Miracle-dz/UniFAR-FTUs huggingface dataset:
Metacommunity structuring in stream networks: roles of dispersal mode, distance type, and regional environmental context

Within a metacommunity, both environmental and spatial processes regulate variation in local community structure. The strength of these processes may vary depending on species traits (e.g., dispersal mode) or the characteristics of the regions studied (e.g., spatial extent, environmental heterogeneity). We studied the metacommunity structuring of three groups of stream macroinvertebrates differing in their overland dispersal mode (passive dispersers with aquatic adults; passive dispersers with terrestrial adults; active dispersers with terrestrial adults). We predicted that environmental structuring should be more important for active dispersers, because of their better ability to track environmental variability, and that spatial structuring should be more important for species with aquatic adults, because of stronger dispersal limitation. We sampled a total of 70 stream riffle sites in three drainage basins. Environmental heterogeneity was unrelated to spatial extent among our study regions, allowing us to examine the effects of these two factors on metacommunity structuring. We used partial redundancy analysis and Moran's eigenvector maps based on overland and watercourse distances to study the relative importance of environmental control and spatial structuring. We found that, compared with environmental control, spatial structuring was generally negligible, and it did not vary according to our predictions. In general, active dispersers with terrestrial adults showed stronger environmental control than the two passively dispersing groups, suggesting that the species dispersing actively are better able to track environmental variability. There were no clear differences in the results based on watercourse and overland distances. The variability in metacommunity structuring among basins was not related to the differences in the environmental heterogeneity and spatial extent. Our study emphasized that (1) environmental control is prevailing in stream metacommunities, (2) dispersal mode may have an important effect on metacommunity structuring, and (3) some factors other than spatial extent or environmental heterogeneity contributed to the differences among the basins.
Adherence to the Mediterranean type of diet is associated with lower prevalence of asthma symptoms, among 10–12 years old children: the PANACEA study

To cite this article: Arvaniti F, Priftis KN, Papadimitriou A, Papadopoulos M, Roma E, Kapsokefalou M, Antracopoulos MB, Panagiotakos DB. Adherence to the Mediterranean type of diet is associated with lower prevalence of asthma symptoms, among 10–12 years old children: the PANACEA study. Pediatr Allergy Immunol 2011; 22: 283–289.
A Motion Retargeting Method for Effective Mimicry-Based Teleoperation of Robot Arms

In this paper, we introduce a novel interface that allows novice users to effectively and intuitively tele-operate robot manipulators. The premise of our method is that an interface that allows its user to direct a robot arm using the natural 6-DOF space of his/her hand would afford effective direct control of the robot; however, a direct mapping between the user's hand and the robot's end effector is impractical because the robot has different kinematic and speed capabilities than the human arm. Our key technical idea that by relaxing the constraint of the direct mapping between hand position and orientation and end effector configuration, a system can provide the user with the feel of direct control, while still achieving the practical requirements for telemanipulation, such as motion smoothness and singularity avoidance. We present methods for implementing a motion retargeting solution that achieves this relaxed control using constrained optimization and describe a system that utilizes it to provide real-time control of a robot arm. We demonstrate the effectiveness of our approach in a user study that shows novice users can complete a range of tasks more efficiently and enjoyably using our relaxed-mimicry based interface compared to standard interfaces.
Screen ecologies, multi-gaming and designing for different registers of engagement

In this paper, we propose the notion of screen ecologies and argue for its importance in the study of contemporary digital game play. We draw on findings from a range of studies to highlight the interplay between screen ecologies, game design, and registers of engagement. We discuss how game play is increasingly mediated by multiple screen configurations, and in turn, how the design of different games are suited to or appropriated within these different screen ecologies. From this analysis we propose a number of modalities of game-engagement that we argue will assist further HCI research into game design and player experience research.
Author ' s personal copy Effective optical properties of highly ordered mesoporous thin fi lms

a r t i c l e i n f o This paper expands our previous numerical studies predicting the optical properties of highly ordered mesoporous thin films from two-dimensional (2D) nanostructures with cylindrical pores to three-dimensional (3D) structures with spherical pores. Simple, face centered, and body centered cubic lattices of spherical pores and hexagonal lattice of cylindrical pores were considered along with various pore diameters and porosities. The transmittance and reflectance were numerically computed by solving 3D Maxwell's equations for transverse electric and transverse magnetic polarized waves normally incident on the mesoporous thin films. The effective optical properties of the films were determined by an inverse method. Reflectance of 3D cubic mesoporous thin films was found to be independent of polarization, pore diameter, and film morphology and depended only on film thickness and porosity. By contrast, reflectance of 2D hexagonal mesoporous films with cylindrical pores depended on pore shape and polarization. The unpolarized reflectance of 2D hexagonal mesoporous films with cylindrical pores was identical to that of 3D cubic mesoporous films with the same porosity and thickness. The effective refractive and absorption indices of 3D films show good agreement with predictions by the 3D Maxwell–Garnett and nonsymmetric Bruggeman effective medium approximations, respectively.
Discontinuous epitope prediction based on mimotope analysis

MOTIVATION Phage display is a widespread technique used to obtain peptide mimotopes selected by binding to a given monoclonal antibody in a similar way as the native epitope. However, the localization of the interaction site mimicked by the mimotopes on the surface of the antigen is not always a straightforward task. MIMOP is a computational tool developed with the aim of helping experimentalists to analyze a set of mimotope sequences and guide them in the identification of the mimicked region. RESULTS To predict potential epitopic regions, MIMOP integrates two different approaches combining two- and three-dimensional analyses: MimAlign starts from degenerated alignment analyses, and MimCons is based on consensus identification. The relevance and usefulness of the tool are illustrated by four use cases corresponding to real-life situations.
Telomere Dynamics in Immune Senescence and Exhaustion Triggered by Chronic Viral Infection

The progressive loss of immunological memory during aging correlates with a reduced proliferative capacity and shortened telomeres of T cells. Growing evidence suggests that this phenotype is recapitulated during chronic viral infection. The antigenic volume imposed by persistent and latent viruses exposes the immune system to unique challenges that lead to host T-cell exhaustion, characterized by impaired T-cell functions. These dysfunctional memory T cells lack telomerase, the protein capable of extending and stabilizing chromosome ends, imposing constraints on telomere dynamics. A deleterious consequence of this excessive telomere shortening is the premature induction of replicative senescence of viral-specific CD8+ memory T cells. While senescent cells are unable to expand, they can survive for extended periods of time and are more resistant to apoptotic signals. This review takes a closer look at T-cell exhaustion in chronic viruses known to cause human disease: Epstein–Barr virus (EBV), Hepatitis B/C/D virus (HBV/HCV/HDV), human herpesvirus 8 (HHV-8), human immunodeficiency virus (HIV), human T-cell leukemia virus type I (HTLV-I), human papillomavirus (HPV), herpes simplex virus-1/2 (HSV-1/2), and Varicella–Zoster virus (VZV). Current literature linking T-cell exhaustion with critical telomere lengths and immune senescence are discussed. The concept that enduring antigen stimulation leads to T-cell exhaustion that favors telomere attrition and a cell fate marked by enhanced T-cell senescence appears to be a common endpoint to chronic viral infections.
Brain-Computer Interface Controlled Cyborg: Establishing a Functional Information Transfer Pathway from Human Brain to Cockroach Brain

An all-chain-wireless brain-to-brain system (BTBS), which enabled motion control of a cyborg cockroach via human brain, was developed in this work. Steady-state visual evoked potential (SSVEP) based brain-computer interface (BCI) was used in this system for recognizing human motion intention and an optimization algorithm was proposed in SSVEP to improve online performance of the BCI. The cyborg cockroach was developed by surgically integrating a portable microstimulator that could generate invasive electrical nerve stimulation. Through Bluetooth communication, specific electrical pulse trains could be triggered from the microstimulator by BCI commands and were sent through the antenna nerve to stimulate the brain of cockroach. Serial experiments were designed and conducted to test overall performance of the BTBS with six human subjects and three cockroaches. The experimental results showed that the online classification accuracy of three-mode BCI increased from 72.86% to 78.56% by 5.70% using the optimization algorithm and the mean response accuracy of the cyborgs using this system reached 89.5%. Moreover, the results also showed that the cyborg could be navigated by the human brain to complete walking along an S-shape track with the success rate of about 20%, suggesting the proposed BTBS established a feasible functional information transfer pathway from the human brain to the cockroach brain.
Learning the post-contact reconfiguration of the hand object system for adaptive grasping mechanisms

A new class of simple, adaptive, under-actuated and compliant robot hands has recently attracted the interest of the robotics community. The under-actuated mechanisms and the structural compliance used in these hands facilitate and robustify not only grasping but also the execution of dexterous, in-hand manipulation tasks. Another significant characteristic of the particular hands is that they are able to efficiently grasp a wide range of everyday life objects even under significant object pose uncertainties. However, these hands, are difficult to model due to kinematic constraints introduced by the underactuation and the use of complex flexure joints. Moreover, adaptive hands tend to reconfigure upon contact with the object surface, imposing certain parasitic object motions. In this paper, we propose a learning scheme that uses the contact force measurements collected from tactile sensors to estimate the post-contact reconfiguration of the hand-object system and the imposed parasitic object motion. The learning scheme's estimates are compared with “ground truth” data that describe the actual motion of the object and that are collected using a vision based motion capture system. The proposed learning scheme can be used with any type of adaptive robot hand and its efficiency is experimentally validated using extensive paradigms involving different hand designs and various everyday life objects.
Consciousness doesn't overflow cognition

Theories of consciousness can be separated into those that see it as cognitive in nature, or as an aspect of cognitive functioning, and those that see consciousness as importantly distinct from any kind of cognitive functioning. One version of the former kind of theory is the higher-order-thought theory of consciousness. This family of theories posits a fundamental role for cognitive states, higher-order thought-like intentional states, in the explanation of conscious experience. These states are higher-order in that they represent the subject herself as being in various world-directed first-order states and thus constitute a kind of cognitive access to one's own mental life. This distinctive cognitive access is postulated to account for what it is like for one to have a conscious experience.
Scoring-and-Unfolding Trimmed Tree Assembler: Algorithms for Assembling Genome Sequences Accurately and Efficiently

The recent advances in DNA sequencing technology and their many potential applications to Biology and Medicine have rekindled enormous interest in several classical algorithmic problems at the core of Genomics and Computational Biology: primarily, the whole-genome sequence assembly problem (WGSA). Two decades back, in the context of the Human Genome Project, the problem had received unprecedented scientific prominence: its computational complexity and intractability were thought to have been well understood; various competitive heuristics, thoroughly explored and the necessary software, properly implemented and validated. However, several recent studies, focusing on the experimental validation of de novo assemblies, have highlighted several limitations of the current assemblers. Intrigued by these negative results, this dissertation reinvestigates the algorithmic techniques required to correctly and efficiently assemble genomes. Mired by its connection to a well-known NP -complete combinatorial optimization problem, historically, WGSA has been assumed to be amenable only to greedy and heuristic methods. By placing efficiency as their priority, these methods opted to rely on local searches, and are thus inherently approximate, ambiguous or error-prone. This dissertation presents a novel sequence assembler, SUTTA, that dispenses with the idea of limiting the solutions to just the approximated ones, and instead favors an approach that could potentially lead to an exhaustive (exponential-time) search of all possible layouts but tames the complexity through constrained search (Branch-and-Bound) and quick identification and pruning of implausible solutions. Complementary to this problem is the task of validating the generated assemblies. Unfortunately, no commonly accepted method exists yet and widely used metrics to compare the assembled sequences emphasize only size, poorly capturing quality and accuracy. This dissertation also addresses these concerns by developing a more comprehensive metric, the Feature-Response Curve, that, using ideas from classical ROC (receiver-operating characteristic) curve, more faithfully captures the trade-off between contiguity and quality. Finally, this dissertation demonstrates the advantages of a complete pipeline integrating base-calling (TotalReCaller) with assembly (SUTTA) in a Bayesian manner.
A Periplasmic and Extracellular c-Type Cytochrome ofGeobacter sulfurreducens Acts as a Ferric Iron Reductase and as an Electron Carrier to Other Acceptors or to Partner Bacteria

ABSTRACT An extracellular electron carrier excreted into the growth medium by cells of Geobacter sulfurreducens was identified as ac-type cytochrome. The cytochrome was found to be distributed in about equal amounts in the membrane fraction, the periplasmic space, and the surrounding medium during all phases of growth with acetate plus fumarate. It was isolated from periplasmic preparations and purified to homogeneity by cation-exchange chromatography, gel filtration, and hydrophobic interaction chromatography. The electrophoretically homogeneous cytochrome had a molecular mass of 9.57 ± 0.02 kDa and exhibited in its reduced state absorption maxima at wavelengths of 552, 522, and 419 nm. The midpoint redox potential determined by redox titration was −0.167 V. With respect to molecular mass, redox properties, and molecular features, this cytochrome exhibited its highest similarity to the cytochromes c of Desulfovibrio salexigensand Desulfuromonas acetoxidans. TheG. sulfurreducens cytochrome c reduced ferrihydrite (Fe(OH)3), Fe(III) nitrilotriacetic acid, Fe(III) citrate, and manganese dioxide at high rates. Elemental sulfur, anthraquinone disulfonate, and humic acids were reduced more slowly. G. sulfurreducens reduced the cytochrome with acetate as an electron donor and oxidized it with fumarate. Wolinella succinogenes was able to reduce externally provided cytochrome c of G. sulfurreducens with molecular hydrogen or formate as an electron donor and oxidized it with fumarate or nitrate as an electron acceptor. A coculture could be established in which G. sulfurreducens reduced the cytochrome with acetate, and the reduced cytochrome was reoxidized by W. succinogenes in the presence of nitrate. We conclude that this cytochrome can act as iron(III) reductase for electron transfer to insoluble iron hydroxides or to sulfur, manganese dioxide, or other oxidized compounds, and it can transfer electrons to partner bacteria.
Improvements on bottleneck matching and related problems using geometry

Let A and B be two sets of n objects in R d. we pro-pose to use bottleneck mat chtng as a convenient way for measuring the resemblance between them, and present several algorithms for computing, as well as approximating, this resemblance. The running time of all these algorithms is close to O(nl 5,. For instance, if the objects are points in the plane, the running time is O(n lslogrr). We also consider the problem of finding a translation of B that maximizes the resemblance to A under the bottleneck matching criterion. When . 4 and B are point-sets in the plane, we present an O (n5 log n) time algorithm for determining whether for some translated copy the resemblance gets below a given p, improving the previous result of . 41t, Mehlhorn, Wagener and Welzl by a factor of almost n. We use this result to compute the smallest such p in time 0(n5 Ioga n), and give an eflicient approximation scheme for this problem.
Efferent projections of the main and the accessory olfactory bulb in the tree shrew (Tupaia glis)

The projections of the main and the accessory olfactory bulb in the tree shrew (Tupaia glis) have been analyzed with anterograde degeneration and autoradiographic methods for identifying axonal projections, and with the horseradish peroxidase method for identifying the distributions of neurons from which these projections originate. The cytoarchitectonic features of the paleocortical areas which receive projections from the main and the accessory olfactory bulb have also been described.
Distributed Intrusion Detection Model in Wireless Sensor Network

The security issues of Wireless Sensor Network (WSN) are significant, among which intrusion detection can improve the defense detection performance of WSN, and also balance the security and energy-saving accurately and efficiently. In this paper, we focus on the intrusion detection problem in WSN. Specifically, we propose a cluster-based collaborative detection structure, and the detection algorithm is based on immunity system and Ant Colony Optimization (ACO). The basic idea is to formulate intrusion detection as an optimization problem and introduce immune mechanism into ACO during iterations. Finally, the experiment shows that proposed algorithm outperforms other methods.
Development of Inhibition During Childhood : Evidence for Situational Specificity and a Two-Factor Model

The inhibition of 99 children was observed from the start ofpnsschool through Grade 1 in multiple settings: adult strangers, dyadic play with unfamiliar and familiar peers, and regular free play in class. A multisetting-multimcthod-multioccasion analysis revealed (a) a high longitudinal stability of inhibition toward strangers and a medium stability of inhibition in class, (b) a decreasing consistency between inhibition in class and inhibition toward strangers, (c) an increasing consistency between inhibition in class and being ignored or rejected by classmates, and (d) no detrimental effect of children's inhibition toward strangers on their dyadic play with familiar peers. These results are discussed in terms of a 2-factor model of inhibition that is linked to Gray's concept of the behavioral inhibition system. It is assumed that both unfamiliarity and social-evaluative concerns contribute to individual differences in inhibition in childhood.
Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

Motivation Analyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets. Results Here we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA). Availability and Implementation CrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.
Rgs6 is Required for Adult Maintenance of Dopaminergic Neurons in the Ventral Substantia Nigra

Parkinson disease (PD) is characterized by the preferential, but poorly understood, vulnerability to degeneration of midbrain dopaminergic (mDA) neurons in the ventral substantia nigra compacta (vSNc). These sensitive mDA neurons express Pitx3, a transcription factor that is critical for their survival during development. We used this dependence to identify, by flow cytometry and expression profiling, the negative regulator of G-protein signaling Rgs6 for its restricted expression in these neurons. In contrast to Pitx3−/− mDA neurons that die during fetal (vSNc) or post-natal (VTA) period, the vSNc mDA neurons of Rgs6 −/− mutant mice begin to exhibit unilateral signs of degeneration at around 6 months of age, and by one year cell loss is observed in a fraction of mice. Unilateral cell loss is accompanied by contralateral degenerating neurons that exhibit smaller cell size, altered morphology and reduced dendritic network. The degenerating neurons have low levels of tyrosine hydroxylase (TH) and decreased nuclear Pitx3; accordingly, expression of many Pitx3 target gene products is altered, including Vmat2, Bdnf, Aldh1a1 (Adh2) and Fgf10. These low TH neurons also express markers of increased dopamine signaling, namely increased DAT and phospho-Erk1/2 expression. The late onset degeneration may reflect the protective action of Rgs6 against excessive DA signaling throughout life. Rgs6-dependent protection is thus critical for adult survival and maintenance of the vSNc mDA neurons that are most affected in PD.