Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers

Abstract Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str. , Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.
Impact and mechanical properties of different composite systems modified with multi-walled carbon nanotubes

Kevlar and glass fiber composites have distinguished mechanical properties such as specific strength and stiffness, resistance to impact loading, and tailoring the overall properties to meet the needs of a specific application. Enhancing their mechanical properties via incorporation of carbon nanotubes (CNTs) into their polymer matrices and proper characterization are very important for automotive and aerospace applications, which is the main objective of this study. This article presents an experimental study on manufacturing and mechanical characterization of six different materials. The tested materials include: CNT-nanocomposites, Kevlar fiber reinforce epoxy (KFRE) and glass fiber reinforced epoxy (GFRE) composites modified with CNTs. The CNTs were ultrasonically dispersed into the epoxy resin at 30% sonication amplitude (225 W) for 30 min to avoid their damage. The results were compared with the control materials (without CNTs). The mechanical tests are drop weight impact, tension, and in-plane shear. All the tests were performed according to ASTMs using computerized testing machines at room temperature. Results from the experimental study showed that the incorporation of the CNTs into the epoxy resin improves their tensile and shear strengths by 11% and 22.2%, respectively. In addition, the tensile and shear moduli of the CNT-nanocomposite were improved respectively by 68.7% and 29%. The absorbed energy and maximum contact force of the CNT-nanocomposite were improved by 11.4% and 9.5%, respectively. The tensile strength of the GFRE/CNT and KFRE/CNT composites showed improvements of 15.3% and 19.6%, respectively. The improvements in the tensile and shear moduli of GFRE/CNT and KFRE/CNT composites are in the range of 15–20%. The CNTs have marginal effects on the impact properties of the modified composite laminates. The tensile properties of the Kevlar composite systems (with and without CNTs) are higher than those of the glass composite systems and vice versa for the shear moduli and the absorbed energies.
β-Cell Adaptation to Insulin Resistance

The β-cell biochemical mechanisms that account for the compensatory hyperfunction with insulin resistance (so-calledβ-cell adaptation) are unknown. We investigated glucose metabolism in isolated islets from 10–12-week-old Zucker fatty (ZF) and Zucker lean (ZL) rats (results expressed per mg/islet of protein). ZF rats were obese, hyperlipidemic, and normoglycemic. They had a 3.8-fold increased β-cell mass along with 3–10-fold increases in insulin secretion to various stimuli during pancreas perfusion despite insulin content per milligram of β-cells being only one-third that of ZL rats. Islet glucose metabolism (utilization and oxidation) was 1.5–2-fold increased in the ZF islets despite pyruvate dehydrogenase activity being 30% lowered compared with the ZL islets. The reason was increased flux through pyruvate carboxylase (PC) and the malate-pyruvate and citrate-pyruvate shuttles based on the following observations (% ZL islets): increasedV max of PC (160%), malate dehydrogenase (170%), and malic enzyme (275%); elevated concentrations of oxaloacetate (150%), malate (250%), citrate (140%), and pyruvate (250%); and 2-fold increased release of malate from isolated mitochondria. Inhibition of PC by 5 mm phenylacetic acid markedly lowered glucose-induced insulin secretion in ZF and ZL islets. Thus, our results suggest that PC and the pyruvate shuttles are increased in ZF islets, and this accounts for glucose mitochondrial metabolism being increased when pyruvate dehydrogenase activity is reduced. As the anaplerosis pathways are implicated in glucose-induced insulin secretion and the synthesis of glucose-derived lipid and amino acids, our results highlight the potential importance of PC and the anaplerosis pathways in the enhanced insulin secretion and β-cell growth that characterize β-cell adaptation to insulin resistance.
Photovoltaic Degradation Rate Affected by Different Weather Conditions: A Case Study Based on PV Systems in the UK and Australia

This article presents the analysis of degradation rate over 10 years (2008 to 2017) for six different photovoltaic (PV) sites located in the United Kingdom (mainly affected by cold weather conditions) and Australia (PV affected by hot weather conditions). The analysis of the degradation rate was carried out using the year-on-year (YOY) degradation technique. It was found that the degradation rate in the UK systems varies from −1.05% and −1.16%/year. Whereas a higher degradation ranging from −1.35% to −1.46%/year is observed for the PV systems installed in Australia. Additionally, it was found that in the Australian PV systems multiple faulty PV bypass diodes are present due to the rapid change in the ambient temperature and uneven solar irradiance levels influencing the PV modules. However, in cold weather conditions (such as in the Northern UK) none of the bypass diodes were damaged over the considered PV exposure period. Furthermore, the number of PV hot spots have also been observed, where it was found that in the UK-based PV systems the number of hot spotted PV modules are less than those found in the Australian systems. Finally, the analysis of the monthly performance ratio (PR) was calculated. It was found that the mean monthly PR is equal to 88.81% and 86.35% for PV systems installed in the UK and Australia, respectively.
Rheoreaction impacts dispersal of fish larvae in restored rivers

Connectivity of nurseries and spawning habitats for young of the year life stage is essential for successful recruitment of fish populations and therefore provides a key indicator for river restoration measures. Models for dispersal offer the potential to draw conclusions regarding restoration scenarios and to fill knowledge gaps about possible implications for fish populations. A newly developed rheoreaction‐based correlated random walk model (RCRW), in combination with a three‐dimensional numerical model and a non‐steady‐state particle tracing model, was applied for nase carp larvae (Chondrostoma nasus) before and after a restoration project on the river Danube, Austria. Spatio‐temporal patterns of dispersal of virtual larvae, attached with rheoreactive behaviour, were analysed within both scenarios. In comparison to the heavily modified river reach, the restored reach enabled a greater amount of upstream movement from the release site and showed a generally higher variability of spatio‐temporal distribution patterns. In contrast, estimated total settlement of rheoreactive larvae was substantially higher for the situation prior to the restoration measure. By comparing model results with a previously field experiment it was found that model simulations including rheoreaction as a single behaviour for navigation could not explain the whole pattern of larval dispersal. Therefore it is highly recommended for future studies to develop larval dispersal models by considering other factors (i.e., behaviour, bio‐energetics and environmental factors) of existing and future individual‐based models, which could serve as a tool to analyse the effect of restoration measures for recruitment of riverine fish populations.
RESURRECTION OF MESOPLODON TRAVERSII (GRAY, 1874), SENIOR SYNONYM OF M. BAHAMONDI REYES, VAN WAEREBEEK, CÁRDENAS AND YÁÑEZ, 1995 (CETACEA: ZIPHIIDAE)

Mesoplodon traversii (Gray, 1874) is shown to be a senior synonym of the recently described beaked whale Mesoplodon bahamondi Reyes et al., 1995 on the basis of a phylogenetic analysis of mitochondrial DNA control region sequences. The mandible and teeth of M. traversii, first reported in 1873 by Hector as Dolichodon layardii, are redescribed. The species can be distin
The Epstein-Barr Virus Nuclear Antigen 2 (EBNA2), a Protein Required for B Lymphocyte Immortalization, Induces the Synthesis of Type I Interferon in Burkitts Lymphoma Cell Lines

Abstract Epstein-Barr virus nuclear antigen 2 (EBNA2), a protein involved in cell transformation, interferes with the cellular response to type I interferons (IFN-α/β). We investigated the function of conditionally expressed EBNA2 in the context of the IFN response in Burkitt's lymphoma cell lines. Expression of EBNA2 led to the transcriptional activation of both endogenous or transfected IFN-stimulated genes (ISGs), genes which contain within their promoters either the interferon-stimulated response element (ISRE) or the gamma interferon activation site (GAS). In search of a molecular mechanism for the transcriptional induction of ISGs, we observed an EBNA2-dependent synthesis of IFN-β mRNA at low levels and the secretion of low amounts of IFN. A transfected IFN-β promoter responded to EBNA2 activation, and a sequence closely resembling a RBP-Jκ binding site was pinpointed as a potential target of EBNA2 activity. EBNA2-dependent transcriptional induction of the IFN-β promoter occurred in EBV-negative Burkitt's lymphoma cells, indicating that other EBV genes were not required for the induction of IFN-β synthesis.
Refuge effects of a cactus in grazed short-grass steppe

Abstract Question: Which factors influence the effectiveness of biotic refuges for harbouring grazing-sensitive species in pastures with a long history of grazing by large herbivores? Previous research showed that spiny clumps of the cactus Opuntia polyacantha provided refuges from cattle grazing for plants and for inflorescence production on short-grass steppe. In this paper, seven factors that may have a potential positive influence on the refuge effects of cactus at a landscape scale were assessed. Location: Short-grass steppe of the Great Plains of North America. Methods: The study was conducted in eight long-term grazed pastures and their respective ungrazed controls that were established 60 years ago. Results: Heavy grazing intensities were necessary for some positive effects of cactus to manifest, and some refuge effects changed to negative effects under lower grazing pressure. Refuge effects increased with plant community productivity due to greater abundances of grazing-sensitive species, and greater grazing intensities in the more productive areas. Cover of cactus cladodes (spine-covered pads) inside clumps appeared to be the main limiting factor for refuge effects, probably by limiting available space for grazing-sensitive species in the clumps. Other factors such as size and density of cactus clumps, and the presence of large refuges in the proximity of clumps had minor influence on the effectiveness of cactus refuges. Conclusions: The effects of biotic refuges largely varied with ecological conditions and structural characteristics of the refuge. Refuge effects were mainly influenced by grazing intensity, plant community productivity, and structural characteristics of the biotic refuges. A conceptual model of factors influencing refuge effects at a local landscape scale in plant communities grazed by large herbivores is presented.
Transforming growth factor‐β and tumor necrosis factor‐α cooperate to induce apoptosis in the oligodendroglial cell line OLI‐neu

As shown previously, transforming growth factor‐β (TGF‐β) plays an important role during the period of developmental cell death in the nervous system. As with neurons, oligodendrocytes are generated in excess and eliminated by apoptosis. The present study was aimed at investigating the possible interaction of TGF‐β with tumor necrosis factor‐α (TNF‐α) in the regulation of cell death in oligodendroglial precursor cells and analyzing the underlying signaling mechanisms. We show that both factors induce apoptosis independently, but cooperate when applied together. The investigation of the signaling events revealed an important role of the JNK pathway during induction of apoptosis. TGF‐β seemed to be more efficient at inducing a release in cytochrome c from mitochondria than TNF‐α. This might be the consequence of decreased Bcl‐xL levels observed in cells treated with TGF‐β but not with TNF‐α. Both factors stimulated caspase‐3 activity, which could be inhibited by caspase‐8 or caspase‐9 inhibitors. Therefore, we conclude that TNF‐α and TGF‐β affect partially common pathways but also regulate different steps in the apoptotic cascade. © 2003 Wiley‐Liss, Inc.
INTRASPECIFIC GENETIC DIFFERENTIATION IN CALIFORNIA SEA LIONS (ZALOPHUS CALIFORNIANUS) FROM SOUTHERN CALIFORNIA AND THE GULF OF CALIFORNIA

Intraspecific patterns of mitochondrial DNA sequence variation were determined among California sea lions (Zalophus califomianus californianus) from three colonies along the Pacific coast of southern and Baja California and one colony in the Gulf of California. We found no variation in 368 base pairs (bp) of cytochrome b sequence among 40 sea lions from these localities, but analysis of 360 base pairs of control region revealed eleven genotypes. The four genotypes found in the Gulf of California population were unique and phylogenetically distinct from those found in sea lions along the Pacific coast. The average sequence divergence between Gulf and Southern California genotypes was 4.3%, suggesting a relatively long period of isolation. However, colonies along the Pacific coast, which are less than 200 km apart, shared mtDNA genotypes, indicating that recent genetic exchange has occurred between them. Therefore, we suggest that regional female philopatry exists in California sea lions. Regional boundaries may be related to oceanic currents or patchiness in the distribution of resources. Further research is needed to better understand the underlying causes of genetic differentiation in the California sea lion.
Evaluating Spatial and Temporal Variability of Fecal Coliform Bacteria Loads at the Pelahatchie Watershed in Mississippi

ABSTRACT Bacterial contaminations of surface waters are an increasing concern for scientists and public health agencies because pathogenic bacteria can cause adverse effects on human health. This research was performed to investigate spatial and seasonal variability of fecal coliform bacteria (FCB) concentrations in the Pelahatchie watershed (527 km2) in Mississippi, USA. Livestock manure, poultry litter, and effluent from failing septic systems were identified as major sources of FCB in the Pelahatchie watershed. The Soil and Water Assessment Tool (SWAT)/microbial sub-model was applied, and model-simulated FCB concentrations were compared with the monthly measured FCB concentrations (years 2001–2008) at the outlet of the watershed. New methodologies were introduced to incorporate bacteria loads into the bacteria model. Results showed coefficients of determination (R 2) of 0.71 to 0.75, and Nash-Sutcliffe efficiency index (NSE) of 0.67 to 0.75 during the bacteria model's calibration and validation periods, respectively. Seasonal analysis of the model-simulated results determined the highest bacteria concentrations in January, whereas the lowest concentrations were simulated in June. Furthermore, the FCB contributions to the watershed outlet from the sources of contamination varied with time of year. This study will help watershed managers to implement best management practices for improvement of water quality.
Development and growth of white lupin: implications for crop management

Grain yield of spring white lupin (Lupinus albus L.) varies greatly with sowing date and density. These effects seem to be related to variability of the canopy architecture. To explain and predict such effects, plant growth and development were characterized at different sowing dates and densities and were related to the distribution of seed number between the main stem and branches. «Lublanc» white lupin was sown in field environments for 9 yr, in the greenhouse for 2 yr, and in a growth cabinet for 1 yr at different densities and at different dates within seasons. Current management techniques were applied. Measurements included successive numbers of main-stem leaf primordia, successive numbers of main-stem leaves, date of flower initiation on the main stem, date of flowering on the main stem (SF), absorbed photosynthetically active radiation (PAR) by linear sensors (1 yr) or by leaf area index measurement (2 yr), and weekly accumulated dry matter (DM). Flowering date varied between 366 and 621 degree-days (base 3°C) from emergence and was closely related to the final number of main-stem leaves. Leaf number was linked to cumulative vernalizing degree-days received by the apex. Thus, SF was dependent on temperatures during early growth. Absorption efficiency of PAR (E a ) varied with plant density, but at high plant densities, regardless of the year, a single curve represented E a change over time. This limit curve gives the maximum possible E a at a given date. Until seed filling began, the coefficient of absorbed PAR conversion was 1.90 g DM MJ −1 . Our results contribute to improved management of lupin crops by suggesting cultural practices to minimize climatic hazards from drought and high temperatures
Phylogenetic relationships between Leymus (Poaceae, Triticeae) and related diploid Triticeae species based on isozyme and genome-specific random amplified polymorphic DNA (RAPD) markers

Abstract To investigate the phylogenetic relationships between Leymus and related diploid species of the Triticeae tribe, the esterase isozyme (EST), superoxide dismutase (SOD) isozymes, and genome-specific random amplified polymorphic DNA (RAPD) markers were used to analyze for 14 Leymus species, together with two Psathyrostachys species (Ns), three Pseudoroegneria species (St), two Hordeum species (H), Lophopyrum elongatum (Ee), Australopyrum retrofractum (W), and Agropyron cristatum (P). The data were used to construct dendrograms by means of UPGMA in the NTSYS-pc computer program. The results suggested that (1) isozyme analysis can be used in the systematic studies of these perennial Triticeae; (2) there is a close relationship between Leymus, Psathyrostachys juncea, three Pseudoroegneria species, and Lophopyrum elongatum; (3) the Ns genome-specific RAPD marker was present in all 14 polyploid species of Leymus, while the Ee and P genome-specific RAPD markers were absent in 14 polyploid species of Leymus; the St, W and H genome-specific RAPD markers were present in some species of Leymus; (4) Leymus species have multiple origins, and different Leymus species derived their genomes from different donors.
Limnology of Lake Bogakain, Bandarban, Bangladesh

Bogakain, a natural high altitude (372 m) lake of Bangladesh has been limnologically investigated for the first time. At mid-point, the depth of the lake was measured 46.54 m and the Secchi visibility was 2.37 m. Water temperature from 1-10 m depth gradient showed slight stratification in the lake which varied from 27.0 - 22.4° C at 1.00 pm. pH at the different depths ranged from 7.8 - 9.1, conductivity from 75 - 80 μS/cm and TDS from 39 - 42 mg/l. Alkalinity ranged from 0.8 - 1.24 meq/l and DO from 0.61 - 11.39 mg/l. A total of 40 species of phytoplank-ton were recorded from the lake of which 21 belonged to Chlorophyceae followed by Cynaophyceae (5), Bacillariophyceae (4), Cryptophyceae (4), Euglenophyceae (3), Dinophyceae (2) and Chrysophyceae (1). Bloom by Synnechocystis salina Wisl was observed at 10 m depth. Water temperature correlated negatively and significantly with depth. Phytoplankton biomass as chl a correlated positively with phytoplankton density and water depth. The former variable showed negative correlation with pH and water temperature. Lake Bogakain is the deepest natural lake of Bangladesh and many of the previous concepts regarding the lake i.e., fishless, highly turbid water and it has got a thermal spring at the bottom was found invalid. Key words : Bogakain; Limnology; Macrophyte; Phytoplankton; Bangladesh DOI: 10.3329/bjb.v39i2. 7301 Bangladesh J. Bot. 39 (2): 153-159, 2010 (December)
GROWTH ATTRIBUTES OF RAPESEED VARIETIES (BRASSICA CAMPESTRIS L.) IN RELATION TO SOWING DATES AND WEEDINGS TREATMENTS

Context: To analyze the effect of sowing dates and weeding treatments on growth attributes such as total dry matter (TDM), leaf area index (LAI), net assimilation rate (NAR), crop growth rate (CGR), leaf area ratio (LAR) of three rapeseed (Brassica campestris L.) Objectives: The objective of the study was to identify the growth in relation to sowing dates and weed competition and identify the weeding number for better growth of rapeseed. Materials and Methods: This investigation was arranged as factorial experiment based on the split-split plot design with three replications. Four sowing dates were including 18 October (S 1 ), 12 November (S 2 ), 17 November (S 3 ) and 3 December (S 4 ) and three weeding treatments were no weeding (W 0 ), one hand weeding (W 1 ) and two hand weeding (W 2 ) and three varieties viz., BINA Sarisha-5, BINA Sarisha-6 and BARI Sarisha-14 were investigated. Results: The results showed that, TDM, LAI, CGR, NAR and LAR were affected by sowing date and weeding treatments. The highest TDM, LAI and CGR were obtained in the first sowing and two weedings treatment. The highest NAR was found in S 2 plants and W0 treatment. The highest LAR was found in S 2 plants and W 1 treatment. Conclusion: The results obtained in this study suggest that the first sowing and two weeding treatments are superior for the production of rapeseed. DOI: http://dx.doi. org/10.3329/jbs.v21i0. 22519 J. bio-sci. 21: 51-59, 2013