Miracle-dz/UniFAR-FTUs huggingface dataset:
Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling

In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA sequence data and an extensive taxon sample. We present the first dated orb weaver phylogeny. Our results suggest that orb weavers appeared by the Middle Triassic and underwent a rapid diversification during the end of the Triassic and Early Jurassic. By the second half of the Jurassic, most of the extant orb-weaving families and web designs were already present. The processes that may have given origin to this diversification of lineages and web architectures are discussed. A combination of biotic factors, such as key innovations in web design and silk composition, as well as abiotic environmental changes, may have played important roles in the diversification of orb weavers. Our analyses also show that increased taxon sampling density in both ingroups and outgroups greatly improves phylogenetic accuracy even when extensive data are missing. This effect is particularly important when addition of character data improves gene overlap.
Analytical solution to bending of stiffened and continuous antisymmetric laminates

Abstract Analytical Strip Method is presented for the analysis of the bending-extension coupling problem of stiffened and continuous antisymmetric thin laminates. A system of three equations of equilibrium, governing the general response of antisymmetric laminates, is reduced to a single eighth-order partial differential equation (PDE) in terms of a displacement function. The PDE is then solved in a single series form to determine the displacement response of antisymmetric cross-ply and angle-ply laminates. The solution is applicable to rectangular laminates with two opposite edges simply supported and the other edges being free, clamped, simply supported, isotropic beam supports, or point supports.
Effect of water deficits on seed development in soybean : I. Tissue water status.

Water deficits during seed filling often decrease seed size in soybean (Glycine max L.). The physiological basis for this response is not known but may result from direct effects of low seed water potential (Psi(w)) on the seed filling process. To determine whether low Psi(w) occurred in reproductive tissues of soybean, we monitored the water status (Psi(w), Psi(s), and Psi(p)) of leaf, pericarp, and seed (embryo and testa) tissue of greenhouse-grown plants subjected to a brief water deficit during the linear period of seed growth. Water deficits were imposed by withholding water and monitored in the reproductive tissues by thermocouple psychrometry. When water was abundant, leaf, pericarp, and seed Psi(w) were -0.5 to -0.7 megapascal at midday. When water was withheld, leaf Psi(w) decreased to -2.3 megapascals within 6 days. Pericarp Psi(w) also decreased to -1.9 megapascal during this time. Pericarp Psi(s) followed the decline in Psi(w), but osmotic adjustment was not evident as the pericarp lost turgor completely by day 6. However, seed Psi(w), Psi(s), and Psi(p) were not significantly different from the controls. These results indicate that the water status of the developing seeds of soybean is not altered by short-term water deficits severe enough to inhibit the metabolic activity of the maternal plant. Maintenance of a favorable water status may be important for the conservation of seed growth rate exhibited by soybean under dry conditions.
Electrostatic tuning of the pre- and post-hydrolytic open states in CFTR

Cystic fibrosis transmembrane conductance regulator (CFTR) is an ion channel that couples adenosine triphosphate (ATP) hydrolysis at its nucleotide-binding domains to gating transitions in its transmembrane domains. We previously reported that the charge-neutralized mutant R352C shows two distinct open states, O1 and O2. The two states could be distinguished by their single-channel current amplitudes: O1 having a smaller amplitude (representing a prehydrolytic open state) and O2 having a larger amplitude (representing a post-hydrolytic open state). In this study, a similar phenotype is described for two mutations of another pore-lining residue, N306D and N306E, suggesting that alterations of the net charge within CFTR’s pore confer this unique conductance aberration. Because moving either of the two endogenous charges, R303 and R352, to positions further along TM5 and TM6, respectively, also results in this O1O2 phenotype, we conclude that the position of the charged residue in the internal vestibule affects hydrolysis-dependent conductance changes. Furthermore, our data show that the buffer and CFTR blocker morpholino propane sulfonic acid (MOPS−) occludes the O1 state more than it does the O2 state when the net charge of the internal vestibule is unchanged or increased. In contrast, when the net charge in the internal vestibule is decreased, the differential sensitivity to MOPS− block is diminished. We propose a three-state blocking mechanism to explain the charge-dependent sensitivity of prehydrolytic and post-hydrolytic open states to MOPS− block. We further posit that the internal vestibule expands during the O1 to O2 transition so that mutation-induced electrostatic perturbations within the pore are amplified by the smaller internal vestibule of the O1 state and thus result in the O1O2 phenotype and the charge-dependent sensitivity of the two open states to MOPS− block. Our study not only relates the O1O2 phenotype to the charge distribution in CFTR’s internal vestibule but also provides a toolbox for mechanistic studies of CFTR gating by ATP hydrolysis.
BDNF Promotes the Regenerative Sprouting, But Not Survival, of Injured Serotonergic Axons in the Adult Rat Brain

Brain-derived neurotrophic factor (BDNF) has trophic effects on serotonergic (5-HT) neurons in the adult brain and can prevent the severe loss of cortical 5-HT axons caused by the neurotoxinp-chloroamphetamine (PCA). However, it has not been determined whether BDNF promotes the survival of 5-HT axons during PCA-insult or facilitates their regenerative sprouting after injury. We show here that BDNF fails to protect most 5-HT axons from PCA-induced degeneration. Instead, chronic BDNF infusions markedly stimulate the sprouting of both intact and PCA-lesioned 5-HT axons, leading to a hyperinnervation at the neocortical infusion site. BDNF treatment promoted the regrowth of 5-HT axons when initiated up to a month after PCA administration. The sprouted axons persisted in cortex for at least 5 weeks after terminating exogenous BDNF delivery. BDNF also encouraged the regrowth of the 5-HT plexus in the hippocampus, but only in those lamina where 5-HT axons normally ramify. In addition, intracortical BDNF infusions induced a sustained local activation of the TrkB receptor. The dose–response profiles for BDNF to stimulate 5-HT sprouting and Trk signaling were remarkably similar, suggesting a physiological link between the two events; both responses were maximal at intermediate doses of BDNF but declined at higher doses (“inverted-U-shaped” dose–response curves). Underlying the downregulation of the Trk signal with excessive BDNF was a decline in full-length TrkB protein, but not truncated TrkB protein or TrkB mRNA levels. Thus, BDNF–TrkB signaling does not protect 5-HT neurons from axonal injury, but has a fundamental role in promoting the structural plasticity of these neurons in the adult brain.
Crowd Simulation for Emergency Response using BDI Agent Based on Virtual Reality

This paper presents a novel VR (virtual reality) trained BDI (belief, desire, intention) software agent used to construct crowd simulations for emergency response. The BDI framework allows modeling of human behavior with a high degree of fidelity. The proposed simulation has been developed using AnyLogic software to mimic crowd evacuation from an area under a terrorist bomb attack. The attributes that govern the BDI characteristics of the agent are studied by conducting human in the loop experiments in VR using the CAVE (cave automatic virtual environment). To enhance generality and interoperability of the proposed crowd simulation modeling scheme, input data models have been developed to define environment attributes. Experiments are also conducted to demonstrate the effect of various parameters on key performance indicators such as crowd evacuation rate and densities
Molecular cloning, characterization, and nucleotide sequence of the rfc gene, which encodes an O-antigen polymerase of Salmonella typhimurium

The rfc gene of Salmonella typhimurium was located in a 1.75-kb HindIII fragment and restored wild-type lipopolysaccharide synthesis ability to both an older rfc point mutant and new rfc::IS10 mutants. DNA sequencing of the HindIII fragment revealed an open reading frame which could encode a protein of 407 amino acids with an Mr of 47,472 and also revealed potential translation signals. Modulator codons accounted for 12.5% of the total codon content, providing a possible explanation for the nondetectability of the protein in subcellular systems. Secondary structure analysis suggested the presence of transmembrane beta-sheet structures, implying a possible role for the protein in translocation of hydrophilic O-antigen-containing materials. Salmonella strains of groups A, B, and D1 contained rfc-homologous DNA, but strains of groups C1, C2, C3, D2, and E2 did not.
Statistical model checking of distributed real-time actor systems

This paper proposes an approach to modelling and analysis of distributed real-time actor systems, which is based on the Uppaal statistical model checker (SMC). SMC was chosen because it automatizes simulations, offers a temporal logic language to formalize specifications and exploits statistical techniques to infer quantitative measures about a model. The approach is integrated in a system life-cycle where a same model can be transitioned without distortions from analysis down to design and implementation, currently based on Java. The paper describes the adopted actor modelling language and its architectural framework, illustrates the Uppaal SMC approach and demonstrates its practical usefulness through a running example.
Building a Large Dataset for Model-based QoE Prediction in the Mobile Environment

The tremendous growth in video services, specially in the context of mobile usage, creates new challenges for network service providers: How to enhance the user's Quality of Experience (QoE) in dynamic wireless networks (UMTS, HSPA, LTE/LTE-A). The network operators use different methods to predict the user's QoE. Generally to predict the user's QoE, methods are based on collecting subjective QoE scores given by users. Basically, these approaches need a large dataset to predict a good perceived quality of the service. In this paper, we setup an experimental test based on crowdsourcing approach and we build a large dataset in order to predict the user's QoE in mobile environment in term of Mean Opinion Score (MOS). The main objective of this study is to measure the individual/global impact of QoE Influence Factors (QoE IFs) in a real environment. Based on the collective dataset, we perform 5 testing scenarios to compare 2 estimation methods (SVM and ANFIS) to study the impact of the number of the considered parameters on the estimation. It became clear that using more parameters without any weighing mechanisms can produce bad results.
Statistical testing of baseline differences in sports medicine RCTs: a systematic evaluation

Background/Aim The CONSORT (Consolidated Standards of Reporting Trials) statement discourages reporting statistical tests of baseline differences between groups in randomised controlled trials (RCTs). However, this practice is still common in many medical fields. Our aim was to determine the prevalence of this practice in leading sports medicine journals. Methods We conducted a comprehensive search in Medline through PubMed to identify RCTs published in the years 2005 and 2015 from 10 high-impact sports medicine journals. Two reviewers independently confirmed the trial design and reached consensus on which articles contained statistical tests of baseline differences. Results Our search strategy identified a total of 324 RCTs, with 85 from the year 2005 and 239 from the year 2015. Overall, 64.8% of studies (95% CI (59.6, 70.0)) reported statistical tests of baseline differences; broken down by year, this percentage was 67.1% in 2005 (95% CI (57.1, 77.1)) and 64.0% in 2015 (95% CI (57.9, 70.1)). Conclusions Although discouraged by the CONSORT statement, statistical testing of baseline differences remains highly prevalent in sports medicine RCTs. Statistical testing of baseline differences can mislead authors; for example, by failing to identify meaningful baseline differences in small studies. Journals that ask authors to follow the CONSORT statement guidelines should recognise that many manuscripts are ignoring the recommendation against statistical testing of baseline differences.
A new hepatocytic isoform of PLZF lacking the BTB domain interacts with ATP7B, the Wilson disease protein, and positively regulates ERK signal transduction

The promyelocytic leukemia zinc finger (PLZF) protein has been described as a transcriptional repressor of the BTB‐domain/zinc‐finger family, and shown to regulate the expression of Hox genes during embryogenesis and the expression of cyclin A in the cell cycle progression. Here, a 45‐kDa isoform of PLZF without a BTB domain was identified via yeast two‐hybrid screening using the C‐terminal region of ATP7B as bait in our determination of the biological roles of the Wilson disease protein outside of its copper‐binding domain. Our immunoprecipitation experiments showed that the hepatocytic isoform of PLZF could specifically interact with the C‐terminal region of ATP7B. The immunostaining of HepG2 cells revealed that the ATP7B and PLZF proteins were apparently colocalized into the trans‐Golgi complexes. It was also determined that disruption of PLZF expression in the HepG2 cells affected an attenuation of ERK activity in a dose‐dependent manner. The hepatocytic activities of ERK kinase were found to be enhanced as the result of PLZF or ATP7B expression, but this enhancement was abrogated by the deletion of the C‐terminal region of ATP7B. Furthermore, a transgenic Drosophila strain that ectopically expressed the hepatocytic ΔBTB‐PLZF exhibited phenotypic changes in eye and wing development, and these alterations were fully recovered as the result of ATP7B expression, indicating the obvious in vivo interaction between the two proteins. Those PLZF‐induced abnormalities were attributed to the enhancement of ERK signaling, as was shown by phenotypic reversions with loss‐of‐function mutations in ERK signal transduction in Drosophila. These data suggest the existence of a mechanism that regulates ERK signaling via the C‐terminus of ATP7B and the ATP7B‐interacting hepatocytic PLZF. J. Cell. Biochem. 99: 719–734, 2006. © 2006 Wiley‐Liss, Inc.
Heterotrophic microbial communities use ancient carbon following glacial retreat

When glaciers retreat they expose barren substrates that become colonized by organisms, beginning the process of primary succession. Recent studies reveal that heterotrophic microbial communities occur in newly exposed glacial substrates before autotrophic succession begins. This raises questions about how heterotrophic microbial communities function in the absence of carbon inputs from autotrophs. We measured patterns of soil organic matter development and changes in microbial community composition and carbon use along a 150-year chronosequence of a retreating glacier in the Austrian Alps. We found that soil microbial communities of recently deglaciated terrain differed markedly from those of later successional stages, being of lower biomass and higher abundance of bacteria relative to fungi. Moreover, we found that these initial microbial communities used ancient and recalcitrant carbon as an energy source, along with modern carbon. Only after more than 50 years of organic matter accumulation did the soil microbial community change to one supported primarily by modern carbon, most likely from recent plant production. Our findings suggest the existence of an initial stage of heterotrophic microbial community development that precedes autotrophic community assembly and is sustained, in part, by ancient carbon.
Effect of Blood Exposure on Push-Out Bond Strength of Four Calcium Silicate Based Cements

Introduction: The purpose of this study was to compare the push-out bond strength of white ProRoot Mineral Trioxide Aggregate (MTA), Biodentine, calcium-enriched mixture (CEM) cement and Endosequence Root Repair Material (ERRM) putty after exposure to blood. Methods and Materials: A total of 96 root dentin slices with a standardized thickness of 1.00±0.05 mm and standardized canal spaces were randomly divided into 4 main experimental groups (n=24) according to the calcium silicate based cement (CSC) used: white ProRoot MTA, CEM Cement, ERRM Putty and Biodentine. Specimens were exposed to whole fresh human blood and then subdivided into two subgroups depending on the exposure time (24 or 72 h). Push-out bond strength was measured using a universal testing machine. Failure modes were examined under a light microscope under ×10 magnification. Data were analyzed using the two-way ANOVA test. Results: Biodentine exhibited the highest values regardless of the exposure time. The lowest push-out strength values were seen in white ProRoot MTA and CEM cement in both post exposure times. After exposure to blood, the push-out bond strength of all materials increased over time. This increase was only statistically significant in white ProRoot MTA and ERRM specimens. The dominant failure mode in all CSCs was the adhesive mode. Conclusion: Biodentine showed the highest values of push-out bond strength and may be better options for situations encountering higher dislocation forces in a short time after cement application.
Interspecific Comparison of the Performance of Soaring Migrants in Relation to Morphology, Meteorological Conditions and Migration Strategies

Background Performance of migrating birds can be affected by a number of intrinsic and extrinsic factors like morphology, meteorological conditions and migration strategies. We compared travel speeds of four raptor species during their crossing of the Sahara desert. Focusing the analyses on this region allows us to compare different species under equivalent conditions in order to disentangle which factors affect migratory performance. Methodology/Principal Finding We tracked raptors using GPS satellite transmitters from Sweden, Spain and Italy, and evaluated their migratory performance at both an hourly and a daily scale. Hourly data (flight speed and altitude for intervals of two hours) were analyzed in relation to time of day, species and season, and daily data (distance between roosting sites) in relation to species, season, day length and tailwind support. Conclusions/Significance Despite a clear variation in morphology, interspecific differences were generally very small, and did only arise in spring, with long-distance migrants (>5000 km: osprey and Western marsh-harrier) being faster than species that migrate shorter distances (Egyptian vulture and short-toed eagle). Our results suggest that the most important factor explaining hourly variation in flight speed is time of day, while at a daily scale, tailwind support is the most important factor explaining variation in daily distance, raising new questions about the consequences of possible future changes in worldwide wind patterns.
Board Structures Around the World: An Experimental Investigation

We model and experimentally examine the board structure-performance relationship. We examine single-tiered boards, two-tiered boards, insider-controlled boards and outsider-controlled boards. We find that even insider-controlled boards frequently adopt institutionally preferred rather than self-interested policies. Two-tiered boards adopt institutionally preferred policies more frequently, but tend to destroy value by being too conservative, frequently rejecting good projects. Outsidercontrolled single-tiered boards, both when they have multiple insiders and only a single insider, adopt institutionally preferred policies most frequently. In those board designs where the efficient Nash equilibrium produces strictly higher payoffs to all agents than the coalition-proof equilibria, agents tend to select the efficient Nash equilibria.
A fusion method of data association and virtual detection for minimizing track loss and false track

In this paper, we present a method to track multiple moving vehicles using the global nearest neighborhood (GNN) data association (DA) based on 2D global position and virtual detection based on motion tracking. Unlikely the single target tracking, multiple target tracking needs to associate observation-to-track pairs. DA is a process to determine which measurements are used to update each track. We use the GNN data association not to lost track and not to connect incorrect measurements. GNN is a simple, robust, and optimal technique for intelligent vehicle applications with a stereo vision system that can reliably estimates the position of a vehicle. However, an incomplete detection and recognition technique bring low track maintenance due to missed detections and false alarms. A complementary virtual detection method adds to GNN method. Virtual detection is used to recover the missed detection by motion tracking when the track maintains for some periods. Motion tracking estimates virtual region of interest (ROI) of the missed detection using a pyramidal Lukas-Kanade feature tracker. Next, GNN associates the lost tracks and virtual measurements if the measurement exists in the validation gate. Our experimental results show that our tracking method works well in a stereo vision system with incomplete detection and recognition ability.
Mining Weakly Labeled Web Facial Images for Search-Based Face Annotation

This paper investigates a framework of search-based face annotation (SBFA) by mining weakly labeled facial images that are freely available on the World Wide Web (WWW). One challenging problem for search-based face annotation scheme is how to effectively perform annotation by exploiting the list of most similar facial images and their weak labels that are often noisy and incomplete. To tackle this problem, we propose an effective unsupervised label refinement (ULR) approach for refining the labels of web facial images using machine learning techniques. We formulate the learning problem as a convex optimization and develop effective optimization algorithms to solve the large-scale learning task efficiently. To further speed up the proposed scheme, we also propose a clustering-based approximation algorithm which can improve the scalability considerably. We have conducted an extensive set of empirical studies on a large-scale web facial image testbed, in which encouraging results showed that the proposed ULR algorithms can significantly boost the performance of the promising SBFA scheme.
COUNTABLE BOREL EQUIVALENCE RELATIONS SCOTT SCHNEIDER AND SIMON THOMAS

Introduction. These notes are an account of a day-long lecture workshop presented by Simon Thomas of Rutgers University at the University of Ohio at Athens on November 17, 2007, as part of the Appalachian Set Theory series. The workshop served as an intensive introduction to the emerging theory of countable Borel equivalence relations. These notes have been compiled from the lecture slides by Scott Schneider, an attendee of the workshop.