Miracle-dz/UniFAR-FTUs huggingface dataset:
Incipient speciation driven by hypertrophied lips in Midas cichlid fishes?

Sympatric speciation has been debated in evolutionary biology for decades. Although it has gained in acceptance recently, still only a handful of empirical examples are seen as valid (e.g. crater lake cichlids). In this study, we disentangle the role of hypertrophied lips in the repeated adaptive radiations of Nicaraguan crater lake cichlid fish. We assessed the role of disruptive selection and assortative mating during the early stages of divergence and found a functional trade‐off in feeding behaviour between thick‐ and thin‐lipped ecotypes, suggesting that this trait is a target of disruptive selection. Thick‐lipped fish perform better on nonevasive prey at the cost of a poorer performance on evasive prey. Using enclosures in the wild, we found that thick‐lipped fish perform significantly better in rocky than in sandy habitats. We found almost no mixed pairs during two breeding seasons and hence significant assortative mating. Genetic differentiation between ecotypes seems to be related to the time since colonization, being subtle in L. Masaya (1600 generations ago) and absent in the younger L. Apoyeque (<600 generations ago). Genome‐wide differentiation between ecotypes was higher in the old source lakes than in the young crater lakes. Our results suggest that hypertrophied lips might be promoting incipient sympatric speciation through divergent selection (ecological divergence in feeding performance) and nonrandom mating (assortative mating) in the young Nicaraguan crater lakes. Nonetheless, further manipulative experiments are needed in order to confirm the role of hypertrophied lips as the main cue for assortative mating.
Securing cognitive radio with a combined approach of beamforming and cooperative jamming

The authors consider secret communication through a relay-assisted cognitive interference channel in which primary and secondary base stations (SBSs), respectively, communicate with the primary and secondary receivers (PU-Rx and SU-Rx) in the presence of multiple eavesdroppers. An SBS is allowed to transmit simultaneously with the primary base station (PBS). They propose three cooperative jamming (CJ) schemes based on the available channel state information at the base stations and the relay. The proposed CJ schemes are designed to create additional interference in the direction of eavesdroppers without creating any interference to the PU-Rx and the SU-Rx. A combined approach of beamforming and zero-forcing precoding is developed at the PBS, the SBS and the relay to cancel out jamming interference at the PU-Rx and the SU-Rx. The secrecy rate of SU-Rx is calculated with the constraint of maintaining interference temperature at the PU-Rx under a certain threshold. Compared with the direct transmission schemes that are available in the literature, the authors’ results show that the approach which combined beamforming and CJ significantly improves the secrecy rate of the cognitive interference channel.
Cuticular hydrocarbon cues of immune‐challenged workers elicit immune activation in honeybee queens

Recently, evidence has shown that variations in the cuticular hydrocarbons (CHCs) profile allow healthy honeybees to identify diseased nestmates, eliciting agonistic responses in the former. Here, we determined whether these ‘immunologic cues’ emitted by diseased nestmates were only detected by workers, who consequently took hygienic measures and excluded these individuals from the colony, or whether queens were also able to detect these cues and respond accordingly. Healthy honeybee queens were exposed to (i) healthy, (ii) Ringer‐injected and (iii) lipopolysaccharide (LPS)‐injected nestmates by allowing direct body contact. Quantitative differences in the CHC profiles of these three groups were measured using GC‐MS. The transcript levels of the products of four genes that encode for antimicrobial peptides (AMPs), which are part of the queen's immune response, were measured in bees exposed to direct contact using qPCR. A significant increase in the transcript levels of these AMP genes over baseline levels in queens was observed when body contact was allowed between the queens and the Ringer‐ and LPS‐injected nestmates. These results provide the first evidence that the detection of CHCs contributes to the initiation of an immune response in insects. In an additional experiment, CHCs were extracted from diseased workers and directly presented to queens, which also evoked a similar immune response. A potential mechanism that relied on volatile compounds could be ruled out by conducting a distance experiment. The study helps to expand our knowledge of chemical communication in insects and sheds light on a likely new mechanism of social immunity.
Chronic low back pain

The care of patients with persistent non-specific low back pain is a common situation in general practice. Chronic non-specific low back pain is defined as back pain persisting for more than 6 weeks in the absence of an underlying pathology. Multiple different permutations of the structures in the back, such as joints, discs, muscles, tendons and ligaments, play a part in the development of chronic non-specific low back pain. With the right management, low back pain resolves or improves significantly in the majority of cases. However, if patients do not receive appropriate management in a timely fashion, there is a higher risk of them going on to experience significant negative physical, social, psychological and economic outcomes.
Determination of genetic relatedness from low‐coverage human genome sequences using pedigree simulations

We develop and evaluate methods for inferring relatedness among individuals from low‐coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present‐day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present‐day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present‐day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.
Rehabilitation adherence and anterior cruciate ligament reconstruction outcome

This study examined the relationship between adherence to postoperative physical therapy and outcome after surgical reconstruction of the anterior cruciate ligament (ACL) of the knee in a sample of 72 men and 36 women. Indices of adherence were obtained during the first 6 weeks of postsurgical rehabilitation. Outcome measures were administered before surgery and approximately 6 months after surgery. Results of a canonical correlation analysis indicated a statistically significant association between the adherence variables and the outcome variables (r = 0.56, p < 0.05). Greater attendance at rehabilitation sessions and more favourable practitioner ratings of adherence during rehabilitation sessions were associated with fewer self-reported knee symptoms and greater knee laxity. The findings highlight the complex nature of the adherence – outcome relationship.
Treatment of Very High Triglycerides with Fish Oils: A Review of 2 Cases

Objective: To report 2 cases of serum triglycerides >1000 mg/dL (i.e., very high serum triglycerides) in which fish oil was used because of treatment failure or intolerance with conventional therapeutic modalities. Case Summary: Two individuals with a history of serum triglycerides >1000 mg/dL were referred to a pharmacist-managed lipid clinic by their primary-care provider because of either treatment failure or intolerance to conventional therapeutic modalities. Fish oils were used in lieu of and in addition to conventional treatment modalities in cases 1 and 2, respectively. Both cases demonstrated that fish oil, at doses ranging from 1 to 6 g/d, decrease triglyceride levels to a degree similar to conventional measures. Both patients tolerated fish oil well; however, increases in liver transaminases were observed. Discussion: Published studies have shown that fish oil can reduce elevated plasma triglycerides by an average of 30–52% in subjects with borderline-high (150–199 mg/dL) to high (200–499 mg/dL) triglycerides. Both of our cases reflect similar results in patients with very high triglycerides. Although fish oil has not been reported to induce hepatotoxicity, both of our patients experienced an increase in transaminases while on fish oil therapy. Whether fish oil truly causes hepatic injury remains to be elucidated. Conclusions: Fish oil supplementation is effective and generally well tolerated in patients with very high triglycerides and can be used as either alternative or adjunctive therapy when conventional treatment modalities become ineffective or intolerable.
Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co‐distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo‐Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species‐specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo‐Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species.
Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection

The simultaneous expression of costly immune effectors such as multiple antimicrobial peptides is a hallmark of innate immunity of multicellular organisms, yet the adaptive advantage remains unresolved. Here, we test current hypotheses on the evolution of such defence cocktails. We use RNAi gene knock‐down to explore, the effects of three highly expressed antimicrobial peptides, displaying different degrees of activity in vitro against Staphylococcus aureus, during an infection in the beetle Tenebrio molitor. We find that a defensin confers no survival benefit but reduces bacterial loads. A coleoptericin contributes to host survival without affecting bacterial loads. An attacin has no individual effect. Simultaneous knock‐down of the defensin with the other AMPs results in increased mortality and elevated bacterial loads. Contrary to common expectations, the effects on host survival and bacterial load can be independent. The expression of multiple AMPs increases host survival and contributes to the control of persisting infections and tolerance. This is an emerging property that explains the adaptive benefit of defence cocktails.
Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β‐fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide‐ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.
Gene copy number variations in adaptive evolution: The genomic distribution of gene copy number variations revealed by genetic mapping and their adaptive role in an undomesticated species, white spruce (Picea glauca)

Gene copy number variation (CNV) has been associated with phenotypic variability in animals and plants, but a genomewide understanding of their impacts on phenotypes is largely restricted to human and agricultural systems. As such, CNVs have rarely been considered in investigations of the genomic architecture of adaptation in wild species. Here, we report on the genetic mapping of gene CNVs in white spruce, which lacks a contiguous assembly of its large genome (~20 Gb), and their relationships with adaptive phenotypic variation. We detected 3,911 gene CNVs including de novo structural variations using comparative genome hybridization on arrays (aCGH) in a large progeny set. We inferred the heterozygosity at CNV loci within parents by comparing haploid and diploid tissues and genetically mapped 82 gene CNVs. Our analysis showed that CNVs were distributed over 10 linkage groups and identified four CNV hotspots that we predict to occur in other species of the Pinaceae. Significant relationships were found between 29 of the gene CNVs and adaptive traits based on regression analyses with timings of bud set and bud flush, and height growth, suggesting a role for CNVs in climate adaptation. The importance of CNVs in adaptive evolution of white spruce was also indicated by functional gene annotations and the clustering of 31% of the mapped adaptive gene CNVs in CNV hotspots. Taken together, these results illustrate the feasibility of studying CNVs in undomesticated species and represent a major step towards a better understanding of the roles of CNVs in adaptive evolution.
Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales

Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance vs. host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree—including tree age, size and soil chemistry—and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modelling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free‐living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity—and, surprisingly, not host species—were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil‐mediated systems.
Apolipoprotein e genotype and late paraphrenia

Patients with late paraphrenia or late onset schizophrenia frequently have associated cognitive impairment which may in some cases progress to a recognized dementia. The frequency of the apoE ϵ4 allele is high in individuals who develop Alzheimer's disease. Twenty‐three patients with late paraphrenia were genotyped for ApoE. The frequency of the ϵ4 allele was comparable with that found in a large group of centenarians, but lower than previously reported from populations of normal controls and Alzheimer's disease patients. Two out of three male patients tested had the rare ϵ2/ϵ2 genotype, which was not found in any of the females.
Daphnia magna microRNAs respond to nutritional stress and ageing but are not transgenerational

Maternal effects, where the performance of offspring is determined by the condition of their mother, are widespread and may in some cases be adaptive. The crustacean Daphnia magna shows strong maternal effects: offspring size at birth and other proxies for fitness are altered when their mothers are older or when mothers have experienced dietary restriction. The mechanisms for this transgenerational transmission of maternal experience are unknown, but could include changes in epigenetic patterning. MicroRNAs (miRNAs) are regulators of gene expression that have been shown to play roles in intergenerational information transfer, and here, we test whether miRNAs are involved in D. magna maternal effects. We found that miRNAs were differentially expressed in mothers of different ages or nutritional state. We then examined miRNA expression in their eggs, their adult daughters and great granddaughters, which did not experience any treatments. The maternal (treatment) generation exhibited differential expression of miRNAs, as did their eggs, but this was reduced in adult daughters and lost by great granddaughters. Thus, miRNAs are a component of maternal provisioning, but do not appear to be the cause of transgenerational responses under these experimental conditions. MicroRNAs may act in tandem with egg provisioning (e.g., with carbohydrates or fats), and possibly other small RNAs or epigenetic modifications.
The correlation between the richmond agitation–sedation scale and bispectral index during dexmedetomidine sedation

Background and objectives: The primary objective of sedation in the critically ill patient is to achieve security and comfort. The routine use of standardized and validated sedation scales and monitors are needed. The Richmond agitation sedation scale has been used but some patients cannot be evaluated with subjective assessment tools such as the Richmond agitation sedation scale because they lack motor responsiveness due to therapeutic paralysis or because they are receiving deep sedation. We aimed to assess the correlation of bispectral index with Richmond agitation sedation scale during dexmedetomidine sedation and evaluate the use of the bispectral index in monitoring the levels of sedation in intensive care patients. Methods: This was a single centre, prospective, clinical study. Eleven mechanically‐ventilated critically ill patients, aged 17–82 (50.09 ± 17.76; mean ± SD) yr, 3 males and 8 females, APACHE II score 12.63 ± 3.90, SOFA score 3.27 ± 1.73 were enrolled in the study. Patients received a dexmedetomidine infusion of 1 μg kg−1 over 10 min followed by a maintenance infusion of 0.5 μg kg−1 h−1 for 8 h. Sedation was assessed using the Richmond agitation sedation scale and bispectral index monitoring. Heart rate, blood pressure, respiratory rate and SPO2 were monitored. Wilcoxon signed rank sum test and Spearman's rank correlation analysis were used for statistical analysis. Results: The variation of Richmond agitation sedation scale score was between 0.9 and −1.7 bispectral index varied from 65 to 75. Significant correlations between Richmond agitation sedation scale and bispectral index values were found in this study. (r = 0.900; P = 0.0001) Conclusions: Richmond agitation sedation scale levels significantly correlated with bispectral index values during dexmedetomidine sedation in critically ill patients requiring mechanical ventilation in the intensive care unit.