Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of saproxylic basidiomycetes in Quercus ilex woodlands of central and insular Greece

Abstract The sclerophyllous forests of Quercus ilex (holm oak) possess a unique position in earth’s biosphere, existing only in countries of the Mediterranean basin. However, very little information exists about mushrooms associated with holm oak in east Mediterranean, including Greece, where Q. ilex appears mostly in relict forests and fragmented stands. A pertinent long-term investigation was undertaken in selected Q. ilex dominated habitats of Crete, Andros, Naxos and Ikaria islands (Aegean Archipelago) as well as in mountains of Attica. Specimens of xylotrophic basidiomycetes were collected and identified. As a result, 74 species were recorded; among them Hemimycena cephalotricha, Hyphoderma cremeoalbum, Hyphodontia radula, Irpex litschaueri, Mycena algeriensis, Phanerochaete martelliana, Phloeomana alba and Phlebia unica constitute new records for the Greek mycobiota, while 68 species are reported for the first time on Q. ilex in Greece. Moreover, the presence of Fomitiporia mediterranea on this host was evidenced through ITS sequencing, and comments are made about its relationship to F. punctata and F. pseudopunctata. The importance of findings is discussed in conjunction with their environmental value; five species could be assigned in the “Species of Special Interest” categories, and other five polypores are proposed as suitable indicators for Q. ilex habitat assessment and conservation.
Seed coat and aging conditions affect germination and physiological changes of aging Korean pine seeds

ABSTRACT The study was conducted to obtain information on possible seed aging during the long-term storage period of Korean pine seeds with thick impermeable seed coat. The seeds were artificially aged at 18, 24, 37 and 45°C for 35 days. Germinations percentages (GP) of aged seeds were highest on 25 days at 18°C, 15 days at 24°C and 10 days at 37°C. The seeds exposed at 45°C have completely lost their germinability after 5 days of aging. From 5 days of aging, mean germination times (MGT) were lower than control seed. The electrical conductivity on 10 days at 45°C reached 1.5–2.5 times its control seed, and had a positive correlation with the GP and a negative correlation with the MGT. The K+ was the most in leaching solution, and K+ and Mg2+ showed a high negative correlation between GP and MGT. The ratio of K+/Na+ had a higher correlation with seed vigor. The malondialdehyde (MDA) increased to 21 times of control seeds at 45°C after 35 days of aging, and had a negative correlation with GP and MGT. The antioxidant enzymes showed different sensitivity to aging, depending on storage conditions and enzyme species. Ascorbate peroxidase showed the highest correlation with germination following glutathion reductase and Catalase. In conclusion, the seed aging had an effect initially to increase the GP and reduce the MGT. However, as aging treatment continued, the seeds eventually lost vitality due to an increase in physiological damages.
Beyond the novelty effect: EFL learners' attitudes towards ICT use in the classroom

The present study explores high school students' (aged 16–17) attitudes towards the use of technology Information and Communication Technology (ICT) in the English as foreign language (EFL) classroom. While digital competence has become one of the core skills in our society, ICT is gaining more presence in the EFL teaching and learning. However, it is not widespread in the mainstream education, as it is the case of Spain, especially at high school level. There is also still some reticence on the part of the teachers to let the ICT be part and parcel of their daily practice. Since adolescents often experience a motivational drop as far as learning a foreign language (FL) in school setting is concerned, EFL teachers should promote the integration of ICT in classroom activities, as research has shown that technology-supported activities may contribute to engaging students in the process of learning a FL and act as a motivating factor. This paper examines 77 EFL learners' responses to a questionnaire administered before and after the implementation of an 18-month ICT-based intervention in their classroom. The main findings reveal that attitudes towards technology were positive and they were maintained beyond the possible “novelty effect”, which supports the claims in favor of ICT's integration in EFL teaching.
Developing a taper model for the Pinus elliottii × P. caribaea var. hondurensis hybrid in South Africa

A relatively new hybrid, Pinus elliottii × P. caribaea var. hondurensis (Pexc), for which a taper model does not exist, is being planted commercially in South Africa. This study primarily focused on developing a taper model for Pexc in South Africa. Taper data were collected from a total of 363 trees, in the Mpumalanga and Limpopo provinces, using a random sampling method. A subsample was selected to determine if altitude, rainfall, temperature or soil have a significant influence on the taper of Pexc. Only rainfall significantly influenced the overall taper. The Max and Burkhart segmented polynomial taper model, as well as the Kozak88, Kozak01 and Kozak02 variable exponent taper models, were fitted, compared and tested using the statistical analysis system (SAS). The predictive ability of the models was evaluated based on the results from the mean bias, standard deviation, the standard error of prediction and the average percentage deviation. The Kozak02 model had the best fit overall followed by the Max and Burkhart model (MB76). The MB76 model, however, predicted the volumes more accurately than the Kozak02 model.
Molecular evolution of biological sequences

The work presented in this thesis has been supported by the Wellcome Trust as part of the PhD programme in Mathematical Genomics and Medicine at the University of Cambridge, by the Sanger Early Career Innovation Award, by Fundacion Ibercaja, and partially supported by the National Science Foundation during a research stay at the Kavli Institute for Theoretical Physics (University of California, Santa Barbara).
Rice crop classification and yield estimation using multi-temporal sentinel-2 data: a case study of Terai districts of Nepal

Crop monitoring, especially in developing countries, can improve food production, address food security issues, and support sustainable development goals. Crop type mapping and yield estimation are the two major aspects of crop monitoring that remain challenging due to the problem of timely and adequate data availability. Existing approaches rely on ground-surveys and traditional means which are time-consuming and costly. In this context, we introduce the use of freely available Sentinel-2 (S2) imagery with high spatial, spectral and temporal resolution to classify crop and estimate its yield through a deep learning approach. In particular, this study uses patch-based 2D and 3D Convolutional Neural Network (CNN) algorithms to map rice crop and predict its yield in the Terai districts of Nepal. Firstly, the study reviews the existing state-of-art technologies in this field and selects suitable CNN architectures. Secondly, the selected architectures are implemented and trained using S2 imagery, groundtruth and auxiliary data in addition for yield estimation. We also introduce a variation in the chosen 3D CNN architecture to enhance its performance in estimating rice yield. The performance of the models is validated and then evaluated using performance metrics namely overall accuracy and F1-score for classification and Root Mean Squared Error (RMSE) for yield estimation. In consistency with the existing works, the results demonstrate recommendable performance of the models with remarkable accuracy, indicating the suitability of S2 data for crop mapping and yield estimation in developing countries. Reproducibility self-assessment (https://osf.io/j97zp/): 2, 2, 2, 1, 2 (input data, preprocessing, methods, computational environment, results).
Mapeamento físico e análise evolutiva em Phaseolus vulgaris L. e P. lunatus L., utilizando hibridação in situ fluorescente (FISH)

26 Introduction 26 Materials and methods 27 Plant material 27 Chromosome preparation 27 DNA probes 27 Fluorescence in situ hybridization (FISH) 27 Data analysis 27 Results 28 Discussion 32 Mechanisms of rDNA variation 32 Differential 45S rDNA amplication in common bean 33 Acknowledgements 34 References 34 5. CAPÍTULO II – Citogenética comparada de duas espécies de Phaseolus: P. lunatus L. e P. vulgaris L. 36
A revision of Peronina Plate, 1893 (Gastropoda : Euthyneura : Onchidiidae) based on mitochondrial and nuclear DNA sequences, morphology and natural history

Abstract. Peronina Plate, 1893 is a genus of onchidiids that live on the mud in mangrove forests. Peronina can be identified in the field by the lung opening at the margin between the ventral hyponotum and the dorsal notum, and by the distinctive scalloped notum edge. This genus was previously known only from the holotype of the type species, Peronina alta Plate, 1893, from eastern India. Onchidium tenerum Stoliczka, 1869 is moved to Peronina and applies to the same species as Peronina alta. Peronina species are described using an integrative approach (natural history, comparative anatomy and DNA sequences). Mitochondrial COI and 16S sequences and nuclear ITS2 and 28S sequences are used to independently test species boundaries. Mitochondrial sequences yielded three units separated by a large barcode gap, but nuclear sequences yielded two units. Because these two units are congruent with differences in the male copulatory apparatus, they are accepted as species. Explanations for highly divergent COI haplotypes within one species are discussed. Peronina tenera (Stoliczka, 1869) is distributed in the Bay of Bengal and the Strait of Malacca, while P. zulfigari Goulding & Dayrat, sp. nov. is endemic to the Strait of Malacca. The two species differ internally but are cryptic externally.
Pyrethroid exposure alters Anopheles albimanus microbiota and resistant mosquitoes harbor more insecticide-metabolizing bacteria

A deeper understanding of the mechanisms underlying insecticide resistance is needed to mitigate its threat to malaria vector control. Building upon our earlier identified associations between mosquito microbiota and insecticide resistance, we demonstrate for the first time, type-specific effects of pyrethroid exposure on internal and cuticle surface bacteria in adult progeny of field-collected Anopheles albimanus. In contrast, larval cuticle surface—but not internal—bacteria were affected by pyrethroid exposure. Being over five-folds more abundant in pyrethroid resistant adults, as compared to susceptible or non-insecticide-exposed mosquitoes, Klebsiella (alphacypermethrin), Pantoea and Asaia (permethrin) were identified as potential markers of pyrethroid resistance in An. albimanus. We also show for the first time that An. albimanus larvae and adult cuticles harbor more diverse bacterial communities than their internal microbial niches. Our findings indicate insecticide selection pressures on mosquito microbiota, and support the hypothesis of an undescribed microbe-mediated mechanism of insecticide metabolism in mosquitoes. Competing interest statement This work was supported by the US Centers for Disease Control and Prevention (CDC) through the American Society for Microbiology’s (ASM) Infectious Disease and Public Health Microbiology Postdoctoral Fellowship program, and the CDC’s Advanced Molecular Detection (AMD) program. The findings and conclusions in this paper are those of the authors and do not necessarily represent the official position of the CDC or ASM.
Lethal and sublethal effects of five insecticides on the demography of a parasitoid wasp

Abstract Habrobracon hebetor Say (Synonym: Bracon hebetor) is an important ectoparasitoid wasp of lepidopteran pests. In this research, the effects of chemical and botanical insecticides including fenvalerate, propargite, buprofezin, dayabon and palizin were investigated on this biocontrol agent. The contact exposure bioassays showed that LC50 values under insecticides treatment were 0.52, 47.44, 23.30, 31.35 and 62.47 mg a.i./L, respectively. Then, the young female wasps of H. hebetor (<24 h old) were exposed to LC30 of selected insecticides for 24 h and their demography was investigated. The sublethal results showed that adult longevity, survival, fecundity, fertility, hatch rate and sex ratio of H. hebetor negatively were affected by the tested insecticides. Finally, the intrinsic rate of increase (rm) was obtained after treatment and was 0.27 day−1 for the control versus 0.14, 0.18, 0.21, 0.19 and 0.24 day−1 for the insecticides, respectively. The effects of dayabon and palizin have not been evaluated yet on moth pests and must be investigated in the future. Our results show that palizin has the lowest negative effects on the demography of H. hebetor and therefore is a compatible insecticide for integrated pest management programs.
Trafficking and Quality Control of Inward-Rectifying Potassium Channels in the Model Eukaryote Saccharomyces cerevisiae

Humans express 15 different inward-rectifying potassium (Kir) channels that play a variety of roles in epithelial transport, nerve conduction, and muscle contraction. Polymorphisms in Kir channels underlie numerous genetic diseases. In order to investigate the function and regulation of Kir channels, researchers have long recognized the potential of expressing them in strains of Saccharomyces cerevisiae (Bakers’ yeast) engineered for sensitivity to growth in a low potassium medium. These studies capitalize on the wide variety of genetic and biochemical tools available in yeast, namely the ease of transforming large quantities of cells with recombinant DNA and the availability of comprehensive mutant libraries for high-throughput screening. Due to the longstanding popularity of yeast as model eukaryotes, the mechanisms underlying cellular phenomena are relatively well-documented and are also conserved in multicellular organisms. In this document, I will first review the history and diversity of techniques for studying potassium channels in potassium-sensitized yeast. Next, I will describe the results of a genetic screen to identify the key regulatory factors for a particular Kir channel: the renal outer medullary potassium (ROMK) channel. ROMK, also known as Kir1.1, is the major route for potassium secretion into the pro-urine and plays an indispensable role in regulating serum potassium. However, the cellular machinery that regulates ROMK trafficking has not been fully defined. I used a synthetic genetic array to identify nonessential genes that reduce the plasma membrane pool of ROMK in potassium uptake-deficient yeast. Through this screen, I identified several members of the endosomal complexes required for transport (ESCRT) and the class-C core vacuole/endosome tethering (CORVET) complexes. Moreover, silencing of ESCRT and CORVET components increased ROMK levels at the plasma membrane in a mammalian cell line, therefore establishing that post-endocytic sorting influences the cell-surface density of ROMK and modulates its activity. Finally, I will briefly delineate potential future studies in yeast with ROMK and other Kir channels and will describe several investigations into various aspects of Kir channel biology to which I have contributed through collaboration.
Local government and urban forest governance: insights from Scotland

ABSTRACT While the benefits of urban forests (UFs) are well-researched, less is known about how to steer collective action for conserving and strengthening this resource, and particularly the role of local government. We address this knowledge gap through a study of urban forest governance in Scotland, United Kingdom. Applying a mixed-methods approach including semi-structured interviews, document analysis and surveys, covering 26 out of the total of 32 Scottish local authorities (LAs), we show that UF management by Scottish LAs is largely reactive. This can be explained by limited funding and knowledge of the resource, poor knowledge of the scale and state of the UF, fragmented management structures, and the tendency to perceive trees as a liability as opposed to an asset. However, some LAs successfully resist this trend through city officials acting as frontrunners within their organisations. They do so by championing activities such as investing in tools for socioeconomic valuation of the UF, pursuing grant funding, breaking down silos through organisational reorganisation, preparing city-level trees and woodland strategies, cross-sectoral partnership working and community engagement. Fundamental change, however, relies on the combination of these activities and therefore requires a whole-organisation commitment to UF sustainability across different domains relevant to predicting UF outcomes.
Culture media for the multiplication of wild Manihot species

ABSTRACT The cassava propagation system is slow and favors disease transmission through successive generations. Micropropagation is an alternative to overcome the aforementioned limitations, besides allowing the generation of a larger number of pest- and pathogen-free plants. Therefore, the aim of the present study is to investigate the effect of culture media on the multiplication in vitro of five wild Manihot species. The experiment followed a completely randomized design, at factorial arrangement 5 (wild Manihot species) x 6 (culture media), with 11 repetitions. Explants consisted in nodal segments (91 cm long and one lateral bud) of species Manihot flabellifolia, M. tristis, M. caerulescens, M. chlorosticta and M. jacobinensis, which were extracted in vitro from the collection of wild cassava species. One segment was placed in each test tube added with 10 mL of MS media 0.01, 17N, 12A3, 4E, 8S and WPM, and kept for 90 days in growth room under 30 μmol m-2 s-1irradiance, temperature 27 ± 1 °C and 16h photoperiod. Variables plant height (cm), number of green leaves, number of senescent leaves, number of shoots, number of microcuttings, fresh and dry shoot mass, fresh and dry root mass (mg) and callus mass (mg) were analyzed. Our results showed that the culture medium 12A3 was not responsive to any of the species; however, if one takes into consideration variables plant height and number of microcuttings, this medium can possibly be used in the micropropagation of other wild species belonging to genus Manihot.
The evolution and distribution of recycled oceanic crust in the Earth’s mantle: Insight from geodynamic models

<p>A better understanding of the Earth&#8217;s compositional structure is needed to place the geochemical record of surface rocks into the context of Earth accretion and evolution. Cosmochemical constraints imply that lower-mantle rocks may be enriched in silica relative to upper-mantle pyrolite, whereas geophysical observations support whole-mantle convection and mixing. To resolve this discrepancy, it has been suggested that subducted mid-ocean ridge basalt (MORB) segregates from subducted harzburgite to accumulate in the mantle transition zone (MTZ) and/or the lower mantle. However, the key parameters that control basalt segregation and accumulation remain poorly constrained. Here, we use global-scale 2D thermochemical convection models to investigate the influence of mantle-viscosity profile, planetary-tectonic style and bulk composition on the evolution and distribution of mantle heterogeneity. Our models robustly predict that, for all cases with Earth-like tectonics, a basalt-enriched reservoir is formed in the MTZ, and a harzburgite-enriched reservoir is sustained at 660~800 km depth, despite ongoing whole-mantle circulation. The enhancement of basalt and harzburgite in and beneath the MTZ, respectively, are laterally variable, ranging from ~30% to 50% basalt fraction, and from ~40% to 80% harzburgite enrichment relative to pyrolite. Models also predict an accumulation of basalt near the core mantle boundary (CMB) as thermochemical piles, as well as moderate enhancement of most of the lower mantle by basalt. While the accumulation of basalt in the MTZ does not strongly depend on the mantle-viscosity profile (explained by a balance between basalt delivery by plumes and removal by slabs at the given MTZ capacity), that of the lowermost mantle does: lower-mantle viscosity directly controls the efficiency of basalt segregation (and entrainment) near the CMB; upper-mantle viscosity has an indirect effect through controlling slab thickness. Finally, the composition of the bulk-silicate Earth may be shifted relative to that of upper-mantle pyrolite, if indeed significant reservoirs of basalt exist in the MTZ and lower mantle. </p>
Multiple isotopic models using various kinetic fractionation coefficients to estimate δ18O of leaf water

Investigation of δ18O of leaf water may improve our understanding of the evapotranspiration partitioning and material exchange between the inside and outside of leaves. In this study, δ18O of bulk leaf water (δL,b) was estimated by both isotopic–steady–state (ISS) and non–steady–state (NSS) assumptions considering the Péclet effect. Specifically, we carefully modified kinetic fractionation coefficients (αk). The results showed that the Péclet effect is required to predict δL,b. On the diel time scale, both NSS assumption + Péclet effect (NSS + P) and ISS assumption + Péclet effect (ISS + P) using modified αk (αk–modified) for δL,b showed a good agreement with observed δL,b (p > 0.05). When using previously proposed αk, however, both NSS + P and ISS + P were not reliable estimators of δL,b (p < 0.05). On a longer time scale (days), estimates of daily mean δL,b from ISS + P outperformed the estimates from NSS + P when using the same αk values. Also, the employment of αk–modified improved model performance in predicting daily mean δL,b compared to the use of previously proposed αk. Clearly, special care must be taken concerning αk when using isotopic models to estimate δL,b. Highlight For hourly and daily mean data sets, the employment of modified kinetic fractionation coefficients significantly improved model performance for δ18O of bulk leaf water.
The development of a parent–child activity based on the principles of perceptual control theory

Abstract Problems most frequently reported by young people in school counselling relate to family difficulties. During adolescence, conflict between parents and young people increases as young people move towards independence whilst still being reliant on parents. The quality of communication during this period has implications for young people’s well-being. The current study explored how the principles of perceptual control theory (PCT) could be used to develop a structured activity aimed at helping young people to talk to their parents about their goals and goal conflicts. PCT proposes that individuals function well when they are able to control things that are important to them. Every individual has numerous goals/wants and if two or more are incompatible, conflict arises. The current study focused on supporting young people to explore conflict that might arise due to incompatible goals held by them and their parent. Six families (child and parent/carer) were recruited to try a goal-setting and monitoring activity. The activity was facilitated by a Method of Levels researcher over a 10-week period. There were two follow-up appointments at 2 and 4 months. Two families were retained for the entire study. On completion, four families provided qualitative feedback. On the basis of participants’ feedback, the activity was modified to incorporate discussions on incompatible goals. Two families piloted the modified activity and provided feedback. Both families completed the study. Results suggest that a parent–child activity using the principles of PCT is feasible and acceptable among parents and young people. Key learning aims (1) To understand how the principles of PCT can be used to support young people in communicating with their parents. (2) To understand how talking about important goals/wants impacts young people and their parents. (3) To understand how the principles of PCT can be used to resolve parent–child conflict.