Miracle-dz/UniFAR-FTUs huggingface dataset:
The roles of diet, speciation and extinction on the diversification of birds, and on the assembly of frugivory networks

To understand how diversity varies through time and/or space we need to understand speciation and extinction dynamics, and ultimately which factors (biotic or abiotic) affect such dynamics. It has been argued that biological interactions play an important role on the diversification of organisms, but macroevolutionary studies have usually adopted a simple characterization of species interactions. On the other hand ecological studies usually focus on well-characterized interactions of very few species. A network approach can augment our understanding of the ecological roles played by different species but it still lacks an evolutionary perspective preventing us to fully understand how ecological interactions are assembled. Using the available phylogeny, dietary data for virtually all bird species (approximately 9965 species) and a large collection of frugivory networks, we tested the effect of diet on the diversification of birds, and the relationship between ecological roles within interaction networks and diversification dynamics of frugivorous species. Lastly, using computational simulations, we assessed the performance of two state-of-the-art methods to estimate diversification rates using molecular phylogenies. We suggest that omnivory acts as macroevolutionary sink where its ephemeral nature is retrieved through transitions from other guilds rather than from omnivore speciation. We propose that these dynamics result from competition within and among dietary guilds, influenced by the deep-time availability and predictability of food resources. We also observed that in the temperate zone, lineages with high-paced evolutionary dynamics (e.g. higher turnover rates) typically do not occupy central roles in frugivory networks, and that these restrictions are modulated by water availability/predictability. Lastly, we found that the two state-of-the
Programmed Variations of Cytokinesis Contribute to Morphogenesis in the C. elegans embryo

While cytokinesis has been intensely studied, how it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant lineage of the C. elegans embryo and find that several parameters are reproducibly altered in different stages. During early divisions, cells undergo consistent patterns of furrow ingression asymmetry and midbody inheritance, suggesting specific regulation of these events. During morphogenesis, in the intestine, pharynx, and amphid sensilla, we find several alterations including migration of midbodies to the apical surface during cellular polarization. In each tissue, Aurora B kinase localizes to the apical membrane after internalization of other midbody components. Perturbations of cytokinesis disrupt lumen formation and dendrite formation. Therefore, cytokinesis shows surprising diversity during development, and may regulate the final interphase architecture of a terminally dividing cell during morphogenesis.
Effets biologiques et mécanismes d'action de ligands environnementaux du récepteur nucléaire de la progestérone chez le poisson zèbre

Chez les vertebres, la progesterone (P4) est un progestatif endogene agissant via les recepteurs nucleaires et membranaires de la progesterone pour medier des processus cles du developpement et de la reproduction. De nombreuses molecules sont concues pour mimer l’action de la P4. Ces progestatifs synthetiques et la P4 sont tres utilises en tant que substances pharmaceutiques et certains sont retrouvees dans l’environnement aquatique, posant un risque pour les organismes. Cependant, les informations sont insuffisantes pour evaluer les dangers et les risques de ces substances pour l’environnement. Dans ce travail de these, les mecanismes d’action et les effets biologiques des progestatifs sur le poisson zebre ont ete etudies grâce a une combinaison d’outils in vitro et in vivo de type gene-rapporteur bases sur le mecanisme d’action des perturbateurs endocriniens. Nous avons caracterise le profil toxicologique complexe de 26 progestatifs vis-a-vis de differents recepteurs nucleaires steroidiens humain et poisson zebre et vis-a-vis de l’expression tissu-specifique de genes de la steroidogenese (cyp19a1b dans le cerveau et cyp11c1 dans les interrenales). Nos resultats montrent que certains progestatifs peuvent perturber differentes voies de signalisation chez les larves en developpement au niveau moleculaire, cellulaire et tissulaire ainsi qu’au niveau physiologique. Dans l’ensemble, les resultats de cette these permettent une meilleure caracterisation des dangers des progestatifs sur differentes cibles endocriniennes.
Effects of water stress on phenolic content and antioxidant activity of African nightshades

Okello OP, Gweyi JPO, Nawiri Mp, Musila W. 2017. Effects of water stress on phenolic contents and antioxidant activity of African nightshades. Biofarmasi J Nat Prod Biochem 15: 79-95. This study aimed at mapping out the distribution of different African Nightshade species in Siaya and Kisii Counties of Kenya and to determine water stress effect on total antioxidant capacity and total phenolic content of two selected African nightshade namely, giant nightshade (Solanum scabrum) and black nightshade (Solanum villosum). Before selection of the two varieties, the study involved farmer field visits, mapping of nightshades present and administration of semi-structured questionnaires to farmers to determine the indigenous vegetables being grown, the nightshade species grown and factors affecting their production. The experiments were conducted both in the field and greenhouse conditions. Watering intervals were at 15 cbars, 50 cbars, and 85 cbars. Data on the number of secondary buds, leaf area, shoot height, shoot and root dry weights were gathered. The total antioxidant capacity and the total phenolic content were recorded using DPPH radical scavenging method and Folin-Ciolcalteu method, respectively. The data collected were subjected to ANOVA. In both counties where production was 100% under small scale, Solanum scabrum was the main variety grown is Siaya County (36%) while in Kisii the main variety was Solanum villosum (32%). There were significant differences (Pâ‰¤0.05) among treatments in leaf area, plant height, shoot biomass, number of secondary buds, leaf and root total phenolic content and leaf and root antioxidant activity. At all stress levels, Solanum scabrum exhibited the tallest plants with a maximum height of 45.17cm at 15cbars, while Solanum villosum had the shortest plants at all stress levels, with the shortest one being recorded at 16.65 cm at 85 cbars. S. scabrum also had the highest root dry weight (7.78g), shoot dry weight (50.78g) and highest leaf area of (304.45cm2). However, Solanum villosum had the highest number of secondary buds at all stress levels with the highest being 24 at 15 cbars. Concerning phytochemicals, Solanum villosum had a higher concentration of both the total phenolics and antioxidant activity in the shoots (46.41g GAE/Kg DM total phenolic content and 52.68% total antioxidant activity). Meanwhile, Solanum scabrum had a higher concentration in the roots (25.06gGAE/Kg DM total phenolic content and 27.18% total antioxidant activity). Water stress cause a decline in all growth parameters but increased phytochemical accumulation in nightshade accessions grown. It is therefore suggested that for better yields, irrigation should be performed at every 15 cbars, however for adequate phytochemical accumulation, the irrigation should be carried out at 50 cbars. Further research to explore and quantify other phytochemical components as affected by different watering regimes need to be undertaken.
Identifying Envirogenomic Signatures for Predicting the Clinical Outcomes of Crohn's Disease

A complex interplay between genetic susceptibility, environmental factors and clinical indicators seem to cause the development of Crohn’s disease (CD). Few disorders in clinical medicine are associated with as much chronic morbidity as CD. Genetic factors are the predetermined cause, whereas non-genetic factors seem to further trigger the development of CD. From epidemiological data, based on concordance statistics in family studies, via linkage analysis to Genome Wide Association Studies (GWAS) and Whole Genome Analysis (WGA), robust evidence have been gathered, implicating distinct genomic loci involved in genetic susceptibility to CD. Most recently, a meta-analysis has been able to implicate 71 distinct genomic loci that seem to be associated with CD development. A study published in the American Journal of Human Genetics has also recently identified more than 200 genes associated with CD, which is more than what have been found for any other disease so far. Monozygotic twins show approximately 50-60% disease concordance, with much lower rates in dizygotic twins (~10%), highlighting the role of both environmental and genetic components in the development of CD.
Chemical composition and antimalarial activity of extracts of Sudanese Tamarindus indica L. (Fabaceae)

Tamarindus indica L. (Asteraceae) is a multipurpose tree, either nutritional or medicinal and grows wild throughout Sudan and other parts of the world. The plant fruits are claimed for their antimalarial activity and treatment of fever and gastrointestinal disorders. Crude 96% ethanolic and water extracts in addition to hexane, chloroform, methanol and water successive extracts were prepared to assess their antiplasmodial activity. The chloroform successive extract exhibited the highest activity (IC50= 34.8 g/mL) and was subjected for GC-MS analysis. It was composed of aliphatic saturated alcohols (12.15%), aliphatic saturated fatty acids and their derivatives (17.41%) phenolic compounds (2.67%); aromatic acids (0.58%); -sitosterol (2.33%) and the most dominant compound 5-hydroxymethyl furfural (30.74%). The activity may be due to one or a combination of these constituents and further studies should be done to spot more light on the observed antimalarial activity and chemical composition of the chloroform extract.
The complete chloroplast genome sequence of Angelica Tsinlingensis (Apioideae)

Abstract Angelica tsinlingensis is endemic in Shaanxi province (China), and is used as Angelica sinensis in folk. Owing to important medicinal value, wild A. sinensis has been over-exploited and become quite rare in China during over 2000 years. Angelica sensu lato (s.l.; Apiaceae subfamily Apioideae) is a taxonomically complex and controversial group, and A. tsinlingensis is clearly different from members of the Angelica s.s. clade with the morphological and molecular results. The complete chloroplast DNA sequence of A. tsinlingensis (GenBank accession number: MF924726) was determined in our study. The size of chloroplast genome of A. tsinlingensis is 147,104 bp, including a large single-copy (LSC) region of 93376 bp and a small single-copy (SSC) region of 17,574 bp separated by a pair of identical inverted repeat regions (IRs) of 18,077 bp each. A total of 125 genes were successfully annotated containing 83 protein-coding genes, 34 tRNA genes and 8 rRNA genes. GC content of IRs region is the highest (44.5%). The result of Phylogenomic analysis supports the difference of A. tsinlingensis from Angelica s.s. clade.
Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta)

Abstract. The problem of reconciling earthworm taxonomy and phylogeny has shown advances with the application of molecular techniques, yet they have proven insufficient. Integrative systematics could solve this by combining multiple sources of evolutionary information. Relatively low diversity, restricted range and low nomenclatural conflict make Hormogastridae Michaelsen, 1900 a desirable target for an integrative systematics approach. The main systematic conflicts within this family are the polyphyly of the species Hormogaster pretiosa Michaelsen, 1899, the widespread presence of cryptic lineages, the lack of resolution of supraspecific relationships and the paraphyly of the genus Hormogaster Rosa, 1877 (found to be composed of four well-supported genus-level clades by molecular phylogenetic inference). This work integrates all the existing information by performing phylogenetic inference based on morphological, molecular and total evidence datasets, comparing their performance with the topology obtained by phylogenomic analyses. It also includes a comparative study of representatives of the main clades based on microcomputed tomography (µCT) reconstructions. The addition of morphological characters improved the resolution of the Hormogastridae tree; ancestral state reconstruction displayed the evolution of character states and provided morphological diagnoses for the genera within a new system, which incorporates information about ecological niches and biogeography.
Nonlinear Analysis of a New Car-Following Model Based on Internet-Connected Vehicles

: A new car-following model is proposed based on Internet-connected vehicles. In this model, a vehicle is controlled by the information of arbitrary number of vehicles obtained from the Internet-connected vehicles system. The stability condition is investigated by using the linear stability theory. The result shows that the stability of traffic flow is improved by taking into account the headway of vehicles ahead and the relative velocity. By applying the nonlinear analysis, the modified Korteweg-de Vries (mKdV) equation is derived to describe the traffic jams. From the numerical simulation, it is shown that the traffic jams are suppressed efficiently by taking into account the headway of vehicles ahead and the relative velocity.
Wildland Recreation: Ecology and Management

Wildland Recreation and Resource Impacts. IMPACTS TO RESOURCE COMPONENTS. Soil. Vegetation. Wildlife. Water. IMPACT PATTERNS AND TRENDS. Impact Patterns. Trends in Wildland Recreation Use and Impacts. FACTORS AFFECTING IMPACTS. Environmental Durability. Visitor Use. MANAGEMENT ALTERNATIVES. Strategies and Concepts of Management. Monitoring Recreational Impacts. Visitor Management. Site Management. International Impact Research and Management. CONCLUSION. A Lasting Impact. Index.
Management of eggplant shoot and fruit borer (Leucinodes orbonalis guenee) by integrating different non-chemical approaches.

Eggplant (Solanum melongena L.) also known as brinjal and aubergine is an important solanaceous vegetable and is extensively cultivated in South Asia (Bangladesh, India and Pakistan) which constitutes about 50% of the total area under eggplant cultivation in the world (Alam et al., 2003). Among all the summer grown vegetables with semi-perennial nature, eggplant is almost available throughout the year and is consumed in various forms by all classes of people. It has high nutritive value and contains all the essential minerals, vitamins and amino acids. In Pakistan, eggplant is cultivated on large scale, but it lags behind many countries in terms of productivity. Several factors are responsible for low productivity of eggplant in Pakistan (Hussain et al., 2014, 2016; Iqbal and Mukhtar, 2014; Kayani et al., 2017; Mukhtar et al., 2013a,b; 2014, 2017a,b; Shahbaz et al., 2015; Tariq-Khan et al., 2017). Among biotic factors, eggplant shoot and fruit borer (ESFB) (Leucinodes orbonalis Guenee) is considered by far the most damaging pest of eggplant (Taylo et al., 2016). The pest is active in moderate climates throughout the year. The females lay approximately 250 eggs one by one on developing fruits and young shoots of eggplant. The caterpillar is pink in color and is covered with sparsely distributed hairs all over the body. Fully grown larva measures about 20 mm long and pupates in a tough silken cocoon. The entire life cycle is completed in 3-6 weeks. There are five overlapping generations of the pest in a year. Severe damage to fruits and shoots is caused by the larvae of the pest. The petioles, midribs of large leaves and young tender shoots are bored by newly hatched larvae. Due to larval activity, translocation of nutrients towards shoots is affected. This causes withering and drooping of shoots, resultantly the growth of eggplant and size and number of fruits are significantly reduced (Atwal and Dhaliwal, 2007). The larvae then enter into young fruits, make tunnels and start feeding on internal tissues. The tunnels are clogged with frass and render the fruits unmarketable (Alam et al., 2003; Mainali, 2014). Sometimes, secondary infection by bacteria causes rotting of fruits and further deteriorates the quality of fruits. The pest is a serious threat due to its high reproduction, fast turnover of generations and tremendous damage. A single larva is enough to damage 4-6 healthy fruits (Jayaraj and Manisegaran, 2010). The infestations and losses caused by the pest vary from location to location and season to season Pak. J. Agri. Sci., Vol. 54(1), 65-70; 2017 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/17.5282 http://www.pakjas. com.pk
The complete plastome sequence of Lilium wahingtonianum Kellogg (Liliaceae)

Abstract Lilium washingtonianum Kellogg is native to Western America and grows on slope in high subalpine. In the present study, the complete plastome of L. washingtonianum was sequenced. The plastome sequence was 151,967 bp long, with a large single copy region of 81,393 bp, a small single copy region of 17,352 bp, and two inverted repeat regions of 26,611 bp each. Total 133 genes were identified, including 83 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 4 pseudogenes. Among four pseudogenes, pseudo ndhF gene was the first to report among Lilium species so far. The phylogenetic position of L. washingtonianum was sister to L. superbum but American lilies were not monophyletic.
Negative effects of litter richness on root decomposition in the presence of detritivores

1.Decomposition is a vital process underlying many ecosystem functions. Although a growing number of studies have tested how litter richness affects the decomposition of aboveground plant organs, knowledge remains limited about the decomposition of root mixtures. Here, we used a field experiment in a subtropical forest to investigate how species richness in root litter mixtures (air-dried fresh fine roots) affects the decomposition of root litter material. 2.Based on the concept of resource complementarity, we hypothesized that root litter would decompose faster as the richness of the root litter mixture increased. In addition, we expected the presence of detritivores to modify the effect of root richness on mass loss, because detritivores might experience bottom-up effects from specific plant species and might affect microbial decomposer communities. 3.We found that the richness level of root litter mixtures did not affect mass loss in the absence of detritivores. In the presence of detritivores, all root litter types decomposed faster. Notably, the positive effect of detritivores was stronger at low root litter richness than at high root litter richness, particularly during the early stages of decomposition (the first two sampling points) when litter mass loss was roughly double at low root litter richness compared to that at high root litter richness. The composition of the root fungal community measured at the last sampling point did not differ significantly across root richness levels, and was not affected by the presence of detritivores. 4.Synthesis. Our findings demonstrate that detritivores modify the relationship between root litter diversity and root litter decomposition in subtropical forest ecosystems. This highlights an importance of cascade effects between different trophic organisms on ecosystem functioning.
Germline cells derived from mesenchymal stem cells, with the focus on Wharton's jelly

Previous attempts have indicated that mesenchymal stem cells (MSCs) are a valuable source and candidate and new approach for tissue engineering and reproductive medicine. MSCs have this potential to be induced and differentiated in an appropriate in vivo and in vitro condition toward various cell lineages and then they can be applied in cell therapies and clinical applications. During recent two decades, various sources have demonstrated they are a great source for MSCs, including bone marrow, the human umbilical cord as well as Wharton's jelly. Due to discarding after birth, easily accessible cells and less ethical concerns, these cells have attracted more and more scientists' attention. Infertility and reproduction diseases have provided special opportunity to examine the efficiency of MSCs in this kind of application. Based on recent investigations, MSCs embedded in Wharton's jelly tissue are more appealing for cell therapies, especially in infertility treatment purposes. So, differentiation of MSCs embedded in Wharton's jelly tissue into germ layer cells for cell-based therapy purposes is now under intensive study.
Contrasting responses in community structure and phenology of migratory and non‐migratory pollinators to urbanization

Anthropogenic landscape change, such as urbanization, can affect community structure and ecological interactions. Furthermore, changes in ambient temperature and resource availability due to urbanization may affect migratory and non‐migratory species differently. However, the response of migratory species to urbanization is poorly investigated, and knowledge for invertebrates in particular is lacking. Our aim was to investigate whether there was a shift in community structure and phenology of hoverflies in urban landscapes, depending on migratory status.
Evaluating cell lines as models for metastatic cancer through integrative analysis of open genomic data

Metastasis is the most common cause of cancer-related death and, as such, there is an urgent need to discover new therapies to treat metastasized cancers. Cancer cell lines are widely-used models to study cancer biology and test drug candidates. However, it is still unknown to what extent they adequately resemble the disease in patients. The recent accumulation of large-scale genomic data in cell lines, mouse models, and patient tissue samples provides an unprecedented opportunity to evaluate the suitability of cell lines for metastatic cancer research. In this work, we used breast cancer as a case study. The comprehensive comparison of the genetic profiles of 57 breast cancer cell lines with those of metastatic breast cancer samples revealed substantial genetic differences. In addition, we identified cell lines that more closely resemble different subtypes of metastatic breast cancer. Surprisingly, a combined analysis of mutation, copy number variation and gene expression data suggested that MDA-MB-231, the most commonly used triple negative cell line for metastatic breast cancer research, had little genomic similarity with Basal-like metastatic breast cancer samples. We further compared cell lines with organoids, a new type of preclinical model which are becoming more popular in recent years. We found that organoids outperformed cell lines in resembling the transcriptome of metastatic breast cancer samples. However, additional differential expression analysis suggested that both types of models could not mimic the effects of tumor microenvironment and meanwhile had their own bias towards modeling specific biological processes. Our work provides a guide of cell line selection in metastasis-related study and sheds light on the potential of organoids in translational research.