title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=408
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Inter-rater and test-retest reliabilities of lumbar stiffness measurement in the postero-anterior direction using a portable algometer and the Kinovea program
link: https://peerj.com/articles/16148
last-modified: 2023-10-02
description: BackgroundBack pain negatively impacts a person’s quality of life and can cause major disability or even death. The measurement of spinal stiffness can be utilized as a promising tool to guide therapeutic decisions regarding physical therapy that result in effective back pain management. This study aimed to determine the reliability of instrumented postero-anterior (PA) stiffness assessment of the lumbar spine in asymptomatic participants by novice assessors using a portable algometer and the Kinovea program.MethodsThirty asymptomatic participants aged 18–25 years were enrolled in this study. Two novice assessors examined the participants for lumbar spinal stiffness at L1–L5 for two consecutive days. The algometer was applied to measure the PA force that applied to each lumbar. The stiffness assessment of each lumbar region was recorded as a video. The 600 data sets of assessment videos were imported into the Kinovea program to perform displacement measurements of each lumbar level. Spinal displacement values at 15 N were defined by graph plotting between force and displacement. The spinal stiffness values were defined by slope calculation. Both variables were analyzed for inter-rater and test-retest reliabilities using intra-class correlation coefficients (ICCs) and standard error of measurement (SEM). Bland-Altman analysis was applied to assess the inter-rater and test-retest systematical bias and limits of agreement of measuring displacement and stiffness.ResultsThe inter-rater reliability of measuring the displacement and the stiffness of L1–L5 was moderate to good (displacement ICCs: 0.67–0.83, stiffness ICCs: 0.60–0.83). The test-retest reliability of measuring the displacement and stiffness of L1–L5 were moderate to good, ICCs: 0.57–0.86 and ICCs: 0.51–0.88, respectively. The inter-rater analysis’s Bland-Altman plot showed that the systematic bias was 0.83 when measuring displacement and 0.20 when measuring stiffness and the bias of both parameters were in both directions. While the test-retest systematically biased measurements of displacement and stiffness were −0.26 mm and 0.22 N/mm, respectively, and the bias of both parameters were in both directions.ConclusionsThe moderate-to-good inter-rater and test-retest reliabilities of the portable instrumented spinal stiffness assessment using a digital algometer and the Kinovea program by novice assessors were demonstrated in this study. Bland-Altman analysis showed that measuring stiffness was more stable and had less systematic bias than measuring displacement. To figure out how reliable the device is in general, more comprehensive studies should be comparatively conducted in the future on subgroups of patients with normal vertebra, hypomobile or hypermobile conditions.
creator: Wantanee Yodchaisarn
creator: Sunthorn Rungruangbaiyok
creator: Maria de Lourdes Pereira
creator: Chadapa Rungruangbaiyok
uri: https://doi.org/10.7717/peerj.16148
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Yodchaisarn et al.

title: Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat
link: https://peerj.com/articles/16181
last-modified: 2023-10-02
description: Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in “Avena sativa, a genus Avena in the grass family Poaceae,” have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function.
creator: Wenbo Mi
creator: Kaiqiang Liu
creator: Guoling Liang
creator: Zhifeng Jia
creator: Xiang Ma
creator: Zeliang Ju
creator: Wenhui Liu
uri: https://doi.org/10.7717/peerj.16181
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Mi et al.

title: Serotypes, virulence factors and multilocus sequence typing of Glaesserella parasuis from diseased pigs in Taiwan
link: https://peerj.com/articles/15823
last-modified: 2023-09-29
description: BackgroundGlaesserella parasuis (G. parasuis) belongs to the normal microbiota of the upper respiratory tract in the swine, but virulent strains can cause systemic infections commonly known as Glässer’s disease that leads to significant economic loss in the swine industry. Fifteen serotypes of G. parasuis have been classified by gel immunodiffusion test while the molecular serotyping based on variation within the capsule loci have further improved the serotype determination of unidentified field strains. Serovar has been commonly used as an indicator of virulence; however, virulence can be significantly differ in the field isolates with the same serotype. To date, investigations of G. parasuis isolated in Taiwan regarding antimicrobial resistance, serotypes, genotypes and virulence factors remain unclear.MethodsA total of 276 G.parasuis field isolates were collected from 263 diseased pigs at the Animal Disease Diagnostic Center of National Chiayi University in Taiwan from January 2013 to July 2021. Putative virulence factors and serotypes of the isolates were identified by polymerase chain reaction (PCR) and antimicrobial susceptibility testing was performed by microbroth dilution assay. Additionally, the epidemiology of G. parasuis was characterized by multilocus sequence typing (MLST).ResultsSerotype 4 (33.3%) and 5 (21.4%) were the most prevalent, followed by nontypable isolates (15.9%), serotype 13 (9.4%), 12 (6.5%), 14 (6.2%), 7 (3.3%), 1 (1.8%), 9 (1.1%), 11 (0.7%) and 6 (0.4%). Nine out of 10 putative virulence factors showed high positive rates, including group 1 vtaA (100%), fhuA (80.4%), hhdA (98.6%), hhdB (96.0%), sclB7 (99.6%), sclB11 (94.9%), nhaC (98.2%), HAPS_0254 (85.9%), and cirA (99.3%). According to the results of antimicrobial susceptibility testing, ceftiofur and florfenicol were highly susceptible (>90%). Notably, 68.8% isolates showed multidrug resistance. MLST revealed 16 new alleles and 67 new sequence types (STs). STs of these isolated G. parasuis strains were classified into three clonal complexes and 45 singletons by Based Upon Related Sequence Types (BURST) analysis. All the G. parasuis strains in PubMLST database, including strains from the diseased pigs in the study, were defined into two main clusters by Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Most isolates in this study and virulent isolates from the database were mainly located in cluster 2, while cluster 1 included a high percentage of nasal isolates from asymptomatic carriers. In conclusion, this study provides current prevalence and antimicrobial susceptibility of G. parasuis in Taiwan, which can be used in clinical diagnosis and treatment of Glässer’s disease.
creator: Ching-Fen Wu
creator: Chia-Yu Hsu
creator: Chi-Chung Chou
creator: Chao-Min Wang
creator: Szu-Wei Huang
creator: Hung-Chih Kuo
uri: https://doi.org/10.7717/peerj.15823
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Wu et al.

title: Genome-wide identification and analysis of Lateral Organ Boundaries Domain (LBD) transcription factor gene family in melon (Cucumis melo L.)
link: https://peerj.com/articles/16020
last-modified: 2023-09-29
description: BackgroundLateral Organ Boundaries Domain (LBD) transcription factor (TF) gene family members play very critical roles in several biological processes like plant-spesific development and growth process, tissue regeneration, different biotic and abiotic stress responses in plant tissues and organs. The LBD genes have been analyzed in various species. Melon (Cucumis melo L.), a member of the Cucurbitaceae family, is economically important and contains important molecules for nutrition and human health such as vitamins A and C, β-carotenes, phenolic acids, phenolic acids, minerals and folic acid. However, no studies have been reported so far about LBD genes in melon hence this is the first study for LBD genes in this plant.ResultsIn this study, 40 melon CmLBD TF genes were identified, which were separated into seven groups through phylogenetic analysis. Cis-acting elements showed that these genes were associated with plant growth and development, phytohormone and abiotic stress responses. Gene Ontology (GO) analysis revealed that of CmLBD genes especially function in regulation and developmental processes. The in silico and qRT-PCR expression patterns demonstrated that CmLBD01 and CmLBD18 are highly expressed in root and leaf tissues, CmLBD03 and CmLBD14 displayed a high expression in male-female flower and ovary tissues.ConclusionsThese results may provide important contributions for future research on the functional characterization of the melon LBD gene family and the outputs of this study can provide information about the evolution and characteristics of melon LBD gene family for next studies.
creator: Ebru Derelli Tufekci
uri: https://doi.org/10.7717/peerj.16020
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Derelli Tufekci

title: Poor sleep quality and suicidal ideation among pregnant women during COVID-19 in Ethiopia: systematic review and meta-analysis
link: https://peerj.com/articles/16038
last-modified: 2023-09-29
description: IntroductionCOVID-19 has profoundly impacted the mental health and well-being of pregnant women worldwide. In Ethiopia, the poor sleep quality and suicidal ideation among pregnant women has increased due to the COVID-19 pandemic. This study aimed to provide comprehensive evidence on the prevalence and associated factors of poor sleep quality and suicidal ideation among pregnant women during COVID-19 in Ethiopia.Materials and MethodsThis study is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendation. Data were searched from PubMed, Google Scholar, and African Journals Online from the occurrence of the COVID-19 pandemic to February 2023. Two researchers extracted the data and performed the methodological quality assessment independently. Random-effect model was used to estimate the pooled effect size and I2was used to check heterogeneity. Stata 14.0 (StataCorp, Collage Station, Texas, USA) was used for statistical analysis.ResultsFrom six studies the pooled prevalence of poor sleep quality was 55% (95% CI [0.42–0.69], I2 = 98.1%, p < 0.001). Age ≥ 30 years pooled AOR = 1.95, 95% CI (0.85, 3.06), 3rd trimester pooled AOR = 3.20, 95% CI (1.82, 4.58), substance use pooled AOR = 2.51, 95% CI (0.99, 4.04), depression pooled AOR = 2.97, 95% CI (0.92, 5.02) and stress pooled AOR 2.14, 95% CI (0.24, 4.03) were associated factors of poor sleep quality. Three studies reported about suicidal ideation and pooled prevalence was 11% (95% CI: 0.09, 0.13, I2 = 48.2%, p = 0.145). Depression pooled AOR = 3.19, 95% CI (1.68, 4.71) was the only associated factor of suicidal ideation.ConclusionDue to COVID-19 pregnant women in Ethiopia were affected by poor sleep quality and suicidal ideation. Thus, suitable and well designed programs proposing awareness of COVID-19, mental health counseling and involvement should be designed to improve the general mental health of pregnant women.Trial registrationPROSPERO registration number CRD42023389896.
creator: Aragaw Asfaw Hasen
creator: Abubeker Alebachew Seid
creator: Ahmed Adem Mohammed
uri: https://doi.org/10.7717/peerj.16038
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Hasen et al.

title: Analysis of cerebral Interleukin-6 and tumor necrosis factor alpha patterns following different ventilation strategies during cardiac arrest in pigs
link: https://peerj.com/articles/16062
last-modified: 2023-09-29
description: Hypoxia-induced neuroinflammation after cardiac arrest has been shown to be mitigated by different ventilation methods. In this prospective randomized animal trial, 35 landrace pigs were randomly divided into four groups: intermittent positive pressure ventilation (IPPV), synchronized ventilation 20 mbar (SV 20 mbar), chest compression synchronized ventilation 40 mbar (CCSV 40 mbar) and a control group (Sham). After inducing ventricular fibrillation, basic life support (BLS) and advanced life support (ALS) were performed, followed by post-resuscitation monitoring. After 6 hours, the animals were euthanized, and direct postmortem brain tissue samples were taken from the hippocampus (HC) and cortex (Cor) for molecular biological investigation of cytokine mRNA levels of Interleukin-6 (IL-6) and tumor necrosis factor alpha (TNFα). The data analysis showed that CCSV 40 mbar displayed low TNFα mRNA-levels, especially in the HC, while the highest TNFα mRNA-levels were detected in SV 20 mbar. The results indicate that chest compression synchronized ventilation may have a potential positive impact on the cytokine expression levels post-resuscitation. Further studies are needed to derive potential therapeutic algorithms from these findings.
creator: Miriam Renz
creator: Lea Müller
creator: Manuel Herbst
creator: Julian Riedel
creator: Katja Mohnke
creator: Alexander Ziebart
creator: Robert Ruemmler
uri: https://doi.org/10.7717/peerj.16062
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Renz et al.

title: Reproductive characteristics and gametogenic cycle of the scleractinian coral Dendrophyllia ramea
link: https://peerj.com/articles/16079
last-modified: 2023-09-29
description: The present study marks a pioneering investigation into the reproductive cycle of the scleractinian coral Dendrophyllia ramea. This is one of the first reproduction studies conducted in the Mediterranean Sea for a colonial azooxanthellate coral. Coral samples were collected in 2017 (May and October) and 2018 (February and July) in the Alborán Sea (SW Mediterranean). This location was selected due to its rarity as one of the few sites where this species thrives at depths shallower than 40 m. These samples were used to study the sexual patterns, fertilization mechanisms and gametogenic cycles by means of histological techniques. To broaden the scope, Sea Surface Temperature (SST) and Chlorophyll-a (Chl-a) data from open access databases have been considered to explore the potential influence of these environmental factors as triggers for gamete development and spawning time. The findings cast D. ramea as a gonochoric species, since no hermaphroditic specimens were observed among the analysed samples. Additionally, the lack of larvae and embryos in any of the analysed polyps, suggest that this species is fertilised externally. Two oocyte cohorts have been detected simultaneously, hinting at a yearly reproductive cycle, characterised by a prolonged oocyte maturation and seasonal spawning period taking place between August and October. Nevertheless, D. ramea display a low fecundity compared to other scleractinians inhabiting deep waters. Lastly, the early stages of gametogenesis seem to be coupled with the highest Chl-a values (i.e., March and December), whereas spawning takes place throughout the warmest period of the year (August to October).
creator: Covadonga Orejas
creator: Silvia Antón-Sempere
creator: Alexis Terrón-Sigler
creator: Amalia Grau
uri: https://doi.org/10.7717/peerj.16079
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Orejas et al.

title: Pathway2Targets: an open-source pathway-based approach to repurpose therapeutic drugs and prioritize human targets
link: https://peerj.com/articles/16088
last-modified: 2023-09-29
description: BackgroundRecent efforts to repurpose existing drugs to different indications have been accompanied by a number of computational methods, which incorporate protein-protein interaction networks and signaling pathways, to aid with prioritizing existing targets and/or drugs. However, many of these existing methods are focused on integrating additional data that are only available for a small subset of diseases or conditions.MethodsWe have designed and implemented a new R-based open-source target prioritization and repurposing method that integrates both canonical intracellular signaling information from five public pathway databases and target information from public sources including OpenTargets.org. The Pathway2Targets algorithm takes a list of significant pathways as input, then retrieves and integrates public data for all targets within those pathways for a given condition. It also incorporates a weighting scheme that is customizable by the user to support a variety of use cases including target prioritization, drug repurposing, and identifying novel targets that are biologically relevant for a different indication.ResultsAs a proof of concept, we applied this algorithm to a public colorectal cancer RNA-sequencing dataset with 144 case and control samples. Our analysis identified 430 targets and ~700 unique drugs based on differential gene expression and signaling pathway enrichment. We found that our highest-ranked predicted targets were significantly enriched in targets with FDA-approved therapeutics for colorectal cancer (p-value < 0.025) that included EGFR, VEGFA, and PTGS2. Interestingly, there was no statistically significant enrichment of targets for other cancers in this same list suggesting high specificity of the results. We also adjusted the weighting scheme to prioritize more novel targets for CRC. This second analysis revealed epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase (PI3K), and two mitogen-activated protein kinases (MAPK14 and MAPK3). These observations suggest that our open-source method with a customizable weighting scheme can accurately prioritize targets that are specific and relevant to the disease or condition of interest, as well as targets that are at earlier stages of development. We anticipate that this method will complement other approaches to repurpose drugs for a variety of indications, which can contribute to the improvement of the quality of life and overall health of such patients.
creator: Mauri Dobbs Spendlove
creator: Trenton M. Gibson
creator: Shaney McCain
creator: Benjamin C. Stone
creator: Tristan Gill
creator: Brett E. Pickett
uri: https://doi.org/10.7717/peerj.16088
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Dobbs Spendlove et al.

title: Leaf morpho-physiological traits of Populus sibirica and Ulmus pumila in different irrigation regimes and fertilizer types
link: https://peerj.com/articles/16107
last-modified: 2023-09-29
description: BackgroundThe impacts of climate change, such as increased soil dryness and nutrient deficiency, highlight the need for environmentally sustainable restoration of forests and groundwater resources. However, it is important to consider that extensive afforestation efforts may lead to a depletion of groundwater supply due to higher evapotranspiration rates, exacerbating water scarcity issues. Consequently, we conducted a study to examine how the fast-growing tree species Populus sibirica (Horth ex Tausch) and Ulmus pumila (L.) respond morpho-physiologically to varying watering regimes and types of fertilizers, aiming to better understand their specific water and nutrient requirements.MethodsWe used two-year-old nursery-growth seedlings (N = 512) of P. sibirica and U. pumila with initial root collar diameter (RCD) and the height of 0.51 ± 0.02 mm and 68 ± 2.94 cm and 0.33 ± 0.01 mm and 51 ± 1.14 cm, respectively. The leaf area (LA), specific leaf area (SLA), chlorophyll concentration, stomatal conductance (gs), chlorophyll fluorescence, and predawn and midday leaf water potential were measured across treatments. Four different irrigation regimes and two different fertilizer types were applied: no irrigation (control, 0 L h−1), 2 L h−1 = 0.25 mm m−2, 4 L h−1 = 0.5 mm m−2, 8 L h−1 = 1.0 mm m−2 and 120 g and 500 g tree−1 of NPK and compost (COMP). Twelve plots (600 m2) were established in the study site for each species and treatments.ResultsDuring the first growing season (2021), the LA of P. sibirica was larger in the 4–8 L h−1 without fertilizer, but it was smaller in the 4 L h−1+ COMP during the second growing season (2022). The 2 L h−1 without fertilizer and 2 L h−1 + NPK had larger LA compared with the control (CONT) for the first and second growing seasons, respectively, for U. pumila. P. sibirica seedlings at 4 L h−1 without fertilizer had the highest SLA for 2021 and at 2 L h−1 + NPK for 2022, whereas CONT and 4 L h−1 had the highest SLA than the other treatments for 2021 and 2022 growing seasons, respectively, for U. pumila. The chlorophyll concentration of P. sibirica seedlings in the first year was generally higher in CONT, while the 2 L h−1 without any fertilizer yielded a significantly higher chlorophyll concentration of U. pumila. Chlorophyll fluorescence parameters (PIABS and Fm) were generally lower in CONT with/without NPK or COMP for both species. The CONT with NPK/COMP generally had a higher gs compared with the other treatments in both experimental periods for U. pumila, whereas CONT and 2 L h−1+ NPK-treated P. sibirica seedlings had a significantly greater gs during the first year and second year, respectively. The predawn and midday leaf water potentials of both species were generally the lowest in CONT, followed by 2 L h−1+ NPK/COMP during the first growing season, but a different pattern was observed during the second growing season. Overall, the morpho-physiological traits of the two species were affected by watering and fertilizer treatments, and the magnitude of the effects varied depending on growing season, amount of irrigation, and fertilizer type, and their interactions.
creator: Ser-Oddamba Byambadorj
creator: Jonathan Ogayon Hernandez
creator: Sarangua Lkhagvasuren
creator: Ge Erma
creator: Khulan Sharavdorj
creator: Byung Bae Park
creator: Batkhuu Nyam-Osor
uri: https://doi.org/10.7717/peerj.16107
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Byambadorj et al.

title: clrDV: a differential variability test for RNA-Seq data based on the skew-normal distribution
link: https://peerj.com/articles/16126
last-modified: 2023-09-29
description: BackgroundPathological conditions may result in certain genes having expression variance that differs markedly from that of the control. Finding such genes from gene expression data can provide invaluable candidates for therapeutic intervention. Under the dominant paradigm for modeling RNA-Seq gene counts using the negative binomial model, tests of differential variability are challenging to develop, owing to dependence of the variance on the mean.MethodsHere, we describe clrDV, a statistical method for detecting genes that show differential variability between two populations. We present the skew-normal distribution for modeling gene-wise null distribution of centered log-ratio transformation of compositional RNA-seq data.ResultsSimulation results show that clrDV has false discovery rate and probability of Type II error that are on par with or superior to existing methodologies. In addition, its run time is faster than its closest competitors, and remains relatively constant for increasing sample size per group. Analysis of a large neurodegenerative disease RNA-Seq dataset using clrDV successfully recovers multiple gene candidates that have been reported to be associated with Alzheimer’s disease.
creator: Hongxiang Li
creator: Tsung Fei Khang
uri: https://doi.org/10.7717/peerj.16126
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Li and Khang