ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management.

BACKGROUND: The increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic data often undergo similar preprocessing across projects, leading to redundant or inconsistent datasets and inefficient use of computing resources. This is especially pertinent for bioinformaticians engaged in multiple projects. Tools have been created to address challenges in managing and accessing curated genomic datasets, however, the practical utility of such tools becomes especially beneficial for users who seek to work with specific types of data or are technically inclined toward a particular programming language. Currently, there exists a gap in the availability of an R-specific solution for efficient data management and versatile data reuse. RESULTS: Here we present ReUseData, an R software tool that overcomes some of the limitations of existing solutions and provides a versatile and reproducible approach to effective data management within R. ReUseData facilitates the transformation of ad hoc scripts for data preprocessing into Common Workflow Language (CWL)-based data recipes, allowing for the reproducible generation of curated data files in their generic formats. The data recipes are standardized and self-contained, enabling them to be easily portable and reproducible across various computing platforms. ReUseData also streamlines the reuse of curated data files and their integration into downstream analysis tools and workflows with different frameworks. CONCLUSIONS: ReUseData provides a reliable and reproducible approach for genomic data management within the R environment to enhance the accessibility and reusability of genomic data. The package is available at Bioconductor ( https://bioconductor.org/packages/ReUseData/ ) with additional information on the project website ( https://rcwl.org/dataRecipes/ ).

Microalgal glycerol-3-phosphate acyltransferase role in galactolipids and high-value storage lipid biosynthesis.

Glycerolipids are the most abundant lipids in microalgae, and glycerol-3-phosphate:acyl-CoA acyltransferase (GPAT) plays an important role in their biosynthesis. However, the biochemical and biological functions of algal GPAT remain poorly characterized. Here, we characterized the endoplasmic reticulum (ER)-associated GPAT of the model unicellular green alga Chlamydomonas reinhardtii (CrGPATer). Enzymatic assays indicated that CrGPATer is an sn-1 acyltransferase using a variety of acyl-CoAs as the acyl donor. Subcellular localization revealed that CrGPATer was associated with ER membranes and lipid droplets. We constructed overexpression (OE) and knockdown (KD) transgenic C. reinhardtii lines to investigate the in vivo function of CrGPATer. Lipidomic analysis indicated that CrGPATer OE enhanced the cellular content of galactolipids, especially monogalactosyldiacylglycerol, under nitrogen deficiency stress. Correspondingly, CrGPATer KD lines contained lower contents of galactolipids than the control. Feeding experiments with labeled phosphatidic acid revealed that the intermediate of the eukaryotic Kennedy pathway could be used for galactolipid biosynthesis in the chloroplasts. These results provided multiple lines of evidence that the eukaryotic Kennedy pathway mediated by CrGPATer may be involved in galactolipid biosynthesis in C. reinhardtii. OE of CrGPATer significantly increased the content of triacylglycerol and the yield of biomass. Moreover, the content and yield of 1, 3-olein-2-palmitin, a high-value lipid that can be used as an alternative for human milk fat in infant formula, were significantly enhanced in the OE transgenic lines. Taken together, this study provided insights into the biochemical and biological functions of CrGPATer and its potential as a genetic engineering target in functional lipid manufacturing.

Correlative relationship between body mass index and heart rate variability in psychiatric disorders.

OBJECTIVE: Indicators of heart rate variability (HRV) have been used to assess the autonomic activity. However, the influence of obesity on HRV in these patients remains to be determined. This study aimed to examine how obesity (measured with the body mass index [BMI]) affects HRV and determine whether the effect varies among different psychiatric disorders. We recruited 3159 consecutive patients, including 1744 with schizophrenia, 966 with mood disorders, and 449 with anxiety disorders. Patients were divided into four groups based on BMI: underweight (< 18.5), normal weight (18.5-23.9), overweight (24-27.9), and obese (≥ 28). The cardiovascular status was assessed using several time- and frequency-based HRV indicators, measured via electrocardiogram signals recorded for 5 min. The mean BMI of the participants was 23.6 ± 4.0. The patients in the overweight and obese groups were 29.4% and 13.6% of the total, respectively. The HRV indicators were higher in underweight and normal-weight patients than in the overweight and obese ones. After stratification based on the psychiatric diagnosis, the patients with mood disorders showed lower HRV than those with schizophrenia or anxiety disorder in the normal-weight group. In contrast, in the overweight and obese groups the patients with mood disorders showed higher HRV than those with the other disorders. The HRV variables were significantly associated with BMI, and higher BMI was associated with higher heart rates and lower HRV. These results indicate that weight gain in psychiatric disorders is associated with an imbalance in autonomic nerve activity. However, the relationship between autonomic activity, weight gain, and psychiatric disorders warrants further investigation.

Risk Factors for Acute Kidney Injury in Adult Patients Under Veno-Arterial Extracorporeal Membrane Oxygenation Support.

OBJECTIVE: To investigate the incidence and risk factors of acute kidney injury (AKI) stage 3 in adult patients under veno-arterial extracorporeal membrane oxygenation (VA-ECMO) support. DESIGN: A retrospective case-control study. SETTING: Single center, Fuwai Hospital. PARTICIPANTS: Adult VA-ECMO patients age ≥18 years and older treated between January 2020 and December 2022 were included. INTERVENTIONS: The patients were grouped by whether they developed AKI Kidney Disease: Improving Global Outcomes (KDIGO) stage 3 or <3. Multivariate logistic regression was performed t"o evaluate risk factors of AKI stage 3. MEASUREMENTS AND MAIN RESULTS: Among enrolled patients, 40 (53.3%) developed AKI stage 3. The in-hospital mortality of AKI stage 3 patients was significantly higher than that of AKI stage <3 patients (67.5% vs 34.3%; p = 0.004). Multivariate logistic regression analysis revealed that concomitant hypertension (odds ratio [OR], 0.250; 95% confidence interval [CI], 0.063, 0.987), p = 0.048), pre-ECMO hemoglobin (OR, 0.969; 95% CI, 0.947-0.992; p = 0.009), pre-ECMO lactate (OR, 1.173; 95% CI, 1.028-1.339; p = 0.018), and pre-ECMO creatinine (OR, 1.014; 95% CI, 1.003-1.025; p = 0.011) were independent risk factors for AKI stage 3. CONCLUSIONS: This study found a high incidence (53.3%) of AKI stage 3 in adult patients with VA-ECMO support and an association with increased in-hospital mortality. Concomitant hypertension, low pre-ECMO hemoglobin, and elevated pre-ECMO lactate and pre-ECMO creatinine were independent risk factors for AKI stage 3 in patients receiving VA-ECMO. It is imperative to identify and adjust these risk factors to enhance outcomes for those supported by VA-ECMO.

Huperzine A ameliorates neurological deficits after spontaneous subarachnoid hemorrhage through endothelial cell pyroptosis inhibition.

Spontaneous subarachnoid hemorrhage (SAH) is a kind of hemorrhagic stroke which causes neurological deficits in survivors. Huperzine A has a neuroprotective effect, but its role in SAH is unclear. Therefore, we explore the effect of Huperzine A on neurological deficits induced by SAH and the related mechanism. In this study, Evans blue assay, TUNEL staining, immunofluorescence, western blot analysis, and ELISA are conducted. We find that Huperzine A can improve neurological deficits and inhibit the apoptosis of nerve cells in SAH rats. Huperzine A treatment can improve the upregulation of brain water content, damage of blood-brain barrier, fibrinogen and matrix metalloprotein 9 expressions and the downregulation of ZO-1 and occludin expressions induced by SAH. Huperzine A inhibit the expressions of proteins involved in pyroptosis in endothelial cells in SAH rats. The increase in MDA content and decrease in SOD activity in SAH rats can be partly reversed by Huperzine A. The ROS inducer H 2O 2 can induce pyroptosis and inhibit the expressions of ZO-1 and occludin in endothelial cells, which can be blocked by Huperzine A. In addition, the increase in the entry of p65 into the nucleus in endothelial cells can be partly reversed by Huperzine A. Huperzine A may delay the damage of blood-brain barrier in SAH rats by inhibiting oxidative stress-mediated pyroptosis and tight junction protein expression downregulation through the NF-κB pathway. Overall, Huperzine A may have clinical value for treating SAH.

Integrated machine learning reveals aquatic biological integrity patterns in semi-arid watersheds.

Semi-arid regions present unique challenges for maintaining aquatic biological integrity due to their complex evolutionary mechanisms. Uncovering the spatial patterns of aquatic biological integrity in these areas is a challenging research task, especially under the compound environmental stress. Our goal is to address this issue with a scientifically rigorous approach. This study aims to explore the spatial analysis and diagnosis method of aquatic biological based on the combination of machine learning and statistical analysis, so as to reveal the spatial differentiation patterns and causes of changes of aquatic biological integrity in semi-arid regions. To this end, we have introduced an innovative approach that combines XGBoost-SHAP and Fuzzy C-means clustering (FCM), we successfully identified and diagnosed the spatial variations of aquatic biological integrity in the Wei River Basin (WRB). The study reveals significant spatial variations in species number, diversity, and aquatic biological integrity of phytoplankton, serving as a testament to the multifaceted responses of biological communities under the intricate tapestry of environmental gradients. Delving into the depths of the XGBoost-SHAP algorithm, we discerned that Annual average Temperature (AT) stands as the pivotal driver steering the spatial divergence of the Phytoplankton Integrity Index (P-IBI), casting a positive influence on P-IBI when AT is below 11.8 °C. The intricate interactions between hydrological variables (VF and RW) and AT, as well as between water quality parameters (WT, NO3-N, TP, COD) and AT, collectively sculpt the spatial distribution of P-IBI. The fusion of XGBoost-SHAP with FCM unveils pronounced north-south gradient disparities in aquatic biological integrity across the watershed, segmenting the region into four distinct zones. This establishes scientific boundary conditions for the conservation strategies and management practices of aquatic ecosystems in the region, and its flexibility is applicable to the analysis of spatial heterogeneity in other complex environmental contexts.

Assessing postoperative wound infection rates in ultrasound-guided microwave ablation versus conventional surgery for varicose veins.

Varicose veins are the prevalent vascular disorder that has conventionally been managed via risky postoperative wound infections and conventional surgery. While ultrasound-guided microwave ablation (UMA) has gained attention as a minimally invasive alternative, there is still a lack of research examining its comparative effectiveness. A prospective comparative investigation was undertaken in the Zhejiang region of China from January to November 2023, involving 140 patients who had received the diagnosis of primary varicose veins. An equal number of 70 patients underwent UMA and conventional surgery. Exclusion criteria for the study encompassed adult patients aged 18-65, with the exception of those who had undergone prior venous surgery, deep vein thrombosis or peripheral arterial disease. The demographical characteristics, procedural details and complication profiles of patients who developed postoperative wound infections within 30 days were analysed statistically. The outcomes demonstrated that postoperative wound infections were significantly diminished (5.7%) with UMA in comparison to conventional surgery (17.1%). In addition, the average duration of procedures and length of hospital stay for UMA patients were both reduced, although neither of these differences was found to be statistically significant (p > 0.05). Infection management, age and gender distribution of varicose veins were comparable between the two groups (p > 0.05). A significant inverse correlation was observed between the severity of varicose veins and postoperative outcomes, as determined by the regression analysis (p < 0.05). Using UMA to treat varicose veins showed promise as an alternative to conventional surgery, specifically in minimizing the incidence of postoperative wound infections. Additional research and clinical consideration are needed regarding the potential transition toward minimally invasive techniques in treatment of varicose veins, as suggested by these results.

Comparison of the immunogenicity of nasal-spray rVSV vector, adenovirus vector, and inactivated COVID-19-based vaccines in rodent models.

Intranasal (i.n.) vaccines can induce mucosal and systemic immunity against respiratory pathogens. Previously, we demonstrated that the recombinant vesicular stomatitis virus (rVSV)-based COVID-19 vaccine rVSV-SARS-CoV-2, with poor immunogenicity via the intramuscular route (i.m.), is more suitable for i.n. administration in mice and nonhuman primates. Here, we found that the rVSV-SARS-CoV-2 Beta variant was more immunogenic than the wild-type strain and other variants of concern (VOCs) in golden Syrian hamsters. Furthermore, the immune responses elicited by rVSV-based vaccine candidates via the i.n. route were significantly higher than those of two licensed vaccines: the inactivated vaccine KCONVAC delivered via the i.m. route and the adenovirus-based Vaxzevria delivered i.n. or i.m. We next assessed the booster efficacy of rVSV following two i.m. doses of KCONVAC. Twenty-eight days after receiving two i.m. doses of KCONVAC, hamsters were boosted with a third dose of KCONVAC (i.m.), Vaxzevria (i.m. or i.n.), or rVSVs (i.n.). Consistent with other heterologous booster studies, Vaxzevria and rVSV elicited significantly higher humoral immunity than the homogenous KCONVAC. In summary, our results confirmed that two i.n. doses of rVSV-Beta elicited significantly higher humoral immune responses than commercial inactivated and adeno-based COVID vaccines in hamsters. As a heterologous booster dose, rVSV-Beta induced potent, persistent, and broad-spectrum humoral and mucosal neutralizing responses against all VOCs, highlighting its potential to be developed into a nasal-spray vaccine.

Favorable factors for the survival of ST-segment elevation myocardial infarction patients with medium- and high-risk thrombolysis in myocardial infarction scores.

OBJECTIVE: ST-segment myocardial infarction (STEMI) is a time-sensitive emergency. This study screened the favorable factors for the survival of STEMI patients with medium- and high-risk thrombolysis in myocardial infarction (TIMI) scores. METHODS: According to the TIMI scores at admission, 433 STEMI patients were retrospectively and consecutively selected and allocated into low-/medium-/high-risk groups, with their general information/blood routine/biochemical indicators/coagulation indicators documented. The factors influencing the in-hospital survival of STEMI patients were analyzed using univariate and multivariate logistic regression analyses. Moreover, the predictive value of favorable factors was analyzed by receiver operating characteristics (ROC) curve, and patients were assigned into high/low level groups based on the cut-off value of these factors, with their in-hospital survival rates compared. RESULTS: The in-hospital survival rate of the medium-/high-risk groups was lower than that of the low-risk group. Emergency percutaneous coronary intervention (PCI), lymphocyte (LYM), total protein (TP), albumin (ALB), and sodium (Na) were independent favorable factors for in-hospital survival in the medium-/high-risk groups. Besides, LYM > 1.275 × 109/L, TP > 60.25 g/L, ALB > 34.55 g/L, and Na > 137.9 mmo1/L had auxiliary predictive value for the survival of STEMI patients with medium-/high-risk TIMI scores. Patients with high levels of LYM, TP, ALB, and Na exhibited higher in-hospital survival rates than patients with low levels. CONCLUSION: For STEMI patients with medium- and high-risk TIMI scores, accepting emergency PCI and normal levels of LYM, TP, ALB, and Na were more conducive to in-hospital survival.

Genome-wide analysis of growth-regulating factor genes in grape (Vitis vinifera L.): identification, characterization and their responsive expression to osmotic stress.

KEY MESSAGE: Identification, characterization and osmotic stress responsive expression of growth-regulating factor genes in grape. The growth and fruit production of grape vine are severely affected by adverse environmental conditions. Growth-regulating factors (GRFs) play a vital role in the regulation of plant growth, reproduction and stress tolerance. However, their biological functions in fruit vine crops are still largely unknown. In the present study, a total number of nine VvGRFs were identified in the grape genome. Phylogenetic and collinear relationship analysis revealed that they formed seven subfamilies, and have gone through three segmental duplication events. All VvGRFs were predicted to be nucleic localized and contained both the conserved QLQ and WRC domains at their N-terminals, one of the typical structural features of GRF proteins. Quantitative real-time PCR analyses demonstrated that all VvGRFs, with a predominant expression of VvGRF7, were constitutively expressed in roots, leaves and stems of grape plants, and showed responsive expression to osmotic stress. Further growth phenotypic analysis demonstrated that ectopic expression of VvGRF7 promoted the growth and sensitivity of transgenic Arabidopsis plants to osmotic stress. Our findings provide important information for the future study of VvGRF gene functions, and potential gene resources for the genetic breeding of new fruit vine varieties with improved fruit yield and stress tolerance.

Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers.

We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relationship of exon choice to known cancer driver alterations. To do so, we compiled a metadataset composed of 876 RNA-sequencing (RNA-Seq) samples from five publicly available sources representing a range of prostate phenotypes from normal tissue to drug-resistant metastases. We subjected these samples to exon-level analysis with rMATS-turbo, purpose-built software designed for large-scale analyses of splicing, and identified 13,149 high-confidence cassette exon events with variable incorporation across samples. We then developed a computational framework, pathway enrichment-guided activity study of alternative splicing (PEGASAS), to correlate transcriptional signatures of 50 different cancer driver pathways with these alternative splicing events. We discovered that Myc signaling was correlated with incorporation of a set of 1,039 cassette exons enriched in genes encoding RNA binding proteins. Using a human prostate epithelial transformation assay, we confirmed the Myc regulation of 147 of these exons, many of which introduced frameshifts or encoded premature stop codons. Our results connect changes in alternative pre-mRNA splicing to oncogenic alterations common in prostate and many other cancers. We also establish a role for Myc in regulating RNA splicing by controlling the incorporation of nonsense-mediated decay-determinant exons in genes encoding RNA binding proteins.

Preliminary study on dosimetry characteristics of a novel cylindrical dose verification system.

OBJECTIVE: To develop a novel ionization chamber array dosimetry system, study its dosimetry characteristics, and perform preliminary tests for plan dose verification. METHODS: The dosimetry characteristics of this new array were tested, including short-term and long-term reproducibility, dose linearity, dose rate dependence, field size dependence, and angular dependence. The open field and MLC field plans were designed for dose testing. Randomly select 30 patient treatment plans (10 intensity-modulated radiation therapy [IMRT] plans and 20 volumetric modulated arc therapy [VMAT] plans) that have undergone dose verification using Portal Dosimetry to perform verification measurement and evaluate dose verification test results. RESULTS: The dosimetry characteristics of the arrays all performed well. The gamma passing rates (3%/2 mm) were more than 96% for the combined open field and MLC field plans. The average gamma pass rates were (99.54 ± 0.58)% and (96.70 ± 3.41)% for the 10 IMRT plans and (99.32 ± 0.89)% and (94.91 ± 6.01)% for the 20 VMAT plans at the 3%/2 mm and 2%/2 mm criteria, respectively, which is similar to the Portal Dosimetry's measurement results. CONCLUSIONS: This novel ionization chamber array demonstrates good dosimetry characteristics and is suitable for clinical IMRT and VMAT plan verifications.

Different Geographic Strains of Dinoflagellate Karlodinium veneficum Host Highly Diverse Fungal Community and Potentially Serve as Possible Niche for Colonization of Fungal Endophytes.

In numerous studies, researchers have explored the interactions between fungi and their hosting biota in terrestrial systems, while much less attention has been paid to the counterpart interactions in aquatic, and particularly marine, ecosystems. Despite the growing recognition of the potential functions of fungi in structuring phytoplankton communities, the current insights were mostly derived from phytoplankton hosts, such as diatoms, green microalgae, and cyanobacteria. Dinoflagellates are the second most abundant group of phytoplankton in coastal marine ecosystems, and they are notorious for causing harmful algal blooms (HABs). In this study, we used high-throughput amplicon sequencing to capture global snapshots of specific fungal assemblages associated with laboratory-cultured marine dinoflagellate. We investigated a total of 13 clonal cultures of the dinoflagellate Karlodinium veneficum that were previously isolated from 5 geographic origins and have been maintained in our laboratory from several months to more than 14 years. The total recovered fungal microbiome, which consisted of 349 ASVs (amplicon sequencing variants, sequences clustered at a 100% sequence identity), could be assigned to 4 phyla, 18 classes, 37 orders, 65 families, 97 genera, and 131 species. The fungal consortium displayed high diversity and was dominated by filamentous fungi and ascomycetous and basidiomycetous yeasts. A core set of three genera among all the detected fungi was constitutively present in the K. veneficum strains isolated from geographically distant regions, with the top two most abundant genera, Thyridium and Pseudeurotium, capable of using hydrocarbons as the sole or major source of carbon and energy. In addition, fungal taxa previously documented as endophytes in other hosts were also found in all tested strains of K. veneficum. Because host-endophyte interactions are highly variable and strongly case-dependent, these fungal taxa were not necessarily genuine endosymbionts of K. veneficum; instead, it raised the possibility that dinoflagellates could potentially serve as an alternative ecological niche for the colonization of fungal endophytes. Our findings lay the foundation for further investigations into the potential roles or functions of fungi in the regulation of the growth dynamics and HABs of marine dinoflagellates in the field.

Assessment of greenhouse gases emissions and intensity from Chinese marine aquaculture in the past three decades.

Marine aquaculture is increasingly gaining importance as a source of food with high nutritional value. However, the expansion of aquaculture could be responsible for water contamination that influences the environmental quality of coastal ecosystems, and emissions of greenhouse gases (GHG) that affect global climate. China is the world's largest producer of marine aquaculture protein, which demands robust studies to assess the corresponding GHG emissions and intensity. To fill in this knowledge gap, the current study quantifies and analyzes GHG emissions and intensity (emission intensity is defined as GHG emissions per unit of production) from Chinese marine aquaculture (marine aquaculture production) over the past 30 years (1991-2020). The production of marine aquaculture comes from the China Fisheries Statistical Yearbooks. And the GHG emissions and intensity were calculated based on five sectors (commercial feed, trash fish, N2O, CH4, and energy) by Emission-Factor Approach. The results suggest that, excluding shellfish and algae, GHG emissions of ten coastal provinces (excluding Shanghai, Hong Kong, Taiwan, and Macau) increased from 2 Mt (109 kg) CO2-eq in 1991 to 25 Mt CO2-eq in 2020. In contrast, GHG emission intensity decreased in the same period from 7.33 (t CO2-eq/t production) to 6.34 (t CO2-eq/t production), indicating a progressive mitigation in GHG emissions per unit of product, hence sustainably satisfying a growing demand for food. As a result, China's marine aquaculture seems to be paving a promising way towards the neutrality of GHG emissions. In most provinces, GHG is on the rise, and only in Tianjin is on the decline in recent years. For the emissions intensity, the values of more than half provinces showed the downtrends. In addition, by considering the ratio of shellfish and algae, Chinese marine aquaculture can improve the net zero goal for GHG emissions of the sector. Finally, results also reveal for the first time the changes in taxonomic composition and spatial GHG emissions and intensity, providing new understanding and scientific bases to elaborate consistent mitigation strategies for an expanding global marine aquaculture.

Advanced treatment and Resource recovery of brewery wastewater by Co-cultivation of filamentous microalga Tribonema aequale and autochthonous Bacteria.

To use unicellular microalgae to remove waste nutrients from brewery wastewater while converting them into algal biomass has been explored but high-cost treatment and low-value biomass associated with current technologies have prevented this concept from further attempts. In this study, a filamentous microalga Tribonema aequale was introduced and the alga can grow vigorously in brewery wastewater and algal biomass concentration could be as high as 6.45 g L-1 which can be harvested by a cost-effective filtration method. The alga together with autochthonous bacteria removed majority of waste nutrients from brewery wastewater. Specifically, 85.39% total organic carbon (TOC), 79.53% total dissolved nitrogen (TN), 93.38% ammonia nitrogen (NH3-N) and 71.33% total dissolved phosphorus (TP) in brewery wastewater were rapidly removed by co-cultivation of T. aequale and autochthonous bacteria. Treated wastewater met the national wastewater discharge quality, and resulting algal biomass contained large amounts of high-value products chrysolaminarin, palmitoleic acid (PLA) and eicosapentaenoic acid (EPA). It is anticipated that reduced cost of algal harvesting coupled with value-added biomass could make T. aequale as a promising candidate for brewery wastewater treatment and resource utilization.

A nomogram for accurately predicting the surgical site infection following transforaminal lumbar interbody fusion in type 2 diabetes patients, based on glycemic variability.

Surgical site infection (SSI) is a common and serious complication of transforaminal lumbar interbody fusion (TLIF), and the occurrence of SSI usually leads to prolonged hospitalisation, increased medical costs, poor prognosis, and even death. The objectives of this study were to compare the incidence of SSI in patients with type 2 diabetes, investigate the correlation between perioperative glycemic variability and postoperative SSI, and develop a nomogram model to predict the risk of SSI. This study retrospectively analysed 339 patients with type 2 diabetes who underwent TLIF in the spinal surgery department of the Affiliated Zhongda Hospital of Southeast University from January 2018 to September 2021. The medical records of all patients were collected, and postoperative infection cases were determined according to the diagnostic criteria of surgical site infection. The risk factors for postoperative SSI were analysed by univariate and multivariate logistic regression. And Nomogram prediction model was established and validated. The nomogram incorporated seven independent predictors. Preoperative FPG-CV was the most important independent risk predictor of SSI, followed by preoperative MFBG, duration of drain placement, postoperative FPG-CV, preoperative blood glucose control scheme, duration of diabetes >5 years, and the number of fused vertebrae ≥2. The nomogram showed good diagnostic accuracy for the SS of both the training cohort and the validation cohort (AUC = 0.915 and AUC = 0.890). The calibration curves for the two cohorts both showed optimal agreement between nomogram prediction and actual observation. In conclusion, preoperative and postoperative glycemic variability is closely related to the occurrence of SSI. We developed and validated a nomogram to accurately predict the risk of SSI after TLIF surgery. It's helpful for spinal surgeons to formulate reasonable treatment plans and prevention strategies for type 2 diabetes patients.

A nomogram for accurately predicting the pathological upgrading of prostate cancer, based on 68 Ga-PSMA PET/CT.

PURPOSE: To develop and validate a nomogram for preoperative predicting the pathological upgrading of prostate cancer (PCa). METHODS: The prediction model was developed in a primary cohort that consisted of 208 PCa patients. All patients included in the study possessed both biopsy pathology specimens and radical prostatectomy pathology specimens, and completed the (68 Ga-prostate-specific membrane antigen [PSMA]) positron emission tomography/computed tomography (PET/CT) detection. The R function "createDataPartition" was used in a 7:3 ratio to randomly divide the patients into training and validation cohorts. In the training cohort, the independent predictors of pathological upgrading of PCa were determined by univariate analysis, univariate regression analysis and multivariate regression analysis. Based on these independent predictors, a nomogram was developed, and its performance was evaluated by receiver operating characteristic (ROC) curve, area under the curve (AUC) and calibration curve of training cohort and validation cohort. RESULTS: The nomogram incorporated five independent predictors including prostate volume (PV), SUVmax of the 68 Ga-PSMA PET/CT examination on prostate lesions (SUVmax ), body mass index (BMI); percentage of cancer positive biopsy cores (PPC) and biopsy International Society of Urological Pathology (ISUP) grade. The nomogram showed good diagnostic accuracy for the pathological upgrading of both the training cohort and the validation cohort (AUC = 0.818 and 0.806, respectively). The calibration curves for the two cohorts both showed optimal agreement between nomogram prediction and actual observation. CONCLUSIONS: We developed and validated a nomogram to accurately predict the risk of pathological upgrading after radical PCa surgery, which can provide accurate basis for therapeutic schedule and prognostic data of PCa patients.

White Light Afterglow in Carbon Dots Achieved via Synergy between the Room-Temperature Phosphorescence and the Delayed Fluorescence.

Carbon dot (CD) based long-lived afterglow emission materials have attracted attention in recent years, but demonstration of white-light room-temperature afterglow remains challenging, due to the difficulty of simultaneous generation of multiple long-lived excited states with distinct chromatic emission. In this work, a white-light room-temperature long-lived afterglow emission from a CD powder with a high efficiency of 5.8% and Commission International de l'Eclairage (CIE) coordinates of (0.396, 0.409) is realized. The afterglow of the CDs originates from a synergy between the phosphorescence of the carbon core and the delayed fluorescence associated with the surface CN moieties, which is accomplished by matching the singlet state of the surface groups of the CDs with the long-lived triplet state of the carbon core, resulting in an efficient energy transfer. It is demonstrated how the long-lived afterglow emission of CDs can be utilized for fabrication of white light emitting devices and in anticounterfeiting applications.

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines.

SUMMARY: The Common Workflow Language (CWL) is used to provide portable and reproducible data analysis workflows across different tools and computing environments. We have developed Rcwl, an R interface to CWL, to provide easier development, use and maintenance of CWL pipelines from within R. We have also collected more than 100 pre-built tools and pipelines in RcwlPipelines, ready to be queried and used by researchers in their own analysis. A single-cell RNA sequencing preprocessing pipeline demonstrates use of the software. AVAILABILITY AND IMPLEMENTATION: Project website: https://rcwl.org (Rcwl: https://bioconductor.org/packages/Rcwl; RcwlPipelines: https://bioconductor.org/packages/RcwlPipelines). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Kinopus chlorellivorus gen. nov., sp. nov. (Vampyrellida, Rhizaria), a New Algivorous Protist Predator Isolated from Large-Scale Outdoor Cultures of Chlorella sorokiniana.

The large-scale culture of low-cost algal biomass can be significantly affected by microbial grazing on the algae. To minimize the impact, it is necessary to manage the predators. In this study, we describe a new genus and species of vampyrellid amoeba, Kinopus chlorellivorus, which caused the loss of Chlorella sorokiniana in large-scale cultures. We assigned it to the family Leptophryidae (Vampyrellida) based on morphology and small-subunit (SSU) rRNA gene sequence comparisons. Using transmission electron microscopy, we found spherical lucent inclusions, which have not been reported for any leptophryids or other vampyrellids. The gene sequence of SSU rRNA did not match any recognized genera or species and contained four characteristic regions. K. chlorellivorus preys on algae by engulfment. Laboratory feeding experiments confirmed that its grazing rate was as high as 131 Chlorella cells day-1 individual-1. Results of prey-range experiments demonstrated that it could consume other chlorophyte microalgae (e.g., Scenedesmus, Coelastrella, and Haematococcus) but with a strong feeding ability on Chlorella spp., with ingestion rates ranging from 2.67 to 3.15 prey predator-1 h-1 and growth rates of the amoeba ranging from 0.039 to 0.045 h-1. On the basis of its high grazing ability on Chlorella, capacity to form large populations in a short period of time, and capacity to form resistant resting stages, this contaminant has the potential to cause serious problems in large-scale Chlorella culture and should be of concern to operators of algal production facilities. IMPORTANCE The vampyrellids (Vampyrellida, Rhizaria) are a major group of predatory amoebae that have attracted significant attention because of their diversity of feeding strategies. The crucial roles they play in important processes such as suppressing soil disease and controlling aquatic algae, and as microbial contaminants in outdoor large-scale algal cultures, have also received increasing attention. In this study, a new genus and species of algivorous vampyrellid amoeba, Kinopus chlorellivorus, is described as a significant grazer responsible for losses in outdoor industrial Chlorella cultures. We found that the amoeba's detrimental effects on Chlorella cultures may be related to its specific feeding characteristics. This study provides phenotypic and genetic information on a previously unknown vampyrellid, emphasizes the impact of contaminating vampyrellids in commercial microalgal cultures, and will contribute to the development of management strategies for predicting this kind of contaminant in large-scale microalgal cultivation.