gebhart/patrepeval huggingface dataset:
Improved Outcomes and Staging in Non-Small-Cell Lung Cancer Guided by A Molecular Assay (2021)

There remains a critical need for improved staging of non-small-cell lung cancer, as recurrence and mortality due to undetectable metastases at the time of surgery remain high even after complete resection of tumors currently categorized as 'early stage.' A 14-gene quantitative PCR-based expression profile has been extensively validated to better identify patients at high-risk of 5-year mortality after surgical resection than conventional staging - mortality that almost always results from previously undetectable metastases. Furthermore, prospective studies now suggest a predictive benefit in disease-free survival when the assay is used to guide adjuvant chemotherapy decisions in early-stage non-small-cell lung cancer patients.
Data from A Simplified Synthesis of Novel Dictyostatin Analogues with <i>In Vitro</i> Activity against Epothilone B–Resistant Cells and Antiangiogenic Activity in Zebrafish Embryos (2023)

&lt;div&gt;Abstract&lt;p&gt;The natural product (−)-dictyostatin is a microtubule-stabilizing agent that potently inhibits the growth of human cancer cells, including paclitaxel-resistant clones. Extensive structure–activity relationship studies have revealed several regions of the molecule that can be altered without loss of activity. The most potent synthetic dictyostatin analogue described to date, 6-&lt;i&gt;epi&lt;/i&gt;-dictyostatin, has superior &lt;i&gt;in vivo&lt;/i&gt; antitumor activity against human breast cancer xenografts compared with paclitaxel. In spite of their encouraging activities in preclinical studies, the complex chemical structure of the dictyostatins presents a major obstacle for their development into novel antineoplastic therapies. We recently reported a streamlined synthesis of 16-desmethyl-25,26-dihydrodictyostatins and found several agents that, when compared with 6-&lt;i&gt;epi&lt;/i&gt;-dictyostatin, retained nanomolar activity in cellular microtubule-bundling assays but had lost activity against paclitaxel-resistant cells with mutations in β-tubulin. Extending these studies, we applied the new, highly convergent synthesis to generate 25,26-dihydrodictyostatin and 6-&lt;i&gt;epi&lt;/i&gt;-25,26-dihydrodictyostatin. Both compounds were potent microtubule-perturbing agents that induced mitotic arrest and microtubule assembly &lt;i&gt;in vitro&lt;/i&gt; and in intact cells. &lt;i&gt;In vitro&lt;/i&gt; radioligand binding studies showed that 25,26-dihydrodictyostatin and its C6-epimer were capable of displacing [&lt;sup&gt;3&lt;/sup&gt;H]paclitaxel and [&lt;sup&gt;14&lt;/sup&gt;C]epothilone B from microtubules with potencies comparable to (−)-dictyostatin and discodermolide. Both compounds inhibited the growth of paclitaxel- and epothilone B–resistant cell lines at low nanomolar concentrations, synergized with paclitaxel in MDA-MB-231 human breast cancer cells, and had antiangiogenic activity in transgenic zebrafish larvae. These data identify 25,26-dihydrodictyostatin and 6-&lt;i&gt;epi&lt;/i&gt;-25,26-dihydrodictyostatin as candidates for scale-up synthesis and further preclinical development. &lt;i&gt;Mol Cancer Ther; 10(6); 994–1006. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Precise 3-D Measurement using Uncalibrated Pattern Projection (2007)

Three-dimensional measurement methods using structured light projection enable accurate depth measurements by decoding the disparity between the projector-camera pair from an observed pattern. However, actual projection devices have various systematic error sources that distort the structured light pattern, directly affecting the accuracy of 3-D measurements. We propose a new method of measuring depth that is not affected by the systematic errors in the projected pattern. In our method, the image of a pattern projected onto a plane is referenced to cancel errors. Based on the invariance of the cross-ratio under perspective projections, depth is obtained from the disparity determined on the referenced image. In experiments, our method removed the systematic errors and improved the accuracy of depth measurement without any extra calibration or measurement.
Introduction (2010)

Arithmetic is one of the old topics in computing. It dates back to the many early civilizations that used the abacus to perform arithmetic operations. The seventeenth and eighteenth centuries brought many advances with the invention of mechanical counting machines like the slide rule, Schickard's Calculating Clock, Leibniz's Stepped Reckoner, the Pascaline, and Babbage's Difference and Analytical Engines. The vacuum tube computers of the early twentieth century were the first programmable, digital, electronic, computing devices. The introduction of the integrated circuit in the 1950s heralded the present era where the complexity of computing resources is growing exponentially. Today's computers perform extremely advanced operations such as wireless communication and audio, image, and video processing, and are capable of performing over 1015 operations per second.
Kernel-based Reconstruction of Space-time Functions on Dynamic Graphs (2017)

Graph-based methods pervade the inference toolkits of numerous disciplines including sociology, biology, neuroscience, physics, chemistry, and engineering. A challenging problem encountered in this context pertains to determining the attributes of a set of vertices given those of another subset at possibly different time instants. Leveraging spatiotemporal dynamics can drastically reduce the number of observed vertices, and hence the sampling cost. Alleviating the limited flexibility of the existing approaches, the present paper broadens the kernel-based graph function estimation framework to reconstruct time-evolving functions over possibly time-evolving topologies. This approach inherits the versatility and generality of kernel-based methods, for which no knowledge on distributions or second-order statistics is required. Systematic guidelines are provided to construct two families of space-time kernels with complementary strengths: the first facilitates judicious control of regularization on a space-time frequency plane, whereas the second accommodates time-varying topologies. Batch and online estimators are also put forth. The latter comprise a novel kernel Kalman filter, developed to reconstruct space-time functions at affordable computational cost. Numerical tests with real datasets corroborate the merits of the proposed methods relative to competing alternatives.
High-sensitivity laser-induced fluorescence detection for capillary electrophoresis (1991)

Capillary electrophoresis provides very high efficiency separations of biological molecules. Laser-induced fluorescence produces very high sensitivity detection. The combination of the two techniques results in an analytical tool with unprecedented properties: separations with more than a million theoretical plates and detection limits of a few hundred analyte molecules. This paper considers the design of high-sensitivity laser-induced fluorescence detection for capillary zone electrophoresis separation of labeled amino acids and capillary gel electrophoresis separation of DNA sequencing fragments.
Cross-Polarization Treatment in Linearly Polarized Vivaldi Array Apertures (2022)

This paper examines how cross-polarization can be effectively reduced in two-dimensional array apertures of linearly-polarized Vivaldi antennas. In previous work it was demonstrated how metallic cross walls, positioned orthogonal to the linear Vivaldi antenna elements in a two-dimensional array, reduce cross-polarization significantly - e.g., -15dB levels for 45° diagonal plane scans. This cross-polarization mitigation technique is expanded upon by showing that slices in the metallic cross walls can further reduce cross-polarization, e.g. -25dB levels for 45° diagonal plane scans. For demonstration, an 8×8 single-pol. Vivaldi array comprising 8 rows of 8-element sub-arrays arranged onto a uniform grid with slots between elements is presented. Cross-polarization measurements are compared to infinite array simulations with and without ‘sliced’ metallic cards inserted (orthogonally) into the slots between radiating elements.
Continuing education in power electronics (2004)

Continuing education has become an increasingly important part of the mission of higher education in the United States and around the world. The objective of engineering continuing education is to help practicing engineers stay current with technological advances relevant to their current or future job assignments. This paper presents the strategies and guidelines for continuing education in power electronics. Critical issues pertaining to engineering education, such as how to identify learning needs, define learning outcomes, design course contents, select instructional methods, assess student performance, and conduct course evaluation, are discussed in detail. © 2005 IEEE.
Optical microfiber loop resonator (2005)

We experimentally demonstrate an optical microfiber loop resonator. The resonator was formed in free space by creating a loop from the subwavelength-diameter waist of a short biconical optical fiber taper. The loop length was chosen so that the free spectrum range of the resonator was ∼100GHz at the optical communication wavelengths near 1.5μm. In order to change and optimize the spectral characteristics such as the effect of birefringence, the shape of resonances, and the free spectrum range, we manually varied the microfiber self-coupling by alignment of the input and output ends of the loop, which were attached to each other by Van der Waals and electrostatic forces. In particular, we tuned the microfiber loop resonator to exhibit resonances with a Q-factor exceeding 15 000 (finesse ≈10) and, also, to the regime of critical coupling with the extinction ratio of transmission oscillations exceeding 34dB. This paper was in press when we achieved the values of 95 000 and 630 000 for the loaded and intrinsic Q-factor, respectively (see note added in proof). We believe that the demonstrated Q-factor can be significantly enhanced with the more uniform microfiber.
Size-Dependent Structural, Energetic, and Spectroscopic Properties of MoS3 Polymorphs (2020)

In spite of the interest of a-MoS3 based nanomaterials, the amorphous nature of the MoS3 phase makes it challenging to control and understand its chemical reactivity. In particular, the type of the structural building unit such as Mo3 triangular vs Mo chain is still debated, while the ambivalent interpretation of the nature of sulfur species (S2–, S22–) and Mo–Mo bonds leads to ambiguous interpretations of spectroscopic data and reactivity. By density functional theory (DFT), we simulate the energetic, structural, and spectroscopic features of relevant zero-dimensional 0D-, 1D-, and 2D-MoS3 triangular, chain-like polymorphs, including unprecedented ones (ring, wave, and helix) and revisit the interpretation of EXAFS, IR-RAMAN, and XPS experimental data. We analyze how MokS3k clusters of a few k atoms may grow up to infinite (periodic replica) MoS3 polymorphs. The evolution of the growth energy and the computed IR spectra within the density functional perturbation theory level suggest the coexistence of various polymorphs in the MoS3 phase as a function of sizes. Molecular dynamics simulations reveal how the small triangular MokS3k oligomers may transform into condensed MoS3 patches resembling embryos of the 2D 1T′-MoS2 phase. Finally, we discuss some plausible transformation pathways from one polymorph to another.
Identifying molecular fluorophore impurities in the synthesis of low-oxygen-content, carbon nanodots derived from pyrene (2022)

Determination of the formation of bright molecular fluorphores during the synthesis of pyrene-derived CNDs, through extensive separation and systematic characterization.
Novel Phenotypic Fluorescent Three-Dimensional Co-Culture Platforms for Recapitulating Tumor in vivo Progression and for Personalized Therapy (2013)

Because three-dimensional (3D) in vitro models are more accurate than 2D cell culture models and faster and cheaper than animal models, they have become a prospective trend in the biomedical and pharmaceutical fields, especially for personalized and targeted therapies. Because appropriate 3D models can be customized to mimic the in vivo microenvironment wherein various cell populations grow within an intricate but well organized extracellular matrix (ECM), they can accurately recapitulate physiological and pathophysiological progressions. The majority of cancers are carcinomas, which originate from epithelial cells, and dynamically interact with non-malignant cells including stromal cells (fibroblasts), vascular cells (endothelial cells and pericytes), immune cells (macrophages and mast cells), and the ECM. Employing a tumor monoclonal colony, tumor xenograft or patient cancer biopsy into an in vivo-like microenvironment, the native signaling pathways, cell-cell and cell-matrix interactions, and cell phenotypes are preserved and our fluorescent phenotypic 3D co-culture platforms can then accurately recapitulate the tumor in vivo scenario including tumor induced angiogenesis, tumor growth, and metastasis. In this paper, we describe a robust and standardized method to co-culture a tumor colony or biopsy with different cell populations, e.g., endothelial cells, immune cells, pericytes, etc. The procedures for recovering cells from the co-culture for molecular analyses, imaging, and analyzing are also described. We selected ECM solubilized extract derived from Engelbreth-Holm-Swam sarcoma cells. Because the 3D co-culture platforms can provide drug chemosensitivity data within 9 days that is equivalent to the results generated from mouse tumor xenograft models in 50 days, the 3D co-culture platforms are more accurate, efficient, and cost-effective and may replace animal models in the near future to predict drug efficacy, personalize therapies, prevent drug resistance, and improve the quality of life.
China Joins the World: Progress and Prospects (1999)

Since the 1970s, the United States has facilitated China's entry into world affairs. What are the results of the effort to integrate China into the international community at an early stage in its rise? How has the international system affected Chinese behavior, and how has China influenced the international system? Each chapter in this volume explores the record of Chinese participation in a specific issue area: the United Nations, arms control, the environment, human rights, banking and finance, trade, energy, telecommunications, and international law. These in-depth and timely studies reveal considerable success--more than most forecasts expected--but the road ahead may prove tougher than the terrain already covered. In addition to the editors, the contributors include Todd M. Johnson, Samuel S. Kim, Nicholas R. Lardy, Andrew J. Nathan, Margaret M. Pearson, Alexander H. Platt, Lester Ross, Michael D. Swaine, Frederick S. Tipson, and Ko-Yung Tung.
Preliminary evaluation of four-layer BGO DOI-detector for PET (2006)

We found that Bi/sub 4/Ge/sub 3/ O/sub 12/ (BGO) scintillator can be elements of a four-layer depth of interaction (DOI) detector and it was proved with a 12/spl times/12/spl times/4 array of BGO crystals in dimensions of 2.9 mm/spl times/2.9 mm/spl times/7.5 mm coupled to a 256-channel flat panel position sensitive photomultiplier tube. Appropriate reflector insertion in the array makes all crystal identification possible on one position histogram. Despite the large refractivity and small light output of BGO, the four-layer BGO detector showed no significant variation in the full energy peaks among all crystal elements. When no optical grease was used in the construction of the BGO DOI-block and irradiated with gamma-rays from /sup 137/Cs, a top layer crystal has 80% of light output relative to the bottom layer. The obtained two-dimensional position histogram by the irradiation was clear enough to allow identification of the crystals of interaction. Profiles of the histogram show peak-to-valley ratio of 1.9:1 for the top layer crystals and larger ratio for other layer crystals in the experiment.
ChemInform Abstract: CONJUGATE ADDITION OF METHYL GROUPS TO αβ‐UNSATURATED ALDEHYDES: USE OF ME5CU3LI2 (1981)

Abstract Mit dem aus 5 Äquival.
Biotechnological Production of Flavonoids: An Update on Plant Metabolic Engineering, Microbial Host Selection, and Genetically Encoded Biosensors (2020)

Flavonoids represent a diversified family of phenylpropanoid-derived plant secondary metabolites. They are widely found in fruits, vegetables, and medicinal herbs. There has been increasing interest on flavonoids because of their proven bioactivity associated with anti-obesity and anti-cancer, anti-inflammatory and anti-diabetic activity. Low bioavailability of flavonoids is a major challenge restricting their applications. Due to safety and economic issues, plant extraction or chemical synthesis could not provide a scalable route for large-scale production. Alternatively, reconstruction of biosynthetic gene clusters in plants and industrially relevant microbes offer significant promise for discovery and scalable synthesis of flavonoids. This review provides an update on biotechnological production of flavonoids. The recent advances on plant metabolic engineering, microbial host, and genetically encoded biosensors are summarized. Plant metabolic engineering holds the promise to improve the yield of specific flavonoids and expand the chemical space of novel flavonoids. The choice of microbial host provides the cellular chassis that could be tailored for various stereo- or regio-selective chemistries that are crucial for their bioactivities. When coupled with transcriptional biosensing, genetically encoded biosensors could be welded into cellular metabolism to achieve high throughput screening or dynamic carbon flux re-allocation to deliver efficient microbial workhorse. The convergence of these technologies will translate the vast majority of plant genetic resources into valuable flavonoids with pharmaceutical/nutraceutical values in the foreseeable future.
Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases (2014)

Neurodegenerative diseases share common pathologic features including neuroinflammation, mitochondrial dysfunction and protein aggregation, suggesting common underlying mechanisms of neurodegeneration. We undertook a meta-analysis of public gene expression data for neurodegenerative diseases to identify a common transcriptional signature of neurodegeneration. Using 1,270 post-mortem central nervous system tissue samples from 13 patient cohorts covering four neurodegenerative diseases, we identified 243 differentially expressed genes, which were similarly dysregulated in 15 additional patient cohorts of 205 samples including seven neurodegenerative diseases. This gene signature correlated with histologic disease severity. Metallothioneins featured prominently among differentially expressed genes, and functional pathway analysis identified specific convergent themes of dysregulation. MetaCore network analyses revealed various novel candidate hub genes (e.g. STAU2). Genes associated with M1-polarized macrophages and reactive astrocytes were strongly enriched in the meta-analysis data. Evaluation of genes enriched in neurons revealed 70 down-regulated genes, over half not previously associated with neurodegeneration. Comparison with aging brain data (3 patient cohorts, 221 samples) revealed 53 of these to be unique to neurodegenerative disease, many of which are strong candidates to be important in neuropathogenesis (e.g. NDN, NAP1L2). ENCODE ChIP-seq analysis predicted common upstream transcriptional regulators not associated with normal aging (REST, RBBP5, SIN3A, SP2, YY1, ZNF143, IKZF1). Finally, we removed genes common to neurodegeneration from disease-specific gene signatures, revealing uniquely robust immune response and JAK-STAT signaling in amyotrophic lateral sclerosis. Our results implicate pervasive bioenergetic deficits, M1-type microglial activation and gliosis as unifying themes of neurodegeneration, and identify numerous novel genes associated with neurodegenerative processes.
KIC RawMaterials: Iron Balance—Austria (2019)

An evaluation of the iron flow in Austria was executed at the RIC ESEE at the Montanuniversitaet Leoben within the context of the European network EIT RawMaterials. The main idea was to develop a system that visualizes the mass flow of iron and steel of Austria. To build up the system, it was essential to provide all necessary information regarding the production, consumption and inventory as well as information about the trading (including import and export) of semi-finished products, goods and scrap. The boundary conditions for the system were the national economics of Austria in the year 2010. The mass flow software STAN2 was used for visualization of the system. A main objective of the project was the calculation and visualization of the required iron scrap for the steel production in Austria. The influencing factors on the iron balance were identified and the question of the steady state of scrap return was answered.
Maskless Lithography using Diffractive-Optical Arrays (2005)

An optical maskless-lithography system is described that is capable of patterning complex geometries at very high resolution, and in a cost-effective manner with potential applications in the fabrication of nanostructures for photonic devices.
<b><i>Porphyromonas gingivalis</i></b> Peptidyl Arginine Deiminase Can Modulate Neutrophil Activity via Infection of Human Dental Stem Cells (2018)

Periodontitis (PD) is a widespread chronic inflammatory disease in the human population. Porphyromonas gingivalis is associated with PD and can citrullinate host proteins via P. gingivalis peptidyl arginine deiminase (PPAD). Here, we hypothesized that infection of human dental follicle stem cells (hDFSCs) with P. gingivalis and subsequent interaction with neutrophils will alter the neutrophil phenotype. To test this hypothesis, we established and analyzed a triple-culture system of neutrophils and hDFSCs primed with P. gingivalis. Mitogen-activated pathway blocking reagents were applied to gain insight into stem cell signaling after infection. Naïve hDFSCs do not influence the neutrophil phenotype. However, infection of hDFSCs with P. gingivalis prolongs the survival of neutrophils and increases their migration. These phenotypic changes depend on direct cellular contacts and PPAD expression by P. gingivalis. Active JNK and ERK pathways in primed hDFSCs are essential for the phenotypic changes in neutrophils. Collectively, our results confirm that P. gingivalis modifies hDFSCs, thereby causing an immune imbalance.
Graphene‐Wrapped Nanoporous Nickel‐Cobalt Oxide Flakes for Electrochemical Supercapacitors (2018)

Abstract A novel approach for hybridizing nanoporous NiCo oxide flakes with graphene sheets is reported. Positively charged cyano‐bridged CoNi coordination polymer flakes (CoNi‐CP) are mixed with graphene (G) suspension with negatively charged surface. Due to effective electrostatic interaction, both the materials are hybridized to form CoNi‐CP/G composite. The as‐prepared CoNi‐CP/G composite is thermally treated in air, to remove the organic components without affecting the integrity of the parent G sheets. Through the thermal treatment, the CoNi‐CP flakes wrapped into G sheets are converted to NiCo oxide, resulting in a new composite consisting of NiCo oxide flakes and G sheets. The NiCo‐oxide/G composite shows the high specific capacitance (∼ 199 F g‐1) at 5 mV/s, and features the good capacitance retention of ∼68% at 100 mV(∼ 135 F g −1 ).