Miracle-dz/UniFAR-FTUs huggingface dataset:
Disappearance of pollinating bees in natural and agricultural systems: Is there an explanation?

Since the last decade, the disappearance of pollinating bee populations has been apparent in several countries. This group is responsible for the pollination and maintenance of hundreds of plant species used in human food, in addition to contributing significantly to the socioeconomic development of several communities associated to family farming. In this study, the possible causes of this disappearance are discussed, among which we highlight deforestation, reinforced by the lack of natural flora, inadequate hive management by beekeepers, increasing infestations of pests in the colonies, and the use of agrochemicals. Conservation strategies for native and domesticated bees are suggested, namely: (a) maintenance of the natural landscape that surrounds agricultural areas; (b) beekeepers’ professionalization in the nutritional management and conservation of beehives; and (c) the continuous development of detailed studies about the lethal and sublethal effects of agrochemicals on pollinators.
Development of Functional Enzymes and Diet Supplement Products through Microbial Cereal Grain Cultivation Technology

Background/Objectives: This study aims to develop enzyme products with live enzyme activity through cereal grain fermentation and develop enzyme diet products containing natural substances by mixing with plant extracts effective for diet. Methods/Statistical analysis: An appropriate fermentation method for the enzyme production was selected to commercialize the product. The enzyme activity was analyzed/ evaluated pursuant to the food standards/ specifications by food under the Korean Food Standards Codex (KFSC) by Dongkang College Food Health Research Institute as there was no state-certified analyzing institution. Nutritive components including crude protein, aflatoxin, and food stability were tested by a state-certified institution in test methods under the KFSC. Findings: Diet enzyme products with a-amylase, protease, and lipase activity and antioxidant activity were developed from the fermentation product. The antioxidant activity of the natural substance was identified and applied to diet products. Fermentation conditions for enzyme production were established and the fermentation time was shortened. Consumer sensory evaluation and experience results were analyzed to identify the diet effects of the developed products. The stability of the developed products was identified through heavy metal analysis including aflatoxin analysis and Escherichia coli tests. Improvements/Applications: The developed products with enzyme activity and antioxidant activity will be mass-produced and developed into main products of the company, the quality of the products will be improved through continuous research & development hereafter, and the products will be utilized to become products competitive not only in the domestic market but also in the world market through diverse marketing activities.
Analysis of factors related to varietal differences in the yield of rice (Oryza sativa L.) under Free-Air CO2 Enrichment (FACE) conditions

ABSTRACT Enhancing crop traits that increase grain yield under elevated CO2 concentrations is an important option for increasing the future productivity of rice. Here, we compared the growth and yield of five varieties with different genetic background under Free-Air CO2 Enrichment (FACE) conditions to identify traits responsible for varietal differences in yield increase under elevated CO2. Three high-yielding and two standard rice varieties grown under FACE conditions commonly had (1) shorter growth periods, (2) higher dry matter production, (3) higher numbers of spikelets (sink capacity) and panicles; and (4) higher yield than those grown under ambient CO2. Yield enhancement by elevated CO2 (FACE/Ambient), however, differed significantly among varieties, ranging from 1.10 to 1.25. The greater response of the sink capacity, defined as the product of spikelet number and single grain mass, was the main factor involved in yield increase. Three high-yielding varieties (Momiroman, Takanari, and Hokuriku 193) had greater sink capacity than two standard varieties and the sink capacity of these varieties significantly increased under FACE condition. However, yield enhancement in elevated CO2 was lower in Hokuriku 193 than in Momiroman and Takanari. In Hokuriku 193, sink production was relatively low while dry matter production was similar to the others. Therefore, larger increase in sink production efficiency per unit of dry matter production under FACE was found to be a particularly important varietal trait, suggesting that efforts to develop varieties suited to the predicted elevated CO2 condition should focus on this and the related traits.
Occurrences of infections caused by the bacteria clostridium difficile on the territory of Belgrade

Introduction/Aim: The aim of the study was to show the characteristics of infections caused by the bacteria Clostridium difficile (C. difficile) originating in the territory of Belgrade in the period between 2013 and 2017. Methods: Data for this report was collected from the reports of infectious diseases and hospital infections, as well as surveys of the patients, medical documentation, and from annual reports on the prevention, treatment and elimination of infectious diseases. Results of epidemiological and laboratory testing were also included. Incidence rates, mortality rates and proportions were used in analysis. Results: In the observed 5 year period the incidence rate was between 34.0/100,000 (2013) and 75.1/100,000 (2016). The mortality rate ranged between 1.1/100,000 (2013) and 2.1/100,000 (2016). The highest average incidence rates were observed in the elderly. Most cases of mortality belonged to the age category 70 and more years of age (11.3/100,000) and were the smallest in the age group 30-39 years (0.1/100,000). Infections with C. difficile were most common in the month of March (608 affected, with an incidence rate of 11.3/100,000). In the observed period there were 12 registered epidemics with 51 cases. Conclusion: The effective prevention and control of the C. difficile infection is predicated upon the continuation of active implementation of disease management in accordance with the incidence rate.
A Graph-Directed Approach for Creation of a Homology Modeling Library: Application to Venom Structure Prediction

Many toxins are short, cysteine-rich peptides that are of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. To perform initial candidate identification for design of a drug impacting a particular receptor or for threat assessment as a harmful toxin, one requires a set of candidate structures of reasonable accuracy with potential for interaction with the target receptor. In this article, we introduce a graph-based algorithm for identifying good extant template structures from a library of evolutionarily-related cysteine-containing sequences for structural determination of target sequences by homology modeling. We employ this approach to study the conotoxins, a set of toxin peptides produced by the family of aquatic cone snails. Currently, of the approximately six thousand known conotoxin sequences, only about three percent have experimentally characterized three-dimensional structures, leading to a serious bottleneck in identifying potential drug candidates. We demonstrate that the conotoxin template library generated by our approach may be employed to perform homology modeling and greatly increase the number of characterized conotoxin structures. We also show how our approach can guide experimental design by identifying and ranking sequences for structural characterization in a similar manner. Overall, we present and validate an approach for venom structure modeling and employ it to expand the library of extant conotoxin structures by almost 300% through homology modeling employing the template library determined in our approach.
Nutritional Manipulations and Its Effects on Yield and Quality of Beef

In recent years, innovations in animal nutrition have yielded several products in the forms of feed additives/supplements for improving feed utilization and also producing novel meat products and quality to meet the demand of consumers. Consumption of meat from ruminant animals and its derivatives is also on the increase. In addition, nowadays, consumers are exceedingly interested in the quality of the products they eat, especially when this refers to meat, either white or red. A large amount progress is completed in the exploitation of the nutrition of pigs and poultry than in the ruminant animals. Beef quality can be manipulated by a variety of nutritional manipulations and many have been implemented successfully in finishing operations world-wide. This paper provides a brief overview of beef quality and the manipulation of beef quality through feeding.
Using stable isotope analysis to answer fundamental questions in invasion ecology: Progress and prospects

What makes some species successful invaders while others fail, and why some invaders have major impacts in invaded ecosystems are pivotal questions that are attracting major research effort. The increasing availability of high resolution, georeferenced stable isotope landscapes (‘isoscapes’), coupled with the commercialization of stable isotope‐enriched tracer molecules and the development of new analytical approaches, is facilitating novel applications of stable isotope techniques in ecology. We can now address ecological questions that were previously intractable. We review and discuss how stable isotope analysis (SIA) can complement fundamental research themes in the study of biological invasions, especially in answering questions relating to the physiological and ecological mechanisms underlying invasion processes and invader impacts. SIA was first used for simply describing the diet of invaders but, more recently, SIA‐informed metrics of population and community trophic structure have been advanced. These approaches now permit the comparison of diets across space and time and provide quantitative tools to compare food webs across different stages of invasion. SIA has also been pivotal in quantifying competition for resources between native and non‐native species (e.g. competition for food, water, or nutrient use). Specific questions related to modes of dispersal (e.g. origin and distance/direction travelled) and mechanisms of establishment can also be addressed using SIA in diverse taxa. An overarching goal is to highlight examples of recent studies that have used SIA in key areas of invasion ecology and use these to synthesize testable predictions where SIA could be applied to future studies. We conclude by highlighting several paths forward and describing how unresolved challenges in quantifying the rates, impacts, and mechanisms underlying invasions could potentially benefit from the use of SIA.
The characterisation of Theileria annulata sporozoite surface antigens

Theileria annulata is a major protozoan parasite of cattle in tropical and subtropical countries, transmitted by the tick Hyalomma anatolicum The infection in the host is initiated by the sporozoite, which rapidly attaches to and invades host cells. A humoral response to sporozoites has been identified in immune cattle (Preston and Brown 1985). Two McAbs which block sporozoite invasion of lymphocytes "in vitro", McAb 1A7 and 4B11, have been identified in previous work (Williamson 1988). These McAbs recognise different sets of polypeptides on Western blots. T. annulata sporozoite antigen 1 (SPAGl), which contains the epitope recognised by McAb 1A7, has been cloned and sequenced [Hall et al 1992). This work describes research to analyse the bovine T and B cell response to the T. annulata SPAGl. The SPAGl polypeptide, and a range of subclones covering different regions of the antigen, were expressed using pGEX vectors in E. coli and purified in large quantities for the purpose of B and T cell epitope mapping. The recombinant SPAGl polypeptides were used to analyse humoral responses of immunised cattle by Western blotting and enzyme linked immuno-sorbant assay. A number of regions of SPAG1 containing B cell epitopes recognised by bovine antisera raised against T. annulata sporozoites were also identified, and the relevance of this data to SPAGl neutralising determinants discussed. T cell responses to SPAGl were analysed in proliferation assays using peripheral blood mononuclear cells and antigen specific T cell lines. A bovine T cell response was found to be induced to SPAG 1 in cattle immunised with the recombinant antigen. In addition, the SPAGl molecule was found to be highly polymorphic according to restriction fragment analysis on Southern blots. Work was also undertaken to prove the surface location of the SPAGl molecule on sporozoites using immuno-electron microscopy techniques. The final part of this work was to identify, express and characterise the T. annulata sporozoite antigen gene containing the McAb 4B11 epitope. McAb 4B11 was used to screen a lambdagtl 1 T. annulata genomic expression library, and two positive recombinants were subcloned into the expression vector pGEX1lambdaT to give pGEX1lambdaT-KP6 and pGEX1lambdaT-KP8. Southern and Northern blot analysis of the KP6 and KPS inserts confirmed they were parasite sequences expressed at high levels in sporozoites as a 3.1 kb mRNA. However, KPS and KPS did not cross-hybridise, indicating that they contained different sequences coding for the 4B11 epitope. The pGEX1lambdaT-KPS fusion protein was expressed in E. coli and purified. The fusion protein was found to affinity bind antibodies from bovine antisera raised against T. annulata sporozoites, and evoked antibodies capable of blocking sporozoite infectivity of leukocytes "in vitro" and recognising sporozoite antigens in immunofluorescence assays or on Western blots when used to immunise a rabbit.
BDKANN – Biological Domain Knowledge-based Artificial Neural Network for drug response prediction

One of the main goals of precision oncology is to predict the response of a patient to a given cancer treatment based on their genomic profile. Although current models for drug response prediction are becoming more accurate, they are also "black boxes" and cannot explain their predictions, which is of particular importance in cancer treatment. Many models also do not leverage prior biological knowledge, such as the hierarchical information on how proteins form complexes and act together in pathways. In this work, we use this prior biological knowledge to form the architecture of a deep neural network to predict cancer drug response from cell line expression data. We find that our approach not only has low prediction error compared to baseline models but also allows for meaningful interpretation of the network. These interpretations can both explain predictions made and discover novel connections in the biological knowledge that could lead to new hypotheses about mechanisms of drug action.
Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing

In melanoma, the lymphocytic infiltrate is a prognostic parameter classified morphologically into “brisk”, “non-brisk” and “absent” entailing a functional association that has never been proved. Recently, it has been shown that lymphocytic populations can be very heterogeneous, and that anti-PD-1 immunotherapy supports activated T cells. Here, we characterize the immune landscape in primary melanoma by high-dimensional single cell multiplex analysis in tissue sections (MILAN technique) followed by image analysis, RT-PCR and shotgun proteomics. We observed that the brisk and non-brisk patterns are heterogeneous functional categories that can be further sub-classified into active, transitional or exhausted. The classification of primary melanomas based on the functional paradigm also shows correlation with spontaneous regression, and an improved prognostic value than that of the brisk classification. Finally, the main inflammatory cell subpopulations that are present in the microenvironment associated with activation and exhaustion and their spatial relationships are described using neighbourhood analysis.
Hierarchical phylogeny construction

xi CHAPTER 1. OVERVIEW . 1 1.
Soil Water Carrying Capacity for Vegetation

Non-native plantation can effectively conserve soil and water and improve ecological environment,but soil desiccation occurs and then changes to severe desiccation in most forest and grass lands of water-limited regions, which causes soil degradation, vegetation decline and crop failure, so it is necessary to regulate the changed relationship between plant growth and soil water. However, there is a lack of a universally accepted theory to provide guidance of sustainable use of soil water resources and sustainable management of forest and sustainable produce of crop in such regions. The theory of regulating the relationship between plant growth and soil water in water-limited regions includes the Soil Water Resources Use Limit by Plant (SWRULP) and Soil Water Carrying Capacity for Vegetation (SWCCV). The SWCCV is the population in a plant population or density of indicator plants in a plant community when the soil water supply is equal to soil water consumption in the root zone and a given time, and changes with plant community type, location and time. The degree of coverage, productivity and benefits of a plant community when population quantity of an indicator plant equals SWCCV should be the theoretical basis for ensuring sustainable use of soil water resources and sustainable development of forest.
Non-Equilibrial Dynamics in Under-Saturated Communities

The concept of the evolutionary stable strategy (ESS) has been fundamental to the development of evolutionary game theory. It represents an equilibrial evolutionary state in which no rare invader can grow in population size. With additional work, the ESS concept has been formalized and united with other stability concepts such as convergent stability, neighborhood invasion stability, and mutual invisibility. Other work on evolutionary models, however, shows the possibility of unstable and/or non-equilibrial dynamics such as limit cycles and evolutionary suicide. Such “pathologies” remain outside of a well-defined context, especially the currently defined stability concepts of evolutionary games. Ripa et al. (2009) offer a possible reconciliation between work on non-equilibrial dynamics and the ESS concept. They noticed that the systems they analyzed show non-equilibrial dynamics when under-saturated and “far” from the ESS and that getting “closer” to the ESS through the addition of more species stabilized their systems. To that end, we analyzed three models of evolution, two predator-prey models and one competition model of evolutionary suicide, to see how the degree of saturation affects the stability of the system. In the predator-prey models, stability is linked to the degree of saturation. Specifically, a fully saturated community will only show stable dynamics, and unstable dynamics occur only when the community is under-saturated. With the competition model, we demonstrate it to be permanently under-saturated, likely showing such extreme dynamics for this reason. Though not a general proof, our analysis of the models provide evidence of the link between community saturation and evolutionary dynamics. Our results offer a possible placement of these evolutionary “pathologies” into a wider framework. In addition, the results concur with previous results showing greater evolutionary response to less biodiversity and clarifies the effect of extrinsic vs. intrinsic non-equilibrial evolutionary dynamics on a community.
Rangelia vitalii infection in a dog from São Paulo city, Brazil: case report

Canine rangeliosis is an extravascular hemolytic disease caused by the protozoan Rangelia vitalii, which is transmitted by ticks of the species Amblyomma aureolatum. Te most common clinical signs are apathy, hyperthermia and spontaneous bleeding. Anemia and thrombocytopenia are the most common hematological fndings. Tis work reports a clinical case of canine Rangeliosis treated at a private veterinary hospital, in São Paulo city in 2017. A dog was treated at a veterinary hospital in the north of São Paulo, with progressive weight loss, apathy and tail injury. Anemia and thrombocytopenia were observed on the hemogram. Rangelia vitalii DNA was detected in animal blood by real-time PCR (qPCR). In addition to the supportive treatment, doxycycline and subcutaneous imidocarb applications were used. Te sample collected afer treatment with the antibiotic continued to present protozoal DNA. Te disease should be considered as a diferential diagnosis and there is a great need for further studies about the therapy used.
Functional Connectivity Evoked by Orofacial Tactile Perception of Velocity

The cortical representation of orofacial pneumotactile stimulation involves a complex network, which is still unknown. This study aims to identify the characteristics of functional connectivity (FC) elicited by different saltatory velocities over the perioral and buccal surface of the lower face using functional magnetic resonance imaging (fMRI) in twenty neurotypical adults. Our results showed 25 cm/s evoked more functional coupling in the right hemisphere, suggesting 25 cm/s might be optimal velocity if bilateral brain damages occur. The decreased FC between the right secondary somatosensory cortex and right posterior parietal cortex for 5 cm/s versus All-on showed that the relatively slow velocity evoked less coupling in the ipsilateral hemisphere, which suggesting functional coupling in the contralateral hemisphere is in charge of orofacial tactile perception of velocity. The increased FC between the right thalamus and bilateral secondary somatosensory cortex for 65 cm/s versus All-on indicated that the neural encoding of relatively fast tactile velocity is more coupling between the right thalamus and bilateral secondary somatosensory cortex. Our results have shown different characteristics of FC for each seed at various velocity contrasts (5 > 25 cm/s, 5 > 65 cm/s, and 25 > 65 cm/s), suggesting the neuronal networks encoding the orofacial tactile perception of velocity. The difference of functional connectivity among three velocities may indicate the optimal stimulation setting for better therapeutic effects on stroke recovery.
Revisión del género Boletus L. (Boletales, Basidiomycota) en Chile

El género Boletus cuenta con alrededor de 300 especies, las cuales se encuentran ampliamente distribuidas en el mundo, formando micorrizas con diversos árboles. En Chile se han documentado seis especies: Boletus loyo, B. loyita, B. chilensis, B. putidus, B. bresinskyanus y B. araucariae, asociadas exclusivamente a Nothofagus spp. , siendo Boletus loyo actualmente clasificada en el género Butyriboletus. En esta revisión, se describen los caracteres macro y microscópicos junto con la distribución climática de las seis especies nativas presentes en nuestro país de acuerdo a la literatura. Además, se presenta una clave dicotómica basada en bibliografía relevante para ayudar a su determinación.