Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat use by a mixed feeder: impala Aepyceros melampus in a heterogeneous protected area

Abstract: Although large herbivore habitat use has been extensively studied, more information is still required on the use of heterogeneous vegetation types. Over 3 y we carried out monthly road transects in the Zambezi National Park (ZNP), Zimbabwe, to determine the impala density in each of five vegetation types. In addition we determined grass and browse chemical composition to test if at the time the impala switches from grass to browse, grass nutritive quality had declined below that of browse. Furthermore, grass height was measured in the five vegetation types. The impala used mixed, acacia and terminalia vegetation types, which constituted 37% of the protected area and avoided grassland and the predominant Zambezi teak (60% of ZNP) vegetation types. At the time of the diet switch by the impala from grass to browse, woody plant leaf nutritive quality was higher than grass in terms of nitrogen, calcium and acid detergent fibre content. The three vegetation types used by the impala had short to medium grass height. We concluded that when the impala switched from grass to browse the grass nutritive quality was lower than that of the browse.
Divergence-Based Introgression Polarization

Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression (IG) in whole-genome data has been a major area of focus. While existing techniques are able to identify the taxa that exchanged genes during IG using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during IG (i.e. polarization of IG directionality). The existing methods that do polarize IG are only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in IG. Here, we present Divergence-based Introgression Polarization (DIP), a method for polarizing IG using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of IG when additional taxa are not available. We use simulations to show that DIP can polarize IG and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin IG event.
Exploring resilience capacities with food innovators: a narrative approach

Non-technical summary We interviewed grassroots food innovators in South Africa to explore the diverse ways in which their narratives expressed different capacities for resilience, such as dealing with surprise and shaping desirable change. We drew on key resilience themes of rootedness, resourcefulness and resistance (the 3Rs) as lenses through which to view their personal stories and efforts to build resilience and reshape the future. We used narrative and interpretative methods to connect the personal and context-specific experiences of food innovators to the 3Rs, exploring a new approach to uncovering resilience capacities. We suggest that this approach could be usefully employed to understand potential resilience capacities that could help address diverse sustainability challenges around the world. Technical summary As direct accounts of human experience, narratives offer a way of exploring the subjective and contextual dimensions of different capacities that influence resilience – the capacity to deal with surprise and unexpected change. In this study, we analysed the stories of food innovators in South Africa through combined narrative and interpretative methods, and we developed a novel approach to tease out some of the unique and particular aspects of resilience expressed in their stories. Using a combination of narrative enquiry and interpretative phenomenological analysis, we drew on the key resilience themes of rootedness, resourcefulness and resistance (the 3Rs) as lenses through which to view the personal reflections of food innovators and to identify important capacities that may contribute towards their efforts to build resilience and reshape the future. Amongst the diverse set of narratives, we found that resilience capacities were strongly influenced by an ethos of connectedness and care; attunement to co-creative processes; and experimenting with novelty and diverse narratives. We suggest that this narrative-based methodology could be usefully employed to surface latent rich and multidimensional resilience capacities in relation to various sustainability challenges in diverse contexts around the world. Social media summary A narrative approach to explore resilience capacities that can help reshape the future of South African food innovators.
Morphological variation associated with dispersal capacity in a tree‐killing bark beetle Dendroctonus ponderosae Hopkins

Intrinsic factors influencing the dispersal of insect pests during outbreaks are poorly understood, yet these factors need to be quantified to parameterize dispersal in models that predict population spread. The present study related wing and body morphology of female mountain pine beetles (Dendroctonus ponderosae) to flight distance, as measured by flight mill bioassays. Beetles that flew long distances (> 11 km) had a greater body weight and larger wings than beetles that flew short distances (< 1 km). These heavier female beetles should also be more capable pioneers because other studies have shown that body weight is positively correlated with lipid content. Wing and body morphology of females are significant predictors of flight distance; heavy beetles with large wings generally flew further than smaller beetles, although this relationship is heteroscedastic. Dispersion of flight distance values increases with wing loading (weight/wing area) as a result of a cohort of ‘lazy’ individuals that fly short distances (< 1 km) regardless of flight phenotype. The observed morphology explained less than 20% of the variation in flight capacity, indicating a substantial contribution from other intrinsic factors that remain to be investigated. The present study may have implications for dispersal modelling, providing estimates of flight capacity using morphological measurements.
Two new species of Okenia (Gastropoda: Nudibranchia: Goniodorididae) from eastern Australia and Tanzania

Two new species of the nudibranch genus Okenia Menke, 1830 (Goniodorididae) are described, one from eastern Australian waters and one from the western Indian Ocean. Okenia atkinsonorum sp. nov. is the third Australian species reported to feed on the bryozoan Pleurotoichus clathratus (Harmer, 1902) and is very similar in external shape and colour to the other two species, O. hallucigenia Rudman, 2004 and O. stellata Rudman, 2004. Okenia rhinorma sp. nov. is reported from Tanzania and the Red Sea. Its body shape and anatomy suggest it is related to the ascidian-feeding group in the genus characterised by O. aspersa (Alder & Hancock, 1845).
Linking gas diffusion electrode composition to CO2 reduction in a flow cell

Gas diffusion electrodes (GDEs) mediate the transport of reagents, products, and electrons in electrochemical reactors designed to reduce CO2 into fuels or chemicals. While the ratio of ionomer to electrocatalyst in the precursor catalyst ink is typically assumed not to change after being deposited on the GDE, we show herein that this assumption is likely not valid. Moreover, we discovered that the faradaic efficiency for formate, which is considered to be inconsequential relative to CO when using Ag electrocatalysts, can be modulated by 20% by a mere 5 wt% change in GDE Nafion® content. We were able to resolve these small differences in GDE composition by developing an X-ray fluorescence (XRF) spectroscopic protocol that quantifies the sulfonate groups appended to the polytetrafluoroethylene (PTFE) backbone of Nafion®. Using this protocol, we were able to determine how to precisely control the relative amount of ionomer to electrocatalyst for each GDE. We also found that maintaining a uniform ionomer–catalyst composition across the entire GDE can likely be done more effectively with automated spray coating than with manual deposition methods. We recommend following these procedures in order to generate reproducible CO2RR performance parameters in flow cells.
The introduced terrestrial slugs Ambigolimax nyctelius (Bourguignat, 1861) and Ambigolimax valentianus (Férussac, 1821) (Gastropoda: Limacidae) in California, with a discussion of taxonomy, systematics, and discovery by citizen science

ABSTRACT Ambigolimax valentianus and Ambigolimax nyctelius are synanthropic terrestrial slugs that have been dispersed widely by human activity. Herein, these species are reported from Los Angeles County, California, as a result of contributions to SLIME (Snails and Slugs Living in Metropolitan Environments), a citizen science project initiated by the Natural History Museum of Los Angeles County and hosted online by iNaturalist. Importantly, collected specimens and specimen data of A. nyctelius are the first of this species in California and the first records to document it in North America since 1960. Species identifications of A. valentianus and A. nyctelius, which are phenotypically similar, were made by examination of specimens’ distal genitalia and analysis of their mtDNA barcoding gene, COI (A. nyctelius, n = 18 and A. valentianus, n = 11). Slug radulae and jaws were examined and are figured, but were not diagnostic to species. Phylogenetic analyses of COI haplotypes from both Ambigolimax species and six other limacids resolve A. nyctelius and A. valentianus as monophyletic sister taxa. However, morphological and molecular data from taxa not included in this study are needed to substantiate this relationship and inform a revision of at least 10 genera in the family Limacidae. Inconsistencies in the literature regarding the year of Férussac’s species description of A. valentianus (as Limax valentianus) are also discussed and resolved.
Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori

Bacillus bombyseptieus is a pathogen of Bombyx mori; it can cause bacterial septicemia in silkworm. One of the components of the parasporal crystal toxin of B. bombyseptieus, α-toxin, plays an important role in the process of infection in silkworm. In this study, we investigated the immune response of silkworm induced by α-toxin by using RNA-seq. We compared the changes in gene expression in the midgut, fatbody, and hemocytes of silkworm and in the B. mori embryonic cell line (BmE) after treatment with α-toxin and identified 952 differentially expressed genes and 353 differentially expressed long noncoding RNAs (lncRNAs). These regulated genes in different tissues were found to be enriched in different pathways. The upregulated genes in the midgut were mainly involved in peptidoglycan catabolic process and tyrosine kinase signaling pathway, whereas the downregulated genes were mainly involved in chitin metabolic pathways. The upregulated genes in fatbody were also involved in peptidoglycan catabolic process, but they were for a different peptidoglycan subtype. Further, genes encoding cecropins were enriched in the fatbody. The downregulated genes were mainly involved in the metabolic pathways of fundamental substances such as cellular protein metabolic process and nucleobase-containing compound metabolic process. These results suggest that α-toxin can induce various immune responses in silkworm, and further studies are warranted to understand the mechanism of α-toxin action in silkworm. Further, lncRNAs and differentially expressed genes were correlated using coexpression network analysis. Our findings revealed potential candidate genes and lncRNAs that might play important physiological functions in the immune response to α-toxins in silkworm.
Neuroprotective micrornas combat HIV-1 associated neurocognitive disorder (HAND) pathogenesis

HIV-1 associated neurocognitive disorder (HAND) is one of the major HIV-1 co- morbidities prevalent around the world. Early during HIV-1 infection, virus crosses the blood - brain barrier (BBB) and enters central nervous system (CNS) through infiltrating infected monocytes/macrophages. These infiltrating infected monocytes/macrophages serve as the source to initiate secondary infection of resident monocytic cells and glial cells in CNS. Neurons are not directly infected by HIV-1 virus. However, pro-inflammatory cytokines and chemokines as well as viral proteins released by infected/exposed immune and glial cells are neurotoxic and contribute to the neuronal stress and apoptosis. Nearly more than half of individuals living with HIV-1 infection present with some degree of neuronal impairment. Currently, no treatment is available to prevent or treat HAND. Thus, devising a strategy to manage HAND progression and improve the quality of life in HIV-1 positive population will be highly valuable and is of great public health significance. MicroRNAs are small non-coding RNAs which play an important role in post- transcriptional regulation. Previous studies in our laboratory have identified specific miRNAs that may have a neuro-protective role. In this study, my goal is to evaluate the role of these candidate miRNAs on inflammatory response of monocytes/macrophages and microglia during HIV-1 infection. I hypothesize that these candidate miRNAs can reduce the proinflammatory response of monocytes/macrophages and microglia, and these inhibitory effects of miRNAs are conserved during HIV-1 infection. In order to test this hypothesis, candidate miRNAs were over expressed in monocytic cell line (THP1) and microglia by using lentiviral expression vectors. Results suggest that miR-20a and miR-106b expression in monocytic cell lines inhibits TNF-α production, while miR-let-7a significantly downregulates IL-6 secretion in response to LPS either in the presence or absence of HIV-1 infection. Similarly, in microglia cells, miR-106b inhibits both IL-6 and IL-8 secretion upon LPS stimulation and miR-20a reduces IL-6 production upon TNF-α stimulation. Evaluation of these candidate miRNAs in J-Lat cells, which contain a single copy of HIV-1 latent HIV-1 virus suggest that, miR-20a, miR-106b, miR-124 and let-7a were able to reduce HIV-1 reactivation. These results indicate that neuroprotective miRNAs may have a direct role in reducing specific neuroinflammatory factor production and may also affect HIV- 1 virus production. Thus, these candidate miRNAs could have a potential therapeutic role to minimize neuroinflammatory cytokine induced neuronal dysfunction and thus aid in management of HAND.
Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.
Estimation of variability parameters for certain quantitative traits in cocoa (Theobroma cacao L.) genotypes

Cocoa (Theobroma cacao L.) is an important plantation crop of Malvaceae family and its center of origin is Upper Amazon basin of South America. In India, it is grown as an intercrop in coconut and arecanut gardens especially in South India. Morpho-agronomic characters of pods and seeds can be used to evaluate the relationship between cocoa genotypes. In the present study, significant variations inthe mean performance of 20 genotypes for 13 traits were observed which revealed that the germplasm collections being maintained have high breeding value. The GCV and PCV ranged from moderate to high. Traits like plant height, first branching height, canopy area, leaf area, pod weight and single dry bean weight recorded high PCV and GCV indicating the high variability. High heritability ranging from 52.81 per cent for number of beans per pod to 99.84 per cent for first branching height was recorded. High genetic advance as per cent of mean was recorded for canopy area (89.33 per cent). High heritability coupled with high genetic advance for all the traits except pod girth, bean length and pod value indicated that all these traits are controlled by additive gene action and has least environmental influence. Further, correlation analysis revealed association of various traits which can be used as selection criteria for efficient planning of cocoa breeding program.
Efficacy of Purified Amino Acids in Practical Diets for Pacific White Shrimp Litopenaeus vannamei

In view of the variability in recommendations for essential amino acid (EAA) and the use of amino acids supplements in shrimp diets, this study was designed to evaluate the efficacy of crystalline amino acids (CAA) in practical shrimp feeds. The basal diet was designed to contain 30% protein and 6% lipid. The primary protein source of the basal diet included: 5% fishmeal, 37% soybean meal, and 5% gelatine. The intact protein was incrementally reduced to produce diets with 28, 26, 24, and 22% protein. In a second series of diets, CAA were supplemented to the reduced protein diets to return the diets to 30% crude protein. Thus, producing a series of diets containing 30% crude protein with 2, 4, 6, and 8% CAA. The trial was conducted twice to confirm results. Replicates within treatments for both trials were variable, resulting in limited statistical differences. Intact crude protein significantly influenced, percentage weight gain (PWG) and mean final weight (MFW) and these parameters decreased with intact protein level of the diet. None of the diets with supplemented CAA appeared to have reached the same MFW or PWG as the basal diet (R-value (PWG), trial 1: 0.38, trial 2: 0.34, R-value, (MFW) trial 1: 0.44, trial 2: 0.38). Another trial was run using a fishmeal-based diet (30% CP), which in theory should be replete in all essential amino acids, and a soybean meal-based diet at two different protein levels (30 and 35% CP). The soybean meal-based diets were supplemented with essential CAA in one set and
Visuo-Haptic Grasping of Unknown Objects through Exploration and Learning on Humanoid Robots

Die vorliegende Arbeit befasst sich mit dem Greifen unbekannter Objekte durch humanoide Roboter. Dazu werden visuelle Informationen mit haptischer Exploration kombiniert, um Greifhypothesen zu erzeugen. Basierend auf simulierten Trainingsdaten wird auserdem eine Greifmetrik gelernt, welche die Erfolgswahrscheinlichkeit der Greifhypothesen bewertet und die mit der grosten geschatzten Erfolgswahrscheinlichkeit auswahlt. Diese wird verwendet, um Objekte mit Hilfe einer reaktiven Kontrollstrategie zu greifen. Die zwei Kernbeitrage der Arbeit sind zum einen die haptische Exploration von unbekannten Objekten und zum anderen das Greifen von unbekannten Objekten mit Hilfe einer neuartigen datengetriebenen Greifmetrik.
Fine scale waterbody data improve prediction of waterbird occurrence despite coarse species data

While modelling habitat suitability and species distribution, ecologists must deal with issues related to the spatial resolution of species occurrence and environmental data. Indeed, given that the spatial resolution of species and environmental datasets range from centimeters to hundreds of kilometers, it underlines the importance of choosing the optimal combination of resolutions to achieve the highest possible modelling prediction accuracy. We evaluated how the spatial resolution of land cover/waterbody datasets (meters to 1 km) affect waterbird habitat suitability models based on atlas data (grid cell of 12 × 11 km). We hypothesized that the area, perimeter and number of waterbodies computed from high resolution datasets would explain distributions of waterbirds better because coarse resolution datasets omit small waterbodies affecting species occurrence. Specifically, we investigated which spatial resolution of waterbodies better explain the distribution of seven waterbirds nesting on ponds/lakes with areas ranging from 0.1 ha to hundreds of hectares. Our results show that the area and perimeter of waterbodies derived from high resolution datasets (raster data with 30 m resolution, vector data corresponding with map scale 1:10 000) explain the distribution of the waterbirds better than those calculated using less accurate datasets despite the coarse grain of the species data. Taking into account the spatial extent (global vs regional) of the datasets, we found the Global Inland Waterbody Dataset to be the most suitable for modelling distribution of waterbirds. In general, we recommend using land cover data of a resolution sufficient to capture the smallest patches of the habitat suitable for a given species’ presence for both fine and coarse grain habitat suitability and distribution modelling.
Genetic Diversity and Variation in Captive Asian Elephants (Elephas maximus) in Thailand

Numbers of wild Asian elephants (Elephas maximus) have been decreasing gradually throughout Asia due primarily to human activities, such as poaching, and habitat encroachment and destruction that lead to human–elephant conflict. Sustainability problems exist in captive populations as well, where morbidity and mortality rates are high and reproduction is low. Determining the genetic diversity of these populations is essential for conservation and sustainable utilization efforts. Intersimple sequence repeat markers were used to assess the genetic variation and differentiation in 97 captive Asian elephants from seven elephant camps in Chiang Mai, Thailand. The nine primers chosen for the analysis revealed 88 bands in male and 115 bands in female elephants, of which 37 (42.05%) and 83 (63.64%) were polymorphic, respectively. Shannon’s index information (I = 2.415 ± 0.054) and expected heterozygosity (He = 0.892 ± 0.008) indicated high species-level genetic diversity. The fixation index (Fst) was −0.130 ± 0.016, demonstrating there was no genetic subdivision between populations. A cluster analysis was performed using Unweight Pair-Group Method with Arithmetic Mean and dendrograms, which illustrated genetic relationships among captive Asian elephants that included 2 main clusters across the seven camps and 27 clusters for the 97 individual elephants. This high variability may be due to the different origins of these individuals, including originating from other Asian countries. Thus, this study showed that intersimple sequence repeat marker analysis was effective in demonstrating high genetic diversity among captive Asian elephants in Chiang Mai province and found cluster differences that could be used to guide breeding management to decrease the risk of inbreeding among Asian elephant groups.