Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatio-temporal study of wood formation of Quercus robur L. and Q. pyrenaica Willd. in the Northwest of the Iberian Peninsula

/Castellano/ Este estudio sobre anatomia ecologica de la madera aporta el conocimiento sistematico de los procesos de formacion del xilema y los patrones climaticos asociados, que son fundamentales para establecer una correcta interpretacion de las relaciones causa-efecto en los resultados retrospectivos dendrocronologicos en especies de anillo poroso. Para ello se llevo a cabo el seguimiento del proceso de formacion de madera (xilogenesis) y fenologia foliar durante dos anos de crecimiento en 14 localidades de bosques naturales de robles (nueve para Quercus robur y cinco para Q. pyrenaica). Tambien se realizo un estudio retrospectivo (dendrocronologico) de anillos de crecimiento y variables anatomicas (vasos conductores de madera temprana) en cuatro localidades de las 14 seleccionas. Se analizaron las relaciones entre el clima y la dinamica de formacion de madera en los 14 sitios, se establecio la sincronizacion entre crecimiento de madera y desarrollo de la hoja, y se cuantifico el contenido en agua de los organos de la copa (ramas, yemas, hojas) para minimizar la subjetividad del observador. /Enghis/ This study on ecological wood anatomy contributes to the knowledge on the process of xylem formation and its associated climatic patterns, which are fundamental to establish a correct interpretation of the cause-effect relationships observed in dendrochronological retrospective analyses of ring-porous species. For this purpose, the process of wood formation (xylogenesis) and leaf phenology were monitored during two years at 14 sites of natural forests (nive for Quercus robur, and five for Q. pyrenaica). A retrospective (dendrochronological) study of tree rings and anatomical variables (earlywood vessels) was also carried out at four out of the 14 sites. Climate-growth relationships at the 14 sites were analyzed, the synchronicity between wood growth and leaf development was described, and the water content of crown organs (branches, buds, leaves) was quantified to minimize observer’s subjectivity for leaf phenology.
Infant killers of Budongo revisited: infanticide and counterstrategies in wild, eastern chimpanzees

Infanticide, the killing of infants, is well documented in chimpanzees. However, despite multiple reports of this behaviour, no comprehensive study has attempted to explicitly test the various different hypotheses for its adaptive function in this species. In this thesis, I use records from the Sonso community of chimpanzees in the Budongo Forest, Uganda, to address the question of the function of infanticide. While infanticide has been recorded in several communities of chimpanzees, rates vary dramatically. In order to shed light on this variation, this thesis investigates risk factors for infanticidal behaviour and counter-strategies by parents. I found that the majority of infanticides adhere to the predictions of the sexual selection hypothesis for male committed infanticide, that instability in the male hierarchy is a key risk factor, and that mothers, but not fathers employ counterstrategies to protect their infants. Avoidance of potentially infanticidal individuals appears to be a key maternal counterstrategy to infanticide. Mothers are responsive to the varying risks posed by different individuals and how they change over time and they selectively avoid high risk individuals, both at the between and within party level.
Genetic identification, origin and sanitary status of grapevine cultivars (Vitis vinifera L.) grown in Babar, Algeria

This research focused on present grapevine biodiversity of neglected cultivars grown in 'Babar' region, Northeastern Algeria. The obtained results demonstrate the complex, rich, and even surprising inheritance of grapevine biodiversity in such a small region, with currently residual viticulture practiced only for direct consumption. Babar is one of the oldest inhabited areas in Algeria and part of the Atlas Mountains, considered very favorable for wild and cultivated vine growing since protohistoric times. Thirty-seven vines from the traditional growing area were analyzed using nuclear microsatellite (SSR) markers for cultivar identification and RT-qPCR analysis for virus detection and sanitary status evaluation. As a result, thirteen different genotypes were found, most of them showing a very good sanitary status, then constituting a valuable biological source for clonal selection. A close relatedness was evidenced with some Mediterranean varieties, resulting from previous exchanges of grapevine cultivars in the past. Furthermore, the present study highlighted the existence of three new genotypes, highly probably autochthonous of Babar region, with proposed names 'Babari', 'Babar-Algeria', and 'Amesski-Babar'. They could represent unique Algerian varieties, probably preserved over time. The conservation of these endangered genotypes is highly recommended.
Physiological responses to light explain competition and facilitation in a tree diversity experiment

Ecologists often invoke interspecific facilitation to help explain positive biodiversity-ecosystem function relationships in plant communities, but seldom test how it occurs. One mechanism through which one species may facilitate another is by ameliorating abiotic stress. Physiological experiments show that a chronic excess of light can cause stress that depresses carbon assimilation. If shading by a plant’s neighbors reduces light stress enough, it may facilitate that plant’s growth. If light is instead most often a limiting factor for photosynthesis, shading may have an adverse, competitive effect. In a temperate tree diversity experiment, we measured stem growth rates and photosynthetic physiology in broadleaf trees across a gradient of light availability imposed by their neighbors. At the extremes, trees experienced nearly full sun (monoculture), or were shaded by nearby fast-growing conifers (shaded biculture). Most species had slower growth rates with larger neighbors, implying a net competitive effect. On the other hand, the two most shade-tolerant species (Tilia americana and Acer negundo) and the most shade-intolerant one (Betula papyrifera) had faster stem growth rates with larger neighbors. The two most shade-tolerant species had large increases in photoinhibition (reduced dark-acclimated Fv/Fm) across the gradient of increasing light availability, which suggests they are more vulnerable to chronic light stress. While most species had lower carbon assimilation rates in the shaded biculture treatment, T. americana had rates up to 25% higher. T. americana also dropped its leaves 3-4 weeks earlier in monocultures, curtailing its growing season. We conclude that although large neighbors can cause light limitation in shade-intolerant species, they can also increase growth through abiotic stress amelioration in shade-tolerant species. Finally, in shade-intolerant B. papyrifera, we find a pattern of stem elongation in trees with larger neighbors, which may suggest that a shade avoidance response accounts for the apparent positive trend in stem volume. Synthesis: Both positive and negative species interactions in our experiment can be explained in large part by the photosynthetic responses of trees to the light environment created by their neighbors. We show that photosynthetic physiology can help explain the species interactions that underlie biodiversity-ecosystem function relationships. The insights that ecologists gain by searching for such physiological mechanisms may help us forecast species interactions under environmental change.
Global identification and analysis of microRNAs involved in salt stress responses in two alfalfa (Medicago sativa ‘Millennium’) lines

Abstract: Alfalfa is an important economic crop; a mutant (M) strain was identified during planting and production. M plants consistently had better relative water content and relative electrical conductivity under higher salt conditions compared with the wild type (WT) plants, suggesting that M plants have higher tolerance for salt. To understand the microRNAs (miRNAs) involved in salt stress response in alfalfa, 128 miRNAs were identified from the WT and M alfalfa plants under normal and saline conditions. Of the 128 miRNAs, 29 and 23 differentially expressed miRNAs were identified in the M vs. WT control (M-CK vs. WT-CK) and salt-stressed M vs. WT (M-salt vs. WT-salt) comparison, respectively. These miRNAs responded to salt stress and showed different expression patterns after salt treatment. Their potential target genes were predicted and further analysed by GO classification and KEGG pathway analysis, where the majority of target genes were associated with plant growth and development, and exhibited significant changes in WT and M plants. In addition, compared with the WT plants, miR172-CNGC, miR319-CAX2, miR408-NHX and miR2590-CHX14/15 showed significant upregulation in M alfalfa plants, suggesting that M plants have higher ion transport levels. The differential expression profiles of miRNAs and putative target genes were further validated by quantitative real-time polymerase chain reaction. It is speculated that these miRNAs are involved in the increased salt tolerance of the M alfalfa plants.
The transcription factor AtMYC2 shapes plant defense responses in Arabidopsis upon Pieris rapae herbivory

Plants have to cope with a variety of biotic stresses, including insect herbivory and pathogen attack. To minimize damage caused by pathogen or insect attack, plants have evolved sophisticated defense mechanisms. Hormones such as jasmonic acid (JA), ethylene (ET), salicylic acid (SA), and abscisic acid (ABA) are important players for determining the proper defense mechanism by the plant. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack.
Federated queries of clinical data repositories: balancing accuracy and privacy

Researchers use large federated clinical data networks that connect dozens of healthcare organizations to access data on millions of patients. However, because patients often receive care from multiple sites in the network, queries frequently double-count patients. Using the probabilistic streaming algorithm HyperLogLog and adding obfuscation, we developed a scalable method for estimating the number of distinct lives that match a query, which balances accuracy and privacy in a “tunable” way.
Clinical significance of preoperative neutrophil-lymphocyte ratio(NLR) in gastric cancer prognosis

Objective:To evaluate the clinical significance of the preoperative NLR in patients following curative resection of gastric cancer.Methods: The clinical and pathological data of 344 patients with gastric cancer,received curative resection in our hospital from January 2003 to January 2006,were analyzed retrospectively.With 231 men(67.2%) and 113 women(32.8%),a mean age of 67.6 years(24years-83years). Radical proximal gastrectomy(PG+D2) was performed in 45cases,radical distal gastrectomy(DG+D2) in 203 cases,radical total gastrectomy(TG+D2) in 76 cases,and extended radical gastrectomy(adjacent organ resection) in 20 cases.N/L ratio was calculated from lymphocyte and neutrophil counts on routine blood tests taken prior to surgery,with an NLR of 3.0 or more were classified as high NLR individuals,patients were followed up regularly.Univariate and multivariate analysis was produced on the clinicopathological factors affecting survival.Results: The 5-year survival of patients with a high NLR was significantly worse than that of patients with a low NLR(51%vs 74%,P0.001),and the disease-free survival is(67%vs 85%,P0.001). Univariate analyses evealed high NLR,depth of tumor,positive lymph nodes,distant metastasis,and poorly differentiated type were significant risk factors for reduced survival.On multivariate analyses,high NLR was independent risk factor of poorer prognosis(P0.001,HR95% confidence interval 1.768-2.174). Conclusion: A high preoperative NLR may be a convenient biomarker to predict recurrence of gastric cancer after resection.
High-dimensional Causal Mediation Analysis with a Large Number of Mediators Clumping at Zero to Assess the Contribution of the Microbiome to the Risk of Bacterial Pathogen Colonization in Older Adults

Causal mediation analysis is conducted in biomedical research with the goal of investigating causal mechanisms that consist of both direct causal pathways between the treatment and outcome variables and intermediate causal pathways through mediators. Recently, this type of analysis has been applied in the context of bioinformatics; however, it encounters the obstacle of high-dimensional and semi-continuous mediators with clumping at zero. In this article, we develop a methodology to conduct high-dimensional causal mediation analysis with a modeling framework that involves (i) a nonlinear model for the outcome variable, (ii) two-part models for semi-continuous mediators with clumping at zero, and (iii) sophisticated variable-selection techniques using machine learning. We conducted simulations and investigated the performance of the proposed method. It is shown that the proposed method can provide reliable statistical information on the causal effects with high-dimensional mediators. The method is adopted to assess the contribution of the intestinal microbiome to the risk of bacterial pathogen colonization in older adults from US nursing homes. The proposed high-dimensional causal mediation analysis with nonlinear models is an innovative and reliable approach to conduct causal inference with high-dimensional mediators.
Haematopoiesis and haematopoietic organs in fish

Haematopoiesis is a complex process in which haematopoietic stem cells, the most immature elements of the haematopoietic hierarchy, proliferate and differentiate into various classes of haematopoietic progenitor cells. These progenitor cells have been shown to be able to differentiate into mature blood cells: erythrocytes, lymphocytes, thrombocytes, granulocytes, and monocytes. The pronephros, or head kidney, is a basic organ forming the blood elements, and is also a reservoir of blood cells. Basic haematopoietic structures and mechanisms in fish are similar to those functioning in other vertebrates, and all haematopoietic cell types are very similar to those of mammals.
Epidemic spruce beetle outbreak changes drivers of Engelmann spruce regeneration

Climate-mediated disturbances outside the range of historical variability can have severe consequences on vital, post-disturbance regeneration processes. High-elevation forests of the Rocky Mountains that are dominated by Engelmann spruce (Picea engelmannii) and subalpine fir (Abies lasiocarpa) are expected to be sensitive to climate change. Additionally, these forests have experienced recent epidemic spruce beetle (Dendroctonus rufipennis) outbreaks that have often resulted in >95% mortality of overstory Engelmann spruce. Therefore, the future distribution of Engelmann spruce forests depends largely on natural regeneration processes. We examined Engelmann spruce seedlings across gradients in soil moisture and stand structural conditions 20 yr post-disturbance on the Markagunt Plateau in southern Utah. All Engelmann spruce seedlings were mapped, measured, and aged, and aspects of stand structure and the microclimate were measured. The goal of our research was to infer processes affecting Engelmann spruce establishment by determining if patterns of advance regeneration that established before the outbreak (~60% of individuals) differed from seedlings that established during and immediately following the outbreak (combined into one group, ~40% of individuals). A generalized linear multi-model approach identified that the density of advance regeneration (seedlings/saplings) was negatively influenced by historical competition with overstory trees. In contrast, post-outbreak regeneration was related to microclimate conditions, including positive relationships with climatic moisture deficit and July soil water content. All seedlings were not significantly clustered around Engelmann spruce snags; however, there was evidence of facilitation of post-outbreak seedlings by pre-outbreak seedlings at higher elevation sites with lower moisture deficit. Together, these findings suggest post-outbreak seedlings were not moisture-limited at lower elevations but instead encouraged by higher evapotranspiration. Moreover, facilitation at higher elevations likely resulted from how pre-outbreak seedlings modify snowpack and associated seedbed environments. Our study provides insight for managing Engelmann spruce after a beetle outbreak. In these forests, preand post-outbreak regeneration can increase resilience to climate–disturbance interactions, but are patchy and structured at different scales. Therefore, the presence of advance regeneration and the likelihood of post-outbreak seedlings depend on local environment (soil moisture and stand structure) and could be taken into account to most effectively plan post-disturbance planting activities.
Genetic identification of native populations of Mediterranean brown trout Salmo trutta L. complex (Osteichthyes: Salmonidae) in central Italy

Abstract Italian native populations of Mediterranean brown trout belong to the Salmo trutta complex. This species complex includes many mitochondrial lineages and phenotypes that have caused taxonomic controversies over time. The spatial distribution and the genetic diversity of these fishes are threatened by habitat destruction, global warming and, mainly, by the introduction of domestic trout of Atlantic origin. Indeed allochthonous trouts were massively restocked in Italian rivers for a century and they admixed with native populations. In order to identify residual native populations of Mediterranean brown trout, a genetic analysis of specimens collected within Latium region, on the Tyrrhenian slope of central Italy, was undertaken. To this purpose, 210 trout specimens were collected from six different rivers and analyzed for the identification of their nuclear (LDH-C1* RFLP) and mitochondrial (Control Region sequences) genotypes. Genetic characterization with these molecular markers allowed a quantitative estimate of allochthonous genotypes, which are present in all brown trout populations of the six sites, even if not equally distributed across the sampling area. At least three populations, inhabiting diverse lotic ecosystems (mountain, hilly and coastal streams respectively), are characterized by a high percentage of native nuclear allele *100 at locus LDH-C1* and typical Mediterranean haplotypes (of AD and ME lineages), which can be considered as different management units (MUs). This finding highlighted the aquatic ecosystems of the Latium Region as an important hotspot of salmonid biodiversity within the Italian peninsula, with important implications from a conservation perspective.
Alpha 6 Integrins Regulate the Expression of Laminin-511 and CXCR4 to Promote Endothelial Tubular Morphogenesis

During angiogenesis, endothelial cells engage components of the extracellular matrix through integrin-mediated adhesion. Endothelial cells express laminin-411 and laminin-511 that bind to integrins, including the α6 integrins, α6β1 and α6β4. However, little is known about the contribution of these laminins to endothelial tubular morphogenesis and stability. We used two organotypic angiogenesis assays in conjunction with RNAi approaches to demonstrate that endothelial depletion of either the α4 chain of laminin-411 or the α5 chain of laminin-511 inhibited sprouting and tube formation. Depletion of α6 integrins resulted in similar phenotypes. Interestingly, depletion of α6 integrins also inhibited the expression of laminin-511, which correlated with the loss of tubular stability. Loss of either α6 integrins or laminin-511 resulted in the inhibition of the expression of CXCR4, a gene previously associated with sprouting endothelial cells. Pharmacological inhibition of CXCR4 signaling suppressed endothelial sprouting and morphogenesis, suggesting that α6 integrins and laminin-511 promotes endothelial tubular morphogenesis in part by regulating the expression of CXCR4. Taken together, our results suggest that α6 integrins regulate gene expression to promote both early events in tubular morphogenesis, as well as the stability of established endothelial tubes. Summary statement Endothelial-secreted laminin-511 and its receptors, α6 integrins promote tubular morphogenesis by regulating the expression of the chemokine receptor, CXCR4. Additionally, the depletion of α6 integrins from established tubes results in the loss of tubular integrity and laminin-511 expression.
Uncovering patterns of atomic interactions in static and dynamic structures of proteins

The number of structures and molecular dynamics simulations of proteins is exploding owing to dramatic advances in cryo-electron microscopy, crystallography, and computing. One of the most powerful ways to analyze structural information involves comparisons of interatomic interactions across different structures or simulations of the same protein or related proteins from the same family (e.g. different GPCRs). Such comparative analyses are of interest to a wide range of researchers but currently prove challenging for all but a few. To facilitate comparative structural analyses, we have developed tools for (i) rapidly computing and comparing interatomic interactions and (ii) interactively visualizing interactions to enable structure-based interpretations. Using these tools, we have developed the Contact Comparison Atlas, a web-based resource for the comparative analysis of interactions in structures and simulations of proteins. Using the Contact Comparison Atlas and our tools, we have identified patterns of interactions with functional implications in structures of G-protein-coupled receptors, G proteins and kinases and in the dynamics of muscarinic receptors. The Contact Comparison Atlas can be used to enable structure modeling, drug discovery, protein engineering, and the prediction of disease-associated mutations. Contact Comparison Atlas website: https://getcontacts.github. io/atlas/