Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in Bacillus subtilis

Gene expression during spore development in Bacillus subtilis is controlled by cell type-specific RNA polymerase sigma factors. σFand σE control early stages of development in the forespore and the mother cell, respectively. When, at an intermediate stage in development, the mother cell engulfs the forespore, σF is replaced by σG and σE is replaced by σK. The anti-sigma factor CsfB is produced under the control of σF and binds to and inhibits the auto-regulatory σG, but not σF. A position in region 2.1, occupied by an asparagine in σG and by a glutamate in οF, is sufficient for CsfB discrimination of the two sigmas, and allows it to delay the early to late switch in forespore gene expression. We now show that following engulfment completion, csfB is switched on in the mother cell under the control of σK and that CsfB binds to and inhibits σE but not σK, possibly to facilitate the switch from early to late gene expression. We show that a position in region 2.3 occupied by a conserved asparagine in σE and by a conserved glutamate in σK suffices for discrimination by CsfB. We also show that CsfB prevents activation of σG in the mother cell and the premature σG-dependent activation of σK. Thus, CsfB establishes negative feedback loops that curtail the activity of σE and prevent the ectopic activation of σG in the mother cell. The capacity of CsfB to directly block σE activity may also explain how CsfB plays a role as one of the several mechanisms that prevent σE activation in the forespore. Thus the capacity of CsfB to differentiate between the highly similar σF/σG and σE/σK pairs allows it to rinforce the cell-type specificity of these sigma factors and the transition from early to late development in B. subtilis, and possibly in all sporeformers that encode a CsfB orthologue.
Meshing Roundtable ( IMR 24 ) Moving mesh methods on parametric surfaces

Many phenomena in the applied and natural sciences occur on surfaces. To solve accurately the corresponding partial differential equations (PDEs), it is often necessary to adapt the mesh, based upon the geometry of the surface, or based upon the behaviour of the PDE solution. Moving mesh methods are particularly efficient strategies in many situations. PDEs explicitly involving the mesh speed, called moving mesh PDEs (MMPDEs), offer a robust technique to adapt the mesh. In this work, we implement, with the C++ finite element library deal.II, a mesh adaptation based on Winslow’s adaptation functional. We generalize the moving mesh problem to curved surfaces by deriving appropriate mathematical and finite element formulations. Furthermore, a simple method using surface parameterization is developed and implemented using deal.II. The results, for both fixed and dynamically adapting meshes, demonstrate the effectiveness of the method. c © 2015 The Authors. Published by Elsevier Ltd. Peer-review under responsibility of organizing committee of the 24th International Meshing Roundtable (IMR24).
Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation

After encounter with antigen, the antibody repertoire is shaped by somatic hypermutation (SHM), which leads to an increase in the affinity of antibodies for the antigen, and class-switch recombination (CSR), which results in a change in the effector function of antibodies. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID), which deaminates deoxycytidine to deoxyuridine in single-stranded DNA (ssDNA). The precise mechanism responsible for the formation of ssDNA in V regions undergoing SHM has yet to be experimentally established. In this study, we searched for ssDNA in mutating V regions in which DNA–protein complexes were preserved in the context of chromatin in human B cell lines and in primary mouse B cells. We found that V regions that undergo SHM were enriched in short patches of ssDNA, rather than R loops, on both the coding and noncoding strands. Detection of these patches depended on the presence of DNA-associated proteins and required active transcription. Consistent with this, we found that both DNA strands in the V region were transcribed. We conclude that regions of DNA that are targets of SHM assemble protein–DNA complexes in which ssDNA is exposed, making it accessible to AID.
Robust supervisor synthesis for automated manufacturing systems using Petri nets

In order to engage automated manufacturing systems in practice, a prerequisite is that they must be immune to deadlocks, which have been extensively investigated for decades by numerous researchers. To ease their effort, resources are presumptively and arbitrarily assumed never to fail; nevertheless, this is quite the opposite in reality. Actually, failures occur frequently due to various causes. In this paper, resource failures will be taken into consideration. In the paradigm of Petri nets, a robust control supervisor is developed to guarantee that the system will not be in stagnation when failures occur unexpectedly. Processes not requiring the failed resources can continue their progress smoothly. Three algorithms are proposed to achieve the tractability in deadlock-freeness, robustness, and concurrency matters, respectively. At each state, they are executed in sequence so as to attain a set of fireable transitions. Anyone of them is legal to fire by obeying these three properties. As a consequence, an appropriate firing sequence is derived so as to lead the system to a desired state. Experimental results show that the proposed approach is effective in response to resource failures.
Curved DNA in promoter sequences

Sequence-dependent DNA curvature is known to play an important role in initiation of transcription of many genes. We compared the distribution of predicted intrinsic curvature of Escherichia coli and human promoter sequences with the distribution of curvature of randomly selected coding and non-coding fragments from these organisms. Different methods of curvature calculation were found to yield mostly similar overall tendencies of DNA curvature in all groups of sequences. According to all methods of calculation, E. coli promoters were found to be more curved than coding sequences from the same genome and random sequences with the same nucleotide composition. By contrast, the average curvature of human promoter sequences was only marginally greater than the average curvature of human coding sequences. Non-coding intron sequences were found to be the most curved of the human sequences examined. Based on these observations, we hypothesize about the role of DNA curvature in promoter sequences.
Learning about Risk

The special issue "Learning about Risk" draws on the launch conference of the ESRC "Social Contexts and Responses to Risk" network (SCARR) held at 28th – 29th January 2005 in Canterbury. The SCARR network is an interdisciplinary network on risk which examines perceptions of and responses to risk in a range of areas, including sexual behaviour and partnering choices, the mass media, faith and ethnicity, pensions and financial planning, industrial pollution, crime, transport, energy policy and environmental hazards. The network's launch conference reflected the interdisciplinary character of risk research including a range of different methods and approaches to risk, directed at diverse objects of interest. The idea of the special issue is to link together this diversity and interdisciplinarity in risk research, and to encourage perspectives that look beyond the boundaries of single disciplines and methodological approaches. The papers in this publication demonstrate the value of insights from different disciplinary backgrounds in this area and point to the opportunities and challenges in the work that remains to be done in drawing these several perspectives more closely together.
A Review of Mobile Location-based Games for Learning across Physical and Virtual Spaces

In this paper we review mobile location-based games for learning. These games are played in physical space, but at the same time, they are supported by actions and events in an interconnected virtual space. Learning in these games is related to issues like the narrative structure, space and game rules and content that define the virtual game space. First, we introduce the theoretical and empirical considerations of mobile location based games, and then we discuss an analytical framework of their main characteristics through typical examples. In particular, we focus on their narrative structure, the interaction modes that they afford, their use of physical space as prop for action, the way this is linked to virtual space and the possible learning impact the game activities have. Finally we conclude with an outline of future trends and possibilities that these kinds of playful activities can have on learning, especially outside school, like in environmental studies and visits in museums and other sites of cultural and historical value.
INFLUÊNCIAS NÃO LINEARES DA INDÚSTRIA NO DESEMPENHO DA FIRMA

This paper aims to investigate the effects of the industry environment on firm’s performance, by using a non-linear regression model. The samples used range from 178 (2005) to 252 (2012) publicly traded Brazilian firms, active in the period from 2005 to 2012. The analysis, which uses the variance decomposition method, allows one to identify a tendency for the influence of rivalry to increase a firm’s performance. The quadratic relationship identified here points to an equilibrium point of the industry environment effect that, if exceeded, may cause a reverse effect on profitability. These results are in line with the view that as rivalry increases, as measured in terms of rivals’ performance, so the possibility of obtaining a better sales performance also increases, until the point where the level of rivalry intensity becomes a barrier to increasing sales any further.
Including threat actor capability and motivation in risk assessment for Smart GRIDs

The SEGRID (Security for Smart Electricity GRIDs) collaboration project, funded by the EU under the FP7 program investigates risk assessment methodologies and their possible need for enhancement. In this paper we discuss the need to include threat actor analysis in threat, vulnerability and risk assessments for smart grids based on the first findings of the practical application of the SEGRID approach to risk assessment. We motivate and propose an approach for including the threat actor's capability and motivation in such a threat, vulnerability and risk assessment.
How elevated pCO 2 modi¢es total and metabolicallyactive bacterial communities in the rhizosphere of two perennial grasses grown under ¢eld conditions

The response of total (DNA-based analysis) and active (RNA-based analysis) bacterial communities to a pCO 2 increase under ﬁeld conditions was assessed using two perennial grasses: the nitrophilic Lolium perenne and the oligonitrophilic Molinia coerulea . PCR- and reverse transcriptase-PCR denaturing gradient gel electrophoresis analysis of 16S rRNA genes generated contrasting proﬁles. The pCO 2 increase inﬂuenced mainly the active and root-associated component of the bacterial community. Bacterial groups responsive to the pCO 2 increase were identiﬁed by sequencing of corresponding denaturing gradient gel electrophoresis bands. About 50% of retrieved sequences were afﬁliated to Proteobacteria . Our data suggest that Actinobacteria in soil and Myxococcales ( Deltaproteobacteria ) in root are stimulated under elevated pCO 2 .
Real-Time NPR System with Multiple Styles

Getting the most from modern video card is important in applications ranging from computer vision to computer gaming and entertainment. To use the full power of modern graphic processing unit (GPU), we must write fragments of code that can be executed by a video card. These fragments are referred to as shaders. We implement a set of non-photorealistic shaders that can be applied to a 3D scene to produce an interactive nonphotorealistic animation. Using shaders we are able to generate scenes with different drawing styles and levels of abstraction. Produced scenes are special and temporal coherent have applications in animation, gaming and landscaping. This paper implemented as a part of “Advanced Topics in Computer Graphics” COMP-767 course in the winter of 2005 at McGill University, under supervision of prof. Allison Klein.
Additional Losses of Inverter Fed Asynchronous Induction Machines of Traction Drives – Comparison of Modelling and Measurements

Additional losses of asynchronous induction machines utilized in traction drives caused by the inverter have a great impact of the thermal behaviour of such machines. Therefore, an accurate modelling and evaluation of these additional losses is a very important task in particular with the initial design. Based on detailed measurement data from already built machines, a fast and reliable calculation method of these additional losses suitable for the initial design of new machines is presented based on equivalent circuits of the induction machine for each higher harmonic components of the terminal voltages applied by the inverter.
Coincident Activation of NMDA and Dopamine D1Receptors within the Nucleus Accumbens Core Is Required for Appetitive Instrumental Learning

The nucleus accumbens, a brain structure ideally situated to act as an interface between corticolimbic information-processing regions and motor output systems, is well known to subserve behaviors governed by natural reinforcers. In the accumbens core, glutamatergic input from its corticolimbic afferents and dopaminergic input from the ventral tegmental area converge onto common dendrites of the medium spiny neurons that populate the accumbens. We have previously found that blockade of NMDA receptors in the core with the antagonist 2-amino-5-phosphonopentanoic acid (AP-5; 5 nmol) abolishes acquisition but not performance of an appetitive instrumental learning task (Kelley et al., 1997). Because it is currently hypothesized that concurrent dopamine D1 and glutamate receptor activation is required for long-term changes associated with plasticity, we wished to examine whether the dopamine system in the accumbens core modulates learning via NMDA receptors. Co-infusion of low doses of the D1receptor antagonist SCH-23390 (0.3 nmol) and AP-5 (0.5 nmol) into the accumbens core strongly impaired acquisition of instrumental learning (lever pressing for food), whereas when infused separately, these low doses had no effect. Infusion of the combined low doses had no effect on indices of feeding and motor activity, suggesting a specific effect on learning. We hypothesize that co-activation of NMDA and D1 receptors in the nucleus accumbens core is a key process for acquisition of appetitive instrumental learning. Such an interaction is likely to promote intracellular events and gene regulation necessary for synaptic plasticity and is supported by a number of cellular models.
The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia’s macronucleus has a very unusual architecture, comprised variably and highly amplified “nanochromosomes,” each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.
On the transition from the web to the cloud

Although in principle two independent technologies, cloud computing is closely associated with the web in contemporary web applications. Such applications, usually developed using web frameworks, are increasingly often deployed on servers that reside in cloud to gain commonly assumed benefits from the cloud infrastructure. These benefits include scalability and elasticity, which liberates the developer from considering such issues during the development. Unfortunately, since the traditional origins of web applications and frameworks used to development them are very different from cloud computing platforms, a mismatch may emerge between the web application and the hosting cloud platform. Then, strengths of the cloud computing may be invalidated by the design of the web application. In this paper, we analyze the consequences of the transition of web application to the cloud by considering the fundamental assumptions in web frameworks and the potential challenges they introduce when used in cloud context.
A corpus of Australian contract language: description, profiling and analysis

Written contracts are a fundamental framework for economic and cooperative transactions in society. Little work has been reported on the application of natural language processing or corpus linguistics to contracts. In this paper we report the design, profiling and initial analysis of a corpus of Australian contract language. This corpus enables a quantitative and qualitative characterisation of Australian contract language as an input to the development of contract drafting tools. Profiling of the corpus is consistent with its suitability for use in language engineering applications. We provide descriptive statistics for the corpus and show that document length and document vocabulary size approximate to log normal distributions. The corpus conforms to Zipf's law and comparative type to token ratios are consistent with lower term sparsity (an expectation for legal language). We highlight distinctive term usage in Australian contract language. Results derived from the corpus indicate a longer prepositional phrase depth in sentences in contract rules extracted from the corpus, as compared to other corpora.
Molecular basis of protein S deficiency

Summary Protein S deficiency (PSD) has been the most difficult to study among the classical inherited thrombophilic factors. This is in part due to the peculiar biology of protein S (PS), which has an anticoagulant role but no enzymatic activity,and because it interacts with plasma components that function in both haemostasis and inflammation.Clinically,it also has been difficult to define and standardise valuable assays to determine PS status and implication in thrombosis. Despite these drawbacks, at present heterozygous PS deficiency is well established as an autosomal dominant trait associated with an increased risk of thrombosis from data on familial and population studies. Almost twohundred mutations have been characterised in PROS1, and approximately 30% of them have been characterised in vitro,clarifying the mechanisms leading to PSD. Furthermore, recent studies on the presence of large deletions in PROS1 have increased the number of PSD associated to PROS1 mutations. Finally, the discovery of new functions for PS, both in the anticoagulant system as well as in the interaction with cellular components through receptor tyrosine kinases, is broadening the importance of this molecule in the context of biomedicine.
Guidelines for Designing Computational Models of Emotions

Rapid growth in computational modeling of emotion and cognitive-affective architectures occurred over the past 15 years. Emotion models and architectures are built to elucidate the mechanisms of emotions and enhance believability and effectiveness of synthetic agents and robots. Despite the many emotion models developed to date, a lack of consistency and clarity regarding what exactly it means to 'model emotions' persists. There are no systematic guidelines for development of computational models of emotions. This paper deconstructs the often vague term 'emotion modeling' by suggesting the view of emotion models in terms of two fundamental categories of processes: emotion generation and emotion effects. Computational tasks necessary to implement these processes are also identified. The paper addresses how computational building blocks provide a basis for the development of more systematic guidelines for affective model development. The paper concludes with a description of an affective requirements analysis and design process for developing affective computational models in agent architectures.
Reactive nitrogen species regulate autophagy through ATM-AMPK-TSC2–mediated suppression of mTORC1

Significance NO exposure triggered an ATM-mediated damage response in breast cancer cells involving activation of the LKB1 and TSC2 tumor suppressors, repression of mTORC1, ULK phosphorylation, and increased autophagic flux. The associated loss of cell viability indicates that autophagy can function as a cytotoxic response to nitrosative stress in tumor cells. Collectively, the data identify a nitrosative-stress signaling pathway that regulates autophagy. A more comprehensive understanding of signaling pathways regulating autophagy holds promise for developing new therapeutic approaches compromising prosurvival autophagic pathways that enable tumor cells to evade therapy, or promoting prodeath autophagic pathways that kill cancer cells. Reactive intermediates such as reactive nitrogen species play essential roles in the cell as signaling molecules but, in excess, constitute a major source of cellular damage. We found that nitrosative stress induced by steady-state nitric oxide (NO) caused rapid activation of an ATM damage-response pathway leading to downstream signaling by this stress kinase to LKB1 and AMPK kinases, and activation of the TSC tumor suppressor. As a result, in an ATM-, LKB1-, TSC-dependent fashion, mTORC1 was repressed, as evidenced by decreased phosphorylation of S6K, 4E-BP1, and ULK1, direct targets of the mTORC1 kinase. Decreased ULK1 phosphorylation by mTORC1 at S757 and activation of AMPK to phosphorylate ULK1 at S317 in response to nitrosative stress resulted in increased autophagy: the LC3-II/LC3-I ratio increased as did GFP-LC3 puncta and acidic vesicles; p62 levels decreased in a lysosome-dependent manner, confirming an NO-induced increase in autophagic flux. Induction of autophagy by NO correlated with loss of cell viability, suggesting that, in this setting, autophagy was functioning primarily as a cytotoxic response to excess nitrosative stress. These data identify a nitrosative-stress signaling pathway that engages ATM and the LKB1 and TSC2 tumor suppressors to repress mTORC1 and regulate autophagy. As cancer cells are particularly sensitive to nitrosative stress, these data open another path for therapies capitalizing on the ability of reactive nitrogen species to induce autophagy-mediated cell death.