gebhart/patrepeval huggingface dataset:
Detection of Antibodies to the Feline Leukemia Virus (FeLV) Transmembrane Protein p15E: an Alternative Approach for Serological FeLV Detection Based on Antibodies to p15E (2014)

The aim of this report was to investigate whether the diagnosis of feline leukemia virus (FeLV) infection by serology might be feasible and useful. Among the various viral proteins, the FeLV env-gene product (SU) and the envelope transmembrane protein p15E were considered promising candidates for the serological diagnosis of FeLV infection. Thus, we evaluated p15E and three other FeLV antigens, namely, a recombinant env-gene product, whole FeLV, and a short peptide from the FeLV transmembrane protein, for their potential to detect FeLV infection. To evaluate possible exposure of cats to FeLV, we tested serum and plasma samples from experimentally and naturally infected and vaccinated cats for the presence of antibodies to these antigens by enzyme-linked immunosorbent assays (ELISAs). The serological results were compared with the p27 and proviral real-time PCR results. We found that p15E displayed a diagnostic sensitivity of 95.7% and a specificity of 100% in experimentally infected cats. In naturally infected cats, p15E showed a diagnostic sensitivity of 77.1% and a specificity of 85.6%. Vaccinated cats displayed minimal antibody levels to p15E, suggesting that anti-p15E antibodies indicate infection rather than vaccination. The other antigens turned out to be too unspecific. The lower specificity in cats exposed to FeLV under field conditions may be explained by the fact that some cats become infected and seroconvert in the absence of detectable viral nucleic acids in plasma. We conclude that p15E serology may become a valuable tool for diagnosing FeLV infection; in some cases, it may replace PCR.
A novel framework for automatic segmentation of kidney from DW-MRI (2015)

The segmentation of the kidney tissues is a key step in developing any non-invasive computer-aided diagnostic (CAD) system for early detection of acute renal transplant rejection. This paper introduces a geometric (level-set)-based deformable model approach for the 3D kidney segmentation from diffusion-weighted magnetic resonance imaging (DW-MRI). The proposed deformable model is guided by a stochastic speed relationship based on an adaptive shape prior guided by the visual appearance of the DW-MRI data. The voxel-wise guiding of the level-sets is obtained by integrating these three image features into a joint Markov-Gibbs random field (MGRF) model of the kidney and its background. The segmentation approach was evaluated for 40 DW-MRI data sets acquired at b-values ranging from 0 to 1000 s/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and compared against other segmentation methods using three evaluation metrics: the Dice similarity coefficient (DSC), the 95-percentile modified Hausdorff distance, and the absolute kidney volume difference. Experimental results' evaluation between manually drawn and automatically segmented contours confirm the robustness and accuracy of the proposed approach.
Cloning and Expression of a β-Galactosidase Gene of<i>Bacillus circulans</i> (2011)

A gene of β-galactosidase from Bacillus circulans ATCC 31382 was cloned and sequenced on the basis of N-terminal and internal peptide sequences isolated from a commercial enzyme preparation, Biolacta(®). Using the cloned gene, recombinant β-galactosidase and its deletion mutants were overexpressed as His-tagged proteins in Escherichia coli cells and the enzymes expressed were characterized.
Sculpture paintings (2018)

We present a framework for automatically creating a type of artwork in which 2D and 3D contents are mixed within the same composition. These artworks create plausible effects for the viewers by showing a different relationship between 2D and 3D at each viewing angle. As the viewing angle is changed, we can clearly see 3D elements emerging from the scene. When creating such artwork, we face several challenges. The main challenge is to ensure the continuity between the 2D and the 3D parts in terms of geometry and colors. We provide a 3D synthetic environment in which the user selects the region of interest (ROI) from a given scene object to be shown in 3D. Then we create a flat rendering grid that matches the topology of the ROI and attach the ROI to the rendering grid. Next we create textures for the flat part and the ROI. To enhance the continuity between the 2D and the 3D parts of the object, we include bas-relief profiles around the ROI. Our framework can be used as a tool in order to assist artists in designing such sculpture paintings. Furthermore, it can be applied by amateur users to create decorative objects for exhibitions, souvenirs, and homes.
Graceful Restart Mechanism for Label Distribution Protocol (2003)

This document describes a mechanism that helps to minimize the negative effects on MPLS traffic caused by Label Switching Router's (LSR's) control plane restart, specifically by the restart of its Label Distribution Protocol (LDP) component, on LSRs that are capable of preserving the MPLS forwarding component across the restart.
Spectroscopy of the IR transitions in Pr3+ doped heavy metal selenide glasses (1997)

The spectral properties of Pr 3+ doped BaInGaGeSe chalcogenide glasses are reported. Absorption spectra, emission spectra, and lifetimes of the lower lying manifolds have been measured. Radiative transition rates are calculated and compared with measured experimental lifetimes. The strong mid-IR emission and spectral properties of this glass make this glass a strong candidate for lasers, amplifiers, and high brightness sources in the mid-IR.
Cytotoxicity of VEGF121/rGel on vascular endothelial cells resulting in inhibition of angiogenesis is mediated via VEGFR-2 (2011)

Taken together, these data confirm the selectivity of VEGF(121)/rGel for VEGFR-2-overexpressing endothelial cells and represent the first analysis of genes governing intoxication of mammalian endothelial cells by a gelonin-based targeted therapeutic agent.
Ultrapotent vinblastines in which added molecular complexity further disrupts the target tubulin dimer–dimer interface (2016)

Approaches to improving the biological properties of natural products typically strive to modify their structures to identify the essential pharmacophore, or make functional group changes to improve biological target affinity or functional activity, change physical properties, enhance stability, or introduce conformational constraints. Aside from accessible semisynthetic modifications of existing functional groups, rarely does one consider using chemical synthesis to add molecular complexity to the natural product. In part, this may be attributed to the added challenge intrinsic in the synthesis of an even more complex compound. Herein, we report synthetically derived, structurally more complex vinblastines inaccessible from the natural product itself that are a stunning 100-fold more active (IC50 values, 50-75 pM vs. 7 nM; HCT116), and that are now accessible because of advances in the total synthesis of the natural product. The newly discovered ultrapotent vinblastines, which may look highly unusual upon first inspection, bind tubulin with much higher affinity and likely further disrupt the tubulin head-to-tail α/β dimer-dimer interaction by virtue of the strategic placement of an added conformationally well-defined, rigid, and extended C20' urea along the adjacent continuing protein-protein interface. In this case, the added molecular complexity was used to markedly enhance target binding and functional biological activity (100-fold), and likely represents a general approach to improving the properties of other natural products targeting a protein-protein interaction.
A Fast Method For Scaling Color Images (2009)

Publication in the conference proceedings of EUSIPCO, Glasgow, Scotland, 2009
Towards rhombohedral SiGe epitaxy on 150mm c-plane sapphire substrates (2015)

Previous work demonstrated for the first time the ability to epitaxially grow uniform single crystal diamond cubic SiGe (111) films on trigonal sapphire (0001) substrates. While SiGe (111) forms two possible crystallographic twins on sapphire (0001), films consisting primarily of one twin were produced on up to 99.95% of the total wafer area. This permits new bandgap engineering possibilities and improved group IV based devices that can exploit the higher carrier mobility in Ge compared to Si. Models are proposed on the epitaxy of such dissimilar crystal structures based on the energetic favorability of crystallographic twins and surface reconstructions. This new method permits Ge (111) on sapphire (0001) epitaxy, rendering Ge an economically feasible replacement for Si in some applications, including higher efficiency Si/Ge/Si quantum well solar cells. Epitaxial SiGe films on sapphire showed a 280% increase in electron mobility and a 500% increase in hole mobility over single crystal Si. Moreover, Ge possesses a wider bandgap for solar spectrum conversion than Si, while the transparent sapphire substrate permits an inverted device structure, increasing the total efficiency to an estimated 30-40%, much higher than traditional Si solar cells. Hall Effect mobility measurements of the Ge layer in the Si/Ge/Si quantum well structure were performed to demonstrate the advantage in carrier mobility over a pure Si solar cell. Another application comes in the use of microelectromechanical devices technology, where high-resistivity Si is currently used as a substrate. Sapphire is a more resistive substrate and offers better performance via lower parasitic capacitance and higher film carrier mobility over the current Si-based technology.
Large stable magnetic domains (1982)

Large, thin-film single domain areas have been observed, in the absence of a bias field, in garnets with magnetization perpendicular to the film plane.1,2 The domain stability in the work by Krumme1 was attributed to a combination of low saturation magnetization and a low Curie temperature. Uchishiba2 relates the stability in his double layer system to appropriate anisotropy fields in one layer compared to the magnetization in the other layer. A more complete model for large domain stability in a bias field free environment is given in this work. Three distinct stability regimes are predicted by the model and all have been observed experimentally. Areas 3.5-cm in diameter have been made into stable single domains. This was achieved in a material showing a zero bias strip width of 4.5 μm. The single domain diameter was, therefore, 7500 times the equilibrium energy domain width. The technique developed and the model have led to a new means for observing magnetic defects. More importantly, it also offers a means for measuring the strength of the defects. Possible applications of the model are also discussed.
From 2D to 1D Electronic Dimensionality in Halide Perovskites with Stepped and Flat Layers Using Propylammonium as a Spacer (2019)

Two-dimensional (2D) hybrid halide perovskites are promising in optoelectronic applications, particularly solar cells and light-emitting devices (LEDs), and for their increased stability as compared to 3D perovskites. Here, we report a new series of structures using propylammonium (PA<sup>+</sup>), which results in a series of Ruddlesden-Popper (RP) structures with the formula (PA)<sub>2</sub>(MA)<sub><i>n</i>-1</sub>Pb<sub><i>n</i></sub>I<sub>3<i>n</i>+1</sub> (<i>n</i> = 3, 4) and a new homologous series of "step-like" (SL) structures where the PbI<sub>6</sub> octahedra connect in a corner- and face-sharing motif with the general formula (PA)<sub>2<i>m</i>+4</sub>(MA)<sub><i>m</i>-2</sub>Pb<sub>2<i>m</i>+1</sub>I<sub>7<i>m</i>+4</sub> (<i>m</i> = 2, 3, 4). The RP structures show a blue-shift in bandgap for decreasing <i>n</i> (1.90 eV for <i>n</i> = 4 and 2.03 eV for <i>n</i> = 3), while the SL structures have an even greater blue-shift (2.53 eV for <i>m</i> = 4, 2.74 eV for <i>m</i> = 3, and 2.93 eV for <i>m</i> = 2). DFT calculations show that, while the RP structures are electronically 2D quantum wells, the SL structures are electronically 1D quantum wires with chains of corner-sharing octahedra "insulated" by blocks of face-sharing octahedra. Dark measurements for RP crystals show high resistivity perpendicular to the layers (10<sup>11</sup> Ω cm) but a lower resistivity parallel to them (10<sup>7</sup> Ω cm). The SL crystals have varying resistivity in all three directions, confirming both RP and SL crystals' utility as anisotropic electronic materials. The RP structures show strong photoresponse, whereas the SL materials exhibit resistivity trends that are dominated by ionic transport and no photoresponse. Solar cells were made with <i>n</i> = 3 giving an efficiency of 7.04% (average 6.28 ± 0.65%) with negligible hysteresis.
Electron Bunch Length Diagnostic With Coherent Smith-Purcell Radiation (1997)

We have designed a new technique for measuring subpicosecond electron bunch lengths using coherent Smith-Purcell radiation. This new diagnostic technique involves passing the electron beam in close proximity of a grating with period comparable to the electron bunch length. The emitted Smith-Purcell radiation will have a coherent component whose angular position and distribution are directly related to the electron bunch length and longitudinal profile, respectively. This new diagnostic technique is inherently simple, inexpensive and non-intercepting. We show that the new technique is also scaleable to femtosecond regime. 1
Quantitative Analysis of In-Field Defects in Image Sensor Arrays (2007)

Growth of pixel density and sensor array size increases the likelihood of developing in-field pixel defects. An ongoing study on defect development in imagers has now provided us sufficient data to be able to quantify characteristics of defect growth. Preliminary investigations have shown that defects are distributed randomly and the closest distance between two defective pixels is approximately 79-340 pixels apart. Furthermore, from an observation of 98 cluster-free defects, the diameter of the defect is estimated to be less than 2.3% of a pixel size at 99% confidence level. The fact that no defect clusters were found in the study of various digital cameras allows us to conclude that defects are not likely to be related to material degradation or imperfect fabrication but are due to environmental stress such as radiation. Furthermore, as verified by a statistical study, the absence of defect clustering provides information on the size of defects and insight into the nature of the defect development.
The Dolaflexin-based Antibody–Drug Conjugate XMT-1536 Targets the Solid Tumor Lineage Antigen SLC34A2/NaPi2b (2021)

Target selection for antibody-drug conjugates (ADC) frequently focuses on identifying antigens with differential expression in tumor and normal tissue, to mitigate the risk of on-target toxicity. However, this strategy restricts the possible target space. SLC34A2/NaPi2b is a sodium phosphate transporter expressed in a variety of human tumors including lung and ovarian carcinoma, as well as the normal tissues from which these tumors arise. Previous clinical trials with a NaPi2b targeting MMAE-ADCs have shown objective durable responses. However, the protein-based biomarker assay developed for use in that study was unable to discern a statistically significant relationship between NaPi2b protein expression and the probability of response. XMT-1536 is a NaPi2b targeting ADC comprised of a unique humanized antibody conjugated with 10-15 auristatin F- hydroxypropylamide (AF-HPA) payload molecules via the Dolaflexin platform. AF-HPA is a cell-permeable, antimitotic compound that is slowly metabolized intratumorally to an active, very low-permeable metabolite, auristatin F (AF), resulting in controlled bystander killing. We describe the preclinical <i>in vitro</i> and <i>in vivo</i> antitumor effects of XMT-1536 in models of ovarian and lung adenocarcinoma. Pharmacokinetic analysis showed approximately proportional increases in exposure in rat and monkey. Systemic free AF-HPA and AF concentrations were observed to be low in all animal species. Finally, we describe a unique IHC reagent, generated from a chimeric construct of the therapeutic antibody, that was used to derive a target expression and efficacy relationship in a series of ovarian primary xenograft cancer models.
Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody (2013)

The henipaviruses, represented by Hendra (HeV) and Nipah (NiV) viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia, Southeast Asia, India and Bangladesh. The high morbidity and mortality rates associated with infection and lack of licensed antiviral therapies make the henipaviruses a potential biological threat to humans and livestock. Henipavirus entry is initiated by the attachment of the G envelope glycoprotein to host cell membrane receptors. Previously, henipavirus-neutralizing human monoclonal antibodies (hmAb) have been isolated using the HeV-G glycoprotein and a human naïve antibody library. One cross-reactive and receptor-blocking hmAb (m102.4) was recently demonstrated to be an effective post-exposure therapy in two animal models of NiV and HeV infection, has been used in several people on a compassionate use basis, and is currently in development for use in humans. Here, we report the crystal structure of the complex of HeV-G with m102.3, an m102.4 derivative, and describe NiV and HeV escape mutants. This structure provides detailed insight into the mechanism of HeV and NiV neutralization by m102.4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines.
Novel Synthetic Antimicrobial Peptides against <i>Streptococcus mutans</i> (2007)

Streptococcus mutans, a common oral pathogen and the causative agent of dental caries, has persisted and even thrived on the tooth surface despite constant removal and eradication efforts. In this study, we generated a number of synthetic antimicrobial peptides against this bacterium via construction and screening of several structurally diverse peptide libraries where the hydrophobicity and charge within each library was varied incrementally in order to generate a collection of peptides with different biochemical characteristics. From these libraries, we identified multiple peptides with robust killing activity against S. mutans. To further improve their effectiveness, the most bactericidal peptides from each library were synthesized together as one molecule, in various combinations, with and without a flexible peptide linker between each antimicrobial region. Many of these "fusion" peptides had enhanced killing activities in comparison with those of the original nonconjoined molecules. The results presented here illustrate that small libraries of biochemically constrained peptides can be used to generate antimicrobial peptides against S. mutans, several of which may be likely candidates for the development of anticaries agents.
The Mechanism of Operation of Lateral and Vertical Organic Field Effect Transistors (2014)

Abstract In this contribution, we describe the working principles of organic field effect transistors. To place it in context, we start with a brief description of some aspects of semiconductor field effect transistors. We then describe the standard structure and properties of laterally aligned field effect transistors and at the end, touch upon some properties of the newly developed vertically stacked field effect transistors.
On the role of three-dimensional inverse design methods in turbomachinery shape optimization (1999)

The application of a three-dimensional (3D) inverse design method in which the blade geometry is computed for a specified distribution of circulation to the design of turbomachinery blades is explored by using two examples. In the first instance the method is applied to the design of radial and mixed flow impellers to suppress secondary flows. Based on our understanding of the fluid dynamics of the flow in the impeller, simple guidelines are developed for input specification of the inverse method in order to systematically design impellers with suppressed secondary flows and a more uniform exit flow field. In the second example the method is applied to the design of a vaned diffuser. Again based on the understanding of the detailed flow field in the diffuser obtained by using 3D viscous calculations and oil flow visualizations, simple design guidelines are developed for input specification to the inverse method in order to suppress corner separation. In both cases the guidelines are verified numerically and in the case of the diffuser further experimental validation is presented.
Anatomical location of Macrophage Migration Inhibitory Factor in urogenital tissues, peripheral ganglia and lumbosacral spinal cord of the rat (2003)

Therefore, MIF, a pro-inflammatory cytokine, is localized to pelvic organs and also in neurons of the peripheral and central nervous tissues that innervate those organs. Changes in MIF's expression at the end organ and at peripheral and central nervous system sites suggest that MIF is involved in pelvic viscera inflammation and may act at several levels to promote inflammatory changes.
A study of virtual memory MTU reassembly within the PowerPC architecture (2002)

Message transfer unit (MTU) reassembly schemes in modern operating systems cause I/O performance degradation when MTU sizes are larger than the architecture's page size. This can happen with emerging network technologies, such as Asynchronous Transfer Mode (ATM), where MTUs can be 64 KB or greater Traditional solutions either reassemble using memory copy or preallocate contiguous memory; these, however lack speed or consume excess resources, respectively. This paper presents an alternative scheme called Virtual Memory MTU Reassembly (VMMR) which reassembles non-contiguous pages through virtual memory remapping. VMMR allows hardware/software interfaces to efficiently DMA large MTUs in hardware pages and remap them to a contiguous address space. Studies done on a PowerPC 601 show that this method can outperform memcopy by one to two orders of magnitude (the maximum VMMR bandwidth is 14.7 Gbits/sec). High-performance multimedia applications, such as video on demand and video conferencing, can greatly benefit from such a performance boost.
Spiral Parallel Magnetic Resonance Imaginga (2006)

Spiral k-space scanning is a rapid magnetic resonance imaging (MRI) technique that can provide an order of magnitude reduction in scan time compared to conventional spin warp techniques. Parallel imaging is another method for reducing scan time that exploits spatially varying radiofrequency (RF) coil sensitivities to reduce the amount of data required to reconstruct an image. Combining spiral scanning with parallel imaging provide a scan time reduction factor that is the product of the reduction factors for each of the techniques and thus can permit very rapid imaging. Image reconstruction for spiral parallel MRI is more involved than for spin warp parallel MRI and is an area of active research. Two techniques for performing this image reconstruction are PILS, a simple image-domain method that relies on localized coil sensitivities, and BOSCO, a method that is based on successive convolution operations in k-space.