Miracle-dz/UniFAR-FTUs huggingface dataset:
It is Never as Good the Second Time Around: Brain Areas Involved in Salience Processing Habituate During Repeated Drug Cue Exposure in Methamphetamine and Opioid Users

Introduction The brain response to drug-related cues is an important marker in addiction-medicine, however, the temporal dynamics of this response in repeated exposure to the cues are not well known yet. In an fMRI drug cue-reactivity task, the presence of rapid habituation or sensitization was investigated by modeling time and its interaction with condition (drug>neutral) using an initial discovery-sample. Replication of this temporal response was tested in two other clinical populations. Methods Sixty-five male participants (35.8±8.4 years-old) with methamphetamine use disorder (MUD) were recruited as the discovery-sample. A linear mixed effects model was used to identify areas with a time-by-condition interaction in the discovery-sample. Replication of these effects was tested in two other samples (29 female with MUD and 22 male with opioid use disorder). The second replication-sample was re-tested within two weeks. Results In the discovery-sample, clusters within the VMPFC, amygdala and ventral striatum showed both significant condition and condition-by-time interaction with a habituation response for the drug-related cues but not neutral cues. The estimates for the main effects and interactions were generally consistent between the discovery and replication-samples across all clusters. The re-test data showed consistent lack of drug>neutral and habituation response within all selected clusters in the second cue-exposure session. Conclusions VMPFC, amygdala and ventral striatum show a habituation in response to drug-related cues which is consistent among different clinical populations. Habituation in response in the first session of cue-exposure and lack of reactivity in the second session of exposure provide foundations for development of cue-desensitization interventions.
Heritability estimates of antler and body traits in white-tailed deer (Odocoileus virginianus) from genomic-relatedness matrices

Estimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimating h2 in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where phenotypic and SNP data are available. We estimated the heritability of five body and three antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated GRMs from >10,000 SNPs: dressed body mass and peroneus muscle mass had moderate h2 values of 0.49 and 0.56, respectively. Heritability in male-only antler features ranged from 0.00 to 0.51 and had high standard errors. We explored the influence of minor allele frequency and data completion filters on h2: GRMs derived from fewer SNPs had reduced h2 estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs increase variance around h2 estimates. This is the first study to estimate h2 on a free-ranging population of white-tailed deer and should be informative for breeding designs and management.
Quantitative partition of the rhizosphere microbiota assembly processes

The soil microbial reservoir and plant recruitment are predominant forces determining microbiota assembly in rhizosphere (i.e. active and passive processes respectively), but to date, no straightforward method to evaluate the respective contribution of forces to the rhizospheric microbiota assembly rules is available. We propose herein a promising way to quantitatively partition the assembling forces of rhizosphere microbiota using ordination metrics. We anticipate that this new method can not only weight the plants individual contributions to microbiota assembly in rhizosphere, but can also indirectly provide a way to quantitatively evaluate soil health by the contribution from plant selection.
The Coevolution of Promoters and Transcription Factors in Animal and Plant Cells

Coevolution has been acknowledged to play a significant role in driving the evolution of molecules and species. Promoters and transcription factors (TFs), especially their interactions, are key determinants for the regulation of gene expression. However, the evolutionary processes and mechanisms of promoter and TF interactions are still poorly understood. Here we conduct extensive physicochemical analyses of multi-omics sequences in 440 animal species and 223 plant species which span nearly one billion years of phylogeny. We demonstrate that promoters and TFs obey antagonistic coevolution in the animal kingdom while follow mutualistic coevolution in the plant kingdom. Furthermore, we reveal that such two coevolutionary strategies result in different evolutionary transitions of transcriptional networks in the two kingdoms. These results suggest that the two distinct coevolutionary mechanisms are likely to be major drivers of far greater genetic divergence between animals and plants, and open a new door to understanding the roles of promoters and TFs in tumor initiation and progression, and human ageing as well in molecular interactions and evolution.
Assessing the variation in Manganese Use Efficiency Traits in Scottish Barley Landrace Bere (Hordeum vulgare L.).

BACKGROUND AND AIMS Manganese (Mn) deficiency in barley is a global problem. It is difficult to detect in the early stages of symptom development and is commonly pre-emptively corrected by Mn foliar sprays that can be costly. Landraces adapted to marginal lands around the world represent a genetic resource for potential sustainability traits including mineral use efficiency. This research aims to confirm novel Mn use efficiency traits from the Scottish landrace Bere and use an association mapping approach to identify genetic loci associated with the trait. METHODS A hydroponic system was developed to identify and characterise the Mn deficiency tolerance traits in a collection of landraces, including a large number of Scottish Bere barleys, a group of 6-rowed heritage landraces grown in the highlands and islands of Scotland. Measuring chlorophyll fluorescence, the effect of Mn deficiency was identified in the early stages of development. Genotypic data, generated using the 50k Illumina iSelect genotyping array, was coupled with the Mn phenotypic data to create a genome-wide association study (GWAS) identifying candidate loci associated with Mn use efficiency. KEY RESULTS The Bere lines generally had good Mn use efficiency traits. Individual Bere lines showed large efficiencies, with some Bere lines recording almost double chlorophyll fluorescence readings in limited Mn conditions compared to the elite cultivar Scholar. The Mn efficient Bere lines had increased accumulation of Mn in their shoot biomass compared with elite cultivars, which was highly correlated to the chlorophyll fluorescence. Several candidate genes were identified as being associated with Mn use efficiency in the GWAS. CONCLUSIONS Several genomic regions for Mn use efficiency traits originating from the Bere lines were identified. Further examination and validation of these regions should be undertaken to identify candidate genes for future breeding for marginal lands.
Application de la complémentation de fluorescence bi-moléculaire à l'étude du mode d'action des protéines Hox in vivo

My current laboratory aims to tackle the issue of specificity and diversity of regulatory molecules, taking the Drosophila Hox transcription factors as a paradigm for the analysis. During my PhD, I developed three connected research lines.Project 1: Visualization of protein interactions in living Drosophila embryos by the BiFC assayOur results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development.Project 2: Investigation of Hox/PBC complex formation in vivo using BiFC Our findings challenge the current paradigm of Hox/Pbx complex assembly: (a) highlighting the existence of alternative modes of Pbx recruitment, (b) demonstrating that unique Hox-PBC interaction modes can provide specific regulatory function in absence of DNA-binding selectivity.To achieve this project BiFC was also performed with vertebrate Hox proteins in chicken embryos.Project 3: Realization of a candidate interaction screen based on BiFC to identify novel Hox protein partners in vivo(a) We have revealed that Hox proteins establish specific interactions with different subunits of the general mediator complex. These results constituted one of the rare studies making a direct link between the Hox regulators and components of the basal transcriptional machinery, in a physiological context. (b) We have discovered that Hox proteins can interact with importin proteins. This result allows us to assess the importance of controlling the nuclear localization of Hox proteins for controlling their regulatory activities during embryogenesis.
Behavioural effects of extracellular matrix protein Fras1 depletion in the mouse

Fras1 is an extracellular protein of the basement membranes that surround embryonic epithelia, choroid plexuses and meninges in foetal mouse brain. Depletion of Fras1 in knockout mice results in sub‐epidermal blistering and fusion of eyelids and digits as well as malformation of lungs and kidneys. Mutations in the human counterpart FRAS1 are responsible for the Fraser Syndrome with clinical manifestations similar to the murine phenotype. In addition, brain deformities or mental impairments have occasionally been reported in patients with Fraser Syndrome. In the present study, we explored the possible involvement of Fras1 in brain function, analysing its expression pattern in mouse brain and investigating aspects of Fras1−/− mice behaviour, related to the function of brain regions expressing Fras1. Transcripts were detected in choroid plexuses and in certain brain regions including cortical, hippocampal and amygdalar areas in juvenile mice. Behavioural tests revealed that Fras1−/− mice exhibit impaired egocentric spatial memory, aberrant olfactory learning and memory, markedly reduced fear memory in an auditory fear conditioning task, as well as reduced anxiety expression in open field and elevated plus maze tests. Moreover, the extracellular matrix organization has been severely affected in cortical and subcortical areas as demonstrated by Wisteria floribunda agglutinin immunolabelling. The widespread detection of Fras1 transcripts in the brain of both pre‐ and postnatal mice, as well as the behavioural and cellular disturbances exhibited by Fras1−/− adult mice provide evidence for the involvement of Fras1 in brain organization and function.
Evaluation of Khat (Catha edulis) Use as a Risk Factor of Cancer: A Systematic Review

Background: Conducting systematic review to evaluate plant use as a risk factor to cancer could be challenging. A systematic and well-balanced method should be applied to accommodate in vivo and in vitro studies to make a final decision. In this article, khat, a recreational plant used in some Arabic and African regions, was employed as an example to systematically determine its relationships to the premalignant and cancerous conditions. Methods: Systematic database search was performed to recruit original human, animal or in vitro studies on khat and cancer. Sixteen studies fulfilled the inclusion criteria and subjected to assessment using Risk of Bias (RoB). Office of Health and Translation (OHAT) approach was used to rate the confidence level in the body of evidence. The evidence was integrated to establish the relationships between khat, premalignant conditions and cancer. Results: Seven out of eight studies showed that khat causes premalignant oral lesions with moderate evidence level. Four studies showed that khat causes cancer with low evidence level and another three studies showed that khat has anti-cancer effect with moderate to high evidence level. Only one study suggested that khat is unrelated to cancer. Conclusion: RoB and OHAT approach are reliable systematic tools to evaluate plant risk to cancer and provide objective and uniform summary regardless of the study type. In conclusion, our pooled analysis did not find a direct relationship between khat and cancer but anti-cancer effect would require to be proofed on human studies.
Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species.

BACKGROUND AND AIMS Sugar composition is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this paper was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modeling approach. METHODS We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of other compounds than sugar and starch, synthesis and hydrolysis of starch, water dilution) involved in the accumulation of soluble sugars during fruit development. KEY RESULTS Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwi). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared to all other species. CONCLUSIONS Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the coordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not tightly affected by ethylene-associated events.
The Dynamics of Bird Diversity in the New World

Abstract Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient. ]
Renewal and Differentiation of GCD Necklace Olfactory Sensory Neurons.

Both canonical olfactory sensory neurons (OSNs) and sensory neurons belonging to the guanylate cyclase D (GCD) "necklace" subsystem are housed in the main olfactory epithelium, which is continuously bombarded by toxins, pathogens and debris from the outside world. Canonical OSNs address this challenge, in part, by undergoing renewal through neurogenesis; however, it is not clear whether GCD OSNs also continuously regenerate, and if so whether newborn GCD precursors follow a similar developmental trajectory to that taken by canonical OSNs. Here we demonstrate that GCD OSNs are born throughout adulthood and can persist in the epithelium for several months. Phosphodiesterase 2A is upregulated early in the differentiation process, followed by the sequential downregulation of β-tubulin and the upregulation of CART protein. The GCD and MS4A receptors that confer sensory responses upon GCD neurons are initially expressed midway through this process, but become most highly expressed once CART levels are maximal late in GCD OSN development. GCD OSN maturation is accompanied by a horizontal migration of neurons towards the central, curved portions of the cul-de-sac regions where necklace cells are concentrated. These findings demonstrate that - like their canonical counterparts - GCD OSNs undergo continuous renewal, and define a GCD-specific developmental trajectory linking neurogenesis, maturation and migration.
Plant Growth-Promoting Effects of Rhizobacteria on Abiotic Stressed Plants. Azospirillum-Grasses Model

Plant growth-promoting rhizobacteria exert beneficial effects on plants when re-introduced by inoculation in a soil containing competitive micro flora. Amongst them Azospirillum is one of the most studied genera. Even though it colonizes different plant species in an ample variety of soils, it was first described in association with grass roots. In Argentina over 220,000 ha of wheat and corn were commercially inoculated with Azospirillum in 2008. In this review the management conditions leading to enhanced crop productivity are discussed. The beneficial effects of inoculation on abiotic stressed plants are also described. We present results showing how wheat and maize stress tolerance are enhanced due to Azospirillum brasilense Sp245 inoculation. _____________________________________________________________________________________________________________
Strong solutions to the nonhomogeneous Boussinesq equations for magnetohydrodynamics convection without thermal diffusion

We are concerned with the Cauchy problem of nonhomogeneous Boussinesq equations for magnetohydrodynamics convection in R2. We show that there exists a unique local strong solution provided the initial density, the magnetic field, and the initial temperature decrease at infinity sufficiently quickly. In particular, the initial data can be arbitrarily large and the initial density may contain vacuum states.
Highly accurate k-l approximation to sum of M independent non-identical Ricean variates

A scheme to approximate the distribution of the sum of M independent, non-identically distributed Ricean random variables by the k-m distribution is proposed. To this end, appropriate k-m distribution parameters are derived. The summands are assumed to have arbitrary mean powers and arbitrary fading parameters. The differences between exact and approximate distribution curves are almost imperceptible.
PROCALCITONIN FOR DIAGNOSING POSTOPERATIVE INFECTION AFTER CARDIAC SURGERY POSTOPERATIVE INFECTION AND PROCALCITONIN

In cardiac surgery practice, systemic inflammatory response (SIRS) is a clinical condition that develops secondary to cardiopulmonary bypass (CPB) and increases mortality and morbidity. Postoperative infection among patients undergoing cardiac surgery, manifests itself in a way similar to SIRS and also increases mortality. Early diagnosis and treatment of infectious complications reduce mortality and morbidity. Procalcitonin, the precursor of calcitonin, is a specificity and sensitivity for early detection of bacterial sepsis have recently been confirmed by multiple studies Its serum level exceeds that level when postoperative infection or sepsis develops, depending on the severity of the either clinical condition. Despite being elevated in the event of bacterial and fungal infections; it is not affected by viral infections. Monitoring postoperative serum PCT kinetics is useful for making an early diagnosis of postoperative complications. Serum PCT should be routinely monitored in all patients undergoing cardiac surgery. PCT levels failing to drop by 24 hours postoperatively, or those exceeding 5 ng/ml, should be interpreted in favor of infection or any postoperative complication. Its marked superiority over CRP and WBC allows making a timely diagnosis of infectious complications and commencing antibiotic therapy without delay. Serum PCT level is an important biomarker that offers promise for routine use to reduce postoperative morbidity and mortality after cardiac surgery.