Miracle-dz/UniFAR-FTUs huggingface dataset:
Species composition and structure of an exotic Quercus suber stand on the island of Gran Canaria (Canary Islands)

Aim of the study: Although introduced tree species have been recognized as adversely affecting native ecosystems, conversely, some studies suggest they can facilitate recovery and promote the establishment of native plant communities. This study tests whether a native plant community is established under the closed canopies of an exotic species by analyzing regeneration and plant species composition.Area of study: Finca de Osorio, a public property of the Cabildo de Gran Canaria included in the Doramas Rural Park (Canary Islands, Spain). Main results: The results reveal that sapling regeneration is dominated by the exotic species, though some native ones are also present. The sapling regeneration community did not differ from the tree canopy composition, so, a native plant community recovery cannot be expected to occur. In addition, other introduced species were also present in the sapling composition community.Research highlights: The laurel forest of the Canary Islands is the most emblematic plant community of the Canary Island archipelago. The studied area dominated by Q. suber does not favor the regeneration of the native plant community. Thus, restoration programs will be required to enhance the native plant community and the area covered by this highly disturbed plant ecosystem on the island of Gran Canaria.Keywords: catalytic effect; invasion; laurel forest; plant community.
The identification and characterization of novel haemolysin genes from Clostridium difficile

Clostridium difficile is a Gram positive spore forming bacteria that is the leading cause of antibiotic associated diarrhoea and pseudomembranous colitis. C. difficile infection is a significant health care burden in hospital settings and in the community. One of the main factors that lead to C. difficile infection is the prolonged use of antimicrobial agents that disturb the microflora of the gut. This allows it to colonize and produce toxins which disrupt the integrity of the intestinal epithelium. Other than toxin production, C. difficile has a number of virulence factors including surface proteins and enzymes that aid in bacterial attachment and spread of infection. Another possible virulence factor that was described in clostridia and other bacteria is the production of haemolysins. These are proteins (sometimes lipids) produced by the bacterium and cause cytolysis of red blood and eukaryotic cells for example epithelial cells, leukocytes, lymphocytes, and macrophages. This work is the first report of C. difficile showing haemolytic activity and the aim of this thesis is to identify genes responsible for haemolysis in C. difficile. A CD630 genomic library was constructed in E. coli and six genes were found to confer haemolysis. One clone contained a gene (designated atlf) encoding a peptide homologous to an anthrax toxin lethal factor which exhibited large zones of haemolysis. Clostron and CRISPR-Cas9 based CD630 mutants were constructed with insertion and deletion in atlf respectively. The haemolysis of the mutants was tested on agar and by a quantitative assay, which revealed no change in the haemolytic phenotype compared to the wild type. This work suggests that haemolysis is a multifactorial phenomenon in C. difficile and may involve several genes. The CRISPR-Cas9 mutagenesis system constructed in this work will aid in many mutagenic studies to understand haemolysis and other virulence mechanisms in C. difficile.
Fæðuofnæmi og fæðuóþol Íslendinga á aldrinum 20-44 ára

Inngangur: Ýmis einkenni tengd neyslu akveðinna faeðutegunda eru algeng umkvortunarefni. I faestum tilvikum er þo haegt að staðfesta faeðuofnaemi/-oþol við profanir. I islenska hluta European Community Respiratory Health Survey var kannað algengi faeðutengdra einkenna meðal fullorðinna Islendinga. Efniviður og aðferðir: Rannsokuð voru 3600 karlar og konur 20-44 ara og ur þeim hopi voru 800 valin af handahofi og rannsokuð serstaklega. Einnig voru skoðuð oll þau sem notuðu astmalyf, eða hofðu astmaeinkenni. Spurt var meðal annars um einkenni fra ondunarfaerum, matarvenjur og einkenni tengd mat. Auk þess var herlendis spurt um lyfjaoþol, ofsaklaða, ofsabjug, barnaeksem, migreni og sora. Oll gengust undir huðprof fyrir 12 algengum ofnaemisvokum, blastursprof og maelingu a berkjuauðreitni með metakolini. Maeld voru sertaek IgE motefni fyrir fimm loftbornum ofnaemisvokum og sex algengum faeðutegundum. Niðurstoður: Af einstaklingum með faeðutengd einkenni hofðu 68% einkenni fra meltingarvegi, 22% utbrot eða klaða, 15% slaeman hofuðverk, 11% maeði, 8% nefrennsli/nefstiflur og 4% þreytu. Samtals voru 42 faeðuefni talin vold að þeim einkennum sem nefnd voru. I slembiurtakinu toldu 22% ser hafa orðið illt af akveðinni faeðu, 15% toldu sig alltaf veikjast með sama haetti af þessari serstoku faeðu. Konur lýstu oftar faeðuoþoli en karlar (17% a moti 13% (p=0,21)). Af slembiurtakinu hofðu einungis 1,8% motefni fyrir akveðinni faeðutegund. Marktaekt samband faeðutengdra einkenna var við einkenni um migreni, ofsaklaða og ofsabjug en þo serstaklega við aetlað lyfjaofnaemi. Konur voru i miklum meirihluta þeirra sem toldu sig hafa migreni (p<0,0001), ofsaklaða (p<0,01), ofsabjug (p<0,05) og lyfjaofnaemi (p<0,002). Engin tengsl voru milli faeðutengdra einkenna og metakolinprofa.
Endocarps of Pyrenacantha (Icacinaceae) from the Early Oligocene of Egypt

Premise of research. The fossil record of Pyrenacantha (Phytocreneae tribe, Icacinaceae) includes well-documented species from the Paleogene of North and South America, but to date, no fossils have been described from its present geographic range, the Old World tropics. We document endocarp remains from the early Oligocene Jebel Qatrani Formation, Fayum Province, Egypt, representing the first fossil evidence of this genus from Africa. We discuss the systematic affinities of these fossils as well as their biogeographic and paleoecological implications. Methodology. The fossil endocarps were studied by a combination of computed tomography scanning and reflected light microscopy and were extensively compared with modern fruits from multiple herbaria (representing all extant genera of Phytocreneae and numerous species of Pyrenacantha) to assess their systematic affinities. We also compared the Jebel Qatrani material with previously described Phytocreneae fossils. Pivotal results. The Jebel Qatrani fossils conform to Pyrenacantha in their overall size, surface ornamentation (pitted), and tubercle morphology and size (tubercles are peg shaped to spiny, like the tubercles of numerous extant species of Pyrenacantha, and the tubercle length-to-diameter ratio is well above 1.0, a feature that further distinguishes Pyrenacantha from other Phytocreneae genera). However, the combination of characters shown by the Jebel Qatrani fossils is unique among modern and fossil species of Pyrenacantha, and therefore we describe them herein as a new species: P. simonsii Stull, Tiffney, Wing & Manchester, sp. nov. Conclusions. The fossils described here indicate that Pyrenacantha has been present in Africa since at least the earliest Oligocene. Although Pyrenacantha is known from the Eocene of midlatitude North America and probably Europe, suggesting a Holarctic origin with subsequent restriction to the tropics in response to climatic cooling, the absence of older Paleogene fossils in Africa could instead reflect inadequate sampling. Given that all modern species of Pyrenacantha (and Phytocreneae in general) are climbers, we can infer that P. simonsii likely also had a climbing growth form, which is consistent with ecological interpretations of the Jebel Qatrani flora as representing at least a gallery forest if not a more widespread forest with appreciable rainfall.
Enhancing Transcriptomics-Based Model-Driven Performance via Stoichiometric Gene-to-Reaction Associations: Metabolic Reprogramming in Prostate Cancer

Genome-scale metabolic models (GSMMs) have been widely used to study the molecular mechanisms underlying a variety of diseases with a strong metabolic component such as diabetes or cancer. GSMMs incorporate logical rules associating genes, proteins, and reactions (GPR rules), enabling the integration of either proteomics or transcriptomics. However, current GPR formulation do not account for the necessary stoichiometry to describe the number of transcript copies that are necessary to generate a catalytically active enzyme, which limits our understanding of how gene expression modulates metabolism. Thus, in this short commentary article, we introduce the stoichimetric-GPR (S-GPR) concept, presented in Marin de Mas et al. The novel S-GPRs associations were implemented to study the metabolic reprogramming in DU145 prostate cancer cells associated to the chronic exposure to the endocrine disruptor Aldrin. The results showed that S-GPRs outperformed previous approaches by significantly improving the GSMM predictions. Thus, the novel S-GPR concept that we have developed enables a more precise integration of transcriptomics data into GSMM-based methods and can be extended to proteomics data, with an important impact in the environmental and the clinical fields.
Leaf resistance traits influence endophytic fungi colonization and community composition in a South American temperate rainforest

Despite the ubiquitous presence of fungal endophytes in woody plants, mechanisms underlying variation in foliar fungal endophyte communities are poorly understood. Given that endophytes in woody plants are predominantly horizontally transmitted, fungal endophyte colonization of foliar tissues is likely to be influenced by plant resistance traits. Here, we evaluated the association between leaf resistance traits and colonization and community composition of horizontally transmitted endophytes (HTE) in 10 dominant trees species in a temperate rainforest in Southern Chile. Because resistance traits might restrict colonization of HTE, it was hypothesized that host trees with similar leaf resistance traits would show similar HTE communities. We measured leaf traits with reported roles in plant resistance against pathogens and/or herbivores: cell wall polysaccharides, leaf toughness, flavonoids, anthocyanins, terpenoids and chitinases. We also determined variation in fungal read counts, number of operational taxonomic units (OTUs), diversity and community structure across tree species. Foliar fungal endophyte communities were characterized using Illumina MiSeq sequencing of tagged amplicons of the ITS1 region. Fungal read counts were significantly different among host trees, while number of OTUs and diversity were similar among them. Multivariate analyses showed that community composition of endophytic fungi significantly differed among hosts, and that variation in cell wall, flavonoids, anthocyanins and terpenoids was associated with differences in HTE communities. We found that host trees sharing leaf resistance traits harbour similar HTE communities. Fungal read counts decreased with increasing content of cell wall polysaccharides, while endophyte diversity decreased with increasing anthocyanin levels. Fungal read counts, in contrast, were positively associated with terpenoids. Additionally, culture‐based data indicated that some HTE strains inhibited the growth of the common fungal pathogen Botrytis cinerea. Synthesis. Overall, we found that leaf resistance traits may influence fungal endophyte colonization and community composition in tree species, likely through deterrent effects of structural and chemical traits. We suggest that endophytic fungi that overcome resistance traits might play a role in plant protection.
Economic impacts of space allowance per animal on beef cattle feedlot

The objective of this study was to assess the economic outcomes of three space allowances (6, 12, and 24 m2 per animal) for outdoor feedlots-finished beef cattle. Simulations considered confinement systems with a static capacity of 5,000 animals per cycle and two 86-day cycles per year. Performance data were obtained from 1,350 uncastrated bovine males. An increase in space allowance elevated the fixed cost per animal. Fixed and variable costs represented 3% and 93% of the total operating cost, respectively. For variable costs, around 70% was used for purchasing cattle and 17% for purchasing feed. The operating profit per animal increased as space allowance increased (R$ 80.90, R$ 102.00, and R$ 109.00 for 6, 12, and 24 m2 per animal, respectively). The three feedlot systems recovered the initial investment and had a positive net present value. In addition, the internal rates of return were 22%, 27%, and 25%, and the probabilities of financial loss were 33%, 29%, and 26% for pen sizes of 6, 12, and 24 m2 per animal, respectively. Therefore, larger space allowances improve profitability and reduce the risk of financial loss.
Regulatory roles of small RNAs in prokaryotes: parallels and contrast with eukaryotic miRNA

Small non-coding RNAs continue to be identified that regulate the processes of translation and transcription in prokaryotes. A variety of regulatory mechanisms have been characterized by these regulatory RNAs that occur by complementary base pairing between the small regulatory RNA (sreRNA) and a target mRNA, including transcription attenuation, translation inhibition, translation activation, and mRNA protection. Here, we discuss the description of these mechanisms, and the key components that contribute to the interactions between the sreRNA and the target mRNA. Additionally, we classify sreRNAs into categories based on their origins. Antisense RNA (asRNA) is defined strictly as cis-encoded, trans-acting regulatory RNA, while small RNA (sRNA) is strictly defined as trans-encoded, trans-acting regulatory RNA. Although both RNAs bind the target mRNA by Watson-Crick base pairing to the complementary sequence of mRNA, sRNA binding typically requires the presence of a chaperone protein, is only partially complementary to the target mRNA, and often targets multiple mRNAs. Therefore, we characterize the mechanism of sRNA as similar to the well characterized eukaryotic miRNA and discuss the parallels and differences between the two. The binding of asRNA to its target mRNA, by contrast, is typically independent of a chaperone protein, is completely or almost completely complementary to the mRNA target sequence and targets only a single mRNA. While this categorization is likely to evolve as the research identifies more relevant and distinguishing characteristics to classify sreRNAs, the classification used here of prokaryotic sreRNAs should lead to a more refined approach to the discussion and investigation of regulatory RNAs until then.
Rutin, a Natural Inhibitor of IGPD Protein, Inhibits the Biofilm Formation in Staphylococcus xylosus ATCC700404

The biofilm of bacteria plays an important role in antibiotic resistance and chronic infection. Thus, in order to solve the problem of resistant bacteria, it is very important to find new drugs that can inhibit the formation of biofilms. In recent years, researchers have shifted their attention to natural products. As a flavonoid, rutin has been reported to have a variety of biological activities, interestingly, in this study, the inhibitory effect of rutin on the biofilm of Staphylococcus xylosus was investigated. We confirmed that rutin could effectively inhibit the biofilm formation of S. xylosus, then, for the sake of discussion on how it interferes with the biofilm formation, the interaction between rutin and imidazolyl phosphate dehydratase (IGPD) which has been identified as the key enzyme that plays a vital role in the process of biofilm formation was analyzed by molecular docking, the results showed that rutin had a strong affinity with IGPD, it occupied the hydrophobic cavity of the active center forming four hydrogen bonds and many other interactions. In addition, we proved that rutin was able to combine with IGPD using SPR technique. Therefore, we determined the enzyme activity and histidine content of IGPD, the result indicated that rutin could simultaneously inhibit the activity of IGPD and abrogate the synthesis of histidine. Interestingly, the hisB gene encoding for IGPD and IGPD in S. xylosus were also significantly inhibited when the bacterial culture was treated with rutin. Taken together, the results have provided evidence that rutin is a natural drug that has the ability to interfere with the formation of biofilm in S. xylosus. It is therefore a potential enzyme inhibitor of IGPD. Author’s Summary Staphylococcus xylosus has been isolated from a variety of infections, and the biofilm formed by S. xylosus can help the bacteria evade the immune system of the host and cause chronic infections. Here, we dealt with this menace by establishing a highly effective drug with the ability to interfere with the process involved in the formation of biofilm in S. xylosus. IGPD has been reported to be directly involved in the formation of biofilm in Staphylococcus xylosus and it is known to be present in a variety of microorganisms. Based on this study, we developed a drug therapy targeting IGPD and at the same time interfere with the formation of biofilm in S. xylosus
Cotas para a soma de autovalores de grafos

xi 1 INTRODUÇÃO . 1 2 NOÇÕES BÁSICAS . 9 2.1 Noções Básicas Sobre Grafos . 9 2.1. 1 Operações entre Grafos . 13 2.1. 2 Classes de Grafos e Subgrafos . 17 2.2 Noções Básicas Sobre Matrizes . 24 2.2.1 Polinômio Caracteŕıstico, Autovalores e Autovetores . 25 2.2.2 Resultados Sobre Matrizes . 27 3 REPRESENTAÇÕES MATRICIAIS . 29 3.1 Matriz de Adjacência . 29 3.1. 1 Resultados sobre A-autovalores . 31 3.2 Matriz Laplaciana . 31 3.2.1 Resultados sobre L-autovalores . 33 3.3 Matriz Laplaciana sem Sinal . 36 3.3.1 Resultados sobre Q-autovalores . 37 iv 4 O PROBLEMA NORDHAUS-GADDUM . 43 4.1 O Problema de Nordhaus-Gaddum para μ1 . 44 4.2 O Problema de Nordhaus-Gaddum para μ2 . 47 4.3 O Problema de Nordhaus-Gaddum para q2 . 53 4.4 O Problema de Nordhaus-Gaddum para qn . 62 5 A SOMA DOS Q-AUTOVALORES . 66 5.1 Cotas para q1 + · · ·+ qk . 66 5.1. 1 Generalização do Argumento . 67 5.1. 2 Grafos livres de K2,s+1 . 70 5.1. 3 Grafos Livres de Ciclos Pares/Ímpares . 71 5.2 Conjectura de Brouwer . 73 5.2.1 Cografos: Resultados Parciais . 75 5.2.2 Grafos Threshold: Resultados Parciais . 78 6 CONCLUSÕES . 83 6.1 Sobre o problema de Nordhaus-Gaddum . 83 6.2 Sobre cotas para q1 + · · ·+ qk . 85 6.3 Sobre a conjectura de Brouwer . 86 REFERÊNCIAS BIBLIOGRÁFICAS . 88 ÍNDICE . 99
High-resolution in vivo identification of miRNA targets by Halo-Enhanced Ago2 Pulldown

The identification of miRNA targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily translated to an in vivo setting. To overcome these limitations and to facilitate the investigation of miRNA functions in mice, we have developed a method (HEAP: for Halo-Enhanced Ago2 Pulldown) to map miRNA-mRNA binding sites. This method is based on a novel genetically engineered mouse harboring a conditional, Cre-regulated, Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be efficiently purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, in developing embryos, in adult tissues and in autochthonous mouse models of human brain and lung cancers. The tools and the datasets we have generated will serve as a valuable resource to the scientific community and will facilitate the characterization of miRNA functions under physiological and pathological conditions.
EFFICACY OF CERTAIN INSECTICIDES AGAINST RED PALM WEEVIL, Rhynchophorus ferrugineus (OLIVIER) UNDER LABORATORY AND FIELD CONDITIONS.

The present work was conducted to evaluate the effect of eight insecticides against red palm weevil (RPW), Rhynchophorus ferrugineus under laboratory and field conditions. The insecticides were studied namely, Chlorpyrifos, Diazinon, Ethion, Fenitrothion, Fipronil, Methomyl, Phenthate and Profenofos. Under laboratory condition results showed that, Chlorpyrifos was the most effective insecticide against the egg stage of RPW, while Fipronil was the most effective one against larval and pupal stage, and Methomyl recorded the highest effect against the adult stages (♀, ♂). At field condition Data revealed that, at the concentration of 3ml/L, all level of the tested insecticides caused 100% recovery expect Methomyl which reached 90% recovery only. Using 2ml/L of the tested insecticides revealed 100% recovery with Fipronil, and 90% with Chlorpyrifos and Phenthoate, while it was 80% with Ethion, Fenitrothion and Profenofos. Diazinon and Methomyl revealed only 60 and 50% recovery, respectively. It worth mentioning that Fipronil seams as the most effective one followed by Chlorpyrifos and Phenthoate.
Spiritual Direction with Women Who Have Autoimmune Diseases: A Model of Psychospiritual Care

Rheumatoid arthritis (RA), multiple sclerosis (MS), and systemic lupus erythematosus (lupus) are incurable autoimmune diseases affecting a gr owing number of people in the U.S. Women typically receive medical care for the physical eff ects of these diseases, but psychospiritual dimensions of illness experiences are often neglect ed. Common autoimmune illness experiences include delayed diagnosis; chronic pain, fatigue, depression; and liminality (being neither healthy nor sick) . Women with RA, MS, and lupus also experience ongoing losses (which may be disenfranchised), such as losses of identity, relationships, self-agency, and spiritual beliefs and practices . As a result of ongoing experiences of suffering and loss, women can “get stuck” in spiritual str uggles that negatively affect her overall health and well-being. Provisional theolo gica claims about the psychospiritual needs of women with RA, MS, and lupus assert that they would benefit from ongoing (over the course of years) acknowledgment of losses and complex, contextual theological meaning making, tested through coping strategies and s piritual practices that help them establish and/or sustain well-integrated spiritua lities nd lifeenhancing relationships with God/the transcendent (a naming convention that ref lects diverse spiritualities and spiritual direction practices). Evaluation of medi cal, psychological, and pastoral caregiving approaches finds contemporary intercul tural spiritual direction, grounded in the Christian tradition, to be an optimal context for long term care that addresses these needs. A model of spiritual direction for women w ith iii autoimmune disorders calls for (1) spiritual directors informed by women’s ex peri nces of autoimmune disease and prepared to balance a woman’s need to engage in transformative spiritual struggle with the risks posed by getting stuck in c hroni struggles, (2) an intercultural and feminist approach that privileges women’s experiences and understandings of illness and God/the transcendent, (3) ongoing complex and contextual theological meaning making through narrative and ritual pract ices that address the shifting perspectives of chronic illness (recurrent vacillation betwee n illn ss-in-theforeground and wellness-in-the-foreground), (4) attention to coping strategies and spiritual practices that enact life-enhancing understandings of illness a d God/the transcendent, and (5) co-construction and performance of rituals that acknowledge losses and facilitate transitions between illness-in-the-foreground and wellne ss-i -theforeground perspectives. This model of spiritual direction can be used in one-on-one or group settings.