Development of multiplex real-time PCR for simultaneous detection of common fungal pathogens in invasive mycoses
Background Fungi are common opportunistic pathogens that pose a significant threat to immunocompromised patients, particularly when late detection occurs. Methods In this study a multiplex real-time PCR has been developed for simultaneous detection of common fungal pathogens associated with invasive mycoses in a diagnostic setting. Results The specificity of the assay was rigorously tested on 40 types of organisms (n = 65), demonstrating 100% specificity. The limit of detection was determined to be 100 pg/μl (106 copies/μl), achievable within a rapid 3-h timeframe. The PCR assay efficiency exhibited a range between 89.77% and 104.30% for each target organism, with linearity falling between 0.9780 and 0.9983. Conclusion This multiplex real-time PCR assay holds promise for enhancing the timely and accurate diagnosis of invasive mycoses, particularly in immunocompromised patient populations.
Ismadi et al. (2024) Development of multiplex real-time PCR for simultaneous detection of common fungal pathogens in invasive mycoses. PeerJ 12:e18238 https://doi.org/10.7717/peerj.18238
Diabetes self-care and its associated factors among type 2 diabetes mellitus with chronic kidney disease patients in the East Coast of Peninsular Malaysia
Introduction Diabetes self-care among diabetic patients is crucial as it determines how patients care for their illness in their daily routine for better diabetes control. This study aims to calculate the average score for diabetes self-care among patients with type 2 diabetes mellitus and chronic kidney disease and to identify factors that are associated with this score. Materials and Methods This cross-sectional study enrols patients over 18 years old with type 2 diabetes mellitus and chronic renal disease with an eGFR of less than 60 mL/min/1.73 m2 in a tertiary hospital in Malaysia. The Malay version of the Summary of Diabetic Self-Care Activities (SDSCA) was used to assess diabetes self-care, the Malay version of the diabetes-related distress questionnaire (DDS-17) was used to assess diabetes distress, and the Malay version of the Patient Health Questionnaire-9 (PHQ-9) was used to assess depression. Data analysis was performed using both simple and multiple linear regression models to determine the associations between variables. Result One hundred and seventy-six eligible patients were recruited for this study. The mean score for diabetes self-care is 3.62. The eGFR (p = 0.002) and diabetes distress (p = 0.004) are the significant associated factors for diabetes self-care among type 2 diabetes mellitus patients with chronic kidney disease. Conclusion The mean score for diabetes self-care indicated a moderate level of self-care. The eGFR level and diabetes distress were important factors influencing diabetes self-care practices.
Ramli et al. (2024) Diabetes self-care and its associated factors among type 2 diabetes mellitus with chronic kidney disease patients in the East Coast of Peninsular Malaysia. PeerJ 12:e18303 https://doi.org/10.7717/peerj.18303
Oral reading promotes predictive processing in Chinese sentence reading: eye movement evidence
Background Fluent sentence reading is widely acknowledged to depend on top-down contextual prediction, wherein sentential and contextual cues guide the pre-activation of linguistic representations before encountering stimuli, facilitating subsequent comprehension. The Prediction-by-Production hypothesis posits an explanation for predictive processes in language comprehension, suggesting that prediction during comprehension involves processes associated with language production. However, there is a lack of eye movement evidence supporting this hypothesis within sentence reading contexts. Thus, we manipulated reading mode and word predictability to examine the influence of language production on predictive processing. Methods Participants engaged in silent or oral reading of sentences containing either high or low-predictable target words. Eye movements were recorded using the Eyelink1000 eye tracker. Results The findings revealed a higher skipping rate and shorter fixation times for high-predictable words compared to low-predictable ones, and for silent compared to oral reading. Notably, interactive effects were observed in the time measures (FFD, SFD, GD) during first-pass reading, indicating that word predictability effects were more pronounced during oral reading than silent reading. Discussion The observed pattern of results suggests that the activation of the production system enhances predictive processing during the early lexical access, providing empirical support for the Prediction-by-Production hypothesis in eye movement sentence reading situations, extending the current understanding of the timing and nature of predictions in reading comprehension.
Chang et al. (2024) Oral reading promotes predictive processing in Chinese sentence reading: eye movement evidence. PeerJ 12:e18307 https://doi.org/10.7717/peerj.18307
Comparative transcriptome analysis to identify the important mRNA and lncRNA associated with salinity tolerance in alfalfa
Salinity represents a fatal factor affecting the productivity of alfalfa. But the regulation of salinity tolerance via lncRNAs and mRNAs remains largely unclear within alfalfa. For evaluating salinity stress resistance-related lncRNAs and mRNAs within alfalfa, we analyzed root transcriptomics in two alfalfa varieties, GN5 (salinity-tolerant) and GN3 (salinity-sensitive), after treatments with NaCl at 0 and 150 mM. There were altogether 117,677 lncRNAs and 172,986 mRNAs detected, including 1,466 lncRNAs and 2,288 mRNAs with significant differential expression in GN5150/GN50, GN3150/GN30, GN50/GN30, and GN5150/GN3150. As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as HPCA1-LRR, PP2C60, PP2C71, CRK1, APX3, HXK2, BAG6, and ARF1, had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased CNGC1 expression in GN5. According to co-expressed network analyses, six lncRNAs (TCONS_00113549, TCONS_00399794, TCONS_00297228, TCONS_00004647, TCONS_00033214 and TCONS_00285177) modulated 66 genes including ARF1, BAG6, PP2C71, and CNGC1 in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 vs. GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas.
Yang et al. (2024) Comparative transcriptome analysis to identify the important mRNA and lncRNA associated with salinity tolerance in alfalfa. PeerJ 12:e18236 https://doi.org/10.7717/peerj.18236
Proteomic analysis of giant panda testicular tissue of different age groups
Background The reproductive ability of male giant pandas has been a major complicating factor in the ex-situ conservation of the species. While it is well known that the testis produces sperm and secretes androgens, a process that requires precise regulation of various proteins, at present, there has been no systematic study on the composition of proteins in the testis of the giant pandas. Therefore, this study aims to apply proteomics to explore the regulation of proteins in the testes of giant pandas. Methods Samples from the testes of three giant pandas (22 years, 18 years, 8 days) were studied to assess the protein’s function. A label-free quantitative method was used to isolate testicular proteins from each male, 139,039 peptides and 11,435 proteins were obtained. Results Gene Ontology (GO) annotates most of the proteins involved in the processes of protein phosphorylation, oxidation-reduction, proteolysis, and signal transduction. KEGG pathway indicated that most of the proteins were involved in the pathway of signal transduction, transport, and catabolism. The protein kinase and WD40 repeats were involved in protein-protein interaction, which in turn regulates gene expression in the testicular tissue of giant pandas. Conclusions This study is the first to conduct an in-depth proteomic analysis of testicular tissue in giant pandas. The results revealed the important role of proteins in testicular tissue on spermatogenesis, testosterone production, and testicular microenvironment, providing clues for further research on male giant panda reproduction.
Peng et al. (2024) Proteomic analysis of giant panda testicular tissue of different age groups. PeerJ 12:e18249 https://doi.org/10.7717/peerj.18249
Factors associated with quality of life among newly diagnosed acute ischemic stroke patients: a community-based case-control study
Background Stroke burden is expected to increase and surviving a bout of stroke may leave one with a chronic or disabling outcome decreasing significantly the quality of life of the sufferer. The study aimed to explore the association between quality of life (QoL) in stroke and non-stroke individuals in a predominantly agricultural community. Method A community-based case-control study was conducted among 154 cases aged 18 and 75 diagnosed with incident stroke. Controls were 554 non-stroke individuals (n = 554) recruited from a community where cases resided. Cases and controls were matched for age, gender and residential area. Using a self-reported questionnaire of the World Health Organization Quality of Life (WHOQOL-BREF), socio-demographic characteristics and lifestyle habits were measured in association with QoL. Statistical analyses included multivariable logistic regression models, adjusted odds ratio (aOR) and 95% confidence interval (CI). Results Significant predictors associated with low-medium QoL were having a larger waist circumference (aOR = 1.619, 95%CI [1.003–2.612]) and being a farmer (aOR = 2.976, 95%CI [1.143–7.750]) but having a current smoking habit and being male were at lesser odds with low-medium QoL (aOR = 0.381, 95%CI [0.191–0.757]) and (aOR = 0.564, 95%CI [0.323–0.985]) respectively. In all domains, women were at a higher risk of low-medium QoL while in physical health and environment domains, it was having a larger waist circumference. In both physical health and psychological domains, being married was protective to low-medium QoL so also being age 39 or younger and having a higher education in social relationship domain. Conclusion Waist circumference, occupation, smoking habit and gender are associated with low-medium QoL. Addressing the influence of such factors could create an additional therapeutic line in the primary prevention of stroke in at-risk populations.
Abdulsalam et al. (2024) Factors associated with quality of life among newly diagnosed acute ischemic stroke patients: a community-based case-control study. PeerJ 12:e18266 https://doi.org/10.7717/peerj.18266
Estimation methods for the variance of Birnbaum-Saunders distribution containing zero values with application to wind speed data in Thailand
Thailand is currently grappling with a severe problem of air pollution, especially from small particulate matter (PM), which poses considerable threats to public health. The speed of the wind is pivotal in spreading these harmful particles across the atmosphere. Given the inherently unpredictable wind speed behavior, our focus lies in establishing the confidence interval (CI) for the variance of wind speed data. To achieve this, we will employ the delta-Birnbaum-Saunders (delta-BirSau) distribution. This statistical model allows for analyzing wind speed data and offers valuable insights into its variability and potential implications for air quality. The intervals are derived from ten different methods: generalized confidence interval (GCI), bootstrap confidence interval (BCI), generalized fiducial confidence interval (GFCI), and normal approximation (NA). Specifically, we apply GCI, BCI, and GFCI while considering the estimation of the proportion of zeros using the variance stabilized transformation (VST), Wilson, and Hannig methods. To evaluate the performance of these methods, we conduct a simulation study using Monte Carlo simulations in the R statistical software. The study assesses the coverage probabilities and average widths of the proposed confidence intervals. The simulation results reveal that GFCI based on the Wilson method is optimal for small sample sizes, GFCI based on the Hannig method excels for medium sample sizes, and GFCI based on the VST method stands out for large sample sizes. To further validate the practical application of these methods, we employ daily wind speed data from an industrial area in Prachin Buri and Rayong provinces, Thailand.
Environmental Contamination and Remediation
Ratasukharom et al. (2024) Estimation methods for the variance of Birnbaum-Saunders distribution containing zero values with application to wind speed data in Thailand. PeerJ 12:e18272 https://doi.org/10.7717/peerj.18272
Larval growth rate is not a major determinant of adult wing shape and eyespot size in the seasonally polyphenic butterfly Melanitis leda
Background Insects often show adaptive phenotypic plasticity where environmental cues during early stages are used to produce a phenotype that matches the environment experienced by adults. Many tropical satyrine butterflies (Nymphalidae: Satyrinae) are seasonally polyphenic and produce distinct wet- and dry-season form adults, providing tight environment-phenotype matching in seasonal environments. In studied Mycalesina butterflies, dry-season forms can be induced in the laboratory by growing larvae at low temperatures or on poor food quality. Since both these factors also tend to reduce larval growth rate, larval growth rate may be an internal cue that translates the environmental cues into the expression of phenotypes. If this is the case, we predict that slower-growing larvae would be more likely to develop a dry-season phenotype. Methods We performed the first experimental study on seasonal polyphenism of a butterfly in the tribe Melanitini. We measured both larval growth rate and adult phenotype (eyespot size and wing shape) of common evening brown butterflies (Melanitis leda), reared at various temperatures and on various host-plant species. We constructed provisional reaction norms, and tested the hypothesis that growth rate mediates between external cues and adult phenotype. Results Reaction norms were similar to those found in Mycalesina butterflies. We found that both among and within treatments, larvae with lower growth rates (low temperature, particular host plants) were more likely to develop dry-season phenotypes (small eyespots, falcate wing tips). However, among temperature treatments, similar growth rates could lead to very different wing phenotypes, and within treatments the relationships were weak. Moreover, males and females responded differently, and eyespot size and wing shape were not strongly correlated with each other. Overall, larval growth rate seems to be weakly related to eyespot size and wing shape, indicating that seasonal plasticity in M. leda is primarily mediated by other mechanisms.
Molleman et al. (2024) Larval growth rate is not a major determinant of adult wing shape and eyespot size in the seasonally polyphenic butterfly Melanitis leda. PeerJ 12:e18295 https://doi.org/10.7717/peerj.18295
A pooled analysis of the incidence and mortality risk of atrial fibrillation in patients with COVID-19
Background There exist serious cardiovascular complications subsequent to SARS-Cov2 infection (COVID-19); however, the association between COVID-19 and atrial fibrillation (AF) remains to be elucidated. We aimed to assess the prevalence of AF among COVID-19 patients and its associated risk of death. Methods The present systematic review was performed in accordance with the PRISMA guidelines. The protocol was registered with CRD42022306523. A comprehensive literature search was performed across PubMed, Embase, and Cochrane databases to identify studies reporting on the prevalence of pre-existing or new-onset fibrillation (AF), and/or the associated clinical outcomes in patients with COVID-19 from January 2020 to December 2023. The random-effect model was used to estimate the prevalence of AF and its related mortality. Results A total of 80 studies, including 39,062,868 COVID-19 patients, were identified in the present investigation. The prevalence rates of pre-existing AF or new-onset AF were 10.5% (95% CI [9.3–11.7%]) or 10.3% (95% CI [6.2–14.5%]), respectively. Subgroup analysis revealed a two fold higher incidence of AF in older patients (≥65 years) compared to younger patients (<65 years) (14.4% vs. 6.4%). The highest rate of AF was observed in Europeans (10.7%, 95% CI [10.2–11.2%]), followed by Northern Americans (10.0%, 95% CI [8.2–11.7%]), while Asians demonstrated a lower prevalence (2.7%, 95% CI [2.2–3.3%]). Notably, severe COVID-19 patients displayed a significantly elevated prevalence of AF at 14.l% (95% CI [13.3–14.9%]), which was approximately 2.5-fold higher than that in non-severe patients (5.2%, 95% CI [4.8–5.5%]). Both pre-existing (HR: 1.83, 95% CI [1.49–2.17]) and new-onset AF (HR: 3.47, 95% CI [2.26–5.33]) were associated with an increased mortality risk among COVID-19 patients. Furthermore, the effect on mortality risk was more significant in Asians (HR: 5.33, 95% CI [1.62–9.04]), compared to Europeans (HR: 1.68, 95% CI [1.24–2.13]) and North Americans (HR: 2.01, 95% CI [1.18–2.83]). Conclusion This study comprehensively investigated the association between AF and COVID-19 in a real-world setting. Notably, a high prevalence of AF was observed among older individuals, severe COVID-19 patients, and in Europe and Northern America. Moreover, co-existing AF was found to be associated with an increased risk for mortality. Further investigations are warranted to improve the management and outcomes of COVID-19 patients with AF.
Shen et al. (2024) A pooled analysis of the incidence and mortality risk of atrial fibrillation in patients with COVID-19. PeerJ 12:e18330 https://doi.org/10.7717/peerj.18330
Determination of natural populations to be included in breeding program in St. John’s wort species (Hypericum perforatum L.)
St. John’s wort (Hypericum perforatum L.) is a medicinal and aromatic plant of rapidly increasing importance. The cultural production of this species, which is of economic importance due to its medicinal properties, is limited. One of the main ways to increase production is to develop cultivars. Thus, the homogeneous raw material required for a standard product will be provided. This study aimed to determine the characteristics of natural populations to obtain productive cultivars with high hypericin and hyperforin that can meet market demands. In addition to yield and quality values, other characteristic features of the plant such as flower diameter, petal length and petal width, which directly affect productivity, were revealed in the study. The study was conducted under field conditions for two years with three replications. Fresh flower weight among the populations varied between 30.15 and 240.28 g/plant, while the hypericin ratio varied between 51.32 and 105.31 (mg/100 g). The study determined a wide variation among the populations, and the populations with superior characteristics were included in the breeding program.
Uysal Bayar (2024) Determination of natural populations to be included in breeding program in St. John’s wort species (Hypericum perforatum L.). PeerJ 12:e18336 https://doi.org/10.7717/peerj.18336