Miracle-dz/UniFAR-FTUs huggingface dataset:
The Clp Proteases of Bacillus subtilisAre Directly Involved in Degradation of Misfolded Proteins

ABSTRACT The presence of the heat stress response-related ATPases ClpC and ClpX or the peptidase ClpP in the cell is crucial for tolerance of many forms of stress in Bacillus subtilis. Assays for detection of defects in protein degradation suggest that ClpC, ClpP, and ClpX participate directly in overall proteolysis of misfolded proteins. Turnover rates for abnormal puromycyl peptides are significantly decreased in clpC, clpP, and clpXmutant cells. Electron-dense aggregates, most likely due to the accumulation of misfolded proteins, were noticed in studies of ultrathin cryosections in clpC and clpP mutant cells even under nonstress conditions. In contrast, in the wild type orclpX mutants such aggregates could only be observed after heat shock. This phenomenon supports the assumption thatclpC and clpP mutants are deficient in the ability to solubilize or degrade damaged and aggregated proteins, the accumulation of which is toxic for the cell. By using immunogold labeling with antibodies raised against ClpC, ClpP, and ClpX, the Clp proteins were localized in these aggregates, showing that the Clp proteins act at this level in vivo.
A Free Associative File System

The Free Associative File System is an alternative in file system structure from the hierarchical directory model. Files can be freely associated with various keywords that pertain to the file. I present a design for such a system with various alternatives that could be taken along the way and describe a simple prototype that I have built to test usability of the system using a simple shell interface.
The Importance of Being Hybrid for Spatial Epidemic Models: A Multi-Scale Approach

This work addresses the spread of a disease within an urban system, defined as a network of interconnected cities. The first step consists of comparing two different approaches: a macroscopic one, based on a system of coupled Ordinary Differential Equations (ODE) Susceptible-Infected-Recovered (SIR) systems exploiting populations on nodes and flows on edges (so-called metapopulational model), and a hybrid one, coupling ODE SIR systems on nodes and agents traveling on edges. Under homogeneous conditions (mean field approximation), this comparison leads to similar results on the outputs on which we focus (the maximum intensity of the epidemic, its duration and the time of the epidemic peak). However, when it comes to setting up epidemic control strategies, results rapidly diverge between the two approaches, and it appears that the full macroscopic model is not completely adapted to these questions. In this paper, we focus on some control strategies, which are quarantine, avoidance and risk culture, to explore the differences, advantages and disadvantages of the two models and discuss the importance of being hybrid when modeling and simulating epidemic spread at the level of a whole urban system.
Trans-Reality Gaming

Trans-reality games are games that take advantage of pervasive, mobile, ubiquitous, locationbased and mixed reality technical infrastructures to deliver new modes of game play experience in which the different contexts of staging are integrated within a unified game space that crosses over technical borders. The development of trans-reality games involves meeting specific design challenges concerning variations between the roles of technology and the player in different game staging environments. The result must be a design methodology in which diverse demands upon and opportunities for player creativity are integrated within the mechanics of a specific trans-reality game design.
Exploring the most appropriate feature detector and descriptor algorithm for on-board UAV image processing

With the development of computer vision technology, many researches about feature detectors and descriptors have been published in the last decades. In order to explore what kind of approaches are appropriate for unmanned aerial vehicle (UAV) onboard video processing, the popular feature detectors and descriptors are analyzed and combined with each other. Three practical videos captured in indoor environments and outdoor environments are used to test the accuracy, runtime and robustness of these combined algorithms. Results validate that the combinations of different feature detectors and descriptors balance well the accuracy and runtime. This will provide references for choosing appropriate onboard video processing algorithms.
Opentrad Apertium Open-Source Machine Translation System: an Opportunity for Business and Research

Work partially funded by Spanish Government through grants FIT-340101-2004-3, FIT-340001-2005-2 and TIC2003-08681-C02-01. Felipe Sanchez-Martinez is supported by the Spanish Government and the European Social Fund through research grant BES-2004-4711. The extension of Apertium is being funded by the Generalitat de Catalunya.
Institution Formation in Public Goods Games

Centralized sanctioning institutions are of utmost importance for overcoming free-riding tendencies and enforcing outcomes that maximize group welfare in social dilemma situations. However, little is known about how such institutions come into existence. In this paper we investigate, both theoretically and experimentally, the endogenous formation of institutions in a public goods game. Our theoretical analysis shows that players may form sanctioning institutions in equilibrium, including those where institutions govern only a subset of players. The experiment confirms that institutions are formed frequently as well as that institution formation has a positive impact on cooperation rates and group welfare. However, the data clearly reveal that players are unwilling to implement institutions in which some players have the opportunity to free ride. In sum, our results show that individuals are willing and able to create sanctioning institutions, but that the institution formation process is guided by behavioral principles not taken into account by standard theory.
Optimization of capacity and operational scheduling for microgrid system using two-stage stochastic linear programming

This paper presents the determination of capacity and operational schedule for a grid-tied microgrid system based on a stochastic optimization method. A photovoltaic power system is used as a renewable energy source, while battery system is utilized as energy storage systems. The microgrid system can be operated using the usual priority scheme or the proposed scheduling scheme. The mathematical model for the microgrid system is developed. The objective function is formulated from a capital and operational costs. The constraints for the optimization are formulated based on system model, physical limitations, and performance requirements. Performances required for microgrid system are high renewable energy penetration with low curtailed renewable energy. Two-stage stochastic linear programming method is used to solve the optimization problem. Proposed scheduling scheme is able to increase renewable energy penetration ratio by 4% and reduce curtailed renewable energy production ratio by 7%. The combination of scheduling scheme and stochastic optimization to improve performances of microgrid system are the key outcomes of this research.
Gene Regulation and Epigenetic Remodeling in Murine Embryonic Stem Cells by c-Myc

Background The Myc oncoprotein, a transcriptional regulator involved in the etiology of many different tumor types, has been demonstrated to play an important role in the functions of embryonic stem (ES) cells. Nonetheless, it is still unclear as to whether Myc has unique target and functions in ES cells. Methodology/Principal Findings To elucidate the role of c-Myc in murine ES cells, we mapped its genomic binding sites by chromatin-immunoprecipitation combined with DNA microarrays (ChIP-chip). In addition to previously identified targets we identified genes involved in pluripotency, early development, and chromatin modification/structure that are bound and regulated by c-Myc in murine ES cells. Myc also binds and regulates loci previously identified as Polycomb (PcG) targets, including genes that contain bivalent chromatin domains. To determine whether c-Myc influences the epigenetic state of Myc-bound genes, we assessed the patterns of trimethylation of histone H3-K4 and H3-K27 in mES cells containing normal, increased, and reduced levels of c-Myc. Our analysis reveals widespread and surprisingly diverse changes in repressive and activating histone methylation marks both proximal and distal to Myc binding sites. Furthermore, analysis of bulk chromatin from phenotypically normal c-myc null E7 embryos demonstrates a 70–80% decrease in H3-K4me3, with little change in H3-K27me3, compared to wild-type embryos indicating that Myc is required to maintain normal levels of histone methylation. Conclusions/Significance We show that Myc induces widespread and diverse changes in histone methylation in ES cells. We postulate that these changes are indirect effects of Myc mediated by its regulation of target genes involved in chromatin remodeling. We further show that a subset of PcG-bound genes with bivalent histone methylation patterns are bound and regulated in response to altered c-Myc levels. Our data indicate that in mES cells c-Myc binds, regulates, and influences the histone modification patterns of genes involved in chromatin remodeling, pluripotency, and differentiation.
Order-memory and association-memory.

Two highly studied memory functions are memory for associations (items presented in pairs, such as SALT-PEPPER) and memory for order (a list of items whose order matters, such as a telephone number). Order- and association-memory are at the root of many forms of behaviour, from wayfinding, to language, to remembering people's names. Most researchers have investigated memory for order separately from memory for associations. Exceptions to this, associative-chaining models build an ordered list from associations between pairs of items, quite literally understanding association- and order-memory together. Alternatively, positional-coding models have been used to explain order-memory as a completely distinct function from association-memory. Both classes of model have found empirical support and both have faced serious challenges. I argue that models that combine both associative chaining and positional coding are needed. One such hybrid model, which relies on brain-activity rhythms, is promising, but remains to be tested rigourously. I consider two relatively understudied memory behaviours that demand a combination of order- and association-information: memory for the order of items within associations (is it William James or James William? ) and judgments of relative order (who left the party earlier, Hermann or William? ). Findings from these underexplored procedures are already difficult to reconcile with existing association-memory and order-memory models. Further work with such intermediate experimental paradigms has the potential to provide powerful findings to constrain and guide models into the future, with the aim of explaining a large range of memory functions, encompassing both association- and order-memory.
Intestinal Immunomodulatory Cells (T Lymphocytes): A Bridge between Gut Microbiota and Diabetes

Diabetes mellitus (DM) is one of the most familiar chronic diseases threatening human health. Recent studies have shown that the development of diabetes is closely related to an imbalance of the gut microbiota. Accordingly, there is increasing interest in how changes in the gut microbiota affect diabetes and its underlying mechanisms. Immunomodulatory cells play important roles in maintaining the normal functioning of the human immune system and in maintaining homeostasis. Intestinal immunomodulatory cells (IICs) are located in the intestinal mucosa and are regarded as an intermediary by which the gut microbiota affects physiological and pathological properties. Diabetes can be regulated by IICs, which act as a bridge linking the gut microbiota and DM. Understanding this bridge role of IICs may clarify the mechanisms by which the gut microbiota contributes to DM. Based on recent research, we summarize this process, thereby providing a basis for further studies of diabetes and other similar immune-related diseases.
Genome methylation patterns across castes and generations in a parasitoid wasp

Abstract Environmental influences shape phenotypes within and across generations, often through DNA methylations that modify gene expression. Methylations were proposed to mediate caste and task allocation in some eusocial insects, but how an insect's environment affects DNA methylation in its offspring is yet unknown. We characterized parental effects on methylation profiles in the polyembryonic parasitoid wasp Copidosoma koehleri, as well as methylation patterns associated with its simple caste system. We used methylation‐sensitive amplified fragment length polymorphism (MS‐AFLP) to compare methylation patterns, among (1) reproductive and soldier larvae; and (2) offspring (larvae, pupae, and adults) of wasps that were reared at either high or low larval density and mated in the four possible combinations. Methylation frequencies were similar across castes, but the profiles of methylated fragments differed significantly. Parental rearing density did not affect methylation frequencies in the offspring at any developmental stage. Principal coordinate analysis indicated no significant differences in methylation profiles among the four crossbreeding groups and the three developmental stages. Nevertheless, a clustering analysis, performed on a subset of the fragments, revealed similar methylation patterns in larvae, pupae, and adults in two of the four parental crosses. Nine fragments were methylated at two cytosine sites in all larvae, and five others were methylated at two sites in all adults. Thus, DNA methylations correlate with within‐generation phenotypic plasticity due to caste. However, their association with developmental stage and with transgenerational epigenetic effects is not clearly supported.
Asymptotics for generalized linear segmentedregression models with an

We consider asymptotic theory for the maximum likelihood esti-mator in the generalized linear model with an unknown breakpoint. A proof for the asymptotic normality is given. The methods are based on the work of Huber (1967). The main problem is the non{ diierentiability of the likelihood and the score function, which requires non{standard methods. An example from epidemiology is presented, where conndence intervals for the parameters are calculated with the asymptotic results.
The exponential Rosenbrock-Euler method for nonsmooth initial data

We consider the exponential Rosenbrock-Euler method for the solution of nonlinear parabolic abstract ordinary dierential equations. For smooth solutions the convergence analysis is known, and the method is of order two. Here we investigate the convergence of the method in the case of nonsmooth initial conditions which result in derivatives of the solution with singularities at the origin. We give an error analysis that applies to the nonsmooth case and identify conditions on the problems for which we can still observe convergence order two. Furthermore we discuss examples with respect to these assumptions.
On the Utility of Automatically Generated Wordnets

Lexical resources modelled after the original PrincetonWordNet are being compiled for a considerable number of languages, however most have yet to reach a comparable level of coverage. In this paper, we show that automatically built wordnets, created from an existing wordnet in conjunction with translation dictionaries, are a suitable alternative for many applications, despite the errors introduced by the automatic building procedure. Apart from analysing the resources directly, we conducted tests on semantic relatedness assessment and cross-lingual text classification with very promising results.
Global, Regional, and National Prevalence, Incidence, and Disability-Adjusted Life Years for Oral Conditions for 195 Countries, 1990–2015: A Systematic Analysis for the Global Burden of Diseases, Injuries, and Risk Factors

The Global Burden of Disease 2015 study aims to use all available data of sufficient quality to generate reliable and valid prevalence, incidence, and disability-adjusted life year (DALY) estimates of oral conditions for the period of 1990 to 2015. Since death as a direct result of oral diseases is rare, DALY estimates were based on years lived with disability, which are estimated only on those persons with unmet need for dental care. We used our data to assess progress toward the Federation Dental International, World Health Organization, and International Association for Dental Research’s oral health goals of reducing the level of oral diseases and minimizing their impact by 2020. Oral health has not improved in the last 25 y, and oral conditions remained a major public health challenge all over the world in 2015. Due to demographic changes, including population growth and aging, the cumulative burden of oral conditions dramatically increased between 1990 and 2015. The number of people with untreated oral conditions rose from 2.5 billion in 1990 to 3.5 billion in 2015, with a 64% increase in DALYs due to oral conditions throughout the world. Clearly, oral diseases are highly prevalent in the globe, posing a very serious public health challenge to policy makers. Greater efforts and potentially different approaches are needed if the oral health goal of reducing the level of oral diseases and minimizing their impact is to be achieved by 2020. Despite some challenges with current measurement methodologies for oral diseases, measurable specific oral health goals should be developed to advance global public health.
Perspective: The Stage‐Gate® Idea‐to‐Launch Process—Update, What's New, and NexGen Systems*

Stage-Gate has become a popular system for driving new products to market, and the benefits of using such a robust idea-to-launch system have been well documented. However, there are many misconceptions and challenges in using Stage-Gate. First, Stage-Gate is briefly outlined, noting how the system should work and the structure of both stages and gates. Next, some of the misconceptions about Stage-Gate—it is not a linear process, nor is it a rigid system—are debunked, and explanations of what Stage-Gate is and is not are provided. The challenges faced in employing Stage-Gate are identified, including governance issues, overbureaucratizing the process, and misapplying cost-cutting systems such as Six Sigma and Lean Manufacturing to product innovation. Solutions are offered, including better governance methods such as “gates with teeth,” clearly defined gatekeepers, and gatekeeper rules of engagement, as well as ways to deal with bureaucracy, including leaner gates. Next-generation versions of Stage-Gate are introduced, notably a scalable system (to handle many different types and sizes of projects), as well as even more flexible and adaptable versions of Stage-Gate achieved via spiral development and simultaneous execution. Additionally, Stage-Gate now incorporates better decision-making practices including scorecards, success criteria, self-managed gates, electronic and virtual gates, and integration with portfolio management. Improved accountability and continuous improvement are now built into Stage-Gate via a rigorous postlaunch review. Finally, progressive companies are reinventing Stage-Gate for use with “open innovation,” whereas others are applying the principles of value stream analysis to yield a leaner version of Stage-Gate.
Study on the Performance Evaluation and Weight of Knowledge Management Based on Value-Chain

Using the thought of the value -chain to represent the valuable activities of information management, also importing the concept of the important contribution of the knowledge activity , thus lays the foundation on the theory for the performance prism to evaluate information management, pointing out the framework of the performance prism. Point out the concrete indices of every panel. Calculate the weight of every index with the approach of the level, which is favorable to next appraisal research.
The Soviet Experiment: Russia, the USSR, and the Successor States . By Ronald Grigor Suny. New York: Oxford University Press, 1998. 540p. $35.00.

without a better understanding of how these more positive developments affect and coexist with the very real problems Rochlin has identified. We are also left without a clear sense of what is needed to ameliorate these problems in Mexico and of how that change might come about. The conclusion is not only vague but also remarkably moderate. The "fusion between state and societal security" can be achieved with "a functional economic system paired with legitimate political structures" (p. 187). There is no reason to believe that the author is referring to anything other than a capitalist democracy. It is puzzling, therefore, that Rochlin should call this a "fairy-tale scenario of major structural reform" (p. 187), given the modesty of the prescription as well as recent advances in Mexican economic growth and democratization. What is needed, Rochlin says in the final paragraph of the book, is "good government and. policies that generate social consent" (p. 190). Unfortunately, the book does not move us beyond this selfevident conclusion to a better appreciation of what such policies should be.
Real vs. acted emotional speech

Even though the use of actors is a popular method for researching the expression of emotion, little is known about the relation between acted and real emotions. To shed some light on this, we set up a novel experiment, based on the Velten mood induction procedure, during which participants have to utter pre-defined sentences with a strong emotional content. In one group of participants, real positive or negative emotions were induced, while another group was instructed to act positive or negative while uttering Velten sentences. Results of a mood questionnaire revealed that participants in the real emotion condition, indeed felt positive or negative, depending on whether they read positive or negative sentences, while participants in the acted emotion condition felt neutral afterwards. In a second, perception experiment, it was found that acted emotions (especially negative ones) were perceived more strongly than the real emotions. This suggests that actors do not feel the acted emotion, and may engage in overacting, which casts doubt on the usefulness of actors as a way to study real emotions.
Use of OWL within the Gene Ontology

The Gene Ontology (GO) is a ubiquitous tool in biological data analysis, and is one of the most well-known ontologies, in or outside the life sciences. Commonly conceived of as a simple terminology structured as a directed acyclic graph, the GO is actually well-axiomatized in OWL and is highly dependent on the OWL tool stack. Here we outline some of the lesser known features of the GO, describe the GO development process, and our prognosis for future development in terms of the OWL representation.
Effects of Game and Game-like Training on Neurocognitive Plasticity

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