Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of bacterial communities in roots of selected trees with and without summer truffle (Tuber aestivum) ectomycorrhiza

Abstract In this study, we examined the effect of the presence of mycorrhiza and ascomata of summer truffle (Tuber aestivum) on the bacterial composition of roots from small trees growing in selected sites of the Nida Basin. Qualitative DNA sequencing methods such as Sanger and next-generation sequencing (NGS) were used. The Sanger method revealed different bacterial species compositions between the samples where summer truffle ascomata was recorded and control samples. Five genera of bacteria could be distinguished: Bacillus, Erwinia, Pseudomonas, Rahnella and Serratia, among which the most numerous were Pseudomonas (Gammmaproteobacteria class) at 32.9%. The results obtained by the NGS method also showed differences in species composition of the bacteria depending on the study sample. Seven genera of bacteria were distinguished: Rhizorhabdus, Methylotenera, Sphingomonas, Nitrosospira, Streptomyces, Methyloceanibacter and Niastella, which dominated in roots from the truffle sites. Telmatobacter, Roseiarcus, Granulicella, Paludibaculum, Acidipila, Acidisphaera and Aliidongia dominated in roots from the control sites. With the NGS method, it is possible to identify the microbiome of a whole root, while only a root fragment can be analysed by the Sanger method. These results extend the scope of knowledge on the preferences of certain groups of bacteria associated with truffles and their influence on the formation of ascomata in summer truffles. Our results may also be useful in selecting and monitoring sites that promote ascomata of Tuber aestivum.
Access routes in transcatheter aortic valve replacement: All roads lead to Rome but only one is paved

• The transfemoral approach is used in most patients undergoing transcatheter aortic valve replacement (TAVR) and is associated with low mortality rates as compared with alternative access sites. • The technical aspects of the procedure rather than the patient's risk profile explain most of the differences in mortality rates observed across different access routes. • Future TAVR studies are needed to establish the optimal access site when the ilio-femoral artery anatomy is unfavorable.
Alpha and beta rhythms differentially support the effect of symbols on visual object recognition

Hearing spoken words can enhance visual object recognition, detection and discrimination. Yet, the mechanisms that underpin this facilitation are incompletely understood. On one account, words do not bias early visual processing, but rather affect later semantic or decision-making stages. However, recent proposals suggest that words can alter early visual processes by activating category-specific priors in sensory regions. A prediction of this account is that top-down priors evoke changes in occipital areas in anticipation of visual stimuli. Here, we tested the hypothesis that neural oscillations serve as a mechanism to activate language-generated visual priors. Participants performed a cue-picture matching task where cues were either spoken words, in their native or second language, or natural sounds, while their EEG and reaction times were recorded. Behaviorally, we replicated the previously reported label-advantage effect, with images cued by words being recognized faster than those cued by natural sounds. A time-frequency analysis of cue-target intervals revealed that this behavioral label-advantage was associated with enhanced power in posterior alpha (9-11 Hz) and beta oscillations (17-19 Hz), both of which were larger when the image was preceded by a word compared to a natural sound. Importantly, object recognition performance improved with high alpha power but slowed down with enhancement of beta synchronization. These results suggest that alpha and beta rhythms play distinct functional roles to support language-mediated visual object recognition: alpha might function to amplify sensory priors in posterior regions, while beta may (re)activate the network states elicited by the auditory cue.
Presynaptic FMRP and local protein synthesis support structural and functional plasticity of glutamatergic axon terminals

Learning and memory critically rely on long-lasting, synapse-specific modifications. While postsynaptic forms of plasticity typically require local protein synthesis, whether and how local protein synthesis contributes to presynaptic changes remains unclear. Here, we examined the hippocampal mossy fiber (MF)-CA3 synapse which expresses both structural and functional presynaptic plasticity. We report that MF boutons synthesize protein locally and contain ribosomes. Long-term potentiation of MF-CA3 synaptic transmission (MF-LTP) was associated with translation-dependent enlargement of MF boutons. Moreover, increasing in vitro and in vivo MF activity enhanced protein synthesis in MFs. Remarkably, deletion of presynaptic Fragile X mental retardation protein (FMRP), an RNA-binding protein expressed in MF boutons and previously implicated in local postsynaptic protein synthesis-dependent plasticity, blocked structural and functional MF-LTP, suggesting that FMRP is a critical regulator of presynaptic function. Thus, presynaptic FMRP and protein synthesis dynamically control presynaptic structure and function in the mature brain. Highlights Mossy fiber boutons (MFBs) synthesize protein locally and contain ribosomes Local presynaptic translation is increased by in vitro and in vivo GC activity MFB structural plasticity relies on de novo protein synthesis. Presynaptic FMRP is required for MF-CA3 structural and functional plasticity In Brief Monday et al. report that FMRP and protein synthesis in hippocampal mossy fiber boutons mediate functional and structural presynaptic plasticity.
Linking parasitism to network centrality and the impact of sampling bias in its interpretation

Group living is beneficial for individuals, but also comes with costs. One such cost is the increased possibility of pathogen transmission because increased numbers or frequencies of social contacts are often associated with increased parasite abundance or diversity. The social structure of a group or population is paramount to patterns of infection and transmission. Yet, for various reasons, studies investigating the links between sociality and parasitism in animals, especially in primates, have only accounted for parts of the group (e.g., only adults), which is likely to impact the interpretation of results. Here, we investigated the relationship between social network centrality and an estimate of gastrointestinal helminth infection intensity in a whole group of Japanese macaques (Macaca fuscata). We then tested the impact of omitting parts of the group on this relationship. We aimed to test: (1) whether social network centrality – in terms of the number of partners (degree), frequency of interactions (strength), and level of social integration (eigenvector) – was linked to parasite infection intensity (estimated by eggs per gram of faeces, EPG); and, (2) to what extent excluding portions of individuals within the group might influence the observed relationship. We conducted social network analysis on data collected from one group of Japanese macaques over three months on Koshima Island, Japan. We then ran a series of knock-out simulations. General linear mixed models showed that, at the whole-group level, network centrality was positively associated with geohelminth infection intensity. However, in partial networks with only adult females, only juveniles, or random subsets of the group, the strength of this relationship - albeit still generally positive - lost statistical significance. Furthermore, knock-out simulations where individuals were removed but network metrics were retained from the original whole-group network showed that these changes are partly a power issue and partly an effect of sampling the incomplete network. Our study indicates that sampling bias can thus hamper our ability to detect real network effects involving social interaction and parasitism. In addition to supporting earlier results linking geohelminth infection to Japanese macaque social networks, this work introduces important methodological considerations for research into the dynamics of social transmission, with implications for infectious disease epidemiology, population management, and health interventions.
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA

Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative ‘Hoogsteen’ bps, expanding the functional complexity of DNA. We developed ‘Hoog-finder’, which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson-Crick in crystal structures of protein-DNA complexes. We uncovered seventeen Hoogsteen bps, seven of which were in complex with six proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks, and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
Identifying Charismatic Bird Species and Traits with Community Science Observations

Identifying which species are perceived as charismatic can improve the impact and efficiency of conservation outreach, as charismatic species receive more conservation funding and have their conservation needs prioritized (9; 17; 13). Sociological experiments studying animal charisma have relied on stated preferences to find correlations between hypothetical “willingness to pay” or “empathy” for a species’ conservation and species’ size, color, and aesthetic appeal (51; 13; 16). Recognizing the increasing availability of digital records of public engagement with animals that reveal preferences, an emerging field of “culturomics” uses Google search results, Wikipedia article activities, and other digital modes of engagement to identify charismatic species and traits (46; 31; 10; 41). In this study, we take advantage of community science efforts as another form of digital data that can reveal observer preferences. We apply a multi-stage analysis to ask whether opportunistic birders contributing to iNaturalist engage more with larger, more colorful, and rarer birds relative to a baseline, from eBird contributors, approximating unbiased detection. We find that body mass, color contrast, and range size all predict over-representation in the opportunistic dataset. We also find evidence that, across 473 modeled species, 52 species are significantly overreported and 158 are significantly underreported, indicating a wide variety of species-specific effects. Understanding which birds are charismatic can aid conservationists in creating impactful outreach materials and engaging new naturalists. The quantified differences between two prominent community science efforts may also be of use for researchers leveraging the data from one or both of them to answer scientific questions of interest.
Enrichment analysis of GWAS data in autoimmunity delineates the multiple sclerosis-Epstein Barr virus association

We exploited genetic information to assess non-genetic influences in autoimmunity. We isolated gene modules whose products physically interact with environmental exposures related to autoimmunity, and analyzed their nominal statistical evidence of association with autoimmune and non-autoimmune diseases in genome-wide association studies (GWAS) data. Epstein Barr virus (EBV) and other Herpesviruses interactomes emerged as specifically associated with multiple sclerosis (MS), possibly under common regulatory mechanisms. Analyses of MS blood and brain transcriptomes, cytofluorimetric studies of endogenous EBV-infected lymphoblastoid lines, and lesion immunohistochemistry, confirmed a dysregulation of MS-associated EBV interactors, suggesting their contribution to CD40 signaling alterations in MS. These interactors resulted enriched in modules from inherited axonopathies-causing genes, supporting a link between EBV and neurodegeneration in MS, in accord with the observed transcriptomic dysregulations in MS brains. They were also enriched with top-ranked pharmaceutical targets prioritized on a genetic basis. This study delineates a disease-specific influence of herpesviruses on MS biology.
An accurate assignment test for extremely low-coverage whole-genome sequence data

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.
Visual Gene Expression Reveals a cone-to-rod Developmental Progression in Deep-Sea Fishes

Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive (“green”) cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone-followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study: Idiacanthus fasciola, Chauliodus sloani; Stomiiformes; Coccorella atlantica, and Scopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rod RH1 opsin gene, and up to seven copies of the cone RH2 opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.
Visualisation of Control Software for Cyber-Physical Systems

Cyber-physical systems are typically composed of a physical system (plant) controlled by a software (controller). Such a controller, given a plant state s and a plant action u, returns 1 iff taking action u in state s leads to the physical system goal or at least one step closer to it. Since a controller K is typically stored in compressed form, it is difficult for a human designer to actually understand how “good” K is. Namely, natural questions such as “does K cover a wide enough portion of the system state space? ”, “does K cover the most important portion of the system state space? ” or “which actions are enabled by K in a given portion of the system space? ” are hard to answer by directly looking at K. This paper provides a methodology to automatically generate a picture of K as a 2D diagram, starting from a canonical representation for K and relying on available open source graphing tools (e.g., Gnuplot). Such picture allows a software designer to answer to the questions listed above, thus achieving a better qualitative understanding of the controller at hand.
Students’ Class Perceptions and Ratings of Instruction: Variability Across Undergraduate Mathematics Courses

The primary purpose of this study was to examine whether students’ motivation-related perceptions of mathematics courses were related to their ratings of instruction while controlling for their academic major, type of math class, and expected grade in the class. We investigated these relationships at both the student- and class-level because little is known about whether students’ motivation-related perceptions vary across mathematics courses and whether this variance is related to overall class ratings of instruction. The sample included 795 students nested within 43 different mathematics course sections. Students provided their course perceptions of autonomy, utility value, expectancies for success, situational interest, instructor caring, expected grade, and their overall perceptions of the course and instructor. Multilevel modeling techniques were used to investigate potential student- and class-level effects as well as compositional effects. Students’ class perceptions varied significantly across mathematics courses. In addition, students’ motivation-related course perceptions were positively related to their instructor and course ratings at both the student-level and class-level; however, the strength of these relationships sometimes varied across courses for some of the motivation-related perceptions. These results suggest that the motivational climate (i.e., the psychological environment) can affect students’ instructor and course ratings. Moreover, these findings suggest that instructors have some control over their instructor and course ratings through the teaching strategies that they implement. For example, they may be able to increase their ratings by implementing teaching strategies that support students’ autonomy, goals, success, interests, and relationships.
Disrupted Structural Brain Connectome Is Related to Cognitive Impairment in Patients With Ischemic Leukoaraiosis

Ischemic leukoaraiosis (ILA) is related to cognitive impairment and vascular dementia in the elderly. One possible mechanism could be the disruption of white matter (WM) tracts and network function that connect distributed brain regions involved in cognition. The purpose of this study was to investigate the relationship between structural connectome and cognitive functions in ILA patients. A total of 89 patients with ILA (Fazekas score ≥ 3) and 90 healthy controls (HCs) underwent comprehensive neuropsychological examinations and diffusion tensor imaging scans. The tract-based spatial statistics approach was employed to investigate the WM integrity. Graph theoretical analysis was further applied to construct the topological architecture of the structural connectome in ILA patients. Partial correlation analysis was used to investigate the relationships between network measures and cognitive performances in the ILA group. Compared with HCs, the ILA patients showed widespread WM integrity disruptions. The ILA group displayed increased characteristic path length (Lp) and decreased global network efficiency at the level of the whole brain relative to HCs, and reduced nodal efficiencies, predominantly in the frontal–subcortical and limbic system regions. Furthermore, these structural connectomic alterations were associated with cognitive impairment in ILA patients. The association between WM changes (i.e., fractional anisotropy and mean diffusivity measures) and cognitive function was mediated by the structural connectivity measures (i.e., local network efficiency and Lp). In conclusion, cognitive impairment in ILA patients is related to microstructural disruption of multiple WM fibers and topological disorganization of structural networks, which have implications in understanding the relationship between ILA and the possible attendant cognitive impairment.
University Teachers' Teaching Style and Their Students' Agentic Engagement in EFL Learning in China: A Self-Determination Theory and Achievement Goal Theory Integrated Perspective

As a relatively new dimension of student engagement, agentic engagement has received growing research interest in recent years, as it not only predicts academic achievement and other positive outcomes, but also benefits reciprocal teacher-student relations. In the educational context, teachers' teaching style exerts a crucial impact on students' engagement. However, research on how perceived teachers' teaching style influences students' agentic engagement is inconclusive. To address this lacuna, this study, taking an integrated perspective that draws on Self-determination Theory and Achievement Goal Theory, investigated the relationship of three types of teaching style (i.e., perceived autonomy support, social relatedness, and controlling) to university students' agentic engagement in EFL learning in China, especially through the mediation of mastery-approach goals and performance approach goals. Structural equation modeling showed that perceived autonomy support positively predicted agentic engagement through the mediation of mastery-approach goals, whereas perceived controlling negatively predicted agentic engagement through the mediation of performance-approach goals. Comparatively, the relationship of perceived social relatedness to agentic engagement was fully mediated by both mastery-approach and performance-approach goals. After discussing these results, practical implications as well as suggestions for future studies were given.