Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma.

Bile cell-free DNA (cfDNA) has been reported as a promising liquid biopsy tool for cholangiocarcinoma (CCA), however, the whole-genome mutation landscape and structural variants (SVs) of bile cfDNA remains unknown. Here we performed whole-genome sequencing on bile cfDNA and analyzed the correlation between mutation characteristics of bile cfDNA and clinical prognosis. TP53 and KRAS were the most frequently mutated genes, and the RTK/RAS, homologous recombination (HR), and HIPPO were top three pathways containing most gene mutations. Ten overlapping putative driver genes were found in bile cfDNA and tumor tissue. SVs such as chromothripsis and kataegis were identified. Moreover, the hazard ratio of HR pathway mutations were 15.77 (95% CI: 1.571-158.4), patients with HR pathway mutations in bile cfDNA exhibited poorer overall survival (P = 0.0049). Our study suggests that bile cfDNA contains genome mutations and SVs, and HR pathway mutations in bile cfDNA can predict poor outcomes of CCA patients.

Identifying MiR-140-3p as a stable internal reference to normalize MicroRNA qRT-PCR levels of plasma small extracellular vesicles in lung cancer patients.

Exploration of a stably expressed gene as a reference is critical for the accurate evaluation of miRNAs isolated from small extracellular vesicles (sEVs). In this study, we analyzed small RNA sequencing on plasma sEV miRNAs in the training dataset (n = 104) and found that miR-140-3p was the most stably expressed candidate reference for sEV miRNAs. We further demonstrated that miR-140-3p expressed most stably in the validation cohort (n = 46) when compared to two other reference miRNAs, miR-451a and miR-1228-3p, and the commonly-used miRNA reference U6. Finally, we compared the capability of miR-140-3p and U6 as the internal reference for sEV miRNA expression by evaluating key miRNAs expression in lung cancer patients and found that miR-140-3p was more suitable as a sEV miRNA reference gene. Taken together, our data indicated miR-140-3p as a stable internal reference miRNA of plasma sEVs to evaluate miRNA expression profiles in lung cancer patients.

Spatiotemporal consistency analysis of cerebral small vessel disease: an rs-fMRI study.

Introduction: Cerebral small vessel disease (SVD) affects older adults, but traditional approaches have limited the understanding of the neural mechanisms of SVD. This study aimed to explore the effects of SVD on brain regions and its association with cognitive decline using the four-dimensional (spatiotemporal) consistency of local neural activity (FOCA) method. Methods: Magnetic resonance imaging data from 42 patients with SVD and 38 healthy controls (HCs) were analyzed using the FOCA values. A two-sample t test was performed to compare the differences in FOCA values in the brain between the HCs and SVD groups. Pearson correlation analysis was conducted to analyze the association of various brain regions with SVD scores. Results: The results revealed that the FOCA values in the right frontal_inf_oper, right temporal_pole_sup, and default mode network decreased, whereas those in the temporal_inf, hippocampus, basal ganglia, and cerebellum increased, in patients with SVD. Most of these varying brain regions were negatively correlated with SVD scores. Discussion: This study suggested that the FOCA approach might have the potential to provide useful insights into the understanding of the neurophysiologic mechanisms of patients with SVD.

Comparison of balanced crystalloids versus normal saline in patients with diabetic ketoacidosis: a meta-analysis of randomized controlled trials.

Purpose: The optimal resuscitative fluid for patients with diabetic ketoacidosis (DKA) remains controversial. Therefore, our objective was to assess the effect of balanced crystalloids in contrast to normal saline on clinical outcomes among patients with DKA. Methods: We searched electronic databases for randomized controlled trials comparing balanced crystalloids versus normal saline in patients with DKA, the search period was from inception through October 20th, 2023. The outcomes were the time to resolution of DKA, major adverse kidney events, post-resuscitation chloride, and incidence of hypokalemia. Results: Our meta-analysis encompassed 11 trials, incorporating a total of 753 patients with DKA. There was no significant difference between balanced crystalloids and normal saline group for the time to resolution of DKA (MD -1.49, 95%CI -4.29 to 1.31, P=0.30, I2 = 65%), major adverse kidney events (RR 0.88, 95%CI 0.58 to 1.34, P=0.56, I2 = 0%), and incidence of hypokalemia (RR 0.80, 95%CI 0.43 to 1.46, P=0.46, I2 = 56%). However, there was a significant reduction in the post-resuscitation chloride (MD -3.16, 95%CI -5.82 to -0.49, P=0.02, I2 = 73%) among patients received balanced crystalloids. Conclusion: Among patients with DKA, the use of balanced crystalloids as compared to normal saline has no effect on the time to resolution of DKA, major adverse kidney events, and incidence of hypokalemia. However, the use of balanced crystalloids could reduce the post-resuscitation chloride. Systematic review registration: https://osf.io, identifier c8f3d.

No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials.

Purpose: The optimal range of protein dosage and effect of high-dose protein on critically ill patients remain controversial. We conducted a meta-analysis to compare higher and lower doses of protein supplementation for nutritional support in critically ill patients. Methods: We searched the PubMed, Embase, Scopus, and Cochrane Library databases for randomized controlled trials that compared higher (≥1.2 g/kg per day) versus lower (<1.2 g/kg per day) doses of protein supplementation among critically ill adult patients. This search spanned from the inception of relevant databases to November 20, 2023. Our primary endpoint of interest was overall mortality, while secondary endpoints included length of stay in the intensive care unit, length of hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury. Results: Seventeen studies including 2,965 critically ill patients were included in our meta-analysis. The pooled analyses showed no significant difference in overall mortality (RR 1.03, 95%CI [0.92-1.15], P = 0.65, I2 = 0%), length of intensive care unit stay (MD 0.19, 95%CI [-0.67 to 1.04], P = 0.66, I2 = 25%), length of hospital stay (MD 0.73, 95%CI [-1.59 to 3.04], P = 0.54, I2 = 27%), duration of mechanical ventilation (MD -0.14, 95%CI [-0.83 to 0.54], P = 0.68, I2 = 8%), and incidence of acute kidney injury (RR 1.11, 95%CI [0.87-1.41], P = 0.38, I2 = 0%) between critically ill patients receiving higher or lower doses of protein supplementation. Conclusions: For critically ill patients, the protein supplementation dose had no significant effect on clinical outcomes, including overall mortality, length of intensive care unit and hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury.

Detection and characterization of pancreatic and biliary tract cancers using cell-free DNA fragmentomics.

BACKGROUND: Plasma cell-free DNA (cfDNA) fragmentomics has demonstrated significant differentiation power between cancer patients and healthy individuals, but little is known in pancreatic and biliary tract cancers. The aim of this study is to characterize the cfDNA fragmentomics in biliopancreatic cancers and develop an accurate method for cancer detection. METHODS: One hundred forty-seven patients with biliopancreatic cancers and 71 non-cancer volunteers were enrolled, including 55 patients with cholangiocarcinoma, 30 with gallbladder cancer, and 62 with pancreatic cancer. Low-coverage whole-genome sequencing (median coverage: 2.9 ×) was performed on plasma cfDNA. Three cfDNA fragmentomic features, including fragment size, end motif and nucleosome footprint, were subjected to construct a stacked machine learning model for cancer detection. Integration of carbohydrate antigen 19-9 (CA19-9) was explored to improve model performance. RESULTS: The stacked model presented robust performance for cancer detection (area under curve (AUC) of 0.978 in the training cohort, and AUC of 0.941 in the validation cohort), and remained consistent even when using extremely low-coverage sequencing depth of 0.5 × (AUC: 0.905). Besides, our method could also help differentiate biliopancreatic cancer subtypes. By integrating the stacked model and CA19-9 to generate the final detection model, a high accuracy in distinguishing biliopancreatic cancers from non-cancer samples with an AUC of 0.995 was achieved. CONCLUSIONS: Our model demonstrated ultrasensitivity of plasma cfDNA fragementomics in detecting biliopancreatic cancers, fulfilling the unmet accuracy of widely-used serum biomarker CA19-9, and provided an affordable way for accurate noninvasive biliopancreatic cancer screening in clinical practice.

Global daily mask use estimation in the pandemic and its post environmental health risks: Analysis based on a validated dynamic mathematical model.

The outbreak of the COVID-19 pandemic led to a sharp increase in disposable surgical mask usage. Discarded masks can release microplastic and cause environmental pollution. Since masks have become a daily necessity for protection against virus infections, it is necessary to review the usage and disposal of masks during the pandemic for future management. In this study, we constructed a dynamic model by introducing related parameters to estimate daily mask usage in 214 countries from January 22, 2020 to July 31, 2022. And we validated the accuracy of our model by establishing a dataset based on published survey data. Our results show that the cumulative mask usage has reached 800 billion worldwide, and the microplastics released from discarded masks due to mismanagement account for 3.27% of global marine microplastic emissions in this period. Furthermore, we illustrated the response relationship between mask usage and the infection rates. We found a marginally significant negative correlation existing between the mean daily per capita mask usage and the rate of cumulative confirmed cases within the range of 25% to 50%. This indicates that if the rate reaches the specified threshold, the preventive effect of masks may become evident.

The Association Between Modified Albumin-Bilirubin (mALBI) and Survival in Advanced Non-small Cell Lung Cancer Patients Treated With Immunotherapy.

OBJECTIVE: This study aimed to assess the clinical value of the modified albumin-bilirubin (mALBI) grade in predicting the survival of patients with advanced non-small cell lung cancer (NSCLC) treated with immunotherapy. METHODS: We conducted a retrospective cohort study of patients with advanced NSCLC who received immune checkpoint inhibitors (ICIs) from January 2020 to May 2022. The primary endpoints were overall survival (OS), treatment response, and the association between different mALBI grades and survival. RESULTS: In these 67 patients, 85.1% (57/67) were male, and the median age was 63 years. The patients with mALBI grades 1 and 2a at baseline had a median OS of 12.83 months (95% CI: 9.4 to 16.27 months), whereas it was 3.2 months (95% CI: NA to 11.59 months) for patients with mALBI grades 2b and 3. The OS for patients with dynamic mALBI grades 1 and 2a was 13.27 months (95% CI: 8.72 to 17.81 months), significantly longer than five months (95% CI: 2.47 to 7.53 months) for dynamic mALBI grades 2b and 3 patients (p<0.01).  Conclusion: In conclusion, mALBI grade may be a potential dynamic biomarker for predicting the prognosis in advanced NSCLC patients treated with immunotherapy.

Multiregion WES of metastatic pancreatic neuroendocrine tumors revealed heterogeneity in genomic alterations, immune microenvironment and evolutionary patterns.

Pancreatic neuroendocrine tumors (PanNETs), though uncommon, have a high likelihood of spreading to other body parts. Previously, the genetic diversity and evolutionary patterns in metastatic PanNETs were not well understood. To investigate this, we performed multiregion sampling whole-exome sequencing (MRS-WES) on samples from 10 patients who had not received prior treatment for metastatic PanNETs. This included 29 primary tumor samples, 31 lymph node metastases, and 15 liver metastases. We used the MSK-MET dataset for survival analysis and validation of our findings. Our research indicates that mutations in the MEN1/DAXX genes might trigger the early stages of PanNET development. We categorized the patients based on the presence (MEN1/DAXXmut, n = 7) or absence (MEN1/DAXXwild, n = 3) of these mutations. Notable differences were observed between the two groups in terms of genetic alterations and clinically relevant mutations, confirmed using the MSK-MET dataset. Notably, patients with mutations in MEN1/DAXX/ATRX genes had a significantly longer median overall survival compared to those without these mutations (median not reached vs. 43.63 months, p = 0.047). Multiplex immunohistochemistry (mIHC) analysis showed a more prominent immunosuppressive environment in metastatic tumors, especially in patients with MEN1/DAXX mutations. These findings imply that MEN1/DAXX mutations lead PanNETs through a unique evolutionary path. The disease's progression pattern indicates that PanNETs can spread early, even before clinical detection, highlighting the importance of identifying biomarkers related to metastasis to guide personalized treatment strategies.

Long non-coding RNA Linc00657 up-regulates Skp2 to promote the progression of cervical cancer through lipid reprogramming and regulation of immune microenvironment.

More and more evidence shows that long non-coding RNA (lncRNA) plays an important role in the biological behavior of many kinds of malignant tumors, but the specific function of lncRNA Linc00657 in cervical cancer is still unknown. The purpose of this study is to explore the effect of Linc00657 on the malignant progression of cervical cancer and its potential mechanism. In two kinds of cervical cancer cell lines and normal cervical epithelial cells, qRT-PCR showed increased expression of Linc00657 in cervical cancer cells. Through MTT, clone formation test, flow cytometry, wound healing test and Transwell test, it has been found that overexpression of Linc00657 could promote the proliferation,migration and invasion of cervical cancer cells，and inhibit apoptosis. Through the StarBase database, it was found that there may be a mutual regulatory relationship between Linc00657 and Skp2, and Skp2 may be the downstream target of Linc00657. QRT-PCR detection confirmed that the expression of Skp2 was increased in cervical cancer cells with overexpression of Linc00657. TIMER2 database found that Skp2 was associated with lipid metabolic enzymes and immune cell infiltration. It was found that Linc00657 knockdown inhibited tumor growth and metastasis and inhibited the expression of Skp2 in vivo. In short, our research shows that Linc00657 has carcinogenic properties in cervical cancer, and LINC00657 promotes the occurrence of cervical cancer by up-regulating the expression of Skp2. We predict that Linc00657/mir30s/Skp2 axis plays a role in the malignant progression of cervical cancer. In addition, Skp2 may participate in cancer immune response and promote lymph node metastasis of cervical cancer through lipid reprogramming. These findings also provide promising targets for the diagnosis and treatment of cervical cancer.

Microbial resistance and resilience to drought and rewetting modulate soil N2O emissions with different fertilizers.

Future climate models indicate an enhanced severity of regional drought and frequent rewetting events, which may cause cascading impacts on soil nitrogen cycle and nitrous oxide (N2O) emissions, but the underlying microbial mechanism remains largely unknown. Here we report an incubation study that examined the impacts of soil moisture status and nitrification inhibitor (DCD) on the N2O-producers and N2O-reducers following the application of urea and composted swine manure in an acid soil. The soil moisture treatments included 100 % water-holding capacity (WHC) (wetting, 35.3 % gravimetric soil water content), 40 % WHC (drought, 7 % gravimetric soil water content), and 40 % to 100 % WHC (rewetting). The results showed that N2O emissions were significantly decreased under drought conditions and were significantly increased after rewetting. The resistance of ammonia-oxidizing bacteria and nosZII, which was inhibited by urea or manure application, modulated N2O emissions under drought conditions. The resilience of the functional guilds modulated their dominant role in N2O emissions with rewetting. Ammonia-oxidizing bacteria, nirS-type denitrifying bacteria and nosZI showed significant resilience in response to rewetting. Significant negative relationships were observed between N2O emissions and nosZII clade under wetting condition and between N2O emissions and nosZI clade after rewetting. Our results highlighted the importance of microbial resistance and resilience in modulating N2O emissions, which help to better understand the dominant way of N2O emissions, and consequently make efficient mitigation strategies under the global climate change.

Genetic Intratumor Heterogeneity Remodels the Immune Microenvironment and Induces Immune Evasion in Brain Metastasis of Lung Cancer.

INTRODUCTION: Brain metastasis, with the highest incidence in patients with lung cancer, significantly worsens prognosis and poses challenges to clinical management. To date, how brain metastasis evades immune elimination remains unknown. METHODS: Whole-exome sequencing and RNA sequencing were performed on 30 matched brain metastasis, primary lung adenocarcinoma, and normal tissues. Data from The Cancer Genome Atlas primary lung adenocarcinoma cohort, including multiplex immunofluorescence, were used to support the findings of bioinformatics analysis. RESULTS: Our study highlights the key role of intratumor heterogeneity of genomic alterations in the metastasis process, mainly caused by homologous recombination deficiency or other somatic copy number alteration-associated mutation mechanisms, leading to increased genomic instability and genomic complexity. We further proposed a selection model of brain metastatic evolution in which intratumor heterogeneity drives immune remodeling, leading to immune escape through different mechanisms under local immune pressure. CONCLUSIONS: Our findings provide novel insights into the metastatic process and immune escape mechanisms of brain metastasis and pave the way for precise immunotherapeutic strategies for patients with lung cancer with brain metastasis.

Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma.

Cholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation patterns in each cell line. In addition, specific expression patterns with distinct biological functions and pathways involved were also observed in the PDPCs at the transcriptomic level. Furthermore, the drug-sensitivity results revealed that the PDPCs exhibited different responses to the six commonly used compounds. Our findings indicate that the established PDPCs can serve as novel in vitro reliable models to provide a crucial molecular basis for improving the understanding of tumorigenesis and its treatment.

The effect of intermittent versus continuous enteral feeding for critically ill patients: a meta-analysis of randomized controlled trials.

Objectives: The appropriate strategy for enteral feeding in critically ill patients still remains controversial. Therefore, we conducted this meta-analysis to compare the effect of intermittent versus continuous enteral feeding method for critically ill patients. Methods: Electronic databases including PubMed, Embase, Scopus, and Cochrane Library were searched up to April 10th, 2023 for randomized controlled trials evaluating the effect of intermittent versus continuous enteral feeding for critically ill patients. The primary outcomes were feeding intolerances, including diarrhea, vomiting, distension, constipation, gastric retention, and aspiration pneumonia. The secondary outcomes were mortality in intensive care unit (ICU), length of stay in ICU, and achievement of nutritional goal. Results: Thirteen studies with a total of 884 patients were analyzed in this meta-analysis. Overall, the use of intermittent enteral feeding was associated with higher incidence of diarrhea (OR 1.66, 95%CI 1.13 to 2.43, I2 = 16%) and distension (OR 2.29, 95%CI 1.16 to 4.51, I2 = 0%), lower incidence of constipation (OR 0.58, 95%CI 0.37 to 0.90, I2 = 0%), and longer length of ICU stay (MD 1.09, 95%CI 0.53 to 1.64, I2 = 0%). Moreover, no significant difference was identified for other outcome measures. Conclusion: In critically ill patients, the implementation of intermittent enteral feeding was associated with higher incidence of diarrhea and distension, longer length of ICU stay, but lower occurrence of constipation. Nevertheless, the absence of sufficient high-quality randomized controlled clinical trials precludes any definitive conclusions regarding the optimal approach to enteral feeding in this population. There is an imperative need for more studies to further assess the efficacy of the two enteral feeding strategies.

Coupling of soil methane emissions at different depths under typical coastal wetland vegetation types.

As an important source of atmospheric methane, methane emissions from coastal wetlands are affected by many factors. However, the methane emission process and interrelated coupling mechanisms in coastal wetland soils of a variety of environments remain unclear owing to complex interactions between intensified anthropogenic activities and climate change in recent years. In this study, we investigated methane cycling processes and the response mechanisms of environmental and microbial factors in soils at different depths under four typical coastal wetland vegetation types of the Yellow River Delta, China, using laboratory culture and molecular biology techniques. Our results show that methane generation pathways differed among the different soil layers, and that the methane emission process has a special response to soil N compounds (NO3-, NH4+). We found that nitrogen can indirectly affect methane emission by impacting key physicochemical properties (pH, oxidation reduction potential, etc.) and some functional communities (mcrA, ANME-2d, sulfate-reducing bacteria (SRB), narG, nosZII). Methane production processes in shallow soils compete closely with sulfate reduction processes, while methane emissions facilitated in deeper soils due to denitrification processes. We believe that our results provide a reference for future research and wetland management practices that seek to mitigate the global greenhouse effect and climate change.

Interleukin-33 Potentiates TGF-ß Signaling to Regulate Intestinal Stem Cell Regeneration After Radiation Injury.

Epithelial regeneration is critical for barrier maintenance and organ function after intestinal radiation injury. Accumulating evidence indicates that the interleukin family members play critical roles in intestinal stem-cell-mediated epithelial regeneration. However, little is known about the relationship between interleukin 33 (IL-33)/ST2 axis and intestinal regeneration after radiation injury. We demonstrate here that IL-33 expression significantly increased after radiation treatment. Deficiency of IL-33/ST2 promotes intestinal epithelial regeneration, resulting in a reduction of mortality during radiation-induced intestine injury. Using ex vivo organoid cultures, we show that recombinant IL-33 promotes intestinal stem cell differentiation. Mechanistically, the effects of IL-33 were mediated by activation of transforming growth factor-ß signaling. Our findings reveal a fundamental mechanism by which IL-33 is able to regulate the intestinal crypt regeneration after tissue damage.

Polypyrrole modification on BiVO4 for photothermal-assisted photoelectrochemical water oxidation.

The bismuth vanadate (BiVO4) photoanode receives extensive attention in photoelectrochemical (PEC) water splitting. However, the high charge recombination rate, low electronic conductivity, and sluggish electrode kinetics have inhibited the PEC performance. Increasing the reaction temperature for water oxidation is an effective way to enhance the carrier kinetics of BiVO4. Herein, a polypyrrole (PPy) layer was coated on the BiVO4 film. The PPy layer could harvest the near-infrared light to elevate the temperature of the BiVO4 photoelectrode and further improve charge separation and injection efficiencies. In addition, the conductive polymer PPy layer acted as an effective charge transfer channel to facilitate photogenerated holes moving from BiVO4 to the electrode/electrolyte interface. Therefore, PPy modification led to a significantly improved water oxidation property. After loading the cobalt-phosphate co-catalyst, the photocurrent density reached 3.64 mA cm-2 at 1.23 V vs the reversible hydrogen electrode, corresponding to an incident photon-to-current conversion efficiency of 63% at 430 nm. This work provided an effective strategy for designing a photothermal material assisted photoelectrode for efficient water splitting.

Soil nitrogen content and key functional microorganisms influence the response of wetland anaerobic oxidation of methane to trivalent iron input.

Trivalent iron (Fe3+)-dependent anaerobic oxidation of methane (Fe-AOM), which is mediated by metal-reducing bacteria, is widely recognized as a major sink for the greenhouse gas methane (CH4), and is a key driver of the carbon (C) biogeochemical cycle. However, the effect of Fe3+ addition on AOM in the present investigation is still ambiguous, and the mechanism is vague. In this study, we investigated the mechanism of changes in AOM response to Fe3+ input at different wetlands by using laboratory incubation methods combined with molecular biology techniques. Results indicated that Fe3+ input did not always lead to promoted AOM rates, which may be mediated by complex environmental factors, while lower soil total nitrogen (TN) had a positive effect on the response of AOM subjected to Fe3+ input. Notably, the promoted response of AOM was regulated by higher soil microbial diversity, of which the Shannon index was a key indicator leading to variation in the AOM response. Additionally, several biomarkers, including Planctomycetota and Burkholderiaceae, were key microorganisms responsible for alterations in AOM response. Our results suggest that the capacity of Fe3+ cycling-mediated AOM may gradually decrease in light of increasing anthropogenic N and Fe inputs to global estuarine wetlands, while its reaction processes will become more complex and more strongly coupled with multiple environmental factors. This finding contributes to the enhanced understanding and prediction of the wetland CH4-related C with Fe cycles, as well as provides theoretical support for the underlying mechanisms.