Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Characterization of a (E)-β-Ocimene Synthase Gene Contributing to the Defense against Spodoptera litura

Soybean is a worldwide crop that offers valuable proteins, fatty acids, and phytonutrients to humans but is always damaged by insect pests or pathogens. Plants have captured sophisticated defense mechanisms in resisting the attack of insects and pathogens. How to protect soybean in an environment- or human-friendly way or how to develop plant-based pest control is a hotpot. Herbivore-induced plant volatiles that are released by multiple plant species have been assessed in multi-systems against various insects, of which (E)-β-ocimene has been reported to show anti-insect function in a variety of plants, including soybean. However, the responsible gene in soybean is unknown, and its mechanism of synthesis and anti-insect properties lacks comprehensive assessment. In this study, (E)-β-ocimene was confirmed to be induced by Spodoptera litura treatment. A plastidic localized monoterpene synthase gene, designated as GmOCS, was identified to be responsible for the biosynthesis of (E)-β-ocimene through genome-wide gene family screening and in vitro and in vivo assays. Results from transgenic soybean and tobacco confirmed that (E)-β-ocimene catalyzed by GmOCS had pivotal roles in repelling a S. litura attack. This study advances the understanding of (E)-β-ocimene synthesis and its function in crops, as well as provides a good candidate for further anti-insect soybean improvement.
Management of Gastro-Intestinal Toxicity of the Pi3 Kinase Inhibitor: Optimizing Future Dosing Strategies

Simple Summary Targeted therapies are becoming more widespread in the treatment of indolent B-cell malignancies, as has been the case for chronic lymphocytic leukemias and small B-cell non-Hodgkin lymphomas. Due to the severity of these diseases, several drugs have received fast track approval since 2014 including the BTK inhibitor ibrutinib, the Bcl2 inhibitor venetoclax and various P13 kinase inhibitors. Of the Pi3 kinase inhibitors, idelalisib was the first of this class to be approved, followed by the second-generation drugs copanlisib, duvelisib and umbralisib. However, the last of these agents have now been withdrawn, partly due to severe gastrointestinal side effects. We herein describe these gastrointestinal effects, as reported in clinical trials, and then review real-world data for these targeted inhibitors using world-wide pharmacovigilance evidence. Our own single-center experience of 15 patients with an indolent B-cell malignancy, from with six biopsies were derived, has helped us to describe the incidence and severity of Pi3 kinase-induced colitis. Histological analysis of these cases yielded clues toward an immunopathological hypothesis. We finally speculate on future directions in relation to managing this severe toxicity and thereby optimizing the safe use of these drugs. Abstract The phosphatidylinositol 3-kinase (PI3K) pathway plays a key role in cancer progression and in host immunity. Idelalisib was the first of this class to be approved with the second-generation Pi3 kinase inhibitors copanlisib, duvelisib and umbralisib, subsequently being approved in the United States. Real-world data are lacking, however, in relation to the incidence and toxicity of Pi3 kinase inhibitor-induced colitis. We here review, in the first instance, the general landscape of the Pi3K inhibitors in the context of hematological malignancies, with a focus on the adverse gastrointestinal side effects reported by various clinical trials. We further review the available worldwide pharmacovigilance data in relation to these drugs. Finally, we describe our own real-world experience with idelalisib-induced colitis management in our center and in a national setting.
Comparison of intracellular cytokine staining versus an ELISA‐based assay to assess CMV‐specific cell‐mediated immunity in high‐risk kidney transplant recipients

The best method for monitoring cytomegalovirus (CMV)‐specific cell‐mediated immunity (CMV‐CMI) among high‐risk kidney transplant (KT) recipients remains uncertain. We assessed CMV‐CMI by intracellular cytokine staining (ICS) by flow cytometry and a commercial interferon (IFN)‐γ release assay (QuantiFERON®‐CMV [QTF‐CMV]) at posttransplant months 3, 4, and 5 in 53 CMV‐seropositive KT recipients that had received induction therapy with antithymocyte globulin (ATG) and a 3‐month course of valganciclovir prophylaxis. The discriminative capacity (areas under receiver operating characteristics curve [auROCs]) and diagnostic accuracy to predict immune protection against CMV infection from the discontinuation of prophylaxis to month 12 were compared between both methods. There was significant although moderate correlations between CMV‐specific IFN‐γ‐producing CD8+ T‐cell counts enumerated by ICS and IFN‐γ levels by QTF‐CMV at months 3 (rho: 0.493; p = 0.005) and 4 (rho: 0.440; p = 0.077). The auROCs for CMV‐specific CD4+ and CD8+ T‐cells by ICS were nonsignificantly higher than that of QTF‐CMV (0.696 and 0.733 vs. 0.678; p = 0.900 and 0.692, respectively). The optimal cut‐off of ≥0.395 CMV‐specific CD8+ T‐cells yielded a sensitivity of 86.4%, specificity of 54.6%, positive predictive value of 79.2% and negative predictive value of 66.7% to predict protection. The corresponding estimates for QTF‐CMV (IFN‐γ levels ≥0.2 IU/mL) were 78.9%, 37.5%, 75.0%, and 42.9%, respectively. The enumeration of CMV‐specific IFN‐γ‐producing CD8+ T‐cells at the time of cessation of prophylaxis performed slightly better than the QTF‐CMV assay to predict immune protection in seropositive KT recipients previously treated with ATG.
Can Bone-Specific Alkaline Phosphatase be a Marker of Vascular Calcification in Type 2 Diabetes Mellitus?

Background and Aims: Alkaline phosphatase (ALP) enzyme has been linked to vascular calcification. Unexplained elevations in serum ALP levels have been reported in patients with type 2 diabetes mellitus (T2DM). We assessed bone-specific alkaline phosphatase (BAP) levels in patients with T2DM who had unexplained ALP elevations and studied the association between BAP and other markers of vascular calcification. Methods: Patients with T2DM who had high serum ALP in the absence of known causes of ALP elevation were studied. The control group was T2DM patients with normal ALP. We measured the serum levels of BAP along with the leptin, fetuin-A, and vitamin K2 levels. Ankle–brachial index (ABI) was also measured in both groups. Results: Serum BAP levels were significantly higher in the group with high ALP when compared with the normal ALP group. A significant positive correlation was present between BAP and serum fetuin-A as well as between BAP and Vit K2 levels. There was no correlation between BAP and serum leptin. ABI was comparable between the two groups. Conclusions: Patients with T2DM may have unexplained elevation in ALP due to an increase in BAP. Elevation in BAP may be associated with other markers of vascular calcification suggesting an increased risk of vascular calcification.
Prevalence of hypertension links with body mass index by academic population in Babylon city

Many risk factors have been listed that predispose to the occurrence of high blood pressure (BP). Although high body mass index (BMI) is a recognized risk factor for hypertension, the cutoff value for the high BMI was not taken into consideration as a predictor risk. There is no clear data on the occurrence of hypertension in Iraq in the highly educated population. Moreover, studies on hypertension in Iraq have been limited to a few studies. To assess and study the prevalence of BP in the academic population of Babylon city, a prospective study of 100 people was conducted. In the course of 3 months, during their work at the university in the morning, the questionnaire was filled out along with the body weight measurement. The receiver operating characteristic curve was used to measure the maximum area under the curve for the BMI score. Outcomes demonstrated that despite the high level of education, the prevalence of hypertension remains unacceptable. Awareness raising about the risk factors should be addressed through ongoing health education in health sectors and media. BMI of more than 25 could be considered a predictable risk value.
Innovation and competition under weak institutions: An empirical analysis of Russian firms

﻿This study examines the relationship between competition and innovation of Russian firms. We mainly explore (i) the role of competition in stimulating or suppressing product and process innovation and (ii) if the relationship is affected by institutional conditions, such as court fairness, corruption, and informal competition. The results show that innovation, particularly process innovation, has an inverted U-shaped relationship with competition but that product innovation is negatively associated with competition. Further, the negative relationship with product innovation is observed only among firms confronting problems in institutional conditions. The results imply that, whereas the promotion of competition can both encourage and discourage innovation, depending on the initial competition level, an improvement in institutional conditions can mitigate the negative effect of competition on innovation.
Structure and Dynamics of ?CDM Haloes

In the standard model (? CDM) galaxies form and evolve within underlying dark matter structures which are assumed to have grown hierarchically. As such there should be observational signatures of the merging process in the structure and dynamics of the remnant galaxy. State-of-the-art high-resolution cosmological simulations have been used to explore three such signatures: the abundance of substructure, the spin and shape of haloes, and the orbital content of these haloes.The Millennium Simulation, combined with semi-analytic galaxy catalogues, is used to compare the predicted frequency of bright central satellites to observations of field and lens galaxies. The predicted frequency is largely independent of galaxy type, but is shown to increase with redshift and halo mass. The predicted frequency is found to be lower than that observed in the Compact Lens All Sky Survey, but considerably higher than that observed in the lens sample of the Sloan Lens ACS Survey and in the field galaxies of the Sloan Digital Sky Survey and the Cosmic Evolution Survey. The distributions of the spin and shape of haloes are explored and the roles of baryons and the physical prescriptions of stellar and black hole feedback are investigated. Baryons act to make the haloes more spherical and are shown to have a significant effect on the shape of the dark matter. The shapes of the simulated haloes are in broad agreement with a wide range of observational estimates of elliptical galaxies. Results of spectral analyses of the orbital content of simulations with different feedback prescriptions are presented. Dark matter only haloes are dominated by box orbits in the central region, but the fraction of box orbits is found to decrease when baryons are included. The orbits of the stellar particles are found to be remarkably similar to those of dark matter particles.
Cardiac Reverse Remodeling in Ischemic Heart Disease with Novel Therapies for Heart Failure with Reduced Ejection Fraction

Despite the improvements in the treatment of coronary artery disease (CAD) and acute myocardial infarction (MI) over the past 20 years, ischemic heart disease (IHD) continues to be the most common cause of heart failure (HF). In clinical trials, over 70% of patients diagnosed with HF had IHD as the underlying cause. Furthermore, IHD predicts a worse outcome for patients with HF, leading to a substantial increase in late morbidity, mortality, and healthcare costs. In recent years, new pharmacological therapies have emerged for the treatment of HF, such as sodium-glucose cotransporter-2 inhibitors, angiotensin receptor-neprilysin inhibitors, selective cardiac myosin activators, and oral soluble guanylate cyclase stimulators, demonstrating clear or potential benefits in patients with HF with reduced ejection fraction. Interventional strategies such as cardiac resynchronization therapy, cardiac contractility modulation, or baroreflex activation therapy might provide additional therapeutic benefits by improving symptoms and promoting reverse remodeling. Furthermore, cardiac regenerative therapies such as stem cell transplantation could become a new therapeutic resource in the management of HF. By analyzing the existing data from the literature, this review aims to evaluate the impact of new HF therapies in patients with IHD in order to gain further insight into the best form of therapeutic management for this large proportion of HF patients.
Investigation of dual-balanced crossover designs for two treatments

An overview of properties of two-period two-treatment crossover designs without and with baseline measurements is presented. In many situations, especially in biomedical experiments, investigators are often limited to the use of two-period designs. For two-period crossover experiments, the optimality of a design is largely affected by the presence or absence of carry-over effects. In this paper, a nearly optimal four-sequence two-period crossover design is discussed.
String Theory and Quantum Field Theories in Three Dimensions

Declaration This thesis is a presentation of my original research work. Wherever contributions of others are involved, every effort is made to indicate this clearly, with due reference to the literature, and acknowledgement of collaborative research and discussions. In my capacity as supervisor of the candidate's thesis, I certify that the above statements are true to the best of my knowledge. Date i Acknowledgment I would like to thank my advisor, Prof Sandip Trivedi, for all his help and encouragement during my time at TIFR and for sharing with me his knowledge, insight and invaluable physical intuition. I would like to thank all my collaborators for their invaluable contributions to my understanding of theoretical physics; it was a privilege to work with them. I would also like to thank members of the string theory group, other members of the department and other members of the institute with whom I have interacted for their invaluable contribution to my education. I would like to thank all the former and present graduate students with whom I have shared an office for teaching me a great deal of physics.
Solution of 0-1 Knapsack Problem Applying Improved CSA Algorithm

This paper proposed an improved Clonal Selection Algorithm(CSA),which combined greedy strategy with an extended boundary,and modified individuality's gene bit to improve population by using the good gene bit information in the immaturate subpopulation.Meanwhile an additional memory cell of the best individuality was set up to avoid population devolution.The simulation test of two 0-1 Knapsack Problems shows that the algorithm can search for the best solution more quickly than the current CSA,and its efficiency is higher and its stability is better than the CSA and Genetic Algorjthm(GA).
Effect of the Consolidation Level on Organic Volatile Compound Emissions from Maize during Storage

The aim of this study was to determine the emission of organic volatile compounds from maize grain as a function of granularity and packing density of bulk material in conditions imitating processes occurring in silos. The study was carried out with the use of a gas chromatograph and an electronic nose, which was designed and constructed at the Institute of Agrophysics of PAS and has a matrix of eight MOS (metal oxide semiconductor) sensors. A 20-L volume of maize grain was consolidated in the INSTRON testing machine with pressures of 40 and 80 kPa. The control samples were not compacted, and the maize bed had bulk density. The analyses were carried out at a moisture content of 14% and 17% (w.b.—wet basis). The measurement system facilitated quantitative and qualitative analyses of volatile organic compounds and the intensity of their emission during 30-day storage. The study determined the profile of volatile compounds as a function of storage time and the grain bed consolidation level. The research results indicated the degree of grain degradation induced by the storage time. The highest emission of volatile compounds was recorded on the first four days, which indicated a dynamic nature of maize quality degradation. This was confirmed by the measurements performed with electrochemical sensors. In turn, the intensity of the volatile compound emission decreased in the next stage of the experiments, which showed a decline in the quality degradation dynamics. The sensor responses to the emission intensity decreased significantly at this stage. The electronic nose data on the emission of VOCs (volatile organic compounds) as well as grain moisture and bulk volume can be helpful for the determination of the quality of stored material and its suitability for consumption.
Design and Implementation of an Simulation of Water Wave Transformation Using Higher Order Mild-Slope Equation

A higher-order mild-slope equation (HOMSE) is derived based on theory of Hsu et al. [14]. Depth function is approximated up to third-order accurate in terms of both wave nonlinearity and bottom slope. Classical Galerkin method is used to solve HOMSE. Developed model is verified with a series of benchmark tests, including propagation of a sinusoidal wave past a submerged bar, wave propagating on a sloping bed, wave propagating over an elliptic shoal on a uniform slope, and wave propagating through a semicircular slope bottom, respectively. Computed results are compared with experiment data and prediction of low-order mild-slope equation model as well as Boussinesq equations model, and show good agreement.
GrapevineXL reliably predicts multi-annual dynamics of vine water status, berry growth, and sugar accumulation in vineyards

Abstract Climate and water availability greatly affect each season’s grape yield and quality. Using models to accurately predict environment impacts on fruit productivity and quality is a huge challenge. We calibrated and validated the functional-structural model, GrapevineXL, with a data set including grapevine seasonal midday stem water potential (Ψxylem), berry dry weight (DW), fresh weight (FW), and sugar concentration per volume ([Sugar]) for a wine grape cultivar (Vitis vinifera cv. Cabernet Franc) in field conditions over 13 years in Bordeaux, France. Our results showed that the model could make a fair prediction of seasonal Ψxylem and good-to-excellent predictions of berry DW, FW, [Sugar] and leaf gas exchange responses to predawn and midday leaf water potentials under diverse environmental conditions with 14 key parameters. By running virtual experiments to mimic climate change, an advanced veraison (i.e. the onset of ripening) of 14 and 28 days led to significant decreases of berry FW by 2.70% and 3.22%, clear increases of berry [Sugar] by 2.90% and 4.29%, and shortened ripening duration in 8 out of 13 simulated years, respectively. Moreover, the impact of the advanced veraison varied with seasonal patterns of climate and soil water availability. Overall, the results showed that the GrapevineXL model can predict plant water use and berry growth in field conditions and could serve as a valuable tool for designing sustainable vineyard management strategies to cope with climate change.
Data Representation via Attribute Selection- Propagation Neural Network

Graph Convolutional Networks (GCNs) have been commonly studied for attribute graph data representation. It is known that the core of Graph Convolution (GC) operation is to define a specific graph propagation operation for graph node's attributes. Existing GCs mainly perform propagation over node's all attributes. However, this ‘full’ propagation may be unreasonable on some practical learning tasks and also be vulnerable to the noisy attributes. To address this issue, in this article, we propose a novel Attribute Selection-Propagation (ASP) mechanism for attribute graph data representation by incorporating attribute selection into GCs. The main aspect of the proposed ASP is that it can be formulated as a regularization model based on which we can derive a simple update rule to implement ASP in a self-supervised manner. ASP aims to adaptively propagate some optimal attributes of node to better serve message passing in GCs. Using ASP, we then present a novel graph neural network, named ASPNet for attribute graph representation and learning. Experiments on several graph learning tasks including node classification, clustering and link prediction demonstrate the effectiveness of the proposed ASPNet.
Accurate mapping of seaweed farms with high-resolution imagery in China

Abstract Seaweed aquaculture is vital in protecting the marine eco-environment and mitigating climate change. China generates more than half of the world’s total seaweed production. However, despite multiple local studies, accurate and reliable information on broad-scale seaweed farms is still scarce. Using an object-based method to classify 3 m spatial resolution Planet Scope images along offshore China, a total of 129,494 ha of cultured seaweed was identified and delineated with an overall accuracy of 95.70% and a KAPPA index of 0.912, respectively. Then, a seaweed map in offshore China in 2018–2019 was developed. The results provided basic information about seaweed farms in China. The approach reported in this work is accurate and efficient, which can be used to replace the conventional method to obtain the culture seaweed information. This study can be of reference for mapping seaweed on a broader or global scale.
ON LIMIT CYCLES OF PLANAR QUADRATIC SYSTEM

Let a quadratic system of differential equations (E_2) possess a focus of order 3 and a uniquesimple singular point at infinity. Then it possesses another focus with odd number of limit cyclesaround it. By suitable variations of the coefficients of the system,three limit cycles jump out ofthe focus of order 3 so that there exist at least four limit cycles for (E_2), and the global structureis completely determined.
A Three-Year Retrospective Study Assessing the Quality of the Course of Management of Infective Endocarditis in a Tertiary Hospital in Riyadh, Saudi Arabia

Background: Infective endocarditis (IE) is one of the most misdiagnosed diseases in Saudi Arabia because of the variable treatment regimen. This study aims to assess the quality of the management of infective endocarditis in a tertiary care teaching hospital. Methods: A single-center retrospective cohort study was conducted, based on electronic medical records extracted from the BestCare electronic medical record system, of all patients who presented with infective endocarditis as a final diagnosis from 2016 to 2019. Results: Out of a total of 99 patients diagnosed with infective endocarditis, 75% of our patients had blood cultures ordered before initiating empirical antibiotic therapy. Positive blood cultures were reported in 60% of patients. Staphylococcus aureus was the most common organism, identified in 18% of our patients, followed by Streptococcus viridans at 5%. Empirical antibiotics were initiated in 81% of patients. Proper antibiotic coverage was initiated within a week for 53% of the patients, and 14% had proper antibiotic coverage within two weeks. On echocardiography, 62% of the patients had vegetation that was present in a single valve. The mitral valve had the highest incidence of vegetation (24%), followed by the aortic valve (21%). Follow-up echocardiography was done in 52% of patients. It showed regressed vegetation in 43% of patients, while only 9% of patients had no vegetation regression. Valve repair was done in 25% of patients. Out of 99 patients, 47 required ICU admission. The mortality rate was 18%. Conclusion: Overall management of infective endocarditis in the study hospital was appropriate and highly compliant with guidelines, with a few areas that could be improved further.