Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Vascular Endothelial Growth Factor by Retinal Pigment Epithelial Cells Induced by Amyloid-β Is Depressed by an Endoplasmic Reticulum Stress Inhibitor

Purpose: Amyloid-β (Aβ) is a 36- to 43-amino-acid peptide that is a constituent of drusen, and it has been demonstrated to upregulate vascular endothelial growth factor (VEGF) expression by retinal pigment epithelial (RPE) cells. This study aimed to determine whether 4-phenylbutyl phosphonylacetate (PBA), a known endoplasmic reticulum (ER) stress inhibitor, can reduce Aβ-induced expression of VEGF in RPE cells. Methods: Aβ was added to the medium of regularly cultured or polarized ARPE-19 cells, a human RPE cell line, with or without PBA. The levels of VEGF and ER stress markers, namely GRP78/Bip, cleaved caspases 4 and 12 and GADD153/C-EBP homologous protein, were determined by enzyme-linked immunoassay, immunocytochemistry and Western blotting. Results: Exposure of ARPE-19 cells to Aβ induced GRP78/Bip expression and activated caspases 4 and 12; however, their expression was decreased by simultaneous exposure to PBA. Aβ increased the expression of VEGF both in regularly cultured and polarized ARPE-19 cells, but it was suppressed by PBA. PBA did not cause RPE cell apoptosis. Conclusion: Aβ has been suggested to be involved in the development of age-related macular degeneration; therefore, our findings suggest that drugs that target ER stress should be considered for the treatment of age-related macular degeneration.
Zero-knowledge using garbled circuits: how to prove non-algebraic statements efficiently

Zero-knowledge protocols are one of the fundamental concepts in modern cryptography and have countless applications. However, after more than 30 years from their introduction, there are only very few languages (essentially those with a group structure) for which we can construct zero-knowledge protocols that are efficient enough to be used in practice. In this paper we address the problem of how to construct efficient zero-knowledge protocols for generic languages and we propose a protocol based on Yao's garbled circuit technique. The motivation for our work is that in many cryptographic applications it is useful to be able to prove efficiently statements of the form e.g., "I know x s.t. y = SHA-256(x)" for a common input y (or other "unstructured" languages), but no efficient protocols for this task are currently known. It is clear that zero-knowledge is a subset of secure two-party computation (i.e., any protocol for generic secure computation can be used to do zero-knowledge). The main contribution of this paper is to construct an efficient protocol for the special case of secure two-party computation where only one party has input (like in the zero-knowledge case). The protocol achieves active security and is essentially only twice as slow as the passive secure version of Yao's garbled circuit protocol. This is a great improvement with respect to the cut-n-choose technique to make Yao's protocol actively secure, where the complexity grows linearly with the security parameter.
Recycling of a spent iron based catalyst for the complete oxidation of toluene: effect of palladium

Complete oxidation of volatile organic compound (toluene) was carried out to assess the property and activity of the palladium-spent iron based catalyst. The properties of the prepared catalysts were characterized by using the Brunauer–Emmett–Teller method and by conducting temperature-programmed reduction, X-ray diffraction, X-ray photoelectron spectroscopy and field emission transmission electron microscopy. The addition of palladium to the spent iron based catalyst pretreated with oxalic acid shifted the conversion curve for the total oxidation of toluene to lower temperature. An increase in the toluene conversion due to palladium was highly related to the easier lattice oxygen mobility of the catalysts. Instrumental analysis suggested the presence of a strong interaction between palladium and iron oxide species. Moreover, in the case of reducing the Pd/Fe catalyst with hydrogen, palladium accelerated the reducing iron oxides, subsequently decreasing the toluene conversion. As a result, the oxidation states of palladium and iron had an important effect on the catalytic activity.
Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8

Takashi Wada, Mikako Shirouzu, Takaho Terada, Yuki Kamewari, Sam-Yong Park, Jeremy R.H. Tame, Seiki Kuramitsu Shigeyuki Yokoyama* RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan 230-0045 RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo, Japan 679-5148 Graduate School of Integrated Science, Yokohama City University, Tsurumi, Yokohama, Japan 230-0045 Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan 560-0043 Graduate School of Science, University of Tokyo, Bunkyo, Tokyo, Japan 113-0033
Methodology to Support Semantic Resources Integration in the Construction Sector

Ontologies, taxonomies, and other semantic resources, are used in a variety of sectors to facilitate knowledge reuse and information exchange between people and applications. In recent years, the need to access multiple semantic resources has led to the development of a variety of projects and tools aiming at integrating existing resources. This paper describes the methodology used during the FUNSIEC project, to develop an open infrastructure for the European Construction sector (OSIECS). This infrastructure aims towards facilitating integration among Construction related semantic resources, providing a base for the development of a new generation of e-services for the domain.
Investigation of defect microstructures responsible for NBTI degradation using effective dipole moment extraction

The identification of the microstructure defects responsible of metal-oxide-silicon field effect transistor (MOSFET) reliability problems is important to understand, the physical mechanisms behind these problems. In this paper, the effective dipole moment of bond precursors that contribute to negative bias temperature instability (NBTI) permanent components is investigated, using the conventional charge pumping method (CCP). In addition, the contribution of the several precursors to the extracted effective dipole moment is modelled. The model is in agreement with the experimental data. The results show that the effective dipole moments responsible of NBTI permanent component correspond to Si-H and stretched Si-O bonds. The Si-H bond dipole moment clearly dominates at low stress electric field (Eox) and when their density is higher than that Si-O bond. While, the effective dipole moment of Si-O bonds is obviously observable at high stress electric field even with low density. However, for intermediate stress electric field, both effective dipole moments contribute and lead an inaccurate extraction. Moreover, the profiling of the effective dipole moment along the transistor channel, shows that Si-H and stretched Si-O bonds are mostly located in the vicinity of the LDD region.
The Pathway Tools software

MOTIVATION Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.
Microbubble distribution and incorporation in an ex-vivo perfused porcine

9 INTRODUCTION . 11 Basics of Ultrasound:. 13 US Imaging: . 15 Image Enhancement Principles and Techniques: . 16 Microwave ablation in clinical practice: . 18 Understanding microwave physics . 18 Ablative techniques for treating hepatic tumours: . 23 Characterisation of liver tumours using CEUS: . 24 Contrast-enhanced ultrasound in the preoperative, intraoperative and postoperative assessment of liver lesions: . 25 Contrast agents for the study of liver lesions: . 25 Types of microbubbles used in the assessment of liver lesion: . 34 Contrast-enhanced intraoperative ultrasound during percutaneous radiofrequency ablation: . 37 CHAPTER ONE . 40 MBs and US Image Enhancement. 40 Methods of producing microbubbles: . 43 Generations of microbubbles: . 44 Microbubble behaviour in US: . 45 Mechanical index: . 48 Microbubbles’ response relative to mechanical index: . 49 Image Enhancement: . 50
Quetol 651: Not just a low viscosity resin

Quetol 651, a low viscosity epoxy resin, is miscible with alcohols, acetone, and water. It is versatile and can be used as a single epoxide or mixed with other epoxides and anhydrides. The most important characteristic is that the addition of Quetol 651 to a formulation results in a lower viscosity embedding medium and allows for good detection of antigenic activity. Properly formulated and mixed resins containing Quetol 651 have excellent sectioning properties and good beam stability. The decrease in viscosity lends to lower specific gravity of the embedding medium and less interfering electron density between specimen elements resulting in better spatial resolution. New formulations and viscosity data are presented and compared to long used, embedding formulations and the extensive uses of Quetol 651 are reviewed. Microsc. Res. Tech. 79:50–57, 2016. © 2015 Wiley Periodicals, Inc.
Plasma Clozapine, Norclozapine, and the Clozapine:Norclozapine Ratio in Relation to Prescribed Dose and Other Factors: Data From a Therapeutic Drug Monitoring Service, 1993–2007

Therapeutic drug monitoring of plasma clozapine and of its principal plasma metabolite N-desmethylclozapine (norclozapine) (predose or “trough” sample) can help in monitoring adherence, in dose adjustment, and in minimizing the risk of toxicity. To obtain data to assist in the interpretation of analytical results, the results from a clozapine therapeutic drug monitoring service, 1993-2007, have been audited. There were 104,127 samples from 26,796 patients [18,750 (70%) men aged at time of first sample (median, range) 34 (10-89) years, and 7763 (30%) female aged 38 (12-90) years]. Clozapine was not detected (plasma concentration <0.01 mg/L) in 1.5% of samples (prescribed clozapine dose up to 900 mg/d). Plasma clozapine was either below 0.35 mg/L or greater than 0.60 mg/L in 42.5% and 28.4% of samples, respectively; in 0.4% samples plasma clozapine was 2.0 mg/L or more. Although plasma clozapine was broadly related to prescribed dose, there was much variation: 1.2% of samples had plasma clozapine >1.0 mg/L at prescribed clozapine doses up to 150 mg/d (76.2% < 0.35 mg/L), whereas 23.3% of samples had plasma clozapine < 0.35 mg/L at doses of 850 mg/d and over (18.0% > 1.0 mg/L). The highest plasma clozapine and norclozapine concentrations encountered were 4.95 and 2.45 mg/L, respectively. Although the median plasma clozapine:norclozapine ratio was 1.25 at plasma clozapine concentrations < 0.35 mg/L, the median ratio was 2.08 at plasma clozapine concentrations > 1.0 mg/L. Data (median, 10th-90th percentile) for both clozapine and norclozapine by prescribed clozapine dose band are useful in assessing partial adherence. Analysis of the plasma clozapine:norclozapine ratio by clozapine concentration provides clear evidence that clozapine N-demethylation becomes saturated at higher plasma clozapine concentrations and adds urgency to the requirement for dose adjustment should smoking habit change. A clozapine:norclozapine ratio greater then 2 suggests either a nontrough sample, or that clozapine N-demethylation has become saturated.
NOTCH1 Gain of Function in Germ Cells Causes Failure of Spermatogenesis in Male Mice

NOTCH1 is a member of the NOTCH receptor family, a group of single-pass trans-membrane receptors. NOTCH signaling is highly conserved in evolution and mediates communication between adjacent cells. NOTCH receptors have been implicated in cell fate determination, as well as maintenance and differentiation of stem cells. In the mammalian testis expression of NOTCH1 in somatic and germ cells has been demonstrated, however its role in spermatogenesis was not clear. To study the significance of NOTCH1 in germ cells, we applied a cre/loxP approach in mice to induce NOTCH1 gain- or loss-of function specifically in male germ cells. Using a Stra8-icre transgene we produced mice with conditional activation of the NOTCH1 intracellular domain (NICD) in germ cells. Spermatogenesis in these mutants was progressively affected with age, resulting in decreased testis weight and sperm count. Analysis of downstream target genes of NOTCH1 signaling showed an increased expression of Hes5, with a reduction of the spermatogonial differentiation marker, Neurog3 expression in the mutant testis. Apoptosis was significantly increased in mouse germ cells with the corresponding elevation of pro-apoptotic Trp53 and Trp63 genes' expression. We also showed that the conditional germ cell-specific ablation of Notch1 had no effect on spermatogenesis or male fertility. Our data suggest the importance of NOTCH signaling regulation in male germ cells for their survival and differentiation.
News Tuner: a simple interface for searching and browsing radio archives

We present in this paper a new Web-based application, called the News Tuner, for searching and browsing large radio archives. While popular search engines provide means for finding text and images, our approach combines semantic and acoustic search for efficient retrieval of audio documents. Semantic search allows the user to retrieve stories for a given concept, while acoustic search allows random access within stored audio files. Our experiments on over 1700 programs show that our method is effective at quickly retrieving stories that would be difficult to find otherwise. The News Tuner paradigm is intended primarily for news and talk radio programs, however it may be applied to browsing and searching any spoken word audio content
Conductive paper fabricated by layer-by-layer assembly of polyelectrolytes and ITO nanoparticles

A new salt-free approach was developed for fabricating conductive paper by layer-by-layer (LBL) assembly of conductive indium tin oxide (ITO) nanoparticles and polyelectrolytes onto wood fibers. Subsequent to the coating procedure, the fibers were manufactured into conductive paper using traditional paper making methods. The wood fibers were first coated with polyethyleneimine (PEI) and then LBL assembled with poly(sodium 4-styrenesulfonate) (PSS) and ITO for several bilayers. The surface charge intensity of both the ITO nanoparticles and the coated wood fibers were evaluated by measuring the ζ-potential of the nanoparticles and short fibers, respectively. The ITO nanoparticles were found to preferentially aggregate on defects on the fiber surfaces and formed interconnected paths, which led to the formation of conductive percolation paths throughout the whole paper. With ten bilayer coatings, the as-made paper was made DC conductive, and its σdc was measured to be 5.2 × 10−6 S cm−1 in the in-plane (IP) direction, while the conductivity was 1.9 × 10−8 S cm−1 in the through-the-thickness (TT) direction. The percolation phenomena in these LBL-assembled ITO-coated paper fibers was evaluated using scanning electron microscopy (SEM), current atomic force microscopy (I-AFM), and impedance measurements. The AC electrical properties are reported for frequencies ranging from 0.01 Hz to 1 MHz. A clear transition from insulating to conducting behavior is observed in the AC conductivity.
The 18 kDa Translocator Protein and Atherosclerosis in Mice Lacking Apolipoprotein E

© 2013 Dimitrova-Shumkovska et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The 18 kDa Translocator Protein and Atherosclerosis in Mice Lacking Apolipoprotein E
Principles of model checking

Our growing dependence on increasingly complex computer and software systems necessitates the development of formalisms, techniques, and tools for assessing functional properties of these systems. One such technique that has emerged in the last twenty years is model checking, which systematically (and automatically) checks whether a model of a given system satisfies a desired property such as deadlock freedom, invariants, and request-response properties. This automated technique for verification and debugging has developed into a mature and widely used approach with many applications. Principles of Model Checking offers a comprehensive introduction to model checking that is not only a text suitable for classroom use but also a valuable reference for researchers and practitioners in the field. The book begins with the basic principles for modeling concurrent and communicating systems, introduces different classes of properties (including safety and liveness), presents the notion of fairness, and provides automata-based algorithms for these properties. It introduces the temporal logics LTL and CTL, compares them, and covers algorithms for verifying these logics, discussing real-time systems as well as systems subject to random phenomena. Separate chapters treat such efficiency-improving techniques as abstraction and symbolic manipulation. The book includes an extensive set of examples (most of which run through several chapters) and a complete set of basic results accompanied by detailed proofs. Each chapter concludes with a summary, bibliographic notes, and an extensive list of exercises of both practical and theoretical nature.
Hormone Therapy for the Management of Menopausal Symptoms

Nearly 50 million women each year are projected to reach menopause by 2030. Many of these women will experience vasomotor symptoms such as night sweats and hot flashes as they enter the menopausal transition. Up until the release of the findings of the Women’s Health Initiative (WHI) studies, women were frequently prescribed hormone therapy (HT) to alleviate bothersome and sometimes debilitating menopausal symptoms as well as to prevent osteoporosis and coronary heart disease (CHD). Although the WHI studies were the first large, randomized, controlled trials that contradicted what was historically believed about the benefits of HT in postmenopausal women, important limitations including baseline demographics of WHI participants and investigation of only one HT strength/dosage form exist. HT may be a reasonable pharmacotherapy option for the management of menopausal symptoms following complete patient evaluation by experienced clinicians. Updated recommendations addressing management of menopausal symptoms, a new HT product containing the spironolactone-analogue drospirenone (DRSP), and discontinuation methods of HT are also discussed in this review.
Evaluation of Chemically-Sensitive Field-Effect Transistors for Detection of Organophosphorus Compounds

This study resulted in the design, fabrication, and evaluation of an interdigitated gate electrode ChemicallySensitive Field-Effect Transistor (CHEMFET). The electrical performance of the CHEMFET sensors coated with the following thin films was evaluated in frequency domain for detecting the gas concentration changes of organophosphorus compounds (diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP)) in the air: cobalt phthalocyanine, nickel phthalocyanine, lead phthalocyanine, copper phthalocyanine, 2-naphthol(1), succinylchloride, succinylcholine chloride, and L-histidine dihydrochloride. The change in the chemical state of a film was manifested as a change in the CHEMFET sensors' output response, when the CHEMFET sensor was excited with a pulse. The results showed the CHEMFET sensor coated with cobalt phthalocyanine produced consistent responses upon exposure, with respect to three concentrations of DIMP and DMMP, at two measurement temperatures. The resulted also revealed that the CHEMFET sensors coated with 2-naphthol(3), succinylchloride, and succinylcholine chloride had promising gas exposure
Ge-rich graded-index Si1-xGex racetrack resonators for long-wave infrared photonics

Mid-infrared racetrack resonators are demonstrated working at 8μm wavelength. The devices are based on a graded SiGe platform providing low propagation loss on a large wavelength range in the mid-IR. Different resonators designs have been fabricated, with varying gap distances in the directional coupler. Q factors of more than 3000 have been experimentally demonstrated. These results pave the way towards compact mid-IR sensors or efficient active devices.
Spatial variation of the cooling lines in the reflection nebula NGC 7023

Context. The north-west photo-dissociation region (PDR) in the reflection nebula NGC 7023 displays a complex structure. Filament-like condensations at the edge of the cloud can be traced via the emission of the main cooling lines, offering a great opportunity to study the link between the morphology and energetics of these regions.Aims. We study the spatial variation of the far-infrared fine-structure lines of [C ii] (158 μm) and [O i] (63 and 145 μm). These lines trace the local gas conditions across the PDR. We also compare their emission with molecular tracers including rotational and ro-vibrational lines of H2 and high-rotational lines of CO.Methods. We used observations from the Herschel/PACS instrument to map the spatial distribution of these fine-structure lines. The observed region covers a square area of about 110″ × 110″ with an angular resolution that varies from 4′′ to 11′′. We compared this emission with ground-based and Spitzer observations of H2 lines, Herschel/SPIRE observations of CO lines, and Spitzer/IRAC 3.6 μm images that trace the emission of polycyclic aromatic hydrocarbons. We used a PDR code to model the [O i]145 μm line and infer the physical conditions in the region.Results. The [C ii] (158 μm) and [O i] (63 and 145 μm) lines arise from the warm cloud surface where the PDR is located and the gas is warm, cooling the region. We find that although the relative contribution to the cooling budget over the observed region is dominated by [O i]63 μm (>30%), H2 contributes significantly in the PDR (~35%), as does [C ii]158 μm outside the PDR (30%). Other species contribute little to the cooling ([O i]145 μm 9%, and CO 4%). Enhanced emission of these far-infrared atomic lines trace the presence of condensations, where high-excitation CO rotational lines and dust emission in the submillimetre are detected as well. The [O i] maps resolve these condensations into two structures and show that the peak of [O i] is slightly displaced from the molecular H2 emission. The size of these structures is about 8″ (0.015 pc) and in surface cover about 9% of the PDR emission. We have tested whether the density profile and peak densities that were derived in previous studies to model the dust and molecular emission can predict the [O i]145 μm emission. We find that the model with a peak density of 106 cm-3, and 2 × 104−5 cm-3 in the oxygen emitting region predicts an [O i]145 μm line that is only 30% lower than the observed emission. Finally, we did not detect emission from [N ii]122 μm, suggesting that the cavity is mostly filled with non-ionised gas.