Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Validation of a Mechanistic Model That Predicts Infection by Diaporthe ampelina, the Causal Agent of Phomopsis Cane and Leaf Spot of Grapevines

Phomopsis cane and leaf spot (PCLS), known in Europe as “excoriose,” is an important fungal disease of grapevines caused by Diaporthe spp. , and most often by Diaporthe ampelina (synonym Phomopsis viticola). PCLS is re-emerging worldwide, likely due to climate change, changes in the management of downy mildew from calendar- to risk-based criteria that eliminate early-season (unnecessary) sprays, and the progressive reduction in the application of broad-spectrum fungicides. In this study, a mechanistic model for D. ampelina infection was developed based on published information. The model accounts for the following processes: (i) overwintering and maturation of pycnidia on affected canes; (ii) dispersal of alpha conidia to shoots and leaves; (iii) infection; and (iv) onset of disease symptoms. The model uses weather and host phenology to predict infection periods and disease progress during the season. Model output was validated against 11 independent PCLS epidemics that occurred in Italy (4 vineyards in 2019 and 2020) and Montenegro (3 vineyards in 2020). The model accurately predicted PCLS disease progress, with a concordance correlation coefficient (CCC) = 0.925 between observed and predicted data. A ROC analysis (AUROC>0.7) confirmed the ability of the model to predict the infection periods leading to an increase in PCLS severity in the field, indicating that growers could use the model to perform risk-based fungicide applications.
A Novel Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Yersinia pestis

Rapid detection of Yersinia pestis, the causative agent of plague, is essential during field investigations to enable prompt control measures for prevention of the spread of the disease. Affordable, efficient, reliable, and simple detection assays are extremely useful, particularly in plague-endemic regions with limited resources. We developed a loop-mediated isothermal amplification (LAMP) assay that detects Y. pestis within 30 min by simply incubating at 65°C on a dry bath heater. The assay targeted the caf1A gene that is situated on the pMT1 plasmid using six specific primers. Y. pestis presence is visually detected based on the color change in the reactions. For comparison of the assay performance, a real-time LAMP with fluorescent dye detection was conducted on a real-time PCR instrument using the same six primers. Sensitivity assessment showed that the limit of detection (LOD) was 0.2 and 0.03 pg when performed on the dry bath heater and on the real-time PCR instrument, respectively. The assay was 100% specific, having no cross-reactivity with closely related Yersinia spp. and other bacterial species. We tested the LAMP assay on field-collected fleas and showed that it successfully detected Y. pestis with identical results to that of a previously published pentaplex real-time PCR assay. These findings suggest that the relatively inexpensive and simpler LAMP assay could be used to support field investigations, yielding comparable results to more expensive and complex PCR assays.
Male Meiosis as a Biomarker for Endo- to Ecodormancy Transition in Apricot

Dormancy is an adaptive strategy in plants to survive under unfavorable climatic conditions during winter. In temperate regions, most fruit trees need exposure to a certain period of low temperatures to overcome endodormancy. After endodormancy release, exposure to warm temperatures is needed to flower (ecodormancy). Chilling and heat requirements are genetically determined and, therefore, are specific for each species and cultivar. The lack of sufficient winter chilling can cause failures in flowering and fruiting, thereby compromising yield. Thus, the knowledge of the chilling and heat requirements is essential to optimize cultivar selection for different edaphoclimatic conditions. However, the lack of phenological or biological markers linked to the dormant and forcing periods makes it difficult to establish the end of endodormancy. This has led to indirect estimates that are usually not valid in different agroclimatic conditions. The increasing number of milder winters caused by climatic change and the continuous release of new cultivars emphasize the necessity of a proper biological marker linked to the endo- to ecodormancy transition for an accurate estimation of the agroclimatic requirements (AR) of each cultivar. In this work, male meiosis is evaluated as a biomarker to determine endodormancy release and to estimate both chilling and heat requirements in apricot. For this purpose, pollen development was characterized histochemically in 20 cultivars over 8 years, and the developmental stages were related to dormancy. Results were compared to three approaches that indirectly estimate the breaking of dormancy: an experimental methodology by evaluating bud growth in shoots collected periodically throughout the winter months and transferred to forcing chambers over 3 years, and two statistical approaches that relate seasonal temperatures and blooming dates in a series of 11–20 years by correlation and partial least square regression. The results disclose that male meiosis is a possible biomarker to determine the end of endodormancy and estimate AR in apricot.
Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms

Interactions between bacteria and phytoplankton in aqueous ecosystems are both complex and dynamic, with associations that range from mutualism to parasitism. This review focuses on algicidal interactions, in which bacteria are capable of controlling algal growth through physical association or the production of algicidal compounds. While there is some evidence for bacterial control of algal growth in the field, our understanding of these interactions is largely based on laboratory culture experiments. Here, the range of these algicidal interactions is discussed, including specificity of bacterial control, mechanisms for activity, and insights into the chemical and biochemical analysis of these interactions. The development of algicidal bacteria or compounds derived from bacteria for control of harmful algal blooms is reviewed with a focus on environmentally friendly or sustainable methods of application. Potential avenues for future research and further development and application of bacterial algicides for the control of algal blooms are presented.
Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea

Rusts are among the most important foliar biotrophic fungal diseases in legumes. Lathyrus cicera crop can be severely damaged by Uromyces pisi, to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in L. cicera. To prioritise the causative variants controlling partial resistance to rust in L. cicera, a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs’ U. pisi disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to U. pisi resistance in L. cicera was quantified for each RIL individual and used for eQTL mapping. One cis-eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance – a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.
Rapid and Facile Preparation of Giant Vesicles by the Droplet Transfer Method for Artificial Cell Construction

Giant vesicles have been widely used for the bottom-up construction of artificial (or synthetic) cells and the physicochemical analysis of lipid membranes. Although methods for the formation of giant vesicles and the encapsulation of molecules within them have been established, a standardized protocol has not been shared among researchers including non-experts. Here we proposed a rapid and facile protocol that allows the formation of giant vesicles within 30 min. The quality of the giant vesicles encapsulating a cell-free protein expression system was comparable to that of the ones formed using a conventional method, in terms of the synthesis of both soluble and membrane proteins. We also performed protein synthesis in artificial cells using a lyophilized cell-free mixture and showed an equivalent level of protein synthesis. Our method could become a standard method for giant vesicle formation suited for artificial cell research.
Design and Simulation of Model for Energy Harvesting from Vehicle Tires Using Piezoelectric Modules

Piezoelectric materials hold the unique feature of development of electric potential upon application of mechanical stress and vice versa technically known as direct and indirect effect respectively. Many developments in the field of vibration-based energy harvesting in past few decades has been done and the accelerated depletion rate of conventional sources of energy in the recent years has drawn attention of science community towards sustainable energy development and researchers towards development of new energy harvesting techniques to tap the energy lost to the environment. This paper proposes a new design to harvest energy from vehicle tires by the use of PZT modules in the tire carcass utilizing the stresses developed at the tube and tire interface. The design has been modelled in MATLAB Simscape and simulated using COMSOL Multiphysics 5.0. The output voltage can be used to charge batteries for energy storage for future use.
Research on Pathogenic Hippocampal Voxel Detection in Alzheimer's Disease Using Clustering Genetic Random Forest

Alzheimer's disease (AD) is an age-related neurological disease, which is closely associated with hippocampus, and subdividing the hippocampus into voxels can capture subtle signals that are easily missed by region of interest (ROI) methods. Therefore, studying interpretable associations between voxels can better understand the effect of voxel set on the hippocampus and AD. In this study, by analyzing the hippocampal voxel data, we propose a novel method based on clustering genetic random forest to identify the important voxels. Specifically, we divide the left and right hippocampus into voxels to constitute the initial feature set. Moreover, the random forest is constructed using the randomly selected samples and features. The genetic evolution is used to amplify the difference in decision trees and the clustering evolution is applied to generate offspring in genetic evolution. The important voxels are the features that reach the peak classification. The results demonstrate that our method has good classification and stability. Particularly, through biological analysis of the obtained voxel set, we find that they play an important role in AD by affecting the function of the hippocampus. These discoveries demonstrate the contribution of the voxel set to AD.
Use of Prophylactic Indomethacin in Preterm Infants: A Systematic Review and Meta-Analysis

Background Prophylactic indomethacin has been widely used as an effective intervention for reducing mortalities and morbidities in preterm infants including the cardiopulmonary and neurodevelopmental morbidities such as intraventricular hemorrhage (IVH), but many studies have reported contradictory outcomes regarding its significance. Therefore, we aim to systematically review and meta-analyze the data of prophylactic indomethacin on preterm infants. Methods Our systematic search included the following databases: Pubmed, Google Scholar, Scopus, Web of Science, The New York Academy of Medicine (NYAM), Virtual health library (VHL), and the System for Information on Grey Literature in Europe (SIGLE) to include studies that assessed the use of prophylactic indomethacin in preterm infants until 12 August 2021. Results The final list of our included studies is comprised of 23 randomized trials and cohort studies. Among all the studies outcomes, significant favorable outcome was lowering the rate of PDA, surgical PDA ligation (P < 0.001) and severe IVH (P = 0.008) while no significance was recorded with BPD, pulmonary hemorrhage, intraventricular hemorrhage, necrotizing enterocolitis, intestinal perforation, mortality, and length of hospital stay. Conclusion Since the meta-analysis results regarding effectiveness of prophylactic indomethacin varied based on the study design particularly with regard to outcomes such as surgical PDA ligation and severe IVH, this warrants the need for more evidence regarding the effectiveness of prophylactic indomethacin in very low birth weight infants.
Evaluation of a Restoration Approach After One Century – Effects of Admixed European Beech on the Natural Regeneration Potential and Humus Condition in Spruce Stands

About 100 years ago, groups of European beech were reintroduced into Norway spruce stands in some parts of Germany as a restoration approach. The aim of this approach was to maintain or rehabilitate the ecological function of soil fertility and the regeneration option of beech for the next generation. The effect of beech groups on surrounding spruce stands was studied in the Ore Mountains by recording natural regeneration of beech and humus layer thickness and form. Point pattern statistics were used to analyse the spread of beech regeneration and to determine factors influencing its establishment. It was found that the density of regeneration decreases with increasing distance from the beech group. However, beech regeneration was found up to distances of 69 m. Furthermore, it becomes evident that PAR radiation (maximum regeneration densities at PAR values of 35 W/m2) and fencing (3.41 times higher regeneration density compared to unfenced areas) against deer have a positive influence on beech regeneration density. Ordered categorical models were used to model humus form and non-linear models were used to model humus layer thickness. It could be proven that the most bioactive humus forms and lowest humus layer thicknesses were found within the beech group. With increasing distance to the beech group, the total humus layer thickness and the proportion of mormoder in the spruce stand increased. The positive influence of the beech group on the humus composition extends to about 40 m from the centre of the beech group. Due to the former arrangement of the beech groups in the terrain, the effects can also extend to the spruce stands in between. The hypotheses on the restoration approach of reintroducing groups of beech into spruce stands formulated by foresters 100 years ago can thus be confirmed. For future restoration approaches of spruce stands, groupwise mixtures of beech should be established with a distance of 40–50 m.
Fabrication of Microbicidal Silver Nanoparticles: Green Synthesis and Implications in the Containment of Bacterial Biofilm on Orthodontal Appliances

Among various metal-based nanoparticles, silver nanoparticles (AgNPs) manifest superior inhibitory effects against several microorganisms. In fact, the AgNP-based treatment has been reported to inhibit both sensitive and resistant isolates of bacteria and other disease-causing microbes with equal propensity. Keeping this fact into consideration, we executed bio-mediated synthesis of AgNPs employing extract of flower and various other parts (such as bud and leaf) of the Hibiscus rosa-sinensis plant. The physicochemical characterization of as-synthesized AgNPs was executed employing transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential, Fourier transform infrared (FTIR) spectroscopy, and UV-Vis spectroscopy, etc. The as-synthesized AgNPs demonstrated strong antimicrobial activity against both Gram-positive and Gram-negative bacteria with equal propensity. The as-synthesized AgNPs successfully inhibited Streptococcus mutans (S. mutans), one of the main causative bacteria responsible for dental caries. Considering the fact that orthodontic appliances facilitate infliction of the oral cavity with a range of microbes including S. mutans, we determined the growth inhibitory and anti-adherence activities of AgNPs on orthodontic appliances. We performed microbiological assays employing AgNPs adsorbed onto the surface of nickel–titanium (Ni-Ti) orthodontic wires. A topographic analysis of the decontaminated Ni-Ti orthodontic wires was performed by scanning electron microscopy. In addition to antimicrobial and anti-biofilm activities against oral S. mutans, the as-fabricated AgNPs demonstrated significant inhibitory and anti-biofilm properties against other biofilm-forming bacteria such as Escherichia coli and Listeria monocytogenes.
Identification of Candidate Chromosome Region Related to Melon (Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study

The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers’ requirements in different regions. In this study, genetic inheritance analysis of three F2 populations derived from six parental lines revealed that the fsg trait is controlled by a simple recessive inherited gene. Through bulked segregant analysis sequencing (BSA-seq), the Cmfsg locus was detected in an 8.96 Mb interval on chromosome 11 and then initially mapped to a region of approximately 1.15 Mb. Further fine mapping with a large F2 population including 1,200 plants narrowed this region to 207 kb containing 11 genes. A genome-wide association study (GWAS) with 187 melon accessions also produced the same chromosome region for the Cmfsg locus. Due to the rare molecular markers and lack of mutations in the coding and promoter regions of the 11 candidate genes in the fine-mapped interval, we conducted in silico BSA to explore the natural melon panel to predict candidate genes for the Cmfsg locus. A 1.07 kb segment upstream of MELO3C019694.2 (annotated as the AGAMOUS MADS-box transcription factor) exhibited a correlation with the grooved and non-grooved accessions among the F2 individuals, and a natural panel consisted of 17 melon accessions. The expression level of MELO3C019694.2 in the pericarp was higher in grooved lines than in non-grooved lines and was specifically expressed in fruit compared with other tissues (female flower, male flower, root, and leaf). This work provides fundamental information for further research on melon fsg trait formation and molecular markers for melon breeding.
How do Independent Directors View Carbon Information Disclosure? Evidence From China

This study examines the effect of independent directors on carbon information disclosure (CID) in China from 2011 to 2017. Additionally, this study investigates the effect of independent director’s attributes (gender, academic experience, and political connection) on the CID. To test our hypothesis, we collected data of 511 Chinese listed firms. The empirical results show that independent directors have a positive influence on the CID. Moreover, the independent female directors, independent academic directors and independent politically connected directors also enhances the CID. Our findings offer shareholders, regulators, and other stakeholders an integrating perspective on motivating firms to disclose high quality carbon information.
Global Research Status and Trends in Venous Thromboembolism After Hip or Knee Arthroplasty From 1990 to 2021: A Bibliometric Analysis

Background Venous thromboembolism (VTE) after hip or knee arthroplasty has attracted increasing attention over the past few decades. However, there is no bibliometric report on the publications in this field. The purpose of this study was to analyze the global research status, hotspots, and trends in VTE after arthroplasty. Methods All articles about VTE research after hip or knee arthroplasty from 1990 to 2021 were retrieved from the Web of Science Core Collection database. The information of each article including citation, title, author, journal, country, institution, keywords, and level of evidence was extracted for bibliometric analysis. Results A total of 1,245 original articles from 53 countries and 603 institutions were retrieved. The USA contributed most with 457 articles, followed by England and Canada. McMaster University in Canada was the leading institution for publications. The journals with the highest output and citation were the Journal of Arthroplasty and the Thrombosis and Haemostasis, respectively. The median number of citations was significantly different among the levels of evidence (F = 128.957, P < 0.001). The research hotspots switched from VTE diagnosis and heparin to factor Xa inhibitors (fondaparinux, rivaroxaban, apixaban) and direct thrombin inhibitors (dabigatran etexilate, ximelagatran), and finally to aspirin, risk factor studies, which can be observed from the keyword analysis and co-cited reference cluster analysis. Conclusions This study observed an increasing trend of research articles on VTE after arthroplasty. Publications with higher levels of evidence gained further popularity among researchers and orthopedic surgeons. Additionally, individualized VTE prevention and the development of new, safe, effective, and inexpensive oral agents would be emerging trends in the future.
The Two Classes of Ceramide Synthases Play Different Roles in Plant Immunity and Cell Death

Ceramide synthases (CSs) produce ceramides from long-chain bases (LCBs). However, how CSs regulate immunity and cell death in Arabidopsis thaliana remains unclear. Here, we decipher the roles of two classes of CS, CSI (LAG1 HOMOLOG 2, LOH2) and CSII (LOH1/3), in these processes. The loh1-2 and loh1-1 loh3-1 mutants were resistant to the bacterial pathogen Pseudomonas syringae pv maculicola (Psm) DG3 and exhibited programmed cell death (PCD), along with increased LCBs and ceramides, at later stages. In loh1-2, the Psm resistance, PCD, and sphingolipid accumulation were mostly suppressed by inactivation of the lipase-like proteins ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and PHYTOALEXIN DEFICIENT 4 (PAD4), and partly suppressed by loss of SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2). The LOH1 inhibitor fumonisin B1 (FB1) triggered EDS1/PAD4-independent LCB accumulation, and EDS1/PAD4-dependent cell death, resistance to Psm, and C16 Cer accumulation. Loss of LOH2 enhances FB1-, and sphinganine-induced PCD, indicating that CSI negatively regulates the signaling triggered by CSII inhibition. Like Cer, LCBs mediate cell death and immunity signaling, partly through the EDS1/PAD4 pathway. Our results show that the two classes of ceramide synthases differentially regulate EDS1/PAD4-dependent PCD and immunity via subtle control of LCBs and Cers in Arabidopsis.