Miracle-dz/UniFAR-FTUs huggingface dataset:
Fire History Sampling Strategy of Fire Intervals Associated with Mixed- to Full-Severity Fires in Southern Alberta, Canada

We propose a series of methods to conduct a ﬁeld-based ﬁre history in landscapes regulated by mixed- to high-severity ﬁres, where repeated lethal ﬁres create a scarcity of trees bearing more than a single scar and pose a challenge for calculating ﬁre return intervals (FRIs). In the context of applied forest and ﬁre management, we use a case study based on six sampling units across the Montane, Subalpine, and Upper Foothills natural subregions of the southern Canadian Rockies of Alberta. The methods use historical aerial photography and a targeted paired-plot sampling strategy along ﬁre boundaries and edges of unburned island remnants. This process allows for the calculation of point FRIs even when ﬁre scars are absent. The Kaplan-Meier nonparametric likelihood estimator is used for the ﬁre frequency analysis. A total of 814 sampling sites were visited, from which 3,123 tree cross-sections containing 522 ﬁre scars were collected. The period of data analysis ranged from the oldest stands sampled in the unit (1535–1770) to 1948, before effective ﬁre suppression. Spatial variability in the probability median FRIs between natural regions was identiﬁed. It ranged from 26 to 35 years in the Montane and was 39 years for the single Upper Foothills unit sampled, whereas the two Subalpine units sampled recorded values of 65 and 85 years. We concluded that the approach was sound for landscape-scale study areas regulated by large ﬁres with signiﬁcant tree mortality and with an average ﬁre interval greater than 20 years. Government and by Spray Lake Sawmills via funds from The Forest Resource Improvement Association of Alberta. A number of individuals were involved with the ﬁre history data collection process and sanding: M. Heathcott, P. Vera, M. Farris, J. Newsome, C. Rigby, G. Irwin, and L. Irwin. Assistance with tree-ring counting was provided by P. Vera. Study area ﬁgures were produced by M. Bradley with Alberta Agriculture and Forestry. The assistance of Xianli Wang from the University of Alberta with R programming was invaluable. Stimulating conversations with Rick Arthur, Mark Heathcott, and Brad Hawkes about the ﬁre regimes of southern Alberta contributed to the interest in publishing the results of this multiyear ﬁre history study. We also thank Brad Hawkes and anonymous reviewers for a detailed review of the article.
Epstein Barr virus EBNA2 : interactions of intrinsically disordered proteins with host cell factors.

It was recently reported that the physiological interaction between the nuclear protein SMRT and the cellular transcription factor STAT3 could be disrupted by the Epstein-Barr-virus protein EBNA2. Binding of SMRT to STAT3 decreases its transcriptional activity. EBNA2 releases SMRT from this complex and therefore enhances the transcription of both host and viral STAT3 regulated genes. STAT3 regulates several immunosuppressive as well as pro-proliferative and anti-apoptotic effects in the host organism and so may have importance for the viral survival strategy of Epstein-Barr-virus. Both EBNA2 and SMRT are intrinsically disordered proteins (IDPs) in common with about one third of all eukaryotic proteins and 70% of cancer-related. Despite their abundance, our understanding of how they function is limited, in part due to difficulties in production of stable samples in the large quantities necessary for structural and biophysical studies. The EPRIT technology was used to overcome these problems and generate well-behaving and -expressing EBNA2 and SMRT fragments. These fragments covered large parts of the EBNA2 and SMRT genes and were in a suitable size for NMR experiments. This enabled interaction studies of these proteins with STAT3. As both proteins are mainly intrinsically disordered all interaction data were analysed with attention to the disordered properties of both proteins. In order to complement the interaction data all fragments used for the interaction studies were as well characterized as IDPs using biochemical and biophysical methods. Fragments of both proteins, EBNA2 and SMRT together with the STAT3 dimer were subjected to binding analysis using various biophysical methods. The kinetics of the binding could be determined and the binding regions could be narrowed down to the amino acid level. Because of its biological significance and higher affinity interaction the EBNA2-STAT3 part was prioritized and first preliminary results investigating the interaction in mammalian cells could be obtained. Also, the interaction between EBNA2 and other cellular proteins was studied briefly. The obtained results aim to improve our understanding of how EBV succeeds to persist lifelong in the host organism.
In vitro Shoot multiplication of Physalis minima L. - an important Medicinal Herb

The present study was to develop an efficient protocol for shoot multiplication of Physalis minima L. Shoots were cultured using nodal segments from 20 days old field grown young plant. The nodal explants were cultured on MS medium supplemented with different concentrations of BAP and KIN. The two cytokinins tested, KIN was found to respond well in shoot multiplication and number of shoots from the nodal explants when compared to BAP. Large number of shoots was induced from all the concentrations of both BAP and KIN. BAP was found to develop in shoot multiplication and higher number of shoots from the nodal explants when compared to KIN. The highest frequency of 100% shoot induction was observed on MS basal medium supplemented with 8μM BAP and 10 μM KIN. Matured shoots are isolated and then transferred to the MS basal medium supplemented with different concentration of NAA and IBA for root induction. The higher number of roots were produced in 30 days on MS basal medium supplemented with 10 μM IBA and 6 μM NAA. The well rooted plantlets were isolated and transplanted to the paper cup for hardening and the well established plants were transferred to the field for acclimatization.
Maize–common bean intercropping to optimize maize-based crop production

SUMMARY Maize (Zea mays L.)–common bean (Phaseolus vulgaris L.) intercropping is a recent practice in north-western Ethiopia and there is limited information on its productivity. A field experiment was conducted at South Achefer and Mecha in north-western Ethiopia during the 2012 and 2013 crop growing seasons to determine combinations of intercrop planting arrangement (IPA) with nitrogen (N) and phosphorus (P) rates for optimizing maize–common bean intercrop productivity and profitability. Treatments consisted of factorial combinations of two IPA (single row of common bean between maize rows and paired rows of common bean between paired rows of maize), two N rates (92 and 128 kg N/ha) and two P rates (20 and 40 kg P/ha). A sole crop maize with recommended fertilizer rate of 128/40 kg N/P/ha was used as a control treatment. The treatments were laid out in a randomized complete block design with three replications. Results indicated that land equivalent ratio was more than unity, and the intercrop system was 20% more productive relative to the sole crop. Maize equivalent yields were highest for most of the intercrop treatments relative to mono-crop maize with yield advantage of 14% from single row IPA with 128/20 kg N/P/ha. Single row IPA with 128/20 kg N/P/ha and paired row IPA with 92/20 kg N/P/ha increased financial returns by 16 and 8% relative to sole crop maize, respectively. Smallholder maize-based cropping of north-western Ethiopia could be nutritionally, agronomically and financially improved through maize–common bean intercropping of single row IPA with appropriate nutrient management.
Z-cells and oogonia/oocytes in the advanced process of autophagy are the dominant altered cells in the ovaries of hypothyroid newborn rats

Abstract Induced prenatal hypothyroidism in rat pups leads to accelerated primordial follicle assembly and premature follicular atresia with ovary failure. This work investigates the influence of maternal hypothyroidism induced with 6-n-propyl-2-thyouracil (PTU) on the number and morphology of oogonia/oocytes in newborn rat pups with light and transmission electron microscopy. Expression of apoptosis and autophagy markers in oogonia/oocytes were examined using immunohistochemistry. Hypothyroid newborn pups had a decreased number of mitotic and resting oogonia, while the number of altered oogonia/oocytes was increased. Ultrastructural observations revealed the increased presence of degenerated pachytene oocytes (Z-cells) and oogonia/oocytes undergoing autophagy, apoptosis and combined apoptosis and autophagy, in this group. The most abundant altered oogonia/oocytes in the hypothyroid group were those with morphological features of advanced autophagy and Z-cells. The percentage of TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) positive oogonia/oocytes was significantly lower in the hypothyroid group. No significant difference was recorded in the expression of caspase-3, ATG7 and LC3 possibly reflecting that these proteins were not involved in the oogonia/oocyte alteration process during prenatal rat hypothyroidism. The obtained results indicate that developmental hypothyroidism in the offspring enhances the number of Z-cells and oogonia/oocytes altered with the advanced process of autophagy.
Phylogeny of the Troidine butterflies (Lepidoptera: Papilionidae) revisited: Are the red-bodied swallowtails monophyletic?

The phylogenetic relationships and biogeography of troidine butterflies are reassessed. The subtribe Troidina is considered to comprise the following generic groups, representing vicariant separation within western, central and eastern Gondwana respectively: 'Parides' Hubner + 'Euryades' C. and R, Felder; the 'red-bodied swallowtails' 'Atrophaneura' Reakirt + ('Pachliopta' Reakirt + ('Losaria' Moore, stat. rev. + 'Cressida' Swainson)); and the 'birdwings' 'Trogonoptera' Rippon + ('Troides' Hubner + 'Ornithoptera' Boisduval). 'Pharmacophagus' Haase, with its sole species 'P. antenor' (Drury) from Madagascar, is retained as a subgenus of 'Pachliopta'. The suggestion that 'Pharmacophagus', 'Cressida' and 'Euryades' are relict taxa is rejected.
ANALYSIS OF AVIAN INFLUENZA A (H7N9) MODEL BASED ON THE LOW PATHOGENICITY IN POULTRY

The avian influenza A (H7N9) virus is one subtype of influenza viruses, which has previously been isolated only in birds. Recently, an outbreak of a new avian influenza (H7N9) in China has resulted in numerous infections and high mortality in the humans. The H7N9 virus is low pathogenic in poultry and high pathogenic in human and that is critically different from other avian influenza viruses. An increasing number of the new H7N9 cases and the high mortality have caused a serious global concern. Here, based on the reported data, we propose and analyze an SE-SEIS avian–human influenza model. We prove the global stability results for both the disease-free equilibrium point and the endemic equilibrium point by using a general Bendixson–Dulac theorem. Our reported theoretical results of this paper are expected to help in exploring the development of efficient methods to controlling the spread of avian influenza A(H7N9).
Cold tolerance of the spring-feeding larvae of the eyespotted bud moth, Spilonota ocellana (Lepidoptera: Tortricidae)

Abstract In this study, we explore the low-temperature thresholds of a pest of apple (Malus pumila Miller; Rosaceae), the eyespotted bud moth, Spilonota ocellana Denis and Schiffermüller (Lepidoptera: Tortricidae), in the context of spring frost. Spilonota ocellana overwinters as a larva, resuming activity and feeding early in the growing season when it could be vulnerable to unexpected freezing temperatures. We determined that the mean supercooling point of spring instars did not differ for larvae within or outside leaf shelters and ranged from −9.1±0.2 °C for fourth instars, to −7.9±0.2 °C for sixth instars. Larval weight increased with instar and was positively related to the supercooling point. As some insects are freeze tolerant and able to recover from freezing, we also exposed larvae to brief freeze events between −4.5 °C and −9.5 °C and found that the median lower lethal temperature, was −7.3±0.4 °C across all instars; indicating that S. ocellana spring instars are susceptible to freezing temperatures above their supercooling point. These low-temperature thresholds suggest that in the spring, S. ocellana larvae are chill susceptible, and a hard frost (<−7 °C) would be necessary to cause significant larval mortality.
Successful interspecific hybridization between Phaseolus vulgaris L. and P. costaricensis Freytag & Debouck

More than 35 difíerent species oí Phaseolus native to the Americas are known (Delgado Salinas 1985). Although this Neotropical genus extends fi-om New York south to San Luis in Argentina (Debouck 1994), a large majority of species is found in Mexico. In general, the different species exhibit specificity in ecological adaptation and large variation in morphological traits, but some species can be grouped together because of apparently closer affinities or evolutionary relationships. They are also comparatively more similar morphologically, and in their ability to adapt ecologically. They also show an afiSnity for crossing and gene exchange. The species forming the secondary gene pool with P. vulgaris, on the basis of commonly shared cpDNA polymorphisms (Schmit et al. 1993) are P. polyanthus Crreenman, P. costaricensis, and probably 1 or 2 more taxa. Along the same line of evidence, P. coccineus L. would be already somewhat distant fi-om that group (Llaca et al. 1994; Schmit et al. 1993).
Construction, validation, and application of nocturnal pollen transport networks in an agro‐ecosystem: a comparison using light microscopy and DNA metabarcoding

1. Moths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant–pollinator interaction networks are traditionally constructed using either flower‐visitor observations or pollen‐transport detection using microscopy. Recent studies have shown the potential of DNA metabarcoding for detecting and identifying pollen‐transport interactions. However, no study has directly compared the realised observations of pollen‐transport networks between DNA metabarcoding and conventional light microscopy.
Cell wall metabolism in Bacillus subtilis

Cell wall is a unique and essential component of bacterial cell. It defines cell shape and protects cell from bursting through its own internal osmotic pressure. It also represents a significant drain on the cells resources, particularly in Gram positives, where the wall accounts for more than 20 % of the dry weight of the cell, and approximately 50 % of ‘‘old’’ cell wall is degraded and new material made to permit cell growth. After the discovery of penicillin, there has been active study of bacterial cell wall structure and metabolism, as it represents the major target for antibacterial compounds. The biosynthetic pathways for cell wall precursors has been well investigated in bacteria generally, but the coordination of cell wall metabolic processes and the fate of turnover cell wall materials have only been well characterised in Gram-negative bacteria (e.g Escherichia coli). In Gram-positive bacteria, it has generally been accepted that the old wall is released from the surface and lost to the environment during growth, with apparent recycling of this material during stationary phase for Bacillus subtilis. It is also known that the Gram-positive wall is subject to significant post-synthetic processing, involving the linkage of wall teichoic acids and the cleavage of molecules from the structure, e.g. D-alanine, although the function of these is unclear. Understanding the importance of these processes has relevance for both the pathogenicity and biotechnological use of bacteria, as well as for understanding bacterial cell biology. As it is known that the peptidoglycan fragments (e.g muropeptides) induce the innate immune response in higher organisms and so act as a signal for infection, particularly for Gram-positive bacteria. Thus, understanding how they are generated and recycled by the bacteria may offer potential insights into novel therapeutics, also the accumulation of cell wall muropeptides should be avoided in biotechnological products. In this thesis, the D-alanine metabolism was manipulated to understand the mechanistic details of cell wall metabolism and D-alanine recycling in B. subtilis, using genetic, biochemical, bioinformatics and fluorescent microscopy approaches. Through these analyses, a Dalanine transporter (DatA, formerly YtnA) was identified by genetic screening. The roles of DatA and the carboxypeptidases, LdcB and DacA, in recycling of cell wall derived D-alanine have experimentally been confirmed. We also found that D-alanine aminotransferase (Dat) can act to synthesis D-alanine under certain conditions. From the data obtained a model for peptidoglycan assembly (coordinated synthesis and turnover) during growth of B. subtilis has been developed to take into account the various aspects of cell wall metabolism.
Insulin-induced Suppression of A-type GABA Receptor Signaling in the INS-1 Pancreatic β-cell Line

GABA and GABA type A receptor (GABAR) are expressed in pancreatic βells and comprise an autocrine signaling system. How the GA BA-GABA AR system is regulated is unknown. In this study, I investigated insulin’ s effect on this system in the INS-1 βcell line. I found that GABA evoked current (I GABA) in INS-1 cells, resulting in membrane depolarization. Perforated-patch recordin gs showed that pre-treatment of insulin or zinc-free insulin suppressed I GABA in INS-1 cells (p < 0.01). Radioimmunossay showed that GABA (30 μM) increased C-peptide secretion from INS-1 cells, which was blocked by GABAAR antagonist picrotoxin, indicating that GABA incre ased insulin secretion through activation of GABA AR. However, insulin significantly reduced the stimulatory effect of GABA on C-peptide secretion ( p < 0.05). These data suggest that GABA released from β-cells positively regulates insulin secretion via G ABA AR activation, and that insulin negatively regulates t he β-cell secretory pathway likely via inhibiting the GABA-GABAAR system in β-cells.
Estimating contemporary migration rates: effect and joint inference of inbreeding, null alleles and mistyping

Microsatellite‐based genetic assignment is used broadly to monitor contemporary effective dispersal among populations. The need to investigate the robustness of this method to common genotyping errors was emphasized more than a decade ago, but it remains unaddressed. We evaluate here for the first time the effect of mistaken and null alleles on estimates of contemporary seed and pollen migration rates obtained with genetic assignment methods. We also introduce a novel Bayesian approach to jointly estimate seed and pollen migration rates, genotyping error rates and null allele frequencies, not requiring independent reference or duplicate genotypic data. Unaccounted‐for mistaken alleles caused positive bias and increased the root mean square error (RMSE) of pollen migration rate estimates, whereas seed migration rate estimates were weakly sensitive to mistyping. Jointly estimating mistyping rates minimized the bias and RMSE they introduce on pollen migration estimates, while yielding seed migration rate estimates with similar or slightly larger bias and RMSE than those obtained when ignoring mistyping. Ignoring genotyping errors can be especially problematic when there is no actual migration, because it can lead to the wrong conclusion that there is statistically significant exchange of pollen and/or seeds among populations that are actually isolated. Unaccounted‐for null alleles are problematic when among‐population pollen dispersal is present, leading to underestimation of pollen migration rates and overestimation of seed migration rates. Jointly estimating null allele frequencies minimized these two biases, reduced the RMSE of seed migration rate estimates and produced relatively small changes in the RMSE of pollen dispersal estimates. Synthesis. Disregarding genotyping errors and null alleles can produce biased and less accurate estimates of the rates at which present‐day plant populations are exchanging seed and pollen. An approach is proposed here to minimize the effect of genotyping problems on contemporary migration rate estimates, which should help avoiding erroneous migration inference, monitoring and management, especially when dealing with low migration rates and their associated uncertainty.
Microsatellite multiplex panels for genetic studies of gray snapper (Lutjanus griseus) and lane snapper (Lutjanus synagris)

Microsatellites are codominantly inherited nuclear-DNA markers (Wright and Bentzen, 1994) that are now commonly used to assess both stock structure and the effective population size of exploited fishes (Turner et al., 2002; Chistiakov et al., 2006; Saillant and Gold, 2006). Multiplexing is the combination of polymerase chain reaction (PCR) amplification products from multiple loci into a single lane of an electrophoretic gel (Olsen et al., 1996; Neff et al., 2000) and is accomplished either by coamplification of multiple loci in a single reaction (Chamberlain et al., 1988) or by combination of products from multiple single-locus PCR amplifications (Olsen et al., 1996). The advantage of multiplexing micro-satellites lies in the significant reduction in both personnel time (labor) and consumable supplies generally required for large genotyping projects (Neff et al., 2000; Renshaw et al., 2006).
Abbreviated title: Glucose uptake in PTP1B -/- neonatal hepatocytes

ABSTRACT The contribution of the liver to glucose utilization is essential to maintain glucose homeostasis. Previous data from protein tyrosine phosphatase (PTP) 1B-deficient mice demonstrated that the liver is a major site for PTP1B action in the periphery. In this study, we have investigated the consequences of PTP1B deficiency in glucose uptake in hepatocytes from neonatal and adult mice. The lack of PTP1B increased basal glucose uptake in hepatocytes from neonatal (3-5 day old), but not adult (10-12 week old) mice. This occurs without changes in hexokinase (HK), glucokinase (GK) and glucose 6-phosphatase (G6Pase) enzymatic activities. By contrast, the glucose transporter GLUT2 was up-regulated at theprotein level in neonatal hepatocytes and livers from PTP1B-deficient neonates. These results were accompanied by a significant increase in the net free intrahepatic glucose levels in the livers of PTP1B -/- neonates. The association between GLUT2 and insulin receptor (IR) A isoform was increased in PTP1B
Red List of Marine Bony Fishes of the Eastern Central Atlantic

The Red List of marine bony fishes of the Eastern Central Atlantic (ECA) is a review of the conservation status of all native marine bony fishes in ECA according to the global Categories and Criteria of the IUCN Red List of Threatened Species. It identifies those species that are threatened with extinction at the global level and occur within the ECA region. This comprehensive assessment, which is the first of its kind in the ECA, aims to provide improved knowledge of species presence and extinction risk status for the purposes of guiding conservation actions and improved policies for these species both globally and regionally.