gebhart/patrepeval huggingface dataset:
Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB‐LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations (2013)

RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.
Analysis and design of distributed transformers for solar power conversion (2011)

In this paper, a high efficiency, low profile design of distributed transformers (DT) for grid-tied photovoltaic (PV) inverter is presented. The proposed DTs fully integrated into the dual-flyback converter maximize the DC/DC stage efficiency in whole load conditions. The developed DTs with the built-in current sensing transformer allows the converter works in boundary conduction mode (BCM) or discontinues conduction mode (DCM) due to the variable nature of solar power with zero current switching (ZCS). Analytical loss model is established to optimize the value of magnetizing inductance which determines the switching frequency and converter overall efficiency. Various techniques are also taken to minimize the winding loss of the DTs. The experimental prototype employing the DTs achieves over 96% efficiency at full load condition.
Powerful change. 1. Batteries and possible alternatives for the mobile market (2003)

Mobile phone companies sell more batteries than phones to consumers. The devices users buy generally include rechargeable batteries so that they are immediately useful. Companies try to protect their batteries with various design and utility patents to keep third-party vendors from competing too heavily with their after-market sales. This protection is necessary because battery technology changes slowly-consumers receive little incentive to upgrade their batteries unless they fail or the consumer desires a larger one. Power is a difficult issue and is often overlooked in mobile computers. However, innovative opportunities abound for exploring this problem. We introduce the issue and propose some alternatives to batteries. In subsequent issues we'll address methods of being more power efficient by using resources both on the body and in the environment.
Universal dynamics during and after ultrafast laser-induced semiconductor-to-metal transitions (2001)

We observe common features in semiconductor-to-metal transitions induced by femtosecond laser pulses in crystalline GaAs, amorphous GaAs, and Sb-rich films of amorphous GeSb, by tracking ultrafast changes in the spectral dielectric function. The dielectric function of the metal-like state reveals a decay in the plasma frequency with time after the transition. In addition, the plasma frequency roughly decreases with increasing excitation fluence.
ChemInform Abstract: A Synthetic Strategy for the Cyclodepsipeptide Core of the Antitumor Antibiotic Verucopeptin. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Zebrafish as a new model to study effects of periodontal pathogens on cardiovascular diseases (2016)

Abstract Porphyromonas gingivalis (Pg ) is a keystone pathogen in the aetiology of chronic periodontitis. However, recent evidence suggests that the bacterium is also able to enter the bloodstream, interact with host cells and tissues, and ultimately contribute to the pathogenesis of cardiovascular disease (CVD). Here we established a novel zebrafish larvae systemic infection model showing that Pg rapidly adheres to and penetrates the zebrafish vascular endothelium causing a dose- and time-dependent mortality with associated development of pericardial oedemas and cardiac damage. The in vivo model was then used to probe the role of Pg expressed gingipain proteases using systemically delivered gingipain-deficient Pg mutants, which displayed significantly reduced zebrafish morbidity and mortality compared to wild-type bacteria. In addition, we used the zebrafish model to show efficacy of a gingipain inhibitor (KYT) on Pg -mediated systemic disease, suggesting its potential use therapeutically. Our data reveal the first real-time in vivo evidence of intracellular Pg within the endothelium of an infection model and establishes that gingipains are crucially linked to systemic disease and potentially contribute to CVD.
Ellipsometric analysis of materials degradation in space (1990)

The fundamentals of variable angle spectroscopic ellipsometry (VASE) are reviewed, and its usefulness in studying the effect of atomic oxygen on space coatings such as indium tin oxide (ITO), silicon dioxide, and aluminum oxide is discussed. Monolayer sensitive and nondestructive VASE is found to be an effective technique for monitoring the atomic oxygen diffusion through the aluminum oxide and silicon dioxide protective overcoatings on space reflectors. Ashing of ITO/silicon samples had the net effect of annealing the film inside the plasma. The annealing effect was supported both by structural changes as verified by X-ray diffraction measurements and by increased absorbance in the spectral range below 3 eV as measured by VASE.
Fine output voltage control for inverter system having nonlinear load and time-delay (2010)

This paper proposes a new output voltage control for inverter system which contains time-delay and nonlinear load. In the next generation X-ray CT system with the contactless power transfer method, the feedback signal often contains some long delay time by AD/DA conversion and error detection/correction time. When the PID controller of inverter system has the harmful influence on the time-delay, it often has an overshoot and an oscillated response. In order to overcome this problem, this paper proposes the compensation method based on Smith predictor for inverter system having the time-delay and the nonlinear load which is the diode bridge rectifier. The proposed compensation method consists of Smith predictor with the equivalent analog circuit. The experimental results confirm the validity of the proposed system.
Resonant-wavelength tuning of a nanocavity by subnanometer control of a two-dimensional silicon-based photonic crystal slab structure (2009)

We demonstrate fine tuning of the resonant wavelength of a nanocavity in a two-dimensional silicon-based photonic crystal slab structure by subnanometer control of the airhole diameter and slab thickness. Theoretical investigation shows that the resonant wavelength depends linearly on the latter two parameters. To experimentally demonstrate the fine tuning of the resonant wavelength, we control these parameters through chemical processes. The resonant-wavelength shift is tuned to 3.25 and 0.36 nm by use of two oxidizing processes. The latter shift, which corresponds to a 0.14 nm thick silicon layer, is considerably smaller than shifts achieved in previous studies.
Comparison of 3-Phase Wide Output Voltage Range PWM Rectifiers (2007)

A three-phase buck boost pulsewidth modulation (PWM) rectifier with a three-switch buck-type rectifier input stage and an integrated dc/dc boost converter output stage, and a three-phase boost buck PWM rectifier system formed by series connection of a boost-type rectifier input stage (Vienna Rectifier) and a dc/dc buck converter output stage are presented and comparatively evaluated. Both systems are characterized by sinusoidal input current and wide output voltage control range. The comparison is for 6 kW rated output power at 400 Vrms line-to-line input and variable output voltage 200 V 600 V and identifies the buck boost approach as significantly superior regarding the overall efficiency, the volume and weight of the passive power components, and the overall system complexity.
Laser‐induced thermoelastic deformation: A three‐dimensional solution and its application to the ablation of biological tissue (1994)

Under certain conditions, laser light incident on a target material can induce an explosive removal of some material, a process called laser ablation. The photomechanical model of laser ablation asserts that this process is initiated when the laser-induced stresses exceed the strength of the material in question. Although one-dimensional calculations have shown that short pulsed lasers can create significant transient tensile stresses in target materials, the stresses last for only a few nanoseconds and the spatial location of the peak stresses is not consistent with experimental observations of material failure in biological tissues. Using the theory of elasticity, analytical expressions have been derived for the thermoelastic stresses and deformations in an axially symmetric three-dimensional solid body caused by the absorption of laser light. The full three-dimensional solution includes three stresses, radial, circumferential and shear, which are necessarily absent in the simple one-dimensional solution. These stresses have long-lived components that exist for eight orders of magnitude longer in time than the acoustic transients, an important point when the details of dynamic fracture are considered. Many important qualitative features are revealed including the spatial location of the peak stresses, which is more consistent with experimental observations of failure.
Complementary Tolls in the periodontium: how periodontal bacteria modify complement and Toll-like receptor responses to prevail in the host (2009)

The complement and the Toll-like receptors are rapidly activatable systems which, in concert, provide first-line innate defense against infection and act as mediators between the innate and the adaptive immune response. The ability of periodontal bacteria to persist and establish chronic infections in the periodontium suggests that they may have evolved strategies to evade, disarm, or subvert these defense systems to their own advantage. Indeed, accumulating evidence indicates that at least some of the major periodontal pathogens utilize ingenious mechanisms to not only undermine each system separately, but also exploit crosstalk points between the complement and the Toll-like receptor pathways. It is conceivable that immune subversive activities by certain keynote periodontal pathogens, such as those comprising the so-called "red complex", may be critical for the persistence of the entire mixed-species biofilm community in the diseased periodontium. This review summarizes and synthesizes recent discoveries in this field, which offers important insights into the pathology associated with the complex periodontal host-microbe interplay.
Sensor based door navigation for a nonholonomic vehicle (2003)

This paper presents a sensor based algorithm for guiding a nonholonomic platform, such as a wheelchair, through a doorway. The controller uses information from a camera system and a laser range finder to perform image-based navigation. Simulations of the resultant switching controller are presented along with experimental results. A simple obstacle avoidance algorithm is also implemented on the experimental platform. Finally, we have considered the input of limited field-of-view constraints on this controller. All of these components together lead to a modal, image-based approach that will safely and robustly navigate a nonholonomic robot with sensor constraints through a doorway.
Carbocationic Polymerization in the Presence of Sterically Hindered Bases. II. Polymerization of a-Methylstyrene (1982)

Abstract The effect of 2,6-di-tert-butylpyridine (DtBP) on a-methyl-styrene (αMeSt) polymerization induced by the “H20”/BC13 initiating system has been studied. Yields, molecular weights, (MW's), and molecular weight distributions (MWD's) obtained in the presence of [DtBP] >1.0 × 10−3 M are invariant with DtBP concentration. Results are explained by the concept of terminative chain transfer, i.e., a process in which the proton which arises in the course of chain transfer to monomer is intercepted by DtBP so that the kinetic chain is terminated. Polymerization goes to completion in the presence of very small amounts of DtBP, i.e., 4.8 × 10−4 M or less; however, MW's and MWD's of the poly(a-methylstyrene) (PaMeSt) formed are still profoundlyjiffected. Thus, in the absence of DtBP, Mn = 1.2 × 104 and Mw /Mn = 3.8, whereas in the presence of [DtBP] = 1.0 ×l(10−4, M M = 4.5 × 10−4 and Mw/Mn = 1.87. According to Mayo plots, a small but nonnegligible extent of chain transfer to monomer persists even in the presence of DtBP, e.g., ktr,M/kp = 6.4 × 10−4 and 2.8 × 10−4 at -30 and -50°C, respectively. This, by DtBP unscavengable chain transfer to monomer, is attributed to a concerted chain transfer process. A mechanism is proposed which explains the experimental facts.
High-Speed Event Counting and Classification Using a Dictionary Hash Technique. (1989)

This paper presents a &amp;quot;dictionary hash&amp;quot; technique that, when presented with a large group of labeled events, can stochastically determine the number of unique labels quickly and with a small amount of memory. This technique is applicable to areas such as signal processing, process monitoring and control, and computer communications network monitoring and control.
Anti-Tumor and Anti-Invasive Effects of ONC201 on Ovarian Cancer Cells and a Transgenic Mouse Model of Serous Ovarian Cancer (2021)

Abstract Background: ONC201 is a promising first-in-class small molecule that has been reported to have anti-neoplastic activity in various types of cancer through activation of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) as well as activation of mitochondrial caseinolytic protease P (ClpP). Methods: Our objective was to evaluate the effect of the ONC201 on (1) proliferation, cellular stress, apoptosis and invasion in human serous ovarian cancer (OC) cell lines, and (2) inhibition of tumor growth in a genetically engineered mouse model of high grade serous OC (K18-gT121+/-;p53fl/fl;Brca1fl/fl; KpB) under obese (high fat diet) and lean (low fat diet) conditions. Results: ONC201 significantly suppressed cell proliferation, induced arrest in G1 phase, and increased cellular stress and apoptosis, accompanied by dual inhibition of the AKT/mTOR/S6 and MAPK pathways in OC cells. ONC201 also resulted in inhibition of adhesion and invasion via epithelial–mesenchymal transition and reduction of VEGF expression. Pre-treatment with the anti-oxidant, N-acetylcysteine (NAC), reversed the ONC201-induced oxidative stress response, and prevented ONC201-reduced VEGF and cell invasion by regulating epithelial–mesenchymal transition protein expression. Knockdown of ClpP in ovarian cancer cells reduced ONC201 mediated the anti-tumor activity and cellular stress. Diet-induced obesity accelerated ovarian tumor growth in the KpB mouse model. ONC201 significantly suppressed tumor growth, and decreased serum VEGF production in obese and lean mice, leading to a decrease in tumoral expression of Ki-67, VEGF and phosphorylation of p42/44 and S6 and an increase in ClpP and DRD5, as assessed by immunohistochemistry. Additionally, ONC201 exhibited greater anti-tumor efficacy in obese (75%) as compared to lean (65%) mice. Interpretation Conclusions: These results suggest that ONC206 may be a promising therapeutic agent to be explored in future clinical trials in high grade serous OC.
Computational Screening of Molecules Approved in Phase-I Clinical Trials to Identify 3CL Protease Inhibitors to Treat COVID-19 (2020)

Ligand and structure based virtual screening approaches were applied to clinical stage drugs as well as those approved for human use in an attempt to repurpose drugs for potential use against COVID-19. This approach involved ligand-based shape similarity searches, structure-based docking and pharmacophore searches with the help of pharmacophore queries derived from available ligands and receptor structures. Several compounds appeared as hits in pharmacophore and shape similarity searches and those docking to the SARS-CoV-2 viral 3CL protease were then ranked on the basis of docking scores.
H1 Hemagglutinin Priming Provides Long-Lasting Heterosubtypic Immunity against H5N1 Challenge in the Mouse Model (2020)

Influenza virus infections leave a signature of immune memory that influences future responses to infections with antigenically related strains. It has been hypothesized that the first exposure in life to H1N1 influenza virus imprints the host immune system, potentially resulting in protection from severe infection with H5N1 later in life through hemagglutinin (HA) stalk-specific antibodies. To study the specific role of the HA on protection against infection without interference of cellular immunity or humoral antineuraminidase immunity, we primed mice with influenza B viruses that express an H1 HA (group 1; B-H1), H3 HA (group 2; B-H3), or wild-type influenza B virus and subsequently challenged them at different time points with an H5N1 virus. Weight loss and survival monitoring showed that the B-H1-primed mice exhibited better protection against H5N1 compared to the control mice. Analysis of H5-specific serum IgG, before and 21 days after H5N1 challenge, evidenced the presence of anti-stalk H5 cross-reactive antibodies in the BH-1 group that were boosted by H5N1 infection. The increased immune responses and protection induced by priming with the B-H1 viruses lasted at least up to 1 year. Hence, a single HA priming based on natural infection induces long-lasting protective immunity against heterosubtypic strains from the same phylogenetic HA group in mice. This study gives mechanistic support to the earlier finding in humans that imprinting by H1 HA protects against H5N1 infections and that highly conserved regions on the HA, like the stalk, are involved in this phenomenon.<b>IMPORTANCE</b> Current studies point out that an HA-mediated immunological imprint is established early in life during the first exposure to influenza viruses, which critically shapes and biases future immune responses. However, studies in animal models are limited and the precise mechanisms of this phenomenon are under investigation. Studies that explore the effect of HA-specific immunity induced during natural infection on future exposures to heterosubtypic influenza strains are needed.
Isothermal crystallisation of PCL/PLA blends (2004)

The thermal properties of a series of poly ε-caprolactone (PCL) and poly lactide (PLA) blends, whose compositions vary with mass fraction were analyzed. Crystallization behavior of the polymer blends was investigated using an isothermal crystallization technique. PCL and PLA were solvent blended using chloroform, and then isothermal crystallization experiments were carried out by differential scanning calorimetry (DSC). The results show that by varying the mass fractions of PCL/PLA blends, it is possible to exert some form of control over their melt temperatures, and the crystallization process of PCL.
Light‐Emitting Diodes with Cu‐Doped Colloidal Quantum Wells: From Ultrapure Green, Tunable Dual‐Emission to White Light (2019)

Copper-doped colloidal quantum wells (Cu-CQWs) are considered a new class of optoelectronic materials. To date, the electroluminescence (EL) property of Cu-CQWs has not been revealed. Additionally, it is desirable to achieve ultrapure green, tunable dual-emission and white light to satisfy the various requirement of display and lighting applications. Herein, light-emitting diodes (LEDs) based on colloidal Cu-CQWs are demonstrated. For the 0% Cu-doped concentration, the LED exhibits Commission Internationale de L'Eclairage 1931 coordinates of (0.103, 0.797) with a narrow EL full-wavelength at half-maximum of 12 nm. For the 0.5% Cu-doped concentration, a dual-emission LED is realized. Remarkably, the dual emission can be tuned by manipulating the device engineering. Furthermore, at a high doping concentration of 2.4%, a white LED based on CQWs is developed. With the management of doping concentrations, the color tuning (green, dual-emission to white) is shown. The findings not only show that LEDs with CQWs can exhibit polychromatic emission but also unlock a new direction to develop LEDs by exploiting 2D impurity-doped CQWs that can be further extended to the application of other impurities (e.g., Mn, Ag).
Species-related luminescence-structure relationships in europium-exchanged mesoporous material (2009)

Europium exchanged into a mesoporous material (Zeotile-1) was extensively characterized with respect to the Si/Al ratio and surface silylation by using time-resolved emission spectroscopy. Qualitative as well as quantitative details of the europium species-related luminescence-structure relationships were obtained and discussed such as the decay associated spectra, local distortion and structure of the bonding environment, crystal-field strength, radiative relaxation rates, and the quantum efficiency. Thus, two europium species were found in the parent as well as in the silylated materials: one species located on the internal surface and the second inside the 2–2.5 nm pores. The species located on the internal surface is characterized by photoluminescence decay times of 105 μs&amp;lt;τ&amp;lt;125 μs, an asymmetry value R of 0.6&amp;lt;R&amp;lt;0.8, and a quantum efficiency of 2%–2.5%. Upon silylation, the photoluminescence decay times, the asymmetry values, and the quantum efficiency were increased to 160 μs&amp;lt;τ&amp;lt;180 μs, 1.7&amp;lt;R&amp;lt;2.1, and ∼4%, respectively. Following silylation, the number of water molecules is reduced in the first coordination shell of the europium species located on the internal surface from eight to nine to about five. On the other hand, the europium species located inside the pores showed a much longer photoluminescence decay time (460 μs&amp;lt;τ&amp;lt;560 μs) and a much higher asymmetry ratio (5&amp;lt;R&amp;lt;6.5). The related photoluminescence efficiency was 26%–30%. An average of one up to two water molecules in the first coordination shell of the europium species located inside the pores was estimated for both parent and silylated materials.
Who Ate My Memory? Towards Attribution in Memory Management (2022)

To understand applications' memory usage details, engineers use instrumented builds and profiling tools. Both approaches are impractical for use in production environments or deployed mobile applications. As a result, developers can gather only high-level memory-related statistics for deployed software. In our experience, the lack of granular field data makes fixing performance and reliability-related defects complex and time-consuming. The software industry needs lightweight solutions to collect detailed data about applications' memory usage to increase developer productivity. Current research into memory attribution-related data structures, techniques, and tools is in the early stages and enables several new research avenues.