Miracle-dz/UniFAR-FTUs huggingface dataset:
Communication and disease management: a qualitative study on coronary disease

This study investigated doctor–patient communication and its role in the management of coronary disease. The aim was to identify patients’ information needs and related issues and to compare these findings with doctors’ perceptions of patients’ needs and communication barriers. Two focus groups were conducted with eight patients who suffered from coronary disease and six cardiologists. Recorded sessions were coded thematically and analyzed with interpretative phenomenological analysis. The results showed a “frustration of understanding” in both groups. Patients reported difficulty in understanding experts’ language, and physicians found it difficult to translate the medical terminology into simple words. However, they accused each other of creating these difficulties. Patients described physicians as an “elite” group with excessive technical language, and physicians reported that patients’ age and education (respectively, high and low) are real obstacles to good communication. Patients evaluated an autonomous search for health information as a way to better manage fear and anxiety related to the illness, but physicians considered it as a lack of trust and, thus, judged it negatively. Patients reported multiple unfilled needs, which were mainly related to information about how other people experienced the same illness and to specific information for their relatives, especially their spouses. Physicians stressed the need to transmit information about drug therapy and the need for adherence to manage chronic conditions. The analysis of patients’ information preferences and the awareness of patients’ information needs might strongly improve the overall quality of chronic disease management by suggesting new communication strategies.
Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range‐wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid‐latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black‐tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.
Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.

Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H(T) and Ac_23_E3(T) were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H(T) and Ac_23_E3(T) were aerobic mesophiles with a broad range of tolerance towards pH (4.0-9.5 and 3.5-10.0, respectively) and temperature (15-44 and 12-47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H(T) and Ac_23_E3(T) were iso-C(15 : 0), summed feature 1 (C(13 : 0) 3-OH/iso-C(15 : 1) H), summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c) and anteiso-C(17 : 0). The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H(T) and Ac_23_E3(T) were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16(T), with 16S rRNA gene sequence identity of 93.2 and 93.3%, respectively. Strains A22_HD_4H(T) and Ac_23_E3(T) displayed 16S rRNA gene sequence similarity of 97.4% to each other. On the basis of the low DNA-DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4H(T) = DSM 26555(T) = LMG 27985(T)) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3(T) = DSM 26558(T) = LMG 27597(T)).
Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.
Pathogen burden, co‐infection and major histocompatibility complex variability in the European badger (Meles meles)

Pathogen‐mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare‐allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e. recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test whether MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen‐mediated selection. We examined individual prevalence (infected or not), infection intensity and co‐infection of 13 pathogens from a range of taxa and examined their relationships with MHC class I and class II variability. This population has a variable, but relatively low, number of MHC alleles and is infected by a variety of naturally occurring pathogens, making it very suitable for the investigation of MHC–pathogen relationships. We found associations between pathogen infections and specific MHC haplotypes and alleles. Co‐infection status was not correlated with MHC heterozygosity, but there was evidence of heterozygote advantage against individual pathogen infections. This suggests that rare‐allele advantages and/or fluctuating selection, and heterozygote advantage are probably the selective forces shaping MHC diversity in this species. We show stronger evidence for MHC associations with infection intensity than for prevalence and conclude that examining both pathogen prevalence and infection intensity is important. Moreover, examination of a large number and diversity of pathogens, and both MHC class I and II genes (which have different functions), provide an improved understanding of the mechanisms driving MHC diversity.
Seonamhaeicola aphaedonensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a tidal flat sediment.

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, AH-M5(T), which was isolated from a tidal flat sediment at Aphae Island in South Korea, was characterized taxonomically. Strain AH-M5(T) grew optimally at 25 °C, at pH 7.0-8.0 and in presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain AH-M5(T) clustered coherently with the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus, showing 93.4-94.3% sequence similarity. The novel strain exhibited 16S rRNA gene sequence similarity values of less than 93.4% to the type strains of other recognized species. Strain AH-M5(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 1) G, iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c) as the major fatty acids. The polar lipid profile of strain AH-M5(T) containing phosphatidylethanolamine and one unidentified lipid as major components was differentiated from those of the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus. The DNA G+C content of strain AH-M5(T) was 34.8 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain AH-M5(T) is distinguished from Mangrovimonas yunxiaonensis and Meridianimaribacter flavus. On the basis of the data presented, strain AH-M5(T) is considered to represent a novel genus and species within the family Flavobacteriaceae, for which the name Seonamhaeicola aphaedonensis gen. nov., sp. nov. is proposed. The type strain of the type species is AH-M5(T) ( = KCTC 32578(T) = CECT 8487(T)).
A quantitative review of MHC‐based mating preference: the role of diversity and dissimilarity

Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC diversity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta‐analysis and meta‐regression techniques, we quantitatively review the existing literature on MHC‐dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC diversity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both diversity‐ and dissimilarity‐based mate choice (r = 0.113 and 0.064, respectively). Importantly, however, meta‐regression models revealed statistically significant support regarding female choice for diversity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa; however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias; thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.
Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen‐mediated selection in wild populations. Here, we examined variation at the MHC class II peptide‐binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in south‐western Alaska. We also obtained genotypes from 90 putatively neutral single nucleotide polymorphisms for each population to compare the relative roles of demography and selection in shaping the observed MHC variation. We found that MHC divergence was generally partitioned by spawning ecotype (lake beaches, rivers and streams) and was 30 times greater than variation at neutral markers. Additionally, we observed substantial differences in modes of selection and diversity among ecotypes, with beach populations displaying higher levels of directional selection and lower MHC diversity than the other two ecotypes. Finally, the level of MHC differentiation in our study system was comparable to that observed over much larger geographic ranges, suggesting that MHC variation does not necessarily increase with increasing spatial scale and may instead be driven by fine‐scale differences in pathogen communities or pathogen virulence. The low levels of neutral structure and spatial proximity of populations in our study system indicate that MHC differentiation can be maintained through strong selective pressure even when ample opportunities for gene flow exist.
Singular value decomposition-based multiuser multiple-input multiple-output vector perturbationaided downlink transmitter and lattice-reductionassisted uplink receiver pair

Abstract: A full-duplex uplink/downlink (UL/DL) system having a UL transmitter/receiver (transceiver) pair and a DL transceiver is considered. Both the UL and DL are improved. The DL is enhanced by a novel vector perturbation (VP)-aided singular value decomposition (SVD)-based precoding scheme, which is capable of exploiting the different-quality SVD eigenbeams and substantially reduces the overall average transmit power requirement of the traditional zero-forcing (ZF) precoder. By contrast, the UL is enhanced by a lattice reduction (LR)-aided receiver scheme designed for SVD-based multiuser multiple-input multiple-output (MU MIMO) UL transmission, when different modulation schemes are employed for different-quality eigenbeams. This new UL scheme avoids the noise-enhancement problem of the classic ZF UL receiver. The authors demonstrate that the proposed VP-aided DL and LR-assisted UL constitute a powerful full-duplex system, which achieves an 15 dB signal to noise ratio (SNR) gain for both SVD-based MU-MIMO DL and UL transmissions over the traditional ZF-aided schemes at a bit error rate (BER) of 1023.
Massive Osteochondral Allografts in the Management of Nontumoral Conditions Around the Knee

Due to the limited ability of cartilage to repair itself, full-thickness articular defects of the knee have a poor prognosis. The healing response to full-thickness articular cartilage injury produces fibrous cartilage (type I collagen) rather than normal hyaline cartilage. The inferiority of fibrous cartilage may lead to secondary osteoarthritis. In young patients, the use of prosthetic replacement components is generally avoided owing to early failure difficulties. Biologic treatments include subchondral drilling, microfracture, autologous chondrocyte transplantation, mosaicplasty, and various cell-, tissue-, or growth factor-mediated processes. Fresh osteochondral bulk allografts (FOBAs) provide a potential biologic solution to focal and diffuse articular cartilage disease of the knee. FOBAs provide instantly viable, fully formed, normally contoured articular surfaces and can restore lost subchondral bone stock. Although the availability of donor tissue may be a challenge with this technique, once donor tissue is obtained, large amounts of graft are available for the management of lesions of almost any size. Further, FOBAs have demonstrated chondrocyte viability for up to 17 years after transplantation.While chondrocytes do not remain viable in frozen allografts, there is evidence that they do remain viable in fresh allografts with maintained matrix. This technique is now an established management option for the treatment of large osteochondral defects of the knee. Survivorships of 95% at 5 years and 80% at 10 years have been reported on the tibial side, and that of 85% was found at 10 years on the femoral side. The risk of transmitting infectious organisms, causing viral or bacterial disease, is one of the most concerning and controversial issues in the use of fresh allograft material. Graft viability is also an issue since many centers require a delay in implantation while waiting for culture results. At the authors' institution, grafts are typically used within 48-72 hours from procurement to maximize chondrocyte viability.
Hybridization and mitochondrial genome introgression between Rana chensinensis and R. kukunoris

Mitochondrial genome (mito‐genome) introgression among metazoans is commonplace, and several biological processes may promote such introgression. We examined two proposed processes for the mito‐genome introgression between Rana chensinensis and R. kukunoris: natural hybridization and sex‐biased dispersal. We sampled 477 individuals from 28 sites in the potential hybrid zone in the western Tsinling Mountains. Mitochondrial gene (cyt‐b) trees were used to examine the introgression events. Microsatellite DNA loci, cyt‐b and morphological data were used to identify hybrids and to examine the extent of natural hybridization. We detected rampant bidirectional introgressions, both ancient and recent, between the two species. Furthermore, we found a wide hybrid zone, and frequent and asymmetric hybridization. The hybrid zone cline analysis revealed a clear mitochondrial–nuclear discordance; while most nuclear markers displayed similar and steep clines, cyt‐b had a displaced cline centre and a more gradual and wider cline. We also detected strong and asymmetric historical maternal gene flow across the hybrid zone. This widespread hybridization and detected low mito‐nuclear conflicts may, at least partially, explain the high frequency of introgression. Lastly, microsatellite data and population genetic methods were used to assess sex‐biased dispersal. A weak pattern of female‐biased dispersal was detected in both species, suggesting it may not play an important role in the observed introgression. Our data are consistent with the hybridization hypothesis, but support for the sex‐biased dispersal hypothesis is weak. We further suggest that selective advantages of the R. kukunoris‐type mito‐genome in thermal adaptation may also contribute to the introgression between the two species.
Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses

Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance‐partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.
Diet strongly influences the gut microbiota of surgeonfishes

Intestinal tracts are among the most densely populated microbial ecosystems. Gut microbiota and their influence on the host have been well characterized in terrestrial vertebrates but much less so in fish. This is especially true for coral reef fishes, which are among the most abundant groups of vertebrates on earth. Surgeonfishes (family: Acanthuridae) are part of a large and diverse family of reef fish that display a wide range of feeding behaviours, which in turn has a strong impact on the reef ecology. Here, we studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea. High‐throughput pyrosequencing results showed that members of the phylum Firmicutes, especially of the genus Epulopiscium, were dominant in the gut microbiota of seven surgeonfishes. Even so, there were large inter‐ and intraspecies differences in the diversity of surgeonfish microbiota. Replicates of the same host species shared only a small number of operational taxonomic units (OTUs), although these accounted for most of the sequences. There was a statistically significant correlation between the phylogeny of the host and their gut microbiota, but the two were not completely congruent. Notably, the gut microbiota of three nonsurgeonfish species clustered with some surgeonfish species. The microbiota of the macro‐ and microalgavores was distinct, while the microbiota of the others (carnivores, omnivores and detritivores) seemed to be transient and dynamic. Despite some anomalies, both host phylogeny and diet were important drivers for the intestinal microbial community structure of surgeonfishes from the Red Sea.