear cells stimulated with the LALF peptide are able to induce in vitro antiviral effects on the Hep-2 cell line mediated by gamma interferon (IFN-gamma) and IFN-alpha. Analysis of the effect of LALF(31-52) on tumor necrosis factor (TNF) and nitric oxide (NO) production by LPS-stimulated peritoneal macrophages revealed that a pretreatment with the peptide decreased LPS-induced TNF production but did not affect NO generation. This indicates that the LALF peptide modifies the LPS-induced response. In a model in mice with peritoneal fulminating sepsis, LALF(31-52) protected the mice when administered prophylactically, and this effect is related to reduced systemic TNF-alpha levels. This study demonstrates, for the first time, the anti-inflammatory properties of the LALF-derived peptide. These properties widen the spectrum of the therapeutic potential for this LALF-derived peptide and the molecules derived from it. These agents may be useful in the prophylaxis and therapy of viral and bacterial infectious diseases, as well as for septic shock.
Extreme Compression of Weather Radar Data (2007)

A method for achieving extreme levels of compression of high-volume weather radar data is presented. Weather reflectivity contours, as per National Weather Service or custom thresholds, are processed by tracing their departure from a smoothed version to obtain the local extrema which serve as control points. The control points, which are transmitted in relative coordinates for further compression, are interpolated using a second-degree B-spline to retrieve the contours. The encoding-decoding method is capable of capturing the random undulations inherent in weather contours. It is shown that over two orders of magnitude of compression is possible without perceptible loss of meteorological information. Multiple enhancements to the basic method are quantitatively studied and compared with the existing methods for radar data compression.
Selective Small Molecule Recognition of RNA Base Pairs (2018)

Many types of RNAs exist in the human transcriptome, yet only the bacterial ribosome has been exploited as a small molecule drug target. Aside from rRNA, other cellular RNAs such as noncoding RNAs have primarily secondary structure and limited tertiary structure. Within these secondary structures of noncanonically paired and unpaired regions, more than 50% are base paired, with most efforts to target these structures focused on looped regions. A void exists in the availability of small molecules capable of targeting RNA base pairs. Using chemoinformatics, an RNA-focused library enriched for nitrogen-containing heterocycles was developed and tested for binding RNA base pairs, leading to the identification of six selective and previously unknown binders. While all binders were derivatives of benzimidazoles, those with expanded aromatic polycycles bound selectively to AU pairs, while those with flexible urea side chains bound selectively to GC pairs. Two of the three selective GC pair binders can distinguish between two different orientations, 5'GG/3'CC and 5'GC/3'CG pairs. Furthermore, all six molecules showed >50-fold selectivity for RNA over DNA. These studies provide foundational knowledge to better exploit RNA as targets for small molecule chemical probes or lead therapeutics by using modules that target RNA base pairs.
Safety and Efficacy of Erythrocyte Encapsulated Thymidine Phosphorylase in Mitochondrial Neurogastrointestinal Encephalomyopathy (2019)

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare autosomal recessive disorder of nucleoside metabolism that is caused by mutations in the nuclear thymidine phosphorylase gene (<i>TYMP</i>) gene, encoding for the enzyme thymidine phosphorylase. There are currently no approved treatments for MNGIE. The aim of this study was to investigate the safety, tolerability, and efficacy of an enzyme replacement therapy for the treatment of MNGIE. In this single centre study, three adult patients with MNGIE received intravenous escalating doses of erythrocyte encapsulated thymidine phosphorylase (EE-TP; dose range: 4 to 108 U/kg/4 weeks). EE-TP was well tolerated and reductions in the disease-associated plasma metabolites, thymidine, and deoxyuridine were observed in all three patients. Clinical improvements, including weight gain and improved disease scores, were observed in two patients, suggesting that EE-TP is able to reverse some aspects of the disease pathology. Transient, non-serious adverse events were observed in two of the three patients; these did not lead to therapy discontinuation and they were managed with pre-medication prior to infusion of EE-TP. To conclude, enzyme replacement therapy with EE-TP demonstrated biochemical and clinical therapeutic efficacy with an acceptable clinical safety profile.
Real‐time imaging of two‐dimensional cardiac strain using a harmonic phase magnetic resonance imaging (HARP‐MRI) pulse sequence (2003)

The harmonic phase (HARP) method provides automatic and rapid analysis of tagged magnetic resonance (MR) images for quantification and visualization of myocardial strain. In this article, the development and implementation of a pulse sequence that acquires HARP images in real time are described. In this pulse sequence, a CINE sequence of images with 1-1 spatial modulation of magnetization (SPAMM) tags are acquired during each cardiac cycle, alternating between vertical and horizontal tags in successive heartbeats. An incrementing train of imaging RF flip angles is used to compensate for the decay of the harmonic peaks due to both T(1) relaxation and the applied imaging pulses. The magnitude images displaying coarse anatomy are automatically reconstructed and displayed in real time after each heartbeat. HARP strain images are generated offline at a rate of four images per second; real-time processing should be possible with faster algorithms or computers. A comparison of myocardial contractility in non-breath-hold and breath-hold experiments in normal humans is presented.
Novel quadrature birdcage coil for a verticalB0 field open MRI system (2000)

A birdcage coil possesses various intrinsic resonant modes. One of the modes produces sinusoidal current distribution around the rung elements of the birdcage and generates a highly uniform B(1) field in the transverse plane. Another mode is the end-ring resonant mode, in which there are no currents in the rungs of the birdcage, leaving the currents flowing in the top and bottom end-rings. Thus, this mode behaves like a "Helmholtz pair," producing a highly uniform B(1) field along the axis of the birdcage. By combining the sinusoidal resonant mode and the end-ring resonant mode at the same frequency, a quadrature birdcage coil for a vertical B(0) field is made possible. In particular, the coil dimension can be chosen such that the two end-ring loops behave as a Helmholtz pair, assuring the optimized B(1) field uniformity around the coil center region. The coil is well suited for a vertical B(0) MRI system, as both B(1) fields are perpendicular to the vertical B(0) field. To mimic a vertical B(0) field orientation, an existing horizontal bore MRI system was used with the RF coil oriented to simulate a "vertical" B(0) field. This is a report of the successful quadrature implementation of this novel birdcage coil.
Modeling and Control for Deadlock-Free Operation of Single-Arm Cluster Tools With Concurrently Processing Multiple Wafer Types via Petri Net (2021)

Nowadays, cluster tools tend to concurrently process multiple types of wafers with similar recipes in order to improve their utilization and flexibility in semiconductor manufacturing. Different wafer types may have different wafer flow patterns, resulting in that cluster tools are deadlock-prone. It is challenging to develop a general method to solve the deadlock problem of cluster tools without restriction on the wafer types. This work aims at solving such a challenging problem for single-arm cluster tools. To do so, a general Petri net model is developed for single-arm cluster tools. Given the wafer flow patterns of all wafer types to be processed in a single-arm cluster tool, such a Petri net model can be easily obtained by defining the relationship between places and transitions. Then, a control method by using self-loops is presented to prevent the model from deadlocks during the evolutions from the initial state to the final state. Furthermore, such a control method is proved to be optimal. Illustrative examples are given to verify the proposed method at last.
Electrode design for coplanar-grid detectors (1997)

The coplanar-grid charge sensing technique provides a method for improving the spectral response of gamma-ray detectors based on compound semiconductors, which typically have poor charge transport properties. The technique functions by effectively modifying the charge induction characteristics of the detector such that the dependence of detector signal on the depth of radiation interaction is minimized. The effectiveness of this technique however can be compromised by non-uniform charge induction characteristics across the detector. This paper examines such non-uniformity due to fringe effects near the detector edges. Alternate electrode configurations are studied that provide effective compensation for such effects. Results from experimental measurements and computer simulations are presented.
Spongy Degeneration of the Brain, Canavan Disease: Biochemical and Molecular Findings (1998)

Canavan disease is a severe progressive leukodystrophy characterized by swelling and spongy degeneration of the white matter of the brain. It is an autosomal recessive disease found more frequently among Ashkenazi Jews. The clinical features are those of severe mental retardation with inability to gain developmental milestones. Hypotonia, head lag and macrocephaly are characteristic of Canavan disease and become apparent after 5–6 months of age. Massive excretion in the urine of N-acetylaspartic acid is the biochemical marker for Canavan disease, which is caused by deficiency of the enzyme aspartocylase. This discovery allowed for accurate diagnosis of Canavan disease, while prior to that, a brain biopsy was needed. The gene for aspartoacylase has been cloned and two mutations predominate among Ashkenazi Jewish individuals with Canavan disease and account for more than 98% of the Ashkenazi Jewish patients. The mutations among other ethnic groups are more diverse. The carrier frequency for the two common mutations among Ashkenazi Jews was found to be surprisingly high, 1: 37. Screening for carriers is now common practice for this population. A knock-out mouse for Canavan disease is being genetically engineered in our laboratory. The mouse model will allow for development of strategies for gene therapy.
Proposal of a Single-Transistor-Type Ferroelectric Memory Using an SOI Structure and Experimental Study on Interference Problem in Write Operation (1996)

1996 International Conference on Solid State Devices and Materials,Proposal of a Single-Transistor-Type Ferroelectric Memory Using an SOI Structure and Experimental Study on Interference Problem in Write Operation
Metal-assisted exfoliation (MAE): green, roll-to-roll compatible method for transferring graphene to flexible substrates (2015)

Graphene is expected to play a significant role in future technologies that span a range from consumer electronics, to devices for the conversion and storage of energy, to conformable biomedical devices for healthcare. To realize these applications, however, a low-cost method of synthesizing large areas of high-quality graphene is required. Currently, the only method to generate large-area single-layer graphene that is compatible with roll-to-roll manufacturing destroys approximately 300 kg of copper foil (thickness = 25 μm) for every 1 g of graphene produced. This paper describes a new environmentally benign and scalable process of transferring graphene to flexible substrates. The process is based on the preferential adhesion of certain thin metallic films to graphene; separation of the graphene from the catalytic copper foil is followed by lamination to a flexible target substrate in a process that is compatible with roll-to-roll manufacturing. The copper substrate is indefinitely reusable and the method is substantially greener than the current process that uses relatively large amounts of corrosive etchants to remove the copper. The sheet resistance of the graphene produced by this new process is unoptimized but should be comparable in principle to that produced by the standard method, given the defects observable by Raman spectroscopy and the presence of process-induced cracks. With further improvements, this green, inexpensive synthesis of single-layer graphene could enable applications in flexible, stretchable, and disposable electronics, low-profile and lightweight barrier materials, and in large-area displays and photovoltaic modules.
Protective Immunogenicity of Group A Streptococcal M-Related Proteins (2015)

Many previous studies have focused on the surface M proteins of group A streptococci (GAS) as virulence determinants and protective antigens. However, the majority of GAS isolates express M-related protein (Mrp) in addition to M protein, and both have been shown to be required for optimal virulence. In the current study, we evaluated the protective immunogenicity of Mrp to determine its potential as a vaccine component that may broaden the coverage of M protein-based vaccines. Sequence analyses of 33 mrp genes indicated that there are three families of structurally related Mrps (MrpI, MrpII, and MrpIII). N-terminal peptides of Mrps were cloned, expressed, and purified from M type 2 (M2) (MrpI), M4 (MrpII), and M49 (MrpIII) GAS. Rabbit antisera against the Mrps reacted at high titers with the homologous Mrp, as determined by enzyme-linked immunosorbent assay, and promoted bactericidal activity against GAS emm types expressing Mrps within the same family. Mice passively immunized with rabbit antisera against MrpII were protected against challenge infections with M28 GAS. Assays for Mrp antibodies in serum samples from 281 pediatric subjects aged 2 to 16 indicated that the Mrp immune response correlated with increasing age of the subjects. Affinity-purified human Mrp antibodies promoted bactericidal activity against a number of GAS representing different emm types that expressed an Mrp within the same family but showed no activity against emm types expressing an Mrp from a different family. Our results indicate that Mrps have semiconserved N-terminal sequences that contain bactericidal epitopes which are immunogenic in humans. These findings may have direct implications for the development of GAS vaccines.
High-contrast, synchronous volumetric imaging with selective volume illumination microscopy (2020)

Light-field fluorescence microscopy uniquely provides fast, synchronous volumetric imaging by capturing an extended volume in one snapshot, but often suffers from low contrast due to the background signal generated by its wide-field illumination strategy. We implemented light-field-based selective volume illumination microscopy (SVIM), where illumination is confined to only the volume of interest, removing the background generated from the extraneous sample volume, and dramatically enhancing the image contrast. We demonstrate the capabilities of SVIM by capturing cellular-resolution 3D movies of flowing bacteria in seawater as they colonize their squid symbiotic partner, as well as of the beating heart and brain-wide neural activity in larval zebrafish. These applications demonstrate the breadth of imaging applications that we envision SVIM will enable, in capturing tissue-scale 3D dynamic biological systems at single-cell resolution, fast volumetric rates, and high contrast to reveal the underlying biology.
Semiconductor nanomembranes: a platform for new science and technology (2011)

Semiconductor nanomembranes, extremely thin (<10 to ~1000 nm) single-crystal sheets, promise considerable new science and technology. They are flexible, they are readily transferable to other hosts and conform and bond easily, and they can take on a large range of shapes (tubes, spirals, ribbons, wires) via appropriate strain engineering and patterning. The ready ability to stack membranes allows the integration of the properties of different materials and/or orientations. A brief review of nanomembrane fabrication and manipulation with a view toward different types of applications is provided.
Optics for Encoders and Integration (2007)

Optics for encoders is studied from the point of view of signal improvement and miniaturization. Basis of optical encoder is the superposition of two gratings. Moire encoder consisting of two superimposed gratings is simple but the encoder signal is often affected by the variation of air gap due to the Fourier image effect. In this paper, basic optics of the encoders is summarized and some advanced optics for the Moire encoders are explained to suppress the influence.
Immunogenicity and protective efficacy of adenoviral and subunit RSV vaccines based on stabilized prefusion F protein in pre-clinical models (2021)

Respiratory Syncytial Virus (RSV) remains a leading cause of severe respiratory disease for which no licensed vaccine is available. We have previously described the derivation of an RSV Fusion protein (F) stabilized in its prefusion conformation (preF) as vaccine immunogen and demonstrated superior immunogenicity in naive mice of preF versus wild type RSV F protein, both as protein and when expressed from an Ad26 vaccine vector. Here we address the question if there are qualitative differences between the two vaccine platforms for induction of protective immunity. In naïve mice, both Ad26.RSV.preF and preF protein induced humoral responses, whereas cellular responses were only elicited by Ad26.RSV.preF. In RSV pre-exposed mice, a single dose of either vaccine induced cellular responses and strong humoral responses. Ad26-induced RSV-specific cellular immune responses were detected systemically and locally in the lungs. Both vaccines showed protective efficacy in the cotton rat model, but Ad26.RSV.preF conferred protection at lower virus neutralizing titers in comparison to RSV preF protein. Factors that may contribute to the protective capacity of Ad26.RSV.preF elicited immunity are the induced IgG2a antibodies that are able to engage Fcγ receptors mediating Antibody Dependent Cellular Cytotoxicity (ADCC), and the induction of systemic and lung resident RSV specific CD8 + T cells. These data demonstrate qualitative improvement of immune responses elicited by an adenoviral vector based vaccine encoding the RSV preF antigen compared to the subunit vaccine in small animal models which may inform RSV vaccine development.
Water Solubility in Ionic Liquids and Application to Absorption Cycles (2010)

The absorption cooling cycle has been in use for more than 100 years. Although the vapor compression cycle is now used for most air-conditioning and refrigeration applications, the well-known refrigerant−absorbent systems (water−LiBr and ammonia−water) are still being used for space cooling and industrial refrigeration. Recently, absorption cooling cycles using water + room-temperature ionic liquids (RTILs) have been proposed as a replacement for the water + LiBr system. There have been a few reports in the literature since about the year 2000 on the solubility of water in RTILs, and some of the hydrophilic RTILs show extremely high mutual solubility with water, indicating formation of chemical complexes. Almost all solubility data have been correlated with the use of activity (or solution) models. In the present report, we apply an equation of state (EOS) model in order to understand the solubility characteristics, as well as the chemical complex formation, consistently with the same thermodynamic model. Also, such a model is convenient for estimating the performance of the absorption cooling cycle, as we have demonstrated in the past for the absorption cycle performance of various hydrofluorocarbons (HFCs) + solvents and ammonia + RTILs. The present purpose is to examine the feasibility of using water and RTILs in an absorption cooling cycle and to show some promising results for this application.
Propeller EPI in the other direction (2006)

A new propeller EPI pulse sequence with reduced sensitivity to field inhomogeneities is proposed. Image artifacts such as blurring due to Nyquist ghosting and susceptibility gradients are investigated and compared with those obtained in previous propeller EPI studies. The proposed propeller EPI sequence uses a readout that is played out along the short axis of the propeller blade, orthogonal to the readout used in previous propeller methods. In contrast to long-axis readout propeller EPI, this causes the echo spacing between two consecutive phase-encoding (PE) lines to decrease, which in turn increases the k-space velocity in this direction and hence the pseudo-bandwidth. Long- and short-axis propeller EPI, and standard single-shot EPI sequences were compared on phantoms and a healthy volunteer. Diffusion-weighted imaging (DWI) was also performed on the volunteer. Short-axis propeller EPI produced considerably fewer image artifacts compared to the other two sequences. Further, the oblique blades for the long-axis propeller EPI were also prone to one order of magnitude higher residual ghosting than the proposed short-axis propeller EPI.