Miracle-dz/UniFAR-FTUs huggingface dataset:
Micropropagation of Banana: Reversion, Rooting, and Acclimatization of Hyperhydric Shoots

Hyperhydricity is a physiological disorder impacting plant growth and multiplication and acclimatization of regenerated plantlets. We report the use of calcium nitrate for reversion and acclimatization of banana ‘Grand Naine’ hyperhydric shoots cultured on Murashige and Skoog medium containing agar or gellan. Although 100% rooting of hyperhydric shoots occurred at all concentrations of calcium nitrate, only 50% rooting was recorded in the absence of calcium nitrate. Electrolyte leakage decreased significantly in the reverted banana tissues compared with the hyperhydric tissues. Histochemical staining for reactive oxygen species indicated that reverted banana tissues possess lower levels of both hydrogen peroxide (H2O2) and superoxide (O2-) than do hyperhydric tissues. Rooting, growth, and survival of the reverted banana plantlets were significantly influenced by calcium nitrate concentrations as well as the type of gelling agent. Reverted banana plantlets in medium containing calcium nitrate (0.5–1 g·L−1) were acclimatized with 100% survival in a growing substrate of peatmoss and vermiculite (1:1).
Physiological and Psychological Effects of Viewing Forests on Young Women

Research Highlights: This study demonstrated that viewing forest landscapes induced physical and mental health benefits on young women. Background and Objectives: The health-promoting effects of spending time in forests have received increasing attention; however, there is a lack of evidence-based research investigating the effects of spending time in forests on women. This study aimed to evaluate the physiological and psychological effects of viewing forest landscapes on young women. Materials and Methods: The experiments were conducted in six forests and six city areas and included 65 women (mean age, 21.0 ± 1.3 years). Participants viewed a forest and a city area for 15 min, during which their heart rate variability and heart rate were measured continuously. Blood pressure and pulse rate were measured before and after the viewing. After the viewing, participants’ psychological responses were assessed using the modified semantic differential method, Profile of Mood States (POMS), and the State–Trait Anxiety Inventory (STAI). Results: Compared with viewing city areas, viewing forest landscapes was associated with significantly higher parasympathetic nervous activity and lower sympathetic nervous activity and heart rate. Moreover, scores of the comfortable, relaxed, and natural parameters and vigor subscales of POMS were significantly higher with forest viewing. The scores of negative feelings, such as tension–anxiety, depression–dejection, anger–hostility, fatigue, and confusion, were significantly lower, as were scores for the total mood disturbance observed using POMS and the anxiety dimension observed using STAI. Conclusions: Viewing forest landscapes resulted in physiological and psychological relaxations in young women.
Genetic Gains in Wheat Breeding and Its Role in Feeding the World

Wheat is the leading global food crop providing 19% of the daily calories and 21% of protein requirements for humans. The wheat production has increased from 220 million tons in 1961 to 750 million tons in 2018 with total production area of 220 million hectares which showed insignificant changes across years. The development of high yielding and widely adapted semi-dwarf input responsive wheat varieties, application of fertilizer, pesticides, irrigation, mechanization and implementation of favorable policies have contributed to such significant jump in wheat production at global level. The average annual genetic gain of wheat has been reported to be 1% while the demand for wheat increases by 1.7% annually reaching a total of 1 billion tons in 2050. To this end, conventional and molecular breeding strategies and approaches such as inter-country shuttle breeding, doubled haploid breeding, speed breeding, marker assisted selection, genomic selection, key location phenotyping and hybrid wheat breeding should be utilized intensively. The international wheat breeding programs at CIMMYT and ICARDA have developed and distributed germplasm to the world in the past 4 or more decades during which hundreds of high yielding and widely adapted wheat varieties with resistance tolerance to the major prevailing abiotic and biotic stresses have been released and adopted. Breeding progress or genetic gains in wheat has been determined by different authors with average relative gains reaching up to 2.5% per year. This paper reviews the global challenges facing demand and supply of wheat, the strategies to increase breeding efficiency and genetic gains, the impacts of the international wheat breeding and its progress, and future strategies to increase wheat production while conserving the natural resource base.
What can goby otolith morphology tell us

The taxonomic information inscribed in otoliths has been widely ignored in ichthyological research, especially in descriptions of new fish species. One reason for this is that otolith descriptions are per se qualitative, and only a few studies have presented quantitative data that can support assignments of otoliths to individual species or permit differentiation between higher taxonomic levels. On the other hand, in palaeontology, otoliths have been employed for the identification and taxonomic placement of fossil fish species for over 100 years. However, palaeontological otolith data is generally regarded with suspicion by ichthyologists. This is unfortunate because, in the Cenozoic, the fossil otolith record is much richer than that based on skeletons. Thus fossil otoliths are a unique source of information to advance our understanding of the origin, biogeographical history and diversification of the Teleostei. This case study deals with otoliths of the Oxudercidae, which, together with the Gobiidae, encompasses the 5-branchiostegal-rayed gobiiforms. The objective was to determine whether the five lineages of the Oxudercidae, and individual species of the European Pomatoschistus lineage, could be distinguished based on the quantification of otolith variations. The data set comprises otoliths from a total of 84 specimens belonging to 20 recent species, which represent all five lineages of the Oxudercidae (Mugilogobius, Acanthogobius, Pomatoschistus, Stenogobius, Periophthalmus), and five fossil otoliths of dagger Pomatoschistus sp. (sensu Brzobohaty, 1994). Ten measurements were taken on each otolith and 23 otolith variables were computed and used for univariate and multivariate analyses. The results indicate that otolith morphometry (i) is capable of identifying the Pomatoschistus and Periophthalmus lineages among the Oxudercidae, but is of limited use in the separation of the other three lineages;(ii) can reliably distinguish the sand gobies (a distinct Glade within the Pomatoschistus lineage) from other members of the Pomatoschistus lineage;and (iii) supports a previous assignment of fossil otoliths to dagger Pomatoschistus sp. as an ancient genus of the sand gobies. With its middle Miocene age (15 m.y. ago), dagger Pomatoschistus sp. represents the oldest record of a sand goby species to date. We discuss possible relationships between distinct otolith morphologies, biogeographic distribution and lifestyles for Pomatoschistus and the Periophthalmus lineage, and also for the sand gobies. We conclude that otolith morphology, combined with morphometry, can be considered as an autapomorphy for an individual species from the studied groups. In addition, it also appears to contain a phylogenetic signal, but more work is needed to evaluate this fully.
Cerebral Perfusion Monitoring Using Near-Infrared Spectroscopy During Head-Up Tilt Table Test in Patients With Orthostatic Intolerance

The head-up tilt table test (HUT) is one of the primary clinical examinations for evaluating orthostatic intolerance (OI). HUT can be divided into three phases: dynamic tilt phase (supine to tilt up), static tilt phase (remain tilted at 70°), and post tilt phase (tilt down back to supine position). Commonly, blood pressure (BP) and heart rate (HR) are monitored to observe for OI symptoms, but are indirect measurements of cerebral perfusion and can lead to inaccurate HUT evaluation. In this study, we implemented a 108-channel near-infrared spectroscopy (NIRS) probe to characterize HUT performance by monitoring cerebral hemodynamic changes for healthy controls (HCs), OI patients with normal HUT results, and OI patients with positive HUT results: vasovagal syncope (VS), postural orthostatic tachycardia syndrome (POTS), orthostatic hypotension (OH), and orthostatic hypertension (OHT). By the end of the static tilt phase, OI patients typically did not show a complete recovery back to baseline cerebral oxygenation and total blood volume compared to HCs. We characterized the return to cerebral homeostasis by polynomial fitting total blood volume changes and determining the inflection point. The OI patients with normal HUT results, VS, OH, or OHT showed a delay in the return to cerebral homeostasis compared to the HC group during HUT.
Ligand nanovectorization using graphene to target cellular death receptors of cancer cell

Tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL) is nowadays envisaged as a natural cytokine useful in nanomedicine to eradicate the cancer cells and not the healthy surrounding ones. However, it suffers from cell resistance and strong dispersion in body to prove its efficiency. The understanding at the molecular level of the TRAIL interaction with death receptors (DRs) on cancer cells is thus of fundamental importance to improve its action. We demonstrate here via molecular simulations that TRAIL can bind to its both agonistic DRs (ie, DR4 and DR5) with a preference for DR4. In this study, the role of a graphene nanoflake as a potential cargo for TRAIL is examined. Furthermore, both TRAIL self‐assembling and TRAIL affinity when adsorbed on graphene are considered to enhance efficacy toward the targeted cancer cell. Our modelization results show that TRAIL can bind to DR4 and DR5 when transported by graphene nanoflake, as a proof of concept.
Effect of Ulva reticulata Extract in Increasing Hemocyte Count and Phagocytosis Activity in Tiger Shrimp (Penaeus monodon)

Tiger shrimp is one of Indonesia's foreign export commodities. Tiger shrimp has decreased production due to various diseases. Ulva reticulata seaweed is known to have polysaccharide sulfate and secondary metabolites that can enhance immunity in shrimp. This study was conducted to analyze the potential of Ulva reticulata extract in increasing the immune response in tiger shrimp. The study design used a Completely Randomized Design (CRD) with 4 treatments with 3 replications. As a treatment, mixing Ulva reticulata extract on commercial feed with a dose of 0, 0.5, 1.0 and 1.5 g kg-1 feed for 14 days. The observation parameters consisted of hemocyte counts and phagocytic activity. The results showed the highest hemocytes and the highest phagocytic activity was shown in the treatment of 1.5 g kg-1 with total hemocytes of 3.0 x 105 cells/ml and the percentage of phagocytic activity was 77%.
A Toxicological Evaluation of Mango Leaf Extract (Mangifera indica) Containing 60% Mangiferin

A battery of OECD- and GLP-compliant toxicological studies was performed on mango leaf extract (Mangifera indica) containing 60% mangiferin (MLE). No evidence of genotoxicity was found in a bacterial reverse mutation test (Ames). While evidence of clastogenic activity was noted in an in vitro chromosomal aberration test, an in vivo mammalian micronucleus test showed no findings up to the limit dose (2000 mg/kg bw). A 90-day repeated dose oral toxicity study was conducted in rats using doses of 0 (vehicle control), 500, 1000, and 2000 mg/kg bw/day. Based on the lack of mortality or toxic effects in the 90-day study, the NOAEL for MLE in Han:Wist male and female rats was determined to be 2000 mg/kg bw/day, the highest dose tested.
Multiclass Disease Classification from Microbial Whole-Community Metagenomes

There is a wealth of information contained within one’s microbiome regarding their physiology and environment, and this is a promising avenue for developing non-invasive diagnostic tools. Here, we utilize 5643 aggregated, annotated whole-community metagenomes from 19 different diseases to implement the first multiclass microbiome disease classifier of this scale. We compared three different machine learning models: random forests, deep neural nets, and a novel graph convolutional architecture which exploits the graph structure of phylogenetic trees as its input. We show that the graph convolutional model outperforms deep neural nets in terms of accuracy (achieving 75% average test-set accuracy), receiver-operator-characteristics (92.1% average AUC), and precision-recall (50% average AUPR). Additionally, the convolutional net’s performance complements that of the random forest, achieving similar accuracy but better receiver-operator-characteristics and lower area under precision-recall. Lastly, we are able to achieve over 90% average top-3 accuracy across all of our models. Together, these results indicate that there are predictive, disease specific signatures across microbiomes which could potentially be used for diagnostic purposes.
Environmental niche adaptation revealed through fine scale phenological niche modelling

Phenology, the temporal response of a population to its climate, is a crucial behavioural trait shared across life on earth. How species adapt their phenologies to climate change is poorly understood but critical in understanding how species will respond to future change. We use a group of flies (Rhaphiomidas) endemic to the North American deserts to understand how species adapt to changing climatic conditions. Here, we explore a novel approach for taxa with constrained phenologies aimed to accurately model their environmental niche and relate this to phenological and morphological adaptations in a phylogenetic context.
Poly(lactic-co-glycolic acid) nanoparticle-mediated interleukin-12 delivery for the treatment of diabetic retinopathy

Background Diabetic retinopathy (DR) is a complication of diabetes that affects the eyes and vision. It is a leading cause of visual impairment and blindness in working-age people. Vascular endothelial growth factor-A (VEGF-A) is a primary initiator and potential mediator of DR. Matrix metalloproteinase-9 (MMP-9) plays a progressive role in the onset and severity of DR. Interleukin-12 (IL-12) is a cytokine of the chemokine family that could reduce the levels of MMP-9 and VEGF-A and suppress tumor angiogenesis. We hypothesize that IL-12 may also have superior therapeutic efficacy against DR. However, protein drugs are prone to degradation by various proteases after drug injection. Therefore, they have short half-lives and low blood concentrations. The objective of this study was to develop IL-12-loaded nanoparticles for long-term and sustained DR treatment. Methods IL-12-loaded poly(lactic-co-glycolic acid) (PLGA) nanoparticles (IL-12-PNP) were developed by double emulsion. The characteristics, anti-DR activity, and mechanisms of IL-12-PNP were examined in vitro and in vivo. Results The nanoparticles had suitable particle size (~132.8 nm), drug encapsulation efficiency (~34.7%), and sustained drug release profile. Compared with IL-12 and blank nanoparticles, IL-12-PNP showed better inhibitory efficacy against VEGF-A and MMP-9 expression in rat endothelial cells and DR mouse retina. Intraocular IL-12-PNP administration significantly reduced retinal damage in DR mice as they presented with increased thickness and decreased neovascularization after treatment. Conclusion These data indicate that IL-12-PNP is an effective drug delivery platform for DR therapy. It restores the thickness and reduces neovascularization of the retinas of DR mice.
The role of atoh1 genes in the development of the lower rhombic lip during zebrafish hindbrain morphogenesis

BACKGROUND The Lower Rhombic Lip (LRL) is a transient neuroepithelial structure of the dorsal hindbrain, which expands from r2 to r7, and gives rise to deep nuclei of the brainstem, such as the vestibular and auditory nuclei and most posteriorly the precerebellar nuclei. Although there is information about the contribution of specific proneural-progenitor populations to specific deep nuclei, and the distinct rhombomeric contribution, little is known about how progenitor cells from the LRL behave during neurogenesis and how their transition into differentiation is regulated. RESULTS In this work, we investigated the atoh1 gene regulatory network operating in the specification of LRL cells, and the kinetics of cell proliferation and behavior of atoh1a-derivatives by using complementary strategies in the zebrafish embryo. We unveiled that atoh1a is necessary and sufficient for specification of LRL cells by activating atoh1b, which worked as a differentiation gene to transition progenitor cells towards neuron differentiation in a Notch-dependent manner. This cell state transition involved the release of atoh1a-derivatives from the LRL: atoh1a progenitors contributed first to atoh1b cells, which are committed non-proliferative precursors, and to the lhx2b-neuronal lineage as demonstrated by cell fate studies and functional analyses. Using in vivo cell lineage approaches we showed that the proliferative cell capacity, as well as their mode of division, relied on the position of the atoh1a progenitors within the dorsoventral axis. CONCLUSIONS Our data demonstrates that the zebrafish provides an excellent model to study the in vivo behavior of distinct progenitor populations to the final neuronal differentiated pools, and to reveal the subfunctionalization of ortholog genes. Here, we unveil that atoh1a behaves as the cell fate selector gene, whereas atoh1b functions as a neuronal differentiation gene, contributing to the lhx2b neuronal population. atoh1a-progenitor cell dynamics (cell proliferation, cell differentiation, and neuronal migration) relies on their position, demonstrating the challenges that progenitor cells face in computing positional information from a dynamic two-dimensional grid in order to generate the stereotyped neuronal structures in the embryonic hindbrain.
Effect of Reproductive Status on Yield and in Vitro Maturation of Oocytes of Egyptian Sheep

The current study investigated the effect of breeding season and presence of corpora lutea (CLs) on the ovaries with, ovarian characteristics, and yield, quality and oocyte recovery rate in sheep. Also, the effect of addition of sheep serum (SS) and bovine serum albumin (BSA) to maturation medium of sheep oocytes during breeding and non-breeding season was studied. Ovaries were collected during breeding and non-breeding seasons from slaughterhouses. Ovaries were classified with or without CLs during both seasons. Oocytes were collected by slicing and their yield, category and recovery rate were determined. Only compact oocytes (COCs) were in vitro matured as affected by breeding vs. non-breeding season and addition of 10% SS vs. BSA. Results show that only ovarian weight was higher (P<0.05) in breeding than in non-breeding season and with CL-ovaries than without CLs. Ovaries were longer and thicker in breed in than in non-breeding season. CL-ovaries during breeding season showed the highest ovarian characteristics. Number of all visible follicles/ovary tended to be higher (P<0.05) in breeding than in non-breeding season and of ovaries with than without CLs (P≥0.05). Oocyte yield/ovary was greater (P<0.05) by 41.7% in breeding than in non-breeding season. Oocyte yield was insignificantly greater on ovaries with CLs than those without CLs. Oocyte recovery rate was insignificantly higher in breeding and on ovaries with CLs than in non-breeding season and on those without CLs. Number/ovary and percentage of COCs were higher, while number/ovary were lower in breeding than in non-breeding season (P<0.05). Number and percentage of all categories were higher for oocytes recovered from ovaries with than without CLs. Percentage of oocytes at M-I stage was slightly higher in non-breeding than in breeding season. Percentage of oocytes at M-II showed an opposite trend, reflecting insignificantly higher maturation rate in breeding than in nonbreeding season. Percentage of oocytes at M-I and M-II stages was insignificantly higher in BSA than in SS-medium. Oocyte maturation rate with SS than with BSA in breeding and non-breeding season. In conclusion, sheep oocytes were available to be harvested during non-breeding season from slaughtered ewes with acceptable yield, quality and the maturation rate in vitro by addition sheep serum (10%) to maturation medium.
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred only from data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes including ancestral states, paleobiogeography and diversification dynamics, the role that fossils play in inferring the tree of life itself is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Here we show paleontological data has a remarkable effect in phylogenetic inference. Fossils often have higher levels of topological influence than extant taxa, while inducing unique topological rearrangements. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses.
Willow Short-Rotation Coppice as Model System for Exploring Ecological Theory on Biodiversity–Ecosystem Function

Plantations of willow (Salix spp.) are today grown as short-rotation coppice (SRC) for the sustainable production of biomass. While developing these production systems in the past, much ecological knowledge on plant–plant, plant–environment and trophic interactions has been generated. This knowledge can contribute to the further development of biodiversity–ecosystem function (BEF) theory, which frequently lacks a sound understanding of the complex mechanisms behind the observed patterns of diversity-productivity relationships. Thus, willow SRC systems are suitable models to explore BEF theory; they are simple enough to allow the study of the complex ecological mechanisms involved and they have many similarities to grassland systems in which much of recent BEF theory development has been achieved. This paper briefly reviews the current observational and mechanistic knowledge on diversity–productivity relationships in willow SRC, as well as the most important above- and below-ground trophic interactions that are likely to affect them. If the available knowledge is integrated and combined with further experimental work targeting mechanisms behind patterns, research on willow SRC as a model offers a great opportunity for filling the gaps in the understanding what presently hampers the development of predictive BEF theory.