Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversidade de isolados brasileiros de Ralstonia solanacearum da biovar 2.

A bacteria de solo Ralstonia solanacearum (Rs), responsavel pela murcha bacteriana em diversas especies hospedeiras, e um complexo especifico devido a sua diversidade genetica. Historicamente, Rs tem sido classificada em biovares, baseado na utilizacao de acucares e alcoois como fonte de carbono, e em racas, baseado na capacidade de infectar diferencialmente especies hospedeiras. Esses sistemas de classificacao, entretanto, nao sao adequados para explicar toda a variabilidade deste patogeno. Por isso, Fegan e Prior (2005) propuseram uma nova classificacao em filotipos com base na regiao ITS (Intergenic Transcribed Sequence) entre os genes de RNA ribossomal 16S e 23S e sequevares baseados na sequencia do gene da enzima endoglucanase . As recentes pesquisas indicam que o filotipo I foi originado na Asia, o filotipo II nas Americas, o filotipo III originado na Africa e o filotipo IV na Indonesia. Neste trabalho, foram analisados 60 isolados brasileiros de Ralstonia solanacearum de procedencia geografica variada, a maioria deles associados a cultura da batata. Todos os isolados, pertencentes a colecao da Embrapa Hortalicas, foram confirmados como pertencentes ao complexo especifico Ralstonia solanacearum por meio de PCR com primers universais e posteriormente foram confirmados como sendo pertencentes a biovar 2. A classificacao em filotipos, realizada por meio de uma PCR multiplex, indicou que todos os isolados apresentaram fragmento amplificado correspondente ao filotipo II, com excecao de um isolado, obtido de pimentao em Brasilia (filotipo IV). Esses resultados corroboram a expectativa da prevalencia do filotipo II nas Americas. Sequenciamento e analise do gene endoglucanase (egl/0, mostrou que eles pertencem a sequevar 1 e 5 e que a variacao entre linhagens de uma mesma regiao e baixa. Resultados de "fingerprint" de Box-PCR indicam que os isolados brasileiros sao agrupados por regiao onde foram isolados e epoca de sua ocorrencia.
Immunomodulation by Food: Allergy Mitigation by Dietary Components

Proper and well-balanced immune functioning is of pivotal importance to health and well-being. In the past decades, there has been an apparent decrease in the prevalence of classical infectious diseases, with a concomitant increase in immune-related disorders, including allergies. Causally, a relationship with changes in life-style-related factors, amongst which hygienic practice, is often laid. Diet and nutrition can affect functioning of various immune parameters. This concept can be explored to prevent or mitigate allergic reactions via the development of targeted food products or ingredients. This review describes recent findings with respect to food products and ingredients that show potential in this respect, with special emphasis on pro- and prebiotics, s-glucans, fungal immunomodulatory proteins and ? -3 polyunsaturated fatty acids. The micro-organism-related products appear to strengthen Th1-mediated immunity, thus possibly restoring defective immune maturation due to overly hygienic living conditions. Also ? -3-PUFAs may hold promise to attenuate allergic symptoms, although this concept appears to function via mechanisms that are clearly distinct from the micro-organism derived compounds.
Genetic Diversity and Population Structure of the Threatened Giant Arapaima in Southwestern Guyana: Implications for Their Conservation

Information on population genetic structure and connectivity among populations is essential for the implementation of effective conservation and management strategies for threatened species. The giant Arapaima is one of the most heavily exploited and threatened freshwater fishes in Guyana. Using nuclear microsatellite markers and mitochondrial (mtDNA) sequences (partial 16S rRNA gene, tRNA-Leu gene, and ND1 gene), we evaluated the genetic structure of Arapaima from the Essequibo and Branco (i.e., Amazon) river basins in Guyana. Both markers showed low genetic diversity compared to previously reported studies of Arapaima from the Amazon. Only two mtDNA haplotypes were recovered in Guyana that differed in a single nucleotide position. One was novel and restricted to the Branco basin; the other had previously been reported from the Amazon but, in this study, was restricted to the Essequibo basin. Surprisingly, STRUCTURE analysis of microsatellite markers grouped Arapaima from Guyana into three distinct clusters; one was again restricted to the Branco basin, while the other two were sympatric at multiple sites in the Essequibo basin. This is the first time genetically distinct groups of Arapaima have been found in sympatry at multiple sites. Results have important implications for management of Arapaima and conservation of their genetic diversity.
Wood versus concrete and steel in house construction a life cycle assessment

The environmental friendliness of building materials can be measured in life cycle assessments of the total energy inputs for the product, from cradle to grave. How do the environmental costs of wood compare with concreteand steel in housing construction? First we compare energy values for each material and for house components. Taking the viewpoint of a consumer, we then compare three typical houses in which steel, concrete, or wood is the dominant component. It appears that wood, wood components, and houses built primarily of wood require lesseramounts of energy in their manufacture, assembly, and operation. The robustness ofthe conclusions is shown by the degree of agreement among researchers and through an assessment of the impact of uncertainties in the analysis.
Suppression of Off-Flavor Development in Freeze-Dried Plasma

It was attempted to find the components responsible for development of off-flavor in freeze-dried Porcine plasma during storage and to find a simple and offective method to remove them. Off-flavor degree (OFD) noticeably developed in freeze-dried plasma after storage at 37°C for 3 weeks and OFD was significantly (p<0.01) correlated to the amount of TBA reactive substances and fluorescence intensity (FI). Off-flavor development was greatly suppressed in freeze-dried plasma processed by ultracentrifugation and charcoal treatment at low pH for diminishing the amount of free fatty acids and phospholipids. The addition of arachidonic acid and phospholipid to the acid-charcoal treated plasma or hemoglobin
Designing “Metamolecules” for Photonic Function: Reduced Backscattering

Metamaterials, subwavelength nanostructured materials, can exhibit novel optical properties such as a negative index of refraction. Dielectric core–nanoparticle satellite clusters, termed “metamolecules,” can have strong optical magnetic resonances in the visible wavelength range—a requirement to achieve negative refractive index materials. However, achieving the desired photonic properties is challenging due to limited control in forming the metamolecule structures. Here, polystyrene (PS) core–gold nanoparticle (AuNP) satellite metamolecules with highly ordered single layers (monolayers) of AuNPs are fabricated and single particle spectroscopy, electron tomography structural measurements, and electrodynamics simulations are conducted to study the photonic properties of metamolecules constituted of ≈100 AuNPs. The simulated and experimental spectra of the many metamolecules studied, including excitation with azimuthally and radially polarized light, are in excellent agreement. It is shown that the scattering properties of the metamolecules are dominated by the AuNPs near the “equator” of the cluster, and that backscattering is strongly suppressed when different multipolar modes (e.g., dipolar and quadrupolar) of electric or optical magnetic character have comparable intensity due to the π‐phase shift of their scattering. Both the optical excitation fields and the ordering of the nanoparticles within metamolecules affect their optical excitation and scattering properties, providing new insights into designing novel photonic metamaterials.
Révision des espèces ouest-paléarctiques du genre Mediimorda Méquignon, 1 946 et description de deux nouvelles espèces d'Afrique du Nord (Coleoptera Mordellidae)

Les especes ouest-palearctiques du genre Mediimorda Mequignon, 1946 sont revisees. Mediimorda bipunctata var. attalica (Schilsky, 1895) est eleve au rang d'espece et M. fallaciosa (Stshegoleva-Barovskaja, 1930) est un synonyme junior. Deux nouvelles especes d'Afrique du Nord sont decrites Mediimorda horaki n. sp. et M. serrahimai n. sp. Des lectotypes sont designes pom Mediimorda bipunctata (Germar. 1827) et M. bipunctata var. abbreviate i (Schilsky. 1899). Des nouvelles attributions avec designation de lectotypes sont donnees pour M bipunctata var. induta (Schilsky. 1895) qui devient M. attalica var. induta (Schilsky . 1895) ; M. bipunctata var. obtecta (Schilsky. 1899) qui devient M attalica x ar. obtecta (Schilsky. 1899) et M. bipunctata var. basicornis (Schilsky, 1899) qui devient M attalica var. basicornis (Schilsky. 1 899). Deux cles d'identification, une pour les mâles et une pour les femelles, sont proposees, suivies du catalogue de l'ensemble des especes revisees, mentionnant leur distribution.
Distribution and habitat properties of Carex pulicaris and Pedicularis sylvatica at their range margin in NW Poland

This paper presents the distribution dynamics, soil and phytocoenotical conditions of the occurrence of Carex pulicaris and Pedicularis sylvatica at the margin of their range in NW Poland. Dynamic cartograms of these species were made on the basis of our field studies and available contemporary and historical records. The studies showed that the plants grow on organic hemic-muck soils, mucky soils and typical muckous soils. The occurrence of these two species on different types of soils proves that they are able to adapt easily to varying habitat conditions of post-bog areas. Populations of C. pulicaris and P. sylvatica were most frequently not numerous and occurred in small community patches. Analyzed phytocoenoses with C. pulicaris have been classified as the community of the alliance Caricion davallianae or the alliance Molinion . Phytocoenoses with P. sylvatica are represented by the association Nardo-Juncetum squarrosi and the community of the class Molinio-Arrhenatheretea . The distribution dynamics of these species shows that they are disappearing from some parts of this region, which proves the recessive trends. This process is more intensive for P. sylvatica , which should be included in the red list of Polish plants like C. pulicaris . The disappearance of the populations of both species has been caused by worsening habitat conditions (insufficient moisture, eutrophication), expansion of competitive plant species and land abandonment.
First report of sugar beet nematode, Heterodera schachtii Schmidt, 1871 (Nemata: Heteroderidae) in sugar beet growing areas of Şanlıurfa, Turkey

The sugar beet nematode, Heterodera schachtii , is the major pest of sugar beet and causes serious yield losses of about 10-70%. H eterodera schachtii occurs in more than 50 countries and regions, however, there has be limited investigation of H. schachtii in Turkey. Therefore, a survey of H. schachtii in the sugar beet producing regions of Şanliurfa was conducted in 2014 and 2015 growing seasons. Using morphological and molecular methods, 12 samples collected from three districts, Bozova, Karakopru and Siverek, in Şanliurfa Province, Turkey, were identified as H. schachtii . In pathogenicity test, the seedling emergence was delayed and reduced, the seedlings were stunted and necrotic, and the white females of H. schachtii were evident 25 days after inoculation. Phylogenetic analyses were also conducted. The 12 H. schachtii populations from Şanliurfa Province clustered together with populations from Europe and Morocco at the value of 99%. Sugar beet is the second largest crop in Turkey with the annual production of more 16 Mt. To our best knowledge, this is the first report of H. schachtii in Şanliurfa Province of Turkey.
Contributions to shrimp taxonomy — Editorial

The idea of devoting a special issue of Zootaxa to shrimp taxonomy was born during a late night meeting between the two editors in Leiden in November 2008. We discussed inviting all currently active shrimp taxonomists to come together in a single volume, dedicated to the description of new taxa in this fascinating group of animals. To be honest, our plan was not entirely altruistic, as at the time we were entering the final phase of compiling a species level list of all described taxa within the shrimp-like Decapoda (Dendrobranchiata, Stenopodidea and Caridea). As was done prior to publication of the crab list (Ng et al. 2008), we liked the idea of compiling a volume to bring to light as many descriptions as possible, both in order for the catalogue, once completed, to remain current for perhaps a few more months (in this fast paced field), but also to offer our colleagues a chance to publish upon (and sort out) some of the nomenclatorial problems any branch of descriptive taxonomy faces.
2 Protein Secretion, Membrane Biogenesis, and Endocytosis

I. INTRODUCTION A growing yeast cell doubles its surface area every division cycle. The principal function of the yeast secretory pathway is to generate and deliver new membrane and protein to the growing surface of the bud. The pathway that newly synthesized proteins follow to the cell surface has the same outline in Saccharomyces cerevisiae as that originally defined in mammalian cells (Palade 1975). The principal steps in the pathway are outlined below and are diagrammed in Figure 1. The gene products responsible for the function of the secretory pathway are given at the end of this chapter in Table 1. Secretory proteins are translocated from the cytosol into the lumen of the endoplasmic reticulum (ER). For some proteins, translocation occurs cotranslationally and for other proteins, translocation can occur posttranslationally, i.e., after completion of protein synthesis. Secretory proteins assume a functional conformation within the lumen of the ER. This can involve covalent modifications of the protein such as cleavage of signal peptide, addition of N-linked and O-linked carbohydrate chains, disulfide bond formation, and addition of glycosylphosphatidylinositol (GPI) anchors. Catalyzed protein folding and, in some cases, assembly of multimeric protein complexes also take place in the ER lumen. Secretory proteins are then packaged into 60-nm vesicles that bud from the ER. These vesicles then deliver their contents to the Golgi by fusion with the Golgi membrane. The Golgi apparatus is composed of three biochemically distinguishable compartments. Secretory proteins are carried through successive compartments of the Golgi.
UPLAND RICE CULTIVAR RESPONSES TO ROW SPACING AND WATER STRESS ACROSS MULTIPLE ENVIRONMENTS

SUMMARY Upland rice (Oryza sativa L., UR) could be an option under soybean–maize crop rotation system. However, the recommended row spacing for UR (0.30 m) is shorter than that recommended for soybean and corn (0.40 m), limiting the use of UR in this rotation. We hypothesize that cultivar adaptation to wider than recommended row spacing and local environmental conditions harbour significant potential for overcoming the yield constraints of wider row spacing. We evaluated the row spacing effects on rice grain yield and their components in UR cultivars grown under different water deficit conditions. The experiments were designed as a randomized block in a split–split-plot scheme with sites (the cities of Santo Antônio de Goiás, Porangatu and Formoso) as main plots, row spacing (0.25, 0.35, 0.45 and 0.55 m) as the subplots and UR cultivars (one old and two modern genotypes) as the sub-subplots. We found that, in the less stressful environments, the modern cultivars, BRSMG Curinga and BRS Primavera, presented the highest grain yield. By contrast, in environments with moderate to intense water stress, the traditional cultivar, Douradão, presented the best performance, regardless of row spacing used. We conclude that UR is a viable option for soybean–maize rotation systems, as the UR cultivars tested presented no noticeable yield losses when sown with the same row spacing used for soybean and maize crops (0.40 m). In terms of impact, it can lead to an increase in UR cropped area in Brazil, and decrease in dependence on flooded rice harvested in the south of the country.
Production and application of chitin

For some years now, biopolymers have attracted great interest from both academia and industry. Some of them have been investigated for a long time, such as rubbers [1], the interest in others, such as starch, cellulose [2] or PHA [3], is mainly being driven by ecology concerns. Chitin is somehow apart from this mainstreaming interest in biopolymers. Indeed, as the second major biopolymer worldwide after cellulose, it is mainly produced as a byproduct in shellfish industry. Therefore its production was less a concern for its valorization through different applications and subsequent purifications and derivatizations [4, [5]. Chitin is a polysaccharide, more precisely an aminoglucopyranan, composed of N-acetylated glucosamine (GlcNAc) and glucosamine (GlcN) units (Figure 1), linked by β(1,4) covalent bonds [6]. Due to this specific linkage, chitin exhibits an extremely robust structure towards chemical and biological aggression, indeed the β(1,4) chitin bond is similar to the one found in cellulose, contrary to starch, that is much more easily digested by enzymes of several (micro)organisms than cellulose and presents an α(1,4) covalent bond between its monomeric units.
Low‐cost grass restoration using erosion barriers in a degraded African rangeland

Rangeland degradation, typified by extensive bare ground and soil erosion, is a serious problem around the world. In sub‐Saharan Africa, rangeland degradation threatens the food security of millions of people who depend on livestock and the region's large mammalian wildlife diversity. We tested the ability of five simple, low‐cost erosion barriers to promote grass and forb establishment in a bare ground‐dominated rangeland in Kenya. These treatments were: (1) trenches with small berms; (2) bundles of branches; and bundles of branches with (3) elephant dung balls, (4) burlap sacking, or (5) nylon mesh sacking inside them. We also tested whether barrier performance depended on (1) supplemental seeding with the grass Cenchrus ciliaris and (2) whether a barrier was located next to existing vegetation patches versus in the open. Within months, the trench and nylon mesh barriers had accumulated 20–50% more sediment than other treatments and had greater grass and forb seedling establishment. Seeding with Cenchrus resulted in higher herbaceous cover but was not necessary for other grasses to establish. After 3 years, the trench and nylon mesh barriers had created patches of new vegetation averaging 18–63% larger than patches created by the other treatments. Barriers that were initially adjacent to existing vegetation had created new vegetation patches averaging 65% larger than those created by solitary barriers. Results suggest that all barrier types increase grass cover but that trenches—especially if placed next to existing vegetation patches—are a particularly cost‐effective way to reduce bare ground and erosion in degraded rangelands.
Analysis of complete mitochondrial genome of fiddler crab Uca (Tubuca) arcuata (De Haan, 1835) (Arthropoda, Malacostraca, Decapoda)

Abstract In this study complete nucleotide sequences of the mitochondrial genome of fiddler crab Uca arcuata (De Haan, 1835) were determined and characterized. The length of mitochondrial genome for U. arcuata is 15,955 bp. This is the third and the longest record of complete mitochondrial genome from the family Ocypodidae. Furthermore, phylogenetic relationships were evaluated due to mitochondrial protein-coding genes. Phylogenetic tree suggests that U. arcuata belongs to the monophyletic family Ocypodidae and has sister group relationship with the genus Ocypode.
Metalloproteinases in Human Invasive Breast Carcinomas

Activation of the zymogen of matrix metalloprotelnase 2 (proMMP-2, progelatinase A) possibly is one ofthe key steps In Invasion and metastasis of various human carcinomas.Three differentmembrane-typeMMPS (MT-MMPs), MT1. , MT2-, and MT3-MMPS are thought to be activators of proMMP-2Inthe tissues.MT4. MMPIsstructurallydifferentfromthe other three enzymes, sad Its function as proMMP-2 activator is uncertain. In the presentstudyof humanInvasivebreastcarcinomas, examineda correlation between the expression of MT1-, MT2-, and MT3-MMPs, immunolocalizatlon of MT1. and MT2.MMPs, and proMMP.2 activation. Northern blot analysis demonstrated the predominant expression of MT1- MMPmRNAIn carcinomatissues(20 of 20 cases),whereasMT2-MMP was detected In only 25% of the cases (5 of 20 cases), and no detectable expressionof MT3.MMPwas observed.The expressionlevels of MT1- MMP but not MT2.MMP correlated well with the presence oflymph node and distant metastases, clinical stages, and size of tumors. Immunohisto chemically, MT1-MMP was localized predominantly in the carcinoma cells In all of the samples (32 of 32 cases). Immunostaining of MT2-MMP In the carcinoma cells was observed in only 38% of the cases (12 of 32 cases). Immunoblot analysis of tumor homogenates confirmed the pres ence of these MT-MMPs. Activation of proMMP-2 was significantly higher in the carcinoma samples with lymph node or distant metastasis comparedto carcinomawithoutmetastasis,normalcontrol,or fibrocystic disease (P < 0.05). An Increase in the activation ratio of proMMP.2 correlated directly with the expression of MT1.MMP but not MT2.MMP, as measured by either Northern blot analysis or immunostaining. These results suggest that MT1-MMP may play a key role in human breast carcinoma invasion and metastasis by being predominantly responsible for activationof proMMP.2.
True causal effect size heterogeneity is not required to explain trans-ethnic differences in GWAS signals

Through genome-wide association studies (GWASs), researchers have identified hundreds of genetic variants associated with particular complex traits. Previous studies have compared the pattern of association signals across different populations in real data, and these have detected differences in the strength and sometimes even the direction of GWAS signals. These differences could be due to a combination of (1) lack of power (insufficient sample sizes); (2) minor allele frequency (MAF) differences (again affecting power); (3) linkage disequilibrium (LD) differences (affecting power to ‘tag’ the causal variant); and (4) true differences in causal variant effect sizes (defined by relative risks). In the present work, we sought to assess whether the first three of these reasons are sufficient on their own to explain the observed incidence of trans-ethnic differences in replications of GWAS signals, or whether the fourth reason is also required. We simulated case-control data of European, Asian and African ancestry, drawing on observed MAF and LD patterns seen in the 1000-Genomes reference dataset and assuming the true causal relative risks were the same in all three populations. We found that a combination of Euro-centric SNP selection and between-population differences in LD, accentuated by the lower SNP density typical of older GWAS panels, was sufficient to explain the rate of trans-ethnic differences previously reported, without the need to assume between-population differences in true causal SNP effect size. This suggests a cross-population consistency that has implications for our understanding of the interplay between genetics and environment in the aetiology of complex human diseases.