title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=470 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Biochar improves the growth and physiological traits of alfalfa, amaranth and maize grown under salt stress link: https://peerj.com/articles/15684 last-modified: 2023-08-18 description: PurposeSalinity is a main factor in decreasing seed germination, plant growth and yield. Salinity stress is a major problem for economic crops, as it can reduce crop yields and quality. Salinity stress occurs when the soil or water in which a crop is grown has a high salt content. Biochar improve plant growth and physiological traits under salt stress. The aim of the present study, the impact of biochar on growth, root morphological traits and physiological properties of alfalfa, amaranth and maize and soil enzyme activities under saline sands.MethodsWe studied the impact of biochar on plant growth and the physiological properties of alfalfa, amaranth and maize under salt stress conditions. After 40 days, plant growth parameters (plant height, shoot and root fresh weights), root morphological traits and physiological properties were measured. Soil nutrients such as the P, K and total N contents in soil and soil enzyme activities were analyzed.ResultsThe results showed that the maize, alfalfa, and amaranth under biochar treatments significantly enhanced the plant height and root morphological traits over the control. The biochar on significantly increased the total root length, root diameter, and root volume. Compared to the control, the biochar significantly increased the chlorophyll a and b content, total chlorophyll and carotenoid content under salt stress. Furthermore, the biochar significantly increased enzyme activities of soil under salt stress in the three crops.ConclusionsBiochar treatments promote plant growth and physiological traits of alfalfa, amaranth, and maize under the salt stress condition. Overall, biochar is an effective way to mitigate salinity stress in crops. It can help to reduce the amount of salt in the soil, improve the soil structure, and increase the availability of essential nutrients, which can all help to improve crop yields. creator: Dilfuza Jabborova creator: Tokhtasin Abdrakhmanov creator: Zafarjon Jabbarov creator: Shokhrukh Abdullaev creator: Abdulahat Azimov creator: Ibrahim Mohamed creator: Maha AlHarbi creator: Abdelghafar Abu-Elsaoud creator: Amr Elkelish uri: https://doi.org/10.7717/peerj.15684 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jabborova et al. title: A novel immune-related prognostic signature based on Chemoradiotherapy sensitivity predicts long-term survival in patients with esophageal squamous cell carcinoma link: https://peerj.com/articles/15839 last-modified: 2023-08-18 description: BackgroundThere is a heterogenous clinical response following chemoradiotherapy (CRT) in esophageal squamous cell carcinoma (ESCC). Therefore, we aimed to study signaling pathway genes that affect CRT sensitivity and prognosis.MethodsGene expression analyses were performed in the GEO and TCGA datasets. A immunohistochemistry (IHC) analysis was performed in pretreatment biopsies.ResultsMMP13 was found to be highly expressed in the “Pathologic Complete Response (pCR)” and “Complete Remission (CR)” and “Alive” groups. Th17 cells and MMP9/13 showed a negative correlation in immune infiltration analysis. In GSEA analysis, IL-4 and IL-13 signaling pathways were highly enriched in patients exhibiting high MMP expression in pCR and CR groups. IHC results suggested higher MMP13 & IL-4 and lower IL-17A & RORC expression in the CR group compared to the 0.70, and the model could well distinguish high-risk and low-risk subgroups.ConclusionThe above results may provide guidance for developing novel treatment and prognostic strategies in ESCC patients. creator: Zewei Zhang creator: Shiliang Liu creator: Tiantian Gao creator: Yuxian Yang creator: Quanfu Li creator: Lei Zhao uri: https://doi.org/10.7717/peerj.15839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Transcription factor EB (TFEB) improves ventricular remodeling after myocardial infarction by inhibiting Wnt/β-catenin signaling pathway link: https://peerj.com/articles/15841 last-modified: 2023-08-18 description: BackgroundAdverse left ventricular remodeling after myocardial infarction (MI) compromises cardiac function and increases heart failure risk. Until now, comprehension of the role transcription factor EB (TFEB) plays after MI is limited.ObjectivesThe purpose of this study was to describe the effects of TFEB on fibroblasts differentiation and extracellular matrix expression after MI.MethodsAAV9 (adeno-associated virus) mediated up- and down-regulated TFEB expressions were generated in C57BL/6 mice two weeks before the MI modeling. Echocardiography, Masson, Sirius red staining immunofluorescence, and wheat germ agglutinin staining were performed at 3 days, and 1, 2, and 4 weeks after MI modeling. Fibroblasts collected from SD neonatal rats were transfected by adenovirus and siRNA, and cell counting kit-8 (CCK8), immunofluorescence, wound healing and Transwell assay were conducted. Myocardial fibrosis-related proteins were identified by Western blot. PNU-74654 (100 ng/mL) was used for 12 hours to inhibit β-catenin-TCF/LEF1 complex.ResultsThe up-regulation of TFEB resulted in reduced fibroblasts proliferation and its differentiation into myofibroblasts in vitro studies. A significant up-regulation of EF and down-regulation of myocyte area was shown in the AAV9-TFEB group. Meanwhile, decreased protein level of α-SMA and collagen I were observed in vitro study. TFEB didn’t affect the concentration of β-catenin. Inhibition of TFEB, which promoted cell migration, proliferation and collagen I expression, was counteracted by PNU-74654.ConclusionsTFEB demonstrated potential in restraining fibrosis after MI by inhibiting the Wnt/β-catenin signaling pathway. creator: Cong Liu creator: Dawang Zhou creator: Qiang Zhang creator: Hongyan Wei creator: Yuanzheng Lu creator: Bo Li creator: Haohong Zhan creator: Jingge Cheng creator: Chuyue Wang creator: Yilin Yang creator: Shuhao Li creator: Chunlin Hu creator: Xiaoxing Liao uri: https://doi.org/10.7717/peerj.15841 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Do feeding responses of a non-native bivalve outperform the native one in a coastal lagoon? A possible explanation for the invasion success of the dark false mussel Mytilopsis leucophaeata link: https://peerj.com/articles/15848 last-modified: 2023-08-18 description: The present study aimed to evaluate and compare feeding responses of the non-native and native bivalves, the dark false mussel Mytilopsis leucophaeata and the scorched mussel Brachidontes darwinianus, respectively, by offering different concentrations of seston from the coastal lagoon where these species coexist after dark false mussel introduction (Rodrigo de Freitas Lagoon, Rio de Janeiro-Brazil). For this purpose, independent laboratory experiments were carried out under five concentrations of seston to test the differences in clearance and ingestion rates of bivalves as a function of increasing concentrations of suspended particulate matter (SPM) on seston. In addition, from the integrated analysis of data obtained in experiments, it can be inferred about the efficiency levels of these species to remove SPM from seston and their effects on water turbidity and nutrient concentrations (total carbon, nitrogen, and phosphorus). Our hypothesis was that the non-native bivalve is more efficient to clear and ingest SPM from seston compared to the native one, which may lead to competitive advantages to the successful invasion of M. leucophaeata in coastal lagoons. Native species did not show a significant difference in clearance and ingestion rates with increasing concentrations of seston. Whereas the non-native bivalve showed a slight tendency to increase its clearance and ingestion rates with the increase in seston concentrations, evidencing its plasticity to adjust its feeding responses. The native bivalve was significantly more efficient to clear and ingest SPM at the lower seston concentration (i.e., close to natural concentrations found in the lagoon) compared to the non-native bivalve, which, on the other hand, showed a significant increase in its ingestion rates at the higher concentration tested (140 mg SPM L−1). Thus, the present results did not suggest food competition between the non-native M. leucophaeata and the native B. darwinianus in the introduced system. However, M. leucophaeata increased its feeding response with experimental increment in seston concentration, which suggests species ability to benefit from conditions of increased inputs of organic matter and higher primary production that could mediate its establishment in introduced systems. creator: Nathalia Rodrigues creator: Danielle Ribeiro creator: Igor C. Miyahira creator: Samira G. M. Portugal creator: Luciano N. Santos creator: Raquel A. F. Neves uri: https://doi.org/10.7717/peerj.15848 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodrigues et al.