Miracle-dz/UniFAR-FTUs huggingface dataset:
MINIMUM ESTIMATES OF SURVIVAL AND POPULATION GROWTH FOR CERULEAN WARBLERS (DENDROICA CERULEA) BREEDING IN ONTARIO, CANADA

Abstract The Cerulean Warbler (Dendroica cerulea) tops many lists of species of conservation concern because of severe population declines and habitat loss. Here we present the first robust estimates of annual survival and population growth rates for this species. We used capture—mark—recapture models to estimate survival of adult male Cerulean Warblers in an eastern Ontario population that has been studied since 1994. Adult male survival probability (ϕ) was constant over time in our best-supported model. Our second-best-supported model indicated a negative effect of a 1998 ice storm on survival. The third-best-supported model indicated a significant year effect on survival. On the basis of those results and previously published estimates of annual fecundity, we calculated a population growth rate using a two-stage Leslie matrix. Population growth rate (λ) was 0.73, using the estimate for constant survival. Model elasticities imply that adult mortality had a stronger effect on λ than did seasonal fecundity. Oversummer survival estimates suggest that events during migration or on wintering grounds are responsible for most adult male mortality. It appears that our study population, thought to be one of the healthiest known for this species, may not be currently reproducing at a high enough rate to accommodate adult mortality. However, caution must be used when interpreting those results, given the possibility of underestimating survival and fecundity of this species.
Omnivores as seasonally important predators in a stream food web1

Abstract. Omnivory is prevalent in terrestrial and aquatic food webs. However, the extent and seasonality of predatory feeding by omnivores in stream food webs is largely unknown. To understand better these aspects of omnivory in stream food webs, we investigated seasonal changes in the trophic positions of 2 omnivores in a small forested stream. We selected the amphipod, Gammarus pulex, and the caddisfly larvae, Hydropsyche spp. , as key organisms because both taxa are common, reach high biomasses in many stream ecosystems, and have broad food spectra. We used stable-isotope analysis of the most prevalent taxa in the benthic macroinvertebrate community to assess the trophic positions of the 2 omnivorous taxa in different seasons. We estimated the degree of predatory feeding by quantifying the importance of different food resources with a stable-isotope mixing model (IsoSource). The predation capacity of omnivores, defined as the fraction of omnivore biomass associated with predation, was compared to the biomass of strictly predatory invertebrates. Our analysis indicated a predation capacity of Hydropsyche spp. similar to that of strict invertebrate predators, whereas the predatory biomass of G. pulex was even higher than those of the other invertebrate predators because of a combination of high biomass and large proportions of animal prey (50–90%) in the diets of both omnivores. The trophic position of omnivores in winter was comparable to that of invertebrate predators (trophic level 3), whereas in summer, their trophic position was comparable to primary consumers (level 2). These shifts might be caused by seasonally varying prey availability for Hydropsyche spp. and life-cycle patterns for G. pulex. Predation by omnivores was generally high in our study stream and probably has been underestimated in other stream ecosystems where omnivores, such as Hydropsyche spp. and G. pulex, are common.
A global biome model based on plant physiology and dominance, soil properties and climate

A model to predict global patterns in vegetation physiognomy was developed from physiological considera- tions influencing the distributions of different functional types of plant. Primary driving variables are mean coldest- month temperature, annual accumulated temeprature over 5"C, and a drought index incorporating the seasonality of precipitation and the available water capacity of the soil. The model predicts which plant types can occur in a given environment, and selects the potentially dominant types from among them. Biomes arise as combinations of domi- nant types. Global environmental data were supplied as monthly means of temperature, precipitation and sunshine (interpolated to a global 0.5" grid, with a lapse-rate correc-
Uygun Simulasyon Sayısının Belirlenmesi: Monte Carlo Simülasyon Çalışması

Simulation is an important method for modeling biological, social, agricultural, medicine and economic processes. Therefore, at the planning stage of a simulation modeling the question of number of simulation runs (N) is very critical. Because, stabilization of parameter estimation changes depend on number of simulation. This study aimed to investigate effect of number of simulation on stabilize of actual Type I error rate. For this aim, Type I error rates were estimated for 16 different number of simulation conditions. Results of this simulation study suggested that while number of simulation was small, differences among the actual Type I error rates increased. On the other hand, it could be said that 50000-700000 simulation numbers were optimum for all sample sizes.
HOX/PBX interaction as a therapeutic target in acute myeloid leukaemia

Acute myeloid leukaemia (AML) is a disorder characterised by the accumulation of blast cells or progenitors of one of several non-lymphoid haematopoietic cell lineages and is classified into two types: primary and secondary. HOX genes are over-expressed in both AML and other cancers. This over-expression is associated with an intermediate/unfavourable cytogenetic subset of AML. Although HOX over-expression is a common feature of AML, conventional knockout methods have failed to fully evaluate their functions due to their functional redundancy. We have applied an alternative approach by using a synthetic peptide called HXR9 to antagonise the interaction between HOX proteins and their cofactor PBX, which interacts with HOX proteins in groups 1-10. AML cell lines derived from different AML types express different subsets of HOX genes at different levels due to the heterogeneity of AML. It is showed for the first time that targeting the HOX-PBX interaction using HXR9 led to cell death of the tested AML cell lines. This cell death did not appear to be through apoptosis, as there were no signs of the caspase activation and nuclear fragmentation. Likewise, there was also no activation of key necrotic markers such as cypD and PARP1. Instead, cell death involved, at least in part, the expression of c-FOS and p21 in p53-independentmanner. In addition, HXR9 caused cell death in MEK/ERK and p38 independent pathways, but the JNK pathway exerted a resistant effect in K562 cells. It was found that inhibiting the Ca2+ downstream mediators CaM, PKC and HO-1 significantly sensitised tested AML cell lines to HXR9. Taken together, these findings indicate a novel cell death pathway in AML cells. In vivo modelling also showed that HXR9 could delay tumour growth in a mouse model of AML.
Studies on Colombian cryptogams. XVI Taxonomy and ecology of Kingiobryum paramicola (Dicranaceae, Musci)

Kingiobryurn paramicola, a rare species of a monotypic endemic genus of Dicranaceae (Musci), has been collected several times in pararnos of Colombia and Venezuela. It was previously reported from only a single specimen. Kingiobryum paramicola is redescribed, including details of the newly discovered sporophyte and discussion of the perforate and fissured walls of the inner basal cells. The ecology of K. paramicola is deliniated and phytosociological data are supplied.
Improved orthotopic and metastatic breast cancer models incorporating key elements of the tumour microenvironment enabling patient-relevant drug testing

Breast cancer (BC) is the most commonly diagnosed cancer in the UK and the second leading cause of cancer-related deaths in women worldwide. Limited treatment is available to patients with metastatic BCs, which are resistant to therapy. There is a strong link between metastatic BC and Epithelial Mesenchymal Transition (EMT). There is a need to target EMT, in order to prevent metastasis for which the therapy is not effective. Therefore, there is a need for improved pre-clinical models that will allow studying EMT in real-time. This study aimed to refine current in vivo models of BC, by incorporating inducible bioluminescent reporter(s) that will allow real-time read-out of EMT. The cell-lines used were classified according to their expression of EMT markers and cancer stem cell (CSC) profile. Inducible bioluminescent EMT reporters based on the S100A4 or E-cadherin or N-cadherin promoter driving firefly luciferase were constructed and used to transduce the cell lines. The activity of the S100A4 reporter was validated in hypoxic conditions in MCF-7 and BT549 cells, where it was shown that induction of S100A4-generated bioluminescence was associated with upregulation in S100A4. In vivo it was shown that human mesenchymal stem cells promoted the tumour growth of MCF-7 cells and/or induced EMT-related traits, including downregulation/loss of E-cadherin, upregulation of Vimentin and/or upregulation of S100A4. The activity of the S100A4 reporter was tested in a similar in vivo model, where it was shown that S100A4-generated bioluminescence correlated with protein expression of S100A4. Taken all the data together, we generated an inducible bioluminescent EMT reporter that can detect the baseline levels and changes in the S100A4 expression. The model can be potentially used for giving a real-time read out of EMT/early stages of EMT and subsequently for testing novel drugs targeted at the onset of EMT.
EVALUATION OF ANTIDERMATOPHYTIC ACTIVITY OF PEDALIUM MUREX L.

Dermatophyte infections are very common in India where hot and humid climate along with poor hygienic conditions play an important role in the growth of these fungi. Trichophyton and Microsporum species forms the commonest etiological agent of dermatophytosis. In the present investigation, different solvent extracts of Pedalium murex L. were screened against two dermatophytes viz., Trichophyton rubrum and Microsporum gypseum. The prominent zone of inhibitions was observed in methanol and petroleum ether extract of Pedalium murex against in Microsporum gypseum at 200 µg/ml concentration. The distilled water and methanol extracts of Pedalium murex showed significant activity against Trichophyton rubrum. The standard drugs griseofulvin, fluconazole and ketoconazole were used as the positive control and zones of inhibition were from 10 to 20 mm.
Enhancing soybean rust resistance through Rpp2, Rpp3 and Rpp4 pair wise gene pyramiding

The threat posed by soybean rust (Phakopsora pachyrhizi) on soybean production is worsened by resistance breakdown associated with single gene resistance present in most cultivars. Few studies have however been undertaken to use mapped simple sequence markers for gene pyramiding to enhance rust resistance. This study validated use of identified simple sequence repeat markers for gene pyramiding, and determined the most effective pairwise gene combination for three independent soybean rust resistance genes, Rpp2, Rpp3 and Rpp4. Markers Satt460 and AF162283 were polymorphic for the three resistance genes among the parents and were therefore used in selections made in the F2 and F3 families. In the F2 generation, soybean plants (homozygous dominant or heterozygous at both loci) with two gene combinations had relatively lower disease severity and sporulation than the parents, suggesting complementary epistatic gene action for resistance. Similarly, homozygous F3 families showed lower severity, lesion density and sporulation. Gene Rpp3 contributed positively to resistance with various genetic backgrounds for most parameters measured, compared to Rpp2 and Rpp4 resistance genes. Overall, the results suggest that marker gene pyramiding is feasible and can substantially increase resistance to soybean rust through reduced severity and reduced sporulating lesions.
The impact of gender on personal, health and workplace psychosocial risk factors for carpal tunnel syndrome

Between 2001 and 2010 six research groups conducted coordinated multi-year, prospective studies of upper extremity musculoskeletal disorders in US workers from various industries and collected detailed subject-level exposure information with follow-up symptom, physical examination, electrophysiological measures, and job changes. Objective. This analysis of the pooled cohort examined the incidence of dominant-hand carpal tunnel syndrome (CTS) in relation to demographic characteristics and estimated associations with occupational psychosocial factors, adjusting for confounding by personal risk factors. Methods. 3,515 participants, without baseline CTS, were followed up to 7 years. Case criteria included symptoms and an electrodiagnostic study consistent with CTS. Adjusted hazard ratios were estimated in Cox proportional hazard models. Workplace biomechanical factors were collected but not evaluated in this analysis. Results. Females were at elevated, though statistically non-significant, risk for CTS (HR=1.30; 95%CI: 0.98-1.72). The incidence of CTS increased linearly with both age and BMI over most of the observed range. High job strain increased risk (HR=1.86; 95%CI: 1.11-3.14) and social support was protective (HR=0.43; 95%CI: 0.23-0.78). There was no effect modification of gender on age, BMI or high job strain. Conclusions. Personal factors associated with an increased risk of developing CTS were BMI, age and being female, though no effect modification by gender was evident. Workplace risk factors were high job strain while social support was protective.
Thermal environment of New Zealand's gradual and abrupt treeline ecotones

In New Zealand, there are treelines of two main forms: abrupt southern beech treelines and gradual conifer-broadleaved treelines. At similar latitudes, abrupt treelines form at higher elevation than gradual treelines, but it is unclear whether this difference is also reflected in the climatic conditions experienced at the contrasting treeline ecotones. In this study, we measured soil and air temperatures across four gradual and two abrupt treelines ecotones in New Zealand for 2 years, and compared the climatic conditions between the treeline forms. Although gradual treelines form at lower elevations, they experience similar summer temperatures as the higher abrupt treelines. In contrast, temperatures in the shoulder season and during winter differed between sites of contrasting treeline forms. Soil scarcely froze and air temperature did not fall below −6°C at the gradual treeline sites, whereas freezing soils and snow were more common (extreme air frosts down to −9°C) at the abrupt treeline sites. Air and soil temperatures mirror the change in tree stature in the ecotone: with increasing altitude through the gradual treeline ecotone, temperature decreased gradually; whereas abrupt temperature changes were found at the abrupt treeline-grassland interface. These altitudinal patterns provide insights into potential mechanisms that drive treeline form and position, and their response to climatic change.
The invasive ctenophore Mnemiopsis leidyi poses no direct threat to Baltic cod eggs and larva

Since its invasion in to the Baltic Sea in 2006, the ctenophore Mnemiopsis leidyi has been suspected of serious predation on the early life stages of Baltic cod (Gadus morhua callarias L.) due to a temporal and spatial overlap in the most important cod spawning ground, the Bornholm Basin. We conducted laboratory incubation experiments and video observations to quantify feeding rates on Baltic cod eggs and larvae. Ingestion rates increased with cod larvae concentrations up to 8 prey L−1, beyond which ingestion remained constant. Neither Mnemiopsis size nor egg concentration (1–16 prey L−1) affected feeding rates on cod eggs. Observed feeding rates pooled from all experiments conducted at nonsaturating prey concentrations were low, with the highest volume‐specific clearance on < 4.5‐d‐old yolk‐sac larvae (0.05 ± 0.02 L (mL Mnemiopsis)−1 h−1), and lower rates on 4.5‐8‐d‐old larvae (0.02 ± 0.02 L (mL Mnemiopsis)−1 h−1) and eggs (0.02 ± 0.03 L (mL Mnemiopsis)−1 h−1). When offered Artemia salina and cod eggs simultaneously, Mnemiopsis passively selected against cod eggs. Video recordings showed that eggs did not trigger the capture response that Mnemiopsis shows toward motile prey, and ingested eggs were often ejected (88%, n = 8). Applying our clearance rates to in situ abundances of cod eggs, larvae, and Mnemiopsis for the peak of the spawning season, we demonstrate that the predation pressure of the invasive ctenophore is negligible. We conclude that Mnemiopsis constitutes no direct threat to the Baltic cod population.
New Species of Jupiaba (Characiformes: Characidae) from Rio Tiquié, Upper Rio Negro Basin, Brazil

Abstract Jupiaba poekotero, new species, is described from the Rio Tiquié, a tributary of the Rio Uaupés, in the upper Rio Negro system, estado do Amazonas, Brazil. It is distinguished from its congeners by the presence of an unpigmented, horizontally-oriented, roughly oval area on the proximal portion of the caudal-fin lobes, bordered posteriorly by dark pigmentation. Comments on the putative relationships of the new species are provided.
Use of Keeling plots to determine sources of dissolved organic carbon in nearshore and open ocean systems

We apply a Keeling mixing model commonly used in atmospheric sciences to oceanic dissolved organic carbon (DOC) 14C and concentrations to demonstrate that DOC distribution across spatial transects or depth profiles can be modeled as two‐component mixtures; one component consists of an old refractory pool to which a newly synthesized component pool is added. We then use the Keeling approach to determine the Δ14C signature of excess DOC added to background concentrations in nearshore and open ocean systems. Our analysis indicates enrichment in 14C of excess DOC in coastal waters relative to offshore waters, particularly in spring when river discharge increases. These findings are consistent with the export of 14C‐enriched terrestrial DOC to the ocean and inconsistent with the idea of selective degradation of young terrestrial DOC in estuaries, resulting in export of old refractory component to the ocean. In the middle Atlantic Bight region, during the spring, excess DOC has a 14C signature similar to that of DOC in the major rivers, whereas during the peak primary productivity of the summer season, excess DOC has a signature more similar to that of dissolved inorganic carbon. Variability in the Δ14C of excess DOC in the open ocean was lower than that of the coastal ocean. Minima in Δ14C values of excess DOC in the open ocean were measured during periods of high particulate organic matter (POC) flux, indicating that POC can interact with DOC and selectively remove 14C‐enriched components from the surface ocean. The Keeling plot provides a powerful approach for determining the isotopic composition of excess DOC from an entire DOC profile or transect.
Effects of an experimentally clumped food resource on raccoon Procyon lotor home-range use

Abstract Some species of carnivores fluctuate between a primarily solitary lifestyle and a group-living lifestyle, depending on resource availability. Understanding the ontogeny of this transition requires analyzing changes in space use. We analyzed radio-telemetry data from 41 adult raccoons Procyon lotor to assess the influence of an experimentally maintained clumped food source on spatial structure. We compared home-range size, two-dimensional overlap and volume of intersection (VI) values between 22 raccoons with access to the clumped food resource and 19 raccoons on an adjacent control site that received similar food quantities, but for which food was distributed in a non-clumped and spatially-temporally unpredictable pattern. No between-sex differences in home-range size occurred within either food site, nor did differences in home-range size occur between the two sites. However, the experimental-site animals had two-dimensional home-range overlap values and volume of intersection (VI) scores that were nearly twice those of raccoons inhabiting the control site. These differences appear to be driven by increased overlap among females from the experimental site, as males from the two treatment sites had similar home-range overlap and VI scores. Collectively, these results indicate that the distribution of resources can significantly change the extent of spatial overlap among individuals, even when the mean home-range size of the population does not change. This further suggests that while a site's overall resource availability influences population size, the spatial clumping of resources facilitates the formation of local aggregations.
Brazilian research on extremophiles in the context of astrobiology

Abstract Extremophiles are organisms adapted to grow at extreme ranges of environmental variables, such as high or low temperatures, acid or alkaline medium, high salt concentration, high pressures and so forth. Most extremophiles are micro-organisms that belong to the Archaea and Bacteria domains, and are widely spread across the world, which include the polar regions, volcanoes, deserts, deep oceanic sediments, hydrothermal vents, hypersaline lakes, acid and alkaline water bodies, and other extreme environments considered hostile to human life. Despite the tropical climate, Brazil has a wide range of ecosystems which include some permanent or seasonally extreme environments. For example, the Cerrado is a biome with very low soil pH with high Al+3 concentration, the mangroves in the Brazilian coast are anaerobic and saline, Pantanal has thousands of alkaline–saline lakes, the Caatinga arid and hot soils and the deep sea sediments in the Brazilian ocean shelf. These environments harbour extremophilic organisms that, coupled with the high natural biodiversity in Brazil, could be explored for different purposes. However, only a few projects in Brazil intended to study the extremophiles. In the frame of astrobiology, for example, these organisms could provide important models for defining the limits of life and hypothesize about life outside Earth. Brazilian microbiologists have, however, studied the extremophilic micro-organisms inhabiting non-Brazilian environments, such as the Antarctic continent. The experience and previous results obtained from the Brazilian Antarctic Program (PROANTAR) provide important results that are directly related to astrobiology. This article is a brief synopsis of the Brazilian experience in researching extremophiles, indicating the most important results related to astrobiology and some future perspectives in this area.
Comparison of methods for total community DNA extraction and purification from soilless substrate

Four protocols of soilless substrate DNA extraction were tested in three soilless substrates with different characterization, in order to find an efficient unbiased DNA extraction procedure which could analyze the microbial community structure in soilless substrate samples. Total DNA was extracted from each soilless substrate by the four protocols, and then was purified by Sephadex G-200 spin column after being precipitated by PEG8000. The results showed that more than 97.5% of the humic acids were also removed by Sephadex G-200 spin column. The agarose gel electrophoresis showed that the fragments of crude and purified DNA had a length of about 23 kb. In addition, the restriction map digested by restriction endonucleases showed that each of the protocols was adapted to extract microbial genome DNA from soilless substrate samples. Moreover, the protocol iii showed more bands by denaturing gradient gel electrophoresis analysis and was adapted to extract microbial genome DNA from soilless substrates with higher organic matter and humic.