Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index
Background This study investigated the relationship between the systemic immune inflammation index (SII) and catheter-related infections and their effects on prognosis in pediatric patients. Methods A total of 56 pediatric patients diagnosed with ventriculoperitoneal (V-P) shunt infection between January 2017 and October 2019 were included. V-P shunt infection diagnosis was made based on clinical findings. All cerebrospinal fluid (CSF) samples were subjected to direct microscopic examination and culture. Protein, glucose, and sodium levels in CSF, CSF leukocytes, and hematological and biochemical parameters were measured. Results Fifty-six patients with growth in CSF culture were included in this study. 55.4% of the cases were female and 44.6% male. V-P shunt was detected in 82.1% of the cases and external ventricular drainage (EVD) catheter-related infection in 17.9%. The CSF/blood glucose ratio was significantly lower (p = 0.046), and SII was significantly increased (p = 0.002) in non-coagulase-negative staphylococci. Conclusions Early and appropriate antibiotic therapy reduces morbidity and mortality in catheter-related infections. However, it is important to start empirical antibiotherapy until culture results are expected. Therefore, further research on the estimation of possible factors is needed.
Nergiz et al. (2023) Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index. PeerJ 11:e15905 https://doi.org/10.7717/peerj.15905
Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum
The plant hormone auxin regulates numerous aspects of plant growth and development, and small auxin-up RNA (SAUR) is the largest family of early auxin response genes in higher plants. SAUR has been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in Lycium ruthenicum. L. ruthenicum is a thorny shrub with very pronounced salt and drought tolerance, and studies have shown that stem thorns are related to drought tolerance in L. ruthenicum. In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT-qPCR). A total of 33 putative LrSAURs were identified and divided into three clusters in a phylogenetic tree of L. ruthenicum. MEME analysis identified 10 motifs in L. ruthenicum, and the results suggested that motif 1 and motif 3 were widely distributed. Analyzing the transcriptome data of stem thorns at four developmental stages indicated that LrSAURs were differentially expressed in L. ruthenicum, and could be divided into six expression patterns. The RT-qPCR analysis of 21 genes showed that LrSAUR2, LrSAUR8, LrSAUR9, LrSAUR11, LrSAUR12, and LrSAUR19 were mainly expressed in stems and stem thorns, and may be related to stem thorn development.
Hu et al. (2023) Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum. PeerJ 11:e15941 https://doi.org/10.7717/peerj.15941
The evolution of SARS-CoV-2 and the COVID-19 pandemic
Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
Si et al. (2023) The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 11:e15990 https://doi.org/10.7717/peerj.15990
Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK
Following school closures and changes in contact behavior of children and adults a reduced head louse prevalence has been reported from across the globe. In parallel, sales of treatments were observed to fall, partly because of supply problems of some products following the pandemic, but this did not appear to result in more cases of infestation. Surveys of schools in and around Cambridge, UK, found that infestation rates were significantly reduced particularly in city schools compared with similar surveys conducted before the COVID-19 pandemic. Contrary to expectation the number of cases in schools has only risen slowly since schools returned to normal full time working in 2022–2023.
Burgess et al. (2023) Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK. PeerJ 11:e16001 https://doi.org/10.7717/peerj.16001
Structural and functional brain changes in people with knee osteoarthritis: a scoping review
Background Knee osteoarthritis is a highly prevalent disease worldwide that leads to functional disability and chronic pain. It has been shown that not only changes are generated at the joint level in these individuals, but also neuroplastic changes are produced in different brain areas, especially in those areas related to pain perception, therefore, the objective of this research was to identify and compare the structural and functional brain changes in knee OA versus healthy subjects. Methodology Searches in MEDLINE (PubMed), EMBASE, WOS, CINAHL, SCOPUS, Health Source, and Epistemonikos databases were conducted to explore the available evidence on the structural and functional brain changes occurring in people with knee OA. Data were recorded on study characteristics, participant characteristics, and brain assessment techniques. The methodological quality of the studies was analysed with Newcastle Ottawa Scale. Results Sixteen studies met the inclusion criteria. A decrease volume of the gray matter in the insular region, parietal lobe, cingulate cortex, hippocampus, visual cortex, temporal lobe, prefrontal cortex, and basal ganglia was found in people with knee OA. However, the opposite occurred in the frontal lobe, nucleus accumbens, amygdala region and somatosensory cortex, where an increase in the gray matter volume was evidenced. Moreover, a decreased connectivity to the frontal lobe from the insula, cingulate cortex, parietal, and temporal areas, and an increase in connectivity from the insula to the prefrontal cortex, subcallosal area, and temporal lobe was shown. Conclusion All these findings are suggestive of neuroplastic changes affecting the pain matrix in people with knee OA.
Salazar-Méndez et al. (2023) Structural and functional brain changes in people with knee osteoarthritis: a scoping review. PeerJ 11:e16003 https://doi.org/10.7717/peerj.16003
Application of bubble streams to control biofouling on marine infrastructure—pontoon-scale implementation
There is a lack of cost-effective, environmentally-friendly tools available to manage marine biofouling accumulation on static artificial structures such as drilling rigs, wind turbines, marine farms, and port and marina infrastructure. For there to be uptake and refinement of tools, emerging technologies need to be tested and proven at an operational scale. This study aimed to see whether biofouling accumulation could be suppressed on marine infrastructure under real-world conditions through the delivery of continuous bubble streams. Submerged surfaces of a floating marina pontoon were cleaned in-situ by divers, and the subsequent colonisation by biofouling organisms was monitored on treated (bubbles applied) and untreated sections. Continuous bubble streams proved highly effective (>95%) in controlling macrofouling accumulation on the underside surface of the marina pontoon for the first 2 months after deployment, but efficacy dropped off rapidly once bubble stream delivery was partially obscured due to biofouling accumulation on the diffuser itself. Although extensive macrofouling cover by mussels, bryozoans and hydroids was observed on treated surfaces by 4 months (27.5%, SE = 4.8%), biofouling % cover and diversity was significantly higher on untreated surfaces (79.6%, SE = 2.9%). While this study demonstrates that continuous bubble streams greatly restrict biofouling accumulation over short-to-medium timescales, improved system design, especially the incorporation of diffusers resistant to fouling, is needed for the approach to be considered a viable long-term option for biofouling management on static artificial structures.
Hopkins et al. (2023) Application of bubble streams to control biofouling on marine infrastructure—pontoon-scale implementation. PeerJ 11:e16004 https://doi.org/10.7717/peerj.16004
Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population
Background Due to the deficiencies of vaccines and effective medicine, the human immunodeficiency virus (HIV) infection mechanism should be studied. The C19orf66 gene, one of the interferon-stimulated genes (ISGs), expresses broad-spectra anti-viral activity, including inhibiting HIV replication. Methods In this study, we collect 421 HIV-1 infected patients and 448 controls to genotype three SNPs in the C19orf66 gene. Then, the association between SNPs and biochemical indices/ HIV-1 subtypes are analyzed. Results Genotypes CC and CT of rs12611087 show statistically lower and higher frequencies in HIV-1 infected patients than in controls, respectively. Alleles C and T of rs12611087 play protective and risk roles in Yunnan HIV population, respectively. Biochemical indices analysis shows that HIV-1 infected persons carried genotype TT of rs77076061 express significantly lower CD3+/CD45+ ratio level and higher IBIL level. The epidemic subtypes of HIV-1 patients in this study are CRF 07_BC and CRF 08_BC. Moreover, subtype CRF 08_BC tends to infect persons with genotype CC of rs12611087. Conclusion The genetic polymorphisms of the C19orf66 gene are firstly studied and reported to associate with HIV-1 infection and biochemical indices of patients in Yunnan. Furthermore, subtype CRF 08_BC infection could be influenced by genotypes of SNP in the C19orf66 gene.
Zhang et al. (2023) Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population. PeerJ 11:e16005 https://doi.org/10.7717/peerj.16005
Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology
In the literature there are numerous reports of developmental deformities in arthropods collected in their natural habitat. Since such teratogenically affected individuals are found purely by chance, the causes of their defects are unknown. Numerous potential physical, mechanical, chemical, and biological teratogens have been considered and tested in the laboratory. Thermal shocks, frequently used in teratological research on the spider Eratigena atrica, have led to deformities on both the prosoma and the opisthosoma. In the 2020/2021 breeding season, by applying alternating temperatures (14 °C and 32 °C, changed every 12 h) for the first 10 days of embryonic development, we obtained 212 postembryos (out of 3,007) with the following anomalies: oligomely, heterosymely, bicephaly, schistomely, symely, polymely, complex anomalies, and others. From these we selected six spiders with defects on the prosoma and two with short appendages on the pedicel for further consideration. The latter cases seem particularly interesting because appendages do not normally develop on this body part, viewed as the first segment of the opisthosoma, and appear to represent examples of atavism. In view of the ongoing development of molecular techniques and recent research on developmental mechanisms in spiders, we believe the observed phenotypes may result, at least in part, from the erroneous suppression or expression of segmentation or appendage patterning genes. We consider “knockdown” experiments described in the literature as a means for generating hypotheses about the sources of temperature-induced body abnormalities in E. atrica.
Napiórkowska et al. (2023) Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology. PeerJ 11:e16011 https://doi.org/10.7717/peerj.16011
The current landscape of m6A modification in urological cancers
N6-methyladenosine (m6A) methylation is a dynamic and reversible procession of epigenetic modifications. It is increasingly recognized that m6A modification has been involved in the tumorigenesis, development, and progression of urological tumors. Emerging research explored the role of m6A modification in urological cancer. In this review, we will summarize the relationship between m6A modification, renal cell carcinoma, bladder cancer, and prostate cancer, and discover the biological function of m6A regulators in tumor cells. We will also discuss the possible mechanism and future application value used as a potential biomarker or therapeutic target to benefit patients with urological cancers.
Zeng et al. (2023) The current landscape of m6A modification in urological cancers. PeerJ 11:e16023 https://doi.org/10.7717/peerj.16023
Temporal variation of the relationships between rice yield and climate variables since 1925
Background Long-term time-series datasets of crop yield and climate variables are necessary to study the temporal variation of climate effects on crops. The aim of this study was to broadly assess assessment of the effects of climate on rice, and the associated temporal variations of the effects during the long-term period. Methods We conducted field experiments in Taiwan from 1925 to 2019 to collect and analyze rice yield data and evaluate the impacts of changes in average temperature, diurnal temperature range (DTR), rainfall, and sunshine duration on rice yield during cool and warm cropping seasons. We then estimated the relationships between annual grain yield and the climate variables using the time series of their first difference values. We also computed the total relative and annual actual yield changes using regression coefficients for each climate variable for the intervals 1925–1944, 1945–1983, and 1996–2019 to reveal the impacts of climate change on yields and the associated temporal variations during the overall experimental period. Results The annual daily average temperature calculated from the trend of the regression lines increased by 0.94–1.03 °C during the 95-year period. The maximum temperature remained steady while the minimum temperature increased, leading to decreased DTR. The total annual rainfall decreased by 237–352 mm and the annual total sunshine duration decreased by 93.9–238.9 h during the experimental period. We observed that during the cool cropping season, yield response to temperature change decreased, while that to DTR and rainfall changes increased. During the warm cropping season, all the yield responses to temperature, DTR, and rainfall changes were negative throughout the experimental period. In recent years (1996–2019) the estimated annual actual rice yield changes during the cool cropping season were negatively affected by climate variables (except for sunshine duration), and slightly positively affected (except for temperature) during the warm cropping season. Compared to the effects of temperature and DTR, those of rainfall and sunshine duration on rice yield changes were weak. This study contributes to provide impacts of climate change on rice yield and associated long-term temporal variations over nearly a century.
Chen et al. (2023) Temporal variation of the relationships between rice yield and climate variables since 1925. PeerJ 11:e16045 https://doi.org/10.7717/peerj.16045