Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution and Ecology of Flyingfishes (Teleostei:Exocoetidae)

The flyingfishes (Teleostei: Exocoetidae) are a family of 53 epipelagic marine species distributed throughout tropical and subtropical surface waters. They form a key mid-trophic link between zooplankton and predators, and have evolved special adaptations to survive in the open ocean. However, little is known about their basic evolutionary history and ecology. Here, I apply a multidisciplinary approach to better understand the evolution and ecology of flyingfishes. I propose the first species-level phylogenetic hypothesis for the group, based on nuclear and mtDNA sequences, and show that the most speciose genus (Cheilopogon) is paraphyletic. Gliding evolved progressively from twoto four-wing strategies, and habitat preference is correlated with species range size. I also analyzed patterns of genetic diversity within the most abundant genus, Exocoetus, and found no evidence of cryptic species. Instead, I found that this genus likely consists of three genetically distinct species (in contrast to the five currently recognized) and two indistinct species that diverged very recently. Population genetic analysis of Exocoetus volitans (266 samples from 97 localities) indicates a single, circum-tropical population that is well connected; yet the Isthmus of Panama and an Equatorial barrier limit gene flow. Finally, I investigated species abundance, richness, diversity, and distributions within the eastern tropical Pacific Ocean (11,125 specimens). My results provide critical updates on species distributions and habitat preferences. Predictive modeling indicates that sea surface temperature iii is important for defining flyingfish habitat. This thesis addresses central issues concerning both evolution and ecology in the epipelagic zone, and highlights the need for better understanding remote marine regions and organisms.
Odour‐evoked [Ca2+] transients in mitral cell dendrites of frog olfactory glomeruli

We measured Ca2+ concentration, [Ca2+], transients in mitral cell distal apical dendritic tufts produced by physiological odour stimulation of the olfactory epithelium and electrical stimulation of the olfactory nerve (ON) using two‐photon scanning and conventional wide‐field microscopy of Ca2+‐Green‐1 dextran in an in vitro frog nose–brain preparation. Weak or strong ON shock‐evoked fluorescence transients always had short latency with an onset 0–10 ms after the onset of the bulb local field potential, rapidly increasing to a peak of up to 25% fractional fluorescence change (ΔF/F) in 10–30 ms, were blocked by 10 µm CNQX, decaying with a time constant of about 1 s. With stronger ON shocks that activated many receptor axons, an additional, delayed, sustained AP5‐sensitive component (peak at ≈ 0.5 s, up to 40% ΔF/F maximum) could usually be produced. Odour‐evoked [Ca2+] transients sometimes displayed a rapid onset phase that peaked within 50 ms but always had a sustained phase that peaked 0.5–1.5 s after onset, regardless of the strength of the odour or the amplitude of the response. These were considerably larger (up to 150% ΔF/F) than those evoked by ON shock. Odour‐evoked [Ca2+] transients were also distinguished from ON shock‐evoked transients by tufts in different glomeruli responding with different delays (time to onset differed by up to 1.5 s between different tufts for the same odour). Odour‐evoked [Ca2+] transients were increased by AMPA‐kainate receptor blockade, but substantially blocked by AP5. Electrical stimulation of the lateral olfactory tract (5–6 stimuli at 10 Hz) that evoked granule cell feedback inhibition, blocked 60–100% of the odour‐evoked [Ca2+] transient in tufts when delivered within about 0.5 s of the odour. LOT‐mediated inhibition was blocked by 10 µm bicuculline.
Restoration of Impaired Metabolic Energy Balance (ATP Pool) and Tube Formation Potential of Endothelial Cells under “high glucose”, Diabetic Conditions by the Bioinorganic Polymer Polyphosphate

Micro-vascularization is a fast, energy-dependent process that is compromised by elevated glucose concentrations such as in diabetes mellitus disease. Here, we studied the effect of the physiological bioinorganic polymer, polyphosphate (polyP), on the reduced ATP content and impaired function of endothelial cells cultivated under “high glucose” (35 mM diabetes mellitus conditions) concentrations. This high-energy biopolymer has been shown to provide a source of metabolic energy, stored in its phosphoanhydride bonds. We show that exposure of human umbilical vein endothelial cells (HUVEC cells) to “high glucose” levels results in reduced cell viability, increased apoptotic cell death, and a decline in intracellular ATP level. As a consequence, the ability of HUVEC cells to form tube-like structures in the in vitro cell tube formation assay was almost completely abolished under “high glucose” conditions. Those cells were grown onto a physiological collagen scaffold (collagen/basement membrane extract). We demonstrate that these adverse effects of increased glucose levels can be reversed by administration of polyP to almost normal values. Using Na-polyP, complexed in a stoichiometric (molar) ratio to Ca2+ ions and in the physiological concentration range between 30 and 300 µM, an almost complete restoration of the reduced ATP pool of cells exposed to “high glucose” was found, as well as a normalization of the number of apoptotic cells and energy-dependent tube formation. It is concluded that the adverse effects on endothelial cells caused by the metabolic energy imbalance at elevated glucose concentrations can be counterbalanced by polyP, potentially opening new strategies for treatment of the micro-vascular complications in diabetic patients.
Transcriptome and microRNome of Theileria annulata Host Cells

Tropical Theileriosis is a parasitic disease of calves with a profound economic impact caused by Theileria annulata, an apicomplexan parasite of the genus Theileria. Transmitted by Hyalomma ticks, T. annulata infects and transforms bovine lymphocytes and macrophages into a cancer-like phenotype characterized by all six hallmarks of cancer. In the current study we investigate the transcriptional landscape of T. annulata-infected lymphocytes to define genes and miRNAs regulated by host cell transformation using next generation sequencing. We also define genes and miRNAs differentially expressed as a result of the attenuation of a T.annulata-infected macrophage cell line used as a vaccine. By comparing the transcriptional landscape of one attenuated and two transformed cell lines we identify four genes that we propose as key factors in transformation and virulence of the T. annulata host cells. We also identify miR126-5p as a key regulator of infected cells proliferation, adhesion, survival and invasiveness. In addition to the host cell trascriptome we studied T. annulata transcriptome and identified the role of ROS and TGF-β2 in controlling parasite gene expression. Moreover, we have used the deep parasite ssRNA-seq data to refine the available T. annulata annotation. Taken together, this study provides the full list of host cell’s genes and miRNAs transcriptionally perturbed after infection with T. annulata and after attenuation and describes genes and miRNAs never identified before as players in this type of host cell transformation. Moreover, this study provides the first database for the transcriptome of T. annulata and its host cells using next generation sequencing.
Genome-wide association studies for small intestine length in an F2 population of chickens

Abstract Small intestine length is an important physiological index that is effected by nutrient intake and thus plays roles in growth and egg-laying in chickens. Although there are some studies about small intestine length, little information is available regarding the genetic architecture of small intestine. The current study was conducted to investigate the genetic architecture of small intestine length. A total of 1435 F2 hens from a White Leghorn and Dongxiang reciprocal cross were phenotyped for the duodenum lengths (DL), jejunum length (JL) and ileum length (IL), and genotyped using a chicken 600 K single nucleotide polymorphism (SNP) genotyping array. SNP-based heritability estimation was performed by SAS algorithm and univariate genome-wide association studies (GWAS) were performed by GEMMA, a genome-wide efficient mixed-model association algorithm. The JL and IL exhibited high SNP-based heritability estimation (0.43 and 0.49, respectively), while the heritability estimation was moderate for the DL (0.36). Three independent univariate genome-wide screens for these small intestine lengths identified 202, 298 and 119 SNPs that were significantly associated with the DL, JL and IL, respectively. The significant genomic regions indicated that ∼170 Mb on GGA1 is an important region for these small intestine lengths. In this region, 78 SNPs were associated with them, of which 4 were involved in cell proliferation and development, corresponding to RB1 (rs313207223), CKAP2 (rs312737959) and SIAH3 (rs312771221, rs15494052) genes. Small intestine length exhibited good SNP-based heritability estimation and the GWAS results indicated that an important genomic region was located on GGA1.
Development of successive cambia and formation of flat stems in Rhynchosia pyramidalis (Lam.) Urb. (Fabaceae)

Abstract Stem flattening in Rhynchosia pyramidalis (Fabaceae) is achieved by the development of crescent-shaped successive cambia on two opposite sides of the stem (referred hereafter as distal side). Other lateral sides of the stem (adjacent to supporting host and its opposite side, referred as proximal sides) usually possess single cambium. In the young stems, parenchymatous cells located outside to protophloem of distal side dedifferentiate and develop small segments of cambium. Concomitant to bidirectional differentiation of the secondary xylem and phloem, these newly developed cambial segments also extend in tangential directions. Differential activity of newly developed crescent-shaped cambial segments deposits more secondary xylem at median position as compared to their terminal ends of the stem on distal side; consequently, it pushes the cambial segment outside, thus resulting in crescent-shaped arcs of the cambia only on two opposite sides. After the production of 1–2 mm of secondary xylem, they cease to divide and new segments of cambial arc develop on the same side in a similar fashion. Such repeated behaviour of successive cambia development consequently leads to the formation of tangentially flat stems. The secondary xylem is diffusely porous with indistinct growth rings and is composed of vessels (wide and narrow), fibres, axial ray parenchyma cells, while phloem consisted of sieve elements, companion cells, axial and ray parenchyma. Rays in both xylem and phloem are uni- to multiseriate and heterocellular. The structure of secondary xylem and development of successive cambia is correlated with climbing habit.
Predicting Protein Binding Affinity With Word Embeddings and Recurrent Neural Networks

At the core of our immunological system lies a group of proteins named Major Histocompatibility Complex (MHC), to which epitopes (also proteins sometimes named antigenic determinants), bind to eliciting a response. These responses are extremely varied and of widely different nature. For instance, Killer and Helper T cells are responsible for, respectively, counteracting viral pathogens and tumorous cells. Many other types exist, but their underlying structure can be very similar due to the fact that they all are proteins and bind to the MHC receptor in a similar fashion. With this framework in mind, being able to predict with precision the structure of a protein that will elicit a specific response in the human body represents a novel computational approach to drug discovery. Although many machine learning approaches have been used, no attempt to solve this problem using Recurrent Neural Networks (RNNs) exist. We extend the current efforts in the field by applying a variety of network architectures based on RNNs and word embeddings (WE). The code is freely available and under current development at https://github.com/carlomazzaferro/mhcPreds
Automatic fish species classification in underwater videos: exploiting pre-trained deep neural network models to compensate for limited labelled data

There is a need for automatic systems that can reliably detect, track and classify fish and other marine species in underwater videos without human intervention. Conventional computer vision techniques do not perform well in underwater conditions where the background is complex and the shape and textural features of fish are subtle. Data-driven classification models like neural networks require a huge amount of labelled data, otherwise they tend to over-fit to the training data and fail on unseen test data which is not involved in training. We present a state-of-the-art computer vision method for fine-grained fish species classification based on deep learning techniques. A cross-layer pooling algorithm using a pre-trained Convolutional Neural Network as a generalized feature detector is proposed, thus avoiding the need for a large amount of training data. Classification on test data is performed by a SVM on the features computed through the proposed method, resulting in classification accuracy of 94.3% for fish species from typical underwater video imagery captured off the coast of Western Australia. This research advocates that the development of automated classification systems which can identify fish from underwater video imagery is feasible and a cost-effective alternative to manual identification by humans.
Sequence Characterization of Bovine Antisense to Insulin-Like Growth Factor Type 2 Receptor Non-Coding RNA (AIRN)

Bovine insulin-like growth factor type 2 receptor (IGF2R) is an imprinted gene whose aberrant expression has been implicated in development of abnormal offspring syndrome. Bovine AIRN (AIRN) is expressed in post-implantation fetal tissues coinciding with imprinted expression of IGF2R. Although expression patterns of bovine AIRN have been reported based on PCR analysis, characteristics of this transcript are unknown. Therefore, the objective of this work was to sequence characterize the AIRN ncRNA transcript. PCR primer sets (n = 19) were designed based on genomic sequence to “walk” down the predicted AIRN ncRNA sequence. Total RNA extracted from gestational Day 150 bovine fetal liver was used as source material for analysis. Extracted RNA was DNase-treated prior to cDNA synthesis, PCR amplified, and sequenced. A putative bAIRN promoter was located 623 base-pairs upstream of differentially methylated region 2 (DMR2) within intron 2 of IGF2R. A polyadenylation signal was found 117 kb downstream of the promoter. Primer sets designed upstream of the promoter as well as downstream of the polyadenylation signal yielded no PCR amplicons, suggesting that the length of AIRN is approximately 117 kb. In conclusion, bovine AIRN appears to be an antisense transcript of approximately 117 kb in length with a promoter region located 623 bp upstream of DMR2 within intron 2 of IGF2R.
ENVIRONMENTAL IMPACTS OF ARTHROPODS AS BIOLOGICAL CONTROL AGENTS

Biological control is an important component in the integrated management of pests. It is used to reduce or mitigate pests and it has been the focus of discussions for a long time. Hundreds of species of natural enemies were introduced, resulting in the successful control of various pests. However, the ecological processes involved for its success are generally very complex. In this way, this review focused on all the process of introducing species of arthropods as biological control agents and how they can affect the environment. The evaluation of environmental risk is the most critical and difficult partof the procedures and should contain some elements such as the identification of potential risks to which the environment will be exposed. The problems caused by the invasion of exotic species have increased and the high frequency of invasion is associated in large part with human activities, such as accidental transport and introduction. All these questions should be analysed based on rigorous studies and risk analysis, in which ecological interactions, competition, intraguild predation, and the effects of introduction on non-target organisms as well are considered.
Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability

All biological systems exhibit cell-to-cell variability, and this variability often has functional implications. To gain a thorough understanding of biological processes, the latent causes and underlying mechanisms of this variability must be elucidated. Cell populations comprising multiple distinct subpopulations are commonplace in biology, yet no current methods allow the sources of variability between and within individual subpopulations to be identified. This limits the analysis of single-cell data, for example provided by flow cytometry and microscopy. In this study, we present a data-driven modeling framework for the analysis of populations comprising heterogeneous subpopulations. Our approach combines mixture modeling with frameworks for distribution approximation, facilitating the integration of multiple single-cell datasets and the detection of causal differences between and within subpopulations. The computational efficiency of our framework allows hundreds of competing hypotheses to be compared, giving unprecedented depth of a study. We demonstrated the ability of our method to capture multiple levels of heterogeneity in the analyzes of simulated data and data from highly heterogeneous sensory neurons involved in pain initiation. Our approach identified the sources of cell-to-cell variability and revealed mechanisms that underlie the modulation of nerve growth factor-induced Erk1/2 signaling by extracellular scaffolds. Highlights Mechanistic model for populations consisting of multiple heterogeneous subpopulations Scalable parameter estimation and model selection using multivariate single-cell data Study of pain sensitization in primary sensory neurons Proof of principle for fitting of mechanistic model with single-cell data
The effect of essential oil of Lavandula angustifolia on amyloid beta polymerization: An in vitro study

Alzheimer’s disease (AD) is a progressive neurological disorder associated with cognitive and memory deficits. Accumulation of amyloid beta (Aβ) plaques is one of the major causes of AD. Therefore, inhibition of the plaque formation has been aimed to play a preventive role in the disease. Lavender, through some neuroprotective roles such as antioxidant effects, is known to be an effective candidate in treatment of neurodegenerative disorders. In this study using Thioflavin T Measurement and Atomic Force Microscope (AFM) Imaging we evaluated effect of essential oil of lavender on Aβ polymerization.Thioflavin T Method showed that the essential oil enhances the Aβ aggregation. The results of AFM method also confirmed it. Our data antagonizes previous results indicating clearing effect of aqueous extract of lavender on Aβ plaque. It seems that the different combination of essential oil and aqueous extract considerably determines if or not the aggregation occurs.
Optimising sampling methods for small mammal communities in Neotropical rainforests

Quantifying mammalian biodiversity is a critical yet daunting challenge, particularly in species-rich ecosystems. Non-volant small mammals account for >60% of the mammalian diversity and often require several survey methods to estimate their species richness and abundance, because of differences in their size and behaviour. Using 117 studies at 278 sites in a species-rich biome, the Brazilian Atlantic Forest, we determined the influence of trap configuration, trap type, and sampling effort on measures of species richness and abundance. We used generalised linear mixed-effects models to determine which methodological approaches influenced estimates of species richness and abundance at the sampling sites. We used estimates of beta (β) to determine which methods improved species richness and abundance estimates, and generated predicted values for the overall species richness as a function of trap configuration (line transect, grid, or both), trap type (pitfall traps, live-traps or both), and sampling effort (number of trap-nights). Our results indicated that sites in which pitfall traps alone were used generated higher estimates of the overall small mammal species richness and abundance, and rodent abundance, than sites in which only live-traps were used. Sites in which pitfall traps alone were used also produced higher estimates of species richness and abundance, and rodent species richness and abundance, than sites in which both trap types were used. Increased sampling effort led to increased estimates of species richness, but sites in which pitfall traps were used alone or together with live-traps had higher estimates of species richness with less sampling effort than sites in which live-traps only were used. Using pitfall traps greatly reduced the number of trap-nights necessary to obtain a good estimate of small mammal species richness in a community. We found no influence of trap configuration (line transects or grids) on estimates of species richness, but the abundance of rodents was estimated to be higher in sites where both line transects and grids were used, than in sites where only one trap configuration was used. Our review shows the importance of using pitfall traps in research, monitoring, and environmental impact studies on species-rich small mammal communities.
Phenyl or pyridyl amide compounds as prostaglandin e2 antagonists

The present invention is (wherein A to provide compounds of formula (I) represents a phenyl group, B represents an aryl, E is represents a 1,4-phenylene group, R These compounds are useful in the treatment of disease states mediated prostaglandins such as pain in a mammal. Compounds act as antagonists of prostaglandin E2 receptor. The present invention also provides a pharmaceutical composition comprising the above compound. [Formula 1] . BACKGROUND
Effect of plant secondary metabolites on common cutworm, Spodoptera litura (Lepidoptera: Noctuidae)

The effect of various flavonoids, lectins and phenyl β‐D‐glucoside on larval survival, weights and the activities of digestive (total serine protease and trypsin) and detoxifying (esterase and glutathione‐S‐transferase) enzymes of Spodoptera litura larvae at 7 days after treatment was studied through diet incorporation assay. Flavonoids (rutin, chlorogenic acid, quinic acid, caffeic acid, naringenin, quercitin, kaempferol, myricetin, catechin, and ferulic acid) were incorporated in artificial diet at 100, 500 and 1000 ppm, lectins: groundnut leaf lectin (GLL), concavalin A (ConA) and phenyl β‐D‐glucoside at 1, 2 and 5 μg/mL. Flavonoids such as rutin, quercitin and kaempferol at 1000 ppm were more toxic to S. litura larvae than quinic acid, caffeic acid, naringenin, myricetin, catechin, and ferulic acid. Larval growth and development were significantly reduced in S. litura larvae fed on a diet with GLL and ConA at 5 μg/mL compared to the larvae fed at 2 and 1 μg/mL concentrations. The larvae fed on flavonoid‐treated diets showed significant reduction in serine protease, trypsin and esterase activities. The flavonoids such as rutin, chlorogenic acid, quinic acid, naringenin, quercitin, kaempferol and myricetin, and lectins, GLL and ConA can be utilized in insect control programs.