The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study
Background We 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. Methods We 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. Results The 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). Conclusion A high preoperative LAR is an independent predictor of the prognosis of colon cancer patients.
Xie et al. (2022) The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study. PeerJ 10:e13091 https://doi.org/10.7717/peerj.13091
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
Background Cervical 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. Methods In 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. Results GJH 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). Conclusion GJH 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.
Reddy et al. (2022) 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. PeerJ 10:e13097 https://doi.org/10.7717/peerj.13097
Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults
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.
Wilson et al. (2022) Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults. PeerJ 10:e13110 https://doi.org/10.7717/peerj.13110
Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses
Background The 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. Methods In 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. Results As 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.
Rashid et al. (2022) Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses. PeerJ 10:e12674 https://doi.org/10.7717/peerj.12674
Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes
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.
Aski et al. (2022) Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes. PeerJ 10:e12766 https://doi.org/10.7717/peerj.12766
A versatile isothermal amplification assay for the detection of leptospires from various sample types
Background Leptospirosis 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. Results Several 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. Conclusions In 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.
Othman et al. (2022) A versatile isothermal amplification assay for the detection of leptospires from various sample types. PeerJ 10:e12850 https://doi.org/10.7717/peerj.12850
Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways
Background Immediate 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. Methods The 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. Results A 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. Conclusion IER3 may be a potential prognostic marker for HCC. The molecular mechanisms of IER3 in HCC warrant further study.
He et al. (2022) Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways. PeerJ 10:e12944 https://doi.org/10.7717/peerj.12944
First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842
Background Females 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. Methods Histological 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. Results Ovarian 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. Conclusions All 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.
Durkina et al. (2022) First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842. PeerJ 10:e12950 https://doi.org/10.7717/peerj.12950
Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study
Background Sepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis. Methods In total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths. Results Serum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HSP90α and IL-1β, IL-18, and MIP-3α. Conclusion HSP90α is of favorable clinical significance in sepsis diagnosis and prognosis, laying a foundation for future clinical applications.
Li et al. (2022) Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study. PeerJ 10:e12997 https://doi.org/10.7717/peerj.12997
Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements
Objectives To determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions. Methods An experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05). Results During the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture positions (p < 0.01) and neck angulation (p < 0.01); the use of these loupes did not affect muscle activation in the regions evaluated (p > 0.05). Conclusion The use of Galilean loupes had a positive effect on dental students’ working posture during the restoration procedures performed.
Pazos et al. (2022) Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements. PeerJ 10:e13021 https://doi.org/10.7717/peerj.13021