Miracle-dz/UniFAR-FTUs huggingface dataset:
`Ocean triads' in the Mediterranean Sea: physical mechanisms potentially structuring reproductive habitat suitability (with example application to European anchovy, Engraulis encrasicolus)

Summaries of maritime weather reports and mean seasonal satellite-sensed ocean colour distributions for the Mediterranean Sea are used to identify characteristic configurations of physical mechanisms promoting (i) nutrient enrichment, (ii) concentration of larval food distributions, and (iii) local retention of eggs and larvae. Five subbasin scale ‘ocean triads’, hypothesized to be particularly favourable groupings, are identified in the Aegean Sea, the Gulf of Lions and nearby Catalan Coast, the Alboran Sea, the Straits of Sicily/Tunisian Coast, and the Adriatic Sea. These are examined in relation to available knowledge of anchovy spawning grounds. All areas are characterized by patterns of linked wind-driven Ekman upwelling and downwelling. All areas except the Straits of Sicily are found to have inputs of less saline surface waters offering raised nutrient concentrations, enhanced upper layer stability, and frontal density contrasts, and to have areas where the characteristic rate of turbulent mixing energy input by the wind fall below a reference intensity level. All areas, except the Sicilian Channel/ Tunisian Coast, also contain abundant locally reproducing anchovy populations.
A multiscale analysis of canopy structure in Fagus sylvatica L. and Quercus cerris L. old‐growth forests in the Cilento and Vallo di Diano National Park

Abstract Broadleaved forest is one of the most severely exploited and threatened ecosystems worldwide such that many authors have highlighted the scarcity of undisturbed old‐growth broadleaved forests, especially in southern Europe. From an ecological perspective, old‐growth forests are considered to be significant for their structural diversity and complex ecological relationships among species. In this paper, we compare ground measurements of leaf area index (LAI) and the remotely sensed normalized difference vegetation index (NDVI) autocorrelation pattern of two old‐growth forest stands in the Cilento National Park (southern Italy) with two nearby managed forests stands of the same type. Results show that old‐growth forests have higher fine‐scale variability in both LAI and NDVI values and longer autocorrelation ranges than the corresponding managed forests. The potential relevance of these findings for the single large or several small (SLOSS) debate is also briefly discussed.
Role of sea surface temperature and rainfall in determining the stock and fishery of the common octopus (Octopus vulgaris, Mollusca, Cephalopoda) in Tunisia

Octopus (Octopus vulgaris, Mollusca, Cephalopoda) is an important and valuable fishery resource on the eastern and southern coasts of Tunisia, but its landings are highly variable. This paper explores the effect of environment on octopus catch per unit effort (CPUE) during a 12-year period, through correlation analyses and the incorporation into surplus production models of sea surface temperature (SST) and rainfall data collected during cold (January–May) and hot (August–October) seasons. CLIMPROD software was used to select the appropriate model and fit it to the fishery and environment data. In both seasons, SST significantly contributed to CPUE variability; fishery production was influenced positively by cold season SST but negatively by hot season SST. Due to a poor fit with cold season data, the impact of rainfall was analysed only for the hot season, during which it has a positive effect on production. Results are discussed in view of the life-cycle of octopus and the dynamics of the Tunisian fishery. This first study of octopus variability in Tunisia highlights the necessity to incorporate environmental influence into stock assessment and management advice.
Physical activity of the civilian chemical victims of Sardasht 20 years after sulfur mustard exposure

Sulfur mustard was employed as a chemical warfare agent by the Iraqi forces in the borderline regions of Iran during the Iraq-Iran war (1980–1988). The short- and long-term biological effects of sulfur mustard agent have been studied in both basic and clinical aspects. One organ that was primarily affected was the respiratory system. Among the adults, regular physical activity positively affects the respiratory system as well as the individual’s ability to perform important daily tasks. We investigated the self reported physical activity in chemical victims 20 years after sulfur mustard exposure, compared the data with those of the matched counterparts, and explored any potential association with BMI. The exposed group was 357 and the control group was 125 individuals. Physical activity was measured using the global physical activity questionnaire (GPAQ) that evaluates work, recreational, transport and sitting activities. A significant difference was found between the control and exposed groups in terms of total physical activity MET (metabolic equivalent), total physical activity min/week and total transport-related physical activity min/week in BMI >30 kg/m2. In addition, total work-related physical activity showed a significant difference between the control and exposed groups with BMI <25 kg/m2. The results show that a significant correlation was present between the increase of body weight and the reduction of total physical activity and MET in exposed group 20 years after sulfur mustard exposure.
First nesting record of the Bay-Capped Wren-Spinetail Spartonoica maluroides (Aves, Furnariidae) in Brazil, with nest and nestling descriptions and notes on breeding behavior

O unico registro de reproducao de Spartonoica maluroides (d'Orbigny & Lafresnaye, 1837) no Brasil e baseado na observacao de um filhote recem-saido do ninho no sul do Rio Grande do Sul em janeiro de 1976. Em 7 de dezembro de 2005, descobrimos um ninho contendo tres filhotes na extremidade sudoeste da Lagoa Pequena, municipio de Pelotas, Rio Grande do Sul. O ninho estava oculto na base de uma cavidade dentro de uma touceira de Spartina densiflora (Poaceae) situada na margem de uma marisma. O ninho era constituido de pedacos delgados de folhas mortas de Scirpus olneyi (Cyperaceae) e S. densiflora firmemente entrelacados as folhas da touceira. Folhas vivas de S. densiflora que orlavam a cavidade compreendiam uma parte substancial da arquitetura do ninho, constituindo a maior parte da porcao superior das paredes laterais e o teto. A secao inferior era mais elaborada, similar a uma taca profunda e formando uma câmara incubatoria distinta. Os adultos acessavam o ninho atraves de uma abertura apical de formato irregular por entre as folhas. O ninho media 244 mm de altura e 140 mm de largura. A câmara incubatoria apresentava um diâmetro externo de 138,5 mm, um diâmetro interno de 79,4 mm e uma profundidade de 86 mm, sendo forrada de folhas delgadas e fibras vegetais brancas. Os ninhegos tinham de cinco a seis dias de idade. Um ninhego exibiu um total de 107 neossoptilas restritas aos tratos capital, espinal e alar. A distribuicao das neossoptilas na regiao ocular de S. maluroides forma um padrao distinto que pode ser tipico de Furnariidae e familias afins. Dois adultos atendiam o ninho, trazendo pequenos insetos para os ninhegos e removendo sacos fecais. Registramos pelo menos 74 visitas ao ninho em um periodo de ca. 6 h durante uma tarde. O numero medio de visitas por hora foi de 12,8 ± 1,3. Os adultos permaneceram em media 0,7 ± 0,56 minutos dentro do ninho atendendo os filhotes. O ninho permaneceu sem atendimento em media por 3,61 ± 3,13 minutos. O horario do dia nao influenciou o tempo de permanencia dos adultos no ninho ou longe deste. Retornamos ao local em 15 de dezembro de 2005 e encontramos o ninho abandonado. Observacoes confirmam que S. maluroides e um residente reprodutor no sul do Brasil e que as marismas do estuario da Lagoa dos Patos constituem um importante habitat para a especie durante todo o ano. Um ninhego e o ninho foram coletados para documentar o registro.
Intermediate Gel Immunoelectrophoresis

By interposing an intermediate gel between the first-dimension and the second-dimension gel (the reference gel) of a crossed IE, it is possible to compare the content of an unknown antiserum (Ab-x)with that ofa reference antiserum (Ref-Ab) by using a reference antigen (Ref-Ag) [37, 51, 6281. The two antisera are compared by running two plates that are identical apart from the lack of Ab-x in the intermediate gel of the test plate. The antibody specificities and titres of Ab-x can be expressed relative to Ref-Ab specificities and titres, but ‘free’ antigens present in Ab-x will also be revealed if corresponding antibodies are present in Ref-Ab. The method can be used for antigen analysis of an unknown antigen sample if the antibodies of the reference gel (Ref-Ab I) and of the intermediate gel (Ref-Ab 11) react with different molecules in the sample. This set-up is also useful for detecting fragments of antigens if Ref-Ab I and Ref-Ab I1 react with different determinants of an intact molecule. The intermediate gel principle is easily applicable also to rocket IE and to fused rocket IE.
Nonlinear Mixed-effects Scalar-on-function Models and Variable Selection for Kinematic Upper Limb Movement Data

This paper arises from collaborative research the aim of which was to model clinical assessments of upper limb function after stroke using 3D kinematic data. We present a new nonlinear mixed-effects scalar-on-function regression model with a Gaussian process prior focusing on variable selection from large number of candidates including both scalar and function variables. A novel variable selection algorithm has been developed, namely functional least angle regression (fLARS). As they are essential for this algorithm, we studied the representation of functional variables with different methods and the correlation between a scalar and a group of mixed scalar and functional variables. We also propose two new stopping rules for practical usage. This algorithm is able to do variable selection when the number of variables is larger than the sample size. It is efficient and accurate for both variable selection and parameter estimation. Our comprehensive simulation study showed that the method is superior to other existing variable selection methods. When the algorithm was applied to the analysis of the 3D kinetic movement data the use of the non linear random-effects model and the function variables significantly improved the prediction accuracy for the clinical assessment.
Extinction of Organelles in Differentiating Epidermis

In the dorsal skin of fetal rats, the epidermis on day 16 of gestation consisted of a single or a few layers of undifferentiated cells, and it developed to display the full strata, i. e the stratum (s.) corneum (horny layer), s. granulosum (granular layer), s. spinosum (spinous layer), and s. germinativum (basal layer) by the day of birth. Perinuclear electron lucent special areas, which were also detectable by conventional staining under light microscope, appeared in the cells of the s. spinosum or the s. granulosum on the day of birth. We call such an area the “peri-nuclear compartment (PNC) ”. The PNC was not partitioned by membranous structures either. Typical PNCs became recognizable on the day of birth. The cell nuclei seemed to be digested inside of the PNC of the cells located in the outermost area of the s. granulosum or sometimes in the boundary between the s. granulosum and the s. corneum. In the initial phase of nuclear extinction, morphology of the nucleus undergoing degeneration resembles that of apoptotic cells. In comparison to the morphological degeneration of the nucleus, DNA fragmentation was suggested to occur earlier. Localization of cathepsin B and cathepsin D in the s. spinosum and s. granulosum as revealed by immunohistochemistry, together with an electron microscopic study on the appearance of autophagosomes in those areas, suggested a contribution of autophagy to the digestion of organelles including mitochondria and endoplasmic reticula in the terminal differ-entiation of epidermal cells.
Marine Mangrove Fungi

Driftwood, prop roots and other mangrove samples were collected from the intertidal regions of Brillant and Anse Boileau mangrove stands, in the Seychelles. This material was examined for the presence of higher marine fungi. Forty seven species of marine fungi were collected (37 Ascomycotina, 1 Basidiomycotina, 9 Deuteromycotina), with Halocypluna villosu the most common fungus, while Aniptodera mungrovii, Antennospora quudricorruita, Halosarpheia marina, Ascomyccte sp. (4), and Lulworthiu grandispora were collected frequently. The mycota of the two mangrove stands arc compared. A list of fungi recorded from mangroves is compiled.
Automated docking of α‐(1→4)‐ and α‐(1→6)‐linked glucosyl trisaccharides and maltopentaose into the soybean β‐amylase active site

The Lamarckian genetic algorithm of AutoDock 3.0 was used to dock α‐maltotriose, methyl α‐panoside, methyl α‐isopanoside, methyl α‐isomaltotrioside, methyl α‐(61‐α‐glucopyranosyl)‐maltoside, and α‐maltopentaose into the closed and, except for α‐maltopentaose, into the open conformation of the soybean β‐amylase active site. In the closed conformation, the hinged flap at the mouth of the active site closes over the substrate. The nonreducing end of α‐maltotriose docks preferentially to subsites −2 or +1, the latter yielding nonproductive binding. Some ligands dock into less optimal conformations with the nonreducing end at subsite −1. The reducing‐end glucosyl residue of nonproductively‐bound α‐maltotriose is close to residue Gln194, which likely contributes to binding to subsite +3. In the open conformation, the substrate hydrogen‐bonds with several residues of the open flap. When the flap closes, the substrate productively docks if the nonreducing end is near subsites −2 or −1. Trisaccharides with α‐(1→6) bonds do not successfully dock except for methyl α‐isopanoside, whose first and second glucosyl rings dock exceptionally well into subsites −2 and −1. The α‐(1→6) bond between the second and third glucosyl units causes the latter to be improperly positioned into subsite +1; the fact that isopanose is not a substrate of β‐amylase indicates that binding to this subsite is critical for hydrolysis. Proteins 2000;40:299–309. © 2000 Wiley‐Liss, Inc.
The Influence of 17β-Estradiol on Patterns of Cell Division in the Uterus

Uteri from immature (21-day-old) and adult mice show different patterns of cell division in response to a physiological dose of 17β-estradiol. In the immature mouse uterus, estradiol increased stromal and epithelial cell proliferation by shortening the cell generation time (Tc). The epithelial Tc was reduced from 100 to 14.5 h; the stromal Tc was reduced to 16 h. In both cell types, the reduction in Tc was primarily due to a reduction of the G1 phase of the cell cycle. In the adult mouse uterus, estradiol stimulated epithelial but not stromal cell proliferation. Here, estradiol reduced the epithelial Tc from 86 to 13 h, mostly by reducing the G1 phase of the cell cycle. Therefore, estrogens stimulate uterine hyperplasia by selectively decreasing the G1 phase of the cell cycle in specific cell populations. At some point during reproductive tract maturation, uterine stromal cells lose their ability to divide in response to estrogen stimulation. A developmental study showed that in the intact mouse, the stro.
Prolonged maximal sexual swelling in wild bonobos facilitates affiliative interactions between females

Perineal sexual skin swelling in relation to menstrual cycle occurs in a variety of primate taxa. However, sexual swelling with exaggerated size and colour is found only in some Old World monkeys and the two Pan species. Although several hypotheses have been proposed (e.g., reliable indicator hypothesis and graded signal hypothesis), it seems unlikely that a single explanation can account for the significance of the sexual swelling in all of these species. Bonobos (Pan paniscus) provide an excellent opportunity for studying sexual swelling since they have the most prolonged maximal swelling periods among primates. In this study we propose a new hypothesis that sexual swelling in female bonobos increases their attractiveness to other females and thereby facilitates affiliative social interaction with them. We found that free-ranging female bonobos with maximal sexual swelling engaged in affiliative social interactions with other females, including genito-genital rubbing, staying in close proximity and grooming, more frequently than females without maximal swelling. These tendencies suggest that females with maximal swelling were attractive to other females. The results also suggest that the benefits of maximal swelling might vary among females depending on their life-history stage. In particular, young females may get more benefits from prolonged maximal swelling through increased grooming reciprocity and staying in close proximity to other females. Thus our study supported the hypothesis that one function of prolonged maximal swelling in bonobos is to increase attractiveness to other females, thereby enhancing affiliative relationships between females in a male-philopatric social system.
Intraspecific interactions in the mangrove crab Ucides cordatus (Decapoda: Ocypodidae) during the metamorphosis and post-metamorphosis periods under laboratory conditions

Current efforts for restocking natural populations of the mangrove crab Ucides cordatus (Linnaeus, 1763) in Brazil have focused on developing a methodology for stimulating the metamorphosis of U. cordatus larvae at a large scale. The aim of the present study was to compare the mortality rates both in individual and mass conditions, during the induction of metamorphosis of megalopa to juvenile in U. cordatus, without the use of mangrove sediment as substrate. Furthermore, the importance of intraspecific antagonistic behavior on survivorship rates during early post-metamorphosis period was investigated. Metamorphosis was induced by the use of water conditioned with conspecific adults (30 indiv. 100 L-1 for 24 hours). In the first assay, megalopae were stimulated into metamorphosis in experimental vials, both under individual and mass rearing conditions. The second assay assessed the interactions between megalopae and first instar juveniles, which have metamorphosed for more than 24 hours. In the third assay, the existence of cannibalistic behavior among first instar juveniles under different experimental densities was investigated. Significant differences between survivorship rates of individuals that metamorphosed under individual and mass rearing conditions were detected. However no cannibalistic behavior between juveniles and megalopae was observed in the second assay. Juveniles reared at a density of 200 indiv.m-2 showed survivorship rates similar to those obtained under individual conditions. Yet 500 juveniles.m-2 treatments showed significantly lower survivorship rates. Intraspecific interactions appear to be an important problem in U. cordatus specifically during the metamorphosis, but not during larval and post-larval rearing.
On the analysis and classification of sleep stages from cardiorespiratory activity

A method of adapting the boundaries when extracting the spectral features from heart rate variability (HRV) for sleep and wake classification is described. HRV series can be derived from electrocardiogram (ECG) signals obtained from single-night polysomnography (PSG) recordings. Conventionally, the HRV spectral features are extracted from the spectrum of an HRV series with fixed boundaries specifying bands of very low frequency (VLF), low frequency (LF), and high frequency (HF). However, because they are fixed, they may fail to accurately reflect certain aspects of autonomic nervous activity which in turn may limit their discriminative power, e.g. in sleep and wake classification. This is in part related to the fact that the sympathetic tone (partially reflected in the LF band) and the respiratory activity (modulated in the HF band) vary over time. In order to minimize the impact of these variations, we adapt the HRV spectral boundaries using time-frequency analysis. Experiments were conducted on a data set acquired from two groups with 15 healthy and 15 insomnia subjects each. Results show that adapting the HRV spectral features significantly increased their discriminative power when classifying sleep and wake. Additionally, this method also provided a significant improvement of the overall classification performance when used in combination with other HRV non-spectral features. Furthermore, compared with the use of actigraphy, the classification performed better when combining it with the HRV features.
Digestive and metabolic efficiencies of grizzly and black bears

Digestive and metabolic efficiencies of black bears (Ursus americanus) and grizzly bears (Ursus arctos) were determined in 7-day total collection trials using seven single foods and four mixed diets. No significant interspecific differences in digestive or metabolic efficiencies were observed. Dry matter and energy digestibilities were inversely related to the dietary fiber content, whereas digestible protein was directly correlated with dietary protein content. Mean retention time for hair in a meat diet was 13 h, whereas the retention time for clover was 7 h and did not differ between species. Giant pandas (Ailuropoda melanoleuca), grizzly bears, and black bears appear to have very similar digestive efficiencies and passage rates. The relationships between diet composition and digestive efficiency can be used to begin evaluating the nutritional quality of diets consumed by free-ranging bears.
Syntheses and Biological Activities of New Plant Growth Inhibitors Structurally Related to Abscisic Acid Part I

Several analogs of abscisic acid (ABA) were prepared and their biological activities were assayed. Among the compounds tested, 5-(l, 2-epoxy-2, 6, 6-trimethyl-l-cyclohexyl)-, 5-(l-hydroxy-2, 6, 6-trimethyl-2-cyclohexen-l-yl)- and 5-(l-hydroxy-2-methylene-6, 6-dimethyl-l-cyclohexyl)-3-methyl-cis, trans-2, 4-pentadienoic esters (V, IX, XXIII and XXV) were found to be potent plant growth inhibitors. Their activities were superior or comparable to that of ABA.