T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese.

Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version - T2T-CHM13 - reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete diploid human genome reference for the Han Chinese, the largest population in the world, we assembled the genome of a male Han Chinese individual, T2T-YAO, which includes T2T assemblies of all the 22 + X + M and 22 + Y chromosomes in both haploid. The quality of T2T-YAO is much better than all currently available diploid assemblies, and its haploid version, T2T-YAO-hp, generated by selecting the better assembly for each autosome, reaches the top quality of fewer than one error per 29.5 Mb, even higher than that of T2T-CHM13. Derived from an individual living in the aboriginal region of the Han population, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors. Each haplotype of T2T-YAO possesses ∼ 330-Mb exclusive sequences, ∼ 3100 unique genes, and tens of thousands of nucleotide and structural variations as compared with CHM13, highlighting the necessity of a population-stratified reference genome. The construction of T2T-YAO, a truly accurate and authentic representative of the Chinese population, would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.

Lung microbiome and cytokine profiles in different disease states of COPD: a cohort study.

Increasing evidence indicates that respiratory tract microecological disorders may play a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Understanding the composition of the respiratory microbiome in COPD and its relevance to respiratory immunity will help develop microbiome-based diagnostic and therapeutic approaches. One hundred longitudinal sputum samples from 35 subjects with acute exacerbation of COPD (AECOPD) were analysed for respiratory bacterial microbiome using 16S ribosomal RNA amplicon sequencing technology, and the sputum supernatant was analysed for 12 cytokines using a Luminex liquid suspension chip. Unsupervised hierarchical clustering was employed to evaluate the existence of distinct microbial clusters. In AECOPD, the respiratory microbial diversity decreased, and the community composition changed significantly. The abundances of Haemophilus, Moraxella, Klebsiella, and Pseudomonas increased significantly. Significant positive correlations between the abundance of Pseudomonas and TNF-α, abundance of Klebsiella and the percentage of eosinophils were observed. Furthermore, COPD can be divided into four clusters based on the respiratory microbiome. AECOPD-related cluster was characterized by the enrichment of Pseudomonas and Haemophilus and a high level of TNF-α. Lactobacillus and Veillonella are enriched in therapy-related phenotypes and may play potential probiotic roles. There are two inflammatory endotypes in the stable state: Gemella is associated with the Th2 inflammatory endotypes, whereas Prevotella is associated with the Th17 inflammatory endotypes. Nevertheless, no differences in clinical manifestations were found between these two endotypes. The sputum microbiome is associated with the disease status of COPD, allowing us to distinguish different inflammatory endotypes. Targeted anti-inflammatory and anti-infective therapies may improve the long-term prognosis of COPD.

Is the traction table necessary to treat femoral fractures with intramedullary nailing? A meta-analysis.

BACKGROUND: The traction table is generally used in femoral intramedullary nailing surgery. Recently, some published studies have shown that the same or better treatment effects can be gotten without a traction table. It remains no consensus on this issue. METHODS: The Preferred Reporting Items for Systematic Reviews and Meta-analyses guideline was applied in this study. We searched PubMed, Embase, Web of Science, and Cochrane Library databases for eligible studies. The random-effect model was used to calculate the standardized mean difference (SMD) and risk ratios with 95% CIs. Trial sequential analysis (TSA) was performed to verify the results. RESULTS: The pooled estimates of seven studies, including 266 cases each in the manual traction group and traction table group, indicated that manual traction could shorten operative time [SMD, - 0.77; 95% CI (- 0.98, - 0.55); P < 0.00001] and preoperative set-up time [SMD, - 2.37; 95% CI (- 3.90, - 0.84); P = 0.002], but it would not reduce intraoperative blood loss volume and fluoroscopy time. No statistical difference was found in their fracture healing time, postoperative Harris scores, and malunion rate. The use of a Traction repositor could reduce the set-up time [SMD, - 2.48; 95% CI (- 4.91, - 0.05); P < 0.00001]. CONCLUSIONS: Compared with manual traction, the traction table in femoral intramedullary nailing surgery lengthened operative time and preoperative set-up time. At the same time, it did not show significant advantages in reducing blood loss volume and fluoroscopy time, or improving prognosis. In clinical practice, the optimal surgical plan must be made on a case-by-case basis to avoid unnecessary traction table use.

Collateral sensitivity between tetracyclines and aminoglycosides constrains resistance evolution in carbapenem-resistant Klebsiella pneumoniae.

AIMS: The acquisition of resistance to one antibiotic may confer an increased sensitivity to another antibiotic in bacteria, which is an evolutionary trade-off between different resistance mechanisms, defined as collateral sensitivity (CS). Exploiting the role of CS in treatment design could be an effective method to suppress or even reverse resistance evolution. METHODS: Using experimental evolution, we systematically studied the CS between aminoglycosides and tetracyclines in carbapenem-resistant Klebsiella pneumoniae (CRKP) and explored the underlying mechanisms through genomic and transcriptome analyses. The application of CS-based therapies for resistance suppression, including combination therapy and alternating antibiotic therapy, was further evaluated in vitro and in vivo. RESULTS: Reciprocal CS existed between tetracyclines and aminoglycosides in CRKP. The increased sensitivity of aminoglycoside-resistant strains to tetracyclines was associated with the alteration of bacterial membrane potential, whereas the unbalanced oxidation-reduction process of tetracycline-resistant strains may lead to an increased bacterial sensitivity to aminoglycosides. CS-based combination therapy could efficiently constrain the evolution of CRKP resistance in vitro and in vivo. In addition, alternating antibiotic therapy can re-sensitize CRKP to previously resistant drugs, thereby maintaining the trade-off. CONCLUSIONS: These results provide new insights into constraining the evolution of CRKP resistance through CS-based therapies.

Metabolic landscape dysregulation in bronchoalveolar lavage fluid of checkpoint inhibitor pneumonitis.

BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is a potentially fatal adverse event resulting from immunotherapy in patients with malignant tumors. However, the pathogenesis of CIP remains poorly understood. METHODS: We collected bronchoalveolar lavage fluid (BALF) from cohorts of patients with CIP, new-onset lung cancer (LC), and idiopathic pulmonary fibrosis (IPF). Non-targeted metabolomics analysis was conducted to analyze metabolic signatures. Flow cytometry was used to evaluate immune cell subsets. RESULTS: Lymphocytes were predominant in the BALF of patients with CIP. A total of 903 metabolites were identified, among which lipid compounds were the most abundant. In a comparison between patients with CIP and LC, enrichment analysis of the altered metabolites showed suppressed amino sugar metabolism, and spermidine and spermine biosynthesis in the CIP group. Metabolism of alpha linolenic acid, linoleic acid, and their fatty acid derivatives was enriched in the CIP group relative to the IPF group. The twelve metabolites found to be enriched in the CIP group were positively correlated with the proportion of CD8+ T cells. One cluster of BALF metabolites, 57.14% of which were lipid molecules, was inversely correlated with the proportion of natural killer cells. CONCLUSIONS: In this study, the metabolomic landscape of BALF in patients with CIP was determined. We elucidated suppressed tumor metabolic signatures, enhanced pulmonary inflammatory signaling, and the characteristics of responsible immune cells, which helps to understand the pathogenesis of CIP.

Resistance to Cefiderocol Involved Expression of PER-1 ß-Lactamase and Downregulation of Iron Transporter System in Carbapenem-Resistant Acinetobacter baumannii.

Background: Cefiderocol (CFDC) is a promising antimicrobial agent against multidrug resistant Gram-negative bacteria. However, CFDC resistance has emerged in carbapenem-resistant Acinetobacter baumannii (CR-AB) but the underlying mechanisms remain unclear. Methods: Whole-genome sequencing and transcriptome sequencing were performed on CFDC-non-susceptible and CFDC-susceptible isolates. Two different recombinant plasmids was electro-transformed into the E. coli BL21 strain to determine the impact of blaPER and the combined impact of blaPER-1 and blaOXA-23 on CFDC resistance. Results: Fifty-five CR-AB isolates with minimum inhibitory concentrations (MICs) ranged from 0.06 mg/L to >256 mg/L were sequenced, including 47 CFDC-non-susceptible and eight CFDC-susceptible isolates. Two CFDC-non-susceptible isolates belonged to ST104 whereas the remaining isolates belonged to ST2, and blaPER-1 was present only in CFDC-non-susceptible isolates. Amino acid substitutions were noted in penicillin-binding proteins (PBPs) in four CFDC-susceptible isolates, with slightly elevated MICs. The MICs of recombinant E. coli BL21 carrying the blaPER-1 gene increased 64-fold and recombinant E. coli BL21 carrying both the blaPER-1 and blaOXA-23 genes increased 8-fold but both remained within the susceptibility range. Transcriptome sequencing of 17 CFDC-non-susceptible isolates and eight CFDC-susceptible isolates revealed that transcriptional levels of various iron transport proteins, such as fiu, feoA, and feoB, and the energy transduction system, TonB-ExbB-ExbD, were relatively downregulated in CFDC-non-susceptible isolates. GO enrichment analysis revealed that the upregulated genes in CFDC-non-susceptible isolates were mainly associated with redox homeostasis and stress response. Besides, the expression levels of the blaOXA-23 and exbD genes were negatively correlated with the MICs. Conclusion: PER-1 production, iron transport system downregulation, and mutations in PBPs may synergistically impart high-level resistance to CFDC in CR-AB.

Characteristics of lower respiratory tract microbiota in the patients with post-hematopoietic stem cell transplantation pneumonia.

Background: Pneumonia is a leading cause of non-relapse mortality after hematopoietic stem cell transplantation (HSCT), and the lower respiratory tract (LRT) microbiome has been proven to be associated with various respiratory diseases. However, little is known about the characteristics of the LRT microbiome in patients with post-HSCT compared to healthy controls (HC) and community-acquired pneumonia (CAP). Methods: Bronchoalveolar lavage samples from 55 patients with post-HSCT pneumonia, 44 patients with CAP, and 30 healthy volunteers were used to detect microbiota using 16S rRNA gene sequencing. Results: The diversity of the LRT microbiome significantly decreased in patients with post-HSCT pneumonia, and the overall community was different from the CAP and HC groups. At the phylum level, post-HSCT pneumonia samples had a high abundance of Actinobacteria and a relatively low abundance of Bacteroidetes. The same is true for non-survivors compared with survivors in patients with post-HSCT pneumonia. At the genus level, the abundances of Pseudomonas, Acinetobacter, Burkholderia, and Mycobacterium were prominent in the pneumonia group after HSCT. On the other hand, gut-associated bacteria, Enterococcus were more abundant in the non-survivors. Some pathways concerning amino acid and lipid metabolism were predicted to be altered in patients with post-HSCT pneumonia. Conclusions: Our results reveal that the LRT microbiome in patients with post-HSCT pneumonia differs from CAP patients and healthy controls, which could be associated with the outcome. The LRT microbiota could be a target for intervention during post-HSCT pneumonia.

Minimize the extent and morbidity of axillary dissection for node-positive breast cancer patients: implementation of axillary lymph node dissection based on breast lymphatics level.

BACKGROUND: Breast cancer-related lymphedema (BCRL) is associated with extensive axillary dissection. Axillary lymph node dissection (ALND) based on breast lymphatics level (BLL) was proposed to minimize the surgical extent for node-positive breast cancer patients. METHODS: A total of 156 consecutive sentinel lymph node-positive (SLN+) or clinically node-positive (cN+) patients underwent sentinel lymph node biopsy (SLNB) with indocyanine green and methylene blue (MB). The SLNs were injected with 0.1 ml MB before removal, and a standard ALND was subsequently performed. The nodes adjacent to the blue-stained axillary lymph nodes from the breast (bALNs) were sent for pathological examination separately by resecting serial tissue every 0.5 cm away from the marginal blue-stained bALNs. Then, a pilot study comparing ALND based on BLL and standard ALND was performed. RESULTS: BLL were successfully identified in 20 SLN+ (100%) and 134 cN+ (98.5%) patients. The median number of BLL was four, ranging from three to six. A horizontal line 1.0 cm away from the superior blue-stained bALN and a vertical line 1.0 cm away from the medial blue-stained bALN formed BLL II, III, and IV. All of the additional positive nodes were within 1.0 cm of the blue-stained bALNs. The minimized axillary dissection should resect upwards from the lowest BLL that contains the first confirmed negative blue-stained bALNs. In the pilot study, no patient developed axillary recurrence. CONCLUSION: The ALND surgical procedure based on BLL could minimize the surgical extent for pathological node-positive breast cancer patients and potentially reduce the BCRL rate. TRIAL REGISTRATION: ChiCTR1800014247 .

Increased KIAA0101 gene expression associated with poor prognosis in breast cancer.

BACKGROUND: Breast cancer (BC) has long been a major death threat facing women worldwide. With the development of comprehensive treatment methods, the prognosis of BC was improved but still unsatisfactory. This study was aimed to identify the key genes in BC tumorigenesis and investigate potential prognostic predictors. METHODS: Differential expression genes were analyzed in TCGA BRCA dataset using Genevestigator software. The expression profile of target gene was explored, and the correlations between selected genes with important clinical parameters were evaluated as well. The prognostic values of target genes were also carried out through Kaplan-Meier plotter OncoLnc and BC gene-expression miner. RESULTS: KIAA0101 gene was selected for further analysis from the differential expression genes identified. At both mRNA and protein levels, the expression of KIAA0101 in BC was higher than that in normal tissues. Further analysis indicated that overexpression of KIAA0101 was significantly correlated with worse clinical outcome parameters. KIAA0101 was highly expressed in older patients, in the luminal group, and in patients with advanced stages. Moreover, BC patients with elevated KIAA0101 expression had worse overall survival (OS), relapse-free survival (RFS), distant metastasis-free survival (DMFS) and disease-free survival (DFS). CONCLUSIONS: Taken together, KIAA0101 could be considered as a diagnostic biomarker or predictor for BC prognosis.

Heated fennel therapy promotes the recovery of gastrointestinal function in patients after complex abdominal surgery: A single-center prospective randomized controlled trial in China.

BACKGROUND: Postoperative gastrointestinal dysfunction remains a major determinant of the duration of stay after complex abdominal surgery. This study was performed to evaluate the effectiveness of heated fennel therapy in accelerating the recovery of gastrointestinal function. METHODS: This surgeon-blinded, prospective randomized controlled study included 381 patients with hepatobiliary, pancreatic, and gastric tumors who were divided into 2 groups. The patients in the experimental groups received heated fennel therapy, and those in the control groups received heated rice husk therapy. We compared the baseline characteristics, time to first postoperative flatus and defecation, fasting time, duration of postoperative hospital stay, grading of abdominal pain, classification of abdominal distension, inflammatory markers, and nutritional status indicators. RESULTS: The time to first flatus and first defecation and the fasting time were statistically significantly less in the heated fennel therapy group than those in the control groups (P < .05 each); and abdominal distension was also relieved in the experimental groups (P < .001). Heated fennel therapy had no obvious beneficial effect on inflammatory markers but improved the serum albumin (ALB) level of the patients at postop day 9 (P < .001). Among the patients with alimentary tract reconstruction, those in the heated fennel therapy group had a clinically important, lesser hospital stay than those in the control group (9.2 5 ± 5.1 versus 11.1 ± 6.4; P < .023). CONCLUSION: Heated fennel therapy facilitated the gastrointestinal motility function of patients early postoperatively.

regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants.

Predicting the functional or pathogenic regulatory variants in the human non-coding genome facilitates the interpretation of disease causation. While numerous prediction methods are available, their performance is inconsistent or restricted to specific tasks, which raises the demand of developing comprehensive integration for those methods. Here, we compile whole genome base-wise aggregations, regBase, that incorporate largest prediction scores. Building on different assumptions of causality, we train three composite models to score functional, pathogenic and cancer driver non-coding regulatory variants respectively. We demonstrate the superior and stable performance of our models using independent benchmarks and show great success to fine-map causal regulatory variants on specific locus or at base-wise resolution. We believe that regBase database together with three composite models will be useful in different areas of human genetic studies, such as annotation-based casual variant fine-mapping, pathogenic variant discovery as well as cancer driver mutation identification. regBase is freely available at https://github.com/mulinlab/regBase.

Is blood transfusion associated with an increased risk of infection among spine surgery patients?: A meta-analysis.

BACKGROUND: Blood transfusions are associated with many adverse outcomes among spine surgery patients, but it remains unclear whether perioperative blood transfusion during spine surgery and postoperative infection are related. Recently, many related cohort studies have been published on this topic. METHODS: This study was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. The PubMed, Embase, and Cochrane Library databases were searched for eligible published studies. The Newcastle-Ottawa Scale (NOS) was used to assess the methodological quality of the studies, and a random-effects model was used to calculate the odds ratios (ORs) with 95% CIs. Sensitivity analyses were conducted to explore the source of heterogeneity. RESULTS: The final analysis included 8 cohort studies with a total of 34,185 spine surgery patients. These studies were considered to be of high or moderate quality based on their NOS scores, which ranged from 5 to 9. Pooled estimates indicated that blood transfusion increased the infection rate (OR, 2.99; 95% CI, 1.95 to 4.59; I = 86%), which was consistent with the sensitivity analyses. CONCLUSIONS: Our results suggest that perioperative blood transfusion is a risk factor for postoperative infection among spine surgery patients. Further study is necessary to identify other influencing factors and to establish the mechanism underlying this relationship. Additional measures may be needed to reduce unnecessary blood transfusions during spine surgery.

Surgical Management of the Axilla in Breast Cancer Patients with Negative Sentinel Lymph Node: A Method to Reduce False-Negative Rate.

BACKGROUND: False-negative rate (FNR) of sentinel lymph node dissection (SLND) has not been eliminated. The study was conducted to optimize the surgical resection of axilla in patients with negative sentinel lymph node (SLN) for the purpose of eradicating false-negative (FN) events of SLND. METHODS: A total of 312 clinically node-negative patients without neoadjuvant therapy underwent SLND with indocyanine green (ICG), methylene blue and the combination of ICG and methylene blue. Axillary dissection was performed subsequently regardless of the status of SLN. Lymph nodes were sent for pathological examination separately by serial resection every 0.5 cm away from marginally visualized SLNs. RESULTS: SLND was successfully conducted in 98.1% (306/312) of patients using methylene blue, ICG, and its combination. Further examination revealed 97 true-positive, 189 true-negative, and 13 FN results. The overall FNR was 11.8% (13/110). A horizontal line 1.5 cm away from the superior vSLN and a vertical line 1.5 cm away from the medial vSLN formed a zone of lower outer quadrant (LOQ) in axilla. Surgical resection of LOQ 'en bloc' showed a FNR of zero. CONCLUSIONS: The surgical management of axilla may benefit negative SLN patients with potential nodal involvement, reducing the FNR of SLND to zero. TRIAL REGISTRATION NUMBER AND AGENCY: This study was registered with the Chinese Clinical Trial Registry (ChiCTR1800014247).

Biosurfactant surfactin with pH-regulated emulsification activity for efficient oil separation when used as emulsifier.

In the present study, the pH-regulated emulsification activity of surfactin was studied and its potential application in oil separation towards enhanced oil recovery (EOR) was investigated. As demonstrated, surfactin can stabilize emulsions quite well beyond pH 7.4. An oil emulsification ratio of about 98% was obtained at pH 11.0; while this emulsification activity was rapidly and completely lost when pH decreased to below 3.0, having an oil separation ratio of over 98%. This pH-sensitive property is probably due to surfactin dissolution-precipitation induced by the ionization-protonation of a carboxyl group in its structure under alkaline or acidic conditions. This property allows oil emulsification or oil separation to be readily achieved via simple pH adjustments when surfactin is used as an emulsifier. Furthermore, surfactin sustained its activity after demulsification and can be readily reused many times. The above obtained results indicated surfactin-based EOR processes have great application feasibility.

New idea for treatment strategies for Barcelona Clinic Liver Cancer stages based on a network meta-analysis.

BACKGROUND: Currently, the Barcelona Clinic Liver Cancer staging (BCLC) system still remains controversies in the management of hepatocellular carcinoma. We are trying to determine the best therapeutic strategy for each BCLC stage through a network meta-analysis and provide a new treatment idea. METHODS: We conducted a systematic literature search of the PubMed, EMBASE, and Cochrane Library databases and extracted data from randomized controlled trials (RCTs) that compared various strategies. Network meta-analyses were conducted in ADDIS by evaluating different overall survival of each stage. Cumulative probability was used to rank the included strategies. A node-splitting model assessed whether direct and indirect evidence on a specific node was in agreement. RESULTS: Of the 24 included RCTs, 3667 patients were included. Based on the probability P values, the results showed that TACE plus surgical resection (SR) was the first choice for BCLC Stage A (P = .38 and P = .52 for 3- and 5-year OS, respectively). The application of SR was the best strategy for BCLC Stage B (P = .51 and P = .95 for 1- and 3-year OS, respectively). For Stage C, whole net connections could not be established in this research, but combined therapy seemed to produce better results based on 3 separated net connections (P = .92, P = .80, and P = .69 for 1-year OS). CONCLUSIONS: The updated therapy strategies discussed in this study are recommended. More importantly, we deemed that the recommended strategy for each patient may be subject to adjustment due to individual clinical factors. The applicable scope of each strategy should also be evaluated before application.

Feasibility and Efficacy of S-Adenosyl-L-methionine in Patients with HBV-Related HCC with Different BCLC Stages.

Aims. To understand the feasibility and efficacy of treatment with SAMe in patients with hepatitis B-related HCC with different Barcelona Clinic Liver Cancer (BCLC) stages. Methods. We retrospectively enrolled 697 patients with BCLC early-stage (stages 0-A) and advanced-stage (stages B-C) HCC who underwent SAMe therapy (354 cases) or no SAMe therapy (343 cases). The baseline characteristics, postoperative recoveries, and 24-month overall survival rates of the patients in the 2 groups were compared. Cox regression model analysis was performed to confirm the independent variables influencing the survival rate. Results. For patients in the early-stage (BCLC stages A1-A4) group, little benefit of SAMe therapy was observed. For advanced-stage (BCLC B-C) patients, SAMe therapy reduced alanine aminotransferase (ALT) and aspartate transaminase (AST) levels and effectively delayed the recurrence time and enhanced the 24-month survival rate. Cox regression model analysis in the advanced-stage group revealed that treatment with SAMe, preoperative viral load, and Child-Pugh grade were independent variables influencing survival time. Conclusion. SAMe therapy exhibited protective and therapeutic efficacy for BCLC advanced-stage HBV-related HCC patients. And the efficacy of SAMe therapy should be further explored in randomized prospective clinical trials.