gebhart/patrepeval huggingface dataset:
Abstract PR5: Therapeutic targeting of oncogene-specific tyrosine kinase networks during prostate cancer progression (2012)

Abstract Dominant activating mutations or DNA amplification of tyrosine kinases are not readily observed despite the numerous oncogenic alterations implicated in prostate cancer. We demonstrate that castration resistant prostate cancer (CRPC) exhibits increased tyrosine phosphorylation, raising the question of whether enhanced tyrosine kinase activity is observed in this disease in the absence of specific tyrosine kinase mutations. We generated a mouse model of prostate cancer progression using combinations of commonly perturbed non-tyrosine kinase oncogenes and pathways, including myristoylated Akt (Akt), androgen receptor (AR), Erg, and activated Kras (KrasG12V). We recapitulated the different stages of prostate cancer ranging from prostatic intraepithelial neoplasia (PIN) (Akt) to low grade cancer (Akt+Erg) to highly aggressive prostatic adenocarcinoma (Akt+AR or Akt+KrasG12V). We detected a significant upregulation of tyrosine phosphorylation at the advanced adenocarcinoma stage. Phosphotyrosine peptide enrichment and quantitative mass spectrometry identified oncogene-specific tyrosine kinase signatures, including activation of Egfr Y1172 (Akt+Erg), EphA2 Y595 (Akt+KrasG12V), and Jak2 Y1007/08 (Akt+AR). Kinase:substrate relationship analysis of the phosphopeptides also revealed Abl Y245 and Src Y416 tyrosine kinase activation in Akt+AR tumors; known targets of the tyrosine kinase inhibitor Dasatinib. We are currently evaluating the efficacy of tyrosine kinase inhibitors Dasatinib or Erlotinib on non-tyrosine kinase driven tumors Akt+AR or Akt+Erg, respectively. In summary, the observation of elevated phosphotyrosine signaling in advanced prostate cancer and identification of specific tyrosine kinase pathways from genetically-defined tumor models points to new therapeutic approaches using tyrosine kinase inhibitors for advanced prostate cancer. This abstract is also presented as Poster C35. Citation Format: Justin M. Drake, Jiaoti Huang, Thomas G. Graeber, Owen N. Witte, Nicholas A. Graham, Tanya Stoyanova, Amir Sedghi, Andrew S. Goldstein, Houjian Cai, Daniel A. Smith, Hong Zhang, Evangelia Komisopoulou. Therapeutic targeting of oncogene-specific tyrosine kinase networks during prostate cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr PR5.
Joint Priors for Variational Shape and Appearance Modeling (2007)

We are interested in modeling the variability of different images of the same scene, or class of objects, obtained by changing the imaging conditions, for instance the viewpoint or the illumination. Understanding of such a variability is key to reconstruction of objects despite changes in their appearance (e.g. due to non-Lambertian reflection), or to recognizing classes of objects (e.g. cars), or individual objects seen from different vantage points. We propose a model that can account for changes in shape or viewpoint, appearance, and also occlusions of line of sight. We learn a prior model of each factor (shape, motion and appearance) from a collection of samples using principal component analysis, akin a generalization of "active appearance models" to dense domains affected by occlusions. The ultimate goal of this work is stereo reconstruction in 3D, but first we have developed the first stage in this approach by addressing the simpler case of 2D shape/radiance detection in single images. We illustrate our model on a collection of images of different cars and show how the learned prior can be used to improve segmentation and 3D stereo reconstruction.
Post-poliomyelitis syndrome (2004)

Post-poliomyelitis syndrome (PPS) is a common neurological disorder that occurs in a large proportion of individuals who have recovered from paralytic poliomyelitis. The main clinical features are new weakness, muscular fatigability, general fatigue, and pain. The primary criteria necessary for the diagnosis of PPS are a history of paralytic poliomyelitis, partial or complete recovery of neurological function followed by a period of stability (usually several decades), persistent new muscle weakness or abnormal muscle fatigability, and the exclusion of other causes of new symptoms. The cause of PPS remains unclear, but is likely due to a distal degeneration of enlarged post-poliomyelitis motor units. Contributing factors to PPS may be aging (with motor neuron loss), overuse, and disuse. PPS is usually a slowly progressive neuromuscular disease. Although there is no specific treatment for PPS, an interdisciplinary management program can be useful in controlling symptoms.
ChemInform Abstract: A Highly dl‐Stereoselective Pinacolization of Aromatic Aldehydes Mediated by Titanium Trichloride in Dichloromethane. (1996)

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.
Chirospecific synthesis of 1,4-dideoxy-1,4-imino-D-arabinitol and 1,4-dideoxy-1,4-imino-L-xylitol via one-pot cyclisation (1998)

The multi-protected compounds 4 and 5 were treated with 20% iodine in methanol to give 1,4-dideoxy-1,4-imino-D-arabinitol 1 and 1,4-dideoxy-1,4-imino-L-xylitol 2 directly. Iodine was an efficient catalyst for deprotection of O-isopropylidene, O-(tert-butyldimethylsilyl), N-(9-phenylfluoren-9-yl) and N-benzyloxycarbonyl groups, resulting in intramolecular cyclisation.
CAPA: The Spirit of Beaver against Physical Attacks. (2017)

In this paper we introduce two things: On one hand we introduce the Tile-Probe-and-Fault model, a model generalising the wire-probe model of Ishai et al. extending it to cover both more realistic side-channel leakage scenarios on a chip and also to cover fault and combined attacks. Secondly we introduce CAPA: a combined Countermeasure Against Physical Attacks. Our countermeasure is motivated by our model, and aims to provide security against higher-order SCA, multiple-shot FA and combined attacks. The tile-probe-and-fault model leads one to naturally look (by analogy) at actively secure multi-party computation protocols. Indeed, CAPA draws much inspiration from the MPC protocol SPDZ. So as to demonstrate that the model, and the CAPA countermeasure, are not just theoretical constructions, but could also serve to build practical countermeasures, we present initial experiments of proof-of-concept designs using the CAPA methodology. Namely, a hardware implementation of the KATAN and AES block ciphers, as well as a software bitsliced AES S-box implementation. We demonstrate experimentally that the design can resist second-order DPA attacks, even when the attacker is presented with many hundreds of thousands of traces. In addition our proof-of-concept can also detect faults within our model with high probability in accordance to the methodology.
Cultural heritage 'in-The-wild': Considering digital access to cultural heritage in everyday life (2018)

As digital cultural heritage applications begin to be deployed out with 'traditional' heritage sites (such as museums, open-Air museums or galleries), there is an increased need to consider their use amongst individuals who are open to learning about the heritage of a site, but where that is a clearly secondary purpose of their visit. Parks, recreational areas and the everyday built environment represent places that although often rich in heritage, are often not visited primarily to access that heritage. We present the results of a study of a mobile application, called Explore, that supports accessing heritage on a Finnish recreational island. Evaluation with 45 participants, who were not visiting primarily to access the heritage, provided insight into how digital heritage applications can be developed for this user group. Our results showed how low immersion and lightweight interaction support individuals to integrate cultural heritage around their primary visit purpose. Although participants were willing to include heritage as part of their visit, they were not willing to be directed by Explore. Our work outlines future directions that should be considered when expanding the reach of heritage access beyond 'traditional' sites.
ChemInform Abstract: Alkyne Metathesis by Molybdenum and Tungsten Alkylidyne Complexes (2013)

Abstract Review: 33 refs.
Coordinately unsaturated O2c–Ti5c–O2c sites promote the reactivity of Pt/TiO2 catalysts in the solvent-free oxidation of n-octanol (2021)

Coordination unsaturated O<sub>2c</sub>–Ti<sub>5c</sub>–O<sub>2c</sub> of TiO<sub>2</sub> (001) facets promote the formation of low-coordinate Pt metal clusters, which enhances catalytic performance in aerobic 1-octanol oxidation.
(Late) Reliability and performance considerations for NMOSFET pass gates in FPGA applications (2013)

The NMOSFET-only pass gates used in some digital CMOS applications, such as the Field-Programmable Gate Arrays (FPGAs), are apparently vulnerable to Positive Bias Temperature Instability (PBTI). Here we discuss the impact of PBTI frequency and workload on high-k/metal-gate NMOSFETs in terms of Capture-and-Emission Time (CET) maps and quantitatively explain the degradation of our test circuit. From individual trapping events in deeply-scaled NMOSFETs we then project PBTI distributions at 10 years. Finally, we show that at increased supply voltage the pass gate speed degradation is outweighed by signal transfer speedup, resulting in a net performance improvement.
Mechanical Strength of PhotoFix® and Glutaraldehyde Treated Porcine Aortic Valve Wall Tissue (1999)

Abstract The use of prosthetic heart valves manufactured from porcine aortic valves is commonplace. The standard design incorporates a valve mounted on a plastic or metal stent to facilitate implantation. More recently stentless valves have gained favor. These valves include the intact aortic root or a composite design. Composite valves are assembled using tissue from different valves cut axially along the aorta between valve leaflets. Composite designs are used to eliminate the right coronary leaflet substantially reducing the associated muscle shelf which has been the cause of high re-operation rates in the past (1). We are developing a tri-composite, PhotoFix® stentless valve, combining three non-coronary leaflets and it is the goal of this study to examine the mechanical strength of the associated aortic tissue. This is being done to ensure adequate strength of the material to withstand physiological loading. The strength will be compared to estimated in vivo loading conditions as well as to the strength of tissue from a commercially available glutaraldehyde fixed product.
A new finite element method for inverse problems in structural analysis: application to atherosclerotic plaque elasticity reconstruction (2014)

International audience
Surface micromachined tunable 155 μm-VCSEL with 102 nm continuous single-mode tuning (2011)

For the first time a vertical-cavity surface-emitting laser (VCSEL) with a single-mode wavelength-tuning over 102 nm in the range of 1550 nm is demonstrated. The fiber-coupled optical output power has a maximum of 3.5 mW and is > 2 mW over the entire tuning range. The sidemode suppression ratios are > 45 dB. The wavelength tuning is achieved with the micro-electro mechanical actuation of a mirror membrane fabricated with surface micro-machining for on-wafer mass production. The mirror membrane consists of low cost dielectric materials (SiOx/SiNy) deposited with low temperature (< 100°C) Plasma Enhanced Chemical Vapor Deposition (PECVD).
GeneTrail--advanced gene set enrichment analysis (2007)

We present a comprehensive and efficient gene set analysis tool, called 'GeneTrail' that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, 'Over-Representation Analysis' (ORA) comparing a reference set of genes to a test set, and 'Gene Set Enrichment Analysis' (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de.
Synthesis and Characterization of Ionic Polymer Networks in a Room-Temperature Ionic Liquid (2012)

Ionic liquid gels (ILGs) for potential use in ion transport and separation applications were generated via a free radical copolymerization of 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and N,N'-methylene(bis)acrylamide (MBA) using 1-ethyl-3-methylimidazolium ethylsulfate (IL) as a room temperature ionic liquid solvent medium. The AMPS and MBA monomer solubility window in the IL in the temperature range of 25 to 65 °C was determined. In situ ATR-FTIR showed near complete conversion of monomers to a cross-linked polymer network. ILGs with glass transition temperatures (T(g)s) near -50 °C were generated with T(g) decreasing with increasing IL content. The elastic moduli in compression (200 to 6600 kPa) decreased with increasing IL content and increasing AMPS content while the conductivities (0.35 to 2.14 mS cm⁻¹) increased with increasing IL content and decreasing MBA content. The polymer-IL interaction parameter (χ) (0.48 to 0.55) was determined via a modified version of the Bray and Merrill equation.
Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images (2018)

The majority of computational methods for predicting toxicity of chemicals are typically based on "nonmechanistic" cheminformatics solutions, relying on an arsenal of QSAR descriptors, often vaguely associated with chemical structures, and typically employing "black-box" mathematical algorithms. Nonetheless, such machine learning models, while having lower generalization capacity and interpretability, typically achieve a very high accuracy in predicting various toxicity endpoints, as unambiguously reflected by the results of the recent Tox21 competition. In the current study, we capitalize on the power of modern AI to predict Tox21 benchmark data using merely simple 2D drawings of chemicals, without employing any chemical descriptors. In particular, we have processed rather trivial 2D sketches of molecules with a supervised 2D convolutional neural network (2DConvNet) and demonstrated that the modern image recognition technology results in prediction accuracies comparable to the state-of-the-art cheminformatics tools. Furthermore, the performance of the image-based 2DConvNet model was comparatively evaluated on an external set of compounds from the Prestwick chemical library and resulted in experimental identification of significant and previously unreported antiandrogen potentials for several well-established generic drugs.
Temperature-Sensitive Mutants of Influenza Virus. IV. Induction of Interferon in the Nasopharynx by Wild-Type and a Temperature-Sensitive Recombinant Virus (1973)

The temperature-sensitive (ts) live influenza A virus vaccine (ts-1[E]), administered intranasally, induced interferon in the nasopharyngeal (NP) washes of volunteers. The amount of interferon in the NP washes of these volunteers was 15-fold less than that induced by wild-type virus. In addition, interferon was detected for a shorter period in men infected with the ts-1[E] virus. There was a strong correlation between the level of virus multiplication and the amount of interferon induced in the NP washes by either the ts or wild-type virus. In vitro, the ts and wild-type viruses had similar sensitivities to interferon; in addition, under conditions that were permissive for the ts virus (34 C), it stimulated as much interferon and interference in tissue culture as wild-type virus. It appeared that the low levels of interferon induced in the nasopharynx by the ts virus in vivo were a consequence of the low level of virus multiplication at that site. Furthermore, the mechanism(s) responsible for the attenuation of this ts virus does not seem to be related to an increased production of interferon in the nasopharynx or to an enhanced sensitivity of this virus to interferon.
Iron-Catalyzed Synthesis of C2 Aryl- and N-Heteroaryl-Substituted Tetrahydropyrans (2015)

An iron-catalyzed cyclization of hydroxy allylic derivatives into tetrahydropyrans possessing an N-heteroaryl at C2 is disclosed. The reaction proceeds with good yield and in high diastereoselectivity in favor of the more stable isomer. The diastereoselectivity results from an iron-induced reopening of the tetrahydropyrans, allowing a thermodynamic equilibration. The method allows access to a variety of 2,6-disubstituted as well as 2,4,6-trisubstituted tetrahydropyrans that could be considered as attractive scaffolds for the pharmaceutical industry.
Development and characterization of a sparse ellipsoidal 256 element array for volumetric ultrasound imaging (2021)

Sparse 2D matrix arrays represent an alternative to fully populated arrays for a more efficient use of available electronic channels. While individually driving the elements of fully populated matrix arrays requires electronics with thousands of elements, the requirements to the multichannel electronics can be dramatically reduced with sparse arrays. In our work, we developed and characterized a sparse 2D array with a spiral element pattern. The array consists of 256 elements in a 513 µm pitched matrix. An elliptical geometry was chosen in view of a later use in volumetric transperineal imaging. The array was processed on a conductive backing. An average centre frequency of 4,2 MHz (1,4 MHz −6 dB bandwidth) was measured. A wire phantom was used for assessment of the imaging performance. When excited with a single plane wave (0°), the FWHM ranged between 750 µm and 1100 µm (in x- and y- direction respectively).
Genome-wide unmasking of epigenetically silenced genes in lung adenocarcinoma from smokers and never smokers (2014)

Lung cancer in never smokers (NS) shows striking demographic, clinicopathological and molecular distinctions from the disease in smokers (S). Studies on selected genetic and epigenetic alterations in lung cancer identified that the frequency and profile of some abnormalities significantly differ by smoking status. This study compared the transcriptome of lung adenocarcinoma cell lines derived from S (n = 3) and NS (n = 3) each treated with vehicle (control), histone deacetylation inhibitor (trichostatin A) or DNA methylation inhibitor (5-aza-2'-deoxycytidine). Among 122 genes reexpressed following 5-aza-2'-deoxycytidine but not trichostatin A treatment in two or more cell lines (including 32 genes in S-only and 12 NS-only), methylation was validated for 80% (98/122 genes). After methylation analysis of 20 normal tissue samples and 14 additional non-small cell lung cancer cell lines (total 20), 39 genes frequently methylated in normal (>20%, 4/20) and 21 genes rarely methylated in non-small cell lung cancer (≤10%, 2/20) were excluded. The prevalence for methylation of the remaining 38 genes in lung adenocarcinomas from S (n = 97) and NS (n = 75) ranged from 8-89% and significantly differs between S and NS for CPEB1, CST6, EMILIN2, LAYN and MARVELD3 (P < 0.05). Furthermore, methylation of EMILIN2, ROBO3 and IGDCC4 was more prevalent in advanced (Stage II-IV, n = 61) than early (Stage I, n = 110) tumors. Knockdown of MARVELD3, one of the novel epigenetically silenced genes, by small interfering RNA significantly reduced anchorage-independent growth of lung cancer cells (P < 0.001). Collectively, this study has identified multiple, novel, epigenetically silenced genes in lung cancer and provides invaluable resources for the development of diagnostic and prognostic biomarkers.
Formation of Carbide‐Derived Carbon on β‐Silicon Carbide Whiskers (2005)

Carbon was synthesized on β‐SiC whiskers by extraction of Si atoms from SiC. In this study, three different elevated temperature extraction methods were used to remove Si atoms from SiC: treatments in either Cl 2 or HCl and vacuum decomposition. In all chlorination experiments and vacuum treatment at 1700°C, carbon preserved the original shape of SiC whiskers. At higher temperatures (2000°C), vacuum decomposition led to a distortion in the shape of the whiskers. High‐resolution transmission electron microscopy and Raman spectroscopy showed that the structure of carbide‐derived carbon depends on the Si extraction method and the process parameters. Chlorination of SiC resulted in the formation of mostly amorphous nanoporous carbon. High‐temperature treatment of SiC in HCl environment produced fullerene‐like structures, while high‐temperature vacuum decomposition resulted in the formation of graphite. Transmission electron microscopy studies of the carbon coating thickness produced in Cl 2 at various chlorination times revealed linear reaction kinetics at 700°C. Raman studies showed that the carbon structure became more ordered with increasing chlorination temperature. The results obtained demonstrate that by using the silicon extraction technique, one can precisely control the thickness and morphology of the carbon coating.
Biology of the BKPyV: An Update (2017)

The BK virus (BKPyV) is a member of the <i>Polyomaviridae</i> family first isolated in 1971. BKPyV causes frequent infections during childhood and establishes persistent infections with minimal clinical implications within renal tubular cells and the urothelium. However, reactivation of BKPyV in immunocompromised individuals may cause serious complications. In particular, with the implementation of more potent immunosuppressive drugs in the last decade, BKPyV has become an emerging pathogen in kidney and bone marrow transplant recipients where it often causes associated nephropathy and haemorrhagic cystitis, respectively. Unfortunately, no specific antiviral against BKPyV has been approved yet and the only therapeutic option is a modulation of the immunosuppressive drug regimen to improve immune control though it may increase the risk of rejection. A better understanding of the BKPyV life cycle is thus needed to develop efficient treatment against this virus. In this review, we provide an update on recent advances in understanding the biology of BKPyV.
Pegylated-interferon-λ treatment-induced peripheral interferon stimulated genes are associated with SARS-CoV-2 viral load decline despite delayed T cell response in older individuals (2022)

Abstract Interferons (IFNs) are antiviral cytokines induced very early after SARS-CoV-2 infection and are crucial for viral clearance, shaping immunity, and preventing the development of severe COVID-19. We previously demonstrated that a single injection of peginterferon-lambda1 (PEG-IFN-λ) accelerated viral clearance in COVID-19 patients. To determine if the rapid viral decline was mediated by enhanced immunity, we assessed in vivo responses to PEG-IFN-λ by single cell RNA sequencing and measured SARS-CoV-2-specific T cell and antibody responses between placebo and PEG-IFN-λ-treated patients. PEG-IFN-λ treatment induced interferon stimulated genes in peripheral immune cells expressing IFNLR1 , with plasmacytoid dendritic cells having the greatest response, followed by B cells. PEG-IFN-λ did not significantly affect SARS-CoV-2-specific antibody levels in plasma or the magnitude or functionality of virus-specific T cells. However, we identified a delayed T cell response in older adults, suggesting that PEG-IFN-λ can overcome the delay in adaptive immunity to accelerate viral clearance in patients most at risk for severe disease. Taken together, PEG-IFN-λ offers an early COVID-19 treatment option for outpatients to boost innate antiviral defenses without dampening peripheral SARS-CoV-2 adaptive immunity