Miracle-dz/UniFAR-FTUs huggingface dataset:
Cortical Inactivation Does Not Block Response Enhancement in the Superior Colliculus

Repetitive visual stimulation is successfully used in a study on the visual evoked potential (VEP) plasticity in the visual system in mammals. Practicing visual tasks or repeated exposure to sensory stimuli can induce neuronal network changes in the cortical circuits and improve the perception of these stimuli. However little is known about the effect of visual training at the subcortical level. In the present study, we extend the knowledge showing positive results of this training in the rat’s superior colliculus (SC). In electrophysiological experiments, we showed that a single training session lasting several hours induces a response enhancement both in the primary visual cortex (V1) and in the SC. Further, we tested if collicular responses will be enhanced without V1 input. For this reason, we inactivated the V1 by applying xylocaine solution onto the cortical surface during visual training. Our results revealed that SC’s response enhancement was present even without V1 inputs and showed no difference in amplitude comparing to VEPs enhancement while the V1 was active. These data suggest that the visual system plasticity and facilitation can develop independently but simultaneously in different parts of the visual system.
A pragmatic approach to produce theoretical syntheses in ecology

Theoretical syntheses have the role of describing and guiding knowledge generation, and are usually done by enunciating the conceptual bases that guide research in a given field. In fields that develop axiomatically, the conceptual basis can be easily identified in the set of axioms guiding model building. However, ecology does not develop axiomatically but rather pragmatically, i.e., ecologists do not build models based on a predefined set of assumptions (axioms). They rather resort to any information that seems useful to learn about ecological phenomena. Therefore, a theoretical synthesis in ecology cannot rely on the enunciation of axioms; instead, it requires identifying what information and knowledge ecologists use (i.e., what they decide is useful to learn). Here we present an approach for producing theoretical syntheses based on the information/knowledge most frequently used to learn about the world. The approach consists of (i) defining a phenomenon of interest; (ii) defining a collective of scientists studying the phenomenon; (iii) surveying the scientific studies about the phenomenon published by this collective; (iv) identifying the most relevant publications used in these studies; (v) identifying how the studies refer to the most relevant publications; (vi) synthesizing what is being used by this collective to learn about the phenomenon. We implemented the approach in a case study on the phenomenon of ecological succession, defining the collective as the scientists currently studying succession. We identified three propositions that synthesize the views of the defined collective about succession. The theoretical synthesis revealed that there is no clear division between “classical” and “contemporary” succession models, and that neutral models are being used to explain successional patterns alongside with models based on niche assumptions.By implementing the pragmatic approach in a case study, we show that it can be successfully used to produce syntheses describing the conceptual bases of a field, which have the potential to guide knowledge generation. As such, these syntheses fulfil the roles ascribed to scientific theories in the epistemological literature.
Decoding Neural Responses to Motion-in-Depth Using EEG

Two stereoscopic cues that underlie the perception of motion-in-depth (MID) are changes in retinal disparity over time (CD) and interocular velocity differences (IOVD). These cues have independent spatiotemporal sensitivity profiles, depend upon different low-level stimulus properties, and are potentially processed along separate cortical pathways. Here, we ask whether these MID cues code for different motion directions: do they give rise to discriminable patterns of neural signals, and is there evidence for their convergence onto a single ‘motion-in-depth’ pathway? To answer this, we use a decoding algorithm to test whether, and when, patterns of electroencephalogram (EEG) signals measured from across the full scalp, generated in response to CD- and IOVD-isolating stimuli moving towards or away in depth can be distinguished. We find that both MID cue type and 3D-motion direction can be decoded at different points in the EEG timecourse and that direction decoding cannot be accounted for by static disparity information. Remarkably, we find evidence for late processing convergence: IOVD motion direction can be decoded relatively late in the timecourse based on a decoder trained on CD stimuli, and vice versa. We conclude that early CD and IOVD direction decoding performance is dependent upon fundamentally different low-level stimulus features, but that later stages of decoding performance may be driven by a central, shared pathway that is agnostic to these features. Overall, these data are the first to show that neural responses to CD and IOVD cues that move towards and away in depth can be decoded from EEG signals, and that different aspects of MID-cues contribute to decoding performance at different points along the EEG timecourse.
Animal personality adds complexity to the processes of adaptive divergence and speciation

Divergent selection is a powerful driver of speciation and has been widely studied in relation to the physical characters of organisms. Because evolution of behavioural traits may contribute to evolutionary processes, we explored how consistent variation in behaviours may affect the process of adaptive divergence and speciation. We studied whether two sympatric morphs of Arctic charr (Salvelinus alpinus) have recently evolved genetically-based differences in personality that conform to their respective ecological niches, and whether these differences contribute to reproductive isolation by generating maladaptive hybrid behaviours. Studying three aspects of behavioural variation (average trait value, consistent individual differences and trait covariance), we assessed the sociality and risk-taking propensity of hybrid and pure-morph offspring reared in common conditions. Contrary to expectations, the two morphs did not differ in the average values of these traits but showed different behavioural syndromes (trait covariances). While the hybrids did not differ from either morph in their average behavioural responses, they showed less individual consistency in these behaviours and a different set of behavioural syndromes. Differences between morphs and their hybrids in other behavioural aspects than their average behavioural responses suggest that our understanding of speciation processes can benefit from an integrative view of behavioural variation.
Association between bone discordance and dietary pattern among Iranian postmenopausal women

Introduction: Bone discordance is new challenge in order to diagnosis of osteoporosis especially among postmenopausal women, there are many causes have been proposed for occurrence of this phenomenon. Objective: This study was conducted to evaluate the effect of major dietary pattern on bone discordance. Design: Cross-sectional study Settings: The volunteer had completed demographic data. Dietary intake was assessed with a 147- item food frequency questionnaire (FFQ). Dietary patterns were created by factor analysis from 25 food groups. Dual-energy x-ray absorptiometry (DXA) was performed on the lumbar (L2-L4) and hip for cases. Subjects: We designed a cross-sectional survey of 258 postmenopausal women From June 2015 to February 2016. Results: Three major dietary patterns were identified by using factor analysis based on baseline intake data: Unhealthy, Mediterranean and Western diet. After analysis we found 53.4% were concordance and 42.8% (4% were in the major discordance group) of participants were discordance. We found discordance group were younger, and obese participants were more talented to be in the major discordance group. We found inversely relationship between unhealthy dietary pattern and hip and lumbar Z score, while there was positive relationship between Mediterranean dietary pattern and hip BMD. No associations were found between dietary pattern and bone discordance. Conclusions: This study concluded that bone discordance was directly related to obesity in other words, and obese and younger women were at risk of bone discordance. Unhealthy and Mediterranean dietary pattern were negatively and positively related to bone density among postmenopausal women. This study showed, there was no association between any bone discordance situation and dietary pattern.
De novo transcriptome assembly, annotation, and identification of low-copy number genes in the flowering plant genus Silene (Caryophyllaceae)

Phylogenetic methods that rely on information from multiple, unlinked genes have recently been developed for resolving complex situations where evolutionary relationships do not conform to bifurcated trees and are more adequately depicted by networks. Such situations arise when successive interspecific hybridizations in combination with genome duplications have shaped species phylogenies. Several processes such as homoeolog loss and deep coalescence can potentially hamper our ability to recover the historical signal correctly. Consequently the prospect of reconstructing accurate phylogenies lies in the combination of several low-copy nuclear markers that when, used in concert, can provide homoeologs for all the ancestral genomes and help to disentangle gene tree incongruence due to deep coalescence events. Expressed sequence tag (EST) databases represent valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. The genus Silene L. is a prime example of a plant group whose evolutionary history involves numerous events of hybridization and polyploidization. As for many groups there is currently a shortage of low-copy nuclear markers, for which phylogenetic usefulness has been demonstrated. Here, we present two EST libraries for two species of Silene that belong to large phylogenetic groups not previously investigated with next generation technologies. The assembled and annotated transcriptomes are used for identifying low copy nuclear regions, suitable for sequencing.
An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

Cellular biology has a uniformity not shared amongst viruses. This is perhaps best exemplified by negative-sense RNA viruses that encode their genetic material as a ribonucleoprotein complex composed of genome, RNA-dependent RNA polymerase, and the nucleoprotein. Here we demonstrate that limiting nucleoprotein availability not only universally culminates in a replicative catastrophe for negative-sense RNA viruses, but it results in the production of aberrant genomic material and induction of the interferon-based host defenses. This dynamic illustrates the tremendous stress imposed on negative-sense RNA viruses during replication as genomic products accumulate in an environment that requires an increasing demand on nucleoprotein availability. We show that limiting NP by RNA interference or drug targeting blocks replication and primes neighboring cells through the production of interferon. Together, these results demonstrate that the nucleoprotein represents the Achilles heel of the entire phylum of negative-sense RNA viruses. Here we establish this principle for a diverse collection of human pathogens and propose that the nucleoprotein should be a primary target for the development of future antiviral drugs. HIGHLIGHTS Limited levels of NP result in production of defective viral genomes Defective viral genomes and viral antagonists are key determinants of the host antiviral response The host response and defective viral genome generation further exasperate NP availability NP is an optimal drug target for the whole phylum of negative-sense RNA viruses
Loss of Hem1 disrupts macrophage function and impacts on migration, phagocytosis and integrin-mediated adhesion

The hematopoietic-specific protein 1 (Hem1) comprises an essential subunit of the WAVE Regulatory Complex (WRC) in immune cells. WRC has a fundamental role in Arp2/3 complex activation and the protrusion of branched actin networks in motile cells. Hem1 deficiency leads to suppression of the entire WRC in immune cells. Defective WRC function in macrophages results in loss of lamellipodia and migration defects. Moreover, phagocytosis, commonly accompanied by lamellipodium protrusion during cup formation, is altered in Hem1 null cells concerning frequency and efficacy. When analyzing cell spreading, adhesion and podosome formation, we found that Hem1 null cells are capable, in principle, of podosome formation and consequently, do not show any quantitative differences in extracellular matrix degradation. Their adhesive behavior, however, was significantly altered. Specifically, adhesion as well as de-adhesion of Hem1 null cells was strongly compromised, likely contributing to the observed reduced efficiency of phagocytosis. In line with this, phosphorylation of the prominent adhesion component paxillin was diminished. Non-hematopoietic somatic cells disrupted in expression for both Hem1 and its ubiquitous orthologue Nck-associated protein 1 (Nap1) or the essential WRC components Sra-1/PIR121 did not only confirm defective paxillin phosphorylation, but also revealed that paxillin turnover in focal adhesions is accelerated in the absence of WRC. Finally, adhesion assays using platelets lacking functional WRC as model system unmasked radically decreased αIIbβ3 integrin activation. Our results thus demonstrate that WRC-driven actin networks impact on integrin-dependent processes controlling formation and dismantling of different types of cell-substratum adhesion. One sentence summary Interference of Hem1 function in mice and cells uncovers a hitherto unrecognized role in integrin-mediated cell adhesion that is crucial for macrophage function and connects to recently discovered immunodeficiencies in patients carrying Hem1 mutations.
Multi-scale analysis of schizophrenia risk loci: Integrating centenarian genomes and spatio-temporal expression profiles suggests the need for adjunctive therapeutic interventions for neuropsychiatric disorders

Schizophrenia (SZ) is a debilitating mental illness with multigenic etiology and significant heritability. Despite extensive genetic studies the molecular etiology has remained enigmatic. A recent systems biology study suggested a protein-protein interaction (PPI) network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominantly during adolescence often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan atlas data allowed us to re-examine the genes present in SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and non-psychiatric ExAC database allowed us to identify the variants of criticality. The expression of SZ candidate genes responsible for cognition and disease onset were studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene-expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by the previous interactome study to 10 proteins. These proteins belonging to 81 biological pathways, are targeted by 34 known FDA approved drugs that have distinct potential for treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to Celecoxib pharmacodynamics, Gα signaling and cGMP-PKG signaling pathways, that are non-specific to schizophrenia etiology.
Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. High-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multilayer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to allow other omics data input and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research. The open-source tool is freely available at http://www.chomics. org.
Different temporal trends in vascular plant and bryophyte communities along elevational gradients over four decades

Despite many studies showing biodiversity responses to warming, the generality of such responses across taxonomic groups remains unclear. Very few studies have tested for evidence of bryophyte community responses to warming, even though bryophytes are major contributors to diversity and functioning in many ecosystems. Here we report an empirical study comparing long-term change of bryophyte and vascular plant communities in two sites with contrasting long-term warming trends, using “legacy” botanical records as a baseline for comparison with contemporary resurveys. We hypothesized that ecological changes would be greater in sites with a stronger warming trend, and that vascular plant communities, with narrower climatic niches, would be more sensitive than bryophyte communities to climate warming. For each taxonomic group in each site, we quantified the magnitude of changes in species’ distributions along the elevation gradient, species richness, and community composition. We found contrasted temporal changes in bryophyte vs. vascular plant communities, which only partially supported the warming hypothesis. In the area with a stronger warming trend, we found a significant increase of local diversity and beta-diversity for vascular plants, but not for bryophytes. Presence absence data did not provide sufficient power to detect elevational shifts in species distributions. The patterns observed for bryophytes are in accordance with recent literature showing that local diversity can remain unchanged despite strong changes in composition. Regardless of whether one taxon is systematically more or less sensitive to environmental change than another, our results suggest that vascular plants cannot be used as a surrogate for bryophytes in terms of predicting the nature and magnitude of responses to warming. Thus, to assess overall biodiversity responses to global change, abundance data from different taxonomic groups and different community properties need to be synthesized.