title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=595 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma link: https://peerj.com/articles/14622 last-modified: 2023-01-06 description: Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC. creator: Jingze Yang creator: Xin Yang creator: Jinlu Guo creator: Shi Liu uri: https://doi.org/10.7717/peerj.14622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Evaluating the effect of the incidence angle of ALOS-2 PALSAR-2 on detecting aquaculture facilities for sustainable use of coastal space and resources link: https://peerj.com/articles/14649 last-modified: 2023-01-06 description: BackgroundDriven by the growing world population, aquaculture plays a key role in meeting the increasing demand for food. However, aquaculture facilities in Japan are widely installed in coastal waters where natural disasters, such as typhoons and tsunamis, might wash these facilities away, thereby interfering with maritime navigation safety. Therefore, it is imperative to efficiently monitor the state of aquaculture facilities daily, particularly after a disaster in real time. To this end, several new space-borne L-band synthetic aperture radars (SARs) continue to be launched now and in the future, whose utilizations are expected to increase nationally and internationally. An example is the Japan Aerospace Exploration Agency, currently operating a SAR that can be operated day and night, and even under cloudy conditions, called ALOS-2 PALSAR-2.MethodsBased on the above facts, this study evaluated the effect of the incidence angle of ALOS-2 PALSAR-2 HH single-polarization data, using 3 m spatial resolution, on aquaculture raft detection. As the study site, we selected Ago Bay, located on the Pacific coast of Mie Prefecture in central Japan since the Nankai Trough Megathrust Earthquake and tsunamis have been predicted to occur in the future around this area. Then, we analyzed the sigma zero (backscattering coefficient) of aquaculture rafts and their surrounding sea surfaces, including the relationships between satellite orbits and aquaculture raft directions.ResultsInvestigations revealed that the optimum incidence angle for detecting aquaculture rafts in this study was 33.8°–45.1°. Differences in the sigma zero values existed between the ascending and descending orbits. However, the incidence angles differed on the orbits. Then, differences in the median sigma zero values across a range of incidence angles were evaluated under the descending orbit. In addition, when the directions of the aquaculture rafts were closely perpendicular to the satellite orbit, aquaculture rafts tended to show the highest values of sigma zero due to Bragg resonance scattering. Hence, this knowledge may allow for the rapid detection of aquaculture rafts during an emergency without going on-site. creator: Hiroki Murata creator: Toyonobu Fujii creator: Chinatsu Yonezawa uri: https://doi.org/10.7717/peerj.14649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Murata et al. title: Depletion of PSMD14 suppresses bladder cancer proliferation by regulating GPX4 link: https://peerj.com/articles/14654 last-modified: 2023-01-06 description: ObjectiveThe aim of this study was to investigate the role of deubiquitinase (DUB) 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in patients with bladder cancer.MethodsFrom 2016 to 2018, 181 patients diagnosed with primary bladder cancer at the Affiliated Hospital of Qingdao University were recruited. The expression of PSMD14 in bladder cancer tissues was tested by immunochemistry. The association between PSMD14 expression and clinical and pathological data and outcomes of bladder cancer patients was determined. Overexpression and knockdown cells were constructed to evaluate the effects of PSMD14 on proliferation of bladder cancer cells.ResultsOur results showed that PSMD14 was significantly overexpressed in bladder cancer tissues compared to adjacent non-tumor tissues (76.24% vs 23.76%, P = 0.02). The expression of PSMD14 was significantly higher in patients with larger tumor diameters (85.14% vs 70.09%, P = 0.019) and patients with a family history of cancer (92.16% vs 70.00%, P = 0.002). Patients with high expression of PSMD14 had poor disease-free survival (DFS) (HR = 2.89, 95% CI [1.247–6.711], P = 0.013). Gain and loss of function experiments demonstrated that PSMD14 deficiency inhibited bladder cancer cell proliferation. Additionally, depletion of PSMD14 suppressed bladder cancer cell growth via down-regulation of GPX4, and the promotion of PSMD14-induced cell growth was observably reversed by the GPX4 inhibitor RSL3.ConclusionWe determined that PSMD14 is highly expressed in bladder cancer tissues, and that PSMD14 expression correlated with poor disease-free survival. Depletion of PSMD14 could inhibit the proliferation of bladder cancer cells through the downregulation of GPX4. Therefore, PSMD14 may be an effective target for the treatment of bladder cancer. creator: Changxin Jia creator: Xin Zhang creator: Tingting Qu creator: Xiuyun Wu creator: Yu Li creator: Yang Zhao creator: Lijiang Sun creator: Qing Wang uri: https://doi.org/10.7717/peerj.14654 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jia et al. title: Immune fitness and lifestyle habits of Saudi medical students: a cross sectional study link: https://peerj.com/articles/14363 last-modified: 2023-01-05 description: IntroductionImmune function reaches an optimum level in young adults. However, young adults are more likely to adopt potentially harmful habits that may pose a risk to their long-term health and immune fitness, and which eventually may put a substantial burden on the healthcare system. This study aimed to assess the status of medical students’ immune fitness, using the immune status questionnaire (ISQ) and exploring the association with the commonly adopted lifestyle habits hypothesized to have an impact on immune functions.MethodsA descriptive, cross-sectional study was conducted among preclinical students attending the medical school of King Abdulaziz University. An online self-reported questionnaire was used to assess the immune status (ISQ), perceived (momentary) immune fitness, general health, lifestyle habits and students’ perception of these lifestyle-associated impacts on immune fitness. Descriptive, Spearman’s correlation and stepwise linear regression analyses were performed.ResultsIn a pooled sample of 211 participants, the overall ISQ score was 6.00 ± 5.0 with statistically significant abnormally lower scores in females (ISQ 5.00 ± 5.0, p < 0.001). 49.29% of respondents experienced poor immune fitness as measured by the ISQ (<6). The ISQ score was significantly correlated with fast and fatty food consumption (p = 0.003), daytime sleepiness (p = 0.001), and BMI subgroups (p = 0.028) negatively and positively correlated with adherence to a program of exercise (p = 0.005). A total of 41.23% of participants who reported a normal immune health, rated at ≥6 were graded below 6 on the ISQ score. Only 62.6% of students were able to correctly identify the effects of fast and fatty food consumption on immune fitness.ConclusionPoor immune fitness was common among medical students in KAU and associated significantly with their adopted lifestyle habits. Although, other factors can be significant contributors, biased immune health perception and lack of awareness of these lifestyle-associated impacts on immune fitness and general health may hinder the adoption of healthier habits. Immune biomarkers should be implemented in future work. creator: Azzah S. Alharbi uri: https://doi.org/10.7717/peerj.14363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alharbi title: Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review link: https://peerj.com/articles/14399 last-modified: 2023-01-05 description: Serratia marcescens is a ubiquitous bacterium from order Enterobacterales displaying a high genetic plasticity that allows it to adapt and persist in multiple niches including soil, water, plants, and nosocomial environments. Recently, S. marcescens has gained attention as an emerging pathogen worldwide, provoking infections and outbreaks in debilitated individuals, particularly newborns and patients in intensive care units. S. marcescens isolates recovered from clinical settings are frequently described as multidrug resistant. High levels of antibiotic resistance across Serratia species are a consequence of the combined activity of intrinsic, acquired, and adaptive resistance elements. In this review, we will discuss recent advances in the understanding of mechanisms guiding resistance in this opportunistic pathogen. creator: Faviola Tavares-Carreon creator: Karla De Anda-Mora creator: Idalia C. Rojas-Barrera creator: Angel Andrade uri: https://doi.org/10.7717/peerj.14399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tavares-Carreon et al. title: Validation of low-density lipoprotein cholesterol equations in pediatric population link: https://peerj.com/articles/14544 last-modified: 2023-01-05 description: Several studies have shown a high prevalence of dyslipidemia in children. Since childhood lipid concentrations continue into adulthood, recognition of lipid abnormalities in the early period is crucial to prevent the development of future coronary heart disease (CHD). Low density lipoprotein cholesterol (LDL-C) is one of the most used parameters in the initiation and follow-up of treatment in patients with dyslipidemia. It is a well known fact that LDL-C lowering therapy reduces the risk of future CHD. Therefore, accurate determination of the LDL-C levels is so important for the management of lipid abnormalities. This study aimed to validate different LDL-C estimating equations in the Turkish population, composed of children and adolescents. A total of 3,908 children below 18 years old at Sivas Cumhuriyet University Hospital (Sivas, Turkey) were included in this study. LDL-C was directly measured by direct homogeneous assays, i.e., Roche, Beckman, Siemens and estimated by Friedewald’s, Martin/Hopkins’, extended Martin-Hopkins’ and Sampson’s formulas. The concordances between the estimations obtained by the formulas and the direct measurements were evaluated both overall and separately for the LDL-C, triglycerides (TG) and non-high-density lipoprotein cholesterol (non-HDL-C) sublevels. Linear regression analysis was performed and residual error plots were generated between each estimation and direct measurement method. Coefficient of determination (R2) and mean absolute deviations were also evaluated. The overall concordance of Friedewald, Sampson, Martin-Hopkins and the extended Martin-Hopkins formula were 64.6%, 69.9%, 69.4%, and 84.3% for the Roche direct assay, 69.8%, 71.6%, 73.6% and 80.4% for the Siemens direct assay, 66.5%, 68.8%, 68.9% and 82.1% for the Beckman direct assay, respectively. The extended Martin-Hopkins formula had the highest concordance coefficient in both overall and all sublevels of LDL-C, non-HDL-C, and TG. When estimating the LDL-C categories, the highest underestimation degrees were obtained with the Friedewald formula. Our analysis, conducted in a large pediatric population, showed that the extended Martin-Hopkins equation gives more reliable results in estimation of LDL-C compared to other equations. creator: Gözde Ertürk Zararsız creator: Serkan Bolat creator: Ahu Cephe creator: Necla Kochan creator: Serra Ilayda Yerlitaş creator: Halef Okan Doğan creator: Gökmen Zararsız uri: https://doi.org/10.7717/peerj.14544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ertürk Zararsız et al. title: Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China link: https://peerj.com/articles/14592 last-modified: 2023-01-05 description: The study compare the diversity patterns and processes of microbial community assembly in the water and sediment of Lake Wuchang (China) using high-throughput sequencing of 16S rRNA gene amplicons. A higher microbial α-diversity in the sediment was revealed (P < 0.01), and the most common bacterial phyla in water column were Proteobacteria, Cyanobacteria and Actinobacteria, while Proteobacteria, Acidobacteria, Chloroflexi and Nitrospirae were dominant in sediment. Functions related to phototrophy and nitrogen metabolism primarily occurred in the water column and sediment, respectively. The microbial communities in water column from different seasons were divided into three groups, while no such dispersion in sediment based on PCoA and ANOSIM. According to Pearson correlation analysis, water temperature, dissolved oxygen, water depth, total nitrogen, ammonium, and nitrite were key factors in determining microbial community structure in water column, while TN in sediment, conductivity, and organic matter were key factors in sediment. However, the stochastic processes (|βNTI| < 2) dominated community assembly in both the water column and sediment of Lake Wuchang. These data will provide a foundation for microbial development and utilization in lake water column and sediment under the circumstances of increasing tendency of lake ecological fishery in China. creator: Xuemei Li creator: Zihao Meng creator: Kang Chen creator: Feifei Hu creator: Lu Liu creator: Tingbing Zhu creator: Deguo Yang uri: https://doi.org/10.7717/peerj.14592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa link: https://peerj.com/articles/14629 last-modified: 2023-01-05 description: Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance. creator: Tanya Singh creator: Kazuhiko Sakai creator: Jun Ishida-Castañeda creator: Akira Iguchi uri: https://doi.org/10.7717/peerj.14629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Singh et al. title: A systematic analysis of anti-diabetic medicinal plants from cells to clinical trials link: https://peerj.com/articles/14639 last-modified: 2023-01-05 description: BackgroundDiabetes is one of the fastest-growing health emergencies of the 21st century, placing a severe economic burden on many countries. Current management approaches have improved diabetic care, but several limitations still exist, such as decreased efficacy, adverse effects, and the high cost of treatment, particularly for developing nations. There is, therefore, a need for more cost-effective therapies for diabetes management. The evidence-based application of phytochemicals from plants in the management of diseases is gaining traction.MethodologyVarious plants and plant parts have been investigated as antidiabetic agents. This review sought to collate and discuss published data on the cellular and molecular effects of medicinal plants and phytochemicals on insulin signaling pathways to better understand the current trend in using plant products in the management of diabetes. Furthermore, we explored available information on medicinal plants that consistently produced hypoglycemic effects from isolated cells to animal studies and clinical trials.ResultsThere is substantial literature describing the effects of a range of plant extracts on insulin action and insulin signaling, revealing a depth in knowledge of molecular detail. Our exploration also reveals effective antidiabetic actions in animal studies, and clear translational potential evidenced by clinical trials.ConclusionWe suggest that this area of research should be further exploited in the search for novel therapeutics for diabetes. creator: Simeon Omale creator: Kennedy I. Amagon creator: Titilayo O. Johnson creator: Shaun Kennedy Bremner creator: Gwyn W. Gould uri: https://doi.org/10.7717/peerj.14639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Omale et al. title: Retrospective validation of bone risk stratification criteria for men with de novo metastatic hormone-naive prostate cancer in China link: https://peerj.com/articles/14500 last-modified: 2023-01-04 description: BackgroundBone metastasis has been suggested to be a significant impactor on the prognosis of newly diagnosed de novo metastatic hormone-sensitive prostate cancer (mHSPC), and some risk stratification models have been proposed on the basis of this hypothesis. However, the effectiveness of these risk stratification criteria has not been fully evaluated in China. This study aimed to evaluate the effectiveness of the risk stratification models in China.MethodsA total of 140 patients who were newly diagnosed with metastatic prostate cancer followed by primary androgen deprivation-based therapy from January 2008 to June 2021 at our institution were enrolled in this study. The patients were divided into different groups on the basis of high- and low-volume disease (H/LVD) criteria, high-and low-risk disease (H/LRD) criteria, extremity bone metastasis criteria (EBM), and extent of disease (EOD) criteria. The area under the receiver operating characteristic (ROC) curve (AUC) and decision curve analysis (DCA) were used to compare the validity and net benefit of these models. Using the Cox proportional hazards model, we performed univariable and multivariable analyses of the factors influencing overall survival (OS) and the time of progression to metastatic castration-resistant prostate cancer (CRPC).ResultsThe median patient age was 72 years. Most patients had a Gleason score ≥8 (102 cases, 72.9%) and clinical T stage >2 (75 cases, 53.6%). The median follow-up time was 25 months (range, 2–95 months). Ninety-two patients progressed to CRPC and fifty-seven patients died during the follow-up. The AUC of OS and CRPC showed that the EOD model had higher validity than the other risk stratification models. DCA shows that the net benefit of the EOD model on OS was better than that of the other risk stratification models. As for CRPC, the net benefit of the EOD model was second only to that of the H/LRD model when the threshold was <0.5; however, when the threshold was >0.5, the EOD model outperformed the other models. The effectiveness of EOD as an independent prognostic variable was verified through univariable and multivariable analyses.ConclusionThe EOD model yields reasonable risk stratification for use in Chinese mHSPC patients, providing further evidence supporting its role in clinical decision-making. creator: Yang Zhang creator: Li Ding creator: Yuxin Zheng creator: Kun Wang creator: Wentao Xia creator: Junqi Wang creator: Peng Ge uri: https://doi.org/10.7717/peerj.14500 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al.