Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants

Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of natural selection along a transmission chain. Many viruses exhibit tight bottlenecks, and studies of early SARS-CoV-2 lineages identified a bottleneck of 1-3 infectious virions. While increased force of infection, host receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here, we compare the transmission bottleneck of non-variant-of-concern (non-VOC) SARS-CoV-2 lineages to those of the Alpha, Delta, and Omicron variants. We sequenced viruses from 168 individuals in 65 multiply infected households in duplicate to high depth of coverage. In 110 specimens collected close to the time of transmission, within-host diversity was extremely low. At a 2% frequency threshold, 51% had no intrahost single nucleotide variants (iSNV), and 42% had 1-2 iSNV. In 64 possible transmission pairs with detectable iSNV, we identified a bottleneck of 1 infectious virion (95% CI 1-1) for Alpha, Delta, and Omicron lineages and 2 (95% CI 2-2) in non-VOC lineages. The latter was driven by a single iSNV shared in one non-VOC household. The tight transmission bottleneck in SARS-CoV-2 is due to low genetic diversity at the time of transmission, a relationship that may be more pronounced in rapidly transmissible variants. The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive their evolution.
Thalamocortical networks involved in Pusher Syndrome

Indirect quantification of functional and structural disconnection increases the knowledge derived from focal brain lesions by inferring subsequent brain network damage from the respective lesion. We applied both measures to a sample of 124 stroke patients to investigate brain disconnection in pusher syndrome – a disorder characterized by a disturbed perception of one’s own upright body posture. Our results suggest a hub-like function of the posterior and lateral portions of the thalamus in the perception of one’s own postural upright and identified dysfunction in a thalamo-cortical network as one likely cause of pusher syndrome. Lesion network-symptom-mapping investigating functional disconnection indicated cortical diaschisis in cerebellar, frontal, parietal, occipital, and temporal areas in patients with thalamic lesions suffering from pusher syndrome, but there was no evidence for functional diaschisis in cortical stroke and no evidence for the convergence of thalamic and cortical lesions onto a common functional network. Structural disconnectivity mapping identified several thalamo-cortical disconnections. Many of the thalamic and cortical regions disconnected by lesions that lead to pusher behavior correspond to previously reported lesion sites associated with pusher syndrome. Thus, while the presence of both, isolated thalamic and cortical lesions in context with pusher behavior has been reported previously and led to the conclusion that the correct estimation of one’s own postural upright might depend on a thalamo-cortical network, our analyses offer the first evidence for a direct thalamo-cortical (or cortico-thalamic) interconnection and, more importantly, shed light on the location of the respective thalamo-cortical disconnections.
Body size as a magic trait in two plant-feeding insect species

When gene flow accompanies speciation, recombination can decouple divergently selected loci and loci conferring reproductive isolation. This barrier to sympatric divergence disappears when assortative mating and disruptive selection involve the same “magic” trait. Although magic traits could be widespread, the relative importance of different types of magic traits to speciation remains unclear. Because body size frequently contributes to host adaptation and assortative mating in plant-feeding insects, we evaluated several magic trait predictions for this trait in a pair of sympatric Neodiprion sawfly species adapted to different pine hosts. A large morphological dataset revealed that sawfly adults from populations and species that use thicker-needled pines are consistently larger than those that use thinner needled-pines. Fitness data from recombinant backcross females revealed that egg size is under divergent selection between the preferred pines. Lastly, mating assays revealed strong size-assortative mating within and between species in three different crosses, with the strongest prezygotic isolation between populations that have the greatest interspecific size differences. Together, our data support body size as a magic trait in pine sawflies and possibly many other plant-feeding insects. Our work also demonstrates how intraspecific variation in morphology and ecology can cause geographic variation in the strength of prezygotic isolation.
Patterns of litigation in France during two decades of recovery of a large carnivore

The recovery of large carnivores in Europe’s human dominated landscapes is an unexpected conservation success. In France, where the wolf disappeared in 1937, the species population is now approaching one thousand individuals after the species naturally returned in the country in 1992 from Italy. Large carnivores in Europe are protected by several legal instruments, ranging from international law, to European, national or regional laws (in federal countries). There has been a limited attention allocated to how this legal protection is in practice activated in Member States of the European Union. In particular, there is little research on the role of public interest environmental litigation for large carnivore conservation. We take the example of the wolf (Canis lupus) in France and describe wolf-related litigation in the country during two decades. We compiled a database of case law decisions (i.e. court rulings) relating to administrative litigation about the protection of the wolf and collected a total of 275 court rulings. We found that wolf litigation occurred unsurprisingly more often in administrative courts located in regions where wolves first returned (i.e. South-East of France). Animal welfare or protection associations were the most active and successful plaintiffs. The State administration represented by its Préfets was also a plaintiff in lawsuits against illegal culling decisions made by mayors. The Préfet des Alpes Maritimes and the Minister of the Environment were regular defendants for decisions to cull wolves that were litigated by nature protection associations. Nature protection associations overall had a case winning rate higher than 50%. There were no immediately obvious inter-annual trends in wolf litigation. Our database did not allow us to quantify the total number of wolves that were effectively protected from culling decisions because court rulings made after the execution of administrative decisions did not specify whether the animals were killed or not. Bet it as it may, nature protection associations appear to conduct legally relevant litigation in view of the high success rate they achieve and conservation lawsuits belong to the portfolio of available conservation instruments.
SKEW POLYNOMIAL RINGS OVER σ-QUASI-BAER AND σ-PRINCIPALLY QUASI-BAER RINGS

Let R be a ring R and be an endomorphism of R. R is called -rigid (resp. reduced) if for any implies a = 0. An ideal I of R is called a -ideal if . R is called -quasi-Baer (resp. right (or left) -p.q. -Baer) if the right annihilator of every -ideal (resp. right (or left) principal -ideal) of R is generated by an idempotent of R. In this paper, a skew polynomial ring A = R[] of a ring R is investigated as follows: For a -rigid ring R, (1) R is -quasi-Baer if and only if A is quasi-Baer if and only if A is -quasi-Baer for every extended endomorphism on A of (2) R is right -p.q. -Baer if and only if R is -p.q. -Baer if and only if A is right p.q. -Baer if and only if A is p.q. -Baer if and only if A is -p.q. -Baer if and only if A is right -p.q. -Baer for every extended endomorphism on A of .
Are female scientists underrepresented in self-correcting science for honest error?

Retractions are among the effective measures to strengthen the self-correction of science and the quality of the literature. When it comes to self-retractions for honest errors, exposure of one’s own failures is not a trivial matter for researchers. However, self-correcting data, results and/or conclusions has increasingly been perceived as good research practice, although rewarding such practice challenges traditional models of research assessment. In this context, it is timely to investigate who have self-retracted for honest error in terms of country, field, and gender. We show results on these three factors, focusing on gender, as data is scarce on the representation of female scientists in efforts to set the research record straight. We collected 3,822 retraction records, including research articles, review papers, meta-analyses, letters, and others, from the Retraction Watch Database (2010-2021). We screened the dataset collected for research articles retracted for honest error, excluding retractions by publishers, editors, or third parties, and those mentioning any investigation issues. We then categorized the records according to country, field, and gender, after selecting research articles with a sole corresponding author. Our results show that female scientists account for 25% of self-retractions for honest error, with the highest share for women affiliated with US institutions.
Identifying human islet microRNAs associated with donor sex, age and body mass index

Human islets are widely used in research for understanding pathophysiological mechanisms leading to diabetes. Sex, age, and body mass index (BMI) are key donor traits influencing insulin secretion. Islet function is also regulated by an intricate network of microRNAs. Here, we profiled 754 microRNAs and 58,190 transcripts in up to 131 different human islet donor preparations (without diabetes) and assessed their association with donor traits. MicroRNA analyses identified miR-199a-5p and miR-214-3p associated with sex, age and BMI; miR-147b with sex and age; miR-378a-5p with sex and BMI; miR-542-3p, miR-34a-3p, miR-34a-5p, miR-497-5p and miR-99a-5p with age and BMI. There were 959 mRNA transcripts associated with sex (excluding those from sex-chromosomes), 940 with age and 418 with BMI. MicroRNA-199a-5p and miR-214-3p levels inversely associate with transcripts critical in islet function, metabolic regulation, and senescence. Our analyses identify human islet cell microRNAs influenced by donor traits. Graphical abstract
Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - the Ligula intestinalis species complex

Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapeworm Ligula intestinalis a promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the current Ligula lineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between different Ligula lineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.
Pnictogen height as a possible switch between high- T c nodeless and low- T c nodal pairings in the iron-based superconductors

We study the effect of the lattice structure on the spin-fluctuation-mediated superconductivity in the iron pnictides adopting the five-band models of several virtual lattice structures of LaFeAsO, as well as actual materials such as NdFeAsO and LaFePO obtained from the maximally localized Wannier orbitals. Random phase approximation is applied to the models to solve the Eliashberg equation. This reveals that the gap function and the strength of the superconducting instability are determined by the cooperation or competition among multiple spin-fluctuation modes arising from several nestings among disconnected pieces of the Fermi surface, which is affected by the lattice structure. Specifically, the appearance of the Fermi surface $\ensuremath{\gamma}$ around $(\ensuremath{\pi},\ensuremath{\pi})$ in the unfolded Brillouin zone is sensitive to the pnictogen height ${h}_{\text{Pn}}$ measured from the Fe plane, where ${h}_{\text{Pn}}$ is shown to act as a switch between high-${T}_{c}$ nodeless and low-${T}_{c}$ nodal pairings. We also find that reduction in the lattice constants generally suppresses superconductivity. We can then combine these to obtain a generic superconducting phase diagram against the pnictogen height and lattice constant. This suggests that NdFeAsO is expected to exhibit a fully gapped, sign-reversing $s$-wave superconductivity with a higher ${T}_{c}$ than in LaFeAsO, while a nodal pairing with a low ${T}_{c}$ is expected for LaFePO, which is consistent with experiments.
Biotic and abiotic stress distinctly drive the phyllosphere microbial community structure

While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance to these stresses. We evaluated the impact of one such abiotic stress, elevated tropospheric ozone (O3), under open-top chamber field conditions on host susceptibility and phyllosphere microbiome associated with pepper cultivars resistant and susceptible to Xanthomonas. Pathogen challenge resulted in distinct microbial community structures in both cultivars under an ambient environment. Elevated O3 alone affected microbial community structure associated with resistant cultivar but not the susceptible cultivar, indicating the role of host genotypic background in response to abiotic stress. Elevated O3 did not influence overall host susceptibility but did increase disease severity on the resistant cultivar, indicating a possible compromise in the resistance. Interestingly, combined stress resulted in a shift in microbial composition and structure like that observed with pathogen challenge alone. It indicates the possible prioritization of community response towards the most significant stress and pathogen being most influential regardless of the cultivar. Despite community composition differences, overall functional redundancy was observed in the phyllosphere community. To gain insights into community-level interactions, network topology assessment indicated a stable network with enhanced taxon connectedness upon pathogen challenge. However, an observation of destabilized random network with a shift in hub taxa in the presence of combined stress warrants future studies on the consequences of such unstable microbial communities on host response to pathogens in the face of climate change.
Suspect macrocyclic lactone resistance cases with the canine heartworm ( Dirofilaria immitis ): mismatch between microfilarial suppression test and SNP results in Australia

Canine heartworm disease is a potentially deadly cardiopulmonary disease caused by the mosquito-borne filarial nematode Dirofilaria immitis . In Australia, the administration of 27 macrocyclic lactone (ML) drugs has successfully reduced the prevalence of D. immitis 28 infection. However, the recent re-emergence of D. immitis in dogs in Queensland, Australia 29 and the identification of ML-resistant isolates in the USA poses an important question of 30 whether ML-resistance has emerged in this parasite in Australia. The aim of this study was to 31 utilise phenotypic and genotypic assays to determine the presence of ML-resistant D. immitis 32 in Australia. To do this, we surveyed 45 (n=45) dogs from Queensland and New South Wales 33 across 3 years (2019-2022) for the presence of D. immitis infection using an antigen test, 34 quantitative Modified Knott’s test, and qPCR targeting both D. immitis and the D. immitis 35 symbiont Wolbachia . A phenotypic assay utilising a microfilarial suppression test for 23/45 36 dogs was coupled with genetic testing of filtered microfilariae for SNPs previously associated 37 with ML-resistance in isolates from the USA. Sixteen (16/45) dogs tested positive for D. 38 immitis infection despite reportedly receiving ‘rigorous’ heartworm prevention for 12 months 39 prior to the study. The phenotypic and genotypic assays in this study did not unequivocally 40 demonstrate the presence of ML-resistant D. immitis in Australia. Although the failure of 16 41 dogs to reduce microfilaremia by >90% after ML treatment was considered phenotypic 42 evidence of suspect ML-resistance, no genotypic evidence was discovered using the genetic SNP analysis. It is possible that the presence of ML-resistance in this study was masked by the high initial of moxidectin (microspheres, 500 µg/kg s.c.) administered to eighteen 45 (18/23) dogs at the time of diagnosis, which had the potential to clear any ML-resistant D.
Re-evaluating homoploid reticulate evolution in the annual sunflowers

Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best studied examples of homoploid hybrid speciation. To understand the broader picture of hybridization within the annual sunflowers, we used whole genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (H. anomalus, H. deserticola, and H. paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
Macro-scale patterns in functional connectivity associated with ongoing thought patterns and dispositional traits

Complex macro-scale patterns of brain activity that emerge during periods of wakeful rest provide insight into the organisation of neural function, how these differentiate individuals based on their traits, and the neural basis of different types of self-generated thoughts. Although brain activity during wakeful rest is valuable for understanding important features of human cognition, its unconstrained nature makes it difficult to disentangle neural features related to personality traits from those related to the thoughts occurring at rest. Our study builds on recent perspectives from work on ongoing conscious thought that highlight the interactions between three brain networks - ventral and dorsal attention networks, as well as the default mode network. We combined measures of personality with state-of-the-art indices of ongoing thoughts at rest and brain imaging analysis, and explored whether this ‘tri-partite’ view can provide a framework within which to understand the contribution of states and traits to observed patterns of neural activity at rest. To capture macro-scale relationships between different brain systems, we calculated cortical gradients to describe brain organisation in a low dimensional space. Our analysis established that for more introverted individuals, regions of the ventral attention network were functionally more aligned to regions of the somatomotor system and the default mode network. At the same time, a pattern of detailed self-generated thought was associated with a decoupling of regions of dorsal attention from regions in the default mode network. Our study, therefore, establishes that interactions between attention systems and the default mode network are important influences on ongoing thought at rest and highlights the value of integrating contemporary perspectives on conscious experience when understanding patterns of brain activity at rest.
Personalized Functional Brain Network Topography Predicts Individual Differences in Youth Cognition

Individual differences in cognition during childhood are associated with important social, physical, and mental health outcomes in adolescence and adulthood. Given that cortical surface arealization during development reflects the brain’s functional prioritization, quantifying variation in the topography of functional brain networks across the developing cortex may provide insight regarding individual differences in cognition. We test this idea by defining personalized functional networks (PFNs) that account for interindividual heterogeneity in functional brain network topography in 9-10 year olds from the Adolescent Brain Cognitive DevelopmentSM Study. Across matched discovery (n=3,525) and replication (n=3,447) samples, the total cortical representation of fronto-parietal PFNs positively correlated with general cognition. Cross-validated ridge regressions trained on PFN topography predicted cognition across domains, with prediction accuracy increasing along the cortex’s sensorimotor-association organizational axis. These results establish that functional network topography heterogeneity is associated with individual differences in cognition before the critical transition into adolescence.