Miracle-dz/UniFAR-FTUs huggingface dataset:
Adult lung side population cells have mesenchymal stem cell potential.

BACKGROUND The development of stem cell therapy for pulmonary diseases remains a challenge. Many diverse cell types reside within the lung and a common stem cell has not yet been identified. A basic understanding of lung stem cell fate during disease may prove important for drug intervention as well as autologous therapies. Niches for resident mesenchymal stem cells (MSC) have been identified in many adult tissues and more recently in the lung. We present data to confirm the observation that non-hematopoietic CD45(neg) lung side population (SP) cells contain MSC, single cells capable of multilineage differentiation. METHODS We carried these observations forward by analyzing the MSC potential of single-cell clones, as well as their chromosomal stability and telomerase activity. RESULTS The expression of MSC markers was characterized in mouse CD45(neg) lung SP by flow cytometry on freshly isolated or cultured clonal populations. The karyotype of these cells was subsequently assayed by banding analysis, and telomerase activity was assessed using quantitative polymerase chain reaction. MSC differentiation potential was confirmed by the characteristic ability of single-cell clones to differentiate into cells of three mesenchymal lineages, chondrocytes, adipocytes and osteocytes. Differentiation was confirmed by histochemical analysis. All analyzed populations of CD45(neg) lung SP expressed mesenchymal markers (CD44, CD90, CD105, CD106, CD73 and Sca-I) and lacked hematopoietic markers (CD45, c-kit, CD11b, CD34 and CD14). The cultured and clonal CD45(neg) lung SP had normal chromosomal structures and expressed high levels of telomerase. After being expanded and cultured in differentiation medium, all populations of CD45(neg) lung SP demonstrated adipogenic, osteogenic and chrondrogenic potential. Adult CD45(neg) lung SP cells are a source of MSC. DISCUSSION In defining this tissue-specific stem cell population in the lung, we are now better able to clarify a potential role for them in lung diseases.
Optimizing stream program performance on CGRA-based systems?

Coarse-Grained Reconfigurable Architectures (CGRAs), often used as coprocessors for DSP and multimedia kernels, can deliver highly energy-efficient execution for compute-intensive kernels. Simultaneously, stream applications, which consist of many actors and channels connecting them, can provide natural representations for DSP applications, and therefore be a good match for CGRAs. We present our results of mapping DSP applications written in StreamIt language to CGRAs, along with our mapping flow. One important challenge in mapping is how to manage the multitude of kernels in the application for the limited local memory of a CGRA, for which we present a novel integer linear programming-based solution. Our evaluation results demonstrate that our software and hardware optimizations can help generate highly efficient mapping of stream applications to CGRAs, enabling far more energy-efficient executions (7× worse to 50× better) compared to using state-of-the-art GP-GPUs.
Semantics Preserving Model Composition

Separation of concerns (SoC) and modularisation are well established strategies for managing complex specifications [1, 2]. However, although software is designed with SoC in mind, the language mechanisms at hand often lead to tangling and scattering of concerns. This has motivated a range of language extensions to support concern specification, such as aspects and subjects in programming and modelling. The current trend is modularisation of cross-cutting concerns into units, e.g. aspects, that can later be composed by some transformation process (composition/merging/weaving). An important issue in this process is how the semantics of the models/programs is preserved. The focus of this PhD work is on composition and configuration of software specifications from a modelling perspective. Standard mechanisms in modelling (e.g. in UML) provide composition and configuration with well understood characteristics. Examples from UML are class redefinitions, composite structures, composite states, structured activities, interaction decomposition, and package merge. This work goes beyond those by exploring modelling and composition of concerns at a collaboration level, focusing on their architecture and interaction dimensions. The semantics governing such compositions and their results is of particular interest in this regard. I will address how generative techniques can be used for implementing the compositions and guide semantics preservation. I will also address what semantics preservation means in different modelling and composition contexts. UML is used as the language for experimentation, as this is the de-facto standard for software modelling.
Epstein-Barr Virus (EBV) DNA in Plasma Is Not Encapsidated in Patients With EBV-Related Malignancies

Epstein-Barr Virus (EBV), a ubiquitous gamma herpes virus, infects more than 95% of the human population before adulthood. Life-long persistence, usually without adverse health consequences, relies on a balance between viral latency, viral replication, and host immune response. Patients with EBV-related disease often have high levels of EBV DNA in their plasma. This study addresses whether this circulating, cell-free EBV DNA is encapsidated in virions or exists as naked genomes. First, an assay was developed, combining DNase I and quantitative real-time PCR, to discriminate encapsidated from naked EBV DNA. EBV DNA was almost always naked in the plasma of AIDS-related lymphoma patients (n = 11) and immunosuppressed/posttransplantation patients (n = 8). In contrast, infectious mononucleosis patients (n = 30) often had a mixture of encapsidated and naked EBV DNA. These findings may be important in understanding how viral load relates to disease status and in predicting response to nucleoside analogs and other antiviral therapies.
Selective Constraints in Experimentally Defined Primate Regulatory Regions

Changes in gene regulation may be important in evolution. However, the evolutionary properties of regulatory mutations are currently poorly understood. This is partly the result of an incomplete annotation of functional regulatory DNA in many species. For example, transcription factor binding sites (TFBSs), a major component of eukaryotic regulatory architecture, are typically short, degenerate, and therefore difficult to differentiate from randomly occurring, nonfunctional sequences. Furthermore, although sites such as TFBSs can be computationally predicted using evolutionary conservation as a criterion, estimates of the true level of selective constraint (defined as the fraction of strongly deleterious mutations occurring at a locus) in regulatory regions will, by definition, be upwardly biased in datasets that are a priori evolutionarily conserved. Here we investigate the fitness effects of regulatory mutations using two complementary datasets of human TFBSs that are likely to be relatively free of ascertainment bias with respect to evolutionary conservation but, importantly, are supported by experimental data. The first is a collection of almost >2,100 human TFBSs drawn from the literature in the TRANSFAC database, and the second is derived from several recent high-throughput chromatin immunoprecipitation coupled with genomic microarray (ChIP-chip) analyses. We also define a set of putative cis-regulatory modules (pCRMs) by spatially clustering multiple TFBSs that regulate the same gene. We find that a relatively high proportion (∼37%) of mutations at TFBSs are strongly deleterious, similar to that at a 2-fold degenerate protein-coding site. However, constraint is significantly reduced in human and chimpanzee pCRMS and ChIP-chip sequences, relative to macaques. We estimate that the fraction of regulatory mutations that have been driven to fixation by positive selection in humans is not significantly different from zero. We also find that the level of selective constraint in our TFBSs, pCRMs, and ChIP-chip sequences is negatively correlated with the expression breadth of the regulated gene, whereas the opposite relationship holds at that gene's nonsynonymous and synonymous sites. Finally, we find that the rate of protein evolution in a transcription factor appears to be positively correlated with the breadth of expression of the gene it regulates. Our study suggests that strongly deleterious regulatory mutations are considerably more likely (1.6-fold) to occur in tissue-specific than in housekeeping genes, implying that there is a fitness cost to increasing “complexity” of gene expression.
The relationship between lightning type and convective state of thunderclouds

Thunderstorm case studies and earlier observations are described which illuminate the relationship between cloud vertical development and the prevalence of intracloud (IC) and cloud-to-ground (CG) lightning. A consistent temporal evolution starting with peak IC activity changing to predominant CG activity and concluding with strong outflow (microburst) suggests that ice is responsible for both the electrical (i.e., lightning) and dynamical (i.e., microburst) phenomena. The IC activity is attributed to the updraft-driven accumulation of graupel particles in the central dipole region, and the subsequent CG activity to the descent of ice particles beneath the height of the main negative charge. The subsequent descent and melting of ice particles beneath the height of the 0°C isotherm are associated with the acceleration of the downdraft and outflow. The IC lightning precursor can provide a valuable short-term (5–10 min) warning for microburst hazard at ground level.
Recognition of Schistosome Glycolipids by Immunoglobulin E: Possible Role in Immunity

ABSTRACT To investigate the role of antibody responses to (glyco)lipids in immunity to schistosome infection, lipids extracted fromSchistosoma mansoni eggs and adult worms were fractionated, and the antibody isotype profile reactive to the fractionated lipids in a well-characterized S. haematobium-infected population was investigated. In tests of 10 plasma samples it was found that immunoglobulin G (IgG) reactivity was highest to the fraction containing ceramidepolyhexosides, whereas IgE reactivity was most prominent to both cerebroside- and ceramidepolyhexoside-containing fractions. The fraction containing ceramidepolyhexosides was then tested for reactivity with IgG subclasses and IgE in plasma samples from 66 S. haematobium-infected patients. Considering IgG4 and IgE, isotypes of particular interest in helminth infections, we found that both isotypes recognized egg (glyco)proteins in more than 90% of the infected subjects. However, in the case of glycolipids, IgE reactivity was much more prominent than IgG4 reactivity (found in 80 and 41% of the subjects, respectively). Furthermore, worm glycolipid-specific IgE prior to treatment of the subjects with praziquantel was negatively correlated with egg counts at 2 years posttreatment, indicating that IgE directed towards glycolipids could play an important role in resistance to reinfection.
Entrepreneurial and innovative behavior in spanish smes: essays on profitability, growth and export intensity.

En esta tesis doctoral, presentamos tres estudios empiricos que tratan de responder a diferentes preguntas de investigacion: (1) ? Que efecto tiene la orientacion emprendedora sobre la rentabilidad financiera de las PYMEs? La relacion entre la orientacion emprendedora y la rentabilidad financiera depende de la hostilidad del entorno operativo? (2) ? Podria la utilizacion de las redes fortalecer la orientacion emprendedora? Que efectos tienen el uso de la redes y la orientacion emprendedora sobre el crecimiento de la PYMEs? y ? Que efecto tiene la capacidad de innovacion sobre la propension y la intensidad exportadora de la pequena empresa? La propension a exportar impulsa la capacidad innovadora de la pequena empresa? En consecuencia, nos basamos en diferentes perspectivas teoricas para desarrollar las hipotesis propuestas. Ademas, utilizamos varias tecnicas de investigacion para poner en prueba dichas hipotesis, tales como: regresion lineal, modelo de ecuaciones estructurales, regresion ordinal, regresion logistica, etc. Los resultados confirman la mayoria de las relaciones propuestas. Finalmente, discutimos las implicaciones de nuestros hallazgos y proponemos futuras lineas de investigacion.
The Mevalonate Pathway of Staphylococcus aureus

ABSTRACT Isoprenoids are a class of ubiquitous organic molecules synthesized from the five-carbon starter unit isopentenyl pyrophosphate (IPP). Comprising more than 30,000 known natural products, isoprenoids serve various important biological functions in many organisms. In bacteria, undecaprenyl pyrophosphate is absolutely required for the formation of cell wall peptidoglycan and other cell surface structures, while ubiquinones and menaquinones, both containing an essential prenyl moiety, are key electron carriers in respiratory energy generation. There is scant knowledge on the nature and regulation of bacterial isoprenoid pathways. In order to explore the cellular responses to perturbations in the mevalonate pathway, responsible for producing the isoprenoid precursor IPP in many gram-positive bacteria and eukaryotes, we constructed three strains of Staphylococcus aureus in which each of the mevalonate pathway genes is regulated by an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible promoter. We used DNA microarrays to profile the transcriptional effects of downregulating the components of the mevalonate pathway in S. aureus and demonstrate that decreased expression of the mevalonate pathway leads to widespread downregulation of primary metabolism genes, an upregulation in virulence factors and cell wall biosynthetic determinants, and surprisingly little compensatory expression in other isoprenoid biosynthetic genes. We subsequently correlate these transcriptional changes with downstream metabolic consequences.
A Study of Negative Reputation in the Workplace

In an attempt to better understand how a negative reputation may affect one’s career, a series of hypotheses which offer an overview of negative personal reputation are tested, utilizing both a lab and a field study. Based upon the existing theory, these hypotheses explore negative reputation in the context of employees in organizations, suggesting that although often negative reputations are undesirable, at times individuals may be motivated to develop such reputations because they may confer benefits to one’s career.
Generalizability theory in psychotherapy research: The impact of multiple sources of variance on the dependability of psychotherapy process ratings

Abstract A central task of psychotherapy process measurement development is the assessment of reliability and validity. The convention of reporting intraclass correlations (ICCs) for coding procedures assumes that variance in scores can be adequately explained by differences between individuals and error resulting from differences in coders. Given the complex coding procedures that are common in psychotherapy process studies (multiple sessions may be rated by multiple coders on one or more multi-item scales), an ICC may fail to account for all of the relevant sources of variability in obtained scores. If process studies are to provide useful information about the mutative agents in psychotherapy, assessment procedures must be developed that dependably assess the constructs of interest. Generalizability theory provides a framework within which multiple sources of error can be simultaneously evaluated, thus improving the accuracy of reliability estimates and providing critical information for modification and improvement of coding procedures. To illustrate the applicability of generalizability theory to psychotherapy process research, the authors present the design and findings of a study investigating the generalizability of technique scales in the Psychotherapy Process Rating Scale for Borderline Personality Disorder. Implications for measurement development and procedural modifications are discussed.
Cardiomyocytes with disrupted CFTR function require CaMKII and Ca2+‐activated Cl− channel activity to maintain contraction rate

The physiological role of the cystic fibrosis transmembrane conductance regulator (CFTR) in cardiomyocytes remains unclear. Using spontaneously beating neonatal ventricular cardiomyocytes from wild‐type (WT) or CFTR knockout (KO) mice, we examined the role of CFTR in the modulation of cardiomyocyte contraction rate. Contraction rates of spontaneously beating myocytes were captured by video imaging. Real‐time changes in intracellular ([Ca2+]i) and protein kinase A (PKA) activity were measured by fura‐2 and fluorescence resonance energy transfer, respectively. Acute inhibition of CFTR in WT cardiomyocytes using the CFTR inhibitor CFTRinh‐172 transiently inhibited the contraction rate. By contrast, cardiomyocytes from CFTR KO mice displayed normal contraction rates. Further investigation revealed that acute inhibition of CFTR activity in WT cardiomyoctyes activated L‐type Ca2+ channels, leading to a transient increase of [Ca2+]i and inhibition of PKA activity. Additionally, we found that contraction rate normalization following acute CFTR inhibition in WT cardiomyocytes or chronic deletion in cardiomyocytes from CFTR KO mice requires the activation of Ca2+/calmodulin‐dependent kinase II (CaMKII) and Ca2+‐activated Cl− channels (CaCC) because simultaneous addition of myristoylated‐autocamtide‐2‐related inhibitory peptide or niflumic acid and CFTRinh‐172 to WT cardiomyocytes or treatment of cardiomyoctes from CFTR KO mice with these agents caused sustained attenuation of contraction rates. Our results demonstrate that regulation of cardiomyocyte contraction involves CFTR. They also reveal that activation of CaMKII and CaCC compensates for loss of CFTR function. Increased dependence on CaMKII upon loss of CFTR function might leave cystic fibrosis patients at increased risk of heart dysfunction and disease.
Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation

According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-β (Aβ) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Aβ assemblies is accompanied by a conformational change toward a high content of β-structure. Here, we report the solution structure of Aβ(1–40) in complex with the phage-display selected affibody protein ZAβ3, a binding protein of nanomolar affinity. Bound Aβ(1–40) features a β-hairpin comprising residues 17–36, providing the first high-resolution structure of Aβ in β conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Aβ. ZAβ3 stabilizes the β-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Aβ hairpin within a large hydrophobic tunnel-like cavity. Consequently, ZAβ3 acts as a stoichiometric inhibitor of Aβ fibrillation. The selected Aβ conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates.
Health index assessment for power transformers with thermal upgraded paper up to 230kV using fuzzy inference systems

This document presents a proposal to asset health index of transformers up to 230 kV. with upgraded thermal paper using fuzzy logic. The health index is a useful asset management tool, and provides a warning of the status of the unit allowing the correct operation and maintenance. This method use oil as inputs routine tests, such as humidity, acidity, dielectric strength, dissipation factor, dissolved gas analysis and, unlike other authors, it will include in the degree of analysis of polymerization. It is well known that thermal papers will not produce furans. Using current standards, the permissible limits will be obtained within the membership functions and parameters. Once obtain the six membership functions, relating them between with the help of expert judgment and thereby obtain the result of the health index.
Planning and execution of grasping motions on a humanoid robot

In this paper we present an approach for generating collision-free grasping motions and robustly execute them on a humanoid robot. The proposed MultiEEF-RRT algorithm for planning collision-free grasping trajectories exploits the enlarged goal space of a humanoid robot that results from the parallelized search of grasping trajectories for each arm. Here, multiple paths are searched simultaneously and the planner automatically chooses the first found solution. The reactive execution component operates on the planned C-Space trajectories and observes the movements in workspace with visual servoing approaches. The proposed algorithms do not rely on hand-eye calibrations, however it is possible to reliably execute given trajectories. The approach is fault-tolerant against changing execution speed, inaccurate sensor data and inexact executions of velocities. Since the hand and the target poses are visually tracked, the Cartesian error between the estimated position on a trajectory and the visually retrieved hand pose can be determined in workspace. This value is projected in the configuration space and used as a correction factor when calculating the joint velocities. We realized a grasping scenario with the humanoid robot ARMAR-III, where an object in front of the robot should be grasped. This demonstration shows how the proposed components play together to build a reactive and robust system integrating planning and execution of collision-free motions.
Deriving the Type Flaw Attacks in the Otway-Rees Protocol by Rewriting

This paper presents an approach to formalizing and verifying security protocol specifications based on rewriting techniques. A rewrite system Rp describes the steps of a protocol and the properties under consideration, and a rewrite system RI defines an intruder's ability of decomposing and decrypting messages. The equational theory generated by R = RP∪RI characterizes the recognizability of terms by an intruder, i.e. how an intruder can learn (parts of) messages exchanged among principals communicating over an insecure network. Security properties, such as authentication and secrecy, can be expressed by means of intruder's recognizability, and verifying whether a term is recognized by an intruder reduces to checking whether such a term can be rewritten to a normal form in the intruder's initial knowledge. A rewriting strategy is defined that, given a term t that represents a property to be proved, suitably expands and reduces t using the rules in R to derive whether or not t is recognized by an intruder. The approach is applied on the Otway-Rees symmetric-key protocol by deriving its well-known type flaw attacks.
Design and analysis of an optimal hopper for use in resonance-based locomotion

Quadrupedal running is an efficient form of locomotion found in nature, which serves as an inspiration for robotics. We believe that a resonance-based approach is the path towards energy-efficient legged locomotion and running robots. The first step in working towards this goal is creating an energy-efficient one-legged hopper. Such a one-legged hopper was designed and constructed. The impact efficiency of the mechanism is calculated analytically, determined in simulation and measured with the prototype. The impact efficiency as calculated from the experiments is found to be in agreement with the analytical expectation and simulation results. Finally, using an electric motor to inject energy by creating a virtual spring with reverse hysteresis, hopping is achieved.