Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Biodiversity: a Phylogenetic Perspective

Quantification of biodiversity presents a two-fold problem. First, there is the question of what exactly we should be counting. If that question is not difficult enough, it leads straight to the second practical question of how we can possibly accomplish such a count. At the species level, for example, even if we can decide what a species is (for discussion see Wheeler & Meier 2000), we must in practice use surrogate information to quantify relative numbers of species in different places. These same issues recur when biodiversity is defined below the species level. Debates about taxonomic distinctiveness in biodiversity conservation (Vane-Wright et al. 1991; Faith 1992a; Williams et al. 1994), although initially concerned with quantification of biodiversity at the level of species, led to a recognition that what we would like to count when setting species priorities is biodiversity below the species level-broadly, "feature diversity" (Faith 1992a, 1992b; 1994a, 1994b; Williams et al. 1994). Furthermore, the rationale in such prioritization, conserving feature diversity to maximize "option value" (Faith 1992a, 1992b)-dictates that those "features" must include not only observed characters of organisms but also unobserved characters. Clearly, we cannot count all those features and so must turn to something like taxonomy and phylogenetic pattern to capture character diversification (Faith 1992a, 1992b; but also see Faith 1996). Representation of "evolutionary history" (Faith 1994b), encompassing processes of cladogenesis and anagenesis, is assumed to provide representation of the feature diversity of organisms. Specifically, the phylogenetic diversity (PD) measure estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those phylogenetic branches spanned by the set (Faith 1992a, 1992b, 1994b). Although that method has subsequently been used in various biodiversity toolboxes (BioRap [Faith & Walker 1996] and Worldmap [Williams
Does hormesis foster organism resistance to extreme events

future stressors. Hormetic responses have been described across a wide range of taxa, from bacteria to plants and vertebrates (Mattson and Calabrese 2010). Importantly, hormetic responses can generalize across environmental stressors, where exposure to, say, heat stress may prime the organism to withstand other kinds of stressors, such as chemical toxicity (Mattson and Calabrese 2010; Costantini 2014). The degree to which hormetic priming to future stressors will shape a resistant phenotype strongly depends on the timing of the first (mild-level) exposure: for example, if there is a critical time window or developmental stage in which the priming effect can occur. For instance, individuals that experience heat stress early in life may be better able to cope with subsequent temperature extremes if the initial exposure induced a hormetic response (Costantini 2014). There is empirical support for thermal hormesis priming the individual to withstand stressors over time and consequently extending lifespan; a recent meta-analysis demonstrated that the hormetic response to stress induced by high ambient temperatures is very similar across invertebrate species, suggesting that there has been evolutionary pressure not to change it (Lagisz et al. 2013). Stimulatory effects of mild heat stress have also been described in vertebrates; avian studies showed that early conditioning to mild heat stress primed individuals to withstand episodes of high ambient temperatures experienced later in life (Costantini et al. 2012). Thermal hormetic priming also occurs in aquatic organisms; for instance, mild heat stress improved the ability of juvenile rainbow trout (Oncorhynchus mykiss) to resist salinity stress (Niu et al. 2008). Furthermore, short-term drought exposure can prime organisms to 209
Impacts of Climatic Factors on Evolution of Molecular Diversity and the Natural Distribution of Wild Stocks of the Giant Freshwater Prawn (Macrobrachium rosenbergii)

Abstract: Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor ∼1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.
Exigências de metionina + cistina para frangos de corte machos em diferentes fases de criação

Three assays were carried out to determine methionine + cystine requirement and the digestible methionine + cystine: digestible lysine ratio of males broilers, Avian Farms, from 1 to 20, 24 to 38 and 44 to 56 days of age. Each experiment was a completely randomized design with five levels of methionine + cystine, six replications and 20 birds per pen from 1 to 20 and 24 to 38 and 16 birds per pen from 44 to 56 day of age, respectively. The digestible methionine + cystine levels were 0.731-0.916% (in increments of 0.046); 0.712-0.881% (in increments of 0.042) and 0.631-0.781% (in increments of 0.037) for 1 to 20, 24 to 38 and 44 to 56 days of age, respectively. Feed intake, weight gain, feed conversion and carcass quality were evaluated. There were linear positive and quadratic effects of the methionine + cystine levels on body weight gain and feed conversion, respectively, in the 1 to 20 days phase. Using the broken line model, the requirement of digestible methionine + cystine (total) and the ratio of digestible methionine + cystine:digestible lysine for the 1 to 20 days phase was 0.808 (0.907% total) and 70%, respectively, according to the results of feed conversion. For the phase 24 to 38 days, weight gain, feed conversion and absolute leg quarter weight responded quadratically to increasing levels of digestible methionine + cystine. Using the broken line model, the requirement of digestible methionine + cystine (total) and the ratio of digestible methionine + cystine:digestible lysine for the 24-38 days phase were 0.767 (0.844% total) and 72%, respectively, according to the results of body weight gain. The absence of a significant response for body weight gain and feed conversion in the third phase (44-56 days) demonstrates that the lowest level of methionine + cystine met the birds requirement. Nevertheless, according to the best biological response the digestible (total) methionine + cystine were 0.668% (0.738% total) and 71%, respectively. Methionine + cystine quadratically affected breast yield and breast fillet yield in the 44 to 56 days phase.
REMEDIAL MEASURES FOR IMMOBOLIZATION OF HEAVY METALS FROM CONTAMINATED SOIL

To understand the remedial measures of heavy metals from contaminated soil, three vegetable ( Brassica juncea, Brassica rapa and Lepidium sativum ) were grown on soil artificially contaminated with 300 mg kg -1 CuCl 2 , 500 mg kg -1 Pb(NO 3 ) 2 , 800 mg kg -1 ZnCl 2 or their mixed metal (1600 mg kg -1 ). This experiment showed that Cu and Pb accumulation in vegetables are higher in lime treatments than in 20% cowdung treatments. Zinc accumulation increased in B. rapa and L. sativum in both cow dung and lime treatments compared to control. Accumulation of Cu, Pb and Zn from mixed metal treatment was highest in L. sativum (at lime 9 g kg -1 for Cu and Pb, and 20% cow dung for Zn). Morphological changes such as fresh weight, dry weight, shoot length, root length, mostly increased significantly (P≤0.01) with Zn and cow dung treatment, but none with lime treatment. Fresh and dry weight increased only in L. sativum grown in 3 g kg -1 lime treatment. Immobilization of Cu, Pb and Zn in both single and mixed treatments was found to be high in cow dung amended soil. From this it can be ascertained that 20% cow dung treatment is suitable for immobilization of supplied heavy metals than lime treatments. DOI: http://dx.doi. org/10.3126/eco.v19i0. 9853 Ecoprint An International Journal of Ecology Vol. 19, 2012 Page: 1-5 Uploaded date : 2/14/2014
Thyroid hormone stimulates the shift of erythrocyte populations during metamorphosis of the flounder

Hormonal control of changes in circulating erythrocytes was studied in the metamorphosing flounder (Paralichthys olivaceus). Premetamorphic flounder larvae had large, round erythrocytes with small, round and pyknotic nuclei. At metamorphic climax, many smaller erythroid cells with larger nuclei appeared in the circulation. These cells developed into elliptical, adult-type erythrocytes in fully metamorphosed juveniles. Larval erythrocytes were not observed in juvenile fish. Biochemical analysis of hemoglobins are different between larvae and juveniles. L-thyroxine (T4) treatment at 100 ppb in ambient seawater clearly stimulated a precocious morphological shift in the erythrocyte populations within 15 days, while the predominant blood cells in control fish were the larval erythrocytes throughout the experiment. The erythrocyte shift found in T4-treated larvae coincided with metamorphic changes in external appearance and behavior of the fish. These results indicate the presence of the two distinct populations of erythroid cells, larval type and adult type, in developing flounder larvae, and suggest that thyroid hormone suppresses larval erythropoiesis and stimulates establishment of adult, or definitive erythropoiesis.
Pharmacogenomics and animal models of schizophrenia

Schizophrenia is a syndromal brain disease of largely unknown pathophysiology and most likely heterogeneous etiology in which genetic predisposition constitutes the major risk factor. In recent years, a shift from a monolithic view of the disorder is leading to its dissection into component phenotypic modules or endophenotypes that may differ in pathophysiology, underlying genetic diathesis, or treatment response. Reducing phenotypic heterogeneity by focusing on endophenotypes will facilitate the production of valid animal models to be used in experimental approaches, improve our chances of uncovering genes predisposing to the disease in linkage or association approaches, and simplify generation of novel molecular targets for the drug discovery process. We hereby review some recently generated mouse models that replicate specific endophenotypes observed in schizophrenia and that implicate putative contributing genes that may be exploited to explore novel drug targets. These are derived from opposing but complementary perspectives. One approach developed in our work begins with mouse models of schizophrenia traits to uncover candidate schizophrenia genes. Another approach followed by several other groups begins with putative schizophrenia vulnerability genes to investigate the corresponding endophenotype in mouse models. Combined with global analysis of gene expression, these mouse models offer the hope that the disease‐causing and treatment pathways implicated in schizophrenia will finally be unraveled. Drug Dev. Res. 60:95–103, 2003. © 2003 Wiley‐Liss, Inc.
Feeding habits of the maned wolf, Chrysocyon brachyurus (Carnivora: Canidae), in southeast Brazil

The feeding habits of the maned wolf were studied in southeast Brazil to understand its response towards changes in the environment and in relation to its prey. By occurrence, miscellaneous fruits, small mammals and wolf's fruit were the most consumed items. Armadillos, small mammals and wolf's fruit (Solanum lycocarpum) provided most of the ingested biomass. While wolf's fruit and small mammals were mainly consumed in the dry season, other miscellaneous fruits were taken mostly in the wet season. There was selectivity in the predation on some small mammal species. The maned wolf's diet followed patterns similar to those found in more pristine areas. O hábito alimentar do lobo guará foi estudado no sudeste do Brasil para descrever suas respostas as alterações do ambiente e em relação as suas presas. Por frequência de ocorrência, as frutas silvestres, os pequenos mamíferos e a fruta-do-lobo foram os itens mais consumidos. Tatus, pequenos mamíferos e a frutas-do-lobo (Solanum lycocarpum) constituíram os itens mais importantes em relação à biomassa ingerida. A fruta-do-lobo e os pequenos mamíferos foram consumidos principalmente na estação seca, enquanto os demais frutos silvestres na época das chuvas. Houve seleção de algumas espécies de pequenos mamíferos. A dieta do lobo guará apresentou padrões semelhantes aqueles encontrados em áreas mais preservadas.
Cities, the social economy and inclusive growth: a practice review

The social economy constitutes a range of organisations that have a core social mission, different levels of participative and democratic control by members, and use financial surpluses or profits primarily to achieve their social missions. This research examined the actual and potential roles of the social economy in bringing about inclusive growth that generates more and better jobs in UK cities, particularly for people who are either in or at risk of poverty.
Viral haemorrhagic septicaemia virus multiplication and interferon production in rainbow trout and in rainbow trout × brook trout hybrids

Abstract Rainbow trout ( Oncorhynchus mykiss ) susceptible to Viral Haemorrhagic Septicaemia (VHS) Virus type 1 and rainbow trout × brook trout ( Salvelinus fontinalis ) triploid hybrids were challenged with VHSV by either immersion or i.p. injection of the virus. In both cases susceptible rainbow trout displayed an increasing viraemia which was paralleled by high interferon titres in the serum. In contrast virus multiplication as well as serum interferon production remained low in resistant hybrids. When blood leucocytes were infected in vitro the adsorption of virus appeared low and there was no obvious multiplication of the virus and trout and hybrid leucocytes released similar levels of interferon in the culture medium. When leucocytes were stimulated by monolayers of VHSV infected cells fixed with glutarldehyde at the time virus was budding at their surface, interferon production was the same in kidney leucocytes but was much lower in hybrid than in trout blood leucocyte cultures.
Generation time extension for cost‐effective strain maintenance of transgenic Mediterranean fruit fly, Ceratitis capitata [Diptera: Tephritidae]

Molecular technologies have enabled the generation of various transgenic insect strains for the area‐wide control of agricultural pests and vectors of human diseases. Individual maintenance of several diverse transgenic lines or strains involves a lot of resources, and sometimes problems arise that threaten the strains being maintained. Here, we present a way to cost‐effectively maintain transgenic lines or strains of the Mediterranean fruit fly Ceratitis capitata by extending their generation time. Immature stages were kept at 20°C instead of 28°C, and the subsequent generation of transgenic flies kept at different temperatures were found to have laboratory fecundity comparable to the untreated transgenic flies. Extension of generation time offers inexpensive strain maintenance as it reduces the resources, time and energy spent on maintenance of transgenic medfly strains, in addition to minimizing exposure of strains to problems sometimes associated with strain maintenance.
Gene therapy for inherited retinal diseases

Inherited retinal diseases include a number of disorders which typically affect photoreceptor/retinal pigment epithelial function, and can lead to severe visual impairment. Advances in molecular genetics have allowed the identification of many of the genes responsible for particular conditions, and progress in viral gene transfer technology has enabled the replacement of specific genes into the retina. The first human clinical trial of gene therapy for inherited retinal disease was carried out at Moorfields Eye Hospital and UCL Institute of Ophthalmology, involving 12 patients with RPE65 deficiency - an early-onset retinal dystrophy. The results from this trial are described and provide evidence for the safe administration of viral vectors in the eye, and also demonstrate improvements in retinal function in a number of patients. However, the extent and duration of the response did not match that observed in prior animal studies, suggesting improvements in gene expression level may be required in humans. In addition, consideration for future involvement of the foveal region is highlighted, since retinal thinning was observed in a number of patients following subretinal delivery. Achromatopsia is an inherited disorder of congenitally absent cone photoreceptor function. Gene replacement therapy in animal models of achromatopsia has shown evidence of restored cone function, suggesting that this condition may be an appropriate target for gene therapy in humans. Recent studies have suggested that achromatopsia is a progressive condition with deterioration in cone structure with age, implying that the window of opportunity for therapeutic intervention may be narrow. In this study of retinal structure and function (in preparation for a gene therapy trial) in 40 patients with achromatopsia, an age-associated deterioration in cone structure was not identified, suggesting that the age range for potential intervention is wider than recently suggested, and prospective patients should be assessed on an individual basis, irrespective of age.
Embryonic mutants of Arabidopsis thaliana

Genetic analysis of plant em-bryogenesis has been approached in part through the isolation and characterization of recessive embryonic mutants. The most extensive studies have dealt with maize and Arabidopsis. The high frequency of mutants defective in plant embryogenesis is consistent with the presence of many target genes with essential functions at this stage of the life cycle. Some mutants are likely to be defective in genes with general housekeeping functions. Others should facilitate the identification of genes with a more direct role in the regulation of morphogesis. Over 300 embryonic mutants of Arabidopsis isolated following chemical mutagenesis and T-DNA insertional mutagenesis are currently being analyzed. This collection includes embryonic le-thals, defectives, and pattern mutants. Developmental abnormalities include the presence of fused cotyledons, twin embryos, abnormally large suspensors, distorted epidermal layers, single cotyledons, enlarged shoot apices, pattern deletions and duplications, embryos with altered patterns of symmetry, bloated embryos with giant vacuolated cells, reduced hypocotyls that fail to produce roots, and embryos that protrude through the seed coat late in maturation. This review describes the isolation and characterization of embryonic mutants of Arabidopsis and their potential application to plant biology. © 1992 Wiley-Liss, Inc.
Occurrence of Zearalenone-4-β-d-glucopyranoside in Wheat

An LC-MS method was developed for the analysis of zearalenone-4-β-d-glucopyranoside and zearalenone in wheat (Triticum aestivum). The limit of determination for zearalenone-4-β-d-glucopyranoside and zearalenone was 10 μg/kg. The recovery rates were calculated to be 69% and 89% at a concentration of 100 μg/kg for zearalenone-4-β-d-glucopyranoside and zearalenone, respectively. Twenty-four Bavarian wheat samples from a 1999 harvest were analyzed. Zearalenone was present in 22 of 24 field samples, the levels ranged from 11 to 860 μg/kg. Zearalenone-4-β-d-glucopyranoside was found in 10 of the zearalenone positive samples (42%) at levels ranging from 17 to 104 μg/kg. The amounts of zearalenone-4-β-d-glucopyranoside were correlated to those of zearalenone (r 2 = 0.86, b = 0.10). After gastrointestinal hydrolyzation, zearalenone-4-β-glucopyranoside might be implicated in the development of a zearalenone-syndrome. Therefore, more attention should be focused on conjugated mycotoxins in food and feed. Keywords: Ze.
Variation with Fish Length, Sex, Stage of Sexual Maturity, and Season in the Appearance and Volume of the Drumming Muscles of the Swim-Bladder in the Haddock, Melanogrammus aeglefinus (L.)

Observations made as early as 1947 and data collected in 1953 to 1954 and 1956 to 1957 indicate that there is considerable variation in the size and appearance of the drumming muscles of the swim-bladder of haddock with fish length, sex, sexual maturity, and season on the Grand Bank and St. Pierre Bank. For haddock of the same length the data indicate that the drumming muscles of mature male haddock are larger than those of immature males and also of immature and mature females of the same length. In addition the data indicate that a periodicity is exhibited in the size of the muscles of the mature male, the muscles being nearly twice as large during the pre-spawning and spawning period in May and June as they are in October and November. This phenomenon does not occur in female haddock, the drumming muscles of which are considerably smaller than those of male fish of the same size and show no variation in size with the season.It is suggested that the difference in size of the drumming muscles of male and.
Effects of Freezing and Thawing Methods and Storage Time on Physicochemical Properties of Freshwater Prawns (Macrobrachium rosenbergii)

Abstract Physicochemical changes in prawn muscle as related to freezing and thawing procedures were monitored during 6 months frozen (-29°C) storage. Lipid oxidation (formation of TBARS) in raw muscle tissue reached a maximum between 1 and 3 months and then decreased thereafter. The kinetics of TBARS formation depended on the presence or absence of shell and rate of thawing. Texture (shear force) of raw muscle decreased slightly (3.5–8.1%) but shear force of cooked prawns increased considerably (13–27.9%) during storage. Cooking loss was higher for shell-off (20.2%) prawns than for shell-on prawns (14.4%), and correlated with increased toughness of cooked muscle. Shells did not protect raw muscle against lipid oxidation but reduced its cooking loss. Electrophoretic analysis showed no protein changes except that the intensity of all protein bands decreased slightly after 6 months storage.