title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=244 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A method for evaluating sediment-induced macroinvertebrate community composition changes in Idaho streams link: https://peerj.com/articles/18060 last-modified: 2024-10-04 description: Human activities can increase sediment delivery to streams, changing the composition, distribution, and abundance of stream aquatic life. Few U.S. states have numeric water quality standards for streambed sediment under the Clean Water Act, so managers often need to develop local application-specific benchmarks. This study developed stream surface fine sediment <2 mm (sand and fines, SF) and macroinvertebrate fine sediment biotic index (FSBI) benchmarks and an application framework to test for sediment-induced macroinvertebrate community composition changes in 1st–4th order Idaho streams. FSBI reference benchmarks were calculated as the 25th percentile FSBI value among reference sites within three ecoregion-based site classes. Two approaches were used to develop SF benchmarks. Quantile regression was used to define reach-specific SF benchmarks representing an upper bound value expected under reference conditions. In addition, logistic regression was used to predict SF values with 50% and 75% probability that FSBI is worse than reference within each stream order and site class. The strength of association between SF benchmarks and macroinvertebrate community condition was evaluated by calculating relative risk using multiple datasets and examining responses of multiple macroinvertebrate indicators to SF benchmark status. SF reference benchmarks generally had stronger associations with poor macroinvertebrate condition than SF stressor-response benchmarks. Across datasets and macroinvertebrate indicators, poor macroinvertebrate condition was 1.8–3 times more likely when SF reference benchmarks were exceeded than when achieved. We propose rating the strength of evidence for a surface fine sediment-induced macroinvertebrate community composition change at the sample event scale as ‘unlikely’ if both SF and FSBI reference benchmarks are achieved, having ‘mixed evidence’ if only one reference benchmark is achieved, and ‘likely’ if both reference benchmarks are not achieved. We recommend combining ratings with other relevant data in a weight-of-evidence approach to assess if sediment impairs aquatic life. creator: Jason Williams creator: James Efta uri: https://doi.org/10.7717/peerj.18060 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Williams and Efta title: Beyond graft function impairment after liver transplantation: the prolonged cold ischemia time impact on recurrence of hepatocellular carcinoma after liver transplantation—a single-center retrospective study link: https://peerj.com/articles/18126 last-modified: 2024-10-04 description: PurposeHepatocellular carcinoma (HCC) is one of the malignant tumors responsible for high mortality and recurrence rates. Although liver transplantation (LT) is an effective treatment option for HCC, ischemia-reperfusion injury (IRI) is a contributor to HCC recurrence after LT. Moreover, prolonged cold ischemia time (CIT) is a risk factor for IRI during LT, and there is insufficient clinical evidence regarding the impact of CIT on HCC recurrence after LT.Patients and MethodsThis retrospective study analyzed 420 patients who underwent LT for HCC between February 2015 and November 2020 at The First Affiliated Hospital, Sun Yat-sen University. The duration of CIT was defined as the time from clamping of the donor aorta until portal reperfusion.ResultsA total of 133 patients (31.7%) experienced tumor recurrence after LT, and CIT > 568 min was the independent risk factor for HCC recurrence (OR, 2.406; 95% CI [1.371–4.220]; p = 0.002). Multivariate Cox’s regression analysis revealed that the recipients’ gender, exceeding Milan criteria, poor differentiation, and alpha-fetoprotein (AFP) ≥400 ng/ml in CIT > 568 min group were independent risk factors for disease-free survival. The peak 7-day postoperative alanine aminotransferase (ALT) level (p < 0.001), the peak 7-day postoperative aspartate aminotransferase (AST) level (p < 0.001), the peak 7-day postoperative peak total bilirubin (TBIL) level (p = 0.012), and the incidence of early allograft dysfunction (EAD) (p = 0.006) were significantly higher in the CIT > 568 min group compared to the CIT ≤ 568 min group. Moreover, the amount of fresh frozen plasma (FFP) infusion during the operation increased (p = 0.02), and the time of mechanical ventilation postoperative was longer (p = 0.045).ConclusionAn effective strategy to improve the prognosis is to reduce CIT; this strategy lowers the recurrence of HCC in patients undergoing LT, especially those within the Milan criteria. creator: Jia Yu creator: Tang Yunhua creator: Yiwen Guo creator: Yuqi Dong creator: Jin long Gong creator: Tielong Wang creator: Zhitao Chen creator: Maogen Chen creator: Weiqiang Ju creator: Xiaoshun He uri: https://doi.org/10.7717/peerj.18126 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: Impact of foam rolling with and without vibration on muscle oxidative metabolism and microvascular reactivity link: https://peerj.com/articles/18180 last-modified: 2024-10-04 description: Background and PurposeThere is a growing interest in use vibration foam rolling as a warm up and recovery tool. However, whether vibration foam rolling offers additional benefits to traditional foam rolling is unclear. The current study aims to compare the effects of acute foam rolling, with and without vibration, on skeletal muscle metabolism and microvascular reactivity.MethodsFifteen physically active young males were tested on two different days, with gastrocnemius muscle microvascular function assessed using near-infrared spectroscopy coupled with the post-occlusive reactive hyperemia technique, before and after foam rolling, performed with or without vibration. The slope of tissue saturation index (TSI) decrease during occlusion between 120 s to 150 s (TSI occlusion slope) was assessed for muscle metabolic rate. Three commonly used microvascular function indexes, including the first10s TSI slope after occlusion (TSI10), time for TSI to reach half of peak magnitude (TSI1/2), and TSI peak reactive hyperemia, were also assessed.ResultsNone of the measured indexes showed significance for interaction or method (all p > 0.05). However, there was a main effect for time for TSI occlusion slope, TSI1/2, and TSI peak reactive hyperemia (p = 0.005, 0.034 and 0.046, respectively). No main effect for time for TSI10 was detected (p = 0.963).ConclusionsThe application of foam rolling can decrease muscle metabolism, and may improve some aspects of muscle microvascular function. However, vibration foam rolling does not seem to offer any additional benefits compared to traditional foam rolling alone. creator: Haizhen Huang creator: Bin Leng creator: Chuan Zhang uri: https://doi.org/10.7717/peerj.18180 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Huang et al. title: Association between triglyceride glycemic index and ejection fraction preserved heart failure in hypertensive patients link: https://peerj.com/articles/18220 last-modified: 2024-10-04 description: BackgroundThe triglyceride-glucose (TyG) index is regarded as an independent predictor of cardiovascular disease consequences and a reliable surrogate measure of insulin resistance (IR). However, the correlation analysis between triglyceride glucose index and heart failure with preserved ejection fraction in patients with essential hypertension remains unknown.MethodsA single-center, retrospective study was conducted with patients diagnosed with essential hypertension at the First Affiliated Hospital of Xinjiang Medical University, from December 2018 to September 2020. Participants were selected based on specific inclusion and exclusion criteria, with their clinical data and laboratory tests collected. The study employed Spearman’s correlation analysis, logistic regression models, restricted cubic spline plots, and receiver operating characteristic (ROC) curves to investigate the relationships between the TyG index and HFpEF.ResultsOut of 1,602 enrolled hypertensive patients, 992 were included in the analysis after applying exclusion criteria. Patients were categorized into tertiles based on the TyG index, which showed that patients in the highest tertile had characteristics associated with a higher risk of HFpEF, including age, body mass index (BMI), systolic blood pressure (SBP), N-terminal pro-B-type natriuretic peptide (NT-proBNP), and left ventricular mass index (LVMI). A significant, independent association between the TyG index and HFpEF was confirmed, with an odds ratio (OR) of 5.127 (95% CI [3.894–6.856]). Furthermore, an S-shaped nonlinear relationship was observed between the TyG index and the incidence of HFpEF (nonlinear p < 0.001). TyG index (AUC: 0.824, 95% CI [0.795–0.854]), NT-proBNP (AUC: 0.840, 95% CI [0.816–0.864]), and LVMI (AUC: 0.847, 95% CI [0.820–0.875]) showed good predictive ability for HFpEF. In addition, the TyG+LVMI combination demonstrated the strongest predictive ability (AUC: 0.907, 95% CI [0.887–0.927]).ConclusionThe study underscores a significant association between IR, as indicated by the TyG index, and the development of HFpEF in hypertensive patients. It highlights the critical role of metabolic dysfunction in the pathophysiology of HFpEF, advocating for a broader perspective on cardiovascular risk management. creator: Xue-Feng Shan creator: Long Yang creator: Xiao-Ming Gao uri: https://doi.org/10.7717/peerj.18220 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Shan et al. title: The non-HDL-C to APOB ratio as a predictor of inaccurate LDL-C measurement in patients with chronic intrahepatic cholestasis and jaundice: a retrospective study link: https://peerj.com/articles/18224 last-modified: 2024-10-04 description: BackgroundCholestasis is characterized by the accumulation of bile in the liver or biliary system due to obstruction or impaired flow, necessitating lipid profiling to assess lipid metabolism abnormalities. Intrahepatic cholestasis, being the most significant type of cholestasis, further complicates the assessment of lipid abnormalities. However, the accuracy of low-density lipoprotein cholesterol (LDL-C) measurement in intrahepatic cholestasis patients remains uncertain.ObjectiveThis study aimed to evaluate the consistency of the homogeneous assay and the Friedewald formula in detecting LDL-C levels and identify factors influencing LDL-C test results in intrahepatic patients with cholestasis.MethodsRetrospective analysis of laboratory data was conducted on intrahepatic cholestatic patients. Correlations between LDL-C values obtained using the homogeneous method (LDL-C(D)) and the Friedewald formula (LDL-C(F)), as well as associations between high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A1 (ApoA1), LDL-C(D) and LDL-C(F), and apolipoprotein B (ApoB), were analyzed. Logistic regression analyses were employed to identify diagnostic indicators for inaccurate LDL-C measurements in intrahepatic cholestatic patients.ResultsCompared to patients with intrahepatic cholestasis without jaundice, the correlation between LDL-C(F) and LDL-C(D) was weaker in those with jaundice. Additionally, HDL-C exhibited a strong correlation with ApoA1 in both jaundice and non-jaundice cholestasis cases. Elevated non-HDL-C to APOB ratio (NH-C/B Ratio) levels (>4.5) were identified as a reliable predictor of inaccurate LDL-C measurements in patients with chronic intrahepatic cholestasis accompanied by jaundice.ConclusionsLDL-C measurement reliability is moderately weaker in patients with intrahepatic cholestasis accompanied by jaundice. Elevated levels of the NH-C/B ratio serve as a significant predictor of inaccurate LDL-C measurements in this chronic patient population, highlighting its clinical relevance for diagnostic assessments. creator: Yongjiang Cheng creator: Jingyan Ye creator: Junyuan Huang creator: Yang Wang uri: https://doi.org/10.7717/peerj.18224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng et al. title: Reliability and reproducibility of an Italian questionnaire on “Knowledge of high social impact Eye Diseases” (KED-IT) link: https://peerj.com/articles/17906 last-modified: 2024-10-03 description: BackgroundHealth literacy plays an important role in public health. Although this has been demonstrated in the field of ophthalmology, there are very few specific instruments available to assess eye health literacy. This work aims to develop an Italian questionnaire on knowledge of eye diseases (Knowledge on Eye Disease, Italian version; KED-IT) and to evaluate its reliability and reproducibility. The KED-IT focuses on diseases with high social impact, specifically glaucoma, macular degeneration, diabetic retinopathy and keratoconus, which is the main cause of corneal transplant in Italy.MethodsA cross-sectional study was conducted. The KED-IT was self-administered by the study participants twice. The interval between each administration (T0 and T1) was 5 to 8 days. Reliability was assessed using the KR-20 coefficient. The test-retest Cohen’s Kappa coefficient was estimated to measure the stability and reproducibility of the results obtained between T0 and T1.ResultsA total of 60 subjects participated in the study. The response rate at T1 was 92%. The KR-20 reliability coefficient of the 14-item KED-IT questionnaire was good with a value of 0.878. The Cohen’s kappa value for all 14 items of the KED-IT questionnaire was k = 0.747, indicating good agreement.ConclusionsThe KED-IT is the first specific ophthalmic knowledge questionnaire validated in the Italian language and we hope that it may be a starting point for the study of eye health literacy in the Italian population. creator: Valeria Iannucci creator: Alice Bruscolini creator: Tiziano Melchiorre creator: Alessandro Lambiase creator: Alice Mannocci uri: https://doi.org/10.7717/peerj.17906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Iannucci et al. title: Nanotechnology in action: silver nanoparticles for improved eco-friendly remediation link: https://peerj.com/articles/18191 last-modified: 2024-10-03 description: Nanotechnology is an exciting area with great potential for use in biotechnology due to the far-reaching effects of nanoscale materials and their size-dependent characteristics. Silver and other metal nanoparticles have attracted a lot of attention lately because of the exceptional optical, electrical, and antimicrobial characteristics they possess. Silver nanoparticles (AgNPs) stand out due to their cost-effectiveness and abundant presence in the earth’s crust, making them a compelling subject for further exploration. The vital efficacy of silver nanoparticles in addressing environmental concerns is emphasized in this thorough overview that dives into their significance in environmental remediation. Leveraging the distinctive properties of AgNPs, such as their antibacterial and catalytic characteristics, innovative solutions for efficient treatment of pollutants are being developed. The review critically examines the transformative potential of silver nanoparticles, exploring their various applications and promising achievements in enhancing environmental remediation techniques. As environmental defenders, this study advocates for intensified investigation and application of silver nanoparticles. Furthermore, this review aims to assist future investigators in developing more cost-effective and efficient innovations involving AgNPs carrying nanoprobes. These nanoprobes have the potential to detect numerous groups of contaminants simultaneously, with a low limit of detection (LOD) and reliable reproducibility. The goal is to utilize these innovations for environmental remediation purposes. creator: Suresh Babu Naidu Krishna creator: Abdul Gaffar Sheik creator: Karen Pillay creator: Manhal Ahmed Hamza creator: Mohammed Yagoub Mohammed Elamir creator: Samy Selim uri: https://doi.org/10.7717/peerj.18191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Krishna et al. title: PotatoG-DKB: a potato gene-disease knowledge base mined from biological literature link: https://peerj.com/articles/18202 last-modified: 2024-10-03 description: BackgroundPotato is the fourth largest food crop in the world, but potato cultivation faces serious threats from various diseases and pests. Despite significant advancements in research on potato disease resistance, these findings are scattered across numerous publications. For researchers, obtaining relevant knowledge by reading and organizing a large body of literature is a time-consuming and labor-intensive process. Therefore, systematically extracting and organizing the relationships between potato genes and diseases from the literature to establish a potato gene-disease knowledge base is particularly important. Unfortunately, there is currently no such gene-disease knowledge base available.MethodsIn this study, we constructed a Potato Gene-Disease Knowledge Base (PotatoG-DKB) using natural language processing techniques and large language models. We used PubMed as the data source and obtained 2,906 article abstracts related to potato biology, extracted entities and relationships between potato genes and related disease, and stored them in a Neo4j database. Using web technology, we also constructed the Potato Gene-Disease Knowledge Portal (PotatoG-DKP), an interactive visualization platform.ResultsPotatoG-DKB encompasses 22 entity types (such as genes, diseases, species, etc.) of 5,206 nodes and 9,443 edges between entities (for example, gene-disease, pathogen-disease, etc.). PotatoG-DKP can intuitively display associative relationships extracted from literature and is a powerful assistant for potato biologists and breeders to understand potato pathogenesis and disease resistance. More details about PotatoG-DKP can be obtained at https://www.potatogd.com.cn/. creator: Congjiao Xie creator: Jing Gao creator: Junjie Chen creator: Xuyang Zhao uri: https://doi.org/10.7717/peerj.18202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xie et al. title: Feasibility and acceptability pilot study of an online weight loss program in rural, underserved communities link: https://peerj.com/articles/18268 last-modified: 2024-10-03 description: BackgroundThe purpose of this intervention was to investigate the feasibility, acceptability, and preliminary effectiveness of an online weight loss program, EMPOWER, in rural, underserved communities.MethodsAdults with a body mass index (BMI) ≥ 25 kg/m2 living in rural counties were recruited through collaboration with University of Illinois Extension. The intervention lasted 1 year including online educations sessions, nutrition and lifestyle coaching, and diet and weight monitoring via a novel web application, MealPlot. Feasibility was measured by enrollment attainment, participant retention, online education session completion, and completion of anthropometric and dietary measures. Acceptability was measured by survey using Likert scales of satisfaction for all program components. Anthropometric measurements, 24-h dietary records, and food frequency questionnaires (FFQs) were measures of program efficacy. Additionally, two interviews were collected for program feedback.ResultsEnrollment of 16 participants was attained, however due to higher than anticipated dropout (retention 62.5%, N = 10) at 3-months, 62.5% of the education sessions were completed and 75.0% of anthropometric and dietary measures. The average satisfaction rating for the comprehensive program was 4.2/5 with lowest satisfaction being the MealPlot web application 2.7/5 (N = 11). On average a clinically significant (≥5% baseline weight) weight loss of 6.2 ± 6.0% body weight or 5.7 ± 5.3 kg and improvements to protein and fiber intake at 12 months (N = 10) were observed.ConclusionsA novel online weight loss program showed adequate to strong feasibility and acceptability and preliminary results indicating efficacy among a pilot sample of rural residents. Future studies are required to investigate means of improving retention and reducing the burden on program collaborators. creator: Ashleigh Oliveira creator: Nouf Alfouzan creator: Jin Yu creator: Asma Yahya creator: Kayla Lammy creator: Mary Liz Wright creator: Diane Reinhold creator: Lisa Peterson creator: Ashley Brewer creator: Janet Liechty creator: Manabu T. Nakamura uri: https://doi.org/10.7717/peerj.18268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oliveira et al. title: A new species of frog of the genus Noblella Barbour, 1930 (Amphibia: Strabomantidae) from the Cordillera del Cóndor, Ecuador link: https://peerj.com/articles/17939 last-modified: 2024-10-02 description: We describe a new species of leaflitter frog of the genus Noblella from southern Ecuador, province of Zamora Chinchipe. The new species is diagnosed from all its congeners by having one or two tubercles on the upper eyelids; distal phalanges strongly T-shaped; phalangeal formula on hands 2-2-3-3; phalangeal formula on feet 2-2-3-4-3; heel with a small subconical tubercle; disc on all toes with papillae; dorsum brown or brown with gray, with V-shaped inverted or scattered irregular darker marks. We include a detailed description of its osteology and a study of its phylogenetic relationships. Finally, we evaluate its conservation status and discuss the threats that are currently impacting at the type locality. creator: David Brito-Zapata creator: Juan D. Chávez-Reyes creator: Matheo David Pallo-Robles creator: Julio C. Carrión-Olmedo creator: Diego F. Cisneros-Heredia creator: Carolina Reyes-Puig uri: https://doi.org/10.7717/peerj.17939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Brito-Zapata et al.