Miracle-dz/UniFAR-FTUs huggingface dataset:
Rare-Earth Doped Aluminum Oxide Lasers for Silicon Photonics by Emir

A reliable and CMOS-compatible deposition process for amorphous Al2O3 based active photonic components has been developed. Al2O3 films were reactively sputtered, where process optimization was achieved at a temperature of 250 C, with a deposition rate of 8.5 nm/min. With a surface roughness of 0.3 nm over a 1 μm area, background optical losses as low as 0.1 dB/cm were obtained for undoped films. The development of active photonics components has been realized by use of rare-earth metals as dopants. By cosputtering aluminum and erbium targets, Er dopants at concentrations on the order of 1.0x10 cm have been added to the Al2O3 host medium. Resulting Er3+:Al2O3 films have been characterized, and over 3 dB/cm absorption has been measured over a 20 nm bandwidth. Following the material development, distributed Bragg reflector lasers were designed and fabricated in a CMOS foundry. The laser cavity was created by introducing gratings on either side of a Si3N4 waveguide. Er 3+:Al2O3 was deposited in SiO2 trenches on top of the Si3N4 layer, eliminating the need for any subsequent etching steps. On-chip laser output of 3.9 μW has been recorded at a wavelength of 1533.4 nm, with a side mode suppression ratio over 38.9 dB. Thesis Supervisor: Leslie A. Kolodziejski Title: Professor of Electrical Engineering and Computer Science
Applications of Alternative Nucleases in the Age of CRISPR/Cas9

Breakthroughs in the development of programmable site-specific nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases (MNs), and most recently, the clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (including Cas9) have greatly enabled and accelerated genome editing. By targeting double-strand breaks to user-defined locations, the rates of DNA repair events are greatly enhanced relative to un-catalyzed events at the same sites. However, the underlying biology of each genome-editing nuclease influences the targeting potential, the spectrum of off-target cleavages, the ease-of-use, and the types of recombination events at targeted double-strand breaks. No single genome-editing nuclease is optimized for all possible applications. Here, we focus on the diversity of nuclease domains available for genome editing, highlighting biochemical properties and the potential applications that are best suited to each domain.
The Crystal Structures of Substrate and Nucleotide Complexes of Enterococcus faecium Aminoglycoside-2′′-Phosphotransferase-IIa [APH(2′′)-IIa] Provide Insights into Substrate Selectivity in the APH(2′′) Subfamily

ABSTRACT Aminoglycoside-2′′-phosphotransferase-IIa [APH(2′′)-IIa] is one of a number of homologous bacterial enzymes responsible for the deactivation of the aminoglycoside family of antibiotics and is thus a major component in bacterial resistance to these compounds. APH(2′′)-IIa produces resistance to several clinically important aminoglycosides (including kanamycin and gentamicin) in both gram-positive and gram-negative bacteria, most notably in Enterococcus species. We have determined the structures of two complexes of APH(2′′)-IIa, the binary gentamicin complex and a ternary complex containing adenosine-5′-(β,γ-methylene)triphosphate (AMPPCP) and streptomycin. This is the first crystal structure of a member of the APH(2′′) family of aminoglycoside phosphotransferases. The structure of the gentamicin-APH(2′′)-IIa complex was solved by multiwavelength anomalous diffraction methods from a single selenomethionine-substituted crystal and was refined to a crystallographic R factor of 0.210 (R free, 0.271) at a resolution of 2.5 Å. The structure of the AMPPCP-streptomycin complex was solved by molecular replacement using the gentamicin-APH(2′′)-IIa complex as the starting model. The enzyme has a two-domain structure with the substrate binding site located in a cleft in the C-terminal domain. Gentamicin binding is facilitated by a number of conserved acidic residues lining the binding cleft, with the A and B rings of the substrate forming the majority of the interactions. The inhibitor streptomycin, although binding in the same pocket as gentamicin, is orientated such that no potential phosphorylation sites are adjacent to the catalytic aspartate residue. The binding of gentamicin and streptomycin provides structural insights into the substrate selectivity of the APH(2′′) subfamily of aminoglycoside phosphotransferases, specifically, the selectivity between the 4,6-disubstituted and the 4,5-disubstituted aminoglycosides.
Consolidating Heterogeneous Enterprise Data for Named Entity Linking and Web Intelligence

Linking named entities to structured knowledge sources paves the way for state-of-the-art Web intelligence applications which assign sentiment to the correct entities, identify trends, and reveal relations between organizations, persons and products. For this purpose this paper introduces Recognyze, a named entity linking component that uses background knowledge obtained from linked data repositories, and outlines the process of transforming heterogeneous data silos within an organization into a linked enterprise data repository which draws upon popular linked open data vocabularies to foster interoperability with public data sets. The presented examples use comprehensive real-world data sets from Orell Fussli Business Information, Switzerland's largest business information provider. The linked data repository created from these data sets comprises more than nine million triples on companies, the companies' contact information, key people, products and brands. We identify the major challenges of tapping into such sources for named entity linking, and describe required data pre-processing techniques to use and integrate such data sets, with a special focus on disambiguation and ranking algorithms. Finally, we conduct a comprehensive evaluation based on business news from the New Journal of Zurich and AWP Financial News to illustrate how these techniques improve the performance of the Recognyze named entity linking component.
Graphics Tools for the Generation of Large Scale Urban Scenes

The acquisition of 3D city and landscape models has been a topic of major interest within the photogrammetric community and a number of algorithms became available both for the automatic and semiautomatic data collection. Usually, these 3D models are used for visualisation in order to generate realistic scenes and animations e.g. for planning and navigation purposes. Such real-time visualisations of artificial or real-word scenes are one of the main goals in computer graphics. Due to the rapid developments in that field, realistic visualisations are feasible even for complex and area covering 3D datasets and are integrated in an increasing number of applications. However, the benefit of applying computer graphics tools within photogrammetric data processing is not limited to the visualisation and presentation of 3D geodata. As it will be demonstrated within the paper, also photogrammetric data collection can take considerable advantage of a direct integration of these tools for the generation of large scale urban scenes.
Motives for volunteering are associated with mortality risk in older adults.

OBJECTIVE The purpose of this study is to examine the effects of motives for volunteering on respondents' mortality risk 4 years later. METHODS Logistic regression analysis was used to examine whether motives for volunteering predicted later mortality risk, above and beyond volunteering itself, in older adults from the Wisconsin Longitudinal Study. Covariates included age, gender, socioeconomic variables, physical, mental, and cognitive health, health risk behaviors, personality traits, received social support, and actual volunteering behavior. RESULTS Replicating prior work, respondents who volunteered were at lower risk for mortality 4 years later, especially those who volunteered more regularly and frequently. However, volunteering behavior was not always beneficially related to mortality risk: Those who volunteered for self-oriented reasons had a mortality risk similar to nonvolunteers. Those who volunteered for other-oriented reasons had a decreased mortality risk, even in adjusted models. CONCLUSIONS This study adds to the existing literature on the powerful effects of social interactions on health and is the first study to our knowledge to examine the effect of motives on volunteers' subsequent mortality. Volunteers live longer than nonvolunteers, but this is only true if they volunteer for other-oriented reasons.
Mfn2 downregulation in excitotoxicity causes mitochondrial dysfunction and delayed neuronal death

Mitochondrial fusion and fission is a dynamic process critical for the maintenance of mitochondrial function and cell viability. During excitotoxicity neuronal mitochondria are fragmented, but the mechanism underlying this process is poorly understood. Here, we show that Mfn2 is the only member of the mitochondrial fusion/fission machinery whose expression is reduced in in vitro and in vivo models of excitotoxicity. Whereas in cortical primary cultures, Drp1 recruitment to mitochondria plays a primordial role in mitochondrial fragmentation in an early phase that can be reversed once the insult has ceased, Mfn2 downregulation intervenes in a delayed mitochondrial fragmentation phase that progresses even when the insult has ceased. Downregulation of Mfn2 causes mitochondrial dysfunction, altered calcium homeostasis, and enhanced Bax translocation to mitochondria, resulting in delayed neuronal death. We found that transcription factor MEF2 regulates basal Mfn2 expression in neurons and that excitotoxicity‐dependent degradation of MEF2 causes Mfn2 downregulation. Thus, Mfn2 reduction is a late event in excitotoxicity and its targeting may help to reduce excitotoxic damage and increase the currently short therapeutic window in stroke.
POSTER: A footprint of third-party tracking on mobile web

In this paper, we investigate the footprints of third-party tracking on the mobile web. The survey of 100 popular mobile versions of web applications indicates that third-party tracking is also prevalent on mobile web. The results show that 62 sites are tracking users' activities on mobile web and Google Analytics is the most widespread tracker on mobile web. We believe that this study will help raise awareness about the tracking situation on the mobile web side.
VERY DEEP NETWORKS VIA VOLUME CONSERVATION

Recently, very deep neural networks set new records across many application domains, like Residual Networks at the ImageNet challenge and Highway Networks at language processing tasks. We expect further excellent performance improvements in different fields from these very deep networks. However these networks are still poorly understood, especially since they rely on non-standard architectures. In this contribution we analyze the learning dynamics which are required for successfully training very deep neural networks. For the analysis we use a symplectic network architecture which inherently conserves volume when mapping a representation from one to the next layer. Therefore it avoids the vanishing gradient problem, which in turn allows to effectively train thousands of layers. We consider highway and residual networks as well as the LSTM model, all of which have approximately volume conserving mappings. We identified two important factors for making deep architectures working: (1) (near) volume conserving mappings through x = x+f(x) or similar (cf. avoiding the vanishing gradient); (2) Controlling the drift effect, which increases/decreases x during propagation toward the output (cf. avoiding bias shifts);
Production of the Main Celiac Disease Autoantigen by Transient Expression in Nicotiana benthamiana

Celiac Disease (CD) is a gluten sensitive enteropathy that remains widely undiagnosed and implementation of massive screening tests is needed to reduce the long term complications associated to untreated CD. The main CD autoantigen, human tissue transglutaminase (TG2), is a challenge for the different expression systems available since its cross-linking activity affects cellular processes. Plant-based transient expression systems can be an alternative for the production of this protein. In this work, a transient expression system for the production of human TG2 in Nicotiana benthamiana leaves was optimized and reactivity of plant-produced TG2 in CD screening test was evaluated. First, a subcellular targeting strategy was tested. Cytosolic, secretory, endoplasmic reticulum (C-terminal SEKDEL fusion) and vacuolar (C-terminal KISIA fusion) TG2 versions were transiently expressed in leaves and recombinant protein yields were measured. ER-TG2 and vac-TG2 levels were 9- to 16-fold higher than their cytosolic and secretory counterparts. As second strategy, TG2 variants were co-expressed with a hydrophobic elastin-like polymer (ELP) construct encoding for 36 repeats of the pentapeptide VPGXG in which the guest residue X were V and F in ratio 8:1. Protein bodies (PB) were induced by the ELP, with a consequent two-fold-increase in accumulation of both ER-TG2 and vac-TG2. Subsequently, ER-TG2 and vac-TG2 were produced and purified using immobilized metal ion affinity chromatography. Plant purified ER-TG2 and vac-TG2 were recognized by three anti-TG2 monoclonal antibodies that bind different epitopes proving that plant-produced antigen has immunochemical characteristics similar to those of human TG2. Lastly, an ELISA was performed with sera of CD patients and healthy controls. Both vac-TG2 and ER-TG2 were positively recognized by IgA of CD patients while they were not recognized by serum from non-celiac controls. These results confirmed the usefulness of plant-produced TG2 to develop screening assays. In conclusion, the combination of subcellular sorting strategy with co-expression with a PB inducing construct was sufficient to increase TG2 protein yields. This type of approach could be extended to other problematic proteins, highlighting the advantages of plant based production platforms.
A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known enzymes, many of them acting in metabolism, providing opportunities to directly connect intermediary metabolism with posttranscriptional gene regulation. We mapped the RNA targets for 13 proteins identified in this screen and found that they were associated with distinct groups of mRNAs, some of them coding for functionally related proteins. We also found that overexpression of the enzyme Map1 negatively affects the expression of experimentally defined mRNA targets. Our results suggest that many proteins may associate with mRNAs and possibly control their fates, providing dense connections between different layers of cellular regulation.
Interactive manipulation of rigid body simulations

Physical simulation of dynamic objects has become commonplace in computer graphics because it produces highly realistic animations. In this paradigm the animator provides few physical parameters such as the objects' initial positions and velocities, and the simulator automatically generates realistic motions. The resulting motion, however, is difficult to control because even a small adjustment of the input parameters can drastically affect the subsequent motion. Furthermore, the animator often wishes to change the end-result of the motion instead of the initial physical parameters. We describe a novel interactive technique for intuitive manipulation of rigid multi-body simulations. Using our system, the animator can select bodies at any time and simply drag them to desired locations. In response, the system computes the required physical parameters and simulates the resulting motion. Surface characteristics such as normals and elasticity coefficients can also be automatically adjusted to provide a greater range of feasible motions, if the animator so desires. Because the entire simulation editing process runs at interactive speeds, the animator can rapidly design complex physical animations that would be difficult to achieve with existing rigid body simulators.
Interaction interfaces-towards a scientific foundation of a methodological usage of message sequence charts

We introduce the formal notion of an interaction interface. Its purpose is to specify formally the interaction between two or more components that co-operate as subsystems of a distributed system. We suggest the use of interaction interfaces for the description not of the behaviour of a single component in isolation but of the interface, the co-operation, between two or more components that are interacting within a distributed system. Typical examples are the interaction between an embedded system and its environment or the interaction between a sender and a receiver in a communication protocol. An interaction interface can be formally described by predicates characterising sets of interaction histories. We understand the specification of interaction histories as a typical step in system development that prepares the decomposition of a system into interacting subcomponents. After fixing the distribution structure of the system, an interaction interface is worked out that describes how the introduced subcomponents interact. In a successive development step we systematically derive the individual component specifications from the interface description. We show how such an interaction interface can be decomposed systematically into component specifications.
Maximum Likelihood Estimation of a Unit Root Bilinear Model with an Application to Prices

We estimate a unit root bilinear process using the Maximum Likelihood method with log-likelihood function constructed by means of the Kalman filter, and evaluate the finite sample properties of this estimator.One hundred and five world-wide price series are tested for unit root bilinearity applying the test suggested by Charemza et al. (forthcoming). Applying the Maximum Likelihood estimator based on the Kalman filter, the null hypothesis of no bilinearity is rejected for 39 out of 105 series at the 5% level of significance. Most of the significant unit root bilinear coefficient estimates are explosive.
Timed k-Tail: Automatic Inference of Timed Automata

Accurate and up-to-date models describing the behavior of software systems are seldom available in practice. To address this issue, software engineers may use specification mining techniques, which can automatically derive models that capture the behavior of the system under analysis. So far, most specification mining techniques focused on the functional behavior of the systems, with specific emphasis on models that represent the ordering of operations, such as temporal rules and finite state models. Although useful, these models are inherently partial. For instance, they miss the timing behavior, which is extremely relevant for many classes of systems and components, such as shared libraries and user-driven applications. Mining specifications that include both the functional and the timing aspects can improve the applicability of many testing and analysis solutions. This paper addresses this challenge by presenting the Timed k-Tail (TkT) specification mining technique that can mine timed automata from program traces. Since timed automata can effectively represent the interplay between the functional and the timing behavior of a system, TkT could be exploited in those contexts where time-related information is relevant. Our empirical evaluation shows that TkT can efficiently and effectively mine accurate models. The mined models have been used to identify executions with anomalous timing. The evaluation shows that most of the anomalous executions have been correctly identified while producing few false positives.
ΔNp63-mediated regulation of hyaluronic acid metabolism and signaling supports HNSCC tumorigenesis

Significance The p63 isoform ΔNp63, a master regulator of epithelial biology, is overexpressed/amplified in the majority of head and neck squamous cell carcinoma (HNSCC), the sixth most common cancer worldwide. Here, we provide a demonstration of a molecular and functional link between the activity of ΔNp63 and hyaluronic acid (HA), a major component of the extracellular matrix. We unveiled a ΔNp63-dependent transcriptional program involving genes regulating the metabolism (HAS3 and HYAL proteins) and the signaling (CD44) of HA. By directly controlling the expression of these HA-related genes, ΔNp63 contributes to the activation of proproliferative and prosurvival pathway in HNSCC. Accordingly, the p63/HA pathway is a negative prognostic factor of HNSCC patient survival. Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, and several molecular pathways that underlie the molecular tumorigenesis of HNSCC have been identified. Among them, amplification or overexpression of ΔNp63 isoforms is observed in the majority of HNSCCs. Here, we unveiled a ΔNp63-dependent transcriptional program able to regulate the metabolism and the signaling of hyaluronic acid (HA), the major component of the extracellular matrix (ECM). We found that ∆Np63 is capable of sustaining the production of HA levels in cell culture and in vivo by regulating the expression of the HA synthase HAS3 and two hyaluronidase genes, HYAL-1 and HYAL-3. In addition, ∆Np63 directly regulates the expression of CD44, the major HA cell membrane receptor. By controlling this transcriptional program, ∆Np63 sustains the epithelial growth factor receptor (EGF-R) activation and the expression of ABCC1 multidrug transporter gene, thus contributing to tumor cell proliferation and chemoresistance. Importantly, p63 expression is positively correlated with CD44, HAS3, and ABCC1 expression in squamous cell carcinoma datasets and p63-HA pathway is a negative prognostic factor of HNSCC patient survival. Altogether, our data shed light on a ∆Np63-dependent pathway functionally important to the regulation of HNSCC progression.
Cytotoxic and insect-repellent activities of surface flavonoids from Datura stramonium L . Grown in Egypt

Three flavonoidal aglycones viz; F1 (Chrysin), F2 (Kampferol) and novel F3( 3,7dimethylether quercetin), were isolated from acetone wash of fresh leaves of Datura stramomium L. Isolated compounds were identified on the basis of their physico-chemical properties, Co-TLC, H-NMR, C-NMR and CIMS specrtum. Significant cytotoxic activity against three tumor cell lines (liver, cervix & breast), was recorded for the isolated compounds. In addition, remarkable repellent action of surface flavonoids against House Flies (Musca domestica) was recorded. [K. M. Meselhy. Cytotoxic and insect -repellent activities of surface flavonoids from Datura stramonium L. Grown in Egypt. Life Sci J 2012;9(4):3154-3158] (ISSN:1097-8135). http://www.lifesciencesite. com. 462