bluuebunny/crossref_metadata_2025 huggingface dataset:
Folate intake and the risk of endometrial cancer: A dose–response meta-analysis
Authors: Long Jiaye , Wang Du , Yang Miyang , Pang Yingrong , Li Meiqiong , Qin Shuxin , Cui Kai
Published: September 2024

Background:

The relationship between folate intake and risk of endometrial cancer (EC) is debatable. The goal of this study was to examine the relationship between folate consumption and EC and then conduct a dose–response analysis in accordance with this.

Methods:

Up until February 1, 2024, we conducted a thorough search using PubMed, EMBASE, the Cochrane Library, and Web of Science. Stata 14 software was used to analyze the findings of the article. The study protocol was registered in PROSPERO (CRD42024505943), and the meta-analysis was conducted in accordance with PRISMA guidelines.

Results:

Nine case-control studies and 6 cohort studies were included, comprising 379,570 participants and 8660 EC cases. The highest level of folate consumption was associated with a 10% reduction in the occurrence of EC (relative risk [RR] = 0.90, 95% confidence intervals [CIs]: 0.78–1.05, I
2 = 63.2%) compared to the lowest level of intake. The association exhibited a statistically significant linear trend (P = .231), with a combined RR of 0.974 (95% CI: 0.968–0.981) for each daily intake of 50 µg folate.

Conclusion:

Folate intake may reduce the risk of EC.
Causal relationship between smoking and spinal stenosis: Two-sample Mendelian randomization
Authors: Deng Guang-Hua
Published: September 2024

Objective:

Currently, the number of patients with spinal stenosis is increasing, and most of the patients are found to have a history of smoking in the clinic. In this study, we used the Mendelian randomization (MR) method to investigate the causal relationship between smoking and spinal stenosis.

Methods:

Genetic loci independently associated with smoking and spinal stenosis in people of European ancestry were selected as instrumental variables using pooled data from large-scale genome-wide association studies (GWAS). Three MR analyses, MR-Egger, Weighted median and inverse variance weighting (IVW), were used to investigate the causal relationship between smoking and spinal stenosis. The results were tested for robustness by heterogeneity and multiplicity tests, and sensitivity analyses were performed using the “leave-one-out” method.

Results:

The IVW results showed an OR (95% CI) of 2.40 (0.31–18.71), P = .403, indicating that there was no causal relationship between smoking and spinal stenosis. And no heterogeneity and multiplicity were found by the test and sensitivity analysis also showed robust results.

Conclusion:

In this study, genetic data were analyzed and explored using 2-sample MR analysis, and the results showed that there is a causal relationship between smoking and the occurrence of spinal stenosis, and more studies need to be included.
Ultrasonography as a way of evaluating the diaphragm muscle in patients with chronic obstructive pulmonary disease
Authors: Figueira Silva Bianca Carmo , Abreu Diego Condesso , Souza Yves Raphael , Figueiredo Manoele , Macêdo Joseane Felix , Mafort Thiago Thomaz , Rufino Rogerio , Costa Claudia Henrique da
Published: September 2024

The respiratory muscles in chronic obstructive pulmonary disease (COPD) patients have reduced strength and resistance, leading to loss of the functional ability of these muscles. Lung hyperinflation is one of the main alterations, and air trapping is the main factor limiting diaphragmatic mobility (DM) in these patients; however, its correlation with functional parameters, exercise capacity, and indicators of disease severity remains underexplored. This study aimed to assess DM in stable COPD patients and relate the findings with parameters such as the 6-minute walk test distance, forced expiratory volume in 1 second (FEV1) %predicted, residual volume (RV) %predicted, and dyspnea. An observational cohort study was conducted to measure DM using ultrasound both at rest (DMrest) and during deep inspiration (DMmax). Forty-nine patients with stable COPD were included in this study. There was a correlation between DMmax and FEV1 %predicted (R = 0.36; P = .012), RV %predicted (r = −0.42; P = .01), RV/total lung capacity (r = −0.61; P < .001), and distance reached in the 6MWT (R = 0.46; P = .001). Patients with a modified Medical Research Council score <2 exhibited greater DM than those with a score ≥2 (mean difference = 13.20 ± 4.6 mm; P = .0059). Similarly, patients with a Body Mass Index, Airflow Obstruction, Dyspnea and Exercise Capacity index ≤4 showed greater DM (61.95 mm) than those with a Body Mass Index, Airflow Obstruction, Dyspnea and Exercise Capacity index >4 (47.89 mm; mean difference = 14.05 ± 5.3 mm; 95% confidence interval = 25.09–3.01 mm). DM is correlated with bronchial obstruction (FEV1), lung hyperinflation (RV and RV/total lung capacity), exercise capacity, and dyspnea in patients with COPD, suggesting its utility as an evaluative tool in this population.
Predictive value of neutrophil-to-lymphocyte ratio for adverse outcomes in hospitalized patients with acute exacerbation of chronic obstructive pulmonary disease: A retrospective study
Authors: Vu-Hoai Nam , Ly-Phuc Duc , Duong-Minh Ngoc , Tran-Ngoc Nguyen , Nguyen-Dang Khoa
Published: September 2024

Chronic obstructive pulmonary disease (COPD) stands as one of the leading causes of mortality worldwide. Acute exacerbations of COPD (AECOPD) lead to rapid respiratory function decline and worsened disease status. Despite recent studies, the ability of the neutrophil-to-lymphocyte ratio (NLR) to predict outcomes in patients with COPD remains controversial. We investigated the predictive value of NLR for adverse outcomes in hospitalized patients with AECOPD. A retrospective study was conducted at the Department of Pulmonary Medicine, Cho Ray Hospital (Vietnam) from November 2019 to November 2021. The study extracted data from patients diagnosed with AECOPD at discharge and met the inclusion criteria. NLR is calculated by dividing the number of neutrophils by the number of lymphocytes in the peripheral blood test. Adverse outcomes are defined as invasive mechanical ventilation, admission to intensive care unit, or in-hospital mortality. Multivariable regression analysis was conducted to identify variables predicting adverse outcomes. The cutoff, sensitivity, specificity, area under the curve, and receiver operating characteristic of NLR were determined for predicting adverse outcomes. Two hundred eighty-seven patients with AECOPD were included in the final analysis, with a mean age of 70.9, and males comprising 92.7%. The rate of adverse outcomes was 15.7%. Multivariable logistic regression identified reduced consciousness at admission (adjusted odds ratio = 0.08, 95% confidence interval [CI]: 0.02–0.38, P = .001) and high NLR (adjusted odds ratio = 1.17, 95% CI: 1.10–1.24, P < .001) as predictors of adverse outcomes. The receiver operating characteristic of NLR’s predictive value yielded an area under the curve of 0.877 (95% CI: 0.83–0.93). An NLR cutoff of 11.0 predicted adverse outcomes with a sensitivity of 80.0%, specificity of 77.7%, and an odds ratio of 13.9 (95% CI: 6.3–30.7), P < .001. NLR is a simple, routine, and cost-effective tool for predicting adverse outcomes in hospitalized patients with AECOPD. Future studies should evaluate the kinetics of NLR in predicting treatment response in patients with AECOPD.
H-marker via bronchoscopy under LungPro navigation combined with cone-beam computed tomography for locating multiple pulmonary ground-glass nodules: A case report and literature review
Authors: Fang Wanlan , Zhang Jisong , Chen Enguo , Ying Kejing
Published: September 2024

Rationale:

Pulmonary ground-glass nodules (GGNs) pose challenges in intraoperative localization due to their primarily nonsolid composition. This report highlights a novel approach using H-marker deployment guided by LungPro navigation combined with cone-beam computed tomography (CBCT) for precise localization of multiple GGNs.

Patient concerns:

A 55-year-old female patient presented at Sir-Run-Run-Shaw Hospital, Zhejiang University School of Medicine, in June 2021, requiring thoracoscopic surgery for the management of multiple GGNs in her right lung. She had a recent history of thoracoscopic wedge resection for a lesion in her lower left lung 3 months prior.

Diagnoses:

Computed tomography scans revealed the presence of 3 mixed GGNs in the right lung, with further confirmation identifying these as solitary pulmonary nodules, necessitating surgical intervention.

Interventions:

The patient underwent thoracoscopic surgery, during which the multiple nodules in her right lung were precisely localized utilizing an H-marker implanted bronchoscopically under the guidance of LungPro navigation technology, with CBCT providing additional confirmation of nodule positioning. This innovative combination of technologies facilitated accurate targeting of the lesions.

Outcomes:

Postoperative histopathological analysis confirmed the nodules to be microinvasive adenocarcinomas. Radiographic examination with chest X-rays demonstrated satisfactory lung expansion, indicating effective lung function preservation following the procedure. Follow-up assessments have shown no evidence of tumor recurrence, suggesting successful treatment.

Lessons:

The employment of H-marker implantation guided by the LungPro navigation system with CBCT confirmation presents a feasible and efficacious strategy for localizing multiple pulmonary GGNs. To further validate its clinical utility and safety, large-scale, multicenter, prospective studies are warranted. This approach holds promise in enhancing the precision and outcomes of surgeries involving GGNs.
Construction and validation of a predictive model for preoperative lower extremity deep vein thrombosis risk in elderly hip fracture patients: An observational study
Authors: Yang Chang-Song , Tan Zhe
Published: September 2024

The aim of this study was to identify independent risk factors for preoperative lower extremity deep vein thrombosis (DVT) in elderly hip fracture patients and to construct a nomogram prediction model based on them. We collected clinical data from elderly hip fracture patients from Ya’an Hospital of Traditional Chinese Medicine (2021–2023), and used univariate and multivariate logistic regression analyses to identify independent risk factors for preoperative DVT. In this way, a nomogram prediction model was established. In addition, external validation of the model was performed by patient data from Ya’an Mingshan District Hospital of Traditional Chinese Medicine. Receiver operating characteristic curve analysis was used to calculate the area under the curve, and calibration and decision curves were plotted to assess the predictive performance of the model. Of the 223 elderly hip fracture patients, 23 (10.31%) developed DVT of the lower extremities before surgery. A total of 6 variables were identified as independent risk factors for preoperative lower extremity DVT in elderly hip fracture patients by logistic regression analysis: age > 75 years (OR = 1.932; 95% CI: 1.230–3.941), diabetes mellitus (OR = 2.139; 95% CI: 1.149–4.342), and prolonged duration of disease (OR. 2.535; 95% CI: 1.378–4.844), surgical treatment (OR = 1.564; 95% CI: 1.389–3.278), D-dimer > 0.5 mg/L (OR = 3.365; 95% CI: 1.229–7.715) fibrinogen > 4 g/L (OR = 3.473; 95% CI: 1.702–7.078). The constructed nomogram model has high accuracy in predicting the risk of preoperative DVT in elderly hip fracture patients, providing an effective tool for clinicians to identify high-risk patients and implement early intervention.
Efficacy and safety of upadacitinib in the treatment of moderate-to-severe atopic dermatitis in adolescents: A systematic review and meta-analysis of randomized controlled trials
Authors: Huang Lingmei , Zhao Danjie , Lin Haixia , Zheng Hong , Li Xia , Chen Long , Tang Peng
Published: September 2024

Background:

To assess the efficacy and safety of upadacitinib in adolescents with moderate-to-severe atopic dermatitis (AD).

Methods:

A comprehensive search was conducted using PubMed, Medline, Embase, Web of Science, Clinical Trials Website, and Cochrane Library databases, spanning from their inception until February 18, 2024. The review incorporated all randomized controlled trials examining upadacitinib’s efficacy in managing moderate to severe AD among adolescent patients. The methodological quality of the selected studies underwent thorough assessment utilizing the Cochrane systematic review methodology. Statistical analyses of the outcome measures were executed employing the Review Manager 5.3 software.

Results:

The meta-analysis encompassed 4 studies in total. Compared to placebo, upadacitinib at doses of both 15 and 30 mg was associated with a significant enhancement in the eczema area and severity index-75% ([odds ratio, OR = 11.06, 95% confidence interval, CI (6.78–18.04), P < .00001]; [OR = 21.73, 95% CI (12.73–37.11), P < .00001]), a reduction in the numerical rating scale of ≥4 ([OR = 6.16, 95% CI (3.56–10.64), P < .00001]; [OR = 10.58, 95% CI (6.12–18.29), P < .00001]), and improvement in the investigator’s global assessment to 0/1 ([OR = 8.85, 95% CI (4.86–16.10), P < .00001]; [OR = 21.43, 95% CI (11.64–39.46), P < .00001]). Regarding safety, upadacitinib at both 15 and 30 mg doses was linked to a statistically significant rise in the overall incidence of adverse events when juxtaposed with placebo ([OR = 1.57, 95% CI (1.01–2.44), P = .04]; [OR = 2.21, 95% CI (1.44–3.41), P = .0003]). Nevertheless, no statistically significant disparity was discovered in the occurrence of serious adverse events between upadacitinib and placebo ([OR = 1.02, 95% CI (0.27–3.84), P = .98]; [OR = 0.42, 95% CI (0.09–1.93), P = .26]).

Conclusion:

The findings from this meta-analysis indicate that upadacitinib demonstrates substantial effectiveness and tolerability in treating moderate to severe AD in adolescents. Moreover, upadacitinib provides a rapid reduction in pruritus and markedly ameliorates symptoms and signs, with the 30 mg dosage showing a more pronounced therapeutic effect relative to the 15 mg dosage.
Patients’ experience of telehealth clinics during the COVID-19 pandemic: Cross-sectional study
Authors: AlRadini Faten A. , Abdulrahim Maha , AlOtaibi Naif , Al Amri Fahad A. , Amer Samar Ahmed
Published: September 2024

Globally, the Coronavirus disease (COVID-19) pandemic in 2019 has accelerated the adoption of telehealth technologies. The implementation of the Saudi Telemedicine Network (STN) and other digital health initiatives, such as the telehealth clinic (THC) at King Abdullah bin Abdulaziz University Hospital (KAAUH), exemplifies this trend in Saudi Arabia. The aim of this study was to explore the patients’ experience of THC in KAAUH during the COVID-19 pandemic and their’ beliefs about their readiness to replace the traditional onsite clinical visits with THC from March to September 2020. A cross-sectional study targeted all 1398 patients who utilized THC at KAAUH. A self-administrated, validated survey collected the data. The survey used a Likert scale and included questions on satisfaction with THC services and the perceived effectiveness of telehealth as a substitute for in-person visits. The collected data was analyzed using frequency and percentage. A total of 252 patients responded to the THC postvisit survey. Overall, 217 patients (86%) were satisfied, 32 patients (13%) were dissatisfied, and only 3 patients (1%) were neutral about THC. Most patients (65.5%) agree that THC provided enough information about their health conditions, which can substitute for clinical visits. About 18.3% of patients were neutral, while 16.3% disagreed with the effectiveness of THC services and believed that they could not replace onsite visits. During the COVID-19 pandemic, most patients were satisfied at KAAUH-THC in Saudi Arabia and believed that it could replace the onsite visit to a physician’s clinic. The 2 main causes of the patient’s belief that THC could not replace an onsite clinical visit were: First, nonadherence to appointments led to missed calls and a complete medical service. Second, the patient’s perception is that a physical examination and lab investigation cannot be completed through THC.
Process Evaluation of a Pilot Food Insecurity Resource Navigation Program Integrated Within Pediatric Primary Care: Utilizing RE-AIM to Inform Program Scale-up
Authors: Stuenkel Mackenzie , Koob Caitlin , Richardson Emily , Smolens Nicole , Eicken Meredith , Amati J. Blakely , Sease Kerry
Published: September 2024

Objective:

The purpose of this study was to examine the implementation and effectiveness of a novel pediatric food navigation program through a structured, comprehensive evaluation using the RE-AIM framework.

Design and Participants:

Data were collected from October 2021 through August 2022 for 166 pediatric patients and their families who were screened as food insecure or high-risk for food insecurity and were referred to this pilot food resource navigation program (FRNP). A total of 88 patients’ guardians consented to participate in this FRNP, receiving initial service connection. Participants were contacted via telephone by trained navigators within this health system to assess food security status across three time points (baseline, follow-up 1 [1- <3 months], and follow-up 2 [3-6 months]) and facilitate connection to appropriate community-based resources related to food assistance.

Results:

In this sample, we had an overrepresentation of Hispanic patients and an underrepresentation of Non-Hispanic Black and White patients relative to the available clinic population. Patients participating in the navigation program showed incremental shifts toward food security from baseline to two follow-up points. Integration within primary care was supported by physician champions across participating clinics and alignment with systemwide, updated universal screening guidelines to support projected increases in families requiring connecting to assistance programs. Through this evaluation, a comprehensive list of community-based food resource programs related to food assistance was integrated into electronic documentation for navigators to alleviate navigator burden and sustain the effect of this FRNP’s implementation.

Conclusions:

These findings may be used to inform expansion of current programming efforts within this FRNP and to clarify process evaluations of broader health system-based programming. Further research, building on the findings of this pilot study, is needed to examine the longitudinal, causal effect of FRNPs in pediatric food security and long-term health outcomes for replication across health systems nationwide.
New Metabolomic Insights Into Cancer
Authors: Zhu Jiangjiang
Published: September 2024

Cancer has been marked by metabolic irregularities that fuel various aggressive activities such as rapid cell proliferation, evasion of the immune system, and spread to distant organs. Therefore, exploiting cancer metabolism for diagnosis, monitoring, or treatment has been extensively studied in the past couple of decades with various molecular and cellular techniques. More recently, investigating cancer diagnostics and treatments through advanced metabolomics has emerged, and these comprehensive approaches provide a holistic understanding of cancer metabolism, which supported the discovery of metabolic targets relevant across multiple cancer types and the development of more effective treatments. This study offers highlights of new knowledge on cancer metabolism enabled by recent metabolomics studies and their potential applications in aiding cancer research and predicting cancer treatment outcomes. Specifically, we discussed the use of advanced metabolomics in cancer metabolism, tumor microenvironment, and cancer immunotherapy studies to provide valuable insights that can shape future research efforts in the dynamic field of cancer metabolism research.
Ecosystemic Approach to Understanding Gut Microbiome–Mediated Prevention of Colorectal Cancer
Authors: Lutsiv Tymofiy , Hussan Hisham , Thompson Henry J.
Published: September 2024

Humans and their associated microorganisms coexist in complex symbiotic relationships. Continuously advancing research is demonstrating the crucial role of host-associated microbiota in the pathophysiology and etiology of disease and in mediating the prevention thereof. As an exemplar, the gut microbiota, especially colonic bacteria, have been extensively studied in colorectal cancer (CRC), and the growing body of evidence establishes new oncomicrobes and their oncometabolites associated with the initiation and promotion of carcinogenesis. Herein, we discuss the importance of approaching the gut microbiome as an ecosystem rather than an assortment of individual factors, especially in the context of cancer prevention. Furthermore, we argue that a dietary pattern effectively drives multiple nodes of the gut microbial ecosystem toward disease- or health-promoting qualities. In the modern circumstances of excessive consumption of ultraprocessed and animal-based foods and concomitant escalation of chronic disease burden worldwide, we focus on whole food–derived dietary fiber as a key to establishing a health-promoting eubiosis in the gut.
Forehead shape analysis following surgical and conservative treatment in metopic synostosis: a 3D photogrammetry analysis
Authors: Tio Pauline A.E , Abdel Alim Tareq , Roshchupkin Gennady , Versnel S.L. , Pleumeekers Mieke M. , van Veelen Marie-Lise C. , Mathijssen Irene M.J.
Published: September 2024

Background:

The aim of this study is to describe and compare head shape in surgically and conservatively treated patients using 3D photogrammetry.

Methods:

A retrospective review (2017-2020) of consecutive patients with isolated metopic synostosis based on 3D photogrammetry was conducted at the age of 4 years old. Images were aligned using a healthy age-matched template, and mean head shapes were reconstructed to evaluate shape development. A comparative sub-analysis based on phenotype was performed between patients that have been treated surgically and conservatively.

Results:

44 patients with isolated metopic synostosis were included: 22 received conservative treatment and 22 underwent fronto-orbital advancement. At 4 years of age the surgical group showed retrusion of the complete frontal area, while the conservative group showed a slight frontal prominence. Both groups showed temporal depression with respect to the control. In the sub-analysis, a similar degree of temporal depression was observed between surgical and conservative treatment. Head shape patterns showed considerable similarity across all severity phenotypes.

Conclusion:

This study shows a deviation in forehead shape from normal controls in patients with metopic synostosis following both surgical and conservative treatment by the age of 4 years. Comparison between surgical and conservative treatment shows a similar degree of temporal depression, a slight prominence in the center of the forehead in the conservative group, and retrusion of the entire frontal area in the surgical group. This observed difference is of considerable similarity across all severity types.

Level of evidence (therapeutic):

III
Pediatric Firearm Deaths and State Policies on Social, Emotional, and Academic Development
Authors: Hatchimonji Justin S , Haddad Diane N , Scantling Dane R , Kaufman Elinore J , Hatchimonji Danielle R
Published: September 2024

Objective:

To determine whether state-level SEAD policies are associated with pediatric firearm homicides and suicides.

Summary Background Data:

Firearm deaths continue to rise among United States (US) children. School-based efforts to promote social, emotional, and academic development (SEAD) may be a means to reduce such deaths, but state-level policies vary and the effect on firearm deaths is unknown.

Methods:

We used Education Trust data regarding state-level SEAD policies, averaging 6 domains to create a cumulative score and investigating each domain individually. The primary outcomes were pediatric firearm homicides and suicides, using covariates from the American Community Survey and State Firearm Laws database. We mapped SEAD policies and pediatric death rates. Poisson regression was used to investigate associations between SEAD policies and pediatric firearm deaths.

Results:

Annual statewide pediatric firearm deaths ranged from 0.85 to 7.81 per 100,000; homicides from 0.64 to 5.69, and suicides from 0.21 to 4.75. Univariate analyses demonstrated associations between SEAD scores and both homicides (P=0.003) and suicides (P=0.032), but these were nonsignificant after adjustment. Professional Development and Engagement policies were associated with lower rates of pediatric firearm homicides after adjustment (IRR=0.33, P=0.004 and IRR=0.46, P=0.014, respectively). There was no significant association between any domain and pediatric firearm suicide.

Conclusion:

Professional Development and Student, Family and Community Engagement policies are associated with lower rates of pediatric firearm homicides, however, there was no significant association between pediatric firearm deaths and summary SEAD measures after adjustment. Certain SEAD policies may be helpful in decreasing pediatric firearm deaths.
Xanthomonas citri pv. eucalyptorum 4866-2_S43 strain (formerly X. axonopodis pv. eucalyptorum): Causal agent of bacterial leaf blight on eucalypt recovered in Argentina

Authors: Traglia German Matias , Poudel Mousami , Miño Samuel , Canteros Blanca Isabel , Minsavage Gerald V. , Sharma Anuj , Goss Erica M. , Jones Jeffrey B. , Gochez Alberto
Published: September 2024

We report the draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by Xanthomonas citri pv. eucalyptorum (Xce). The genome size is 5,188,607 bp, with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is Xce LPF 602, isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96%. between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated Xanthomonas spp. These results revealed that strain 4866-2_S43 had greater than 95% with X. citri pv. citri,and X. citri pv. phaseoli, and less than 95% with X. euvesicatoria pv. alfalfae, X. euvesicatoria pv. perforans, and X. euvesicatoria pathovars euvesicatoria and eucalyptii.
Dongia sedimenti sp. nov., isolated from river sediment
Authors: Jiang Xueting , Ruan Luyao , Wu Ningning , Mao Dongmei , He Jian , Wang Shimei , Jiang Jiangdong , Shen Qirong
Published: September 2024

A Gram-stain-negative, non-spore-forming and strictly aerobic bacterial strain, designated R-7T, was isolated from river sediment in Wuxi, Jiangsu, PR China. Cells (1.6–3.8 µm long and 0.6–0.8 µm wide) were slightly curved to straight rods and motile by means of a polar flagellum. The strain grew optimally on Reasoner's 2A medium at 30 °C, pH 7.0 and with 1.0% (w/v) NaCl. Strain R-7T exhibited closest 16S rRNA gene sequence similarities to Dongia mobilis CGMCC 1.7660T (95.4%), D. rigui 04SU4-PT (94.6%) and D. soli D78T (93.8%). The phylogenetic trees based on genomic and 16S rRNA gene sequences showed that strain R-7T was clustered in the genus Dongia. The obtained average nucleotide identity and digital DNA–DNA hybridization values between R-7T and the three type strains of the genus Dongia were 73.4, 72.8 and 72.4% and 19.5, 19.0 and 18.7%, respectively. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, two unidentified aminophospholipids and nine unidentified polar lipids. The major cellular fatty acids (>5% of the total) were cyclo-C19 : 0
 ω8c, C16 : 0 and C16 : 0 2-OH. The DNA G+C content was 65.5 mol%. On the basis of the evidence presented in this study, strain R-7T represents a novel species of the genus Dongia, for which the name Dongia sedimenti sp. nov. is proposed, with strain R-7T (=KCTC 8082T=MCCC 1K08805T) as the type strain.
Effects of host heterogeneity on epidemiological dynamics are mediated by how host infectiousness is determined
Authors: Cohen Jacob A. , Dean Andrew D. , Viney Mark E. , Fenton Andy
Published: September 2024

It is well established that heterogeneities in host susceptibility and infectiousness can affect population-level parasite transmission. However, the role played by the underlying ‘infectiousness determination scenario’, or how infectious a newly infected host (the ‘recipient’) becomes upon infection, in mediating the effects of host heterogeneity on parasite transmission is unknown.

Broadly, host infectiousness may be an inherent, pre-determined trait of the recipient (which we call ‘Recipient-Dependent’ (RD)), or it may be determined by the infectiousness of the ‘donor’ host that infected them (which we call ‘Donor-Dependent’ (DD)). To investigate how these alternative infectiousness determination scenarios mediate the epidemiological consequences of host heterogeneity we developed two Susceptible-Infected compartmental models which incorporate host heterogeneity in both susceptibility and infectiousness, under the contrasting RD and DD scenarios. We then quantified how changing initial population-level heterogeneity affected three epidemiological measures in each case: the basic reproduction number (R0), temporal changes in heterogeneity, and equilibrium host abundance. We found that the primary driver ofR0differs between the two scenarios – covariance between host susceptibility and infectiousness drivesR0in the RD scenario, versus maximum infectiousness in the DD scenario. Heterogeneity stayed the same over time in both scenarios, though there were differences between the scenarios in the consequences of host heterogeneity on equilibrium host abundance. Overall, the findings we present demonstrate that the infectiousness determination scenario can change epidemiological outcomes considerably and should be accounted for when modelling host heterogeneities in parasite transmission.
Global trends in occupational disease reporting: a systematic review
Authors: Khoe Levina Chandra , Saldi Siti Rizny Fitriana , Isbayuputra Marsen , Mansyur Muchtaruddin , Wiseman Virginia , Asante Augustine
Published: September 2024

Background

Disease reporting is often unreliable and faces many challenges, making it difficult to estimate the true burden of occupational diseases, defined as any disease that is caused by the work activity or environment. This study aimed to assess the global reporting and underreporting rate of occupational diseases, and to identify the factors affecting the underreporting of occupational diseases.

Methods

Following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, this study searched Medline (PubMed), CINAHL, EMBASE, Scopus, Web of Science, WHO Institutional Repository for Information Sharing (IRIS) database, Dimensions, and Google Scholar. We used search terms related to reporting and underreporting of occupational diseases or illnesses. The selected records were screened, and data extracted using the Covidence software tool. Screening and quality assessment were conducted by two independent researchers and finalized by a third researcher. The quality of the evidence was assessed with the Mixed Methods Appraisal Tool. This study is registered on PROSPERO, number CRD42023417814.

Results

A total of 121 studies from 29 countries were identified, all coming from high-income and upper-middle-income countries. The incidence rate of occupational disease varied widely, ranging between 1.71 to 1,387 per 100,000 employees yearly. The highest number of annual cases was reported in the agricultural sector (ranging from 33 to 6,431), followed by the health sector (146 to 5,508), and then the construction sector (264). Two studies evaluated rates of underreporting, which varied from 50% to 95%. The main factor contributing to underreporting was employee concerns about job security.

Conclusions

The results reveal a significant gap in the reporting of occupational diseases among high-income and low-middle-income countries. This review also identifies variations in reporting mechanisms across different countries. Our findings highlight the need to establish a national system for reporting occupational diseases that engages employers, employees, and healthcare providers.
Temperature-dependent predation predicts a more reptilian future
Authors: Grady John M. , Amme Jacob L. , Bhaskaran-Nair Kiran , Sinha Varun , Brunwasser Samuel J. , Record Sydne , Dell Anthony I. , Hengen Keith B.
Published: September 2024

Diversity increases toward the tropics, but the strength of this pattern diverges with thermo-regulatory strategy. Synthesizing over 30,000 species distributions, we quantified patterns of richness in terrestrial vertebrates, and present evidence for a latitudinal gradient of community composition. We observe a two orders of magnitude shift in comparative diversity with temperature, from endothermic mammal and avian dominance near the poles, toward ectothermic reptile and amphibian majority in the tropics. Next, we provide mechanistic support for a corresponding latitudinal gradient of predatory interactions. Using automated video tracking in>4500 trials, we show that differences in thermal sensitivity of locomotion in endothermic predators and ectothermic prey favors endotherms in colder environments and yields theoretically predicted foraging outcomes across thermal conditions, including the number of strikes, the distance traveled, and the time to capture prey. We also present evidence that endotherms use thermal cues to anticipate prey behavior, modulating the impact of temperature. Finally, we integrate theory and data to forecast future patterns of diversity, revealing that as the world get warmer, it will become increasingly reptilian. Overall, our results point toward a broad reorganization of vertebrate diversity with latitude, elevation, and temperature: from endotherm dominance in cold systems toward ectotherm dominance in warm.
Insecticide resistance inMyzus persicaecollected from sweet pepper
Authors: Beekman Mariska M. , Ruan Xinyan , Dicke Marcel , Zwaan Bas J. , Pannebakker Bart A. , Verhulst Eveline C.
Published: September 2024

Populations of the green peach aphid,Myzus persicae, rapidly develop resistance to insecticides applied in agriculture, necessitating regular resistance monitoring of pest populations. Previous research identified two dominant multilocus genotypes (MLGs) in conventional (using insecticides + biological control agents) Dutch sweet pepper greenhouses: MLG-A under pymetrozine application and MLG-R under flonicamid application. This suggests positive selection for the genotypes by the application of these insecticides. However, no resistance ofM. persicaeto these insecticides has been reported yet. To investigate whether the insecticides were selectively driving the emergence of these specific MLGs, we compared the sensitivity of MLG-A and MLG-R to pymetrozine and flonicamid to that of six other genotypes from the same crop system. Additionally, we screened theM. persicaepopulations from Dutch sweet pepper greenhouses for known mutations conferring resistance to carbamates, pyrethroids, neonicotinoids, and tetronic and tetramic acid derivatives. Our results show that both MLG-A and MLG-R are less sensitive to pymetrozine compared to the other genotypes investigated. Furthermore, full mortality for MLG-R, the genotype least sensitive to flonicamid, was not achieved at the recommended field dose for this insecticide. Resistance mutations for carbamates and pyrethroids were prevalent among the MLGs, including MLG-A and MLG-R, while mutation A2226V, which is linked to resistance to tetronic and tetramic acid derivatives, was absent. Notably, the neonicotinoid resistance mutation R81T was found only in MLG-R, making this the northernmost detection of R81T inM. persicaeto date. This study shows that various resistance mechanisms can accumulate in a single aphid genotype and that insecticides likely play a role in selecting for the dominant genotypes ofM. persicaein conventional greenhouses.
A helper NLR targets organellar membranes to trigger immunity
Authors: Ibrahim Tarhan , Yuen Enoch Lok Him , Wang Hung-Yu , King Freddie J. , Toghani AmirAli , Kourelis Jiorgos , Vuolo Cristina , Adamkova Vanda , Castel Baptiste , Jones Jonathan D. G. , Wu Chih-Hang , Kamoun Sophien , Bozkurt Tolga O.
Published: September 2024

In plants, NLR (nucleotide-binding domain and leucine-rich repeat) proteins execute innate immunity through the formation of resistosomes that accumulate at the plasma membrane. However, the extent to which NLR resistosomes target other cellular membranes is unknown. Here, we show that the helper NLR NRG1 engages with multiple organellar membranes to trigger innate immunity. Compared to other helper NLRs, NRG1 and closely related RPW8-like NLRs (CCR-NLRs) possess extended N-termini with distinctive sequence signatures, enabling their assembly into longer structures than canonical coiled coil NLR (CC-NLR) resistosomes. Activated NRG1 associates with single- and double-membrane organelles via its N-terminal RPW8-like domain. Our findings reveal that plant NLR resistosomes accumulate at a variety of cellular membrane sites to activate immunity.
Optical photothermal infrared imaging using metabolic probes in biological systems
Authors: Shuster Sydney O. , Curtis Anna E. , Davis Caitlin M.
Published: September 2024

Infrared spectroscopy is a powerful tool for identifying biomolecules. In biological systems, infrared spectra provide information on structure, reaction mechanisms, and conformational change of biomolecules. However, the promise of applying infrared imaging to biological systems has been hampered by low spatial resolution and the overwhelming water background arising from the aqueous nature of in cell andin vivowork. Recently, optical photothermal infrared microscopy (OPTIR) has overcome these barriers and achieved both spatially and spectrally resolved images of live cells and organisms. Here, we determine the most effective modes of collection on a commercial OPTIR microscope for work in biological samples. We examine three cell lines (Huh-7, differentiated 3T3-L1, and U2OS) and three organisms (E. coli, tardigrades, and zebrafish). Our results suggest that the information provided by multifrequency imaging is comparable to hyperspectral imaging while reducing imaging times twenty-fold. We also explore the utility of IR active probes for OPTIR using global and site-specific noncanonical azide containing amino acid probes of proteins. We find that photoreactive IR probes are not compatible with OPTIR. We demonstrate live imaging of cells in buffers with water.13C glucose metabolism monitored in live fat cells andE. colihighlights that the same probe may be used in different pathways. Further we demonstrate that some drugs (e.g. neratinib) have IR active moieties that can be imaged by OPTIR. Our findings illustrate the versatility of OPTIR, and together, provide a direction for future dynamic imaging of living cells and organisms.
A repeatedly evolved mutation in Cryptochrome-1 of subterranean animals alters behavioral and molecular circadian rhythms
Authors: Swaminathan Amruta , Kenzior Alexander , McCoin Colin , Price Andrew , Weaver Kyle , Hintermann Aurélie , Morris NatiCia , Keene Alex C. , Rohner Nicolas
Published: September 2024

The repeated evolution of similar phenotypes in independent lineages often occurs in response to similar environmental pressures, through similar or different molecular pathways. Recently, a repeatedly occurring mutation R263Q in a conserved domain of the protein Cryptochrome-1 (CRY1) was reported in multiple species inhabiting subterranean environments. Cryptochromes regulate circadian rhythms, and glucose and lipid metabolism. Subterranean species show changes to their circadian rhythm and metabolic pathways, making it likely that this mutation in CRY1 contributes to adaptive phenotypic changes. To identify the functional consequences of the CRY1 R263Q mutation, we generated a mouse model homozygous for this mutation. Indirect calorimetry experiments revealed delayed energy expenditure, locomotor activity and feeding patterns of mutant mice in the dark phase, but no further metabolic phenotypes – unlike a full loss of function of CRY1. Gene expression analyses showed altered expression of several canonical circadian genes in the livers of the mutant mice, fortifying the notion that CRY1 R263Q impacts metabolism. Our data provide the first characterization of a novel mutation that has repeatedly evolved in subterranean environments, supporting the idea that shared environmental constraints can drive the evolution of similar phenotypes through similar genetic changes.
Modelling dynamics of human NDPK hexamer structure, stability and interactions
Authors: Lim Yee Ying , Natarajan Kedar Nath
Published: September 2024

Nucleoside diphosphate kinases (NDPKs) are evolutionarily conserved multifunctional enzymes involved in energy metabolism and gene regulation. NDPKs primarily regulate nucleotide pool turnover by catalyzing the transfer between nucleoside triphosphate (NTPs) and their deoxy derivatives, maintaining cellular homeostasis. The NDPK hexameric assembly is needed for kinase activity, but its precise assembly into homo-/hetero-oligomeric complexes remains poorly understood. How quaternary structure affects NDPK activity is limited by high subunit homology, experimental challenges in isolatingin vivoheterohexamers and subunit abundances across cellular compartments. We identify conserved Arg27 across group I NDPKs (NME1-4) as the key residue for hexamer assembly. The Arg27 ensures similar hexameric assembly across subunits and mediates inter- and intra-molecular monomeric interactions, while Arg27 mutation leads to decreased binding affinity, dynamics, and complex destabilization. The double and triple Arg NME4 mutations destabilize hexamer into dimer due to shorter C-terminal region. Simulating NME1-3 with Arg mutations and shortened C-terminal recapitulates hexameric destabilization, highlighting role of the C-terminal region in stabilizing NDPK hexamers. Comparing heterohexameric complexes, we report NME1-NME2 (A1B5) complex as most stable and abundant, owing to predominant subunit nuclear localization. We propose that Arginine residues, C-terminal sequence and subunit abundances contribute to formation and stabilization of NDPK heterohexameric complexes.
Evaluating the Radiation Sensitivity Index and 12-chemokine gene expression signature for clinical use in a CLIA laboratory
Authors: Berglund Anders , Puskas John , Yoder Sean , Smith Andrew T. , Marchion Douglas C. , Qian Dahui , Mulé James J. , Torres-Roca Javier F. , Eschrich Steven A.
Published: September 2024

Background

The radiation sensitivity index (RSI) and 12-chemokine gene expression signature (12CK GES) are two gene expression signatures (GES) that were previously developed to predict tumor radiation sensitivity or identify the presence of tertiary lymphoid structures in tumors, respectively. To advance the use of these GES into clinical trial evaluation, their assays must be assessed within the context of the Clinical Laboratory Improvement Amendments (CLIA) process.

Methods

Using HG-U133Plus 2.0 arrays, we first established CLIA laboratory proficiency. Then the accuracy (limit of detection and macrodissection impact), precision (variability by time and operator), sample type (surgery vs. biopsy), and concordance with reference laboratory were evaluated.

Results

RSI and 12CK GES were reproducible (RSI: 0.01 mean difference, 12CK GES 0.17 mean difference) and precise with respect to time and operator. Taken together, the reproducibility analysis of the scores indicated a median RSI difference of 0.06 (6.47% of range) across samples and a median 12CK GES difference of 0.92 (12.29% of range). Experiments indicated that the lower limit of input RNA is 5 ng. Reproducibility with a second CLIA laboratory demonstrated reliability with the median RSI score difference of 0.065 (6% of full range) and 12CK GES difference of 0.93 (12 % of observed range).

Conclusions

Overall, under CLIA, RSI and 12CK GES were demonstrated by the Moffitt Cancer Center Advanced Diagnostic Laboratory to be reproducible GES for clinical usage.
Natural history of a parasite-induced biliary cancer
Authors: Crellen Thomas , Vita Francesca , Braconi Chiara , Sithithaworn Paiboon , Hollingsworth T. Déirdre
Published: September 2024

Pathogens are major drivers of cancer globally. Quantifying the relationship between infection and carcinogenesis is therefore crucial for developing preventative programs. The foodborne trematodeOpisthorchis viverriniis a primary cause of biliary cancer (cholangiocarcinoma) and infects 12 million people in Southeast Asia. In tumours from patients exposed toO. viverriniwe found that the earliest chromosomal amplification of driver genes occurred at 30 years old on average, two to four decades before cancer diagnosis, and disproportionately containedFGFR2, TP53andPTENgenes. We then fitted transmission models to parasitological data from Thailand spanning 27 years (n= 11,517) finding that, for people born between 1960–1989, first exposure occurred at two years old and by 30 years individuals had been cumulatively infected with a median of 72 worms. Trematodes are long-lived and our analysis quantifies the average lifespan ofO. viverrinias 13 years (90% credible interval [CrI] 6–23 years) within human hosts. Finally, we calculate the lifetime probability of diagnosis with cholangiocarcinoma as 1.2% (90% CrI 1.0–1.4%) given prior exposure to the parasite. Overall, our study demonstrates how pathogen exposure drives patterns of cancer within human populations.