Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematics and evolution of extinct and extant Pan-Alcidae (Aves, Charadriiformes) : combined phylogenetic analyses, divergence estimation, and paleoclimatic interactions

Although the ecological interactions and ethology of the wing-propelled diving seabirds known as the Alcidae (Aves, Charadriiformes) have been intensively studied, systematic studies of the clade have been overwhelmingly limited to extant taxa. Pan-Alcidae have the richest fossil record among Charadriiformes, with specimens representing more than 35 million years of evolutionary history. Morphometric and apomorphy-based taxonomic revision of previously named extinct pan-alcids along with description of new species of extinct pan-alcids facilitated refined estimates of species richness. Combined phylogenetic analyses of morphological and molecular sequence data including pan-alcid fossils elucidated the poorly understood evolutionary history of the clade. Divergence estimation analysis for Charadriiformes placed previously hypothesized episodes of pan-alcid radiation and extinction in context with proposed paleoclimatic drivers of alcid evolution.
Cornification in developing claws of the common Australian skink (Lampropholis guichenoti) (Squamata, Lacertidae)

An ultrastructural and immunocytochemical study on developing lizard claws has been done. Claws originate from an epidermal thickening covering the tip of digits under which mesenchymal cells aggregate. The outer side of the dorsal terminal scale of a digit gives origin to the unguis, and suggests that claws are modified scales sustained by the last phalanx. Beneath four–seven layers of embryonic alpha‐keratin cells, beta‐keratin cells are differentiated but no shedding complex is formed. Beta‐keratin cells extends also over the apical part of the ventral side (sub‐unguis) which is mainly formed by alpha‐keratin cells. Initially beta‐keratin filaments have a prevalent oblique orientation along the plane containing the proximal–apical axis of the digit. Later bundles become more irregularly distributed. Beta‐keratin cells of the unguis remain largely separated and do not merge into a syncitium like in the beta‐layer of scales. The thickness of the horny layer is higher in the unguis than in the sub‐unguis and decreases from the claw tip toward its basal most part. It is hypothesized that the evolution of claws occurred by the extension of the outer scale surface of the terminal scales beyond the digit tip under the influence of the apical mesenchyme in the terminal phalange.
Phase difference between calcification and organic matrix formation in the diurnal growth of otoliths in rainbow trout, Salmo gairdneri

The relative role of calcium and organic matrix deposition in the formation of daily increments in otoliths was studied in in vitro preparations of otolith-containing sacculi of rainbow trout, Salmo gairdneri. Sacculi were incubated in a Ringer solution containing both /sup 45/Ca and /sup 3/H-glutamic acid for 2 hours at 6-h intervals throughout a 24-h period and then the uptake of these isotopes was determined for both otolith and saccular tissue fractions. Serum calcium and sodium concentrations were also analyzed for diurnal variations. Serum calcium concentrations varied diurnally by 8% in a single phasic pattern, reaching a peak at dusk (1600 h) and a nadir at night (2200 h), while sodium concentrations remained almost constant throughout a 24-h period. Diurnal variation in the otolith's uptake of calcium and glutamic acid showed discrete, antiphasic cycles. The rate of calcium uptake varied in a pattern closely resembling that of serum calcium (the peak at 1600 h and the nadir at 2200 h); glutamic acid uptake remained almost constant during the daytime and peaked at night (2200 h). The results indicate that in rainbow trout daily increments of otoliths are formed by the antiphasic deposition of calcium and organic matrix.
Distribution, Density, Diet and Habitat Use of the Otter in Relation to Land Use in the Araglin Valley, Southern Ireland

Abstract:The distribution, density, diet and habitat use of the otter (Lutra lutra) were examined in the Araglin Valley, in counties Cork, Tipperary and Waterford. Otter signs (tracks, spraints, anal secretions, holts, etc.) and environmental conditions (river depth, river width, flow regime, vegetation cover, etc.) were recorded at 112 sites across three habitat types (agriculture, moorland and forestry) in the river valley. Three definite home range boundaries were delineated by high levels of sprainting and scraping, and results indicated the presence of six or seven otters. Significant correlations were recorded between otter signs and river depth, river width, lying-up availability and presence of holts, but no trends were found between otter signs and vegetation cover or flow velocity. A positive relationship was recorded between spraints and vegetation cover in the agriculture and moorland habitats, but a negative correlation was found in the forested sites. Percentage frequency of occurrence, relative percentage of frequency, and percentage bulk (Sc%) were calculated for twelve food categories based on seasonal data sets. Fish (mainly salmonids and eels) were the predominant food category in each season (Sc% = 70.03). Other significant food categories included small quantities of mammals, birds, frogs and crayfish (both in February and March). Considerable variation in otter diet was revealed and was related to differences among three different habitat types and to the location of the home range. In home range 3, fish prey were relatively scarce, while birds and frogs were more important. In contrast, fish was the more important food in home ranges 1 and 2. The trophic niche breadth of otter, evaluated using Levin's index, varied little throughout the study period, with a peak in spring/early summer and a minimum value in late autumn (October-November).
Mining protein-protein interaction networks for the analysis of disease

Interactions between proteins regulate signaling, gene expression and many other cellular functions. Therefore, characterizing the entire human interactome is a key effort in current proteomics research. The existing knowledge of protein-protein interactions (PPIs) is stored in a number of databases. However, PPIs have properties that make their interpretation difficult and that are not adequately represented in a unified way in these databases. On the one hand, the experimental reliability of the techniques used to detect PPIs can have widely different quality with some methods being associated with high error rates. Another problem of PPI detection methods is that many interactions are measured under artificial conditions (for example, yeast cells are transfected with human genes in yeast two-hybrid assays) or even if detected in a physiological context, this information is missing from the common PPI databases. We implement a resource that integrates human PPI data from the major expertcurated PPI databases. To address the high uncertainty associated with experimentally detected PPIs, we develop a scoring scheme that has been optimized both computationally and by human experts to reflect the amount and quality of evidence for a given PPI. To deal with the problem of missing context, we develop a method that assigns information to PPIs inferred from various attributes of the interacting proteins: gene expression, functional and disease annotations, and inferred pathways. We demonstrate that context annotation helps to detect interactions of higher experimental reliability and how context-filtered networks are enriched in bona fide pathways and disease proteins. We use these context-specific networks to identify PPIs that likely play a role in disease. Finally, we use the integrated human PPI network for the study of the wild type function of polyglutamine (polyQ) stretches. Expansions of these stretches have been observed in the proteins of a large number of patients with different neurodegenerative diseases such as Huntington’s and several Ataxias. Protein aggregation, which is a key feature of most of these diseases, is thought to be triggered by these expanded polyQ sequences in disease-related proteins. However, polyQ tracts are a normal feature of many human proteins, suggesting that they have an important cellular function. To clarify the potential function of polyQ repeats in biological systems, we study the characteristics of polyQ-containing proteins in the human PPI network. We complement the network analysis studying the repeats at nucleotide, protein and organism level. Together, our observations suggest that polyQ tracts in proteins stabilize protein interactions, likely through structural changes whereby the polyQ sequence extends a neighboring coiled-coil region to facilitate its interaction with a coiled-coil region in another protein.
αvβ3 and macrophage colony‐stimulating factor: partners in osteoclast biology

Summary: Osteoclasts, the sole bone‐resorbing cells, arise by fusion and differentiation of monocyte/macrophage precursors. Matrix degradation requires adhesion of the osteoclast to bone, an integrin αvβ3‐mediated event that also stimulates signals which polarize the cell and secrete resorptive molecules such as hydrochloric acid and acidic proteases. Two cytokines are necessary and sufficient for osteoclastogenesis, receptor activator of nuclear factor κB ligand (RANKL) and macrophage colony‐stimulating factor (M‐CSF), both produced by mesenchymal cells in the bone marrow environment. M‐CSF promotes survival and proliferation of osteoclast precursors. It also contributes to their differentiation and regulates the cytoskeletal changes that accompany bone resorption. Binding of M‐CSF to c‐Fms, its receptor, recruits adapter proteins and cytosolic kinases, thereby activating a variety of intracellular signals. We herein review how αvβ3 and M‐CSF, alone and in concert, impact production, survival, and function of the osteoclast, thereby controlling skeletal mass. Signals from αvβ3 and/or c‐Fms activate Syk and Vav3, originally defined by their function in lymphoid cells. Genetic depletion of either protein generates a strong bone phenotype, underscoring the promise of osteoimmunobiology.
Improving assessments of marine protected areas

1. The use of experimental design and statistical analysis to evaluate the effects of marine protected areas (MPAs) is increasingly popular throughout the world. 2. However, in looking at historical approaches to MPA evaluations, flaws were identified in the execution of theoretically correct designs, as well as disconnects between the stated objectives of MPAs and those of assessment studies. 3. MPA assessments can be improved by: (1) considering the enforcement/compliance level; (2) linking explicitly the choice of indicator(s) to the MPA objectives; (3) accounting for habitat structure; (4) taking into account the age and size of the MPA; and (5) quantifying the fishing pressure outside the MPA (including possible displacement effects). 4. Neglecting social factors, using inappropriate indicators, and/or ignoring relevant covariates, carries the risk of having MPAs dismissed as an effective management tool. Societal expectations are strong that MPAs will confer benefits, and thus assessment studies need to be progressively improved using new methodologies and the best available scientific evidence. Copyright © 2009 John Wiley & Sons, Ltd.
Facilitation by herbivore‐mediated nurse plants in a threatened tree, Taxus baccata: local effects and landscape level consistency

We investigated the regeneration of a threatened tree, the yew Taxus baccata, in relation to the presence of fleshy-fruited woody plants acting as seed dispersal foci as well as protecting yew recruits against ungulate herbivores. We seek to determine if local facilitative effects are consistent across landscape in the Cantabrian range (NW Spain). Yew seed rain by birds mostly concentrated under yew trees and beneath hollies Ilex aquifolium. Seedling emergence distributed similarly to seed rain, but first-year seedling survival was higher beneath hollies. In one site where woody vegetation was structured as nucleation centres (multispecific patches of fleshy-fruited plants acting as foci for seed rain) yew recruits mostly occurred in yew-dominated centres, suggesting dispersers-mediated facilitation. However, holly was the main nurse plant for most of these recruits, considering the nurse as the species whose canopy covered directly the yew recruit. Living beneath nurse plants reduced herbivore damage on saplings and enhanced seedling survival. A planting experiment with yew rooted-cuttings beneath different spiny shrubs corroborated this effect. Additional evidence on yew recruitment limitation by herbivory emerged from one population where ungulates were fence-excluded. Our results suggest that nurse plants mitigate the negative effect of herbivores on yew regeneration, by providing defence against browsing and trampling. Shelter ability related to nurse structure, cone-shaped shrubs with branches at their bases acting better as a barrier. Paradoxically, this structure resulted from heavy browsing on nurse plants. The study of yew regeneration and habitat structure in seven sites provided evidence for the consistency of facilitation by holly at the landscape level, since local values of yew recruitment positively related to nurse ground cover. Range-scale yew management must consider the local functioning of the interaction among avian seed-dispersers, nurse fleshy-fruited plants and ungulate herbivores, in combination with regional measures, targeting the habitats where facilitation emerges.
Intimate Partner Violence

Abstract: This review examines multiple forms of intimate partner violence, including women's use of violence, and argues for development of more complex conceptualizations of intimate partner violence. As new victims are identified, partner violence has been reconceptualized. Research findings indicate that women are both victims and perpetrators in intimate partner violence, challenging previous conceptualizations and explanations. The authors argue that how researchers conceptualize intimate partner violence influences how they study and measure it. The authors call for researchers to develop more complex constructions of gender, and to distinguish between distinct forms of intimate partner violence.
Quality of Potatoes Treated With Selected Insecticides and Potato-haulm Killers

SummaryTreatment with aldicarb and demeton-S-methyl had no influence on the dry weight or on the starch or protein contents, but increased the content of ascorbic acid by up to 25%. Diquat, dinoseb and metoxuron had no effect on dry weight or starch content; dinoseb and metoxuron increased the protein and ascorbic acid contents by up to 20%. The effects of the pesticide treatments on the chemical composition of freshly harvested potatoes were maintained during their cold storage.
Variation for Fruit Morphological Characteristics in a Capsicum chinense Jacq. Germplasm Collection

Mature fruit of 330 accessions of Capsicum chinense Jacq. from the USDA/ARS Capsicum germplasm collection were characterized for fruit length, width, weight, and color. Mean fruit length was determined to be 47 mm with a range from 7.9 mm to 113.7 mm. Mean fruit width was 21.17 mm with a range of 6.18 mm to 40.0 mm. Mean fruit weight was 6.31 g with a range of 0.18 g to 22.7 g. Distributions of all characteristics were positively skewed. Distributions of fruit length, fruit weight, and fruit length/width failed the Kolmogorov-Smirnov test for normality. The distribution for fruit width was normal. Ninety-two percent of the accessions examined were elongate. Mature fruit colors included red, orange, yellow, brown (chocolate), and cream. The germplasm collection contained primarily pendent larger-fruited cultivated forms of the species, but also contained upright small-fruited primitive and semipendent transitional forms. These data define the variability for mature fruit characteristics within this germplasm collection and provide a baseline against which future introductions/acquisitions can be compared. Additional sampling of the gene pool might be expected to substantially enhance the genetic variability within the primitive forms of this species.
Resistance to Pierce’s Disease in Muscadinia rotundifolia and Other Native Grape Species

Pierce’s disease (PD), caused by the bacterium Xylella fastidiosa , is a major disease of grapevines. Grape species native to southern areas of North America where the disease is severe have evolved resistance to PD. Using controlled greenhouse trials, a quantitative assessment of the level of resistance in cultivated and wild selections of five native grape species was made. Conclusions were based on estimates of bacterial concentrations in stem tissue via ELISA and subjective evaluations of disease symptoms. Vitis labrusca, native to the northeast United States where PD is absent, appears to be as susceptible as Vitis vinifera . California natives Vitis californica and Vitis girdiana appear to be moderately susceptible, although there was significant variation among the V. girdiana selections. In contrast, Muscadinia rotundifolia and Vitis arizonica , both native to areas of severe disease pressure, appear to be very resistant. A pattern of resistance correlating with geographic variation in disease pressure was also evident within species. Wild accessions of M. rotundifolia from cooler areas such as Tennessee, where PD is uncommon, supported up to 20x higher concentrations of bacteria than the accessions from Florida where PD is severe. Trials with wild accessions of V. girdiana showed a similar pattern, with susceptible selections supporting up to 100x higher bacterial concentrations. Results demonstrated a gradient of resistance both among and within species, consistent with the hypothesis that PD resistance has evolved in response to disease pressure. This study identifies candidate plant material for breeding projects and provides insight into the genetic and physiological basis of PD resistance in native grapes.
NUTRITIVE VALUE OF FISH MEAT COMPARATIVE TO SOME ANIMALS MEAT

Fish has always been seen as a food necessary for good health - since ancient times fish was recognized as being a 'brain food', a reference to its importance in the development of a healthy brain. Research over the past few decades has confirmed the importance of the nutritional components of fish in brain development and reproduction and highlighted a role for fish in a variety of other functions in the body. There is strong evidence that fish plays a major role in protecting against heart disease and may also play a role in the prevention of other illnesses. Components of fish are also important in the development and maintenance of the eyes, skin and nervous system. The chemical composition of fish varies greatly from one species and one individual to another depending on age, sex, environment and season. Fish has between 13 and 25% protein, which accounts for 80 to 90% of the energy content of the fish. The protein found in fish is of high biological value, which means that fish can be used as the sole source of protein in the diet. Fish proteins contain all the essential amino-acids for the human organism.
MYCORRHIZAS OF AUTOTROPHIC HIGHER PLANTS

(1) The range of mycorrhizal types is briefly compared, with respect to structure and nutritional mode of the symbionts. Ectotrophic, vesicular‐arbuscular and erica‐ceous mycorrhizas of autotrophic plants are selected for further consideration, both because the symbionts have nutritional similarities, and because recent experimental work provides a basis for useful comparisons.
Antibodies against pseudorabies virus in feral swine in southeast Brazil

Soros de 358 javalis (Sus scrofa), criados em sistema de semiconfinamento em propriedades do estado de Sao Paulo, foram coletados entre 1998 e 2000 e testados para anticorpos contra o virus da doenca de Aujeszky (VDA), pela tecnica de soroneutralizacao (SN) e ensaio imunoenzimatico (ELISA). Foram detectados animais soropositivos em tres das sete propriedades analisadas. Do total de javalis testados, 30,7% apresentaram anticorpos neutralizantes contra o VDA, com variacao de 25,2% a 100% nas propriedades com animais sororreagentes. O ELISA detectou menor numero de sororeagentes (19,3%), sendo a sensibilidade e a especificidade 57,3% e 97,6%, respectivamente, e a correlacao observada de 85,2% (P<0,0001). Os resultados mostram que a infeccao pelo virus da doenca de Aujeszky ocorre em criacoes de javalis no estado de Sao Paulo, e compromete o sucesso de um futuro programa de erradicacao da doenca na regiao.
Phyllodiaptomus thailandicus , a new fresh-water copepod (Copepoda, Calanoida, Diaptomidae) from Thailand

[Examination of freshwater diaptomid copepods from Thailand resulted in the discovery of a new species belonging to the genus Phyllodiaptomus, namely P. thailandicus n. sp. It belongs to the blanci-group and is most similar to P. christineae Dumont, Reddy & Sanoamuang, 1996 and P. blanci (Guerne & Richard, 1890). The new species is the tenth member of the genus and the fourth species recorded from Thailand. It is rare and has been recorded only in 15 permanent ponds in eastern and southern Thailand. L'examen des copepodes diaptomides d'eau douce de Thailande a permis de decouvrir une nouvelle espece appartenant au genre Phyllodiaptomus, P. thailandicus n. sp. Elle appartient au groupe blanci et est proche de P. christineae Dumont, Reddy & Sanoamuang, 1996 et P. blanci (Guerne & Richard, 1890). La nouvelle espece est le dixieme membre du genre et la quatrieme reconnue en Thailande. Elle est rare et a ete trouvee dans seulement 15 mares permanentes dans l'est et le sud de la Thailande. , Examination of freshwater diaptomid copepods from Thailand resulted in the discovery of a new species belonging to the genus Phyllodiaptomus, namely P. thailandicus n. sp. It belongs to the blanci-group and is most similar to P. christineae Dumont, Reddy & Sanoamuang, 1996 and P. blanci (Guerne & Richard, 1890). The new species is the tenth member of the genus and the fourth species recorded from Thailand. It is rare and has been recorded only in 15 permanent ponds in eastern and southern Thailand. L'examen des copepodes diaptomides d'eau douce de Thailande a permis de decouvrir une nouvelle espece appartenant au genre Phyllodiaptomus, P. thailandicus n. sp. Elle appartient au groupe blanci et est proche de P. christineae Dumont, Reddy & Sanoamuang, 1996 et P. blanci (Guerne & Richard, 1890). La nouvelle espece est le dixieme membre du genre et la quatrieme reconnue en Thailande. Elle est rare et a ete trouvee dans seulement 15 mares permanentes dans l'est et le sud de la Thailande. ]
Importance and utilization of amaranth in food industry Part I. Characteristic of grain and average chemical constitution of whole amaranth flour

Amaranth seeds are very small. Their bulk density is 843 g dm−3. Basic analysis of amaranth whole flour from Slovakia proved evidently a high content of proteins (17.7% on dry basis), what is typical for amaranths. The lipid content of amaranth grains is rather high (7.32% on d. b.). Amaranths with their high content of fat are similar to oats. From the point of storage time of the amaranth flour the high content of fat was assumed as an unfavourable factor. The quantity of fiber (4.91% on d.b.) is comparable with more varieties of amaranth cultivated abroad. Amaranth has a relatively high content of Ca, Mg, P, K and Fe. The quantity of thiamine corresponds to the average values of amaranth grown abroad. Riboflavin is present up to quadruple amount in comparison to the literature. The acidity of flour during 6 weeks of resting increased relatively little.