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In evidence synthesis, dealing with zero-events studies is an important and complicated task that has generated broad discussion. Numerous methods provide valid solutions to synthesizing data from studies with zero-events, either based on a frequentist or a Bayesian framework. Among frequentist frameworks, the one-stage methods have their unique advantages to deal with zero-events studies, especially for double-arm-zero-events. In this article, we give a concise overview of the one-stage frequentist methods. We conducted simulation studies to compare the statistical properties of these methods to the two-stage frequentist method (continuity correction) for meta-analysis with zero-events studies when double-zero-events studies were included. Our simulation studies demonstrated that the generalized estimating equation with unstructured correlation and beta-binomial method had the best performance among the one-stage methods. The random intercepts generalized linear mixed model showed good performance in the absence of obvious between-study variance. Our results also showed that the continuity correction with inverse-variance heterogeneous (IVhet) analytic model based on the two-stage framework had good performance when the between-study variance was obvious and the group size was balanced for included studies. In summary, the one-stage framework has unique advantages to deal with studies with zero events and is not susceptive to group size ratio. It should be considered in future meta-analyses whenever possible.

Abstract Background In the US, stimulant use is associated with a 3–6 times greater rate of HIV seroconversion in sexual minority men (SMM) than in those who do not use stimulants. Annually, 1 in 3 SMM who HIV seroconvert will be persistent methamphetamine (meth) users. The primary objective of this qualitative study was to explore experiences of stimulant use in SMM living in South Florida, a high priority region for the Ending the HIV Epidemic initiative. Methods The sample included 25 SMM who use stimulants, recruited via targeted ads on social networking apps. Participants completed one-on-one semi-structured qualitative interviews, conducted from July 2019 through February 2020. A general inductive approach was used to identify themes relating to experiences, motivations, and overall relationship with stimulant use. Results Mean age of participants was 38.8, ranging from 20 to 61 years old. Participants were 44% White, 36% Latino, 16% Black and 4% Asian. Most participants were born in the US, self-identified as gay, and preferred meth as their stimulant of choice. Themes included: (1) stimulants as cognitive enhancements for focus or task completion, including transitioning to meth after first using prescription psychostimulants; (2) unique South Florida environment where participants could be open regarding their sexual minority status while also being influential on their stimulant use; (3) stimulant use as both stigmatizing and a coping mechanism for stigma. Participants anticipated stigma by family and potential sexual partners due to their stimulant use. They also reported using stimulants to cope with feelings of stigma due to their minoritized identities. Conclusion This study is among the first to characterize motivations for stimulant use in SMM living in South Florida. Results highlight both the risk and protective factors of the South Florida environment, psychostimulant misuse as a risk for meth initiation, and the role of anticipated stigma on stimulant use in SMM. Understanding stimulant use motivations can help to shape intervention development. This includes developing interventions that address individual, interpersonal, and cultural factors that drive stimulant use and increase risk of HIV acquisition. Trial registration NCT04205487.

Abstract Background Thymic squamous cell carcinoma and type B3 thymoma are primary neoplasms of the anterior mediastinum that are sometimes difficult to differentiate from one another histologically. However, only a few immunohistochemical markers are available for the differential diagnosis. The purpose of this study was to discover a novel marker for differentiating between thymic squamous cell carcinoma and type B3 thymoma. Methods We used histological samples of thymic carcinomas (n = 26) and type B3 thymomas (n = 38) which were resected between 1986 and 2017. To search for candidates of differential markers, gene expression levels were evaluated in samples using promoter analysis by cap analysis of gene expression (CAGE) sequencing. Results Promoter level expression of CALML5 genes was significantly higher in thymic carcinomas than in type B3 thymomas. We further validated the results of the CAGE analysis in all 26 thymic carcinomas and 38 type B3 thymomas by immunohistochemistry (IHC). CALML5 was strongly expressed in the cytoplasm in 19 of 26 cases with thymic carcinoma, whereas positivity at the protein level was shown in two of 38 type B3 thymomas. Thus, the sensitivity (73.1%) and specificity (94.7%) of CALML5 as markers for immunohistochemical diagnosis of thymic carcinoma were extremely high. Conclusion We identified CALML5 as a potential marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. It is assumed that future clinical use of CALML5 may improve the diagnostic accuracy of differentiating between these two diseases.

ABSTRACT: Objectives: The purpose of this study was to characterize the strains of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) isolated from municipal and hospital wastewater by detecting antibiotic resistance genes (ARGs) as well as antibiotic susceptibility. To identify the source of ESBL-EC, multi-locus sequence typing and typing plasmids that may carry ESBL-producing genes were conducted. Methods: Wastewater was sampled twice a month from February 2019 to February 2020 from a municipal wastewater treatment plant and hospital located in a city in northeastern Japan. Throughout the study period, 279 and 37 strains of ESBL-EC were isolated from municipal and hospital wastewater, respectively. Results: All 316 isolates were resistant to ampicillin and cefotaxime and susceptible to imipenem and tigecycline. Almost all (98.1%) of the ESBL-EC isolates possessed blaCTX-M, and the blaCTX-M-9 group was detected most frequently (62.3%). Multi-locus sequence typing revealed a higher diversity of sequence types (STs) in the isolates from municipal wastewater than in those from hospital wastewater; although ST131, which recently caused nosocomial- and community-associated infections worldwide, was dominant in both types of wastewater. All ST131 isolates possessed the IncFII plasmid, which is often reported to carry blaCTX-M. Conclusions: These results demonstrated that healthy people carry clinically important antibiotic-resistant bacteria and ARGs, motivating routine monitoring of municipal wastewater to detect such antibiotic-resistant bacteria and ARGs from a variety of sources supported by the high diversity of STs in the present study.

Abstract Despite Japan’s high vaccination coverage, daily numbers of new COVID-19 cases have been high. However, studies on the seroprevalence among Japanese people and the causative factors for rapid spread have remained limited. In this study, we aimed to examine the seroprevalence and associated factors in healthcare workers (HCWs) of a medical center in Tokyo using blood samples drawn at annual check-ups from 2020 to 2022. We found that of the 3,788 HCWs in 2022 (by mid-June), 669 were seropositive for N-specific antibodies (tested by Roche Elecsys Anti-SARS-CoV-2 assay); the seroprevalence surged from 0.3% in 2020 and 1.6% in 2021 to 17.7% in 2022. Notably, our study found 325 (48.6%; 325/669) cases were infected without awareness. Among those with a previously PCR-confirmed SARS-CoV-2 infection during the past three years, 79.0% (282/357) were found after January 2022, after the Omicron variant was first detected in Tokyo at the end of 2021. This study indicates the fast spread of the SARS-CoV-2 among HCWs during the Omicron surge in Japan. The high percentage of infection without awareness may be a key driving factor causing rapid person-to-person transmission, as shown in this medical center with high vaccination coverage and strict infection control measures.

Abstract Background Studies included in a meta-analysis are often heterogeneous. The traditional random-effects models assume their true effects to follow a normal distribution, while it is unclear if this critical assumption is practical. Violations of this between-study normality assumption could lead to problematic meta-analytical conclusions. We aimed to empirically examine if this assumption is valid in published meta-analyses. Methods In this cross-sectional study, we collected meta-analyses available in the Cochrane Library with at least 10 studies and with between-study variance estimates > 0. For each extracted meta-analysis, we performed the Shapiro–Wilk (SW) test to quantitatively assess the between-study normality assumption. For binary outcomes, we assessed between-study normality for odds ratios (ORs), relative risks (RRs), and risk differences (RDs). Subgroup analyses based on sample sizes and event rates were used to rule out the potential confounders. In addition, we obtained the quantile–quantile (Q–Q) plot of study-specific standardized residuals for visually assessing between-study normality. Results Based on 4234 eligible meta-analyses with binary outcomes and 3433 with non-binary outcomes, the proportion of meta-analyses that had statistically significant non-normality varied from 15.1 to 26.2%. RDs and non-binary outcomes led to more frequent non-normality issues than ORs and RRs. For binary outcomes, the between-study non-normality was more frequently found in meta-analyses with larger sample sizes and event rates away from 0 and 100%. The agreements of assessing the normality between two independent researchers based on Q–Q plots were fair or moderate. Conclusions The between-study normality assumption is commonly violated in Cochrane meta-analyses. This assumption should be routinely assessed when performing a meta-analysis. When it may not hold, alternative meta-analysis methods that do not make this assumption should be considered.

Abstract Background Alzheimer’s disease (AD) is one of the neurodegenerative diseases and characterized by the appearance and accumulation of amyloid-β (Aβ) aggregates and phosphorylated tau with aging. The aggregation of Aβ, which is the main component of senile plaques, is closely associated with disease progression. App NL-G-F mice, a mouse model of AD, have three familial AD mutations in the amyloid-β precursor gene and exhibit age-dependent AD-like symptoms and pathology. Gut-brain interactions have attracted considerable attention and inflammatory bowel disease (IBD) has been associated with a higher risk of dementia, especially AD, in humans. However, the underlying mechanisms and the effects of intestinal inflammation on the brain in AD remain largely unknown. Therefore, we aimed to investigate the effects of intestinal inflammation on AD pathogenesis. Methods Wild-type and App NL-G-F mice at three months of age were fed with water containing 2% dextran sulfate sodium (DSS) to induce colitis. Immune cells in the brain were analyzed using single-cell RNA sequencing (scRNA-seq) analysis, and the aggregation of Aβ protein in the brain was analyzed via immunohistochemistry. Results An increase in aggregated Aβ was observed in the brains of App NL-G-F mice with acute intestinal inflammation. Detailed scRNA-seq analysis of immune cells in the brain showed that neutrophils in the brain increased after acute enteritis. Eliminating neutrophils by antibodies suppressed the accumulation of Aβ, which increased because of intestinal inflammation. Conclusion These results suggest that neutrophils infiltrate the AD brain parenchyma when acute colitis occurs, and this infiltration is significantly related to disease progression. Therefore, we propose that neutrophil-targeted therapies could reduce Aβ accumulation observed in early AD and prevent the increased risk of AD due to colitis.

Abstract Objectives In evidence synthesis practice, dealing with studies with no cases in both arms has been a tough problem, for which there is no consensus in the research community. In this study, we propose a method to measure the potential impact of studies with no cases for meta-analysis results which we define as harms index (Hi) and benefits index (Bi) as an alternative solution for deciding how to deal with such studies. Methods Hi and Bi are defined by the minimal number of cases added to the treatment arm (Hi) or control arm (Bi) of studies with no cases in a meta-analysis that lead to a change of the direction of the estimates or its statistical significance. Both exact and approximating methods are available to calculate Hi and Bi. We developed the “hibi” module in Stata so that researchers can easily implement the method. A real-world investigation of meta-analyses from Cochrane reviews was employed to evaluate the proposed method. Results Based on Hi and Bi, our results suggested that 21.53% (Hi) to 26.55% (Bi) of Cochrane meta-analyses may be potentially impacted by studies with no cases, for which studies with no cases could not be excluded from the synthesis. The approximating method shows excellent specificity (100%) for both Hi and Bi, moderate sensitivity (68.25%) for Bi, and high sensitivity (80.61%) for Hi compared to the exact method. Conclusions The proposed method is practical and useful for systematic reviewers to measure whether studies with no cases impact the results of meta-analyses and may act as an alternative solution for review authors to decide whether to include studies with no events for the synthesis or not.

The spatial and frontal QRS-T angles are electrocardiographic (ECG) predictors for arrhythmia. This work used genetic analyses to identify associated loci and pathways, and explore their relationships with other ECG traits and cardiovascular disease.

Rapid reviews have been widely employed to support timely decision-making, and limiting the search date is the most popular approach in published rapid reviews. We assessed the accuracy and workload of search date limits on the meta-analytical results to determine the best rapid strategy. The meta-analyses data were collected from the Cochrane Database of Systematic Reviews (CDSR). We emulated the rapid reviews by limiting the search date of the original CDSR to the recent 40, 35, 30, 25, 20, 15, 10, 7, 5, and 3 years, and their results were compared to the full meta-analyses. A random sample of 10% was drawn to repeat the literature search by the same timeframe limits to measure the relative workload reduction (RWR). The relationship between accuracy and RWR was established. We identified 21,363 meta-analyses of binary outcomes and 7683 meta-analyses of continuous outcomes from 2693 CDSRs. Our results suggested that under a maximum tolerance of 5% and 10% on the bias of magnitude, a limit on the recent 20 years can achieve good accuracy and at the same time save the most workload. Under the tolerance of 15% and 20% on the bias, a limit on the recent 10 years and 15 years could be considered. Limiting the search date is a valid rapid method to produce credible evidence for timely decisions. When conducting rapid reviews, researchers should consider both the accuracy and workload to make an appropriate decision.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only, and its association with lower leptin concentrations was specific to this ancestry (P = 2 × 10-16, n = 3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting that leptin regulates early adiposity.

The Escherichia coli (E. coli)-based protein synthesis using recombinant elements (PURE) system is a cell-free protein synthesis system reconstituted from purified factors essential for E. coli translation. The PURE system is widely used for basic and synthetic biology applications. One of the major challenges associated with the PURE system is that the protein yield of the system varies depending on the protein. Studies have reported that the efficiency of translation is significantly affected by nucleotide and amino acid sequences, especially in the N-terminal region. Here, we investigated the inherent effect of various N-terminal sequences on protein synthesis using the PURE system. We found that a single amino acid substitution in the N-terminal region significantly altered translation efficiency in the PURE system, especially at low temperatures. This result gives us useful suggestions for the expression of the protein of interest in vitro and in vivo.

Information regarding Klebsiella aerogenes haboring carbapenemase in Japan is limited. A comprehensive nationwide survey was conducted from September 2014 to December 2022, and 67 non-duplicate strains of carbapenem-resistant K. aerogenes were isolated from 57 healthcare facilities in Japan. Through genetic testing and whole-genome sequencing, six strains were found to possess carbapenemases, including imipenemase (IMP)-1, IMP-6, New Delhi metallo-β-lactamase (NDM)-1, and NDM-5. The strain harboring blaNDM-5 was the novel strain ST709, which belongs to the clonal complex of the predominant ST4 in China. The novel integron containing blaIMP-1 featured the oxacillinase-101 gene, which is a previously unreported structure, with an IncN4 plasmid type. However, integrons found in the strains possessing blaIMP-6, which were the most commonly identified, matched those reported domestically in Klebsiella pneumoniae, suggesting the prevalence of identical integrons. Transposons containing blaNDM are similar or identical to the transposon structure of K. aerogenes harboring blaNDM-5 previously reported in Japan, suggesting that the same type of transposon could have been transmitted to K. aerogenes in Japan. This investigation analyzed mobile genetic elements, such as integrons and transposons, to understand the spread of carbapenemases, highlighting the growing challenge of carbapenem-resistant Enterobacterales in Japan and underscoring the critical need for ongoing surveillance to control these pathogens.

The automotive industry needs to improve energy efficiency rapidly to achieve carbon neutrality while creating a safe, secure, and comfortable driving environment for customers. Porous sound-absorbing materials and porous thermal insulators are typically used to satisfy these requirements despite limitations in mass and space. While these porous materials are similar, the microstructures they offer for high performance differ in the size and connectivity of their fluid phases, which enhances the difficulty of achieving excellent sound absorption and thermal insulation in the same material. In this study, a hydrophobic cellulose nanofiber–poly(methylsiloxane) xerogel composite was developed using computational microstructure modeling. This porous material has high porosity and excellent thermal insulation and sound absorption properties.

Introduction: Educational attainment, widely used in epidemiologic studies as a surrogate for socioeconomic status, is a predictor of cardiovascular health outcomes.Methods: A two-stage genome-wide meta-analysis of low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), and triglyceride (TG) levels was performed while accounting for gene-educational attainment interactions in up to 226,315 individuals from five population groups. We considered two educational attainment variables: “Some College” (yes/no, for any education beyond high school) and “Graduated College” (yes/no, for completing a 4-year college degree). Genome-wide significant (p < 5 × 10−8) and suggestive (p < 1 × 10−6) variants were identified in Stage 1 (in up to 108,784 individuals) through genome-wide analysis, and those variants were followed up in Stage 2 studies (in up to 117,531 individuals).Results: In combined analysis of Stages 1 and 2, we identified 18 novel lipid loci (nine for LDL, seven for HDL, and two for TG) by two degree-of-freedom (2 DF) joint tests of main and interaction effects. Four loci showed significant interaction with educational attainment. Two loci were significant only in cross-population analyses. Several loci include genes with known or suggested roles in adipose (FOXP1, MBOAT4, SKP2, STIM1, STX4), brain (BRI3, FILIP1, FOXP1, LINC00290, LMTK2, MBOAT4, MYO6, SENP6, SRGAP3, STIM1, TMEM167A, TMEM30A), and liver (BRI3, FOXP1) biology, highlighting the potential importance of brain-adipose-liver communication in the regulation of lipid metabolism. An investigation of the potential druggability of genes in identified loci resulted in five gene targets shown to interact with drugs approved by the Food and Drug Administration, including genes with roles in adipose and brain tissue.Discussion: Genome-wide interaction analysis of educational attainment identified novel lipid loci not previously detected by analyses limited to main genetic effects.

Background Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways. Methods To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses. Results Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology. Conclusions Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.

Background: Data extraction is the foundation for research synthesis evidence, while data extraction errors frequently occur in the literature. An interesting phenomenon was observed that data extraction error tend to be more common in trials of pharmaceutical interventions compared to non-pharmaceutical ones. The elucidation of which would have implications for guidelines, practice, and policy. Methods and analyses: We propose a crossover, multicenter, investigator-blinded trial to elucidate the potential variants on the data extraction error rates. Eligible 90 participants would be 2nd year or above post-graduate students (e.g., masters, doctoral program). Participants will be randomized to one of the two groups to complete pre-defined data extraction tasks: 1) group A will contain 10 randomized controlled trials (RCTs) of pharmaceutical interventions; 2) group B will contain 10 RCTs of non-pharmaceutical interventions. Participants who finish the data extraction would then be assigned to the alternative group for another round of data extraction after a 30 min washout period. Finally, those participants assigned to A or B group will be further 1:1 randomly matched based on a random-sequenced number for the double-checking process on the extracted data. The primary outcome will be the data extract error rates of the pharmaceutical intervention group and non-pharmaceutical group, before the double-checking process, in terms of the cell level, study level, and participant level. The secondary outcome will be the data error rates of the pharmaceutical intervention group and non-pharmaceutical group after the double-checking process, again, in terms of the cell level, study level, and participant level. A generalized linear mixed effects model (based on the above three levels) will be used to estimate the potential differences in the error rates, with a log link function for binomial data. Subgroup analyses will account for the experience of individuals on systematic reviews and the time used for the data extraction. Discussion: This trial will provide useful evidence for further systematic review of data extraction practices, improved data extraction strategies, and better guidelines. Trial registration: Chinese Clinical Trial Register Center (Identifier: ChiCTR2200062206).

Background: Cellulitis is a common complication of cystic lymphatic malformations (cLM) and Klippel–Trenaunay syndrome (KTS). Cellulitis in the pediatric population requires hospitalization and reduces a patients’ quality of life. This study aimed to clarify the seasonality and characteristics of cellulitis in patients with cLM and KTS. Methods: We retrospectively reviewed the clinical records of patients with cLM and KTS who were admitted for cellulitis between January 2014 and December 2021. Results: One hundred and seventeen hospitalizations of 33 patients with cellulitis were examined. There were 80 and 37 hospitalizations for cLM and KTS oatients, respectively. The number and percentage of hospitalizations in spring, summer, autumn, and winter were 26 (22.2%), 43 (36.8%), 19 (16.2%), and 29 (24.8%), respectively, showing a significantly different frequency (P = 0.018). The number of hospitalization days per season was not significantly different between the seasons (P = 0.335). Seasonality and hospitalization duration did not differ significantly between the cLM and KTS groups. Of the 117 hospitalized cases, only 5 (4.3%) had positive blood cultures. The number of hospitalizations remarkably correlated with temperature and humidity from April to November. Conclusions: Cellulitis associated with lymphatic malformations, such as cLM and KTS, occurs more frequently in the summer. Patients should take precautions to prevent their lesions from progressing to cellulitis, particularly in summer. Levels of evidence: Level Ⅲ

We demonstrated an endovascular technique excluding an ascending aorta pseudoaneurysm using an aortic extension. A 32-year-old woman, 3 years after lung transplantation with extracorporeal membrane oxygenation presented with an ascending aortic pseudoaneurysm. Vascular surgery was consulted after open repair was deemed high risk. An aortic extension stent graft was placed in a hybrid operating room with the aid of intraoperative transesophageal echocardiography. Ascending aorta pseudoaneurysms are complex and life-threatening complications. Traditional repair involves high surgical and anesthetic risks whereas endovascular treatment is technically feasible.