gebhart/patrepeval huggingface dataset:
Categorization of gene expression subtypes in clear cell renal cell carcinoma with sarcomatoid features. (2017)

519 Background: Presence of sarcomatoid features in Renal Cell Carcinoma (sRCC) tumors signals aggressive clinical behavior and poor prognosis compared to Clear Cell Renal Cell Carcinoma (ccRCC). However, the underlying gene expression patterns of sRCC are poorly understood. We sought to categorize ccRCC and sRCC gene expression subtypes and compare survival outcomes, as well as evaluate whether sRCC gene expression patterns are similar to non-renal sarcomas. Methods: We identified 511 ccRCC cases, of which 36 had a sarcomatoid component from The Cancer Genome Atlas. Enrichment analysis was used to measure associations between gene expression signatures for soft tissue sarcomas and expression profiles of sRCC and ccRCC cases measured by RNA-Seq. The resulting scores were used to identify distinct patient groups using K-means clustering. Overall survival (OS) was evaluated by Kaplan-Meier, log rank, and Cox regression methods. Results: Our analysis identified 4 distinct clusters that differ in enrichment for soft-tissue sarcoma gene expression profiles. The clusters showed significantly different OS distributions (p-value&lt;0.001 log rank). Most sRCC cases (69%) segregated into a single cluster with the worst prognosis. Among ccRCC cases, 57% of patients with higher levels of sarcoma signature enrichment were associated with a shorter OS, which is independent of tumor stage. 5-year/median OS survival estimates for ccRCC cases in the 4 clusters, by increasing levels of sarcoma profile enrichment, were 83%/NR, 75%/NR, 67%/90.9 mo, and 49%/56.7 mo. We also validated existence of these clusters in another sRCC cohort (Sircar 2015). Conclusions: We identified strong associations between sarcoma expression signatures and gene expression profiles of sRCC. We also found that 57% of morphologically non-sRCC cases demonstrate enrichment for sarcoma expression signatures, and these patients have worse OS than their non-sarcoma enriched ccRCC counterparts. The presence of sarcoma expression signatures has not been previously evaluated in RCC. These signatures portend poor survival and may be clinically actionable, as they describe unique subtypes of RCC that may not correspond to histologic characterization.
Highly Efficient and Tunable Synthesis of Dioxabicyclo[4.2.1] Ketals and Tetrahydropyrans via Gold-Catalyzed Cycloisomerization of 2-Alkynyl-1,5-diols (2009)

A highly efficient gold(I) chloride catalyzed cycloisomerization of 2-alkynyl-1,5-diol (1) to dioxabicyclo[4.2.1] ketal (2) and its further transformation to tetrahydropyran (3) are reported. The diol is readily obtained by the reduction of 2-alkynyl-substituted glutarates, isolated from the Michael addition of allenoates to methyl acrylate. These reactions proceeded smoothly under very mild conditions. A plausible mechanism for the formation of the said tetrahydropyran from the corresponding ketal is proposed.
Surface and interface analysis of GaAs–oxyfluorides (1983)

AES, XPS, and SIMS analysis of the plasma grown oxyfluorides on GaAs are presented. These data indicate that the films are composed of three basic layers. Region 1 is a mixed As2O3, Ga2O3 glass with low concentrations of fluorine. In the second region, fluorine concentrations increase and a shoulder on the As-3d and Ga-3d peaks are observed. As2O3 and Ga2O3 are still the major constituents of the film. At the interface between the oxyfluoride glass and the substrate is a thin metallic As region. The difference between pure oxides and this oxyfluoride is the incorporation of fluorine in the films and lower concentrations of metallic As at the interface.
Control of Nitrogen Depth Profile near Silicon Oxynitride/Si(100) Interface Formed by Radical Nitridation (2006)

Depth profiles of composition and chemical structures in radical nitrided silicon oxynitride films formed with Ar/N2, Xe/N2, or Ar/NH3 plasma excited by microwave have been investigated by X-ray photoelectron spectroscopy combined with step etching in HF solution. The relationship between the intensities of emission from N2+ radical in these plasmas and the concentration of nitrogen atoms forming Si3≡N configuration near the silicon oxynitride film/Si substrate interface nitrided using these plasmas was studied. The emission intensities from N2+ radical generated in Xe/N2 or Ar/NH3 plasma are a quarter or one-sixth of that from N2+ radical generated in Ar/N2 plasma respectively. However, the emission from NH radical is also detected in Ar/NH3 plasma. Although the nitrogen concentration of Xe/N2 plasma is smaller than that of Ar/N2 plasma at the film/substrate interface, that of Ar/NH3 plasma is larger than that of Ar/N2 plasma at the interface. It is important for the reduction of the nitrogen concentration near the film/substrate interface to use Xe/N2 plasma in which both of the generation efficiencies of N2+ and NH radicals are low.
Influenza A Virus Migration and Persistence in North American Wild Birds (2013)

Wild birds have been implicated in the emergence of human and livestock influenza. The successful prediction of viral spread and disease emergence, as well as formulation of preparedness plans have been hampered by a critical lack of knowledge of viral movements between different host populations. The patterns of viral spread and subsequent risk posed by wild bird viruses therefore remain unpredictable. Here we analyze genomic data, including 287 newly sequenced avian influenza A virus (AIV) samples isolated over a 34-year period of continuous systematic surveillance of North American migratory birds. We use a Bayesian statistical framework to test hypotheses of viral migration, population structure and patterns of genetic reassortment. Our results reveal that despite the high prevalence of Charadriiformes infected in Delaware Bay this host population does not appear to significantly contribute to the North American AIV diversity sampled in Anseriformes. In contrast, influenza viruses sampled from Anseriformes in Alberta are representative of the AIV diversity circulating in North American Anseriformes. While AIV may be restricted to specific migratory flyways over short time frames, our large-scale analysis showed that the long-term persistence of AIV was independent of bird flyways with migration between populations throughout North America. Analysis of long-term surveillance data provides vital insights to develop appropriately informed predictive models critical for pandemic preparedness and livestock protection.
α(V)β(6) integrin expression is induced in the POET and Pten(pc-/-) mouse models of prostatic inflammation and prostatic adenocarcinoma. (2012)

Chronic inflammation is proposed to prime the development of prostate cancer. However, the mechanisms of prostate cancer initiation and development are not completely understood. The α(v)β(6) integrin has been shown to play a role in epithelial development, wound healing and some epithelial cancers [1, 2]. Here, we investigate the expression of α(v)β(6) in mouse models of prostatic inflammation and prostate cancer to establish a possible relationship between inflammation of the prostate, α(v)β(6) expression and the progression of prostate cancer. Using immunohistochemical techniques, we show expression of α(v)β(6) in two in vivo mouse models; the Pten(pc)-/- model containing a prostate- specific Pten tumor suppressor deletion that causes cancer, and the prostate ovalbumin-expressing transgenic (POET) inflammation mouse model. We show that the α(v)β(6) integrin is induced in prostate cancer and inflammation in vivo in these two mouse models. α(v)β(6) is expressed in all the mice with cancer in the Pten(pc-/-) model but not in age-matched wild-type mice. In the POET inflammation model, α(v)β(6) is expressed in mice injected with activated T-cells, but in none of the control mice. In the POET model, we also used real time PCR to assess the expression of Transforming Growth Factor Beta 1 (TGFβ1), a factor in inflammation that is activated by α(v)β(6). In conclusion, through in vivo evidence, we conclude that α(v)β(6) integrin may be a crucial link between prostatic inflammation and prostatic adenocarcinoma.
FAS LIGAND AND NK CELLS ARE IMPORTANT MEDIATORS OF LATE SKIN GRAFT REJECTION (1998)

6 We have previously demonstrated prolonged but not indefinite survival of MHC mismatched murine skin allografts with combined perioperative blockade of the CD40 and CD28 costimulatory pathways. The purpose of this study was to determine the role of NK cells, the Fas/Fas ligand, and perforin effector pathways in late skin allograft rejection after combined costimulatory pathway blockade. This will allow the development of strategies to improve the efficacy of this therapy. To determine the effector pathway, three groups of recipients: 1) C57BL/6(B6), 2) B6mn.C3H-Faslgld (mutation in Fas ligand, B6-gld), 3) C57BL/6-Pfptmlsdz (B6-perforin-/-) received BALB/c skin grafts with or without combined CD40/CD28 blockade. The hamster anti-murine CD40L antibody, MR1, and human CTLA4Ig were administered at doses of 500 μg intraperitoneally on postoperative days 0, 2, 4, and 6. In all of the untreated groups, the skin grafts were rejected promptly (MST =8d≈12d). CTLA4Ig and MR1 treatments prolonged the survival in C57BL/6 mice (n=5, MST=40d). The treated B6-perforin-/- group showed mild improved survival (n=5, MST=65d). In contrast, the treated B6-gld group demonstrated excellent survival (n=5, MST>175d). To determine the role of NK cells in late graft loss, C57BL/6 mice received BALB/c skin allografts and treatment in one of three groups: 1) no treatment, 2) CD40/CD28 blockade, 3) CD40/CD28 blockade plus anti-NK antibodies(anti-asialo-GM1 antisera). Polyclonal rabbit anti-asialo-GM1 antisera (50μl) was given on days 0, 4, 8, and 12 post-transplant. In addition, BALB/c skins were transplanted on to C57BL/6 or C57BL/6-Lystbg/+ (beige mouse with impaired NK cell cytotoxicity) with or without CD40/CD28 blockade. In all the untreated groups including the beige mice, the skin grafts were rejected promptly (MST =8d ≈12d). CTLA4Ig and MR1 treatments prolonged the survival in C57BL/6 mice (n=5, MST=40d). The addition of anti-NK antibodies augmented survival (n=5, MST=106d). The treated beige mice also showed marked improved survival (n=7, MST>56d) compared to the treated C57BL/6 group (n=7, MST=28d). The Fas ligand effector pathway and NK cells are important mediators of late skin graft loss after combined costimulatory pathway blockade. These results raise the possibility that NK cells and Fas ligand may be important targets for novel therapies to prevent chronic allograft loss.
Crystal Structure, Morphology, and Phase Transitions in Aromatic Polyimide Oligomers. 1. Poly(4,4'-oxydiphenylene pyromellitimide) (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal Structure, Morphology, and Phase Transitions in Aromatic Polyimide Oligomers. 1. Poly(4,4'-oxydiphenylene pyromellitimide)Jiang Liu, Stephen Z. D. Cheng, Frank W. Harris, Benjamin S. Hsiao, and Kenncorwin H. GardnerCite this: Macromolecules 1994, 27, 4, 989–996Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/ma00082a016https://doi.org/10.1021/ma00082a016research-articleACS PublicationsRequest reuse permissionsArticle Views768Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Predictive Simulation Strategies for the 2-Stroke Scavenging Process within the Scope of the Development Process (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Cylindrical photonic bandgap fibers for high-power laser transmission (Abstract Only) (2004)

The problem of transmitting light through fibers has been synonymous with the identification of low loss materials, since the transparency of a conventional index-guided fiber cannot exceed that of its constituents. To date, precious few materials have been shown to exhibit high transparency at any wavelength and none have been found to exhibit it over wide wavelength ranges. The focus of our research at MIT has been on the elucidation of strategies for creating optical fibers where transparency is determined by the fiber microstructure, the ultimate goal being to create a fiber that is "more transparent than the materials that it is made from." This talk will present the underlying physics, materials selection and processing methodology which have resulted in the design and draw of hollow fibers lined with an interior omnidirectional dielectric mirror. A pair of glassy materials with substantially different indices of refraction but with similar thermo-mechanical properties was used to construct a fiber with multiple layers of alternating high and low refractive indices surrounded by a tough polymer cladding. Confinement of light in the hollow core is provided by the large photonic bandgaps established by the multiple alternating sub-micrometer-thick layers of a high-refractive-index chalcogenide glass and a low-index polymer. The fundamental and higher order transmission windows are determined by the layer thicknesses and can be scaled from 0.75 to 10.6 microns in wavelength. Recent transmission loss measurements were found to be orders of magnitude lower than those of the intrinsic fiber material, thus demonstrating that low attenuation can be achieved by structural design rather than high-transparency material selection. Scaling laws as well as device applications will be surveyed, recent results pertaining to CO<sub>2</sub> laser transmission will be presented, and future directions will be discussed.
Back from the Tip of the Nose (2001)

About 130 years ago, Giulio Bizozzero, then in Pavia, made a seminal observation [1]. He divided the tissues of the vertebrate body into three categories: those that divide constantly (labile), such as blood and skin, those that never divide, such as striated muscle and brain (perennial), and those that normally do not divide but can do so if injured (stable). As a consequence, diseases that perturb cell division, such as cancer, affect labile tissues, while degenerative diseases affect perennial tissues where repair is inefficient. Epithelia and blood possess a reservoir of cells that divide and maintain a progenitor pool throughout life (the stem cells) whereas striated muscle and brain were supposed not to contain stem cells. Furthermore, stem cells were supposed to generate only the cells of the tissue where they belong.
Recombinant host cells and nucleic acid constructs encoding polypeptides having cellulolytic enhancing activity (2023)

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.
Cost of Lost Productivity Due to Erectile Dysfunction and Impact of Employer Benefit Exclusion of Penile Prosthesis Implantation Treatment (2021)

Productivity loss due to ED and PPI benefit exclusion have considerable economic impacts on men with ED and their employers. continuous advocacy for benefit exclusion removal is needed to ensure appropriate patient access.
Computers, Robotics, and the Human Brain (2008)

We dedicate this issue to the theme of computers, robotics, and the human brain, exploring the full potential of both biological systems and machines and the synergistic interaction between them. The human brain is considered the most fascinating and complex signal processing machine in existence. Promising to tap into the ultimate power of the biological machine, brain-computer interface (BCI) is an emerging cross-disciplinary field that has attracted much interest from the signal processing, machine learning, and biology communities. Research in this area tackles a wide spectrum of challenges ranging from robust interface design, spatial signal filtering, multimodal imaging and explores important applications, such as motor control for handicapped users and information triage in real-time situations. The guest editors of the special issue, Sajda, Muller and Shenoy, serve as our guides venturing into this burgeoning field. They have selected nine outstanding articles, providing a comprehensive survey of important signal processing issues at the forefront of BCI research. What could be a better way to understand brain structures and functions than learning how meditation practitioners (especially Buddhist monks) improve their mental states and skills? The “In the Spotlight”
Scene-Graph Augmented Data-Driven Risk Assessment of Autonomous Vehicle Decisions (2021)

There is considerable evidence that evaluating the subjective risk level of driving decisions can improve the safety of Autonomous Driving Systems (ADS) in both typical and complex driving scenarios. In this paper, we propose a novel data-driven approach that uses scene-graphs as intermediate representations for modeling the subjective risk of driving maneuvers. Our approach includes a Multi-Relation Graph Convolution Network, a Long-Short Term Memory Network, and attention layers. To train our model, we formulate subjective risk assessment as a supervised scene classification problem. We evaluate our model on both synthetic lane-changing datasets and real-driving datasets with various driving maneuvers. We show that our approach achieves a higher classification accuracy than the state-of-the-art approach on both large (96.4% vs. 91.2%) and small (91.8% vs. 71.2%) lane-changing synthesized datasets, illustrating that our approach can learn effectively even from small datasets. We also show that our model trained on a lane-changing synthesized dataset achieves an average accuracy of 87.8% when tested on a real-driving lane-changing dataset. In comparison, the state-of-the-art model trained on the same synthesized dataset only achieved 70.3% accuracy when tested on the real-driving dataset, showing that our approach can transfer knowledge more effectively. Moreover, we demonstrate that the addition of spatial and temporal attention layers improves our model’s performance and explainability. Finally, our results illustrate that our model can assess the risk of various driving maneuvers more accurately than the state-of-the-art model (86.5% vs. 58.4%, respectively).
DOLCE: A Model-Based Probabilistic Diffusion Framework for Limited-Angle CT Reconstruction (2022)

Limited-Angle Computed Tomography (LACT) is a non-destructive evaluation technique used in a variety of applications ranging from security to medicine. The limited angle coverage in LACT is often a dominant source of severe artifacts in the reconstructed images, making it a challenging inverse problem. We present DOLCE, a new deep model-based framework for LACT that uses a conditional diffusion model as an image prior. Diffusion models are a recent class of deep generative models that are relatively easy to train due to their implementation as image denoisers. DOLCE can form high-quality images from severely under-sampled data by integrating data-consistency updates with the sampling updates of a diffusion model, which is conditioned on the transformed limited-angle data. We show through extensive experimentation on several challenging real LACT datasets that, the same pre-trained DOLCE model achieves the SOTA performance on drastically different types of images. Additionally, we show that, unlike standard LACT reconstruction methods, DOLCE naturally enables the quantification of the reconstruction uncertainty by generating multiple samples consistent with the measured data.
Shape statistics for cell division detection in time-lapse videos of early mouse embryo (2014)

We describe a statistical approach to the problem of estimating the times of cell-division cycles in time-lapse movies of early mouse embryos. Our method is based on the likelihoods for cells of certain radii ranges to be in each frame — without actually locating or counting the cells. Computing the likelihoods consists of a voting scheme where votes come form quadruples of points in a way similar to the first step of the Randomized Hough Transform for ellipse detection. To locate divisions, we search for points of abrupt change in the matrix of likelihoods (built for all frames), and pick the two optimal division points using a dynamic programming algorithm. Our results for the first and second cell division cycles differ less than two frames from the medians of the annotated times in a database of 100 annotated videos, and outperform two other recent methods in the same set.
A slim patient with polycystic ovary syndrome (PCOS) (2015)

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ChemInform Abstract: 4‐DIISOPROPYLAMINOMETHYLTRIPHENYLPHOSPHINE: A WATER SOLUBLE WITTIG REAGENT (1985)

Abstract Das aus der Bromverbindung (I) und dem Chlorphosphin (II) erhältliche Triphenylphosphin‐De?vat (III) kann nach Alkylierung mit Propyliodid (IV) als wasserlösliches Wittig‐Reagens z.B. mit Benzaldehyd (V) zum Olefin (VI) umgesetzt werden.
Advances in fiber optics (2002)

This paper describes the development of fiber optics technology — an essential element of the telecommunications revolution — and reviews the remarkable progress in fiber design and fabrication, optical amplifiers, UV-induced fiber gratings, novel microstructured optical fibers, and integrated optics. The paper also explores the limits of optical fiber channel capacity and considers the future of optical communications.