Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features

Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA‐based methods to identify mycorrhizal fungi from eleven E. firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine‐scale environmental factors and macro‐evolutionary patterns of change in mycorrhizal specificity. Thus, E. firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.
A comparison of carers needs for service users cared for both in and out of area

Purpose – This paper describes an ongoing process of engagement with carers of people with intellectual disabilities currently being monitored by an out of area service for both carers of people placed both in area and out of area within a local Mental Health Learning Disabilities team in South London.Design/methodology/approach – Using a series of consultation events, carers were asked to participate in a free dialogue which focussed on everyday issues for carers. This included financial implications of caring, knowledge of care pathways/systems in care, carer's needs and expectations and the support they currently receive.Findings – This paper highlighted a number of issues and concerns that carers face in their daily lives when supporting one or more people. These include lack of recognition, financial difficulties, lack of training and support.Originality/value – This project offered a valuable insight into current carer perceptions and will help develop further discussion and promote greater engageme.
A metabolic approach to study algal–bacterial interactions in changing environments

Increasing evidence exists that bacterial communities interact with and shape the biology of algae and that their evolutionary histories are connected. Despite these findings, physiological studies were and still are generally carried out with axenic or at least antibiotic‐treated cultures. Here, we argue that considering interactions between algae and associated bacteria is key to understanding their biology and evolution. To deal with the complexity of the resulting ‘holobiont’ system, a metabolism‐centred approach that uses combined metabolic models for algae and associated bacteria is proposed. We believe that these models will be valuable tools both to study algal–bacterial interactions and to elucidate processes important for the acclimation of the holobiont to environmental changes.
Recent speciation and secondary contact in endemic ants

Gene flow is the main force opposing divergent selection, and its effects are greater in populations in close proximity. Thus, complete reproductive isolation between parapatric populations is not expected, particularly in the absence of ecological adaptation and sharp environmental differences. Here, we explore the biogeographical patterns of an endemic ant species, Cataglyphis floricola, for which two colour morphs (black and bicolour) coexist in parapatry throughout continuous sandy habitat in southern Spain. Discriminant analyses of six biometric measurements of male genitalia and 27 cuticular hydrocarbons reveal high differentiation between morphs. Furthermore, the low number of shared alleles derived from nuclear markers (microsatellites) between the morphs at their contact zone suggests the absence of recent gene flow. Mitochondrial DNA (COI) phylogenetic analysis and median‐joining networks show that the black morph is basal to the bicolour morph, with unique haplotypes recovered for each morph. Mismatch distribution analysis and Bayesian skyline plots suggest that they are undergoing different demographic changes, with the bicolour and black morphs at demographic equilibrium and expansion, respectively. Thus, our results show complete reproductive isolation between the two colour morphs as evidenced from genetic, chemical and morphological data. We suggest that these divergence events could be explained by historical vicariance during the Pleistocene, in which reproductive traits experienced strong divergent selection between the morphs initiating or culminating speciation.
Theoretical models of the influence of genomic architecture on the dynamics of speciation

A long‐standing problem in evolutionary biology has been determining whether and how gradual, incremental changes at the gene level can account for rapid speciation and bursts of adaptive radiation. Using genome‐scale computer simulations, we extend previous theory showing how gradual adaptive change can generate nonlinear population transitions, resulting in the rapid formation of new, reproductively isolated species. We show that these transitions occur via a mechanism rooted in a basic property of biological heredity: the organization of genes in genomes. Genomic organization of genes facilitates two processes: (i) the build‐up of statistical associations among large numbers of genes and (ii) the action of divergent selection on persistent combinations of alleles. When a population has accumulated a critical amount of standing, divergently selected variation, the combination of these two processes allows many mutations of small effect to act synergistically and precipitously split one population into two discontinuous, reproductively isolated groups. Periods of allopatry, chromosomal linkage among loci, and large‐effect alleles can facilitate this process under some conditions, but are not required for it. Our results complement and extend existing theory on alternative stable states during population divergence, distinct phases of speciation and the rapid emergence of multilocus barriers to gene flow. The results are thus a step towards aligning population genomic theory with modern empirical studies.
Expression of hypoxia-inducible factor 1α and 2α in choroidal neovascular membranes associated with age-related macular degeneration

Hypoxia-inducible factors (HIF-1α and HIF-2α) play pivotal roles in angiogenesis. However, their involvement in choroidal neovascular membranes (CNVMs) is still unknown. This study investigates the distribution of HIF-1α and HIF-2α proteins in six CNVMs associated with age-related macular degeneration (AMD). By means of immunohistochemical analysis, HIF-1α and HIF-2α were detected in 5 and 6 eyes, respectively. Endothelial cells and macrophages were immunostained by both HIF-1α and HIF-2α antibodies, whereas no staining was observed in retinal pigment epithelial (RPE) cells. Our study raises the possibility that HIF-1α and HIF-2α are involved in CNV formation. HIF-1α and HIF-2α are transcription factors that transactivate the expression of pro-angiogenic genes in response to hypoxic conditions, and play important roles in vasculogenesis …
Optimisation of low-density parity-check codes with deterministic unequal error protection properties

In this study, the authors propose a systematic method of designing low-density parity-check codes with deterministic unequal-error-protection characteristics over an additive white Gaussian noise channel. The proposed method optimises the code rate or the noise threshold while at the same time guaranteeing that different classes of code bits can achieve their respective target error probabilities within a specified number of decoding iterations. The authors also derive the necessary and sufficient stability condition for the optimisation method.
Hannaella pagnoccae sp. nov., a tremellaceous yeast species isolated from plants and soil.

Several independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118(T) ( = CBS 11142(T) = ATCC MYA-4530(T)).
Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

Phenotypic plasticity is predicted to facilitate individual survival and/or evolve in response to novel environments. Plasticity that facilitates survival should both permit colonization and act as a buffer against further evolution, with contemporary and derived forms predicted to be similarly plastic for a suite of traits. On the other hand, given the importance of plasticity in maintaining internal homeostasis, derived populations that encounter greater environmental heterogeneity should evolve greater plasticity. We tested the evolutionary significance of phenotypic plasticity in coastal British Columbian postglacial populations of threespine stickleback (Gasterosteus aculeatus) that evolved under greater seasonal extremes in temperature after invading freshwater lakes from the sea. Two ancestral (contemporary marine) and two derived (contemporary freshwater) populations of stickleback were raised near their thermal tolerance extremes, 7 and 22 °C. Gene expression plasticity was estimated for more than 14 000 genes. Over five thousand genes were similarly plastic in marine and freshwater stickleback, but freshwater populations exhibited significantly more genes with plastic expression than marine populations. Furthermore, several of the loci shown to exhibit gene expression plasticity have been previously implicated in the adaptive evolution of freshwater populations, including a gene involved in mitochondrial regulation (PPARAa). Collectively, these data provide molecular evidence that highlights the importance of plasticity in colonization and adaptation to new environments.
Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above‐ and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap‐plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.
The Diagnostic Performance of Computer Programs for the Interpretation of Electrocardiograms

Background. Computer programs for the interpretation of electrocardiograms (ECGs) are now widely used. However, a systematic assessment of various computer programs for the interpretation of ECGs has not been performed. Methods. We undertook a large international study to compare the performance of nine electrocardiographic computer programs with that of eight cardiologists in interpreting ECGs in 1220 clinically validated cases of various cardiac disorders. ECGs from the following groups were included in the sample: control patients (n = 382); patients with left ventricular hypertrophy (n = 183), right ventricular hypertrophy (n = 55), or biventricular hypertrophy (n = 53); patients with anterior myocardial infarction (n = 170), inferior myocardial infarction (n = 273), or combined myocardial infarction (n = 73); and patients with combined infarction and hypertrophy (n = 31). The interpretations of the computer programs and the cardiologists were compared with the clinical diagnoses made independently of the ECGs, and the computer interpretations were compared with those of the cardiologists. Results. The percentage of ECGs correctly classified by the computer programs (median, 91.3 percent) was lower than that for the cardiologists (median, 96.0 percent; P < 0.01). The median sensitivity of the computer programs was also significantly lower than that of the cardiologists in diagnosing left ventricular hypertrophy (56.6 percent vs. 63.9 percent, P < 0.02), right ventricular hypertrophy (31.8 percent vs. 46.6 percent, P < 0.01), anterior myocardial infarction (77.1 percent vs. 84.9 percent, P < 0.001), and inferior myocardial infarction (58.8 percent vs. 71.7 percent, P < 0.0001). The median total accuracy level (the percentage of correct classifications) was 6.6 percent lower for the computer programs (69.7 percent) than for the cardiologists (76.3 percent; P < 0.001). However, the performance of the best programs nearly matched that of the most accurate cardiologists. Conclusions. Our study shows that some but not all computer programs for the interpretation of ECGs perform almost as well as cardiologists in identifying seven major cardiac disorders.
Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird‐pollinated, cloud forest shrub in northern Mesoamerica

Recent empirical work on cloud forest‐adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6–3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding–contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.
Stress modulation of cellular metabolic sensors: interaction of stress from temperature and rainfall on the intertidal limpet Cellana toreuma

In the natural environment, organisms are exposed to large variations in physical conditions. Quantifying such physiological responses is, however, often performed in laboratory acclimation studies, in which usually only a single factor is varied. In contrast, field acclimatization may expose organisms to concurrent changes in several environmental variables. The interactions of these factors may have strong effects on organismal function. In particular, rare events that occur stochastically and have relatively short duration may have strong effects. The present experiments studied levels of expression of several genes associated with cellular stress and metabolic regulation in a field population of limpet Cellana toreuma that encountered a wide range of temperatures plus periodic rain events. Physiological responses to these variable conditions were quantified by measuring levels of mRNA of genes encoding heat‐shock proteins (Hsps) and metabolic sensors (AMPKs and Sirtuin 1). Our results reveal high ratios of individuals in upregulation group of stress‐related gene expression at high temperature and rainy days, indicating the occurrence of stress from both prevailing high summer temperatures and occasional rainfall during periods of emersion. At high temperature, stress due to exposure to rainfall may be more challenging than heat stress alone. The highly variable physiological performances of limpets in their natural habitats indicate the possible differences in capability for physiological regulation among individuals. Our results emphasize the importance of studies of field acclimatization in unravelling the effects of environmental change on organisms, notably in the context of multiple changes in abiotic factors that are accompanying global change.
Hibernation alters the diversity and composition of mucosa‐associated bacteria while enhancing antimicrobial defence in the gut of 13‐lined ground squirrels

The gut microbiota plays important roles in animal nutrition and health. This relationship is particularly dynamic in hibernating mammals where fasting drives the gut community to rely on host‐derived nutrients instead of exogenous substrates. We used 16S rRNA pyrosequencing and caecal tissue protein analysis to investigate the effects of hibernation on the mucosa‐associated bacterial microbiota and host responses in 13‐lined ground squirrels. The mucosal microbiota was less diverse in winter hibernators than in actively feeding spring and summer squirrels. UniFrac analysis revealed distinct summer and late winter microbiota clusters, while spring and early winter clusters overlapped slightly, consistent with their transitional structures. Communities in all seasons were dominated by Firmicutes and Bacteroidetes, with lesser contributions from Proteobacteria, Verrucomicrobia, Tenericutes and Actinobacteria. Hibernators had lower relative abundances of Firmicutes, which include genera that prefer plant polysaccharides, and higher abundances of Bacteroidetes and Verrucomicrobia, some of which can survive solely on host‐derived mucins. A core mucosal assemblage of nine operational taxonomic units shared among all individuals was identified with an average total sequence abundance of 60.2%. This core community, together with moderate shifts in specific taxa, indicates that the mucosal microbiota remains relatively stable over the annual cycle yet responds to substrate changes while potentially serving as a pool for ‘seeding’ the microbiota once exogenous substrates return in spring. Relative to summer, hibernation reduced caecal crypt length and increased MUC2 expression in early winter and spring. Hibernation also decreased caecal TLR4 and increased TLR5 expression, suggesting a protective response that minimizes inflammation.
NEIGHBORHOODS AND HEALTH

Drawing on the expertise of a renowned cast of researchers, this book presents a state-of-the art account of the theories, methods, and empirical evidence linking neighborhood conditions to population health. Represented in the volume are contributions from the world's leading investigators in the field, including social epidemiologists, demographers, medical geographers, sociologists, and medical practitioners.
Effect of a γ-aminobutyric acid-enriched dairy product on the blood pressure of spontaneously hypertensive and normotensive Wistar–Kyoto rats

We investigated the blood-pressure-lowering effects of γ-aminobutyric acid (GABA) and a GABA-enriched fermented milk product (FMG) by low-dose oral administration to spontaneously hypertensive (SHR/Izm) and normotensive Wistar–Kyoto (WKY/Izm) rats. FMG was a non-fat fermented milk product produced by lactic acid bacteria, and the GABA contained in FMG was made from the protein of the milk during fermentation. A single oral dose of GABA or FMG (5 ml/kg; 0·5 mg GABA/kg) significantly (P>0·05) decreased the blood pressure of SHR/Izm from 4 to 8 h after administration, but did not increase that of WKY/Izm rats. The hypotensive activity of GABA was dose-dependent from 0·05 to 5·00 mg/kg in SHR/Izm. During the chronic administration of experimental diets to SHR/Izm, a significantly slower increase in blood pressure with respect to the control group was observed at 1 or 2 weeks after the start of feeding with the GABA or FMG diet respectively (P>0·05) and this difference was maintained throughout the period of feeding. The time profile of blood-pressure change due to administration of FMG was similar to that of GABA. FMG did not inhibit angiotensin 1-converting enzyme. Furthermore, an FMG peptide-containing fraction from reverse-phase chromatography lacked a hypotensive effect in SHR/Izm rats. The present results suggest that low-dose oral GABA has a hypotensive effect in SHR/Izm and that the hypotensive effect of FMG is due to GABA.