Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Applications in Genetics and Molecular Biology MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection

MicroRNAs (miRNAs) are non-coding, short (21-23nt) regulators of protein-coding genes that are generally transcribed first into primary miRNA (pri-miR), followed by the generation of precursor miRNA (pre-miR). This finally leads to the production of the mature miRNA. A large amount of information is available on the preand mature miRNAs. However, very little is known about the pri-miRs, due to a lack of knowledge about their transcription start sites (TSSs). Based on the genomic loci, miRNAs can be categorized into two types —intragenic (intra-miR) and intergenic (inter-miR). While it is already an established fact that intra-miRs are commonly transcribed in conjunction with their host genes, the transcription machinery of intermiRs is poorly understood. Although it is assumed that miRNA promoters are similar in structure to gene promoters, since both are transcribed by RNA polymerase II (Pol II), computational validations exhibit poor performance of gene promoter prediction methods on miRNAs. In this paper, we concentrate on the problem of TSS prediction for miRNAs. The present study begins with the identification of positive and negative promoter samples from recently published data stemming from RNA-sequencing studies. From these samples of experimentally validated miRNA TSSs, a number of standard sequence features are extracted. Furthermore, to account for potential footprints related to promoter regulation by CpG dinucleotide targeted DNA methylation, a number of novel features are defined. We develop a support vector machine (SVM) with RBF kernel for the prediction of miRNA TSSs trained on human miRNA promoters. A novel feature reduction technique based on archived multi-objective simulated annealing (AMOSA) identifies the final set of features. The resulting model trained on miRNA promoters shows improved performance over the one trained on protein-coding gene promoters in terms of classification accuracy, sensitivity and specificity. Results are also reported for a completely independent biologically validated test set. In a part of the investigation, the proposed approach is used to predict protein-coding gene TSSs. It shows a significantly improved performance when compared to previously published gene TSS prediction methods.
Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism

Microbes are usually believed to have cosmopolitan distributions. However, for estimating the global distributions of microorganisms, discriminating among cryptic species and eliminating undersampling biases are important challenges. We used a novel approach to address these problems and infer the global distribution of a given fungal ecological guild. We collected mushroom‐forming fungi from Yakushima, Japan. We sequenced the internal transcribed spacer 2 (ITS2) from these samples and queried their sequences against GenBank. After identifying similar sequences, we tracked down the geographical origins of samples that yielded those sequences. We used Bayesian zero‐inflated models to allow for species whose DNA sequences have not yet been deposited in GenBank. Results indicated that the geographical distribution of ectomycorrhizal (ECM) fungi was strongly constrained by host specificity, resulting in the occurrence of these fungi intensively in the neighbouring regions. On the other hand, saprotrophic (SAP) fungi were less constrained by climatic conditions, resulting in a much broader distribution range. We inferred that differences in constraints during colonization between ECM and SAP fungi were responsible for the different geographical distribution ranges. We hypothesize that the degree of host/habitat specificity and the degree of isolation of potentially suitable habitats determine microbial biogeographic patterns.
Not That Alternative: Short-term Volunteer Tourism at an Organic Farming Project in Costa Rica

Drawing on interview-based research with seven young Canadian women who volunteered briefly at an organic farming project in Costa Rica, supplemented by participant observation with a larger group of volunteers and conversations with local people and the farm’s owners, this paper offers an empirically grounded critique of short-term international volunteering. It demonstrates that, despite the claims of the voluntourism industry and the hopeful rhetoric of much academic literature, international volunteering does not reliably yield discernable material contributions to social development or environmental sustainability in ‘host communities’, meaningful trans-cultural understanding between locals and volunteers, or, in the short-term at least, transformative reflexive self-development among volunteers. Nor in the case under examination did it “challenge the very foundations of contemporary tourism and capitalist globalisation” (Higgins-Desboilles and Russell-Mundine, 2008, 186). Rather, “volunteerism” was almost entirely subordinated to “tourism” as a framework for imagining, understanding, coordinating, and performing Northern selves in the context of participants’ trips to Costa Rica. The paper traces five main dimensions of this ‘transformative failure’: (a) the hierarchical binary between Northern subject and Southern object on which discourses of international volunteering depend, (b) short-term volunteering’s reliance on a tourism infrastructure, (c) the farm’s specific characteristics as a volunteering project, (d) the short duration of participants’ volunteering stint, and (e) the behavioural outcomes of volunteers’ consequent disillusionment with their experience over the course of the trip.
Does autonomic arousal distinguish good and bad decisions? Healthy individuals’ skin conductance reactivity during the Iowa Gambling Task

The somatic marker hypothesis (SMH) proposes that physiological feedback to the brain influences cognitive appraisal and human decisions, however, the strength of evidence in support of the SMH is equivocal. We examined the validity of the SMH by measuring physiological arousal in a population of healthy individuals playing the Iowa Gambling Task (IGT), which is a computerized card game designed to assess real-life decisions. We also examined the influence of reinforcer type on IGT performance and physiological reactivity. Skin conductance level (SCL) reactivity was measured in 41 participants performing the IGT using either facsimile or real money. Participants were categorized as normal (i.e., nonimpaired) or impaired on the basis of their IGT performance, and differences in performance and physiological reactivity between groups were examined. No differences in SCL were found between normal and impaired groups. However, greater SCL rises were borderline significant when anticipating choices from bad de.
Crime control and community: The new politics of public safety

Introduction: community-based crime control in retrospect and prospects by Adam Edwards and Gordon Hughes 1. Plotting the rise of community safety: critical reflections on research, theory and politics by Gordon Hughes 2. 'Same bed, different dreams': postmodern reflections on crime prevention and community safety by Eugene McLaughlin 3. The rediscovery of learning by Nick Tilley 4. People pieces: the neglected but essential elements of community crime prevention by Janet Foster 5. Power, politics and partnerships: the state of crime prevention on Merseyside by Roy Coleman, Joe Sim and Dave Whyte 6. Community safety in England by Kevin Stenson 7. Deficits of power and simulations of control: local crime control strategies in London by Simon Hallsworth 8. The strategic dilemmas of community-based crime control: learning from diversity in the East Midlands by Adam Edwards Conclusion: drawing lessons about community-based crime control and safety politics by Adam Edwards, Gordon Hughes and Henry Shaftoe
Comparative Analysis and Classification of Cassette Exons and Constitutive Exons

Alternative splicing (AS) is a major engine that drives proteome diversity in mammalian genomes and is a widespread cause of human hereditary diseases. More than 95% of genes in the human genome are alternatively spliced, and the most common type of AS is the cassette exon. Recent discoveries have demonstrated that the cassette exon plays an important role in genetic diseases. To discover the formation mechanism of cassette exon events, we statistically analyze cassette exons and find that cassette exon events are strongly influenced by individual exons that are smaller in size and that have a lower GC content, more codon terminations, and weaker splice sites. We propose an improved random-forest-based hybrid method of distinguishing cassette exons from constitutive exons. Our method achieves a high accuracy in classifying cassette exons and constitutive exons and is verified to outperform previous approaches. It is anticipated that this study will facilitate a better understanding of the underlying mechanisms in cassette exons.
Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species

The Marinobacter genus comprises widespread marine bacteria, found in localities as diverse as the deep ocean, coastal seawater and sediment, hydrothermal settings, oceanic basalt, sea-ice, sand, solar salterns, and oil fields. Terrestrial sources include saline soil and wine-barrel-decalcification wastewater. The genus was designated in 1992 for the Gram-negative, hydrocarbon-degrading bacterium Marinobacter hydrocarbonoclasticus. Since then, a further 31 type strains have been designated. Nonetheless, the metabolic range of many Marinobacter species remains largely unexplored. Most species have been classified as aerobic heterotrophs, and assessed for limited anaerobic pathways (fermentation or nitrate reduction), whereas studies of low-temperature hydrothermal sediments, basalt at oceanic spreading centers, and phytoplankton have identified species that possess a respiratory repertoire with significant biogeochemical implications. Notable physiological traits include nitrate-dependent Fe(II)-oxidation, arsenic and fumarate redox cycling, and Mn(II) oxidation. There is also evidence for Fe(III) reduction, and metal(loid) detoxification. Considering the ubiquity and metabolic capabilities of the genus, Marinobacter species may perform an important and underestimated role in the biogeochemical cycling of organics and metals in varied marine habitats, and spanning aerobic-to-anoxic redox gradients.
Swearing: A "Bad" Part of Language; A Good Part of Language Learning

This article proposes that class treatment of taboo language can be beneficial for language learning students. This is not to say that all groups of ESL learners would benefit, nor that instructors should teach their students how to swear in English. However, I suggest that learners need to understand what constitutes "obscene" language in North American contexts, why native speakers choose to use it, and what it signifies sociolinguistically. Arguments are made as to why an ESL classroom may be one of the better places (i.e., a more responsible, mature environment) where L2 speakers can receive explanations about the usage and paradoxes involved in swearing. The author's experience related to the use of taboo language by L2 speakers in a non-English speaking environment is described. In addition, some non-linguistic variables relevant to cursing are also discussed. As a means to open this topic for discussion, this article suggests that there is, in terms of sociolinguistics, study value in the nature and use of obscene language for language learners.
Perceptions of peer pressure, peer conformity dispositions, and self-reported behavior among adolescents.

Chez deux echantillons d'adolescents des grades 6 a 12 sont etudiees les dispositions a acceder a la pression des pairs, les perceptions de cette pression et les auto-appreciations de la frequence des comportements lies au degre de socialisation avec les amis et aux mauvaises conduites
Predicting Type 2 Diabetes Based on Polymorphisms From Genome-Wide Association Studies

OBJECTIVE—Prediction of type 2 diabetes based on genetic testing might improve identification of high-risk subjects. Genome-wide association (GWA) studies identified multiple new genetic variants that associate with type 2 diabetes. The predictive value of genetic testing for prediction of type 2 diabetes in the general population is unclear. RESEARCH DESIGN AND METHODS—We investigated 18 polymorphisms from recent GWA studies on type 2 diabetes in the Rotterdam Study, a prospective, population-based study among homogeneous Caucasian individuals of 55 years and older (genotyped subjects, n = 6,544; prevalent cases, n = 686; incident cases during follow-up, n = 601; mean follow-up 10.6 years). The predictive value of these polymorphisms was examined alone and in addition to clinical characteristics using logistic and Cox regression analyses. The discriminative accuracy of the prediction models was assessed by the area under the receiver operating characteristic curves (AUCs). RESULTS—Of the 18 polymorphisms, the ADAMTS9, CDKAL1, CDKN2A/B-rs1412829, FTO, IGF2BP2, JAZF1, SLC30A8, TCF7L2, and WFS1 variants were associated with type 2 diabetes risk in our population. The AUC was 0.60 (95% CI 0.57–0.63) for prediction based on the genetic polymorphisms; 0.66 (0.63–0.68) for age, sex, and BMI; and 0.68 (0.66–0.71) for the genetic polymorphisms and clinical characteristics combined. CONCLUSIONS—We showed that 9 of 18 well-established genetic risk variants were associated with type 2 diabetes in a population-based study. Combining genetic variants has low predictive value for future type 2 diabetes at a population-based level. The genetic polymorphisms only marginally improved the prediction of type 2 diabetes beyond clinical characteristics.
Surface Learning with Applications to Lipreading

Most connectionist research has focused on learning mappings from one space to another (eg. classification and regression). This paper introduces the more general task of learning constraint surfaces. It describes a simple but powerful architecture for learning and manipulating nonlinear surfaces from data. We demonstrate the technique on low dimensional synthetic surfaces and compare it to nearest neighbor approaches. We then show its utility in learning the space of lip images in a system for improving speech recognition by lip reading. This learned surface is used to improve the visual tracking performance during recognition.
Using Butterfly-Patterned Partial Sums to Draw from Discrete Distributions

We describe a SIMD technique for drawing values from multiple discrete distributions, such as sampling from the random variables of a mixture model, that avoids computing a complete table of partial sums of the relative probabilities. A table of alternate ("butterfly-patterned") form is faster to compute, making better use of coalesced memory accesses; from this table, complete partial sums are computed on the fly during a binary search. Measurements using CUDA 7.5 on an NVIDIA Titan Black GPU show that this technique makes an entire machine-learning application that uses a Latent Dirichlet Allocation topic model with 1024 topics about about 13% faster (when using single-precision floating-point data) or about 35% faster (when using double-precision floating-point data) than doing a straightforward matrix transposition after using coalesced accesses.
Re-usable features in a hierarchical concept network for autonomous learning in complex games

The use of re-usable features to define conceptual elements is a recognised trait in many models of semantic memory, and provides advantages in efficiency of representation, and a manner to preserve links between related concepts. In order to form scalable and generalisable representations, autonomous systems are advantaged by the ability to re-use features, and to develop such a network of features autonomously. Existing learning systems that build knowledge structures in a reinforcement based environment tend to use separately defined rules, rather than re-use of shared features. The system described is a form of Learning Classifier System, based on the Activation-Reinforcement Classifier System that reinforces rules according to separate properties of expected reward and accessibility. This provides a useful platform for examining the construction of rules from re-used features. An implementation is described that constructs a network of features, that are used to define rules. This is able to operate successfully on the game of Dots and Boxes, providing stable operation and the ability to activate rules from a body of 4000 autonomously developed features. Examining the network produced shows a scale-free connectivity distribution, which is a property common in human semantic networks.
Developing Industrial Multi-Agent Systems †

problem solving and to interact with other community members. The interactions typically involve agents cooperating and communicating with one another in order to enhance their individual problem solving and to better solve the overall application problem. Each agent consists of an ARCHON Layer (AL) and an application program (known as an Intelligent System (IS)). Purpose-built ISs can make use of the ARCHON functionality to enhance their problem solving and to improve their robustness. However pre-existing ISs can also be incorporated, with a little adaptation, and can experience similar benefits (Jen-nings et al., 1993). This latter point is important because in many cases developing the entire application afresh would be considered too expensive or too large a change away from proven technology (Jennings and Wittig, 1992). To successfully incorporate both purpose-built and pre-existing systems, community design must be carried out from two different perspectives simultaneously. A top down approach is needed to look at the overall needs of the application and a bottom up approach is needed to look at the capabilities of the existing systems. Once the gap between what is required and what is available has been identified, the system designer can choose to provide the additional functionality through new systems, through additions to the existing systems, or through the ARCHON software itself. This methodology, which is described more thoroughly in Varga et al. (1994), shapes the design process by providing guidelines for problem decomposition and distribution which reduce inefficiencies. This paper is organised along the following lines: section two provides an overview of the ARCHON architecture. Section three describes the Iberdrola application-it involves seven heterogeneous agents, a substantial number of which were purpose built, which perform three main types of activity (data acquisition, fault diagnosis, and service restoration) and cooperate in a number of different styles. Finally, section four highlights some key experiences which impact upon the design and implementation of future DAI systems. The ARCHON software has been used to integrate a wide variety of application program types under the general assumption that the ensuing agents will be loosely coupled and semi-autonomous. The ISs themselves can be heterogeneous in terms of their programming language, their 1. Iberdrola is a large Spanish electric utility. Their transport network , on which this application operates, is controlled by the North Dispatch Control Room (DCR) located in Bilbao. Abstract The development and deployment of multi-agent systems in real world settings raises …
On Young Neutron Stars as Propellers and Accretors with Conventional Magnetic Fields

The similarity of rotation periods of the anomalous X-ray pulsars (AXPs), the soft gamma-ray repeaters (SGRs), and the dim isolated thermal neutron stars (DTNs) suggests a common mechanism with an asymptotic spin-down phase, extending through the propeller and early accretion stages. The DTNs are interpreted as sources in the propeller stage. Their luminosities arise from frictional heating in the neutron star. If the 8.4 s rotation period of the DTN RX J0720.4-3125 is close to its rotational equilibrium period, the estimated propeller torque indicates a magnetic field in the 1012 G range. The mass inflow rate onto the propeller is on the order of the accretion rates of the AXPs. The limited range of rotation periods, taken to be close to equilibrium periods, and conventional magnetic fields in the range 5 × 1011 to 5 × 1012 G correspond to a range of mass inflow rates 3.2 × 1014 g s-1< Ṁ < 4.2 × 1017 g s-1. Observed spin-down rates of the AXPs and SGRs also fit in with estimates for these magnetic fields and equilibrium periods. The source of the mass inflow is a remnant accretion disk formed as part of the fallback during the supernova explosion. These classes of sources thus represent the alternative pathways for those neutron stars that do not become radio pulsars. For the highest mass inflow rates the propeller action may support enough circumstellar material so that the optical thickness to electron scattering destroys the X-ray beaming, and the rotation period is not observable. These are the radio-quiet neutron stars at the centers of supernova remnants Cas A, Puppis A, RCW 103, and 296.5+10. The statistics and ages of DTNs suggest that sources in the propeller phase are quite common, maybe accounting for the majority of neutron stars formed in supernovae. AXPs are the rare cases whose Ṁ history has allowed them to evolve rapidly to the post-propeller accretion phase. The different classes represent alternative pathways rather than consecutive phases of evolution. Thus, for example, the AXPs are not descendants of the DTNs. This model obviates the need to postulate magnetars for AXPs and DTNs. Frequently sampled timing observations of AXPs, SGRs, and DTNs can distinguish between this explanation and the magnetar model.
Mechanisms of retroaxonal barrage firing in hippocampal interneurons

• Persistent firing can be triggered in a population of inhibitory interneurons found in the hippocampus and neocortex. Repeated stimulation eventually triggers an autonomous barrage of spikes that is generated and maintained in the axon, followed by antidromic propagation to the soma. • This barrage of spikes is generated and maintained in the axon, followed by antidromic propagation to the soma. The mechanisms underlying this ‘retroaxonal barrage firing’ are unknown. • We find that retroaxonal barrage firing is Ca2+ dependent, is inhibited by the L‐type Ca2+ channel blockers cadmium, nifedipine and verapamil, and does not require synaptic transmission. Loading the stimulated interneuron with BAPTA did not block barrage firing, suggesting that the required Ca2+ entry may occur in other cells. • Retroaxonal barrage firing was observed in mice lacking the Cx36 isoform (most common neuronal isoform), indicating that this particular isoform is not required.
Metodologías multicriterio para toma de decisiones en gestión de proyectos: la integración de los agentes gestores como beneficio indirecto

Correct decision making in project management takes into account all of the components and the whole life-cycle of the project, but primarily focuses on all of the stakeholders. An example (deciding between alternative homes to buy) shows the integration of economic, functional, social and environmental requirements. In order to score alternatives, costs, vulnerability, location, aesthetics, natural resources, sustainability, etc. are considered. It is also justified, in an indirect way, that the proper application of the methodology integrates agents, lessening the possibility of conflict and achieving greater efficiency in management. The methodology, as described, is ready to be applied to any project.