Miracle-dz/UniFAR-FTUs huggingface dataset:
Potato genetical genomics: investigating the genetic basis of primary metabolism and its relationship to the phenotype

Primary metabolism is essential for plant growth and survival and it is therefore involved in all physiological processes of the plant. In the past years the advancements in large-scale and high-throughput technologies have enhanced our ability to characterize the plant metabolome. The development of methods for the simultaneous analysis of many different plant metabolites and the necessary software for subsequent data analysis have further expanded the possibilities to investigate plant responses from a system-oriented perspective. This allows the comparison of genetic and phenotypic variation at different molecular levels, enabling us to find associations between genotype and phenotype and their intermediate levels of information transduction. Metabolomics has become increasingly important for the characterization of the metabolic status of plants under different environmental and genetic perturbations. The economic importance of potato and the increasing availability of genetic and molecular resources have stimulated research on many different aspects of the physiology of this crop and the regulation of complex traits. We used the available tools to explore the genetic basis of the composition and content of primary metabolites in a potato population. In this research, the possibilities to combine metabolite profiling with genetic information are explored to identify the genetic factors determining primary metabolism and to infer links between metabolites and agronomic phenotypes.
Structural and Functional Principles of the Small Heat Shock Protein alpha-Crystallin

Alpha-crystallins are molecular chaperones which belong to the small heat shock protein family. They contribute to the maintenance of the cellular protein homeostasis by binding to partially unfolded substrate proteins preventing deleterious protein aggregation. A remarkable feature of alpha-crystallins is the formation of dynamic oligomers with a variable number of subunits. In this work, the molecular architecture of these complexes was elucidated using different biochemical and biophysical methods. Furthermore, the functional principles of the chaperone activity of alpha-crystallins were studied. These results show that the N-terminal domain provides a phosphorylation-controlled switch for oligomerization and activation of substrate binding. In addition, the release and refolding of denatured substrates by the interplay between alpha-crystallins and the Hsp70 system was revealed.
Interface modification of SnO2 layer using p–n junction double layer for efficiency enhancement of perovskite solar cell

In this work, interface modification of SnO2 layer using p–n junction double layer is investigated for the efficiency enhancement of perovskite solar cell (PSC). For the double layer, a Sn additive layer was applied on a SnO2 layer by using the DC magnetron sputtering technique at various deposition times. The highest power conversion efficiency of 15.11% is obtained for PSC with a SnOx additive layer at 5 s sputtering time, compared to 12.89% for the best PSC without the additive layer. The effect of the SnOx additive layer on PSCs at optimum sputtering time is further explored via the photoconversion properties of both optical and electrical properties. From the results, it is found that the SnOx additive layer is essential for efficiency enhancement by forming the p-n junction with a SnO2 electron transporting layer (ETL) and modifying the interface between the ETL and the perovskite layer. The p-n junction of the ETL is observed via the diode-like behavior of I–V characteristics. The interface modification can enhance the PSC efficiency by improving the quality of the perovskite layer due to the larger grain size and higher absorbance, and by improving the charge transfer. The faster photogenerated charge transfer is confirmed by lower PL intensity and the shorter charge transfer lifetime is confirmed by the fitted open-circuit voltage decay. In addition, the SnOx additive layer can also eliminate the hysteresis effect of PSCs. This interface modification technique for PSC efficiency enhancement could be further explored for other ETLs.
Optogenetics reprogramming of planktonic cells for biofilm formation

Single-cell behaviors play essential roles during early-stage biofilms formation. In this study, we evaluated whether biofilm formation could be guided by precisely manipulating single cells behaviors. Thus, we established an illumination method to precisely manipulate the type IV pili (TFP) mediated motility and microcolony formation of Pseudomonas aeruginosa by using a combination of a high-throughput bacterial tracking algorithm, optogenetic manipulation and adaptive microscopy. We termed this method as Adaptive Tracking Illumination (ATI). We reported that ATI enables the precise manipulation of TFP mediated motility and microcolony formation during biofilm formation by manipulating bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) levels in single cells. Moreover, we showed that the spatial organization of single cells in mature biofilms can be controlled using ATI. Thus, the established method (i.e., ATI) can markedly promote ongoing studies of biofilms.
Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays considerably extended the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species confirms previous findings in model animals. Overall, these results emphasize the value of FAANG for research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.
Evidence for Allopolyploid Speciation in Nymphoides (Menyanthaceae)

Abstract The floating-leaved aquatic plant genus Nymphoides includes diploid and polyploid species that are distributed worldwide. Prior studies found widespread incongruence between nuclear and plastid phylogenies, and this has prevented the construction of a unified phylogenetic hypothesis for the genus. In order to examine whether phylogenetic incongruence resulted from ancestral polyploidization events, we obtained DNA sequence data from two nuclear loci, phytoene desaturase (PDS) and transmembrane nine (TMN1), as well as the plastid trnT—trnF region. Multiple divergent copies of the nuclear genes were recovered from several species, and species with the most divergent copies were inferred to have originated through allopolyploidization. Our data support a scenario in which three groups of species descended from allopolyploidization events: a clade of North American species (N. aquatica and N. cordata), a clade of neotropical species (N. fallax, N. grayana, and N. humboldtiana), and the Australian species N. montana. Trees constructed using novel nuclear gene data also were incongruent with previously generated nuclear and plastid data, however we were able to combine data from four independently evolving regions (PDS, TMN1, nuclear internal transcribed spacer, and plastid) to generate a single species tree that received strong support at several nodes. Sources of incongruence on the species tree involved a relatively small subset of species. Overall, the increased data from nuclear loci have dramatically improved our understanding of the Nymphoides phylogeny.
Summer season induced heat stress impact on the expression patterns of different toll-like receptor genes in Malabari goats

Abstract The study was conducted with the primary objective of establishing the impact of heat stress on the expression pattern of different toll-like-receptors (TLRs) in Malabari goats. The study was conducted for a period of 45 days using twelve Malabari goats. The goats were randomly allocated into two groups: MC (n = 6; Malabari control) and MHS (n = 6; Malabari heat stress). At the end of study, all 12 animals were slaughtered and their mesenteric lymph node (MLN) tissues were collected for gene expression. Heat stress significantly (p < 0.05) down regulated TLR1, TLR4, TLR5 and TLR6 and significantly increased (p < 0.05) TLR2 expression pattern. A negative correlation (p < 0.01) was also established between THI and different TLRs except TLR3, TLR7 and TLR10. The study indicated that TLR2 could serve as ideal immunological marker for establishing the superior thermo-tolerance ability of Malabari breed in terms of maintaining the immune status during heat stress challenges.
Model selection for the North American Breeding Bird Survey: A comparison of methods

ABSTRACT The North American Breeding Bird Survey (BBS) provides data for >420 bird species at multiple geographic scales over 5 decades. Modern computational methods have facilitated the fitting of complex hierarchical models to these data. It is easy to propose and fit new models, but little attention has been given to model selection. Here, we discuss and illustrate model selection using leave-one-out cross validation, and the Bayesian Predictive Information Criterion (BPIC). Cross-validation is enormously computationally intensive; we thus evaluate the performance of the Watanabe-Akaike Information Criterion (WAIC) as a computationally efficient approximation to the BPIC. Our evaluation is based on analyses of 4 models as applied to 20 species covered by the BBS. Model selection based on BPIC provided no strong evidence of one model being consistently superior to the others; for 14/20 species, none of the models emerged as superior. For the remaining 6 species, a first-difference model of population trajectory was always among the best fitting. Our results show that WAIC is not reliable as a surrogate for BPIC. Development of appropriate model sets and their evaluation using BPIC is an important innovation for the analysis of BBS data.
Zeylanidium as Pollution Indicators: Live Sensors to Water Parameters

Podostemaceae family is well known as a group of aquatic angiosperms with enigmatic characters. The present work was performed to trace ecological aspects, phenology, water analysis and phylogenetic analysis of the genus Zeylanidium, in order to establish the uniqueness of the species in the fresh water habitats S-1 (9.9559°N, 76.8339°E) and S-2 (10.0538°N, 76.8294°E). Through water analysis it is revealed that the species of plants could be used as an indicator of pollution as they are present in very sensitive area of running fresh water. The phenology of the taxa understudy paved light to the co-existence of Zeylanidium maheshwari and Zeylanidium lichenoides. The data on comparison of molecular and phylogenic tree reveal that the species are highly related genetically for a sustainable coexistence.
The heterotrimeric G protein г Stgg1 is required for conidiation, secondary metabolite production and pathogenicity of Setosphaeria turcica

ABSTRACT Heterotrimeric G proteins are best known for their role in the transduction of extracellular signals to various downstream effectors. G proteins in higher eukaryotes are intensively studied; however, their roles in foliar pathogens are still elusive. In this study, we cloned the gene Stgg1 encoding G protein γ subunit in Setosphaeria turcica and investigated its function by RNA interference technology. Three independent Stgg1 targeted RNAi mutants R3, R5 and R6 with diverse silencing efficiency were generated. Knock-down of Stgg1 resulted in a significant reduction in mRNA levels of the genes encoding Gα (Stga1, Stga2, Stga3) but not for Gβ (Stgb1). Stgg1 RNAi mutants exhibited significantly elongated hyphal cells with blocked conidium production. In addition, Stgg1 RNAi mutants all appeared in lighter colony colour compatible with inhibited secondary metabolites. Further assays demonstrated that Stgg1 was required for biosynthesis of melanin and HT-toxin activity. Furthermore, down-regulation of Stgg1 largely inhibited the inflection capacity. Thus, we proposed that Stgg1 played crucial roles in conidiation, secondary metabolite production and pathogenicity of S. turcica and is, therefore, an ideal target for drug design against foliar pathogens.
BIODIVERSITY STATE OF ALGERIAN SHEEP BREEDS

The richness of the variability of the sheep genetic resources is untapped. We have noted the presence of 12 sheep breeds in Algeria such as Ouled Djellal, Rembi, Hamra, Berber, Barbarine, D'man, Sidaou, Tadmit, Tazegzawt, Ifilene, Srandi and Daraa, which are well adapted to the conditions of the environments. Unfortunately, anarchic crossings lead to dispersion and an erosion of the genetic capital of the breeds, the increase of consanguinity in the herds and a decrease of the returns of the farms. The medium-term risk is the absorption of certain «breeds" by others, and the loss of certain characters that make the specificity of our breeds. In addition, the documentation on the diversity of sheep breeds in Algeria is minimal or absent, so several breeds require a phenotypic and zootechnical description to know their performance. This document describes the sheep genetic resources present in Algeria and the diversity between them based on surveys that have been carried out for more than 17 years, in 40 wilayas, based on the phenotypic characterization of these "breeds" in their cradles, in order to make an updated breed distribution map and a new breed classification.
Resilient Leadership as Paradox Work: Notes from COVID-19

In such situations there is always the expectation that ‘something has to be said’ in response to commentators and authorities calling for a clear unambiguous direction (in politics, in business, and in communities) and that it is best said by ‘the leader’ Contradictory tensions (such as anticipation/adaptation;solidity/flexibility;efficiency/redundancy;boldness/prudence;compassion/hardiness;profit/purpose;updating information/being aware that information may not mean knowing;courage to make unpopular decisions/humility to listen the crowd, etc ) must be synthesized into an overarching whole to characterize resilient leadership The COVID-19 pandemic has tested the capacity of leaders to be both firm and flexible, gritty and empathic, tough and compassionate, directive and empowering, willing to set the pace and to be responsive to the emerging realities, steering and sharing leadership, leading while being led by experts (Wilson, 2020);in other words, conducting paradox work in the purposeful balancing of interdependent yet opposing forces (Smith & Lewis, 2011) The COVID-19 lockdown is providing countless opportunities for employing ‘generative doubt’ and the ability to ‘learn to unlearn and learn’, as well as other expressions of paradox work: engaging the base while offering clear direction from the top;focusing on central processes while scrutinizing the more opaque periphery in order to stay alert to unexpected developments;making short-term improvised decisions while considering long-term implications;providing flexibility for adapting to changing circumstances while maintaining control;conducting deliberate search while being open to serendipitous emergence
Functional independent components: revealing cortico-cortical, cross-frequency interactions

In its most classical and simple setting, the statistical analysis of functional brain images consists of comparing one group of subjects under two different conditions, or comparing two independent groups of subjects, using voxel-by-voxel statistics with correction for multiple testing. This approach is widely used in almost all brain imaging literature, where the aim is the “localization of brain function”. An alternative approach consists of abandoning the concept that brain function can be localized to a small number of hotspots, and to embrace the notion that brain function is more adequately characterized by the spatio-temporal/frequency distributions of activity. Recently, this concept is becoming popular with the use of independent component analysis (ICA) of fMRI data. In this paper, using insights from a novel field in statistics called “functional data analysis”, a new formulation for the discovery of interaction patterns of brain activity across space, time and frequency is presented. The method is illustrated by comparing EEG data between schizophrenic patients and normal control subjects.
Deformable Quaternion Gabor Convolutional Neural Network For Color Facial Expression Recognition

In facial expression recognition (FER), convolutional neural networks (CNNs) have been shown great capability of learning features. In this paper, we propose a new CNN framework for FER in color images, which incorporates deformable Gabor filters into a quaternion CNN. Deformable Gabor filters reinforce the network’s ability of extracting different orientations of facial wrinkles information. Quaternion CNNs have greater advantages over the regular CNNs in handling the coupling between color channels. The proposed deformable quaternion Gabor convolutional neural network (DQG-CNN) not only learns FER feature representation excellently, but also processes spectral correlation between color channels naturally. Moreover, it can also effectively reduce training complexity compared to other reference models. Experimental results on three benchmark color datasets Oulu-CASIA, MMI, and SFEW, demonstrate that the proposed DGQ-CNN outperforms other state-of-the-art methods clearly.
EEG Power Spectrum Correlates of Working Memory in Children with Learning Disorders

Learning disorders (LD) are diagnosed in children whose academic skills of reading, writing or mathematics are impaired and lagged according to their age, schooling and intelligence. Children with LD experience substantial working memory (WM) deficits, even more pronounced if more than one of the academic skills is affected. We compared the task-related EEG power spectral density of children with LD (n= 23), with a control group of children with good academic achievement (n= 22), during the performance of a WM task. sLoreta was used to estimate the current distribution at the sources, and 18 brain regions of interests (ROIs) were chosen with an extended version of the eigenvector centrality mapping technique. In this way, we lessen some drawbacks of the traditional EEG at the sensor space by an analysis at the brain sources level over data-driven selected ROIs. Results: The LD group showed fewer correct responses at the WM task, an overall slower EEG with more theta activity in all ROIs, less upper-alpha power at posterior areas, and less high-frequency beta activity in frontal areas. We explain these EEG patterns in LD children as indices of an inefficient neural resource management related with a delay in the neural development.
The evaluation of the mitochondrial genomics in Atlantic salmon (Salmo salar)

Abstract The mitochondrial genomic of Atlantic salmon (Salmo salar) was sequenced and deposited in GenBank accession no. LC012541.1. In this study for the evolutionary analysis of Mtgenomic between S. salar and other salmonid species such as S. t. fario, S.t. trutta and S.t. caspius were conducted by using MEGA Software Version 7. The results showed that there is a major homology between S. salar and other salmonids like S.t. fario and S.t. trutta, and we can see it in Figure 1 showing the close relationship between them.
Population coupling predicts the plasticity of stimulus responses in cortical circuits

Long-term imaging of sensory cortex reveals a diverse range of stimulus response stability: some neurons retain stimulus responses that are stable over days whereas other neurons have highly plastic stimulus responses. Using a recurrent network model, we explore whether this observation could be due to an underlying diversity in the synaptic plasticity of neurons. We find that, in a network with diverse learning rates, neurons with fast rates are more coupled to population activity than neurons with slow rates. This phenomenon, which we call a plasticity-coupling link, surprisingly predicts that neurons with high population coupling exhibit more long-term stimulus response variability than neurons with low population coupling. We substantiate this prediction using recordings from the Allen Brain Observatory which track the orientation preferences of 15,000 neurons in mouse visual cortex. In agreement with our model, a neuron’s population coupling is correlated with the plasticity of its orientation preference. Finally, we show that high population coupling helps plastic neurons alter their stimulus preference during perceptual learning, but hinders the ability of stable neurons to provide an instructive signal for learning. This suggests a particular functional architecture: a stable ‘backbone’ of stimulus representation formed by neurons with slow synaptic plasticity and low population coupling, on top of which lies a flexible substrate of neurons with fast synaptic plasticity and high population coupling.
Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake

The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria, Nitrospirae, Chloroflexi, Firmicutes and Ignavibacteriae. The dominant groups of archaea consisted of Euryarchaeota, Woesearchaeota DHVEG-6, Bathyarchaeota and WSA2. Lastly, the meta-analysis results highlighted that the low TOC (LT) prokaryotic community structure is larger and more complex compared to moderate TOC (MT). On the whole, the prokaryotic community structure is obviously distinct among groups with different TOC levels, and LT communities may interact with each other strongly in the Dianchi Lake sediment. This study can provide more insights into prokaryotic assemblages in eutrophic lake sediment and provide suggestions for the restoration and maintenance of sediment ecosystems.