Online Software Tool Research Articles

The presence of genes encoding carbapenem-hydrolyzing oxacillinase and lack of carbapenem resistance in non-baumannii Acinetobacter misidentified as Acinetobacter baumannii causing bloodstream infections in a tertiary hospital over a 3-year period

ObjectiveThis study aims to analyze the genomic and clinical characteristics of Non-baumannii Acinetobacter strains misidentified as A. baumannii, causing bloodstream infections (BSIs) in our hospital. Materials and methodsWhole genome sequencing was performed and average nucleotide identity (ANI) was analyzed. Susceptibility testing was conducted using micro-broth methods. The distribution of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) was examined using online software tools. The prevalence of virulence factors (VFs) was investigated through nucleotide coding sequence comparisons. Genetic structures of blaOXA genes were analyzed by Gcluster software. Clinical information was collected from electronic medical records for patient characterization. ResultsANI analysis identified five strains as Acinetobacter pittii, with the remaining four identified as A. geminorum, A. nosocomialis, A. soli and A. bereziniae. The GC content of all isolates was less than 38.9 % except for A. soli 16,294. All Non-baumannii Acinetobacter strains were relatively susceptible to antibiotics, except for one A. pittii isolate. Nine blaOXA variants were identified in seven isolates, with two isolates co-carrying 2 different types of blaOXA. Twenty-four insertion sequences (ISs) were identified, with ISAba and IS17 being the primary ISs. Five A. pittii isolates shared the same genetic structures around blaOXA. Genes related to adherence, immune modulation, and nutritional/metabolic factors were the most frequent. Few VFs were detected in A. soli 16,294 and A.bereziniae 14,325. ConclusionsThe presence of carbapenem hydrolyzing oxacillinase encoding genes did not confer carbapenem resistance, possibly due to the lack of ISs in the blaOXA flanking sequences. Different blaOXA variants within distinct strains shared the same genetic structures, suggesting potential for multidrug resistance development, which warrants our attention.

Analysis of virus gene subtypes and drug resistance monitoring results of newly reported HIV/AIDS population in Anhui Province from 2020 to 2023

Objective: To investigate the genetic subtypes and drug resistance monitoring of newly reported human immunodeficiency virus (HIV) infection/AIDS virus in Anhui Province from 2020 to 2023. Methods: An observational design study was used to collect blood samples from patients diagnosed with HIV/AIDS in the AIDS Prevention and Control Department of Anhui Provincial Center for Disease Control and Prevention from January 2020 to December 2023.The HIV-1 pol gene was amplified by reverse transcription-nested PCR, and the genetic subtypes were identified by phylogenetic tree analysis using MEGA 7.0 software. The mutation sites of drug resistance were analyzed by the online software tool of Stanford University's HIV Drug resistance database. The influencing factors of drug resistance before treatment were analyzed by multivariate logistic analysis. Results: A total of 335 plasma samples were collected, and 332 HIV-1 pol gene sequences were obtained successfully. The main gene subtypes were CRF01-AE, accounting for 35.55% (118/332), followed by CRF07-BC, B and B+C types [29.22% (97/332), 11.74% (39/332), 9.93% (33/332)]. The total drug resistance rate before treatment was 30.12%(32/100), and the drug resistance rate of protease inhibitor (PIs) in HIV-1 was 6.33% (21/332). The drug resistance rate of nucleoside reverse transcriptase inhibitors (NRTI) before treatment was 6.33% (21/332). The drug resistance rate of non-nucleoside reverse transcriptase inhibitors (NNRTI) before treatment was 17.47% (58/332).The comparison of drug resistance rate of different drug types showed statistical significance (χ2=30.435, P<0.05).Among the 100 cases of drug resistance, the main mutation point of HIV-1 protease inhibitor was Q58E (21.00%), and the main mutation point of nucleoside reverse transcriptase inhibitor was M184V/I (6.00%). Non-nucleoside reverse transcriptase inhibitor resistance mutation points mainly K103N (22.00%).There were statistically significant differences in the starting time of antiviral therapy, the number of CD4+T cells at baseline and the drug resistance rate of gene subtypes (the chi-square values are respectively 24.152, 32.516, 11.652, P<0.05).Multivariate logistic analysis showed that the baseline CD4+T cell count was <200/μl, subtype B, subtype B+C, CRF01-AE subtype, CRF55-01B subtype and 01-BC subtype was the influential factor of drug resistance before treatment (the chi-square values are respectively 4.577, 8.202, 4.416, 5.206, 7.603 and 4.804, P<0.05). Conclusion: The newly reported HIV/AIDS population in Anhui Province from 2020 to 2023 has a variety of viral gene subtypes, and NNRTIs are the main types of drug resistance gene mutations before treatment. Attention should be paid to the number of baseline CD4+T cells, the duration of antiviral treatment, and the distribution of gene subtypes to reduce the drug resistance of HIV/AIDS patients before treatment.

Some peculiarities of effective online interaction

The study in this article is aimed at assessing the effectiveness of virtual communication and analyzing the needs of representatives of various fields of activity in the online communication process. To provide the communication process effectiveness, a combination of different interaction forms is required to compensate for the lack of personal communication through virtual communication. The data was gathered through an online survey. The survey was formed using the Google Forms online tool and was carried out in the form of anonymous survey sent by link through social networks. The aim of the presented study review was to reveal the current situation with the beneficial implementation of online interaction tools to solve variety of communication problems. The questionnaire analyze showed that online communicators consider the ZOOM platform an important online communication tool. According to the study, language in remote communication is endowed with new functions related to communication tactics and strategy. Social and cultural factors affecting the structure and properties of the communicative situation, as well as the characteristics of communicants, determine the success or failure of communication. Qualitative and quantitative indicators of online software tools are of interest for research of online discourse from different aspects.

Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma

ABSTRACT To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05–0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.

Prednisone combined with Dihydroartemisinin attenuates systemic lupus erythematosus by regulating M1/M2 balance through the MAPK signaling pathway

ObjectiveDihydroartemisinin (DHA) plays a very important role in various diseases. However, the precise involvement of DHA in systemic lupus erythematosus (SLE), relation to the equilibrium between M1 and M2 cells, remains uncertain. Therefore, we aimed to investigate the role of DHA in SLE and its effect on the M1/M2 cells balance. MethodsSLE mice model was established by pristane induction. Flow cytometry was employed to measure the abundance of M1 and M2 cells within the peripheral blood of individuals diagnosed with SLE. The concentrations of various cytokines, namely TNF-α, IL-1β, IL-4, IL-6, and IL-10, within the serum of SLE patients or SLE mice were assessed via ELISA. Immunofluorescence staining was utilized to detect the deposition of IgG and complement C3 in renal tissues of the mice. We conducted immunohistochemistry analysis to assess the expression levels of Collagen-I, a collagen protein, and α-SMA, a fibrosis marker protein, in the renal tissues of mice. Hematoxylin-eosin staining, Masson’s trichrome staining, and Periodic acid Schiff staining were used to examine histological alterations. In this study, we employed qPCR and western blot techniques to assess the expression levels of key molecular markers, namely CD80 and CD86 for M1 cells, as well as CD206 and Arg-1 for M2 cells, within kidney tissue. Additionally, we investigated the involvement of the MAPK signaling pathway. The Venny 2.1 online software tool was employed to identify shared drug-disease targets, and subsequently, the Cytoscape 3.9.2 software was utilized to construct the “disease-target-ingredient” network diagram. Protein-protein interactions of the target proteins were analyzed using the String database, and the network proteins underwent enrichment analysis for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. ResultsThe results showed that an increase in M1 cells and a decrease in M2 cells within the peripheral blood of individuals diagnosed with SLE. Further analysis revealed that prednisone (PDN) combined with DHA can alleviate kidney damage and regulate the balance of M1 and M2 cells in both glomerular mesangial cells (GMC) and kidney. The MAPK signaling pathway was found to be involved in SLE kidney damage and M1/M2 balance in the kidney. Furthermore, PDN and/or DHA were found to inhibit the MAPK signaling pathway in GMC and kidney. ConclusionWe demonstrated that PDN combined with DHA attenuates SLE by regulating M1/M2 balance through MAPK signaling pathway. These findings propose that the combination of PDN and DHA could serve as a promising therapeutic strategy for SLE, as it has the potential to mitigate kidney damage and reinstate the equilibrium of M1 and M2 cells.

A Readability Study of Carpal Tunnel Release in 2023.

The National Institutes of Health (NIH) and the American Medical Association (AMA) recommend a sixth-grade reading level for patient-directed content. This study aims to quantitatively evaluate the readability of online information sources related to carpal tunnel surgery using established readability indices. Web searches for "carpal tunnel release" and "carpal tunnel decompression surgery" queries were performed using Google, and the first 20 websites were identified per query. WebFX online software tools were utilized to determine readability. Indices included Flesch Kincaid Reading Ease, Flesch Kincaid Grade Level, Coleman Liau Index, Automated Readability Index, Gunning Fog Score, and the Simple Measure of Gobbledygook Index. Health-specific clickthrough rate (CTR) data were used in order to select the first 20 search engine results page from each query. "Carpal tunnel release" had a mean readability of 8.46, and "carpal tunnel decompression surgery" had a mean readability of 8.70. The range of mean readability scores among the indices used for both search queries was 6.17 to 14.0. The total mean readability for carpal tunnel surgery information was found to be 8.58. This corresponds to approximately a ninth-grade reading level in the United States. The average readability of carpal tunnel surgery online content is three grade levels above the recommended sixth-grade level for patient-directed materials. This discrepancy indicates that existing online materials related to carpal tunnel surgery are more difficult to understand than the standards set by NIH and AMA.

Validating the credibility of solar simulation tools using a real-world case study

Solar energy is being recognized around the world for generating clean power using photovoltaic (PV) panels. Inadequate planning and sizing of PV panel systems leads to increased costs, emphasising the significance of reviewing solar energy simulationtools for accuracy and credibility. Even with the current literature, it could be challenging to select the software tools that are appropriate for the research. This paper identified, reviewed and validated four system-based (System Advisor Model (SAM), PVsyst, PV*Sol and Solarius PV) and three online software tools (Helioscope, PV-Watts and PV-GIS). It provides necessary information on the software tools which compiled in a features matrix under seven categories. The validation process involves using real-world data from an 84.5KW solar plant installed on a building in Nagpur, India, to assess the accuracy and performance of the software tools. The statistical metrics used for validation are Absolute Deviation (AD), Root Mean Square Error (RMSE) accompanied by Mean Bias Error (MBE) and Nash-Sutcliffe Efficiency (NSE) for a comprehensive understanding of the accuracy and reliability. The findings show a discrepancy in the simulated output data and the recorded data of the tools with PV*Sol and Solarius PV showcasing the least error. In conclusion, the findings of this research provide valuable insights and guidance for users seeking to make informed decisions in selecting the most appropriate Solar PV simulation tool tailored to their specific needs and requirements.

FUT1 variants responsible for Bombay or para-Bombay phenotypes in a database

Rare individuals with Bombay and para-Bombay phenotypes lack or have weak expression of the ABO(H) antigens on surface of red blood cells due to no or very weak H-type α(1,2)fucosyltransferase activity encoded by FUT1. These phenotypes are clinically important because subjects with these phenotypes can only accept transfusions of autologous blood or blood from subjects with the same phenotypes due to the anti-H antibody. To survey FUT1 alleles involved in Bombay and para-Bombay phenotypes, the effect of 22 uncharacterized nonsynonymous SNPs in the Erythrogene database on the α(1,2)fucosyltransferase activity were examined by transient expression studies and in silico analysis using four different online software tools. Two nonfunctional alleles (FUT1 with c.503C>G and c.749G>C) and one weakly functional allele (with c.799T>C) were identified in transient expression studies, while the software predicted that the proteins encoded by more alleles including these would be impaired. Because both nonfunctional FUT1 alleles appear to link to the nonsecretor alleles, homozygotes of these alleles would be of the Bombay phenotype. The present results suggest that functional assays are useful for characterization of nonsynonymous SNPs of FUT1 when their phenotypes are not available.

Insight into (Z)-ethyl-2-(2-((E)-2,4-dinitro benzylidene amino)-4-oxo-3-phenylthiazolidin-5-ylidene) acetate in-silico anti-SARS-CoV-2 performance: Synthesis, structural-spectral characterizations and DFT computations

This study reports on the synthesis of a 4-thiazolidinone derivative (EN2Th), namely, (Z)-Ethyl-2-(2-((E)-2,4-dinitro benzylidene amino)-4-oxo-3-phenylthiazolidin-5-ylidene) acetate. Its crystal structure has been determined by single crystal X-ray diffraction and the spectral characterizations were carried out by means of 1H and 13C NMR, and FT-IR techniques. The molecule of EN2Th crystallizes in the monoclinic P21/c symmetry and its crystal structure consists of a herringbone packing along [100]. The density functional theory (DFT) at the B3LYP/6-311G (d,p) level has been employed for structure optimization, the results confirm a good consistency between the theoretical and the experimental geometrical data. Hirshfeld surface and 2D fingerprints indicate C−H···O (29.7%) and H···H (24.5%) as the most relevant intermolecular interactions in the crystal packing of EN2Th. According to the reduced density gradient (RDG) analysis, EN2Th exhibits vdW to weak repulsive regions with low electron densities. The theoretical electronic circular dichroism (ECD) spectrum displays an exciton coupled transitions associated with the Z-configuration of the thiazolidin-4-one moiety reflecting the steric effect of the ester group. Charge transfer inside the 4-thiazolidinone derivative EN2Th was considered via the frontier molecular orbitals (FMOs) and natural bond orbital (NBO) investigations along with molecular electrostatic potential (MEP) distribution maps. The HOMO and LUMO energies allowed the estimation of the chemical reactivity descriptors. In accordance with the NBO results, the predicted hyperpolarizabilities indicate a strong donor to acceptor π-electrons delocalization in EN2Th. The anti-viral performance of EN2Th was evaluated in silico against SARS-CoV-2 main protease (MPro) via molecular docking simulations. Finally, ADMET (absorption, distribution, metabolism, excretion and toxicity) online software tools were utilized to uncover the title compound's potential cytotoxicity.

Indapamide analogue a promising drug: Synthesis, a novel crystal structure, HSA/DFT/XRD, greener pastures biological study

A new indoline derivative, N-allyl-4-chloro-3-(N,N-diallylsulfamoyl)-N-(2-methylindolin-1-yl)benzamide (ASIB), indapamide analogue, has been synthesized via the N-allylation reaction and characterized by ESI-MS, IR, 1H & 13C NMR. The geometric parameters of the title compound, whose crystallographic structure has been defined by X-ray diffraction, have been calculated by Density Functional Theory (DFT), B3LYP, 6–311++G(d,p) basis set. For these operations, the data obtained by X-ray diffraction was used as initial values, and the calculated geometric parameters and experimental results were compared. In order to understand intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis (HSA) studies were figured out for the molecule. Frontier Molecular Orbitals (FMO's) were created, and Energy Gap between Lowest Unoccupied Molecular Orbital (LUMO) and Highest Occupied Molecular Orbital (HOMO) was calcculated. Adapting Greener Pastures Biological Study (GPBS) aims to conduct a fair comparative study using accessible computer-aided software. ASIB, Indapamide, Asunaprevir, Danoprevir, and Vaniprevir were docked together using the same conditions and parameters to ensure a fair comparison. The binding scores against 6LU7 were −6.6, −7.1, −8.4, 7.6, and −7.9 kcal/mol−1 for ASIB, Indapamide, Asunaprevir, Danoprevir, and Vaniprevir, respectively. A relation between the molecule's binding score was due to the hydrophobic and hydrogen interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the free energy and environmentally friendly in Silico molecular docking method aims mainly to rank ASIB, and Indapamide with respect to the approved drugs used in this study. Results support further investigation of ASIB as non-toxic a Diuretic, anti-COVID-19 and powerful antiviral drug as an indapamide derivative. Way2drug-PASS, Pro Tox-II and SwissADME are online software tools used in this study. Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of ASIB and its starting material (Indapamide) were compared.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin.

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.

Effects of SARS-CoV-2 Pandemic on computer communication: delayed consequences and new behavioral standards

The relevance of this study is revealed in a selection of online communication tools with the forced consequences of the spread of SARS-CoV-2 in the world, revealing the effectiveness of distance learning. Objective: to trace the transformation of the speech and behavioral standard depending on the internal understanding of their own knowledge about computer-mediated communication in comparison with traditional methods of communication; to evaluate the effectiveness of virtual communication based on the analysis of the needs of communicants in the process of online communication. The presented analysis of the form of communication demonstrates the processes of transformation of the speech and behavioral profile of communicants, which allows for additional research for a wide range of readers who practice online interaction on an observable basis. The material was data from an online questionnaire in which 261 respondents from Kazakhstan took part. The methodology is based on the psychological verbal-communicative method of anonymous online questioning using Google Forms via social networks. Results: online communicants identified the ZOOM platform as an important tool for online communication as an important factor in maintaining stable interaction in a professional environment, training and social communication. Effective computer communication poses the problem of compliance with the norms of online communication for successful interaction. Further study of qualitative and quantitative indicators of various online software tools is of interest for improving the linguistic modeling of educational online discourse with the prediction of the result.

Virtual Screening and Pharmacokinetic Studies of Vaccinium oxycoccos L. Phytonutrients in Ulcer Induced Proinflammatory Mediated Targets

Molecular docking is a computational online software tool for analyzing ligand-protein interactions. Phytoconstituents have rich antioxidant properties that play a leading role in treating various diseases. Generally, the incidence of peptic ulcers increases day by day due to the concomitant use of NSAIDs. Medicament that induces ulcers can suppress the release of all pro-inflammatory targets such as prostaglandin-endoperoxide synthase-1(COX 1), prostaglandin- endoperoxide-2 (COX 2), Prostin E-2 (EP2), Prostaglandin E-3 (EP3), Prostin E-4 (EP4), and stimulate histamine-2 (the H2 receptor). Herbal medicaments are generally used for treatment because they have decreased adverse effects. Docking studies on Phytonutrients are helpful for the investigation of complementarity of the ligand with the receptor at the molecular level. The main aim of this docking study is to target all mediators and compare the affinity of Phytomedicines. Chem Draw Pro 8.0, RCSB protein data bank, is the software used for docking. Additionally, pharmacokinetic studies are conducted on the herbal constituents to analyze the therapeutic efficacy.

MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction.

The applications of artificial intelligence, machine learning, and deep learning techniques in the field of materials science are becoming increasingly common due to their promising abilities to extract and utilize data-driven information from available data and accelerate materials discovery and design for future applications. In an attempt to assist with this process, we deploy predictive models for multiple material properties, given the composition of the material. The deep learning models described here are built using a cross-property deep transfer learning technique, which leverages source models trained on large data sets to build target models on small data sets with different properties. We deploy these models in an online software tool that takes a number of material compositions as input, performs preprocessing to generate composition-based attributes for each material, and feeds them into the predictive models to obtain up to 41 different material property values. The material property predictor is available online at http://ai.eecs.northwestern.edu/MPpredictor.

Digital natives and streaming TV platforms: an integrated perspective to explain continuance usage of over-the-top services

PurposeDigital natives constitute a substantial part of consumers nowadays. Yet, a theoretical understanding of the factors driving their engagement with new-age digital services is lacking. This study therefore aims to examine digital natives’ continuance usage of the proliferating over-the-top (OTT) services. To address these objectives, the study uses a comprehensive model that primarily integrates perceived value, cognitive absorption and customer brand engagement theories.Design/methodology/approachData were collected using an online personal questionnaire targeting active digital natives OTT service users using the online software tool SurveyMonkey. A sample of 1,415 digital natives was analysed using structural equation modelling.FindingsThe findings indicated that continuance usage is predicted by all three theories. The results illustrate that cognitive absorption and customer brand engagement are the most critical in enhancing continuance usage. Gender effects on digital natives’ value perceptions were found. The model explains 57% of the variance in users’ continuance usage.Originality/valueThe study adds valuable contributions to the existing literature that are relevant to digital natives’ engagement with new-age digital services. The proposed integrated model and the role of gender in value formations provide managers with novel insights when designing effective strategies to increase continuance usage for the largest consuming generation.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-03-2022-0133

ConstraintID: An online software tool to assist grain growers in Australia identify areas affected by soil constraints

Soil constraints, such as soil sodicity, salinity and acidity, are one cause of yield loss for grain growers globally. A first step towards reducing the associated yield gap is the identification of the area affected and the soil constraint/s responsible for the yield loss. Within a single field, persistent spatial variation of crop growth that repeats year after year is likely due to some form of soil constraint. Vegetation indices derived from satellite imagery can provide a valuable alternative to yield maps for assessing these persistent patterns. The variation identified from remote-sensing data can be compared with soil data from the field to help identify which soil constraints are potentially causing yield differences. This application note describes ConstraintID (www.constraintid.com.au), a web-based software tool that makes it easy for growers to use and interact with remote-sensing data to (1) reveal the persistent long-term variation of crop growth within their fields, (2) devise targeted soil sampling plans and (3) interpret the resulting soil data in view of critical values for certain soil constraints.

Magnetic resonance imaging T2* of the pancreas value using an online software tool and correlate with T2* value of myocardium and liver among patients with transfusion-dependent thalassemia major.

Patients with thalassemia major do require lifetime blood transfusions that eventually result in iron accumulation in different organs. We described the usefulness of using magnetic resonance imaging (MRI) T2*imaging values for the evaluation of pancreatic iron load in these patients, and we correlated it with MRI T2* haemosiderosis of the myocardium and liver that has been recognized as a non-invasive assessment of iron overload among patients with thalassemia major. We conducted a cross-sectional study on 39 patients with thalassemia major in one of the tertiary university hospitals for a 1-year period. Demographic data were collected from the patient's history. MRI T2* of the pancreas, liver, and heart were executed on all patients in the same setting. Objective values of iron overload in these organs were obtained using the MRI post-processing software from online software. A total of 32 (82.1%) patients had pancreatic iron overload including 2 patients (5.1%) with severe iron overload and 15 patients (38.5%) with moderate and mild iron overload, respectively. Nine patients (23.1%) had myocardial iron overload, which included 3 patients (7.7%) who had severe cardiac haemosiderosis. Notably, 37 patients (94.9%) had liver iron overload, which included 15 patients (38.5%) who had severe liver haemosiderosis. There was a moderate positive correlation between the relaxation time of the pancreas and heart haemosiderosis (r = 0.504, P < 0.001). No significant correlation was found between the relaxation time of the pancreas with the liver and the heart with the liver. Pancreatic haemosiderosis precedes cardiac haemosiderosis, which establishes a basis for initiating earlier iron chelation therapy to patients with thalassemia major.

Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

BackgroundThe spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies have identified important ‘disease resistance single nucleotide polymorphisms (SNPs)’, but how these affect the underlying traits is an unresolved question. Recent advances in computational statistics make it now possible to estimate the effects of SNPs on host traits from epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known about how to effectively design disease transmission experiments or field studies to maximise the precision with which these effects can be estimated.ResultsIn this paper, we develop and validate analytical expressions for the precision of the estimates of SNP effects on the three above host traits for a disease transmission experiment with one or more non-interacting contact groups. Maximising these expressions leads to three distinct ‘experimental’ designs, each specifying a different set of ideal SNP genotype compositions across groups: (a) appropriate for a single contact-group, (b) a multi-group design termed “pure”, and (c) a multi-group design termed “mixed”, where ‘pure’ and ‘mixed’ refer to groupings that consist of individuals with uniformly the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than estimates for infectivity. Whereas the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferred because it uses information from naturally-occurring rather than artificial infections. The same design principles apply to estimates of the epidemiological impact of other categorical fixed effects, such as breed, line, family, sex, or vaccination status. Estimation of SNP effect precisions from a given experimental setup is implemented in an online software tool SIRE-PC.ConclusionsMethodology was developed to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables that underlie host susceptibility, infectivity and recoverability. Designs that maximize the precision of estimates were derived.

CASE STUDY OF DEFRAGMENTATION OF CITY SCALE’S GREENHOUSE GAS EMISSION IN MELAKA

The defragmentation of multiple sources of greenhouse gas emissions would allow for more effective climate action at the local level. The adoption of a Global Protocol for Community-Scale (GPC) framework will assist in determining the source of greenhouse gas emissions in Malacca based on inventory data. The online software tool (Harmonised Emissions Analysis Tool (HEAT+)) is used to translate data that can then be used to plan strategic initiatives at the local level. Malacca’s per capita GHG emissions currently stands at 4.59 tonnes of CO2 equivalent (tCO2e). A GPC analysis revealed the industrial sector was the principal offender, who accounted for 39.6% (1,548.412 tCO2e) of the emissions, this was followed by the transport and logistics sector, which accounted for 29.9% (1,160,333 tCO2e), the commercial sector that accounted for 14.7% (574,844 tCO2e) and individual residences which accounted for the balance 12.8% (499,655 tCO2e). Scope 1 dominated GHG emissions by 72.1%, based on the electricity use data from buildings held by the Historical Malacca City Council and Hang Tuah Jaya City Council. The result indicates that the two government buildings need to lead sustainable infrastructure initiatives and reduce emissions by spearheading various energy efficiency programmes. These initiatives can then be followed by businesses and residences using decentralised energy strategies. Making climate change mitigation efforts a priority is recommended. This can be done by implementing a variety of low-carbon-based technologies supported by command and control frameworks and market-based policy interventions. The manufacturing and services sectors are the two most important economic sectors in Malacca, and both have the capacity to adopt more advanced greener and cleaner technologies. Nevertheless, active modes of transportation must be promoted as part of the adaptation strategy for clean, low- carbon modes of transportation.

Morroniside, a novel GATA3 binding molecule, inhibits hepatic stellate cells activation by enhancing lysosomal acid lipase expression

BackgroundLiver fibrosis can be easily developed into irreversible liver cirrhosis or even liver cancer. Lysosomal acid lipase (LAL), encoded by the lipase A (Lipa) gene, is a critical enzyme involved in liver fibrosis development. Morroniside, an iridoid glycoside isolated from Cornus officinalis Sieb. et Zucc., exerts hepatic protective effects. However, the mechanism of action underling the anti-liver fibrosis effects of morroniside have not been fully elucidated. PurposeTo explore whether Lipa served as a biomarker for liver fibrosis and investigate the anti-liver fibrosis effects of morroniside and the underlying action mechanism in liver fibrosis cell models. MethodsLAL expression was examined in the liver tissues of CCl4 and high-fat diet (HFD)-induced liver fibrosis animal models. α-smooth muscle actin (α-SMA) level, collagen and GATA family expressions were analyzed by Real-time PCR and Western blot. Putative transcription factor binding sites in the DNA sequences of Lipa was identified by PROMO-ALGGEN v8.3 online software and ENCODE ChIP-Seq Significance Tool. MD simulation was performed to explore the protein-ligand interaction. ResultsWe found that the expression of hepatic LAL is lower in the liver fibrosis animal models than the control models. The reduced LAL expression is associated with HSCs activation, suggesting LAL is novel liver fibrosis biomarker. More importantly, our data showed that morroniside exerts anti-liver fibrosis effects in vitro. Mechanistic studies reveal that it binds to the hydrophobic sites of GATA3 and also reduces GATA3 expression, which increases LAL expression. ConclusionsThis study, for the first time, suggests LAL is a novel biomarker for liver fibrosis. Besides, morroniside exerts its anti-liver fibrosis effects by targeting GATA3 and LAL and hence inhibits HSC activation. These findings provide strong scientific evidence to support the development of morroniside as novel alternative or complementary therapeutics for liver injury prevention and treatment.