SIRT3/AMPK signaling pathway regulates lipid metabolism and improves vulnerability to atrial fibrillation in Dahl salt sensitive rats.

BACKGROUND: Hypertension may result in atrial fibrillation (AF) and lipid metabolism disorders. The Sirtuins3 (SIRT3) / AMP-activated protein kinase (AMPK) signaling pathway has the capacity to regulate lipid metabolism disorders and the onset of AF. We hypothesize that the SIRT3/AMPK signaling pathway suppresses lipid metabolism disorders, thereby mitigating salt-sensitive hypertension (SSHT)-induced susceptibility to AF. METHODS: The study involved 7-week-old male Dahl salt-sensitive that were fed either high-salt diet (8% NaCl; DSH group) or normal diet (0.3% NaCl; DSN group). Then DSH group were administered either oral metformin (MET, an AMPK agonist) or intraperitoneal injection of Honokiol (HK, a SIRT3 agonist). This experimental model allowed for the measurement of SBP, the expression levels of lipid metabolism-related biomarker, pathological examination of atrial fibrosis and lipid accumulation, as well as AF inducibility and AF duration. RESULTS: DSH decrease SIRT3, phosphorylation-AMPK and VLCAD expression, increased FASN and FABP4 expression and concentrations of FFA and TG, atrial fibrosis and lipid accumulation in atrial tissue, enhanced level of SBP, promoted AF induction rate and prolonged AF duration, which are blocked by MET and HK. Our results also showed that the degree of atrial fibrosis was negatively correlated with VLCAD expression, but positively correlated with the expression of FASN and FABP4. CONCLUSIONS: We have confirmed that high-salt diet can result in hypertension, associated atrial tissue lipid metabolism dysfunction. This condition is linked to the inhibition of the SIRT3/AMPK signaling pathway, which plays a significant role in the progression of susceptibility to AF in SSHT rats.

The surgical interval between robot-assisted SEEG and epilepsy resection surgery is an influencing factor of SSI.

BACKGROUND: In recent years, the development of robotic neurosurgery has brought many benefits to patients, but there are few studies on the occurrence of surgical site infection (SSI) after robot-assisted stereoelectroencephalography (SEEG). The purpose of this study was to collect relevant data from robot-assisted SEEG over the past ten years and to analyze the influencing factors and economic burden of surgical site infection. METHODS: Basic and surgical information was collected for all patients who underwent robot-assisted SEEG from January 2014 to December 2023. Logistic regression was used to analyze the factors influencing SSI according to different subgroups (radiofrequency thermocoagulation or epilepsy resection surgery). RESULTS: A total of 242 subjects were included in this study. The risk of SSI in the epilepsy resection surgery group (18.1%) was 3.5 times greater than that in the radiofrequency thermocoagulation group (5.1%) (OR 3.49, 95% CI 1.39 to 9.05); this difference was statistically significant. SSI rates in the epilepsy resection surgery group were associated with shorter surgical intervals (≤ 9 days) and higher BMI (≥ 23 kg/m2) (6.1 and 5.2 times greater than those in the control group, respectively). Hypertension and admission to the intensive care unit (ICU) were risk factors for SSI in the radiofrequency thermocoagulation group. Patients with SSIs had $21,231 more total hospital costs, a 7-day longer hospital stay, and an 8-day longer postoperative hospital stay than patients without SSI. CONCLUSIONS: The incidence of SSI in patients undergoing epilepsy resection after stereoelectroencephalography was higher than that in patients undergoing radiofrequency thermocoagulation. For patients undergoing epilepsy resection surgery, prolonging the interval between stereoelectroencephalography and epilepsy resection surgery can reduce the risk of SSI; At the same time, for patients receiving radiofrequency thermocoagulation treatment, it is not recommended to enter the ICU for short-term observation if the condition permits.

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.

Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer mismatches overlapping with primers and predicted PCR byproducts. We also compare Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (~90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluate Olivar on real wastewater samples and found that Olivar has up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available online as a web application at https://olivar.rice.edu  and can be installed locally as a command line tool with Bioconda. Source code, installation guide, and usage are available at https://github.com/treangenlab/Olivar .

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet.

Taxonomic profiling is a ubiquitous task in the analysis of clinical and environmental microbiomes. The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling from long-read shotgun metagenomic datasets. Lemur is a marker-gene based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet makes detailed presence/absence calls for bacterial genomes based on whole-genome read mapping. The tools work in sequence: Lemur estimates abundances conservatively, and Magnet operates on the genomes of identified organisms to filter out likely false positive taxa. The result is an increase in precision of as much as 70%, which far exceeds competing methods. By operating only on marker genes, Lemur is a comparatively lightweight software. We demonstrate that it can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs - a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. The reference is available at https://zenodo.org/records/10802546, and the software is open-source and available at https://github.com/treangenlab/lemur.

One-step electrodeposition of MWCNTs-Cu MOF films for the ratiometric electrochemical analysis of glyphosate.

Sensitive and accurate determination of glyphosate (GLYP) is vital for food safety and environmental protection. Herein, a novel electrochemical ratiometric biosensor was designed for the accurate quantification of GLYP through one-step electrodeposition of MWCNTs-Cu MOF films. MWCNTs-Cu MOF nanostructures were directly electro-synthesized in situ on the electrode from the precursor solution. The combination of Cu MOFs with MWCNTs not merely improved the conductivity of MOFs, but also enhanced the sensitivity of the biosensor. Furthermore, Cu sites within Cu MOFs were turned into CuCl to further amplify the current signal and enable the specific recognition of GLYP through competing reactions with the transformation of CuCl into non-electroactive Cu-GLYP. Meanwhile, internal reference molecules of methylene blue (MB) were incorporated to improve the measurement accuracy of GLYP for reducing unpredictable measurement errors aroused by environmental deviations. The ratiometric electrochemical sensor exhibited a high linearity with the logarithmic value of GLYP concentration from 0.5 nM to 400 nM. The detection limit was estimated to be as low as 0.014 nM. Finally, the present sensor with ratiometric signal export was applied for GLYP analysis in real samples with high sensitivity and accuracy. The simplicity and reliability of the ratiometric sensor make it a worthy and powerful tool for food and environmental monitoring. This design strategy also provides an avenue for the development of simple and efficient biosensors for other substances.

Elucidating important factors and corresponding method optimization for sensitive detection of small peptide drugs in human urine by solid-phase extraction and UPLC-HRMS: The influence of MS scan modes, protein precipitants, and ammonium formate.

Small peptide hormones are widely used in sports as performance-enhancing substances, making it crucial to develop sensitive analytical methods for their detection in doping control analysis. Various factors significantly affect analytical sensitivity, such as the selection of ultra-performance liquid chromatography (UPLC) mobile phase, high-resolution mass spectrometry (HRMS) scanning modes, and extraction solvents for pretreatment. Herein, comparative study approach was utilized to investigate the sensitivity of each peptide analyte under both full scan and parallel reaction monitoring (PRM) modes of HRMS and assess the effects of some protein precipitants as a part of extraction solvents on solid-phase extraction (SPE). The results showed that full scan should be selected as the primary scan mode of HRMS, and the combination with PRM mode could effectively compensate for the limitations of full scan, and the addition of protein precipitants would adversely affect the detection of certain small peptide analytes. Meanwhile, influences of ammonium formate in reverse UPLC mobile phase on the charge state distribution of small peptides were investigated and elucidated. Based on these findings, a sensitive and reliable UPLC-HRMS analytical method combining full scan and PRM mode was validated for screening and confirmation of 63 small peptide analytes after SPE, with limits of detection (LODs) ranging between 0.010 and 0.473 ng/ml and limits of identification (LOIs) ranging between 0.015 and 1.512 ng/ml. Additionally, suggestions were provided for the detection of [Arg8]-vasopressin, dermorphin, and its analogues.

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.

Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.

The impact of preoperative biliary drainage on postoperative healthcare-associated infections and clinical outcomes following pancreaticoduodenectomy: a ten-year retrospective analysis.

BACKGROUND: Pancreaticoduodenectomy (PD) is a complex procedure and easily accompanied by healthcare-associated infections (HAIs). This study aimed to assess the impact of PBD on postoperative infections and clinical outcomes in PD patients. METHODS: The retrospective cohort study were conducted in a tertiary hospital from January 2013 to December 2022. Clinical and epidemiological data were collected from HAIs surveillance system and analyzed. RESULTS: Among 2842 patients who underwent PD, 247 (8.7%) were diagnosed with HAIs, with surgical site infection being the most frequent type (n = 177, 71.7%). A total of 369 pathogenic strains were detected, with Klebsiella pneumoniae having the highest proportion, followed by Enterococcu and Escherichia coli. Although no significant association were observed generally between PBD and postoperative HAIs, subgroup analysis revealed that PBD was associated with postoperative HAIs in patients undergoing robotic PD (aRR = 2.174; 95% CI:1.011-4.674; P = 0.047). Prolonging the interval between PBD and PD could reduce postoperative HAIs in patients with cholangiocarcinoma (≥4 week: aRR = 0.292, 95% CI 0.100-0.853; P = 0.024) and robotic PD (≤2 week: aRR = 3.058, 95% CI 1.178-7.940; P = 0.022). PBD was also found to increase transfer of patients to ICU (aRR = 1.351; 95% CI 1.119-1.632; P = 0.002), extended length of stay (P < 0.001) and postoperative length of stay (P = 0.004). CONCLUSION: PBD does not exhibit a significant association with postoperative HAIs or other outcomes. However, the implementation of robotic PD, along with a suitable extension of the interval between PBD and PD, appear to confer advantages concerning patients' physiological recuperation. These observations suggest potential strategies that may contribute to enhanced patient outcomes.

Effects of neighborhood built environment on cognitive function in older adults: a systematic review.

BACKGROUND: In the background of an aging population, the risk of cognitive impairment in the older population is prominent. Exposure to complex neighborhood built environments may be beneficial to the cognitive health of older adults, and the purpose of this study was to systematically review the scientific evidence on the effects of neighborhood built environments on cognitive function in older adults. METHODS: Keywords and references were searched in Web of Science, Pubmed, PsycINFO, and MEDLINE. Studies examining the relationship between the built environment and cognitive function in older adults were included. The neighborhood built environment as an independent variable was classified according to seven aspects: density, design, diversity, destination accessibility, public transportation distance, blue/green space, and built environment quality. The cognitive function as the dependent variable was classified according to overall cognitive function, domain-specific cognitive function, and incidence of dementia. The quality of the included literature was assessed using the National Institutes of Health's Observational Cohort and Cross-Sectional Study Quality Assessment Tool. RESULTS: A total of 56 studies were included that met the inclusion criteria, including 31 cross-sectional studies, 23 longitudinal studies, 1 cross-sectional study design combined with a case-control design, and 1 longitudinal study design combined with a case-control design. Most of the studies reviewed indicate that the built environment factors that were positively associated with cognitive function in older adults were population density, street connectivity, walkability, number of public transportation stops around the residence, land use mix, neighborhood resources, green space, and quality of the neighborhood built environment. Built environment factors that were negatively associated with cognitive function in older adults were street integration, distance from residence to main road. The relationship between residential density, destination accessibility, and blue space with cognitive function in older adults needs to be further explored. CONCLUSION: Preliminary evidence suggests an association between the neighborhood built environment and cognitive function in older adults. The causal relationship between the built environment and cognitive function can be further explored in the future using standardized and combined subjective and objective assessment methods, and longitudinal or quasi-experimental study designs. For public health interventions on the cognitive health of older adults, it is recommended that relevant authorities include the neighborhood built environment in their intervention programs.

Epidemiology and risk factors of nosocomial infections in a Chinese tertiary-care hospital: a 10-year retrospective case-control study.

BACKGROUND: Nosocomial infections (NIs) are the most frequent adverse events among patients and cause a heavy burden on both health and economics. To investigate epidemiology of NIs and identify risk factors for NIs by integrating continuous long-term surveillance data. METHODS: We performed an observational study among inpatients at the Chinese People's Liberation Army General Hospital between January 1, 2010, and December 31, 2019. Infection rates, mortality rates and percentage of NIs were calculated. Trends of yearly infection rates by pathogens were assessed using Mann-Kendall trend test. Controls were matched to cases (2:1) by age (±2 years), sex, admission date (±1 year) and admission diagnosis, and conditional logistic regression was used to estimate odds ratios. RESULTS: A total of 1,534,713 inpatients were included among which 33,468 NIs cases occurred with an infection rate of 2.18%. The most common infections were respiratory system infection (52.22%), bloodstream infection (17.60%), and genitourinary system infection (15.62%). Acinetobacter. baumannii (9.6%), Klebsiella. pneumoniae (9.0%), Pseudomonas. aeruginosa (8.6%), Escherichia. coli (8.6%) and Enterococcus. faecium (5.0%) were the top five isolated pathogens. Infection rates of K. pneumoniae and carbapenems-resistant K. pneumoniae significantly increased. Prior ICU stay, surgery, any device placement (including central venous catheter, mechanical ventilation, urinary catheter, and tracheotomy), prior use of triple or more antibiotics combinations, carbapenem, and ß-Lactamase inhibitors were significantly associated with NIs. CONCLUSION: K. pneumoniae has the potential to cause a clinical crisis with increasing infection rates and carbapenem resistance. Clinical management of invasive operations and antibiotics use should be further strengthened.

The relationship between sleep status and activity of daily living: based on China Hainan centenarians cohort study.

OBJECTIVE: This study, based on the China Hainan Centenarians Cohort Study (CHCCS), aims to comprehensively describe the characteristic of daytime, night and total sleep duration, sleep quality and different sleep mode of Hainan centenarians and their associations with activity of daily living (ADL) functions. METHOD: The baseline data of CHCCS was used. ADL function was evaluated the Bathel index, sleep quality was evaluated by Pittsburgh sleep quality index (PSQI), sleep status including daytime, night and total sleep duration as well as sleep quality and sleep mode. Multivariate logistic regression model was used to explore the association between sleep status and ADL disability and ADL moderate & severe disability. RESULTS: A total of 994 centenarians were included in this study with the age range 100-116 years old. Compared with the centenarians who sleep 6-9 h at night and < 2 h in the daytime, the adjusted OR between sleep > 9 h at night and sleep ≥ 2 h in the daytime and ADL disability was 2.93 (95% CI: 1.02-8.44), and adjusted OR of ADL moderate & severe disability was 2.75 (95% CI: 1.56-4.83). Compared with centenarians who sleep for 7-9 h and have good sleep quality, centenarians who sleep for > 9 h and have poor sleep quality have an increased risk of ADL moderate & severe disability (OR = 3.72, 95% CI: 1.54-9.00). CONCLUSION: Relation between sleep duration and ADL disability was more significant compared with sleep quality in Hainan centenarians. Poor sleep quality can aggravate the relationship between sleep duration and ADL moderate & severe disability.

Epidemiology of healthcare-associated infections and outcomes among open and robotic pancreatoduodenectomy: A retrospective study from 2013 to 2022.

BACKGROUND AND AIM: Healthcare-associated infections (HAIs) after pancreaticoduodenectomy (PD) are one of the common postoperative complications. This study aims to investigate the epidemiology of postoperative HAIs in patients with open pancreaticoduodenectomy (OPD) and robotic pancreaticoduodenectomy (RPD). METHODS: This retrospective cohort study described the trend of HAIs in patients undergoing PD from January 2013 to December 2022 at a tertiary hospital. Patients were divided into OPD and RPD, and the HAIs and outcomes were compared. RESULTS: Among 2632 patients who underwent PD, 230 (8.7%, 95% confidence interval [CI] 7.7-9.9%) were diagnosed with HAIs, with a decreasing trend from 2013 to 2022 (P < 0.001 for trend). The incidence of postoperative HAIs was significantly higher in patients with OPD than RPD (9.6% vs 5.8%; P = 0.003). The incidence of HAIs for patients with OPD showed a decreasing trend (P = 0.001 for trend), and the trend for RPD was not significant (P = 0.554 for trend). Logistic regression showed that RPD was significantly associated with postoperative HAIs after adjusting for covariates (adjusted odds ratio = 0.654; 95% CI 0.443-0.965; P = 0.032), especially in the subgroup of patients without preoperative biliary drainage (adjusted odds ratio = 0.486; 95% CI 0.292-0.809; P = 0.006). Regarding clinical outcomes, RPD has a shorter length of stay and a more expensive charge than OPD (all P < 0.05). CONCLUSION: Postoperative HAIs in patients with PD showed a decreasing trend in recent years, especially in OPD. RPD was significantly associated with reduced postoperative HAIs and length of stay, although the charge is more expensive. Attention should be paid to postoperative HAIs in OPD, and it is imperative to continue reducing the costs of RPD.

Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater.

We present Crykey, a computational tool for rapidly identifying cryptic mutations of SARS-CoV-2. Specifically, we identify co-occurring single nucleotide mutations on the same sequencing read, called linked-read mutations, that are rare or entirely missing in existing databases, and have the potential to represent novel cryptic lineages found in wastewater. While previous approaches exist for identifying cryptic linked-read mutations from specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and for tens of thousands of samples and with increased scrutiny, given their potential to represent either artifacts or hidden SARS-CoV-2 lineages. Crykey fills this gap by identifying rare linked-read mutations that pass stringent computational filters to limit the potential for artifacts. We evaluate the utility of Crykey on >3,000 wastewater and >22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over a three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations representing potential cryptic lineages in wastewater.

Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta.

IMPORTANCE: Our study provides insights into the evolution of the coronavirus disease 2019 (COVID-19) pandemic in Malta, a highly connected and understudied country. We combined epidemiological and phylodynamic analyses to analyze trends in the number of new cases, deaths, tests, positivity rates, and evolutionary and dispersal patterns from August 2020 to January 2022. Our reconstructions inferred 173 independent severe acute respiratory syndrome coronavirus 2 introductions into Malta from various global regions. Our study demonstrates that characterizing epidemiological trends coupled with phylodynamic modeling can inform the implementation of public health interventions to help control COVID-19 transmission in the community.

An electrochemical microsensor based on a specific recognition element for the simultaneous detection of hydrogen peroxide and ascorbic acid in the live rat brain.

A novel electrochemical microsensor was developed for the ratiometric and simultaneous determination of hydrogen peroxide (H2O2) and ascorbic acid (AA) based on the borate-phenol "switch" recognition mechanism and carbon nanotube (CNT) catalytic characteristics. First of all, a carbon fiber microelectrode (CFME) was coated with CNTs. Then, a specific probe, 9-anthraceneboronic acid pinacol ester (9-AP), was screened and decorated on CNTs through π-π stacking for the recognition of H2O2 based on the transformation of boric acid ester into electroactive phenols. CNTs not only served as the amplifiers of current signals, but also as catalysts facilitating AA oxidation. Meanwhile, ferrocenecarboxylic acid (Fc), inert to H2O2 and AA, was modified on another amino-functionalized CNT microelectrode via an amide bond as an internal reference channel for avoiding errors caused by environmental discrepancies. The two-channel ratiometric microsensor enabled the sensitive and accurate detection of H2O2 and AA simultaneously, and the detection limits were estimated to be 0.09 µM and 4.12 µM, respectively. The developed microsensor with remarkable analytical performance was finally applied for the simultaneous detection of H2O2 and AA in the live rat brain.

Prefrontal cortex-specific Dcc deletion induces schizophrenia-related behavioral phenotypes and fail to be rescued by olanzapine treatment.

Multiple genome studies have discovered that variation in deleted in colorectal carcinoma (Dcc) at transcription and translation level were associated with the occurrences of psychiatric disorders. Yet, little is known about the function of Dcc in schizophrenia (SCZ)-related behavioral abnormalities and the efficacy of antipsychotic drugs in vivo. Here, we used an animal model of prefrontal cortex-specific knockdown (KD) of Dcc in adult C57BL/6 mice to study the attention deficits and impaired locomotor activity. Our results supported a critical role of Dcc deletion in SCZ-related behaviors. Notably, olanzapine rescued the SCZ-related behaviors in the MK801-treated mice but not in the cortex-specific Dcc KD mice, indicating that Dcc play a critical in the mechanism of antipsychotic effects of olanzapine. Knockdown of Dcc in prefrontal cortex results in glutamatergic dysfunction, including defects in glutamine synthetase and postsynaptic maturation. As one of the major risk factors of the degree of antipsychotic response, Dcc deletion-induced glutamatergic dysfunction may be involved in the underlying mechanism of treatment resistance of olanzapine. Our findings identified Dcc deletion-mediated SCZ-related behavioral defects, which serve as a valuable animal model for study of SCZ and amenable to targeted investigations in mechanistic hypotheses of the mechanism underlying glutamatergic dysfunction-induced antipsychotic treatment resistance.

A comprehensive and high-throughput screening method for multiple prohibited substances by UPLC-QE Plus-HRMS and HPLC-QQQ-MS in human urine for doping control.

Since the World Anti-Doping Agency's (WADA) Prohibited List is updated on an annual basis, screening methods must be continually adapted to align with these changes. In accordance with Technical Document-MRPL 2022, a newly combined, comprehensive, rapid and high-throughput doping control screening method has been developed for the analysis of 350 substances with different polarities in human urine using ultra-high performance liquid chromatography coupled with Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (UPLC-QE Plus-HRMS) and ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometer (UPLC-QQQ-MS). The limits of detection were in the range of 0.12-50 ng mL-1 for beta-2 agonists, hormone and metabolic modulators, narcotics, cannabinoids and glucocorticoids, 0.1-14 ng mL-1 for the manipulation of blood and blood components, beta blockers, anabolic agents and hypoxia-inducible factor (HIF) activating agents, and 2.5-100 000 ng mL-1 for substances of Appendix A, diuretics & masking agents and stimulants. The sample preparation consisted of two parts: one is the dilute & shoot part analyzed in UPLC-QQQ-MS, another is a mixture of the dilute & shoot part and a liquid-liquid extraction part of hydrolyzed human urine analyzed in UPLC-QE Plus-HRMS in full scan mode with polarity switching and parallel reaction monitoring (PRM) mode. The method has been fully validated for doping control purposes. All the substances were compliant with WADA's required 1/2 minimum requirement performance level (MRPL) or minimum reporting level (MRL), and this method was successfully used in the 2022 Beijing Winter Olympic Games and Winter Paralympic Games for anti-doping purpose.

Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater.

As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).

Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.

Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 2 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer SNPs overlapping with primers and predicted PCR byproducts. We also compared Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (~90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluated Olivar on real wastewater samples and found that Olivar had up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available as a web application at https://olivar.rice.edu. Olivar can also be installed locally as a command line tool with Bioconda. Source code, installation guide and usage are available at https://github.com/treangenlab/Olivar.

Retrospective Analysis of Epidemiology, Risk Factors, and Outcomes of Health Care-Acquired Carbapenem-Resistant Klebsiella pneumoniae Bacteremia in a Chinese Tertiary Hospital, 2010-2019.

INTRODUCTION: In the present study, we aimed to describe the proportion of carbapenem-resistant Klebsiella pneumoniae bloodstream infection (CRKP-BSI) in KP-BSI in one Chinese tertiary hospital over 10 years and determine the risk factors and outcomes of CRKP-BSI. METHODS: We retrospectively analyzed clinical and microbiological data of patients with KP-BSI from January 2010 to December 2019 to identify risk factors, clinical features, and outcomes using multivariate logistic regression analysis. KP-BSI only included monomicrobial BSI and health care-acquired BSI. RESULTS: Among the total 687 isolates of KP-BSI in this study, the rate of CRKP was 39.0% (268/687); this rate in the intensive care unit (ICU) was 65.6% and that in seven high-risk departments (including four ICUs, respiratory medicine, gastroenterology medicine, and hepatobiliary surgery) was 74.6%. The annual rate of CRKP in KP-BSI ranged from 0.0% in 2010 to 54.5% in 2019. The 28-day mortality was 36.2% in patients with CRKP-BSI and 11.7% in those with carbapenem-susceptible K. pneumoniae (CSKP) BSI. Multivariable logistic regression analysis showed that prior ICU stay (odds ratio [OR] 2.485, P < 0.001), hospital stay ≥ 30 days prior to BSI (OR 1.815, P = 0.007), prior mechanical ventilation (OR 2.020, P = 0.014), prior urinary catheter (OR 1.999, P = 0.003), prior carbapenem use (OR 3.840, P < 0.001), hepatobiliary disease (OR 2.943, P < 0.001), pancreatitis (OR 2.700, P = 0.026), and respiratory disease (OR 2.493, P = 0.009) were risk factors of CRKP-BSI. Patients with a first admission (OR 0.662, P = 0.046) had a lower percentage of CRKP-BSI. CONCLUSION: The rapidly rising rate of CRKP-BSI in KP with high mortality requires increased attention. Exposure to carbapenems, ICU stay, invasive mechanical ventilation or urinary catheter, prolonged hospital stay, hepatobiliary disease, pancreatitis, and respiratory disease were found to be risk factors for CRKP-BSI. Strict control measures should be implemented to prevent the emergence and spread of CRKP, especially in high-risk departments.