Miracle-dz/UniFAR-FTUs huggingface dataset:
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração

A cana-de-acucar e uma das principais especies cultivadas para o fornecimento mundial de acucar e energia renovavel. Devido a elevada quantidade de elementos repetitivos e os varios eventos de poliploidizacao, o genoma da especie ainda nao foi montado e anotado, diferentemente de outras especies de interesse agronomico. Assim, as informacoes do transcritoma da especie se tornam ainda mais uteis por dar suporte as iniciativas de analises genomicas. Um draft assembly do transcritoma de cana-de-acucar foi montado a partir do sequenciamento Illumina de bibliotecas paired-ends de cinco orgaos distintos da planta, obtidos de uma amostra de trinta clones elite. Os dados de RNA-seq passaram por analises de controle de qualidade e normalizacao. O software Trinity foi utilizado para montagem de novo do transcritoma. Os scaffolds obtidos identificados como ORFs completas foram anotados conforme os termos do Gene Ontology. O draft assembly obtido para o transcritoma de cana-de-acucar foi caracterizado pela identificacao de marcadores moleculares do tipo microssatelites e SNPs e pela avaliacao da contribuicao dos diferentes orgaos vegetais para constituicao final do transcritoma. O transcritoma obtido compreendeu 178 Mb, distribuidos em 131.831 scaffolds, representando 61.225 genes. O tamanho medio dos transcritos foi de 1.350 pb, com valor de N50 igual a 1.667 pb. Um total de 1.250 transcritos, identificados como ORFs completas, nao apresentaram similaridade com sequencias do banco de dados nr do NCBI, sendo considerados novas regioes transcricionalmente ativas (nTARs). A anotacao realizada atraves do banco de dados do KEGG identificou 234 transcritos codificantes para enzimas integrantes do metabolismo de sacarose e amido, uma importante rota metabolica para compreensao da relacao entre taxa fotossintetica e o acumulo de sacarose no colmo. Os cinco orgaos vegetais utilizados contribuiram igualmente para a constituicao do draft do transcritoma de cana-de-acucar. Foram identificadas 12.931 regioes genomicas contendo microssatelites perfeitos, com predominio de di e tri nucleotideos. Em media, identificou-se um SNP a cada 18 pares de bases, com mais de quatro milhoes de SNPs identificados. A diversidade nucleotidica dos trinta clones elites utilizados e elevada. A identificacao destes marcadores moleculares, principalmente os marcadores SNPs, fornece a possibilidade de utilizacao destes polimorfismos em estudos geneticos e genomicos de cana-de-acucar, incluindo o emprego em abordagens como selecao genomica ampla no melhoramento da especie. O draft assembly do transcritoma de cana-de-acucar proposto neste estudo possui qualidade de dados e de analise suficiente para ser utilizado na tentativa de abranger um transcritoma de referencia para as especies de Saccharum spp.
Decrease of heat shock protein levels in hela tumor cells by red wine extracts

The effect of extracts from two red and one white wine on Hsp70 and Hsp27 levels in HeLa tumor cells was investigated. Each wine was fractionated into three extracts using solid phase extraction and tested. Total phenol content was determined by the Folin-Ciocalteau method and phenolic composition by HPLC-DAD. Hsps levels were determined by Western blot analysis. One extract of each red wine reduced both Hsp70 and Hsp27 levels by about 2-fold, while the other wine extracts gave no significant effect. Both active extracts exhibited much higher total phenolics than the others, and they were rich in anthocyanins and flavanols.
Atypical Enostoses—Series of Ten Cases and Literature Review

Bone islands (BI; enostoses) may be solitary or occur in the setting of osteopoikilosis (multiple bone islands) and are sometimes associated with Gardner’s Syndrome (osteopoikilosis and colonic polyposis). Characteristic features of bone islands are (1) absence of pain or local tenderness, (2) typical radio dense central appearance with peripheral radiating spicules (rose thorn), (3) Mean CT (computerized tomography) attenuation values above 885 Hounsfield units (HU) (4) absence of uptake on bone scan and (5) radiographic stability over time. However, when enostoses display atypical features of pain, unusual radiographic appearance, aberrant HU, increased radiotracer uptake, and/or enlargement, they can be difficult to differentiate from more sinister bony lesions such as osteoblastic metastasis, low grade central osteosarcoma, osteoid osteoma and osteoblastoma. In this retrospective case series, the demographic, clinical, radiographic, treatment and outcome for ten patients with eleven atypical bone islands (ABI) are presented, some showing associated pain (5), some with atypical radiographic appearance (3), some with increased activity on BS (4), some with documented enlargement over time (7), one with abnormal CT attenuation value, some in the setting of osteopoikilosis (2), one in the setting of Gardner’s Syndrome and one osteoid osteoma simulating a bone island. This series represents the spectrum of presentations of ABI. Comprehensive review of the literature reveals that the previous largest series of ABI showing enlargement as the atypical feature was in younger patients with jaw BI. Hence, this represents one of the largest series reported of ABI of all types in adults.
Detecting Selection from Linked Sites Using an F-Model

Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations connected by migration is the F-model, which measures differences in allele frequencies by population specific FST coefficients. This model readily accounts for multiple evolutionary forces by partitioning FST coefficients into locus- and population-specific components reflecting selection and drift, respectively. Here we present an extension of this model to linked loci by means of a hidden Markov model (HMM), which characterizes the effect of selection on linked markers through correlations in the locus specific component along the genome. Using extensive simulations, we show that the statistical power of our method is up to twofold higher than that of previous implementations that assume sites to be independent. We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP).
A Novel HPLC-Based Method to Investigate on RNA after Fixation

RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different fixatives on RNA. By the application of the presented method, which is based on the Nuclease S1 enzymatic digestion of RNA extracts followed by a HPLC analysis, it is possible to quantify the unmodified nucleotide monophosphates (NMPs) in the mixture and recognize their hydroxymethyl derivatives as well as other un-canonical RNA moieties. The results obtained from a set of mouse livers fixed/embedded with different protocols as well from a set of clinical samples aged 0 to 30 years-old show that alcohol-based fixatives do not induce chemical modification of the nucleic acid under ISO standard recommendations and confirm that pre-analytical conditions play a major role in RNA preservation.
Behavioural reaction of root vole (Microtus oeconomus Pallas) males of different social ranks to familiar and novel odour of conspecific males

In this experiment, we tested the hypothesis that males of root voles (Microtus oeconomus Pallas) of different social ranks display different behavioural strategies. To document behavioural differences between social ranks, we investigated patterns in the behavioural responses to urine cues from familiar and novel individu in a choice maze. Ten pairs of male voles were efectively used in this experiment. All behaviour was recorded with OBSERVER 5.0. When experiment was finished, video tapes were transformed into digital data. Then all data were analyzed by SPSS. The results showed that the approach latency of subordinates was shorter for familiar odours than novel ones, dominant individuals preferentially entered the strange odourant box, subordinates preferred familiar odours over novel ones, subordinates spent more time visiting familiar odours compared to the novel odours, dominants preferred novel odours to familiar ones, subordinates approached familiar odours more frequently than novel ones and self-groomed more often in the familiar odourant box than in the novel box, and dominant and subordinate individuals showed significantly different countermarking behaviours to familiar and novel odours. In conclusion, the dominants and subordinates displayed different behaviour patterns when faced to familiar and novel conspecific males' urine cues. The data support our hypothesis that differences in social rank induce differences in behavioural patterns.
The cytokine MIF controls daily rhythms of symbiont nutrition in an animal–bacterial association

Significance Daily biological rhythms are fundamental, evolutionarily conserved features of many symbioses. Here we use the binary squid–vibrio association, the simplicity of which has offered the resolution to explore strategies of symbiosis that are shared with more complex systems, such as those of mammals. We demonstrate a pivotal role for an evolutionarily conserved cytokine, macrophage migration inhibitory factor, or MIF, which is abundant in epithelia supporting the symbionts of both the squid light organ and the mammalian gut. In the mature squid association, MIF regulates the cyclic metabolic dialogue that underlies oscillations in host-provided symbiont nutrients. As such, this study integrates the role of MIF across two distinct time scales: the host’s life history and its daily rhythms. The recent recognition that many symbioses exhibit daily rhythms has encouraged research into the partner dialogue that drives these biological oscillations. Here we characterized the pivotal role of the versatile cytokine macrophage migration inhibitory factor (MIF) in regulating a metabolic rhythm in the model light-organ symbiosis between Euprymna scolopes and Vibrio fischeri. As the juvenile host matures, it develops complex daily rhythms characterized by profound changes in the association, from gene expression to behavior. One such rhythm is a diurnal shift in symbiont metabolism triggered by the periodic provision of a specific nutrient by the mature host: each night the symbionts catabolize chitin released from hemocytes (phagocytic immune cells) that traffic into the light-organ crypts, where the population of V. fischeri cells resides. Nocturnal migration of these macrophage-like cells, together with identification of an E. scolopes MIF (EsMIF) in the light-organ transcriptome, led us to ask whether EsMIF might be the gatekeeper controlling the periodic movement of the hemocytes. Western blots, ELISAs, and confocal immunocytochemistry showed EsMIF was at highest abundance in the light organ. Its concentration there was lowest at night, when hemocytes entered the crypts. EsMIF inhibited migration of isolated hemocytes, whereas exported bacterial products, including peptidoglycan derivatives and secreted chitin catabolites, induced migration. These results provide evidence that the nocturnal decrease in EsMIF concentration permits the hemocytes to be drawn into the crypts, delivering chitin. This nutritional function for a cytokine offers the basis for the diurnal rhythms underlying a dynamic symbiotic conversation.
Durability of Structural Lightweight Concrete with Sintered Fly Ash Aggregate

The aim of this study was to present the problem of durability of structural lightweight concrete made of a sintered fly ash aggregate. The issue of durability was researched for 12 concrete series in terms of their water absorption, water permeability, and freeze-thaw resistance. Additionally, the microstructure of several concretes was analyzed with a scanning electron microscope (SEM). In the durability research, the influences of the following parameters were taken into consideration: The initial moisture content of sintered fly ash (mc = 0, 17–18, and 24–25%); the aggregate grading (4/8 and 6/12 mm); and the water-cement ratio (w/c = 0.55 and 0.37). As a result of various compositions, the concretes revealed different properties. The density ranged from 1470 to 1920 kg/m3, and the corresponding strength ranged from 25.0 to 83.5 MPa. The durability research results of tested lightweight concretes showed that, despite considerably higher water absorption, a comparable water permeability and comparable or better freeze-thaw resistance in relation to normal-weight concrete may be present. Nevertheless, the fundamental requirement of lightweight concrete to achieve good durability requires the aggregate’s initial moisture content to be limited and a sufficiently tight cement matrix to be selected. The volume share of the cement matrix and aggregate, the cement content, and even the concrete strength are of secondary importance.
In Vitro Plant Evaluation Trial: Reliability Test of Salinity Assays in Citrus Plants

Salinity is one of the major abiotic stresses affecting crops worldwide, and breeders are urged to evaluate new genotypes to know their degree of tolerance to this selective agent. However, obtaining a number of plants high enough to make the evaluation can prove to be a long and laborious process which could be overcome by using tissue culture techniques. In the present study, the reliability of tissue culture evaluations is called into question through two parallel experiments, in vitro and ex vitro, using Citrus macrophylla and four mutants thereof, previously selected by their different behavior to salinity, as a plant material. Plants were subjected to salinity for 8 weeks in both in vitro (80 mM NaCl) and ex vitro (100 mM NaCl) experiments, and differences with plants grown in control conditions without salt were analyzed. After the experiments, length, leaf damage, shoot dry weight, chlorophylls and ions were measured in both conditions and experiments. As a result, it was demonstrated that tissue culture is a reliable tool to determine whether a genotype is tolerant to salinity or not, since plants of the same genotype responded in a similar way to salinity in both experiments. Henceforth, in vitro evaluations can be employed to test genotypes in a very early stage and using very little time and space. However, genotypes that showed the biggest or lowest changes when cultured in salinity were not always the same in both experiments. Thus, only ex vitro experiments can be performed if the goal is to compare genotypes and see which genotype is the most or least resistant to salinity.
Point-of-Care Ultrasound for Central Venous Assessment in the Emergency Department

Objectives The objective of this study was to estimate the width, height, and depth of the femoral vein (FV) and internal jugular vein (IJV), both sites of potential central line placement in children, using point-of-care ultrasound. Methods This was a prospective observational study. Point-of-care ultrasound was used to measure the width, height, and depth of the right FV and IJV in 100 children. The primary outcome was a comparison of the widths of the FV and the IJV in the same child. Our primary hypothesis was that the IJV would be wider than the FV. Secondary outcome measures included comparison of the heights and depths the FV and IJV and description of vessel overlap frequency between the 2 sites. Results A total of 106 children were enrolled, with 6 subjects excluded, and equally divided into 5 age groups (0–30 days, 1–24 months, 2–5 years, 6–11 years, and 12–17 years). The FV/IJV width ratios (95% confidence interval) by age were 0.58 (0.49–0.68), 0.53 (0.43–0.66), 0.57 (0.49–0.67), 0.68 (0.55–0.85), and 0.73 (0.62–0.85), all P < 0.002. The FV/IJV height ratios were <1 in all age groups, with P < 0.003 in the 4 youngest age groups. The FV/IJV depth ratios were >1 in 6 to 11 years (P = 0.018) and 12 to 17 years (P < 0.001). Conclusions The IJV was significantly wider and taller than the FV in the same child in all age groups. The FV was significantly deeper than the IJV in children 6 years and older. This supports the use of the IJV as a potential site when placing ultrasound-guided central lines in children.
Comparison of the Effectiveness of Two Different Vaccination Regimes for Avian Influenza H9N2 in Broiler Chicken

Simple Summary The low pathogenic avian influenza H9N2 virus has been associated with severe economic losses in broiler chicken flocks. Problems associated with its control strategy are potential early infection and level of immune response that may be high in one-day-old chicks due to maternally derived antibodies. Herein, two vaccination regimes were evaluated in commercial broilers kept under either field or laboratory conditions. Two different vaccine types and concentrations were used, and the results highlighted a significantly higher protection against early infection when a homologous vaccine of high antigenic mass was applied at 7 days of life. Shedding was significantly reduced in this regime. Abstract Low pathogenic avian influenza virus is one of the major threats that has been affecting the poultry industry in the Middle East region for decades. Attempts to eradicate this disease have failed. Currently, there are commercial vaccines that are either imported or produced locally from recently circulating isolates of H9N2 in Egypt and Middle Eastern countries. This present work focused on comparing the effectiveness of two vaccines belonging to these categories in Egypt. Two commercial broiler flocks (Cobb-500 Broiler) with maternally derived immunity (MDA) against H9N2 virus were employed and placed under normal commercial field conditions or laboratory conditions. Immunity was evaluated on the basis of detectable humoral antibodies against influenza H9N2 virus, and challenge was conducted at 28 days of life using a recent wild H9N2 virus. The results showed that vaccination on the 7th day of life provided significantly higher immune response in both vaccine types, with significantly lower virus shedding compared to vaccination at day 1 of life, regardless of field or laboratory conditions. In addition, the vaccine produced from a recent local H9N2 isolate (MEFLUVAC-H9-16) provided a significantly higher humoral immune response under both field and laboratory conditions, as measured by serology and virus shedding (number of shedders and amount of shedding virus), being significantly lower following challenge on the 28th day of life, contrary to the imported H9 vaccine. In conclusion, use of H9N2 vaccine at 7 days of life provided a significantly higher protection than vaccination at day 1 of life in birds with MDA, suggesting vaccination regimes between 5–8-days of life for broiler chicks with MDA. Moreover, use of a vaccine prepared from a recently circulating H9N2 virus showed significantly higher protection and was more suitable for birds in the Middle East.
Microeukaryotic Communities Associated With the Seagrass Zostera marina Are Spatially Structured

Epibiotic microorganisms link seagrass productivity to higher trophic levels, but little is known about the processes structuring these communities, and which taxa consistently associate with seagrass. We investigated epibiotic microeukaryotes on seagrass (Zostera marina) leaves, substrates, and planktonic microeukaryotes in ten meadows in the Northeast Pacific. Seagrass epibiotic communities are distinct from planktonic and substrate communities. We found sixteen core microeukaryotes, including dinoflagellates, diatoms, and saprotrophic stramenopiles. Some likely use seagrass leaves as a substrate, others for grazing, or they may be saprotrophic organisms involved in seagrass decomposition or parasites; their relatives have been previously reported from marine sediments and in association with other hosts such as seaweeds. Core microeukaryotes were spatially structured, and none were ubiquitous across meadows. Seagrass epibiota were more spatially structured than planktonic communities, mostly due to spatial distance and changes in abiotic conditions across space. Seawater communities were relatively more similar in composition across sites and more influenced by the environmental component, but more variable over time. Core and transient taxa were both mostly structured by spatial distance and the abiotic environment, with little effect of host attributes, further indicating that those core taxa would not show a strong specific association with Z. marina.
Pollen Morphology of Hosta Tratt. (Funkiaceae) and Related Genera

CHUNG, M. G. AND S. B. JONES, JR. (Botany Department, University of Georgia, Athens, GA 30602). Pollen morphology of Hosta Tratt. (Funkiaceae) and related genera. Bull. Torrey Bot. Club 116: 31-44. 1989. -Pollen grains of 22 taxa of Hosta and nine taxa of closely related monocotyledons were investigated by light microscopy (LM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). On the basis of exine omamentation and wall ultrastructure, the pollen of Hosta can be divided into five types; reticulate, reticulate-like, rugulate, rugulate-baculate, and rugulate-granulate. The rugulate-granulate type is the most common and can be divided into eight subtypes based on variation in shape and size of the granules and degree of density of the rugulose exine elements. There is some speciesspecific variation in exine ornamentation. On palynological grounds, it is suggested that Hosta, Hesperocallis, and Leucocrinum may have originated from a common group of ancestral plants.
Effect of a Short-Time Probiotic Supplementation on the Abundance of the Main Constituents of the Gut Microbiota of Term Newborns Delivered by Cesarean Section—A Randomized, Prospective, Controlled Clinical Trial

The gut microbiota plays a pivotal role in the maintenance of human health. Numerous factors, including the mode of delivery, impact early gut colonization in newborns. Recent research focuses on the use of probiotics in the prevention of gut dysbiosis in newborns delivered by cesarean section (CS). The objective of this study was to determine whether a probiotic supplement given to newborns delivered by CS during their stay in the maternity ward alters the pattern of early gut colonization by lactic acid bacteria versus potential pathogens. A prospective, randomized trial was conducted. In total, 150 newborns, born at 38–40 weeks gestational age and delivered by CS, were included in the study. They were randomized into the intervention group, supplemented orally with a probiotic containing Bifidobacterium breve PB04 and Lactobacillus rhamnosus KL53A, and the control group. Stool samples were obtained on days 5 and 6 of life and after one month of life and were analyzed for the presence and abundance of the main groups of bacteria. An application of two probiotic bacteria during the first days of life after CS resulted in quick and abundant colonization by days 5 and 6, with high populations of L. rhamnosus and B. breve. The applied bacterial strains were present in the majority of neonates one month after. The supplementation of term neonates delivered by cesarean section immediately after birth with a mixture of L. rhamnosus and B. breve enriched the gut microbiota composition with lactic acid bacteria.