Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered leaf elemental composition with climate change is linked to reductions in photosynthesis, growth and survival in a semi‐arid shrubland

Climate change will increase heat and drought stress in many dryland areas, which could reduce soil nutrient availability for plants and aggravate nutrient limitation of primary productivity. Any negative impacts of climate change on foliar nutrient contents would be expected to negatively affect the photosynthetic capacity, water use efficiency and overall fitness of dryland vegetation. We conducted a 4‐year manipulative experiment using open top chambers and rainout shelters to assess the impacts of warming (~2°C, W), rainfall reduction (~30%, RR) and their combination (W + RR) on the nutrient status and ecophysiological performance of six native shrub species of contrasting phylogeny in a semi‐arid ecosystem. Leaf nutrient status and gas exchange were assessed yearly, whereas biomass production and survival were measured at the end of the study. Warming (W and W + RR) advanced shoot growth phenology and reduced foliar macro‐ (N, P, K) and micronutrient (Cu, Fe, Zn) concentrations (by 8%–18% and 14%–56% respectively), net photosynthetic rate (32%), above‐ground biomass production (28%–39%) and survival (23%–46%). Decreased photosynthesis and growth in W and W + RR plants were primarily linked to enhanced nutritional constraints on carbon fixation. Poor leaf nutrient status in W and W + RR plants partly decoupled carbon assimilation from water flux and led to drastic reductions in water use efficiency (WUEi; ~41%) across species. The RR treatment moderately decreased foliar macro‐ and micronutrients (6%–17%, except for Zn) and biomass production (22%). The interactive impacts of warming and rainfall reduction (W + RR treatment) on plant performance were generally smaller than expected from additive single‐factor effects. Synthesis. Large decreases in plant nutrient pool size and productivity combined with increased mortality during hotter droughts will reduce vegetation cover and nutrient retention capacity, thereby disrupting biogeochemical processes and accelerating dryland degradation with impending climate change. Increased macro‐ and micronutrient co‐limitation of photosynthesis with forecasted climate change conditions may offset any gains in WUEi and productivity derived from anthropogenic CO2 elevation, thereby increasing dryland vegetation vulnerability to drought stress in a warmer and drier climate. The generalized reduction in leaf nutrient contents with warming compromises plant nutritional quality for herbivores, with potential cascading negative effects across trophic levels.
Evolutionary and Structural Overview of Human Picornavirus Capsid Antibody Evasion

Picornaviruses constitute one of the most relevant viral groups according to their impact on human and animal health. Etiologic agents of a broad spectrum of illnesses with a clinical presentation that ranges from asymptomatic to fatal disease, they have been the cause of uncountable epidemics throughout history. Picornaviruses are small naked RNA-positive single-stranded viruses that include some of the most important pillars in the development of virology, comprising poliovirus, rhinovirus, and hepatitis A virus. Picornavirus infectious particles use the fecal–oral or respiratory routes as primary modes of transmission. In this regard, successful viral spread relies on the capability of viral capsids to (i) shelter the viral genome, (ii) display molecular determinants for cell receptor recognition, (iii) facilitate efficient genome delivery, and (iv) escape from the immune system. Importantly, picornaviruses display a substantial amount of genetic variability driven by both mutation and recombination. Therefore, the outcome of their replication results in the emergence of a genetically diverse cloud of individuals presenting phenotypic variance. The host humoral response against the capsid protein represents the most active immune pressure and primary weapon to control the infection. Since the preservation of the capsid function is deeply rooted in the virus evolutionary dynamics, here we review the current structural evidence focused on capsid antibody evasion mechanisms from that perspective.
Characterization of the complete chloroplast genome of Gerbera jamesonii Bolus in China and phylogenetic relationships

Abstract Gerbera (Gerbera jamesonii Bolus) is one of the most popular ornamental flowers and one of the top five cut flowers worldwide. In this study, we presented the complete chloroplast genome of it using BGISEQ-500 sequencing. Its chloroplast genome is 151,898 bp in size, containing a large single copy region (83,518 bp) and a small single copy region (18,244 bp), and a pair of IR regions (25,068 bp). The chloroplast genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic maximum likelihood analysis based on chloroplast genomes of Gerbera and other 17 plant species indicated that the relationship between Gerbera and other plant species of family Compositae is not very close and its relationship with Atractylodes lancea is the closest.
“Watch Your Language!”: Word Choice in Library Website Usability

Many academic libraries conduct extensive user studies when redesigning their websites, considering characteristics such as design features, information architecture, and link and information placement. One of the less studied aspects impacting library website usability is choice of language. This article presents the results of a usability study conducted at a small Canadian academic library that assessed the impact of word choice on user interactions with its library website. The author provides an overview of the relevant literature and explores the role that word choice, especially on a library website’s home page, can play in user experience. Plusieurs bibliotheques universitaires effectuent des etudes d’utilisabilite lors des refontes de sites Web pour tenir compte de caracteristiques telles les particularites techniques, l’architecture de l’information ainsi que le placement des liens et de l’information. L’un des aspects les moins etudies concernant l’utilisabilite d’un site Web de bibliotheque est le choix du langage. Cet article presente les resultats d’une etude d’utilisabilite effectuee a une petite bibliotheque universitaire canadienne qui a tente d’evaluer l’impact du choix des mots et les interactions des usagers avec son site Web. L’auteur fournit un survol de la litterature pertinente et explore quel role le choix des mots, surtout sur la page d’accueil d’un site Web de bibliotheque, peut avoir sur l’experiences des usagers.
Feather steroid hormone concentrations in relation to age, sex, and molting time in a long‐distance migratory passerine

Abstract In birds, concentrations of testosterone (T) and corticosterone (Cort) are closely connected with many morphological, behavioral, and other physiological traits, including reproduction, metabolism, immunity, and fitness. The direction of the effect of these hormones on above‐mentioned traits, and the potential feedback between hormones are in general unclear; in addition, knowledge on how age and sex can affect T and Cort concentrations is still inconsistent. Our study used a novel method to analyze testosterone and corticosterone in feathers (Tf, Cortf) based on the precolumn chemical derivatization of hormones before liquid chromatography–tandem mass spectrometry (LC‐MS/MS) analysis. Unlike previously used methods (RIA, EIA), our analytical procedure allows simultaneous analysis of both hormones from small amounts of feathers (4–25 mg) and, thus, overcomes the problem of insufficient detection limits. We applied this method to reveal associations between Tf and Cortf hormone concentrations and feather growth, age, and sex in feathers grown during the postbreeding (flanks) and prebreeding (tails) periods in barn swallows (Hirundo rustica). There was neither a correlation between prebreeding and postbreeding Tf, nor between prebreeding and postbreeding Cortf. Tail Cortf concentrations were negatively associated with tail feather growth rates. Feather hormone concentrations were correlated in the prebreeding period, negatively in males but positively in females. Both Cortf and Tf were higher in young birds compared to older ones, indicating either an age‐related decrease in hormone concentrations within individuals, or the selective disappearance of individuals with high steroid concentrations. Males and females did not differ in Cortf, but Tf concentrations were higher in males than females, particularly during the prebreeding period. In this study, we provide an effective method for analyzing hormones in feathers in an ecological context, especially in situations when the total amount of feathers available for the analysis is limited.
Co-targeting among microRNAs is widespread and enriched in the brain

MicroRNAs (miRNAs) play roles in diverse developmental processes and cellular differentiation. Distinct miRNAs have hundreds to thousands of conserved binding sites in mRNAs, but typically exert only modest repression on a single site. Co-targeting of individual mRNAs by multiple different miRNAs could be commonly used to achieve stronger and more complex patterns of repression. Comparing target sets of different miRNAs, we identified hundreds of pairs of miRNAs that share more mRNA targets than expected (often -2-fold or more) relative to stringent controls. For one co-targeting pair, miR-138 and miR-137, we validated functional overlap in neuronal differentiation. Clustering of the pairing relationships revealed a group of 9 predominantly brain-enriched miRNAs that share many targets. In reporter assays, subsets of these miRNAs together repressed gene expression by 5to 10-fold or more, sometimes exhibiting cooperative repression. Our results uncover an unexpected pattern in which certain combinations of miRNAs can collaborate to strongly repress particular targets, and suggest important developmental roles. Thesis Supervisor: Christopher B. Burge, Professor of Biology
Evaluation and prediction of semen parameters of breeding boars and their use in stock management

Article history: Received 14 December 2018 Received in revised form 1 July 2019 Accepted 2 July 2019 Artificial insemination constitutes the main method of pig breeding in Europe. According to literature, statistical models which allow prediction of productive capacity can be used as additional tools which may be helpful in making selection decisions concerning breeding boars. The aim of the research was to evaluate the influence of boar’s age, standardized daily growth rate, standardized meat content in the carcass, the number of nipples, the age when the boar starts to be used for breeding, the number of semen collections per month, and the interval between semen collections on selected qualitative and quantitative parameters of the semen and to calculate multiple regression equations, which would allow prediction of productive capacity of AI landrace boars. The material for the analysis comprised 47596 ejaculates obtained over the period 1995-2014 from 306 Polish Landrace boars. The obtained results show that semen parameters of the examined boars depend on physiological and organizational factors included in the analysis. It was observed that the following factors, measured with the number of produced semen doses, were of particular significance for the efficiency of use of the boars: boar’s age, the daily growth rate, meat content in the carcass, as well as the number of collections and the interval between collections. The conducted statistical analysis points to the possibility of predicting semen parameters accurately using regression analysis. The models are characterized by very high accuracy, which points to their potential for application. The calculated determination coefficients for the multiple regression equations assumed the R2 value of above 0.92. The highest value of the determination coefficient (R2 –0.99) was obtained for the percentage of sperm cells showing progressive motility. The calculated regression equations may be used in the management of the stock of breeding boars and when making selection decisions.
Molecular Characterisation of Feline Mammary Tumours

FMCs are highly malignant tumours characterised by local invasion and early dissemination. Considering the poor outcome of affected cats, identification of useful biomarkers to predict clinical behaviour and suitable therapeutic targets is of major importance. In this study, we used massive-parallel DNA and RNA sequencing to identify structural rearrangements and differentially expressed genes enriching key biological processes characterising FMC-associated malignancy and poor outcome. Important structural rearrangements (CNLs in FCA B1 and CNGs in FCAs B4 and F2) were detected and correlated with poor prognosis. Immunohistochemical and transcriptomic findings showed a high level of correlation with genomic aberrations detected. Different potential biomarkers and therapeutic targets were identified including TUSC3, RRM2, ESRP1, HMGA2 and MYC as well as different components of the p53 and PI3K-Akt signalling pathways. Amplified and upregulated genes were typically involved in pathways correlated with cell motion (SBDS, ITGAM, PDGFA, RAC1, FGFR1, APC and ITGB2), transcription modulation (GATA3, HMGN1, ZEB1, MYC and MYCN), DNA replication and repairing (RFC3, AK2, NUDT5. MCM2, RRM2 and TYMS) and EMT-elicitation (VIM, ZEB1, KRAS, HMGA2, ESRP1, MTDH, YWHAZ, and MYC). On the other hand, deleted and down-regulated genes were typically tumour-suppressors (CSMD1, MSR1, MTUS1, TUSC3, DLC1, NRG1 and LZTS1) or genes involved in biological processes that would normally prevent tumour spreading such as tight junction components (CLDN4, CLDN5 CLDN7, CLDN8, CLDN23, LMO7, PCDH17, PCDH20 and PCDH9) and cell adhesion molecules (CD2, CD8A, CD34, CD40, CDH1, CDH4, CDH5, ICAM2, ITGAM, ITGB2, PECAM1, ESAM and JAM2). FMCs included in this study shared some clinical and molecular similarities with specific molecular subtypes of human breast cancer characterised by worse outcome (i.e. hTNBCs, metaplastic breast carcinomas, and claudin-low breast tumours). Cellular models analysed shared a considerable amount of similarities with original tumours; however, specific alterations mainly correlated with endocrine regulation, circadian rhythm and metabolic pathways showed important differences. Despite the genomic characteristics associated with poor prognosis in solid carcinomas, no separation for the different histological grouping (tubular carcinomas, comedocarcinomas and solid carcinomas) was observed at the transcriptomic level. Molecular characteristics associated with malignancy were more typically observed in solid carcinomas and comedocarcinomas. However, specific cases with tubular carcinomas also shared these molecular characteristics and had a poor survival. DNA and RNA high-throughput sequencing prove to be useful to identify important biomarkers and target genes, resemblances between FMCs and human breast cancer, and advantages and limitations of in vitro models.
Survival-based bioinformatics analysis to identify hub genes and key pathways in non-small cell lung cancer

Background Lung cancer is one of the leading causes of cancer mortality worldwide. Here, we performed an integrative bioinformatics analysis to screen hub genes and critical pathways in non-small cell lung cancer (NSCLC) based on the overall survival rate of differentially expressed genes (DEGs). Methods Four datasets from the gene expression omnibus (GEO) were used to identify the DEGs. To obtain robust DEGs in NSCLC, only the DEGs that co-existed in the four datasets were selected for subsequent analysis. To identify the genes correlated with overall survival, the overall survival of these genes was then analyzed using the Kaplan-Meier plotter database. The genes significantly correlated with survival were used to perform gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis; next, these genes were used to construct a protein-protein interaction network. MCODE and CytoHubba were used to identify the clusters and hub genes. Finally, the hub genes were validated in the Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA). Results We found 522 up-regulated DEGs, and 989 down-regulated DEGs between the NSCLC and normal lung tissue, and 895 of them were correlated with a higher overall survival. GO analysis showed that the DEGs that were associated with a higher overall survival were enriched in cell division, cell cycle, DNA replication, angiogenesis, and cell migration. KEGG analysis was consistent with GO analysis and showed that p53 signaling pathway, pyrimidine metabolism, cGMP-PKG signaling pathway and renin secretion pathway were associated with overall survival in NSCLC. In the protein-protein analysis, we identified seven clusters and six hub genes which were BUB1B, CCNB1, CENPE, KIF18A, NDC10, and MAD2L1. Of these genes, CENPE and KIF18A had not been reported until now. Finally, the dysregulated expression of the six hub genes was validated by the data from the TCGA and HPA. Conclusions We identified the hub genes and potential mechanisms of NSCLC based on multiple-microarray analysis and overall survival; then, validated the hub genes in the TCGA and HPA database. These hub genes may serve as potential therapeutic targets.
Enzyme annotation in UniProtKB using Rhea

Motivation To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ontology ChEBI (Chemical Entities of Biological Interest). Results We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API, and SPARQL endpoint that leverage the chemical structure data, nomenclature, and classification that Rhea and ChEBI provide. Availability and Implementation UniProtKB at https://www.uniprot. org/; UniProt REST API at https://www.uniprot. org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot. org/sparql; Rhea at https://www.rhea-db.org/. Contact anne.morgat@sib.swiss
Complete mitochondrial genome of Hemiptelea davidii (Ulmaceae) and phylogenetic analysis

Abstract Hemiptelea davidii (Hance) Planch is a potential valuable forest tree in arid sandy environments. Here, the complete mitochondrial genome of H. davidii was assembled using a combination of the PacBio Sequel data and the Illumina Hiseq data. The mitochondrial genome is 460,941 bp in length, including 37 protein-coding genes, 19 tRNA genes, and three rRNA genes. The GC content of the whole mitochondrial genome is 44.84%. Phylogenetic analyses indicated that H. davidii is close with Cannabis and Morus species.
The bioinformatics method of polyprenol reductase genes in Elaeis guineensis

Even though led to minor components, Elaeis guineensis is well known to contain vitamin E, carotenoids, fatty acid, triterpenoid, and phytosterols. Recently the occurrence and pattern of long-chain polyisoprenoids from oil palm has been reported. The current study assesses the bioinformatics approaches to assay four probably polyprenol reductase genes from E. guineensis on NCBI database along with predicted the physical chemical, subcellular echolocation, and phylogenetic of polyprenol reductase. Several parameters of physicochemical polyprenol reductase in E. guineensis were varied among the genes observed. Results also showed the implication of understanding the variation and role of physical and chemical characteristics of the changed amino acids in oil palm polyprenol reductase genes. The subcellular location of these three genes has stored in the plasma membrane, Golgi body, endoplasmic reticulum (membrane and lumen). It is surprising to note that all the genes had the same values. The existence polyprenol reductase genes of E. guineensis in the clustering was supported by the dominated of carbon chain length of dolichols in the monocot plants.
Sleep spindles mediate hippocampal-neocortical coupling during sharp-wave ripples

Sleep is pivotal for the consolidation of memories [1]. According to two-stage accounts, experiences are temporarily stored in the hippocampus and gradually translocated to neocortical sites during non-rapid-eye-movement (NREM) sleep [2,3]. Mechanistically, information transfer is thought to rely on interactions between thalamocortical spindles and hippocampal ripples. In particular, spindles may open precisely-timed communication channels, across which reactivation patterns may travel between the hippocampus and cortical target sites when ripples occur. To test this hypothesis, we first derived time-frequency representations (TFRs) in hippocampus (HIPP) and at scalp electrode Cz (neocortex, NC) time-locked to individual hippocampal ripple events. Compared to matched ripple-free intervals, results revealed a concurrent increase in spindle power both in HIPP and NC. As revealed by coherence analysis, hippocampal-neocortical coupling was indeed enhanced in the spindle band around ripples. Finally, we examined the directionality of spindle coupling and observed a strong driving effect from NC to HIPP. Specifically, ∼250 ms prior to the HIPP ripple, NC spindles emerge and entrain HIPP spindles. Both regions then remain synchronised until ∼500 ms after the ripple. Consistent with recent rodent work, these findings suggest that active consolidation is initiated by neocortex and draws on neocortical-hippocampal-neocortical reactivation loops [4], with a role of sleep spindles in mediating this process.
Global Dynamics of an Hepatitis C Virus Mathematical Cellular Model with a Logistic Term

In this paper, the aim is to analyze the global dynamics of Hepatitis C Virus (HCV) cellular mathematical model under therapy with uninfected hepatocytes proliferation. We prove that the solution of the model with positive initial values are global, positive and bounded. In addition, firstly we show that the model is locally asymptotically stable at free virus equilibrium and also at infected equilibrium. Secondly we show that the model is globally asymptotically stable at the free virus equilibrium by using an appropriate lyapunov function.