title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=486
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Effects of hydraulic retention time and influent nitrate concentration on solid-phase denitrification system using wheat husk as carbon source
link: https://peerj.com/articles/15756
last-modified: 2023-07-24
description: 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.
creator: Shuhui Niu
creator: Shuwei Gao
creator: Kai Zhang
creator: Zhifei Li
creator: Guangjun Wang
creator: Hongyan Li
creator: Yun Xia
creator: Jingjing Tian
creator: Ermeng Yu
creator: Jun Xie
creator: Minting Zhang
creator: Wangbao Gong
uri: https://doi.org/10.7717/peerj.15756
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Niu et al.

title: Development of a video camera-type kayak motion capture system to measure water kayaking
link: https://peerj.com/articles/15227
last-modified: 2023-07-21
description: BackgroundIn 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.MethodsIn 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.ResultsRoot 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.ConclusionsThe 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.
creator: Shigeaki Miyazaki
creator: Go Yamako
creator: Ryo Kimura
creator: Niroshan G. Punchihewa
creator: Tsubasa Kawaguchi
creator: Hideki Arakawa
creator: Etsuo Chosa
uri: https://doi.org/10.7717/peerj.15227
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Miyazaki et al.

title: Evaluation of the reliability and quality of YouTube videos as a source of information for transcutaneous electrical nerve stimulation
link: https://peerj.com/articles/15412
last-modified: 2023-07-21
description: BackgroundYouTube 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.MethodsIn 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).ResultsBased 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).ConclusionAccording 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.
creator: Yüksel Erkin
creator: Volkan Hanci
creator: Erkan Ozduran
uri: https://doi.org/10.7717/peerj.15412
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Erkin et al.

title: Protein family neighborhood analyzer—ProFaNA
link: https://peerj.com/articles/15715
last-modified: 2023-07-21
description: BackgroundFunctionally 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.MethodsHere, 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.ResultsSeveral 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.
creator: Bartosz Baranowski
creator: Krzysztof Pawłowski
uri: https://doi.org/10.7717/peerj.15715
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Baranowski and Pawłowski

title: Human disturbances and the daytime activity of sympatric otters along equatorial Amazonian rivers
link: https://peerj.com/articles/15742
last-modified: 2023-07-21
description: BackgroundPrevious 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?MethodsDirect 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.ResultsThe 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.ConclusionsOur 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.
creator: Darren Norris
creator: Fernanda Michalski
uri: https://doi.org/10.7717/peerj.15742
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Norris and Michalski

title: Confirmatory digital subtraction angiography after clinical brain death/death by neurological criteria: impact on number of donors and organ transplants
link: https://peerj.com/articles/15759
last-modified: 2023-07-21
description: BackgroundDemand 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.MethodsAll 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.ResultsWe 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).DiscussionIn 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.
creator: Karen Irgens Tanderup Hansen
creator: Jesper Kelsen
creator: Marwan H. Othman
creator: Trine Stavngaard
creator: Daniel Kondziella
uri: https://doi.org/10.7717/peerj.15759
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Hansen et al.

title: Where are the Penaeids crustins?
link: https://peerj.com/articles/15596
last-modified: 2023-07-20
description: Crustins are antimicrobial peptides and members of the four-disulfide core (4-DSC) domain-containing proteins superfamily. To date, crustins have only been reported in crustaceans and possess a structural signature characterized by a single 4-DSC domain and one cysteine-rich region. The high-throughput sequencing technologies have produced vastly valuable genomic information that sometimes dilutes information about previously sequenced molecules. This study aimed (1) to corroborate the loss of valuable descriptive information regarding crustin identification when high throughput sequencing carries out automatic annotation processes and (2) to detect possible crustin sequences reported in Penaeids to attempt a list considering structural similarities, which allows the establishment of phylogenetic relationships based on molecular characteristics. All crustins sequences reported in Penaeids and registered in the databases were obtained. The first list was made with the proteins reported as crustin or carcinin, excluding those that did not meet the structural characteristics. Subsequently, using local alignments, sequences were sought with high similarity even if they had been reported with a different name of crustin but with a probability of being crustin. This broader list, including proteins with high structural similarity, can help establish phylogenetic relationships of shrimp genes and the evolutionary trajectory of this antimicrobial distributed exclusively among crustaceans. Results revealed that in most sequences obtained by Sanger or transcriptomics, which met the structural criteria, the identification was correctly established as crustin. Contrarily, the sequences corresponding to crustins obtained by whole genome sequencing projects were incorrectly classified or not characterized, being momentarily “buried” in the information generated. In addition, the sequences that complied with the criteria of crustin tended to be grouped into species separated by geographical regions; for example, the crustins of the inhabitant shrimp of the American coasts differ from those corresponding to the natives of the Asian coasts. Finally, the results suggest the convenience of annotations considering the previous but correct information, even if such information was generated with previous technologies.
creator: Marcel Martinez-Porchas
creator: Jorge Hernández-López
creator: Francisco Vargas-Albores
uri: https://doi.org/10.7717/peerj.15596
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Martinez-Porchas et al.

title: A method of constructing a dynamic chart depth model for coastal areas
link: https://peerj.com/articles/15616
last-modified: 2023-07-20
description: The depth is important for vessel navigation at sea. Currently, most vessels use electronic navigation charts to navigate at sea. In coastal areas, especially close to shallow water areas, the dynamic change of the water level is very important to safe navigation. Ships calculate the change of water level by using up-to-date tide tables, to obtain the dynamic water depth in the channels. However, the depth caused by the tide and non-tidal components may reach several meters in some seas, causing the dynamic depth below the safety depth, which can easily lead to grounding of vessels stranding accidents. The channel is regularly dredged to achieve navigational depth. Without regular dredging, the offshore non-channel area becomes the common area of ship grounding. The dynamic chart depth model studied in this article can provide real-time depth, which serves the ships navigation in the non-channel. The model incorporates the chart depth and the dynamic water levels on the same reference datum. The chart depth is from the electronic navigational chart depth. The dynamic water levels are constructed by the simulated tidal levels and continuous series of nontidal residual. We then designed a deviation correction method to reduce the discrepancy of the simulated tidal level with the actual water level, including datum offset correction and residual water level correction. Finally, by merging the revised dynamic water levels with the electronic navigational chart depth, we obtained the dynamic chart depth model of the study region.
creator: Minglei Guan
creator: Chenyang Tian
creator: Bin Wang
creator: Fangzheng Ji
creator: Rui Sun
creator: Song Yu
creator: Chongping Wang
creator: Qi Wang
creator: Jingzhe Wang
creator: Wei Zhang
creator: Dejin Zhang
uri: https://doi.org/10.7717/peerj.15616
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Guan et al.

title: Home hazard modification programs for reducing falls in older adults: a systematic review and meta-analysis
link: https://peerj.com/articles/15699
last-modified: 2023-07-20
description: ObjectiveThis study aims to assess the effect of home modification in preventing falls in older adults.MethodsA systematic review and meta-analysis of randomized studies were performed. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was registered prospectively. Five electronic databases were systematically searched for related articles. The titles and abstracts of the articles found using the key search phrases—home modification and falling—were screened using inclusion and exclusion criteria. The Cochrane risk of bias tool was used to evaluate the studies’ methodology.ResultsA total of 12 trials were included. A meta-analysis was conducted using 10 studies with n = 1, 960 participants showing a clinically meaningful 7% reduction in falls (risk ratio = 0.93; 0.87–1).ConclusionsFalls can be significantly reduced with the use of home modification interventions that are thorough, well-focused, have an environmental-fit perspective, and have adequate follow-up.
creator: Charupa Lektip
creator: Sirawee Chaovalit
creator: Apichai Wattanapisit
creator: Sarawut Lapmanee
creator: Jiraphat Nawarat
creator: Weeranan Yaemrattanakul
uri: https://doi.org/10.7717/peerj.15699
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Lektip et al.

title: Topological data analysis for revealing dynamic brain reconfiguration in MEG data
link: https://peerj.com/articles/15721
last-modified: 2023-07-20
description: In recent years, the focus of the functional connectivity community has shifted from stationary approaches to the ones that include temporal dynamics. Especially, non-invasive electrophysiological data (magnetoencephalography/electroencephalography (MEG/EEG)) with high temporal resolution and good spatial coverage have made it possible to measure the fast alterations in the neural activity in the brain during ongoing cognition. In this article, we analyze dynamic brain reconfiguration using MEG images collected from subjects during the rest and the cognitive tasks. Our proposed topological data analysis method, called Mapper, produces biomarkers that differentiate cognitive tasks without prior spatial and temporal collapse of the data. The suggested method provides an interactive visualization of the rapid fluctuations in electrophysiological data during motor and cognitive tasks; hence, it has the potential to extract clinically relevant information at an individual level without temporal and spatial collapse.
creator: Ali Nabi Duman
creator: Ahmet E. Tatar
uri: https://doi.org/10.7717/peerj.15721
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Duman and Tatar