Arsenic Reduces Methane Emissions from Paddy Soils: Insights from Continental Investigation and Laboratory Incubations.

Arsenic (As) contamination and methane (CH4) emissions co-occur in rice paddies. However, how As impacts CH4 production, oxidation, and emission dynamics is unknown. Here, we investigated the abundances and activities of CH4-cycling microbes from 132 paddy soils with different As concentrations across continental China using metagenomics and the reverse transcription polymerase chain reaction. Our results revealed that As was a crucial factor affecting the abundance and distribution patterns of the mcrA gene, which is responsible for CH4 production and anaerobic CH4 oxidation. Laboratory incubation experiments showed that adding 30 mg kg-1 arsenate increased 13CO2 production by 10-fold, ultimately decreasing CH4 emissions by 68.5%. The inhibition of CH4 emissions by As was induced through three aspects: (1) the toxicity of As decreased the abundance and activity of the methanogens; (2) the adaptability and response of methanotrophs to As is beneficial for CH4 oxidation under As stress; and (3) the more robust arsenate reduction would anaerobically consume more CH4 in paddies. Additionally, significant positive correlations were observed between arsC and pmoA gene abundance in both the observational study and incubation experiment. These findings enhance our understanding of the mechanisms underlying the interactions between As and CH4 cycling in soils.

Bone marrow stromal and anterior cruciate ligament remnant cell co-culture-derived extracellular vesicles promote cell activity in both cell types.

The significance of anterior cruciate ligament (ACL) remnants during reconstruction remains unclear. Co-culturing ACL remnant cells and bone marrow stromal cells (BMSCs) may reduce apoptosis and enhance hamstring tendon activity. This study investigated whether extracellular vesicles (EVs), which facilitate cell-cell interactions, act as the active components, improving graft maturation in this co-culture. The effects of EVs on cell viability, proliferation, migration and gene expression in the rabbit ACL remnant cells and BMSCs were assessed using control (BMSC-only culture), co-culture (ACL remnant cells and BMSCs, CM) and co-culture without EVs (CM ∆ EVs) media. EVs were isolated from control (BMSC-EV) and co-culture (CM-EV) media and characterized. CM significantly enhanced the proliferation, migration and expression of transforming growth factor (TGF-ß)-, vascular endothelial growth factor (VEGF)-, collagen synthesis- and tenogenesis-related genes. However, CM-induced effects were reversed by the CM ∆ EVs treatment. CM-EV treatment exhibited higher potential to enhance proliferation, migration and gene expression in the ACL remnant cells and BMSCs than BMSC-EV and non-EV treatments. In conclusion, EVs, secreted under the coexistence of ACL remnant cells and BMSCs, primarily increase the cell viability, proliferation, migration and gene expression of collagen synthesis-, TGF-ß-, VEGF- and tenogenesis-related genes in both cell types.

Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.

In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate structural and dynamic characteristics of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). Unlike crystallographic beamlines and their role in streamlining acquisition of structures for folded proteins, an integrated experimental and computational approach aimed at IDPs/IDRs has emerged. In this Perspective we aim to provide a robust overview of current computational tools for IDPs and IDRs, and most recently their complexes and phase separated states, including statistical models, physics-based approaches, and machine learning methods that permit structural ensemble generation and validation against many solution experimental data types.

Expressional respones of hsp70 genes against abiotic and entomopathgenic stresses in four different noctuid larval species (Lepidoptera: Noctidae).

Heat shock proteins (Hsps) are stress response proteins. In a previous study, host larval Hsp70s were identified as the structural proteins of virions of Heliothis virescens ascovirus 3h (HvAV-3h), an insect virus that mainly infects noctuid larvae. To investigate the response of hsp70s of healthy Mythimna separata, Spodoptera exigua, Spodoptera frugiperda, and Spodoptera litura larvae to various abiotic or entomopathogenic stresses, quantitative PCR was used to detect larval hsp70s expression patterns. Results showed distinct expression patterns of hsp70s in response to different abiotic stresses. Notably, Mshsp70 expression pattern resembled Slhsp70 under most treatments. In healthy larvae, no tissue tropism was observed concerning the relative expression of Mshsp70, Sfhsp70, and Slhsp70. After infection with HvAV-3h, the expression of hsp70s in all dissected tissues of all tested larval species increased. Significant differences were found in the fat bodies of M. separata, S. exigua, and S. litura as well as in the hemolymph of S. exigua and S. litura. Subsequent silencing of Slhsp70, resulted in a significant decrease in DNA replication levels of HvAV-3h in S. litura larvae at 24 and 72 h post RNA interference, indicating that Slhsp70 is necessary for DNA replication in HvAV-3h. These data can provide references for the studying on the stress response of noctuid larvae to different environmental factors.

Nomogram for assistant diagnosing acute suppurative cholangitis: a case-control study.

BACKGROUND: Acute suppurative cholangitis (ASC) lacks sensitive and specific preoperative diagnostic criteria. Some researchers suggest treating ASC as severe cholangitis. This study aimed to explore the relationship between the Tokyo Guidelines 2018 (TG18) grading system for acute cholangitis (AC) and the diagnosis of acute suppurative cholangitis (ASC), searching for independent risk factors of ASC and develop a nomogram to discriminate ASC from acute nonsuppurative cholangitis (ANSC) accurately. METHODS: After applying the inclusion and exclusion criteria, 401 patients with acute cholangitis (AC) were retrospectively analyzed at Nanjing First Hospital between January 2015 and June 2023. SPSS version 27.0 and R studio software were used to analyze data obtained from medical records. The results were validated in a prospective cohort of 82 AC patients diagnosed at Nanjing First Hospital between July 2023 and February 2024. RESULTS: Among the 401 patients, 102 had suppurative bile (the ASC group; AC grade I: 40 [39.2%], AC grade II: 27 [26.5%], AC grade III: 35 [34.3%]), whereas 299 did not have (the ANSC group; AC grade I: 157 [52.5%], AC grade II: 92 [30.8%], AC grade III: 50 [16.7%]). The specificity of ASC for diagnosing moderate-to-severe cholangitis is 79.7%. Multivariate logistic regression analysis identified concurrent cholecystitis, CRP, PCT, TBA, and bile duct diameter as independent risk factors for suppurative bile, and all of these factors were included in the nomogram. The calibration curve exhibited consistency between the nomogram and the actual observation, and the area under the curve was 0.875 (95% confidence interval: 0.835-0.915), sensitivity was 86.6%, and specificity was 75.5%. CONCLUSION: Suppurative bile is a specific indicator for diagnosing moderate-to-severe cholangitis. However, diagnosing ASC with AC grade II and AC grade III has the risk of missed diagnosis as the sensitivity is only 60.8%. To improve the diagnostic rate of ASC, this study identified concurrent cholecystitis, CRP, PCT, TBA, and preoperative bile duct diameter as independent risk factors for ASC, and a nomogram was developed to help physicians recognize patients with ASC.

Pediatric calcaneal osteomyelitis: an analysis of literature-reported 128 cases.

BACKGROUND: Calcaneal osteomyelitis (CO) poses a formidable challenge in treatment due to the distinct anatomical structure and functional properties of the calcaneus. The present study endeavors to furnish a thorough and comprehensive understanding of the clinical manifestations, therapeutic strategies, and therapeutic outcomes pertaining to pediatric calcaneal osteomyelitis (PCO) by conducting a meticulous synthesis and analysis of cases reported in the literature. METHODS: A systematic search of the PubMed, Embase, and Cochrane Library databases was conducted to identify English-language studies analyzing PCO between 2000 and 2021. The quality of the included studies was assessed using the National Institutes of Health (NIH) assessment scale. Effective data were extracted and analyzed. RESULTS: A total of 42 studies, encompassing 128 patients, fulfilled the established inclusion criteria. The gender distribution revealed a male-to-female ratio of 2:1 (81 boys and 40 girls). The median age at the time of diagnosis was 8 years, while the median duration of symptoms was 0.6 month. Trauma emerged as the primary etiology (41 cases, 54%), and limited activity was the most prevalent symptom (68 cases). The positive rate for pathogen culture was 75.4% (49/65), with Staphylococcus aureus being the most commonly isolated pathogen (28 cases, 57.1%). Surgical intervention was performed in 51% (64/126) of the patients, with debridement serving as the primary surgical strategy. The rate of infection recurrence was 6.8% (8/118), and the risk of below-knee amputation was 0.8% (1/124). CONCLUSIONS: PCO occurred more frequently in male patients, with trauma being the primary underlying cause and Staphylococcus aureus being the most prevalent bacterial pathogen isolated. Over half of the patients underwent surgical intervention. Nonetheless, it is imperative that treatment strategies undergo further refinement, as approximately 7% of patients experienced infection recurrence.

Single nucleotide polymorphisms in the development of osteomyelitis and prosthetic joint infection: a narrative review.

Currently, despite advancements in diagnostic and therapeutic modalities, osteomyelitis and prosthetic joint infection (PJI) continue to pose significant challenges for orthopaedic surgeons. These challenges are primarily attributed to the high degree of heterogeneity exhibited by these disorders, which are influenced by a combination of environmental and host factors. Recent research efforts have delved into the pathogenesis of osteomyelitis and PJI by investigating single nucleotide polymorphisms (SNPs). This review comprehensively summarizes the current evidence regarding the associations between SNPs and the predisposition to osteomyelitis and PJI across diverse populations. The findings suggest potential linkages between SNPs in genes such as IL-1, IL-6, IFN-γ, TNF-α, VDR, tPA, CTSG, COX-2, MMP1, SLC11A1, Bax, NOS2, and NLRP3 with the development of osteomyelitis. Furthermore, SNPs in genes like IL-1, IL-6, TNF-α, MBL, OPG, RANK, and GCSFR are implicated in susceptibility to PJI. However, it is noted that most of these studies are single-center reports, lacking in-depth mechanistic research. To gain a more profound understanding of the roles played by various SNPs in the development of osteomyelitis and PJI, future multi-center studies and fundamental investigations are deemed necessary.

Coronary Computed Tomography Angiography Using an Optimal Acquisition Time Window Based on Heart Rate Determined During Breath-Holding Following Free Breathing.

OBJECTIVES: To compare the image quality and radiation dose in coronary computed tomography angiography (CCTA) based on different acquisition time windows corresponding to the heart rate of breath-holding after free breathing. METHODS: Two hundred patients who underwent CCTA with a basal heart rate between 70 and 85 beats/min were divided into groups A and B, with 100 patients in each group. Patients in groups A and B were scanned with the acquisition time window corresponding to the heart rate determined during a breath hold obtained after free breathing and the basal heart rate during free breathing, respectively. Computed tomography (CT) attenuation values of the coronary artery, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were calculated. The subjective image scores of the groups were assessed blindly by 2 experienced physicians using a 4-point system, and score consistency was compared using the κ test. The volume CT dose index and dose-length product were recorded for each patient, and the effective dose (ED) was calculated. The Kruskal-Wallis H test was performed to evaluate differences in age, heart rate, and body mass index. A χ2 test was used to evaluate sex differences. An independent-sample t test was employed to compare objective and subjective data such as dose-length product, volume CT dose index, ED, SNR, CNR, and averaged subjective assessment scores. Statistical significance was set at P < 0.05. RESULTS: No statistically significant differences occurred in sex, age, or body mass index between patients in group A and group B (all P > 0.05). No significant differences occurred in the mean CT values, mean SNR values, mean CNR values, or mean subjective scores of CCTA images between the patients in groups A and B (P > 0.05). The ED values of the patients in group A were 52.93% lower than those in group B (P < 0.001). CONCLUSION: The radiation dose in CCTA examinations can be significantly reduced while maintaining image quality by narrowing the acquisition time window for breath-holding after free breathing.

Virgibacillus tibetensis sp. nov., isolated from salt lake on the Tibetan plateau of China.

One bacterial strain, designated as C22-A2T, was isolated from Lake LungmuCo in Tibet. Cells of strain C22-A2T were long rod-shaped, Gram-stain-negative, non-spore-forming, with positive catalase and oxidase activity. Optimal growth occurred at 20-25 °C, pH 8.0 and with 3.0-7.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene and whole genome sequences revealed that strain C22-A2T belonged to the genus Virgibacillus, showing the highest 16S rRNA gene similarity to Virgibacillus halodenitrificans DSM 10037T (97.6%). The average nucleotide identity values between strain C22-A2T and the type strains of related species in the genus Virgibacillus were less than 74.4% and the digital DNA-DNA hybridization values were less than 20.2%, both below the species delineation thresholds of 95 and 70% respectively. The genome analysis revealed that strain C22-A2T harboured genes responsible for osmotic and oxidative stress, enabling it to adapt to its surrounding environment. In terms of biochemical and physiological characteristics, strain C22-A2T shared similar characteristics with the genus Virgibacillus, including the predominant cellular fatty acid anteiso-C15 : 0, the major respiratory quinone MK-7, as well as the polar lipids phosphatidylglycerol and diphosphatidylglycerol. Based on the comprehensive analysis of phylogenetic, phylogenomic, morphological, physiological and biochemical characteristics, strain C22-A2T is proposed to represent a novel species of the genus Virgibacillus, named as Virgibacillus tibetensis sp. nov. (=CGMCC 1.19202T=KCTC 43426T).

Efficient CRISPR-mediated genome editing can be initiated by embryonic injection but not by ovarian delivery in the beetle Tribolium castaneum.

The clustered regularly interspaced small palindromic repeats (CRISPR) / CRISPR-associated nuclease 9 (Cas9)-mediated gene editing technology has revolutionized the study of fundamental biological questions in various insects. Diverse approaches have been developed to deliver the single-guide RNA (sgRNA) and Cas9 to the nucleus of insect embryos or oocytes to achieve gene editing, including the predominant embryonic injection methods and alternative protocols through parental ovary delivery. However, a systematic comparative study of these approaches is limited, especially within a given insect. Here, we focused on revealing the detailed differences in CRISPR/Cas9-mediated gene editing between the embryo and ovary delivery methods in the beetle Tribolium castaneum, using the cardinal and tyrosine hydroxylase (TH) as reporter genes. We demonstrated that both genes could be efficiently edited by delivering Cas9/sgRNA ribonucleoproteins to the embryos by microinjection, leading to the mutant phenotypes and indels in the target gene sites. Next, the Cas9/sgRNA complex, coupled with a nanocarrier called Branched Amphiphilic Peptide Capsules (BAPC), were delivered to the ovaries of parental females to examine the efficacy of BAPC-mediated gene editing. Although we observed that a small number of beetles' progeny targeting the cardinal exhibited the expected white-eye phenotype, unexpectedly, no target DNA indels were found following subsequent sequencing analysis. In addition, we adopted a novel approach termed "direct parental" CRISPR (DIPA-CRISPR). However, we still failed to find gene-editing events in the cardinal or TH gene-targeted insects. Our results indicate that the conventional embryonic injection of CRISPR is an effective method to initiate genome editing in T. castaneum. However, it is inefficient by the parental ovary delivery approach.

Prediction model establishment and validation for enteral nutrition aspiration during hospitalization in patients with acute pancreatitis.

BACKGROUND: Acute pancreatitis (AP) is a disease caused by abnormal activation of pancreatic enzymes and can lead to self-digestion of pancreatic tissues and dysfunction of other organs. Enteral nutrition plays a vital role in the treatment of AP because it can meet the nutritional needs of patients, promote the recovery of intestinal function, and maintain the barrier and immune functions of the intestine. However, the risk of aspiration during enteral nutrition is high; once aspiration occurs, it may cause serious complications, such as aspiration pneumonia, and suffocation, posing a threat to the patient's life. This study aims to establish and validate a prediction model for enteral nutrition aspiration during hospitalization in patients with AP. AIM: To establish and validate a predictive model for enteral nutrition aspiration during hospitalization in patients with AP. METHODS: A retrospective review was conducted on 200 patients with AP admitted to Chengdu Shangjin Nanfu Hospital, West China Hospital of Sichuan University from January 2020 to February 2024. Clinical data were collected from the electronic medical record system. Patients were randomly divided into a validation group (n = 40) and a modeling group (n = 160) in a 1:4 ratio, matched with 200 patients from the same time period. The modeling group was further categorized into an aspiration group (n = 25) and a non-aspiration group (n = 175) based on the occurrence of enteral nutrition aspiration during hospitalization. Univariate and multivariate logistic regression analyses were performed to identify factors influencing enteral nutrition aspiration in patients with AP during hospitalization. A prediction model for enteral nutrition aspiration during hospitalization was constructed, and calibration curves were used for validation. Receiver operating characteristic curve analysis was conducted to evaluate the predictive value of the model. RESULTS: There was no statistically significant difference in general data between the validation and modeling groups (P > 0.05). The comparison of age, gender, body mass index, smoking history, hypertension history, and diabetes history showed no statistically significant difference between the two groups (P > 0.05). However, patient position, consciousness status, nutritional risk, Acute Physiology and Chronic Health Evaluation (APACHE-II) score, and length of nasogastric tube placement showed statistically significant differences (P < 0.05) between the two groups. Multivariate logistic regression analysis showed that patient position, consciousness status, nutritional risk, APACHE-II score, and length of nasogastric tube placement were independent factors influencing enteral nutrition aspiration in patients with AP during hospitalization (P < 0.05). These factors were incorporated into the prediction model, which showed good consistency between the predicted and actual risks, as indicated by calibration curves with slopes close to 1 in the training and validation sets. Receiver operating characteristic analysis revealed an area under the curve (AUC) of 0.926 (95%CI: 0.8889-0.9675) in the training set. The optimal cutoff value is 0.73, with a sensitivity of 88.4 and specificity of 85.2. In the validation set, the AUC of the model for predicting enteral nutrition aspiration in patients with AP patients during hospitalization was 0.902, with a standard error of 0.040 (95%CI: 0.8284-0.9858), and the best cutoff value was 0.73, with a sensitivity of 91.9 and specificity of 81.8. CONCLUSION: A prediction model for enteral nutrition aspiration during hospitalization in patients with AP was established and demonstrated high predictive value. Further clinical application of the model is warranted.

Establishment of predictive models and determinants of preoperative gastric retention in endoscopic retrograde cholangiopancreatography.

BACKGROUND: Study on influencing factors of gastric retention before endoscopic retrograde cholangiopancreatography (ERCP) background: With the wide application of ERCP, the risk of preoperative gastric retention affects the smooth progress of the operation. The study found that female, biliary and pancreatic malignant tumor, digestive tract obstruction and other factors are closely related to gastric retention, so the establishment of predictive model is very important to reduce the risk of operation. AIM: To analyze the factors influencing preoperative gastric retention in ERCP and establish a predictive model. METHODS: A retrospective analysis was conducted on 190 patients admitted to our hospital for ERCP preparation between January 2020 and February 2024. Patient baseline clinical data were collected using an electronic medical record system. Patients were randomly matched in a 1:4 ratio with data from 190 patients during the same period to establish a validation group (n = 38) and a modeling group (n = 152). Patients in the modeling group were divided into the gastric retention group (n = 52) and non-gastric retention group (n = 100) based on whether gastric retention occurred preoperatively. General data of patients in the validation group and modeling group were compared. Univariate and multivariate logistic regression analyses were performed to identify factors influencing preoperative gastric retention in ERCP patients. A predictive model for preoperative gastric retention in ERCP patients was constructed, and calibration curves were used for validation. The receiver operating characteristic (ROC) curve was analyzed to evaluate the predictive value of the model. RESULTS: We found no statistically significant difference in general data between the validation group and modeling group (P > 0.05). The comparison of age, body mass index, hypertension, and diabetes between the two groups showed no statistically significant difference (P > 0.05). However, we noted statistically significant differences in gender, primary disease, jaundice, opioid use, and gastrointestinal obstruction between the two groups (P < 0.05). Multivariate logistic regression analysis showed that gender, primary disease, jaundice, opioid use, and gastrointestinal obstruction were independent factors influencing preoperative gastric retention in ERCP patients (P < 0.05). The results of logistic regression analysis revealed that gender, primary disease, jaundice, opioid use, and gastrointestinal obstruction were included in the predictive model for preoperative gastric retention in ERCP patients. The calibration curves in the training set and validation set showed a slope close to 1, indicating good consistency between the predicted risk and actual risk. The ROC analysis results showed that the area under the curve (AUC) of the predictive model for preoperative gastric retention in ERCP patients in the training set was 0.901 with a standard error of 0.023 (95%CI: 0.8264-0.9567), and the optimal cutoff value was 0.71, with a sensitivity of 87.5 and specificity of 84.2. In the validation set, the AUC of the predictive model was 0.842 with a standard error of 0.013 (95%CI: 0.8061-0.9216), and the optimal cutoff value was 0.56, with a sensitivity of 56.2 and specificity of 100.0. CONCLUSION: Gender, primary disease, jaundice, opioid use, and gastrointestinal obstruction are factors influencing preoperative gastric retention in ERCP patients. A predictive model established based on these factors has high predictive value.

Multi-dimensional signals coupling of simultaneous acquisition stripping current with laser-induced breakdown spectroscopy for accurate analysis of Cd(II) in coexisting Cu(II).

BACKGROUND: Despite significant advancements in detecting Cd(II) using nanomaterials-modified sensitive interfaces, most detection methods rely solely on a single electrochemical stripping current to indicate concentration. This approach often overlooks potential inaccuracies caused by interference from coexisting ions. Therefore, establishing multi-dimensional signals that accurately reflect Cd(II) concentration in solution is crucial. RESULTS: In this study, we developed a system integrating concentration, electrochemical stripping current, and laser-induced breakdown spectroscopy (LIBS) characteristic peak intensity through in-situ laser-induced breakdown spectroscopy and electrochemical integrated devices. By simultaneously acquiring multi-dimensional signals to dynamically track the electrochemical deposition and stripping processes, we observed that replacement reactions occur between Cu(II) and Cd(II) on the surface of Ru-doped MoS2 modified carbon paper electrodes (Ru-MoS2/CP). These reactions facilitate the oxidation of Cd(0) to Cd(II) during the stripping process, significantly increasing the currents of Cd(II). Remarkably, the ingenious design of the Ru-MoS2 sensitive interface allowed for the undisturbed deposition of Cu(II) and Cd(II) during the electrochemical deposition process. Consequently, our in-situ integrated device achieved accurate detection of Cd(II) in complex environments, boasting a detection sensitivity of 8606.5 counts µM⁻1. SIGNIFICANCE: By coupling multi-dimensional signals from stripping current and LIBS spectra, we revealed the interference process between Cu(II) and Cd(II), providing valuable insights for accurate electrochemical analysis of heavy metal ions in complex water environments.

Vascular wall microenvironment: Endothelial cells original exosomes mediated melatonin-suppressed vascular calcification and vascular ageing in a m6A methylation dependent manner.

Vascular calcification and vascular ageing are "silent" diseases but are highly prevalent in patients with end stage renal failure and type 2 diabetes, as well as in the ageing population. Melatonin (MT) has been shown to induce cardiovascular protection effects. However, the role of MT on vascular calcification and ageing has not been well-identified. In this study, the aortic transcriptional landscape revealed clues for MT related cell-to-cell communication between endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) in vascular calcification and vascular ageing. Furthermore, we elucidated that it was exosomes that participate in the information transportation from ECs to VSMCs. The exosomes secreted from melatonin-treated ECs (MT-ECs-Exos) inhibited calcification and senescence of VSMCs. Mechanistically, miR-302d-5p was highly enriched in MT-ECs-Exos, while depletion of miR-302d-5p blocked the ability of MT-ECs-Exos to suppress VSMC calcification and senescence. Notably, Wnt3 was a bona fide target of miR-302d-5p and modulated VSMC calcification and senescence. Furthermore, we found that maturation of endothelial derived exosomal miR-302d-5p was promoted by WTAP in an N6-methyladenosine (m6A)-dependent manner. Interestingly, MT alleviated vascular calcification and ageing in 5/6-nephrectomy (5/6 NTP) mice, a chronic kidney disease (CKD) induced vascular calcification and vascular ageing mouse model. MT-ECs-Exos was absorbed by VSMCs in vivo and effectively prevented vascular calcification and ageing in 5/6 NTP mice. ECs-derived miR-302d-5p mediated MT induced anti-calcification and anti-ageing effects in 5/6 NTP mice. Our study suggests that MT-ECs-Exos alleviate vascular calcification and ageing through the miR-302d-5p/Wnt3 signaling pathway, dependent on m6A methylation.

Clinical and pathogen features of COVID-19-associated infections during an Omicron strain outbreak in Guangzhou, China.

Although the Omicron variant has been associated with greater transmissibility and tropism of the upper respiratory tract, the clinical and pathogenic features of patients infected with the Omicron variant during an outbreak in China have been unclear. Adults with COVID-19 were retrospectively enrolled from seven medical centers in Guangzhou, China, and clinical information and specimens ( BALF, sputum, and throat swabs) from participants were collected. Conventional detection methods, metagenomics next-generation sequencing (mNGS), and other methods were used to detect pathogens in lower respiratory tract samples. From December 2022 to January 2023, we enrolled 836 patients with COVID-19, among which 56.7% patients had severe/critical illness. About 91.4% of patients were infected with the Omicron strain (BA.5.2). The detection rate of possible co-infection pathogens was 53.4% by mNGS, including Klebsiella pneumoniae (16.3%), Aspergillus fumigatus (12.2%), and Pseudomonas aeruginosa (11.8%). The co-infection rate was 19.5%, with common pathogens being Streptococcus pneumoniae (11.5%), Haemophilus influenzae (9.2%), and Adenovirus (6.9%). The superinfection rate was 75.4%, with common pathogens such as Klebsiella pneumoniae (26.1%) and Pseudomonas aeruginosa (19.4%). Klebsiella pneumoniae (27.1%% vs 6.1%, P < 0.001), Aspergillus fumigatus (19.6% vs 5.3%, P = 0.001), Acinetobacter baumannii (18.7% vs 4.4%, P = 0.001), Pseudomonas aeruginosa (16.8% vs 7.0%, P = 0.024), Staphylococcus aureus (14.0% vs 5.3%, P = 0.027), and Streptococcus pneumoniae (0.9% vs 10.5%, P = 0.002) were more common in severe cases. Co-infection and superinfection of bacteria and fungi are common in patients with severe pneumonia associated with Omicron variant infection. Sequencing methods may aid in the diagnosis and differential diagnosis of pathogens. IMPORTANCE: Our study has analyzed the clinical characteristics and pathogen spectrum of the lower respiratory tract associated with co-infection or superinfection in Guangzhou during the outbreak of the Omicron strain, particularly after the relaxation of the epidemic prevention and control strategy in China. This study will likely prompt further research into the specific issue, which will benefit clinical practice.

Genetic Evidence for Causal Association Between Hypertension and Chronic Pain: A Bidirectional Two-Sample Mendelian Randomization Study.

Objective The extent to which the association between hypertension and chronic pain in observational studies is either causally linked or influenced by other shared risk factors has not been substantially addressed. In the present study, Mendelian randomization (MR) was employed to examine the potential causal relationship between hypertension and risk of chronic pain. Methods The study data were derived from the pooled dataset of the genome-wide association study (GWAS), enabling the evaluation of the causal effects of hypertension on various types of chronic pain including headache as well as chest, abdominal, joint, back, limb, and multisite chronic pain. We performed a bidirectional two-sample MR analysis using random effect inverse variance weighting (IVW), MR-Egger, and weighted median and weighted mode, quantified by the odds ratio (OR). Results Genetically predicted essential hypertension was associated with an increased risk of chronic headache (OR = 1.007, 95% CI: 1.003-1.011, P = 0.002) and limb pain (OR = 1.219, 95% CI: 1.033-1.439, P = 0.019). No potential causal associations were identified between chronic pain and essential hypertension in the reverse direction MR ( P > 0.05). In addition, there was no potential causal association between secondary hypertension and chronic pain (P > 0.05). Conclusion This study provided genetic evidence that a unidirectional causal relationship exists between essential hypertension and the increased risks of chronic headache and limb pain, and no causal relationship was found between secondary hypertension and chronic pain. These findings offer crucial theoretical underpinnings for future research on managing hypertension and chronic pain.

Risk factor differences in five-year progression of Intracranial artery stenosis and cerebral small vessel disease in general population.

BACKGROUND: Intracranial artery stenosis (ICAS) and cerebral small vessel disease (CSVD) are associated with a heavy socioeconomic burden; however, their longitudinal changes remain controversial. METHODS: We conducted a longitudinal analysis on 756 participants of Shunyi Cohort who underwent both baseline and follow-up brain magnetic resonance imaging (MRI) and MR angiography in order to investigate the risk factors for ICAS and CSVD progression in community population. Incident ICAS was defined as new stenosis occurring in at least one artery or increased severity of the original artery stenosis. CSVD markers included lacunes, cerebral microbleeds (CMB), and white matter hyperintensities (WMH). RESULTS: After 5.58 ± 0.49 years of follow-up, 8.5% of the 756 participants (53.7 ± 8.0 years old, 65.1% women) had incident ICAS. Body mass index (BMI) (OR = 1.09, 95% CI = 1.01-1.17, p = 0.035) and diabetes mellitus (OR = 2.67, 95% CI = 1.44-4.93, p = 0.002) were independent risk factors for incident ICAS. Hypertension was an independent risk factor for incident lacunes (OR = 2.12, 95% CI = 1.20-3.77, p = 0.010) and CMB (OR = 2.32, 95% CI = 1.22-4.41, p = 0.011), while WMH progression was primarily affected by BMI (ß = 0.108, SE = 0.006, p = 0.002). A higher LDL cholesterol level was found to independently protect against WMH progression (ß = -0.076, SE = 0.027, p = 0.019). CONCLUSIONS: Modifiable risk factor profiles exhibit different in patients with ICAS and CSVD progression. Controlling BMI and diabetes mellitus may help to prevent incident ICAS, and antihypertensive therapy may conduce to mitigate lacunes and CMB progression. LDL cholesterol may play an inverse role in large arteries and small vessels.

Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.

The inversion of substrate size specificity is an evolutionary roadblock for proteins. The Duf4243 dioxygenases GedK and BTG13 are known to catalyze the aromatic cleavage of bulky tricyclic hydroquinone. In this study, we discover a Duf4243 dioxygenase PaD that favors small monocyclic hydroquinones from the penicillic-acid biosynthetic pathway. Sequence alignments between PaD and GedK and BTG13 suggest PaD has three additional motifs, namely motifs 1-3, distributed at different positions in the protein sequence. X-ray crystal structures of PaD with the substrate at high resolution show motifs 1-3 determine three loops (loops 1-3). Most intriguing, loops 1-3 stack together at the top of the pocket, creating a lid-like tertiary structure with a narrow channel and a clearly constricted opening. This drastically changes the substrate specificity by determining the entry and binding of much smaller substrates. Further genome mining suggests Duf4243 dioxygenases with motifs 1-3 belong to an evolutionary branch that is extensively involved in the biosynthesis of natural products and has the ability to degrade diverse monocyclic hydroquinone pollutants. This study showcases how natural enzymes alter the substrate specificity fundamentally by incorporating new small motifs, with a fixed overall scaffold-architecture. It will also offer a theoretical foundation for the engineering of substrate specificity in enzymes and act as a guide for the identification of aromatic dioxygenases with distinct substrate specificities.

Discovery of orally bioavailable ALK PROTACs based ceritinib against ALK positive cancers.

Anaplastic lymphoma kinase (ALK) fusion genes promote a variety of human malignancies. Although several ALK inhibitors have significantly improved disease prognosis in patients with ALK positive cancers, the persistent emergence of acquired drug-resistant mutations remain the major problem in clinic treatment. Adoption of new therapeutic strategies such as proteolysis targeting chimera (PROTAC) to overcome drug resistance in BTK/AR-related cancers have shown promising prospect. Herein, we reported the integrate ALK PROTACs through overall optimization of linker, revealed that subtle structural differences can lead to significant activity difference, indicating the key role of conformation of PROTACs in inducing the formation of E3-PROTAC-target protein ternary complexes. A series of rigid ALK PROTACs were developed through conjugation of Ceritinib and thalidomide, orally bioavailable PROTAC 4B (F = 14.22 %) was obtained by overall optimization of molecular properties. 4B effectively induced long lasting degradation of ALK fusion proteins and strong repression of downstream pathway in Karpas 299 cells (DC50 = 119.33 nM, Dmax = 97.1 %) and showed comparable anti-proliferative activity to Ceritinib (IC50 = 3.11 ± 0.08 nM vs IC50 = 1.31 ± 0.43 nM). Furthermore, 4B significantly inhibited the growth of Karpas 299 xenografts in vivo with TGI of 49.5 % and showed superior anti-proliferative activity against G1202R mutation to Ceritinib (IC50 = 52.82 nM vs IC50 = 109.5 nM). Overall, 4B is expected to be a potential treatment for ALK-driven malignancies.