Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphological convergence in the recently diversified Silene gigantea complex (Caryophyllaceae) in the Balkan Peninsula and south-western Turkey, with the description of a new subspecies.

The Silene gigantea complex is characterized by a high degree of morphological variability that resulted in the description of three subspecies across its distribution range from the Balkan Peninsula to South-west Asia and Cyprus. In this work, we used nuclear and plastid markers in Bayesian phylogeographic analyses to investigate the taxonomy and the evolutionary history of S. gigantea . The results from plastid DNA partly support the existing taxonomic assessments since S. gigantea subsp. rhodopea is monophyletic, whereas S. gigantea subspp. gigantea and hellenica are clearly polyphyletic. This pattern suggests that a strong morphological convergence is associated with chasmophytic conditions. The results also suggest that the populations from the Epirus region (north-western Greece) did not arise from hybridization as previously claimed, but correspond to a new evolutionary lineage that is consequently described and named S. gigantea subsp. epirota . An identification key to the four subspecies is also given. Our phylogeographic study further highlights a genetic continuity across populations from the central and eastern Greek mainland to Chios and Turkey, all of them sharing the same plastid DNA haplotype and belonging to the same nuclear cluster. In addition, at least two separate colonization events are suggested for Crete. The Bayesian phylogeographic reconstruction clearly points to a post-Messinian diversification across the Aegean area. Considering the low seed dispersal ability of S. gigantea , a continuum of ancestral populations between islands and the mainland is assumed to have occurred during the last glaciations and to have played a key role in colonization processes.
Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities

In this paper, we report the endophytic microbial diversity of cultivated and wild Oryza sativa plants including their functional traits related to multiple traits that promote plant growth and development. Around 255 bacteria were isolated out of which 70 isolates were selected for further studies based on their morphological differences. The isolates were characterized both at biochemical and at the molecular level by 16s rRNA gene sequencing. Based on 16S rRNA gene sequencing the isolates were categorized into three major phyla, viz, Firmicutes (57.1 %), Actinobacteria (20.0 %) and Proteobacteria (22.8 %). Firmicutes was the dominant group of bacteria of which the most abundant genus was Bacillus. The isolates were further screened in vitro for plant growth promoting activities which revealed a hitherto unreported endophytic bacterial isolate, Microbacteriaceae bacterium RS01 11 as the highest secretor of a phytohormone, IAA (28.39 ± 1.39 μg/ml) and GA (67.23 ± 1.83 μg/ml). Bacillus subtilis RHS 01 displayed highest phosphate solubilizing activity (81.70 ± 1.98 μg/ml) while, Microbacterium testaceum MK LS01, and Microbacterium trichothecenolyticum MI03 L05 exhibited highest potassium solubilizing activity (53.42±0.75μg/ml) and zinc solubilizing efficiency (157.50%) respectively. Bacillus barbaricus LP20 05 produced highest siderophore units (64.8 %). Potential plant growth promoting isolated were tested in vivo in pot culture under greenhouse conditions. A consortium consisting of Microbacteriaceae bacterium RS01 11, Bacillus testaceum MK LS01 and Bacillus subtilis RHS promoted plant growth and increased the yield 3.4 fold in rice when compared to control T0 when tested in pot culture and reduce application rates of chemical fertilizer to half the recommended dose. Our study confirms the potentiality of the rice endophytes isolated as good plant growth promoter and effective biofertilizer.
Indigenous pseudomonas chlororaphis affects growth of Alternaria sp., Phoma sp. and Drechslera tetramera from anise.

Pseudomonas chlororaphis is a bacterium used as a soil inoculant in agriculture and horticulture. It can act as a biocontrol agent against certain phytopathogenic fungi via production of phenazine type antibiotics. Phytopathogenic fungi are responsible for several plant diseases in different medicinal plants and cause very important economic losses in Serbian plantation. Among them, Alternaria sp. , Phoma sp. and Drechslera tetramera are known as major plant pathogens, whereby at least 20% of agricultural spoilage is caused by Alternaria species. In this study, we examined the antifungal activity of indigenous Pseudomonas chlororaphis isolates against the phytopathogenic fungi Alternaria sp. , Phoma sp. and Drechslera tetramera, which had infected anise (Pimpinella anisum L., fam. Apiaceae), using in vitro inhibition tests. The obtained results showed that studied antibioticproducing Ps. chlororaphis isolates inhibited the tested fungi as follows: D. tetramera in the range from 3.85-69.23%, Alternaria sp. in the range from 5-50%, and Phoma sp. in the range from 0-50%. In general, it has been concluded that studied P. chlororaphis isolates have potential in controlling plant diseases caused by phytopathogenic fungi Alternaria sp. , Phoma sp. and D. tetramera, whereby the bacterial isolates with the highest inhibitory potential will be selected for further experiments.
Bet- hedging reproduction strategies in the massive Caribbean coral Favia fragum

Bet- hedging has long been recognised as an adaptive mechanism in unpredictable environments, yet is often overlooked as an evolutionary strategy in corals to adapt to environmental conditions associated with climate change. Most environments vary spatially and temporally over the lifespan of corals, and corals use cues from their natal environments as “predictors” of the environment they will release their offspring into and may optimise phenotypes to maximise fitness to changes in the maternal environment. However, when conditions fluctuate in unpredictably or environmental cues are otherwise lost, producing a single phenotype could cause population bottlenecks. Prolonged summer periods of high sea surface temperatures combined with anthropogenic impacts are inhibiting environmental cues that have previously secured reproductive success in tropical scleractinian corals and enabled them to fine-tune their reproductive patterns to time periods that optimize external fertilization success, appropriate larval dispersal and efficient coral recruitment. This study tested the ability of the brooding species Favia fragum to “hedge their bets” on reproductive strategies in the presence/ absence of lunar cues, a cue known to play an important role in synchronizing reproductive output. Results illustrated F. fragum exhibited dynamic bet-hedging, tailoring larval output and producing a range of larval phenotypes and thus exhibiting plasticity dependent on their environment. In the absence of lunar cues, corals varied the timing of planulae release as well as within-clutch size variation promoting dispersal and retention to their natal environment. Lunar stimulated corals concentrated release to 3-6 days, typically produced a single phenotype aiding retention and re-seeding local reef populations. Reproductive flexibility will enable coral to strategize larval/ gamete release that optimise recruitment success within unstable environmental conditions. The use of such strategies in other brooding species and broadcast spawners should be a focus of further investigation to evaluate the potential for corals to populate environments beyond the familiar and persist future unpredictability
Disabling Gβγ SNARE interaction in transgenic mice disrupts GPCR-mediated presynaptic inhibition leading to physiological and behavioral phenotypes

Gi/o-coupled G-protein coupled receptors modulate neurotransmission presynaptically through inhibition of exocytosis. Release of Gβγ subunits decreases the activity of voltage-gated calcium channels (VGCC), decreasing excitability. A less understood Gβγ–mediated mechanism downstream of calcium entry is the binding of Gβγ to SNARE complexes. Here, we create a mouse partially deficient in this interaction. SNAP25Δ3 homozygote animals are developmentally normalbut impaired gait and supraspinal nociception. They also have elevated stress-induced hyperthermia and impaired inhibitory postsynaptic responses to α2A-AR, but normal inhibitory postsynaptic responses to Gi/o-coupled GABAB receptor activation. SNAP25Δ3 homozygotes have deficits in inhibition of hippocampal postsynaptic responses to 5 HT1b agonists that affect hippocampal learning. These data suggest that Gi/o-coupled GPCR inhibition of exocytosis through the Gβγ-SNARE interaction is a crucial component of numerous physiological and behavioral processes.
Locally Inhibition of Orthodontic Relapse by Injection of Carbonated Hydroxy Apatite-Advanced Platelet Rich Fibrin in a Rabbit Model

Relapse is considered a significant failure after orthodontic treatment. In response to relapse, RANKL expressions will increase, while OPG expressions will decrease. CHA is thought to be one of an ideal candidate for enhancing bone formation. Moreover, a-PRF is a source high levels of growth factors that play a central role in the bone remodeling. This research was intended to investigate the effect of hydrogel CHA-aPRF in preventing relapse. Hydrogel-CHA was initially designed, with its degradation profile and FTIR (Fourie’s Transform Infrared) spectra were investigated as the basis to find out optimum formulation before incorporated with aPRF. Hydrogel-CHA microspheres were prepared in 3 different compositions: those were encoded 30-CHA, 40-CHA, and 50-CHA. After the hydrogel formulation and characterization were completed, 10 mL blood samples were collected, then centrifuged at 1500 rpm for 14 min. At the end of the centrifugation process, the aPRF clot was isolated and then pressed to obtain their releasate. The releasate aPRF was then loaded into the best formulation candidate of hydrogel CHA. The hydrogel incorporated aPRF was then gently injected on the mesial side of incisor gingival sulcus of the rabbit after orthodontic tooth movement. The FTIR analysis showed that carbonated apatite was successfully developed during the fabrication process of hydrogel-CHA microspheres. It was also known that degradation profile of 30-CHA was considered ideal compared to the other compositions. The application of CHA-aPRF (group C) was proven to significantly prevent relapse, indicated by lowest percentage of relapse 21 days after debonding (29.95±3.91%) compared to control group. Furthermore, it has been found that expressions of RANKL were significantly lowest (p<0.05) in group C on day 0, 3, and 7, while OPG expressions showed significantly highest (p<0.05) in group C on day 14 and 21 after debonding. These results indicate that incorporation of hydrogel-CHA has potential effect to enhance alveolar bone remodeling and prevent orthodontic relapse by stimulates OPG expression and suppresses RANKL expression.
Distribution patterns of Kielmeyera (Calophyllaceae): the Rio Doce basin emerges as a confluent area between the northern and southern Atlantic Forest

The Atlantic Forest is one of the most diverse and threatened tropical forests in the world, and the Rio Doce valley seems to represent a limit between biotas from its southern and northern portions. In the present study, we investigated the distribution of Kielmeyera (Calophyllaceae), a woody, typically wind-dispersed genus, with a high endemism rate in the Atlantic Forest. The 351 specimens analysed, representing 21 of 22 species of Kielmeyera from the Atlantic Forest, pointed to a complete dissimilarity between species composition in the southern (Rio de Janeiro state) and northern (Bahia state) portions of the forest. However, the Rio Doce valley in Espírito Santo state, rather than being a limit between these two portions, appear to represent a confluent area. The northern boundary of species from the southern portion is the São Mateus basin, whereas the southern boundary of species from the northern portion is at the Litorânea do Espírito Santo basin. Most specimens of Kielmeyera were collected in areas that currently are not remnants of original vegetation and that are not within any conservation unit, suggesting that an imminent loss of biodiversity is taking place. Studies comprising a broad range of functionally and phylogenetically distinct taxa make individual patterns of distribution obscure and overlook the conservation needs for specific groups. Therefore, our study on the distribution of Kielmeyera in the Atlantic forest highlights the importance of biogeographic analyses of less inclusive taxa of a flora.
Limited functional responses of plankton food webs in northern lakes following diamond mining

There is limited understanding of the impact of diamond mining on the aquatic communities of lakes that receive mining activity residue. For aquatic communities, assessing the response to mining, which can affect multiple variables concurrently, is not trivial, especially when a species-by-species approach is used. Thus, we assessed diamond mine impacts using changes in plankton functional composition, enabling an integrated evaluation of the ecological responses of aquatic ecosystems. Using a 19-year data set, we evaluated the functional responses of lake phytoplankton and zooplankton to water quality changes associated with mining activities in five downstream lakes of the Ekati Diamond Mine (Northwest Territories, Canada). Our results demonstrate that mining activity shifted phytoplankton functional composition toward edible diatoms and more recently the rotifer communities toward parallelepiped types, while for crustacean zooplankton we observed a reinforcement of the original functional composition.
First report of kinorhynchs from singapore, with the description of three new species

The kinorhynch fauna of Singapore, or from any locality close by, has never been explored. For the present study, samples of Kinorhyncha were collected at seven localities around Singapore. This revealed the presence of at least nine different species distributed across four genera. Two species, Echinoderes tchefouensis and Condyloderes paradoxus, are known from other localities in Asia, whereas the remaining seven species are new to science. Three of them, Centroderes impurus sp. nov., Echinoderes annae sp. nov., and Leiocanthus nagini sp. nov., are described, whereas materials representing the remaining, potentially new, species were too limited to allow complete descriptions.
Method Optimization for Synthesis of Trisubstitued Quinazoline Derivatives

A series of new 4-anilinoquinazoline derivatives (IV-XVI) were synthesized in convenient pathway with desirable yields. 4-Aminoquinazoline derivatives corresponding Erlotinib are more active compounds for inhibition of the epidermal growth factor receptor (EGFR) which are used as anticancer agents. Although these categories of compounds have widespread clinical use, most of the reported syntheses protocol for them require multistep and low-yielding reaction pathways. Here we tried a new method with only 3 or 4 steps to prepare 4-anilinoquinazoline derivatives. We synthesized our new compounds in two parts (part I with 3 steps and part II with 4 steps). In the first step of part I, we used ortho-diflouro or ortho-dimethoxy anthranilic acid to get the quinazoline ring with a carbonyl group at its 4 position. Then, in the second and third steps of this part, we replaced the carbonyl group of quinazoline ring by chlorine and amine group respectively (IV-X). In part II, we used dichloro anthranilic acid to get the quinazoline ring with a carbonyl group at its 4 position. In these cases, after synthesis of the quinazoline ring we could etherify it via its substitutions on the starting anthranilic acid (XI-XVI), in order to mimic the erlotinib structure as a tyrosine kinase inhibitor. The next steps of this part (replacing the carbonyl group by chlorine and then by amine) were the same as part I. Our new compounds contain different substitutions at orto (6,7) or meta (5,7) positions of the quinazoline ring.
Resting State Functional Connectivity MRI in the Rodent Brain: Applications to Human Disease

1 Chapter 1: Introduction . 4 Section 1: Bridging the gap between human and animal models using functional connectivity across species . 4 Section 2: Using resting state functional connectivity in rodents . 8 Section 3. Goals of project 1 (validation) and project 2 (applications). 14 Chapter 2: Project 1. Correlated gene expression and anatomical communication support synchronized brain activity in the mouse functional connectome . 18 Introduction . 18 Materials and Methods . 20 Results . 35 Discussion. 48 Supplementary Materials . 54 Chapter 3: Project 2. Chronic gestational inflammation through interleukin-6 (IL-6) inflicts persistent changes in behavior and functional connectivity network topology in rodent offspring . 58 Introduction . 58 Materials and Methods . 61 Results . 73 Discussion. 82 Supplementary Materials . 94 iii Chapter 4: Discussion and Future Directions . 103 Section 1: Validation and biological influences on FC. 103 Section 2: Applying validated techniques to a preclinical models . 106 Section 3: Directly comparing between human and animal models . 110 References . 124
System Biology Modeling with Compositional Microbiome Data Reveals Personalized Gut Microbial Dynamics and Keystone Species

A growing body of literature points to the important roles that different microbial communities play in diverse natural environments and the human body. The dynamics of these communities is driven by a range of microbial interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood, making it hard to predict the response of the community to different perturbations. With the increasing availability of high-throughput sequencing based community composition data, it is now conceivable to directly learn models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is however affected by several experimental limitations, particularly the compositional nature of sequencing data. We present a new computational approach (BEEM) that addresses this key limitation in the inference of generalised Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference in an expectation maximization like algorithm (BEEM). Surprisingly, BEEM outperforms state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM’s application to previously inaccessible public datasets (due to the lack of biomass data) allowed us for the first time to analyse microbial communities in the human gut on a per individual basis, revealing personalised dynamics and keystone species.
A nesting record and vocalisations of the Night Parrot Pezoporus occidentalis from the East Murchison, Western Australia

The Night Parrot Pezoporus occidentalis is a poorly known, nationally endangered species that historically occurred throughout semi-arid and arid Australia, including Western Australia where the type specimen was collected during the 19th century. Despite recent sightings in Western Australia, no evidence has been provided to definitively prove the existence of an extant population in the state. In March 2017, we discovered living Night Parrots in the East Murchison biogeographic subregion of Western Australia, and documented an active nest, associated calling behaviour including previously undescribed duets, and roosting habitat of a pair of this species at the site.
Relevance of brands and beef quality differentials for the consumer at the time of purchase

ABSTRACT The objective of this study was to identify the purchase habits and preferences of beef consumers, their level of knowledge on brands and products with quality differentials (certifications, packaging, premium lines), and the relevance of different attributes in the purchase decision, and to group consumers according to the profile of purchase decision. The methodology consisted of using an information-collecting instrument applied to 271 beef consumers. The data collected were analyzed using descriptive statistical analyses, chi-square analysis, and correspondence analysis, [. ]
Evaluation of the IgE reactivity of common pandora parvalbumin in a Moroccan population and action of heating and enzymatic treatments

ABSTRACT The aim of this study was to evaluate the immunoglobulin E (IgE) sensitivity to common pandora (Pagellus erythrinus) parvalbumin (CPP) in a Moroccan population from the Fez region, and then to study the effect of temperature and enzymatic digestion on the allergenicity of CPP. This work was conducted with a questionnaire completed by a sera-bank, obtained from 500 patients recruited from Fez hospitals. Their sera were analyzed for specific IgE against CPP. Evaluation of specific IgE showed that 11.8% of patients present higher values (>150 IU/ml). Further indirect ELISA and dot-blot results indicated that CPP showed a decrease in the binding of anti-IgE under heating with an average diminution of 41.9%, while pepsin hydrolysis reduced IgE recognition by 22.9%. These results demonstrate that this population was sensitive to CPP and the sensitivity could be reduced by heating and pepsin hydrolysis with an action higher with temperature than enzymatic digestion processing.
Post-fledging habitat use in the Dickcissel

ABSTRACT Effective habitat management requires understanding habitat needs across a species' life history stages. In songbirds, management of breeding habitat is generally focused on the pre-nesting and nesting stages, while habitat use during the critical post-fledging stage remains understudied and is seldom a target for management. In 2014 and 2015, we documented post-fledging habitat use of Dickcissels (Spiza americana) in central Illinois, USA. We examined vegetation characteristics used by fledglings and how fledgling survival varied with habitat use. We also compared fledgling habitat use to nesting site habitat. Fledgling Dickcissels used areas with vegetation that was overall denser and more concealed than at random locations. Fledglings preferentially selected dense vegetation after fledging (days 1–3 post-fledging), and then used even denser vegetation once they became more mobile (days 4–11 post-fledging). Fledglings that used comparatively denser habitat were more likely to survive the critical part of the post-fledgling period (days 0–3 post-fledging), but not during subsequent parts of the post-fledging period (>3 days post-fledging). Habitat characteristics preferred by fledglings did not differ from those preferred by females for nest sites. Our results suggest that dense vegetation is needed for fledglings until they develop adequate mobility to evade predators. Furthermore, our finding of a positive association between fledgling survival and denser habitat during, but not after, the critical part (days 0–3) of the post-fledging period identifies an important window for management to increase fledgling survival. Management for dense habitat, however, must be appropriately timed not to disturb adults, nests, and young, immobile fledglings.