gebhart/patrepeval huggingface dataset:
Time-resolved dual root-microbe transcriptomics reveals early induced Nicotiana benthamiana genes and conserved infection-promoting Phytophthora palmivora effectors (2017)

Abstract Background Plant-pathogenic oomycetes are responsible for economically important losses on crops worldwide. Phytophthora palmivora , a broad-host-range tropical relative of the potato late blight pathogen, causes rotting diseases in many important tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped understanding of how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. Results We employed the model plant N. benthamiana to study the P. palmivora root infections at the cellular and molecular level. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. Conclusions These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.
Immunogenicity of a Recombinant Influenza Virus Bearing Both the CD4+ and CD8+ T Cell Epitopes of Ovalbumin (2011)

Recombinant influenza viruses that bear the single immunodominant CD8+ T cell epitope OVA(257-264) or the CD4+ T cell epitope OVA₃₂₃₋₃₃₉ of the model antigen ovalbumin (OVA) have been useful tools in immunology. Here, we generated a recombinant influenza virus, WSN-OVA(I/II), that bears both OVA-specific CD8+ and CD4+ epitopes on its hemagglutinin molecule. Live and heat-inactivated WSN-OVA(I/II) viruses were efficiently presented by dendritic cells in vitro to OT-I TCR transgenic CD8+ T cells and OT-II TCR transgenic CD4+ T cells. In vivo, WSN-OVA(I/II) virus was attenuated in virulence, highly immunogenic, and protected mice from B16-OVA tumor challenge in a prophylactic model of vaccination. Thus, WSN-OVA(I/II) virus represents an additional tool, along with OVA TCR transgenic mice, for further studies on T cell responses and may be of value in vaccine design.
Use of radiation force for enhancing efficacy of molecular targeted ultrasound contrast agents - in vitro and in vivo (2008)

Intravenously injected modified ultrasound microbubbles possessing molecule specific targeting ligands hold significant promise as a method for “molecular imaging.” Unfortunately, although microbubbles can achieve specific adhesion in regions of vascular pathology, the method breaks down in high blood flow regions where the bond formation process is more problematic. I present results indicating that acoustic radiation does increase the specific targeted adhesion of microbubbles by pushing the bubbles towards the periphery of a vessel. During in vitro studies, radiation force enhanced microbubble adhesion up to 60-fold. Microbubble adhesion is observed to increase approximately with the square of acoustic pressure between 25 and 122 kPa, but decreases at higher pressures as the bubbles rupture. Our in vivo studies involved using intravital microscopy to assess the adherence of P-selectin targeted microbubbles in the mouse cremaster microcirculation and femoral vessels. Acoustic radiation force enhanced microbubble retention four-fold in cremaster venules and in the femoral vein. A 20-fold enhancement was observed in the femoral artery. I discuss the potential for derivatives of the technique to provide molecular targeted therapeutic contribution.
Growth Kinetics Of Photoinduced Gratings And Paramagnetic Centers In High NA, Heavily Ge-Doped Silica Optical Fibers (1997)

The achievement of UV photoinduced refractive index changes in germanosilicate fibers paved the way for the development of fiber Bragg grating (FBG) based optical devices (e.g., filters, fiber lasers, sensors). Although the mechanisms underlying the UV photosensitivity are not fully understood, it is now well established that the refractive index changes are associated with a partial bleaching of an absorption band around 5 eV, arising from the Germanium Oxygen Defect Center (GODC). Several mechanisms have been proposed to explain the photosensitivity in germanosilicate fibers: color centers [1], stress relief [2] and compaction [3]. Depending on the Ge concentration and the experimental conditions used to write the gratings, three types of photosensitivity, type 1, type IIa and type 2 have been identified in unloaded Ge-doped silica fibers. The most commonly observed, type 1, arises in standard fibers ([GeO 2 ] &lt; 20 mol%) under either pulsed or cw UV exposure in the low fluence regime. Type 1 photosensitivity is characterized by a monotonie increase of both the mean refractive index &lt;Δn eff &gt; and the induced refractive index modulation Δn mod under UV exposure. Unlike type 1, the most relevant feature of type IIa photosensitivity ([GeO 2 ] &gt; 25 mol%, ϕ c ≈ 2µm) is the complex behavior of &lt;Δn eff &gt; and Δn mod as a function of exposure time [4]. Indeed, with increasing UV exposure time, a partial or total bleaching of the saturated type I grating is followed by the formation of a new grating spectrum. At the time of the second grating growth, the shift experienced by the Bragg grating wavelength is nulled or slightly negative, indicating a negative refractive index change. Moreover, a noticeable difference between type 1 and type IIa photosensitivities is their markedly different thermal behavior. Type 1 gratings begin to anneal at temperatures as low as 300 C and are no longer observed at 550 C while type IIa gratings experience no annealing at temperatures below 450-500 C; a rapid decay is then observed at annealing temperatures ~600-700 C. Recent experiments have shown that the formation dynamics of type 1/IIa grating spectra are strongly affected when the gratings are written in strained fibers [5]. Using the “Photoelastic densification” model and stress dependence kinetics, it has been demonstrated that, under the assumption of a decrease in densification rate, stretching the fiber will in turn decrease the type 1 index modulation [3], [6]. Nevertheless the origin of type IIa photosensitivity in high NA Ge-doped silica fibers still remains unresolved.
Exploitation Performance and Characterization of a Prototype Compressive Sensing Imaging Spectrometer (2012)

The coded aperture snapshot spectral imager (CASSI) systems are a class of imaging spectrometers that provide a first-generation implementation of compressive sensing themes to the domain of hyperspectral imaging. Via multiplexing of information from different spectral bands originating from different spatial locations, a CASSI system undersamples the three-dimensional spatial/spectral data cube of a scene. Reconstruction methods are then used to recover an estimate of the full data cube. Here we report on our characterization of a CASSI system’s performance in terms of post-reconstruction image quality and the suitability of using the resulting data cubes for typical hyperspectral data exploitation tasks (e.g., material detection, pixel classification). The data acquisition and reconstruction process does indeed introduce trade-offs in terms of achieved image quality and the introduction of spurious spectral correlations versus data acquisition speedup and the potential for reduced data volume. The reconstructed data cubes are of sufficient quality to perform reasonably accurate pixel classification. Potential avenues to improve upon the usefulness of CASSI systems for hyperspectral data acquisition and exploitation are suggested.
Ultra-high sensitivity CO-sensor based on nanocrystalline metal oxide gate AlGaN/GaN heterostructure (2010)

This paper presents a robust sensor to detect low concentration (&lt;1 ppm) of CO gas. The sensor is based on AlGaN/GaN Metal-Oxide-Semiconductor High Electron Mobility Transistor (MOS-HEMT) with a non-conventional gate structure. The performance of the device has been simulated based on the charge control physics of AlGaN/GaN heterostructure transistor. Large sensitivities and widely linear characteristics are obtained for the AlGaN/GaN device based sensor assuming ideal gas-surface kinetics which can be approximated by the proposed gate structure. The sensor generates 0.8 &#956;A of current for 0.5 ppm concentration of CO. The sensor shows linear characteristics for concentration of 1000 ppm CO. The effects of varying aspect ratio on total changes in current, sensitivity and linearity of the device have been simulated.
Effect of Antigen Shedding on Targeted Delivery of Immunotoxins in Solid Tumors from a Mathematical Model (2014)

Most cancer-specific antigens used as targets of antibody-drug conjugates and immunotoxins are shed from the cell surface (Zhang & Pastan (2008) Clin. Cancer Res. 14: 7981-7986), although at widely varying rates and by different mechanisms (Dello Sbarba & Rovida (2002) Biol. Chem. 383: 69-83). Why many cancer-specific antigens are shed and how the shedding affects delivery efficiency of antibody-based protein drugs are poorly understood questions at present. Before a detailed numerical study, it was assumed that antigen shedding would reduce the efficacy of antibody-drug conjugates and immunotoxins. However, our previous study using a comprehensive mathematical model showed that antigen shedding can significantly improve the efficacy of the mesothelin-binding immunotoxin, SS1P (anti-mesothelin-Fv-PE38), and suggested that receptor shedding can be a general mechanism for enhancing the effect of inter-cellular signaling molecules. Here, we improved this model and applied it to both SS1P and another recombinant immunotoxin, LMB-2, which targets CD25. We show that the effect of antigen shedding is influenced by a number of factors including the number of antigen molecules on the cell surface and the endocytosis rate. The high shedding rate of mesothelin is beneficial for SS1P, for which the antigen is large in number and endocytosed rapidly. On the other hand, the slow shedding of CD25 is beneficial for LMB-2, for which the antigen is small in number and endocytosed slowly.
Pressure effect on iron-based superconductor LaFeAsO1−xHx: Peculiar response of 1111-type structure (2016)

A systematic study of the crystal structure of a layered iron oxypnictide LaFeAsO<sub>1-x</sub>H<sub>x</sub> as a function of pressure was performed using synchrotron X-ray diffraction. This compound exhibits a unique phase diagram of two superconducting phases and two parent phases. We established that the As-Fe-As angle of the FeAs<sub>4</sub> tetrahedron widens on the application of pressure due to the interspace between the layers being nearly infilled by the large La and As atoms. Such rarely observed behaviour in iron pnictides implies that the FeAs<sub>4</sub> coordination deviates from the regular tetrahedron in the present systems. This breaks a widely accepted structural guide that the superconductivity favours the regular tetrahedron, albeit the superconducting transition temperature (T<sub>c</sub>) increases from 18 K at ambient pressure to 52 K at 6 GPa for x = 0.2. In the phase diagram, the second parent phase at x ~ 0.5 is suppressed by pressure as low as ~1.5 GPa in contrast to the first parent phase at x ~ 0, which is robust against pressure. We suggest that certain spin-fluctuation from the second parent phase is strongly related to high-T<sub>c</sub> under pressure.
Multi-gate devices for the 32nm technology node and beyond (2007)

Due to the limited control of the short channel effects, the high junction leakage caused by band-to-band tunneling and the dramatically increased V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> statistical fluctuations, the scaling of planar bulk MOSFETs becomes more and more problematic with every technology node. The ITRS roadmap predicts that from the 32 nm technology node on planar bulk devices will not be able to meet the stringent leakage requirements anymore and that multi-gate devices will be required. In this paper, the suitability of FinFET based multi-gate devices for the 32 nm technology and beyond will be discussed. Apart from the benefits, some technological challenges will be addressed.
Data from Detection of Tumor Epidermal Growth Factor Receptor Pathway Dependence by Serum Mass Spectrometry in Cancer Patients (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; We hypothesized that a serum proteomic profile predictive of survival benefit in non–small cell lung cancer patients treated with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI) reflects tumor EGFR dependency regardless of site of origin or class of therapeutic agent.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; Pretreatment serum or plasma from 230 patients treated with cetuximab, EGFR-TKIs, or chemotherapy for recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) or colorectal cancer (CRC) were analyzed by mass spectrometry. Each sample was classified into “good” or “poor” groups using VeriStrat, and survival analyses of each cohort were done based on this classification. For the CRC cohort, this classification was correlated with the tumor EGFR ligand levels and &lt;i&gt;KRAS&lt;/i&gt; mutation status.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In the EGFR inhibitor–treated cohorts, the classification predicted survival (HNSCC: gefitinib, &lt;i&gt;P&lt;/i&gt; = 0.007 and erlotinib/bevacizumab, &lt;i&gt;P&lt;/i&gt; = 0.02; CRC: cetuximab, &lt;i&gt;P&lt;/i&gt; = 0.0065) whereas the chemotherapy cohort showed no survival difference. For CRC patients, tumor EGFR ligand RNA levels were significantly associated with the proteomic classification, and combined &lt;i&gt;KRAS&lt;/i&gt; and proteomic classification provided improved survival classification.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Serum proteomic profiling can detect clinically significant tumor dependence on the EGFR pathway in non–small cell lung cancer, HNSCC, and CRC patients treated with either EGFR-TKIs or cetuximab. This classification is correlated with tumor EGFR ligand levels and provides a clinically practical way to identify patients with diverse cancer types most likely to benefit from EGFR inhibitors. Prospective studies are necessary to confirm these findings. Cancer Epidemiol Biomarkers Prev; 19(2); 358–65&lt;/p&gt;&lt;/div&gt;
Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer (2020)

Clinical outcomes for patients with ovarian and uterine cancers have not improved greatly in the past twenty years. To identify ovarian and uterine cancer vulnerabilities, we analyzed genome-scale CRISPR/ Cas9 loss-of-function screens across 739 human cancer cell lines. We found that many ovarian cancer cell lines overexpress the phosphate importer SLC34A2, which renders them sensitive to loss of the phosphate exporter XPR1. We extensively validated the XPR1 vulnerability in cancer cell lines and found that the XPR1 dependency was retained in vivo. Overexpression of SLC34A2 is frequently observed in tumor samples and is regulated by PAX8 -a transcription factor required for ovarian cancer survival. XPR1 overexpression and copy number amplifications are also frequently observed. Mechanistically, SLC34A2 overexpression and impaired phosphate efflux leads to the accumulation of intracellular phosphate and cell death. We further show that proper localization and phosphate efflux by XPR1 requires a novel binding partner, KIDINS220. Loss of either XPR1 or KIDINS220 results in acidic vacuolar structures which precede cell death. These data point to the XPR1:KIDINS220 complex - and phosphate dysregulation more broadly -as a therapeutic vulnerability in ovarian cancer.
Enhanced Femoral Nerve Regeneration After Tubulization with a Tyrosine-Derived Polycarbonate Terpolymer: Effects of Protein Adsorption and Independence of Conduit Porosity (2013)

Following complete nerve transection, entubulation of the nerve stumps helps guide axons to reconnect distally. In this study, a biodegradable and noncytotoxic tyrosine-derived polycarbonate terpolymer composed of 89.5 mol% desaminotyrosyl tyrosine ethyl ester (DTE), 10 mol% desaminotyrosyl tyrosine (DT), and 0.5 mol% poly(ethylene glycol) (PEG, molecular weight [Mw]=1 kDa) [designated as E10-0.5(1K)] was used to fabricate conduits for peripheral nerve regeneration. These conduits were evaluated against commercially available nonporous polyethylene (PE) tubes. The two materials are characterized in vitro for differences in surface properties, and the conduits are then evaluated in vivo in a critical-sized nerve defect in the mouse femoral nerve model. Conduits were fabricated from E10-0.5(1K) in both porous [P-E10-0.5(1K)] and nonporous [NP-E10-0.5(1K)] configurations. The results illustrate that adsorption of laminin, fibronectin, and collagen type I was enhanced on E10-0.5(1K) compared to PE. In addition, in vivo the E10-0.5(1K) conduits improved functional recovery over PE conduits, producing regenerated nerves with a fivefold increase in the number of axons, and an eightfold increase in the percentage of myelinated axons. These increases were observed for both P-E10-0.5(1K) and NP-E10-0.5(1K) after 15 weeks. When conduits were removed at 7 or 14 days following implantation, an increase in Schwann cell proteins and fibrin matrix formation was observed in E10-0.5(1K) conduits over PE conduits. These results indicate that E10-0.5(1K) is a pro-regenerative material for peripheral nerves and that the porosity of P-E10-0.5(1K) conduits was inconsequential in this model of nerve injury.
Performance data on new tunable attenuating PSM for 193-nm and 157-nm lithography (2004)

A new phase shifting film system based on tantalum and silicon dioxide is presented. The tantalum film works as a transmission control layer and furthermore as an etch stop layer due to its good etch selectivity. The silicon dioxide phase control layer is tuned to 180° phase shift. Excellent laser stability and chemical durability were already shown. The two layer system can be easily tuned to various transmission values for three different lithography wavelengths. Transmission and phase shift uniformity fulfill already the final production specifications according to ITRS. An optimized deposition process yields excellent film surface roughness values equal to an uncoated substrate. Defect density could be significantly reduced recently. First SEM pictures of structured films show promising results.
Amplified Host Defense by Toll-Like Receptor-Mediated Downregulation of the Glucocorticoid-Induced Leucine Zipper (GILZ) in Macrophages (2019)

Activation of toll-like receptors (TLRs) plays a pivotal role in the host defense against bacteria and results in the activation of NF-κB-mediated transcription of proinflammatory mediators. Glucocorticoid-induced leucine zipper (GILZ) is an anti-inflammatory mediator, which inhibits NF-κB activity in macrophages. Thus, we aimed to investigate the regulation and role of GILZ expression in primary human and murine macrophages upon TLR activation. Treatment with TLR agonists, e.g., Pam<sub>3</sub>CSK<sub>4</sub> (TLR1/2) or LPS (TLR4) rapidly decreased GILZ mRNA and protein levels. In consequence, GILZ downregulation led to enhanced induction of pro-inflammatory mediators, increased phagocytic activity, and a higher capacity to kill intracellular bacteria (<i>Salmonella</i> enterica serovar <i>typhimurium</i>), as shown in GILZ knockout macrophages. Treatment with the TLR3 ligand polyinosinic: polycytidylic acid [Poly(I:C)] did not affect <i>GILZ</i> mRNA levels, although GILZ protein expression was decreased. This effect was paralleled by sensitization toward TLR1/2- and TLR4-agonists. A bioinformatics approach implicated more than 250 miRNAs as potential GILZ regulators. Microarray analysis revealed that the expression of several potentially GILZ-targeting miRNAs was increased after Poly(I:C) treatment in primary human macrophages. We tested the ability of 11 of these miRNAs to target GILZ by luciferase reporter gene assays. Within this small set, four miRNAs (hsa-miR-34b<sup>*</sup>,-222,-320d,-484) were confirmed as GILZ regulators, suggesting that GILZ downregulation upon TLR3 activation is a consequence of the synergistic actions of multiple miRNAs. In summary, our data show that GILZ downregulation promotes macrophage activation. GILZ downregulation occurs both via MyD88-dependent and -independent mechanisms and can involve decreased mRNA or protein stability and an attenuated translation.
A comparison between computer-controlled and set work rate exercise based on target heart rate. (1991)

Good exercise prescriptions provide work rates (WRs) that maintain heart rates (HR) in a target zone and at a percent of maximum metabolic equivalent (%METmax). HR and MET were evaluated from computer-controlled and set WR (constant speed) sessions (20 min at 65% METmax). Computer-controlled WR used a control algorithm to adjust speed and grade to maintain the target HR. The set WR (mean +/- S.D.) HR (139 +/- 8 bpm) was lower (p less than 0.05) than the target (147 +/- 3 bpm) and computer-controlled HRs (153 +/- 5 bpm). The set WR MET (8.6 +/- 2.2) was not different than the target (8.6 +/- 2.2), but both were lower than computer-controlled exercise (9.7 +/- 2.2). Computer-control time in target HR zone (16 +/- 5 min) was significantly (p less than 0.004) greater than set WR exercise (6 +/- 5 min). Computer-controlled WR was significantly better in maintaining target HR and the MET values were not physiologically different than target WRs.
A review of recent work on stresses and strains in semiconductor heterostructures (1997)

We first discuss the work on strain and critical thickness of large area lattice mismatched epilayers of GeSi, InGaAs and II-VI semiconductors. A summary of Finite Element (FE) calculations of stresses in stripe-substrate heterostructures is then given. Calculated stresses for novel stripe designs are also given. The results are then applied to interpret experiments. Raman and luminescence experiments on stripes of GaAs/Si, GeSi/Si and InGaAs/GaAs, Raman experiments on LOCOS structures and on GeSi quantum wires and quantum dots and luminescence experiments on InGaAs quantum wires are included in the discussion.
On the sharpness of the interfaces in metallic multilayers (2004)

We show that the three most relevant magnetic properties (magnetic moment, critical temperature, and interlayer exchange coupling) of metallic multilayers can be reproduced with good accuracy by first principles theory, provided that the picture of atomically sharp interfaces is abandoned and one allows instead for both interface alloying and interface roughness. The interface of a metallic multilayer (exemplified by the Fe/V system) is demonstrated to, at best, have interdiffusion essentially over two to three atomic layers on each side of the interface. Our conclusions are the result of combining experimental work with theoretical modeling, and we argue that this approach is the best avenue to obtain accurate information about the interface quality of metallic multilayers.