Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut and Tissue Microbiome Biogeography and Its Response to Environmental Perturbation

The symbiotic relationship between the host and its microbiome, which is composed of trillions of bacteria, archaea, viruses, and fungi, is essential for the host to maintain health. In the past two decades, the intestinal microbiota has become one of the most intensely studied microbial ecosystems on the planet; however, there are few studies on much of the microbiota’s distribution, the factors shaping its composition both within and outside of the gastrointestinal (GI) tract, and the microbial communities’ response to environmental factors, such as fluoride. To understand the extent of intra-intestinal microbiota composition, its representation in the stool and factors dictating site-specificity of microbial taxa within the gut, we systematically collected stool and paired lumenal and mucosal intestinal samples from ten sites distal to the jejunum from the model organism Macaca mulatta (rhesus macaque) and assayed the samples with 16S rRNA amplicon sequencing. We found that stool composition was highly correlated with the microbial composition at the colonic lumen and mucosa, as well as enrichment of oxygen-tolerant bacteria in the mucosa, suggesting that stool is a good representation of distal gut lumenal bacterial communities and that oxygen may be a strong factor in shaping the gut microbial composition. We then tested the hypothesis that environmental factors, such as fluoride, may affect the oral and gut microbial communities, as fluoride is widely prevalent in drinking water and dental products and may have unexpected effects on health. We modeled human fluoride exposure in mice by administering fluoride daily over a 12-week period. We then assayed oral and stool samples for 16S amplicons and
An Overview of Joint Modeling of Time-to-Event and Longitudinal Outcomes

In this review, we present an overview of joint models for longitudinal and time-to-event data. We introduce a generalized formulation for the joint model that incorporates multiple longitudinal outcomes of varying types. We focus on extensions for the parametrization of the association structure that links the longitudinal and time-to-event outcomes, estimation techniques, and dynamic predictions. We also outline the software available for the application of these models.
Efficient low cost seesap (CSUP) technique for micropropagation of newly introduced sweetener plant, Stevia rebaudiana Bertoni

Stevia rebaudiana is a non-caloric sweetening herb, which has a high potential for commercialization. During this study low cost media sterilization, seesap (CSUP) technique which applies sodium hypochlorite was used as an alternative to autoclaving. In vitro cultures were established using nodal segments collected from stevia mother plants. These in vitro shoots were cultured on Murashige & Skoog (MS) medium supplemented with 16 combinations of 6- benzyl amino purine (BAP) and kinetin (KN) with 3% sugar at 5.8 pH, to investigate the in vitro shoot multiplication. The developed shoots were transferred to half MS medium supplemented with 0, 1 and 2 mg/L Indole butyric acid (IBA) with 3, 4 and 5% sugar in nine combinations at 5.8 pH, to investigate the rooting. The well rooted stevia plantlets were transferred to Jiffy™ bags for hardening. The results showed that the combination of 1.0 mg/L BAP and 1.5 mg/L KN resulted in the highest number of shoots (11.8 shoots/shoot). The combination of 2.0 mg/L IBA with 5% sugar in half MS medium resulted in the highest root induction (7.2 roots / plant) and root elongation (1.02 cm). The plants grown in culture medium containing 5% sucrose gave 100% survival rate at acclimatization. Key words: Stevia, micropropagation, shoot induction, root induction, acclimatization, low cost seesap (CSUP).
A précis of Gill-Oxygen Limitation Theory (GOLT), with some Emphasis on the Eastern Mediterranean

A summary of the Gill-Oxygen Limitation Theory (GOLT) is presented, i.e., of a theory seeking to explain a variety of life processes in fish and aquatic invertebrate by the fact that that the surface of their gills (and hence their oxygen supply) cannot, as 2-dimensional objects, keep up with the growth of their 3-dimensional bodies, and thus with their oxygen requirements. Various processes and attributes of fish and aquatic invertebrates are presented which had to date no mechanistic explanation, but which fit within the GOLT, offered here as a tool to interpret phenomena that until now were perceived as unrelated. However, the GOLT should also help to address practical problems, such as arise for fish farming when water temperature increases because of global warming.
An Overview of Quantum Key Distribution Protocols

Quantum key distribution (QKD) is the objects of close attention and rapid progress due to the fact that once first quantum computers are available – classical cryptography systems will become partially or completely insecure. The potential threat to today’s information security cannot be neglected, and efficient quantum computing algorithms already exist. Quantum cryptography brings a completely new level of security and is based on quantum physics principles, comparing with the classical systems that rely on hard mathematical problems. The aim of the article is to overview QKD and the most conspicuous and prominent QKD protocols, their workflow and security basement. The article covers 17 QKD protocols and each introduces novel ideas for further QKD system improvement.
"Country of origin" effect and ethnocentrism in food purchase in Southern Chile - Efecto "país de origen" y etnocentrismo en la compra de alimentos en el sur de Chile

This study sought to determine the relative importance of the country of origin in the selection of four foodstuffs (rice, sugar, chicken meat and oil); to identify consumer segments; and to evaluate which sociodemographic variables affect ethnocentrism in food consumption, through a survey responded by 800 habitual supermarket shoppers in southern Chile. It was determined that the country of origin was the most important attribute in the selection of the four foods. Three consumer segments were distinguished which assigned a different degree of importance to the country of origin, although in two segments the country of origin was highly important in the purchase choice. The consumers of the three segments preferred Chilean foods and expressed a lower preference for food imported from countries that were farther away and more culturally different from Chile. The segments differed significantly in the frequency of purchase of imported foods, reasons for preferring to buy imported foods, and ethnocentrism. It was found that if the respondent was a woman, of older age, belonged to the medium or high socioeconomic level, and had a conservative lifestyle, the probability of being ethnocentric in food consumption increased.
DNA barcodes fail to accurately differentiate species in Hawaiian plant lineages

DNA barcoding has been largely successful in differentiating animal species, but the most effective loci and evaluative methods for plants are still debated. Floras of young, oceanic islands are a challenging test of DNA barcodes, because of rapid speciation, high incidence of hybridization and polyploidy. We used character-based, tree-based and genetic distance-based methods to test DNA barcoding of 385 species of native Hawaiian plants constituting 20 lineages at the nuclear ITS(2) locus, nine lineages at each of the plastid loci trnH-psbA and rbcL, eight lineages at the plastid locus matK and four lineages with concatenated data. We also incorporated geographical range information and tested if varying sample sizes within a lineage influenced identification success. Average discrimination success was low (22% maximum) with all methods of analysis across all loci. The character-based method generally provided the highest identification success, there were limited benefits from incorporating geographical data and no relationship between number of species sampled in a lineage and identification success was found. Percentages of identification success are the lowest reported in a DNA barcoding study of comparable scale, and multi-species groups that radiated in the Hawaiian archipelago probably cannot be identified based on current DNA barcoding loci and methodologies.
Improving Domain-Independent Planning via Critical Section Macro-Operators

Macro-operators, macros for short, are a well-known technique for enhancing performance of planning engines by providing “short-cuts” in the state space. Existing macro learning systems usually generate macros from most frequent sequences of actions in training plans. Such approach priorities frequently used sequences of actions over meaningful activities to be performed for solving planning tasks. This paper presents a technique that, inspired by resource locking in critical sections in parallel computing, learns macros capturing activities in which a limited resource (e.g., a robotic hand) is used. In particular, such macros capture the whole activity in which the resource is “locked” (e.g., the robotic hand is holding an object) and thus “bridge” states in which the resource is locked and cannot be used. We also introduce an “aggressive” variant of our technique that removes original operators superseded by macros from the domain model. Usefulness of macros is evaluated on several stateof-the-art planners, and a wide range of benchmarks from the learning tracks of the 2008 and 2011 editions of the International Planning Competition.
First Survey of Heterobranch Sea Slugs (Mollusca, Gastropoda) from the Island Sangihe, North Sulawesi, Indonesia

Indonesia is famous for its underwater biodiversity, which attracts many tourists, especially divers. This is also true for Sangihe Islands Regency, an area composed of several islands in the northern part of North Sulawesi. However, Sangihe Islands Regency is much less known than, e.g., Bunaken National Park (BNP, North Sulawesi). The main island, Sangihe, has recently experienced an increase in tourism and mining activities with potentially high impact on the environment. Recently, monitoring projects began around BNP using marine Heterobranchia as indicators for coral reef health. No information about this taxon exists from the remote islands in North Sulawesi. The present study represents the first monitoring study ever and focuses on marine Heterobranchia around Sangihe. In total, 250 specimens were collected, which could be assigned to Sacoglossa (3), Anthobranchia (19), and Cladobranchia (1). Despite the low number (23 versus 172 in BNP), at least eight species (35%) are not recorded from BNP, probably indicating differences in habitat, but also influence of a strong El Niño year in 2016. Here we also report for the first time a Chromodoris annae specimen mimicking C. elisabethina, and the discovery of a new Phyllidia species.
Temporal cascade of frontal, motor and muscle processes underlying human action-stopping

Action-stopping is a canonical executive function thought to involve top-down control over the motor system. Here we aimed to validate this stopping system using high temporal resolution methods in humans. We show that, following the requirement to stop, there was an increase of right frontal beta (∼13 to 30 Hz) at ∼120 ms, likely a proxy of right inferior frontal gyrus; then, at 140 ms, there was a broad skeletomotor suppression, likely reflecting the impact of the subthalamic nucleus on basal ganglia output; then, at ∼160 ms, suppression was detected in the muscle, and, finally, the behavioral time of stopping was ∼220 ms. This temporal cascade confirms a detailed model of action-stopping, and partitions it into subprocesses that are isolable to different nodes and are more precise than the behavioral speed of stopping. Variation in these subprocesses, including at the single-trial level, could better explain individual differences in impulse control.
PSATHYRELLA EUTHYGRAMMA (AGARICALES, BASIDIOMYCOTA), A NEW RECORD FROM BRAZIL

Wartchow, F. & A. R. P. Gomes. 2019. Psathyrella euthygramma (Agaricales, Basidiomycota), a new record from Brazil. Darwiniana, nueva serie 7(1): 187-190. PSATHYRELLA EUTHYGRAMMA (AGARICALES, BASIDIOMYCOTA), A NEW RECORD FROM BRAZIL 1 Universidade Federal da Paraíba, Departamento de Sistemática e Ecologia, Pós-Graduação em Biologia de Fungos, CEP 58051-970, João Pessoa, PB, Brazil; fwartchow@yahoo.com. br (author for correspondence). 2 Universidade Federal de Pernambuco, Departamento de Micologia, Av. Nelson Chaves s/n, 50760-420, Recife, PE, Brazil. Felipe Wartchow1 & Ana R. P. Gomes2 Psathyrella euthygramma is reported for the first time from Brazil, growing on rotting wood in the Atlantic Forest. The diagnostic features are the small basidiomes with stipe bearing a fugacious annulus and densely strigose base, the small basidiospores bearing germ pore and cystidia thin to slightly thick walled.
The effect of electric fields on hyaline cartilage: an in vitro and in silico study

Hyaline cartilage is a dense connective tissue with low self-healing capacity when is affected by degenerative pathologies. Therefore, electrical stimulation has been proposed as a possible non-invasive alternative therapy to enhance the restoration of the cartilaginous tissue. Accordingly, this work presents a combined computational and experimental approach to understand better the hyaline cartilage biology and its response to electrical stimulation using different in vitro models. On the one hand, a mechanobiological model was developed to simulate the endochondral ossification process. On the other hand, the electrical stimulation on hyaline cartilage was evaluated in three different scenarios. Initially, cell proliferation and glycosaminoglycans synthesis of chondrocytes, cultured in monolayer and stimulated with electric fields, was analyzed. Then, a histomorphometric analysis was performed to chondroepiphysis explants that were electrically stimulated. Finally, the effects of the electric fields on chondrogenic differentiation of mesenchymal stem cells cultured in hydrogels was assessed. The results indicated that electrical stimulation is a promising biophysical stimulus, due to the fact that this type of stimulation enhances the viability and the proliferation of cells, induces morphological changes in the chondrocytes, and stimulates the synthesis of the main molecules that compose the hyaline cartilage, such as SOX-9, glycosaminoglycans and aggrecan. Moreover, this project is the first step towards the implementation of an alternative biophysical stimulus that modifies the cellular dynamics of growth plate chondrocytes in ex vivo conditions. Additionally, this study highlights the potential effect of electric fields to induce the chondrogenesis process of mesenchymal stem cells cultured in basal conditions. Overall, the assessment of electrical stimulation on chondrocytes, tissues and scaffolds is a useful tool that may contribute to the current knowledge of regenerative therapies focused on hyaline cartilage healing.
TRANSPORT AND TRANSFORMATIONS OF FERTILIZER NITROGEN IN A SANDY FIELD PLOT USING TRACER TECHNIQUES

In a field study utilizing 15N on Manotick sand, leaching, denitrification, clay fixation of NH4+, mineralization, and immobilization all played a significant role in the transport and transformation of fertilizer NH4+. Fertilizer NH4+ applied 24 June was distributed throughout the 75-cm profile by 29 July. The relatively small amount (0.5% of the total 15N recovered) found in the deepest sample (60 to 75 cm) suggested that a larger portion of the 27% unrecovered 15N was denitrified rather than leached. Denitrification, then, was assumed to be more prevalent early, rather than late, in the season. On 4 October, a much larger proportion of the 15N was found deep in the profile, showing that leaching losses after 29 July became more important. Four percent of the fertilizer 15NH4+-N was immediately clay-fixed. By 29 July, 9% of the initially fixed 15NH4+-N was released, but by 4 October, 77% of the initially fixed 15NH4+-N was released. The total amount of immobilized 15N was similar on both 29 July and 4 October samplings. The relatively constant amount of organic 15N during the field season showed that immobilization was more active between 24 June and 29 July than between 29 July and 4 October. Immobilized 15N accounted for 19 to 20% of the applied fertilizer 15N. The dynamics of N transformations were compared with a previously studied adjacent clay loam soil.
Damping-off disease of big onion (Allium cepa L.) in Sri Lanka and evaluation of Trichoderma asperellum and Trichoderma virens for its control

Allium cepa is used as a condiment and reduction of yield due to infectious diseases is a major economical constraint. The present study was aimed at isolation and identification of fungal pathogens associated with damping-off disease of onion in Sri Lanka. Trichoderma spp. present in the soil of the same onion fields were isolated with a view to evaluating them as possible biocontrol agents of damping-off pathogen(s). The diseased seedlings were collected from fifty-five onion fields in Matale and Anuradhapura districts during the yala season. Soil collected from the same onion fields and soil fungi isolated using the Warcup method. Fusarium sp. isolated from diseased seedlings was confirmed to be the causative agent of damping-off disease of big onions by following Koch’s postulates. The pathogenic Fusarium sp. was identified as Fusarium solani based on the similarity matches of the Internal Transcribed Spacer region using Basic Local Alignment Search Tool. Two Trichoderma spp. showing significantly high (p ≤0.05) reduction of growth of F. solani in dual culture assay, higher sporulation capacity and growth rates were identified as T. asperellum (Tr.3) and T. virens (Tr.1). Polymerase Chain Reaction (PCR) using two primer pairs i.e. ITS 1 and ITS 4, FR 1 and NS 1 were used to characterize the seven Trichoderma spp. while ITS 1 and ITS 4 were used to characterize Fusarium spp. Although a lesser degree of polymorphism was detected using these primers, the random amplified polymorphic DNA analysis had the ability to differentiate T. asperellum, T. virens and F. solani. The capability of two Trichoderma spp. to suppress F. solani is through formation of loops and coils and attachment of hyphal tips. They also had the ability to produce Chitinase and volatile metabolites that controlled the growth of F. solani.
Zooxanthellate, Sclerite-Free, and Pseudopinnuled Octocoral Hadaka nudidomus gen. nov. et sp. nov. (Anthozoa, Octocorallia) from Mesophotic Reefs of the Southern Ryukyus Islands

Shallow water coral reefs are the most diverse marine ecosystems, but there is an immense gap in knowledge when it comes to understanding the diversity of the vast majority of marine biota in these ecosystems. This is especially true when it comes to understudied small and cryptic coral reef taxa in understudied ecosystems, such as mesophotic coral reef ecosystems (MCEs). MCEs were reported in Japan almost fifty years ago, although only in recent years has there been an increase in research concerning the diversity of these reefs. In this study we describe the first stoloniferous octocoral from MCEs, Hadaka nudidomus gen. nov. et sp. nov., from Iriomote and Okinawa Islands in the southern Ryukyus Islands. The species is zooxanthellate; both specimens host Cladocopium LaJeunesse & H.J.Jeong, 2018 (formerly Symbiodinium ‘Clade C’) and were collected from depths of ~33 to 40 m. Additionally, H. nudidomus gen. nov. et sp. nov. is both sclerite-free and lacks free pinnules, and both of these characteristics are typically diagnostic for octocorals. The discovery and morphology of H. nudidomus gen. nov. et sp. nov. indicate that we still know very little about stoloniferous octocoral diversity in MCEs, their genetic relationships with shallower reef species, and octocoral–symbiont associations. Continued research on these subjects will improve our understanding of octocoral diversity in both shallow and deeper reefs.
Compatibility between entomopathogenic nematodes and crop protection products used in maize seed treatment

Chemical insecticides are widely used to control soil pests but not always effective. Entomopathogenic nematodes (NEPs) are found in the soil and depend on host insects to complete their life cycle, and therefore have the potential to control soil pests. Thus, we aimed to investigate the possible joint use of these control methods by assessing the compatibility of two nematodes (Heterorhabditis amazonensis GL and Heterorhabditis amazonensis MC01) with five crop protection products used for maize seed treatment (Maxim®, Cruiser 350 FS®, Fortenza 600 FS®, Avicta 500 FS®, and Amulet®), as well as one neem-based product (NeenMax®). The experimental design was completely randomized with five replicates, six treatments, and one control, in which only distilled water was added to nematode suspension. Each replicate consisted of a test tube containing 1 mL suspension with 2,000 infective juveniles (IJs) and 1 mL of diluted product, following the manufacturer's recommendation. The evaluated parameters were viability, infectivity on Tenebrio molitor larvae and IJs production after exposure to products. Both nematodes were compatible with NeenMax® and Fortenza 600 FS® since they did not differ from the control and were classified as innocuous. Cruiser 350 FS ® was also compatible with the nematodes since the effect value of the product was lower than 30%. Amulet® was classified as slightly noxious, reducing H. amazonensis MC01 and H. amazonensis GL infectivity by 17.5% and 28.5%, and production by 18.2% and 22.3%, respectively. Despite not having reduced viability, Avicta 500 FS® and Maxim® were considered harmful. This is because Avicta 500 FS® and Maxim® reduced productivity by 70.0% and 72.5% and production by 66.1% and 65.4% for H. amazonensis MC01, respectively. For H. amazonensis MC01, both Avicta 500 FS® and Maxim® reduced infectivity by 76.19%, and production by 63.7% and 62.3%, respectively.
Image Based Trash Classification using Machine Learning Algorithms for Recyclability Status

This research paper talks about Trash classification which comes across as a social and unique cause where Image processing through Analytics can help with better management of garbage and waste materials. A standout amongst the most proficient approach to process trash as indicated by its recyclability is to comprehend what class that waste has a place. Analytics can make this herculean task achievable through image classification into its proper categorizations. The goal of this task is to take pictures with single items, segregate them and group those pictures into five particular classifications of cardboard, glass, metal, paper and plastic. We will utilize a dataset of around 400-500 pictures from every class indicated previously. This dataset was made accessible freely and the creators of the dataset give full access to it through their GitHub store. The model utilized will be a Convolutional Neural Network (CNN) because of its impressive and efficient capabilities in the world of machine learning, particularly in image classification. Further, an Extreme Gradient Boosting will be implemented and checked if it can perform better than a CNN. Multiple methods were juxtaposed in order to zero in on the best method or combination of methods which can prove beneficial and efficient for image classification.