Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial food webs in hypertrophic fishponds: Omnivorous ciliate taxa are major protistan bacterivores

Despite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia (Czech Republic). We used fluorescently labeled bacteria as bacterivory tracers to estimate how abundant protistan populations in fishponds (4–25 × 103 HNF mL−1 and 55–770 ciliates mL−1) contribute to total bacterial mortality. Fluorescence microscopy, innovative image processing tools, and quantitative protargol staining were combined to detect major bacterivorous and omnivorous ciliate taxa. We quantified bacterial production, bacterivory by individual ciliate species, total ciliates, and total protistan bacterivory in all fishponds. On average, ciliate bacterivory was comparable to that of HNF, accounting for 56% and 44% of total protistan grazing, respectively. We found that primarily bacterivorous Peritrichia (genera Vorticella, Epistylis) and Scuticociliata (Cyclidium spp.) contributed only moderately (mean 26%) to total ciliate bacterivory. Unexpectedly, but highly abundant omnivorous Halteria/Pelagohalteria (Stichotrichia) and, to a lesser extent, also omnivorous Rimostrombidium spp. (Oligotrichia) contributed significantly more (mean 71%) to total ciliate bacterivory than typical bacterivorous taxa. This suggests that unselective grazers, which feed on a broader size spectrum from bacteria to small algae, may have a considerable competitive advantage in hypertrophic environments rich in small particles. Moreover, a meta‐analysis of available literature data supports our hypothesis that the role of ciliate bacterivory increases significantly, relative to HNF bacterivory, along a trophic gradient toward hypertrophic habitats.
A comparison of automated and manual co-registration for magnetoencephalography

Magnetoencephalography (MEG) is a neuroimaging technique that accurately captures the rapid (sub-millisecond) activity of neuronal populations. Interpretation of functional data from MEG relies upon registration to the participant’s anatomical MRI. The key remaining step is to transform the participant’s MRI into the MEG head coordinate space. Although both automated and manual approaches to co-registration are available, the relative accuracy of two approaches has not been systematically evaluated. The goal of the present study was to compare the accuracy of manual and automated co-registration. Resting MEG and T1-weighted MRI data were collected from 90 participants. Automated and manual coregistration were performed on the same subjects, and the inter-rater reliability of the two methods compared using the intra-class correlation. Mean coregistration error for both methods was within acceptable limits. Reliability was in the fair range. These results suggest that the output of the automated coregistation procedure is comparable to that achieved using manual coregistration.
Prune belly syndrome: current perspectives

Abstract Prune belly syndrome (PBS) is a rare but morbid congenital disease, classically defined by a triad of cardinal features that includes cryptorchidism, urinary tract dilation and laxity of the abdominal wall musculature. Children often require numerous surgical interventions including bilateral orchidopexy as well as individually tailored urinary tract and abdominal wall reconstruction. Along with the classic features, patients with PBS often experience gastrointestinal, orthopedic, and cardiopulmonary comorbidities.
CDNA-AFLP ANALYSIS REVEALS INDUCIBLE GENE EXPRESSION IN TOMATO LEAVES IN RESPONSE TO SIMULATED ACID RAIN

Acid rain as an important environmental problem in China and a stressor may cause gene expression, and tomato is one of model plants and the most important vegetable crops in middle and south China. Tomato seedlings were exposed for 7 days to simulated acid rain (SiAR) of pH 3.0 and control (pH 5.6). The cDNA-amplified fragment length polymorphism (cDNA-AFLP) was carried out to separate differentially expressed gene fragments by using selective base pairs including 8 Mse I primers and 8 EcoR I primers, which allowed the identification and cloning of 45 differential expression transcriptderived fragments (TDFs) corresponding to SiAR, among of which 45 TDFs were successfully cloned and sequenced. 31 of them were found homologies in the NCBI, and 19 displayed homology to genes with known functions, 12 to genes with uncharacterized function. 8 TDFs played significant role in tomato resistance to acid rain-stress. Among of them, TDF5 and TDF8 were stressinducible transcription factor. TDF4 and TDF20 played important role in resistance to SiAR stress. TDF2 was related to isoprenoid biosynthesis, TDF7 to transcription regulation, TDF11 to metabolism, TDF24 to plant development and defense. Possible roles of the 8 TDFs in the response of tomato to SiAR are also discussed. Moreover, Homologous of amino acid encoded in TDF5 and TDF8 were analyzed.
No evidence for local adaptation and an epigenetic underpinning in native and non‐native ruderal plant species in Germany

Abstract Many invasive species have rapidly adapted to different environments in their new ranges. This is surprising, as colonization is usually associated with reduced genetic variation. Heritable phenotypic variation with an epigenetic basis may explain this paradox. Here, we assessed the contribution of DNA methylation to local adaptation in native and naturalized non‐native ruderal plant species in Germany. We reciprocally transplanted offspring from natural populations of seven native and five non‐native plant species between the Konstanz region in the south and the Potsdam region in the north of Germany. Before the transplant, half of the seeds were treated with the demethylation agent zebularine. We recorded survival, flowering probability, and biomass production as fitness estimates. Contrary to our expectations, we found little evidence for local adaptation, both among the native and among the non‐native plant species. Zebularine treatment had mostly negative effects on overall plant performance, regardless of whether plants were local or not, and regardless of whether they were native or non‐native. Synthesis. We conclude that local adaptation, at least at the scale of our study, plays no major role in the success of non‐native and native ruderal plants. Consequently, we found no evidence yet for an epigenetic basis of local adaptation.
Woodpecker nest survival, density, and a pine beetle outbreak

ABSRACT Mountain pine beetle ( Dendroctonus ponderosae ) outbreaks in western North American coniferous forests are increasing in size and severity. An understanding of wildlife population responses to pine beetle outbreaks is needed to inform habitat conservation strategies. We monitored 355 nests of 5 woodpecker species during 2 sampling periods, before ( 2003 – 2006 ) and after ( 2009 – 2014 ) the peak of a pine beetle outbreak in dry mixed conifer forest of Montana, USA. Three of 5 woodpecker species represented the beetle ‐ foraging group: American three ‐ toed ( Picoides dorsalis ) , hairy ( Dryobates villosus ) , and downy ( D. pubescens ) woodpeckers. The other 2 species studied were northern ﬂ icker ( Colaptes auratus ) , a foraging and habitat generalist, and red ‐ naped sapsucker ( Sphyrapicus nuchalis ) , a sap forager and bark ‐ gleaning insectivore. We analyzed daily survival rate of nests in relation to pine beetle outbreak ( 445,000 ha ) severity and timing, along with covariates unrelated to the outbreak ( temp, nest height, and nest tree diameter ) . Our results provided stronger evidence for relationships between woodpecker nest survival and the non ‐ outbreak variables than those associated with outbreaks. Our results indicated limited support for nest survival relationships with beetle severity ( annual and cumulative pine tree mortality at 0.81 ‐ ha and 314 ‐ ha scales ) . Nevertheless, we observed a signi ﬁ cant increase in densities of hatched nests for beetle ‐ foraging woodpeckers following the outbreak. Our results suggest that woodpeckers, particularly beetle foragers, respond numerically to pine beetle outbreaks through increased nesting densities more so than functionally via nest survival. © 2019 The Authors. Journal of Wildlife Management Published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.
Karyological notes on seven Trifolium L. taxa from Turkey

Bu calismada uc temel kromozom sayisi belirlendi (x:5,7 ve 8). Mevcut bu calismaya gore T. resupinatum L. var. resupinatum, T. stellatum L. var. stellatum ve T. purpureum Lois. var. purpureum 2n: 16; T. arvense var. arvense, T. hausknechtii Boiss. var. hausknechtii ve T. pauciflorum d’Urv. 2n.14; ve T. hirtum 2n:10 kromozom sayisina sahiptir. Calisilan Trifolium turlerinde butun kromozomlar, median noktali (M), median (m) olarak bulundu ve satellit gozlenmedi. T. haussknechtii Boiss. var. haussknechtii ve T. pauciflorum d’Urv. ’nin kromozom sayilari ve morfolojileri ilk kez rapor edilmistir.
Phylotranscriptomics resolves phylogeny of the Heliozelidae (Adeloidea: Lepidoptera) and suggests a Late Cretaceous origin in Australia

Heliozelidae are a cosmopolitan family of small, day‐flying moths, and include some pest species of commercial crops. Overall, the family is poorly known and lacks a well‐resolved phylogeny. Previous molecular and taxonomic work has revealed rich undescribed diversity within the family, particularly in Australia; however, the relationships amongst the major clades or genera were not resolved. We sequenced the transcriptomes of 39 taxa, representing all major genera of Heliozelidae, and seven outgroups representing most other Adeloidea families and the putative sister superfamily, Andesianoidea. The resulting phylogeny, based on the coding sequences of up to 1049 nuclear genes, provides a robust hypothesis for the generic relationships within Heliozelidae. On the basis of this analysis, the genus Plesiozela, previously proposed as sister group to all other Heliozelidae, is excluded from the family and formally transferred to Incurvariidae. By incorporating fossil and secondary time calibrations into our phylogeny, we estimated that Heliozelidae ancestors first appeared at the beginning of the Late Cretaceous, approximately 95 Ma. We propose an ancestral biogeographical range hypothesis of the family, based on a combination of our transcriptome data and a previous multigene study including over 100 species. Our ancestral range modelling results suggest that Heliozelidae are likely to have originated in the Australian region, with subsequent range expansions to the rest of the world.
Classifying Hybrids of Energy Cane for Production of Bioethanol and Cogeneration of Biomass-Based Electricity by Principal Component Analysis-Linked Fuzzy C-Means Clustering Algorithm

The biggest challenge facing in sugar-energy plants is to move towards the biorefinery concept, without threatening the environment and health. Energy cane is the state-of-the-art of smart energy crops to provide suitable whole-raw material to produce upgraded biofuels, dehydrated alcohol for transportation, refined sugar, yeast-fermented alcoholic beverages, soft drinks, silage and high-quality fodder, as well as to cogenerate heat and bioelectricity from burnt lignocellulose. We, accordingly, present fuzzy c-means (FCM) clustering algorithm interconnected with principal component analysis (PCA) as powerful exploratory data analysis tool to wisely classify hybrids of energy cane for production of first-generation ethanol and cogeneration of heat and bioelectricity. From the orthogonally-rotated factorial map, fuzzy cluster I aggregated the hybrids VX12-0277, VX12-1191, VX12-1356 and VX12-1658 composed of higher contents of soluble solids and sucrose, and larger productive yields of fermentable sugars. These parameters correlated with the X-axis component referring to technological quality of cane juice. Fuzzy cluster III aggregated the hybrids VX12-0180 and VX12-1022 consisted of higher fiber content. This parameter correlated with the Y-axis component referring to physicochemical quality of lignocellulose. From the PCA-FCM methodology, the conclusion is, therefore, hybrids from fuzzy cluster I prove to be type I energy cane (higher sucrose to fiber ratio) and could serve as energy supply pathways to produce bioethanol, while the hybrids from fuzzy cluster III are type II energy cane (lower sucrose to fiber ratio), denoting potential as higher fiber yield biomass sources to feed cogeneration of heat and bioelectricity in high temperature and pressure furnace-boiler system.
Extracellular adenosine enhances the ability of PMNs to kill Streptococcus pneumoniae by inhibiting IL-10 production

PMNs are crucial for initial control of Streptococcus pneumoniae (pneumococcus) lung infection; however, as the infection progresses their persistence in the lungs is detrimental. We found that the progressive inability of PMNs to control infection correlated with phenotypic differences characterized by a decrease in CD73 expression, an enzyme required for production of extracellular adenosine (EAD). EAD production by CD73 was crucial for PMN function as PMNs from CD73-/- mice failed to kill pneumococci and supplementation with EAD reversed this defect. Further, adoptive transfer of PMNs from wild type mice prior to lung challenge was sufficient to boost the resistance of CD73-/- mice to infection. Importantly, CD73 activity was important for the antimicrobial function of PMNs from human donors. We found that CD73-mediated resistance is due to its inhibitory effects on IL-10. PMNs from CD73-/-, but not wild type mice, up-regulated IL-10 production upon pneumococcal infection in the lungs and in vitro. IL-10 inhibited PMN function, as addition of recombinant IL-10 impaired the ability of PMNs from wild type mice to kill pneumococci ex vivo, and treatment with anti-IL-10 boosted the bactericidal activity of CD73-/- PMNs. Blocking IL-10 also boosted the resistance of CD73-/- mice to pneumococcal pneumonia. CD73/IL-10 did not affect apoptosis, bacterial uptake and intracellular killing or production of anti-microbial Neutrophil Elastase and Myeloperoxidase. Rather, inhibition of IL-10 production by CD73 was important for production of extracellular ROS by PMNs upon S. pneumoniae infection. This study demonstrates that CD73 regulates PMN anti-microbial phenotype during pneumococcal pneumonia. Summary Sentence Extracellular adenosine produced by CD73 promotes the ability of PMNs to kill Streptococcus pneumoniae by blunting IL-10 production
Temporal discrimination from the interaction between dynamic synapses and intrinsic subthreshold oscillations

The interaction between synaptic and intrinsic dynamics can efficiently shape neuronal input-output relationships in response to temporally structured spike trains. We use a neuron model with subthreshold oscillations receiving inputs through a synapse with short-term depression and facilitation to show that the combination of intrinsic subthreshold and synaptic dynamics leads to channel-specific nontrivial responses and recognition of specific temporal structures. We employ the Generalized Integrate-and-Fire (GIF) model, which can be subjected to analytical characterization. We map the temporal structure of spike input trains to the type of spike response, and show how the emergence of nontrivial input-output preferences is modulated by intrinsic and synaptic parameters in a synergistic manner. We demonstrate that these temporal input discrimination properties are robust to noise and to variations in synaptic strength, suggesting that they likely contribute to neuronal computation in biological circuits. Furthermore, we also illustrate the presence of these input-output relationships in conductance-based models. Author summary Neuronal subthreshold oscillations underlie key aspects of information processing in single neuron and network dynamics. Dynamic synapses provide a channel-specific temporal modulation of input information. We combine a neuron model that displays subthreshold oscillations and a dynamic synapse to analytically assess their interplay in processing trains of spike-mediated synaptic currents. Our results show that the co-action of intrinsic and synaptic dynamics builds nontrivial input-output relationships, which are resistant to noise and to changes in synaptic strength. The discrimination of a precise temporal structure of the input signal is shaped as a function of the joint interaction of intrinsic oscillations and synaptic dynamics. This interaction can result in channel-specific recognition of precise temporal patterns, hence greatly expanding the flexibility and complexity in information processing achievable by individual neurons with respect to temporal discrimination mechanisms based on intrinsic neuronal dynamics alone.
Systematic Revision and Redefinition of the Genus Scirrotherium Edmund & Theodor, 1997 (Cingulata, Pampatheriidae): Implications for the Origin of Pampatheriids and the Evolution of the South American Lineage Including Holmesina

The intrageneric relationships of the pampatheriid genus Scirrotherium and its affinities with supposedly related genera, i.e. Kraglievichia and Holmesina, are revised through parsimony phylogenetic analyses and new comparative morphological descriptions. For this work was analyzed unpublished material of pampatheriids (numerous osteoderms, one partial skull and a few postcranial bones) from Neogene formations of Colombia. The results show that Scirrotherium is paraphyletic if we include all its referred species, i.e. Scirrotherium hondaensis, S. carinatum and S. antelucanus. The species S. carinatum is closer to Kraglievichia paranensis than to S. hondaensis or S. antelucanus, then it is proposed the new name K. carinatum comb. nov. The relationships between S. hondaensis and S. antelucanus could not be resolved, so these species should be designated in aphyly. In spite of failing to recover S. hondaensis and S. antelucanus as one single clade, here is preferred to maintain the generic name Scirrotherium in both species from diagnostic evidence. New emended diagnoses for Scirrotherium, S. hondaensis and Kraglievichia are provided. The genus Holmesina was found monophyletic and located as the sister clade of Scirrotherium + Kraglievichia. The evolutionary and biogeographical implications of the new phylogeny and taxonomical re-arrangements are discussed. It is claimed a possible geographical origin of the family Pampatheriidae and Scirrotherium in low latitudes of South America as early as Early Miocene (Burdigalian) times. The South American ancestor or sister taxon of Holmesina is predicted as morphologically more similar to Scirrotherium than to Kraglievichia.
Density-dependent effects of mortality on the optimal body size of a habitat shift: Why smaller is better despite increased mortality risk?

Many animal species across different taxa change their habitat during their development. An ontogenetic habitat shift enables the development of early vulnerable-to-predation stages in a safe ‘nursery’ habitat with reduced predation mortality, while less vulnerable stages can exploit a more risky, rich feeding habitat. Therefore, the timing of the habitat shift is crucial for individual fitness. We investigate the effect that size-selectivity in mortality in the rich feeding habitat has on the optimal timing of the habitat shift using a population model and the adaptive dynamics approach. We show that the size-selective nature of mortality in this habitat affects density-dependent body growth rate in the nursery habitat and thus the optimal timing of the habitat shift. This is caused by the effect exerted by size-dependent mortality on the size distribution of the population that results in strong competition in the nursery habitat. We furthermore find that, as a consequence of this effect, increased size-selectivity in mortality in the rich feeding habitat causes the optimal body size to shift habitat to decrease. Our results reveal the interdependence between population structure and life history traits, and highlight the need for integrating ecological interactions in the study of the evolution of life histories.
Evaluation of oxidative stress, blood parameters, and neurocognitive status in cement factory workers

Abstract The current investigation was aimed to evaluate the oxidative stress (OS), blood factors, and neurocognitive state among cement factory workers who are exposed to dust during their work. Totally 41 cement exposed workers and 41 subjects as a control group were selected, and their OS, biochemical parameters, and a neurocognitive questionnaire were assessed. The results indicated that the levels of triglyceride, alanine aminotransferase, and alkaline phosphatase were higher among the exposed workers. The rate of lipid peroxidation and total antioxidant capacity were not significantly differenced among the workers while compared to the control group. Highlights Cement industry may lead to several health impairments among cement workers. A significant association between past dust exposure in the workplace and neurocognitive impairment. Occupational exposures to these dusts may result later in life in adverse mental health outcomes.
Regulation of the immune checkpoint PD-L1 by microRNAs

MicroRNAs are evolutionary conserved non-coding RNAs that control more than 60% of human protein-coding genes at the posttranscriptional level. MicroRNAs can either mediate translational repression or mRNA degradation by complementary base-pairing to the 3’-UTR of mRNA. MicroRNAs have critical roles in the regulation of immune responses and inflammation. The expression of PD-L1 protein is found on some normal and cancer cells and contributes to suppression of T cell activity by acting as a brake on the immune response. Previously, it has been shown that posttranscriptional mechanisms regulate PD-L1 levels in cancer, it remains unknown whether such regulatory networks operate also in non-transformed cells. Here, I tested the hypothesis that expression and function of PD-L1 in stromal, vascular and cancer cells is posttranscriptionally regulated by inflammatory-driven microRNAs. I demonstrate that PD-L1 expression in human dermal lymphatic endothelial cells (HDLECs) can be induced with the treatment of pro-inflammatory cytokines IFN-y and TNF-a. The microRNA landscape in HDLECs was activated by IFN-y and TNF-a treatment including some microRNAs that have predicted binding sites on PD-L1. A highly upregulated microRNA was microRNA-155 (miR-155), a multifunctional microRNA that regulates haematopoiesis, normal immune function and mediates the inflammatory response. I determined that miR-155 can bind to the 3’-UTR of PD-L1 on two functional binding sites, and that the kinetics of PD-L1 induction is fine-tuned by inflammation-induced miR-155 in HDLECs and dermal fibroblasts. Interestingly, I found that miR-155 can also silence PD-L1 expression in renal, breast but only in a subset of lung cancer cell lines. These findings reveal that inflammatory activation induce PD-L1 expression on several different cell types presumably to avoid prolonged immune-mediated tissue damage. However, miR-155 can act in a cell type-specific manner to temporally release PD-L1 immunosuppression to regulate the balance between immune tolerance and autoimmunity.