Miracle-dz/UniFAR-FTUs huggingface dataset:
Water Deficit Triggers Phospholipase D Activity in the Resurrection Plant Craterostigma plantagineum

Phospholipids play an important role in many signaling pathways in animal cells. Signaling cascades are triggered by the activation of phospholipid cleaving enzymes such as phospholipases C, D (PLD), and A2. Their activities result in the formation of second messengers and amplification of the initial signal. In this study, we provide experimental evidence that PLD is involved in the early events of dehydration in the resurrection plant Craterostigma plantagineum. The enzymatic activity of the PLD protein was activated within minutes after the onset of dehydration, and although it was not inducible by abscisic acid, PLD activity did increase in response to mastoparan, which suggests a role for heterotrimeric G proteins in PLD regulation. Two cDNA clones encoding PLDs, CpPLD-1 and CpPLD-2, were isolated. The CpPLD-1 transcript was constitutively expressed, whereas CpPLD-2 was induced by dehydration and abscisic acid. Immunological studies revealed changes in the subcellular localization of the PLD protein in response to dehydration. Taken together, the data on enzymatic activity as well as transcript and protein distributions allowed us to propose a role for PLD in the events leading to desiccation tolerance in C. plantagineum.
Nematicons and Their Electro-Optic Control: Light Localization and Signal Readdressing via Reorientation in Liquid Crystals

Liquid crystals in the nematic phase exhibit substantial reorientation when the molecules are driven by electric fields of any frequencies. Exploiting such a response at optical frequencies, self-focusing supports transverse localization of light and the propagation of self-confined beams and waveguides, namely “nematicons”. Nematicons can guide other light signals and interact with inhomogeneities and other beams. Moreover, they can be effectively deviated by using the electro-optic response of the medium, leading to several strategies for voltage-controlled reconfiguration of light-induced guided-wave circuits and signal readdressing. Hereby, we outline the main features of nematicons and review the outstanding progress achieved in the last twelve years on beam self-trapping and electro-optic readdressing.
Topic Modeling with Document Relative Similarities

Topic modeling has been widely used in text mining. Previous topic models such as Latent Dirichlet Allocation (LDA) are successful in learning hidden topics but they do not take into account metadata of documents. To tackle this problem, many augmented topic models have been proposed to jointly model text and metadata. But most existing models handle only categorical and numerical types of metadata. We identify another type of metadata that can be more natural to obtain in some scenarios. These are relative similarities among documents. In this paper, we propose a general model that links LDA with constraints derived from document relative similarities. Specifically, in our model, the constraints act as a regularizer of the log likelihood of LDA. We fit the proposed model using Gibbs-EM. Experiments with two real world datasets show that our model is able to learn meaningful topics. The results also show that our model outperforms the baselines in terms of topic coherence and a document classification task.
The variance-optimal martingale measure for continuous processes

We prove that for continuous stochastic processes S based on (fQ . P) for which there is an equivalent martingale measure Q0 with square-integrable density d QO/d P, we have that the so-called 'variance optimal' martingale measure Qopt for which the density d gopt/d ~ has minimal L2( )-norm is automatically equivalent to P. The result is then applied to an approximation problem arising in mathematical finance.
Functional Notch signaling is required for BMP4-induced inhibition of myogenic differentiation

The bone morphogenetic protein (BMP) and Notch signaling pathways are crucial for cellular differentiation. In many cases, the two pathways act similarly; for example, to inhibit myogenic differentiation. It is not known whether this inhibition is caused by distinct mechanisms or by an interplay between Notch and BMP signaling. Here we demonstrate that functional Notch signaling is required for BMP4-mediated block of differentiation of muscle stem cells, i.e. satellite cells and the myogenic cell line C2C12. Addition of BMP4 during induction of differentiation dramatically reduced the number of differentiated satellite and C2C12 cells. Differentiation was substantially restored in BMP4-treated cultures by blocking Notch signaling using either theγ -secretase inhibitor L-685,458 or by introduction of a dominant-negative version of the Notch signal mediator CSL. BMP4 addition to C2C12 cells increased transcription of two immediate Notch responsive genes, Hes1 and Hey1, an effect that was abrogated by L-685,458. A 3 kb Hey1-promoter reporter construct was synergistically activated by the Notch 1 intracellular domain (Notch 1 ICD) and BMP4. The BMP4 mediator SMAD1 mimicked BMP activation of the Hey1 promoter. A synthetic Notch-responsive promoter containing no SMAD1 binding sites responded to SMAD1, indicating that DNA-binding activity of SMAD1 is not required for activation. Accordingly, Notch 1 ICD and SMAD1 interacted in binding experiments in vitro. Thus, the data presented here provide evidence for a direct interaction between the Notch and BMP signaling pathways, and indicate that Notch has a crucial role in the execution of certain aspects of BMP-mediated differentiation control.
Microstructural Evolution during Industrial Rolling of a Duplex Stainless Steel

The microstructural evolution of a duplex stainless steel EN 1.4462 during the industrial rolling process has been examined. The ferritic and austenitic phases were analyzed separately after each rolling and annealing step. Optical microscopy and transmission electron microscopy, together with texture measurements, have been used to characterize the morphology and the preferred crystallographic orientations of both phases. Additionally, the hardness evolution in ferrite and austenite after each industrial step was measured by instrumented indentation. The results show that microstructural features observed after hot rolling tend to remain during further processing and they are essentially present in the final cold rolled and annealed product.
OntoSphere: more than a 3D ontology visualization tool

In this paper a new approach to ontology visualization is introduced, using a more than 3-dimensional space. The ontology information is represented on a 3D view-port enriched by visual cues. A preliminary application based on the presented principles is described, and results show that the approach is feasible and can actually lead to a more effective modeling process and to an easy detection of “conceptual inconsistencies”. The opinions of domain experts are also quite positive and seem to indicate that the approach is promising and can be extended for creating “user friendly” ontology editors for people with low ICT skills.
Focus-based design of mixed reality systems

Currently very few techniques are available to support the design of Augmented and Mixed Reality (MR) systems. Task elicitation is more complex for MR systems than for traditional information systems. Having multiple sources of information and two worlds of interaction (real and virtual) involves making choices about what to attend to and when. Interaction based on traditional input and output devices is not effective in a mixed scenario. It distracts the user from the task at hand and may create a severe cognitive seam. Understanding, formalizing and modeling such aspects can help designers to assess interaction at all the stages of development. We are interested in focused applications that require the user's hand free for real world tasks and to understand how the user's task focus drives designing MR systems. The contribution of this paper is twofold: it first illustrates the specific requirements posed by such systems and then it shows through a study case that there is currently no complete support to model these aspects among the tools commonly employed for task modeling.
Genomic and Proteomic Analysis of the Impact of Mitotic Quiescence on the Engraftment of Human CD34+ Cells

It is well established that in adults, long-term repopulating hematopoietic stem cells (HSC) are mitotically quiescent cells that reside in specialized bone marrow (BM) niches that maintain the dormancy of HSC. Our laboratory demonstrated that the engraftment potential of human HSC (CD34(+) cells) from BM and mobilized peripheral blood (MPB) is restricted to cells in the G0 phase of cell cycle but that in the case of umbilical cord blood (UCB) -derived CD34(+) cells, cell cycle status is not a determining factor in the ability of these cells to engraft and sustain hematopoiesis. We used this distinct in vivo behavior of CD34(+) cells from these tissues to identify genes associated with the engraftment potential of human HSC. CD34(+) cells from BM, MPB, and UCB were fractionated into G0 and G1 phases of cell cycle and subjected in parallel to microarray and proteomic analyses. A total of 484 target genes were identified to be associated with engraftment potential of HSC. System biology modeling indicated that the top four signaling pathways associated with these genes are Integrin signaling, p53 signaling, cytotoxic T lymphocyte-mediated apoptosis, and Myc mediated apoptosis signaling. Our data suggest that a continuum of functions of hematopoietic cells directly associated with cell cycle progression may play a major role in governing the engraftment potential of stem cells. While proteomic analysis identified a total of 646 proteins in analyzed samples, a very limited overlap between genomic and proteomic data was observed. These data provide a new insight into the genetic control of engraftment of human HSC from distinct tissues and suggest that mitotic quiescence may not be the requisite characteristic of engrafting stem cells, but instead may be the physiologic status conducive to the expression of genetic elements favoring engraftment.
Vaginal Memory T Cells Induced by Intranasal Vaccination Are Critical for Protective T Cell Recruitment and Prevention of Genital HSV-2 Disease

ABSTRACT Protective immunity against genital pathogens causing chronic infections, such as herpes simplex virus 2 (HSV-2) or human immunodeficiency virus, requires the induction of cell-mediated immune responses locally in the genital tract. Intranasal immunization with a thymidine kinase-deficient (TK−) mutant of HSV-2 effectively induces HSV-2-specific gamma interferon (IFN-γ)-secreting memory T cell production and protective immunity against intravaginal challenge with wild-type HSV-2. However, the precise mechanism by which intranasal immunization induces protective immunity in the distant genital mucosa more effectively than does systemic immunization is unknown. Here, we showed that intranasal immunization with live HSV-2 TK− induced the production of effector T cells and their migration to, and retention in, the vaginal mucosa, whereas systemic vaccination barely established a local effector T cell pool, even when it induced the production of circulating memory T cells in the systemic compartment. The long-lasting HSV-2-specific local effector T cells induced by intranasal vaccination provided superior protection against intravaginal wild-type HSV-2 challenge by starting viral clearance at the entry site earlier than with intraperitoneal immunization. Intranasal immunization is an effective strategy for eliciting high levels of cell-mediated protection of the genital tract by providing long-lasting antigen (Ag)-specific local effector T cells without introducing topical infection or inflammation. IMPORTANCE Intranasal (i.n.) vaccines against sexually transmitted diseases that are caused by viruses such as herpes simplex virus 2 (HSV-2) have long been in development, but no vaccine candidate is currently available. Understanding the cellular mechanisms of immune responses in a distant vaginal mucosa induced by i.n. immunization with HSV-2 will contribute to designing such a vaccine. Our study demonstrated that i.n. immunization with an attenuated strain of HSV-2 generated long-lasting IFN-γ-secreting T cells in vaginal mucosa more effectively than systemic immunization. We found that these vaginal effector memory T cells are critical for the early stage of viral clearance at natural infection sites and prevent severe vaginal inflammation and herpes encephalitis.
A CAT(0)-valued pointwise ergodic theorem

In this note we prove the a pointwise ergodic theorem for functions taking values in a separable complete CAT(0)-space, analogous to Lindenstrauss' pointwise ergodic theorem for real-valued integrable functions on a probability space subject to a probability-preserving action of an amenable l.c. s.c. group, where in the CAT(0) setting the role of ergodic averages is played by the barycentres of the empirical distributions of a CAT(0)-valued map along an orbit of the group action. The proof rests on an approximation argument and an appeal to that result for real-valued maps.
Intermittent ethanol exposure increases the number of cerebellar microglia.

AIMS The number of cerebellar microglia after 5(1)/2 months of continuous or intermittent ethanol exposure was studied using the optical dissector method. METHODS Male Wistar rats were divided into three groups: an intermittently ethanol-exposed group, a continuously ethanol-exposed group and a control group (n = 6 in each group). The intermittently treated rats had two ethanol-withdrawal periods per week throughout the experiment. The number of microglia was measured in the anterior (folium II) and the posterior (folium X) cerebellar vermis. Tomato (Lycopersicon esculentum) lectin was used to stain the cerebellar microglia. RESULTS The volumes of folia II and X were similar in all the groups. The number of microglia increased in the molecular layer of folium II in the intermittently ethanol-exposed group compared with the continuously exposed and control groups. In the granular layer, there were no differences between the groups in the number of microglia. CONCLUSIONS The results suggest that the number of cerebellar microglia increases in the anterior vermis before any ethanol-induced cerebellar atrophy is discernible. Repeated ethanol withdrawals seem to be more essential in inducing microgliosis than ethanol intoxication per se.
Measuring IS-Support: A Conceptual Model

This paper reports on a conceptual model of a larger research effort proceeding from a central interest in the importance of assessing the IS-Support provided to key-user groups. This study conceptualised a new multidimensional IS-Support construct with four dimensions: training, documentation, assistance and authorisation, which form the overarching construct – IS-Support. We argue that a holistic measure for assessing IS-Support should consist of dimensions, and measures, that together assess the variety of the support provided to IS key-user groups. The proposed IS-Support construct is defined as the support the IS key-user groups receive to increase their capabilities in utilising information systems within the organisation. With two interrelated phases, conceptualisation phase and validation phase, to rigorously hypothesise and validate a measurement model, the IS-Support model, proposed in this study, is intended to include the characteristics of analytic theory.
Preclinical Assessment of Efficacy of Radiation Dose Painting Based on Intratumoral FDG-PET Uptake

Purpose: We tested therapeutic efficacy of two dose painting strategies of applying higher radiation dose to tumor subvolumes with high FDG uptake (biologic target volume, BTV): dose escalation and dose redistribution. We also investigated whether tumor response was determined by the highest dose in BTV or the lowest dose in gross tumor volume (GTV). Experimental Design: FDG uptake was evaluated in rat rhabdomyosarcomas prior to irradiation. BTV was defined as 30% of GTV with the highest (BTVhot) or lowest (BTVcold) uptake. To test efficacy of dose escalation, tumor response (time to reach two times starting tumor volume, TGTV2) to Hot Boost irradiation (40% higher dose to BTVhot) was compared with Cold Boost (40% higher dose to BTVcold), while mean dose to GTV remained 12 Gy. To test efficacy of dose redistribution, TGTV2 after Hot Boost was compared with uniform irradiation with the same mean dose (8 or 12 Gy). Results: TGTV2 after 12 Gy delivered heterogeneously (Hot and Cold Boost) or uniformly were not significantly different: 20.2, 19.5, and 20.6 days, respectively. Dose redistribution (Hot Boost) with 8 Gy resulted in faster tumor regrowth as compared with uniform irradiation (13.3 vs. 17.1 days; P = 0.026). Further increase in dose gradient to 60% led to a more pronounced decrease in TGTV2 (10.9 days; P < 0.0001). Conclusions: Dose escalation effect was independent of FDG uptake in target tumor volume, while dose redistribution was detrimental in this tumor model for dose levels applied here. Our data are consistent with the hypothesis that tumor response depends on the minimum intratumoral dose. Clin Cancer Res; 21(24); 5511–8. ©2015 AACR.
A Nonlinear Discriminative Approach to AAM Fitting

The Active Appearance Model (AAM) is a powerful generative method for modeling and registering deformable visual objects. Most methods for AAM fitting utilize a linear parameter update model in an iterative framework. Despite its popularity, the scope of this approach is severely restricted, both in fitting accuracy and capture range, due to the simplicity of the linear update models used. In this paper, we present an new AAM fitting formulation, which utilizes a nonlinear update model. To motivate our approach, we compare its performance against two popular fitting methods on two publicly available face databases, in which this formulation boasts significant performance improvements.
Conducting Polymer/Graphene Filler-based Hybrids: Energy and Electronic Applications

This chapter covers the potentially important conductive polymers and their benefits with effective relevance in number of growing technologies in telecommunication, biomolecular electronics, display devices, electrochemical storage systems, and many more. The most widely investigated polymers in practical applications are polythiophene (PTh), polypyrrole (PPy), and polyaniline (PANI). These polymers have been employed in technical applications depending upon their stability and ease of preparation. Conducting polymers display significantly high values of specific capacitance however in terms of several physical properties they are not up to the mark. Relevance of graphene-based materials incorporated in conducting polymers is also considered in this chapter. Polymer/graphene filler composites have recognized a range of interesting characteristic such as superior mechanical properties, high electron mobility at room temperature, and exceptional thermal conductivity. Conductive polymer/graphene filler composites may involve a three-dimensional network to haulage electrical conductivity. The formation of conducting polymer interconnected graphene network present significant advantages to be employed in a range of applications such as electronics, sensors, Li-ion batteries, solar cells, EMI shielding, etc.
Measurement of pancreatic lipase activity in serum by a kinetic colorimetric assay using a new chromogenic substrate

We evaluate a new assay reagent for lipase determination, based on the use of 1,2-o-dilauryl-rac-glycero-3-glutaric acid-(6'-methylresorufin) ester (DGGR) as substrate. DGGR is cleaved by lipase, resulting in an unstable dicarbonic acid ester which is spontaneously hydrolysed to yield glutaric acid and methylresorufin, a bluish-purple chromophore with peak absorption at 580nm. The rate of methylresorufin formation is directly proportional to the lipase activity in the sample. Bile salts, colipase and calcium chloride are included to provide optimal reactivity and specificity. Analysis of total imprecision gave a coefficient of variation of between 5·7% and 9·6%. Anticoagulants, common interfering substances and carboxylesterase had no effect on the assay, but interference by increased concentrations of serum triglycerides was noted. Good correlations were obtained with turbidimetry and a coupled enzymatic method. The estimated reference interval was 6-38U/L. The unique characteristics of the chromogenic substrate qualify the present method as an innovative approach to serum lipase analysis.
Nanocrystalline Titania Films and Particles by Chemical Vapor Synthesis

Thick crystalline titania films with grain sizes below 30 nm, as well as nanocrystalline titania particles with sizes below 10 nm, are prepared by a modified CVD method called chemical vapor synthesis (CVS). Pyrolysis of titanium tetraisopropoxide (TTIP) is performed in a hot-wall reactor, in a mixed helium/oxygen atmosphere, using liquid precursor delivery. Film thicknesses of up to 150 μm on silicon (100) substrate materials are achieved. The influence of process parameters (particularly reactor position) on the microstructure and growth rate is examined. Process temperatures, starting at film-forming (CVD) conditions and going up to exclusive particle formation (CVS) are investigated. Grain size, particle size, and crystallographic phases are determined by X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET), scanning electron microscopy (SEM), and transmission electron microscopy (TEM).
A mouse embryonic stem cell model of Schwann cell differentiation for studies of the role of neurofibromatosis type 1 in Schwann cell development and tumor formation

The neurofibromatosis Type 1 (NF1) gene functions as a tumor suppressor gene. One known function of neurofibromin, the NF1 protein product, is to accelerate the slow intrinsic GTPase activity of Ras to increase the production of inactive rasGDP, with wide‐ranging effects on p21ras pathways. Loss of neurofibromin in the autosomal dominant disorder NF1 is associated with tumors of the peripheral nervous system, particularly neurofibromas, benign lesions in which the major affected cell type is the Schwann cell (SC). NF1 is the most common cancer predisposition syndrome affecting the nervous system. We have developed an in vitro system for differentiating mouse embryonic stem cells (mESC) that are NF1 wild type (+/+), heterozygous (+/−), or null (−/−) into SC‐like cells to study the role of NF1 in SC development and tumor formation. These mES‐generated SC‐like cells, regardless of their NF1 status, express SC markers correlated with their stage of maturation, including myelin proteins. They also support and preferentially direct neurite outgrowth from primary neurons. NF1 null and heterozygous SC‐like cells proliferate at an accelerated rate compared to NF1 wild type; this growth advantage can be reverted to wild type levels using an inhibitor of MAP kinase kinase (Mek). The mESC of all NF1 types can also be differentiated into neuron‐like cells. This novel model system provides an ideal paradigm for studies of the role of NF1 in cell growth and differentiation of the different cell types affected by NF1 in cells with differing levels of neurofibromin that are neither transformed nor malignant. © 2007 Wiley‐Liss, Inc.