title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=748 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The evolution of reproductive strategies in turtles link: https://peerj.com/articles/13014 last-modified: 2022-03-11 description: Optimal egg size theory assumes that changes in the egg and clutch are driven by selection, resulting in adjustments for the largest possible production of offspring with the highest fitness. Evidence supports the idea that large-bodied turtles tend to produce larger clutches with small and round eggs, while smaller species produce small clutches with large and elongated eggs. Our goals were to investigate whether egg and clutch size follow the predictions of egg size theory, if there are convergent reproductive strategies, and identify ecological factors that influence clutch and egg traits across all clades of living turtles. Using phylogenetic methods, we tested the covariance among reproductive traits, if they are convergent among different turtle lineages, and which ecological factors influence these traits. We found that both egg shape and size inversely correlate with clutch size, although with different evolutionary rates, following the predictions of the egg size theory. We also present compelling evidence for convergence among different turtle clades, over at least two reproductive strategies. Furthermore, climatic zone is the only ecological predictor to influence both egg size and fecundity, while diet only influences egg size. We conclude that egg and clutch traits in Testudines evolved independently several times across non-directly related clades that converged to similar reproductive strategies. Egg and clutch characteristics follow the trade-offs predicted by egg size theory and are influenced by ecological factors. Climatic zone and diet play an important role in the distribution of reproductive characteristics among turtles. creator: Gabriel Jorgewich-Cohen creator: Rafael S. Henrique creator: Pedro Henrique Dias creator: Marcelo R. Sánchez-Villagra uri: https://doi.org/10.7717/peerj.13014 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jorgewich-Cohen et al. title: UAV spraying on citrus crop: impact of tank-mix adjuvant on the contact angle and droplet distribution link: https://peerj.com/articles/13064 last-modified: 2022-03-11 description: Adding tank-mix adjuvants into the spray mixture is a common practice to improve droplet distribution for field crops (e.g., rice, wheat, corn, etc.) when using Unmanned Aerial Vehicle (UAV) sprayers. However, the effectiveness of tank-mix adjuvant for UAV spraying in orchard crops is still an open problem, considering their special canopy structure and leaf features. This study aims to evaluate the effects of a typical tank-mix adjuvant concentrations (i.e., Nong Jian Fei (NJF)) on Contact Angle (CA) and droplet distribution in the citrus tree canopy. Three commonly used parameters, namely dynamic CA, droplet coverage, and Volume Median Diameter (VMD), are adopted for performance evaluation. The dynamic CAs on the adaxial surface of citrus leaves, for water-only and NJF-presence sprays, respectively, are measured with five concentration levels, where three replications are performed for each concentration. The sprays with 0.5‰ NJF are adopted in the field experiment for evaluating droplet distributions, where Water Sensitive Papers (WSPs) are used as collectors. Two multi-rotor UAVs (DJI T20 and T30) which consist of different sizes of pesticide tanks and rotor diameters are used as the spraying platforms. Both water-only and NJF-presence treatments are conducted for the two UAVs, respectively. The results of the CA experiment show that NJF addition can significantly reduce the CAs of the sprays. The sprays with 0.5‰ NJF obtain the lowest CA within the observing time, suggesting a better spread ability on solid surface (e.g., WSPs or/and leaves). With respect to the effects of NJF addition on individual UAVs, the field trial results indicate that NJF addition can remarkably increase both the droplet coverage and VMD at three canopy layers, except for T30 droplet coverage of the inside and bottom layers. Comparing the difference of droplet coverage between two UAVs, while significant difference is found in the same layer before NJF addition, there is no notable difference appearing in the outside and bottom layers after NJF addition. The difference of VMD in the same layer between two UAVs is not affected by NJF addition except for the bottom layer. These results imply that the differences of droplet coverage among different UAVs might be mitigated, thus the droplet distribution of some UAVs could be improved by adding a tank-mix adjuvant into the sprays. This hypothesis is verified by investigating the droplet penetration and the correlation coefficient (CC) of droplet coverage and VMD. After NJF addition, the total percentage of T20 droplet coverage in the bottom and inside layers is increased by 5%. For both UAVs, the CCs indicate that both droplet coverage and VMD increase at the same time in most cases after NJF addition. In conclusion, the addition of a tank-mix adjuvant with the ability to reduce CA of the sprays, can effectively improve droplet distribution using UAV spraying in the citrus canopy by increasing droplet coverage and VMD. creator: Yanhua Meng creator: Wanqiang Zhong creator: Cunjia Liu creator: Jinya Su creator: Jiyuan Su creator: Yubin Lan creator: Zhiguo Wang creator: Meimei Wang uri: https://doi.org/10.7717/peerj.13064 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Meng et al. title: The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study link: https://peerj.com/articles/13091 last-modified: 2022-03-11 description: BackgroundWe explored the relationship between the platelet-lymphocyte ratio (PLR), the prognostic nutritional index (PNI), the lactate dehydrogenase-albumin ratio (LDH/albumin ratio; LAR), the controlling nutritional status (CONUT) score, and the long-term survival of colon cancer patients.MethodsWe conducted a retrospective analysis of the clinical data and follow-up materials of 126 patients with colon cancer who underwent surgical treatment in the Department of Gastrointestinal Surgery of Jiangnan University Affiliated Hospital from June 2012 to December 2015. The receiver operating characteristic curve (ROC) was used to distinguish the high ratio group from the low ratio group. The Kaplan Meier method was used to draw the survival curve in our survival analysis. The log rank test was used for the univariate analysis and the Cox multivariate regression analysis was used to analyze the correlation between preoperative PLR, PNI, LAR, conut scores, and overall survival (OS) and progression free survival (PFS) of patients with colon cancer.ResultsThe median follow-up time was 72 months. The OS rates at 3 and 5 years were 83.3% and 78.5%, respectively. The PFS rates at 3 and 5 years were 79.3% and 77.6%, respectively. The 3-year and 5-year OS rates in the low LAR group (≤4.91) were 90.9% and 87.1%, respectively, and were 56.0% and 44.0% in the high LAR group (>4.91) respectively. Univariate and multivariate analyses showed that the LAR value was correlated with OS and PFS (P < 0.05).ConclusionA high preoperative LAR is an independent predictor of the prognosis of colon cancer patients. creator: Zhihui Xie creator: Hui Zhou creator: Lei Wang creator: Yibo Wu uri: https://doi.org/10.7717/peerj.13091 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xie et al. title: Comparison and correlation of cervical proprioception and muscle endurance in general joint hypermobility participants with and without non-specific neck pain—a cross-sectional study link: https://peerj.com/articles/13097 last-modified: 2022-03-11 description: BackgroundCervical proprioception and muscle endurance are essential for maintaining cervical functional joint stability. Proprioception and muscle endurance may be impaired in those with general joint hypermobility (GJH). Examining these aspects is crucial. This study’s aims are to (1) compare the cervical joint position error (JPE) and muscle endurance holding capacities in GJH individuals with and without non-specific neck pain (NSNP) (2) to assess the relationship between hypermobility Beighton scores, cervical JPE’s, and muscle endurance in GJH individuals with and without NSNP.MethodsIn this cross-sectional comparative study, 33 GJH participants with NSNP (mean age 21.7 ± 1.8 years) and 35 asymptomatic participants GJH (mean age 22.42 ± 1.7 years) participated. Beighton’s score of ≥4 of 9 tests was used as criteria to diagnose GJH. Cervical JPEs were estimated in degrees using a cervical range of motion device, and muscle endurance (flexor and extensor) were estimated in seconds using a stopwatch.ResultsGJH participants with NSNP showed significantly larger cervical JPEs (p < 0.001) and decreased muscle endurance holding times (p < 0.001) compared to asymptomatic participants. Beighton hypermobility scores showed a significant moderate positive correlation with cervical JPEs (flexion: r = 0.43, p = 0.013), left rotation: r = 0.47, p = 0.005, right rotation: r = 0.57, p = 0.001) in NSNP individuals. Also, Beighton hypermobility scores showed a moderate negative correlation with muscle endurance in NSNP (flexor muscles: r = −0.40, p = 0.020, extensor muscles: r = −0.41, p = 0.020, and asymptomatic individuals (flexor muscles: −0.34, p = 0.045, extensor muscles: r = −0.45, p = 0.007).ConclusionGJH individuals with NSNP showed increased cervical JPEs and reduced muscle endurance compared to asymptomatic. Individuals with GJH with higher Beighton scores demonstrated increased cervical JPEs and reduced neck muscle endurance holding ability. In clinical practice, therapists should be aware of these findings, incorporate proprioceptive and muscle endurance assessments, and formulate rehabilitation strategies for NSNP individuals with GJM. creator: Ravi Shankar Reddy creator: Jaya Shanker Tedla creator: Mastour Saeed Alshahrani creator: Faisal Asiri creator: Venkata Nagaraj Kakaraparthi uri: https://doi.org/10.7717/peerj.13097 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Reddy et al. title: Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults link: https://peerj.com/articles/13110 last-modified: 2022-03-11 description: Social communication difficulties are a diagnostic feature in autism. These difficulties are sometimes attributed, at least in part, to impaired ability in making inferences about what other people mean. In this registered report, we tested a competing hypothesis that the communication profile of adults on the autism spectrum can be more strongly characterised by reduced confidence in making inferences in the face of uncertain information. We tested this hypothesis by comparing the performance of 102 autistic and 109 non-autistic adults on a test of implied meaning, using a test of grammaticality judgements as a control task. We hypothesised that autistic adults would report substantially lower confidence, allowing for differences in accuracy, than non-autistic adults on the test of implied meaning compared to the grammaticality test. However, our results did not suggest this. Instead, we found that accuracy and confidence were both reduced to a similar extent on the test of implied meaning in the autistic group compared to the control group, although these were only subtle differences. This pattern of results was specific to inference-making, as the autistic and non-autistic groups did not differ on the grammar test. This supports the idea that specific differences in pragmatic language processing can exist in autism in the absence of core language problems. Importantly, this pattern of results (differences on the test of implied meaning and no differences on the grammar test) was reversed in a group with self-reported reading difficulties, indicating that the differences in inference-making were specific to the autistic group. Lastly, we found relationships between Intolerance of Uncertainty, performance on the test of implied meaning, and self-reported social communication challenges. This supports the idea that discomfort with uncertainty plays a role in the pragmatic language and communication challenges in autism. creator: Alexander C. Wilson creator: Dorothy V.M. Bishop uri: https://doi.org/10.7717/peerj.13110 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wilson and Bishop title: Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses link: https://peerj.com/articles/12674 last-modified: 2022-03-10 description: BackgroundThe rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment.MethodsIn this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions.ResultsAs a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs. creator: Muhammad Abdul Rehman Rashid creator: Rana Muhammad Atif creator: Yan Zhao creator: Farrukh Azeem creator: Hafiz Ghulam Muhu-Din Ahmed creator: Yinghua Pan creator: Danting Li creator: Yong Zhao creator: Zhanying Zhang creator: Hongliang Zhang creator: Jinjie Li creator: Zichao Li uri: https://doi.org/10.7717/peerj.12674 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rashid et al. title: Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes link: https://peerj.com/articles/12766 last-modified: 2022-03-10 description: The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H′) revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly inefficient genotypes. The above contrasting diverse lentil genotypes can be utilized to produce P-efficient lentil cultivars. The lentil germplasm with potentially favorable root traits can be suggested to evaluated for other abiotic stress to use them in crop improvement programme. The scientific breakthroughs in root trait phenotyping have improved the chances of establishing trait–allele relationships. As a result, genotype-to-phenotype connections can be predicted and verified with exceptional accuracy, making it easier to find and incorporate favourable nutrition-related genes/QTLs in to breeding programme. creator: Muraleedhar Aski creator: Reena Mehra creator: Gyan Prakash Mishra creator: Dharmendra Singh creator: Prachi Yadav creator: Neha Rai creator: Venkata Ravi Prakash Reddy creator: Arun Kumar MB creator: Renu Pandey creator: Madan Pal Singh creator: Gayacharan creator: Ruchi Bansal creator: Kuldeep Tripathi creator: Sripada M. Udupa creator: Shiv Kumar creator: Ashutosh Sarker creator: Harsh Kumar Dikshit uri: https://doi.org/10.7717/peerj.12766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aski et al. title: A versatile isothermal amplification assay for the detection of leptospires from various sample types link: https://peerj.com/articles/12850 last-modified: 2022-03-10 description: BackgroundLeptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene.ResultsSeveral reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease.ConclusionsIn short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study. creator: Shuhaidah Othman creator: Pui-Yuei Lee creator: Jia-Yong Lam creator: Noraini Philip creator: Nurul Natasya Azhari creator: Norliza Bahtiar Affendy creator: Siti Norbaya Masri creator: Vasantha Kumari Neela creator: Farah Shafawati Mohd-Taib creator: Hui-Yee Chee uri: https://doi.org/10.7717/peerj.12850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Othman et al. title: Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways link: https://peerj.com/articles/12944 last-modified: 2022-03-10 description: BackgroundImmediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown.MethodsThe expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation.ResultsA significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09–0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61–0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03–1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-related signaling pathways, the p53 signaling pathway, and other signaling pathways. Regulatory factor X5 (RFX5) was identified as a possible regulator of IER3-related TF.ConclusionIER3 may be a potential prognostic marker for HCC. The molecular mechanisms of IER3 in HCC warrant further study. creator: Fei-Yan He creator: Gang Chen creator: Rong-quan He creator: Zhi-Guang Huang creator: Jian-Di Li creator: Wei-Zi Wu creator: Ji-Tian Chen creator: Yu-Lu Tang creator: Dong-Ming Li creator: Shang-Ling Pan creator: Zhen-Bo Feng creator: Yi-wu Dang uri: https://doi.org/10.7717/peerj.12944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842 link: https://peerj.com/articles/12950 last-modified: 2022-03-10 description: BackgroundFemales of the gammaridean amphipod Ampelisca eschrichtii with signs of regenerating, previously atrophied ovaries were recovered from the northeastern shelf of Sakhalin Island (Okhotsk Sea, Russia). Ovarian regeneration was previously unknown for any amphipod species. A. eschrichtii have a predominantly 2-year life cycle (from embryo to adult death) and reproduce once between late winter or early spring at the age of 2 years. Occasionally, females survive to a third year. An adaptive value of extended survival among these females is likely to require that they are also reproductive.MethodsHistological sections from a second-year female with ovarian atrophy, a female with normal ovaries, a third-year female with ovarian regeneration, as well as testes of an immature and a sexually mature male were compared to determine the sources of cells of the germinal and somatic lines necessary for ovarian regeneration.ResultsOvarian regeneration in the third-year female began with the formation of a new germinal zone from germ cells preserved in the atrophied ovaries and eosinophilic cells of the previously starving second-year female. Eosinophilic cells form the mesodermal component of the germinal zone. A mass of these cells appeared in the second-year female that had atrophied ovaries and in large numbers on the intestine wall of the third-year female with regenerating ovaries. These eosinophilic cells appear to migrate into the regenerating ovaries.ConclusionsAll germ cells of the second-year female are not lost during ovarian atrophy and can be involved in subsequent ovarian regeneration. Eosinophilic cells involved in ovarian regeneration are of mesodermal origin. The eosinophilic cell morphologies are similar to those of quiescence cells (cells in a reversible state that do not divide but retain the ability to re-enter cell division and participate in regeneration). These histological data thus indicate that eosinophilic and germ cells of third-year females can participate in the regeneration of the ovaries to reproduce a second brood. The precursors of these third-year females (a small number the second-year females with an asynchronous [summer] breeding period and ovaries that have atrophied due to seasonal starvation) appear to possess sources of somatic and germ cells that are sufficient for ovarian regeneration and that may be adaptations to starvation stress. creator: Valentina B. Durkina creator: John W. Chapman creator: Natalia L. Demchenko uri: https://doi.org/10.7717/peerj.12950 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Durkina et al.