Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling of Heart Repolarization Using Realistic Action Potentials

A computer model for simulation of surface ECG that enables to study heart repolarization changes is introduced. It includes heart geometry and structure description, predefined elemental action potential forms and enables computation of ECG potentials on the surface of an inhomogeneous torso. The influence of the action potentials form on the ST- T part and T-wave of ECG signals is demonstrated.
Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site‐associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average FST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians.
A Molecular Model of Alzheimer Amyloid β-Peptide Fibril Formation*

Polymerization of the amyloid beta (Aβ) peptide into protease-resistant fibrils is a significant step in the pathogenesis of Alzheimer’s disease. It has not been possible to obtain detailed structural information about this process with conventional techniques because the peptide has limited solubility and does not form crystals. In this work, we present experimental results leading to a molecular level model for fibril formation. Systematically selected Aβ-fragments containing the Aβ16–20sequence, previously shown essential for Aβ-Aβ binding, were incubated in a physiological buffer. Electron microscopy revealed that the shortest fibril-forming sequence was Aβ14–23. Substitutions in this decapeptide impaired fibril formation and deletion of the decapeptide from Aβ1–42 inhibited fibril formation completely. All studied peptides that formed fibrils also formed stable dimers and/or tetramers. Molecular modeling of Aβ14–23 oligomers in an antiparallel β-sheet conformation displayed favorable hydrophobic interactions stabilized by salt bridges between all charged residues. We propose that this decapeptide sequence forms the core of Aβ-fibrils, with the hydrophobic C terminus folding over this core. The identification of this fundamental sequence and the implied molecular model could facilitate the design of potential inhibitors of amyloidogenesis.
Calculation of the channel capacity of optical phase damping channel with iteration

The optical signal transmitted on a fiber with phase damping is studied. At the limitation of complete damping, we prove that the channel is in fact a classical channel. The complete phase damping channel maps the coherent state to a Poisson distributed state. Classical information is encoded in the parameter of the coherent state, the general input is a probability distribution of coherent states. The transfer matrix is given after the discretion of the parameter of the coherent state. The quantum Holevo quantity (whose maximum gives the channel capacity) is simplified to Shannon mutual information. We calculate the capacity with iteration. The optimal distribution of the input achieve the channel capacity is a probabilistic mixture of vacuum state (zero input) and a wave packet when the total energy is small, other wave packets appear when the total energy increases. The wave packet phenomenon is apparent
Vertical Contracts and Mandatory Universal Distribution

Abstract An upstream monopoly that provides a new good to a downstream oligopoly might prefer to sell to a single rather than to multiple downstream firms. For example, Apple initially sold its iPhone through one vendor. If a monopoly uses a single vendor, the government may impose a mandatory universal distribution (MUD) requirement that forces the monopoly to sell to all downstream vendors. However, if the income elasticity of demand for the new good is greater than the income elasticity of the existing generic good, the MUD requirement leads to a higher equilibrium price for both the new good and the generic and lowers consumer welfare.
Increased B-Type Natriuretic Peptide Concentration Is Associated with Reduced Coronary Vasoreactivity in Patients with Dilated Cardiomyopathy but Not in Healthy Young Subjects

Background/Aims. Natriuretic peptides are associated with the cardiovascular disease risk under a range of different circumstances. However, less is known about whether this association is found also in young healthy subjects. Methods. 9 patients with dilated cardiomyopathy and 26 healthy young subjects were studied. The myocardial blood flow measurements were performed basally and during adenosine infusion using PET. Results. S-proBNP concentrations were significantly higher (2153 ± 1964 versus 28 ± 17 ng/L, P = .000002) and adenosine-stimulated flow lower (1.6 ± 0.8 versus 3.6 ± 1.1 mL·g−1·min−1, P = .00001) in patients with dilated cardiomyopathy when compared to healthy subjects. S-proBNP concentration was inversely associated with adenosine stimulated flow in patients with dilated cardiomyopathy (r = −0.75, P = .019) but not in healthy subjects (r = −0.06, P = .84). Conclusions. Natriuretic peptides are inversely associated with coronary vasoreactivity in patients with dilated cardiomyopathy but not in healthy young subjects. Since reduced coronary vasoreactivity seems to be one of the earliest abnormalities in the development of coronary artery disease, this might indicate that natriuretic peptides are not predictor of cardiovascular disease risk in healthy young subjects.
Attenuated Shigella as a DNA Delivery Vehicle for DNA-Mediated Immunization

Direct inoculation of DNA, in the form of purified bacterial plasmids that are unable to replicate in mammalian cells but are able to direct cell synthesis of foreign proteins, is being explored as an approach to vaccine development. Here, a highly attenuated Shigella vector invaded mammalian cells and delivered such plasmids into the cytoplasm of cells, and subsequent production of functional foreign protein was measured. Because this Shigella vector was designed to deliver DNA to colonic mucosa, the method is a potential basis for oral and other mucosal DNA immunization and gene therapy strategies.
Why the Fed Should Ignore the Stock Market

James B. Bullard and Eric Schaling study a simple, small dynamic economy which a policymaker is attempting to control with a Taylor-type monetary policy rule. The authors wish to understand the macroeconomic consequences of the policymaker’s decision to include the level of equity prices in the rule. They show that such a policy can be counterproductive because it can interfere directly with the policymaker’s ability to minimize inflation and output variability. In extreme cases, a policy of targeting equity prices can lead to an indeterminate rational expectations equilibrium and hence a more unpredictable form of volatility than would be achieved by maintaining a rule without asset prices included. They thus provide an important and novel theoretical reason why policymakers may wish to ignore equity market developments when setting monetary policy.
About the use of different processing domains for synchronization in non-contiguous FBMC systems

The problem of synchronization in non-contiguous OFDM (NC-OFDM) in the presence of other in-band systems is addressed by means of a comparison between time-and frequency-based signal processing approaches. The filterbank multicarrier scheme with its spectral-efficient offset-QAM (OQAM) OFDM implementation is thereby a good choice for an NC-OFDM system design due to its well-localized spectral signal shape. In this work, we present and discuss two NC-OFDM synchronization methods for OQAM-OFDM, employing the time domain and the already demodulated frequency domain signal for synchronization and evaluate them in terms of sustainable bit-error rate over signal-to-interference ratio and variance of time and frequency offset estimation in different resource allocation scenarios. Additionally, their computational complexity is taken into account to estimate the costs of implementation on hardware. The results show that the task of synchronization can be achieved with comparable performance in both domains with an advantage of frequency domain processing over time domain processing in terms of efficiency in preamble design and complexity.
Writing the Disaster: A Philippine Case Study of the Challenge to Traditional Theodicy in Popular Media

The question initially raised in this paper was on how one’s religious sensibility affects one’s response to suffering. Focusing on three particular disasters that hit the Philippines, we look at the various media sources: the writing about the rains and flooding found in broadsheets and online media, and some ethnographic descriptions coming from the social sciences; we also look at experiential or anecdotal sources. All this provides us with material to establish certain traits and topics that come to fore in times of disaster, including such concerns as the lessons learned during disaster, the wrath of God, and points of cultural pride such as notions of solidarity and resilience. A significant upshot of this study has been the recognition of epistemic and methodological reevaluations that had to constantly be taken. This concludes in a retrieval of the contextuality of suffering (the historic, socio-economic – in addition to the religious – contexts of one who has been through disaster), a redefinition of what it means to say that the response is a Christian one, and finally a proposal that paying closer attention to these points, in addition to non-philosophical sources, might be a way of rethinking the problem of suffering beyond the scope of traditional theodicies.
Augmentable Paraphrase Extraction Framework

Paraphrase extraction relying on a single factor such as distribution similarity or translation similarity might lead to the loss of some linguistic properties. In this paper, we propose a paraphrase extraction framework, which accommodates various linguistically motivated factors to optimize the quality of paraphrase extraction. The major contributions of this study lie in the augmentable paraphrasing framework and the three kinds of factors conducive to both semantic and syntactic correctness. A manual evaluation showed that our model achieves more successful results than the state-of-the-art methods.
Acción, Significado y Estructura en la Teoría de A. Giddens

El objetivo de este trabajo es ofrecer una vision introductoria de la teoria de la estructuracion formulada por An thony Giddens, en la que se intenta re solver el dilema de la relacion en tre accion humana y estructura so cial. Desde el punto de vista de esta teoria, no se trata de afirmar la existencia de un sujeto constituido como fundamento de la historia sino de hacer intervenir a los actores sociales, los cuales no pueden ser pensados al margen del sistema en que estan inscritos. Por ello requiere, para dar cuenta del agente, del proposito expreso de escapar al dualismo subjetivismo objetivismo, asi como tambien de la tarea de superar el funcionalismo y el estructuralismo. Estas dos ultimas teorias vieron disminuida su capacidad explicativa al atribuir a la estructura so cial una eficacia propia al margen de los agentes.
Edinburgh Research Explorer Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background: Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results: Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions: Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
pH-dependent Perforation of Macrophage Phagosomes by Listeriolysin O from Listeria monocytogenes

The pore-forming toxin listeriolysin O (LLO) is a major virulence factor implicated in escape of Listeria monocytogenes from phagocytic vacuoles. Here we describe the pH-dependence of vacuolar perforation by LLO, using the membrane-impermeant fluorophore 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) to monitor the pH and integrity of vacuoles in mouse bone marrow–derived macrophages. Perforation was observed when acidic vacuoles containing wild-type L. monocytogenes displayed sudden increases in pH and release of HPTS into the cytosol. These changes were not seen with LLO-deficient mutants. Perforation occurred at acidic vacuolar pH (4.9–6.7) and was reduced in frequency or prevented completely when macrophages were treated with the lysosomotropic agents ammonium chloride or bafilomycin A1. We conclude that acidic pH facilitates LLO activity in vivo.
Implementing an LU Factorization for the Embedded Network Simplex Algorithm

This paper presents an LU factorization specialized for embedded network simplex algorithms. Specializing the LU factorization in this fashion poses a challenge as the embedded network algorithm uses a very compressed working basis inverse. Using publicly available test problems, we demonstrate the impact of this factorization on the EMNET implementation of the embedded network simplex algorithm. We also compare the impact of the LU factorization when coupled with recent advances in starting, pricing, and basis reduction that have already been implemented in EMNET. We demonstrate that this LU factorization is a vital component of EMNET and offers significant performance improvement for virtually all EMNET configurations. To place our results in context, we compare EMNET's performance with CPLEX.
Nature-Inspired Multi-Agent Coordination in Task Assigment Problems

The main problem when using multi-agent systems (MAS) for ta sk ssignment problems in real-world environments is the limited scalability of trad itional MAS approaches such as centralized planning. Therefore, we look at a scalable, generic methodo logy inspired by nature for multi-agent coordination in large, embodied MAS, operating in noisy, real-t ime environments. More specifically, we look at real-world task assignment problems and use the testbed o f robots performing resource distribution in large storage facilities. As a first step toward a generic methodology for embodied, dis tributed MAS, we analyse the behavior and the scalability of an embodied MAS which is driven by simu lated potential fields. Resources in a storage facility emit a certain simulated potential while robots emit an opposite potential. Applying principles inspired by physics to local behavior, idle robo ts move toward resources but away from other robots. Whenever a resource appears, a central agent system registers this appearance and creates a plan for a robot to pick up the resource and deliver it to some desti nation area. We show that this system is highly scalable with respect to both the environment and t he number of robots, while maintaining functionality, adaptivity and robustness. Furthermore, t h integration of planning helps to prevent local optima and to increase fairness. In future work, the central agent system will be replaced by a distributed system, such as a sensor network, to further increase scalability, adaptivity and r obustness of the system.
Social Identity, Health and Well-Being: An Emerging Agenda for Applied Psychology

The social environment comprising communities, families, neighbourhoods, work teams, and various other forms of social group is not simply an external feature of the world that provides a context for individual behaviour. Instead these groups impact on the psychology of individuals through their capacity to be internalised as part of a person’s social identity. If groups provide individuals with a sense of meaning, purpose, and belonging (i.e. a positive sense of social identity) they tend to have positive psychological consequences. The impact of these identity processes on health and well-being is explored in the contributions to this special issue. In this editorial, we discuss these contributions in light of five central themes that have emerged from research to date. These themes address the relationship between social identity and (a) symptom appraisal and response, (b) health-related norms and behaviour, (c) social support, (d) coping, and (e) clinical outcomes. The special issue as a whole points to the capacity for a social identity approach to enrich academic understanding in these areas and to play a key role in shaping health-related policy and practice.
Leukocyte engagement of fibrin(ogen) via the integrin receptor αMβ2/Mac-1 is critical for host inflammatory response in vivo

The leukocyte integrin αMβ2/Mac-1 appears to support the inflammatory response through multiple ligands, but local engagement of fibrin(ogen) may be particularly important for leukocyte function. To define the biological significance of fibrin(ogen)-αMβ2 interaction in vivo, gene-targeted mice were generated in which the αMβ2-binding motif within the fibrinogen γ chain (N390RLSIGE396) was converted to a series of alanine residues. Mice carrying the Fibγ390–396A allele maintained normal levels of fibrinogen, retained normal clotting function, supported platelet aggregation, and never developed spontaneous hemorrhagic events. However, the mutant fibrinogen failed to support αMβ2-mediated adhesion of primary neutrophils, macrophages, and αMβ2-expressing cell lines. The elimination of the αMβ2-binding motif on fibrin(ogen) severely compromised the inflammatory response in vivo as evidenced by a dramatic impediment in leukocyte clearance of Staphylococcus aureus inoculated into the peritoneal cavity. This defect in bacterial clearance was due not to diminished leukocyte trafficking but rather to a failure to fully implement antimicrobial functions. These studies definitively demonstrate that fibrin(ogen) is a physiologically relevant ligand for αMβ2, integrin engagement of fibrin(ogen) is critical to leukocyte function and innate immunity in vivo, and the biological importance of fibrinogen in regulating the inflammatory response can be appreciated outside of any alteration in clotting function.
Prevalence of Underprescription or Overprescription of Energy Needs in Critically Ill Mechanically Ventilated Adults as Determined by Indirect Calorimetry: A Systematic Literature Review.

BACKGROUND Underfeeding and overfeeding has been associated with adverse patient outcomes. Resting energy expenditure can be measured using indirect calorimetry. In its absence, predictive equations are used. A systematic literature review was conducted to determine the prevalence of underprescription and overprescription of energy needs in adult mechanically ventilated critically ill patients by comparing predictive equations to indirect calorimetry measurements. METHODS Ovid MEDLINE, CINAHL Plus, Scopus, and EMBASE databases were searched in May 2013 to identify studies that used both predictive equations and indirect calorimetry to determine energy expenditure. Reference lists of included publications were also searched. The number of predictive equations that underestimated or overestimated energy expenditure by ±10% when compared to indirect calorimetry measurements were noted at both an individual and group level. RESULTS In total, 2349 publications were retrieved, with 18 studies included. Of the 160 variations of 13 predictive equations reviewed at a group level, 38% underestimated and 12% overestimated energy expenditure by more than 10%. The remaining 50% of equations estimated energy expenditure to within ±10 of indirect calorimetry measurements. On an individual patient level, predictive equations underestimated and overestimated energy expenditure in 13-90% and 0-88% of patients, respectively. Differences of up to 43% below and 66% above indirect calorimetry values were observed. CONCLUSIONS Large discrepancies exist between predictive equation estimates and indirect calorimetry measurements in individuals and groups. Further research is needed to determine the influence of indirect calorimetry and predictive equation limitations in contributing to these observed differences.