title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=467 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of potential functional peptides involved in demyelinating injury in the central nervous system link: https://peerj.com/articles/15846 last-modified: 2023-08-21 description: Multiple sclerosis (MS) is a chronic inflammatory neurologic disease characterized by the demyelinating injury of the central nervous system (CNS). It was reported that the mutant peptide came from myelin proteolipid protein (PLP) and myelin basic protein (MBP) might play a critical role in immunotherapy function of MS. However, endogenous peptides in demyelinating brain tissue of MS and their role in the pathologic process of MS have not been revealed. Here, we performed peptidomic analysis of freshly isolated corpus callosum (CC) from the brains of CPZ-treated mice and normal diet controls of male C57BL/6 mice by LC-MS/MS. Identified a total of 217 peptides were expressed at different levels in MS mice model compared with controls. By performed GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, we found that the precursor protein of these differently expressed peptides (DEPs) were associated with myelin sheath and oxidative phosphorylation. Our study is the first brain peptidomic of MS mice model, revealing the distinct features of DEPs in demyelination brain tissue. These DPEs may provide further insight into the pathogenesis and complexity of MS, which would facilitate the discovery of the potential novel and effective strategy for the treatment of MS. creator: Xiaohua Dong creator: Shuchen Sun creator: Jie Li creator: Sen Shen creator: Wanting Chen creator: Tongqi Li creator: Xinyuan Li uri: https://doi.org/10.7717/peerj.15846 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dong et al. title: Feeding ecology and reproductive biology of small coastal sharks in Malaysian waters link: https://peerj.com/articles/15849 last-modified: 2023-08-21 description: Small coastal demersal sharks form a major proportion of the sharks landed in Malaysia. However, little is known about their feeding ecology and reproduction. This study sought to elucidate the dietary patterns, role of ontogeny in prey consumption, and reproductive biology of four dominant small demersal shark species in Malaysian waters: the Hasselt’s bamboo shark, Chiloscyllium hasseltii; brownbanded bamboo shark, C. punctatum; spadenose shark, Scoliodon laticaudus; and Pacific spadenose shark, S. macrorhynchos. Dietary analyses revealed a high overlap in prey taxa consumed; clear resource partitioning among co-occurring species based on the percentage Prey-specific Index of Relative Importance (%PSIRI), with higher fish %PSIRI for Chiloscyllium hasseltii, higher cephalopod %PSIRI for C. punctatum, and higher crustacean %PSIRI for both Scoliodon species; and an ontogenetic diet shift, seen through changes in prey size. Based on the examination of reproductive organs, the results showed larger sizes at maturity for males compared to females for all four species; no obvious reproductive cycles, based on hepatosomatic and gonadosomatic indices for all species; female bias in the sex ratio of the embryos of Scoliodon species; and increased reproductive output (number of eggs or embryos and size of eggs) with larger female size for C. hasseltii and Scoliodon species. The partitioning of food resources minimizes direct competition for food and supports coexistence within shared coastal habitats. The reproductive strategies of these small coastal sharks appear to be favorable for supporting short-term population productivity; although a reduction in fishing pressure, especially from bottom trawlers, is essential for the long-term sustainable use of these sharks. creator: Kean Chong Lim creator: Amy Yee-Hui Then creator: Kar-Hoe Loh uri: https://doi.org/10.7717/peerj.15849 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lim et al. title: Prediction of soil moisture using BiGRU-LSTM model with STL decomposition in Qinghai–Tibet Plateau link: https://peerj.com/articles/15851 last-modified: 2023-08-21 description: Ali Network data based on the Qinghai-Tibetan Plateau (QTP) can provide representative coverage of the climate and surface hydrometeorological conditions in the cold and arid region of the QTP. Among them, the plateau soil moisture can effectively quantify the uncertainty of coarse resolution satellite and soil moisture models. With the objective of constructing an “end-to-end” soil moisture prediction model for the Tibetan Plateau, a combined prediction model based on time series decomposition and a deep neural network is proposed in this article. The model first performs data preprocessing and seasonal-trend decomposition using loess (STL) to obtain the trend component, seasonal component and random residual component of the original time series in an additive way. Subsequently, the bidirectional gated recurrent unit (BiGRU) is used for the trend component, and the long short-term memory (LSTM) is used for the seasonal and residual components to extract the time series information. The experiments based on the measured data demonstrate that the use of STL decomposition and the combination model can effectively extract the information in soil moisture series using its concise and clear structure. The proposed model in this article has a stable performance improvement of 5–30% over a single model and existing prediction models in different prediction time domains. In long-range prediction, the proposed model also achieves the best accuracy in the shape and temporal domains described by using dynamic time warping (DTW) index and temporal distortion index (TDI). In addition, the generalization performance experiments show that the combined method proposed in this article has strong reference value for time series prediction of natural complex systems. creator: Lufei Zhao creator: Tonglin Luo creator: Xuchu Jiang creator: Biao Zhang uri: https://doi.org/10.7717/peerj.15851 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhao et al. title: Early haemodynamic predictors of poor functional outcomes in patients with acute ischaemic stroke receiving endovascular therapy: a single-centre retrospective study in China link: https://peerj.com/articles/15872 last-modified: 2023-08-21 description: BackgroundChanges in cerebral haemodynamics following endovascular therapy (EVT) for large-vessel occlusion stroke may affect the outcomes of patients with acute ischaemic stroke (AIS); however, evidence supporting this belief is limited. This study aims to identify the early haemodynamic predictors of poor outcomes in patients with AIS caused by anterior circulation large-artery occlusion after undergoing EVT and to evaluate the usefulness of these indicators in predicting functional outcomes at 90 days.MethodsThis retrospective study was conducted at a single academic hospital, using prospectively collected data. We enrolled adult patients with acute anterior circulation stroke who underwent EVT. Transcranial colour-coded sonography (TCCS) examinations of the recanalised and contralateral middle cerebral artery (MCA) were performed within 12 h after undergoing EVT. Haemodynamic indicators were analysed to determine their association with poor functional outcomes (modified Rankin Scale: 3–6) 90 days after stroke. Receiver operating characteristic (ROC) curves were used to evaluate the usefulness of haemodynamic indicators in predicting functional outcomes.ResultsIn total, 108 patients (median age: 66 years; 69.4% males) were enrolled in this study. Complete recanalization was achieved in 93 patients (86.1%); however, 60 patients (55.6%) had a poor 90-day outcome. The peak systolic velocity (PSV) ratio, adjusted PSV ratio, mean flow velocity (MFV) ratio, and adjusted MFV ratio of the MCA were significantly higher in patients with poor prognosis than in patients with good prognosis (p < 0.02). A multivariate logistic regression analysis showed that higher PSV ratio, adjusted PSV ratio, MFV ratio, and adjusted MFV ratio were independently associated with a poor 90-day outcomes (adjusted odds ratio: 1.11–1.48 for every 0.1 increase; p < 0.03). Furthermore, adding the adjusted MFV ratio significantly improved the prediction ability of the basic model for the 90-day poor functional outcome using the ROC analysis, the areas under ROC curves increased from 0.75 to 0.85 (p = 0.013).ConclusionsEarly TCCS examination may help in predicting poor functional outcomes at 90 days in patients with AIS who underwent EVT. Moreover, combining novel TCCS indicators (adjusted MFV ratio) with conventional parameters improved the prediction ability of the base model. creator: Yanyan Hu creator: Shizhong Zhang creator: Jiajun Zhang creator: Xin Wang creator: Feng Zhang creator: Hong Cui creator: Hui Yuan creator: Wei Zheng uri: https://doi.org/10.7717/peerj.15872 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: Clinical dosage of lidocaine does not impact the biomedical outcome of sepsis-induced acute respiratory distress syndrome in a porcine model link: https://peerj.com/articles/15875 last-modified: 2023-08-21 description: BackgroundSepsis is a common disease in intensive care units worldwide, which is associated with high morbidity and mortality. This process is often associated with multiple organ failure including acute lung injury. Although massive research efforts have been made for decades, there is no specific therapy for sepsis to date. Early and best treatment is crucial. Lidocaine is a common local anesthetic and used worldwide. It blocks the fast voltage-gated sodium (Na+) channels in the neuronal cell membrane responsible for signal propagation. Recent studies show that lidocaine administered intravenously improves pulmonary function and protects pulmonary tissue in pigs under hemorrhagic shock, sepsis and under pulmonary surgery. The aim of this study is to show that lidocaine inhalative induces equivalent effects as lidocaine intravenously in pigs in a lipopolysaccharide (LPS)-induced sepsis with acute lung injury.MethodsAfter approval of the local State and Institutional Animal Care Committee, to induce the septic inflammatory response a continuous infusion of lipopolysaccharide (LPS) was administered to the pigs in deep anesthesia. Following induction and stabilisation of sepsis, the study medication was randomly assigned to one of three groups: (1) lidocaine intravenously, (2) lidocaine per inhalation and (3) sham group. All animals were monitored for 8 h using advanced and extended cardiorespiratory monitoring. Postmortem assessment included pulmonary mRNA expression of mediators of early inflammatory response (IL-6 & TNF-alpha), wet-to-dry ratio and lung histology.ResultsAcute respiratory distress syndrome (ARDS) was successfully induced after sepsis-induction with LPS in all three groups measured by a significant decrease in the PaO2/FiO2 ratio. Further, septic hemodynamic alterations were seen in all three groups. Leucocytes and platelets dropped statistically over time due to septic alterations in all groups. The wet-to-dry ratio and the lung histology showed no differences between the groups. Additionally, the pulmonary mRNA expression of the inflammatory mediators IL-6 and TNF-alpha showed no significant changes between the groups. The proposed anti-inflammatory and lung protective effects of lidocaine in sepsis-induced acute lung injury could not be proven in this study. creator: René Rissel creator: Christian Moellmann creator: Victoria Albertsmeier creator: Miriam Renz creator: Robert Ruemmler creator: Jens Kamuf creator: Erik K. Hartmann creator: Alexander Ziebart uri: https://doi.org/10.7717/peerj.15875 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rissel et al. title: Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China link: https://peerj.com/articles/15909 last-modified: 2023-08-21 description: Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos’ desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = −0.924, p < 0.01; r = −0.800, p < 0.01; r = −0.933, p < 0.01) and salinity (r = −0.615, p < 0.05; r = −0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau. creator: Jumei Liu creator: Jingli Yu creator: Wantong Si creator: Ge Ding creator: Shaohua Zhang creator: Donghui Gong creator: Jie Bi uri: https://doi.org/10.7717/peerj.15909 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Development and validation of web-based dynamic nomograms predictive of disease-free and overall survival in patients who underwent pneumonectomy for primary lung cancer link: https://peerj.com/articles/15938 last-modified: 2023-08-21 description: BackgroundThe tumour-node-metastasis (TNM) staging system is insufficient to precisely distinguish the long-term survival of patients who underwent pneumonectomy for primary lung cancer. Therefore, this study sought to identify determinants of disease-free (DFS) and overall survival (OS) for incorporation into web-based dynamic nomograms.MethodsThe clinicopathological variables, surgical methods and follow-up information of 1,261 consecutive patients who underwent pneumonectomy for primary lung cancer between January 2008 and December 2018 at Sun Yat-sen University Cancer Center were collected. Nomograms for predicting DFS and OS were built based on the significantly independent predictors identified in the training cohort (n = 1,009) and then were tested on the validation cohort (n = 252). The concordance index (C-index) and time-independent area under the receiver-operator characteristic curve (AUC) assessed the nomogram’s discrimination accuracy. Decision curve analysis (DCA) was applied to evaluate the clinical utility.ResultsDuring a median follow-up time of 40.5 months, disease recurrence and death were observed in 446 (35.4%) and 665 (52.7%) patients in the whole cohort, respectively. In the training cohort, a higher C-reactive protein to albumin ratio, intrapericardial pulmonary artery ligation, lymph node metastasis, and adjuvant therapy were significantly correlated with a higher risk for disease recurrence; similarly, the independent predictors for worse OS were intrapericardial pulmonary artery and vein ligation, higher T stage, lymph node metastasis, and no adjuvant therapy. In the validation cohort, the integrated DFS and OS nomograms showed well-fitted calibration curves and yielded good discrimination powers with C-index of 0.667 (95% confidence intervals CIs [0.610–0.724]) and 0.697 (95% CIs [0.649–0.745]), respectively. Moreover, the AUCs for 1-year, 3-year, and 5-year DFS were 0.655, 0.726, and 0.735, respectively, and those for 3-year, 5-year, and 10-year OS were 0.741, 0.765, and 0.709, respectively. DCA demonstrated that our nomograms could bring more net benefit than the TNM staging system.ConclusionsAlthough pneumonectomy for primary lung cancer has brought encouraging long-term outcomes, the constructed prediction models could assist in precisely identifying patients at high risk and developing personalized treatment strategies to further improve survival. creator: Xiangyang Yu creator: Feng Wang creator: Longjun Yang creator: Kai Ma creator: Xiaotong Guo creator: Lixu Wang creator: Longde Du creator: Xin Yu creator: Shengcheng Lin creator: Hua Xiao creator: Zhilin Sui creator: Lanjun Zhang creator: Zhentao Yu uri: https://doi.org/10.7717/peerj.15938 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yu et al. title: The fraternal birth-order effect as a statistical artefact: convergent evidence from probability calculus, simulated data, and multiverse meta-analysis link: https://peerj.com/articles/15623 last-modified: 2023-08-18 description: The fraternal-birth order effect (FBOE) is a research claim which states that each older brother increases the odds of homosexual orientation in men via an immunoreactivity process known as the maternal immune hypothesis. Importantly, older sisters supposedly either do not affect these odds, or affect them to a lesser extent. Consequently, the fraternal birth-order effect predicts that the association between the number of older brothers and homosexual orientation in men is greater in magnitude than any association between the number of older sisters and homosexual orientation. This difference in magnitude represents the main theoretical estimand of the FBOE. In addition, no comparable effects should be observable among homosexual vs heterosexual women. Here, we triangulate the empirical foundations of the FBOE from three distinct, informative perspectives, complementing each other: first, drawing on basic probability calculus, we deduce mathematically that the body of statistical evidence used to make inferences about the main theoretical estimand of the FBOE rests on incorrect statistical reasoning. In particular, we show that throughout the literature researchers ascribe to the false assumptions that effects of family size should be adjusted for and that this could be achieved through the use of ratio variables. Second, using a data-simulation approach, we demonstrate that by using currently recommended statistical practices, researchers are bound to frequently draw incorrect conclusions. And third, we re-examine the empirical evidence of the fraternal birth-order effect in men and women by using a novel specification-curve and multiverse approach to meta-analysis (64 male and 17 female samples, N = 2,778,998). When analyzed correctly, the specific association between the number of older brothers and homosexual orientation is small, heterogenous in magnitude, and apparently not specific to men. In addition, existing research evidence seems to be exaggerated by small-study effects. creator: Johannes K. Vilsmeier creator: Michael Kossmeier creator: Martin Voracek creator: Ulrich S. Tran uri: https://doi.org/10.7717/peerj.15623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Vilsmeier et al. title: THAPBI PICT—a fast, cautious, and accurate metabarcoding analysis pipeline link: https://peerj.com/articles/15648 last-modified: 2023-08-18 description: THAPBI PICT is an open source software pipeline for metabarcoding analysis of Illumina paired-end reads, including cases of multiplexing where more than one amplicon is amplified per DNA sample. Initially a Phytophthora ITS1 Classification Tool (PICT), we demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, it can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by non-specialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/ with documentation including installation instructions. creator: Peter J. A. Cock creator: David E. L. Cooke creator: Peter Thorpe creator: Leighton Pritchard uri: https://doi.org/10.7717/peerj.15648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cock et al. title: Process optimization, antioxidant, antibacterial, and drug adjuvant properties of bioactive keratin microparticles derived from porcupine (Hystrix indica) quills link: https://peerj.com/articles/15653 last-modified: 2023-08-18 description: A structural protein called keratin is often employed in the medical industry to create medication carriers. Process improvement, antioxidant, antibacterial, and adjuvant drug studies of synthetic bioactive keratin microparticles made from lipids and keratin derived from porcupine (Hystrix indica) quills are the main objectives of this study. After coating the keratin microparticles with lipids which were obtained from the same porcupine quills, the bioactive keratin microparticles were produced. The response surface technique was applied to optimize the conditions for extraction of the keratin protein and sizing of the keratin microparticles. An infrared spectroscopy was used to analyze the chemical shifts in compositions of keratin microparticles while the optical microscopy was used to measure the size of the keratin microparticles. The results of this work revealed that a yield 27.36 to 42.25% of the keratin protein could be obtained from porcupine quills. The keratin microparticles were sized between 60.65 and 118.87 µm. Through response surface optimization, mercaptoethanol and urea were shown to be the main variables which positively affected the yield and the size of the keratin protein. The lipid stacking on the keratin microparticles’ surface was confirmed by infrared spectroscopy. The 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulphonate) assay confirmed the keratin microparticle’s antioxidant activity of 29.83%. Compared to lipid alone, the antibacterial properties of the keratin microparticles against Escherichia coli—a gram-negative—and Staphylococcus aureus—a gram-positive—bacteria enhanced by up to 55% following the coating of the microparticles with the lipids. The pharmacological action against these bacterial species was further improved by the lipid-loaded erythromycin that was carried on the surface of keratin microparticles. This work has demonstrated the design and uses of the keratin microparticles obtained from porcupine quills for clinical applications. creator: Zahid Majeed creator: Hoorulain Farhat creator: Basharat Ahmad creator: Atia Iqbal creator: Abu ul Hassan Faiz creator: Mater H. Mahnashi creator: Ali O. Alqarni creator: Omaish Alqahtani creator: Amer Al Ali creator: Aiman M. Momenah uri: https://doi.org/10.7717/peerj.15653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Majeed et al.