Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution, degree of damage and risk of spread of Trioza erytreae (Hemiptera: Triozidae) in Kenya

The African citrus triozid (ACT), Trioza erytreae Del Guercio, is a destructive pest particularly on citrus, and vectors, “Candidatus” Liberibacter africanus (CLaf), which is the causal agent of the African citrus greening disease. Our study seeks to establish the distribution and host‐plant relationship of ACT across citrus production areas in Kenya. We also modelled the risk of spread using the maximum entropy modelling algorithm with known occurrence data. Our results infer that ACT is widely distributed and causes severe damage to four alternative host plants belonging to the family Rutaceae. The adults, immature stages (eggs and nymphs), galls and the percentage of infested leaves were significantly higher in shaded than unshaded trees. However, adult ACTs preferred Kenyan highlands to Victoria Lake and coastal regions. The average area under the curve of the model predictions was 0.97, indicating an optimal model performance. The environmental variables that most influenced the prediction were the precipitation of wettest quarter, precipitation of wettest month, mean diurnal range, temperature seasonality and mean temperature of the coldest quarter. The current prediction of ACT exceeded its existing range, especially in the Western, Nyanza, Central, Rift valley and Eastern regions of Kenya. The model predicted a contraction of suitable habitats for a potential spread in 2040 with an inland shift to higher altitudes in the cooler regions. The potential for further expansion to climatically suitable areas was more pronounced for the 2080 forecast. These findings provide relevant information to improve monitoring/surveillance and designing IPM strategies to limit its spread and damage.
New records of Boana icamiaba (Anura: Hylidae) in the Brazilian Amazon rainforest

Boana icamiaba is an Amazonian anuran species reported for sites in the mid-lower Madeira-Rio Tapajós River and lower Tapajós-Rio, and Xingu River interfluves – municipalities of Juruti, Altamira, Santarém, and Itaituba, state of Pará, northern Brazil. We provided the first records of Boana icamiaba for the states of Mato Grosso and Rondônia, central and northern Brazil, which enlarges the knowledge on its distribution in approximately 470 km southmost and circa 886 km southwestmost from the nearest previously recorded locality.
Improved the Shelf Life of Guava Fruits by Salicylic Acid against Postharvest Black Spot Disease

Guava fruit (Psidium guajava L.) is one of the most important popular fruits in the tropical and subtropical zones. It is a perishable and has a short postharvest shelf life at environment temperature due to climacteric ripening with changes in physicochemical properties; However, the most serious microorganisms attacked guava fruits are the fungi. Guava black spot (GBS) is a latent infection disease caused by the ascomycete fungal Phyllosticta capitalensis, that infect immature guava in the field. This postharvest decay can lead to significant economic losses. Since the commercial application of fungicides to control postharvest diseases found harmful to human and the ecosystems. Therefore, the search of finding alternative fungicides, safety and environmentally friendly strategy is a major aim of the researchers worldwide. Salicylic acid (SA) is one of the safe, natural compounds applied in the postharvest treatment of fruit. The present investigation aimed to evaluate the effect of different concentrations of SA on fungal growth in vitro and postharvest treatment of infected fruit to improve the shelf life of guava fruits. Guava fruit collected from local supermarket and measurement of disease incidence and severity (DI & DS%) carried out in the three seasons (2015-2017). SA at different concentrations assessed on mycelial linear growth inhibition (MLGI%) of P. capitalensis in vitro. Exogenous postharvest treatment of guava fruit with SA tested at five concentrations, three times of immersion and kept for three periods time of shelf life. DS% evaluated after three period time. Total soluble solids (TSS) and weight loss (WL) evaluated after three period time. SA concentrations at 6 mmol/L significant on MLGI of P. capitalensis in vitro. Postharvest treatment with SA at 3 mmol/L significantly reduced DS% on guava fruit, at three immersion time and after three periods of shelf life, compared to control. SA with a concentration at 4 mmol/L decreased TSS and WL after three periods of shelf life. Postharvest treatment with SA solutions had an overall positive effect on fruit quality of guava during shelf life. A decay incidence decreased, TSS and weight loss noticed in treated guava fruit compared to control. The present study demonstrated the efficacy and potential of SA solutions in preserving the shelf life of a highly perishable like guava fruits.
Spatial and temporal variation in small mammal abundance and diversity under protection, pastoralism and agriculture in the Serengeti Ecosystem, Tanzania

Land use is an important factor influencing animal abundance, species richness and diversity in both protected and human-dominated landscapes. Increase in human population and activities intensify changes in habitat structure and hence abundance, species richness and diversity. We investigated the influences of land use and seasonality on small mammal abundance, species richness and diversity in 10 habitat types distributed over protected, agricultural and pastoral landscapes in the Serengeti ecosystem in Tanzania. We used live traps (n = 141) and capture-recapture methods in each of 10 fixed plots distributed across three landscapes for a total of 28,200 trap nights of effort. Trapping was carried out in the wet and dry seasons for two consecutive years (April 2017 to October 2018). Small mammal abundance was higher in the pastoral than in the protected and in the agricultural landscape. Abundance was higher in the dry than the wet season across all the three landscapes. Species richness and diversity were higher in the protected, middling in the agricultural and lowest in the pastoral landscape. The high abundance in the pastoral landscape was due to the numerical dominance of two species, namely A. niloticus in the shrubland and M. natalensis in the cropland habitat, resulting in low species richness and diversity. Abundance was more evenly distributed across all habitats in the protected area due to less disturbance. The low abundance in the agricultural landscape, likely reflects disturbance from cultivation. High species richness and diversity in the protected area indicate high habitat heterogeneity while high species diversity in the agricultural landscape was likely due to high food availability during and soon after harvests. These findings emphasize the importance of protection in maintaining habitat heterogeneity for wildlife. They also reaffirm the need for buffer zones around protected areas to cushion them from intensifying human activities.
Life history of Karualona muelleri (Richard, 1897) (Chydoridae, Aloninae)

Many taxonomic issues still need to be solved for the family Chydoridae, but mainly in the subfamily Aloninae. The species Karualona muelleri is an example of a recent taxonomic redefinition, since it was decoupled from the genus Alona and translocated to another genus. In order to expand our knowledge on the species, we investigated population growth and compared the morphometry of the first and second instars, male, parthenogenetic female, ephippial female, and ephippium. An experimental population was obtained by hatching resting eggs collected from the sediment in a temporary lake located in the Serra da Canastra National Park (Minas Gerais, Brazil). The hatched individuals were subjected to morphometric analyses and used in experiments to assess population growth and fecundity. Reproductive age and lifespan were also monitored in two groups of females in different life stages: parthenogenetic and gamogenetic. The reproductive age occurred between the 1st and 15th days of life, and the greatest longevity was 17 days. The start of gamogenetic reproduction was stimulated by elevated population densities and it characterized the slowdown of exponential population growth. Morphometric analyses detected differences between the development phases, as well as similarities in the morphological features of the male, first and second instars, and the two types of females.
Influence of GA3 on seed multiplication of CMS lines used for hybrid rice development

In Pakistan, the F1 seed production ranks very low in the three-line system. One of the reasons is poor panicle exertion and less out crossing rate in the female lines. Gibbrillic Acid (GA3) increase the seed and improve panicle exertion as well as outcrossing. This study was designed to identify the suitable doses of GA3 application in the seed multiplication block of different CMS lines. The material comprising both the parental lines (cytoplasmic male sterility and maintainer) used in the development of hybrid rice. GA3 powder used in the experiment is 90% concentration in three level concentration that is 0, 100, 200, ppm. The outcomes indicated that GA3 positively increased plant height, stigma exertion, panicle exertion, duration of floret opening, angle of floret opening and panicle length. Increased seed production is 0.3 to 1 t/ha compared to the control (0 ppm GA3). Application of GA3 concentration at the rate of 200ppm gave the best results as compared to the other treatments like control and 100 ppm in all the tested CMS lines increased productivity. So, 200 ppm concentration is recommended in seed multiplication of parental lines used in hybrid rice development. Key words: Hybrid rice, CMS lines, GA3, seed multiplication.
Variational Autoencoders for Cancer Data Integration: Design Principles and Computational Practice

International initiatives such as the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) are collecting multiple data sets at different genome-scales with the aim to identify novel cancer bio-markers and predict patient survival. To analyse such data, several machine learning, bioinformatics and statistical methods have been applied, among them neural networks such as autoencoders. Although these models provide a good statistical learning framework to analyse multi-omic and/or clinical data, there is a distinct lack of work on how to integrate diverse patient data and identify the optimal design best suited to the available data. In this paper, we investigate several autoencoder architectures that integrate a variety of cancer patient data types (e.g., multi-omics and clinical data). We perform extensive analyses of these approaches and provide a clear methodological and computational framework for designing systems that enable clinicians to investigate cancer traits and translate the results into clinical applications. We demonstrate how these networks can be designed, built and, in particular, applied to tasks of integrative analyses of heterogeneous breast cancer data. The results show that these approaches yield relevant data representations that, in turn, lead to accurate and stable diagnosis.
Production of Biomass Briquettes Using Coconut Husk and Male Inflorescence of Elaeis guineensis

The decreasing availability of fuel wood coupled with the increasing prices of kerosene and cooking gas in Nigeria has drawn attention on the need to consider alternative sources of energy for domestic and industrial use in the country. The study was undertaken to evaluate the combustion properties (percentage volatile matter, percentage ash content, percentage fixed carbon, heating value) of briquette produced from coconut husk and male inflorescence of Elaeis guineensis. The experiment was laid down using the Randomized Complete Block Design (RCBD). The study involves three particle sizes (2 mm each) of coconut husk, male inflorescence of oil palm tree and cassava starch used as binder. The coconut husk and male inflorescence of Elaeis guineensis were varied into (25:30:40:50:60) respectively and bound together with starch at same ratio. Proximate analysis was carried out to determine the constituent of the briquettes which include ash content, percentage fixed carbon, percentage volatile matter and experimental test to determine the heating value was also determined. All processing variables in this study were significantly different except for heating value at P>0.05. From the result of the percentage ash content, briquette produced from coconut husk, male inflorescence and starch at (20:20:60) has the least fixed carbon (6.5%) with better performance. The highest percentage volatile matter 74.6% was obtained from coconut husk, male inflorescence and starch at (20:20:60) while low fixed carbon (18.8%) was obtained from male inflorescence and starch at (60:40). In conclusion, large quantities of wastes generated in terms of coconut husk and male inflorescence which are disposed indiscriminately can be utilized to produce briquette with enhanced performance.
ASSESSMENT OF PHENOTYPIC DIVERSITY IN TUNISIAN CARROT (Daucus carota subsp. sativus) LANDRACES

Knowledge of the morphological diversity of a germplasm collection is fundamental for genebank managers and plant breeders. The main objective of the present work was to characterize 33 landraces of carrot from 13 different regions of Tunisia, based on 34 agromorphological characters related to leaves and roots. The Shannon-Weaver Diversity (H’) index was used to study the phenotypic diversity. The estimated H’ ranged from 0.19 for core colour compared to cortex colour (RCCCC) to 0.99 for leaf division (LD). Analysis of variance revealed significant differences among landraces for all quantitative characters. Stepwise multivariate analyses were carried out to identify the useful characters that can distinguish among landraces. This study showed that qualitative characters were the best for the delimitation of landraces in this collection. Cluster analysis permitted the subdivision of carrot collection into four distinct groups independent of their geographic distribution. This information will be helpful to curators in the management and improvement of carrot germplasm in Tunisia.
GARDEN-NET and ChAseR: a suite of tools for the analysis of chromatin networks

We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology. We demonstrate the approach on epigenomic and chromatin structure datasets in haematopoietic cells.
Bioactive Compounds and Antioxidant Activity of Common Vegetables and Spices Available in Bangladesh

Giving priority to health-promoting components of plant origin foods, the present investigation is carried out to quantify the levels of bioactive compounds and antioxidant capacity of common vegetables and spices available in Bangladesh. Total polyphenol, flavonoid, anthocyanin contents and antioxidant activity were investigated on seven vegetable i.e., cauliflower, cabbage, carrot, bitter gourd, cucumber, lemon, tomato and three spices i.e., onion, garlic and turmeric in this study. The highest total polyphenol content was found in bitter gourd 87.9±4.6 mg GAE/g of extract and the lowest was found in cabbage 18.7±0.19 mg GAE/g of extract. Total flavonoid content was varying from 28.99 to 133.6 mg QE/g of extract whereas cauliflower has the lowest and onion has the highest content. Anthocyanin the color compound of vegetable was found highest in turmeric and lowest in cauliflower. Consistently, antioxidant capacity was highest in lemon 192.7±0.97 µmol TE/g of extract and lowest in carrot 104.2±0.26 µmol TE/g of extract.The result showed a correlation between phenolic content and antioxidant activities of vegetables and spices. This study provides novel information about common vegetables and spices bioactive composition, which is essential for the understanding of their nutraceutical potential and future application in the food processing industry.
Pruned petioles of papaya as nesting sites of the leafcutting bee, Megachile laticeps Smith and its pollen fidelity

The nest selection and pollen fidelity of the leafcutting bee, Megachile laticeps was studied. Mature and nearly dry petioles of papaya were pruned to simulate hollow stems of other plants to attract females of M. laticeps for construction of its nest. The nest occupancy and adult emergence rate were 64.70% and 89.07% respectively, with an average of 12.7 ± 2.11 cells per nest. Scopal pollen loads from foraging adult female bees were removed and identified to the lowest taxonomic level possible. Pigeon pea, sunnhemp, and field bean pollen (Fabaceae) made up on an average of 54% of total pollen grains carried in the scopae of adult female bees. Nest pollen analysis indicated that Fabaceae pollen was the most prevalent in the brood provision. M. laticeps in a farm landscape utilized the pruned hollow petioles of standing papaya plant and local floral resources. This behavior shows the importance of pollinator species’ characteristics for developing conservation strategies to enhance pollination services in agro-ecosystems.
A neural network for online spike classification that improves decoding accuracy

Separating neural signals from noise can improve brain-computer interface performance and stability. However, “spike-sorting” suffers from a lack of ground truth for classifying waveforms, and most algorithms for separating neural action potentials from noise are not suitable for use in real time and have shown mixed effects on decoding performance. Our goals were to automate the intuition of human spike-sorters to operate in real time with an easily tunable parameter governing the stringency with which spike waveforms are classified. We trained an artificial neural network with one hidden layer on neural waveforms that were hand-labeled as either spikes or noise. The network output was a likelihood metric for each waveform it classified, and we tuned the network’s stringency by varying the minimum likelihood value for a waveform to be considered a spike. Using the network’s labels to exclude noise waveforms, we decoded remembered target location during a memory-guided saccade task from electrode arrays implanted in prefrontal cortex of rhesus macaque monkeys. The network classified waveforms in real time, and its classifications were qualitatively similar to those of a human spike-sorter. Compared to decoding with threshold crossings, in most sessions we improved decoding performance by removing waveforms with low spike likelihood values. Furthermore, decoding with our network’s classifications became more beneficial as time since array implantation increased. Our classifier serves as a feasible preprocessing step, with little risk of harm, that could be applied to both offline neural data analyses and online decoding. New & Noteworthy Analysis of neural data from extracellular electrodes typically involves a manual step in which the experimenter isolates neural signals from noise. This process, known as spike-sorting, is tedious and subjective. We used waveforms sorted by a human as training data to create an artificial neural network to separate spikes from noise. We found that this network operated in real time and was suitable for both offline data processing and online decoding.
Primary morphological characterization of West African dwarf (Djallonk) ewes from Cte dIvoire based on qualitative and quantitative traits

Phenotypic characterization is used to identify and document diversity within and between distinct breeds, based on their observable attributes. Study to assess the body characteristics and variability of 204 Djallonke (West African dwarf) ewes was conducted in three agro-ecological zones (central, western and northern) of Cote d’Ivoire, from November 2016 to April 2017. Animals were described using visual appreciation of the body hair coat (colour type and pattern), hair length, ear orientation, tail type and the facial (head) profile. The linear body measurements, such as ear and tail length, muzzle length and width, height at wither, chest depth, and chest girth were also described. The data collected were subjected to principal component (PCA) and discriminant analysis. Results showed that the most common Djallonke ewes had erected ear (87.25%), thin tail and straight face. The dominant colour pattern of the body hair coat was patchy (64.22%) followed by plain (32.84%) and spotted (2.94%). The agro-ecological zone had a significant (p˂0.01) effect on some linear body measurements (muzzle length, ear length and height wither). Based on PCA performed with all the above morphological variabilities, we were able to segregate the Djallonke ewes’ into three clusters (I, II and III). Discriminant analysis revealed that 76.27% sheep of cluster I, 92.80% sheep of cluster II and 90% sheep of cluster III were correctly classified in their original cluster. This result indicated that Ivorian Djallonke sheep population comprises of three well characterized morphological types of animals. This information could constitute a basis for further characterization and development of conservation strategies for Djallonke sheep breeding in Cote d’Ivoire. Key words: Local, sheep, breed, morphological, variability, West Africa.
Evaluation of the establishment of predatory beetle, Laricobius nigrinus (Coleoptera: Derodontidae) in Virginia, and assessment of its impact on hemlock woolly adelgid (Hemiptera: Adelgidae) at release sites in the eastern U.S.

Academic) ! The predatory beetle, Laricobius nigrinus Fender (Coleoptera: Derodontidae), has been released in the eastern U.S. since 2003 for the management of hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae). The establishment of L. nigrinus at release sites in Virginia was assessed in 2017 and 2018. Sampling was performed in both years to determine presence or absence L. nigrinus. Stand level HWA densities, tree health, predator-prey ratios, and Laricobius spp. identifications were also assessed at each site. Laricobius nigrinus established at 82% of sites and was the primary species recovered. HWA densities appeared to decline, and tree health appeared to improve in year two. Predator-prey ratios were lower than those indicated in the native range, however much is left to be understood about the dynamics of this system in its introduced range. A separate two-year study to assess the impact of L. nigrinus on HWA was initiated in 2014 (Phase One) at nine sites in the eastern U.S. Significant predation of HWA sistens ovisacs was demonstrated during this period, therefore, it was continued from 2016-2018 (Phase Two) to provide longer-term evaluations. Predator exclusion cages were used to monitor predator and prey populations. In Phase Two of the study, mean ovisac disturbance rates on no-cage branches were significantly greater than caged branches and were as high as 80%,