title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=395 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Development and validity of the expectations of physiotherapists questionnaire on practice management software link: https://peerj.com/articles/16246 last-modified: 2023-10-17 description: BackgroundDespite the growing trend in the use of digital technologies in physiotherapy, the overall adoption of both, practice management software (PMS) and electronic health records in physiotherapy clinics has been low and slow over time. In order to learn what factors determine the adoption of these technologies by physiotherapists, there is a need to examine the expectations of physiotherapists (EPs) on specific software attributes. The main aims of this study were to develop a questionnaire to measure and describe the EPs towards PMS. The knowledge of these EPs will be useful to guide PMS design in order to improve physiotherapists‘ satisfaction.MethodsInstrument development study with validity and reliability testing. The development of this questionnaire was conducted in three phases: identification of attributes to be explored, development of the items, pilot study, and psychometric testing. The questionnaire was distributed to chartered physiotherapists. A total of 272 participants completed the questionnaire.ResultsA series of analysis were conducted to assess item reduction, factor structure of the questionnaire and metric properties of multi-item scales. From the initial 43 attributes, the final version of the questionnaire consisted of 26 items on EPs, grouped in nine scales and two areas (clinical care and administrative activities). As a result, all scores had strong item-scale correlations, excellent item scaling success, and good internal consistency (Cronbach alpha coefficients of >.7). Our study also showed that current EPs were high towards most of the items, only two scales concentrated most of the attributes with the least expectations (monitoring quality of care and digital health interventions). Our study included physiotherapists with and without experience with PMS, and it showed that both groups had a similar pattern of expectations. Our study provides a valuable questionnaire of EP on PMS attributes for clinical care and administrative activities and shows a detailed development process. creator: Eduardo Arza-Moncunill creator: Francesc Medina-Mirapeix creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.16246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Arza-Moncunill et al. title: A pilot study: effect of irisin on trabecular bone in a streptozotocin-induced animal model of type 1 diabetic osteopathy utilizing a micro-CT link: https://peerj.com/articles/16278 last-modified: 2023-10-17 description: BackgroundOsteoporosis is a significant co-morbidity of type 1 diabetes mellitus (DM1) leading to increased fracture risk. Exercise-induced hormone ‘irisin’ in low dosage has been shown to have a beneficial effect on bone metabolism by increasing osteoblast differentiation and reducing osteoclast maturation, and inhibiting apoptosis and inflammation. We investigated the role of irisin in treating diabetic osteopathy by observing its effect on trabecular bone.MethodsDM1 was induced by intraperitoneal injection of streptozotocin 60 mg/kg body weight. Irisin in low dosage (5 µg twice a week for 6 weeks I/P) was injected into half of the control and 4-week diabetic male Wistar rats. Animals were sacrificed six months after induction of diabetes. The trabecular bone in the femoral head and neck was analyzed using a micro-CT technique. Bone turnover markers were measured using ELISA, Western blot, and RT-PCR techniques.ResultsIt was found that DM1 deteriorates the trabecular bone microstructure by increasing trabecular separation (Tb-Sp) and decreasing trabecular thickness (Tb-Th), bone volume fraction (BV/TV), and bone mineral density (BMD). Irisin treatment positively affects bone quality by increasing trabecular number p < 0.05 and improves the BMD, Tb-Sp, and BV/TV by 21–28%. The deterioration in bone microarchitecture is mainly attributed to decreased bone formation observed as low osteocalcin and high sclerostin levels in diabetic bone samples p < 0.001. The irisin treatment significantly suppressed the serum and bone sclerostin levels p < 0.001, increased the serum CTX1 levels p < 0.05, and also showed non-significant improvement in osteocalcin levels.ConclusionsThis is the first pilot study to our knowledge that shows that a low dose of irisin marginally improves the trabecular bone in DM1 and is an effective peptide in reducing sclerostin levels. creator: Sahar Mohsin creator: Fiona Brock creator: Suneesh Kaimala creator: Charlene Greenwood creator: Mohsin Sulaiman creator: Keith Rogers creator: Ernest Adeghate uri: https://doi.org/10.7717/peerj.16278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mohsin et al. title: Effects of mental rotation on map representation in orienteers—behavioral and fNIRS evidence link: https://peerj.com/articles/16299 last-modified: 2023-10-17 description: ObjectiveTaking orienteering as an example, this study aimed to reveal the effects of mental rotation on orienteers’ map representation and their brain processing characteristics.MethodsFunctional near-infrared spectroscopic imaging (fNIRS) was used to explore the behavioral performance and cortical oxyhemoglobin concentration changes of map-represented cognitive processing in orienteering athletes under two task conditions: normal and rotational orientation.ResultsCompared to that in the normal orientation, athletes’ task performance in the rotated orientation condition was significantly decreased, as evidenced by a decrease in correct rate and an increase in reaction time; in the normal orientation condition, blood oxygen activation in the dorsolateral prefrontal lobe was significantly greater than that in the ventral prefrontal lobe, which was significantly correlated with the correct rate. With rotating orientation, the brain oxygen average of each region of interest was enhanced, and the brain region specifically processed was the ventral prefrontal lobe, specifically correlating with the correct rate.ConclusionsMental rotation constrains the map representation ability of athletes, and map representation in rotational orientation requires more functional brain activity for information processing. Ventral lateral prefrontal lobe activation plays an important role in the map representation task in rotational orientation. creator: Mingsheng Zhao creator: Jingru Liu creator: Yang Liu creator: Pengyang Kang uri: https://doi.org/10.7717/peerj.16299 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhao et al. title: Daidzein alleviates osteoporosis by promoting osteogenesis and angiogenesis coupling link: https://peerj.com/articles/16121 last-modified: 2023-10-16 description: BackgroundPostmenopausal osteoporosis and osteoporosis-related fractures are world-wide serious public health problem. Recent studies demonstrated that inhibiting caveolin-1 leads to osteoclastogenesis suppression and protection against OVX-induced osteoporosis. This study aimed to explore the mechanism of caveolin-1 mediating bone loss and the potential therapeutic target.MethodsThirty C57BL/6 female mice were allocated randomly into three groups: sham or bilateral ovariectomy (OVX) surgeries were performed for mice and subsequently daidzein or vehicle was administrated to animals (control, OVX + vehicle and OVX + daidzein). After 8-week administration, femurs were harvested for Micro-CT scan, histological staining including H&E, immunohistochemistry, immunofluorescence, TRAP. Bone marrow endothelial cells (BMECs) were cultured and treated with inhibitors of caveolin-1 (daidzein) or EGFR (erlotinib) and then scratch wound healing and ki67 assays were performed. In addition, cells were harvested for western blot and PCR analysis.ResultsMicro-CT showed inhibiting caveolin-1with daidzein alleviated OVX-induced osteoporosis and osteogenesis suppression. Further investigations revealed H-type vessels in cancellous bone were decreased in OVX-induced mice, which can be alleviated by daidzein. It was subsequently proved that daidzein improved migration and proliferation of BMECs hence improved H-type vessels formation through inhibiting caveolin-1, which suppressed EGFR/AKT/PI3K signaling in BMECs.ConclusionsThis study demonstrated that daidzein alleviates OVX-induced osteoporosis by promoting H-type vessels formation in cancellous bone, which then promotes bone formation. Activating EGFR/AKT/PI3K signaling could be the critical reason. creator: Junjie Jia creator: Ruiyi He creator: Zilong Yao creator: Jianwen Su creator: Songyun Deng creator: Kun Chen creator: Bin Yu uri: https://doi.org/10.7717/peerj.16121 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jia et al. title: Effects of 3021 meal replacement powder protect NAFLD via suppressing the ERS, oxidative stress and inflammatory responses link: https://peerj.com/articles/16154 last-modified: 2023-10-16 description: ObjectiveTo explore the specific protective mechanism of 3021 meal replacement powder (MRP) against non-alcoholic fatty liver disease (NAFLD).Materials and MethodsC57BL/6J male mice were divided into four groups: control group, 3021 MRP group, model group and test group. The lipid accumulation and endoplasmic reticulum stress (ERS)-related proteins in hepatocytes of mice were detected by hematoxylin-eosin (HE) staining, oil red O staining and Western blotting.ResultsThe expressions of GRP78, GRP94, p-PERK and p-IRE1α were significantly inhibited in test group compared with those in model group. The protein expressions of p-NF-κB, p-JNK, IL-1β, IL-18 and NOX4 in test group were also significantly lower than those in model group. In vivo and in vitro experiments revealed that the body weight and lipid droplet content, and the expressions of ERS-related proteins (including BIP and XBP-1) in liver tissues all significantly declined in model group compared with those in 3021 MRP group.ConclusionIn conclusion, 3021 MRP can greatly reduce lipid accumulation by inhibiting ERS, oxidative stress and inflammatory response in NAFLD. creator: Qi Xie creator: Shuqing Gao creator: Yuanjudi Li creator: Weifang Xi creator: Zhiyun Dong creator: Zengning Li creator: Min Lei uri: https://doi.org/10.7717/peerj.16154 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al. title: Long non‑coding RNA L13Rik promotes high glucose-induced mesangial cell hypertrophy and matrix protein expression by regulating miR-2861/CDKN1B axis link: https://peerj.com/articles/16170 last-modified: 2023-10-16 description: BackgroundDiabetic nephropathy (DN) is a frequent microvascular complication of diabetes. Glomerular mesangial cell (MC) hypertrophy occurs at the initial phase of DN and plays a critical role in the pathogenesis of DN. Given the role of long non coding RNA (lncRNA) in regulating MC hypertrophy and extracellular matrix (ECM) accumulation, our aim was to identify functional lncRNAs during MC hypertrophy.MethodsHere, an lncRNA, C920021L13Rik (L13Rik for short), was identified to be up-regulated in DN progression. The expression of L13Rik in DN patients and diabetic mice was assessed using quantitative real-time PCR (qRT-PCR), and the function of L13Rik in regulating HG-induced MC hypertrophy and ECM accumulation was assessed through flow cytometry and western blotting analysis.ResultsThe L13Rik levels were significantly increased while the miR-2861 levels were decreased in the peripheral blood of DN patients, the renal tissues of diabetic mice, and HG-treated MCs. Functionally, both L13Rik depletion and miR-2861 overexpression effectively reduced HG-induced cell hypertrophy and ECM accumulation. Mechanistically, L13Rik functioned as a competing endogenous RNA (ceRNA) to sponge miR-2861, resulting in the de-repression of cyclin-dependent kinase inhibitor 1B (CDKN1B), a gene known to regulate cell cycle and MC hypertrophy.ConclusionsCollectively, the current results demonstrate that up-regulated L13Rik is correlated with DN and may be a hopeful therapeutic target for DN. creator: Linlin Sun creator: Miao Ding creator: Fuhua Chen creator: Dingyu Zhu creator: Xinmiao Xie uri: https://doi.org/10.7717/peerj.16170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al. title: Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia) link: https://peerj.com/articles/16188 last-modified: 2023-10-16 description: Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the “C-value enigma”. The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson’s correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements’ amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology. creator: Chloé Julie Loïs Fourreau creator: Hiroki Kise creator: Mylena Daiana Santander creator: Stacy Pirro creator: Maximiliano M. Maronna creator: Angelo Poliseno creator: Maria E.A. Santos creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.16188 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fourreau et al. title: Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae) link: https://peerj.com/articles/16217 last-modified: 2023-10-16 description: BackgroundThoracotremata belong to the large group of “true” crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.MethodsHere we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).ResultsThe results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle. creator: Tao Xu creator: Henrique Bravo creator: Sancia E.T. van der Meij uri: https://doi.org/10.7717/peerj.16217 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Identification and validation of key genes associated with pathogenesis and prognosis of gastric cancer link: https://peerj.com/articles/16243 last-modified: 2023-10-16 description: BackgroundGastric cancer (GC) is the fourth leading cause of cancer-related death worldwide. However, the precise mechanisms and specific biomarkers of GC have not been fully elucidated. We therefore sought to identify and validate the genes associated with GC.MethodsRNA sequencing was performed on gastric tissue specimens from 10 cases each of non-atrophic gastritis (NAG), intestinal metaplasia (IM), and GC. Validation of gene expression was conducted through immunohistochemistry (IHC) staining. The Kaplan–Meier Plotter database was utilized to screen genes associated with prognosis, while protein–protein interaction analysis was conducted to identify hub genes.ResultsIn GC-IM, the differentially expressed genes (DEGs) were predominantly enriched in pathways related to ECM-receptor interaction, focal adhesion, PI3K-Akt pathway, and pathways in cancer. Conversely, in IM-NAG, the DEGs were primarily enriched in pathways associated with fat digestion and absorption, pancreatic secretion, and retinol metabolism. IHC staining revealed elevated expression levels of KLK7 and KLK10 in GC. Specifically, KLK7 expression was found to be correlated with differentiation (P = 0.025) and depth of invasion (P = 0.007) in GC, while both KLK7 and KLK10 were associated with the overall survival (P < 0.05). Furthermore, a total of ten hub genes from DEGs in GC-NAG (COL6A2, COL1A1, COL4A1, COL1A2, SPARC, COL4A2, FN1, PCOLCE, SERPINH1, LAMB1) and five hub genes in IM-NAG (SI, DPP4, CLCA1, MEP1A, OLFM4) were demonstrated to have a significant correlation with the prognosis of GC.ConclusionsThe present study successfully identified and validated crucial genes associated with GC, providing valuable insights into the underlying mechanisms of this disease. The findings of this study have the potential to inform clinical practice. creator: Ai Li creator: Yan Li creator: Yueyue Li creator: Mingming Zhang creator: Hong Zhang creator: Feixue Chen uri: https://doi.org/10.7717/peerj.16243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Developing a semi-pelagic trawl to capture redfish in the Gulf of St. Lawrence, Canada link: https://peerj.com/articles/16244 last-modified: 2023-10-16 description: In this study, we developed a semi-pelagic trawl to target redfish (Sebastes spp.) and potentially reduce the capture of bycatch species and seabed impacts in the Gulf of St. Lawrence, Canada. The new trawl used an innovative technique connecting the upper bridles of the trawl to the warps, anterior of the trawl doors, leading to the trawl system being fished off the seabed. Such a technique can be used to match the heights of redfish as they move above the seabed during their diurnal cycle while allowing bycatch species related to the seabed to escape under the trawl. A 1:10 scale model of the trawl was constructed and evaluated in a flume tank to optimize the rigging and then a full-scale trawl was constructed for sea trials. Two field experiments subsequently evaluated the trawl at sea. The first field experiment concentrated on the experimental trawl’s operation and video observations of redfish behaviour in the trawl mouth and its effect on trawl entry. The second field experiment concentrated on a small-scale preliminary test on the catch of redfish and bycatch species when the trawl was on or off the seabed. Capture results, though preliminary, indicate that redfish can be targeted commercially with a semi-pelagic trawl, though some redfish will escape under the trawl. Additionally, results suggest that the catches of bycatch species may be reduced. In conclusion, this study suggests that a semi-pelagic trawl could be considered an effective technique to harvest redfish sustainably. creator: Vang Y. Nguyen creator: Shannon M. Bayse creator: Paul D. Winger creator: Harold DeLouche creator: George Legge uri: https://doi.org/10.7717/peerj.16244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nguyen et al.