Replicate Tests Research Articles

In-cell Western assay to quantify infection with pathogenic orthohantavirus Puumala virus in replication kinetics and antiviral drug testing

Hemorrhagic fever with renal syndrome (HFRS) represents a serious zoonotic disease caused by orthohantaviruses in Eurasia. A specific antiviral therapy is not available. HFRS is characterized by acute kidney injury (AKI) with often massive proteinuria. Infection of kidney cells may contribute to the clinical picture. However, orthohantaviral replication in kidney cells is not well characterized. Therefore, we aimed to perform a reliable high-throughput assay that allows the quantification of infection rates and testing of antiviral compounds in different cell types. We quantified relative infection rates of Eurasian pathogenic Puumala virus (PUUV) by staining of nucleocapsid protein (N protein) in an in-cell Western (ICW) assay. Vero E6 cells, derived from the African green monkey and commonly used in viral cell culture studies, and the human podocyte cell line CIHP (conditionally immortalized human podocytes) were used to test the ICW assay for replication kinetics and antiviral drug testing. Quantification of infection by ICW revealed reliable results for both cell types, as shown by their correlation with immunofluorescence quantification results by counting infected cells. Evaluation of antiviral efficacy of ribavirin by ICW assay revealed differences in the toxicity (TC) and inhibitory concentrations (IC) between Vero E6 cells and podocytes. IC5O of ribavirin in podocytes is about 12-fold lower than in Vero E6 cells. In summary, ICW assay together with relevant human target cells represents an important tool for the study of hantaviral replication and drug testing.

A-294 Duplicate Testing of Samples Suspected of SARS-CoV-2 Infection Could Prevent Misdiagnosis of Covid-19

Abstract Background There is no doubt that the whole world has been shaken by the SARS-CoV-2 pandemic, which has affected both global health and the global economy. At the same time the importance of molecular methods for the accurate diagnosis of respiratory infections has been reinforced together with the need of testing methodologies that minimize the risk of misleading results. During the last three years of the pandemic, SARS-CoV-2 exhibited a tremendous adaptation capability through numerous mutations, leading to the appearance of the well-known Variants of Concern (VOCs) responsible of increased transmission rates. Therefore, the development of molecular methods capable of detecting all variants has become a challenge. To overcome this, potential genetic targets with low mutation rates have been identified, including ORF1ab, N gene, S gene and E gene. While Real-time PCR based detection assays of viral genomes are very accurate, testing naso/oropharyngeal samples using singlet analysis does not guarantee the error free detection of true positive results for SARS-CoV-2 infections. Furthermore, it has been documented that the probability of a false-negative testing results is influenced by a number of variables . Therefore, testing protocol adaptations, such as replicate testing, has been shown to efficiently reduce the probability of missing SARS-CoV-2 positive cases. The pilot study presented here investigates the outcome of testing 10 014 nasopharyngeal samples collected from patients with a suspected SARS-CoV-2 infection using two separate detection kits. In this study the error rate of single vs duplicate testing is discussed. Methods 10 014 nasopharyngeal swabs, collected from three different U.K. hospital trusts and Kent based care homes, were tested at the North Kent Pathology Service (NKPS). Each swab collected was placed in sterile transport media and stored at 4°C prior to viral genome isolation using the HigherPurity™ Viral RNA extraction kit. All collected specimens were processed within 24 h from collection. Total RNA isolated was immediately analyzed using two commercial CE-IVD kits: Vitassay qPCR SARS-CoV-2 and Primerdesign™ LTD, Coronavirus (COVID-19) Genesig Real-Time PCR assay. All samples were tested in duplicate. Results Following the testing and subsequent analysis, 491 samples (4.9%) were detected positive for SARS-CoV-2 using both assay kits. Of these, 302 samples (61.5%) were reported as duplicate positive (on both replicate 1 and 2) whereas 189 samples (38.5%) were detected positive on either replicate 1 or 2. In particular, 85 (17.3%) were detected positive on replicate 1 and 104 (21.2%) were detected positive on replicate 2. Conclusions Approximately 19% of tested individuals were detected as SARS-CoV-2 positive based on a positive Real-time PCR result in one of the two reactions. This percentage represents the potential SARS-CoV-2 infections that can be missed when a single reaction Real-time PCR testing is employed for infection detection in the wider population, and equates to 940 individuals out of 100 000 potentially being falsely confirmed as SARS-CoV-2 negative The authors believe that in the presence of fast transmitting variants this is a significant number of false negative tests and should be taken into consideration when testing protocols are developed and disease modelling is employed.

A-018 Biological Variation Estimates for N-terminal pro-B-type Natriuretic Peptide from Eight Healthy Turkish Women

Abstract Background B-type natriuretic peptide (BNP) and its precursor N-terminal pro-B-type natriuretic peptide (NT-proBNP) are released primarily by the ventricles in the heart in response to volume or pressure overload. Measurements of NT-proBNP are used as an aid in the diagnosis and assessment of severity of congestive heart failure (CHF). Within- (CVI) and between-subject (CVG) biological variation (BV) estimates for NT-proBNP are limited. Here biological variability (BV) estimates from eight apparently healthy Turkish women for NT-proBNP are provided. Methods Serum samples were collected weekly from 24 healthy subjects (12 male, 12 female) for 10 consecutive weeks and stored at −80 °C prior to analysis. Study participant samples were analyzed in duplicate within a single run using the Atellica® IM NT-proBNP (PBNP) assay* on the Atellica IM Analyzer. Outlier detection, variance homogeneity analyses, and trend analysis were performed followed by CV-ANOVA to determine BV and analytical variation (CVA) estimates with 95% CI. The asymmetrical reference change values (RCV) using the lognormal approach, index of individuality (II), and analytical performance specification (APS), based on the CVA estimate derived in our study, were also calculated. Results PBNP results from 11 males and 3 females were lower than the limit of quantitation (LoQ) of the assay (<35 pg/mL). The remaining male sample was not included in the analysis. One female sample was identified as an outlier between individuals and was excluded from the analysis. To fulfil criteria for variance homogeneity of the data from eight women, 7% of results were excluded. In total, 104 analytical results were included in the analysis. PBNP data for the female group was normally distributed, and no trends were identified by regression analysis. The BV estimates derived from females were CVI: 23.7%, (95% CI 19.0–30.4) and CVG: 8.22%, (95% CI 0.0–24.7). The CVA obtained from replicate test results was 11.2% (95% CI 9.4–13.9), which was lower than the desirable APS for imprecision. The II, calculated as the ratio of CVI/CVG, indicated a low individuality of PBNP (defined as II > 1.6). Thus, use of a population-based reference interval for interpreting serial PBNP measurements is more appropriate than use of the RCV. Conclusions This study provides updated BV estimates for NT-proBNP derived from a protocol consistent with European Federation of Clinical Chemistry and Laboratory Medicine recommendations. The availability of BV estimates allows for refined APS and associated II and RCV, which are applicable when using PBNP as an aid in the diagnosis and assessment of severity of congestive heart failure. *The products/features mentioned here are not commercially available in all countries. Their future availability cannot be guaranteed.

B-095 Determination of Error Rates with Duplicate Analysis in Anti-Drug Antibody Testing

Abstract Background Duplicate measurements can be used to characterize assay imprecision, identify outliers, and estimate error rates. The benefits of duplicate analysis, however, need to be balanced against the increased financial cost. The objective of this study was to evaluate the need for continued replicate measurement in a laboratory developed assay measuring anti-drug antibodies to infliximab (ATI). To this end, duplicate patient sample measurements from the ATI assay over a two-year period were analyzed to calculate outlier and error frequencies. Methods ATI were measured by electrochemiluminescence (ECL) on the MesoScale Discovery (MSD) platform, with a standard curve from 20–1250 U/mL using commercially available monoclonal ATIs. All patient samples tested for ATI over a 27-month period of time (n = 9582) were subject to inclusion in this study. Only patient samples with ATI levels within the analytical measuring range (AMR) of the assay, however, were selected for further analysis. Samples were divided equally into 7 bins across the measuring range based on mean replicate concentration. Within-run imprecision was determined for each bin using the standard deviation (combined from all replicates using sum of squares) and mean concentration derived from all replicates. Outliers were defined as replicate measurements with a percent difference greater than ±3 SD of the calculated assay imprecision. Errors were defined as samples which had replicate values on opposite sides of the clinical cutoff of positive ATI (≥50 U/mL) and a percent difference greater than 3SD of the assay imprecision. Results Of the 9582 total patient samples analyzed, 2467 had ATI values within the AMR and 1655 had levels over the clinical cut-off of 50 U/mL (17.3% positivity rate). Within-run imprecision determined from the mean and combined SD of the duplicate measurements ranged from 15.7% at the lowest concentration bin (20–27.5 U/mL) to 10.0% at the highest concentration bin (358–1243 U/mL). The mean percentage of outliers in each bin ranged from 0.8%–3.4% resulting in an overall outlier frequency of 2.1% when considering all samples within the AMR. There were 66 samples within the AMR which demonstrated qualitative discrepancies between the replicates. However, only 21 (31.8%) of these samples, had a percent agreement greater than 3SD of the assay imprecision resulting in an overall error rate of 0.2% when considering all 9582 samples. Conclusion In this study, the analysis of replicate patient samples enabled the establishment of a precision profile and estimation of error rates for a laboratory developed test measuring ATI. The calculated error rate of 0.2%, however, is well within the reported range of most clinical assays indicating that the continued practice of duplicate measurement may not be necessary. Additionally, updating the laboratory protocol to eliminate replicate testing would have positive impact in laboratory workflow, cost, and turn-around-time for results.

Replicate Testing of Clinical Endpoints Can Prevent No-Go Decisions for Beneficial Vaccines.

In vaccine efficacy trials, inaccurate counting of infection cases leads to systematic under-estimation-or "dilution"-of vaccine efficacy. In particular, if a sufficient fraction of observed cases are false positives, apparent efficacy will be greatly reduced, leading to unwarranted no-go decisions in vaccine development. Here, we propose a range of replicate testing strategies to address this problem, considering the additional challenge of uncertainty in both infection incidence and diagnostic assay specificity/sensitivity. A strategy that counts an infection case only if a majority of replicate assays return a positive result can substantially reduce efficacy dilution for assays with non-systematic (i.e., "random") errors. We also find that a cost-effective variant of this strategy, using confirmatory assays only if an initial assay is positive, yields a comparable benefit. In clinical trials, where frequent longitudinal samples are needed to detect short-lived infections, this "confirmatory majority rule" strategy can prevent the accumulation of false positives from magnifying efficacy dilution. When widespread public health screening is used for viruses, such as SARS-CoV-2, that have non-differentiating features or may be asymptomatic, these strategies can also serve to reduce unneeded isolations caused by false positives.

More spice, less salt: How capsaicin affects liking for and perceived saltiness of foods in people with smell loss

People who lose their sense of smell self-report consuming more salt to compensate for a lack of flavor and enhance eating enjoyment. However, this may contribute to excess sodium intake. Capsaicin may help increase salt taste intensity and eating enjoyment in people with smell loss, but this has not been studied in this population. The purpose of this study was to determine 1) whether salt intake in those with smell loss differs from population averages, 2) whether capsaicin increases flavor and salt taste intensity, and 3) if adding spice to foods increases liking in individuals with smell loss. Thirty-three participants 18–65 years old with confirmed smell loss for at least 12 weeks completed two sets of replicate test sessions (four total). In two sessions participants rated overall flavor intensity, taste qualities' intensities, spicy intensity, and liking for model tomato soups with low or regular sodium content and three levels of capsaicin (none, low, or moderate). In the other two sessions, participants rated the same sensory attributes for model food samples with three levels of added spice (none, low, or moderate). 24-hour urine samples were collected to determine sodium intake. Results indicate that although sodium intake is higher than recommended (<2300 mg/day) in those with smell loss (2893 ± 258 mg/day), they do not consume more sodium than population averages (3039 ± 100 mg/day; p = 0.3). Adding low and moderate amounts of capsaicin to a model tomato soup increased the intensity of overall flavor (p < 0.001) and saltiness (p = 0.004) compared to a model tomato soup without capsaicin. However, capsaicin's effect on liking differed by food type. Thus, capsaicin can improve flavor, salt taste intensity, and eating enjoyment in people with smell loss.

Personality, Sexuality, and Beauty Standards: A Cross-Cultural Exploration of Canadian and German Women's Cosmetic Surgery Behaviours and Attitudes

This study investigated the impact of various psychosocial factors on behaviours and attitudes towards cosmetic surgery among Canadian (n=97) and German (n=115) women, considering cultural differences and beauty standards. The primary objective was to provide valuable insights for physicians and psychologists when selecting suitable candidates for elective procedures, as current pre-surgical assessments often fail to integrate the psychological perspective. A correlation analysis was undergone and revealed that neuroticism moderately influenced interest and motivation for cosmetic surgery in both populations. Additionally, the Canadian group exhibited a moderate negative correlation between motivation for cosmetic surgery and early sexual experiences, effectively destigmatizing cosmetic surgery as a social indicator of early sexual behaviours. However, this correlation was not observed in the German cohort. Notably, Canadians reported a higher overall motivation for undergoing cosmetic surgery compared to Germans, as confirmed by a t-test. Surgeons should inquire about sexuality and personality in pre-surgical consultations to determine candidates who may benefit from the procedure and minimize harm. Future research should develop a standardized test for replication and include diverse demographics.

The causal role of circulating amino acids on neurodegenerative disorders: A two-sample Mendelian randomization study.

Potential associations between the risk of neurodegenerative diseases and circulating levels of amino acids have been implied in both experimental research and observational studies. However, because of the confounding and reverse causality, the findings could be biased. We aimed to determine whether circulating amino acid levels have potential effects on the risk of neurodegenerative diseases through a more robust analysis. So, we performed a total of two MR analyses, a discovery two-sample MR analysis, and a replication test, using summary-level genome-wide association study (GWAS) data, both with circulating levels of amino acids as exposure and risk of neurodegenerative diseases as an outcome. The potential causalities between nine amino acids (Glutamine [Glu], Leucine [Leu], Isoleucine [Ile], Phenylalanine [Phe], Valine [Val], Alanine [Ala], Tyrosine [Tyr], Histidine [His], and Glycine [Gly]) and six neurodegenerative disorders (Alzheimer's disease [AD], Parkinson's disease [PD], Multiple sclerosis [MS], Frontotemporal dementia [FTD], Lewy body dementia [DLB], Amyotrophic lateral sclerosis [ALS]) were explored in this study. According to the discovery MR analysis, 1 SD. increase in circulating levels of Gln was genetically determined to result in a 13% lower risk of AD (IVW ORSD [95% CI] = 0.872 [0.822, 0.926]; FDR = 7.46 × 10-5 ) while PD risk was decreased to 63% per SD. increase of circulating Leu levels (IVW ORSD [95% CI] = 0.628 [0.467, 0.843]; FDR = 0.021). Results from the replication test provide further evidence of the potential association between circulating Gln levels and AD risk (IVW ORSD [95% CI] = 0.094 [0.028, 0.311]; FDR = 9.98 × 10-4 ). Meanwhile, sensitivity analysis demonstrated that the significant relationships revealed by our two-sample MR outcomes were reliable. Our analyses provided robust evidence of causal associations between circulating levels of Gln and AD risk as well as circulating Leu levels and risk of PD. However, the underlying mechanisms remain to be further investigated.

The Wellbeing in Place Perceptions Scale: Structure, Validity, Reliability and Correlates During COVID Times

The influence of place-based factors on the physical and mental health of residents is well established and acknowledged within the population health approach to addressing health and wellbeing inequalities. The COVID-19 pandemic brought to the fore the issues that global communities face. The current UK policy context of ‘levelling up’ represents these concerns and the need to address them. This research examines perceptions of community wellbeing and its determinants as collected within a city region of the North West Coast of England during COVID restrictions between June and August 2020. The paper aims to establish the structure, construct validity and reliability of a new measure of community wellbeing - the Wellbeing in Place Perceptions Scale. Further, it aims to examine how this measure of community wellbeing correlated with symptoms of common mental health as reported by residents of this relatively disadvantaged city region during this unprecedented time. Results indicate that the WIPPS has a reliable and valid structure, correlating significantly with another widely used measure of sense of community and with the Index of Multiple Deprivation. Its relationship to self-reported common mental distress is also clear. Though in need of replication and longitudinal testing, the findings reported here on this new measure remind us that individual and place-based factors combine to influence wellbeing and that community needs to have an increasingly influential role to sustainably prevent future mental health challenges.

Poverty, Brain Development, and Mental Health: Progress, Challenges, and Paths Forward

Poverty is associated with changes in brain development and elevates the risk for psychopathology in childhood, adolescence, and adulthood. Although the field is rapidly expanding, there are methodological challenges that raise questions about the validity of current findings. These challenges include the interrelated issues of reliability, effect size, interindividual heterogeneity, and replicability. To address these issues, we propose a multipronged approach that spans short-, medium-, and long-term solutions, including changes to data pipelines along with more comprehensive data acquisition of environment, brain, and mental health. Additional suggestions are to use open science approaches, more robust statistical analyses, and replication testing. Furthermore, we propose increased integration between advanced analytical approaches using large samples and neuroscience models in intervention research to enhance the interpretability of findings. Collectively, these approaches will expand the application of neuroimaging findings and provide a foundation for eventual policy changes designed to improve conditions for children in poverty.

Empathy and self-regulation in prosocial accountability: Gender and genetic (OXTR SNP rs53576) pathways

ABSTRACT Empathy and self-regulation play key roles in prosocial accountability. Meta-analytic evidence for empathy—in relation to gender and a particular genetic variable (OXTR SNP rs53576) – guided design and power analysis to determine the size of this United States sample. We assessed 311 participants (51.4% female; 19% racial or ethnic minority). We conducted tests of hypothesized indirect effects of gender and genotype through empathy to trait and state accountability – reporting replication and extension tests of gratitude, forgivingness and relational repair in a supplement (https://doi.org/10.17605/OSF.IO/KZDF8). Gender tests controlled for SNP group and vice versa. Gender had indirect effects on accountability via empathy (higher in women than men). SNP group indirect effects on accountability via empathy (higher in GGs than A-carriers) showed roles of gender, race/ethnicity and self-regulation. SNP group also had indirect effects on accountability through self-regulation (higher in A-carriers than GGs). Findings underscore empathy and self-regulation in relational accountability and positive psychology.

A New Repellent for Redbay Ambrosia Beetle (Coleoptera: Curculionidae: Scolytinae), Primary Vector of the Mycopathogen That Causes Laurel Wilt.

The redbay ambrosia beetle, Xyleborus glabratus, was detected in Georgia, USA, in 2002 and has since spread to 11 additional states. This wood-boring weevil carries a symbiotic fungus, Harringtonia lauricola, that causes laurel wilt, a lethal disease of trees in the Lauraceae family. Native ambrosia beetles that breed in infected trees can acquire H. lauricola and contribute to the spread of laurel wilt. Since 2002, laurel wilt has devastated native Persea species in coastal forests and has killed an estimated 200,000 avocado trees in Florida. Since laurel wilt is difficult to manage once it has entered a susceptible agrosystem, this study evaluated piperitone as a candidate repellent to deter attacks by X. glabratus and other ambrosia beetles. Additionally, piperitone was compared to the known repellent verbenone as a potential cost-effective alternative. The repellent efficacy was determined by comparing captures in traps baited with commercial beetle lures containing α-copaene versus captures in traps baited with lures plus a repellent. In parallel 10-week field tests, the addition of piperitone reduced the captures of X. glabratus in α-copaene-baited traps by 90%; however, there was no significant reduction in the captures of native ambrosia beetles in ethanol-baited traps. In two replicate 10-week comparative tests, piperitone and verbenone both reduced X. glabratus captures by 68-90%, with longevity over the full 10 weeks. This study identifies piperitone as a new X. glabratus repellent with potential for pest management.

A reliable and replicable test protocol for the mechanical evaluation of synthetic meshes

Despite the worldwide spread of surgical meshes in abdominal and inguinal surgery repair, the lack of specific standards for mechanical characterization of synthetic meshes, used in hernia repair and urogynecologic surgery, makes performance comparison between prostheses undoubtedly difficult. This consequently leads to the absence of acknowledged specifications about the mechanical requirements that synthetic meshes should achieve in order to avoid patient discomfort or hernia recurrences.The aim of this study is to provide a rigorous test protocol for the mechanical comparison between surgical meshes having the same intended use. The test protocol is composed of three quasi-static test methods: (1) ball burst test, (2) uniaxial tensile test, and (3) suture retention test. For each test, post-processing procedures are proposed to compute relevant mechanical parameters from the raw data. Some of the computed parameters, indeed, could be more suitable for comparison with physiological conditions (e.g., membrane strain and anisotropy), while others (e.g., uniaxial tension at rupture and suture retention strength) are reported as they provide useful mechanical information and could be convenient for comparisons between devices. The proposed test protocol was applied on 14 polypropylene meshes, 3 composite meshes, and 6 urogynecologic devices to verify its universal applicability towards meshes of different types and produced by various manufacturers, and its repeatability in terms of coefficient of variation.The test protocol resulted easily applicable to all the tested surgical meshes with intra-subject variability characterized by coefficient of variations settled around 0.05. Its use within other laboratories could allow the determination of the inter-subject variability assessing its repeatability among users of alternative universal testing machines.

Tracing the development and lifespan change of population-level structural asymmetry in the cerebral cortex.

Cortical asymmetry is a ubiquitous feature of brain organization that is subtly altered in some neurodevelopmental disorders, yet we lack knowledge of how its development proceeds across life in health. Achieving consensus on the precise cortical asymmetries in humans is necessary to uncover the developmental timing of asymmetry and the extent to which it arises through genetic and later influences in childhood. Here, we delineate population-level asymmetry in cortical thickness and surface area vertex-wise in seven datasets and chart asymmetry trajectories longitudinally across life (4-89 years; observations = 3937; 70% longitudinal). We find replicable asymmetry interrelationships, heritability maps, and test asymmetry associations in large-scale data. Cortical asymmetry was robust across datasets. Whereas areal asymmetry is predominantly stable across life, thickness asymmetry grows in childhood and peaks in early adulthood. Areal asymmetry is low-moderately heritable (max h2SNP ~19%) and correlates phenotypically and genetically in specific regions, indicating coordinated development of asymmetries partly through genes. In contrast, thickness asymmetry is globally interrelated across the cortex in a pattern suggesting highly left-lateralized individuals tend towards left-lateralization also in population-level right-asymmetric regions (and vice versa), and exhibits low or absent heritability. We find less areal asymmetry in the most consistently lateralized region in humans associates with subtly lower cognitive ability, and confirm small handedness and sex effects. Results suggest areal asymmetry is developmentally stable and arises early in life through genetic but mainly subject-specific stochastic effects, whereas childhood developmental growth shapes thickness asymmetry and may lead to directional variability of global thickness lateralization in the population.

Optimizing reduction of western blotting analytical variations: Use of replicate test samples, multiple normalization methods, and sample loading positions

Western blot (WB) analysis is widely used, but obtaining consistent results can be problematic, especially when using multiple gels. This study examines WB performance by explicitly applying a method commonly used to test analytical instrumentation. Test samples were lysates from RAW 264.7 murine macrophages treated with LPS to activate MAPK and NF-kB signaling targets.Samples from the pooled cell lysates placed in every lane on multiple gels were analyzed by WBs for levels of p-ERK, ERK, IkBβ and non-target protein. Different normalization methods and sample groupings were applied to the density values and the resulting coefficients of variation (CV) and ratios of maximal to minimal values (Max/Min) were compared. Ideally with identical sample replicates the CVs would be 0 and the Max/Min 1; deviation indicating introduction of variability by the WB process. Common normalizations to reduce analytical variance, total lane protein, % Control, and p-ERK/ERK ratios, did not have the lowest CVs or Max/Min values. Normalization using the sum of target protein values combined with analytical replication most effectively reduced variability, resulting CV and Max/Min values as low as 5–10% and 1.1. These methods should allow reliable interpretation of complex experiments that require samples to be placed on multiple gels.

Asphalt mixture fatigue damage and failure predictions using the simplified viscoelastic continuum damage (S-VECD) model

Fatigue cracking is a primary asphalt pavement distress and various models have been developed to predict the fatigue life of asphalt mixtures using laboratory tests. One such model is the simplified viscoelastic continuum damage (S-VECD) model, which has been implemented in the pavement performance prediction program, FlexPAVETM. The S-VECD model test protocols (AASHTO TP 133 and AASHTO T 400) and data processing tool (FlexMATTM) are widely used around the world. Over the past three decades, this model has been continuously improved and refined. However, questions remain on the model’s ability to predict the material response when stress or strain are used as the model input. Also, different fitting procedures for the model calibration were found to affect the model’s prediction accuracy. In this study, analysis was conducted using data for four typical North Carolina mixes based on single replicate tests and multiple replicate tests to compare the model’s prediction accuracy based on stress versus strain as the model input and by considering fitting errors in the different calculations. The results show that using strain as the model input, which automatically incorporates portions of permanent strain, yields more accurate predictions compared to using stress as the input, regardless of the fitting algorithm. Additionally, in the analysis of individual test data, which is not affected by replicate specimen variability, the model’s predictions match the measured data well, as long as the fitting errors of the damage characteristic curve are controlled. When the data from replicate tests are analyzed together, although specimen variability compromises the S-VECD model’s prediction accuracy, failure can still be reasonably determined when strain is used as the model input.

Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data

International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.

Imprints of Millennial-Scale Monsoonal Events during the MIS3 Revealed by Stalagmite δ13C Records in China

Regions located on the Chinese Loess Plateau are sensitive to changes in the Asian monsoon because they are on the edge of the monsoon region. Based on six 230Th experiments and 109 sets of stable isotope data of LH36 from Lianhua Cave, Yangquan City, Shanxi Province, we obtained a paleoclimate record with an average resolution of 120 years from 54.5 to 41.1 ka BP during the MIS3 on the Chinese Loess Plateau. Both the Hendy test and the replication test indicated an equilibrium fractionation of stable isotopes during the stalagmite deposition. Comparison with four other independently-dated, high-resolution stalagmite δ13C records between 29°N and 41°N in the Asian monsoon region shows that the stalagmite δ13C records from different caves have good reproducibility during the overlapped growth period. We suggest that speleothem δ13C effectively indicates soil CO2 production in the overlying area of the cave, reflecting changes in the cave’s external environment and in the Asian summer monsoon. Five millennial-scale Asian summer monsoon intensification events correspond to the Dansgaard–Oeschger 10–14 cycles recorded in the Greenland ice core within dating errors, and the weak monsoon processes are closely related to stadials in the North Atlantic. The spatial consistency of stalagmite δ13C records in China suggests that the Asian summer monsoon and the related regional ecological environment fluctuations sensitively respond to climate changes at northern high latitudes through sea-air coupling on the millennial timescale.

Evaluation of the response of phytoplankton communities to heavy metal stresses using multi-statistical approaches, Alexandria coast, Egypt

This is the first study to investigate the antioxidant response of the phytoplankton community to heavy metal stress in the open sea. The levels of Cu, Zn, Cd, Mn, Pb, and Fe were determined in the phytoplankton community and water in Abu Talat (AT), and El Dekhella Harbour (DH), Alexandria coast during spring 2018 and autumn 2019. Furthermore, the changes in phytoplankton abundance, the bioconcentration factor (BCF), the metal pollution index (MPI), and the pollution load index (PLI) were used to assess pollution status. The phytoplankton density in the DH stations was 17–42 folds higher than in the AT. The order of BCF during spring was Fe > Zn > Pb > Cu > Mn > Cd. However, Fe > Zn > Mn > Cu > Pb > Cd was found in both areas during the autumn. The BCF, MPI, and PLI of the phytoplankton community revealed that DH is more polluted than AT. The phenol, 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity and total antioxidant activity of the phytoplankton communities achieved higher values in DH than in AT stations, in response to heavy metal stresses. Principal component analysis was performed to follow pollution sources, suggesting that station 3 in both seasons was a hot spot because of stagnant water. A correlation matrix indicated that phenol and DPPH interacted positively in both locations during the two seasons. Analysis of variances with replicate tests on heavy metals in phytoplankton revealed significant seasonal differences across the two areas at a significance level < 0.05.

A service evaluation of phased- and stepped-care psychological support for health and social care workers during the COVID-19 pandemic.

The COVID-19 pandemic has disproportionally affected the mental health of health and social care workers (HSCWs), with many experiencing symptoms of depression, anxiety and post-traumatic stress disorder. Psychological interventions have been offered via mental health services and in-house psychology teams, but their effectiveness in this context is not well documented. To evaluate a stepped-care psychological support pathway for HSCWs from Homerton Healthcare Foundation Trust in London, which offered psychological first aid, evidence-based psychological therapies and group-based well-being workshops. The service evaluation used a pre-post approach to assess depression, anxiety, functional impairment and post-traumatic stress disorder symptom change for those who attended sessions of psychological first aid, low- or high-intensity cognitive-behavioural therapy or a combination of these. In addition, the acceptability of the psychological first aid sessions and well-being workshops was explored via feedback data. Across all interventions, statistically significant reductions of depression (d = 1.33), anxiety (d = 1.37) and functional impairment (d = 0.93) were observed, and these reductions were equivalent between the interventions, as well as the demographic and occupational differences between the HSCWs (ethnicity, staff group and redeployment status). HSCWs were highly satisfied with the psychological first aid and well-being workshops. The evaluation supports the utility of evidence-based interventions delivered as part of a stepped-care pathway for HSCWs with common mental health problems in the context of the COVID-19 pandemic. Given the novel integration of psychological first aid within the stepped-care model as a step one intervention, replication and further testing in larger-scale studies is warranted.