Miracle-dz/UniFAR-FTUs huggingface dataset:
Paintings predict the distribution of species, or the challenge of selecting environmental predictors and evaluation statistics

Aim: Species distribution modelling, a family of statistical methods that predicts species distribu- tions from a set of occurrences and environmental predictors, is now routinely applied in many macroecological studies. However, the reliability of evaluation metrics usually employed to validate these models remains questioned. Moreover, the emergence of online databases of environmental variables with global coverage, especially climatic, has favoured the use of the same set of standard predictors. Unfortunately, the selection of variables is too rarely based on a careful examination of the species’ ecology. In this context, our aim was to highlight the importance of selecting ad hoc variables in species distribution models, and to assess the ability of classical evaluation statistics to identify models with no biological realism. Innovation: First, we reviewed the current practices in the field of species distribution modelling in terms of variable selection and model evaluation. Then, we computed distribution models of 509 European species using pseudo-predictors derived from paintings or using a real set of climatic and topographic predictors. We calculated model performance based on the area under the receiver operating curve (AUC) and true skill statistics (TSS), partitioning occurrences into training and test data with different levels of spatial independence. Most models computed from pseudo- predictors were classified as good and sometimes were even better evaluated than models com- puted using real environmental variables. However, on average they were better discriminated when the partitioning of occurrences allowed testing for model transferability. Main conclusions: These findings confirm the crucial importance of variable selection and the inability of current evaluation metrics to assess the biological significance of distribution models. We recommend that researchers carefully select variables according to the species’ ecology and evaluate models only according to their capacity to be transfered in distant areas. Nevertheless, statistics of model evaluations must still be interpreted with great caution.
Computational Dissection of Composite Molecular Signatures and Transcriptional Modules

This dissertation aims to develop a latent variable modeling framework with which to analyze gene expression profiling data for computational dissection of molecular signatures and transcriptional modules. The biological problem is formalizes as a source separation problem that permits the development of a unified latent variable modeling framework. The framework is implemented in different molecular levels with a top-down approach, i.e., from tissue or cell mixtures to gene modules, and from gene modules to gene regulatory programs. The first part of the dissertation is focused on extracting pure gene expression signals from tissue or cell mixtures. In molecular profiling of solid tumors, it is often needed to process composite gene expression data as obtained from heterogeneous tumor biopsies. The main goal of gene expression profiling is to identify the pure signatures of different cell types (such as cancer cells, stromal cells and inflammatory cells) and estimate the concentration of each cell type. In order to accomplish this, a new blind source separation method is developed, namely, nonnegative partially independent component analysis (nPICA), for tissue heterogeneity correction (THC). The nPICA method is specifically developed to extract nonnegative and partially uncorrelated signals from microarray data based on phenotypic up-regulated genes. The THC problem is formulated as a constrained optimization problem and solved with a learning algorithm based on geometrical and statistical principles. The nPICA method was tested on a series of numerical mixtures of microarray data sets to tackle cell and tissue heterogeneity, and accurately dissected mixtures into pure signals of component cell types. The second part of the dissertation sought to identify gene modules from gene expression data to uncover important biological processes in different types of cells. Since biological processes are latent variables in gene expression data, the problem of gene module identification can be treated as a blind source separation problem as well. A new gene clustering approach, nonnegative independent component analysis (nICA), is
Experimental assay of a fitness landscape on a macroevolutionary scale

Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. The His3 fitness landscape is dominated by synergistic epistasis. For 80% of substitutions, the effect on fitness depended on the genetic background. Furthermore, at 67% of sites, substitutions are under sign epistasis, having both strongly positive and negative effect on different genetic background. 46% of sites were under reciprocal sign epistasis. Sign epistasis affected few genotypes but involved interaction of multiple sites which makes multidimensionality of the His3 fitness landscape essential, with the number of dimensions of the landscape approximately one quarter of the sequence length.
MAK-10 : A Long Shelf-life Charentais Breeding Line Developed by Introgression of a Genomic Region from Makuwa Melon

This work has been carried out in the framework of the Programa de Valorizacion y Recursos Conjuntos de I+D+i de VLC/CAMPUS and has been funded by the Ministerio de Educacion, Cultura y Deporte as part of the Programa Campus de Excelencia Internacional. IL generation, genotyping, and phenotyping were supported by SAFQIM project, AGL2012-40130-C02-02 of the Spanish Ministry of Economy and Competitivity (MINECO). We wish to thank the MINECO project AGL2014-53398-C2-2-R, co-funded with FEDER funds.
The effect of barley meal on dairy cow's dry matter intake, allantoin excretion and microbial protein synthesis in feeding alfalfa silage ad libitum

Four ruminally cannulated Holstein cows in midlactation were randomly assigned to a 4×4 Latin square design to evaluate barley meal effect on alfalfa silage dry matter intake, allantoin excretion and microbial protein synthesis. Cows were fed alfalfa silage (37.2% dry matter and in dry matter 21.9% crude protein, 35.4% NDF and 29.4% ADF) ad libitum and barley meal equivalent to 25, 40, 55 or 70% of their metabolic energy requirement. The preliminary period lasted for 8 and the trial period for 6 days. Urine was collected on the 6 day of the trial period during 12 hours with bladder catheters. Samples of rumen fluid were taken on the 5 and 6 day of the trial period 4 hours after morning feeding. Barley meal proportion in the ration was increased from 25% to 75%. Each additional kg of barley meal in the ration decreased the dry matter intake of alfalfa silage by 1.02 kg. Urinary allantoin excretion correlated with DM intake (r=0.553; P<0.05), ME intake (0.665; P<0.001) non-fibre carbohydrate (NFC) intake (r=0.662; P<0.001), digestible organic matter fermented in the rumen (DOMR) content in the ration (r=0.664; P<0.01), urinary N content (r=0.562; P<0.05) and daily N excretion (r=0.601; P<0.01). Respectively to the trial variant, the amount of synthesized ruminal microbial nitrogen per each kg of DOMR was 24.7; 23.2; 28.3 and 29.8 g and for MJ metabolizable energy these values were 1.03; 0.96; 1.14 and 1.22 g. When alfalfa silage is fed ad libitum, barley meal as the only source of nonstructural carbohydrates in the ration of cows is not sufficient for synchronizing the hydrolysis of energy and protein and for maximizing microbial protein synthesis in the rumen.
Ontogenetic partial migration is associated with environmental drivers and influences fisheries interactions in a marine predator

James S. E. Lea*, Bradley M. Wetherbee, Lara L. Sousa, Choy Aming, Neil Burnie, Nicolas E. Humphries, Nuno Queiroz, Guy M. Harvey, David W. Sims, and Mahmood S. Shivji* The Guy Harvey Research Institute, Nova Southeastern University Oceanographic Centre, 8000 North Ocean Drive, Dania Beach, FL 33004, USA The Laboratory, Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth PL1 2PB, UK Marine Research Facility, PO Box 10646, Jeddah 21443, Saudi Arabia School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, Devon, PL4 8AA, UK Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA Centro de Investigaç~ao em Biodiversidade e Recursos Genéticos, CIBIO – Universidade do Porto, Campus Agrário de Vair~ao, Rua Padre Armando Quintas, Vair~ao 4485-668, Portugal Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK Bermuda Shark Project, Bermuda Aquarium, Museum and Zoo, 40 North Shore Road, Bermuda Centre for Biological Sciences, Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK *Corresponding authors: tel: þ18 005 416 682; fax: þ1 954-262-4098; e-mail: james@eatonlea.co.uk and mahmood@nova.edu These authors contributed equally to this work.
Caracterização funcional do complexo adaptador 1 (AP-1) em Trypanosoma cruzi

The AP-1 Adaptor Complex assists clathrin-coated vesicle assembly in the trans-Golgi network of eukaryotic cells. However, the role of AP-1 in the protozoan Trypanosoma cruzi — the Chagas disease parasite — has not been addressed. Here, we studied the function of AP-1 in different T. cruzi life cycle forms, by generating a gene knockout of the large AP-1 subunit gamma adaptin (TcAP1-γ). Epimastigote (insect form) parasites lacking TcAP1-γ (TcAP1-γKO) have reduced proliferation and differentiation into infective metacyclic trypomastigotes (compared with wild-type parasites). TcAP1-γKO parasites have also displayed significantly reduced infectivity towards mammalian cells. Importantly, TcAP1-γ knockout impaired maturation and transport to lysosome-related organelles (reservosomes) of a key cargo – the major cysteine protease cruzipain, which is important for parasite nutrition, differentiation and infection. To confirm that the absence of cruzipain in the reservosomes of TcAP1-γKO parasites was due the lack of TcAP1-γ expression, TcAP1-γKO parasites were transfected with an episomal construct constitutively expressing TcAP1-γ. Complementation of TcAP1-γ expression in AP1-γKO mutants restored maturation and cruzipain localization to the reservosomes, implicating the AP-1 complex in the formation of reservosome-bound vesicles containing cruzipain, at the trans-Golgi network. In addition, proteomics analysis of complexes associated with GFP-tagged TcAP1-β and TcAP1-μ detected the subunits of AP-1, TcAP1-γ and TcAP1-σ, but not others possible targets, indicating that GFP probably interfered with the association of AP-1 with other auxiliary proteins.
Forget Pixels: Adaptive Particle Representation of Fluorescence Microscopy Images

Modern microscopy modalities create a data deluge with gigabytes of data generated each second, and terabytes per day. Storing and processing these data is a severe bottleneck, not fully alleviated by data compression. We argue that this is because images are processed as regular grids of pixels. To address the root of the problem, we here propose a content-adaptive representation of fluorescence microscopy images called the Adaptive Particle Representation (APR). The APR replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels. We present the ideas, concepts, and algorithms of the APR and validate them using noisy 3D image data. We show that the APR represents the content of an image while maintaining image quality. We then show that the adaptivity of the APR provides orders of magnitude benefits across a range of image processing tasks. Therefore, the APR provides a simple, extendable, and efficient content-aware representation of images that relaxes current data and processing bottlenecks.
Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective

Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.
Molecular dissection of cell division in apicomplexan parasites

Apicomplexa are intracellular parasites that cause important human diseases including malaria and toxoplasmosis. Following invasion of a host cell, Apicomplexa undergo a fascinatingly complex process of division. Apicomplexa proliferate by a unique mechanism that combines closed mitosis of the nucleus with de-novo formation of daughter cells. Mitosis occurs in the presence of a nuclear envelope and with little appreciable chromatin condensation. Nuclear division is not always followed by cytokinesis. In some Apicomplexa, division results in a cytosol in which multiple nuclei and organelles are parceled into multiple daughter cells simultaneously. Budding is remarkably flexible in output and can produce two to thousands of progeny cells depending on the apicomplexan species. How genomes and daughters are counted and coordinated is unknown. Here, we use Toxoplasma gondii as a cell biological model to ask questions pertaining molecular aspects of apicomplexan division. We had shown previously that all centromeres, the sites of kinetochore attachment on each chromosome, are constantly tethered to the centrosome positioned in a specific region of the nuclear periphery. Centromeres are clustered throughout the cell cycle. We show that centromere clustering is mediated by elements of the nuclear envelope. In particular, components of the nuclear pore complex appear to be important for maintenance of centromere tethered to the nuclear envelope. We also show that nuclear events are coordinated with assembly of daughter cells through structures associated to the centrosome during division. A fiber-like structure, derived from the algal past of apicomplexan parasites, assembles on the centrosome during mitosis and initiates daughter cell assembly. This fiber is made of striated fiber assemblin proteins which in algae participate in the positioning and organization of the flagellar basal body. These findings have broad evolutionary implications. We propose that Apicomplexa retained the organizing principle of the flagellar microtubule organizing center. Instead of ensuring appropriate numbers of flagella, the system now positions the microtubule organizing center of the daughter cell. Finally, the results herein presented derive a novel model of regulation of division in which individual elements of the cell are linked through physical tethers to the centrosome providing both spatial organization and temporal control. INDEX WORDS: Toxoplasma, Apicomplexa, division, replication, mitosis, centromere, centrosome, striated fiber, histone, nuclear pore complex, microtubule organizing center. MOLECULAR DISSECTION OF CELL DIVISION IN APICOMPLEXAN PARASITES
Selección de levaduras No-Saccharomyces de las uvas de Merlot y Cabernet Sauvignon en función de su perfil polifenólico.

Yeast strains that intervene in fermentation are responsible for much of the final characteristics of the wines, because they have a decisive influence on the colour, structure, aromatic composition, stability and food safety. The sequential sowing of nonSaccharomyces and Saccharomyces yeasts, like what happens in the spontaneous fermentation of the grape must, contributes to increase the complexity of the wines and to improve their personality, due to the differential characteristics that nonSaccharomyces yeast strains can give to wines. It is studied the effect of different strains of non-Saccharomyces yeast strains isolated in Cabernet Sauvignon and Merlot grapes, from Winery Chozas Carrascal, in the chemical and organoleptic composition of wines with them elaborated. For this purpose, individual fermentations have been made with each of the non-Saccharomyces yeast strains isolated, sowing it in the musts in fermentation with the strain Saccharomyces cerevisiae 22H, previously isolated in the grapes of this winery, so that strain concludes the fermentation process. In the elaborated wines, the conventional and polyphenolic composition has been determined and its sensory profile has been established, with the purpose of determining the best strains of yeast present in the vineyard, and to implement them in the fermentation, to obtain wines of higher quality and personality, which improve the polyphenolic composition of wines and their organoleptic valuation. In general, in wines of the Merlot and Cabernet Sauvignon variety elaborated, the sequential fermentation with non-Saccharomyces-Saccharomyces 22 H strains rise to a better polyphenolic behaviour and a better organoleptic valuation, compared to the wines fermented only with the Saccharomyces 22 H strain. Of all the strains tested, has been the strain non-Saccharomyces 42 d in Merlot wines, and the 58 E for those of Cabernet, chosen to be part of a mixed sequential fermentation together with the yeast S. cerevisiae 22H.
Antibody characterisation of DISC1, a gene identified at a chromosomal translocation associated with psychiatric illness

DISCI (Disrupted in Schizophrenia) was identified at the breakpoint of a chromosomal translocation associated with schizophrenia and other psychiatric illnesses in a large Scottish family. Recent linkage studies have also identified the DISCI locus as a susceptibility factor for schizophrenia in Finnish families and DISCI is emerging as a candidate gene for psychiatric illness. At the time of identification DISCI was novel and the function of the DISCI protein was completely unknown. To characterise the function of DISCI, antibodies were raised against the DISCI protein using both a peptide and bacterially expressed recombinant protein as the antigen. The resulting antibodies were characterised thoroughly to ensure their specificity for DISCI. Multiple transcripts ofDISCI had been identified and the initial aim was to determine which of the transcripts were translated into functional proteins. Multiple DISCI-related proteins were found to exist in human but only a single isoform was identified in mouse and rat. In addition the protein expression levels of DISCI were examined in lymphoblastoid cell lines derived from members of the original translocation family. No evidence for a truncated protein resulting from the translocated chromosome was found but preliminary results suggest that levels of DISCI are significantly reduced in translocation carriers. The subcellular localisation of DISCI was studied in human neuroblastoma and glioblastoma cell lines. DISCI was found to colocalise with mitochondria in a cytoskeletal associated pattern, and in differentiated neuroblastoma cells DISCI localised to the tips of developing neurites suggesting a possible role in neurite outgrowth. Further characterisation of the function of DISCI should now focus on its relationship with the mitochondria to ascertain the significance of this association to both the function and subsequent dysfunction of the nervous system.
The Association Between Endometriosis and Surface Epithelial Ovarian Tumors: A Review of Pathological Data

Background: Endometriosis is a prevalent benign condition arising from female reproductive system and aﬀects about 7% to 10% of females. The association of this disorder with epithelial ovarian tumors has been a matter of interest in gynecology. Objectives: Thepresentstudywasconductedtoassesstheassociationbetweenendometriosisanddiﬀerenttypesof surfaceepithe-lial ovarian tumor. Methods: Microscopicslidesof182caseswiththediagnosisofsurfaceepithelialovariancarcinomaandborderlinetumorfrom2007 to2014werereviewedforthepresenceof endometriosisinatertiarygynecologicalcenter. Additionaldataincludedage,tumorsize and laterality, site of endometriosis, presence of atypical endometriosis, and concomitant uterine endometrial carcinoma. Results: Endometriosiswasfoundin32outof the182(17.58%)of reviewedovarianepithelialtumorcases. Theyincludedendometri-oidcarcinoma(46.87%),clearcellcarcinoma(18.75%),borderlineepithelialtumor(31.25%),andlow-gradeserouspapillarycarcinoma (3.12%). Conclusions: Endometrioid and clear cell types of ovarian tumors were most frequently associated with endometriosis.