AMHconverter: an online tool for converting results between the different anti-Müllerian hormone assays of Roche Elecsys®, Beckman Access, and Kangrun
Background The anti-Müllerian hormone (AMH) is gaining attention as a key factor in determining ovarian reserve and polycystic ovarian syndrome, and its clinical applications are becoming more widespread worldwide. Objective To identify the most accurate formula for converting AMH assay results between different platforms, so that the developed AMH converter can be used to reduce the need for multiple AMH tests at different hospitals. Methods Assuming that the Beckman Access, Kangrun, and Roche Elecsys® AMH assays fit a linear relationship from the lowest to the highest concentration (a global relationship), we used Passing–Bablok regression to determine the conversion equation between each two assays. When the relationship between two AMH assays was a local one, spline regression was used. Bland–Altman plots were drawn to check systemic bias and heterogeneity of variance across different ranges of values. The fitting effects of the models were evaluated using the squared coefficient of determination (r2), adjusted r2, root mean square error (RMSE), Akaike information criterion (AIC), and corrected AIC. Results The coefficient of variance for multiple controls in the Kangrun, Roche, and Beckman assays was lower than 5%, and the bias of multiple controls was lower than 7%. A global linear relationship was observed between the Kangrun and Roche assays, with the intercept being zero, for which Passing-Bablok regression was employed for data conversion between the two platforms. For the other two pairs of platforms, i.e., Roche and Kangrun or Beckman and Kangrun, spline regression was applied, with the intercepts not including zero. The six corresponding formulas were developed into an online AMH converter (http://121.43.113.123:8006/). Conclusion This is the first time Passing–Bablok plus spline regression has been used to convert AMH concentrations from one assay to another. The formulas have been developed into an online tool, which makes them convenient to use in practical applications.
Xu et al. (2023) AMHconverter: an online tool for converting results between the different anti-Müllerian hormone assays of Roche Elecsys®, Beckman Access, and Kangrun. PeerJ 11:e15301 https://doi.org/10.7717/peerj.15301
Development of rapid and cost-effective multiplex PCR assays to differentiate catfish of the genus Brachyplatystoma (Pimelodidae–Siluriformes) sold in Brazil
The catfishes Brachyplatystoma filamentosum (Kumakuma), Brachyplatystoma vaillantii (Laulao catfish), and Brachyplatystoma rousseauxii (gilded catfish) are important fishery resources in Brazil, where they are sold both fresh and in the form of fillets or steaks. These species have morphological similarities, thus, they can be easily misidentified or substituted, especially after processed. Therefore, accurate, sensitive, and reliable methods are needed for the identification of these species to avoid commercial fraud. In the present study, we develop two multiplex PCR assays for the identification of the three catfish species. Each multiplex protocol combined three species-specific forward primers and a universal reverse primer to produce banding patterns able to discriminate the target species unequivocally. The length of the cytochrome C oxidase subunit I (COI) fragments was approximately 254 bp for B. rousseauxii, 405 bp for B. vaillantii, and 466 bp for B. filamentosum, while the control region (CR) assay produced fragments of approximately 290 bp for B. filamentosum, 451 bp for B. vaillantii, and 580 bp for B. rousseauxii. The protocols were sensitive enough to detect the target species at a DNA concentration of 1 ng/µL, with the exception of the CR of B. vaillantii, in which the fragment was only detectable at 10 ng/µL. Therefore, the multiplex assays developed in the present study were sensitive, accurate, efficient, rapid, and cost-effective for the unequivocal identification of the target species of Brachyplatystoma. They can be utilized by fish processing industries to certify their products, or by government agencies to authenticate products and prevent fraudulent commercial substitutions.
Freitas et al. (2023) Development of rapid and cost-effective multiplex PCR assays to differentiate catfish of the genus Brachyplatystoma (Pimelodidae–Siluriformes) sold in Brazil. PeerJ 11:e15364 https://doi.org/10.7717/peerj.15364
Morpho-biochemical characterization and molecular marker based genetic diversity of pearl millet (Pennisetum glaucum (L.) R. Br.)
Pearl millet is a key food for millions living in semi-arid and arid regions and is a main diet for poorer populations. The genetic diversity existing in the pearl millet germplasm can be used to improve the micronutrient content and grain yield. Effective and organized exploitation of diversity at morphological and DNA levels is the strategy for any crop improvement program. In this study, the genetic diversity of 48 pearl millet genotypes was evaluated for eight morphological traits and eleven biochemical characters. All genotypes were also characterized using twelve SSR and six SRAP markers to evaluate genetic diversity. The significant mean difference between morphological and biochemical traits were detected. The productive tillers per plant varied from 2.65 to 7.60 with a mean of 4.80. The grain yield of genotypes varied more than 3× from 15.85 g (ICMR 07222) to 56.75 g (Nandi 75) with an average of 29.54 g per plant. Higher levels of protein, iron, and zinc contents were found to be present in ICMR 12555 (20.6%), ICMR 08666 (77.38 ppm), and IC 139900 (55.48 ppm), respectively, during the experiment. Substantial variability was observed for grain calcium as it ranged from 100.00 ppm (ICMR 10222) to 256.00 ppm (ICMR 12888). The top eight nutrient-dense genotypes flowered in 34–74 days and had 5.71–9.39 g 1,000 grain weight. Genotype ICMR 08666 was superior for Fe, Zn, K and P. The inter-genotype similarity coefficient at the genetic level, generated using DNA markers, ranged from 0.616 to 0.877 with a mean of 0.743. A combination of morpho-biochemical traits and DNA markers based diversity may help to differentiate the genotypes and diverse genotypes can be used in breeding programs to improve the mineral content in pearl millet.
Gunguniya et al. (2023) Morpho-biochemical characterization and molecular marker based genetic diversity of pearl millet (Pennisetum glaucum (L.) R. Br.). PeerJ 11:e15403 https://doi.org/10.7717/peerj.15403
Predictors of cognitive impairment in patients undergoing ileostomy for colorectal cancer: a retrospective analysis
Background Early detection of cognitive impairment in patients undergoing ileostomy for colorectal cancer may help improve patient outcomes and quality of life. Identifying risk factors and clinically accessible factors is crucial for prevention and treatment. Objective This retrospective study aimed to identify risk factors for post-operative cognitive impairment in patients undergoing ileostomy for colorectal cancer and to explore potential factors for its prevention and treatment. Methods A total of 108 cases were selected and included in the study. Patient data including general characteristics, disease stage, complications, and chemotherapy status were collected, and sleep quality and cognitive function were assessed using questionnaires and follow-up. Patients were randomly divided into training and validation groups. A random forest model was used to rank clinical features based on their contribution to predicting the prognosis of cancer-related cognitive impairment (CRCI). Nomograms were constructed using the support vector machine–recursive feature elimination (SVM-RFE) method, and the minimal root-mean-square error (RMSE) values were compared to select the best model. Regression analysis was performed to determine independent predictors. Results Significant differences were observed in age, body mass index (BMI), alcohol consumption, frequency of physical activity, comorbidity, and cancer-related anemia (CRA) between the CRCI and non-CRCI groups. Random forest analysis revealed that age, BMI, exercise intensity, PSQI scores, and history of hypertension were the most significant predictors of outcome. Univariate logistic regression analysis of 18 variables revealed that age, alcohol consumption, exercise intensity, BMI, and comorbidity were significantly associated with the outcome of CRCI (p < 0.05). Univariate and multivariate models with P-values less than 0.1 and 0.2, respectively, showed better predictive performance for CRCI. The results of univariate analysis were plotted on a nomogram to evaluate the risk of developing CRCI after colorectal cancer surgery. The nomogram was found to have good predictive performance. Finally, regression analysis revealed that age, exercise intensity, BMI, comorbidity, and CRA were independent predictors of CRCI. Conclusions This retrospective cohort study revealed that age, exercise intensity, BMI, comorbidity, CRA, and mobility are independent predictors of cognitive impairment in patients undergoing ileostomy for colorectal cancer. Identifying these factors and potential factors may have clinical implications in predicting and managing post-operative cognitive impairment in this patient population.
Xu et al. (2023) Predictors of cognitive impairment in patients undergoing ileostomy for colorectal cancer: a retrospective analysis. PeerJ 11:e15405 https://doi.org/10.7717/peerj.15405
Determinants of acute undernutrition among pregnant women attending primary healthcare unit in Chinaksen District, Eastern Ethiopia: a case-control study
Background Women’s undernutrition during pregnancy increases the risks and burdens of maternal and neonatal morbidity, death, and disability through its vicious cycles of irreversible intergenerational negative effects. Despite the high burden of maternal undernutrition during pregnancy in semi-pastoral communities of eastern Ethiopia, there is a paucity of information on its major risk factors. This study revealed determinants of acute undernutrition among pregnant women attending primary healthcare units in Chinaksen district in rural eastern Ethiopia. Method A facility-based case-control study was conducted among 113 cases and 113 controls in Chinaksen district from February 01 to March 30, 2017. Data were entered using EpiData version 3.1 and analyzed using SPSS version 24. Multivariable logistic regression analyses conducted to identify significant determinants of acute undernutrition. Adjusted odds ratio (AOR) with a 95% confidence interval was used to report the strength of association and statistical significance declared at p value < 0.05. Results Sixty (53.1%) of cases and 56 (49.6%) of controls were in the age group of 25-34 years and their mean ± SD age of cases and controls were 26.6 ± 5.7 and 28 ± 5.5 years, respectively. In this study, larger family size (AOR = 6.98, 95 CI [2.82–17.27]), lack of prenatal dietary advice (AOR = 3.68, 95% CI [1.67–8.00]), did not participate in a cooking demonstration (AOR = 5.41, 95% CI [2.39–12.24]), used substances (AOR = 3.65, 95% CI [1.30–10.23]), absence of basic latrine (AOR = 2.91, 95% CI [1.28–6.58]), low minimum dietary diversity of women (AOR = 2.48, 95% CI [1.20–5.12]), and household food insecurity (AOR = 3.06, 95% CI [1.44–6.51]) were significantly increased the odds of acute undernutrition among pregnant women. Conclusions The study revealed that living in crowded families, lack prenatal dietary advice, did not participate in cooking demonstrations, substances use; lack of toilet, low minimum dietary diversity, and household food insecurity were significant risk factors for acute undernutrition among pregnant women. Strengthening multi-sectoral approaches through improving dietary diversity/quality and food access/quantity would be essential to prevent, and reduce the risks, burdens, and impacts of maternal undernutrition during pregnancy.
Adem et al. (2023) Determinants of acute undernutrition among pregnant women attending primary healthcare unit in Chinaksen District, Eastern Ethiopia: a case-control study. PeerJ 11:e15416 https://doi.org/10.7717/peerj.15416
The diagnostic value of serum insulin-like growth factor binding protein 7 in gastric cancer
Backgrounds Early detection might help in reducing the burden and promoting the survival rate of gastric cancers. Herein, we tried to explore the diagnostic value of insulin-like growth factor binding protein 7 (IGFBP7) in gastric cancers. Methods In this study, we first analyzed the expression levels and prognostic value of IGFBP7 mRNA in gastric cancers from The Cancer Genome Atlas (TCGA) database. Then, we recruited 169 gastric cancer patients and 100 normal controls as training cohort, and 55 gastric cancer patients and 55 normal controls as independent validation cohort. Enzyme-linked immunosorbent assay was applied to test the serum levels of IGFBP7. The receiver operating characteristic curve (ROC) and the area under the curve (AUC) were applied to evaluation the diagnostic value. Results TCGA showed that IGFBP7 mRNA was dysregulated and associated with prognosis in gastric cancer patients. Then, we examined the expression of serum IGFBP7 and found that serum IGFBP7 expressed lower in gastric cancer patients than normal controls both in training and independent validation cohorts (p < 0.0001). In training cohort, with the cutoff value of 1.515 ng/ml, the AUC for distinguishing gastric cancer patients was 0.774 (95% CI [0.713–0.836]) with sensitivity of 36.7% (95% CI [29.5–44.5]) and specificity of 90.0% (95% CI [82.0–94.8]). As for early-stage EJA, the AUC was 0.773 (95% CI [0.701–0.845]) with the sensitivity of 33.3% (95% CI [14.4–58.8]). In independent validation cohort, with the same cutoff value, the AUC reached to 0.758 (95% CI [0.664–0.852]). Similarly, for early-stage gastric cancer diagnosis in the independent validation cohort, the AUC value was 0.778 (95% CI [0.673–0.882]). Conclusions This study indicated that serum IGFBP7 might act as a potential early diagnostic marker for gastric cancers.
Liu et al. (2023) The diagnostic value of serum insulin-like growth factor binding protein 7 in gastric cancer. PeerJ 11:e15419 https://doi.org/10.7717/peerj.15419
Exploring forearm muscle coordination and training applications of various grip positions during maximal isometric finger dead-hangs in rock climbers
Background Maximal isometric finger dead-hangs are used in rock climbing to strengthen finger flexors. Although various grip positions are often used when performing finger dead-hangs, little is known regarding how these grip positions can affect forearm muscle activity. Understanding how forearm muscles are recruited during dead-hangs could help foreseeing the potential for training of different grip positions. The aim of the present study was to explore the training applications of the various grip positions by comparing the activity of forearm muscles during maximal dead-hangs in rock climbers. Materials & Methods Twenty-five climbers performed maximal dead-hangs in three climbing-specific grip positions: CRIMP, SLOPE, and SLOPER. We recorded the maximal loads used and the sEMG of the flexor digitorum profundus (FDP), the flexor digitorum superficialis (FDS), the flexor carpi radialis (FCR), and the extensor digitorum communis (EDC). Individual and global (sum of all muscles) root mean square (RMS) and neuromuscular efficiency (NME) values were computed. Repeated measures analysis were performed to assess grip differences (p < 0.05). Results SLOPER showed the largest maximal load values among the three grip positions (p < 0.001, d ≥ 2.772). Greater global (p ≤ 0.044, d ≥ 0.268), FDS (p ≤ 0.005, d ≥ 0.277), and FCR (p < 0.001, d ≥ 1.049) activity was observed for the SLOPER compared to CRIMP and SLOPE, while EDC (p ≤ 0.005, d ≥ 0.505) showed lower activity in the SLOPER compared to the other two grip positions. SLOPER presented the highest global (p < 0.001, d ≥ 0.629), FDP (p < 0.001, d ≥ 0.777), FDS (only CRIMP vs SLOPER: p < 0.001, d = 0.140), and EDC NME (p < 0.001, d ≥ 1.194). The CRIMP showed greater FDS activity (p = 0.001, d = 0.386) and lower NME (p = 0.003, d = 0.125) compared to SLOPE. Conclusions These results revealed that, under maximum intensity conditions, SLOPER could stimulate the FDS and FCR better than the other grip positions at the expense of using greater loads. Similarly, maximum CRIMP dead-hang could better stimulate the FDS than the SLOPE, even when using similar loads.
Ferrer-Uris et al. (2023) Exploring forearm muscle coordination and training applications of various grip positions during maximal isometric finger dead-hangs in rock climbers. PeerJ 11:e15464 https://doi.org/10.7717/peerj.15464
Ferroptosis-associated gene CISD2 suppresses colon cancer development by regulating tumor immune microenvironment
Background Despite the association of ferroptosis with various tumors, the specific mechanism by which it influences colon adenocarcinoma (COAD) microenvironmental equilibrium remains elusive. This study aims to elucidate how ferroptosis affects COAD microenvironmental homeostasis and its potential impact on COAD research. Objective By employing genetic screening and single-cell analysis of tumor data, we investigated the role of ferroptosis genes in COAD microenvironmental homeostasis. The genes were correlated with immune cell infiltration in tissue samples and patient outcomes. Methods Ferroptosis-associated genes were initially identified through the FerrDb database. Utilizing the tidyverse and Seurat packages, genes with substantial expression differences were extracted, and clustering analysis was performed on the single-cell data. A Venn diagram depicted shared differential genes for ferroptosis and tumors. To screen key ferroptosis genes, further enrichment analysis and immune cell infiltration analysis were conducted. Lastly, human COAD cell lines were employed to overexpress CDGSH iron sulfur domain 2 (CISD2) through cellular assays to validate its function in COAD. Results Following screening of The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, 414 COAD patient samples and 341 normal samples were included. Through the FerrDb database, 259 ferroptosis genes were identified. Clustering the single-cell data revealed 911 tumor marker genes, of which 18 were ferroptosis genes. Analysis of variance (ANOVA) and univariate regression analysis determined that only CISD2 was statistically significantly associated with clinical outcomes. Additionally, CISD2 was found to positively correlate with activated memory T cells and negatively correlate with regulatory T cells (Tregs) and plasma cells in COAD, as well as being significantly associated with several immune-related and cancer-related pathways. CISD2 expression was elevated in most tumors, likely due to cell cycle regulation and immune system activation. Moreover, CISD2 upregulation inhibited COAD cell proliferation and enhanced 5-fluorouracil (5-FU) sensitivity. Our findings indicate, for the first time, that CISD2 governs the cell cycle and stimulates the immune system to impede COAD progression. Conclusion By modulating the cell cycle and mediating immune infiltration, CISD2 may inhibit COAD development by influencing tumor immune microenvironment equilibrium, providing valuable insights into the relevance and potential impact of the research results on the COAD research field.
Xu et al. (2023) Ferroptosis-associated gene CISD2 suppresses colon cancer development by regulating tumor immune microenvironment. PeerJ 11:e15476 https://doi.org/10.7717/peerj.15476
Land use scenarios, seasonality, and stream identity determine the water physicochemistry of tropical cloud forest streams
Background Land use is a major factor determining stream water physicochemistry. However, most streams move from one land use type to another as they drain their watersheds. Here, we studied three land use scenarios in a tropical cloud forest zone in Mexico. We addressed three main goals, to: (1) assess how land use scenarios generate different patterns in stream physicochemical characteristics; (2) explore how seasonality (i.e., dry, dry-to-wet transition, and wet seasons) might result in changes to those patterns over the year; and (3) explore whether physicochemical patterns in different scenarios resulted in effects on biotic components (e.g., algal biomass). Methods We studied Tropical Mountain Cloud Forest streams in La Antigua watershed, Mexico. Streams drained different three scenarios, streams with (1) an upstream section draining forest followed by a pasture section (F-P), (2) an upstream section in pasture followed by a forest section (P-F), and (3) an upstream forest section followed by coffee plantation (F-C). Physicochemistry was determined at the upstream and downstream sections, and at the boundary between land uses. Measurements were seasonal, including temperature, dissolved oxygen, conductivity, and pH. Water was analyzed for suspended solids, alkalinity, silica, chloride, sulfate, magnesium, sodium, and potassium. Nutrients included ammonium, nitrate, and phosphorus. We measured benthic and suspended organic matter and chlorophyll. Results Streams presented strong seasonality, with the highest discharge and suspended solids during the wet season. Scenarios and streams within each scenario had distinct physicochemical signatures. All three streams within each scenario clustered together in ordination space and remained close to each other during all seasons. There were significant scenario-season interactions on conductivity (F = 9.5, P < 0.001), discharge (F = 56.7, P < 0.001), pH (F = 4.5, P = 0.011), Cl− (F = 12.2, P < 0.001), SO42− (F = 8.8, P < 0.001) and NH4+ (F = 5.4, P = 0.005). Patterns within individual scenarios were associated with stream identity instead of land use. Both P-F and F-C scenarios had significantly different physicochemical patterns from those in F-P in all seasons (Procrustes analysis, m12 = 0.05–0.25; R = 0.86–0.97; P < 0.05). Chlorophyll was significantly different among scenarios and seasons (F = 5.36, P = 0.015, F = 3.81, P = 0.42, respectively). Concentrations were related to physicochemical variables more strongly during the transition season. Conclusion Overall, land use scenarios resulted in distinctive water physicochemical signatures highlighting the complex effects that anthropogenic activities have on tropical cloud forest streams. Studies assessing the effect of land use on tropical streams will benefit from assessing scenarios, rather than focusing on individual land use types. We also found evidence of the importance that forest fragments play in maintaining or restoring stream water physicochemistry.
Vázquez et al. (2023) Land use scenarios, seasonality, and stream identity determine the water physicochemistry of tropical cloud forest streams. PeerJ 11:e15487 https://doi.org/10.7717/peerj.15487
Development and validation of a nomogram to predict protein-energy wasting in patients with peritoneal dialysis: a multicenter cohort study
Background Protein-energy wasting (PEW) is a common complication in patients with peritoneal dialysis (PD). Few investigations involved risk factors identification and predictive model construction related to PEW. We aimed to develop a nomogram to predict PEW risk in patients with peritoneal dialysis. Methods We collected data from end-stage renal disease (ESRD) patients who regularly underwent peritoneal dialysis between January 2011 and November 2022 at two hospitals retrospectively. The outcome of the nomogram was PEW. Multivariate logistic regression screened predictors and established a nomogram. We measured the predictive performance based on discrimination ability, calibration, and clinical utility. Evaluation indicators were receiver operating characteristic (ROC), calibrate curve, and decision curve analysis (DCA). The performance calculation of the internal validation cohort validated the nomogram. Results In this study, 369 enrolled patients were divided into development (n = 210) and validation (n = 159) cohorts according to the proportion of 6:4. The incidence of PEW was 49.86%. Predictors were age, dialysis duration, glucose, C-reactive protein (CRP), creatinine clearance rate (Ccr), serum creatinine (Scr), serum calcium, and triglyceride (TG). These variables showed a good discriminate performance in development and validation cohorts (ROC = 0.769, 95% CI [0.705–0.832], ROC = 0.669, 95% CI [0.585–0.753]). This nomogram was adequately calibrated. The predicted probability was consistent with the observed outcome. Conclusion This nomogram can predict the risk of PEW in patients with PD and provide valuable evidence for PEW prevention and decision-making.
Mei et al. (2023) Development and validation of a nomogram to predict protein-energy wasting in patients with peritoneal dialysis: a multicenter cohort study. PeerJ 11:e15507 https://doi.org/10.7717/peerj.15507