title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=653 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cancer, platelet distribution width, and total protein levels as predictors of rebleeding in upper gastrointestinal bleeding link: https://peerj.com/articles/14061 last-modified: 2022-09-15 description: BackgroundRebleeding is associated with poor outcomes in upper gastrointestinal bleeding (UGIB). Identifying predictors of rebleeding can assist in risk assessment. The aim of the study is to investigate the factors affecting rebleeding in patients with UGIB admitted to the emergency department.MethodsThis retrospective, observational, cross-sectional study was conducted on patients with UGIB presented to the emergency department. Patients who did not arrest in the first 24 h, who were not diagnosed with GI malignancy, and who were clinically diagnosed with UGIB were included in the study. Patient demographic characteristics, hemodynamic parameters, patient parameters, and bleeding that may affect rebleeding were evaluated. The primary endpoint was rebleeding within 7 days.ResultsThe study included 371 patients. A total of 55 patients (14.8%) had rebleeding within 7 days, and 62 patients (16.7%) presented without bleeding manifestations. Rebleeding rates were higher in those who presented with bloody or coffee-ground vomitus, had a diagnosis of cancer, had blood in their nasogastric tube, and had peptic ulcers due to endoscopy. Mean cell hemoglobin concentration, lymphocyte, albumin, and total protein values of patients with rebleeding were low; red blood cell distribution width, neutrophil count, platelet distribution width (PDW), and neutrophil lymphocyte ratio were high. In-hospital mortality and 30-day mortality values of patients with rebleeding were significantly increased. In the multivariate analysis, cancer, PDW, and total protein levels were statistically significant.ConclusionThe presence of cancer, low total protein level, and high PDW are effective parameters in predicting 7-day rebleeding in patients with UGIB admitted to the emergency department. creator: Ali Cankut Tatlıparmak creator: Özlem Dikme creator: Özgür Dikme creator: Hakan Topaçoğlu uri: https://doi.org/10.7717/peerj.14061 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tatlıparmak et al. title: miR-378 associated with proliferation, migration and apoptosis properties in A549 cells and targeted NPNT in COPD link: https://peerj.com/articles/14062 last-modified: 2022-09-15 description: BackgroundmicroRNAs contribute to the development and progression of chronic obstructive pulmonary disease (COPD). However, the underlying molecular mechanisms are largely unclear. The goal of this study was to investigate the roles of miR-378 in alveolar epithelial type II cells and identify molecular mechanisms which contribute to the pathogenesis of COPD.Materials and methodsHuman alveolar epithelial (A549) cells were cultured in Dulbecco’s Modified Eagle Medium. Cell proliferation was studied by using a cell counting kit-8 (CCK-8) and colony formation assays. Cell apoptosis and cell cycle were analyzed by flow cytometry and wound healing and Transwell were used to analyze the cell migration and. We performed bioinformatics analysis including target gene prediction, gene ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment and construction of protein-protein interaction (PPI) network. The expression of miR-378 and NPNT from publically available expression microarray of COPD lung tissues was analyzed.ResultsOverexpression of miR-378 significantly increases cell proliferation, migration, and suppress apoptosis. GO analysis demonstrated that the miR-378 involved in transcription, vascular endothelial growth factor receptor signaling pathway, phosphatidylinositol 3-kinase signaling, cell migration, blood coagulation, cell shape, protein stabilization and phosphorylation. Pathway enrichment showed that the 1,629 target genes of miR-378 were associated with mTOR, ErbB, TGF-β, MAPK, and FoxO signaling pathways. Notably, miR-378 directly targets Nephronectin in A549 cells, and miR-378 was upregulated while NPNT was downregulated in COPD lung tissue samples.ConclusionsThese findings suggest that miR-378 can regulate the proliferation, migration, and apoptosis of A549 cells and target NPNT. miR-378 increased in COPD lung tissues while NPNT decreased, and might prove a potential target for novel drug therapy. creator: Guoqing Qian creator: Qi Liao creator: Guoxiang Li creator: Fengying Yin uri: https://doi.org/10.7717/peerj.14062 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qian et al. title: Effects of CRISPR/Cas9-mediated stearoyl-Coenzyme A desaturase 1 knockout on mouse embryo development and lipid synthesis link: https://peerj.com/articles/13945 last-modified: 2022-09-14 description: BackgroundLipid synthesis is an indispensable process during embryo and growth development. Abnormal lipid synthesis metabolism can cause multiple metabolic diseases including obesity and hyperlipidemia. Stearoyl-Coenzyme A desaturase 1 (SCD1) is responsible for catalyzing the synthesis of monounsaturated fatty acids (MUFA) and plays an essential role in lipid metabolism. The aim of our study was to evaluate the effects of SCD1 on embryo development and lipid synthesis in a knockout mice model.MethodsWe used the CRISPR/Cas9 system together with microinjection for the knockout mouse model generation. Ten-week-old female C57BL/6 mice were used for zygote collection. RNase-free water was injected into mouse zygotes at different cell phases in order to select the optimal time for microinjection. Five sgRNAs were designed and in vitro transcription was performed to obtain sgRNAs and Cas9 mRNA. RNase-free water, NC sgRNA/Cas9 mRNA, and Scd1 sgRNA/Cas9 mRNA were injected into zygotes to observe the morula and blastocyst formation rates. Embryos that were injected with Scd1 sgRNA/Cas9 mRNA and developed to the two-cell stage were used for embryo transfer. Body weight, triacylglycerol (TAG), and cholesterol in Scd1 knockout mice serum were analyzed to determine the effects of SCD1 on lipid metabolism.ResultsMicroinjection performed during the S phase presented with the highest zygote survival rate (P < 0.05). Of the five sgRNAs targeted to Scd1, two sgRNAs with relatively higher gene editing efficiency were used for Scd1 knockout embryos and mice generation. Genome sequence modification was observed at Scd1 exons in embryos, and Scd1 knockout reduced blastocyst formation rates (P < 0.05). Three Scd1 monoallelic knockout mice were obtained. In mice, the protein level of SCD1 decreased (P < 0.05), and the body weight and serum TAG and cholesterol contents were all reduced (P < 0.01). creator: Huibin Tian creator: Huimin Niu creator: Jun Luo creator: Weiwei Yao creator: Wenchang Gao creator: Yang Wen creator: Min Cheng creator: Anmin Lei creator: Jinlian Hua uri: https://doi.org/10.7717/peerj.13945 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tian et al. title: Phenotypic spectrum of FGF10-related disorders: a systematic review link: https://peerj.com/articles/14003 last-modified: 2022-09-14 description: FGF10, as an FGFR2b-specific ligand, plays a crucial role during cell proliferation, multi-organ development, and tissue injury repair. The developmental importance of FGF10 has been emphasized by the identification of FGF10 abnormalities in human congenital disorders affecting different organs and systems. Single-nucleotide variants in FGF10 or FGF10-involving copy-number variant deletions have been reported in families with lacrimo-auriculo-dento-digital syndrome, aplasia of the lacrimal and salivary glands, or lethal lung developmental disorders. Abnormalities involving FGF10 have also been implicated in cleft lip and palate, myopia, or congenital heart disease. However, the exact developmental role of FGF10 and large phenotypic heterogeneity associated with FGF10 disruption remain incompletely understood. Here, we review human and animal studies and summarize the data on FGF10 mechanism of action, expression, multi-organ function, as well as its variants and their usefulness for clinicians and researchers. creator: Katarzyna Bzdega creator: Justyna A. Karolak uri: https://doi.org/10.7717/peerj.14003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bzdega and Karolak title: 5-Methylindole kills various bacterial pathogens and potentiates aminoglycoside against methicillin-resistant Staphylococcus aureus link: https://peerj.com/articles/14010 last-modified: 2022-09-14 description: Antibiotic resistance of bacterial pathogens has become a severe threat to human health. To counteract antibiotic resistance, it is of significance to discover new antibiotics and also improve the efficacy of existing antibiotics. Here we show that 5-methylindole, a derivative of the interspecies signaling molecule indole, is able to directly kill various Gram-positive pathogens (e.g., Staphylococcus aureus and Enterococcus faecalis) and also Gram-negative ones (e.g., Escherichia coli and Pseudomonas aeruginosa), with 2-methylindole being less potent. Particularly, 5-methylindole can kill methicillin-resistant S. aureus, multidrug-resistant Klebsiella pneumoniae, Mycobacterium tuberculosis, and antibiotic-tolerant S. aureus persisters. Furthermore, 5-methylindole significantly potentiates aminoglycoside antibiotics, but not fluoroquinolones, killing of S. aureus. In addition, 5-iodoindole also potentiates aminoglycosides. Our findings open a new avenue to develop indole derivatives like 5-methylindole as antibacterial agents or adjuvants of aminoglycoside. creator: Zhongyan Li creator: Fengqi Sun creator: Xinmiao Fu creator: Yajuan Chen uri: https://doi.org/10.7717/peerj.14010 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: The emergence of spiraling tracheary element bundles in incompatible grafts link: https://peerj.com/articles/14020 last-modified: 2022-09-14 description: In distantly-related plant grafting, incompatibility often occurs between scion and rootstock, resulting in growth stagnation, and eventually graft failure. In this study, we found that an emergent structure, or the spiraling tracheary element (TE) bundles consisting of TE masses occurring at the graft interface, was extensively present in the highly incompatible interfamilial graft of Brassica napus/Portulaca oleracea (Bn/Po) and Nicotiana benthamiana/Portulaca oleracea (Nb/Po). This special structure mostly appeared in the local area near the grafting union, and the frequency and quantity of the spiraling tracheary element bundles were much higher in the scion than in the rootstock. Nevertheless, only a small portion of Arabidopsis thaliana/Portulaca oleracea (At/Po) interfamilial grafts showed a less spiraled TEs at the grafting union (usually a circular TE), which is consistent with its growth performance. This study consolidated that spiraling TE bundles were an important indicator for graft incompatibility. The possible reason for the formation of spiraling TE bundles in interfamilial grafts was discussed. creator: Huiyan Wu creator: Zhuying Deng creator: Xue Wang creator: Dacheng Liang uri: https://doi.org/10.7717/peerj.14020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau link: https://peerj.com/articles/14028 last-modified: 2022-09-14 description: Mycorrhizal fungi can form symbiotic associations with tree species, which not only play an important role in plant survival and growth, but also in soil carbon (C) and nitrogen (N) cycling. However, the understanding of differences in soil C and N cycling patterns among forests with different mycorrhizal types is still incomplete. In order to determine the similarities and differences of soil C and N cycling patterns in different mycorrhizal forest types, three primary forests dominated by ectomycorrhizal (EcM), arbuscular mycorrhizal (AM) and ericoid mycorrhizal (ErM) trees respectively were studied on the eastern Qinghai-Tibetan Plateau. Indicators associated with soil C and N cycling, including leaf litter quality, soil C and N contents, soil C and N fluxes, and soil microbial biomass C and N contents were measured in each mycorrhizal type forest. The results showed that leaf litter quality was significantly lower with high C:N ratio and lignin: N ratio in ErM forest than that in AM and EcM forests. Soil CO2 flux (508.25 ± 65.51 mg m−2 h−1) in AM forest was significantly higher than that in EcM forest (387.18 ± 56.19 mg m−2 h−1) and ErM forest (177.87 ± 58.40 mg m−2 h−1). Furthermore, soil inorganic N content was higher in the AM forest than that in EcM and ErM forests. Soil net N mineralization rate (−0.02 ± 0.03 mg kg−1 d−1) was lower in ErM forest than that in EcM and AM forests. We speculated that AM and EcM forests were relatively characterized by rapid soil C cycling comparing to ErM forest. The soil N cycling in EcM and ErM forests were lower, implying they were ‘organic’ N nutrition patterns, and the pattern in ErM forest was more obvious. creator: Miaomiao Zhang creator: Shun Liu creator: Miao Chen creator: Jian Chen creator: Xiangwen Cao creator: Gexi Xu creator: Hongshuang Xing creator: Feifan Li creator: Zuomin Shi uri: https://doi.org/10.7717/peerj.14028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: A novel virtual reality application for autonomous assessment of cervical range of motion: development and reliability study link: https://peerj.com/articles/14031 last-modified: 2022-09-14 description: BackgroundNeck pain, one of the most common musculoskeletal diseases, affects 222 million people worldwide. The cervical range of motion (CROM) is a tool used to assess the neck’s state across three movement axes: flexo-extension, rotation, and lateral flexion. People with neck pain often have a reduced CROM, and they feel pain at the end-range and/or accompany neck movements with compensatory trunk movements. Virtual reality (VR) setups can track the movement of the head and other body parts in order to create the sensation of immersion in the virtual environment. Using this tracking position information, a CROM assessment can be performed using a VR setup that may be carried out autonomously from the user’s home. The objectives of this study were to develop a VR experience that could be used to perform a CROM assessment, and to evaluate the intra-rater and inter-rater reliability of the CROM measures guided by this VR experience. To the best of our knowledge, a study of this type has not been carried out before.Materials & MethodsA total of 30 asymptomatic adults were assessed using a VR device (HTC Vive Pro Eye™). Two raters provided support with the VR setup, and the participants were guided by the VR experience as they performed the movements. Each rater tested each subject twice, in random order. In addition to a head-mounted display (HMD), a tracker located on the subject’s back was used to measure trunk compensatory movements. The CROM was estimated using only the HMD position and this measurement was corrected using the tracker data. The mean and standard deviation were calculated to characterize the CROM. To evaluate the reliability, the interclass correlation coefficients (ICC) were calculated for intra-rater and inter-rater analysis. The standard error of measurement and minimum detectable change were also calculated. The usability of the VR system was measured using the Spanish version of the System Usability Scale.ResultsThe mean CROM values in each axis of movement were compatible with those described in the literature. ICC values ranged between 0.86 and 0.96 in the intra-rater analysis and between 0.83 and 0.97 in the inter-rater analysis; these values were between good and excellent. When applying the correction of the trunk movements, both the intra-rater and inter-rater ICC values slightly worsened except in the case of the lateral flexion movement, where they slightly improved. The usability score of the CROM assessment/VR system was 86 points, which is an excellent usability score.ConclusionThe reliability of the measurements and the usability of the system indicate that a VR setup can be used to assess CROM. The reliability of the VR setup can be affected by slippage of the HMD or tracker. Both slippage errors are additive, i.e., only when the sum of these two errors is less than the compensatory movement do the measurements improve when considering the tracker data. creator: Jose Angel Santos-Paz creator: Álvaro Sánchez-Picot creator: Ana Rojo creator: Aitor Martín-Pintado-Zugasti creator: Abraham Otero creator: Rodrigo Garcia-Carmona uri: https://doi.org/10.7717/peerj.14031 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Santos-Paz et al. title: The effects of rumen-protected tryptophan (RPT) on production performance and relevant hormones of dairy cows link: https://peerj.com/articles/13831 last-modified: 2022-09-13 description: Tryptophan is an essential amino acid that cannot be synthesized in mammals. Therefore, the dietary supply of tryptophan is critical for the health and production performance (e.g., milk) of mammals. In the present study, 36 lactating Holstein cows were used, of which 24 cows were in the rumen-protected tryptophan (RPT) feeding groups with different doses at 14 g/d and 28 g/d, respectively and 12 cows were in the control group. This approach could avoid dietary tryptophan being degraded by the rumen microorganisms and improve its bioavailability for cows. The results showed that RPT increased milk protein percentage, milk protein yield, milk solid non-fat (SNF), and milk yield. In response to RPT treatment, the levels of melatonin (MT), prolactin (PRL), and insulin-like growth factor-1 (IGF-1) were significantly increased in the serum of cows compared to the controls. RPT feeding improved nutrient utilization efficiency and lactation performance of dairy cows, which enhanced the quality of milk. creator: Hui Ma creator: Songyang Yao creator: Libing Bai creator: Sarvvl Bai creator: Guoshi Liu uri: https://doi.org/10.7717/peerj.13831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ma et al. title: High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae) link: https://peerj.com/articles/13912 last-modified: 2022-09-13 description: BackgroundWolbachia bacteria are estimated to occur in more than half of all insect species. In Hymenoptera, Wolbachia often manipulates its host’s reproduction to its own advantage. Wolbachia is likely the reason that males are rare in the uniparental Ooencyrtus mirus Triapitsyn & Power (Hymenoptera: Encyrtidae). The likelihood of producing male offspring can be increased by giving mothers a continuous supply of Bagrada hilaris (Burmeister) (Heteroptera: Pentatomidae) host eggs to parasitize for 2–3 weeks, by feeding the parents antibiotics, or by rearing parent wasps at high temperatures; all variables that have been shown to correlate with depleting Wolbachia titers in other organisms. The purpose of the current study was to determine whether thelytoky in O. mirus is due to Wolbachia, and if so, at what time in development the sex change occurs. We also wished to determine if Wolbachia removal results in the production of intersexes, as in some other hymenopterans. Finally, mating behavior was observed to see if and where it breaks down as a result of the species becoming thelytokous.MethodsFemales were collected from parental lines of O. mirus reared at 26, 30, 31, 32, 33, 34, and 36 °C. The offspring of these females were reared at 26 °C, and their sex-ratio was determined. In a subsequent experiment, the parental generation was switched between 26 °C and 36 °C during development to narrow down the critical period at which changes occurred that subsequently affected the sex-ratio of their offspring.ResultsThe sex ratio was male biased in the offspring of O. mirus parents reared at 34 °C and 36 °C (high temperatures), even if the offspring themselves were reared at 26 °C. The constant temperature at which the percentage of males started to increase after two generations was 31 °C (10% males), rising to 39% males at 33 °C, and 100% males at 34 °C and 36 °C. Lasting more than 2 days, the critical period for the change toward a male biased sex ratio was during the second half of the parent’s development. Molecular diagnostic assays confirmed that O. mirus females contain Wolbachia and males do not. Examination of preserved males and male-female pairs under a dissecting microscope showed no signs of intersex characters. Observation of the mating behavior of live O. mirus showed that males initiate courtship by drumming their antennae on a female’s antennae, but after a few seconds, the females typically turn and walk away. However, a few instances of possible copulation were noted.ConclusionsAs hypothesized, the results indicated that thelytoky in O. mirus is likely mediated by Wolbachia bacteria. To maximize the population growth rate without generating males, the best temperature for mass rearing this species is 30 °C. creator: Nancy R. Power creator: Paul F. Rugman-Jones creator: Richard Stouthamer creator: Fatemeh Ganjisaffar creator: Thomas M. Perring uri: https://doi.org/10.7717/peerj.13912 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Power et al.