Miracle-dz/UniFAR-FTUs huggingface dataset:
Diet, Gastric Parasitism, and Injuries of Caimans (Caiman, Melanosuchus, and Paleosuchus) in the Peruvian Amazon

Abstract. Caimans (Crocodilia: Alligatoridae) are top-level predators in aquatic ecosystems of the Neotropics. This paper presents data on the diet of caimans from the Peruvian Amazon (principally Paleosuchus spp., but also Caiman crocodilus and Melanosuchus niger), including feeding observations and stomach content examinations. A total of 58 stomach content analyses and three in situ feeding observations were made, and incidence of gastric parasitism and external injury were also studied. Insects, crustaceans, and fish were the most frequently encountered prey in the gut of P. trigonatus, but reptiles, fish, crustaceans, and mammals composed the greatest proportion of the diet by stomach content dry mass. We report novel squamate and fish species in the diet of Amazonian caimans and overall dietary findings consistent with that of other caiman diet literature. Gastroliths were absent from C. crocodilus and M. niger, although 44% of P. trigonatus sampled contained gastroliths. Parasitic nematodes were recovered from just under half of sampled C. crocodilus and P. trigonatus and 71% of M. niger. Injury rates were low in M. niger and P. trigonatus (< 10% of individuals) while 35% of C. crocodilus were injured, most often through damage to the tail. These data on caiman diet, gut parasitism, and injury rates help provide a baseline for comparison between species and study populations.
Molecular analysis of northern red oak (Quercus rubra) populations from the Greater Sudbury Region: genetic variation and gene expression

The main objectives of the present study were to 1) analyze genetic variability of Q. rubra populations from the mining region of Sudbury (Ontario) using RAPD marker system and 2) analyze the expression of nickel and copper resistance genes in Q. rubra populations. The level of polymorphic loci within populations was high ranging from 61 % to 72% despite a high level of gene flow (2.4) and the population differentiation (GST) value was low (0.17). All Q. rubra populations analyzed were genetically sustainable. Moreover, this study revealed that all populations were genetically closely related with genetic distance values varying from 0.17 to 0.35. A zinc finger protein of Arabidopsis thaliana (ZAT11) involved in nickel resistance was differentially expressed in samples analyzed. There was a 120x up-regulation of ZAT11 expression in samples from metal contaminated areas of Wahnapitae Dam compared to other sites. No association between soil metal levels and expression of ZAT11 was established.
An Isolated and Expanding Population of the Introduced Toad Bufo marinus in New South Wales

The distribution of Bufo marinus in north-eastern New South Wales (Australia) was surveyed in 1975 and 1978. Hitherto it had been assumed that the toads in New South Wales were derived from a southward migration from Queensland, but the populations proved to be disjunct, being separated by 25km of coastal seaboard. Estimated times of first sightings suggest the the toads have been dispersing at least 12y from an initial introduction near Byron Bay. The mean rate of spread from Byron Bay is 1.07 km y-1. The maximum rate, 3km y-1, is attained across flat or gently undulating rural areas. As there are no major climatological or geographic disjunctions at the present boundaries, the Queensland and New South Wales populations are likely to meet within 4-12 y, and further dispersal southwards appears certain.
Study on larvicidal activity of crude extracts of Ruta graveolens against Aedes aegypti and Anopheles stephensi

The present study was conducted to identify the larvicidal activity of Ruta graveolens against larval cultures of Anopheles stephensi and Aedes aegypti. The larvicidal bioassay of each plant extract was conducted. The % of mortality was calculated. The petroleum ether extract showed maximum larvicidal activity against both the larvae when compared to the hexane and methanol extract. The petroleum ether extract was then subjected to TLC using the solvent system petroleum ether: chloroform: acetone at 0.5: 1.5: 0.5 ratios. The larvicidal activity of the pure compound was checked and the % mortality of different fractions was calculated. It was observed that the fraction 1 showed 100% mortality against An. stephensi and 80% mortality against Ae. aegypti and toxicity was not observed for the cream prepared for fraction 1. The functional groups were analyzed using FTIR analysis.
Genetic basis of transgressive segregation in rice heading phenotypes

Transgressive segregation produces hybrid progeny phenotypes that exceed parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice. Our previous study examined days to flowering (heading; DTH) in six F2 populations for which the parents had distal DTH, and found very few transgressive phenotypes. Here, we demonstrate that transgressive segregation in F2 populations occurred between parents with proximal DTH. DTH phenotypes of the A58 × Kitaake F2 progenies frequently exceeded those of both parents. Both A58 and Kitaake are japonica rice cultivars adapted to Hokkaido, Japan, which is a high-latitude region, and have short DTH. Among the four known loci required for short DTH, three loci had common alleles in A58 and Kitaake, and only the one locus had different alleles. This result indicates that there is a similar genetic basis for DTH between the two varieties. We identified five new quantitative trait loci (QTLs) associated with transgressive DTH phenotypes by genome-wide single nucleotide polymorphism (SNP) analysis. Each of these QTLs showed different degrees of additive effects on DTH, and two QTLs had epistatic effect on each other. These results demonstrated that genome-wide SNP analysis facilitated detection of genetic loci associated with the extreme phenotypes and revealed that the transgressive phenotypes were produced by exchanging complementary alleles of a few minor QTLs in the similar parental genotypes.
Molecular Epidemiology of Helicobacter pylori in Dental Plaque among Jordanians; A Probable Source for Infection and Treatment Failure

The human pathogen Helicobacter pylori infects around 50% of the global population. Significant proportion of infected individuals with H. pylori can undergo gastritis or gastric adenocarcinoma. The major source and reservoir of infection and transmission with H. pylori is not fully understood, yet. Oral cavity has been proposed to be a reservoir for H. pylori and possibly a major source of gastric reinfection; however, the results are still controversial. In this study a total of sixty Jordanian individuals were tested for the presence of H. pylori in their dental plaques. Samples were analyzed by PCR to detect for the presence of H. pylori using specific primers for H. pylori 16s ribosomal RNA gene. Our data show that all individuals tested in this study were found positive for H. pylori. Although, individuals tested in this study were heterogeneous in term of age, sex, education, and geographical region but this did not influence the presence ofH. pylori in the dental plaque of Jordanians. The results of the present study suggest that the oral reinfection route of transmission of H. pylori should be taken into consideration because it may explain the high prevalence of H. pylori associated gastritis in Jordanian people.
A synthesis of tree functional traits related to drought-induced mortality in forests across climatic zones

1. Forest dieback caused by drought-induced tree mortality has been observed world-wide. Forecasting which trees in which locations are vulnerable to drought-induced mortality is important to predict the consequences of drought on forest structure, biodiversity and ecosystem function. 2. In this paper, our central aim was to compile a synthesis of tree traits and associated abiotic variables that can be used to predict drought-induced mortality. We reviewed the literature that specifically links drought mortality to functional traits and site conditions (i.e. edaphic variables and biotic conditions), targeting studies that show clear use of tree traits in drought analysis. We separated the review into five climatic zones to determine global vs. regionally restricted relationships between traits and mortality. 3. Our synthesis identifies a number of traits that have clear relationships with drought-induced mortality (e.g. wood density at the species level and tree size and growth at the individual level). However, the lack of direct relationships between most traits and drought-induced mortality highlights areas where future research should focus to broaden our understanding. 5. Synthesis and applications. Our synthesis highlights established relationships between traits and drought-induced mortality, presents knowledge gaps for future research focus and suggests monitoring and research avenues for improving our understanding of drought-induced mortality. It is intended to assist ecologists and natural resource managers choose appropriate and measurable parameters for predicting local and regional scale tree mortality risk in different climatic zones within constraints of time and funding availability.
Phase-Amplitude Coupling of Neural Oscillations Can Be Effectively Probed with Concurrent TMS-EEG

Despite the widespread use of transcranial magnetic stimulation (TMS), knowledge of its neurophysiological mode of action is still incomplete. Recently, TMS has been proposed to synchronise neural oscillators, and to thereby increase the detectability of corresponding oscillations at the population level. As oscillations in the human brain are known to interact within nested hierarchies via phase-amplitude coupling, TMS might also be able to increase the macroscopic detectability of such coupling. In a concurrent TMS-electroencephalography study, we therefore examined the technique’s influence on theta-gamma, alpha-gamma and beta-gamma phase-amplitude coupling by delivering single-pulse TMS (sTMS) and repetitive TMS (rTMS) over the left motor cortex and right visual cortex of healthy participants. The rTMS pulse trains were of 5 Hz, 11 Hz and 23 Hz for the three coupling variations, respectively. Relative to sham stimulation, all conditions showed transient but significant increases in phase-amplitude coupling at the stimulation site. In addition, we observed enhanced coupling over various other cortical sites, with a more extensive propagation during rTMS than during sTMS. By indicating that scalp-recorded phase-amplitude coupling can be effectively probed with TMS, these findings open the door to the technique’s application in manipulative dissections of such coupling during human cognition and behaviour.
β3 Integrin siRNA-Loaded Multifunctional Nanoparticle Therapy for Metastatic Breast Cancer

While RNA interference (RNAi) holds promise as a novel therapeutic modality for cancer, a number of extracellular and intracellular obstacles have revealed the need for safe and effective siRNA delivery systems in order to translate these RNAi-based technologies into the clinic. We have recently developed a multifunctional cationic lipid-based carrier, ECO, which can efficiently deliver siRNA and induce RNAi in both non-cancerous and cancer cell lines. ECO forms stable nanoparticles with siRNA that protect the payload against degradation, promote endosomal escape following cellular internalization, and facilitate cytosolic siRNA release via a glutathionedependent mechanism. In breast cancer, β3 integrin has been implicated as a key player in the acquisition of a metastatic phenotype through TGF-β-mediated epithelialmesenchymal transition (EMT). Inactivation of β3 integrin has been shown to disrupt the oncogenic properties of TGFβ and as such, ECO nanoparticles delivering β3 integrin siRNA (ECO/siβ3) may prove effective in the prevention and treatment of metastatic breast cancer. In NME cells stimulated with TGF-β, ECO/siβ3 nanoparticles induced sustained β3 integrin silencing up to 7 days posttransfection. Depletion of β3 integrin consequently reduced the acquired mesenchymal markers, such as N-cadherin, while restoring epithelial markers, namely E-cadherin. Delivery of siβ3 concurrently with EMT induction suppressed TGF-β-mediated stress fiber formation, a hallmark event of the transformation process. Cells grown in a 3D organotypic culture revealed that treatment with ECO/siβ3 nanoparticles over a 10 day period significantly inhibited growth in comparison to a control group. This observation was further supplemented by a decrease in invasiveness and proliferation. Together, the in vitro results suggest that ECO/siβ3 nanoparticles are a promising therapeutic strategy to combat metastatic breast cancer.
The Copper Amine Oxidase AtCuAOδ Participates in Abscisic Acid-Induced Stomatal Closure in Arabidopsis

Plant copper amine oxidases (CuAOs) are involved in wound healing, defense against pathogens, methyl-jasmonate-induced protoxylem differentiation, and abscisic acid (ABA)-induced stomatal closure. In the present study, we investigated the role of the Arabidopsis thaliana CuAOδ (AtCuAOδ; At4g12290) in the ABA-mediated stomatal closure by genetic and pharmacological approaches. Obtained data show that AtCuAOδ is up-regulated by ABA and that two Atcuaoδ T-DNA insertional mutants are less responsive to this hormone, showing reduced ABA-mediated stomatal closure and H2O2 accumulation in guard cells as compared to the wild-type (WT) plants. Furthermore, CuAO inhibitors, as well as the hydrogen peroxide (H2O2) scavenger N,N1-dimethylthiourea, reversed most of the ABA-induced stomatal closure in WT plants. Consistently, AtCuAOδ over-expressing transgenic plants display a constitutively increased stomatal closure and increased H2O2 production compared to WT plants. Our data suggest that AtCuAOδ is involved in the H2O2 production related to ABA-induced stomatal closure.
Characterization and genetic diversity of cowpea (Vigna unguiculata L.) genotypes linked to Cowpea yellow mosaic virus

The present research was carried out to investigate the genetic diversity among cowpea tolerant and susseptibe genotypes. For which the fifteen cowpea genotypes were manually infected with Cowpea yellow mosaic virus(CYMV) inoculum and to detect virus by a serological technique. The five most tolerant and sensitive each genotypes had been taken for genetic diversity study in which JCPL-2 and JCPL-11 was found most susceptible and tolerant genotype, having absorbance at 405nm 2.172 and 0.167 respectively. The RAPD, ISSR and SSR marker system were applied to the ten cowpea genotypes. For the RAPD data, based on PIC value, it can be said that primer OPAI-15 was the best primer resulting good amplification with maximum PIC value (0.764). Dendrogram constructed using the RAPD data clearly distinguished all genotypes. It revealed that JCPL-44 and JCPL-45 found in one cluster and shared maximum 96.00% similarity; however, genotype JCPL-2 have out grouped from other 9 genotypes and shared minimum 41.00% similarity. In case of ISSR data, based on PIC value it can be said that the primer 835 was the best primer resulting good amplification with maximum PIC value (0.837). Jaccard’s similarity coefficient ranged from 0.625 and 0.906. The ISSR results indicated that maximum similarity 90.60% was found between JCPL-2 and JCPL-18, while minimum similarity 62.50% was obtained between JCPL-2 and JCP- 87. For the SSR data, based on PIC value it can be said that the primer VM-13 was the best primer resulting good amplification with maximum PIC value (0.668). Jaccard’s similarity coefficient ranged from 0.500to 1.000. So SSR data revealed that JCPL-2 showed maximum variability compared to other nine genotypes. The combined RAPD, ISSR and SSR analysis revealed that out of ten genotypes JCPL-44 and JCPL-45 were showed maximum (91.0%) similarity. The lowest similarity of 58.30% was found between JCPL-2 and JCP-45.
Lateral root priming synergystically arises from root growth and auxin transport dynamics

The root system is a major determinant of plant fitness. Its capacity to supply the plant with sufficient water and nutrients strongly depends on root system architecture, which arises from the repeated branching off of lateral roots. A critical first step in lateral root formation is priming, which prepatterns sites competent of forming a lateral root. Priming is characterized by temporal oscillations in auxin, auxin signalling and gene expression in the root meristem, which through growth become transformed into a spatially repetitive pattern of competent sites. Previous studies have demonstrated the importance of auxin synthesis, transport and perception for the amplitude of these oscillations and their chances of producing an actual competent site. Additionally, repeated lateral root cap apoptosis was demonstrated to be strongly correlated with repetitive lateral root priming. Intriguingly, no single mutation has been identified that fully abolishes lateral root formation, and thusfar the mechanism underlying oscillations has remained unknown. In this study, we investigated the impact of auxin reflux loop properties combined with root growth dynamics on priming, using a computational approach. To this end we developed a novel multi-scale root model incorporating a realistic root tip architecture and reflux loop properties as well as root growth dynamics. Excitingly, in this model, repetitive auxin elevations automatically emerge. First, we show that root tip architecture and reflux loop properties result in an auxin loading zone at the start of the elongation zone, with preferential auxin loading in narrow vasculature cells. Second, we demonstrate how meristematic root growth dynamics causes regular alternations in the sizes of cells arriving at the elongation zone, which subsequently become amplified during cell expansion. These cell size differences translate into differences in cellular auxin loading potential. Combined, these properties result in temporal and spatial fluctuations in auxin levels in vasculature and pericycle cells. Our model predicts that temporal priming frequency predominantly depends on cell cycle duration, while cell cycle duration together with meristem size control lateral root spacing.
The gene task1 is involved in morphological development, mycoparasitism and antibiosis of Trichoderma asperellum

ABSTRACT Competitive activity, mycoparasitism and antibiosis of Trichoderma asperellum are considered essential mechanisms in its suppressive activity against soil-borne plant pathogens. The role of the mitogen-activated protein kinase encoding gene task1 on morphological development, mycoparasitic interaction and the production of cell wall degrading enzymes and secondary metabolites were examined in T. asperellum. The Δtask1 mutant had altered growth morphology, lost its ability to parasitise plant pathogens and showed increased expression of several cell wall degrading enzymes during confrontation with Rhizoctonia solani. T. asperellum task1 expression was negatively correlated with cell wall degrading enzyme activities during inducing experiments using pathogen cell wall compounds. In antibiosis assays, task1 deletion caused increased output of 6-pentyl-α-pyrone and inhibition of pathogen growth.
Antioxidant and antimicrobial activities of various Stachy sieboldii MIQ extracts for application in meat product

In order to analyze bioactive functionalities for application in meat product depending on different parts of leaf, stem and tuber in Stachy sieboldii MIQ (SSM) and extraction solvents, we investigated the antioxidant and antibacterial activities of the various SSM extracts. The leaf methanol and ethanol extracts from SSM maintained more polyphenol and flavonoid contents as well as higher antioxidant activities than those of the stem and tuber extracts. DPPH, ABTS • + and nitrite radical scavenging activities from the methanol extracts maintained a higher or similar value compared with the ethanol extracts. DPPH, ABTS • + and FRAP radical scavenging activities were proportional to total polyphenol and flavonoid contents in the various SSM extracts, whereas nitrite radical scavenging activity was partially related to these materials, which the methanol extracts were observed by the coincident activity with their materials, but the ethanol extracts were not depending on their materials. The SSM leaf and tuber methanol extracts or the tuber ethanol extract were showed by strong antibacterial activities against S. typhimurium. In addition, the SSM leaf methanol extract was showed by strong antibacterial activity against S. aureus. It is assumed that the antioxidant and antibacterial activities of SSM are related to total polyphenol and flavonoid contents extracted by methanol and ethanol. Therefore, we suggest that the SSM extracts have a high possibility for application as a bioac- tive material in meat product.
Integrating islands of knowledge for greater synergy and efficiency in crop research

A transnational approach to plant science is required to address global challenges such as food security and climate change. Action from the plant, crop and agricultural science communities will be required to meet these challenges. Islands of knowledge (e.g. crop, discipline, scale, environment, organization) need to be better integrated. Mapping is needed to identify gaps and make connections between these islands. Translational research, spanning from the molecular to farm scale, should be the focus. We need more integrators' to manage complex global projects and integration should be recognized as an important skill in itself. We need to advocate teamwork over individuality - and reward teams. Impact should be taken much more seriously as an outcome and we need to better understand impact pathways. Focusing on key game-changers will more likely lead to impact rather than attempting to do everything. Building bridges between islands of knowledge should enhance the impact of global research addressing food security (background image from www.world.time.com).
The Development and Evolution of Iridescent Colors in Birds

A key question in evolutionary biology is the origin and evolution of morphological innovations. Iridescent colors in feathers are produced by the interaction of light refracting through nanostructurally organized arrays of keratin and melanin-containing organelles (melanosomes), and are responsible for the brightest and most diverse colors found in birds. Such diversity arises from minute changes to nanostructural components, and birds have evolved extensive modifications to the shape and composition (hollowness) of melanosomes, providing a labile template for selection to act. Further, feather colors play a crucial role in intraspecific communication, sexual and social selection, and prezygotic isolation. Thus, this system is ideal for examining how complex morphologies arise ontogenetically and how they affect color diversification. I explored how this nanostructural arrangement emerges developmentally, showing that organization takes place in the final stages of feather growth, potentially through self-assembly. This implies that the fine-tuning color-producing structures can result from changes in the relative concentrations of different components and the timing of feather maturation. Further, quantitative variation to the degree of long-range order is responsible for variation in the degree of glossiness. Gloss was negatively associated with the thickness of the keratin layer, and positively with the continuity of the underlying melanosome layer. As a consequence, a continuum from matte black to irides-