Variance Component Analysis Research Articles

Batch correction methods for nontarget chemical analysis data: application to a municipal wastewater collection system

Nontarget chemical analysis using high-resolution mass spectrometry has increasingly been used to discern spatial patterns and temporal trends in anthropogenic chemical abundance in natural and engineered systems. A critical experimental design consideration in such applications, especially those monitoring complex matrices over long time periods, is a choice between analyzing samples in multiple batches as they are collected, or in one batch after all samples have been processed. While datasets acquired in multiple analytical batches can include the effects of instrumental variability over time, datasets acquired in a single batch risk compound degradation during sample storage. To assess the influence of batch effects on the analysis and interpretation of nontarget data, this study examined a set of 56 samples collected from a municipal wastewater system over 7 months. Each month’s samples included 6 from sites within the collection system, one combined influent, and one treated effluent sample. Samples were analyzed using liquid chromatography high-resolution mass spectrometry in positive electrospray ionization mode in multiple batches as the samples were collected and in a single batch at the conclusion of the study. Data were aligned and normalized using internal standard scaling and ComBat, an empirical Bayes method developed for estimating and removing batch effects in microarrays. As judged by multiple lines of evidence, including comparing principal variance component analysis between single and multi-batch datasets and through patterns in principal components and hierarchical clustering analyses, ComBat appeared to significantly reduce the influence of batch effects. For this reason, we recommend the use of more, small batches with an appropriate batch correction step rather than acquisition in one large batch.Graphical abstract

Micromorphological characterization and electron microscopic study of parasitic species of the family Loranthaceae Juss.

The Loranthaceae Juss. family includes parasitic species that invade important trees such as fruit trees. In Saudi Arabia, Loranthaceae comprises four genera, which include six species that grow in the western, southwestern, and northern regions: Tapinanthus globifer (A.Rich.) Tiegh, Oncocalyx glabratus (Engl.) M. G. Gilbert, Loranthella deflersii (Tiegh.) S. Blanco & C. E. Wetze, Phragmanthera austroarabica A. G. Mill. & J. Nyberg, Plicosepalus curviflorus (Benth.ex Oliv.) Tiegh. and Plicosepalus acaciae (Zucc.). The species present in the Kingdom of Saudi Arabia have not been the subject of enough studies. This work aims to screen and evaluate the taxonomic importance of the micromorphological traits of leaves and fruits in Loranthaceae species native to Saudi Arabia (SA) using scanning electron microscope (SEM). In this study, cluster dendrogram (CD), principal component analysis (PCA) and analysis of variance (ANOVA) were used to evaluate the ability to discriminate Loranthaceae species using micromorphological characteristics. Most of the micromorphological characteristics of the leaf and fruit surfaces used reflected significant variation between the species of Loranthaceae. The type of stomata, trichome, lenticels, fine relief of the cell wall and wax form were the most taxonomically important characteristics. In addition, the cluster dendrogram of morphological characteristics showed species distribution within branches based on affiliation to subtribes Tapinanthinae and Emelianthinae. To the best of our knowledge, the fruit and leaves of the species under study have never been described using electron microscopy, and this study is considered the first of its kind. It also contributes to solving the classification problems of the family Loranthaceae in general and confirms the importance of the characteristics and methods used as tools for characterizing parasitic species that infect trees and helps to verify their identities. This will help to improve resistance efforts and put effective control plans in place.

Assessment of time of harvest at different moisture contents on seed yield attributes of ten pigeon pea (Cajanus cajan) genotypes

Grain moisture content is a key indicator of an appropriate harvest period of seeds on the field and could also be used to effectively stabilize cereal products especially when physical attributes is to be evaluated. This study evaluated effect of time of harvest at different moisture contents on seed yield attributes of ten pigeon pea genotypes. The ten pigeon pea genotypes used for the experiment were sourced from International Institute of Tropical Agriculture (IITA) Ibadan, Oyo State, Nigeria. The field experiment was a Randomized Completely Block Design (RCBD) with three replications. The seeds were harvested at maturity on the field at 12, 15 and 17 % moisture content. At each harvested moisture content, the following seed yield parameters were evaluated periodically on five observational plants from each net plot-; number of pods per plant, number of seeds/pod, seed yield/plant, pod weight /plant, 100 seed weight/plot and seed production efficiency. Data collected were subjected to analysis of variance and Principal component analysis was used to identify characters that contributed majorly to variation within the genotypes under each treatment. The result showed that NSWCC-18b, NSWCC-19 and NSWCC-18 had an outstanding performance in the entire seed- yield attributes, evaluated for various moisture contents and could therefore, be used as dependable genotypes in pigeon pea seed development programme. It is thereby, recommended that, pigeon pea seeds should be harvested at 15% moisture content for effective maintenance of quality, quantity and vigor.

Impact of environment on morphometric characteristics of pigeon pea (Cajanus cajan (L.) genotypes through seed digital imaging analysis

Computer seed digital imaging was utilized in this study to evaluate the differences in seed metric traits in twenty genotypes of pigeon pea as affected by the seed production environment. InSEEDLE™ software digital imaging analysis was used to differentiate the seed metric characters. For every replication, a hundred seeds were placed on the lighting hood in such a way that the embryo axis of the seed faced the image analysis system. Seeds were automatically analyzed by the scanner and the image of the seed was recorded by the 'WinSEEDLE™'. The procedure was repeated three times. The parameters observed were seed area, straight length, curve length, straight width, curve width, width length, and seed perimeter. Data collected were subjected to analysis of variance (anova) and principal component analysis. The result revealed that the pigeon pea genotypes evaluated were highly variable in all the seed metric traits evaluated. NSWCC-34C, NSWCC-34b, NSWCC-50 and NSWCC-34 were identified with consistent and high seed morphometric characteristic performance for most of the attributes examined, hence, an important tool in selecting superior pigeon pea genotypes and could be used as parental material.

Genotype-by-environment interaction effects on blast disease severity and genetic diversity of advanced blast-resistant rice lines based on quantitative traits

IntroductionAmong the rice diseases, rice blast caused by the pathogen Magnaporthe oryzae is a major threat to the global rice cultivation. This experiment was aimed at investigating the genotype by environment interaction effects on the severity of blast disease and variability of the advanced blast resistant rice lines using quantitative characters.Materials and methodsThe experiment was laid out in randomized complete block design conducted at three locations. Data were collected on 21 traits which included vegetative, physiological, yield and yield components and were subjected to analysis of variance and variance component analysis. Cluster analysis was authenticated using principal component analysis for genotypes’ classification.Results and discussionAll vegetative and yield traits showed highly significant variation among the advanced lines and the check. Seberang Prai showed the highest average yield (5.62t/ha), followed by Tanjung Karang (5.39t/ha) and UPM (4.97t/ha). All the advanced lines showed high resistance to blast disease. Evaluation across the three environments indicated that genotype G3, from MR219 based population, had the highest yield and resistance to blast infection. Genotype G21, from MR263 based population, performed best across the three environments studied and were selected for further breeding programme. The two selected lines, three and four clusters derived from MR219 and MR263 based populations, respectively, were recommended as new lines for further breeding programmes.

Characterization of Oxidation-Reduction Potential Variations in Biological Wastewater Treatment Processes: A Study from Mechanism to Application

Oxidation-reduction potential (ORP) sensors would constitute a robust surveillance and control solution for aeration and external carbon dosing in wastewater biological treatment processes if a clear correlation exists between the ORP values and process variables (e.g., dissolved oxygen (DO), nitrate, and chemical oxygen demand (COD). In this study, ORP values and other water quality variables were analyzed, and principal component analysis (PCA) and analysis of variance were used to study the relationships between ORP and main reactive substances under anoxic conditions. Mathematical models were then established using multiple regression analysis. The results showed that under anoxic conditions, ORP was positively correlated with nitrate, DO, and COD and negatively correlated with ammonia nitrogen, phosphate, and pH. COD had a low correlation with the ORP value change. PCA showed that the mathematical model of ORP can be established by using DO, nitrate, and phosphate, for which the adjusted R² value was 0.7195. The numeric relationships among ORP, COD, and nitrate were clearly established and applied to control external carbon dosing. A precise and clear relationship between ORP and COD offers the possibility to substitute COD monitoring for process control.

Second‐generation fully automated Elecsys cerebrospinal fluid immunoassays demonstrate high precision, reproducibility, and sample stability suitable for clinical use to aid Alzheimer’s disease diagnosis

AbstractBackgroundBeta‐amyloid(1–42) (Abeta42) and phosphorylated tau 181 (pTau) cerebrospinal fluid (CSF) biomarker analysis is recommended alongside cognitive evaluation to aid Alzheimer’s disease (AD) diagnosis. For clinical use, CSF biomarker assays should demonstrate high precision/reproducibility and sample stability. This study evaluated precision, reproducibility, and sample stability of second‐generation fully automated Elecsys® CSF immunoassays.MethodFrozen/pooled CSF and PreciControl samples were analyzed using Elecsys β‐Amyloid(1–42) CSF II/Phospho‐Tau (181P) CSF immunoassays on cobas e 601 (Roche Diagnostics International Ltd). pTau/Abeta42 ratios were calculated. Precision was evaluated at one site per Clinical and Laboratory Standards Institute (CLSI) EP02‐A3 (two runs/day in duplicate over 21 days; n=84). Reproducibility was determined per CLSI EP05‐A3 over five days using a single lot across three sites (site‐to‐site)/three lots at one site (lot‐to‐lot). Coefficients of variation (CVs)/standard deviations (SDs) for repeatability/intermediate precision/reproducibility were calculated using variance component analysis. Sample stability was determined from fresh CSF, collected per manufacturer's instructions. Baseline measurements were taken <6 hours after lumbar puncture and follow‐up measurements (from stored aliquots) at defined intervals for ≤8 days at room temperature (RT; 25°C; n=13), ≤15 days at 6°C (n=14), and ≤13 weeks at ‐20°C (n=25). Storage stability was determined from percent recoveries/ordinary linear regression.ResultRepeatability CVs were <2.4% and <1.9% for Abeta42 and pTau immunoassays, respectively, and <2.4% for pTau/Abeta42 ratio. Intermediate precision CVs were <3.3% and <3.7% for Abeta42 and pTau immunoassays, respectively, and <3.9% for pTau/Abeta42 ratio. Site‐to‐site reproducibility CVs were <5.1% and <3.6% for Abeta42 and pTau immunoassays, respectively, and <6.5% for pTau/Abeta42 ratio (Table 1). For the Abeta42 immunoassay, lot‐to‐lot reproducibility CVs were <5.4%, except for one sample pool (mean concentration: 322 pg/mL; SD: 34.1 pg/mL; Table 2). Lot‐to‐lot reproducibility CVs were <3.6% for the pTau immunoassay and <6.0% for pTau/Abeta42 ratio. At maximum sample storage duration (8 days at RT/15 days at 2−8°C), median recoveries of 95%/98% were observed for Abeta42 and 97%/99% for pTau immunoassays. Stability assessment at ‐20°C is ongoing.ConclusionThe Elecsys immunoassays demonstrated high precision/reproducibility, supporting clinical use in AD diagnosis. Conservative recommendations for sample storage are 5 days at RT/14 days at 2−8°C.

Generating better leaf traits in M2 lines of fourteen Ethiopian sesame (Sesamum indicum L.) genotypes through the treatment of their seeds with sodium azide

The present study explored the effect of sodium azide (NaN3) on quantitative and qualitative leaf traits of M2 lines on 14 Ethiopian sesame genotypes collected from Humera Agricultural Research Center, Tigrai, Ethiopia. Qualitative data on leaf color, leaf hairiness, leaf arrangement, leaf shape, basal leaf profile, basal leaf margin, and leaf angle to main stem as well as quantitative data on length of basal leaf, length of top leaf, width of basal leaf, width of top leaf, length of marginal leaf, and width of marginal leaf were recorded and analyzed using analysis of variance, clustering analysis, Mahalanobis distance, and principal component analysis. Generally, treatment of seeds with NaN3 has brought many distinct and statistically significant phenotypic changes on both quantitative and qualitative leaf traits of the M2 lines. The changes in the NaN3 treated and locally adapted genotypes of Gumero and Zeri Tesfay are promising; producing the highest mean length of basal leaf (p ≤ 0.01). NaN3 treated seeds of Baha Necho, Gumero, and Hirhir developed the highest mean width of basal leaf. Locally adapted genotypes have responded positively to NaN3 treatment, generating better leaf traits as compared to the research improved ones. This study was the first of its kind in exploring the effects of NaN3 seed treatment on leaf traits of sesame genotypes. The findings of this study will, therefore, serve as a steppingstone to look into the effects of the changes in sesame yield and initiate future genetic and molecular studies on the responsive genotypes.

Optimization of stir bar sorptive extraction (SBSE) and multi-stir bar sorptive extraction (mSBSE) to improve must volatile compounds extraction

The aromatic compounds present in grapes are found in very low concentrations, since, for their determination, a previous step of selective extraction is necessary. In this work we optimize and compare, for the first time, the techniques of extraction by stir bar sorption (SBSE) and multi-stir bar sportive extraction (mSBSE), with the aim of analyzing the must volatile composition. For this purpose, two randomized factorial designs were carried out in which the following factors and levels were combined and optimized: for SBSE, extraction mode (headspace (HS), direct immersion (DI), and both at the same time), extraction speed (500/1000 rpm), extraction time (1/3/6 h), extraction temperature (20/40/60 °C) and NaCl addition (with and without NaCl, and sequential); and for mSBSE: extraction speed (500/1000 rpm), extraction time (1/3/6 h), extraction temperature (20/40/60 °C), and NaCl addition (with and without). The results showed that SBSE technique provided a higher extraction of volatile compounds than mSBSE. After performing principal component analysis (PCA) and analysis of variance (ANOVA) multifactorial, it was concluded that the best conditions for SBSE were: HS, 500 rpm, 6 h, 60 °C and adding NaCl (sequential); and for mSBSE were: 500 rpm, 6 h, 60 °C and without NaCl.

Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans.

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%-16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.

Validation of newly developed tasks for the assessment of generic Critical Online Reasoning (COR) of university students and graduates

In recent decades, the acquisition of information has evolved substantially and fundamentally affects students’ use of information, so that the Internet has become one of the most important sources of information for learning. However, learning with freely accessible online resources also poses challenges, such as vast amounts of partially unstructured, untrustworthy, or biased information. To successfully learn by using the Internet, students therefore require specific skills for selecting, processing, and evaluating the online information, e.g., to distinguish trustworthy from distorted or biased information and for judging its relevance with regard to the topic and task at hand. Despite the central importance of these skills, their assessment in higher education is still an emerging field. In this paper, we present the newly defined theoretical-conceptual framework Critical Online Reasoning (COR). Based on this framework, a corresponding performance assessment, Critical Online Reasoning Assessment (CORA), was newly developed and underwent first steps of validation in accordance with the Standards for Educational and Psychological Testing. We first provide an overview of the previous validation results and then expand them by including further analyses of the validity aspects “internal test structure” and “relations with other variables”. To investigate the internal test structure, we conducted variance component analyses based on the generalizability theory with a sample of 125 students and investigated the relations with other variables by means of correlation analyses. The results show correlations with external criteria as expected and confirm that the CORA scores reflect the different test performances of the participants and are not significantly biased by modalities of the assessment. With these new analyses, this study substantially contributes to previous research by providing comprehensive evidence for the validity of this new performance assessment that validly assesses the complex multifaceted construct of critical online reasoning among university students and graduates. CORA results provide unique insights into the interplay between features of online information acquisition and processing, learning environments, and the cognitive and metacognitive requirements for critically reasoning from online information in university students and young professionals.

A software-assisted untargeted liquid chromatography-mass spectrometry method for lipidomic profiling of human plasma samples.

In this paper, an analytical pipeline designed for untargeted lipidomic profiling in human plasma is proposed. The analytical pipeline was developed for case-control studies nested in prospective cohorts. The procedure consisted of isopropanol protein precipitation followed by reverse phase liquid chromatography coupled to high resolution mass spectrometry and software-assisted data processing. The compounds are putatively annotated by matching experimental mass spectrometry data with spectral library data using LipidSearch software. The lipid profile of a pool of plasma samples from 10 healthy volunteers was detected in both positive and negative polarity modes. The impact of the chosen polarity on the number and quality of the lipid identification has been evaluated. More than 1000 lipids from 12 different classes were detected, 1150 in positive mode and 273 in negative mode. Nearly half of them were unambiguously identified by the software in positive mode, and about one-third in negative mode. The method repeatability was assessed on the plasma pool samples by means of variance components analysis. The intra- and inter-assay precision was measured for 10 lipids chosen among the most abundant found within the different lipid classes. The intra-assay coefficients of variation ranged from 2.56% to 4.56% while intra- and inter-day coefficients of variance never exceeded the 15% benchmark adopted. The lipidomic profiles of the 10 healthy volunteers were also investigated. This method detects a wide range of lipids and reports their degree of identification. It is particularly fit and well-designed for large case-control epidemiologic studies.

Utilization of Grain Physical and Biochemical Traits to Predict Malting Quality of Barley (Hordeum vulgare L.) under Sub-Tropical Climate.

Barley is the most popular raw material for malting, and recently, the demand for malt-based products has increased several folds in India and other South Asian countries. The barley growing season is peculiar in the sub-tropical plains region compared to European or Northern American conditions, characterized by a total crop duration of 130-145 days with a maximum grain filling duration of around only 35-40 days. A total of 19 barley genotypes were grown for three years to assess the comparative performance in relation to different quality traits, including grain physical traits and biochemical and malt quality parameters. Analysis of variance, Pearson correlation, and principal component analysis were performed to determine the correlation among different traits. The results showed significant genotypic variation among genotypes for individual grain and malt traits. Despite the shorter window for grain filling, several good malting genotypes have been developed for the sub-tropical climates. The genotypes DWRUB52, DWRB101, RD2849, DWRUB64, and DWRB91 were found suitable for malting. Based on correlation studies, a few grain parameters have been identified which can be used to predict the malting potential of a barley genotype. The hot water extract was found to be positively correlated with the grain test weight, thousand-grain weight, and malt friability but was negatively correlated with the husk content. Beta-glucan content varied from 3.4 to 6.1% (dwb); reducing the grain beta-glucan content and increasing the amylase could be priorities to address in future malt barley improvement programs under sub-tropical climatic conditions.

Surgical Case Volume Needed to Achieve Stable Procedural Proficiency in the General Surgery Chief Resident Year

Introduction: We have previously reported using a resident’s learning curve based on operative time (OT) plateau could determine their procedural proficiency. In this study we hypothesize case volume in the chief resident (CR) year would influence whether a CR could achieve reproducible procedural proficiency based on OT. Methods: We extracted laparoscopic cholecystectomy (LCh), laparoscopic colectomy (LCo), laparoscopic inguinal hernia (LIH) and open inguinal hernia (OIH) performed by general surgery residents in the CR year from 7/2016 to 6/2020 through hospital records with OT, patient type, and case complexity assessed by DRG. We used variance component analyses as well as generalizability and decision studies (D-Study) to determine number of cases needed to achieve desired reliability (> 0.80). Results: In total 1514 cases (LCh=776, LCo=339, LIH=158, OIH=241) were included. On average, CR overall completed 38.3 LCh, 16.9 LCo, 7.8 LIH, and 11.8 OIH. After controlling for CR effect, case complexity (r=0.004) and procedure type (r<0.0001) significantly influenced OT. To achieve stable/reproducible OT in each procedure upon graduation, our CRs (N = 6) were estimated to perform on average 25 LCh, 30 LCo, 26 LIH, and 17 OIH per person. Individual CR had minimal impact on the estimation of case needed. Conclusion: The case volume needed to achieve stable procedural proficiency in LCo, LIH and OIH exceeds average CR case number in our program. This might be also true in other programs. Prospective measurement of OT may allow for individualized CR case assignments and enhance CR readiness for independent practice in general surgery.

Genetic Analyses of Response of Local Ghanaian Tanzanian Chicken Ecotypes to a Natural Challenge with Velogenic Newcastle Disease Virus.

Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.

Characterization of Sugar Reduction in Model Confectionary Gels Using Descriptive Analysis.

Successful sugar reduction in food products mimics the sensory and functional properties of the full sugar counterpart. The initial step of sugar reduction is to determine how the absence of sugar affects these properties. Descriptive analysis was conducted on four gel types (gelatin, ι-carrageenan, κ-carrageenan, and konjac glucomannan) and a range of sugar concentrations from 0–20% w/v to create a sensory profile of model confectionary gels for comparison to instrumental texture profile analysis data. The sensory descriptive data were analyzed using analysis of variance and principal component analysis. Correlation analysis, cluster analysis, and partial least squares regression (PLS-R) were used to compare and correlate sensory and instrumental data. Regardless of sugar concentration, sensory analysis primarily clustered samples by gelling agent type, such as in the case of konjac glucomannan consistently being characterized as chewy. Cohesion and gumminess were correlated highly with melt-in-mouth and a jiggly texture, while adhesion and fracturability were negatively correlated. In the PLS-R samples biplot, gelatin and iota carrageenan samples were located near these attributes indicating their aptness as descriptors. In conclusion, descriptive analysis provided a more discriminating method for characterizing model confectionary gels.

Aspects of a unique natural limnological phenomenon in the Brazilian Pantanal

This study compares physical and chemical parameters of water samples collected in a marginal lake (Castelo Bay) in the Paraguay River Basin in southern Pantanal during a significant natural phenomenon of hypoxia, locally called decoada, and shortly after it. Limnological parameters were analyzed from four sampling sites along the bay. Comparisons of the physical and chemical parameters between decoada and post-decoada periods were performed by Student’s t-test, principal component analysis and multivariate permutational analysis of variance (permanova). During the period of the decoada, there was a significant reduction in mean values of water transparency and concentrations of dissolved oxygen, sodium and nitrite compared to the post-decoada period. On the other hand, water temperature and conductivity, and concentrations of orthophosphate, total nitrogen and total iron have all had higher values during the decoada period. An effect of connectivity between lake and river was found to generate a gradient of water characteristics at Castelo Bay. The limnological characteristics that differed the most between decoada and post-decoada periods are those associated with the reduction of dissolved oxygen that could cause natural death of fish and the increase in nutrients during the decoada, yet they vary on temporal and spatial scales.&#x0D; Keywords: anoxia, dissolved oxygen, floodplain lakes.

Effect of Environment on Morphometric Characteristics of Mung bean (vigna radiata (L.) Genotypes through Seed Digital Imaging Analysis

Digital imaging is a fast and reliable method for cultivar identification and discrimination. Computer seed digital imaging was utilized in this study to evaluate the differences in seed metric traits in ten genotypes of mung bean as affected by the seed production environment. A hundred seeds in each of the mung bean genotypes were subjected to digital imaging analysis using the ‘WinSEEDLE™’ software to differentiate the seed metric characters. For every replication, a hundred seeds were placed on the lighting hood in such a way that the embryo axis of the seed faces the image analysis system and the longitudinal axis runs parallel to the surface of the scanner. Seeds were automatically analyzed by the scanner and the image of the seed was recorded by the ‘WinSEEDLE™’. The procedure of hundred seeds placement on seed digital image was repeated three times for each genotype. The parameters observed were seed area, straight length, curve length, straight width, curve width, width length, and seed perimeter. Scan data collected from ‘WinSEEDLE™’ were subjected to analysis of variance and principal component analysis. The result revealed that the Mung bean genotypes evaluated were highly variable in all the seed metric traits evaluated. The study recommended that attention should be given to genotypes and seed production environments in the seed production of Mung bean. Genotypes Tvr-73, Tvr-27, Tvr-98, and Tvr-78 have been identified with consistent and high seed morphometric characteristic performance for most of the attributes examined, hence, can be important criteria in selecting superior seed physical traits and could be used as parental material, in the development of high seed yielding varieties.

Pandemic Vulnerability Mapping in East Java and Its Connection to Local Economic Resistance

The objectives of this study are to measuring and to mapping pandemic vulnerability in East Java as well as to examine the association between pandemic vulnerability and local economic resistance. To achieve the objectives, this study employs several techniques: descriptive analysis, principal component analysis, cluster analysis, and analysis of variance. The data were acquired from various sources, that cover health, social, economic, and environmental conditions. The results showed that there were seven most vulnerable districts in East Java. They were Kota Surabaya, Kabupaten Sidoarjo, Kabupaten Gresik, Kota Kediri, Kota Malang, Kota Mojokerto and Kota Madiun. The core pandemic indicators were population mobility, the number of COVID-19 cases and its mortality, population density, air pollution, the prevalence of diabetes, and the share of secondary and tertiary sectors. Furthermore, this study found that there were negative association between pandemic vulnerability and local economic resistance in East Java.

Using otolith and body shape to discriminate between stocks of European anchovy (Engraulidae: Engraulis encrasicolus) from the Aegean, Marmara and Black Seas.

European anchovy, a small pelagic fish, plays a significant role in the blue economy, with remarkable commercial, ecological and culinary values. In this study, the variability in the shapes of the body and sagitta otoliths was examined to identify the different anchovy stocks in the Black Sea (26.5°E-39.9°E, 38.7° N-42.1°N) and adjacent regions, i.e., the Sea of Marmara and the Aegean Sea. The body shape was assessed with geometric morphometrics, while shape indices and elliptic Fourier analysis were used to evaluate the shape of the sagitta otoliths. The data were analysed using multivariate and univariate analysis of variance, discriminant function and principal component analysis. The anchovy population could be divided into five distinct stocks based on body shape, with an overall leave-one-out cross-validated correct classification of 85.6%. The geometric morphometrics revealed significant differences in body depth, snout, lower jaw and caudal fin. The differences in sagitta otolith shape also revealed the existence of four distinct stocks with an overall leave-one-out cross-validated correct classification of 46.5%-69.3%. The elliptic Fourier analysis revealed two main stocks of anchovy from the Black Sea as the Eastern-Middle Black Sea stock and the Western Black Sea stock. Based on the elliptic Fourier analysis, the differences in the sagitta otoliths increase in magnitude with increasing geographic separation, first manifested at the otolith anterior notch, followed by changes in the otolith width. The findings affirmed the existence of distinct stocks that should have important implications for effective management of this pelagic fish in the Black Sea and adjacent regions.