Miracle-dz/UniFAR-FTUs huggingface dataset:
Calibrated Bayes factors for model selection and model averaging

The discussion of statistical model selection and averaging has a long history and is still attractive nowadays. Arguably, the Bayesian ideal of model comparison based on Bayes factors successfully overcomes the difficulties and drawbacks for which frequentist hypothesis testing has been criticized. By putting prior distributions on modelspecific parameters, Bayesian models will be completed hierarchically and thus many statistical summaries, such as posterior model probabilities, model-specific posterior distributions and model-average posterior distributions can be derived naturally. These summaries enable us to compare inference summaries such as the predictive distributions. Importantly, a Bayes factor between two models can be greatly affected by the prior distributions on the model parameters. When prior information is weak, very dispersed proper prior distributions are often used. This is known to create a problem for the Bayes factor when competing models that differ in dimension, and it is of even greater concern when one of the models is of infinite dimension. Therefore, we propose an innovative criterion called the calibrated Bayes factor, which uses training samples to calibrate the prior distributions so that they achieve a reasonable level of ”information”. The calibrated Bayes factor is then computed as the Bayes factor over the remaining data. The level of ”information” is tied to the concentration of training-updated prior distributions, which is carefully evaluated by monitoring ii the distribution of symmetrized Kullback-Leibler divergence between two likelihood functions drawn independently from the training-updated prior distribution. Monte Carlo Markov chain algorithms are widely used in this research to generate parameter draws from training-updated prior distributions. Subsampling is applied to reduce dependence among parameter draws. In this thesis, we mainly focus on comparisons of one-sample (i.i.d) models and the variable selection problem under regression settings with a variety of model specific prior distributions. We illustrate through simulation studies that the calibrated Bayes factor yields robust and reliable model preferences under various true models. We further demonstrate use of the calibrated Bayes factor on obesity data from the Ohio Family Health Survey (one-sample model) and the ozone data originally studied in Breiman and Friedman (1985) (variable selection problem). The calibrated Bayes factor is applicable to a large variety of model comparison problems because it makes no assumption on model forms (parametric or nonparametric) and can be used for both proper and improper priors.
Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging

Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include environmental changes and inter-specific ecological interactions that cause ranges of multiple, co-distributed species to contract, expand, or become fragmented. Such processes predict temporally clustered patterns of evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in effective population size, but not both, and the latter has been limited to approximate Bayesian computation (ABC). We introduce a general, full-likelihood Bayesian method that can use genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Applying this method to simulated data, we find that estimating the timing and sharing of demographic changes is much more challenging than divergences. Even under favorable simulation conditions, the ability to infer shared demographic events is quite limited and very sensitive to prior assumptions, which is in sharp contrast to accurate, precise, and robust estimates of shared divergence times. Our results also suggest that previous estimates of co-expansion among five Alaskan populations of threespine sticklebacks (Gasterosteus aculeatus) were likely spurious, and driven by a combination of misspecified prior assumptions and the lack of information about the timing of demographic changes when invariant characters are ignored. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.
Direct effects of a non‐native invader erode native plant fitness in the forest understory

The direct role of non‐native plant invaders in driving negative population‐ and community‐level processes of native species has been recently questioned. Addressing this controversy requires determining quantitatively if invaders negatively affect native population fitness. Because the invasion of non‐natives often coincides with other anthropogenic stressors, experiments that partition the putative impact of non‐natives from other known stressors and assess their potential synergies are required. While many studies have examined the effects of non‐natives on components of native plant performance, studies that decompose the net fitness effects of non‐natives from other anthropogenic stressors on population growth rate are lacking. We used 6 years of detailed demographic data to parameterize a size‐dependent integral projection model to examine the individual and combined effects of an allelochemical‐producing invader (Alliaria petiolata) and an overabundant ungulate herbivore (Odocoileus virginianus) on the population dynamics of an understory perennial (Trillium erectum). We show that Alliaria consistently and negatively affects the population dynamics of Trillium. Specifically, this invader reduces native population growth rate and alters the size distribution of the population at equilibrium. Alliaria also works in concert with the known negative impacts of overabundant white‐tailed deer, illustrating the additive effects of anthropogenic stressors on native plant dynamics. Synthesis. Alliaria's effects on vital rates differed in magnitude and sign across the native's life cycle, highlighting the importance of detailed demographic analyses. Our study provides novel empirical support for the claim that non‐native invasive species can significantly and directly reduce the fitness of native plants.
Perspectives for ecological networks in plant ecology

ABSTRACT Background: Plant communities are usually characterised by species composition and abundance, but also underlie a multitude of complex interactions that we have only recently started unveiling. Yet, we are still far from understanding ecological and evolutionary processes shaping the network-level organisation of plant diversity, and to what extent these processes are specific to certain spatial scales or environments. Aims: Understanding the systemic mechanisms of plant–plant network assembly and their consequences for diversity patterns. Methods: We review recent methods and results of plant–plant networks. Results: We synthetize how plant–plant networks can help us to: (a) assess how competition and facilitation may balance each other through the network; (b) analyse the role of plant–plant interactions beyond pairwise competition in structuring plant communities, and (c) forecast the ecological implications of complex species dependencies. We discuss pros and cons, assumptions and limitations of different approaches used for inferring plant–plant networks. Conclusions: We propose novel opportunities for advancing plant ecology by using ecological networks that encompass different ecological levels and spatio-temporal scales, and incorporate more biological information. Embracing networks of interactions among plants can shed new light on mechanisms driving evolution and ecosystem functioning, helping us to mitigate diversity loss.
Constant Infusion Radiotracer Administration for High Temporal Resolution Positron Emission Tomography (PET) of the Human Brain: Application to [18F]-Fluorodexoyglucose PET (FDG-PET)

Functional Positron Emission Tomography (fPET) provides a method to track molecular dynamics in the human brain. With a radioactively labelled glucose-analogue, [18F]-flurodeoxyglucose (FDG-fPET), it is now possible to index the dynamics of glucose metabolism with temporal resolutions approaching those of functional magnetic resonance imaging (fMRI). This direct measure of glucose uptake has enormous potential for understanding normal and abnormal brain function, and probing the effects of metabolic and neurodegenerative diseases. Further, new advances in hybrid MR-PET hardware makes it possible to capture fluctuations in glucose and blood oxygenation simultaneously using fMRI and FDG-fPET. The temporal resolution and signal-to-noise of the FDG-fPET images is critically dependent upon the administration of the radioactive tracer. In this work we present two alternative continuous infusion protocols and compare them to a traditional bolus approach. We detail a method for acquiring blood samples, time-locking PET, MRI and experimental stimulus, and administrating the non-traditional tracer delivery. By applying a visual stimulus, we demonstrate cortical maps of the glucose-response to external stimuli on an individual level with a temporal resolution of 16-seconds. Summary Radiotracer infusion protocols for positron emission tomography (PET) provide improved temporal resolution over bolus administration. Here, we describe radiotracer administration for two protocols, constant infusion and bolus plus infusion protocol. We compare this to the standard bolus administration protocol. Using [18-F] fluorodeoxyglucose PET (FDG-PET) as an example, we show that temporal resolutions of approximately 16sec are achievable using these protocols.
Levels of oxidative stress markers in the mangrove oyster, Crassostrea gasar from a coastal ecosystem in southwest Nigeria

This study investigated biochemical responses in the ecologically important Mangrove Oyster, Crassostrea gasar along a contamination gradient on the Lagos/Badagry lagoon in Lagos, Nigeria. The antioxidant enzymes and oxidative stress biomarkers, catalase enzyme activity (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx) and Thiobarbituric Acid Reactive Substances (TBARS): Malondialdehyde (MDA) were assessed in gills and muscle tissues of adult Crassostrea gasar using standard biochemical procedures. The muscle tissue of C. gasar exhibited higher oxidative stress enzymes activity than the gills. Relatively higher mean value of MDA was recorded in the gill of C. gasar at Makoko (35.39±1.08 Hmol/mg pro) as compared to the levels in oysters collected from Abule-Agege Creek (26.26±2.78 Hmol/mg pro) and Badagry Creek (25.15±4.54 ± Hmol/mg protein). Similarly, the result of anti-oxidative stress enzyme activities and lipid peroxidation in the muscle tissue of C. gasar from Makoko waters showed significant highest values of SOD (54.24±1.37 Min/mg pro), CAT (6.82 Min/mg pro) and MDA (42.35±0.81 Hmol/mg pro). No significant difference in GPx value was recorded in examined samples of C. gasar across sites. C. gasar collected from Abule-Agege and Badagry Creeks were similar in most values of the measured biochemical enzyme activities. Biological adverse effects were more evident in oysters from Makoko, a recognized contaminated area than those from Abule-Agege Creek and Badagry Creek. The study gave an indication of stress on the health status of the oysters, hence the need for periodic monitoring of the ecosystem. Keywords: Mangrove Oyster, Antioxidant enzymes, Oxidative stress, Estuary
Automatic Operation of Light Tractor with Sprayer in Paddy Fields

When a sprayer spreads pesticides in the field, the operator on board is exposed to the mist of pesticides. The automatic operation without operator on board could certainly alleviate such a shortcoming. A joint research team organized by NARC and Mitsubishi Farm Machinery Co. Ltd. Developed and tested an automatic operation method by the light tractor “Paddy vehicle” with a sprayer. The operation system included a straight line automatic operation which followed the rows of rice plants and a turning action supported by a remote controller handled by the operator. The paddy vehicle equipped with a boom sprayer could carry out automatic spraying operations without an operator on board in the paddy fields. The automatic forward movement of the vehicle following the straight row of rice plants, the automatic turning by the computerized program, and the maneuver remotely controlled by the operator on the road for the accurate position ready for the next stroke were tested. The operation of the paddy vehicle was found to be successful as had been intended from the design stage. This new automatic operation system enables 1 operator to handle 2 or more paddy vehicles simultaneously in paddy fields. Discipline: Agricultural machinery Additional key words: robot, pest control JARQ 30, 239-244 (1996)
Anthropomorphic visualization : depicting participants in online spaces using the human form

Anthropomorphic visualization is a new approach to presenting information about participants in online spaces using the human form as the basis for the visualization. Various data about an individual’s online behavior are mapped to different parts of a humanoid yet abstract form. I hypothesized that using a humanoid form to visualize data about people in online social spaces could serve two purposes simultaneously: communicate statistics about the individuals and evoke a social response. Using the human form in this way has both benefits and drawbacks. Users can quickly scan a set of humanoid representations and get a sense of the character of a group, and may respond socially to the other participants in the group. However, the information we are able to represent is somewhat limited, and a humanoid representation style might lead users to make incorrect assumptions about the people being represented. To investigate these tradeoffs, I created a testbed application that visualized data from messages written in Usenet newsgroups. I conducted user studies to evaluate how users interpreted the data from the visualizations and responded to messages shown with visualizations. In this thesis, I discuss the challenges of designing effective anthropomorphic visualizations and offer guidelines to consider when using the human form to visualize information about participants in online conversations. Thesis Supervisor: Judith S. Donath Assistant Professor of Media Arts & Sciences Director of Sociable Media, Media Laboratory
RECENT CHANGES OF ZOOBENTHOS COMMUNITIES FROM THE REGION CAPE KALIAKRA CAPE GALATA (THE BLACK SEA)

UZUNOVA, S. , 2015. Recent changes of zoobenthos communities from the region Cape Kaliakra – Cape Galata (the Black Sea). Bulg. J. Agric. Sci., Supplement 1, 21: 154–158 In 2006, 2011 and 2013 benthic macrofauna investigations were carried out in the region between Cape Kaliakra and Cape Galata, situated at 1 mile distance in front of the Bulgarian Black Sea coast and two stations in Varna Bay, so that to reveal the present situation with the benthic communities in the studied area in 2013, compared to 2006 and 2011. The results show strong increase in abundance of benthic macrofauna from 2006 to 2013 and reverse trend for the biomass values. Similar results were established for the period 1998–2002, which prove that situation within benthic community is still very unstable. Trend of decrease in mollusk’s share in species composition and increase of polychete number was found in 2013. Shannon – Wiener index shows improvement of the state of benthic communities in the investigated area. Values of Marine Biotic Index (AMBI) and multivariate AMBI (M–AMBI) are in conformity with Shannon – Wiener index and confi rm the relatively good state of the ecosystem in the investigated area.
Transcriptome-wide analysis of roles for tRNA modifications in translational regulation

Covalent nucleotide modifications in noncoding RNAs such as tRNAs affect a plethora of biological processes, with new functions continuing to be discovered for even well-known tRNA modifications. To systematically compare the functions of a large set of ncRNA modifications in gene regulation, we carried out ribosome profiling and RNA-Seq in budding yeast for 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with modifying enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally-regulated mRNAs throughout the yeast genome. Our data also uncover novel roles for tRNA modifying enzymes in transcriptional regulation of TY retroelements, and in rRNA 2’-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.
Altered m6A modification of specific cellular transcripts affects Flaviviridae infection

The RNA modification N6-methyladenosine (m6A) can modulate mRNA fate and thus affect many biological processes. We analyzed m6A modification across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, we found that activation of innate immune sensing or the endoplasmic reticulum (ER) stress response by viral infection contributes to the changes in m6A modification in RIOK3 and CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.
Non-Rhizobial Nodule Associated Bacteria (NAB) From Blackgram (Vigna mungo L.) and their possible role in plant growth promotion

Rhizosphere engineering is one of the means to increase the competitive survivability of rhizobial bio-inoculants. This can be achieved by altering the rhizospheric community structure with a co-compatible and co-operative microbial partner. There exists a proto-cooperative mode of interaction between the non-rhizobial endophytes (NRE) and the endosymbiont Rhizobium, which can be unraveled to enhance their competitive survivability. In the present investigation, 8 isolates of nodule associated bacteria (NAB) and 1 rhizobial species were isolated from the root nodules of black gram (Vigna mungo L.,) cultivar VBN6. Among the NAB isolates, 75% were grampositive bacilli belonging to the phylum firmicutes. The promising NABs that showed maximum PGP features were phylogenetically affiliated as Bacillus subtilis NANEB1 and Paenibacillus taichungensis TNEB6. Among them, P.taichungensis TNEB6 registered significant IAA production (15.39 μg.ml-1), siderophore (10.7%), ammonia, HCN and also ACC deaminase activity (94.3 mg-1 hr-1). Interestingly, 75 % of the NAB isolates could solubilize phosphorous. Furthermore, P.taichungensis TNEB6, when co-inoculated with Rhizobium sp showed significant plant growth promotion with respect to enhanced root and shoot length. The vigor index was also maximum in the treatment that received co-inoculation of Rhizobium sp and P.taichungensis (1812) Hence, the study suggests the scope of enhancing the yield potential and fitness of blackgram using a compatible co-inoculant, comprising a multifunctional NAB, P. taichungensis TNEB6 and Rhizobium sp.
Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects underlying impaired adult neurogenesis

Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NSCs are crucial for regulating stem cell self-renewal and differentiation. We used single-cell RNA profiling to generate an unbiased molecular atlas of all cell types in the largest neurogenic niche of the adult mouse brain, the subventricular zone (SVZ). We characterized > 20 neural and non-neural cell types and gained insights into the dynamics of neurogenesis by predicting future cell states based on computational analysis of RNA kinetics. Furthermore, we apply our single-cell approach to mice lacking LRP2, an endocytic receptor required for SVZ maintenance. The number of NSCs and proliferating progenitors was significantly reduced. Moreover, Wnt and BMP4 signaling was perturbed. We provide a valuable resource for adult neurogenesis, insights into SVZ neurogenesis regulation by LRP2, and a proof-of-principle demonstrating the power of single-cell RNA-seq in pinpointing neural cell type-specific functions in loss-of-function models. HIGHLIGHTS unbiased single-cell transcriptomics characterizes adult NSCs and their niche cell type-specific signatures and marker genes for 22 SVZ cell types Free online tool to assess gene expression across 9,804 single cells cell type-specific dysfunctions underlying impaired adult neurogenesis
Eucalypt forests dominated by epicormic resprouters are resilient to repeated canopy fires

Wildfire occurrence and severity are projected to increase in response to anthropogenic climate change, leading to fire regimes that may exceed the limits of tolerance for some species. Plants capable of regenerating from aerial shoots following high intensity fires, termed ‘epicormic resprouters’, are assumed to be resilient to changes in fire regimes. However, empirical tests of the response of epicormic resprouters to extreme fire regimes, such as repeated canopy fires at short intervals, are currently lacking. This study examined the effect of combinations of understorey fire and canopy fire across two successive wildfires (2007, 2013) on the resilience of eucalypts that resprout epicormically. The study took place in a temperate eucalypt forest in south eastern Australia. Measures used to infer community resilience included stem topkill and damage, and seedling recruitment. It was predicted that: (a) stems will exhibit lower resistance (i.e. increased topkill and damage) to canopy fire than understorey fire; (b) recruitment will be higher following canopy fire than understorey fire; (c) prior exposure to canopy fire will reduce stem resistance and recruitment in response to subsequent wildfires; and (d) stem resistance will vary depending on bark traits. Topkill of saplings and small stems (<30 cm diameter at breast height) was higher in sites that recently (i.e. 2013) experienced canopy fire as opposed to understorey fire. Recent fire severity had no effect on topkill of large trees. Tree species with dense bark on the main stem and larger branches were less prone to topkill or partial stem and branch mortality than species with fibrous bark or exposed branches. Seedling recruitment was greater following canopy fire than understorey fire. Exposure to past canopy fire (i.e. in 2007) did not decrease stem resistance or recruitment. Synthesis. The results of this study suggest that communities of eucalypts that can resprout epicormically following fire will experience demographic shifts following repeated canopy fires. However, given the high resistance of large trees and rapid post‐fire recovery of the seedbank, ecosystem conversion appears unlikely. The findings support the presumption that forest communities of epicormic resprouters are highly resilient to shifts in fire regimes.