Miracle-dz/UniFAR-FTUs huggingface dataset:
Variabilidade genética e associação entre caracteres em germoplasma de pinhão-manso (Jatropha curcas L.)1

A oleaginosa pinhao-manso (Jatropha curcas L.) tem se mostrado uma importante alternativa a producao de biodiesel no Brasil. Objetivando-se conhecer a variabilidade genetica existente na Colecao de germoplasma da UFRRJ, e tambem identificar genotipos de desempenho superior, portadores de atributos importantes ao melhoramento, 60 acessos de J. curcas, aos tres anos de idade, foram caracterizados a partir de 12 descritores morfo-agronomicos. A descricao indicou que as caracteristicas producao de oleo e projecao da copa se mostraram como as de maior variabilidade genetica, ao passo que os atributos intrinsecos as sementes apresentaram os menores valores de variacao. A decomposicao das correlacoes, via analise de trilha, evidenciou importantes associacoes entre a altura de plantas, a projecao da copa, o numero de ramos, o tempo de formacao do fruto e o teor de oleo sobre a producao de oleo por planta. Tal resultado corroborou a possibilidade destas caracteristicas, na Colecao de germoplasma da UFRRJ, serem adotadas como criterio de selecao indireta para a obtencao de genotipos mais produtivos, com porte reduzido e menor periodo de colheita. Pela analise de componentes principais se identificou a producao de oleo e o numero de ramos como as caracteristicas que mais contribuiram para a variacao observada. Os agrupamentos de Tocher e UPGMA promoveram a formacao de sete e oito grupos dissimilares de genotipos, respectivamente, apresentando a possibilidade de serem envolvidos em futuros cruzamentos, e revelando a existencia de uma consideravel variabilidade para as caracteristicas avaliadas.
Foliage Profile by Vertical Measurements

A technique is described for estimating a foilage profile in a forest by a combination of measurements over random lines of points: (1) counts of leaf contacts on a plumb line below a tripod, (2) sightings on the heights of lowest leaves over grids of points, and (3) the proportions of sky unobscured by leaves.
popart: full‐feature software for haplotype network construction

Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production. popart also provides a platform for the implementation and distribution of new network‐based methods – we describe one such new method, integer neighbour‐joining. The software is open source and freely available for all major operating systems.
Specific Heat, Thermal Conductivity and Thermal Diffusivity of Red Lentil Seed as a Function of Moisture Content

Thermal properties of red lentil seeds, including specific heat, thermal conductivity and thermal diffusivity in the moisture content range of 9.5–21.1% (w.b) were determined. The specific heat was measured using method of mixtures and found to be between 1.08 and 2.03 kJ/kg·K as the moisture content increased. The thermal conductivity of seed increased from 0.191 to 0.241 W/m·K by increasing moisture content (P < 0.05). This relationship has been established in the form of a second-order regression equation. Moreover, the thermal diffusivity computed from the values of thermal conductivity, specific heat and bulk density showed polynomial decrease from 2.15 × l0−7 to 1.65 × 10−7 m2/s in the specified range of moisture content (P < 0.05). Determination of these characteristics is practical in modeling thermal behavior of red lentil seeds during thermal processing operations, such as frying, drying and baking. Practical Application Thermal properties of agricultural materials and foods need to be known to better understand their nature and to be able to develop new technologies. Knowledge of thermal properties is important for mathematical modeling and simulation of heat and moisture transport. However, the moisture content significantly affects different thermal characteristics. The presented models and equations in this study allow engineers to predict these properties, thus saving time, material and cost.
Two Groups of Porcine TCRγδ+ Thymocytes Behave and Diverge Differently1

Developmental pathways of γδ T cells are still unknown, largely because of the absence of recognized lineage-specific surface markers other than the TCR. We have shown that porcine γδ thymocytes can be divided into 12 subsets of the following two major groups: 1) CD4− γδ thymocytes that can be further subdivided according to their CD2/CD8αα phenotype, and 2) CD4+ γδ thymocytes that are always CD1+CD2+CD8αβ+ and have no counterpart in the periphery. In this study, we have analyzed γδ thymocyte subsets with respect to behavior during cultivation, cell cycle status, and lymphocyte-specific transcripts. The group of CD4− γδ thymocytes gives rise to all γδ T cells found in the periphery. Proliferating CD2+CD8−CD1+CD45RC− γδ thymocytes are a common precursor of this group. These precursors differentiate into CD2+CD8αα+, CD2+CD8−, and CD2−CD8− γδ T cell subsets, which subsequently mature by loss of CD1 and by eventual gain of CD45RC expression. In contrast, the group of CD4+ γδ thymocytes represents transient and independent subsets that are never exported from thymus as TCRγδ+ T cells. In accordance with the following findings, we propose that CD4+CD8αβ+ γδ thymocytes extinguish their TCRγδ expression and differentiate along the αβ T cell lineage program: 1) CD4+ γδ thymocytes are actively dividing; 2) CD4+ γδ thymocytes do not die, although their numbers decreased with prolonged cultivation; 3) CD4+ γδ thymocytes express transcripts for RAG-1, TdT, and TCRβ; and 4) CD4+ γδ thymocytes are able to alter their phenotype to TCRαβ+ thymocytes under appropriate culture conditions.
Embryo Rescue through in Ovulo Culture in Helianthus

In vitro rescuing of interspecific embryos between sunflower (Helianthus annuus L.) and other Helianthus species has been limited by the inability to culture embryos less developed than the vascular stage. The objective of this research was to develop a technique for rescuing ✕ Helianthus embryos at an earlier growth stage. This objective was achieved by culturing the embryos for 1 wk in ovulo on artificial agar media. During that culture period, 51 to 84% of the embryos from five sunflower genotypes developed to the vascular stage like in vivo sib-embryos of the same age left as checks on greenhouse plants. Survival and development of sunflower embryos grown in ovulo were not affected by the salt composition of the four media tested (B5, B5S, MS and NN), or benefited by high sucrose levels (90 or 120g L⁻¹). The technique of in ovulo culture resulted in rescuing 52% of H. annuus ✕ H. maximiliani Schrad. hybrid embryos. This indicates that sunflower ovules cultured on standard media fulfilled the requirements of Helianthus hybrid embryos at an early stage of development. After excision from the ovule and subsequent culturing for 2 wk on fresh media with the same composition, 40 to 60% of H. annuus embryos and 25% of H. annuus ✕ H. maximiliani hybrid embryos germinated into plantlets. Six H. annuus ✕ H. maximiliani plantlets survived transfer to the greenhouse and grew into flowering plants that exhibited traits from both parents. These are the first reported hybrid plants between H. annuus and H. maximiliani using sunflower as the female parent.
Phylogeny of parasitic Platyhelminthes: a critical study of synapomorphies proposed on the basis of the ultrastructure of spermiogenesis and spermatozoa

Recent cladistic phylogenies of the Platyhelminthes, especially the parasitic species, use for synapomorphies several characters of the spermatozoa, together with other characters. This paper reinvestigates synapomorphies based on sperm characteristics. The outgroup usually chosen for such studies on the parasitic Platyhelminthes (Cercomeria) is the "Dalyelliida" or "Dalyellioida," generally considered a paraphyletic group, but sperm structure in this group shows great variation. In this paper, the Typhloplanoida, which have a plesiomorphic structure (two free axonemes), are considered the outgroup. One of the synapomorphies recently proposed for the Neodermata is "spermatozoon with axonemes incorporated in the cytoplasm. " This definition introduces convergences with several other groups of nonparasitic Platyhelminthes. A more precise definition of spermiogenesis, based on a detailed description, is proposed in this paper and avoids homoplasies: "proximodistal fusion of the axonemes. " This implies the pre.
Effect of Cluster Thinning on Berry Skin Anthocyanin Composition of Vitis vinifera cv. Nebbiolo

Cluster thinning (removal of 50% of the cluster one month after bloom) was tested for three consecutive years in a vineyard located in southern Piedmont (Italy). At harvest, concentrations of total anthocyanins and flavonoids were assessed by spectrophotometry and concentrations of individual anthocyanins were determined by high-performance liquid chromatography. Berry weight and berry skin weight slightly increased following thinning. Soluble solids and berry skin anthocyanins and flavonoids were more concentrated in berries from cluster-thinned plants. Cluster thinning increased the concentrations of cyanidin-3-glucoside, peonidin-3-glucoside, and, to a lesser extent, petunidin-3-glucoside. Concentrations of malvidin-3-glucoside and of acylated anthocyanins were not affected by cluster thinning.
Bases and Experience of Expressing the Protein Content of Milk—England and Wales

Abstract Milk proteins are grouped in three rather arbitrary categories, which are separated by acid precipitations. Each is determined by reference Kjeldahl (N × 6.38) measurement. Quality payment schemes to dairy farmers, which involve a protein payment, are currently almost universally based on total protein. The alternative use of true protein (caseins plus whey proteins and proteosepeptones) has been under debate for some years, and, in France, NPN is discounted in DHI and quality payment testing. Arguments favoring discounting NPN in payments are weighed against the commercial problems that such action creates. The major reason for change is to improve analytical accuracy, but the commercial price to be paid for such a change seems unjustified, and I argue for retention of recording protein as total protein.
Cutting Edge: LFA-1 Is Required for Liver NK1.1+TCRαβ+ Cell Development: Evidence That Liver NK1.1+TCRαβ+ Cells Originate from Multiple Pathways

Using mice deficient for LFA-1, CD44, and ICAM-1, we examined the role of these adhesion molecules in NK1.1+TCRαβ+ (NKT) cell development. Although no defect in NKT cell development was observed in CD44−/− and ICAM-1−/− mice, a dramatic reduction of liver NKT cells was observed in LFA-1−/− mice. Normal numbers of NKT cells were present in other lymphoid organs in LFA-1−/− mice. When LFA-1−/− splenocytes were injected i.v. into wild-type mice, the frequency of NKT cells among donor-derived cells in the recipient liver was normal. In contrast, when LFA-1−/− bone marrow (BM) cells were injected i.v. into irradiated wild-type mice, the frequency of liver NKT cells was significantly lower than that of mice injected with wild-type BM cells. Collectively, these data indicate that LFA-1 is required for the development of liver NKT cells, rather than the migration to and/or subsequent establishment of mature NKT cells in the liver.
Catalog of type specimens in the International Protozoan Type Collection

Cole, Linda. Catalog of Type Specimens in the International Protozoan Type Collection. Smithsonian Contributions to Zoology, number 561, 28 pages, 1994. —The International Protozoan Type Collection, which is located at the National Museum of Natural History, Smithsonian Institution, Washington, D.C., includes holotypes, paratypes, syntypes, neotypes, lectotypes and paralectotypes. As of October 1992, the collection consists of five phyla (Ciliophora, Sarcomastigophora, Apicomplexa, Microspora, and Myxozoa) composing approximately 542 species. This catalog lists types within each Phylum/Subphylum/Superclass/Class/ Order/Suborder/Family/Subfamily in alphabetical order by genus and also by species. The naming authorities and year, nature of type, amount of material, catalog number, and host are given. OFFICIAL PUBLICATION DATE is handstamped in a limited number of initial copies and is recorded in the Institution's annual report, Smithsonian Year. SERIES COVER DESIGN: The coral Montastrea cavernosa (Linnaeus). Library of Congress Cataloging-in-Publication Data Cole. Linda L. Catalog of type specimens in the International Protozoan Type Collection / Linda Cole. p. cm. —(Smithsonian contributions to zoology ; no. 561) Includes bibliographical references. 1. Protozoa—Type specimens—Catalogs and collections—Washington (D.C.) 2. National Museum of Natural History (U.S.)—Catalogs. I. Title. II. Title: International Protozoan Type Collection. III. Series. Qll . S54no. 561 [QL366J 591 s—<lc20 94-9547 [593.1'074'753] CIP ® The paper used in this publication meets the minimum requirements of the American National Standard for Permanence of Paper for Printed Library Materials Z39.48—1984.
ESTUDIO DE LA ENTOMOFAUNA SUCESIONAL ASOCIADA A LA DESCOMPOSICIÓN DE UN CADÁVER DE CERDO DOMÉSTICO (Sus scrofa) EN CONDICIONES DE CAMPO

During July to September of 2003, characterization of entomofauna attracted by decomposition of two pigs (Sus scrofa) was carried out in the experimental farm of Federacion Nacional de Cafeteros de Colombia at Consaca (Narino). One of the two pigs was used as a control sample. Pioneer settler insects of carcass belonged to families Calliphoridae and Sarcophagidae (Diptera). From Calliphoridae individuals from Chrysomya albiceps (Wiedemann 1819), Chrysomya putoria (Wiedemann 1818), Chrysomya rufifacies (Macquart 1843) and Lucilia sp. were captured. C. albiceps and Lucilia sp. were the most abundant species. Families from Coleoptera order were also found: Histeridae, Staphilinidae, Silphidae, as predators, and Dermestidae as necrophagous. Other groups of insects were observed occasionaly. Nevertheless, as predators of Diptera grubs, individuals of Labidus sp. (Formicidae: subfamily Ecitoninae) were present during the entire decomposition process.
TNF gene expression in macrophage activation and endotoxin tolerance

TNF is an inflammatory cytokine that plays a critical role in the acute phase response to infection, and its dysregulation has been implicated in the pathology of several inflammatory and autoimmune disorders. TNF gene expression is regulated in a cell typeand inducer-specific manner that involves chromatin alterations at both the TNF promoter and distal DNase I hypersensitive (DH) sites within the TNF/LT locus. While the mechanisms underlying TNF gene activation in monocytes/macrophages and T cells have been studied intensively, the mechanisms of enhanced, repressed, and restored TNF gene expression in the context of classical macrophage activation and endotoxin tolerance remain largely unknown. We set out to understand how TNF gene expression is modulated during these biological processes by characterizing the chromatin environment of the TNF/LT locus. In the context of classical macrophage activation, IFN-γ primes both circulating monocytes and tissue-resident macrophages so that, upon microbial recognition, there is an enhanced anti-microbial response; importantly, this results in enhanced TNF transcription. The mechanisms involved in priming are unclear; the IFN-γ-inducible transcription factors IRF1 and STAT1 have been implicated, but functional roles for these factors have not been determined. Here, we show in primary human monocyte-derived macrophages (MDMs) that IFN-γ poises the TNF/LT locus for enhanced TNF transcription by exposing the distal enhancer element hHS-8, and that the ability of this element to promote TNF gene expression in response to priming depends on its recruitment of IRF1. We also demonstrate that IFN-γ poises hHS-8 for enhancer function by promoting H3K27me3 enrichment, and that subsequent LPS stimulation triggers hHS-8 enhancer activation through demethylation of H3K27me3 followed by acetylation of H3K27. These experiments provide a mechanistic
The Role of Costimulatory Molecules in the Development of Memory and Effector T Helper 2 Cells During an in vivo Immune Response to the Murine Gastrointestinal Parasite Heligmosomoides polygyrus

Abstract : Previous studies have demonstrated the importance of costimulatory interactions for effector CD4+ T helper (Th) cell development during the primary immune response. However, the role of costimulatory molecules in memory CD4+ T cell differentiation is not well understood. One model used to study the Th immune response involves oral infection of mice with the gastrointestinal nematode parasite Heligmosomoides polygyrus. Although the primary immune response to H. polygyrus is a chronic infection, challenge immunization triggers a T-dependent memory response that impairs adult worm maturation. In the studies presented herein, the effects of costimulatory molecule blockade on T helper effector cell function during the memory response were examined. Effector T cell development was inhibited during the primary response to H. polygyrus in B7-1/B7-2-/- mice; however, memory Th cells developed that produced IL-4 and mediated effective reductions in adult worm egg production, but did not provide effective Ag-specific B cell help or support increased germinal center (GC) formation. Parallel studies in H. polygyrus-challenged CD28-/- mice demonstrated similar IL-4 elevations and decreases in adult worm egg production. However, Ag-specific Ab responses and increased GC formation were significantly restored in H. polygyrusinoculated CD28-/- mice. Although elevations in serum IgG1 and GC formation were intact in H. polygyrus-challenged OX40L-/- mice, elevations in IL-4 and serum IgE were partially inhibited, and associated with decreased worm expulsion and increased egg production. To further examine the role of OX40L in Ag-specific CD4+ T cell IL-4 production following priming, adoptively transferred OVA-specific DO11.10 T cells were analyzed in the context of the H. polygyrus response. Following immunization with OVA plus H. polygyrus, Ag-specific T cell expansion, celThese studies extt
The use of image analysis to estimate population growth rate in Daphnia magna

1. Population growth rate (PGR) is central to the theory of population ecology and is crucial for projecting population trends in conservation biology, pest management and wildlife harvesting. Furthermore, PGR is increasingly used to assess the effects of stressors. Image analysis that can automatically count and measure photographed individuals offers a potential methodology for estimating PGR. 2. This study evaluated two ways in which the PGR of Daphnia magna, exposed to different stressors, can be estimated using an image analysis system. The first method estimated PGR as the ratio of counts of individuals obtained at two different times, while the second method estimated PGR as the ratio of population sizes at two different times, where size is measured by the sum of the individuals' surface areas, i.e. total population surface area. This method is attractive if surface area is correlated with reproductive value (RV), as it is for D. magna, because of the theoretical result that PGR is the rate at which the population RV increases. 3. The image analysis system proved reliable and reproducible in counting populations of up to 440 individuals in 5 L of water. Image counts correlated well with manual counts but with a systematic underestimate of about 30%. This does not affect accuracy when estimating PGR as the ratio of two counts. Area estimates of PGR correlated well with count estimates, but were systematically higher, possibly reflecting their greater accuracy in the study situation. 4. Analysis of relevant scenarios suggested the correlation between RV and body size will generally be good for organisms in which fecundity correlates with body size. In these circumstances, area estimation of PGR is theoretically better than count estimation. 5. Synthesis and applications. There are both theoretical and practical advantages to area estimation of population growth rate when individuals' reproductive values are consistently well correlated with their surface areas. Because stressors may affect both the number and quality of individuals, area estimation of population growth rate should improve the accuracy of predicting stress impacts at the population level.
Technical improvements for analysis of recalcitrant proteins by LC-MS : the myccorhiza responsive membrane proteome as a case study

Arbuscular mycorrhizas (AM) are widespread symbiotic associations between plant roots and AM fungi. Deep membrane alterations are the foremost morphological changes occurring in the host plant in response to AM symbiosis. Two-dimensional gel electrophoresis (2-DE) is the workhorse method in AM proteomics. Membrane proteins are under-represented in 2-DE because of their hydrophobicity, low abundance, and precipitation at their isoelectric point, thereby few are the identified membrane proteins involved in sustaining the AM symbiosis. Membrane proteomics is still challenging due to 2-DE related shortcomings, however latest trends and advancements in mass spectrometry (MS)-based quantitative proteomics offer enormous potential to monitor membrane protein change in abundance in large scale experiments. In the current work microsomal proteins of Medicago truncatula roots inoculated with Rhizophagus irregularis were, for the first time, scrutinised by state-of-the-art MS-based proteomic approaches iTRAQ-OFFGEL-LC-MS/MS and label-free 1-DE-LC-MS/MS. The applied workflows combine two novel proteomic procedures, label-based and -free, targeting an insight view on the membrane proteome changes in AM symbiosis. A subcellular fractionation method is herein described to access the total membrane-associated proteins with sufficient recovery and purity for their subsequent in-depth analysis. In addition to the biological gain by shedding the light on candidate AM-related membrane proteins, a methodological approach was carried out in the present work in order to elucidate the iTRAQ labelling impact on peptide isoelectric points.
Biochemical Changes During Seed Germination of Sterculia urens Roxb.

The present study describes biochemical changes taking place during seed germination of Sterculia urens. The levels of proteins, total amino acids, reducing sugars, total soluble sugars and lipids were studied during various stages of seed germination (0-15 days). Total protein content was decreased in cotyledons during seed germination while free amino acid content increased to its maximum extent by 9th day of germination and reverse trend thereafter. The levels of reducing sugars and total soluble sugars increased till 6th day of germination and decreased thereafter. The lipid content was high at initial stages of germination (0-6 days) but gradually decreased by 15th day of germination.
An Elicitor of Plant Volatiles from Beet Armyworm Oral Secretion

The compound N -(17-hydroxylinolenoyl)-l-glutamine (named here volicitin) was isolated from oral secretions of beet armyworm caterpillars. When applied to damaged leaves of corn seedlings, volicitin induces the seedlings to emit volatile compounds that attract parasitic wasps, natural enemies of the caterpillars. Mechanical damage of the leaves, without application of this compound, did not trigger release of the same blend of volatiles. Volicitin is a key component in a chain of chemical signals and biochemical processes that regulate tritrophic interactions among plants, insect herbivores, and natural enemies of the herbivores.