Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of predator-exclusion cages used in turtle conservation: cost analysis and effects on nest environment and proxies of hatchling fitness

Abstract Context. A main goal of conservation is to mitigate anthropogenic impacts on natural ecosystems, thus conservation tools themselves should not negatively affect target species. Predator-exclusion cages are effectively used to reduce predation of turtle nests; however, their effects on nest environment and developing hatchlings have not been examined. Aims. Our study had the following four goals: (1) to examine effects of cages on the nest environment, (2) determine whether nest caging affects proxies for hatchling fitness, (3) evaluate whether nest predators preferentially interact with certain cage types, and (4) assess the cost-effectiveness of different nest caging designs. Methods. In 2010 and 2011 in Algonquin Provincial Park, Ontario, painted turtle (Chrysemys picta; n = 93) and snapping turtle (Chelydra serpentina; n = 91) nests were assigned to one of three treatments (wooden-sided cages, above- and below-ground wire cages) or a control (no nest cage) and outfitted with a data logger to record incubation temperature. After emergence, hatching success and proxies of hatchling fitness were measured. Key results. Nest temperature, hatching success, frequency of hatchling deformities and locomotor performance did not differ among cage treatments. However, hatchling body condition differed among treatments; wooden-sided and below-ground cages had the most positive influence on body condition in painted and snapping turtles, respectively. Predator interactions did not differ among treatments, and wooden-sided cages were the most inexpensive to construct. Conclusions. Nest cages did not alter the nest environment from natural conditions but did alter hatchling body condition, and nest caging affected species differently. Implications. Nest cages are known to reduce nest depredation, and our data indicated that, in general, nest cages also do not affect the nest environment or proxies for hatchling fitness. Thus, our findings indicated that cages are effective conservation tools that do not present secondary deleterious effects on potential recruitment.
Theoretical habitat templets, species traits, and species richness: aquatic macrophytes in the Upper Rhône River and its floodplain

SUMMARY 1 The objective of this study, which is based on forty-two species of hydrophytes and helophytes, is to investigate: (i) relationships among species traits; (ii) habitat utilization by species; (iii) the relationship between species traits and habitat utilization; (iv) trends in species traits in the framework of spatial–temporal habitat variability, and if trends match predictions from the river habitat templet; and (v) trends in species richness in the framework of spatial–temporal habitat variability, and if trends match predictions of the patch dynamics concept. 2 Two data sets were used for this analysis: species traits (mainly reproductive and morphological characteristics) were documented from the literature; and species distribution across eight habitat types was from field surveys conducted in the floodplain of the Upper Rhone River, France. This information was structured by a fuzzy coding technique and analysed by ordination methods. 3 Several species traits, which are related to disturbances and reflect resistance (e.g. attachment to soil or substrate) or resilience (e.g. potential for regeneration of an individual), are closely related for aquatic macrophytes. 4 Habitat utilization by aquatic macrophytes separates the habitat types along a gradient of connectivity with the main channel, which corresponds to a gradient in flood disturbance frequency and the permanence of the different water-bodies. 5 The relationship between species traits and habitat utilization is highly significant, indicating that a particular set of habitat types is used by taxa with a particular set of species trait modalities. 6 Observations in one habitat templet (in which scaling of the templet is primarily based on water level fluctuations for the temporal variability axis and on substrate characteristics for the spatial variability axis) generally do not support predictions on trends in species traits but do support predictions on trends in species richness. 7 Observations in an alternative habitat templet (in which scaling of the templet is based on frequency of flood scouring for the temporal variability axis and on heterogeneity of the substrate for the spatial variability axis) support theoretical predictions on trends for about half of the species traits for which predictions were available. However, trends in species richness in this alternative habitat templet are only partly in agreement with predictions.
The Most Important Factors Affecting Yield of the Eucalyptus Species

This study was conducted primarily to obtain factors affecting yield for forest plantation Eucalyptus spp in Aek Nauli, North Sumatera, Indonesia. The data in this study used 650 rhombic plots consisting of 106 PSPs and 544 inventory plots with several variations of plot size. Stands features referred to diameter, height, merchantable volume, age, species, spacing, site index, basal area, and density of Eucalyptus species. Geographical features referred to slope, elevation, rain fall and soil of the study area . The most important factors affecting yield of the E. hybrid, E. urophylla, and all Eucalyptus species are rainfall followed by soil group A while for E. grandis, E. pellita and mixed Eucalyptus are stand density, elevation, interaction site index and age, respectively.
ANT‐POLLINATION OF THE GRANITE OUTCROP ENDEMIC DIAMORPHA SMALLII (CRASSULACEAE)

Formica schaufussi, a medium-sized ant common throughout the Piedmont and Coastal Plain of the southeastern United States, has been observed in association with Diamorpha smallii, a self-incompatible annual endemic to granite outcrops in the Southeast, over a 6-yr period. Observations of ants collected on the flowers show large numbers of the sticky pollen grains adhering to hairs and indentations primarily on the thoraces of the ants. Though small native bees and flies are frequent and sometimes effective pollinators, it is highly unlikely that the monotypic genus Diamorpha coevolved with the introduced honeybee, as has been suggested. Characteristics indicative of an "ant-pollination syndrome" include occurrence in hot, dry habitats, a high density of very small plants bearing overlapping inflorescences at a uniform height, and low seed number, pollen volume, and nectar quantity.
Circadian Variations in Plasma Adrenaline and Noradrenaline in the Thoroughbred Horse

Circadian variations in catecholamines (CA) in the Thoroughbred horse were investigated by determining plasma adrenaline (Ad) and noradrenaline (NA) concentrations every 2 hr by high-performance liquid chromatography with an electrochemical detector (HPLC-ED). The HPLC-ED method in the present study was sufficient for determining plasma CA concentrations. The elution of CA from alumina with a mixture of acetic acid and methanol (1:50, v/v) gave a good recovery. The detection limit for both Ad and NA was 10 pg/ml. A significant variation during the 24 hr was observed for plasma NA concentrations (P<0.01), but not for plasma Ad concentrations. From 14:00 hr to 18:00 hr, plasma NA concentrations were significantly higher than those observed from 02:00 hr to 04:00 hr (P<0.01). As a result of the cosinor analysis for individuals, a circadian rhythm of plasma concentrations of Ad and NA was demonstrated (mean ± SE, 26.3 ± 4.6 pg/ml and 66.3 ± 3.8 pg/ml; rhythm amplitude, 9.4 ± 1.4 pg/ml and 12.7 ± 1.2 pg/ml; time of trough, 02:34 hr: min ± 9.7 min and 02:54 hr: min ± 33 min for Ad and NA, respectively). The 6 hr continuous tie-stall-type restraint decreased plasma concentrations of Ad and NA and delayed their peaks by 4 hr and 2 hr, respectively. There was a significant correlation (n=48, r=0.562, P<0.001) between the circadian variations in plasma Ad and NA. In conclusion, it was found that circadian variations in plasma CA in the Thoroughbred horse were similar to those in humans. In addition, the present study suggests that the sustained stress may influence circadian variations in plasma CA.
Land‐use impact on ecosystem functioning in eastern Colorado, USA

Land‐cover change associated with agriculture has had an enormous effect on the structure and functioning of temperate ecosystems. However, the empirical evidence for the impact of land use on ecosystem functioning at the regional scale is scarce. Most of our knowledge on land‐use impact has been derived from simulation studies or from small plot experiments. In this article we studied the effects of land use on (i) the seasonal dynamics and (ii) the interannual variability of the Normalized Difference Vegetation Index (NDVI), a variable linearly related to the fraction of the photosynthetically active radiation (PAR) intercepted by the canopy. We also analysed the relative importance of environmental factors and land use on the spatial patterns of NDVI. We compared three cultivated land‐cover types against native grasslands. The seasonal dynamics of NDVI was used as a descriptor of ecosystem functioning. In order to reduce the dimensionality of our data we analysed the annual integral (NDVI‐I), the date of maximum NDVI (DMAX) and the quarterly average NDVI. These attributes were studied for 7 years and for 346 sites distributed across eastern Colorado (USA).
IFN-αβ Released by Mycobacterium tuberculosis-Infected Human Dendritic Cells Induces the Expression of CXCL10: Selective Recruitment of NK and Activated T Cells 1

We recently reported that dendritic cells (DC) infected with Mycobacterium tuberculosis (Mtb) produce Th1/IFN-γ-inducing cytokines, IFN-αβ and IL-12. In the present article, we show that maturing Mtb-infected DC express high levels of CCR7 and they become responsive to its ligand CCL21. Conversely, CCR5 expression was rapidly lost from the cell surface following Mtb infection. High levels of CCL3 and CCL4 were produced within 8 h after infection, which is likely to account for the observed CCR5 down-modulation on Mtb-infected DC. In addition, Mtb infection stimulated the secretion of CXCL9 and CXCL10. Interestingly, the synthesis of CXCL10 was mainly dependent on the Mtb-induced production of IFN-αβ. Indeed, IFN-αβ neutralization down-regulated CXCL10 expression, whereas the expression of CXCL9 appeared to be unaffected. The chemotactic activity of the Mtb-infected DC supernatants was evaluated by migration assays using activated NK, CD4+, and CD8+ cells that expressed both CCR5 and CXCR3. Mtb-induced expression of CCL3, CCL4, CXCL9, and CXCL10 was involved in the stimulation of NK and T cell migration. In accordance with the data on the IFN-αβ-induced expression of CXCL10, neutralization of IFN-αβ significantly reduced the chemotactic activity of the supernatant from Mtb-infected DC. This indicates that IFN-αβ may modulate the immune response through the expression of CXCL10, which along with CXCL9, CCL3, and CCL4 participates in the recruitment and selective homing of activated/effector cells, which are known to accumulate at the site of Mtb infection and take part in the formation of the granulomas.
Over‐expression of ATR causes autophagic cell death

ATR is highly conserved in all eukaryotes and functions as a cell‐cycle checkpoint kinase to stabilize the nuclear genome. In addition, knockout mouse models indicate that ATR is essential for viability. Here, it is shown that moderate overproduction of ATR, but not of the other phosphatidylinositol 3′ kinase‐related kinases, ataxia‐telangiectasia‐mutated, mTOR and SMG‐1, and a downstream target p53, resulted in cell death. ATR over‐expression induced cellular vacuolization from 12 to 48 h after transfection, before cell death progression. A series of deletion analyses showed that overproduction of the N‐terminal HEAT repeat segments of ATR was sufficient for the induction of the vacuolization. Moreover, post‐transcriptional modification of LC3, a marker of autophagy, and autophagosomes with double membranes were evident in ATR‐overproducing cells. The vacuolization was also suppressed in autophagy‐deficient MCF7 cells. In addition, both cellular vacuolization and cell death were reduced by inhibition of Ras activity using farnesyl thiosalicylic acid. Conversely, neither inhibition of mTOR nor activation of the checkpoint system could be observed in the vacuolated cells. These results suggest that the Ras signaling pathway is involved in the autophagic response caused by ATR overproduction, and tight regulation of ATR protein expression is crucial for cell viability.
Genetic and behavioural analysis in three typical colonies of Jackdaws (Corvus monedula)

Breeding density colonies structure of Jackdaw (Corvus monedula) depends on the existence of appropriate cavities. In this work we report the social behavioural and genetic characteristics of Jackdaw colonies located in three typical hosting structures. To assess genetic structure a microsatellite analysis was performed throughout four polymorphic loci. During field activity a strong hierarchy in “natural cliff” and “modern bridge” colonies was revealed, compared to “mediaeval bell tower” colony. The colony located on the modern bridge showed the lower value of genetic variability. A high variability level was shown in the natural cliff, allowing the bird nesting in casually distributed cavities on a bi-dimensional surface, and in the tower that offers the chance of nesting on four sides of a three-dimensional volume. Hardy-Weinberg equilibrium in the three colonies was discussed considering social structure of the birds.
The Entomologist's Monthly Magazine

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Temperature-sensitive mutants of equine arteritis virus

Sera from patients infected with verocytotoxin-producing Escherichia coli (VTEC) O157, from patients with antibodies to E. coli O157 lipopolysaccharide (LPS) and from healthy controls were examined for antibodies to proteins involved in expressing the attaching and effacing phenotype. After SDS-PAGE, purified recombinant intimin, EspA-filament structural protein, translocated protein EspB and three separate domains of the translocated intimin receptor (Tir) were tested for reaction with patients' sera by immunoblotting. An ELISA was also used to detect antibodies to intimin in sera from E. coli O157 LPS antibody-positive individuals. Seven of nine culture-positive patients and one control patient had antibodies to EspA. Five of these patients and two controls had serum antibodies to the intimin-binding region of Tir, whereas none of the sera contained antibodies binding to either of the intracellular domains of Tir. By immunoblotting, 10 of 14 culture-positive patients had antibodies to the conserved region of intimin, eight of whom were infected with E. coli O157 phage type 2. Thirty-six of 60 sera from culture-negative but E. coli O157 LPS antibody-positive patients had antibodies to intimin as determined by ELISA. The secreted proteins are expressed in vivo during infection and are considered as pathogenic markers. Antibodies to these proteins may form the basis of a serodiagnostic test for the detection of patients infected with VTEC which carry the locus for the enterocyte effacement pathogenicity island and provide an adjunct test to the established serological tests based on VTEC LPS.
Expression and Prognostic Significance of Cadherin 4 (CDH4) in Renal Cell Carcinoma

Background Aberrant expression of cadherin family members and their possible biological function have been widely studied in renal cell carcinoma (RCC). However, the expression of cadherin 4 (CDH4) and its value in RCC diagnosis and prognosis remains elusive. Material/Methods The TCGA database was used to analyze the expression of CDH4 and its clinical parameters and prognosis in 891 RCC patients. In addition, real-time PCR was used to verify the transcription of CDH4 in renal clear cell carcinoma tissue, and the distribution of protein was observed by immunohistochemical staining. Results We found that the mRNA level of CDH4 was elevated in primary RCC in contrast with normal kidney samples using bioinformatics analysis based on the TCGA database. Among the 3 main subtypes of RCC, transcriptional CDH4 was significantly increased in KIRC and KIRP, while it was downregulated in KICH. Interestingly, CDH4 mRNA gradually decreased with the progression of KIRC and KIRP. The transcription of CDH4 in the primary tumor of KIRP patients at T3–T4 stages and KIRC patients with lymph node and distant metastasis were decreased significantly. Overall survival (OS) showed that KIRC and KICH patients with lower expression of CDH4 had worse outcomes. Conclusions The transcriptional level of CDH4 may serve as an effective diagnostic and prognostic biomarker for RCC patients.
Characterization of Superoxide Anion Scavenging Compounds in Roselle (Hibiscus sabdariffa L.) Extract by Electron Spin Resonance and LC/MS

Roselle (Hibiscus sabdariffa L.) is known to possess strong antioxidative capacity mainly due to its high content of anthocyanins and ascorbic acid. This study aimed to elucidate the ratio of contribution of these compounds in Roselle extract towards superoxide anion scavenging capabilities through analysis using electron spin resonance (ESR) coupled with the hypoxanthine/xanthine oxidase system and DMPO spin trapping technique. The ESR analysis indicated that the IC50 of Roselle extract against superoxide anion was 0.25 mg/ml. After depleting the ascorbate in Roselle extract (0.25 mg/ml) with ascorbate oxidase, the remaining superoxide anion scavenging capacity was determined to be 30.5%, which revealed that ascorbic acid substantially facilitated the scavenging process. By both HPLC and LC/MS analyses, the major active anthocyanins in Roselle crude pigments were identified as delphinidin-3-sambubioside (71.2% of total peak area), delphinidin-3-glucoside (8.7% of total peak area) and cyanidin-3-sambubioside (16.1% of total peak area). Approximately 80% of the superoxide anion scavenging capacities of these anthocyanins was from delphinidin-derivatives (delphinidin-3-sambubioside and delphinidin-3-glucoside); the other 20% was from cyanidin-derivative (cyanidin-3-sambubioside).
ACTIN FILAMENTS OF HEPATOCYTES IN EXPERIMENTAL RAT CHOLESTASIS-OBSERVATIONS USING A FLUORESCENT STAINING METHOD BY DACM LABELED HEAVY MEROMYOSIN

Actin filaments of hepatocytes in three types of experimental rat cholestasis were examined by a previously reported method (J. Histochem. Cytochem. 28; 335, 1980). Liver treated with cytochalasin B in vivo showed bile canalicular dilation and the obscure polygonal pattern of hepatocytes depended upon partial loss and granular aggregation in peripheral fluorescence. Liver treated with phalloidin showed an accumulation of fluorescence mainly around bile canaliculi in addition to an accumulation in the cytoplasma and nucleus in hepatocytes. Liver ligated with common bile duct showed increased fluorescence in the peripheral cytoplasma of hepatocytes, particularly around bile canaliculi, but this alteration varied according to the duration of ligation.
BioCovi: A Visualization Service for Comparative Genomics Analysis

Visualization of the homology information is an important method to analyze the evolutionary and functional meanings of genes. With a database containing model genomes of Homo sapiens, Mus muculus, and Rattus norvegicus, we constructed a web­based comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale. The user interface has several features: it marks regions whose identity is greater than that specified, it shows or hides gaps from the result of global sequence alignment, and it inverts the graph when total identity is higher than the threshold specified.
Influence of pre-treatments on microbial load of stored dehydrated onion slices.

Summary Onions slices were pre-treated in potassium meta-bisulphite (KMS) and sodium chloride with different concentration levels to study the microbial load of tray and greenhouse-dried onion slices up to 6 months of storage. Data were analysed as per procedure of one-way classified anova using DMRT of AgRes statistical package for bacteria, yeast, fungi and Lactobacilli. Results revealed that in almost all samples, permissible levels of bacteria [18.33 × 101 colony-forming units (CFU) per gram], yeast (ND), fungi (0.5 × 101 CFU g−1) and Lactobacilli (0.25 × 101 CFU g−1) were observed after 5 months of storage. All the samples were also found to be free from Escherichia coli and no Mac Conkey growth was noticed. Onion slices pre-treated in 0.25% and 0.50% KMS and dried in tray and greenhouse, respectively, were found best after 6 months of storage period.
Factors Controlling Phytoplankton Production in Lake Vanda (77°S)

At least three floristically distinct communities of algae were distributed down the permanently ice-capped water column of Lake Vanda. Phytoplankton at each depth were highly specialized towards specific conditions of light and temperature. Maximum photosynthesis and algal biomass was at the bottom of the euphotic zone (55–57.5 m) immediately above a region of nutrient-rich anoxic water. This Phormidium-dominated community was adapted towards warm temperatures (18–20 °C) but a dim light regime. Dissolved inorganic N to P ratios in this region were extreme (> 5000:1) and the plankton demonstrated strong cellular P deficiency. A much smaller photosynthetic maximum was recorded in the middle of a large thermohaline convection cell at 25–30 m where P deficiency was less severe, but detectable. A microflagellate community immediately under the ice demonstrated the least response to phosphorus enrichment, but photosynthetic characteristics appeared to be more attuned to the low irradiances which prevail early .