Miracle-dz/UniFAR-FTUs huggingface dataset:
Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core

The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.
Actinobacterial endophytes for improved crop performance

Increasing numbers of endophytic bacteria are being isolated and identified revealing a rich vein of microbial interaction within a variety of crop plants. In addition, cultivation-independent studies have exposed a broader diversity, with many of the species belonging to culturable genera. Microscopic evidence of endophytic colonisation has been shown in some cases, proving ‘true’ endophytic status and providing an understanding of how these microorganisms gain entry and deploy through their host.
Community Advisory Boards in Community-Based Participatory Research: A Synthesis of Best Processes

Community-based participatory research (CBPR) is a paradigm to study and reduce disparities in health outcomes related to chronic disease. Community advisory boards (CABs) commonly formalize the academic–community partnerships that guide CBPR by providing a mechanism for community members to have representation in research activities. Researchers and funding agencies increasingly recognize the value of the community's contribution to research and acknowledge that community advisory boards are a key component of successful CBPR projects. In this article, we describe the best processes for forming, operating, and maintaining CABs for CBPR. We synthesize the literature and offer our professional experiences to guide formation, operation, and maintenance of CABs.
A national survey of pediatric dentists on antibiotic use in children.

PURPOSE The purposes of this study were to: (1) examine the antibiotic prescribing practices of pediatric dentists and adherence to professional guidelines; and (2) assess their knowledge of and attitudes toward antibiotic resistance. METHODS A cross-sectional survey regarding antibiotic use, resistance, and knowledge of antibiotic stewardship programs was emailed to 4,636 members of the American Academy of Pediatric Dentistry (AAPD). RESULTS 987 surveys (21 percent) were completed; 984 were analyzed. Lack of adherence to AAPD antibiotic guidelines was noted. There was a trend toward overuse of antibiotics for the following conditions: irreversible pulpitis with (32 percent) and without vital pulp (42 percent); localized dentoalveolar abscess with (68 percent) and without draining fistula (39 percent); mitral valve relapse with regurgitation (43 percent); intrusion (15 percent); extrusion (13 percent); and rheumatoid arthritis (12 percent). Determinants of antibiotic use were: facial swelling (88 percent); pain relief (15 percent); unavailable appointment for several weeks (six percent); and parental satisfaction (four percent). Although 98 percent of respondents believed that antibiotic resistance is of growing concern, only 15 percent were aware of antibiotic stewardship programs. CONCLUSION AAPD members overprescribe antibiotics. Educational programs to increase knowledge of antibiotic resistance and stewardship programs should be implemented to increase adherence to professional guidelines.
An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

Molluscs are the second most species-rich phylum in the animal kingdom, yet only eleven genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72x. The assembly contains 94.6 % of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ~690 Mb compared to the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70 % mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly-available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
Hybrid Spectral Unmixing: Using Artificial Neural Networks for Linear/Non-Linear Switching

Spectral unmixing is a key process in identifying spectral signature of materials and quantifying their spatial distribution over an image. The linear model is expected to provide acceptable results when two assumptions are satisfied: (1) The mixing process should occur at macroscopic level and (2) Photons must interact with single material before reaching the sensor. However, these assumptions do not always hold and more complex nonlinear models are required. This study proposes a new hybrid method for switching between linear and nonlinear spectral unmixing of hyperspectral data based on artificial neural networks. The neural networks was trained with parameters within a window of the pixel under consideration. These parameters are computed to represent the diversity of the neighboring pixels and are based on the Spectral Angular Distance, Covariance and a non linearity parameter. The endmembers were extracted using Vertex Component Analysis while the abundances were estimated using the method identified by the neural networks (Vertex Component Analysis, Fully Constraint Least Square Method, Polynomial Post Nonlinear Mixing Model or Generalized Bilinear Model). Results show that the hybrid method performs better than each of the individual techniques with high overall accuracy, while the abundance estimation error is significantly lower than that obtained using the individual methods. Experiments on both synthetic dataset and real hyperspectral images demonstrated that the proposed hybrid switch method is efficient for solving spectral unmixing of hyperspectral images as compared to individual algorithms.
Gating of O2-sensitive K+ channels of arterial chemoreceptor cells and kinetic modifications induced by low PO2

We have studied the kinetic properties of the O2-sensitive K+ channels (KO2 channels) of dissociated glomus cells from rabbit carotid bodies exposed to variable O2 tension (PO2). Experiments were done using single-channel and whole-cell recording techniques. The major gating properties of KO2 channels in excised membrane patches can be explained by a minimal kinetic scheme that includes several closed states (C0 to C4), an open state (O), and two inactivated states (I0 and I1). At negative membrane potentials most channels are distributed between the left-most closed states (C0 and C1), but membrane depolarization displaces the equilibrium toward the open state. After opening, channels undergo reversible transitions to a short-living closed state (C4). These transitions configure a burst, which terminates by channels either returning to a closed state in the activation pathway (C3) or entering a reversible inactivated conformation (I0). Burst duration increases with membrane depolarization. During a maintained depolarization, KO2 channels make several bursts before ending at a nonreversible, absorbing, inactivated state (I1). On moderate depolarizations, KO2 channels inactivate very often from a closed state. Exposure to low PO2 reversibly induces an increase in the first latency, a decrease in the number of bursts per trace, and a higher occurrence of closed-state inactivation. The open state and the transitions to adjacent closed or inactivated states seem to be unaltered by hypoxia. Thus, at low PO2 the number of channels that open in response to a depolarization decreases, and those channels that follow the activation pathway open more slowly and inactivate faster. At the macroscopic level, these changes are paralleled by a reduction in the peak current amplitude, slowing down of the activation kinetics, and acceleration of the inactivation time course. The effects of low PO2 can be explained by assuming that under this condition the closed state C0 is stabilized and the transitions to the absorbing inactivated state I1 are favored. The fact that hypoxia modifies kinetically defined conformational states of the channels suggests that O2 levels determine the structure of specific domains of the KO2 channel molecule. These results help to understand the molecular mechanisms underlying the enhancement of the excitability of glomus cells in response to hypoxia.
The Economic Cost of Publicly Announced Information Security Breaches: Empirical Evidence from the Stock Market

This study examines the economic effect of information security breaches reported in newspapers or publicly traded US corporations. We find limited evidence of an overall negative stock market reaction to public announcements of information security breaches. However, further investigation reveals that the nature of the breach affects this result. We find a highly significant negative market reaction for information security breaches involving unauthorized access to confidential data, but no significant reaction when the breach does not involve confidential information. Thus, stock market participants appear to discriminate across types of breaches when assessing their economic impact on affected firms. These findings are consistent with the argument that the economic consequences of information security breaches vary according to the nature of the underlying assets affected by the breach.
Measuring productivity dispersion in selected Australian industries

Productivity growth is a key determinant of improvements in living standards in the long run. However, analysis of productivity trends at the aggregate level does not capture the variation of firm and sub-industry productivity performance that underlies industry or aggregate productivity. By examining the differences in productivity performance of firms in particular industries (that is, productivity dispersion) we can enhance our understanding of the rich productivity dynamics of the economy and ultimately help to better inform policy advice. This paper – a collaboration between Treasury and the Australian Bureau of Statistics – uses firm-level data from the Business Longitudinal Analysis Data Environment (BLADE) to measure the dispersion in labour productivity for six Australian industries (Manufacturing; Construction; Retail Trade; Wholesale Trade; Professional, Scientific and Technical Services; and Administrative and Support Services). The study finds labour productivity dispersion to be persistent in the selected industries. Among the six industries, Manufacturing and Professional, Scientific and Technical Services exhibit the smallest labour productivity gap between businesses at the top and bottom quartiles. Contrary to international evidence, there is little evidence of widening labour productivity dispersion over time, with dispersion decreasing to varying degrees over 2001-02 to 2013-14. In particular, labour productivity dispersion declined significantly over the period in Retail Trade and Wholesale Trade. We also explore potential drivers of labour productivity dispersion and its relationship with aggregate labour productivity, and discuss avenues for further research. JEL Classification Numbers: C23, C55, D22, D30, E23, E24
The Shade Avoidance Syndrome in Arabidopsis: The Antagonistic Role of Phytochrome A and B Differentiates Vegetation Proximity and Canopy Shade

Light limitation caused by dense vegetation is one of the greatest threats to plant survival in natural environments. Plants detect such neighboring vegetation as a reduction in the red to far-red ratio (R:FR) of the incoming light. The low R:FR signal, perceived by phytochromes, initiates a set of responses collectively known as the shade avoidance syndrome, intended to reduce the degree of current or future shade from neighbors by overtopping such competitors or inducing flowering to ensure seed production. At the seedling stage these responses include increased hypocotyl elongation. We have systematically analyzed the Arabidopsis seedling response and the contribution of phyA and phyB to perception of decreased R:FR, at three different levels of photosynthetically active radiation. Our results show that the shade avoidance syndrome, induced by phyB deactivation, is gradually antagonized by phyA, operating through the so-called FR-High Irradiance Response, in response to high FR levels in a range that simulates plant canopy shade. The data indicate that the R:FR signal distinguishes between the presence of proximal, but non-shading, neighbors and direct foliar shade, via a intrafamily photosensory attenuation mechanism that acts to suppress excessive reversion toward skotomorphogenic development under prolonged direct vegetation shade.
Vortex imaging: new information gain from tracking cardiac energy loss.

During a cardiac cycle, the filling and emptying of the left ventricle (LV) are associated with characteristic patterns of blood flow motion. Diastolic filling shows an initial rapidly flowing transmitral jet, which decelerates and is subsequently redirected towards the LV outflow track. During this process of flow redirection, the formation of vortices store part of the kinetic energy of the incoming flowinarotarymotion. 1‐3 However,vorticesaredynamicalentities and therefore inherently also show marked, intrinsic instability. When they develop under unfavourable conditions they can give risetoturbulencewithlossofkineticenergyduetoincreasedfriction. The development of LV diastolic vortical intraventricular blood motionhascapturedtheimaginationof researchersin biomechanics and cardiovascular science. Numerous recent studies have demonstrated that anomalies in cardiac function are related to the changes in LV flow. 3‐7 In this issue of the journal, the article by Stugaard et al. 8 analysed the alterations in intraventricular flow in patients with varying severity of aortic regurgitation (AR). The presence of an AR jet is expected to alter the natural swirling motion of blood within the LV and increase turbulence. Authors specifically illustrate this by tracking the two-dimensional (2D) intraventricular flow velocities using a novel echocardiographic technique of Vector Flow Mapping (VFM), which is based on the processing of color Doppler acquisitions. VFM provides the velocity component along the scan line and estimates the transversal motion with the aid of the mass conservation and is therefore useful for deriving the amountofkineticenergythatislostduringthedisturbedflowmotion. Energy loss is expected to increasewith worsening AR and thereforemayprovideanovelindextogradetheseverityofAR.Thestudy by Stugaardet al. 8 in this issue exploresthis hypothesis byan experimental design in a canine model with further clinical verification in patients. The results confirm the hypothesis with highly comparable data from both experimental dog model and observations in the human subjects. The visualizations of blood flow quite remarkably
Visuo-Haptic Systems: Half-Mirrors Considered Harmful

In recent years, systems that allow users to see and touch virtual objects in the same space (visuo-haptic systems) are being investigated. Most research projects are employing a half-mirror, while few use a video see-through, head-mounted display (HMD). The work presented in this paper points out advantages of the HMD-based approach. First, we present an experiment that analyzes human performance in a target acquisition task. We have compared a half-mirror system with an HMD system. Our main finding is, that a half-mirror significantly reduces performance. Second, we present an HMD-based painting application, which introduces new interaction techniques that could not be implemented with a half-mirror display. We believe that our findings could inspire other researchers, employing a half-mirror, to reconsider their approach
Efficient Haplotype Inference with Answer Set Programming

Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. However, due to technological limitations, we have access to genotype data (genetic makeup of an individual), and determining haplotypes (genetic makeup of the parents) experimentally is a costly and time consuming procedure. With these biological motivations, we study a computational problem, called Haplotype Inference by Pure Parsimony (HIPP), that asks for the minimal number of haplotypes that form a given set of genotypes. HIPP has been studied using integer linear programming, branch and bound algorithms, SAT-based algorithms, or pseudo-boolean optimization methods. We introduce a new approach to solving HIPP, using Answer Set Programming (ASP). According to our experiments with a large number of problem instances (some automatically generated and some real), our ASP-based approach solves the most number of problems compared with other approaches. Due to the expressivity of the knowledge representation language of ASP, our approach allows us to solve variations of HIPP, e.g., with additional domain specific information, such as patterns/parts of haplotypes observed for some gene family, or with some missing genotype information. In this sense, the ASP-based approach is more general than the existing approaches to haplotype inference.
The restoration of ecological interactions: plant-pollinator networks on ancient and restored heathlands

1. Attempts to restore damaged ecosystems usually emphasize structural aspects of biodiversity, such as species richness and abundance. An alternative is to emphasize functional aspects, such as patterns of interaction between species. Pollination is a ubiquitous interaction between plants and animals. Patterns in plant-pollinator interactions can be analysed with a food web or complex-systems approach and comparing pollination webs between restored and reference sites can be used to test whether ecological restoration has taken place. 2. Using an ecological network approach, we compared plant-pollinator interactions on four pairs of restored and ancient heathlands 11 and 14 years following initiation of restoration management. We used the network data to test whether visitation by pollinators had been restored and we calculated pollinator importance indices for each insect species on the eight sites. Finally, we compared the robustness of the restored and ancient networks to species loss. 3. Plant and pollinator communities were established successfully on the restored sites. There was little evidence of movement of pollinators from ancient sites onto adjacent restored sites, although paired sites correlated in pollinator species richness in both years. There was little insect species overlap within each heathland between 2001 and 2004. 4. A few widespread insect species dominated the communities and were the main pollinators. The most important pollinators were typically honeybees (Apis mellifera), species of bumblebee (Bombus spp.) and one hoverfly species (Episyrphus balteatus). The interaction networks were significantly less complex on restored heathlands, in terms of connectance values, although in 2004 the low values might reflect the negative relationship between connectance and species richness. Finally, there was a trend of restored networks being more susceptible to perturbation than ancient networks, although this needs to be interpreted with caution. 5. Synthesis and applications. Ecological networks provide a powerful tool for assessing the outcome of restoration programmes. Our results indicate that heathland restoration does not have to occur immediately adjacent to ancient heathland for functional pollinator communities to be established. Moreover, in terms of restoring pollinator interactions, heathland managers need only be concerned with the most common insect species. Our focus on pollination demonstrates how a key ecological service can serve as a yardstick for judging restoration success.
Agency Modulates the Lateral and Medial Prefrontal Cortex Responses in Belief-Based Decision Making

Many real-life decisions in complex and changing environments are guided by the decision maker’s beliefs, such as her perceived control over decision outcomes (i.e., agency), leading to phenomena like the “illusion of control”. However, the neural mechanisms underlying the “agency” effect on belief-based decisions are not well understood. Using functional imaging and a card guessing game, we revealed that the agency manipulation (i.e., either asking the subjects (SG) or the computer (CG) to guess the location of the winning card) not only affected the size of subjects’ bets, but also their “world model” regarding the outcome dependency. Functional imaging results revealed that the decision-related activation in the lateral and medial prefrontal cortex (PFC) was significantly modulated by agency and previous outcome. Specifically, these PFC regions showed stronger activation when subjects made decisions after losses than after wins under the CG condition, but the pattern was reversed under the SG condition. Furthermore, subjects with high external attribution of negative events were more affected by agency at the behavioral and neural levels. These results suggest that the prefrontal decision-making system can be modulated by abstract beliefs, and are thus vulnerable to factors such as false agency and attribution.