Miracle-dz/UniFAR-FTUs huggingface dataset:
Wildfire in wet sclerophyll forests: the interplay between disturbances and fuel dynamics

There are multiple pathways for vegetation to change following disturbances. Understanding those post‐disturbance pathways is critical for managing wildfire risk since vegetation is fuel in a wildfire context. Across forest systems, there is considerable debate about disturbance‐related changes to fuels and flammability. This study investigated post‐disturbance fuel trajectories following three disturbance types—high severity wildfire, low severity wildfire, and clear‐fell logging. Fuels were measured in a chrono‐sequence of 141 sites in Mountain Ash (Eucalyptus regnans)‐dominated wet sclerophyll forest in southeastern Australia, a particularly contentious forest system. Wildfires are an important part of the lifecycle of these forests, but too frequent fire can threaten post‐fire regeneration. Large wildfires (in 2009, 1983 and 1939) and ongoing public and scientific debate over clear‐fell logging highlight the need to better understand post‐disturbance trajectories for fuel and flammability in wet sclerophyll forests. We used empirical data to test 10, sometimes contradictory, hypotheses from the scientific literature regarding post‐disturbance pathways for fuel following wildfire and logging. Only five hypotheses were supported with surface fine fuels, fuel hazard, species composition, and vertical structure driving overall differences in post‐disturbance fuel trajectories. The implications for flammability remain uncertain because the independent and interactive effects of many fuel components on overall flammability remain unquantified. Importantly, we found there were always high quantities of fuel, irrespective of disturbance history, which demonstrates that fire occurrence is not fuel‐limited in wet sclerophyll forests. Under conditions of abundant fuel, fuel moisture could become critical to fire occurrence. Therefore, forest management should prioritize efforts to quantify not only the importance of individual fuel components to flammability but also fuel moisture dynamics in wet sclerophyll forests. As the climate (and fuels) becomes drier under climate change, it will be a major challenge to manage fire regimes in these highly valued forests.
Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria

Despite the remarkable evolutionary and metabolic diversity found within the human microbiome, the vast majority of mechanistic studies focus on two phyla: the Bacteroidetes and the Proteobacteria. Generalizable tools for studying the other phyla are urgently needed in order to transition microbiome research from a descriptive to a mechanistic discipline. Here, we focus on the Coriobacteriia class within the Actinobacteria phylum, detected in the distal gut of 90% of adult individuals around the world, which have been associated with both chronic and infectious disease, and play a key role in the metabolism of pharmaceutical, dietary, and endogenous compounds. We established, sequenced, and annotated a strain collection spanning 14 genera, 8 decades, and 3 continents, with a focus on Eggerthella lenta. Genome-wide alignments revealed inconsistencies in the taxonomy of the Coriobacteriia for which amendments have been proposed. Re-sequencing of the E. lenta type strain from multiple culture collections and our laboratory stock allowed us to identify errors in the finished genome and to identify point mutations associated with antibiotic resistance. Analysis of 24 E. lenta genomes revealed an “open” pan-genome suggesting we still have not fully sampled the genetic and metabolic diversity within this bacterial species. Consistent with the requirement for arginine during in vitro growth, the core E. lenta genome included the arginine dihydrolase pathway. Surprisingly, glycolysis and the citric acid cycle was also conserved in E. lenta despite the lack of evidence for carbohydrate utilization. We identified a species-specific marker gene and validated a multiplexed quantitative PCR assay for simultaneous detection of E. lenta and specific genes of interest from stool samples. Finally, we demonstrated the utility of comparative genomics for linking variable genes to strain-specific phenotypes, including antibiotic resistance and drug metabolism. To facilitate the continued functional genomic analysis of the Coriobacteriia, we have deposited the full collection of strains in DSMZ and have written a general software tool (ElenMatchR) that can be readily applied to novel phenotypic traits of interest. Together, these tools provide a first step towards a molecular understanding of the many neglected but clinically-relevant members of the human gut microbiome.
Beyond core object recognition: Recurrent processes account for object recognition under occlusion

Core object recognition, the ability to rapidly recognize objects despite variations in their appearance, is largely solved through the feedforward processing of visual information. Deep neural networks are shown to achieve human-level performance in these tasks, and explain the primate brain representation. On the other hand, object recognition under more challenging conditions (i.e. beyond the core recognition problem) is less characterized. One such example is object recognition under occlusion. It is unclear to what extent feedforward and recurrent processes contribute in object recognition under occlusion. Furthermore, we do not know whether the conventional deep neural networks that were shown to be successful in solving core object recognition, can perform similarly well in problems that go beyond the core recognition. Here, we characterize neural dynamics of object recognition under occlusion, using magnetoencephalography (MEG), while human subjects were presented with images of objects with various levels of occlusion. We provide evidence from multivariate analysis of MEG data, behavioral data, and computational modelling, demonstrating an essential role for recurrent processes in object recognition under occlusion. Furthermore, the computational model with local recurrent connections, used here, suggests a mechanistic explanation of how the human brain might be solving this problem.
Sepsis: Partial least squares structural equation modelling (PLS-SEM) suggests a critical role for anti-inflammatory responses in clinical severity

Backgorund Despite major advances in medicine, Sepsis remains one of the major killers in critical care wards around the world. For several years it was widely believed that an early pro-inflammatory host response is followed by an overwhelming anti-inflammatory phase. The hypo-inflammatory status, termed as ‘Compensatory anti-inflammatory response syndrome’ (CARS), was proposed to be the primary cause of sepsis-associated mortality. However, this paradiam changed in recent years since there was little evidence to support the linear model of host response and pathogenesis in sepsis. Currently held view is that both inflammatory and anti-inflammatory host responses are stimulated in an overlapping manner. In this study a robust statistical model to study the complex interplay of host cytokines in human sepsis has been developed to evaluate host responses in sepsis that contribute significantly to clinical pathology. Methods Twentyseven cytokines/ chemokines were quantified in 139 sepsis patients and multivariate analysis of variance (MANOVA) was performed to assess differences in host responses in different categories of clinical severity. Partial least squares regression based structural equation modelling (PLS-SEM) was used to assess interactions between different groups of cytokines and their contribution to clinical pathology. An array of 23 cytokines was analysed in a mouse model of endotoxemia and a similar mathematical model was constructed. Results The results of MANOVA demonstrated the ability of combined cytokine response to discriminate sepsis patients according to clinical severity or outcome. Structural equation modelling revealed strong positive association between inflammatory and anti-inflammatory cytokines. In human sepsis, anti-inflammatory cytokines emerged as a significant entity associated with clinical severity as assessed by APACHE II scores. Conclusion PLS-SEM modeling of cytokine responses and APACHE II score in human sepsis revealed that anti-inflammatory molecules contribute significantly towards clinical severity. More critically, the model offers emperical evidence for failures of clinical trials conducted during the last two decades in which antagonists of inflammatory host responses for human Sepsis were used for sepsis. The model also provides credence to the notion that inflammatory and anti-inflammatory host responses occur concurrently in both experimental endotoxemia and in human sepsis.
Comparative water relations of co-occurring trees in a mixed podocarp-broadleaf forest

Aims As extreme climatic events including droughts and heat waves become more common in a changing climate, tree mortality has increased across the globe. In order to determine whether certain species have a competitive advantage over others, we explored the water-relations and leaf-gas exchange of four co-occurring species in a forest in northern Aotearoa-New Zealand. We studied the ecologically and culturally significant foundation species, Agathis australis (a conifer), two additional conifers, Phyllocladus trichomanoides and Podocarpus totara and the angiosperm Knightia excelsa. Methods We measured sap flow, leaf-gas exchange and xylem water potentials of leaves and terminal branches with concurrent measures of micrometeorological data on days with very few clouds. We derived whole tree hydraulic conductance and instantaneous water-use efficiency (WUEi) at our remnant forest in west Auckland during February 2015 (southern hemisphere summer). Important Findings The four species behaved similarly in their diurnal curves of gas exchange and water potential. Rates of assimilation, stomatal conductance and WUEi were similar among trees of different species. Whole tree hydraulic conductance was also similar among species. These results indicate functional convergence in water relations, possibly driven by low nutrient soils at the site. Our results suggest that there is no species with a clear adaptive advantage over the others in the context of climate change.
Applying next-generation sequencing to enable marker-assisted breeding for adaptive traits in common bean (Phaseolus vulgaris L.)

This research establishes molecular breeding capability for adapting common bean (Phaseolus vulgaris L.) to UK growing conditions. A high-resolution linkage map was constructed for a bi-parental recombinant inbred population (large brown x small white haricot) using genotyping-by-sequencing data. Pre-breeding material was exploited to enable genetic mapping and marker-assisted selection of essential adaptive traits, including (1) resistance to halo blight, caused by Pseudomonas syringae pathovar phaseolicola (Psph), (2) root architecture related to abiotic stress tolerance and nutrient acquisition, (3) earliness of maturity, (4) plant architecture amenable to mechanical harvest, and (5) seed coat colour of consumer interest. A 500-kb mapping interval was defined for quantitative resistance to the broadly virulent Psph race 6, a devastating bacterial pathogen that threatens global bean production with losses from halo blight. Complementary research generating high-quality draft genomes for 32 pathogenically and geographically diverse isolates of Psph identified five high-probability candidate determinants of the broad virulence of Psph race 6, including avirulence protein AvrD. Pathogenicity effectors that are highly conserved within the pathovar were identified as candidate targets for potential race-nonspecific resistance to halo blight. Putative QTL for root architecture traits associated with water and nutrient acquisition were detected on chromosome Pv07. A useful breeding strategy may be to select for larger taproot diameter in view of the comparatively high heritability of this trait. Potentially desirable alleles on Pv07 are linked in coupling phase with the dominant allele of seed coat pigmentation factor P. Identification of lines recombinant for these alleles may prove useful for the introgression of genes governing physiological resilience into white-seeded varieties adapted to UK growing conditions. Provisional QTL for morphological and reproductive traits of agronomic importance, including plant architecture, growth stage and yield, were identified using phenotypic data obtained from pilot field and polytunnel evaluations of the recombinant inbred population.
Improved cortical boundary registration for locally distorted fMRI scans

With continuing advances in MRI techniques and the emergence of higher static field strengths, submillimetre spatial resolution is now possible in human functional imaging experiments. This has opened up the way for more specific types of analysis, for example investigation of the cortical layers of the brain. With this increased specificity, it is important to correct for the geometrical distortions that are inherent to echo planar imaging (EPI). Inconveniently, higher field strength also increases these distortions. The resulting displacements can easily amount to several millimetres and as such pose a serious problem for laminar analysis. We here present a method, Recursive Boundary Registration (RBR), that corrects distortions between an anatomical and an EPI volume. By recursively applying Boundary Based Registration (BBR) on progressively smaller subregions of the brain we generate an accurate whole-brain registration, based on the grey-white matter contrast. Explicit care is taken that the deformation does not break the topology of the cortical surface, which is an important requirement for several of the most common subsequent steps in laminar analysis. We show that RBR obtains submillimetre accuracy with respect to a manually distorted gold standard, and apply it to a set of human in vivo scans to show a clear increase in spacial specificity. RBR further automates the process of non-linear distortion correction. This is an important step towards routine human laminar fMRI. We provide the code for the RBR algorithm, as well as a variety of functions to better investigate registration performance in a public GitHub repository, https://github.com/TimVanMourik/OpenFmriAnalysis, under the GPL 3.0 license.
Moderate weather extremes alter phytoplankton diversity—A microcosm study

Funding information Tiroler Wissenschaftsfonds, Grant/Award Number: GZ: UNI-0404/1794 Abstract 1. Moderate weather extremes are predicted to increase in frequency and intensity as a function of climate change. These extremes can result in sudden changes in temperature, light and nutrient levels, which may strongly affect the phytoplankton community in many lakes. 2. We conducted a microcosm experiment with eight freshwater algal species, representing different functional groups, to investigate the interactive effects of these environmental variables on a phytoplankton community typical of an oligomesotrophic temperate lake. 3. We manipulated temperature (6, 16 and 26°C), light (18, 56, 132 lmol m 2 s ) and soluble reactive phosphorus (0, 1, 5 lg/l) concentrations in a 3 9 3 9 3 factorial design and analysed treatment effects on algal biomass, species diversity (SDiv) and functional diversity (FDiv). 4. Strong temperature variations affected phytoplankton biomass and diversity more strongly than moderate changes in nutrient and light levels. In particular, SDiv and FDiv decreased significantly with increasing temperatures. 5. Our results support earlier findings that lake warming favours heterotrophic bacteria, relative to phytoplankton. 6. We conclude that sudden temperature increases as they typically occur in temperate lakes during heat waves may decrease phytoplankton diversity, leading to altered ecosystem functioning. In contrast, heavy rain events usually characterised by decreasing levels of temperature and light intensities, concurrent with increases in nutrient concentrations, may sustain high phytoplankton diversity.
Antimicrobial wound dressing films containing essential oils and oleoresins of pepper encapsulated in sodium alginate films

EnglishMedicated wound dressings are important barriers to avoid contamination and, when they contain antimicrobial additives, can be used as treatment for infected wounds. There are several types of polysaccharide materials that serve as matrices for medicated wound dressings, among them, sodium alginate. For the preparation of the films studied in this paper, sodium alginate was employed in combination with essential oils/oleoresins (EO/OL) of six peppers that are commonly used in cooking. The EO/OL were incorporated at three different concentrations (low, intermediate and high). Most of the films prepared had better dispersion of the EO/OL at the intermediate concentration. All films studied in this research were dissolved in water at different rates. The antibacterial activity of the prepared films showed significant results against Escherichia coli, Staphylococcus aureus and Bacillus cereus, and demonstrated that the films studied may be a new alternative for medicated wound dressings. Key words: medicated wound dressings; alginate-based films; essential oils; oleoresins; antibacterial activity portuguesOs curativos medicamentosos sao importantes barreiras para se evitar contaminacao e ainda, quando contem aditivos antimicrobianos, servem como tratamento para ferimentos infectados. Existem varios tipos de materiais polissacaridicos que servem como matrizes para curativos medicamentosos, dentre eles, destaca-se o alginato de sodio. Para a preparacao dos filmes estudados neste trabalho, utilizou-se alginato de sodio e incorporou-se oleos essenciais/oleoresinas (OE/OL) de seis pimentas utilizadas na culinaria, em tres diferentes concentracoes. A maioria dos filmes preparados apresentou melhor dispersao dos OE/OL na concentracao intermediaria destes. Todos os filmes estudados neste trabalho apresentam solubilidade em agua, em uma certa extensao. A atividade antibacteriana dos filmes preparados mostra resultados significantes contra Escherichia coli, Staphylococcus aureus e Bacillus Cereus, mostrando que os filmes estudados podem ser uma nova alternativa como curativos medicamentos. Palavras-chave: curativos medicamentosos; filmes de alginato; oleos essenciais; oleoresinas; pimentas; atividade antibacteriana
The complete mitochondrial transcript of the red tail loach Yasuhikotakia modesta as assembled from RNAseq (Teleostei: Botiidae)

Abstract Here, we present the first complete mitochondrial genome of the Red Tailed Loach Yasuhikotakia modesta (Teleostei: Botiidae) from Thailand, assembled from next-generation transcriptome sequencing data. The assembled transcript corresponds to the full length mitochondrial genome of Y. modesta, which measured 16,865 bp in length, and contained 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. A slight A + T bias was observed in the mitogenome of Y. modesta with an overall base composition of 32.2% A, 25.8% T, 26.4% C, and 15.4% G, and a GC content of 41.8%. The gene arrangement was identical to that of previously described loach mitogenomes.
Etude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques

L’igname (Dioscorea spp) est un aliment de base de plus de 100 millions de personnes en Afrique. L’objectif de cette these etait d'etudier la diversite genomique de l'igname, comprendre les bases genetiques de sa domestication, et d'etudier son adaptation a differentes zones climatiques. L’etude du processus de domestication de l’igname a ete menee par une approche de genomique comparee entre l’espece cultivee D. rotundata et deux especes sauvages apparentees D. praehensilis et D. abyssinica, en utilisant des donnees de sequencage NGS genomique. Nous avons mis en evidence des selections fortes de genes de la voie de biosynthese de l’amidon. Des genes impliques dans la morphologie des tubercules ou l’aptitude au phototropisme, ainsi que des genes du complexe NADH deshydrogenase ont egalement ete identifies comme selectionnes durant la domestication. Ce meme complexe NADH-DH a egalement ete identifie lors de la recherche de genes associes a la distribution d’une collection d’ignames selon la variabilite climatique. Nous avons aussi cree la premiere banque de novo d’elements transposables (ET) de l’igname. L’etude que nous avons menee sur les elements repetes (ER) du genome de l’igname nous a permis d’identifier une forte correlation entre la variabilite des abondances relatives d’un grand nombre d’ERs et la variabilite climatique. Enfin, nous avons pu proposer une hypothese quant a l’origine de l’igname cultivee D. rotundata. La domestication de l'igname deriverait de l'espece infeodee au milieu forestier, D. praehensilis. Ces resultats remettent en cause l’hypothese d’une origine stricte en zone de savane pour les especes cultivees et l’agriculture en Afrique de l'Ouest.
Molecular determinants of influenza A virus cross-species jumps

Influenza A viruses (IAVs) represent a significant risk to human and animal health and thus determining the mechanisms of cross-species transmission is critical in understanding viral emergence. H3N8 equine influenza virus (EIV) is a virus of avian origin that emerged in horses in the early 1960s and is still circulating in horses despite the availability of vaccines. Therefore, H3N8 EIV provides unique opportunities to study the underpinning mechanisms of cross-species jumps and adaptation in mammalian hosts. The aim of this project was to determine the role of evolution on EIV adaptation to the horse. To this end, equine and avian cell lines were infected as well as horse tracheal explants with a panel of phylogenetically distinct EIVs and compared their infection phenotypes. Viral replication was quantified and changes in the histology and ciliary activity of infected explants were assessed to compare the phenotype of infection of each virus. Phylogenetically distinct EIVs exhibited different infection phenotypes: while early EIVs grew more efficiently in avian cells, late EIVs grew to higher titres in equine explants. This phenotype was demonstrated to be largely due to the late EIV viral polymerase. Using an in vitro measure of polymerase activity, late EIVs were observed to have more efficient activity in mammalian cells than early EIVs. The Polymerase Acidic (PA) and Nucleoprotein (NP) segments were shown to be the greatest drivers of the mammalian-adapted polymerase phenotype. Including either of these segments from a late EIV in the polymerase complex significantly increased minireplicon activity. Our results suggest that EIV adapted to the horse along its evolutionary history partly by mutations in the PA and NP genes.
Forest structure following tornado damage and salvage logging in northern Maine, USA

Understanding forest structural changes resulting from postdisturbance management practices such as salvage logging is critical for predicting forest recovery and developing appropriate management strategies. In 2013, a tornado and subsequent salvage operations in northern Maine, USA, created three conditions (i.e., treatments) with contrasting forest structure: blowdown, blowdown + salvage, and control (undisturbed). We sampled forest structure in five stands representing each of these three treatments. Our results document obvious and predictable changes to forest structure caused by the blowdown and salvage operations; however, they also include unexpected findings: downed coarse woody debris volume remained quite high in the salvaged areas, although its vertical distribution was markedly reduced; salvage operations did not reduce fine woody debris volume; and the salvage operation itself reduced the abundance of upturned root masses. Our study contributes to a growing body of literature highlighting t.