gebhart/patrepeval huggingface dataset:
Abstract A046: Identification and validation of HCC-specific gene transcriptional signature for tumor antigen discovery (2016)

Abstract A novel two-step bioinformatics strategy was applied for identification of signatures with therapeutic implications in hepatitis-associated HCC. Transcriptional profiles from HBV- and HCV-associated HCC samples were compared with normal liver tissue controls. Resulting HCC modulated genes were subsequently compared with different normal tissue samples. Two related signatures were identified, namely “HCC-associated” and “HCC-specific.” Expression data were validated by RNA-Seq analysis carried out on unrelated HCC samples and protein expression was confirmed according to the publicly available database at http://www.proteinatlas.org/. Among all, only two proteins (namely AKR1B10 and IGF2BP3) were found strictly HCC-specific with no expression in 18/20 normal tissues. Target peptides for vaccine design were predicted for both proteins associated with the most prevalent HLA-class I and II alleles. The described novel strategy showed to be feasible for identification of HCC-specific proteins as highly potential target for HCC immunotherapy (Petrizzo et al., Scientific Reports, in press). Citation Format: Annacarmen Petrizzo, Francesca P. Caruso, Maria Tagliamonte, Maria Lina Tornesello, Michele Ceccarelli, Valerio Costa, Marianna Aprile, Roberta Esposito, Gennaro Ciliberto, Franco M. Buonaguro, Luigi Buonaguro. Identification and validation of HCC-specific gene transcriptional signature for tumor antigen discovery [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A046.
Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site (2014)

Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus 'Serpentinomonas'.
Multiomics to investigate the mechanisms contributing to repression of PTPRC and SOCS2 in pediatric T‐ALL: Focus on miR‐363‐3p and promoter methylation (2022)

T-cell acute lymphoblastic leukemia (T-ALL) is a heterogeneous and aggressive malignancy arising from T-cell precursors. MiRNAs are implicated in negative regulation of gene expression and when aberrantly expressed contribute to various cancer types, including T-ALL. Previously we demonstrated the oncogenic potential of miR-363-3p overexpression in a subgroup of T-ALL patients. Here, using combined proteomic and transcriptomic approaches, we show that miR-363-3p enhances cell growth of T-ALL in vitro via inhibition of PTPRC and SOCS2, which are implicated in repression of the JAK-STAT pathway. We propose that overexpression of miR-363-3p is a novel mechanism potentially contributing to overactivation of JAK-STAT pathway. Additionally, by combining the transcriptomic and methylation data of T-ALL patients, we show that promoter methylation may also contribute to downregulation of SOCS2 expression and thus potentially to JAK-STAT activation. In conclusion, we highlight aberrant miRNA expression and aberrant promoter methylation as mechanisms, alternative to mutations of JAK-STAT-related genes, which might lead to the upregulation of JAK-dependent signaling in T-ALL.
All-digital multipoint adaptive delay compensationcircuit for lowskew clock distribution (1995)

The authors describe an all-digital circuit for automatically controlling skew in the distribution of a clock or data signal over a single line. The circuit derives a compensating delay for any location such that a signal applied at one end emerges at the same global time at all sites. This is an alternative to delay-equalised hierarchical trees for use in large ICs, computers, and digital switches. A 3 µm CMOS prototype at eight sites spread over 16 m shows adaptive skew control to within +/- 1.5 primitive buffer delays of the process employed. A novel technique for accommodating metastability is involved in the design.
Nanocomposite thin films for miniaturized multi-layer ceramic capacitors prepared from barium titanate nanoparticle based hybrid solutions (2011)

In the present work a flexible approach for the wet chemical processing of nanocomposite functional thin films is demonstrated. Barium titanate (BTO) based nanocomposite thin films for future miniaturized multi-layer ceramic capacitors are chosen as model systems to introduce the concept of “hybrid solutions” which consist of stabile mixtures of reverse micelle derived BTO nanoparticle dispersions and conventional molecular precursor solutions of either the same (BTO:BTO) or a specifically different material such as zirconia (BTO:ZrO2). While in the case of using BTO:BTO hybrid solutions an interesting mode of microstructure control is found, the use of BTO:ZrO2 hybrid solutions with various BTO : ZrO2 ratios leads to nanocomposite films. BTO:BTO hybrid solutions yield columnar grown films with excellent permittivities up to 1050 with a significantly reduced number of coating steps at 700 °C. Low values of the temperature coefficient of capacitance are realized in the BTO–ZrO2 nanocomposite thin films. The observed dielectric behavior of these films is explained based on the formation of a core–shell type microstructure on the nanoscale. A detailed high resolution transmission electron microscopy study combined with Raman spectroscopy and X-ray diffraction gives evidence for the proposed BTO–ZrO2 nanocomposite character of these thin films.
Synthesis of Geometry Proof Problems (2014)

This paper presents a semi-automated methodology for generating geometric proof problems of the kind found in a high-school curriculum. We formalize the notion of a geometry proof problem and describe an algorithm for generating such problems over a user-provided figure. Our experimental results indicate that our problem generation algorithm can effectively generate proof problems in elementary geometry. On a corpus of 110 figures taken from popular geometry textbooks, our system generated an average of about 443 problems per figure in an average time of 4.7 seconds per figure.
From Kanner Austim to Asperger Syndromes, the Difficult Task to Predict Where ASD People Look at (2020)

Modelling the visual attention of people with autism spectrum disorder (ASD) is attracting more and more interest. This consists in determining where ASD people look and in inferring the important visual features contributing to the gaze deployment. In this article, we investigate whether or not existing neurotypical as well as ASD saliency models perform well over the whole spectrum of autism. For this purpose, we propose two new eye-tracking datasets of ASD people in order to cover a large part of the autism spectrum, going from high-level functioning (e.g. Asperger) to low-level functioning (e.g. Kanner) autism. We demonstrate that current neurotypical and ASD models do not generalize well and perform well only on a small part of the spectrum. Our objective is to raise the awareness of computer scientists to the difficult task we are facing up when it comes to simulate the gaze deployment of ASD people.
Design of Low-molar Mass Thermomesogens in the Search for Biaxial Nematic Liquid Crystals (1998)

Abstract In this article we describe research into the molecular design features for potential thermotropic biaxial nematogens of low-molar mass. We discuss how we can systematically change the shape of molecular structures in view of this aim of our work. The optical biaxialities of the materials prepared were tested through conoscopic and birefringence measurements. So far none of these materials synthesised and tested in this way have unequivocally exhibited the biaxial nematic phase. An overview of numerous further materials different in molecular shape and in part studied by others is also given. Key Words: Biaxial nematicsliquid crystalsgeometrical factorsmetal complexesmetallome-sogensmultifunctional compoundsradial multifacessynthetic routes
ChemInform Abstract: Microwave Promoted Synthesis of 4,7‐Dihydro‐1H‐imidazo[4,5‐e]‐1,2,4‐triazepin‐8‐ones as Ring‐Expanded Hypoxanthine Analogues. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum (2010)

Genetic studies of midgut carcinoid cancer have exclusively focused on genomic changes of the tumor cells. We investigated the role of constitutional genetic polymorphisms in predisposing individuals to ileal carcinoids. In all, 239 cases and 110 controls were collected from three institutions: the Uppsala University Hospital; the Dana-Farber Cancer Institute; and the MD Anderson Cancer Center, and were genotyped using microarrays assaying >300 000 single nucleotide polymorphisms. Association with rs2208059 in KIF16B approached statistical significance (Mantel-Haenszel odds ratio=2.42, P=4.16×10(-7)) at a Bonferroni-corrected level (<1.62×10(-7)). Using two computational algorithms, four copy-number variants (CNVs) were identified in multiple cases that were absent in study controls and markedly less frequent in ∼1500 population-based controls. Of these four constitutional CNVs identified in blood-derived DNA, a 40 kb heterozygous deletion in Chr18q22.1 corresponded with a region frequently showing loss of heterozygosity (LOH) in ileal carcinoid tumor cells based on our meta-analysis of previously published cytogenetic studies (69.7% LOH, 95% confidence interval=60.0-77.9%). We analyzed the constitutional 40 kb deletion on chr18 in our study samples with a real-time quantitative PCR assay; 14/226 cases (6.19%) and 2/97 controls (2.06%) carried the CNV, although the exact boundaries of each deletion have not been determined. Given the small sample size, our findings warrant an independent cohort for a replication study. Owing to the rarity of this disease, we believe these results will provide a valuable resource for future work on this serious condition by allowing others to make efficient use of their samples in targeted studies.
Imaging the Multi-Temporal Photo-Carrier Dynamics at the Nanometer Scale in Organic and Inorganic Solar Cells (2017)

Understanding the interplay between the nanostructure and photo-transport mechanisms is central for the development of many emerging photovoltaic technologies. In recent years. there has been an increasing focus on the need to probe the photo-carrier dynamics at the nanometer scare. Recently we demonstrated that non-contort atomic force microscopy combined with kelvin probe force microscopy under frequent' modulated illumination (FMI-KPFM) can be used to map two-dimensional images of the surface photo-soltage dynamics pith a sub-10 nnm lateral resolution. Here, a detailed overview of this approach including operating principle. instrumental aspects and data treatment will be given. The capability of FMI-KPFM to map spatial variations of the minority carrier lifetime is demonstrated in the case of silicon nanocrystal-based third generation solar cells. The accuracy of the post-data acquisition processing is discussed by analyzing the evolution of the dynamical contrasts as a function of the illumination intensity in organic bulk heterojunction thin films.
Average Property Relations for Nonlinear Polymerization with Unequal Reactivity (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAverage Property Relations for Nonlinear Polymerization with Unequal ReactivityDouglas R. Miller and Christopher W. MacoskoCite this: Macromolecules 1978, 11, 4, 656–662Publication Date (Print):July 1, 1978Publication History Published online1 May 2002Published inissue 1 July 1978https://pubs.acs.org/doi/10.1021/ma60064a008https://doi.org/10.1021/ma60064a008research-articleACS PublicationsRequest reuse permissionsArticle Views409Altmetric-Citations114LEARN 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
Tim-1 Is Essential for Induction and Maintenance of IL-10 in Regulatory B Cells and Their Regulation of Tissue Inflammation (2015)

T cell Ig and mucin domain (Tim)-1 identifies IL-10-producing regulatory B cells (Bregs). Mice on the C57BL/6 background harboring a loss-of-function Tim-1 mutant showed progressive loss of IL-10 production in B cells and with age developed severe multiorgan tissue inflammation. We demonstrate that Tim-1 expression and signaling in Bregs are required for optimal production of IL-10. B cells with Tim-1 defects have impaired IL-10 production but increased proinflammatory cytokine production, including IL-1 and IL-6. Tim-1-deficient B cells promote Th1 and Th17 responses but inhibit the generation of regulatory T cells (Foxp3(+) and IL-10-producing type 1 regulatory T cells) and enhance the severity of experimental autoimmune encephalomyelitis. Mechanistically, Tim-1 on Bregs is required for apoptotic cell (AC) binding to Bregs and for AC-induced IL-10 production in Bregs. Treatment with ACs reduces the severity of experimental autoimmune encephalomyelitis in hosts with wild-type but not Tim-1-deficient Bregs. Collectively, these findings suggest that in addition to serving as a marker for identifying IL-10-producing Bregs, Tim-1 is also critical for maintaining self-tolerance by regulating IL-10 production in Bregs.
The effect of pomegranate fruit extract on testosterone‐induced BPH in rats (2015)

BACKGROUND Benign prostatic hyperplasia (BPH) affects many men after the age of 50 years. Inflammation and oxidative stress along with apoptotic changes are thought to play an important role in the pathology of BPH. Pomegranate contains a variety of polyphenolic compounds that have been studied in a medley of diseases for their anti‐oxidant, anti‐inflammatory and pro‐apoptotic properties. Therefore, this study examined the effect of Pomegranate Fruit Extract (PFE) on the development of BPH using a testosterone‐induced BPH model in rats. METHODS A total of 48 rats were randomly divided into six groups of eight, one group served as the control, BPH was induced by testosterone 3 mg/kg S.C. daily in four groups, three of them received PFE by oral gavage daily at doses of 25, 50, and 100 mg/kg respectively, while one group received PFE at a dose of 50 mg/kg without induction of BPH. RESULTS PFE at a dose of 100 mg/kg was the most effective in decreasing testosterone‐induced increase in prostate weight, prostate weight/body weight ratio, and PAP levels by 30.8%, 55%, and 68% respectively and in preventing the accompanying histological changes. In the BPH model, testosterone significantly decreased GSH, SOD, and CAT to 0.45, 0.64, and 0.88 of the control group values respectively, and significantly increased MDA by &gt;6‐fold. In combination with testosterone, PFE dosed at 100 mg/kg significantly increased GSH, SOD, and CAT to 0.83, 0.92, and 0.93 of the control group values respectively, whereas MDA was significantly decreased by 72% compared with the testosterone treated group. In addition to this, at the range of doses studied, PFE lowered COX‐II, iNOS, Ki‐67 expression, and increased apoptotic index. CONCLUSION The current findings elucidate the effectiveness of PFE in preventing testosterone‐induced BPH in rats. This could be attributed, at least partly, to its anti‐oxidant, anti‐inflammatory, and pro‐apoptotic properties. Prostate 75:679–692, 2015 . © 2015 Wiley Periodicals, Inc.
Heat Transfer Coefficients on a Flat Surface Impinged by the Under-expanded Sonic Jet (2004)

An experimental investigation has been carried out to examine heat-transfer characteristics of an axisymmetric, under-expanded, sonic jet impinging on a flat plate and the local measurement of surface pressures and heat transfer coefficients on a plate have been achieved together with a visualization test of shock structure in a jet. Heat transfer coefficients on a plate have been found to be changed significantly depending on the under- expansion ratio as much as the nozzle-to-plate distance and these phenomena have been explained with other results and discussions by other
Computational and in vitro experimental analyses of the anti-COVID-19 potential of Mortaparib and MortaparibPlus (2021)

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a global health emergency. Although new vaccines have been generated and being implicated, discovery and application of novel preventive and control measures are warranted. We aimed to identify compounds that may possess the potential to either block the entry of virus to host cells or attenuate its replication upon infection. Using host cell surface receptor expression (angiotensin-converting enzyme 2 (ACE2) and Transmembrane protease serine 2 (TMPRSS2)) analysis as an assay, we earlier screened several synthetic and natural compounds and identified candidates that showed ability to down-regulate their expression. Here, we report experimental and computational analyses of two small molecules, Mortaparib and MortaparibPlus that were initially identified as dual novel inhibitors of mortalin and PARP-1, for their activity against SARS-CoV-2. In silico analyses showed that MortaparibPlus, but not Mortaparib, stably binds into the catalytic pocket of TMPRSS2. In vitro analysis of control and treated cells revealed that MortaparibPlus caused down-regulation of ACE2 and TMPRSS2; Mortaparib did not show any effect. Furthermore, computational analysis on SARS-CoV-2 main protease (Mpro) that also predicted the inhibitory activity of MortaparibPlus. However, cell-based antiviral drug screening assay showed 30-60% viral inhibition in cells treated with non-toxic doses of either MortaparibPlus or Mortaparib. The data suggest that these two closely related compounds possess multimodal anti-COVID-19 activities. Whereas MortaparibPlus works through direct interactions/effects on the host cell surface receptors (ACE2 and TMPRSS2) and the virus protein (Mpro), Mortaparib involves independent mechanisms, elucidation of which warrants further studies.
Two-photon spectroscopy and analysis with a white-light continuum probe (2002)

We present a powerful experimental tool and analysis for characterization of two-photon absorption (2PA) spectra. We demonstrate this method with ZnS and then apply it to organic dyes in solution. We also compare the results with those from other methods such as two-photon fluorescence spectroscopy. This femtosecond pump-probe method uses a white-light continuum (WLC) as the probe to produce a nondegenerate 2PA spectrum. The extreme chirp of the WLC requires that transmittance data be collected over a range of temporal delays between pump and probe pulses. These data then need to be corrected for the effects of this chirp as well as for the temporal walk-off of the pulses in the sample that result from the frequency nondegenerate nature of the experiment. We present a simple analytic solution for the transmitted fluence through the sample, which is applicable for most practical cases.
Probe-Based Nanolithography: Self-Amplified Depolymerization Media for Dry Lithography (2009)

peer reviewed
SELECTIVE DRY ETCHING OF GaN OVER AlGaN IN BCL3/SF6 MIXTURES (2005)

Inductively coupled plasma (ICP) etching of GaN with high selectivity over Al.22Ga.78N in BCl3/SF6 mixtures has been studied. Selectivity and surface morphology were investigated over a wide range of pressures (3.75–37.5mTorr), RF powers (30–120 W), ICP powers (100–400 W), and SF6/BCl3 ratios (0.1–0.7). Higher pressures, lower dc biases, and higher SF6/BCl3 ratios increased the GaN to AlGaN selectivity. Selectivities up to 25 were measured by laser interferometry. A root mean square (rms) surface roughness of 0.67 nm was measured by atomic force microscopy (AFM) after removal of 0.5 μm from a GaN template (process selectivity: 15, as-grown rms surface roughness: 0.56 nm). A degradation in surface morphology, with the gradual formation of pits, was observed for selectivities above 10.
Claudin-like protein 24 interacts with the VEGFR-2 and VEGFR-3 pathways and regulates lymphatic vessel development (2010)

The Claudin-like protein of 24 kDa (CLP24) is a hypoxia-regulated transmembrane protein of unknown function. We show here that clp24 knockdown in Danio rerio and Xenopus laevis results in defective lymphatic development. Targeted disruption of Clp24 in mice led to enlarged lymphatic vessels having an abnormal smooth muscle cell coating. We also show that the Clp24(-/-) phenotype was further aggravated in the Vegfr2(+/LacZ) or Vegfr3(+/LacZ) backgrounds and that CLP24 interacts with vascular endothelial growth factor receptor-2 (VEGFR-2) and VEGFR-3 and attenuates the transcription factor CREB phosphorylation via these receptors. Our results indicate that CLP24 is a novel regulator of VEGFR-2 and VEGFR-3 signaling pathways and of normal lymphatic vessel structure.
Microstructural Properties of Gamma Titanium Aluminide Manufactured by Electron Beam Melting (2011)

In recent years, Electron Beam Melting (EBM) has matured as a technology for additive manufacturing of dense metal parts. The parts are built by additive consolidation of thin layers of metal powder using an electron beam. With EBM, it is possible to create parts with geometries too complex to be fabricated by other methods, e.g. fine network structures and internal cavities. The process is run in vacuum, which makes it well suited for materials with a high affinity to oxygen, i.e. . titanium compounds. We present material data from a recently conducted study of how melt strategy affects EBM process for gamma titanium aluminide, Ti-48Al-2Cr-2Nb.The investigation includes microstructural characterization, grain size measurement and tensile testing.
Developmental role of PHD2 in the pathogenesis of pseudohypoxic pheochromocytoma (2022)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)