gebhart/patrepeval huggingface dataset:
Automatic mapping of OWL ontologies into Java (2004)

We present an approach for mapping an OWL ontology into Java. The basic idea is to create a set of Java interfaces and classes from an OWL ontology such that an instance of a Java class represents an instance of a single class of the ontology with most of its properties, classrelationships and restriction-definitions maintained. We note that there exist some fundamental semantic differences between Description Logic (DL) and Object Oriented (OO) systems, primarily related to completeness and satisfiability. We present various ways in which we aim to minimize the impact of such differences, and show how to map a large part of the much richer OWL semantics into Java. Finally, we sketch the HarmonIA framework, which is used for the automatic generation of agent systems from institution specifications, and whose OWL Ontology Creation module was the basis for the tool presented in this paper.
Arthroscopic Reduction with Endobutton Fixation for Glenoid Fracture (2017)

Glenoid rim fractures, accompanied by acute glenohumeral dislocation or subluxation usually results in persistent instability. Traditionally open reduction and internal fixation has been recommended in displaced intra-articular glenoid fractures. However, open reduction is difficult, and it may not be possible to address the associated intra-articular soft-tissue injuries. A few reports of arthroscopic-assisted fixation of these fractures have been recently published. The most anatomic method for addressing an acute glenoid rim lesion is a reduction (either open or arthroscopic) and internal fixation. We are reporting a case of arthroscopic reduction and fixation of a glenoid fracture utilizing Endobuttons with clinical and radiological results at 18 months follow-up.
Comparison of the Immunogenicity and Reactogenicity of Cervarix and Gardasil Human Papillomavirus Vaccines in HIV-Infected Adults: A Randomized, Double-Blind Clinical Trial (2013)

Both vaccines were immunogenic and well tolerated. Compared with Gardasil, Cervarix induced superior vaccine responses among HIV-infected women, whereas in HIV-infected men the difference in immunogenicity was less pronounced.
Design and Optical Properties of Active Polymer-Coated Plasmonic Nanostructures (2011)

The grafting of stimuli-responsive polymer brushes on plasmonic structures provides a perfectly controlled two-dimensional active device with optical properties that can be modified through external stimuli. Herein, we demonstrate thermally induced modifications of the plasmonic response of lithographic gold nanoparticles functionalized by thermosensitive polymer brushes of (poly(N-isopropylacrylamide), PNIPAM). Optical modifications result from refractive local index changes due to a phase transition from a hydrophilic state (swollen regime) to a hydrophobic state (collapsed regime) of the polymer chains occurring in a very small range of temperatures. The refractive index of the polymer in aqueous solution is estimated in both states, deduced from the discrete dipole approximation (DDA) method. The combination of lithographic gold NPs and thermoresponsive polymer chains leads to a new generation of perfectly calibrated and dynamically controlled hybrid gold/polymer system for real-time nanosensors.
Abstract 2237: Involvement of Retinoic Acid Receptors RARβ and RARγ in growth, self-renewal and differentiation on mammary cancer stem cells (2015)

Abstract Retinoids exert different effects on cell differentiation and malignant phenotype reversion through the modulation of Retinoid Acid Receptors (RAR). In this work we have analyzed the involvement of retinoid system induction on proliferation, self-renewal and differentiation of cancer stem cells (CSC) using the triple negative mammary cell line LM38-LP. In order to obtain a CSC enriched culture, cells where cultured under mammosphere conditions. We performed mammosphere cultures in order to enrich in CSC. The treatment with All-trans retinoid acid (ATRA1μM for 96 h) reduced CSC growth rate evaluated as mammosphere diameter (Control: 176±8 μm vs. ATRA: 129±10 μm; p≤0.05). Surprisingly, ATRA pre-treatment for 96 h increased CSC self-renewal evaluated as the number of secondary mammospheres (Control: 313±19; ATRA: 495±21; p≤0.05) and as the clonogenic capacity of LM38-LP CSC (Control: 6±0.5; ATRA: 11±1.2; p≤0.05). Concomitant with these biological effects, the same treatment showed, by RT-PCR, an increase in RARβ and RARγ levels in LM38-LP- CSC. Through the use of specific RAR antagonists, we found that RARγ inhibition impaired ATRA effects on self-renewal but RARβ inhibition increased the number of secondary mammospheres (Control: 382±27; ATRA: 735±11; ATRA/RARγ antagonist: 352±17; ATRA/RARβ Antagonist: 1260±177; p≤0.05). A similar result was observed when clonogenic capacity in RARγ blocked CSC was analyzed. Finally, we performed a matrigel 3D culture using cells from LM38-LP mammospheres. Under these conditions, colonies presented large irregular structures while ATRA treatment led to the formation of differentiated colonies with evidence of lumen. Our findings suggest that RARγ down modulation and RARβ induction could lead to CSC self-renewal inhibition and differentiation in triple negative mammary cancers. Citation Format: Damian E. Berardi, Carolina Flumian, Maria I. Diaz Bessone, Stefano M. Cirigliano, Elisa D. Bal de Kier Joffe, Alejandro J. Urtreger, Laura B. Todaro. Involvement of Retinoic Acid Receptors RARβ and RARγ in growth, self-renewal and differentiation on mammary cancer stem cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2237. doi:10.1158/1538-7445.AM2015-2237
Interpretation and Evaluation of Near Girth Weld, Short Axial Cracks in a Petroleum Pipeline (2014)

A Canadian crude oil pipeline presented a unique cracking mechanism exhibited by short, branched axial cracks located in the vicinity of girth welds. These attributes, among others, translated into added depth sizing complexity for ultrasonic crack in-line inspection (ILI) tools. The scope presented in this paper encompasses results from three crack ILIs carried out between 2011 and 2013. The assessment and mitigation of such atypical cracks required innovative interpretation and evaluation techniques. First, unique ILI analysis approaches and reporting criteria were implemented and validated beyond established design specifications. The goal was to characterize the very short features at girth welds, while understanding and managing sizing limitations associated with conventional ILI analysis methods. This was attained from a laboratory ILI pull-testing program performed on field cut-outs containing cracks of interest, in addition to detailed non-destructive examinations (NDE) completed in field and laboratory settings. Second, customized, depth-independent, likelihood-based evaluation criteria were developed to identify and mitigate cracking with such distinct attributes. The ensuing model was then validated against a comprehensive field NDE program using different sizing techniques (e.g., Phased Array and Multi-angle Shear Wave). This paper highlights the key findings from the analytical, experimental and field studies and describes the novel methodology followed in the assessment of crack-related features reported by ILI.
Nucleoporin 210 Serves a Key Scaffold for SMARCB1 in Liver Cancer (2020)

The roles of chromatin remodelers and their underlying mechanisms of action in cancer remain unclear. In this study, SMARCB1, known initially as a bona fide tumor suppressor gene, was investigated in liver cancer. SMARCB1 was highly upregulated in patients with liver cancer and was associated with poor prognosis. Loss- and gain-of-function studies in liver cells revealed that SMARCB1 loss led to reduced cell proliferation, wound healing capacity, and tumor growth <i>in vivo</i>. Although upregulated SMARCB1 appeared to contribute to switch/sucrose nonfermentable (SWI/SNF) complex stability and integrity, it did not act using its known pathways antagonism with EZH2 or association between TP53 or AMPK. SMARCB1 knockdown induced a mild reduction in global H3K27 acetylation, and chromatin immunoprecipitation sequencing of SMARCB1 and acetylated histone H3K27 antibodies before and after SMARCB1 loss identified Nucleoporin210 (NUP210) as a critical target of SMARCB1, which bound its enhancer and changed H3K27Ac enrichment and downstream gene expression, particularly cholesterol homeostasis and xenobiotic metabolism. Notably, NUP210 was not only a putative tumor supporter involved in liver cancer but also acted as a key scaffold for SMARCB1 and P300 to chromatin. Furthermore, SMARCB1 deficiency conferred sensitivity to doxorubicin and P300 inhibitor in liver cancer cells. These findings provide insights into mechanisms underlying dysregulation of chromatin remodelers and show novel associations between nucleoporins and chromatin remodelers in cancer. SIGNIFICANCE: This study reveals a novel protumorigenic role for SMARCB1 and describes valuable links between nucleoporins and chromatin remodelers in cancer by identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
Native and Denaturing MS Protein Deconvolution for Biopharma: Monoclonal Antibodies and Antibody–Drug Conjugates to Polydisperse Membrane Proteins and Beyond (2019)

Electrospray ionization mass spectrometry (ESI-MS) is a ubiquitously used analytical method applied across multiple departments in biopharma, ranging from early research discovery to process development. Accurate, efficient, and consistent protein MS spectral deconvolution across multiple instrument and detector platforms (time-of-flight, Orbitrap, Fourier-transform ion cyclotron resonance) is essential. When proteins are ionized during the ESI process, a distribution of consecutive multiply charged ions are observed on the <i>m</i>/<i>z</i> scale, either positive [M + <i>n</i>H]<sup><i>n</i>+</sup> or negative [M - <i>n</i>H]<sup><i>n</i>-</sup> depending on the ionization polarity. The manual calculation of the neutral molecular weight (MW) of single proteins measured by ESI-MS is simple; however, algorithmic deconvolution is required for more complex protein mixtures to derive accurate MWs. Multiple deconvolution algorithms have evolved over the past two decades, all of which have their advantages and disadvantages, in terms of speed, user-input parameters (or ideally lack thereof), and whether they perform optimally on proteins analyzed under denatured or native-MS and solution conditions. Herein, we describe the utility of a parsimonious deconvolution algorithm (explaining the observed spectra with a minimum number of masses) to process a wide range of highly diverse biopharma relevant and research grade proteins and complexes (PEG-GCSF; an IgG1<i>k</i>; IgG1- and IgG2-biotin covalent conjugates; the membrane protein complex AqpZ; a highly polydisperse empty MSP1D1 nanodisc and the tetradecameric chaperone protein complex GroEL) analyzed under native-MS, denaturing LC-MS, and positive and negative modes of ionization, using multiple instruments and therefore multiple data formats. The implementation of a comb filter and peak sharpening option is also demonstrated to be highly effective for deconvolution of highly polydisperse and enhanced separation of a low level lysine glycation post-translational modification (+162.1 Da), partially processed heavy chain lysine residues (+128.1 Da), and loss of <i>N</i>-acetylglucosamine (GlcNAc; -203.1 Da).
MO‐D‐144‐02: Ultrasound Transducer Localization Using the CyberKnife's X‐Ray System (2013)

Purpose: 4D ultrasound has become an alternative for image guidance and motion compensation in radiosurgery. Nevertheless, a two‐step localization has to be performed when using ultrasound. In addition to target localization inside the ultrasound volume, the transducer itself has to be localized and the target position has to be transformed into treatment coordinates. Methods: The CyberKnife (Accuray Inc.) features a stereo X‐ray system which is used for patient and fiducial marker localization. Accessing only the raw X‐ray images, we designed a software package for additional marker detection. To measure the physical camera parameters, X‐ray phantoms were designed and a non‐orthogonal stereo camera calibration was performed on 50 calibration X‐ray pairs. Algorithms were developed for three‐dimensional single marker localization and six‐dimensional localization of marker geometries. Different X‐ray marker geometries were designed and attached to the ultrasound transducer. The final system was evaluated and compared to the on‐board localization system using a 6‐axis industrial robot to position different marker geometries at 150 randomly distributed positions over the acquisition volume. Results: Two marker geometries with 20 and 50mm base lengths were localized using the on‐board and newly developed software. The mean translational error for the on‐board localization is 0.202mm, for the new system 0.218mm. The rotational error of the on‐board system could be reduced from 0.212 to 0.053 degrees for the 50mm marker and from 0.272 to 0.076 degrees for the 20mm marker geometry. Conclusion: We have shown that ultrasound transducers can be localized using the CyberKnife x‐ray system. The rotational accuracy of the localization could be increased by a factor of four, which is important for high marker‐to‐ultrasound‐target distances. Furthermore, using the full area of the flat‐panel detectors without pre‐processing steps the tracking volume was increased by 70 percent, which helps detecting patient/fiducials and transducer at the same time.
Supplementary Video S2 from Fluorophore-NanoLuc BRET Reporters Enable Sensitive &lt;i&gt;In Vivo&lt;/i&gt; Optical Imaging and Flow Cytometry for Monitoring Tumorigenesis (2023)

&lt;p&gt;Living Image DLIT 3D reconstruction of Emu-Myc Lymphoma-GpNLuc orthotopic allograft transplant.&lt;/p&gt;
Audio Identification by Sampling Sub-fingerprints and Counting Matches (2017)

It is challenging to retrieve audio clips from large audio datasets not only due to the high dimensionality of audio but also due to the large number of audios. Fingerprinting methods primarily focus on the use of semantic-level techniques to speed up retrieval and neglect low-level support. This paper shows that the performance of audio retrieval can be exploited by properly organizing and manipulating audio fingerprint data. The proposed sampling and counting method markedly improves the retrieval speed while maintaining a high recall rate and high precision for short audio clips. The proposed inverted index structure for fingerprints quickly shrinks the scope of the candidate set while requiring considerably less memory. The experiments show that the proposed method is faster and yields more consistent performance in terms of recall rate and precision than do the state-of-the-art methods. The proposed method is scalable for big audio data and is robust to background noise, resampling, MP3 conversion, white noise addition, bandpass filtering, chorus, echo, flanger, gsm compression, and tremolo. The average precision and recall rates are 99.995% and 99.78%, respectively, for dataset 1 and average 98.97% and 95.15%, respectively, for dataset 2. Specifically, the precision and recall rates for query audio clips of 3 s in length in the targeted dataset 1 are 99.94% and 99.64%, respectively.
Cell Wall Degradation of Spruce, Poplar, and Wheat Straw by MnO<sub>2</sub>/Oxalate: An Overview (2001)

Manganese dioxide and oxalate are two components commonly found in wood during its microbial decay. The degradation of cell wall from wheat straw, spruce and poplar sawdust by the association of MnO2 and oxalate is reviewed here. The Mn oxidants formed are shown to modify the properties of the wood cell wall at the molecular but also ultrastructural levels. Marked reductions in the contents of ether linked Guaiacyl and Syringyl monomers, but also of the main dimers composing the lignins are observed in all samples after MnO2/oxalate oxidation. The Mn oxidants also slightly modify polysaccharides, but in spruce only and probably at the level of hemicellulose. Finally, the cell wall architecture is altered by MnO2/oxalate, in a specific manner depending on the plant considered.
Toward a Biological Replacement of Petroleum (2013)

Petroleum is the source of most of the world’s raw materials and it also provides the majority of the world’s energy. As the price of petroleum fluctuates and its combustion has significant negative environmental impact, there is growing interest in research into alternative sources of energy. Current biorefining schemes use plant biomass or algae to produce ethanol, biodiesel, and some chemicals used as raw materials. While these approaches are the leading processes, next-generation biorefinery should consider other options for starting materials, schemes for manufacturing, and the biofuel itself. For example, direct photosynthetic production of advanced biofuels (such as n-butanol or isobutanol) or raw materials from CO2 would be an attractive and more environmentally friendly alternative; this strategy bypasses the need for lignocellulose deconstruction and algal lipid processing. Non-photosynthetic, electricity-powered CO2 reduction to generate biofuels further by-passes the need for large light exposed surface areas used in photo-bioreactors and represents an option for biochemical and biofuel production as well as electricity storage.
Supplementary Table S1 from Cell Type–specific Adaptive Signaling Responses to KRAS&lt;sup&gt;G12C&lt;/sup&gt; Inhibition (2023)

&lt;p&gt;Supplementary Table S1. Relative quantification of peptides representing total KRAS, WT KRAS, free KRAS G12C protein and drug bound KRAS G12C Protein Levels.&lt;/p&gt;
Segmenting Cutaneous Wounds from Tissue Sections and In Vivo Images using Deep Learning (2020)

Convolutional neural networks were used to accurately segment both H&amp;E-stained tissue sections and in vivo autofluorescence images of skin wounds, which enabled automated, quantitative analysis of a variety of wound features.
A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus (2020)

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif ("CACGTG"), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network.
LITE (2022)

There is a strong need for GPU trusted execution environments (TEEs) as GPU is increasingly used in the cloud environment. However, current proposals either ignore memory security (i.e., not encrypting memory) or impose a separate memory encryption domain from the host TEE, causing a very substantial slowdown for communicating data from/to the host.
Doppler ultrasound flow measurement of non-parallel velocity fields in a deformed elastic tube (2020)

The ultrasonic Doppler velocimetry (UVP) method is well known for the laminar flow stream in a circular tube. In many practical situations, deformed tubes or, non-parallel streamlines are involved. An improved experimental arrangement of the UVP transducer is needed to define the real velocity-vectors of the flow when the streamlines are not parallel to its wall. An experimental approach has been used with two sets of transducers in perpendicular to each other to obtain the magnitude of the real velocity vector (vreal), the direction of velocity-vector, and axial velocity component along the flow direction. The experiments were carried out using a proposed arrangement of UVP transducer for flow visualisation in a squeezed elastic tube. The results show that the 2D velocity profiling found to be more accurate using the present transducer arrangement, which is important for generating further information such as shear rate, flow rate, etc.
Causal Analysis on the Anchor Store Effect in a Location-based Social Network (2022)

A particular phenomenon of interest in Retail Eco-nomics is the spillover effect of anchor stores (specific stores with a reputable brand) to non-anchor stores in terms of customer traffic. Prior works in this area rely on small and survey-based datasets that are often confidential or expensive to collect on a large scale. Also, very few works study the underlying causal mechanisms between factors that underpin the spillover effect. In this work, we analyze the causal relationship between anchor stores and customer traffic to non-anchor stores and employ a propensity score matching framework to investigate this effect more efficiently. First of all, to demonstrate the effect, we leverage open and mobile data from London Datastore and Location-Based Social Networks (LBSNs) such as Foursquare. We then perform a large-scale empirical analysis of customer visit patterns from anchor stores to non-anchor stores (e.g., non-chain restaurants) located in the Greater London area as a case study. By studying over 600 neighbourhoods in the Greater London area, we find that anchor stores cause a 14.2-26.5% increase in customer traffic for the non-anchor stores reinforcing the established economic theory Moreover, we evaluate the efficiency of our methodology by studying the confounder balance, dose difference and performance of the matching framework on synthetic data. Through this work, we point decision-makers in the retail industry to a more systematic approach to estimate the anchor store effect and pave the way for further research to discover more complex causal relationships underlying this effect with open data.