gebhart/patrepeval huggingface dataset:
Chromosomal rearrangements between tomato and <i>Solanum chilense</i> hamper mapping and breeding of the TYLCV resistance gene <i>Ty‐1</i> (2011)

Summary Tomato yellow leaf curl disease, a devastating disease of Solanum lycopersicum (tomato), is caused by a complex of begomoviruses generally referred to as Tomato yellow leaf curl virus (TYLCV). Almost all breeding for TYLCV resistance has been based on the introgression of the Ty‐1 resistance locus derived from Solanum chilense LA1969. Knowledge about the exact location of Ty‐1 on tomato chromosome 6 will help in understanding the genomic organization of the Ty‐1 locus. In this study, we analyze the chromosomal rearrangement and recombination behavior of the chromosomal region where Ty‐1 is introgressed. Nineteen markers on tomato chromosome 6 were used in F 2 populations obtained from two commercial hybrids, and showed the presence of a large introgression in both. Fluorescence in situ hybridization (FISH) analysis revealed two chromosomal rearrangements between S. lycopersicum and S. chilense LA1969 in the Ty‐1 introgression. Furthermore, a large‐scale recombinant screening in the two F 2 populations was performed, and 30 recombinants in the Ty‐1 introgression were identified. All recombination events were located on the long arm beyond the inversions, showing that recombination in the inverted region was absent. Disease tests on progenies of informative recombinants with TYLCV mapped Ty‐1 to the long arm between markers MSc05732‐4 and MSc05732‐14, an interval overlapping with the reported Ty‐3 region, which led to the indication that Ty‐1 and Ty‐3 may be allelic. With this study we prove that FISH can be used as a diagnostic tool to aid in the accurate mapping of genes that were introgressed from wild species into cultivated tomato.
Quantum dot lasers based on a stacked and strain-compensated active region grown by metal-organic chemical vapor deposition (2005)

We demonstrate an InAs∕GaAs quantum dot (QD) laser based on a strain-compensated, three-stack active region. Each layer of the stacked QD active region contains a thin GaP (Δao=−3.8%) tensile layer embedded in a GaAs matrix to partially compensate the compressive strain of the InAs (Δao=7%) QD layer. The optimized GaP thickness is ∼4MLs and results in a 36% reduction of compressive strain in our device structure. Atomic force microscope images, room-temperature photoluminescence, and x-ray diffraction confirm that strain compensation improves both structural and optical device properties. Room-temperature ground state lasing at λ=1.249μm, Jth=550A∕cm2 has been demonstrated.
JTAG-based vector and chain management for system test (2006)

We present an embedded boundary-scan test vector management solution that ensures the correct version of test vectors is applied to the unit under test (UUT). This new vector management approach leverages the system-level boundary-scan multi-drop architecture employed in some high availability electronic systems. Compared to previous methods that do not use system-level boundary-scan resources for vector management, this new approach ensures that the correct boundary-scan vectors are retrieved from the UUT without affecting its operation and requires minimal UUT functionality to execute. The performance and effectiveness of this technique is shown using an actual design example that has been realized in a new product
Self-templated chemically stable hollow spherical covalent organic framework (2015)

Covalent organic frameworks are a family of crystalline porous materials with promising applications. Although active research on the design and synthesis of covalent organic frameworks has been ongoing for almost a decade, the mechanisms of formation of covalent organic frameworks crystallites remain poorly understood. Here we report the synthesis of a hollow spherical covalent organic framework with mesoporous walls in a single-step template-free method. A detailed time-dependent study of hollow sphere formation reveals that an inside-out Ostwald ripening process is responsible for the hollow sphere formation. The synthesized covalent organic framework hollow spheres are highly porous (surface area ∼1,500 m(2 )g(-1)), crystalline and chemically stable, due to the presence of strong intramolecular hydrogen bonding. These mesoporous hollow sphere covalent organic frameworks are used for a trypsin immobilization study, which shows an uptake of 15.5 μmol g(-1) of trypsin.
A Bacteriophage T4 Nanoparticle-Based Dual Vaccine against Anthrax and Plague (2018)

<i>Bacillus anthracis</i> and <i>Yersinia pestis</i>, the causative agents of anthrax and plague, respectively, are two of the deadliest pathogenic bacteria that have been used as biological warfare agents. Although Biothrax is a licensed vaccine against anthrax, no Food and Drug Administration-approved vaccine exists for plague. Here, we report the development of a dual anthrax-plague nanoparticle vaccine employing bacteriophage (phage) T4 as a platform. Using an <i>in vitro</i> assembly system, the 120- by 86-nm heads (capsids) of phage T4 were arrayed with anthrax and plague antigens fused to the small outer capsid protein Soc (9 kDa). The antigens included the anthrax protective antigen (PA) (83 kDa) and the mutated (mut) capsular antigen F1 and the low-calcium-response V antigen of the type 3 secretion system from <i>Y. pestis</i> (F1mutV) (56 kDa). These viral nanoparticles elicited robust anthrax- and plague-specific immune responses and provided complete protection against inhalational anthrax and/or pneumonic plague in three animal challenge models, namely, mice, rats, and rabbits. Protection was demonstrated even when the animals were simultaneously challenged with lethal doses of both anthrax lethal toxin and <i>Y. pestis</i> CO92 bacteria. Unlike the traditional subunit vaccines, the phage T4 vaccine uses a highly stable nanoparticle scaffold, provides multivalency, requires no adjuvant, and elicits broad T-helper 1 and 2 immune responses that are essential for complete clearance of bacteria during infection. Therefore, phage T4 is a unique nanoparticle platform to formulate multivalent vaccines against high-risk pathogens for national preparedness against potential bioterror attacks and emerging infections.<b>IMPORTANCE</b> Following the deadly anthrax attacks of 2001, the Centers for Disease Control and Prevention (CDC) determined that <i>Bacillus anthracis</i> and <i>Yersinia pestis</i> that cause anthrax and plague, respectively, are two Tier 1 select agents that pose the greatest threat to the national security of the United States. Both cause rapid death, in 3 to 6 days, of exposed individuals. We engineered a virus nanoparticle vaccine using bacteriophage T4 by incorporating key antigens of both <i>B. anthracis</i> and <i>Y. pestis</i> into one formulation. Two doses of this vaccine provided complete protection against both inhalational anthrax and pneumonic plague in animal models. This dual anthrax-plague vaccine is a strong candidate for stockpiling against a potential bioterror attack involving either one or both of these biothreat agents. Further, our results establish the T4 nanoparticle as a novel platform to develop multivalent vaccines against pathogens of high public health significance.
Design of a Modular E-Core Flux Concentrating Transverse Flux Machine (2018)

In this paper, a novel E-Core transverse flux machine (TFM) is proposed. The machine has a double stator-single rotor configuration with flux concentrating ferrite magnets and pole windings across each leg of an E-Core stator. E-Core stators with the proposed flux-concentrating rotor arrangement result in better magnet utilization and higher torque density. The machine also has a modular structure facilitating simpler construction. This paper presents a single phase and a two-phase version of the E-Core machine. Case study for a 1 kW, 400 r/min machine for both the single phase and two-phase TFM is presented.
Paintable Room‐Temperature Phosphorescent Liquid Formulations of Alkylated Bromonaphthalimide (2018)

Organic phosphors have been widely explored with an understanding that crystalline molecular ordering is a requisite for enhanced intersystem crossing. In this context, we explored the room-temperature phosphorescence features of a solvent-free organic liquid phosphor in air. While alkyl chain substitution varied the physical states of the bromonaphthalimides, the phosphorescence remained unaltered for the solvent-free liquid in air. As the first report, a solvent-free liquid of a long swallow-tailed bromonaphthalimide exhibits room-temperature phosphorescence in air. Doping of the phosphor with carbonyl guests resulted in enhanced phosphorescence, and hence a large-area paintable phosphorescent liquid composite with improved lifetime and quantum yield was developed.
<title>In-line fiber etalon (ILFE) for internal strain measurement</title> (1994)

This paper describes an optical fiber interferometer that uses a short segment of silica hollow- core fiber spliced between two sections of single-mode fiber to form a mechanically robust in- line optical cavity. The hollow-core fiber is specifically manufactured to have an outer diameter that is equal to the outer diameter of the single mode lead fibers, thereby combining the best qualities of existing intrinsic and extrinsic Fabry-Perot sensors. Uniaxial tension and pure bending strength tests are used to show that the new configuration does not diminish the axial strength of bare fiber and reduces the bending strength by 17% at most. Similar tests confirm that the fiber sensor has 1.96% strain to failure. Axisymmetric finite element analysis is used to investigate the reliability of the in-line etalon during typical thermoset composite cure conditions, and parametric studies are performed to determine the mechanically optimal cavity length. The sensor strain response tests demonstrate a dynamic strain resolution of 21 n(epsilon) /(root)Hz at frequencies > 5 Hz with a sensor gauge length of 137 micrometers .
Freeform microfluidic networks encapsulated in laser printed three-dimensional macro-scale glass objects (2019)

Large-scale microfluidic microsystems with complex three-dimensional (3D) configurations are highly in demand by both fundamental research and industrial application, holding the potentials for fostering a wide range of innovative applications such as lab-on-a-chip and organ-on-a-chip as well as continuous-flow manufacturing of fine chemicals. However, freeform fabrication of such systems remains challenging for most of the current fabrication techniques in terms of fabrication resolution, flexibility, and achievable footprint size. Here, we report ultrashort pulse laser microfabrication of freeform microfluidic circuits with high aspect ratios and tunable diameters embedded in 3D printed glass objects. We achieve uniform microfluidic channel diameter by carefully distributing a string of extra access ports along the microfluidic channels for avoiding the over-etching in the thin microfluidic channels. After the chemical etching is completed, the extra access ports are sealed using carbon dioxide laser induced localized glass melting. We demonstrate a model hand of fused silica with a size of ~3 cm * 2.7 cm * 1.1 cm in which the whole blood vessel system is encapsulated.
Performance of a New Al2O3/Ce–TZP Ceramic Nanocomposite Dental Implant: A Pilot Study in Dogs. (2017)

Although titanium remains as the prevalent material in dental implant manufacturing new zirconia-based materials that overcome the major drawbacks of the standard 3Y-yttria partially-stabilized zirconia (Y-TZP) are now emerging. In this study, a new ceramic nanocomposite made of alumina and ceria-stabilized TZP (ZCe-A) has been used to produce dental implants with the mechanic and topographic characteristics of a pilot implant design to evaluate bone and soft tissue integration in a dog model (<i>n</i> = 5). Histological cross-section analysis of the implanted ceramic fixations (<i>n</i> = 15) showed not only perfect biocompatibility, but also a high rate of osseous integration (defined as the percentage of bone to implant contact) and soft tissue attachment. This clinical success, in combination with the superior mechanical properties achieved by this Al₂O₃/Ce-TZP nanocomposite, may place this material as an improved alternative of traditional 3Y-TZP dental implants.
Spin wave nanofabric update (2012)

We provide a progress update on the spin wave nanofabric. The nanofabric comprises magneto-electric cells and spin wave buses serving for spin wave propagation. The magneto-electric cells are used as the input/output ports for information transfer between the charge and the spin domains, while information processing inside the nanofabric is via spin waves only. Information is encoded into the phase of the propagating spin wave, which makes it possible to utilize waveguides as passive logic elements and take the advantage of using wave superposition for data processing. This provides a fundamental advantage over the conventional transistor-based logic circuitry allowing for functional throughput enhancement and power consumption minimization at the same time. We present recent accomplishments in the magneto-electric element development and integration with spin wave buses. In particular, we show the excitation and detection of the spin waves via multiferroic elements. In addition, we present different approaches to magnonic logic circuit engineering and provide the comparison with CMOS by mapping the designs to 45nm NANGATE standard cell libraries. The estimates show more than 40X power reduction and 53X area reduction for magnonic circuits. These results illustrate the potential advantages over conventional charge based electronics that could be a route to beyond CMOS logic circuitry.
Activation of Skeletal α-Actin Gene Transcription: The Cooperative Formation of Serum Response Factor-Binding Complexes over Positive <i>cis</i> -Acting Promoter Serum Response Elements Displaces a Negative-Acting Nuclear Factor Enriched in Replicating Myoblasts and Nonmyogenic Cells (1991)

Three upstream CBAR cis-acting promoter elements, containing the inner core CC(A/T)6GG of the serum response element (SRE), are required for myogenic cell type-restricted expression of the avian skeletal alpha-actin gene (K.L. Chow and R.J. Schwartz, Mol. Cell. Biol. 10:528-538, 1990). These actin SRE elements display differential binding properties with two distinct nuclear proteins, serum response factor (SRF) and another factor described here as F-ACT1. SRF is able to bind to all actin SREs with various affinities. This multisite interaction is marked by cooperative binding events in that the two high-affinity proximal and distal SREs facilitate the weak central-site interaction with SRF, leading to the formation of a higher-order SRF-promoter complex. Functional analyses reveal that undisrupted multiple SRF-DNA interactions are absolutely essential for promoter activity in myogenic cells. F-ACT1, present at higher levels in nonmyogenic cells and replicating myoblasts than in myotubes, binds solely to the proximal SRE, and its binding is mutually exclusive with that of SRF owing to their overlapping base contacts. The cooperative promoter binding by SRF, however, can effectively displace prebound F-ACT1. In addition, an intact F-ACT1 binding site acts as a negative promoter element by restricting developmentally timed expression in myoblasts. F-ACT1 may therefore act as a repressor of skeletal alpha-actin gene transcription. This interplay between F-ACT1 and SRF may constitute a developmental as well as a physiologically regulated mechanism which modulates sarcomeric actin gene expression.
Rate-Compatible Short-Length Protograph LDPC Codes (2013)

This paper produces a rate-compatible protograph LDPC code at 1k information blocklength with superior performance in both waterfall and error floor regions. The design of such codes has proved difficult in the past because the constraints imposed by structured design (protographs), rate-compatibility, as well as small block length, are not easily satisfied together. For example, as the block length decreases, the predominance of decoding threshold as the main parameter in coding design is reduced, thus complicating the search for good codes. Our rate-compatible protograph codes have rates ranging from 1/3 to 4/5 and show no error floor down to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> FER.
Multiple parasitic microstrip antenna for multifrequency behaviour (2004)

A multifrequency microstrip patch antenna comprising a driven patch and a plurality of parasitic elements placed underneath a driven patch is proposed. The antenna features a multifrequency behavior (5 operating band) with similar performance.
Inheritance of morphological traits of periwinkle mutants with modified contents and yields of leaf and root alkaloids (1999)

Abstract Periwinkle Catharanthus roseus is a medicinally important plant producing anticancer and antihypertension alkaloids. Two mutants, one dwarf and one semidwarf and both, with a high alkaloid content in the roots and one mutant with a wavy leaf margin and a high alkaloid content in its leaves were obtained after induced chemical mutagenesis with ethyl methane sulphonate and N‐nitroso‐N‐ethylurea in the variety ‘Nirmal’, which is resistant to dieback disease. These mutants were evaluated in the M 3 and M 4 generations. The dwarf and semidwarf mutants differed from the parental variety for many morphological characters, while the mutant with the wavy leaf margin differed mainly in leaf size and leaf thickness. Although both dwarf and semidwarf mutants showed a significantly higher alkaloid content in their roots in both generations, only the semidwarf mutant gave a significantly higher (23%) root alkaloid yield than the parental variety. The mutant with the wavy leaf margin showed a significantly higher alkaloid content in the leaves in both the M 3 and M 4 generations and also had a significantly higher (21%) leaf alkaloid yield than the parental variety. All three mutants were found to be controlled by monogenic recessive genes; the genes for ‘dwarfness’ and ‘semidwarfness’ were allelic to each other, with the allele for semidwarfness being dominant over the allele for dwarfness. The gene for the wavy leaf margin was inherited independently of the genes for dwarfness and semidwarfness.
Observation of antisymmetric dispersion-managed solitons in a mode-locked laser (2008)

We report experimental evidence of antisymmetric solitons in a mode-locked fiber laser with a strong dispersion map. A dispersion-managed soliton breathes as it traverses the dispersion map, and the antisymmetric dispersion-managed soliton can be considered a tightly bound soliton pair with pi phase difference between the component solitons. The antisymmetric soliton is observed only at particular values of the net cavity dispersion.
Deep photometric learning (DPL) (2020)

Photometric stereo is a common technique for 3D reconstruction by calculating the surface normals of an object from different illumination angles. The technique is effective to estimate height profile of static objects with large features, but often fails for objects with smaller features or in flat environments with small depressions. We propose a method using deep learning to perform 3D reconstruction of small features. Our method handles sample noise, uneven illumination, and surface tilt. We demonstrate decreased noise susceptibility on synthetic data and promising performance on experimental datasets. This approach enables rapid inspection and reconstruction of complex surfaces without the need to use destructive or expensive analysis methods.
Superconducting Nanowire Single Photon Detectors with High System Detection Efficiency at Telecom Wavelengths (2013)

We report on a fiber-coupled eight-channel single-photon-detection system employing superconducting nanowire single-photon detectors (SNSPDs) based on amorphous tungsten silicide (WSi) with system detection efficiency ranging from 81 to 89 % at 1550 nm wavelength.
Development and validation of a clinical and genetic model for predicting risk of severe COVID-19 (2021)

Clinical and genetic risk factors for severe coronavirus disease 2019 (COVID-19) are often considered independently and without knowledge of the magnitudes of their effects on risk. Using severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) positive participants from the UK Biobank, we developed and validated a clinical and genetic model to predict risk of severe COVID-19. We used multivariable logistic regression on a 70% training dataset and used the remaining 30% for validation. We also validated a previously published prototype model. In the validation dataset, our new model was associated with severe COVID-19 (odds ratio per quintile of risk = 1.77, 95% confidence interval (CI) 1.64-1.90) and had acceptable discrimination (area under the receiver operating characteristic curve = 0.732, 95% CI 0.708-0.756). We assessed calibration using logistic regression of the log odds of the risk score, and the new model showed no evidence of over- or under-estimation of risk (α = -0.08; 95% CI -0.21-0.05) and no evidence or over-or under-dispersion of risk (β = 0.90, 95% CI 0.80-1.00). Accurate prediction of individual risk is possible and will be important in regions where vaccines are not widely available or where people refuse or are disqualified from vaccination, especially given uncertainty about the extent of infection transmission among vaccinated people and the emergence of SARS-CoV-2 variants of concern.
Photonic crystal enhanced fluorescence using a quartz substrate to reduce limits of detection (2011)

A Photonic Crystal surface fabricated upon a quartz substrate using nanoimprint lithography has been demonstrated with a signal enhancement factor as high as 7500× for the detection of LD-700 dye spin-coated upon the PC. The detection of spotted Alexa-647 labeled polypeptide on the PC exhibits a 330× SNR improvement. Using dose-response characterization of deposited fluorophore-tagged protein spots, the PCEF surface demonstrated a 140× lower limit of detection compared to a conventional glass substrate.
Neural network that incorporates direct optical imaging (1995)

A compact neural network architecture is described that can be trained to sense and classify an optical image directly projected onto it. The system is based on the combination of a two-dimensional amorphous silicon photoconductor array and a liquid-crystal spatial light modulator. Appropriate filtering of the incident optical image on capture is incorporated into the network training rules through a modification of the standard backpropagation training algorithm. Training of the network on two image-classification problems is described: the recognition of handprinted digits and facial recognition. The network, once trained, is capable of stand-alone operation, sensing an incident image, and outputting a final classification signal in real time.