Miracle-dz/UniFAR-FTUs huggingface dataset:
Species coexistence in resource-limited patterned ecosystems is facilitated by the interplay of spatial self-organisation and intraspecific competition

The exploration of mechanisms that enable species coexistence under competition for a sole limiting resource is widespread across ecology. Two examples of such facilitative processes are intraspecific competition and spatial self-organisation. These processes determine the outcome of competitive dynamics in many resource-limited patterned ecosystems, classical examples of which include dryland vegetation patterns, intertidal mussel beds and Sub-alpine ribbon forests. Previous theoretical investigations have explained coexistence within patterned ecosystems by making strong assumptions on the differences between species (e.g. contrasting dispersal behaviours or different functional responses to resource availability). In this paper, I show that the interplay between the detrimental effects of intraspecific competition and the facilitative nature of self-organisation forms a coexistence mechanism that does not rely on species-specific assumptions and captures coexistence across a wide range of the environmental stress gradient. I use a theoretical model that captures the interactions of two generic consumer species with an explicitly modelled resource to show that coexistence relies on a balance between species’ colonisation abilities and their local competitiveness, provided intraspecific competition is sufficiently strong. Crucially, the requirements on species’ self-limitation for coexistence to occur differ on opposite ends of the resource input spectrum. For low resource levels, coexistence is facilitated by strong intraspecific dynamics of the species superior in its colonisation abilities, but for larger volumes of resource input, strong intraspecific competition of the locally superior species enables coexistence. Results presented in this paper also highlight the importance of hysteresis in understanding tipping points, in particular extinction events. Finally, the theoretical framework provides insights into spatial species distributions within single patches, supporting verbal hypotheses on co-existence of herbaceous and woody species in dryland vegetation patterns and suggesting potential empirical tests in the context of other patterned ecosystems.
Sequence-Based Methods for Real Value Predictions of Protein Structure

: Recent years observed a growing interest in computational methods that predict and characterize protein structure due to the increasing sequence-structure gap. This includes a spike in development of sequence-based in-silico meth-ods that address prediction of several newly formulated real-value descriptors of protein structure. These descriptors include B-factor, backbone torsion angles, solvent accessibility, residue depth, contact number, residue-wise contact order, secondary structure content, and folding rates. Although they address different structural aspects, such as exposure to the solvent, spatial position and packing of the residues, their flexibility, amount of secondary structures in the protein, and folding time, the methods that are built to address them share similarities that could be exploited to improve future designs. To date, no comprehensive overview that summarizes and contrasts solutions developed for these tasks was published. To address this we compare different designs of real-value predictors based on information concerning input data encoding and prediction algorithms used. We also investigate evaluation standards, which include benchmark datasets, test criteria, and test procedures used in these predictive tasks. Finally, we summarize application areas and problems that use the above-mentioned predictions. We believe that the breath and number of these applications justify further development of more accurate and integrated real-value prediction methods.
Effectiveness of the Natura 2000 Network for the conservation of cave‐dwelling bats in a Mediterranean region

The Natura 2000 Network represents the greatest step forward yet in conservation in Europe, although its effectiveness is sometimes questioned, especially in Mediterranean regions. Bats are protected by the Habitat Directive and the presence of certain species is a prerequisite before Special Areas Conservation (SAC sites) can be included as such in the Natura 2000 Network. However, the effectiveness of SAC sites as regards the protection they offer to bats, especially cave‐dwelling species, remains to be evaluated. We assess the effectiveness of the SAC system for protecting the roosts of six species of cave‐dwelling bats and for protecting suitable and optimal habitats, using ecological niche models. Gap analyses indicate that c. 60% of roosts are protected by SAC sites, with values ranging from 45.8% for Miniopterus schreibersii to 72.2% for Rhinolophus hipposideros. The protection offered to suitable and optimal habitats was found to be much lower in general, with values of below 40% in all cases. Our results emphasize the potential value of non‐natural caves (e.g. mines and buildings) for the conservation of bat populations, and the importance of assessing the efficiency of protected areas by considering distribution models that incorporate different types of information (e.g. roosts and use habitat) concerning species occurrence.
Influence of the choice of physical and chemistry variables on interpreting patterns of sediment contaminants and their relationships with estuarine macrobenthic communities.

A primary objective of contaminated sediment risk assessments is to identify if contaminant enrichment is eliciting an ecological response. Using complementary environmental and biotic datasets, we examined five scenarios with respect to: dataset complexity; metal extraction; normalisation of organics; the inclusion/exclusion of acid-volatile sulfide data, and iron and manganese concentrations. Spatial distributions of abiotic variables were examined by principal components analysis, with canonical correspondence analysis used to examine the total and partitioning of biological variation. Metals were the dominant contaminant and explained the largest proportion of variation in the macrobenthic data. Extraction procedure and carbon normalisation of organics had little influence on the overall analysis. Porewater metal data was essential for interpretation, with excess of acid-volatile sulfide over simultaneously extractable metals being a poor surrogate. In the canonical correspondence analyses, the inclusion of Fe/Mn accentuated the covariation between the ecological and contaminant variables. Multimodel comparisons aided interpretation by emphasising specific relationships among environmental variables and their interactions with the biotic data. Furthermore, for future examinations of the described system, the findings can be used to reduce the collection of redundant environmental variables or variables that are poorly correlated with changes in macrobenthic assemblages.
Adaptability to climate change in forestry species: drought effects on growth and wood anatomy of ponderosa pines growing at different competition levels

More stressful conditions are expected due to climatic change in several regions, including Patagonia, South-America. In this region, there are no studies about the impact of severe drought events on growth and wood characteristics of the most planted forestry species, Pinus ponderosa (Doug. ex-Laws). The objective of this study was to quantify the effect of a severe drought event on annual stem growth and functional wood anatomy of pines growing at different plantation densities aiming to understand how management practices can help to increase their adaptability to climate change. Growth magnitude and period, specific hydraulic conductivity, and anatomical traits (early- and latewood proportion, lumen diameter, cell-wall thickness, tracheid length and bordered pit dimensions) were measured in the ring 2008-2009, which was formed during drought conditions. This drought event decreased annual stem growth by 30-38% and 58-65% respect to previous mean growth, in open vs. closed stand trees, respectively, indicating a higher sensitivity of the latter, which is opposite to reports from the same species growing in managed native forests in USA. Some wood anatomical variables did differ in more water stressed trees (lower cell wall thickness of early wood cells and higher proportion of small-lumen cells in latewood), which in turn did not affect wood function (hydraulic conductivity and resistance to implosion). Other anatomical variables (tracheid length, pit dimensions, early- and latewood proportion, lumen diameter of early wood cells) did not differ between tree sizes and plantation density. The results suggest that severe drought affects differentially the amount but not the function and quality of formed wood in ponderosa pine growing at different competition levels.
Disrupted structural connectivity in ArcAβ mouse model of Aβ amyloidosis

Although amyloid beta (Aβ) deposition is one of the major causes of white matter (WM) alterations in Alzheimer’s disease (AD), little is known about the underlying basis of WM damage and its association with global structural connectivity and network topology. We aimed to dissect the contributions of WM microstructure to structural connectivity and network properties in the ArcAβ mice model of Aβ amyloidosis. We acquired diffusion-weighted images (DWI) of wild type (WT) and ArcAβ transgenic (TG) mice using a 9.4 T MRI scanner. Fixel-based analysis (FBA) was performed to measure fiber tract-specific properties. We also performed three complementary experiments; to identify the global differences in structural connectivity, to compute network properties and to measure cellular basis of white matter alterations. Transgenic mice displayed disrupted structural connectivity centered to the entorhinal cortex (EC) and a lower fiber density and fiber bundle cross-section. In addition, there was a reduced network efficiency and degree centrality in weighted structural connectivity in the transgenic mice. To further examine the underlying neuronal basis of connectivity and network deficits, we performed histology experiments. We found no alteration in myelination and an increased level of neurofilament light (NFL) in the brain regions with disrupted connectivity in the TG mice. Furthermore, TG mice had a reduced number of perineuronal nets (PNN) in the EC. The observed FDC reductions may indicate a decrease in axonal diameter or axon count which would explain the basis of connectivity deficits and reduced network efficiency in TG mice. The increase in NFL suggests a breakdown of axonal integrity, which would reduce WM fiber health. Considering the pivotal role of the EC in AD, Aβ deposition may primarily increase NFL release, damaging PNN in the entorhinal pathway, resulting in disrupted structural connectivity.
LIPID PROFILE AND FATTY ACID COMPOSITIONS IN BODY WALL OF APOSTICHOPUS JAPONICUS (SELENKA)

The lipid profile and fatty acid compositions in the body wall of Apostichopus japonicus (Selenka) have been analyzed. The level of total lipids in the body wall that was 3.93 ± 0.27% of dry weight (w/w) and the amount of phospholipids was 43.32 ± 2.10% of total lipids (w/w), exceeded that of neutral lipids and glycolipids. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were the major phospholipids, and the contents were 58.93 ± 3.42% and 24.77 ± 1.34% of total phospholipids (w/w), respectively. Polyunsaturated fatty acids (PUFAs) were abundant in total lipids, PC and PE, and the main PUFAs were arachidonic acid (AA), eicosapentaenoic acid (EPA) and docosahexaenoic acid. PE contained much higher C18:0 dimethyl acetals and AA, but lower C18:1 and EPA compared with PC. The results indicated that there were some differences in the fatty acid compositions between PE and PC. PRACTICAL APPLICATIONS The cultivation scale of Apostichopus japonicus (Selenka) is on the increase in Northern China, and the consumption of A. japonicus becomes a fashion due to its nutritional and supposed medicinal properties. This study analyzes the lipid profile and phospholipid compositions of the body wall of A. japonicus, and compares the fatty acid compositions between phosphatidylethanolamine and phosphatidylcholine. The results could provide some useful information in the nutritional value of lipids for the exploitation of A. japonicus as a valuable functional and health food.
Quantifying successional changes in response to forest disturbances

ABSTRACT Question: Can dissimilarity measures of individual plots be used to forecast the driving factors among various anthropogenic disturbances influencing understorey successional changes? Location: Yambulla State Forest, south-eastern Australia (37°14′ S, 149°38′ E). Methods: Assessments of understorey vegetation communities were taken prior to anthropogenic disturbances and at three subsequent time periods representing a period of 15 years post-disturbance. Dissimilarities were calculated from the original assessment and modelled in a Bayesian framework to examine the influence of logging, number of prescribed burns and time. Results: All sites underwent significant changes over time independently of the imposed management regimes. Logging resulted in an immediate change in vegetation assemblage which decreased in the subsequent assessments. The number of prescribed fires brought greater change in the shrub vegetation assemblages, but less change in the ground species vegetation assemblages. Conclusions: The anthropogenic disturbances did have some role in the changes of vegetation assemblages but these were minimal. The ongoing changes appear to be a natural response to the last wildfire, which passed through the study area in 1973 (13 years prior to the study). Forest management practices should consider the influence of wildfire succession when planning for the conservation of biodiversity.
Development and characterization of 10 novel microsatellite markers from Chital deer (Cervus axis) and their cross–amplification in other related species

Ten polymorphic microsatellite loci were isolated and characterized from Chital deer (Cervus axis). These loci show high levels of allelic diversity with four to eight alleles per locus in the 22 individuals of the free-ranging population of Chital deer in Nehru Zoological Park, Hyderabad. In addition, we found that all the loci show cross-amplification in closely related as well as distantly related deer species. The amplification of these markers in different genera further indicates that these can be applied to a wide range of endangered deer species for their population genetics studies and conservation management.
Inflammatory markers in Covid-19 Patients: a systematic review and meta-analysis.

Introduction Diagnosis of COVID-19 is based on clinical manifestation, history of exposure, positive findings on chest CT and laboratory tests. It has been shown that inflammation plays a role in pathogenesis of COVID-19. Method We used the necessary transformations to convert the median and IQR to mean and SD Random-effect model using Der Simonian, and Laird methods was used if heterogeneity between studies was significant, the homogeneity among studies was assessed with I2 Statistic, values above 50%, and for the chi-square test, P-values <0.1 was supposed statistically significant Results Twelve studies were included in the analysis that all of which were conducted in China in the year 2020. The result of combining 12 articles with 772 participants showed that the pooled estimate of the mean of lymphocyte with 95% CI was (Mean: 1.01; 95% CI (0.76-1.26); p-value<0.001). About WBC the pooled result of 9 studies with 402 participants was (Mean: 5.11; 95% CI (3.90-6.32); p-value<0.001) Also the pooled mean estimate of 9 studies with 513 patients for the ratio of Neutrophil/lymphocyte was (Mean: 3.62; 95% CI (1.48-5.77); p-value=0.001). The pooled mean from the combination of 7 studies with 521 patients on CRP was (Mean: 28.75; 95% CI (8.04-49.46). Conclusion Inflammatory Markers increase in patients with Covid-19, which can be a good indicator to find patients.
Molecular analysis of the γδ T‐cell receptor repertoire in normal human skin and in Oriental Cutaneous Leishmaniasis

Abstract The extent of diversity of the γδ T‐cell receptor (TCR) in normal human skin and Oriental Cutaneous Leishmaniasis (OCL) was examined by molecular analysis of the variable (V) δ gene segment, junctional (J) δ gene segment and junctional regions. To examine the expression of TCR δ genes, segments of γδ T lymphocytes, DNA isolated from normal human skin and from OCL were subjected to enzymatic gene amplification by the polymerase chain reaction (PCR) method using TCR Vδ‐and Jδ‐specific oligonucleotides as primers. PCR amplification using these primers indicated that the Vδ2 gene segment was predominantly used by γδ T lymphocytes in both normal human skin and OCL. To determine the extent of junctional diversity in the δ gene of γδ T cells in normal human skin and OCL, we sequenced the nucleic acid sequences corresponding to the V δ2/Jδ1 junctional regions. Sequence analysis of junctional regions demonstrated broad junctional diversity in normal skin but only limited diversity in OCL. Our findings support the hypothesis that skin γδ T lymphocytes may derive from a fetal subset of γδ T lymphocytes that leaves the thymus early and colonizes (he periphery. The limited junctional diversity demonstratd in OCL lesions indicates that γδ T cells can undergo oligoclonal expansion following recognition of a specific ligand and supports the idea that junctional regions are important in the recognition of antigenic determinant.
Analysis of Anti-Prolamin Monoclonal Antibody Reactivity Using Prolamin Fractions Purified by Preparative Electrophoresis

Coeliac disease (CD) is a gastrointestinal afliction triggered by the ingestion of prolamins from wheat, barley, rye and possibly oats. The only treatment for CD is a strict diet, free of the toxic components. Immunochemical methods are usually applied to certify foods aimed at coeliac patients. The characterization of a panel of four anti-prolamin monoclonal antibodies (MAbs) to be used to certify gluten-free products is described here. To this aim, purified gliadin, secalin and hordein fractions were obtained by preparative electrophoresis at acid pH. This procedure provides purified fractions not exposed to denaturing conditions. The specificity of the MAbs was tested by ELISA against purified fractions and ethanol extracts of wheat, barley, rye, oats, rice, maize, buckwheat, sorghum and soy. The four MAbs recognized only coeliac-toxic cereals. Each MAb reacted strongly with gliadins and showed differential reactivity against the different prolamin purified fractions. Some MAbs showed a broad pattern of recognition whereas others presented a more restricted one. The reactivity observed corresponded to structural homologies among gliadin, secalin and hordein fractions. It is remarkable that some fractions obtained by electrophoresis in the presence of sodium dodecylsulphate were not recognized by some MAbs, whereas the same components obtained by preparative A-PAGE showed high reactivity. This reinforces the suitability of the purification method employed in this study to isolate prolamin fractions. Using these purified prolamins, characterization of anti-prolamin MAb reactivity was achieved.
Topologically correct synthetic reconstruction of pathogen social behavior found in deep tissue sites

Within deep tissue sites, extracellular bacterial pathogens often replicate in clusters that are surrounded by immune cells. Disease is modulated by interbacterial interactions as well as bacterial-host cell interactions resulting in microbial growth, phagocytic attack and secretion of host antimicrobial factors. To overcome the limited ability to manipulate these infection sites, we established a system for Yersinia pseudotuberculosis (Yptb) growth in microfluidics-driven microdroplets that regenerates microbial social behavior in tissues. Chemical generation of nitric oxide (NO) in the absence of immune cells was sufficient to reconstruct microbial social behavior, as witnessed by expression of the NO-inactivating protein Hmp on the extreme periphery of microcolonies, mimicking spatial regulation in tissues. Similarly, activated macrophages that expressed inducible NO synthase (iNOS) drove peripheral expression of Hmp, allowing regeneration of social behavior observed in tissues. These results argue that topologically correct microbial tissue growth and associated social behavior can be reconstructed in culture.
THE EFFECT OF PHOTON IRRADIANCE ON THE BEHAVIORAL ECOLOGY AND POTENTIAL NICHE SEPARATION OF FRESHWATER PHYTOPLANKTONIC FLAGELLATES 1

Photoresponsive behavior in phytoplanktonic flagellates potentially controls depth regulation, vertical migration, and the accumulation of cells in preferred conditions and hence has major implications for photosynthesis, growth, and species competition. This study used microscale laboratory chambers with cell track analysis and mesoscale lake studies to investigate the responses of five phylogenetically contrasting freshwater flagellates to gradients of light. Laboratory results demonstrated that these species differed in their light preferences despite being grown at the same photon irradiance. Preferred photon irradiances were 20–120, 20, 65–120, 4–20, and>200 μmol photons·m−2·s−1, respectively, for Ceratium furcoides (Levander) Langhans, Chlamydomonas moewusii Gerloff, Dinobryon sertularia Ehrenberg, Euglena gracilis Klebs, and Plagioselmis nannoplanctica (Skuja) Novarino. Analysis of the response of individual cells showed that in all species, photoresponsive preference was the result of positive and negative phototaxis combined with step‐up and step‐down photophobic reactions. There was no evidence for photokinesis or cell memory. Only in C. furcoides did the preferred photon irradiance alter with growth conditions. In C. furcoides, D. sertularia, and P. nannoplanctica, irradiance preference matched the optimal irradiance for growth, whereas in the two remaining species a lower than optimal irradiance was preferred, suggesting that light may be used as an indicator of other ecological conditions. Mesoscale experiments in a lake demonstrated that the laboratory microscale measurements provide information relevant to understanding ecological distributions. Behavioral responses to light contribute to the delineation of vertical niche separation and provide a method for predicting the spatial and temporal distribution of flagellates.
14-3-3ζ mediates an alternative, non-thermogenic mechanism to reduce heat loss and improve cold tolerance

Following prolonged cold exposure, adaptive thermogenic pathways are activated to maintain homeothermy, and elevations in body temperature are generally associated with UCP1-dependent and -independent increases in energy expenditure. One of the earliest, identified functions of the molecular scaffold, 14-3-3ζ, was its role in the synthesis of norepinephrine, a key endogenous factor that stimulates thermogenesis. This suggests that 14-3-3ζ may have critical roles in cold-induced thermogenesis. Herein, we report that transgenic over-expression of TAP-14-3-3ζ in mice significantly improved tolerance to prolonged cold. When compared to wildtype controls, TAP mice displayed significantly elevated body temperatures and paradoxical decreases in energy expenditure. No changes in β-adrenergic sensitivity or oxidative metabolism were observed; instead, 14-3-3ζ over-expression significantly decreased thermal conductance via increased peripheral vasoconstriction. These findings suggest 14-3-3ζ mediates alternative, non-thermogenic mechanisms to mitigate heat loss for homeothermy. Our results point to an unexpected role of 14-3-3ζ in the regulation of body temperature. Graphical abstract