Miracle-dz/UniFAR-FTUs huggingface dataset:
Achromatic body markings as a widespread visual mechanism across group living animals

Grouping is a widespread form of predator defense, with individuals in groups often performing evasive collective movements in response to predators9 attacks. Individuals in these groups use behavioral rules to coordinate their movements, with visual cues about neighbors9 positions and orientations informing movement decisions. Although the exact visual cues individuals use to coordinate their movements with neighbors have not yet been decoded, some studies have suggested that stripes, lines or other body patterns may act as conspicuous conveyors of movement information that could promote coordinated group movement, or promote dazzle camouflage, thereby confusing predators. We used phylogenetic logistic regressions to test whether the contrasting achromatic body patterns of four different taxa vulnerable to predation, including species within two orders of birds (Anseriformes and Charadriiformes), a suborder of Artiodactyla (the ruminants) and several orders of marine fish (predominantly Perciformes) were associated with group living. Contrasting body patterns were significantly more prevalent in social species, and tended to be absent in solitary species or species less vulnerable to predation. We suggest that body patterns taking the form of white lines on dark backgrounds, or vice versa, provide a widespread mechanism across taxa that serves either to inform conspecifics of neighbors9 directional movement, or to confuse predators, when moving in groups. Detection and processing of patterns and of motion in the visual channel is essentially colourblind. That diverse animal taxa with widely different vision systems (including di-, tri- and tetrachromats) appear to have converged on a similar use of achromatic patterns is therefore expected given signal-detection theory. This hypothesis would explain the convergent evolution of conspicuous coloration patterns as an antipredator mechanism in numerous vertebrate species.
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes

Gene prioritisation at GWAS loci necessities careful assembly and examination of different types of molecular evidence to arrive at a set of plausible candidates. In many human traits, common small-effect mutations may subtly dysregulate the function of the very same genes which are impacted by rare, large-effect mutations causing Mendelian disease of similar phenotype. However, information on gene-Mendelian disease associations, rare pathogenic mutations driving the disease, and the disease phenotype ontology is dispersed across many data sources and does not integrate easily with enrichment analysis. MendelVar is a new webserver facilitating transfer of knowledge from Mendelian disease research into interpretation of genetic associations from GWAS of complex traits. MendelVar allows querying of pre-defined or LD-determined genomic intervals against a comprehensive integrated database to find overlap with genes linked to Mendelian disease. Next, MendelVar looks for enrichment of any Human Phenotype Ontology, Disease Ontology and other ontology/pathway terms associated with identified Mendelian genes. In addition, MendelVar provides a list of all overlapping pathogenic and likely pathogenic variants for Mendelian disease sourced from ClinVar. Inclusion of information obtained from MendelVar in post-GWAS gene annotation pipelines can strengthen the case for causal importance of some genes. Moreover, as genes with Mendelian disease evidence may make for more successful drug targets, this may be particularly useful in drug discovery pipelines. Taking GWAS summary statistics for male-pattern baldness, intelligence and atopic dermatitis, we demonstrate the use of MendelVar in prioritizing candidate genes at these loci which are linked to relevant enriched ontology terms. MendelVar is freely available at https://mendelvar.mrcieu. ac.uk/
Extracellular levels of glucose in the hippocampus and striatum during maze training for food or water reward in male rats

Peripheral and central administration of glucose potently enhance cognitive functions. The present experiments examined changes in brain extracellular glucose levels while rats were trained to solve hippocampus-sensitive place or striatum-sensitive response learning tasks for food or water reward. During the first minutes of either place or response training, extracellular glucose levels declined in both the hippocampus and striatum, an effect not seen in untrained, rewarded rats. Subsequently, glucose increased in both brain areas under all training conditions, approaching asymptotic levels ∼15-25 min into training. Compared to untrained-food controls, training with food reward resulted in significant glucose increases in the hippocampus but not striatum; striatal glucose levels exhibited large increases to food intake in both trained and untrained groups. In rats trained to find water, glucose levels increased significantly above the values seen in untrained rats in both hippocampus and striatum. In contrast to results seen with lactate measurements, the magnitude of training-related increases in hippocampus and striatum glucose levels did not differ by task under either reward condition. The decreases in glucose early in training might reflect an increase in brain glucose consumption, perhaps triggering increased brain uptake of glucose from blood, as evident in the increases in glucose later in training. Together with past findings measuring lactate levels under the same conditions, the initial decreases in glucose may also stimulate increased production of lactate from astrocytes to support neural metabolism directly and/or to act as a signal to increase blood flow and glucose uptake into the brain. Highlights Glucose levels in hippocampus and striatum decrease at the start of training. Glucose levels increase in both brain areas later in training. Glucose changes in both brain areas were similar for place and response tasks. Glucose levels responded similarly to training for either food and water rewards. Early decreases in glucose may trigger increased production astrocytic lactate.
A quantitative measure of functional redundancy in microbial ecosystems

Although functional redundancy has received increased attention in the microbial ecology literature, no quantitative functional redundancy measurement is currently available which compares multiple communities and integrates of 9omics data rather than phenotypic traits. Here, we propose an approach for quantifying functional redundancy that use 9omics data. This approach, termed trait contribution evenness (TCE), is based on traditional measures of community diversity. We measure functional redundancy of a trait within a community as the evenness in relative contribution of that trait among taxa within the community. This definition has several appealing properties including: TCE is an extension of established diversity theory, functional redundancy measurements from communities with different richness and relative trait contribution by taxa are easily comparable, and any quantifiable trait data (genes copies, protein abundance, transcript copies, respiration rates, etc.) is suitable for analysis. Resilience of a trait to taxa extinctions is often viewed as an ecological consequence of traits with high functional redundancy. We demonstrate that TCE functional redundancy is closely and monotonically related to the resilience of a trait to extinctions of trait-bearing taxa. Finally, to illustrate the applicability of TCE, we analyzed the functional redundancy of eight nitrogen-transforming pathways using 2,631 metagenome-assembled genomes from 47 TARA Oceans sites. We found that the NH4+ assimilation pathway was the most functionally redundant (0.6 to 0.7) while nitrification had the lowest functional redundancy (0 to 0.1). Here, TCE functional redundancy addresses shortfalls of other functional redundancy measurements by providing a generalizable, quantitative, and comparable functional redundancy measurement.
An Unsupervised Algorithm for Host Identification in Flaviviruses

Early characterization is essential to control the spread of emerging viruses, such as the Zika Virus outbreak in 2014. A major challenge is the identification of potential hosts for novel viruses. We introduce an algorithm to identify the host range of a virus from its raw genome sequence that will be a useful tool to understand host-virus relationships.
Adherens junction serves to generate cryptic lamellipodia required for collective migration of epithelial cells

Collective migration of epithelial cells plays crucial roles in various biological processes such as cancer invasion. In migrating epithelial sheets, leader cells form lamellipodia to advance, and follower cells also form similar motile apparatus at cell-cell boundaries, which are called cryptic lamellipodia (c-lamellipodia). Using adenocarcinoma-derived epithelial cells, we investigated how c-lamellipodia are generated, and found that they sporadically grew from Ecadherin-based adherens junctions (AJs). WAVE and Arp2/3 complexes were localized along the AJs, and silencing them not only interfered with c-lamellipodia formation but also prevented follower cells from trailing the leaders. Disruption of AJs by removing αE-catenin resulted in uncontrolled c-lamellipodia growth, and this was brought about by myosin II activation and the resultant contraction of AJ-associated actomyosin cables. Additional observations indicated that c-lamellipodia tended to grow at mechanically weak sites of the junction. We conclude that AJs not only tie cells together but also generate c-lamellipodia by recruiting actin regulators, enabling epithelial cells to undergo ordered collective migration.
A Timescale for the Radiation of Photosynthetic Eukaryotes

Oxygenic photosynthesis is considered the most important evolutionary innovation in the history of Earth. It depends on two photosystems, responsible for the photolysis of water and the reduction of carbon dioxide. Oxygen and carbohydrates are released at the end of the reaction. Extraordinary, the oxygen released created the stratospheric ozone layer, and transformed the ocean chemistry, whereas the carbohydrates are the primary source of energy for complex cells. Several lines of evidence indicate the photosynthesis arose in the ancestors of cyanobacteria. It was spread over some eukaryotes by the acquisition of a free-living cyanobacterium, which evolved into photosynthetic plastid, the chloroplast. The timing of the chloroplast emergence is still controversy. Estimated ages range from 600 to 2100 million years ago (Mya) in accordance to previous studies. The aim of this study is to clarify several aspects of the origin and diversification of photosynthetic eukaryotes. For this purpose, we utilized a data set based on 27 protein-coding genes from genomes of cyanobacteria and photosynthetic eukaryotes, more genes than other papers that also utilized plastid genes, and performed the Bayesian analysis method to estimate the divergence times of the photosynthetic eukaryotes. Results showed photosynthetic eukaryotes emerged Late Mesoproterozoic about 1342 Mya. The Early Proterozoic oceans did not have adequate conditions for eukaryotes, because chemical elements such as zinc and molybdenum were at reduced concentrations, and they are essential to the formation of eukaryotic proteins.
A neural representation of invisibility: when stimulus-specific neural activity negatively correlates with conscious experience

Although visual awareness of an object typically increases neural responses, we identify a neural response that increases prior to perceptual disappearances, and that scales with the amount of invisibility reported during perceptual filling-in. These findings challenge long-held assumptions regarding the neural correlates of consciousness and entrained visually evoked potentials, by showing that the strength of stimulus-specific neural activity can encode the conscious absence of a stimulus. Significance Statement The focus of attention and the contents of consciousness frequently overlap. Yet what happens if this common correlation is broken? To test this, we asked human participants to attend and report on the invisibility of four visual objects which seemed to disappear, yet actually remained on screen. We found that neural activity increased, rather than decreased, when targets became invisible. This coincided with measures of attention that also increased when stimuli disappeared. Together, our data support recent suggestions that attention and conscious perception are distinct and separable. In our experiment, neural measures more strongly follow attention.
Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen

Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, including human acute myeloid leukemia (AML) and subtypes of acute lymphoblastic leukemia (ALL). HOXA9 overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding of HOXA9 regulation in leukemia is limited, hindering development of therapeutic strategies to treat HOXA9-driven leukemia. To mitigate these challenges, we generated the first HOXA9-mCherry knock-in reporter in an MLL-rearranged (MLLr) B-ALL cell line to dissect HOXA9 regulation. By utilizing the reporter and CRISPR/Cas9 mediated screens, we identified transcription factors controlling HOXA9 expression, including a novel regulator, USF2 and its homolog USF1. USF1/USF2 depletion significantly down-regulated HOXA9 expression and impaired MLLr leukemia cell proliferation. Ectopic expression of HOXA9-MEIS1 fusion protein rescued the impaired leukemia cell proliferation upon USF2 loss. Cut&Run analysis revealed the direct occupancy of USF2 onto HOXA9 promoter in MLLr leukemia cells. Collectively, the HOXA9 reporter facilitated the functional interrogation of the HOXA9 regulome and has advanced our understanding of the molecular regulation network in HOXA9-driven leukemia.
Structural basis for active-site probes targeting Staphylococcus aureus serine hydrolase virulence factors

Staphylococcus aureus is a major cause of infection in the community and in hospitals. Serine hydrolases play key roles in bacterial homeostasis, in particular biofilms. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fphs), which contribute to virulence of S. aureus in the biofilm niche. Here we report structures of the putative tributyrin esterase FphF, alone and covalently bound by a substrate analog, and small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. We show that FphF has promiscuous esterase activity. Building from this, we extended our analysis to the wider Fph protein family using homology modeling and docking tools. We predict that other Fph enzymes, including FphB which was linked directly to virulence, may be more specific than FphF. This study provides insight into Fph function and a template for designing new imaging agents, diagnostic probes, and inhibitors to treat S. aureus infections.
Evolution of cross-tolerance to environmental stresses in populations of Drosophila melanogaster selected for increased resistance to cold stress

Empirical studies on the promiscuous species of Drosophila revealed that the laboratory evolution of resistance to a certain type of environmental stress can impact the ability of the organism to resist other kinds of stresses. The mechanisms of resistance to a particular stress are specialized and costly, then, mechanisms of resistance to other stresses can be negatively affected. However, it is also possible that at least a part of the stress resistance mechanisms is generic. With this premise we aimed to understand whether increased resistance to a cold stress can increase resistance to other types of stresses.To address this issue, we used populations of Drosophila melanogaster (D. melanogaster) that have been selected for 57-71 generations for increased resistance to cold shock (−5°C for one hour). We subjected the selected (FSB; selected for cold shock resistance, derived from BRB population) and control FCB; cold shock control, derived from BRB population) populations to a variety of environmental stresses such as cold shock, heat shock, starvation, desiccation and bacterial infection. We found that the compared to FCB populations, FSB populations had higher resistance to heat stress in terms of adult survivorship and mating ability post cold or heat shock. Desiccation resistance was observed higher in FSB females compared to FCB females but no such difference was found in males. We observed that FSB populations had lower starvation resistance relative to FCB populations. There was no difference between FSB and FCB populations in their ability to survive post bacterial infection. Our findings suggest that resistance to heat stress and desiccation (in females) are positively correlated with increased resistance to cold shock. However, resistance to starvation was negatively correlated with increased resistance to cold shock.
An automatic and efficient pulmonary nodule detection system based on multi-model ensemble

Accurate pulmonary nodule detection plays an important role in early screening of lung cancer. Although there are many presented CAD systems based on deep learning for pulmonary nodule detection, these methods still have some problems in clinical use. The improvement of false negatives rate of tiny nodules, the reduction of false alarms and the optimization of time consumption are some of them that need to be solved as soon as possible. In view of the above problems, in this paper, we first propose a novel full convolution segmentation framework for lung cavity extraction in preprocessing stage to solve the time consumption problem of the existing pulmonary nodule detection systems. Furthermore, a 2D-NestedUNet segmentation network and a 3D-RPN detection network is stacked to get the high recall and low false positive rate on nodule candidate extraction, especially the recall of tiny nodules. Finally, a false positive reduction method based on multi-model ensemble is proposed for the further classification of nodule candidates. Our methods are evaluated on several public datasets, LUNA16, LNDb and ChestCT2019, which demonstrated the superior performance of our CAD system.
Network communication models improve the behavioral and functional predictive utility of the human structural connectome

The connectome provides a structural substrate facilitating communication between brain regions. We aimed to establish whether accounting for polysynaptic communication paths in structural connectomes would improve prediction of interindividual variation in behavior as well as increase structure-function coupling strength. Structural connectomes were mapped for 889 healthy adults participating in the Human Connectome Project. To account for polysynaptic signaling, connectomes were transformed into communication matrices for each of 15 different network communication models. Communication matrices were (i) used to perform predictions of five data-driven behavioral dimensions and (ii) correlated to interregional resting-state functional connectivity (FC). While FC was the most accurate predictor of behavior, network communication models, in particular communicability and navigation, improved the performance of structural connectomes. Accounting for polysynaptic communication also significantly strengthened structure-function coupling, with the navigation and shortest paths models leading to 35-65% increases in association strength with FC. Combining behavioral and functional results into a single ranking of communication models positioned navigation as the top model, suggesting that it may more faithfully recapitulate underlying neural signaling patterns. We conclude that network communication models augment the functional and behavioral predictive utility of the human structural connectome and contribute to narrowing the gap between brain structure and function.
Múltiplas Recidivas Oligometastáticas em Doente com Tumor de Pulmão Não-Pequenas Células

Surgical stages of non-small cell lung carcinoma represent only about 20% of all cases. However, 50% of these patients will relapse after surgery, with metastatic disease and dismal prognosis.In some cases, the pattern of relapse is oligometastatic – a limited number of lesions (1-5) on a single organ (oligoprogressive if there is a short interval after surgery). With aggressive local treatment, long survivals have been documented in these patients, suggesting a particular biology. The authors present the case of a young woman with multiple oligoprogressive relapse of a primary pulmonary adenocarcinoma, (breast, skin and central nervous system) two, 12 and 27 months after curative lung surgery, treated locally with surgery and gamma knife, with a long survival and keeping clinically asymptomatic. Received: 09/05/2017 - Accepted: 31/08/2017
Lack of strong selection pressures maintains wide variation in floral traits in a food-deceptive orchid.

BACKGROUND AND AIMS Angiosperms vary remarkably in traits such as colour, size and shape of flowers, yet such variation generally tends to be low within species. In deceptive orchids, however, large variation in floral traits has been described, not only between, but also within populations. Nonetheless, the factors driving variation in floral traits in deceptive orchids remain largely unclear. METHODS To identify determinants of variation in floral traits, we investigated patterns of fruit set and selection gradients in the food-deceptive orchid Orchis purpurea, which typically presents large within-population variation in the colour and size of the flowers. Using long-term data, fruit set was quantified in two populations during sixteen consecutive years (2004-2019). Artificial hand pollination was performed to test the hypothesis that fruit set was pollinator limited and that selfing led to decreased seed set and viability. Annual variation (2016-2019) in selection gradients was calculated for three colour traits (brightness, contrast and the number of spots on the labellum), flower size (spur length, labellum length and width) and plant size (number of flowers, plant height). KEY RESULTS Fruit set was, on average, low (~12%) and severely pollinator limited. Opportunities for selection varied strongly across years, but we found only weak evidence for selection on floral traits. In contrast, there was strong and consistent positive selection on floral display. Selfing led to reduced production of viable seeds and hence severe inbreeding depression (δ = 0.38). CONCLUSION Overall, these results demonstrate that the large variation in flower colour and size that is regularly observed in natural O. purpurea populations is maintained by the consistent lack of strong selection pressures on these traits through time.