gebhart/patrepeval huggingface dataset:
Strong suppression of radiation states in a slab waveguide sandwiched between omnidirectional mirrors (2005)

Structures in channel or slab waveguides, applied deliberately or due to imperfections, may lead to strong modal losses, corresponding to the excitation of radiation modes. As an example, losses are generally very large in slab photonic crystal (PhC) impurity waveguides (WGs) due to the combined effect of field enhancement and fabrication errors. In the presentation it is shown that for a silicon slab in air such radiation losses can be strongly reduced, by approximately one order of magnitude, by structural optimization of such a slab sandwiched between two omni-directional mirrors. The effect can be used for the production of low loss PhC impurity WGs, high Q-cavities and low-loss transitions between different WG sections.
Quantitative, noninvasive MRI characterization of disease progression in a mouse model of non-alcoholic steatohepatitis (2021)

Non-alcoholic steatohepatitis (NASH) is an increasing cause of chronic liver disease characterized by steatosis, inflammation, and fibrosis which can lead to cirrhosis, hepatocellular carcinoma, and mortality. Quantitative, noninvasive methods for characterizing the pathophysiology of NASH at both the preclinical and clinical level are sorely needed. We report here a multiparametric magnetic resonance imaging (MRI) protocol with the fibrogenesis probe Gd-Hyd to characterize fibrotic disease activity and steatosis in a common mouse model of NASH. Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce NASH with advanced fibrosis. Mice fed normal chow and CDAHFD underwent MRI after 2, 6, 10 and 14 weeks to measure liver T1, T2*, fat fraction, and dynamic T1-weighted Gd-Hyd enhanced imaging of the liver. Steatosis, inflammation, and fibrosis were then quantified by histology. NASH and fibrosis developed quickly in CDAHFD fed mice with strong correlation between morphometric steatosis quantification and liver fat estimated by MRI (r = 0.90). Sirius red histology and collagen quantification confirmed increasing fibrosis over time (r = 0.82). Though baseline T1 and T2* measurements did not correlate with fibrosis, Gd-Hyd signal enhancement provided a measure of the extent of active fibrotic disease progression and correlated strongly with lysyl oxidase expression. Gd-Hyd MRI accurately detects fibrogenesis in a mouse model of NASH with advanced fibrosis and can be combined with other MR measures, like fat imaging, to more accurately assess disease burden.
MLTI-17. DIFFERENTIATION OF RADIATION INJURY FROM RECURRENT BRAIN METASTASIS USING COMBINED FET PET/MRI RADIOMICS (2019)

Abstract BACKGROUND: The aim of this study was to investigate the potential of combined radiomics textural feature analysis of contrast-enhanced MRI (CE MRI) and static O-(2-[18F]fluoroethyl)-L-tyrosine(FET) PET for the differentiation of recurrent brain metastasis from radiation injury. PATIENTS AND METHODS: Fifty-two patients with newly diagnosed or progressive contrast-enhancing brain lesions on MRI after radiotherapy (predominantly radiosurgery, 84% of patients) of brain metastases were additionally investigated using FET PET. Based on histology (n=19) or clinicoradiological follow-up (n=33), local recurrent brain metastases were diagnosed in 21 patients (40%) and radiation injury in 31 patients (60%). Forty-two features (shape-based, first and second order features) were calculated on both unfiltered and filtered CE MRI and summed FET PET images (20–40 min p.i). After feature selection, logistic regression models using a maximum of five features to avoid overfitting were calculated for each imaging modality separately and for the combined FET PET/MRI features. The resulting models were validated using cross-validation. Diagnostic accuracies were calculated for each imaging modality separately as well as for the combined model. RESULTS: For differentiation between radiation injury and brain metastasis recurrence, textural features extracted from CE MRI had a diagnostic accuracy of 81%. FET PET textural features revealed a slightly higher diagnostic accuracy of 83%. However, the highest diagnostic accuracy was obtained when combining CE MRI and FET PET features (accuracy, 89%). CONCLUSION: Our findings suggest that combined FET PET/MRI radiomics using textural feature analysis offers a great potential to contribute significantly to the management of patients with brain metastases. SUPPORT: This work was supported by the Wilhelm-Sander Stiftung, Germany
Trimetallic PtPdRu Dendritic Nanocages with Three-Dimensional Electrocatalytic Surfaces (2015)

Control over composition and structure on the nanoscale level is critical for designing highly active and durable catalyst to implement in electrochemical energy conversion. Herein, we report a facile strategy for an efficient synthesis of trimetallic PtPdRu dendritic nanocages with hollow cavity and porous dendritic shell by eroding the interior of the starting PtPdRu nanodendrites in acidic solution. The newly discovered trimetallic dendritic nanocages with an open-framework surface afford 3D molecular accessibility and can be used as highly active and durable catalysts for oxygen reduction reaction due to the synergetic effect derived from their unique porous structure and multimetallic composition.
Unlocking Cryptic Metabolites with Mass Spectrometry-Guided Transposon Mutant Selection (2020)

The products of most secondary metabolite biosynthetic gene clusters (BGCs) have yet to be discovered, in part due to low expression levels in laboratory cultures. Reporter-guided mutant selection (RGMS) has recently been developed for this purpose: a mutant library is generated and screened, using genetic reporters to a chosen BGC, to select transcriptionally active mutants that then enable the characterization of the "cryptic" metabolite. The requirement for genetic reporters limits the approach to a single pathway within genetically tractable microorganisms. Herein, we utilize untargeted metabolomics in conjunction with transposon mutagenesis to provide a global read-out of secondary metabolism across large numbers of mutants. We employ self-organizing map analytics and imaging mass spectrometry to identify and characterize seven cryptic metabolites from mutant libraries of two different <i>Burkholderia</i> species. Applications of the methodologies reported can expand our understanding of the products and regulation of cryptic BGCs across phylogenetically diverse bacteria.
Protein adsorption from plasma onto poly(n-alkyl methacrylate) surfaces (1992)

Protein adsorption of human serum albumin (HSA), human fibrinogen (Fg), human immunoglobulin G (IgG), high density lipoprotein (HDL) and high molecular weight kininogen (HMWK) from plasma onto poly (n-alkyl methacrylate) (PAMA) surfaces was measured using a semi-quantitative enzyme-immunoassay. Adsorption was investigated for PAMA(n = 1) (n is the number of C-atoms in the n-alkyl side chain), PAMA(n = 8) and PAMA(n = 18). PAMA(n = 1) has a relatively hydrophilic surface as compared to the more hydrophobic PAMA(n = 8) surface. Both polymers have surface chains which do not reorient after contact with water. The PAMA(n = 18) surface is relatively hydrophobic but in this case polymer surface chains and segments are able to reorient after contact with water. Protein adsorption was measured both as a function of time and as a function of the plasma dilution. If adsorption from plasma was measured as a function of time no exchange of proteins could be observed. The amount of adsorbed protein was always larger in the case of the hydrophobic PAMA(n = 8) as compared to PAMAS(n = 1 and 18), probably due to hydrophobic interactions between the proteins and the PAMA(n = 8) surface. At high plasma concentration relatively large amounts of HDL adsorb onto PAMA(n = 8), indicating that this lipoprotein preferentially adsorbs onto this surface.
Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites (2019)

Cultivated maize (<i>Zea mays</i>) has retained much of the genetic diversity of its wild ancestors. Here, we performed nontargeted liquid chromatography-mass spectrometry metabolomics to analyze the metabolomes of the 282 maize inbred lines in the Goodman Diversity Panel. This analysis identified a bimodal distribution of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in <50% of the samples. Whereas leaf bases and tips were differentiated by flavonoid abundance, maize varieties (stiff-stalk, nonstiff-stalk, tropical, sweet maize, and popcorn) showed differential accumulation of benzoxazinoid metabolites. Genome-wide association studies (GWAS), performed for 3,991 mass features from the leaf tips and leaf bases, showed that 90% have multiple significantly associated loci scattered across the genome. Several quantitative trait locus hotspots in the maize genome regulate the abundance of multiple, often structurally related mass features. The utility of maize metabolite GWAS was demonstrated by confirming known benzoxazinoid biosynthesis genes, as well as by mapping isomeric variation in the accumulation of phenylpropanoid hydroxycitric acid esters to a single linkage block in a citrate synthase-like gene. Similar to gene expression databases, this metabolomic GWAS data set constitutes an important public resource for linking maize metabolites with biosynthetic and regulatory genes.
Antisense MDM2 Enhances E2F1-Induced Apoptosis and the Combination Sensitizes Androgen-Dependent and Androgen-Independent Prostate Cancer Cells to Radiation (2008)

We have previously shown in separate studies that MDM2 knockdown via antisense MDM2 (AS-MDM2) and E2F1 overexpression via adenoviral-mediated E2F1 (Ad-E2F1) sensitized prostate cancer cells to radiation. Because E2F1 and MDM2 affect apoptosis through both common and independent pathways, we hypothesized that coupling these two treatments would result in increased killing of prostate cancer cells. In this study, the effect of Ad-E2F1 and AS-MDM2 in combination with radiation was investigated in three prostate cancer cell lines: LNCaP cells, LNCaP-Res cells [androgen insensitive with functional p53 and androgen receptor (AR)], and PC3 cells (androgen insensitive, p53(null), and AR(null)). A supra-additive radiosensitizing effect was observed in terms of clonogenic inhibition and induction of apoptosis (caspase-3 + caspase-7 activity) in response to Ad-E2F1 plus AS-MDM2 treatments in all three cell lines. In LNCaP and LNCaP-Res, these combination treatments elevated the levels of phospho-Ser(15) p53 with significant induction of p21(waf1/cip1), phospho-gammaH2AX, PUMA, and Bax levels and reduction of AR and bcl-2 expression. Similarly, AR(null) and p53(null) PC-3 cells showed elevated levels of Bax and phospho-gammaH2AX expression. These findings show that the combination of Ad-E2F1 and AS-MDM2 significantly increases cell death in prostate cancer cells exposed to radiation and that this effect occurs in the presence or absence of AR and p53.
CORRELATION BETWEEN MORPHOLOGY AND MECHANICAL PROPERTIES OF DIFFERENT STYRENE/BUTADIENE TRIBLOCK COPOLYMERS: A SCANNING FORCE MICROSCOPY STUDY* (2001)

The morphology of different styrene/butadiene (SB) block copolymers with triblock architectures was investigated using tapping mode scanning force microscopy (SFM). Comparative analysis of the morphology of the samples at the polymer/substrate interface of solution-cast films and in bulk was performed. It was found that, besides the total phase volume ratio, the interfacial structure between the incompatible chains determines the phase morphology and mechanical properties of the investigated block copolymers. The asymmetric SBS triblock copolymer (φps( 74 vol%) forms, as expected, a cylindrical morphology with hexagonally packed polybutadiene (PB) cylinders in the polystyrene (PS) matrix. Depending on the interfacial structure, block configuration, and the hard/soft phase ratio, other triblock copolymers (φps( 74 vol% and 65 vol%) show lamellae and randomly distributed PS cylinders in a random styrene/butadiene copolymer S/B matrix, respectively.
Supplementary Video S1 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across <i>FGFR2</i> Alterations and Resistance Mutations (2023)

&lt;p&gt;In this schematic movie, apo FGFR1 (left panel) demonstrates rapid P-loop dynamics, while apo FGFR2 (right panel) displays less P-loop motion.&lt;/p&gt;
The Toxic Effects of Tetrachlorobisphenol A in Saccharomyces cerevisiae Cells via Metabolic Interference (2017)

Tetrachlorobisphenol A (TCBPA) is a common flame retardant detected in different environments. However, its toxic effects on animals and humans are not fully understood. Here, the differential intracellular metabolites and associated gene expression were used to clarify the metabolic interference of TCBPA in Saccharomyces cerevisiae, a simple eukaryotic model organism. The results indicated that TCBPA treatment promoted the glycolysis pathway but inhibited the tricarboxylic acid (TCA) cycle, energy metabolism and the hexose monophosphate pathway (HMP) pathway. Thus, the HMP pathway produced less reducing power, leading to the accumulation of reactive oxygen species (ROS) and aggravation of oxidative damage. Accordingly, the carbon flux was channelled into the accumulation of fatty acids, amino acids and glycerol instead of biomass production and energy metabolism. The accumulation of these metabolites might serve a protective function against TCBPA stress by maintaining the cell membrane integrity or providing a stable intracellular environment in S. cerevisiae. These results enhance our knowledge of the toxic effects of TCBPA on S. cerevisiae via metabolic interference and pave the way for clarification of the mechanisms underlying TCBPA toxicity in animals and humans.
Micromechanical and surface adhesive properties of single saccharomyces cerevisiae cells (2017)

The adhesion and mechanical properties of a biological cell (e.g. cell membrane elasticity and adhesiveness) are often strong indicators for the state of its health. Many existing techniques for determining mechanical properties of cells require direct physical contact with a single cell or a group of cells. Physical contact with the cell can trigger complex mechanotransduction mechanisms, leading to cellular responses, and consequently interfering with measurement accuracy. In the current work, based on ultrasonic excitation and interferometric (optical) motion detection, a non-contact method for characterizing the adhesion and mechanical properties of single cells is presented. It is experimentally demonstrated that the rocking (rigid body) motion and internal vibrational resonance frequencies of a single saccharomyces cerevisiae (SC) (baker's yeast) cell can be acquired with the current approach, and the Young's modulus and surface tension of the cell membrane as well as surface adhesion energy can be extracted from the values of these acquired resonance frequencies. The detected resonance frequency ranges for single SC cells include a rocking (rigid body) frequency of 330 ± 70 kHz and two breathing resonance frequencies of 1.53 ± 0.12 and 2.02 ± 0.31 MHz. Based on these values, the average work-of-adhesion of SC cells on a silicon substrate in aqueous medium is extracted, for the first time, as . Similarly, the surface tension and the Young's modulus of the SC cell wall are predicted as and 9.20 ± 2.80 MPa, respectively. These results are compared to those reported in the literature by utilizing various methods, and good agreements are found. The current approach eliminates the measurement inaccuracies associated with the physical contact. Exciting and detecting cell dynamics at micro-second time-scales is significantly faster than the currently known metabolistic response times of cells (milliseconds to seconds), thus, it has the potential to decouple metabolistic and mechanotransduction effects from external stimuli and to operate at high throughput rates.
Image Transformer (2018)

Image generation has been successfully cast as an autoregressive sequence generation or transformation problem. Recent work has shown that self-attention is an effective way of modeling textual sequences. In this work, we generalize a recently proposed model architecture based on self-attention, the Transformer, to a sequence modeling formulation of image generation with a tractable likelihood. By restricting the self-attention mechanism to attend to local neighborhoods we significantly increase the size of images the model can process in practice, despite maintaining significantly larger receptive fields per layer than typical convolutional neural networks. While conceptually simple, our generative models significantly outperform the current state of the art in image generation on ImageNet, improving the best published negative log-likelihood on ImageNet from 3.83 to 3.77. We also present results on image super-resolution with a large magnification ratio, applying an encoder-decoder configuration of our architecture. In a human evaluation study, we find that images generated by our super-resolution model fool human observers three times more often than the previous state of the art.
The study of structural color filter based on periodic nanohole arrays for bio-detection (2015)

A nanostructure which induces localized surface plasmon resonance (LSPR) can be utilized in visible light and near infrared (NIR) regions and it shows promising features as a bio-detector because LSPR state is changed easily by different bio-related materials. Owing to transparent property of many biomolecules as well as diluted states in base solutions, it is hard to distinguish each other by eye or microscope analysis. However, difference in molecular structure and composition makes difference in optical characteristics such as a refractive index or a dielectric constant. Therefore, our LSPR-based nanohole array structure which has high sensitivity to detect small changes in optical characteristics can be a great candidate for a bio detector. Here, we fabricated structural color filters (SCFs) to detect wavelength shifts for several biomolecules and optimized the nanohole array structures for high sensitivity. Periodic nanohole arrays were designed to present resonance peaks in visible light region for optical analysis and fabricated in Au or Al thin film layer. The spectral shifts were detected caused by biomolecules.
An advanced channel access scheme for integrated multimedia services with various bit rates in CDMA networks (1999)

For efficient code sharing among users, a wireless medium access control (MAC) protocol for CDMA networks is proposed, which supports connection-oriented, as well as connectionless, services and provides the various bit rates needed for the integrated multimedia services. The proposed MAC protocol allows mobile terminals to use multiple slots and spreading codes based on contention and reservation. Optimum frequency resources are allocated to the connection-oriented and connectionless services with various bit rates. Waiting and response times in the first contention are reduced, and the overall mean delay time is typically minimized in the case of connectionless bulky traffic.
Aramco Nano Permeameter ANP: A New Laboratory Technology for Accurate and Efficient Measurements of Stress-Dependent Source Rock Permeability (2022)

Abstract In an unconventional reservoir, rock matrix has a much larger storage capacity for hydrocarbon and significantly lower permeability than the natural and hydraulic fractures. It acts as a bottleneck for hydrocarbon flow from the reservoir to the production well during production and is a key parameter for controlling the well performance over a long period of time. A new laboratory technology is developed to accurately and efficiently measure the matrix permeability. We have developed the Aramco Nano Permeameter (ANP), a new laboratory technology for measuring the stress-dependent source rock permeability. While the conventional laboratory methods can only measure one permeability data point with one test run, ANP, based on the nonlinear solution to the gas flow equation, measures the rock matrix permeability for a non-fractured sample as a function of stress using a single test run and thus is very efficient. Permeability as a function of pore pressure at a given confining stress is measured with ANP for several Eagle Ford rock samples without fractures. The permeability curve shows complex behavior: permeability initially decreases with increasing pore pressure, as a result of Knudsen diffusion effect, and then increases with pore pressure owing to the mechanical deformation. The measured permeability curves are verified by comparing them with permeability values measured with other methods for selected pore pressures. The high measurement efficiency of ANP is also demonstrated. In summary, ANP is a laboratory method that is based on a theoretical idea that is significantly different from those currently used by the industry and thus provides a high measurement efficiency that the conventional methods cannot achieve.
Cell-Based Electrical Impedance Platform to Evaluate Zika Virus Inhibitors in Real Time (2023)

Cell-based electrical impedance (CEI) technology measures changes in impedance caused by a growing or manipulated adherent cell monolayer on culture plate wells embedded with electrodes. The technology can be used to monitor the consequences of Zika virus (ZIKV) infection and adherent cell replication in real time, as this virus is highly cytopathogenic. It is a straightforward assay that does not require the use of labels or invasive methods and has the benefit of providing real-time data. The kinetics of ZIKV infection are highly dependent on the employed cell line, virus strain, and multiplicity of infection (MOI), which cannot be easily studied with conventional endpoint assays. Furthermore, the CEI assay can also be used for the evaluation and characterization of antiviral compounds, which can also have dynamic inhibitory properties over the course of infection. This methods article gives a detailed explanation of the practical execution of the CEI assay and its potential applications in ZIKV research and antiviral research in general.
The effects of postoperative adjuvant chemotherapy and radiotherapy on testicular function in men undergoing treatment for soft tissue sarcoma (1981)

Testicular function was studied in 26 men with sarcoma who received adjuvant treatment with doxorubicin, cyclophosphamide, and high-dose methotrexate (with or without radiotherapy). Testicular size, sperm output, and serum FSH, LH and testosterone levels were assessed after treatment. Five of 17 men who received chemotherapy or chemotherapy with radiotherapy to the neck, arm, chest, or leg, had normal testicular function. Eight of the remaining 12 men who provided ejaculates were oligospermic or azoospermic and serum FSH was increased threefold and LH twofold; testosterone levels were normal. In the five men with normal testicular function, FSH was increased fourfold during therapy but returned to normal six to 21 months after treatment. In men less than 40 years old, the mean FSH was less than that of men over 40 years of age (P = to 0.05), suggesting that recovery from the injury was age-related. By contrast, all nine men who received chemotherapy plus radiotherapy to the abdomen or thigh had decreased testicular size, azoospermia, fourfold increase in FSH, and twofold increase in LH levels; but testosterone concentration was normal. These data increase in FSH, and reversible testicular injury occurs after treatment with doxorubicin, cyclophosphamide, and high-dose methotrexate; recovery is age-related. However, these agents in combination with use of adjuvant radiotherapy to the thigh or abdomen may produce permanent testicular injury even in young patients.