gebhart/patrepeval huggingface dataset:
Donor-to-recipient transmission and reactivation in a kidney transplant recipient of an inherited chromosomally integrated HHV-6A: Evidence and outcomes (2020)

Human herpesvirus (HHV)-6A can be inherited and chromosomally integrated (iciHHV-6A), and donor-to-recipient transmission has been reported in solid organ transplant. However, when HHV-6A reactivation happens after transplant, the source of HHV-6A is often not evident and its pathogenicity remains unclear. Here, we present an exhaustive case of donor-to-recipient transmission and reactivation of iciHHV-6A through kidney transplant. The absence of HHV-6A genome from the nails of the recipient excluded a recipient-related iciHHV-6A. Viral loads > 7 log<sub>10</sub> copies/10<sup>6</sup> cells in donor blood samples and similarities of U38, U39, U69, and U100 viral genes between donor, recipient, and previously published iciHHV-6A strains are proof of donor-related transmission. Detection of noncoding HHV-6 snc-RNA14 using fluorescence in situ hybridization analysis and immunofluorescence staining of HHV-6A gp82/gp105 late proteins on kidney biopsies showed evidence of reactivation in the transplanted kidney. Because HHV-6A reactivation can be life threatening in immunocompromised patients, we provide several tools to help during the complete screening and diagnosis.
Deep-Learning Based Adaptive Ultrasound Imaging From Sub-Nyquist Channel Data (2022)

Traditional beamforming of medical ultrasound images relies on sampling rates significantly higher than the actual Nyquist rate of the received signals. This results in large amounts of data to store and process, imposing hardware and software challenges on the development of ultrasound machinery and algorithms, and impacting the resulting performance. In light of the capabilities demonstrated by deep learning methods over the past years across a variety of fields, including medical imaging, it is natural to consider their ability to recover high-quality ultrasound images from partial data. Here, we propose an approach for deep-learning-based reconstruction of B-mode images from temporally and spatially sub-sampled channel data. We begin by considering sub-Nyquist sampled data, time-aligned in the frequency domain and transformed back to the time domain. The data are further sampled spatially so that only a subset of the received signals is acquired. The partial data is used to train an encoder-decoder convolutional neural network (CNN), using as targets minimum-variance (MV) beamformed signals that were generated from the original, fully-sampled data. Our approach yields high-quality B-mode images, with up to two times higher resolution than previously proposed reconstruction approaches (NESTA) from compressed data as well as delay-and-sum (DAS) beamforming of the fully-sampled data. In terms of contrast-to- noise ratio (CNR), our results are comparable to MV beamforming of the fully-sampled data, and provide up to 2 dB higher CNR values than DAS and NESTA, thus enabling better and more efficient imaging than what is used in clinical practice today.
Impact of gate resistance in graphene radio frequency transistors (2012)

The effect of gate resistance on the high frequency device properties of graphene transistors is explored. Decreasing this resistance does not alter the current gain cutoff frequency (fT), but it does allow for the power gain cutoff frequency (fmax) to be increased. Analysis of this effect reveals that the relative rate of change between fT and fmax is most sensitive to the relationship between the parasitic resistance in the device channel and the output conductance, a manifestation of device scaling in the triode regime. This result underlies the importance of a small output conductance in the scaling of graphene transistors.
Structural characterization of chemically synthesized cubic lanthanum sulphide (γ-La2S3) (1993)

Abstract Cubic lanthanum sulphide (γ-La2S3) belongs to the family of rare-earth chalcogenides and is a potential far-infrared (8-14 μm) transmitting material. Low-temperature chemical techniaues incorporating organometallics have been employed to synthesize ultrafine sulphide precursors (about 20 nm in size) at room temperature. The precursors transform to form cubic (γ-La2S3) powders at 1000°C. The thermal stability, phase evolution characteristics and microstructure of the fine particles have been investigated using differential scanning calorimetry, X-ray diffraction and electron microscopy. Convergent-beam electron diffraction was performed on the crystalline powders and hot-pressed ceramics and the space group was identified to be 143d.
Optical properties of quasicrystalline gold nanoparticle arrays in the visible spectrum (2012)

Optical properties of aperiodic arrays of gold cylinders in the visible range are studied experimentally and analytically. Aperiodic samples based on Ammann-Beenker and Danzer tilings were fabricated and illuminated with visible light. The arrays are composed of gold cylinders with a diameter of 175 nm and a height of 50 nm in a fused silica medium. The images of the arrays showed multiple colors. The presence of several colors in the colorimetric pattern of the aperiodic arrays can be explained by the presence of multiple photonic resonances in aperiodic structures. Numeric simulations based on Generalized Mie Method were performed on aperiodic nanosphere arrays which also confirmed the presence multiple photonic resonances.
Sketch simplification by classifying strokes (2016)

In this paper, we propose a novel approach to creating clean line drawing from a scribbled sketch automatically. The main problem is determining which strokes of a scribbled sketch should be merged. We use a machine learning approach to solve this problem. Our method can automatically generate training data by comparing scribbled sketches with manually drawn line drawings without using annotations. In order to verify the generated training data, we merged strokes and created clean line drawings in accordance with the generated training data. In addition, we trained a support vector machine to estimate the pairs of strokes to be merged. Further, we verified that our method can create line drawings using this estimator.
The activity platform (2015)

In this paper, we advocate to be a central abstraction between people and computing instead of applications. We outline the vision of the activity platform as the next-generation social platform.
Lung nitroxidative stress as a prognostic factor in ventilated septic patients (2007)

During sepsis and mechanical ventilation, nitric oxide (•NO) is produced by lung cells. We study whether pulmonary •NO production is a prognostic factor in mechanically ventilated septic patients.
Glycothermal Synthesis of ZnGa[sub 2]O[sub 4]:Mn[sup 2+] Nanophosphor and Change in Its Photoluminescence Intensity by Heat-Treatment (2007)

nanophosphors were synthesized from zinc acetate dihydrate, gallium acetylacetonate, and manganese(II) acetate tetrahydrate in 1,4-butanediol by glycothermal method at for . Their average particle diameter was . We investigated the influence of temperatures of postheat-treatment in Ar on the luminescent and structural properties. The photoluminescence (PL) intensity slightly decreased after heating below . The PL intensity increased between 900 and , reached at the maximum at and decreased over . The decrease of the PL intensity by heating below occurred by the removal of adsorbed organic species. The X-ray diffraction profile indicated the decomposition of to and ZnO by heating over , resulting in the decrease of the PL intensity. The change in the integrated intensity of electron paramagnetic resonance due to paramagnetic with the temperature of heat-treatment in Ar was similar to that of the PL intensity. This suggests that the PL intensity is correlated to the incorporated amount.
Visuelle Datenanalyse mit Streudiagrammen : Problemlösungen für Ungleichverteilung und Überdeckung (2010)

Scatter plots are one of the most powerful and most widely used techniques for visual data exploration in order to detect patterns and correlations. A well-known problem is that scatter plots often have a high degree of overlap, which may occlude a significant portion of the data values shown. Additionally, scatter plots suffer from unequal data distribution, because dense areas are not visualized as good as sparse areas. The research shown in this master s thesis will cope with these problems using a novel approach called Generalized Scatter Plot. This technique allows an overlap-free representation of large datasets to fit entirely into the display.&lt;br /&gt;The basic idea is to allow the analyst to optimize the degree of overlap and distortion to generate the best possible view. To allow an effective usage, the capability to interpolate smoothly between the traditional and the generalized scatter plots is provided. In particular, an optimization function will be identified, which takes both overlap and distortion of the visualization into account. Furthermore, the generalized scatter plots will be applied to a number of realworld data sets from application domains, such as server performance monitoring, telephone service usage analysis, and geographical data, demonstrating the benefits of the generalized scatter plots over traditional techniques.
Investigating Surface Structure, Chemistry, and Thickness of NMC Cathodes Blended with LFO using EELS (2019)

Rechargeable lithium-ion (Li-ion) batteries have been the battery of choice since the 1990s for portable electronics and, more recently, in hybrid/electric vehicles. In order to meet the rising energy demands, lithium ion batteries require higher power density, gravimetric, and volumetric capacity. The main system that became a commercial success was LiCoO2, developed by Goodenough LiCoO2 is a layered structure with Li and Co sitting in alternating octahedral sites forming a hexagonal symmetry. In order to improve cyclic stability, reduce toxicity, and cost, research became focused on adding dopants such as Ni and Mn, replacing Co sites. These efforts led to the realization of LiNixMnyCozO2 (NMC).
Safety and efficacy of carbon dioxide cryotherapy for treatment of neoplastic Barrett’s esophagus (2015)

CO2 cryotherapy was a safe and effective primary curative or rescue therapy for Barrett's neoplasia.
Technological solutions and operational measures to prevent escapes of Atlantic cod (Gadus morhua) from sea cages (2006)

Escapes of cod (Gadus morhua) from sea cages represent an economic problem for farmers and a potential environmental problem. We estimate that 0–6% of cod held in sea-cage farms in Norway were reported to have escaped each year from 2000 to 2005, which is a high proportion compared with salmon. We interviewed employees at 19 coastal sea-cage cod farms in Norway to investigate both how and why cultured cod escape and to document cage handling and management strategies that were effective in minimizing escapes. Based on the interviews, we describe five working hypotheses that may explain why a greater proportion of cod than salmon escape: (1) cod are more willing to escape than salmon; (2) cod bite the net cage and create wear and tear; (3) net cages have insufficient technical standards for cod culture; (4) cod are placed in sea cages at considerably smaller sizes than salmon; and (5) cod are more popular feed for predators. Preliminary testing of the hypothesis that cod bite netting and create holes was done by placing pre-damaged net panels with cut twines and control panels inside sea cages. Holes in the pre-damaged net panels increased in size over a period of 3 months. The type of damage indicated that biting of netting twines was the likely cause.
Surface modification of semiconductor nanocrystals by a methanofullerene carboxylic acid (2010)

We report, for the first time, on successful binding of a fullerene derivative, namely 3,4-dihexyloxyphenyl-C61-butyric-acid (dPCBA) to PbS and CdSe nanocrystals (NCs). This molecule is an excellent candidate to serve as electroactive ligand for NCs and form novel complexes, which could be very promising building blocks for optoelectronic devices. The surface modification phenomenon was followed by steady-state and time-resolved photoluminescence (PL) experiments. The dramatic PL quenching in the case of both NCs indicates photoinduced charge transfer from NCs to dPCBA molecules as a result of effective coordination of dPCBA to the NC surface. The electrically active nature of the new complexes is proven by current–voltage measurements on thin films of the NC-dPCBA complexes.
Injection of inositol trisphosphorothioate into Limulus ventral photoreceptors causes oscillations of free cytosolic calcium. (1991)

Limulus ventral photoreceptors contain calcium stores sensitive to release by D-myo-inositol 1,4,5 trisphosphate (InsP3) and a calcium-activated conductance that depolarizes the cell. Mechanisms that terminate the response to InsP3 were investigated using nonmetabolizable DL-myo-inositol 1,4,5 trisphosphorothioate (InsPS3). An injection of 1 mM InsPS3 into a photoreceptor's light-sensitive lobe caused an initial elevation of cytosolic free calcium ion concentration (Cai) and a depolarization lasting only 1-2 s. A period of densensitization followed, during which injections of InsPS3 were ineffective. As sensitivity recovered, oscillations of membrane potential began, continuing for many minutes with a frequency of 0.07-0.3 Hz. The activity of InsPS3 probably results from the D-stereoisomer, since L-InsP3 was much less effective than InsP3. Injections of 1 mM InsP3 caused an initial depolarization and a period of densensitization similar to that caused by 1 mM InsPS3, but no sustained oscillations of membrane potential. The initial response to InsPS3 or InsP3 may therefore be terminated by densensitization, rather than by metabolism. Metabolism of InsP3 may prevent oscillations of membrane potential after sensitivity has recovered. The InsPS3-induced oscillations of membrane potential accompanied oscillations of Cai and were abolished by injection of ethyleneglycol-bis (beta-aminoethyl ether)-N,N'-tetraacetic acid. Removal of extracellular calcium reduced the frequency of oscillation but not its amplitude. Under voltage clamp, oscillations of inward current were observed. These results indicate that periodic bursts of calcium release underly the oscillations of membrane potential. After each burst, the sensitivity of the cell to injected InsP3 was greatly reduced, recovering during the interburst interval. The oscillations may, therefore, result in part from a periodic variation in sensitivity to a constant concentration of InsPS3. Prior injection of calcium inhibited depolarization by InsPS3, suggesting that feedback inhibition of InsPS3-induced calcium release by elevated Cai may mediate desensitization between bursts and after injections of InsPS3.
E2F factors rate controls the dual role of CDE/E2F composite element: A model of E2F‐regulated gene expression in plant development (2006)

The promoters of several E2F-regulated genes identified in plants contain a variety of E2F motifs, notably a composite element consisting of a "CDE-like element" C/GGCGG on one strand, described as repressor in animals, associated with an E2F element on the complementary strand. This detailed study throughout plant development using ribonucleotide reductase promoters, allows us to propose a model, where E2F and composite elements play a dual role. Such regulation is mainly conditioned by the availability of E2F factors in tissues and during the cell cycle in tobacco.
Novel Peptide Sequence (“IQ-tag”) with High Affinity for NIR Fluorochromes Allows Protein and Cell Specific Labeling for In Vivo Imaging (2007)

The described method is expected to have broad utility in numerous applications, namely site-specific protein imaging, target identification, cell tracking, and drug development.
DEFENSIVE RESIN BIOSYNTHESIS IN CONIFERS (2001)

Tree killing bark beetles and their vectored fungal pathogens are the most destructive agents of conifer forests worldwide. Conifers defend against attack by the constitutive and inducible production of oleoresin, a complex mixture of mono-, sesqui-, and diterpenoids that accumulates at the wound site to kill invaders and both flush and seal the injury. Although toxic to the bark beetle and fungal pathogen, oleoresin also plays a central role in the chemical ecology of these boring insects, from host selection to pheromone signaling and tritrophic level interactions. The biochemistry of oleoresin terpenoids is reviewed, and the regulation of production of this unusual plant secretion is described in the context of bark beetle infestation dynamics with respect to the function of the turpentine and rosin components. Recent advances in the molecular genetics of terpenoid biosynthesis provide evidence for the evolutionary origins of oleoresin and permit consideration of genetic engineering strategies to improve conifer defenses as a component of modern forest biotechnology.
A three-stage, deep learning, ensemble approach for prognosis in patients with Parkinson’s disease (2021)

The approach showed promise for longitudinal prognostication in PD and demonstrated the synergy of imaging and non-imaging information for the prediction task.
Etch process monitoring by electron beam wafer inspection (2007)

Electron beam inspection (EBI) of wafers has been widely shown to be a powerful tool for random defectivity on wafers, particularly for sub-surface electrical defects that cannot be seen by optical tools. Some types of systematic defects, such as subtle under- or over-etch of contacts, can be difficult to catch using traditional die-die or cell-cell comparison because all contacts may be similarly affected. In this paper we investigated methods for catching systematic process defects using EBI. We used a design of experiment where different dies on the same wafer were etched using a total of 4 different etch parameters. The dies were selected by using multiple resist coat, pattern, and etch steps at a single contact layer. A total of 3 wafers were given the same process treatment. Following the etch steps, one wafer continued through the fabrication process to final test, one wafer was inspected using an eS31 electron beam wafer inspection tool, while the third wafer was held in reserve. The initial inspection did not show any significant difference in defectivity between the dies, although final bit test did show pseudo-systematic defectivity depending on etch process condition. The wafer was then inspected on an eS32 tool using a special e-beam preconditioning step to enhance the contrast of subtle under-etched contacts. In this case, we were able to pick out a defectivity corresponding the etch condition of each die. The in-process defectivity found by the electron beam inspection tool matched well with the end-of-line bit failure map. In summary, subtle systematic etch process variations were detected by varying the etch process parameters across a single wafer, and tuning the electron beam inspection sensitivity to maximize contrast for subtle etch variations. Such techniques can be a powerful tool for optimization of etch process recipes to minimize wafer electrical defectivity.
Conformal Electroless Deposition On monolayers for TSV Applications (2013)

Abstract not Available.
Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440 (2017)

The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar K<sub>M</sub> values, the V<sub>max</sub> of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr-1 and alr-2 respectively.
The Heme Degradation Pathway is a Promising Serum Biomarker Source for the Early Detection of Alzheimer's Disease (2010)

One of the remaining challenges in Alzheimer's disease (AD) research is the establishment of biomarkers for early disease detection. As part of a prospective study spanning a period of five years, we have collected serial serum samples from cognitively normal, mild cognitively impaired (MCI), and mild AD participants, including same patient samples before and after cognitive decline. Using mass spectrometry we identified several promising leads for biomarker development, such as prosaposin, phospholipase D1, biliverdin reductase B, and S100 calcium binding protein A7. Selected candidate markers were verified using reverse phase protein microarray assays. Of 15 protein/protein abundance ratios that were significantly altered in sera from subjects with mild AD compared to Normal or MCI subjects, 14 were composed of ratios containing heme oxygenase-1, biliverdin reductase A, or biliverdin reductase B. Moreover, an increase in the protein abundance ratio of matrix metallopeptidase 9/biliverdin reductase differentiated stable MCI subjects from MCI subjects progressing into mild AD before the onset of cognitive decline. These findings strongly implicate the heme degradation pathway as a promising source of protein biomarkers for the early detection of AD.
Toward Understanding the Mechanism behind Microstructure Development of Aluminum Alloy Powders Additively Manufactured by Selective Laser Melting (2019)

The present article describes a possible mechanism behind the microstructure development in aluminum (Al) alloy (AlSi10Mg: Al–10wt%Si–0.3wt%Mg) parts additively manufactured by selective laser melting (SLM) combined with powder bed system (one of the most conventional additive manufacturing processes for metals). It introduces the thermodynamic calculation applied to the studied alloy to understand the microstructure development during the SLM process and then elaborates microstructural features of SLM-fabricated Al alloy parts characterized by electron microscopy and electron back-scattered diffraction analyses. The aforementioned results are utilized to present the formation process of microstructure through the rapid solidification during the SLM process. An attempt was made to quantify the cooling rate and molten pool dimensions using the preliminary two-dimensional finite element model. The analyzed thermal gradient and cooling rates are presented as well.
A Double-Data- Rate 2 (DDR2) Interface Phase-Change Memory with 533MB/s Read -Write Data Rate and 37.5ns Access Latency for Memory-Type Storage Class Memory Applications (2016)

For the first time, by using a novel multiple individual bank sensing/writing and a memory bank interleave design, we demonstrate a double date rate 2 (DDR2) DRAM like interface phase-change memory (PCM) for M-type storage class memory applications . The write and read bandwidth is equal to 533MB/s, and the random read latency is 37.5ns, while the write latency is 11.25ns supporting a random write cycle of 176.7ns. In addition, a record high switching speed of 128ns with good resistance distribution is demonstrated with a super-fast Set material.