Miracle-dz/UniFAR-FTUs huggingface dataset:
Colonization time on island settings: lessons from the Hawaiian and Canary Island floras

Molecular dating offers a tool for inferring the time of divergence between two lineages. In this study, we discuss how dated molecular reconstructions are informative of two different, albeit often intermingled, time estimates with regard to a fundamental process in island biogeography: the time of island colonization (TIC). We illustrate how stem age estimates provide information on the divergence between the extant island lineage and their closest relatives (i.e. the onset of lineage differentiation). Such estimates, however, are typically poor TIC predictors, as they are strongly affected by spatial and temporal uncertainty, particularly in cases of deep stem ages. Crown ages of endemic island lineages, in contrast, provide information on the temporal onset of island in situ diversification, and may represent a better proxy for TIC when the associated uncertainty is taken into account. Thus, the geographic and temporal distance separating the island and mainland lineages in phylogenetic/phylogeographic reconstructions are key factors for determining the reliability of these two estimates as proxies of TIC. We show how divergence times can be used to investigate the biogeographic patterns of two well-studied oceanic archipelagos: Hawaii and the Canary Islands. A compilation of molecular age estimates for nearly one-third of the endemic plant lineages in each archipelago reveals that Canarian plant lineages exhibit significantly younger mean crown ages (2.1 ± 2.4 Myr) than Hawaiian lineages (3.5 ± 2.9 Myr), despite island substrates being much older in the Canarian archipelago. We postulate that this pattern suggests: (1) a more important role of submerged islands during plant colonization in Hawaii, and (2) higher taxon turnover in the Canaries, mediated by relatively young (Mediterranean) lineages, and probably facilitated by the combination of the high incidence of extinction for the last 5 Myr and the close proximity of mainland source areas as compared to Hawaii.
Appropriate Removal of Forest Litter is Beneficial to Pinus tabuliformis Carr. Regeneration in a Pine and Oak Mixed Forest in the Qinling Mountains, China

Research Highlights: Natural regeneration is important in pine–oak mixed forests (Pinus armandii Franch., Pinus tabuliformis Carr., and Quercus aliena Bl. var. acuteserrata Maxim.ex Wenz.), but allelopathy as a limiting factor has not been studied. Our research provides insights into allelopathy in pine–oak mixed forest litter. Background and Objectives: Allelopathy among tree species occupying the same ecological niche in mixed forests may adversely affect regeneration. We studied allelopathy in pine and oak forest litter to determine the effect on regeneration, whether it is offset by adding activated carbon or plant ash, and what allelopathic substances are present. Materials and Methods: We used laboratory seed culture and field seeding to determine pine and oak litter regeneration effects on P. tabuliformis and P. armandii in the Qinling Mountains, China. In the laboratory, we irrigated seeds with three different litter concentrations. A fourth treatment incorporated activated carbon. The field study established small quadrats in mixed forest to study how removing or retaining litter and spreading plant ash affected sown seeds. High performance liquid chromatography–mass spectrometry was used to compare differences in chemical substances in extracts with and without activated carbon. Results: Litter extracts significantly affected germination rates in both species. Seedling morphological and physiological indexes showed that litter extracts negatively affected growth in both species, but activated carbon alleviated this inhibitory effect on P. armandii. Forest stand and litter did not affect P. armandii seed germination. Pinus tabuliformis germination rates were significantly higher in plots with removed litter than when litter was retained or plant ash spread, and lower in oak than pine forest. Allelopathic substances detected in pine forest were trioctyl trimellitate, amyloid β-Peptide 10–20, and triisobutyl phosphate, potentially affecting P. armandii seed germination and growth. Conclusions: Appropriate removal of litter in mixed forests can improve the natural regeneration ability of P. tabuliformis.
The Frequency of Staphylococcus aureus Classical Enterotoxin Genes in Raw Milk Samples in Zanjan, Iran

Staphylococcus aureus is a gram-positive, non-sporeforming, immotile coccus belonging to the family Micrococcaceae, which is considered to be a leading cause of bacterial food poisoning outbreaks [1-3]. Staphylococcal food poisoning (SFP) is caused by the consumption of contaminated foods containing enterotoxins. Approximately 20-30% of human populations are consistent carriers of this bacterium, while 60% are the transient carriers of S. aureus. Therefore, the insufficient pasteurization and decontamination of food products or their contamination during preparation, processing, and distribution by the carriers of S. aureus are the common risk factors for the outbreaks of staphylococcal food poisoning [3-6]. Some of the food products that are often involved in the transmission of staphylococcal poisoning include meat and its products, poultry and egg products, milk and dairy products, salads, bakery products (especially cream-filled pastries and cakes), and sandwich fillings [7-11]. The most common symptoms of staphylococcal food poisoning are nausea and vomiting, diarrhea, and abdominal cramps, which occur within 2-6 hours after the consumption of enterotoxin-containing foods. Occasionally, SFP may be more severe or even fatal, especially in infants, the elderly or immunocompromised patients [11, 12]. Journal of Human, Environment, and Health Promotion
Robust perisomatic GABAergic self-innervation inhibits basket cells in the human and mouse supragranular neocortex

Inhibitory autapses are self-innervating synaptic connections in GABAergic interneurons in the brain. Autapses in neocortical layers have not been systematically investigated, and their function in different mammalian species and specific interneuron types is poorly known. We investigated GABAergic parvalbumin-expressing basket cells (pvBCs) in layer 2/3 (L2/3) in mice as well as in human neocortical tissue resected in deep-brain surgery. Most pvBCs showed robust GABAAR-mediated self-innervation in both species, but autapses were rare in nonfast spiking GABAergic interneurons. Light- and electron microscopy analyses revealed pvBC axons innervating their own soma and proximal dendrites. GABAergic self-inhibition conductance was similar in human and mouse pvBCs and comparable to that of synapses from pvBCs to other L2/3 neurons. Autaptic conductance prolonged somatic inhibition in pvBCs after a spike and inhibited repetitive firing. Perisomatic autaptic inhibition has evolved in pvBCs of various cortical layers and different mammalian species to control discharge of these interneurons.
ISOLATION ENDOPHYTIC MICROORGANISMS FROM DIFFERENT TEA CULTIVARS

There are a variety of endophytic microorganisms in the roots and leaves of tea plants, which will lead to the pollution during the tissue culture, affecting the growth of cultures and the process of genetically modified breeding. In the present study, endophytic microorganisms in the leaves from three tea cultivars in the same field were isolated. The microscopic morphology observation showed that the dominant endophytic microorganisms were different in three tea cultivars. It is Bacillus in Camellia sinensis cv Huangjinya, Alternaria in C. sinensis cv Longjing 43 and Colletotrichum in C. sinensis cv Jiaming 1, respectively. Therefore, different anti-pollution measures should be taken in tea plant tissue culture.
Interpretable Machine Learning for Perturbation Biology

Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides an informative data resource for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in an enormously complex multi-dimensional solution space and to mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of dynamic cell biological processes with a machine learning framework, implemented in Tensorflow. We tested the modelling framework on a perturbation-response dataset for a melanoma cell line after drug treatments. The models can be efficiently trained to accurately describe cellular behavior, as tested by cross-validation. Even though completely data-driven and independent of prior knowledge, the resulting de novo network models recapitulate known interactions. The main predictive application is the identification of combinatorial candidates for cancer therapy. The approach is readily applicable to a wide range of kinetic models of cell biology.
Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation

Freshwater macro‐organismic environmental DNA (eDNA) is gaining increasing popularity in detecting invasive species, assessing community assemblages, and in mapping the distribution of taxa that are rare or otherwise difficult to monitor. The objectives of this article are to review the targets of published freshwater eDNA research in relation to aquatic conservation with a focus on geographic regions covered, as well as the habitats and species investigated. The analysis of 272 peer‐reviewed articles published between 2005 and 2018 revealed that 57% of the 238 primary research papers have a focus on conservation science, mostly addressing invasive and endangered species, followed by 23% papers investigating methodological developments and 11% biodiversity surveys also using eDNA metabarcoding. A strong geographical pattern emerged, with Africa, South America, and the tropics being under‐represented. Taxonomic coverage was dominated by 123 fish species, followed by 29 amphibian and 28 mollusc species. Freshwater arthropods (27 taxa) were under‐represented in relation to their estimated species richness. Taxonomic bias towards certain species such as fishes observed in freshwater eDNA research is pervasive in biodiversity research and conservation sciences, and thus is not surprising. Geographical representation was biased, with a few industrialized countries from the Northern Hemisphere contributing 72% of the studies. Both findings parallel biases known from other research areas, such as marine eDNA analysis, taxonomy, or invasion biology. The application of eDNA in freshwater conservation will benefit from the development of general standards and guidelines that are necessary to integrate freshwater macrobial eDNA techniques in existing monitoring frameworks. To aid future freshwater conservation, our suggestions are to harmonize eDNA methods for comparable and easier implementation worldwide, and to increase international cooperation and funding for under‐represented geographical regions and neglected taxa. This is especially crucial for the known biodiversity hotspots in developing countries where rapid changes occur to freshwater habitats and biodiversity.
Kocaeli Üniversitesi Umuttepe Yerleşkesi’nde Yayılış Gösteren Kertenkelelerin Moleküler Düzeyde Tür Tayini

Kocaeli Universitesi Umuttepe Yerleskesi’nde siklikla rastlanan kertenkeleler, molekuler duzeyde tur teshisi yapilmak uzere yakalanip, kuyruk bolgelerinden doku ornekleri alindi. Ardindan DNA izolasyonu, evrensel mitokondrial COI ve 16S rRNA primerleri kullanilarak Polimeraz Zincir Reaksiyonu (PZR) ve DNA dizi analizleri yapildi. Elektroferogramlari degerlendirildi ve elde edilen sonuclar NCBI veri tabaninda kayitli kertenkele turleri ile karsilastirildi. Tur bazinda molekuler filogenetik analiz yapilan bu calismada Kocaeli Universitesi’nde yayilis gosteren kertenkelelerin Podarcis siculus turune (Istanbul Kertenkelesi) ait olduklari tespit edildi.
NHJ-1 regulates canonical non-homologous end joining in Caenorhabditis elegans

Canonical non-homologous end joining (cNHEJ) is a near-universally conserved pathway for the repair of DNA double-strand breaks (DSBs). While the cNHEJ pathway encompasses more than a dozen factors in vertebrates and is similarly complex in other eukaryotes, in the nematode C. elegans the entire known cNHEJ toolkit consists of two proteins that comprise the Ku ring complex, cku-70 and cku-80, and the terminal ligase lig-4. Here, we report the discovery of nhj-1 as the fourth cNHEJ factor in C. elegans. Observing a difference in the phenotypic response to ionizing radiation (IR) between two lines of the wild type N2 strain, we mapped the locus causative of IR-sensitivity to a candidate on chromosome V. Using CRISPR-Cas9 mutagenesis, we show that disrupting the nhj-1 sequence induces IR-sensitivity in an IR-resistant background. Double mutants of nhj-1 and the cNHEJ factors lig-4 or cku-80 do not exhibit additive IR-sensitivity, arguing that nhj-1 is a member of the cNHEJ pathway. Furthermore, like the loss of lig-4, the loss of nhj-1 in the com-1 genetic background, in which meiotic DSBs are repaired by cNHEJ instead of homologous recombination, increased the number of DAPI-staining bodies in diakinesis, consistent with increased chromosome fragmentation in the absence of cNHEJ repair. Finally, we show that NHJ-1 localizes to many somatic nuclei in the L1 larva, but not the primordial germline, which is in accord with a role in the predominantly somatically active cNHEJ. Although nhj-1 shares no sequence homology with other known eukaryotic cNHEJ factors and is taxonomically restricted to the Rhadbitid family, its discovery underscores the evolutionary plasticity of even highly conserved pathways, and may represent a springboard for further characterization of cNHEJ in C. elegans.
Dasypus kappleri (Cingulata: Dasypodidae)

Abstract: Dasypus kappleri Krauss, 1862, commonly known as greater long-nosed armadillo, is the second largest extant armadillo and readily distinguishable by the prominent spurs on the hind legs. It is diurnal-nocturnal, solitary, and insectivorous. It is a semi-fossorial species ranging east of the Andes across the central lowlands of South America. It occupies a wide range of habitats including rainforest, riparian forest, and grassland. D. kappleri is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources in light of its wide distribution, which presumedly contains robust populations.
Generic classification of Amaryllidaceae tribe Hippeastreae

A robust generic classification for Amaryllidaceae has remained elusive mainly due to the lack of unequivocal diagnostic characters, a consequence of highly canalized variation and a deeply reticulated evolutionary history. A consensus classification is proposed here, based on recent molecular phylogenetic studies, morphological and cytogenetic variation, and accounting for secondary criteria of classification, such as nomenclatural stability. Using the latest sutribal classification of Hippeastreae (Hippeastrinae and Traubiinae) as a foundation, we propose the recognition of six genera, namely Eremolirion gen. nov., Hippeastrum, Phycella s.l. , Rhodolirium s.str. , Traubia, and Zephyranthes s.l. A subgeneric classification is suggested for Hippeastrum and Zephyranthes to denote putative subclades. In Hippeastrum, we recognize H. subg. Hippeastrum and H. subg. Tocantinia. In Zephyranthes, Z. subg. Eithea, Z. subg. Habranthus, Z. subg. Myostemma (= core Rhodophiala clade), Z. subg. Neorhodophiala subg. nov., and Z. subg. Zephyranthes are recognized. Descriptions, synonymy, taxonomic keys, and new combinations are provided for each genus and subgenus.
Antioxidants and hypoglycemic effect of some medicinal plants

There is an increasing trend to replace synthetic drugs, which are of safety concern, with the natural remedies available from plant extracts. This study investigated the phytoconstituents as well as antioxidants and hypoglycemic effect of Anarcadium occidentales, Huntaria umbellata, Parkia biglobosa, Psidium guajava and Vitellaria paradoxa. Phytochemicals compositions were assayed using standard procedures. Antioxidant assays employed were ferric reducing antioxidant power and scavenging effect on the 1, 1-diphenyl-2-picrylhydrazyl radicals. Oral glucose tolerance test (OGTT) and amylase inhibitory assays were employed for hypoglycemic study. The concentration of phenols ranges from 184.368±0.23 mg/g (Anacardium occidentales) to 120.241±0.01 mg/g (Hunteria umbellata). However, Hunteria umbellata extract had the highest alkaloids (76.76±0.01 mg/g), Parkia biglobosa extract had the highest tanins (137.55±0.05 mg/g) while Vitellaria paradoxa extract had higher saponins (188.50±0.01 mg/g). Flavonoids was higher in Parkia biglobosa (458.06±0.06 mg/g) while Psidium guajava had the least. In DPPH assay A. occidentales extract had the lowest IC50 (217.78±3.45 μg/ml) comparable with the standards while H. umbellata had the highest (IC50=311.72±3.45 μg/ml) and thus lowest activity. Anarcadium occidentales had higher α-amylase inhibitory activity (IC50 =171.13±0.14μg/ml) while Psidium guajava (IC50 =304.64 ±0.14μg/ml) had the least activity. Oral glucose tolerance revealed the activities of the extracts in order of Anacardium occidentales>Hunteria umbellata>Vitellaria paradoxa>Parkia biglobosa>Psidium guajava. In conclusion, five medicinal plants investigated in this study possesses some antioxidants and hypoglycemic properties with Anacardium occidentales extract being the most potent, which may be attributed to their polyphenolic constituents.
Mutoviaspermum krassilovii gen. et sp. nov.: A Peculiar Compound Ovuliferous Conifer Cone from the Lopingian (Late Permian) of European Russia (Vologda Region)

Premise of research. Late Permian Voltziales are interpreted to have given rise to most extant conifer families, although their origin and evolutionary relationships are still poorly understood. The Poldarsa Formation (Kichuga Member) of Mutovino (=Isady) in European Russia yielded a diverse Lopingian (upper Permian) flora including some very peculiar compound ovuliferous cones. Methodology. The micromorphologies of eight specimens of dispersed compound ovuliferous cones—some in organic connection with conifer shoot fragments—are described, and their relationships are tested in a phylogenetic analysis. Pivotal results. Mutoviaspermum krassilovii gen. et sp. nov. is characterized by a stout main axis with helically arranged ovuliferous scales protected by coriaceous bracts. The polysperms have a peltate structure with an apical whorl of segments fused only in the basal part near the stalk and with a seed scar on each segment. The anatomical connection between M. krassilovii and Quadrocladus-like leaves provides the basis for reassessing the botanical affinities of these taxa. Conclusions. A morphological phylogenetic analysis supports the placement of Mutoviaspermum as an early-diverging genus within Voltziales, although a precise relationship of this genus with other early conifers remains uncertain. Results of this analysis underline the ambiguous position of Quadrocladus and highlight its complex and poorly understood relationship within the Permian conifers.
Adaptive Deep Brain Stimulation as an Advanced Parkinson’s disease Treatment (ADAPT): a pseudorandomised clinical trial

Beta-based adaptive Deep Brain Stimulation (aDBS) is effective in Parkinson’s disease (PD), when assessed in the immediate post-operative phase. However, potential benefits of aDBS on stimulation-induced side effects in chronically implanted patients are yet to be assessed. To determine the effectiveness and side-effect profile of aDBS in PD we compared to conventional DBS (cDBS) and no stimulation (NoStim) in the chronically implanted state. 13 PD patients undergoing battery replacement were pseudo-randomised in a crossover fashion, into three conditions (NoStim, aDBS or cDBS). Patient videos were blindly evaluated using a short version of the Unified Parkinson’s Disease Rating Scale (subUPDRS) and the Speech Intelligibility Test (SIT). subUPDRS scores were significantly lower both in aDBS (p=<.001), and cDBS (p=.001), when compared to NoStim. Bradykinesia subscores were significantly lower in aDBS (p=.002), but not in cDBS (p=.08), when compared to NoStim. SIT scores of patients with stimulation-induced dysarthria significantly worsened in cDBS (p=.009), but not in aDBS (p=.407), when compared to NoStim. Beta-based aDBS is effective for PD in chronically implanted patients, especially in controlling bradykinesia symptoms. Furthermore, aDBS has a more favourable speech side-effect profile than cDBS.
In silico and empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

This last decade, environmental DNA metabarcoding approaches have been developed and improved to minimize biological and technical biases; some challenges, however, remain, as the design of primers. Here we have performed a comprehensive assessment of ten COI and two 16S primer sets. We have combined in silico, in vivo-mock community of 33 arthropod taxa from 16 orders and guano analyses to identify primer sets that should maximize arthropod detection and taxonomic identification, whilst identifying bat species and minimizing labour time and cost. We have focused on two insectivorous bat species living in mixed-colonies, the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy’s bat (Myotis emarginatus). We have found that the level of primer degeneracy is the main factor influencing arthropod detection for in silico and mock community analyses, while the amplicon length is critical for the detection of arthropods from degraded DNA samples. Our results confirm the importance of performing predator detection and taxonomic identification, simultaneously with arthropod sequencing, as faeces samples can be contaminated by different insectivorous species. Moreover, amplifying bat DNA does not affect the primers’ capacity to detect arthropods. We therefore recommend the systematic simultaneous identification of predator and prey. Finally, we evidenced that one third of the prey occurrences are unreliable and probably not of primary interest in diet studies, which might decrease the relevance of combining several primer sets instead of using one efficient primer set. In conclusion, this study provides general criteria enabling the selection of primers whilst considering different scientific and methodological constraints.