Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel lytic and lysogenic cyanophages predicted to infect Microcoleus associated with anatoxin-producing benthic mats

Proliferations of toxic benthic cyanobacteria are increasingly being reported around the world. Of particular concern are Microcoleus-dominated mats associated with anatoxin production that have resulted in dog fatalities. Although the impact of cyanophages has been demonstrated in planktonic systems, their role in the population dynamics of benthic cyanobacteria has received little attention. Here we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (WR; New Brunswick, Canada) and Eel River (ER; California, US). Our survey recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A lysogenic cyanophage (predicted as a prophage) was found integrated in the genomes of Microcoleus sp. 3 recovered from five ER mat samples. This Microcoleus phage is related to previously described Phormidium phage counterparts. Also, we recovered lytic cyanophages from WR and ER mats dominated by anatoxin-producing Microcoleus, which was predicted as the putative host. Despite the geographical distance between WR and ER, the lytic Microcoleus phage genomes recovered from each river have similar sizes (circa 239 Kbp) and share similar gene content with high sequence identity. Phylogenetic analysis suggests that these lytic Microcoleus phages are distant from any other cyanophage previously described. Our results constitute the first report of cyanophages predicted to infect and therefore influence the population dynamics of mat-forming Microcoleus spp. associated with anatoxin production.
Finite Element Simulation of Weld Bead Geometry and Temperature Distribution during GTA Welding of Modified 9Cr-1Mo Steel and Experimental Validation

Abstract The thermal analysis of Modified 9Cr-1Mo steel plate during GTA welding is carried out using finite element method employing SYSWELD software. First, the simulation of bead on plate welds for 16 varying process parameter conditions by employing a double ellipsoidal heat source was carried out. Simulated bead on plate weld bead dimensions for the 16 welds were compared with the actual bead dimensions obtained experimentally. Then the simulation of GTA welding of square butt joint on 3 mm thick plates of dimensions 300 × 125 × 3 mm was carried out. The simulated thermal profiles were validated using thermocouple measurements. There was good agreement between the predicted and measured weld bead profiles and thermal cycles for square butt joint. The investigation on the effect of copper back up plate on the peak temperature and the cooling rate has revealed that the peak temperature decreased by 147 °C and the cooling rate increased by 35%.
Isolation and identification of mycorrhizal helper bacteria of Vaccinium uliginosum and their interaction with mycorrhizal fungi

Mycorrhizal helper bacteria (MHB) can promote mycorrhizal fungal colonization and form mycorrhizal symbiosis structures. To investigate the effect of interactions between mycorrhizal beneficial microorganisms on the growth of blueberry, 45 strains of bacteria isolated from the rhizosphere soil of Vaccinium uliginosum were screened for potential MHB strains using the dry-plate confrontation assay and the bacterial extracellular metabolite promotion method. The results showed that the growth rate of mycelium of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was increased by 33.33 and 77.77% for bacterial strains L6 and LM3, respectively, compared with the control in the dry-plate confrontation assay. In addition, the extracellular metabolites of L6 and LM3 significantly promoted the growth of O. maius 143 mycelium with an average growth rate of 40.9 and 57.1%, respectively, the cell wall-degrading enzyme activities and genes of O. maius 143 was significantly increased. Therefore, L6 and LM3 were preliminarily identified as potential MHB strains. In addition, the co-inoculated treatments significantly increased blueberry growth; increased the nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activities in the leaves; and promoted nutrient uptake in blueberry. Based on the physiological, and 16S rDNA gene molecular analyses, we initially identified strain L6 as Paenarthrobacter nicotinovorans and LM3 as Bacillus circulans. Metabolomic analysis revealed that mycelial exudates contain large amounts of sugars, organic acids and amino acids, which can be used as substrates to stimulate the growth of MHB. In conclusion, L6 and LM3 and O. maius 143 promote each other’s growth, while co-inoculation of L6 and LM3 with O. maius 143 can promote the growth of blueberry seedlings, providing a theoretical basis for further studies on the mechanism of ericoid mycorrhizal fungi-MHB-blueberry interactions. It laid the technical foundation for the exploitation of biocontrol strain resources and the development of biological fertilizer.
Variation in Sphingomonas traits across habitats and phylogenetic clades

Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.
Pronouncing and comprehending center-embedded sentences

VP3 VP2 RC1 NP1 RC1 VP3 NP1 VP3 NP S Participants: • 28 English native speakers (19f/9m) • Mean age 30.9 (10.1) Stimuli: 2CE-RC sentences designed either to ENCourage or DISCourage the 3-phrase prosody: • 8 varying in phrase length (see examples in 2.2): long phrases in outer clause or in inner clauses. • 4 varying in phrase ‘weight’ only: Varied were word frequency and default stress. ENC items had low frequency/heavily stressed words in outer clause. DISC items had such words in inner clauses. • ENC: The soufflé that the waitress the boss hired brought disintegrated. Sum of word frequencies • DISC: The drink that the hostess the nightclub employed stirred spilled. matched across sentence pair. • 16 fillers: if not because, early/late closure, NP/clause complement, parenthetical Adverbial clauses Dependent Measures: • by subjects, after reading aloud: Pronounceablility and Comprehensibility • by expert judges: Appropriateness of global prosodic contour and positions of prosodic breaks
Developmental origin of tendon diversity in Drosophila melanogaster

Myogenesis is a developmental process that is largely conserved in both Drosophila and higher organisms. Consequently, the fruit fly is an excellent in vivo model for identifying the genes and mechanisms involved in muscle development. Moreover, there is growing evidence indicating that specific conserved genes and signaling pathways govern the formation of tissues that connect the muscles to the skeleton. In this review, we present an overview of the different stages of tendon development, from the specification of tendon progenitors to the assembly of a stable myotendinous junction across three different myogenic contexts in Drosophila: larval, flight and leg muscle development. We underline the different aspects of tendon cell specification and differentiation in embryo and during metamorphosis that result into tendon morphological and functional diversity.
Diaphragmatic ultrasound can help evaluate pulmonary dysfunction in patients with stroke

Objective Pulmonary dysfunction after stroke is increasingly gaining attention from clinical and rehabilitation specialists. However, owing to cognitive and motor dysfunction in patients with stroke, determining the pulmonary function of these patients remains challenging. The present study aimed to devise a simple method for an early evaluation of pulmonary dysfunction in patients with stroke. Methods Overall, 41 patients with stroke in the recovery period (stroke group) and 22 matched healthy controls (control group) were included in the study. We first collected data regarding baseline characteristics for all participants. Furthermore, the participants with stroke were examined using additional scales, such as the National Institutes of Health Stroke Scale (NIHSS), Fugl–Meyer assessment scale (FMA), and modified Barthel Index (MBI). Subsequently, we examined the participants with simple pulmonary function detection and diaphragm ultrasound (B-mode). Ultrasound indices calculated were as follows: the thickness of the diaphragm under the position of functional residual capacity (TdiFRC), the thickness of the diaphragm under the position of forced vital capacity (TdiFVC), thickness fraction, and diaphragmatic mobility. Finally, we compared and analyzed all data to identify group differences, the correlation between pulmonary function and diaphragmatic ultrasound indices, and the correlation between pulmonary function and assessment scale scores in patients with stroke, respectively. Results Compared with the control group, patients in the stroke group exhibited lower values for indices of pulmonary and diaphragmatic function (p < 0.001), except for TdiFRC (p > 0.05). The majority of the patients with stroke had restrictive ventilatory dysfunction, as indicated by a significantly higher incidence ratio (36 in 41 patients) than that in the control group (0 in 22 patients) (p < 0.001). Moreover, significant correlations were found between pulmonary function and diaphragmatic ultrasound indices (p < 0.05), with the strongest correlation between TdiFVC and pulmonary indices. In the stroke group, pulmonary function indices were negatively correlated with the NIHSS scores (p < 0.001) and positively correlated with the FMA scores (p < 0.001). No (p > 0.05) or weak (p < 0.05) correlation was found between pulmonary function indices and the MBI scores. Conclusion We found that patients with stroke had pulmonary dysfunction even in the recovery period. Diaphragmatic ultrasound can be used as a simple and effective tool for detecting pulmonary dysfunction in patients with stroke, with TdiFVC being the most effective index.
Impaired SARS-CoV-2 specific T-cell response in patients with severe COVID-19

Cellular immune responses are of pivotal importance to understand SARS-CoV-2 pathogenicity. Using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay with wild-type spike, membrane and nucleocapsid peptide pools, we longitudinally characterized functional SARS-CoV-2 specific T-cell responses in a cohort of patients with mild, moderate and severe COVID-19. All patients were included before emergence of the Omicron (B.1.1.529) variant. Our most important finding was an impaired development of early IFN-γ-secreting virus-specific T-cells in severe patients compared to patients with moderate disease, indicating that absence of virus-specific cellular responses in the acute phase may act as a prognostic factor for severe disease. Remarkably, in addition to reactivity against the spike protein, a substantial proportion of the SARS-CoV-2 specific T-cell response was directed against the conserved membrane protein. This may be relevant for diagnostics and vaccine design, especially considering new variants with heavily mutated spike proteins. Our data further strengthen the hypothesis that dysregulated adaptive immunity plays a central role in COVID-19 immunopathogenesis.
Do driver’s characteristics, system performance, perceived safety, and trust influence how drivers use partial automation? A structural equation modelling analysis

The present study surveyed actual extensive users of SAE Level 2 partially automated cars to investigate how driver’s characteristics (i.e., socio-demographics, driving experience, personality), system performance, perceived safety, and trust in partial automation influence use of partial automation. 81% of respondents stated that they use their automated car with speed (ACC) and steering assist (LKA) at least 1–2 times a week, and 84 and 92% activate LKA and ACC at least occasionally. Respondents positively rated the performance of Adaptive Cruise Control (ACC) and Lane Keeping Assistance (LKA). ACC was rated higher than LKA and detection of lead vehicles and lane markings was rated higher than smooth control for ACC and LKA, respectively. Respondents reported to primarily disengage (i.e., turn off) partial automation due to a lack of trust in the system and when driving is fun. They rarely disengaged the system when they noticed they become bored or sleepy. Structural equation modelling revealed that trust had a positive effect on driver’s propensity for secondary task engagement during partially automated driving, while the effect of perceived safety was not significant. Regarding driver’s characteristics, we did not find a significant effect of age on perceived safety and trust in partial automation. Neuroticism negatively correlated with perceived safety and trust, while extraversion did not impact perceived safety and trust. The remaining three personality dimensions ‘openness’, ‘conscientiousness’, and ‘agreeableness’ did not form valid and reliable scales in the confirmatory factor analysis, and could thus not be subjected to the structural equation modelling analysis. Future research should re-assess the suitability of the short 10-item scale as measure of the Big-Five personality traits, and investigate the impact on perceived safety, trust, use and use of automation.
Assessment of a single trial impact on the amplitude of the averaged event related potentials

Widely used in neuroscience the averaging of event related potentials is based on the assumption that small responses to the investigated events are present in every trial but can be hidden under the random noise. This situation often takes place, especially in experiments performed at hierarchically lower levels of sensory systems. However, in the studies of higher order complex neuronal networks evoked responses might appear only under particular conditions and be absent otherwise. We encountered this problem studying a propagation of interoceptive information to the cortical areas in the sleep-wake cycle. Cortical responses to various visceral events were present during some periods of sleep, then disappeared for a while and restored again after a period of absence. Further investigation of the viscero-cortical communication required a method that would allow labeling the trials contributing to the averaged event related responses–“efficient trials,” and separating them from the trials without any response. Here we describe a heuristic approach to solving this problem in the context of viscero-cortical interactions occurring during sleep. However, we think that the proposed technique can be applicable to any situation where neuronal processing of the same events is expected to be variable due to internal or external factors modulating neuronal activity. The method was first implemented as a script for Spike 2 program version 6.16 (CED). However, at present a functionally equivalent version of this algorithm is also available as Matlab code at https://github.com/george-fedorov/erp-correlations.
Virtual reality-induced motor function of the upper extremity and brain activation in stroke: study protocol for a randomized controlled trial

Background The benefits of virtual reality (VR)-based rehabilitation were reported in patients after stroke, but there is insufficient evidence about how VR promotes brain activation in the central nervous system. Hence, we designed this study to explore the effects of VR-based intervention on upper extremity motor function and associated brain activation in stroke patients. Methods/design In this single-center, randomized, parallel-group clinical trial with a blinded assessment of outcomes, a total of 78 stroke patients will be assigned randomly to either the VR group or the control group. All stroke patients who have upper extremity motor deficits will be tested with functional magnetic resonance imaging (fMRI), electroencephalography (EEG), and clinical evaluation. Clinical assessment and fMRI will be performed three times on each subject. The primary outcome is the change in performance on the Fugl-Meyer Assessment Upper Extremity Scale (FMA-UE). Secondary outcomes are functional independence measure (FIM), Barthel Index (BI), grip strength, and changes in the blood oxygenation level-dependent (BOLD) effect in the ipsilesional and contralesional primary motor cortex (M1) on the left and right hemispheres assessed with resting-state fMRI (rs-fMRI), task-state fMRI (ts-fMRI), and changes in EEG at the baseline and weeks 4 and 8. Discussion This study aims to provide high-quality evidence for the relationship between upper extremity motor function and brain activation in stroke. In addition, this is the first multimodal neuroimaging study that explores the evidence for neuroplasticity and associated upper motor function recovery after VR in stroke patients. Clinical trial registration Chinese Clinical Trial Registry, identifier: ChiCTR2200063425.
Exploring control-value motivational profiles of mathematics anxiety, self-concept, and interest in adolescents

In this study, we identified multidimensional profiles in students’ math anxiety, math self-concept, and math interest using data from a large generalizable sample of 16,547 9th grade students in the United States who participated in the National Study of Learning Mindsets. We also analyzed the extent that students’ profile memberships are associated with related measures such as prior mathematics achievement, academic stress, and challenge-seeking behavior. Five multidimensional profiles were identified: two profiles which demonstrated relatively high levels of interest and self-concept, along with low math anxiety, in line with the tenets of the control-value theory of academic emotions (C-VTAE); two profiles which demonstrated relatively low levels of interest and self-concept, and high levels of math anxiety (again in accordance with C-VTAE); and one profile, comprising more than 37% of the total sample, which demonstrated medium levels of interest, high levels of self-concept, and medium levels of anxiety. All five profiles varied significantly from one another in their association with the distal variables of challenge seeking behavior, prior mathematics achievement, and academic stress. This study contributes to the literature on math anxiety, self-concept, and interest by identifying and validating student profiles that mainly align with the control-value theory of academic emotions in a large, generalizable sample.
DEVELOPING PICTORIAL SPACE: INSTRUCTIONAL STRATEGIES FOR EFFECTIVE STATISTICAL GRAPHICS

PURPOSE The overwhelming premise of visual imagery is that of communication. Images can be visual renditions or representations of idea s, dimensions, and events (Dickinson, 2001). Representing statistical ideas and informati on is a complex task-as Tufte relates, ”all communication between the readers of an image must take place on a twodimensional surface” (1990, p.12). Our purpose for this presentation is to share the i nstructional techniques developed within an undergraduate mathematics cours e designed to teach statistical graphics skills; and describe the development of au thentic assessments to measure student learning and assessment tools (rubrics) for multiva riate statistical graphics.
Improved background representation, ionosonde input and independent verification in experimental ionospheric tomography

The lack of near-horizontal ray paths through the ionosphere poses serious problems for the reconstruction of vertical profiles in ionospheric tomography. Additional information from ionosondes on the bottomside profile has been incorporated into the reconstruction process to provide an improved image, but representation of the topside by means of ionospheric models is limited in certain circumstances. An alternative approach to reproduction of the topside profile is described here. Observations by means of incoherent scatter radars, both in the UK and in Scandinavia, have provided a large database of topside electron densities. These profiles have been normalised and averaged to produce a range of topside shapes. The topsides have been attached to bottomside profiles, obtained using information from ionograms, to create a set of model ionospheres for use in the representation of the background ionosphere in the reconstruction process. The success of the method is demonstrated by means of tomographic images that show improved agreement with independent co-ordinated measurements made by the EISCAT radar in the SP-UK-TOMO mode. Limitations to the use of ionograms in the formation of the bottomside profile are also discussed.
A Survey on SPARQL Query Relaxation under the Lens of RDF Reiﬁcation

SPARQL query relaxation has been used to cope with the problem of queries that produce none or insufﬁcient answers. The goal is to modify these queries to be able to produce alternative results close to those expected in the original query. Existing approaches generally relax the query constraints based on logical relaxations through RDFS entailment and RDFS ontologies. Techniques also exist that use the similarity of instances based on resource descriptions. These relaxation approaches deﬁned for SPARQL queries over RDF triples have proved their efﬁciency. Nevertheless, signiﬁcant challenges arise for query relaxation techniques in the presence of statement-level annotations, i.e., reiﬁcation. In this survey, we overview query relaxation works with a particular focus on issues and challenges posed by representative reiﬁcation models, namely, standard reiﬁcation, named graphs, n-ary relations, singleton properties, and