Leveraging Bayesian deep learning and ensemble methods for uncertainty quantification in image classification: A ranking-based approach.

Bayesian deep learning (BDL) has emerged as a powerful technique for quantifying uncertainty in classification tasks, surpassing the effectiveness of traditional models by aligning with the probabilistic nature of real-world data. This alignment allows for informed decision-making by not only identifying the most likely outcome but also quantifying the surrounding uncertainty. Such capabilities hold great significance in fields like medical diagnoses and autonomous driving, where the consequences of misclassification are substantial. To further improve uncertainty quantification, the research community has introduced Bayesian model ensembles, which combines multiple Bayesian models to enhance predictive accuracy and uncertainty quantification. These ensembles have exhibited superior performance compared to individual Bayesian models and even non-Bayesian counterparts. In this study, we propose a novel approach that leverages the power of Bayesian ensembles for enhanced uncertainty quantification. The proposed method exploits the disparity between predicted positive and negative classes and employes it as a ranking metric for model selection. For each instance or sample, the ensemble's output for each class is determined by selecting the top 'k' models based on this ranking. Experimental results on different medical image classifications demonstrate that the proposed method consistently outperforms or achieves comparable performance to conventional Bayesian ensemble. This investigation highlights the practical application of Bayesian ensemble techniques in refining predictive performance and enhancing uncertainty evaluation in image classification tasks.

Globularia arabica Methanolic Leaf Extract Has Higher Efficacy on Burn Wound Healing in Diabetic Rats Compared to Malva slyvestries Methanolic Leaf Extract.

This study aimed to see how effective Globularia arabica and Malva slyvestries-based cream formulations were at healing scald burn wounds in rats. Depending on ointment, preparations of 1%, 5%, and 10% w/w were created. For comparison, an ointment base and a regular burn cream composed soframycine were utilized. Rats introduced a burn by solidifying equipment at 100°C on a 14-mm2 shaved dorsal region. A deep second-degree burn was created, and the percentage of wound contraction was measured over the next 15 days. The rats were euthanized on days 8 and 15, and histological slides were prepared using hematoxylin and eosin staining. Compared to the control group, there was a substantial increase in wound contraction and a significant decrease in the duration of epithelialization in the based ointment-treated groups. However, as paralleled to Globularia arabica, significant (P < .05) results were observed with 10% Globularia arabica cream, whereas Malva slyverstries indicate minimal healing. Soframycine causes a substantial increase in wound contraction (P < .05). Soframycine cream with 10% Globularia arabica therapy resulted in practically complete re-epithelialization and re-structuring of wound tissue on histological examination, whereas Malva slyversries treatment resulted in low epithelization during treatment days. The findings suggest that Globularia arabica-based cream has the wound-healing capability.

Efficacy of methanolic extracts of some medicinal plants on wound healing in diabetic rats.

Background: One of the primary health concerns for diabetes individuals is wounds. The used drugs have several side effects, urging the need for new natural sources for therapeutics. Materials and methods: This study was designed to estimate the wound healing potential of the methanolic extract of Globularia arabica and Malva sylvestris leaves and Rhus coriaria fruits. plant extracts were orally administered to the rats to determine their effect on the wound-healing process. Results: Plant extracts significantly increased the contraction of the wound in non-diabetic and diabetic rats (P < 0.05) and increased the fibroblast's proliferation and migration resulting in a faster healing process. The plant extracts have no cytotoxic effects. The proliferation assay exhibited the lowest cell mortality after treatment with plant extract. Conclusion: These findings may indicate that the methanolic leaf extract of the above plants can be used as new therapeutics for wound healing in diabetic patients.

In Vivo Therapeutic Effect of Some Medicinal Plants' Methanolic Extracts on the Growth and Development of Secondary Hydatid Cyst Infection.

PURPOSE: The current study aimed to explore the in vivo therapeutic effects of the methanolic extracts of Citrullus colocynthis, Ruta graveolens, and Peganum harmala against hydatid cyst secondary infection. METHODS: Aerial parts of P. harmala and R. graveolens, including leaves and stems, and seeds of C. colocynthis were collected and extracted using absolute methanol. Rats that are infected with secondary infection of hydatid cysts were treated orally and intraperitoneally according to the determined lethal doses for 30 days. Histological, hematological, and biochemical investigations were done 8 months after the infection. RESULTS: Compared to Albendazole drug, C. colocynthis, and P. harmala, the methanol extract of R. graveolens showed higher and significant (P < 0.05) therapeutic effects on the secondary hydatid cysts growth. Those effects were represented by the reduction in the cysts' number, size, and weight; as well as the significant changes (P < 0.05) in values of hematological and biochemical parameters, the elevation of IFN-γ levels, and the decline of IL-10 and IL-4 cytokines, compared to the negative control group in both routes of treatment (oral and IP). Moreover, the histological sections showed that R. graveolens has a clear damaging effect on the hydatid cysts GL in the infected rats represented by the detachment of GL from LL and AL. CONCLUSION: This study can open an avenue to find new therapeutics for secondary hydatid cyst infections using the studied plant extracts, especially the extract of R. graveolens.

Ruta graveolens, Peganum harmala, and Citrullus colocynthis methanolic extracts have in vitro protoscolocidal effects and act against bacteria isolated from echinococcal hydatid cyst fluid.

Echinococcosis is a common and endemic disease that affects both humans and animals. In this study, the in vitro activities of methanolic extracts of Ruta graveolens, Peganum harmala aerial parts, and Citrullus colocynthis seeds against protoscolosis and isolated bacterial strains from hydatid cysts were assessed using disc diffusion methods and Minimum Inhibitory Concentration (MIC). The chemical composition of three methanolic extracts was studied using LC-MS. After 3 h of exposure to 40 mg/mL R. graveolens extract, a tenfold protoscolocidal effect was seen when compared to the convintional medication (ABZ) for the same duration (P < 0.05). The bacteria listed below were isolated from hydatid cyst fluid collected from a variety of sick locations, including the lung and liver. Micrococcus spp., E. coli, Klebsiella oxytoca, Enterobacter aerogenes, Enterobacter amnigenus, Pseudomonas aeruginosa, Staphylococcus xylosus, and Achromobacter xylosoxidans are among the bacteria that have been identified. The most effective extract was R. graveolens, followed by P. harmala and C. colocynthis, according to the results of antibacterial activity using the disc diffusion method. R. graveolens extract had the lowest MIC values (less than 2 mg/mL) against all microorganisms tested. This shows that the R. graveolens extract has additional properties, such as the ability to be both scolocidal and bactericidal. Because these bacteria are among the most prevalent pathogenic bacteria that increase the risk of secondary infection during hydatid cysts, the results of inhibitory zones and MICs of the R. graveolens methanol extract are considered highly promising.

Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review.

The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.

Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning.

Modern societies are exposed to a myriad of risks ranging from disease to natural hazards and technological disruptions. Exploring how the awareness of risk spreads and how it triggers a diffusion of coping strategies is prominent in the research agenda of various domains. It requires a deep understanding of how individuals perceive risks and communicate about the effectiveness of protective measures, highlighting learning and social interaction as the core mechanisms driving such processes. Methodological approaches that range from purely physics-based diffusion models to data-driven environmental methods rely on agent-based modeling to accommodate context-dependent learning and social interactions in a diffusion process. Mixing agent-based modeling with data-driven machine learning has become popularity. However, little attention has been paid to the role of intelligent learning in risk appraisal and protective decisions, whether used in an individual or a collective process. The differences between collective learning and individual learning have not been sufficiently explored in diffusion modeling in general and in agent-based models of socio-environmental systems in particular. To address this research gap, we explored the implications of intelligent learning on the gradient from individual to collective learning, using an agent-based model enhanced by machine learning. Our simulation experiments showed that individual intelligent judgement about risks and the selection of coping strategies by groups with majority votes were outperformed by leader-based groups and even individuals deciding alone. Social interactions appeared essential for both individual learning and group learning. The choice of how to represent social learning in an agent-based model could be driven by existing cultural and social norms prevalent in a modeled society.

Intelligent judgements over health risks in a spatial agent-based model.

BACKGROUND: Millions of people worldwide are exposed to deadly infectious diseases on a regular basis. Breaking news of the Zika outbreak for instance, made it to the main media titles internationally. Perceiving disease risks motivate people to adapt their behavior toward a safer and more protective lifestyle. Computational science is instrumental in exploring patterns of disease spread emerging from many individual decisions and interactions among agents and their environment by means of agent-based models. Yet, current disease models rarely consider simulating dynamics in risk perception and its impact on the adaptive protective behavior. Social sciences offer insights into individual risk perception and corresponding protective actions, while machine learning provides algorithms and methods to capture these learning processes. This article presents an innovative approach to extend agent-based disease models by capturing behavioral aspects of decision-making in a risky context using machine learning techniques. We illustrate it with a case of cholera in Kumasi, Ghana, accounting for spatial and social risk factors that affect intelligent behavior and corresponding disease incidents. The results of computational experiments comparing intelligent with zero-intelligent representations of agents in a spatial disease agent-based model are discussed. METHODS: We present a spatial disease agent-based model (ABM) with agents' behavior grounded in Protection Motivation Theory. Spatial and temporal patterns of disease diffusion among zero-intelligent agents are compared to those produced by a population of intelligent agents. Two Bayesian Networks (BNs) designed and coded using R and are further integrated with the NetLogo-based Cholera ABM. The first is a one-tier BN1 (only risk perception), the second is a two-tier BN2 (risk and coping behavior). RESULTS: We run three experiments (zero-intelligent agents, BN1 intelligence and BN2 intelligence) and report the results per experiment in terms of several macro metrics of interest: an epidemic curve, a risk perception curve, and a distribution of different types of coping strategies over time. CONCLUSIONS: Our results emphasize the importance of integrating behavioral aspects of decision making under risk into spatial disease ABMs using machine learning algorithms. This is especially relevant when studying cumulative impacts of behavioral changes and possible intervention strategies.

Effects of the main extraction parameters on chemical and microbial characteristics of compost tea.

The rising popularity of compost tea as fertilizer or foliar spray against pathogens has encouraged many researchers to evaluate its performance without standardizing its quality, so obtaining inconsistent and controversial results. The fertilizing and pesticide-like effects of compost tea are due to its chemical and microbiological properties. Therefore, this study aimed to identify the best combination of the compost tea extraction parameters for exalting both chemical and microbiological features. A factorial design was adopted to evaluate the effects of compost/water ratio, extraction time, storage duration and storage temperature in different combination on physical, chemical and microbiological characteristics of compost tea, and the results were elaborated through different statistical analyses. Compost tea nutrients and microorganisms were influenced by compost/water ratio and extraction time. In addition, the storage duration affected the microbial populations, whereas the storage temperature influenced only the fungal population of compost tea. Results suggested that the best combination of the studied parameters was: 1:2.5 compost/water ratio, 2days of extraction time and the compost tea should be utilized immediately after the extraction, since the storage reduced the microbial populations.

First Report of Citrus Root Rot Caused by Phytophthora palmivora in Egypt.

During spring-summer 2009, a survey was conducted to determine the species of Phytophthora present in citrus nurseries in Egypt. A total of 300 samples of soil and fibrous roots were collected from the rhizosphere of symptomatic Volkameriana lemon (Citrus volkameriana Tan. & Pasq.) plants growing in Delta (Benha-Qalyubia) and a desert (Cairo/Alexandria desert road) citrus nurseries. Plants showed various symptoms. Canopies of affected plants showed few and yellowish leaves, a general stunted growth, no new vegetation, and sometimes sudden desiccation; the root system showed few dark brown feeder roots, no new yellow-white apexes, and a fibrous appearance of the rootlets due to disintegration of the cortical bark but not of the xylem. Collected rootlets and soil were plated in Petri dishes containing a selective medium for the oomycete Phytophthora (2) and incubated for 3 to 6 days at 19 ± 1°C as described by Ippolito et al. (1). Pure cultures were obtained by single-hypha transfers and the isolates were identified as Phytophthora palmivora (Butler) Butler on the basis of morphological and cultural characteristics (3). Isolates formed stoloniferous colonies on potato dextrose agar (PDA) and grew between 10 and 30°C, with the optimum at 25°C. On V8 juice agar, they showed a highly fluffy pattern and produced terminal and intercalary globose chlamydospores. Sporangia were papillate, elliptical (45 to 51 × 29 to 35 µm; length/breadth ratio of 1.3:1.8), and were caducous with short pedicel. All isolates were A2 mating type, forming spherical oogonia and amphigynous antheridia in dual cultures with reference P. palmivora isolate of A1 mating type. Identification of the isolates was further confirmed by amplification and sequencing of the internal transcribed spacer (ITS) region using the universal primers ITS4 and ITS6. BLASTn analysis of ITS sequences (GenBank Accession No. HE583183) showed 99% homology with P. palmivora isolates available in GenBank. Pathogenicity tests for P. palmivora were conducted by inoculating three groups of ten 6-month-old Volkameriana lemon plants, transplanted into 1.4 liter pots with growing medium artificially inoculated at the rate of 1% (v/v) of P. palmivora inoculum produced according to Yaseen (4). Ten uninoculated plants served as a control. Two months after the inoculation, plants were analyzed for canopy symptoms and the presence of pathogen in feeder roots. More than 50% of inoculated plants showed foliage symptoms and extensive decay of feeder roots. Colonies of Phytophthora were recovered from necrotic rootlets and identified as P. palmivora, fulfilling Koch's postulates. To the best of our knowledge, this is the first report of P. palmivora as a pathogen to citrus plants in the Egyptian nurseries. P. palmivora should be considered a potential threat to the Egyptian citrus industry since it may negatively influence the nurseries and orchards production in the future. References: (1) A. Ippolito, V. De Cicco, and M. Salerno. Rivista di Patologia Vegetale 2:57, 1992. (2) H. Masago, M. Yoshikawa, M. Fukada, and N. Nakanishi. Phytopathology 67:425, 1977. (3) D. J. Stamps. Revised tabular key to the species of Phytophthora. CAB International Mycological Institute, Kew, Surrey, 1990. (4) T. Yaseen. Molecular diagnosis and biological control of Phytophthora-citrus root rot. PhD thesis. University of Bari, Italy, 2004.

First report of blood parasites in fishes from Kashmir and their effect on the haematological profile.

Cyprinus carpio communis Linnaeus, Carassius carassius Linnaeus, Schizothorax curvifrons Heckel and Triplophysa marmorata species of fishes were captured from Anchar Lake and river Jhelum of Kashmir Himalaya for hematological and parasitological analysis. During the investigation haemoflagellates from the genus Babesiosoma and Trypanosoma were recorded in the blood smears. Trypanosomes were present in all the species except C. carpio, whereas Babesiosoma were only found in T. marmorata. Haematological analysis revealed a significant (p<0.01) reduction in red blood cell count in the fishes infected with Babesiosoma and Trypanosoma. A significant decrease (p<0.05) was recorded in haemoglobin value and packed cell volume in the infected fishes in comparison to the non-infected fishes.

First Report of Cylindrocarpon pauciseptatum Associated with Root Rot and Decline of Peach in Southern Italy (Apulia Region).

During a survey for the sanitary status of stone fruits in southern Italy (Apulia region), symptoms of low vigor, sparse foliage, and chlorosis of leaves, frequently leading to decline or death of the plants, were observed on 3- to 5-year-old peach trees (Prunus persica) cvs. Tardi Belle, Zee Lady, and O'Henry grafted on GF677. Brown-to-black discolorations of the wood were observed in cross-sections of the trunks just below the graft union. Samples were collected from May to June 2010 from two symptomatic orchards in Brindisi and Foggia provinces. Small pieces of brownish, vascular wood and necrotic root tissues were surface disinfested, placed onto potato dextrose agar (PDA), and incubated for 7 days at 25°C in the dark. Single-conidial isolates were subsequently grown on PDA at 25°C for 10 days. Fungal colonies were presumptively identified as members of the genus Cylindrocarpon on the basis of their morphological and conidial characteristics. On PDA, the isolates developed abundant mycelium, which gradually became yellowish or partially brownish. Macroconidia were predominantly three septate, straight and cylindrical with both ends broadly rounded. Chlamydospores and ovoidal microconidia were observed on synthetic nutrient-poor agar (1). Sequence of the ribosomal internal transcribed spacer (ITS) region was obtained using universal primers (ITS6-ITS4) and deposited in GenBank (Accession No. HE577846). This sequence revealed 100% genetic identity with a sequence from Cylindrocarpon pauciseptatum Schroers & Crous (Accession No. EF607090), a recently described species (3). In nature, several species of the genus Cylindrocarpon affect a large number of woody plants, mainly grapevine, olive, and stone fruits, in which they attack the root surface (2). To verify Koch's postulates, the roots of 20 3-month-old peach seedlings (GF305) were dipped for 30 min in a spore suspension of the fungus (1 × 108 conidia ml-1). Seedlings were then transplanted in an artificial soil mix and held under controlled conditions in a greenhouse at 24°C. Typical black-foot symptoms developed on 92% of the inoculated plants within 3 months, whereas the control plants, whose roots had been dipped in distilled water, remained healthy. C. pauciseptatum was reisolated from infected tissues and internal vascular lesions of 45% of the inoculated plants, but none of the plants used as controls, fulfilling Koch's postulates. To our knowledge, this is the first report of this pathogen on peach in the Apulia Region of Italy. Currently, C. pauciseptatum is limited to a few orchards where presumably it was introduced with infected propagating material from extra-regional nurseries. C. pauciseptatum has the potential to negatively affect the stone fruit industry in Italy including reducing nursery production and productivity and vigor of trees in orchards, or even rapid death of young trees. References: (1) W. Gams et al. CBS Course of Mycology. 4th ed. Centraalbureau voor Schimmelcultures, Baarn, the Netherlands, 1998. (2) M. E. S. Hernandez et al. Eur. J. Plant Pathol. 104:347, 1998. (3) H. J. Schroers et al. Mycol. Res. 112:82, 2008.

Macro invertebrate community from Sonamarg streams of Kashmir Himalaya.

This study analyses a macroinvertebrate community survey for River Sindh and its tributary including Baltal, Yashmarg, Sonamarg and Thajwas Grar considering the extreme hydrological conditions linked with the seasonal low-flow period typical for some streams in this area. This study attempts to provide an overview of the macro invertebrate assemblages and physico-chemical variables of the River Sindh and its important tributary. Four study sites were selected from the River Sindh and its tributary including Baltal, Yashmarg, Sonamarg and Thajwas Grar for studying the ecological distribution of Macroinvertebrate assemblages. Totally, 33 taxa of macroinvertebrates were recorded from the two streams belonging to Mollusca-3 (Gastropoda-2 and Bivalvia-1), Annelida-1 and Arthropoda-29 (Insecta-29). Among insects Ephemeroptera (7), Trichoptera (6) and Diptera (13) dominated. Except Yashmrag all sites were found devoid of annelids while as the mollusks were found absent at Sonamarg. Highest values of Shannon Weiner Index were found at Yashmarg (2.42) and lowest at Sonamarg (1.99) while as highest and lowest Sorensen's similarity coefficient were found between Baltal/Thajwas Grar (0.68) and Yashmarg/Thajwas Grar (0.39), respectively. A perusal of the data on physico-chemical characteristics showed that these streams were hard water type with high dissolved oxygen content. The ionic composition of the stream waters revealed the predominance of bicarbonate and calcium. Insecta dominated both qualitatively as well as quantitatively and the study revealed that the substrate compositions dominated by gravel, pebble and leaf litters are primary determinants of the invertebrate community structure recording maximum species diversity and abundance. Sample locations impacted by Amarnath yatris pilgrimage comparatively reflected slightly higher increase in nutrients than Thajwas Grar almost devoid of pilgrimage effect.

Early detection of Aspergillus carbonarius and A. niger on table grapes: a tool for quality improvement.

Aspergillus carbonarius and A. niger aggregate are the main fungal contaminants of table grapes. Besides their ability to cause black rot, they can produce ochratoxin A (OTA), a mycotoxin that has attracted increasing attention worldwide. The objective of this work was to set up a simple and rapid molecular method for the early detection of both fungi in table grapes before fungal development becomes evident. Polymerase chain reaction (PCR)-based assays were developed by designing species-specific primers based on the polyketide synthases (PKS(S)) sequences of A. carbonarius and A. niger that have recently been demonstrated to be involved in OTA biosynthesis. Three table grape varieties (Red globe, Crimson seedless, and Italia) were inoculated with A. carbonarius and A. niger aggregate strains producing OTA. The extracted DNA from control (non-inoculated) and inoculated grapes was amplified by PCR using ACPKS2F-ACPKS2R for A. carbonarius and ANPKS5-ANPKS6 for A. niger aggregate. Both primers allowed a clear detection, even in symptomless samples. PCR-based methods are considered to be a good alternative to traditional diagnostic means for the early detection of fungi in complex matrix for their high specificity and sensitivity. The results obtained could be useful for the definition of a 'quality label' for tested grapes to improve the safety measures taken to guarantee the production of fresh table grapes.