bluuebunny/crossref_metadata_2025 huggingface dataset:
Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing
Authors: Chen Zhao , Grim Christopher J. , Ramachandran Padmini , Meng Jianghong
Published: April 2024

Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant
Salmonella enterica
serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant
Pseudomonas aeruginosa
in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at
https://github.com/jackchen129/MAGenie
) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.

IMPORTANCE

By examining diverse bacterial communities, particularly those housing multiple
Salmonella enterica
serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.
In vitro
enhancement of Zika virus infection by preexisting West Nile virus antibodies in human plasma-derived immunoglobulins revealed after P2 binding site-specific enrichment
Authors: He Yong , Zhong Lilin , Yan Hailing , Virata Maria Luisa , Deng Lu , Mishra Ashish K. , Struble Evi , Scott Dorothy , Zhang Pei
Published: April 2024

Human immunoglobulin preparations contain a diverse range of polyclonal antibodies that reflect past immune responses against pathogens encountered by the blood donor population. In this study, we examined a panel of intravenous immunoglobulins (IGIVs) manufactured over the past two decades (1998–2020) for their capacity to neutralize or enhance Zika virus (ZIKV) infection
in vitro
. These IGIVs were selected specifically based on their production dates in relation to the occurrences of two flavivirus outbreaks in the U.S.: the West Nile virus (WNV) outbreak in 1999 and the ZIKV outbreak in 2015. As demonstrated by enzyme-linked immunosorbent assay (ELISA) experiments, IGIVs made before the ZIKV outbreak already harbored antibodies that bind to various peptides across the envelope protein of ZIKV because of the WNV outbreak. Using phage display, the most dominant binding site was mapped precisely to the P2 peptide between residues 211 and 230 within domain II, where BF1176-56, an anti-ZIKV monoclonal antibody, also binds. When tested in permissive Vero E6 cells for ZIKV neutralization, the IGIVs, even after undergoing rigorous enrichment for P2 binding specificity, failed, as did BF1176-56. Meanwhile, BF1176-56 enhanced ZIKV infection in both FcγRII-expressing K562 cells and human peripheral blood mononuclear cells. However, for enhancement by the IGIVs to be detected in these cells, a substantial increase in their P2 binding specificity was required, thus linking the P2 site with ZIKV enhancement
in vitro
. Our findings warrant further study of the significance of elevated levels of anti-WNV antibodies in IGIVs, considering that various mechanisms operating
in vivo
may modulate ZIKV infection outcomes.

IMPORTANCE

We investigated the capacity of intravenous immunoglobulins manufactured previously over two decades (1998–2020) to neutralize or enhance Zika virus infection
in vitro
. West Nile virus antibodies in IGIVs could not neutralize Zika virus initially; however, once the IGIVs were concentrated further, they enhanced its infection. These findings lay the groundwork for exploring how preexisting WNV antibodies in IGIVs could impact Zika infection, both
in vitro
and
in vivo
. Our observations are historically significant, since we tested a panel of IGIV lots that were carefully selected based on their production dates which covered two major flavivirus outbreaks in the U.S.: the WNV outbreak in 1999 and the ZIKV outbreak in 2015. These findings will facilitate our understanding of the interplay among closely related viral pathogens, particularly from a historical perspective regarding large blood donor populations. They should remain relevant for future outbreaks of emerging flaviviruses that may potentially affect vulnerable populations.
Genetic predisposition, modifiable lifestyles, and their joint effects on human lifespan: evidence from multiple cohort studies
Authors: Bian Zilong , Wang Lijuan , Fan Rong , Sun Jing , Yu Lili , Xu Meihong , Timmers Paul R H J , Shen Xia , Wilson James F , Theodoratou Evropi , Wu Xifeng , Li Xue
Published: April 2024

Objective

To investigate the associations across genetic and lifestyle factors with lifespan.

Design

A longitudinal cohort study.

Setting

UK Biobank.

Participants

353 742 adults of European ancestry, who were recruited from 2006 to 2010 and were followed up until 2021.

Exposures

A polygenic risk score for lifespan with long (highest quintile) risk categories and a weighted healthy lifestyle score, including no current smoking, moderate alcohol consumption, regular physical activity, healthy body shape, adequate sleep duration, and a healthy diet, categorised into favourable, intermediate, and unfavourable lifestyles.

Main outcome measures

Lifespan defined as the date of death or the censor date minus the date of birth.

Results

Of the included 353 742 participants of European ancestry with a median follow-up of 12.86 years, 24 239 death cases were identified. Participants were grouped into three genetically determined lifespan categories including long (20.1%), intermediate (60.1%), and short (19.8%), and into three lifestyle score categories including favourable (23.1%), intermediate (55.6%), and unfavourable (21.3%). The hazard ratio (HR) of death for individuals with a genetic predisposition to a short lifespan was 1.21 (95% CI 1.16 to 1.26) compared to those with a genetic predisposition to a long lifespan. The HR of death for individuals in the unfavourable lifestyle category was 1.78 (95% CI 1.71 to 1.85), compared with those in the favourable lifestyle category. Participants with a genetic predisposition to a short lifespan and an unfavourable lifestyle had 2.04 times (95% CI 1.87 to 2.22) higher rates of death compared with those with a genetic predisposition to a long lifespan and a favourable lifestyle. No multiplicative interaction was detected between the polygenic risk score of lifespan and the weighted healthy lifestyle score (p=0.10). The optimal combination of healthy lifestyles, including never smoking, regular physical activity, adequate sleep duration, and a healthy diet, was derived to decrease risk of premature death (death before 75 years).

Conclusion

Genetic and lifestyle factors were independently associated with lifespan. Adherence to healthy lifestyles could largely attenuate the genetic risk of a shorter lifespan or premature death. The optimal combination of healthy lifestyles could convey better benefits for a longer lifespan, regardless of genetic background.
Mismatch repair deficiency and microsatellite instability in urothelial carcinoma: a systematic review and meta-analysis
Authors: Chandran Elias B A , Iannantuono Giovanni Maria , Atiq Saad O , Akbulut Dilara , Sinaii Ninet , Simon Nicholas I , Banday Abdul Rouf , Boudjadi Salah , Gurram Sandeep , Nassar Amin H , Rosenberg Jonathan E , Butera Gisela , Teo Min Yuen , Sonpavde Guru , Coleman Jonathan A , Apolo Andrea B
Published: April 2024

Background

Mismatch repair deficiency (dMMR) and microsatellite instability-high (MSI-H) occur in a subset of cancers and have been shown to confer sensitivity to immune checkpoint inhibition (ICI); however, there is a lack of prospective data in urothelial carcinoma (UC).

Methods and analysis

We performed a systematic review to estimate the prevalence of dMMR and MSI-H in UC, including survival and clinical outcomes. We searched for studies published up to 26 October 2022 in major scientific databases. We screened 1745 studies and included 110. Meta-analyses were performed if the extracted data were suitable.

Results

The pooled weighted prevalences of dMMR in bladder cancer (BC) and upper tract UC (UTUC) were 2.30% (95% CI 1.12% to 4.65%) and 8.95% (95% CI 6.81% to 11.67%), respectively. The pooled weighted prevalences of MSI-H in BC and UTUC were 2.11% (95% CI 0.82% to 5.31%) and 8.36% (95% CI 5.50% to 12.53%), respectively. Comparing localised versus metastatic disease, the pooled weighted prevalences for MSI-H in BC were 5.26% (95% CI 0.86% to 26.12%) and 0.86% (95% CI 0.59% to 1.25%), respectively; and in UTUC, they were 18.04% (95% CI 13.36% to 23.91%) and 4.96% (95% CI 2.72% to 8.86%), respectively. Cumulatively, the response rate in dMMR/MSI-H metastatic UC treated with an ICI was 22/34 (64.7%) compared with 1/9 (11.1%) with chemotherapy.

Conclusion

Both dMMR and MSI-H occur more frequently in UTUC than in BC. In UC, MSI-H occurs more frequently in localised disease than in metastatic disease. These biomarkers may predict sensitivity to ICI in metastatic UC and resistance to cisplatin-based chemotherapy.
Effect of visual impairment on subjective cognitive decline in older adults: a cross-sectional study in China
Authors: Luo Liyan , Jiang Ning , Zheng Xiaolei , Wang Ping , Bi Jianzhong , Xu Feng , Xie Zhaohong , Yang Liping
Published: April 2024

Objective

People with visual impairment have more functional limitations associated with subjective cognitive decline (SCD), and those with SCD are extremely susceptible to transitioning to irreversible cognitive impairment. This study aimed to explore if visual impairment is a significant predictor of SCD compared with other socioeconomic and health factors associated with SCD.

Design

Cross-sectional study.

Setting and participants

The investigation aimed to assess the factors influencing SCD among 428 participants aged 60 and above in Zhaoyuan, China.

Primary outcome measures

The primary outcome variable was SCD, measured by the Chinese version of SCD questionnaire. Multiple logistic regression and propensity score matching (PSM) were used to analyse the influence of visual impairment on the subjective cognition of the elderly.

32.2% of the elderly were experiencing SCD. Older adults with SCD showed a higher prevalence of visual impairment (72.5%) than the elderly without SCD (58.6%) (P=0.006). Multivariate logistic regression analysis showed that bad self-reported health status, lack of physical exercise and visual impairment were the risk factors for SCD in older adults, while more than 9 years of education was a protective factor. In addition, PSM model showed that after eliminating the dominant biases caused by the individual observable heterogeneity of older adults with and without visual impairment, the risk of SCD in the elderly with visual impairment was increased by 13.6%–14.5% and the difference was statistically significant (P<0.05).

Conclusions

It was found that older adults experiencing visual impairments are at an elevated risk of developing SCD compared with their counterparts without such impairments. Additionally, visual impairment remains a significant risk factor for SCD in the elderly, even adjusting for potential biases arising from individual observable heterogeneity.
Adjuvant Wilms’ tumour 1-specific dendritic cell immunotherapy
complementing conventional therapy for paediatric patients with high-grade
glioma and diffuse intrinsic pontine glioma: protocol of a monocentric phase
I/II clinical trial in Belgium
Authors: Van Genechten Toon , De Laere Maxime , Van den Bossche Jolien , Stein Barbara , De Rycke kim , Deschepper Caroline , Hazes Katja , Peeters Renke , Couttenye Marie-Madeleine , Van De Walle Katrien , Roelant Ella , Maes Sabine , Vanden Bossche Stephanie , Dekeyzer Sven , Huizing Manon , Caluwaert Kim , Nijs Griet , Cools Nathalie , Verlooy Joris , Norga Koen , Verhulst Stijn , Anguille Sebastien , Berneman Zwi , Lion Eva
Published: April 2024

Introduction

Diffuse intrinsic pontine glioma (DIPG) and paediatric high-grade
glioma (pHGG) are aggressive glial tumours, for which conventional
treatment modalities fall short. Dendritic cell (DC)-based immunotherapy
is being investigated as a promising and safe adjuvant therapy. The
Wilms’ tumour protein (WT1) is a potent target for this type of
antigen-specific immunotherapy and is overexpressed in DIPG and pHGG.
Based on this, we designed a non-randomised phase I/II trial, assessing
the feasibility and safety ofWT1mRNA-loaded
DC (WT1/DC) immunotherapy in combination with conventional treatment in
pHGG and DIPG.

Methods and analysis

10 paediatric patients with newly diagnosed or pretreated HGG or
DIPG were treated according to the trial protocol. The trial protocol
consists of leukapheresis of mononuclear cells, the manufacturing of
autologous WT1/DC vaccines and the combination of WT1/DC-vaccine
immunotherapy with conventional antiglioma treatment. In newly diagnosed
patients, this comprises chemoradiation (oral temozolomide
90 mg/m2daily+radiotherapy 54 Gy in 1.8 Gy
fractions) followed by three induction WT1/DC vaccines
(8–10×106cells/vaccine) given on a weekly basis
and a chemoimmunotherapy booster phase consisting of six 28-day cycles
of oral temozolomide (150–200 mg/m2on days 1–5) and
a WT1/DC vaccine on day 21. In pretreated patients, the induction and
booster phase are combined with best possible antiglioma treatment at
hand. Primary objectives are to assess the feasibility of the production
of mRNA-electroporated WT1/DC vaccines in this patient population and to
assess the safety and feasibility of combining conventional antiglioma
treatment with the proposed immunotherapy. Secondary objectives are to
investigate in vivo immunogenicity of WT1/DC vaccination and to assess
disease-specific and general quality of life.

Ethics and dissemination

The ethics committee of the Antwerp University Hospital and the
University of Antwerp granted ethics approval. Results of the clinical
trial will be shared through publication in a peer-reviewed journal and
presentations at conferences.

Trial registration number

NCT04911621
Metformin for sepsis-associated AKI: a protocol for the Randomized Clinical Trial of the Safety and FeasibiLity of Metformin as a Treatment for sepsis-associated AKI (LiMiT AKI)
Authors: Saraiva Ivan E , Hamahata Natsumi , Huang David T , Kane-Gill Sandra L , Rivosecchi Ryan M , Shiva Sruti , Nolin Thomas D , Chen Xinlei , Minturn John , Chang Chung-Chou H , Li Xiaotong , Kellum John , Gómez Hernando
Published: April 2024

Introduction

Acute kidney injury (AKI) is a common complication of sepsis associated with increased risk of death. Preclinical data and observational human studies suggest that activation of AMP-activated protein kinase, an ubiquitous master regulator of energy that can limit mitochondrial injury, with metformin may protect against sepsis-associated AKI (SA-AKI) and mortality. The Randomized Clinical Trial of the Safety and FeasibiLity of Metformin as a Treatment for sepsis-associated AKI (LiMiT AKI) aims to evaluate the safety and feasibility of enteral metformin in patients with sepsis at risk of developing SA-AKI.

Methods and analysis

Blind, randomised, placebo-controlled clinical trial in a single-centre, quaternary teaching hospital in the USA. We will enrol adult patients (18 years of age or older) within 48 hours of meeting Sepsis-3 criteria, admitted to intensive care unit, with oral or enteral access. Patients will be randomised 1:1:1 to low-dose metformin (500 mg two times per day), high-dose metformin (1000 mg two times per day) or placebo for 5 days. Primary safety outcome will be the proportion of metformin-associated serious adverse events. Feasibility assessment will be based on acceptability by patients and clinicians, and by enrolment rate.

Ethics and dissemination

This study has been approved by the Institutional Review Board. All patients or surrogates will provide written consent prior to enrolment and any study intervention. Metformin is a widely available, inexpensive medication with a long track record for safety, which if effective would be accessible and easy to deploy. We describe the study methods using the Standard Protocol Items for Randomized Trials framework and discuss key design features and methodological decisions. LiMiT AKI will investigate the feasibility and safety of metformin in critically ill patients with sepsis at risk of SA-AKI, in preparation for a future large-scale efficacy study. Main results will be published as soon as available after final analysis.

Trial registration number

NCT05900284.
Life skills and reproductive health empowerment intervention for newly married women and their families to reduce unintended pregnancy in India: protocol for the TARANG cluster randomised controlled trial
Authors: Diamond-Smith Nadia , Gopalakrishnan Lakshmi , Leslie Hannah , Katz Elizabeth , Harper Cynthia , Weiser Sheri , Patil Sumeet R
Published: April 2024

Introduction

In South Asia, younger women have high rates of unmet need for family planning and low empowerment. Life skills interventions can equip young women with agency, but the effectiveness of these interventions in reproductive and sexual autonomy and contraception has not been examined.

Methods and analysis

A two-arm, parallel, cluster randomised controlled trial will evaluate the impact of TARANG (Transforming Actions for Reaching and Nurturing Gender Equity and Empowerment), a life skills and reproductive health empowerment group-based intervention for newly married women, compared with usual services in the community in rural and tribal Rajasthan, India. TARANG will also provide light-touch sessions to husbands and mothers-in-law of newly married women. We will test the impact of TARANG in 80 village clusters among 800 eligible households comprising newly married women aged 18–25 years who are at risk of pregnancy but do not want a pregnancy within 1 year at the time of enrolment, their husbands and mothers-in-law who consent to participate. Women in the intervention villages will receive 14 sessions over a 6-month period, while husbands and mothers-in-law will receive 1 and 4 sessions (respectively) each. Three rounds of surveys will be collected over 18 months. Control villages will receive the intervention after the endline surveys. Primary outcomes include rate of unintended pregnancy and modern contraceptive use. We plan to start recruitment of participants and data collection in April 2024. We will estimate unadjusted and adjusted intention-to-treat effects using survival analysis and mixed models.

Ethics and dissemination

Study protocols have been reviewed and approved by the human subjects review boards at the University of California, San Francisco, and the Centre for Media Studies, India (IRB00006230) and ACE Independent Ethics Committee, Bangalore (NET0062022). Results will be disseminated in international peer-reviewed journals and conferences, to stakeholders including local government and non-governmental organisations, and directly to the communities and individuals that participated in the intervention.

Trial registration number

NCT06024616.
Digital micro-banking as a health and protection intervention for street-connected children and youth? Analysis from a Togolese pilot
Authors: Howard Neil
Published: April 2024

Background

The SaVa pilot offered street-connected children and youth (C&Y) access to digital micro-banking services to help them save money and thus avoid the violence associated with theft at night. It further used the micro-banking service as a gateway to attract C&Y towards other health and protection services. It took place over 12 months in Lomé, Togo and involved one social worker (SW) plus volunteers running ‘the bank’ in a non-governmental organisation-funded drop-in centre.

Methods

C&Y peer researchers were trained to interview and use collective drawing with peers, which they did on a bi-monthly basis. The SW recorded information about case management, training and additional services offered. He administered a survey to C&Y at the point of entry into the project and after 1 year, asking questions about recent experiences of violence or theft. At the end of 12 months, the author conducted interviews with C&Y using the bank, C&Y researchers who used the bank, project staff and steering committee partners and child protection stakeholders. One focus group was conducted with C&Y participants, alongside limited participant observation of where C&Y sleep and work.

Results

Findings suggest that the intervention was successful in encouraging children to open accounts and save money, and in contributing to a reduction in theft and associated violence. The incidence of theft reduced 90%; 95% of C&Y account holders were happy with the service; 200 accounts were opened. The project supported the delivery of additional services, including counselling, school reinsertion and removal from the streets.

Conclusions

Analysis suggests that it is possible to offer street-connected C&Y formal financial services but that this offer has potential as a health and protection intervention, especially in combination with the provision of a safe space, dedicated SW support and add-on services.
Assessing quality of direct-to-consumer telemedicine in China: a cross-sectional study using unannounced standardised patients
Authors: Zeng Zhen , Xu Dong (Roman) , Cai Yiyuan , Gong Wenjie
Published: April 2024

Direct-to-onsumer telemedicine (DTCT) has become popular as an alternative to traditional care. However, uncertainties about the potential risks associated with the lack of comprehensive quality evaluation could influence its long-term development. This study aimed to assess the quality of care provided by DTCT platforms in China using unannounced standardised patients (USP) between July 2021 and January 2022. The study assessed consultation services on both hospital and enterprise-sponsored platforms using the Institute of Medicine quality framework. It employed 10 USP cases, covering conditions such as diabetes, asthma, common cold, gastritis, angina, low back pain, child diarrhoea, child dermatitis, stress urinary incontinence and postpartum depression. Descriptive and regression analyses were employed to examine platform characteristics and compare quality across platform types. The results showed that of 170 USP visits across 107 different telemedicine platforms, enterprise-sponsored platforms achieved a 100% success in access, while hospital-sponsored platforms had a success rate of only 47.5% (56/118). Analysis highlighted a low overall correct diagnosis rate of 45% and inadequate adherence to clinical guidelines across all platforms. Notably, enterprise-sponsored platforms outperformed in accessibility, response time and case management compared with hospital-sponsored platforms. This study highlights the suboptimal quality of DTCT platforms in China, particularly for hospital-sponsored platforms. To further enhance DTCT services, future studies should compare DTCT and in-person care, aiming to identify gaps and potential risks associated with using DTCT as alternatives or supplements to traditional care. The potential of future development in enhancing DTCT services may involve exploring the integration of hospital resources with the technology and market capabilities of enterprise-sponsored platforms.
ScRNA-seq reveals novel immune-suppressive T cells and investigates CMV-TCR-T cells cytotoxicity against GBM
Authors: Long Xinmiao , Zhang Zuping , Li Yuzhe , Deng Kun , Gao Wei , Huang Meng , Wang Xiangyu , Lin Xiang , She Xiaoling , Zhao Yiming , Zhang Minfu , Huang Cheng , Wang Shiyi , Du Yinfei , Du Peng , Chen Shuai , Liu Qing , Wu Minghua
Published: April 2024

Background

Glioblastoma (GBM) is a fatal primary brain malignancy in adults. Previous studies have shown that cytomegalovirus (CMV) is a risk factor for tumorigenesis and aggressiveness for glioblastoma. However, little is known about how CMV infection affects immune cells in the tumor microenvironment of GBM. Furthermore, there has been almost no engineered T-cell receptor (TCR)-T targeting CMV for GBM research to date.

Methods

We evaluated the CMV infection status of patients with GBM’s tumor tissue by immune electron microscopy, immunofluorescence, and droplet digital PCR. We performed single-cell RNA sequencing for CMV-infected GBM to investigate the effects of CMV on the GBM immune microenvironment. CellChat was applied to analyze the interaction between cells in the GBM tumor microenvironment. Additionally, we conducted single-cell TCR/B cell receptor (BCR) sequencing and Grouping of Lymphocyte Interactions with Paratope Hotspots 2 algorithms to acquire specific CMV-TCR sequences. Genetic engineering was used to introduce CMV-TCR into primary T cells derived from patients with CMV-infected GBM. Flow cytometry was used to measure the proportion and cytotoxicity status of T cells in vitro.

Results

We identified two novel immune cell subpopulations in CMV-infected GBM, which were bipositive CD68+SOX2+tumor-associated macrophages and FXYD6+T cells. We highlighted that the interaction between bipositive TAMs or cancer cells and T cells was predominantly focused on FXYD6+T cells rather than regulatory T cells (Tregs), whereas, FXYD6+T cells were further identified as a group of novel immunosuppressive T cells. CMV-TCR-T cells showed significant therapeutic effects on the human-derived orthotopic GBM mice model.

Conclusions

These findings provided an insight into the underlying mechanism of CMV infection promoting the GBM immunosuppression, and provided a novel potential immunotherapy strategy for patients with GBM.
Prednisone use, disease activity and the occurrence of hyperglycaemia and diabetes in patients with early rheumatoid arthritis: a 10-year subanalysis of the BeSt study
Authors: van der Pol Joy Ardjuna , Allaart Cornelia F , Lems Willem , van der Kooij Sjoerd M , Huizinga Tom W J , Bergstra Sytske Anne
Published: April 2024

Objectives

To assess whether prednisone use and/or disease activity score (DAS) are associated with the development of hyperglycaemia and diabetes in rheumatoid arthritis (RA).

Methods

We included 504 non-diabetic early RA patients from the BeSt study (Dutch acronym for treatment strategies). Patients were randomised to four DAS-steered treatment arms and followed for 10 years. The associations between DAS and prednisone use with glucose levels and the occurrence of hyperglycaemia over time were assessed with linear and logistic mixed effects regression models. Development of diabetes was analysed with Cox regression. Sensitivity analyses were performed in patients who had a first episode of hyperglycaemia.

Results

31 of 504 patients (6.2%) with a mean age of 54 years developed diabetes during follow-up; 11 of these (35%) had received prior treatment with prednisone. Prednisone use was not associated with development of hyperglycaemia or diabetes after correction for multiple testing in main or sensitivity analyses. In the main analyses, DAS was significantly associated with development of diabetes (HR 1.802 per 1 point DAS increase, 95% CI 1.284 to 2.529) but not with glucose levels nor hyperglycaemia. In patients with previous hyperglycaemia, DAS was associated with glucose levels, recurrence of hyperglycaemia and diabetes.

Conclusions

In non-diabetic early RA patients, the use of prednisone was not associated with developing hyperglycaemia or diabetes. However, high DAS increased the risk of diabetes. Potential risks associated with prednisone use may have been mitigated by its effect on DAS.
Cadre législatif québécois pour la protection des espèces sauvages en situation précaire: évaluation critique et recommandations pour une révision majeure
Authors: Pelletier Fanie , Dumont Pierre , de Walle Joanie Van , Jauvin Daniel , Rodrigue David
Published: April 2024

In Quebec, the Act Respecting Threatened or Vulnerable species (ARTV), adopted in 1989, aims to safeguard Quebec's wild genetic diversity by protecting species at risk. However, since its implementation about 30 years ago, it has been repeatedly pointed out that the application of the Quebec legislative framework for the protection of wildlife species at risk was often slow and inadequate. The aim of this article is therefore to make a series of observations on the limits of current legislation and then propose nine urgent recommendations to improve the effectiveness of conservation efforts for species at risk in Quebec. Our recommendations aim to increase the efficiency and transparency of the designation process, reconsider compensation mechanisms for the loss of critical habitat, and harmonize species status between the federal and provincial levels. We hope that our article will pave the way for a constructive discussion leading to an improved protection of wildlife species in precarious situations and their persistence for future generations. The English version of this article is available in the Supplementary material file.
Cr-Coot: Chronological Coot Algorithm-Based Deep Learning Model for Video Demosaicing
Authors: Babitha A. , Boyed Wesley A.
Published: April 2024

Usually, digital cameras comprise sensor arrays enclosed by Color Filter Arrays (CFAs), mosaics of minute color filters. Thus, every pixel sensor usually records limited spectral data regarding relevant pixels. Demosaicing is defined as the procedure of deducing the misplaced data for every pixel, which plays a vital role in recreating high-quality full-color images. Denoising and demosaicing are the major processes in the camera imaging chain for both videos and images. Here, reconstruction errors occur in these points and have undesirable effects on the final outcome, when it is not appropriately managed. The demosaicing process provokes color and spatial correlation of noises, and it is improved by means of imagining a pipeline. This organized noise usually destroys the quality of the image as well as fails to prevent accurate interpretation of an image. During the mitigation of this structured noise on processed data, denoising techniques diminish the texture and information. Therefore, an effectual demosaicing technique is essential for recreating the full-color image from the defective color samples. Thus, in this paper, an effectual video demosaicing model is proposed using an optimized deep learning system. The designed video demosaicing system achieved better performance with a Peak Signal-to-Noise Ratio (PSNR) of 59.74 dB, Second Derivative, like Measure of Enhancement (SDME) of 63.51, and Root Mean Squared Error (RMSE) of 0.3660.
Aerodynamic and Structural Design Procedures Supported by Fabrication and Flight Testing of a Small Unmanned Helicopter
Authors: Mansour Amr , Kassem Mohammed , Abdel-Rahman A. M. , Zakaria Mohamed Y.
Published: April 2024

In this work, typical design, production, and testing procedures for a small unmanned helicopter are explained and performed. In doing so, preliminary sizing of the helicopter and three main disciplines are conducted: aerodynamic analytical and numerical simulations, power calculations, and structure analysis assessment. First, a thorough survey is implemented to obtain the trends for the maximum take-off weight versus some design constraints such as rotor diameter, motor power, payload, and empty weight. Performance calculation results are obtained to figure out all aspects that correspond to the specified mission. The designed rotor geometry along with the aerodynamic characteristics and flight performance variables is then validated using the blade element theory and numerical simulations. Second, based on the power curves obtained for different flight regimes, an electric brushless motor is selected. The numerical simulations (Computational Fluid Dynamics) analysis is used to enhance the selection which implies that the motor power should be greater than 5.4 kW to overcome the drag forces. The motor power selection corresponds to a maximum rotor pitch angle of 15∘ and a maximum rotor speed of 1450 RPM. Then, the aerodynamic loads are used as an input for the structural analysis using one-way coupling of fluid–structure interaction (FSI) and consequently designing the internal structure of the blade. Eventually, the internal structure manufactured using carbon fiber-reinforced polymer (CFRP) by applying a combined technique between wet layup and compression molding. The blade is statically tested compared with numerical finite element model results. The fuselage structure along with hub and tail units is manufactured and assembled with the existing on-shelf components to examine the helicopter lift capability with different payloads up to 9 kg. The results show that the detailed design process is significant for manufacturing such blades and the helicopter is capable of lifting off the ground with various payloads depending on the rotor pitch angles (8∘, 12∘, and 15∘) at a constant rotor speed of 1450 RPM.
The Effect of Sulfuric Acid Anodization on the Electrochemical Properties of Aluminum Alloy AlSi10Mg Prepared by Selective Laser Melting
Authors: Walton Jack W. , Dwyer Jonathan H. , Rice Lucas , Rueger Zachariah , Swain Greg M.
Published: April 2024

Aluminum alloy, AlSi10Mg, prepared by selective laser melt (SLM) fabrication was anodized in 9.8% sulfuric acid (Type II) at 15 V for a total of 23 min. Experiments were performed to study the potentiostatic anodization process and its effects on the oxide coating morphology, thickness, and electrochemical properties of the alloy. Prior to anodization, the alloy microstructure is composed of aluminum cells encapsulated in a silicon network. Anodizing the abraded and polished AlSi10Mg surface produced a porous oxide layer with a thickness of 5 μm. The oxide coating weight was 698 ± 29 mg/ft2. The oxide coating forms in the aluminum cells that are isolated from one another by the silicon eutectic phase. In electrochemical tests, the anodic and cathodic potentiodynamic polarization currents were suppressed by factors of 15× and 215×, respectively, as compared to the unanodized controls. The data indicate the anodic oxide coating suppresses the cathodic more than the anodic reaction rate. Linear polarization resistance (R
p) values increased by 279× after anodization. The corrosion current density values (j
corr) decreased by 133× after anodization. Taken together, the electrochemical data indicate the anodic oxide coating (unsealed) increases the corrosion resistance of the SLM alloy by two orders of magnitude.
Impact of Cobalt-Doping on the Optical, Magnetic, and Electronic Features of Hexagonal Cadmium Sulfide
Authors: Heiba Zein K. , Abd Ellatief Ah , Mohamed Mohamed Bakr , El-naggar A. M. , Elshimy Hassan , Ahmed Sameh I. , Ibrahim Ismail A.M.
Published: April 2024

CdS and Cd0.9Co0.1S samples were prepared under an N2 atmosphere. The structural analysis was conducted using X-ray diffraction. The structural and microstructure parameters were determined using Rietveld refinement method. The incorporation of cobalt ions into CdS matrix was confirmed by energy-dispersive spectroscopy and Fourier-transform infrared analysis. CdS sample has a non-magnetic feature while the Co-doped sample exhibited a magnetic behavior. The origin of magnetic property transformation has been investigated, revealing the emergence of ferromagnetic ordering and the conversion to a diluted magnetic semiconductor (DMS) with a calculated magnetic moment of 2.56 μ
B upon Co doping. We also investigated how this Cobalt-doping-driven transformation affected optical, photoluminescence, and electronic properties. These effects correlated with the emergence of hyper-deep defect states. Electronic properties were calculated using density functional theory (DFT) with the HSE06 hybrid functional approximation. The calculated energy bandgaps for both Co-doped and pure CdS were 2.13 and 2.12 eV, respectively, while experimental measurements from our UV analysis yielded values of 2.26 and 2.15 eV. DFT calculations were employed to explore the magnetic properties, absorption coefficients, refractive indices, real and imaginary dielectric components, and energy loss spectra in both samples.
Stability, Thermophysical, Optical and Photothermal Properties of ZnO Nanofluids with Added Anionic/Cationic Mixed Surfactants
Authors: Zhang XuSheng , Yang Bin , Shi Yue , Yu XiaoHui , Ma XiuQin
Published: April 2024

Metal oxide nanofluid is a new type of heat transfer medium with good thermal performance, which can be used to improve the heat collection and photothermal conversion performance of the collector. The development of new nanofluids with excellent stability, thermophysical and photothermal properties is very important for solar thermal utilization. In this paper, the ZnO nanofluids with SDS/CTAB mixed surfactants were prepared by two-step method. Their stability, thermophysical, optical and photothermal properties were studied based on experimental data. Then, the optimum concentration and preparation conditions of the proposed ZnO nanofluids adding SDS/CTAB with good photothermal performance were obtained. The results showed that the ZnO nanofluids with the addition of SDS/CTAB hybrid surfactant has good dispersion stability and its thermal conductivity can reach 0.772 W/(m·K). The transmittance was as low as 19.0.10% and the extinction coefficient was as high as 7.25 cm−1. In addition, the addition of the SDS/CTAB hybrid surfactant caused the ZnO nanofluids to exhibit better photothermal conversion efficiency up to 87%, which was superior to that of the control group with the addition of other surfactants. Therefore, ZnO nanofluids with the addition of SDS/CTAB have great potential as DASC working fluids.
A DIRIGENT Gene GmDIR26 Regulates Pod Dehiscence in Soybean
Authors: Wang Zheng , Zhang Xiaofang , Hou Rui , Zhang Huiying , Guo Xu , Ma Xiaofei , Xu Aiqin , Zhu Hong , Li Shuai
Published: April 2024

Pod dehiscence brings much loss for modern agricultural production, and multiple pod dehiscence components have been identified in many plant species. However, the pod dehiscence regulation factors in soybean are limited. In this study, we investigate the function of GmDIR26, a close homologues gene of pod dehiscence genes GmPdh1, PvPdh1, and CaPdh1, in the regulation of pod dehiscence in soybean. The secondary and tertiary structure analysis reveals that GmDIR26 protein has a similar structure with GmPdh1, PvPdh1, and CaPdh1 proteins. Synteny analysis of soybean and chickpea genomes shows that the genomic region surrounding GmDIR26 and CaPdh1 might be evolved from the same ancestor, and these two genes might have similar function. GmDIR26 shows an increased expression pattern during pod development and reaches a peak at beginning seed stage. Meanwhile, GmDIR26 exhibits high expression levels in dorsal suture and pod wall, but low expression pattern in ventral suture. In addition, GmDIR26 shows higher expression levels in pod dehiscence genotype than that in pod indehiscence accessions. Overexpression of GmDIR26 in soybean increases pod dehiscence in transgenic plants, of which the lignin layer in inner sclerenchyma pods is thicker and looser. The expression levels of several pod dehiscence genes are altered. Our study provides important information for further modification of pod dehiscence resistance soybean and characterization of soybean pod dehiscence regulation network.
Exploring Physics‐Informed Neural Networks for the Generalized Nonlinear Sine‐Gordon Equation
Authors: Deresse Alemayehu Tamirie , Dufera Tamirat Temesgen
Published: April 2024

The nonlinear sine‐Gordon equation is a prevalent feature in numerous scientific and engineering problems. In this paper, we propose a machine learning‐based approach, physics‐informed neural networks (PINNs), to investigate and explore the solution of the generalized non‐linear sine‐Gordon equation, encompassing Dirichlet and Neumann boundary conditions. To incorporate physical information for the sine‐Gordon equation, a multiobjective loss function has been defined consisting of the residual of governing partial differential equation (PDE), initial conditions, and various boundary conditions. Using multiple densely connected independent artificial neural networks (ANNs), called feedforward deep neural networks designed to handle partial differential equations, PINNs have been trained through automatic differentiation to minimize a loss function that incorporates the given PDE that governs the physical laws of phenomena. To illustrate the effectiveness, validity, and practical implications of our proposed approach, two computational examples from the nonlinear sine‐Gordon are presented. We have developed a PINN algorithm and implemented it using Python software. Various experiments were conducted to determine an optimal neural architecture. The network training was employed by using the current state‐of‐the‐art optimization methods in machine learning known as Adam and L‐BFGS‐B minimization techniques. Additionally, the solutions from the proposed method are compared with the established analytical solutions found in the literature. The findings show that the proposed method is a computational machine learning approach that is accurate and efficient for solving nonlinear sine‐Gordon equations with a variety of boundary conditions as well as any complex nonlinear physical problems across multiple disciplines.
A Systematic Review on Effects of Nitrogen Fertilizer Levels on Cabbage (Brassica oleracea var. capitata L.) Production in Ethiopia
Authors: Gelaye Yohannes
Published: April 2024

Cabbage (Brassica oleracea var. capitata L.) holds significant agricultural and nutritional importance in Ethiopia; yet, its production faces challenges, including suboptimal nitrogen fertilizer management. The aim of this review was to review the possible effect of nitrogen fertilizer levels on the production of cabbage in Ethiopia. Nitrogen fertilization significantly influences cabbage yield and quality. Moderate to high levels of nitrogen application enhance plant growth, leaf area, head weight, and yield. However, excessive nitrogen levels can lead to adverse effects such as delayed maturity, increased susceptibility to pests and diseases, and reduced postharvest quality. In Ethiopia, small-scale farmers use different nitrogen levels for cabbage cultivation. In Ethiopia, NPSB or NPSBZN fertilizers are widely employed for the growing of various crops such as cabbage. 242 kg of NPS and 79 kg of urea are the blanket recommendation for the current production of cabbage in Ethiopia. The existing rate is not conducive for farmers. Therefore, small-scale farmers ought to utilize an optimal and cost-effective nitrogen rate to boost the cabbage yield. Furthermore, the effectiveness of nitrogen fertilization is influenced by various factors including the soil type, climate, cabbage variety, and agronomic practices. Integrated nutrient management approaches, combining nitrogen fertilizers with organic amendments or other nutrients, have shown promise in optimizing cabbage production while minimizing environmental impacts. The government ought to heed suggestions concerning soil characteristics such as the soil type, fertility, and additional factors such as the soil pH level and soil moisture contents.
Investigation on Dynamic Stability of Cement‐Stabilized Expansive Soil Subgrades Subjected to Repeated Heavy‐Haul Train Loads
Authors: Shang Yonghui , Xu Linrong , Hao Xiaofei , Zhu Qichuan , Li Donghong
Published: April 2024

The dynamic characteristics of the filler are intricately linked to the stability of the subgrade. In this investigation, relying on Haoji (Haolebaoji‐Ji’an, China) heavy‐haul railway engineering, cyclic triaxial tests were executed to scrutinize the dynamic attributes exhibited by the 3%–5% cement‐stabilized expansive soil (CSES) across a series of diverse cyclic stress, confining pressures, and frequencies. Concurrently, in situ vibration trials were undertaken to dissect the dynamic characteristics inherent to the CSES subgrade. The outcomes of cyclic triaxial tests indicate that the augmentation in both the dynamic shear strength and modulus of CSES by a factor of 2–3, coupled with an escalation of the critical dynamic stress threshold by five tosix times, is attributed to the heightened internal structural density within the CSES compared to virgin expansive soil. In identical settings, it is noteworthy that the mean critical dynamic stress threshold observed for CSES surpasses that of Group A filling by a factor of 1.5–1.7. Furthermore, the maximum critical dynamic stress exhibited by CSES achieves a 1.2‐fold superiority over its lime‐stabilized expansive soil (LSES). The outcomes gleaned from the in situ vibration tests elucidate that, when subjected to the passage of a high‐velocity train traveling at 120 km/hr, bearing the load of 25–30 tons per axle, the subgrade surface exhibits dynamic stress ranging from 98.57 to 116.07 kPa. Meanwhile, the dynamic stress undergoes a notable escalation due to rainfall infiltration, intensifying by a factor of 1.02–1.28 times its original magnitude. The influence depth of dynamic stress extends 1.4–1.6 times beyond the designed subgrade bed thickness of 2.5 m. Notably, the critical dynamic stress of the filler surpasses the dynamic stress at the same position, underscoreing the capacity of 3%–5% CSES filling for heavy‐haul railways to ensure long‐term dynamic stability.