Identifying the critical state of cancers by single-sample Markov flow entropy
Background The progression of complex diseases sometimes undergoes a drastic critical transition, at which the biological system abruptly shifts from a relatively healthy state (before-transition stage) to a disease state (after-transition stage). Searching for such a critical transition or critical state is crucial to provide timely and effective scientific treatment to patients. However, in most conditions where only a small sample size of clinical data is available, resulting in failure when detecting the critical states of complex diseases, particularly only single-sample data. Methods In this study, different from traditional methods that require multiple samples at each time, a model-free computational method, single-sample Markov flow entropy (sMFE), provides a solution to the identification problem of critical states/pre-disease states of complex diseases, solely based on a single-sample. Our proposed method was employed to characterize the dynamic changes of complex diseases from the perspective of network entropy. Results The proposed approach was verified by unmistakably identifying the critical state just before the occurrence of disease deterioration for four tumor datasets from The Cancer Genome Atlas (TCGA) database. In addition, two new prognostic biomarkers, optimistic sMFE (O-sMFE) and pessimistic sMFE (P-sMFE) biomarkers, were identified by our method and enable the prognosis evaluation of tumors. Conclusions The proposed method has shown its capability to accurately detect pre-disease states of four cancers and provide two novel prognostic biomarkers, O-sMFE and P-sMFE biomarkers, to facilitate the personalized prognosis of patients. This is a remarkable achievement that could have a major impact on the diagnosis and treatment of complex diseases.
Liu et al. (2023) Identifying the critical state of cancers by single-sample Markov flow entropy. PeerJ 11:e15695 https://doi.org/10.7717/peerj.15695
Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia
Background Oleanolic acid (OA) and moderate drinking have been reported to attenuate diabetes. However, the underlying mechanism of OA and moderate drinking alone or in combination on the islet β-cell deficiency induced diabetes is not fully elucidated. Methods Male Sprague Dawley (SD) rats were intraperitoneally injected with 55 mg/kg streptozotocin (STZ) to induce β-cell deficiency. OA, 5% ethanol (EtOH), or a mixture of OA in 5% ethanol (OA+EtOH) were applied to three treatment groups of hyperglycemia rats for 6 weeks. Results STZ caused the increase of fast blood glucose (FBG) level.OA and EtOH treatment alone or in combination decreased the STZ increased FBG level during the 6 weeks of treatment. In addition, OA treatment also significantly increased the β-cell to total islet cell ratio. Both EtOH and OA+EtOH treatments promoted the increase of total islet cell number and α-cell to β-cell ratio when compared to OA group. STZ induced hyperglycemia dramatically reduced the glucagon-like peptide-1 receptor (GLP-1R) positive cells in islets, all the three treatments significantly increased the pancreatic GLP-1R positive cell number. In the meantime, STZ induced hyperglycemia suppressed the insulin mRNA expression and boosted the glucagon mRNA expression. EtOH and OA+EtOH treatments increased the insulin mRNA expression, but none of the 3 treatments altered the elevated glucagon level. Conclusion GLP-1R positive cell ratio in islets is crucial for the blood glucose level of diabetes. OA and 5% ethanol alone or in combination suppresses the blood glucose level of β-cell deficiency induced diabetes by increasing islet GLP-1R expression.
Xu et al. (2023) Oleanolic acid and moderate drinking increase the pancreatic GLP-1R expression of the β-cell mass deficiency induced hyperglycemia. PeerJ 11:e15705 https://doi.org/10.7717/peerj.15705
Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis
Background Uncertainty exists regarding the pain scores and the success rate of intraligamentary anesthesia compared to other infiltration anesthesia. Based on the conditions of clinical anesthesia techniques, we conducted a systematic review and meta-analysis to compare the efficacy of intraligamentary anesthesia with other infiltration anesthesia. Methods The search was carried out in PubMed Central, Cochrane Central Register of Controlled Trials, MEDLINE (via OVID), Embase (via OVID), and Scopus from the inception to March 26, 2023. Results Seven eligible randomized controlled trials were included in the meta-analysis. The results indicated no significant difference in the success rate (RR = 0.96; 95% CI [0.81–1.14]; p = 0.65; I2= 73%) and visual analog scale (VAS) during dental procedures (MD = 3.81; 95% CI [−0.54–8.16]; p = 0.09; I2= 97%) between intraligamentary anesthesia and other infiltration anesthesia. However, intraligamentary anesthesia exhibited a higher VAS score during injection than other infiltration anesthesia (MD = 8.83; 95% CI [4.86–12.79]; p < 0.0001; I2= 90%). A subgroup analysis according to infiltration techniques showed that supraperiosteal anesthesia had a lower VAS score during dental procedures than intraligamentary anesthesia. Conclusions Intraligamentary anesthesia and other infiltration anesthesias have the same success rate and pain during dental procedures. However, the pain during injection of intraligamentary anesthesia is heavier than that of other infiltration anesthesia.
Pan et al. (2023) Comparison of dental anesthetic efficacy between the periodontal intraligamentary anesthesia and other infiltration anesthesia: a systematic review and meta-analysis. PeerJ 11:e15734 https://doi.org/10.7717/peerj.15734
Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata
Background Gastrodia elata is widely used in China as a valuable herbal medicine. Owing to its high medicinal and nutrient value, wild resources of G. elata have been overexploited and its native areas have been severely damaged. Understanding the impacts of climate change on the distribution of this endangered species is important for the conservation and sustainable use of G. elata. Methods We used the optimized maximum entropy model to simulate the potential distribution of G. elata under contemporary and future time periods (1970–2000, 2050s, 2070s, and 2090s) and different climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Under these conditions, we investigated the key environmental factors influencing the distribution of G. elata as well as the spatial and temporal characteristics of its niche dynamics. Results With high Maxent model accuracy (AUCmean = 0.947 ± 0.012, and the Kappa value is 0.817), our analysis revealed that annual precipitation, altitude, and mean temperature of driest quarter are the most important environmental factors influencing the distribution of G. elata. Under current bioclimatic conditions, the potentially suitable area for G. elata in China is 71.98 × 104 km2, while the highly suitable region for G. elata growth is 7.28 × 104 km2. Our models for three future periods under four climate change scenarios indicate that G. elata can maintain stable distributions in southern Shaanxi, southwestern Hubei, and around the Sichuan basin, as these areas are highly suitable for its growth. However, the center of the highly suitable areas of G. elata shift depending on different climatic scenarios. The values of niche overlap for G. elata show a decreasing trend over the forecasted periods, of which the niche overlap under the SSP3-7.0 scenario shows the greatest decrease. Discussions Under the condition of global climate change in the future, our study provides basic reference data for the conservation and sustainable utilization of the valuable and endangered medicinal plant G. elata. It is important to carefully choose the protection area of G. elata wild resources according the suitable area conditions modeled. Moreover, these findings will be valuable for providing insights into the breeding and artificial cultivation of this plant, including the selection of suitable areas for planting.
Hu et al. (2023) Impact of climate change on the geographical distribution and niche dynamics of Gastrodia elata. PeerJ 11:e15741 https://doi.org/10.7717/peerj.15741
Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source
Solid-phase denitrification shows promise for removing nitrate (NO3−-N) from water. Biological denitrification uses external carbon sources to remove nitrogen from wastewater, among which agriculture waste is considered the most promising source due to its economic and efficiency advantages. Hydraulic retention time (HRT) and influent nitrate concentration (INC) are the main factors influencing biological denitrification. This study explored the effects of HRT and INC on solid-phase denitrification using wheat husk (WH) as a carbon source. A solid-phase denitrification system with WH carbon source was constructed to explore denitrification performance with differing HRT and INC. The optimal HRT and INC of the wheat husk-denitrification reactor (WH-DR) were 32 h and 50 mg/L, respectively. Under these conditions, NO3−-N and total nitrogen removal rates were 97.37 ± 2.68% and 94.08 ± 4.01%, respectively. High-throughput sequencing revealed that the dominant phyla in the WH-DR operation were Proteobacteria, Bacteroidetes, and Campilobacterota. Among the dominant genera, Diaphorobacter (0.85%), Ideonella (0.38%), Thiobacillus (4.22%), and Sulfurifustis (0.60%) have denitrification functions; Spirochaeta (0.47%) is mainly involved in the degradation of WH; and Acidovorax (0.37%) and Azospira (0.86%) can both denitrify and degrade WH. This study determined the optimal HRT and INC for WH-DR and provides a reference for the development and application of WH as a novel, slow-release carbon source in treating aquaculture wastewater.
Environmental Contamination and Remediation
Niu et al. (2023) Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source. PeerJ 11:e15756 https://doi.org/10.7717/peerj.15756
Development of a video camera-type kayak motion capture system to measure water kayaking
Background In kayaking, trunk motion is one of the important factors that prevent injury and improve performance. Kinematic studies in kayaking have been reported in laboratory settings using paddling simulators and ergometers. However, such studies do not reflect kayaking on water, the actual competitive environment. Therefore, we developed a video camera-type kayak motion capture system (KMCS) wherein action cameras were fixed to a kayak to capture images of markers attached to an athlete’s body. This study aimed to compare the kinematic data between KMCS and an optical motion capture system (OMCS) in kayaking and to determine the accuracy of the KMCS analysis. Methods In a competition, five elite junior female kayak athletes performed kayak paddling under the unloaded condition using a kayak. The kayak was secured using a tri-folding bench and a towel, and twenty strokes were recorded during maximal paddling. One stroke was defined as the period from right catch to left catch, and the first six strokes were used to evaluate the accuracy. Trunk angles (tilting, turning, and rotation) were examined with the simultaneous use of KMCS and OMCS, and the differences between these systems were evaluated. To ensure reliability, intraclass correlation coefficient (ICC; a two-way mixed model for absolute agreement) was calculated for each angle. Furthermore, Bland–Altman analysis was performed to understand the agreement between the two systems. Results Root mean square errors (RMSEs) were 1.42° and 3.94° for turning and rotation, respectively, and mean absolute errors (MAEs) were 1.08° and 3.00° for turning and rotation, respectively. The RMSE and MAE for tilting were 2.43° and 1.76°, respectively, which indicated that the validity was comparable to that of other angles. However, the range of motion in tilting was lower than that in turning and rotation. Bland–Altman analysis showed good agreement in the total range of motion, with mean bias values of −0.84°, −0.07°, and −0.41° for tilting, turning, and rotation, respectively. The ICCs for tilting, turning, and rotation were 0.966, 0.985, and 0.973, respectively, and showed excellent reliability. Conclusions The newly developed KMCS effectively measured the trunk motion with good accuracy in kayaking. In future studies, we intend to use KMCS to measure kayaking on water and collect data for performance improvement and injury prevention.
Miyazaki et al. (2023) Development of a video camera-type kayak motion capture system to measure water kayaking. PeerJ 11:e15227 https://doi.org/10.7717/peerj.15227
Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation
Background YouTube plays an influential role in disseminating health-related information in the digital age. This study aimed to evaluate YouTube videos on transcutaneous electrical nerve stimulation (TENS) in terms of their information value and quality. Methods In this descriptive study, we ranked the first 100 videos that met the inclusion criteria using the search term “transcutaneous electrical nerve stimulation” on October 30, 2022. These videos were classified according to the number of views, likes, dislikes, comments, duration, popularity and content categories. Reliability, quality, and accuracy of the videos were assessed using the Journal of American Medical Association (JAMA) Benchmark Criteria and Modified DISCERN Questionnaire and Global Quality Score (GQS). Video popularity were calculated by the Video Power Index (VPI). Results Based on the GQS results, we found that 59, 27, and 14 videos had low, intermediate, and high quality, respectively. In addition, based on the JAMA results, 79 and 21 videos had poor and high reliability, respectively. No statistically significant difference was found between the JAMA, modified DISCERN and GQS scores in terms of the sources of videos (p = 0.226, p = 0.115, p = 0.812). Notably, there was a weak positive correlation between the JAMA scores and the number of views (r = 0.204, p = 0.041). Conclusion According to our study results, most YouTube videos on TENS were of low quality and reliability. Additionally, most videos were uploaded from sources created by doctors; the most frequently found content was about the TENS procedure, and content on complications of the procedure became less frequent as the videos became more recent. In particular, it was found that videos uploaded by academics have longer duration. It has been found that reliable videos with high JAMA scores also have high number of views. Accordingly, it can be concluded that videos with higher quality and more reliability that are created by healthcare providers will be more useful for patients seeking information about TENS.
Erkin et al. (2023) Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation. PeerJ 11:e15412 https://doi.org/10.7717/peerj.15412
Protein family neighborhood analyzer—ProFaNA
Background Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
Baranowski et al. (2023) Protein family neighborhood analyzer—ProFaNA. PeerJ 11:e15715 https://doi.org/10.7717/peerj.15715
Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers
Background Previous studies suggest coexistence between sympatric neotropical (Lontra longicaudis) and giant otters (Pteronura brasiliensis) maybe facilitated by temporal and spatial differences in activity. Yet, to date there has been no systematic evaluation of activity of these species in sympatry. Here we use extensive multi-year field data to compare temporal and spatial patterns in the diurnal activity of sympatric giant and neotropical otters to answer three questions: Do temporal patterns in daytime river use change in relation to seasonal river levels (low, rising, high and declining river levels), do they change due to human disturbances (boats and fishing nets) and do patterns in neotropical otter activity change due to the presence of the larger sized giant otter? Methods Direct observations of both species were recorded using standardized boat surveys along 218 km of rivers over 53 months during nine years (2011–2013 and 2015–2020). Complementary techniques (Generalized Additive Models, Kernel density estimates and non-parametric tests,) were used to compare diurnal activity patterns along rivers subdivided into 41 river reaches. Results The presence of giant otters decreased threefold from 67% of the least disturbed reaches (few boats no fishing nets) to 18% of the most disturbed reaches with many boats and fishing nets. In contrast neotropical otter presence nearly doubled from 44% of the least disturbed to 73% of the most disturbed reaches with fewest giant otter detections. Both species were observed across all daytime hours but were observed rarely on the same day. There was no evidence to suggest simultaneous use of the same reach. When species were detected on the same day, they were separated spatially (median distance between species 12.5 km) and temporally (median time difference 3.0 hours). There was little change in activity of either species among seasons. Giant otters were less active in river reaches with fishing nets and boat use, whereas neotropical otter activity did not appear to be strongly affected by these activities. Conclusions Our findings support evidence that diurnal activity in both otter species is flexible, with daytime activity changing due to human disturbances in the case of giant otters.
Norris et al. (2023) Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers. PeerJ 11:e15742 https://doi.org/10.7717/peerj.15742
Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants
Background Demand for organs exceeds the number of transplants available, underscoring the need to optimize organ donation procedures. However, protocols for determining brain death (BD)/death by neurological criteria (DNC) vary considerably worldwide. In Denmark, digital subtraction angiography (DSA) is the only legally approved confirmatory test for diagnosing BD/DNC. We investigated the effect of the time delay caused by (repeat) confirmatory DSA on the number of organs donated by patients meeting clinical criteria for BD/DNC. We hypothesized that, first, patients investigated with ≥2 DSAs donate fewer organs than those investigated with a single DSA; second, radiological interpretation of DSA is subject to interrater variability; and third, residual intracranial circulation is inversely correlated with inotropic blood pressure support. Methods All DSAs performed over a 7-year period as part of BD/DNC protocols at Rigshospitalet, Copenhagen University Hospital, Denmark, were included. Clinical data were extracted from electronic health records. DSAs were reinterpreted by an independent neurinterventionist blinded to the original radiological reports. Results We identified 130 DSAs in 100 eligible patients. Patients with ≥2 DSAs (n = 20) donated fewer organs (1.7 +/− 1.6 SD) than patients undergoing a single DSA (n = 80, 2.6 +/− 1.7 organs, p = 0.03), and they became less often donors (n = 12, 60%) than patients with just 1 DSA (n = 65, 81.3%; p = 0.04). Interrater agreement of radiological DSA interpretation was 88.5% (Cohen’s kappa = 0.76). Patients with self-maintained blood pressure had more often residual intracranial circulation (n = 13/26, 50%) than patients requiring inotropic support (n = 14/74, 18.9%; OR = 0.23, 95% CI [0.09–0.61]; p = 0.002). Discussion In potential donors who fulfill clinical BD/DNC criteria, delays caused by repetition of confirmatory DSA result in lost donors and organ transplants. Self-maintained blood pressure at the time of clinical BD/DNC increases the odds for residual intracranial circulation, creating diagnostic uncertainty because radiological DSA interpretation is not uniform. We suggest that avoiding unnecessary repetition of confirmatory investigations like DSA may result in more organs donated.
Hansen et al. (2023) Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants. PeerJ 11:e15759 https://doi.org/10.7717/peerj.15759