gebhart/patrepeval huggingface dataset:
P4‐709: PROTEOLIPIDOME ANALYSIS OF HIPPOCAMPAL TISSUE FROM A MURINE ALZHEIMER'S DISEASE MODEL TO FACILITATE THERAPEUTIC TARGET IDENTIFICATION (2019)

Mass spectrometry-based proteomics has potential for uncovering the molecular mechanisms underlying Alzheimer's Disease (AD). However, proteins with atypical biochemical/biophysical properties may go understudied as they may not survive the typical proteomics workflow. Utilizing a unique approach, we have assessed differences across the proteolipidome between the E4FAD murine model of AD and wildtype mice. A liquid-liquid extraction adapted from the Bligh and Dyer method [J. Biochem. Physiol. 1959] was used to isolate proteolipids from hippocampal tissue from apoliprotein E4-5XFAD transgenic and wild-type C57BL/6 mice. Proteolipids were digested with trypsin, labeled with isobaric tandem mass tags (TMT) to provide relative quantitation. Peptides were injected onto a laser-pulled nanobore C18 column and resolved on a liquid chromatograph using an optimized 3-hour gradient coupled to a hybrid quadrupole-Orbitrap mass spectrometer operating in the dd-MS2 mode. Relative peptide abundance was determined using a Proteome Discoverer 2.2. Proteins with a p-value ≤ 0.05 that exhibited a log2-fold change of 0.5 or greater were subjected to functional protein association network analysis as well as comprehensive gene set enrichment analysis. By comparison with results obtained using an optimized bottom-up proteomics workflow, it is evident that many of the proteins found in this experiment are unique to this technique and do not appear in experiments using standard detergent-based aqueous extraction buffers. The relative abundance of many proteins differed between E4FAD and wildtype hippocampi and Protein Center gene ontology analysis revealed numerous proteins to be membrane-specific with protein binding functions. Additionally, many proteins had post-translational modifications (PTMs) such as phosphorylation and acetylation, revealing an interconnected signaling network of proteins that differ in wildtype and E4FAD hippocampus. This novel approach analyzing organically extracted proteolipid fractions provides supplemental coverage of the proteome not revealed by conventional proteomics workflows, including changes in protein expression and PTMs distinctive for the E4FAD as compared to wildtype mice. This method has provided new information regarding the pathological mechanisms in this model, and will be used to facilitate identification of new targets for potential therapeutic development in the treatment of AD.
IgM monoclonal antibodies recognizing FcαR but not FcγRIII trigger a respiratory burst in neutrophils although both trigger an increase in intracellular calcium levels and degranulation (1995)

The role of IgG receptor, Fc gamma RIII, in the triggering of neutrophil functions has been controversial. Here we show that IgM monoclonal antibodies, Leu 11b and 1D3, recognizing Fc gamma RIII, bind to human neutrophils triggering an increase in intracellular calcium concentration and release of myeloperoxidase upon degranulation but do not trigger a respiratory burst detectable as lucigenin-enhanced chemiluminescence. Although many fewer molecules of IgM monoclonal antibody, MY43, recognizing Fc alpha R, bind to the same cells they trigger a much greater increase in intracellular calcium concentration, release of myeloperoxidase and a strong respiratory burst. Since the respiratory bursts triggered by IgG and IgA are equivalent, this demonstrates that Fc gamma RII is responsible for the IgG-mediated response. IgM monoclonal antibody MC2, recognizing the abundant neutrophil cell-surface carbohydrate CD15, also triggers a small rise in intracellular calcium but no respiratory burst.
The Influence of the Support Nature and the Metal Precursor in the Activity of Pd‐based Catalysts for the Bromate Reduction Reaction (2021)

Abstract Palladium catalysts supported on different materials (alumina, activated carbon and mixed oxide derived from hydrotalcite) and prepared with different metal precursors (nitrate, chloride and acetate) have been characterized and tested for the bromate reduction reaction. The catalytic behavior depends on the support nature and on the metallic precursor used for the catalyst preparation. Pd catalyst supported on a mixed oxide has a low activity due to the high affinity of the reconstructed support for the Br − formed, preventing the reactants to approximate the active Pd sites. Pd catalyst supported on activated carbon has a surface negative charge and a microporous structure, making difficult the interaction of the active sites with the reactants. The best results are obtained with the catalyst supported on alumina due to its physical‐chemical properties, i. e . mesoporosity, positive surface charge and reversible adsorption of reactants and products. These characteristics make easy bromate and H 2 adsorption on the active sites and subsequent reaction, thus resulting in a better activity. The Pd precursor salt also influences the catalytic activity as it has an effect on the Pd nanocrystal size. The best results are obtained with the metal precursor that produces homogeneous and large Pd metallic crystallites.
SIMON, an automated machine learning system reveals immune signatures of influenza vaccine responses (2019)

Abstract Machine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. Here, we developed Sequential Iterative Modelling “OverNight” or SIMON, an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4 + and CD8 + T cell subsets strongly associated with a robust antibody response to influenza antigens. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.
Interfacial Effects During Thermal Cycling of Cu-Filled Through-Silicon Vias (TSV) (2011)

Large shear stresses may develop at interfaces between dissimilar materials during thermal excursions when there is a significant difference in their coefficients of thermal expansion. The shear stress may cause interfaces to slide via diffusional process, thereby accommodating the relative dimensional changes between the two materials. This phenomenon presents a significant reliability issue in three-dimensional (3-D) interconnect structures involving through-silicon vias (TSVs), which are subjected not only to continuous thermal cycling but also to large electric current densities during service. This paper reports experimental evidence of interfacial sliding between Cu and Si in Cu-filled TSVs during thermal cycling conditions, and in the presence of electric current. Two different thermal cycling conditions were used: (i) small ΔT thermal cycling (−25°C to 135°C) and (ii) large ΔT thermal cycling (25°C to 425°C). Prior to thermal cycling, a few Cu-filled TSV samples were annealed for 30 min at 425°C. Cu intruded inside Si in nonannealed samples during small ΔT thermal cycling, whereas protrusion of Cu relative to Si occurred during all other thermal excursions. Application of electric current biased the net displacement of the Cu in the direction of electron flow, leading to enhanced protrusion (or intrusion) of Cu relative to the thermal cycling only (i.e., without electric current) condition. A simple one-dimensional analytical model and associated numerical simulations are utilized to rationalize the experimental observations.
Some Metal Chelates of Ethylenediaminetetraacetic Acid, Diethylenetriaminepentaacetic Acid, and Triethylenetetraminehexaacetic Acid (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome Metal Chelates of Ethylenediaminetetraacetic Acid, Diethylenetriaminepentaacetic Acid, and Triethylenetetraminehexaacetic AcidRobert E. Sievers and John C. Bailar Jr.Cite this: Inorg. Chem. 1962, 1, 1, 174–182Publication Date (Print):February 1, 1962Publication History Published online1 May 2002Published inissue 1 February 1962https://pubs.acs.org/doi/10.1021/ic50001a035https://doi.org/10.1021/ic50001a035research-articleACS PublicationsRequest reuse permissionsArticle Views541Altmetric-Citations79LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A short peptide potentially promotes the healing of skin wound (2019)

Skin wound, a common form of skin damage in daily life, remains a serious challenge in clinical treatment. Bioactive peptides with high efficiency have been considered as potential therapeutic candidates for wound healing. In this report, a novel short linear peptide, with mature peptide sequence of 'GLLSGINAEWPC' and no obvious similarity with other known bioactive peptides, was identified by genomic method from the skin of odorous frog, <i>Odorrana andersonii</i> Our results suggested that OA-GL12 (OA: abbreviation of species (<i>O. andersonii</i>), GL: two initial amino acids, 12: peptide length) obviously accelerated the scratch-healing of keratinocytes and human fibroblasts in a time- and concentration-dependent manner. Meanwhile, OA-GL12 showed significant effect in promoting the wound healing on the full-thickness skin wound model. Inflammatory assay results demonstrated that OA-GL12 induced the secretion of tumor necrosis factor (TNF) and transforming growth factor β1 (TGF-β1) on murine macrophage cell line (RAW264.7), which might explain the powerful accelerating capacity of wound healing. Moreover, results also indicated that epidermal growth factor receptor (EGFR) was involved in the mechanisms underlying the scratch-healing promoting activity of OA-GL12. In addition, OA-GL12 showed obvious free radical scavenging activity. Results supported that OA-GL12 did not exert risk in acute toxicity, hemolytic activity, and direct antibacterial activity. The remarkable effect of OA-GL12 on promoting wound healing verified in this research made it potential to be a novel template for the development of wound healing-promoting agents.
Low-cost and TSV-free monolithic 3D-IC with heterogeneous integration of logic, memory and sensor analogy circuitry for Internet of Things (2015)

For the first time, a CO2 far-infrared laser annealing (CO2-FIR-LA) technology was developed as the activation solution to enable highly heterogeneous integration without causing device degradation for TSV-free monolithic 3DIC. This process is capable to implement small-area-small-load vertical connectors, gate-first high-k/metal gate MOSFETs and non-Al metal inter-connects. Such a far-infrared laser annealing exhibits excellent selective activation capability that enables performance-enhanced stacked sub-40nm UTB-MOSFETs (Ion-enhanced over 50 %). Unlike TSV-based 3D-IC, this 3D Monolithic IC enables ultra-wide-IO connections between layers to achieve high bandwidth with less power consumption. A test chip with logic circuits, 6T SRAM, ReRAM, sense amplifiers, analog amplifiers and gas sensors was integrated to confirm the superiority in heterogeneous integration of proposed CO2-FIR-LA technology. This chip demonstrates the most variable functions above reported 3D Monolithic ICs. This CO2-FIR-LA based TSV-free 3D Monolithic IC can realize low cost, small footprint, and highly heterogeneous integration for Internet of Things.
A Performance Evaluation of Post-Processing Algorithms for Disparity Refinement of Stereo Vision (2017)

스테레오 비전은 두 대의 카메라 영상으로부터 시차를 추출하여 실제 거리정보를 계산하는 기술로서 다양한 분야에서 활용될 수 있어 활발하게 연구되는 분야이다. 기존의 스테레오 비전 연구들은 정합 과정에 초점을 맞추고 있어, 상대적으로 후처리에 관한 연구는 부족한 편이다. 이에 본 논문은 후처리 알고리즘을 세 가지로 분류하고, 분류별로 시차 개선 성능의 평가 및 분석을 수행한다. 실험 결과에 따르면, 시드 픽셀 검출 방법에서는 좌-우 일관성 검사가 시차 개선에 있어 가장 좋은 성능을 보여주고, 홀 필링 방법으로는 양방향 보간이 효과적이며, 필터 처리 방법에서는 가중 메디안 필터가 시차의 경계를 보존하면서 정확도를 향상시키는데 가장 효과적임을 확인할 수 있다.
Spring Season in Western Nepal Himalaya is not yet Warming: A 400-Year Temperature Reconstruction Based on Tree-Ring Widths of Himalayan Hemlock (Tsuga dumosa) (2020)

The Himalayan region has already witnessed profound climate changes detectable in the cryosphere and the hydrological cycle, already resulting in drastic socio-economic impacts. We developed a 619-yea-long tree-ring-width chronology from the central Nepal Himalaya, spanning the period 1399–2017 CE. However, due to low replication of the early part of the chronology, only the section after 1600 CE was used for climate reconstruction. Proxy climate relationships indicate that temperature conditions during spring (March–May) are the main forcing factor for tree growth of Tsuga dumosa at the study site. We developed a robust climate reconstruction model and reconstructed spring temperatures for the period 1600–2017 CE. Our reconstruction showed cooler conditions during 1658–1681 CE, 1705–1722 CE, 1753–1773 CE, 1796–1874 CE, 1900–1936 CE, and 1973 CE. Periods with comparably warmer conditions occurred in 1600–1625 CE, 1633–1657 CE, 1682–1704 CE, 1740–1752 CE, 1779–1795 CE, 1936–1945 CE, 1956–1972 CE, and at the beginning of the 21st century. Tropical volcanic eruptions showed only a sporadic impact on the reconstructed temperature. Also, no consistent temperature trend was evident since 1600 CE. Our temperature reconstruction showed positive teleconnections with March–May averaged gridded temperature data for far west Nepal and adjacent areas in Northwest India and on the Southwest Tibetan plateau. We found spectral periodicities of 2.75–4 and 40–65 years frequencies in our temperature reconstruction, indicating that past climate variability in central Nepal might have been influenced by large-scale climate modes, like the Atlantic Multi-decadal Oscillation, the North Atlantic Oscillation, and the El Niño-Southern Oscillation.
Solar Array Fault Detection using Neural Networks (2019)

In this paper, we describe a Cyber-Physical system approach to fault detection in Photovoltaic (PV) arrays. More specifically, we explore customized neural network algorithms for fault detection from monitoring devices that sense data and actuate at each individual panel. We develop a framework for the use of feedforward neural networks for fault detection and identification. Our approach promises to improve efficiency by detecting and identifying eight different faults and commonly occurring conditions that affect power output in utility scale PV arrays.
Metamaterial antenna array fed by distributed Bragg deflector for beam steering on SOI platform (2023)

The capability to radiate collimated steerable beams of light is crucial for many applications, such as remote sensing and free-space optical communications. Here we experimentally demonstrate a novel 1D-antenna array architecture that exhibits a far-field Gaussian profile with an angular divergence of 1.8° x 0.2°.
FIGURE 5 from Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness (2023)

&lt;p&gt;Profiling of LUAD TME by single-cell RNA-seq analysis. &lt;b&gt;A,&lt;/b&gt; Uniform Manifold Approximation and Projection (UMAP) representation colored by cell type using all cells (left) and by density grouped by risk group (right). &lt;b&gt;B,&lt;/b&gt; UMAP representation colored by gene expression of top lineage gene markers for each main cell type. Reclustering analysis for T cells (&lt;b&gt;C&lt;/b&gt;), myeloid cells (&lt;b&gt;D&lt;/b&gt;), and B cells (&lt;b&gt;E&lt;/b&gt;). UMAP representation colored by cluster, followed by UMAP representation colored by gene expression of some subset representative markers. On the far right, we have UMAP by density grouped by risk group (top) and differential abundance analysis (bottom). &lt;i&gt;Y&lt;/i&gt; axis corresponds to the fraction of cells per patient sample. ns, &lt;i&gt;P&lt;/i&gt; &gt; 0.05; *, &lt;i&gt;P&lt;/i&gt; &lt; 0.05; **, &lt;i&gt;P&lt;/i&gt; &lt; 0.001.&lt;/p&gt;
Integration of enhancement and depletion‐mode AlGaN/GaN MIS‐HFETs by fluoride‐based plasma treatment (2007)

Abstract Enhancement‐mode AlGaN/GaN metal–insulator–semiconductor HFETs (MIS‐HFETs) are demonstrated by combining CF 4 plasma treatment technique and a two‐step Si 3 N 4 deposition process. The threshold voltage has been shifted from –4 to 2 V using this technique. A 15 nm Si 3 N 4 layer is inserted under the gate to provide additional isolation between the gate metal and AlGaN surface, which can lead to higher gate turn‐on voltage. The two‐step Si 3 N 4 deposition process is developed to reduce the gate coupling capacitances in the source and drain access regions, while assuring the plasma‐treated gate region being fully covered by the gate electrode. The forward gate turn‐on voltage can be as large as 6.8 V. By tuning the plasma treatment parameters, the threshold voltage of the enhancement‐mode MIS‐HFETs can be raised to as high as 4.3 V. By integrating with depletion‐mode MIS‐HFETs, a direct‐coupled FET logic inverter has been fabricated, with logic low and high noise margins of 2.1 and 2 V. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Bifocal, Electrically Switched Intraocular And Eyeglass Molecular Lenses (1986)

A bifocal electronic molecular lens is described which can be switched between two foci without any grossly visible change in displacement, geometry, temperature or chemical composition. The lens requires very little power to change focus (on the order of tens to hundreds of nanoamps) so that long-term remote operation is anticipated. The principle of operation is based upon electronic control of optical polarization through a birefringent lens. Switching of focus is accomplished by controlling the molecular alignment of a film of liquid crystal molecules and thereby selecting between two orthogonal optical polarizations (P1 and P2). Polarization P1 is associated with focal point S1 and P2 is associated with focal point S2 through the birefringent lens. A number of useful new products are made possible by this lens. Specifically discussed are an electronic intraocular lens and electronic eyeglasses, both of which can be powered independently.
Expression and secretion of alpha-amylase and glucoamylase in Saccharomyces cerevisiae. (1994)

alpha-Amylase genes of Bacillus licheniformis and glucoamylase cDNA of Aspergillus niger were ligated to a E. coli-yeast shuttle vector. The resultant plasmid was used to transform Saccharomyces cerevisiae to construct starch-degrading yeast strain. The results of enzyme activity assay and enzyme property analysis show that alpha-amylase and glucoamylase genes have been expressed simultaneously in yeast under the control of promoters and terminators of yeast MF-alpha 1 factor and PGK genes and over 99% of enzyme activities were secreted to the medium. The engineered yeast strain hydrolyses 97% of the starch (10%) in the medium after 6 days. The recombinant plasmid exists stably in yeast.
High-silica single-mode optical reflection bending and intersecting waveguides (1985)

Single-mode high-silica optical reflection bending and intersecting waveguides are examined under conditions of large bending and intersecting angles (5–90 degrees). The reflection bending waveguide shows a loss of 2 dB at the bending angle of less than 50 degrees. When the intersecting angle was 30 degrees or more, a small intersecting loss (less than 0.1 dB) and a low crosstalk (less than −20 dB) were attained.
Analysis of a 24-kilodalton protein associated with the polyhydroxyalkanoic acid granules in Alcaligenes eutrophus (1995)

A 5.0-kbp genomic EcoRI restriction fragment which complemented a third subclass of polyhydroxyalkanoic acid (PHA)-leaky mutants of A. eutrophus that accumulated PHA at a lower rate than the wild type was cloned from Alcaligenes eutrophus H16. A 687-bp phaPAe gene on this fragment encoded a 24-kDa protein (M(r) = 23,963), which was referred to as the GA24 protein. The GA24 protein was solubilized from the granules and purified to electrophoretic homogeneity, and antibodies against the GA24 protein were obtained. The GA24 protein bound to the surface of PHA granules, as revealed by immunoelectron microscopy of whole cells and of artificial PHA granules. The GA24 protein contributed approximately 5% (wt/wt) of the total cellular protein, and it was the predominant protein present in the granules. It was synthesized only in cells accumulating PHA and only in amounts that could be bound to the granules; no soluble GA24 protein was detected. Tn5::mob-induced phaPAe mutants which were unable to synthesize intact GA24 protein formed only one large PHA granule per cell. The amino acid sequence of the GA24 protein revealed two closely related stretches consisting exclusively of nonhydrophilic amino acids at the C-terminal region, which are presumably involved in the binding of GA24 to the granules, as was recently proposed for a similar protein in Rhodococcus ruber. The GA24 protein seems to be a representative of phasins, which are a new class of protein that form a layer at the surface of PHA granules, like oleosins, which form a layer at the surface of triacylglycerol inclusions in oilseed plants.