Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha)

The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes), and Acanthopterygii, we find weak support (bootstrap value < 48%) for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu Miya et al. (2005) including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular timetrees.
Online interventions for depression and anxiety – a systematic review

Background: Access to mental health care is limited. Internet-based interventions (IBIs) may help bridge that gap by improving access especially for those who are unable to receive expert care. Aim: This review explores current research on the effectiveness of IBIs for depression and anxiety. Results: For depression, therapist-guided cognitive behavioral therapy (CBT) had larger effect sizes consistently across studies, ranging from 0.6 to 1.9; while stand-alone CBT (without therapist guidance) had a more modest effect size of 0.3–0.7. Even other interventions for depression (non-CBT/non-randomized controlled trial (RCT)) showed modestly high effect sizes (0.2–1.7). For anxiety disorders, studies showed robust effect sizes for therapist-assisted interventions with effect sizes of 0.7–1.7 (efficacy similar to face-to-face CBT) and stand-alone CBT studies also showed large effect sizes (0.6–1.7). Non-CBT/Non-RCT studies (only 3) also showed significant reduction in anxiety scores at the end of the interventions. Conclusion: IBIs for anxiety and depression appear to be effective in reducing symptomatology for both depression and anxiety, which were enhanced by the guidance of a therapist. Further research is needed to identify various predictive factors and the extent to which stand-alone Internet therapies may be effective in the future as well as effects for different patient populations.
Instruction Scheduling Based on Subgraph Isomorphism for a High Performance Computer Processor

This paper 1 presents an instruction scheduling algorithm based on the Subgraph Isomorphism Problem. Given a Directed Acyclic Graph (DAG) G1 ,o ur algorithm looks for a subgraph G2 in a base graph G2, such that G 2 is isomorphic to G1. The base graph G2 represents the arrangement of the processing elements of a high performance computer architecture named 2D-VLIW and G2 is the set of those processing elements required to execute operations in G1 . W e have compared this algorithm with a greedy list scheduling strategy using programs of the SPEC and MediaBench suites. In our experiments, the average Operation Per Cycle (OPC) and Operations Per Instruction (OPI) achieved by our algorithm are 1.45 and 1.40 times better than the OPC and OPI obtained by the list scheduling algorithm.
P3 & Beyond: Solving Energies with Higher Order Cliques

In this paper we extend the class of energy functions for which the optimal alpha-expansion and alphabeta-swap moves can be computed in polynomial time. Specifically, we introduce a class of higher order clique potentials and show that the expansion and swap moves for any energy function composed of these potentials can be found by minimizing a submodular function. We also show that for a subset of these potentials, the optimal move can be found by solving an st-mincut problem. We refer to this subset as the P3 Potts model. Our results enable the use of powerful move making algorithms i.e. alpha-expansion and alphabeta-swap for minimization of energy functions involving higher order cliques. Such functions have the capability of modelling the rich statistics of natural scenes and can be used for many applications in computer vision. We demonstrate their use on one such application i.e. the texture based video segmentation problem.
Structural-context-preserving image abstraction by using space-filling curve based on minimum spanning tree

We propose a novel image abstraction method which generates a non-photographic painting-like image automatically from a photographic natural image while preserving its structural context, detailed structure, and so on. In the proposed method, concretely, one-dimensional vector є-filter is applied to an input image along a space-filling curve. This spacefilling curve is constructed by using a minimum spanning tree reflecting structural context of the input image. This novel image abstraction approach is completely different from conventional approaches. By using the proposed method, aggregation of texture details and enhancement of sharp edges are effectively realized while preserving structural contexts such as thin lines, sharp corners, and so on. The structural-context-preserving abstraction capability of the proposed method is verified by some experimental results and examples.
Fast Algorithms and Lower Bounds for Temporal Reasoning

We introduce two new tractable temporal constraint languages, which both strictly contain the class Ord-Horn of B(cid:127)urkert and Nebel. The presented algorithms decide whether a given set of constraints from these languages is consistent in time that is quadratic in the input size; this also yields a new algorithm for Ord-Horn constraints, where the best known algorithms also have quadratic running time. We also prove that the two languages are maximally tractable , i.e., if we add a new temporal relation to one of these constraint languages, the corresponding constraint satisfaction problem becomes NP-complete. Our proof applies the so-called product Ramsey theorem, which we believe will be useful in similar contexts of constraint satisfaction complexity classi(cid:12)cation. Finally, we prove that (unlike Ord-Horn) the two languages cannot be solved by Datalog or by establishing local consistency.
A Boolean Rule-Based Approach for Manufacturability-Aware Cell Routing

An approach for cell routing using gridded design rules is proposed. It is technology-independent and parameterizable for different fabrics and design rules, including support for multiple-patterning lithography. The core contribution is a detailed-routing algorithm based on a Boolean formulation of the problem. The algorithm uses a novel encoding scheme, graph theory to support floating terminals, efficient heuristics to reduce the computational cost, and minimization of the number of unconnected pins in case the cell is unroutable. The versatility of the algorithm is demonstrated by routing single- and double-height cells. The efficiency is ascertained by synthesizing a library with 127 cells in about one hour and a half of CPU time. The layouts derived by the implemented tool have also been compared with the ones from a commercial library; thus, showing the competitiveness of the approach for gridded geometries.
Optimizing degree distributions in LT codes by using the multiobjective evolutionary algorithm based on decomposition

Luby Transform code (LT code) is the first practical digital fountain code and has been widely used as basic components in many communication applications. The coding behavior of LT code is mainly decided by a probability distribution of codeword degrees. In order to customize a degree distribution for different purposes, multi-objective evolutionary algorithm is introduced to optimize degree distributions in this paper. Two critical performance indicators of LT code are considered in our experiments. Some applications hope to minimize the overhead of extra packets and some require to limit the computational cost of the coding system. To handle this problem, MOEA/D is applied to optimize two objectives simultaneously. We expect to obtain the Pareto front (PF) formed by partial optimal solutions and provide those available degree distributions to different LT code applications. Not only promising results are represented in this paper but also the behavior of LT code is thoroughly explored by optimizing the degree distribution according to multi-objectives.
Introspective Active Learning for Scalable Semantic Mapping

This paper proposes an active learning framework for semantic mapping in mobile robotics. In particular, our work explores the benefits of an introspective classifier over that of a more traditional non-introspective approach for active data selection. We extend the notion of introspection to a particular sparse Gaussian Process classifier, the Informative Vector Machine (IVM), and show that the use of an IVM leads to more informative questions being asked during active learning. We further leverage the information-theoretic nature of the IVM to formulate a principled mechanism for forgetting stale data. The result is an efficient and highly effective end-to-end active learning framework which outperforms both passive approaches as well as active approaches based on the more commonly used Support Vector Machine (SVM) in terms of classification performance and learning rate on a publicly available dataset.
Comparative Study of Convolution Based Inpainting Algorithms

Image Inpainting refers to restoring a damaged image in such a manner that manipulation and modification in an image is not recognizable by the observer. In this paper we have simulated and compared results of two different existing algorithms that are based on convolution as given by Oliveira and Hadhoud. The algorithm given by Hadhoud gives faster results but produces strokes in the resultant image while algorithm given by Oliveira is slow but fills the region from all the sides.
Myotubes differentiate optimally on substrates with tissue-like stiffness

Contractile myocytes provide a test of the hypothesis that cells sense their mechanical as well as molecular microenvironment, altering expression, organization, and/or morphology accordingly. Here, myoblasts were cultured on collagen strips attached to glass or polymer gels of varied elasticity. Subsequent fusion into myotubes occurs independent of substrate flexibility. However, myosin/actin striations emerge later only on gels with stiffness typical of normal muscle (passive Young's modulus, E ∼12 kPa). On glass and much softer or stiffer gels, including gels emulating stiff dystrophic muscle, cells do not striate. In addition, myotubes grown on top of a compliant bottom layer of glass-attached myotubes (but not softer fibroblasts) will striate, whereas the bottom cells will only assemble stress fibers and vinculin-rich adhesions. Unlike sarcomere formation, adhesion strength increases monotonically versus substrate stiffness with strongest adhesion on glass. These findings have major implications for in vivo introduction of stem cells into diseased or damaged striated muscle of altered mechanical composition.
“Bad Romance”: Links between Psychological and Physical Aggression and Relationship Functioning in Adolescent Couples

Assortative mating is an important issue in explaining antisocial, aggressive behavior. It is yet unclear, whether the similarity paradigm fully explains frequent displays of aggression in adolescents’ romantic relationships. In a sample of 194 romantic partner dyads, differences between female and male partners’ reports of aggression (psychological and physical) and different measures of relationship functioning (e.g., jealousy, conflicts, and the affiliative and romantic quality of the relationship) were assessed. A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of psychological and physical aggression: nonaggressive couples, couples with higher perceived aggressiveness (both physical and psychological) by females, couples with higher aggressiveness perceived by males and mutually aggressive couples. A substantial number of non-aggressive dyads emerged. Of note was the high number of females showing one-sided aggression, which was, however, not countered by their partner. The mutually aggressive couples showed the least adaptive relationship functioning, with a lack of supportive, trusting relationship qualities, high conflict rates and high jealousy. The discussion focuses on the different functions of aggression in these early romantic relations, and the aggravating impact of mutual aggression on relationship functioning and its potential antisocial outcomes.
The conformational state of Tes regulates its zyxin-dependent recruitment to focal adhesions

The function of the human Tes protein, which has extensive similarity to zyxin in both sequence and domain organization, is currently unknown. We now show that Tes is a component of focal adhesions that, when expressed, negatively regulates proliferation of T47D breast carcinoma cells. Coimmunoprecipitations demonstrate that in vivo Tes is complexed with actin, Mena, and vasodilator-stimulated phosphoprotein (VASP). Interestingly, the isolated NH2-terminal half of Tes pulls out α-actinin and paxillin from cell extracts in addition to actin. The COOH-terminal half recruits zyxin as well as Mena and VASP from cell extracts. These differences suggest that the ability of Tes to associate with α-actinin, paxillin, and zyxin is dependent on the conformational state of the molecule. Consistent with this hypothesis, we demonstrate that the two halves of Tes interact with each other in vitro and in vivo. Using fibroblasts lacking Mena and VASP, we show that these proteins are not required to recruit Tes to focal adhesions. However, using RNAi ablation, we demonstrate that zyxin is required to recruit Tes, as well as Mena and VASP, but not vinculin or paxillin, to focal adhesions.
Enhancing Synchronized Cellular Forward Links by Exploiting Spatial-Temporal Signatures using Extended Subspace Approach

Pilot signals are often used to ease mobile channel acquisition and detection. Cochannel signals are usually treated as interference. However, for synchronized cellular CDMA forward links, all cochannel signals from the same base station share a spatial and temporal channel signature. We propose an extended blind subspace approach to exploit this feature to enhance channel estimation. We demonstrate the performance gain by simulating two transmission schemes for MIMO cellular base stations: fixed beam and adaptive beam.
"Release Early, Release Often"? An Empirical Analysis of Release Strategy in Open Source Software Co-Creation

“Release early, release often” is becoming a popular new product introduction strategy in open source software development. We study the influence of release strategies on the download market share of open source projects. Using a panel data set collected from Sourceforge.net, we find that while more frequent releases are associated with better subsequent download market share, the relationship is curvilinear. Too frequent releases could backfire due to the subtle effects on the demand and supply sides of open source software production. From the demand side, we find that releasing frequently may work less effectively in projects with higher adoption costs. From the supply side, fast releases may work less effectively in projects with weak community contributions. Even when the community contributions are strong, the restrictiveness of open source license moderates the effectiveness of releasing early and often. These results have implications for managing open source projects and research on open source software, open innovation, and software adoption.
Highly Variable Spike Trains Underlie Reproducible Sensorimotor Responses in the Medicinal Leech

The nervous system of the leech is a particularly suitable model to investigate neural coding of sensorimotor responses because it allows both observation of behavior and the simultaneous measurement of a large fraction of its underlying neuronal activity. In this study, we used a combination of multielectrode recordings, videomicroscopy, and computation of the optical flow to investigate the reproducibility of the motor response caused by local mechanical stimulation of the leech skin. We analyzed variability at different levels of processing: mechanosensory neurons, motoneurons, muscle activation, and behavior. Spike trains in mechanosensory neurons were very reproducible, unlike those in motoneurons. The motor response, however, was reproducible because of two distinct biophysical mechanisms. First, leech muscles contract slowly and therefore are poorly sensitive to the jitter of motoneuron spikes. Second, the motor response results from the coactivation of a population of motoneurons firing in a statistically independent way, which reduces the variability of the population firing. These data show that reproducible spike trains are not required to sustain reproducible behaviors and illustrate how the nervous system can cope with unreliable components to produce reliable action.
Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Many studies are uncovering functional roles for long noncoding RNAs (lncRNAs), yet few have been tested for in vivo relevance through genetic ablation in animal models. To investigate the functional relevance of lncRNAs in various physiological conditions, we have developed a collection of 18 lncRNA knockout strains in which the locus is maintained transcriptionally active. Initial characterization revealed peri- and postnatal lethal phenotypes in three mutant strains (Fendrr, Peril, and Mdgt), the latter two exhibiting incomplete penetrance and growth defects in survivors. We also report growth defects for two additional mutant strains (linc–Brn1b and linc–Pint). Further analysis revealed defects in lung, gastrointestinal tract, and heart in Fendrr−/− neonates, whereas linc–Brn1b−/− mutants displayed distinct abnormalities in the generation of upper layer II–IV neurons in the neocortex. This study demonstrates that lncRNAs play critical roles in vivo and provides a framework and impetus for future larger-scale functional investigation into the roles of lncRNA molecules. DOI: http://dx.doi. org/10.7554/eLife.01749. 001
Evaluating different strategies for estimating treatment effects in observational studies

ABSTRACT Since the introduction of the propensity score (PS), methods for estimating treatment effects with observational data have received growing attention in the literature. Recent research has added substantially to the number of available statistical approaches for controlling confounding in such analyses. However, researchers need guidance to decide on the optimal analytic strategy for any given scenario. To address this gap, we conducted simulations evaluating both well-established methods (regression, PS weighting, stratification, and matching) and more recently proposed approaches (tree-based methods, local control, entropy balancing, genetic matching, prognostic scoring). The simulation scenarios included tree-based and smooth regression models as true data-generation mechanisms. We evaluated an extensive number of analysis strategies combining different treatment choices and outcome models. Key findings include 1) the lack of a single best strategy across all potential scenarios; 2) the importance of appropriately addressing interactions in the treatment choice model and/or outcome model; and 3) a tree-structured treatment choice model and a polynomial outcome model with second-order interactions performed well. One limitation to this initial assessment is the lack of heterogeneous simulation scenarios allowing treatment effects to vary by patient.
Inducing broadcast coral spawning ex situ: Closed system mesocosm design and husbandry protocol

Abstract For many corals, the timing of broadcast spawning correlates strongly with a number of environmental signals (seasonal temperature, lunar, and diel cycles). Robust experimental studies examining the role of these putative cues in triggering spawning have been lacking until recently because it has not been possible to predictably induce spawning in fully closed artificial mesocosms. Here, we present a closed system mesocosm aquarium design that utilizes microprocessor technology to accurately replicate environmental conditions, including photoperiod, seasonal insolation, lunar cycles, and seasonal temperature from Singapore and the Great Barrier Reef (GBR), Australia. Coupled with appropriate coral husbandry, these mesocosms were successful in inducing, for the first time, broadcast coral spawning in a fully closed artificial ex situ environment. Four Acropora species (A. hyacinthus, A. tenuis, A. millepora, and A. microclados) from two geographical locations, kept for over 1 year, completed full gametogenic cycles ex situ. The percentage of colonies developing oocytes varied from ~29% for A. hyacinthus to 100% for A. millepora and A. microclados. Within the Singapore mesocosm, A. hyacinthus exhibited the closest synchronization to wild spawning, with all four gravid colonies releasing gametes in the same lunar month as wild predicted dates. Spawning within the GBR mesocosm commenced at the predicted wild spawn date but extended over a period of 3 months. Gamete release in relation to the time postsunset for A. hyacinthus, A. millepora, and A. tenuis was consistent with time windows previously described in the wild. Spawn date in relation to full moon, however, was delayed in all species, possibly as a result of external light pollution. The system described here could broaden the number of institutions on a global scale, that can access material for broadcast coral spawning research, providing opportunities for institutions distant from coral reefs to produce large numbers of coral larvae and juveniles for research purposes and reef restoration efforts.