Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating national population sizes: Methodological challenges and applications illustrated in the common nightingale, a declining songbird in the UK

1. Estimation of national population size can be important for setting conservation priorities, but its methodology has received little critical attention. Sites for highly aggregated species are often prioritised if they contain 1% of national or biogeo-graphic populations, but the utility of this approach for other species is unclear. 2. To make recommendations for study design, we present methods used to estimate the UK population size of the common nightingale Luscinia megarhynchos . We assess the sensitivity of the population estimate to the analytical method used and identify sites of national importance for this territorial songbird. 3. Survey effort was directed by prior knowledge of the species distribution and the survey design maximised detectability by focussing on the period of greatest song output. We used three different statistical methods to account for detectability, estimating that 55%–65% of the national population was detected during surveys. 4. Birds in areas not known to contain the species accounted for 13%–23% of the population estimate. Methods to account for these individuals contributed the greatest uncertainty to the results, due to the difficulty of surveying a very large sample of random sites and consequent
Consequences of invasion by Pseudosuccinea columella on the dynamics of native lymnaeids living on the acid soils of central France

ABSTRACT Eight road ditches located on granite and colonised by the native lymnaeids Galba truncatula or Omphiscola glabra were studied for 2 years to follow the distribution and density of these species in their habitats when the invasive lymnaeid Pseudosuccinea columella was introduced. Six other ditches populated only by a native lymnaeid or by P. columella were used as controls. The same experiment was also carried out for 3 years in seven water tanks placed in semi-natural conditions. The colonisation of P. columella was more rapid in habitats with G. truncatula than in those with O. glabra. Similarly, this colonisation led to a progressive decrease in the number of native lymnaeids in these ditches and this decrease was also faster for G. truncatula than for O. glabra. A similar decrease of G. truncatula and O. glabra was also noted when P. columella was introduced into water tanks placed in semi-natural conditions. The habitats of G. truncatula or O. glabra on the acid soils of central France can be successfully colonised by P. columella, and the establishment of this invasive species may lead to a decrease of the two native lymnaeids or even the local extinction of one of these (G. truncatula).
Quantifying landscape‐level land‐use intensity patterns through radar‐based remote sensing

The increasing availability of high resolution and high frequency, radar-based remote sensing data (i.e. observations on land surface characteristics, insensitive to cloud interference), makes it possible to track land-use intensity more precisely at the whole landscape scale. Here, we develop a new radar-based remote sensing technique for large-scale quantification of agricultural land-use intensity across human-dominated landscapes. We compare the respective abilities of Sentinel-1 C-band radar (C-SAR, C-band synthetic aperture radar) remote sensing data with the more traditional optical data, as MODIS enhanced vegetation indices (MODIS EVI), in capturing seasonality and the magnitude of land-use intensity (quantity and frequency of biomass removal). Linking our novel radar-based change detection algorithm to agricultural management activities on the ground, we quantify a whole landscape according to timing of mowing, a key grassland disturbance, thus capturing the dynamics of mowing regimes in grasslands. We found that the radar-based proxy provides a rapid and reliable measure of land-use intensity, reliably predicting plant community composition at the landscape scale. We tested this methodology using data on black-tailed godwits (Limosa limosa limosa), a specialist breeder of lowland meadows which, over the last 50 years, has shown dramatic declines. During territory establishment, black-tailed godwits preferentially used fields corresponding to intermediate radar-sensed land-use intensities. However, the present-day timing of mowing in these habitats was such that most godwit broods were less likely to be successful than broods in grasslands used at a lower intensity. Synthesis and applications. The newly developed radar-based land-use intensity quantification is a powerful tool that makes it possible for ecologists and land managers to include agricultural land-use intensity measurements in population studies of the plants, insects, birds and mammals using these landscapes, at the spatial scale of entire populations. Applications of this tool include evaluating the effectiveness of European agri-environment schemes aiming to increase biodiversity through decreased land-use intensity or expanding the quantification of agricultural land-use intensity to other geographic regions.
Sociality in rabbits

Two populations of rabbits (Oryctolaqus cuniculus) were investigated to see whether polygynous, multi-male groups formed in the absence of large multi-entranced warrens. They did not. Rabbits neither gathered in space nor time. The small warrens were spread out evenly across homogeneous patches and the females were well spaced out. Monogamy, distinguished by a battery of tests, was prevalent, with the more dominant males as 'mate' rabbits. That the polygyny frequently mentioned in the literature was a result of male dominance and female defense was considered. The genetic structure of each population was investigated by taking blood from rabbits and having it analysed electrophoretically and for immunoglobulins. A method for assessing relatedness between groups of pairs of animals was implemented, then validated and developed with Monte Carlo simulations. With the seven polymorphic allele obtained, no non-zero relatedness was found but it was sometimes possible to exclude high relatedness. The bearing of sociality on vigilance during feeding was investigated. Although a rabbit's vigilance decreased as its 'mate' approached, the presence of other rabbits was correlated with increased vigilance. It was concluded that the need for social vigilance outweighed the benefit of 'many eyes' watching for predators. This conclusion was tested by experiment, using stuffed animals as stimuli. Rabbits increased their vigilance during grazing bouts both by increasing the length and frequency of scans. Scans could be short or long: the probability of ending a scan decreased sharply at a certain point; a form of positive feedback. The durations of short 'maintenance' scans were dependent on chewlength (the amount of food in the mouth). This fitted a timesharing definition as supported by experiment. Long scans in response to a visible threat did not involve chewing.
Transcription-driven Chromatin Repression of Intragenic Promoters

Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a “positional information system” for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The FACT histone chaperone complex is required for this repression mechanism. Genome-wide mapping of Transcription Start Sites (TSSs) reveals thousands of discrete intragenic TSS positions in FACT mutants. Histone 3 lysine 4 mono-methylation poises exonic sites to initiate RNAPII transcription in FACT mutants. Uncovering the mechanism for intragenic TSS repression through the act of RNAPII elongation has important implications for understanding pervasive RNAPII transcription and the regulation of transcript isoform diversity.
PROCAMBARUS (SCAPULICAMBARUS) CLARKII (GIRARD, 1852), (CRUSTACEA: DECAPODA: CAMBARIDAE). UNA LANGOSTILLA NO NATIVA EN COLOMBIA

La langostilla Procambarus (Scapulicambarus) clarkii (Girard, 1852) se registra para la Sabana de Bogot´a, Colombia. Esta especie se diferencia de otras especies del g´enero por algunas caracter´ısticas morfol´ogicas en el caparaz´on y en el primer gonopodo del macho. La especie P. (S.) clarkii es originaria de la regi´on nor-oriental de M´exico y de las regiones central y sur de los Estados Unidos. La distribuci´on actual incluye todos los continentes, con excepci´on de Australia y la Ant´artica. Posiblemente en Colombia esta especie fue introducida para cultivo en la d´ecada de 1980, pero no hay evidencia de que se hayan cumplido con las formalidades de ley que protegen las comunidades nativas.
Comprehensive Assessment of Long-Term Changes of the Black Sea Surface Waters Quality in the Zmiinyi Island Area

In the last decades one of the main problems in degradation of coastal ecosystems’ health of European seas (EEA, 2001), including the Black Sea (BSC, 2008), was eutrophication caused by excessive content of nitrogen and phosphorus compounds in marine coastal waters. To decrease the nutrients flow and bring down eutrophication the European countries are spending significant efforts aimed at revealing the marine areas that are the most sensitive to nutrient pollution in accordance with the methodology proposed by the Water Framework Directive (WFD, 2000). The general approach of the WFD to environmental state of sea waters assessment is characterized by quite complex integrated registration of biological communities’ functioning and hydromorphological and physicochemical parameters. Recently simple method of coastal water quality integrated assessment using the TRIX trophic index proposed by (Vollenweider et al., 1998) for some areas of Adriatic Sea is gaining ground more and more for other European seas including the Black Sea (Baytut, 2010; Dyatlov et al., 2010; Medinets et al., 2010; Moncheva et al., 2002; Zaika, 2003). Results of recent studies of the coastal waters ecosystem adjacent to the Zmiinyi Island in the Black Sea (Medinets and Proschenko, 2008; Medinets et al., 2008b) have also shown that the main factor influencing the North-Western Black Sea (NWBS) water quality is eutrophication caused by nutrients input from coastal and land-based sources, reaching the Sea mainly through river inflow and atmospheric transport. The Marine Research Station “Zmiinyi Island” (MRS) of the Odessa National I.I. Mechnikov University, active since 2003, is carrying out a set of hydrological, hydrochemical, hydrobiological and other observations, that is enabling us to use the TRIX trophic index (Vollenweider et al., 1998), which integrally considers four parameters (Chlorophyll “a”, Total Phosphorous and Nitrogen, Dissolved Oxygen) to determine sea water quality for living organisms. The objective of our work is to study the dynamics of marine waters trophic state changes using TRIX index in the coastal waters of the Zmiinyi Island in the Black Sea, which according to the results of our investigations practically refer to open-sea water, though occasionally being influenced by the Danube, Dniester and Dnieper rivers discharge. Nataliia Kovalova 1, *, Volodymyr Medinets 1
Mass-independent maximal metabolic rate predicts geographic range size of placental mammals

M.B.A. is funded through the NICHE project (CGL2011‐26852) of the Spanish Ministry of Economy and Competitiveness and the Spanish Research Council (CSIC), the Rui Nabeiro Biodiversity Chair and the Danish NSF. M.B.A. acknowledges support from FCT project PTDC/AAG‐MAA/3764/2014.
A new species of Gyroporus (Gyroporaceae, Boletales) from Atlantic Forest in Southern Brazil

: Surveys of boletoid fungi in the Brazilian Atlantic Forest resulted in the discovery of a new species similar to Gyroporus castaneus named Gyroporus austrobrasiliensis. Macro- and microscopic descriptions, molecular data (nrDNA ITS and LSU sequences), photographs of the basidiomata, and scanning electron microscopy images of the basidiospores are provided.
Power spectrum slope and motor function recovery after focal cerebral ischemia in the rat

EEG changes across vigilance states have been observed after ischemic stroke in patients and experimental stroke models, but their relation to functional recovery remains unclear. Here, we evaluate motor function, as measured by single pellet reaching (SPR), as well as local EEG changes in NREM, REM and wakefulness during a 30-day recovery period after middle cerebral artery occlusion (MCAO) or sham surgery in rats. Small cortical infarcts resulted in poor SPR performance and induced widespread changes in EEG spectra in the ipsilesional hemisphere in all vigilance states, without causing major changes in sleep-wake architecture. Ipsilesional 1–4 Hz power was increased after stroke, whereas power in higher frequencies was reduced, resulting in a steeper slope of the power spectrum. Multielectrode array analysis of ipsilesional M1 showed that these spectral changes were present on the microelectrode level throughout M1 and were not related to increased synchronization between electrodes. Spectrum slope was significantly correlated with post-stroke motor function.
The role of the schmutzdecke in Escherichia coli removal in slow sand and riverbank filtration

A series of studies was conducted on laboratory scale sand columns under varying operational and design conditions with spiked concentrations of E. coli to investigate the role of the schmutzdecke, a biologically active layer that develops at the interface of the water and filter in slow sand filtration (SSF) and riverbank filtration (RBF). Results confirmed that E. coli removals in slow-rate biological filters occur primarily at the interface and are related to schmutzdecke ripening state, empty bed contact time, biological activity, temperature, and protistan abundance. Using a suite of analyses characterizing the biofilm growing on the schmutzdecke, no connection was found between the preexisting extent of biological ripening and a filter's ability to recover from a scouring or scraping event that removed the schmutzdecke. Biological activity, as measured by CO2 respiration in the top 2.5 cm, as well as protistan abundance in the top 0.5 cm of the schmutzdecke did, however, correlate positively to E. coli removal. The role of predation deserves further investigation, and filters should be operated in such a way as to enhance biological activity and protistan abundance in the schmutzdecke.
Evaluation of sensory attributes of Hanwoo Longissimus dorsi muscle and its relationships with intramuscular fat, shear force, and environmental factors

Abstract: We examined the relationship of Hanwoo (Bos taurus coreana) beef sensory attributes with intramuscular fat (IMF), Warner–Bratzler shear force (WBSF), and other environmental factors. Samples of 458 beef carcasses including 32 cows, 34 steers, and 392 bulls were analyzed for IMF percentage, WBSF, and important sensory attributes (tenderness, juiciness, and flavour-likeness). Results revealed that steer beef had significantly higher scores for all three sensory attributes than beef from cows and bulls. While juiciness and flavour-likeness differed (p < 0.05) among bulls and cows, they were not associated an effect on tenderness. All sensory attributes and WBSF were correlated (p < 0.001) with IMF; the highest correlation coefficient was for tenderness (0.55) while a negative coefficient (-0.39) was found for WBSF. The influence of IMF level on all three sensory attributes of bull beef significantly increased with IMF level. All sensory attributes of steer and bull beef showed negative relationship (p < 0.01) with WBSF, where highest correlation coefficient (-0.8) found for steer beef tenderness. Furthermore, tenderness and flavour-likeness showed lower ranks for meats slaughtered during the winter season; however, juiciness did not differ (p < 0.05) among seasons.
Orchid bees (Apidae: Euglossini) in Cerrado remnants in northeast Brazil

ABSTRACT There is a general lack of information concerning the diversity of bees belonging to the Euglossini tribe in Cerrado areas closest to the Brazilian Amazon. The state of Maranhão is situated in the northeast Brazilian Cerrado and has become the agricultural frontier of the country due to the advancement of monoculture and cattle farming. These activities have suppressed animal and plant populations in large areas of the Cerrado remnants, for which we have not yet obtained adequate scientific knowledge of local species. The objective of this study was to conduct a survey of Euglossini fauna in the northeast Cerrado. We evaluated the variation in species richness, composition and abundance between two distinct vegetation types: Cerrado sensu stricto (s.s.) and gallery forest. Male bees were captured from 7:00 a.m. to 5:00 p.m. over two consecutive days. Captures were carried out once per month from July 2012 to December 2013, using a combination of passive and active collection techniques, including baited traps, as well as a collector with an entomological net to collect bees near traps. We collected a total of 766 Euglossini males belonging to 24 species and five genera. The most abundant species were Eulaema bombiformis, Eulaema nigrita and Eulaema cingulata for the gallery forest site, whereas Eulaema nigrita, Euglossa melanotricha and Euglossa cordata were more abundant in the Cerrado s.s. The gallery forest yielded a higher number of male Euglossini (n = 503, 21 species) compared with the Cerrado s.s. (n = 263, 16 species). The presence of seven exclusive species in the gallery forest and three in the Cerrado s.s. indicated that both environments are important for the maintenance of Euglossini species in this region and highlight the increasing need for conservation programmes for the protection of Cerrado environments.
Choosing the right sigmoid growth function using the unified‐models approach

Growth of the young is an important part of the life history in birds. However, modelling methods have paid little attention to the choice of regression model used to describe its pattern. The aim of this study was to evaluate whether a single sigmoid model with an upper asymptote could describe avian growth adequately. We compared unified versions of five growth models of the Richards family (the four‐parameter U‐Richards and the three‐parameter U‐logistic, U‐Gompertz, U‐Bertalanffy and U4‐models) for three traits (body mass, tarsus‐length and wing‐length) for 50 passerine species, including species with varied morphologies and life histories. The U‐family models exhibit a unified set of parameters for all models. The four‐parameter U‐Richards model proved a good choice for fitting growth curves to various traits – its extra d‐parameter allows for a flexible placement of the inflection point. Which of the three‐parameter U‐models was the best performing varied greatly between species and between traits, as each three‐parameter model had a different fixed relative inflection value (fraction of the upper asymptote), implying a different growth pattern. Fixing the asymptotes to averages for adult trait value generally shifted the model preference towards one with lower relative inflection values. Our results illustrate an overlooked difficulty in the analysis of organismal growth, namely, that a single traditional three‐parameter model does not suit all growth data. This is mostly due to differences in inflection placement. Moreover, some biometric traits require more attention when estimating growth rates and other growth‐curve characteristics. We recommend fitting either several three‐parameter models from the U‐family, where the parameters are comparable between models, or only the U‐Richards model.
Larval development and fatty acid composition of Ostrea edulis (L.) fed four different single diets from conditioning to pre‐settlement

Survival, growth and fatty acid composition of Ostrea edulis larvae (L.) fed four different single species, microalgal diets, Tisochrysis lutea (T), Chaetoceros neogracile (Cg), Skeletonema marinoi (Sm) or Tetraselmis suecica (Ts) from broodstock to pre-settlement, were studied. Lower larval growth (5.5m to 6.5m/d) was recorded in progeny continuously fed single S.marinoi or T.suecica, whereas good growth was achieved with single T.lutea (7.8m/d). Larvae, originated from broodstock receiving Sm or Ts, exhibited growth compensation when fed a bispecific balanced diet (TCg). This did not occur when broodstock and larvae were fed Cg or T, for which single or mixed diets led to similar larval growth. Furthermore, survival was high (\textgreater90%) regardless of microalgal diet, except for larvae fed from broodstock to pre-settlement T (53%) or Ts (2%). There were significant differences in 20:5 (n-3) and 22: 6 (n-3) contents in polar and neutral fractions of O.edulis expelled larvae dependent on broodstock diet, as well as throughout larval development, but no clear trend was apparent when comparing fatty acid (FA) relative composition of both fractions of O.edulis larvae fed different diets at release or prior to settlement. In contrast, such correlation occurred when FA was expressed in absolute content but exclusively for larvae-fed single diets and was particularly noticeable between 22: 6 (n-3) and growth and survival. In the present work, broodstock nutritional deficiencies have been revealed in O.edulis progeny, compensated thereafter by feeding the larvae a mixed diet, and in this balanced condition, no obvious relation with larval development indicators was found with main fatty acid contents.
Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts

The in vivo erythropoiesis, which is the generation of mature red blood cells in the bone marrow of whole organisms, has been described by a variety of mathematical models in the past decades. However, the in vitro erythropoiesis, which produces red blood cells in cultures, has received much less attention from the modelling community. In this paper, we propose the first mathematical model of in vitro erythropoiesis. We start by formulating different models and select the best one at fitting experimental data of in vitro erythropoietic differentiation. It is based on a set of linear ODE, describing 3 hypothetical populations of cells at different stages of differentiation. We then compute confidence intervals for all of its parameters estimates, and conclude that our model is fully identifiable. Finally, we use this model to compute the effect of a chemical drug called Rapamycin, which affects all states of differentiation in the culture, and relate these effects to specific parameter variations. We provide the first model for the kinetics of in vitro cellular differentiation which is proven to be identifiable. It will serve as a basis for a model which will better account for the variability which is inherent to experimental protocol used for the model calibration.