gebhart/patrepeval huggingface dataset:
Myocardial and blood T1 quantification in normal volunteers at 3T (2011)

T1 mapping is a novel quantitative method for myocardial tissue characterization. Reference values of myocardium and blood have been established at 1.5T (Messroghli, MRM, 2007). CMR at 3T is a rapidly maturing field, and T1 values generally increase with magnetic field strength, making it necessary to establish new reference values at this higher field strength. The aim of this study is to establish pre- and post-contrast myocardium and blood reference T1 values at 3T.
Comparison of approaches for rational siRNA design leading to a new efficient and transparent method (2007)

Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver operating characteristics (ROC) and correlation analyses, the best programs were BioPredsi, ThermoComposition and DSIR. We also studied individual parameters that significantly and consistently correlated with siRNA efficacy in different databases. As a result of this work we developed a new method which utilizes linear regression fitting with local duplex stability, nucleotide position-dependent preferences and total G/C content of siRNA duplexes as input parameters. The new method's discrimination ability of efficient and inefficient siRNAs is comparable with that of the best methods identified, but its parameters are more obviously related to the mechanisms of siRNA action in comparison with BioPredsi. This permits insight to the underlying physical features and relative importance of the parameters. The new method of predicting siRNA efficiency is faster than that of ThermoComposition because it does not employ time-consuming RNA secondary structure calculations and has much less parameters than DSIR. It is available as a web tool called 'siRNA scales'.
ChemInform Abstract: Novel Catalysts for Thiophene Synthesis at Lower Temperatures (1999)

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.
Supplementary Data from Comprehensive Molecular Profiling of Olfactory Neuroblastoma Identifies Potentially Targetable <i>FGFR3</i> Amplifications (2023)

&lt;p&gt;Figure S1. (A) Overexpression of p53 in olfactory neuroblastoma tumor harboring an inactivating TP53 mutation. (B) Representative example of p53 expression in olfactory neuroblastoma tumor lacking TP53 mutation. Immunohistochemistry, 400x magnification. figure S2. (A) Nuclear localization of beta catenin in olfactory neuroblastoma tumor harboring an activating CTNNB1 mutation. (B) Representative example of membranous beta catenin expression in olfactory neuroblastoma tumor lacking CTNNB1 mutation. Immunohistochemistry, 400x magnification. Table S1: Immunohistochemistry protocols Table S2: Clinicopathologic features of olfactory neuroblastoma cohort Table S3: DNA sequencing statistics for profiled olfactory neuroblastoma samples Table S4: Prioritized somatic nonsynonymous mutations in olfactory neuroblastoma cases identified by next generation sequencing Table S5: FGFR3 copy number in olfactory neuroblastomas by next generation sequencing Table S6. Targeted multiplexed PCR based RNA sequencing statistics for ONB samples&lt;/p&gt;
The Antitumor Cytotoxic Response: If the Killer Cells Play the Music, the Microenvironmental Hypoxia Plays the Tune (2020)

The immune system is a potent defense mechanism regulating tumor development and progression. However, immune cells are often functionally compromised in cancer patients, and tumor rejection does not follow successful induction of a CTL response. This is, in part, due to the existing conflict between the tumor system and an unfavorable tumor microenvironment (TME) that is able to neutralize or paralyze the immune system of the host. The recent advances in the field of immune checkpoint inhibitors have changed the focus from targeting the tumor to targeting T lymphocytes. It has been well established that the TME and associated multiple factors contribute to the failures in cancer therapies, including immunotherapy. In this regard, hypoxia, which is a hallmark of solid tumors, is strongly associated with advanced disease stages and poor clinical outcomes. Hypoxia plays a crucial role in tumor promotion and immune escape by conferring tumor resistance, immunosuppression, and tumor heterogeneity, which contribute to the generation of diverse cancer invasion programs and enhanced stroma plasticity. Tumor hypoxic stress interferes with the mesenchymal transition EMT, conferring to cancer cells a high degree of plasticity and the capacity to escape from immune surveillance. Tumors have been also shown to take advantage of hypoxic conditions that impede normal cells. Thus, tumor progression may be mediated by hypoxia-induced phenotypic changes and subsequent clonal selection of malignant cells that overexpress hypoxia-responsive molecules, such as HIF-1α. Currently, the resistance of tumor cells to cell-mediated cytotoxicity remains a drawback in the immunotherapy of cancer, and its molecular basis is poorly understood. In this review, I focus on hypoxia as a key process that evolved in the TME, and I discuss how solid tumors use hypoxic stress as a potent saboteur of the antitumor immune reaction by shaping a compromised cytotoxic cell function through the alteration of tumor target susceptibility to cell-mediated cytotoxicity. Exploiting hypoxia-associated tumor escape capacities may hold promise for attenuating tumor heterogeneity and plasticity, overcoming alteration of antitumor cytotoxic response and improving its effectiveness in cancer patients.
Modular Inorganic Nanocomposites by Conversion of Nanocrystal Superlattices (2010)

Inorganic nanocomposites have been prepared by assembling colloidal nanocrystals and then replacing the organic ligands with precursors to an inorganic matrix phase. Separate synthesis and processing of the nanocrystal and matrix phases allows complete compositional modularity and retention of the superlattice morphologies for sphere (see scheme; top) or rod (bottom) assemblies.
Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway (2020)

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.&lt;br&gt;
Visual memes in social media (2011)

We propose visual memes, or frequently reposted short video segments, for tracking large-scale video remix in social media. Visual memes are extracted by novel and highly scalable detection algorithms that we develop, with over 96% precision and 80% recall. We monitor real-world events on YouTube, and we model interactions using a graph model over memes, with people and content as nodes, and meme postings as links. This allows us to define several measures of influence. These abstractions, using more than two million video shots from several large-scale event datasets, enable us to quantify and efficiently extract several important observations: over half of the videos contain re-mixed content, which appears rapidly; video view counts, particularly high ones, are poorly correlated with the virality of content; the influence of traditional news media versus citizen journalists varies from event to event; iconic single images of an event are easily extracted; and content that will have long lifespan can be predicted within a day after it first appears. Visual memes can be applied to a number of social media scenarios: brand monitoring, social buzz tracking, ranking content and users, among others.
Long-Term Culture of Functional Liver Tissue: Three-Dimensional Coculture of Primary Hepatocytes and Stellate Cells (2003)

One of the greatest challenges in the attempt to create functional liver tissue in vitro is the maintenance of hepatocyte-specific functions. The pharmaceutical industry has long awaited the development of engineered liver tissue, which could represent a long-term, inducible, high-fidelity model for high-throughput screening of new drug compounds. It is also anticipated that such engineered models could one day be used in liver transplants, where replacement is limited by chronic donor shortages. As isolated hepatocytes dedifferentiate rapidly in culture the use of hepatocytes in long-term studies has proved to be a difficult challenge. Here we report a system of rat hepatocytes cocultured with primary rat hepatic stellate cells on a biodegradable poly(DL-lactic acid) substratum. These coculture conditions were found to encourage the rapid self-organization of three-dimensional spheroids. The spheroids formed exhibit hepatocyte-specific functionality (CYP-450 activity and albumin secretion) after almost 2 months in static culture.
Self-Assembly of Pyrrole–Ferrocene Hybrids, Determined Inter Alia by a New Chemically Induced Electrospray Mass Spectrometry Technique (1998)

An interesting example of a noncovalently linked organometallic superstructure (shown right) is obtained from the self-assembly of tetrapyrrole-substituted ferrocene. As a result of the self-associating properties of the pyrrole–ester subunits, this system forms ribbon-like infinite chains in the solid state and small but well-characterized oligomers in organic solvents. Selective oxidation of the ferrocene moiety provides a cationic ferrocenium species amenable to electrospray mass spectrometric analysis.
The α Subunit of the Granulocyte-Macrophage Colony-stimulating Factor Receptor Interacts with c-Kit and Inhibits c-Kit Signaling (2006)

The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) regulates hematopoiesis and the function of mature host defense cells through the GM-CSF receptor (GMR), which is composed of alpha (alphaGMR) and beta (betaGMR) subunits. Stem cell factor is another important hematopoietic cytokine that signals through c-Kit, a receptor tyrosine kinase, and regulates hematopoietic stem cell maintenance and erythroid development. Like other cytokine receptors, GMR and c-Kit are generally deemed as independent adaptor molecules capable of transducing cytokine-specific signals. We found that the alphaGMR directly interacts with c-Kit and that the interaction is mediated by the cytoplasmic domains. Furthermore, alphaGMR inhibited c-Kit auto-phosphorylation induced by the ligand stem cell factor. Consistent with the inhibitory effect, the expression of alphaGMR was suppressed in cells whose viability was dependent on c-Kit signaling. In contrast, the alternatively spliced alpha2 isoform of the alphaGMR could not inhibit c-Kit signaling, providing a rationale for the existence of the alpha2 isoform. Our results suggest that in addition to having the commonly appreciated roles in cytokine signal transduction, the receptors alphaGMR and c-Kit could interact to coordinate their signal initiation.
A Subset of Mouse Colonic Goblet Cells Expresses the Bitter Taste Receptor Tas2r131 (2013)

The concept that gut nutrient sensing involves taste receptors has been fueled by recent reports associating the expression of taste receptors and taste-associated signaling molecules in the gut and in gut-derived cell lines with physiological responses induced by known taste stimuli. However, for bitter taste receptors (Tas2rs), direct evidence for their functional role in gut physiology is scarce and their cellular expression pattern remained unknown. We therefore investigated Tas2r expression in mice. RT-PCR experiments assessed the presence of mRNA for Tas2rs and taste signaling molecules in the gut. A gene-targeted mouse strain was established to visualize and identify cell types expressing the bitter receptor Tas2r131. Messenger RNA for various Tas2rs and taste signaling molecules were detected by RT-PCR in the gut. Using our knock-in mouse strain we demonstrate that a subset of colonic goblet cells express Tas2r131. Cells that express this receptor are absent in the upper gut and do not correspond to enteroendocrine and brush cells. Expression in colonic goblet cells is consistent with a role of Tas2rs in defense mechanisms against potentially harmful xenobiotics.
A Crash Course in Calcium Channels (2017)

Much progress has been made in understanding the molecular physiology and pharmacology of calcium channels. Recently, there have been tremendous advances in learning about calcium channel structure and function through crystallography and cryo-electron microscopy studies. Here, I will give an overview of our knowledge about calcium channels, and highlight two recent studies that give important insights into calcium channel structure.
Design of a multichannel photonic crystal dielectric laser accelerator (2020)

To be useful for most scientific and medical applications, compact particle accelerators will require much higher average current than enabled by current architectures. For this purpose, we propose a photonic crystal architecture for a dielectric laser accelerator, referred to as a multi-input multi-output silicon accelerator (MIMOSA), that enables simultaneous acceleration of multiple electron beams, increasing the total electron throughput by at least 1 order of magnitude. To achieve this, we show that the photonic crystal must support a mode at the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="m1"> <mml:mrow> <mml:mi mathvariant="italic">Γ</mml:mi> </mml:mrow> </mml:math> point in reciprocal space, with a normalized frequency equal to the normalized speed of the phase-matched electron. We show that the figure of merit of the MIMOSA can be inferred from the eigenmodes of the corresponding infinitely periodic structure, which provides a powerful approach to design such devices. Additionally, we extend the MIMOSA architecture to electron deflectors and other electron manipulation functionalities. These additional functionalities, combined with the increased electron throughput of these devices, permit all-optical on-chip manipulation of electron beams in a fully integrated architecture compatible with current fabrication technologies, which opens the way to unconventional electron beam shaping, imaging, and radiation generation.
Elastic shared resource scheduling SOC interconnect architecture for real-time system (2006)

We developed an elastic shared resource scheduling SoC interconnect architecture for SoCs that execute various real-time tasks in parallel. It provides both reliability for the hard real-time executions and an optimized overall performance. To meet these requirements, we introduced a hybrid-type scheduling architecture with a static scheduling block for the reliability and a dynamic scheduling block for the efficiency improvement. The dynamic scheduling block taking into consideration the progress of each task makes use of the shared resource utilizations of some tasks that have timing margins for deadlines, and optimizes the overall system's performance. We evaluated the architecture using simple model simulations and benchmarks for multimedia operations. The benchmarks show that the architecture improves the system performance by 23%. This is suitable for consumer-oriented embedded SoCs with severe restrictions on their real-time executions and system costs
Trade-Off Relationship between Si Recess and Defect Density Formed by Plasma-Induced Damage in Planar Metal–Oxide–Semiconductor Field-Effect Transistors and the Optimization Methodology (2011)

Physical damage induced by high-energy ion bombardment during plasma processing is characterized from the viewpoint of the relationship between surface-damaged layer (silicon loss) and defect site underneath the surface. Parameters for plasma-induced damage (PID), Si recess depth (dR) and residual (areal) defect density after wet-etch treatment (Ndam), are calculated on the basis of a modified range theory, and the trade-off relationship between dR and Ndam is presented. We also model their effects on device parameters such as off-state leakage (Ioff) and drain saturation current (Ion) of n-channel metal–oxide–semiconductor field effect transistors (MOSFETs). Based on the models, we clarify the relationship among plasma process parameters (ion energy and ion flux), dR, Ndam, Ioff, and Ion. Then we propose a methodology optimizing ion energy and ion flux under the constraints defined by device specifications Ioff and Ion, via dR and Ndam. This procedure is regarded as so-called optimization problems. The proposed methodology is applicable to optimizing plasma parameters that minimize degradation of MOSFET performance by PID.
Fault tolerance techniques for wireless ad hoc sensor networks (2003)

Embedded sensor network is a system of nodes, each equipped with a certain amount of sensing, actuating, computation, communication, and storage resources. One of the key prerequisites for effective and efficient embedded sensor systems is development of low cost, low overhead, high resilient fault-tolerance techniques. Cost sensitivity implies that traditional double and triple redundancies are not adequate solutions for embedded sensor systems due to their high cost and high energy-consumption. We address the problem of embedded sensor network-fault-tolerance by proposing heterogeneous back-up scheme, where one type of resource is substituted with another. First we propose a broad spectrum of heterogeneous fault-tolerance techniques for sensor networks including the ones where communication and sensing are mutually backing up each other. Then, we focus our attention on two specific approaches where we back-up one type of sensors with another type of sensor. In the first, we assume faults that manifest through complete malfunctioning and in the second, we assume sensors where fault manifest through high level of error.
Policy recommendations on ecotourism for the countries of the Danube region (2021)

EcoVelo Tour Project (Fostering enhanced ecotourism planning along the Eurovelo cycle route network in the Danube region (DTP-055-2.2) along with the EuroVelo 6, 11 and 13 cycling routes at the Danube develops ecotourism and cycling tourism and ecotourism. The project aims to exploit synergies with the EuroVelo network, communicate effectively about ecotourism in the region, ensure the preservation of cultural and natural assets including biodiversity, landscape elements, and air quality while developing local ecotourism strategies. Ecotourism is a new form of travel that seeks to reduce the negative effects of mass tourism in the 20th century. The International Union for Conservation of Nature and Natural Resources defined ecotourism as "environmentally responsible visiting of relatively unspoilt natural areas, in order to enjoy and appreciate nature (and any accompanying cultural features - both past and present), that promotes conservation, has low negative visitor impact, and provides for beneficially active socio-economic involvement of local populations" (Hector Ceballos-Lascurain, Tourism, Ecotourism and Protected Areas, 1996). Ecotourism is thus a complex concept that emphasizes the importance of preserving local values, the natural environment and culture. This study builds upon the research on ecotourism in the Danube region carried out by national stakeholders from Austria, Bulgaria, Germany, Hungary, Romania, Serbia, and Slovakia. The study aims to provide a helping hand for project partners in formulating policy recommendations at national as well as regional levels. In addition, this study also provides professional support and exchange of experiences to those countries where ecotourism is not yet on an advanced level.
ChemInform Abstract: Total Synthesis of Taxusin: An Initial Step Toward Taxol Synthesis (1992)

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.
Data from Dasatinib (BMS-354825) Selectively Induces Apoptosis in Lung Cancer Cells Dependent on Epidermal Growth Factor Receptor Signaling for Survival (2023)

&lt;div&gt;Abstract&lt;p&gt;Mutations of the epidermal growth factor receptor (EGFR) selectively activate Akt and signal transducer and activator of transcription (STAT) pathways that are important in lung cancer cell survival. Src family kinases can cooperate with receptor tyrosine kinases to signal through downstream molecules, such as phosphatidylinositol 3-kinase/PTEN/Akt and STATs. Based on the importance of EGFR signaling in lung cancer, the known cooperation between EGFR and Src proteins, and evidence of elevated Src activity in human lung cancers, we evaluated the effectiveness of a novel orally bioavailable Src inhibitor dasatinib (BMS-324825) in lung cancer cell lines with defined EGFR status. Here, we show that cell fate (death versus growth arrest) in lung cancer cells exposed to dasatinib is dependent on EGFR status. In cells with EGFR mutation that are dependent on EGFR for survival, dasatinib reduces cell viability through the induction of apoptosis while having minimal apoptotic effect on cell lines with wild-type (WT) EGFR. The induction of apoptosis in these EGFR-mutant cell lines corresponds to down-regulation of activated Akt and STAT3 survival proteins. In cell lines with WT or resistant EGFR mutation that are not sensitive to EGFR inhibition, dasatinib induces a G&lt;sub&gt;1&lt;/sub&gt; cell cycle arrest with associated changes in cyclin D and p27 proteins, inhibits activated FAK, and prevents tumor cell invasion. Our results show that dasatinib could be effective therapy for patients with lung cancers through disruption of cell growth, survival, and tumor invasion. Our results suggest EGFR status is important in deciding cell fate in response to dasatinib. (Cancer Res 2006; 66(11): 5542-8)&lt;/p&gt;&lt;/div&gt;