gebhart/patrepeval huggingface dataset:
Use of quantitative histomorphometrics to classify disease progression in HPV-positive squamous cell carcinoma. (2012)

73 Background: Oropharyngeal squamous cell carcinoma (SCC) is now recognized as distinct because of its strong association with high-risk human papillomavirus (HPV) and favorable prognosis. Although these tumors have some specific morphologic features, none have been shown to predict prognosis, particularly on small specimens such as biopsies. Methods: We present a novel cluster cell graph (CCG) that is computationally efficient and provides an effective tool to quantitatively describe histopathologic images according to the spatial distribution and clustering of cells. CCG is generated by firstly automatically identifying all cells/nuclei within the histologic image and then identifying nuclear clusters. These clusters are then represented via a single node corresponding to center of mass of the cluster. Any pair of nodes is connected via a link if the probability of such an association is greater than a pre-defined threshold, the probability being calculated as a decaying function of the Euclidean distance between node pairs. Once links have been identified between cluster nodes, subgraphs are constructed as series of topological features defined on each node of the subgraph, i.e., local graph metrics (e.g. clustering coefficients and skewness of edge lengths). Results: We leverage CCG to capture structural characteristics of HPV-related (p16+) oropharyngeal SCC (oSCC) from formalin-fixed, paraffin-embedded tissue microarray images. A series of quantitative histomorphometric descriptors are extracted for each image and used to train a random forest (RF) classifier to distinguish patients with p16+ oSCC who develop disease progression from those that do not. Over 25 runs of 3-fold cross validation in a cohort of 140 studies (116 non-progressors and 26 progressors) the RF classifier yielded a mean accuracy of over 87% in distinguishing between progressors and non-progressors. Conclusions: The ability to quantitatively describe the spatial distribution/clustering of nuclei via CCG allows for building of classifiers that can distinguish between progressors and non-progressors in p16+ oSCC tissue images. The approach should be extensible to outcome prediction for other cancers as well.
<title>Structure and navigation for electronic publishing</title> (1998)

The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.
Clean dialogue loudness measurements based on Deep Neural Networks (2021)

Loudness normalization based on clean dialogue loudness improves consistency of the dialogue level compared to the loudness of the full program measured at speech or signal activity. Existing loudness metering methods can not estimate clean dialogue loudness from mixture signals comprising speech and background sounds, e.g. music, sound effects or environmental sounds. This paper proposes to train deep neural networks with input signals and target values obtained fromisolated speech and backgrounds to estimate the clean dialogue loudness. Furthermore, the proposed method outputs estimates for loudness levels of background and mixture signal, and Voice Activity Detection. The presented evaluation reports a mean absolute error of 1.5 LU for momentary loudness, 0.5 LU for short-term and 0.27 LU for long-term loudness of the clean dialogue given the mixture signal.
Sequence of two gonadotropin releasing hormones from tunicate suggest an important role of conformation in receptor activation (1997)

The primary structure of two forms of gonadotropin releasing hormone (GnRH) from tunicate (Chelyosoma productum) have been determined based on mass spectrometric and chemical sequence analyses. The peptides, tunicate GnRH-I and -II, contain features unprecedented in vertebrate GnRH. Tunicate GnRH-I contains a putative salt bridge between Asp5 and Lys8. A GnRH analog containing a lactam bridge between Asp5 and Lys8 was found to increase release of estradiol compared with that of the native tunicate GnRH-I and -II. Tunicate GnRH-II contains a cysteine residue and was isolated as a dimeric peptide. These motifs suggest that the conformation plays an important role in receptor activation.
Derivation of dispersion-managed soliton (DMS) parameters for a given dispersion map by second-order moments (2000)

We derive approximate expressions to predict the chirp and peak power of a pulse propagating through a given dispersion map with lumped amplifiers. We use second-order moments to derive expressions for the evolution of the root-mean-square (RMS) width and chirp parameters within one period of the map. Numerical simulations confirm the accuracy of the analytical model.
Two-Way Nesting in a Split-Implicit Ocean Model: NCOM (2023)

Abstract Presented is the approach, implementation, and evaluation of two-way nesting in a split-implicit ocean model, the Navy Coastal Ocean Model (NCOM). Emphasis is on the strategies applied to feed back fields from the fine-mesh nest (child grid) to the coarse mesh (parent grid). On an appropriate separation of dynamic and feedback interfaces, attention is especially needed for the feedback interface of surface elevation. One particular issue addressed is the inconsistency between the 3D baroclinic velocities and 2D barotropic transports in the feedback. The discrepancy is inherently associated with bathymetry, depth integration, and the need to average over spatial grid points. A simple remedy is proposed and proven to be effective and necessary in realistic coastal applications. In addition to the full two-way nesting, a simplified two-way nesting approach is provided in which only the temperature and salinity are fed back from the nest, and the velocity fields are assumed to self-adjust according to the geostrophic balance. The performance of both approaches is evaluated using the idealized benchmark, propagation of a baroclinic vortex, and an application to the Mississippi River outflow in the northeast Gulf of Mexico, including a comparison with available observations. Discussions are also made on the computational efficiency of the two-way nesting and its sensitivity to the open boundary conditions in regard to noise suppression. Significance Statement The two-way nesting approach reported here can be adapted to other structured-grid ocean models, in particular those using the split-implicit technique. The treatment of the feedback interface for surface elevation is especially important for suppressing the noise production and improving the feedback consistency. An effective procedure is given to amend the inconsistency in the velocity field feedback that is inherently due to bathymetry.
NIMG-12. RADIOGENOMICS ON VENUS AND MARS: IMPACT OF SEX-DIFFERENCES ON MRI AND GENETIC CORRELATIONS IN GLIOBLASTOMA (2018)

patients) were labeled as either pathologically confirmed treatment effect or having no tumor cells (tumor score=0) within the imaging abnormality (TxE; 80/51 samples/patients) or rHGG (tumor score=2-3; 252/118 samples/patients) by a pathologist. Preoperative 3T MRI scans included T1w-Gd and T2w FLAIR; diffusion tensor imaging (b=1000s/mm2); 3D MRSI; and dynamic susceptibility-contrast perfusion MRI. Univariate models were created using generalized estimating equations to evaluate each variable's ability to distinguish TxE from rHGG tissue samples. Normalized choline (median=1.1 TxE & 1.2 rHGG), choline-to-NAA index (CNI, median=2.4 TxE & 3.5 rHGG), and normalized cerebral blood volume (nCBV, me-dian=1.2 TxE & 1.4 rHGG) were significantly associated with biopsy-level classification (p=0.034, 0.015, 0.017). These results are being consolidated into a multiparametric algorithm for predicting TxE or rHGG, which could be of clinical importance in managing patients with recurrent rHGG. Downstream analysis will create a spatial map of rHGG to help guide future surgical sampling.
Method to produce nanocrystalline powders of oxide-based phosphors for lighting applications (2023)

Some embodiments of the present invention are directed toward nanocrystalline oxide-based phosphor materials, and methods for making same. Typically, such methods comprise a steric entrapment route for converting precursors into such phosphor material. In some embodiments, the nanocrystalline oxide-based phosphor materials are quantum splitting phosphors. In some or other embodiments, such nanocrystalline oxide based phosphor materials provide reduced scattering, leading to greater efficiency, when used in lighting applications.
Image understanding from thermal emission polarization (2002)

Existing polarization-based image understanding techniques use information only from reflected light. Apart from incandescent bodies thermally emitted light radiation from elements of a scene in the visible spectrum is insignificant. However, at longer wavelengths such as in the infrared thermal emission is typically quite prevalent from a number of scene elements of interest. FLIR imagery of both indoor and outdoor scenes reveals that many objects thermally emit a significant amount of radiation. Polarization from thermally emitting objects has been observed as long as 170 years ago from incandescent objects but since then there have only been a limited number of empirical investigations into this phenomenon. This paper presents a comprehensive model for explaining polarization of thermal emission from both rough and smooth surfaces, in agreement with empirical data, that can significantly enhance the image understanding of FLIR imagery. In particular it is possible to discern metal from dielectric materials under certain conditions, and from an accurate model for thermally emitted polarization it is possible to predictively model polarization signatures from CAD models of importance to automatic target recognition.
Underline detection and removal in a document image using multiple strategies (2004)

This work presents a novel three-module approach for underline detection and removal in Chinese/English OCR. The detection module uses strategies of connected component analysis and bottom edge analysis. The removal module uses different methods for different kinds of underlines. The disambiguation module is effected via recognition confidence comparison for reducing the risk of removing wrongly doubtful underlines. Our approach can deal with untouched, touched, broken and slightly curved underlines. In a benchmark test using single text line images extracted from UW-I database and images captured by C-Pen, we demonstrate that our approach has little negative effect on pure-text images, and can detect and remove reliably underlines in text line images with underlines.
Supplementary Table 1 from Succinate Dehydrogenase Mutation Underlies Global Epigenomic Divergence in Gastrointestinal Stromal Tumor (2023)

&lt;p&gt;Supplementary Table 1 XLS file 22K, Tumors and reference tissues for methylation microarray analysis&lt;/p&gt;
SOLIS: Autonomous Solubility Screening using Deep Neural Networks (2022)

Accelerating material discovery has tremendous societal and industrial impact, particularly for pharmaceuticals and clean energy production. Many experimental instruments have some degree of automation, facilitating continuous running and higher throughput. However, it is common that sample preparation is still carried out manually. This can result in researchers spending a significant amount of their time on repetitive tasks, which introduces errors and can prohibit production of statistically relevant data. Crystallisation experiments are common in many chemical fields, both for purification and in polymorph screening experiments. The initial step often involves a solubility screen of the molecule; that is, understanding whether molecular compounds have dissolved in a particular solvent. This usually can be time consuming and work intensive. Moreover, accurate knowledge of the precise solubility limit of the molecule is often not required, and simply measuring a threshold of solubility in each solvent would be sufficient. To address this, we propose a novel cascaded deep model that is inspired by how a human chemist would visually assess a sample to determine whether the solid has completely dissolved in the solution. In this paper, we design, develop, and evaluate the first fully autonomous solubility screening framework, which leverages state-of-the-art methods for image segmentation and convolutional neural networks for image classification. To realise that, we first create a dataset comprising different molecules and solvents, which is collected in a real-world chemistry laboratory. We then evaluated our method on the data recorded through an eye-in-hand camera mounted on a seven degree-of-freedom robotic manipulator, and show that our model can achieve 99.13% test accuracy across various setups.
Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome (2004)

The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar.
Observation of a shape resonance of the positronium negative ion (2016)

When an electron binds to its anti-matter counterpart, the positron, it forms the exotic atom positronium (Ps). Ps can further bind to another electron to form the positronium negative ion, Ps(-) (e(-)e(+)e(-)). Since its constituents are solely point-like particles with the same mass, this system provides an excellent testing ground for the three-body problem in quantum mechanics. While theoretical works on its energy level and dynamics have been performed extensively, experimental investigations of its characteristics have been hampered by the weak ion yield and short annihilation lifetime. Here we report on the laser spectroscopy study of Ps(-), using a source of efficiently produced ions, generated from the bombardment of slow positrons onto a Na-coated W surface. A strong shape resonance of (1)P(o) symmetry has been observed near the Ps (n=2) formation threshold. The resonance energy and width measured are in good agreement with the result of three-body calculations.
N⋅⋅⋅Br Halogen Bonding: One‐Dimensional Infinite Chains through the Self‐Assembly of Dibromotetrafluorobenzenes with Dipyridyl Derivatives (2003)

The N.Br halogen bonding drives the self-assembly of 1,4-dibromotetrafluorobenzene (1 a) and its 1,3 or 1,2 analogues (1 b,c, respectively) with dipyridyl derivatives 2 a,b. The isomeric supramolecular architectures 3 a-f are obtained as cocrystals that are stable in the air at room temperature. The solid-state features of these 1D infinite chains 3 have been fully characterized by single-crystal X-ray, Raman, and IR analyses. The occurrence of N.Br halogen bonding in solution has been detected with (19)F NMR spectroscopy. The N.Br halogen bonding is highly selective and directional and the geometry of the single strands of noncovalent copolymers 3 is programmed by the geometry of halogen-bonding donor and acceptor sites on the starting modules. The composition and topology of the instructed networks can be predicted with great accuracy. Experiments of competitive cocrystal formation established the strength of the N.Br interaction relative to other halogen bondings and the ability of different modules 1 to be involved in site-selective supramolecular syntheses.
Experimental comparison of the RZ-DPSK and NRZ-DPSK modulation formats (2005)

The RZ-DPSK and NRZ-DPSK modulation formats were experimentally compared using installed undersea fiber links. Our results show a 1-1.5 dB RZ benefit with optimized RZ modulation depth for both 25-GHz and 33-GHz spaced channels.
Measurement of the $CP$-violating phase $\phi_\mathrm{s}$ in the B$^0_\mathrm{s}\to$ J$/\psi\, \phi$(1020) $\to \mu^+\mu^-$K$^+$K$^-$ channel in proton-proton collisions at $\sqrt{s} =$ 13 TeV (2021)

The CP -violating weak phase ϕs and the decay width difference ΔΓs between the light and heavy Bs0 mass eigenstates are measured with the CMS detector at the LHC in a sample of 48500 reconstructed Bs0→J/ψϕ(1020)→μ+μ−K+K− events. The measurement is based on a data sample corresponding to an integrated luminosity of 96.4fb−1 , collected in proton-proton collisions at s=13TeV in 2017–2018. To extract the values of ϕs and ΔΓs , a time-dependent and flavor-tagged angular analysis of the μ+μ−K+K− final state is performed. The analysis employs a dedicated tagging trigger and a novel opposite-side muon flavor tagger based on machine learning techniques. The measurement yields ϕs=−11±50(stat)±10(syst)mrad and ΔΓs=0.114±0.014(stat)±0.007(syst)ps−1 , in agreement with the standard model predictions. When combined with the previous CMS measurement at s=8TeV , the following values are obtained: ϕs=−21±44(stat)±10(syst)mrad , ΔΓs=0.1032±0.0095(stat)±0.0048(syst)ps−1 , a significant improvement over the 8 TeV result.
The Leading Edge: Aerodynamic Design of Ultra-Streamlined Land Vehicles (1999)

This book provides a basic understanding of the aerodynamics involved in designing an ultra-streamlined land vehicle. It describes many of the important design goals and parameters for producing a low-drag body. The book provides details for the design of solar cars and ultra-light land vehicles including solar bikes. Electrathon racers, hybrid vehicles, electric vehicles and fuel-economy record cars are included. It is explained that the best body shape for such vehicles may not be the body of absolute lowest drag. The vehicle system, including the driver, chassis, and energy / drive system must work in concert to provide the maximum output. In-the-field testing and the history of ultra-streamlined land vehicle development are included.
Inside Cover: Ultrasound‐ and Microwave‐Assisted Preparation of Lead‐Free Palladium Catalysts: Effects on the Kinetics of Diphenylacetylene Semi‐Hydrogenation (ChemCatChem 6/2015) (2015)

The cover picture shows the pivotal role of ultrasound and microwaves in the one-pot preparation of a lead-free Pd-catalyst for selective hydrogenation. In their Full Paper, Z. Wu et al. show that sonication in the presence of a capping agent and reduction by microwave heating gives monodisperse Pd nanoparticles supported on boehmite. The catalyst is approximately seven times as active as a commercial Lindlar catalyst per unit of Pd mass taken, and only 6 % (at 95 % conversion) less selective towards semi-hydrogenation. This investigation was performed by the Universities of Turin (Italy) and Hull (UK) in collaboration with DSM Nutritional products Ltd, Basel (Switzerland) and was funded by the FP7 project MAPSYN. The article highlighted by this cover can be found on p. 952 ff. of Issue 6, 2015.
COMBINATION INTRAVITREAL BEVACIZUMAB/PANRETINAL PHOTOCOAGULATION VERSUS PANRETINAL PHOTOCOAGULATION ALONE IN THE TREATMENT OF NEOVASCULAR GLAUCOMA (2008)

Combination treatment resulted in more rapid decrease in IOP. In addition, the combination group had increased frequency and rapidity of regression of neovascularization. This study provides a foundation for further research and suggests consideration for a possible new paradigm for the treatment of NVG.
The Single Cell Proteome Project - Cell-Cycle Dependent Protein Expression in Breast Cancer Cell Lines (2005)

Abstract : Protein fingerprints of single MCF7 breast cancer cells were mapped using both one-dimensional and two-dimensional capillary electrophoresis (CE). While one-dimensional CE can resolve dozens of proteins, two-dimensional CE has the potential to resolve hundreds or thousands of proteins with broad dynamic range. Cellular proteins are labeled on column by coupling lysine residues with the fluorogenic reagent 3-(2-furoyl)quinoline-2 carboxaldehyde. Labeled proteins are detected by laser-induced fluorescence in a sheath flow cuvette. Capillary sieving electrophoresis and capillary micellar electrophoresis were used to characterize proteins in single cells in one-dimensional separations, while the two techniques were combined to generate two-dimensional protein fingerprints from single cells.
Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a thermophilic, chemolithoautotrophic bacterium capable of respiratory ammonification of nitrate with elemental sulfur (2017)

An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain ST65T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the south-western Pacific Ocean, at a depth of 1870 m. Cells of strain ST65T were non-motile straight or slightly curved short rods, 0.5-0.6 µm in diameter and 0.8-1.5 µm in length. The temperature range for growth was 47-75 °C, with an optimum at 65 °C. The pH range for growth was 5.5-7.5, with an optimum at pH 6.5. Growth of strain ST65T was observed at NaCl concentrations ranging from 1.5 to 4.5 % (w/v), with an optimum at 2.0-2.5 %. Strain ST65T grew anaerobically with inorganic carbon as a carbon source and with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. It was also able to grow by disproportionation of elemental sulfur, thiosulfate and sulfite. Sulfate was not utilized as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to a deep lineage in the phylum Thermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents a novel species of a new genus, Thermosulfuriphilus ammonigenes gen. nov., sp. nov. ST65T (=DSM 102941T=VKM B-2855T) is the type strain of the type species.
Supplemental Figure Legend from Toll-like Receptor Agonist Imiquimod Facilitates Antigen-Specific CD8<sup>+</sup> T-cell Accumulation in the Genital Tract Leading to Tumor Control through IFNγ (2023)

&lt;p&gt;Supplemental Figure Legend&lt;/p&gt;