bluuebunny/crossref_metadata_2025 huggingface dataset:
Methodology of Teaching English in the Military System
Authors:   National Defense University, Aliyeva Ramila
Published: September 2024

In our country's military education system, which is integrated with the military education systems of developed countries, special attention is given to teaching English, a global language, to military personnel. All methods and techniques that can contribute to successful language teaching are thoroughly studied. While modern methodologies offer countless approaches for teachers and students, there remains a need to explore and refine productive methods in this area. This article discusses the importance of teaching English as a foreign language to military personnel and emphasizes the use of effective methods. It also highlights the main challenges faced by English language teachers today, particularly the difficulties in developing and adapting teaching models that can be seamlessly integrated into the unique language structure of the armed forces. With this perspective in mind, the article examines both the scientific and theoretical foundations of English teaching methods in the military system, as well as their practical and applied aspects. It also explores the productive methods and techniques used in teaching English to military personnel.
A key-feature-based clustering approach to assess the impact of technology integration on cow health in Austrian dairy farms
Authors: Matzhold Caspar , Schodl Katharina , Klimek Peter , Steininger Franz , Egger-Danner Christa
Published: September 2024

In the domain of precision livestock farming, the integration of diverse data sources is crucial for advancing sustainability and evaluating the implications of farm management practices on cow health. Addressing the challenge of data heterogeneity and management diversity, we propose a key-feature-based clustering method. This approach, merging knowledge-driven feature selection with unsupervised machine learning, enables the systematic investigation of management effects on cow health by forming distinct clusters for analysis. Utilizing data from 3,284 Austrian farms, including 80 features related to feeding, milking, housing, and technology systems, and health information for 56,000 cows, we show how this methodology can be applied to study the impact of technological systems on cow health resulting from the incidence of veterinary diagnoses. Our analysis successfully identified 14 distinct clusters, further divided into four main groups based on their level of technological integration in farm management: “SMART,” “TRADITIONAL,” “AMS (automatic milking system),” and “SENSOR.” We found that “SMART” farms, which integrate both AMS and sensor systems, exhibited a minimally higher disease risk for milk fever (OR 1.09) but lower risks for fertility disorders and udder diseases, indicating a general trend toward reduced disease risks. In contrast, farms with “TRADITIONAL” management, without AMS and sensor systems, showed the lowest risk for milk fever but the highest risk of udder disease (OR 1.12) and a minimally higher incidence of fertility disorders (OR 1.07). Furthermore, across all four groups, we observed that organic farming practices were associated with a reduced incidence of milk fever, udder issues, and particularly fertility diagnoses. However, the size of the effect varied by cluster, highlighting the complex and multifactorial nature of the relationship between farm management practices and disease risk. The study highlights the effectiveness of the key-feature-based clustering approach for high-dimensional data analyses aimed at comparing different management practices and exploring their complex relationships. The adaptable analytical framework of this approach makes it a promising tool for planning optimizing sustainable and efficient animal husbandry practices.
Exploring the Catrina, an autochthonous cattle breed of the Azores, for a comparative analysis of methane emissions with Holstein-Friesian dairy cows
Authors: Azevedo Ana Rita , Lopes Maria Susana , Borba Alfredo , da Câmara Machado Artur , Mendonça Duarte
Published: September 2024

Introduction

The struggle against climate change in agriculture requires an increased understanding of greenhouse gas emissions, mainly from cattle farming. Through precise and accessible methods to monitor the methane (CH4) emissions of these animals, it is possible to assess the influence of several factors.Therefore, this study evaluates CH4 emissions from Catrina cattle, an autochthonous breed from the Azores, and Holstein-Friesian cattle, aiming to assess the potential environmental impact and sustainability of this native breed.

Materials and methods

The present study was performed on a total of 15 dry cows, seven Catrina and eight Holstein-Friesian, housed by breed, in groups of five animals. The laser methane detector was used to assess the repeatability and reproducibility of CH4 values, including peaks and respiration. Descriptive statistics for raw data, CH4 breath and peaks, and the amount of CH4 emitted per day and year were calculated.

Results

From the Catrina breed, the average of CH4 emissions were 37.04 ± 40.09 ppm x m for raw data, 33.15 ± 28.59 ppm x m for CH4 breath, and 218.65 ± 67.13 ppm x m for CH4 peaks. From the Holstein-Friesian, the values obtained were 65.62 ± 87.11 ppm x m, 57.57 ± 52.59 ppm x m, and 514.19 ± 266.02 ppm x m, respectively. Linear mixed models, the Chisquare method and ANOVA, which showed a significant breed effect (p < 0.001) across all datasets, with trends favoring higher emissions in Holstein-Friesian were also applied. Similarly, Pearson correlation analyses yielded consistent trends, however, with no statistical significance (p > 0.05).

Discussion and conclusion

The findings underscore the importance of preserving cultural and genetic heritage while addressing climate change and environmental challenges. Furthermore, the study highlights the adaptive capacity of autochthonous breeds to their local environments, suggesting their role in sustainable systems. However, methane emissions will be influenced by several factors, besides breed variable, so this study emphasizes the need to integrate the assessment of the microbiome, which depends on the composition of the diet, genetic characteristics, and other aspects, for the development of methane mitigation strategies, with the inclusion of native breeds in sustainable resource management and climate adaptation efforts.
Standardization and quality assessment for human intestinal organoids
Authors: Lee Hana , Yang Seunghye , Lee Kyung Jin , Kim Si-Na , Jeong Ji-Seon , Kim Ki Young , Jung Cho-Rok , Jeon Sooyeon , Kwon Dayeon , Lee Sungin , Lee Hanbyeol , Park Chihye , Ahn Sun-Ju , Yoo Jongman , Son Mi-Young
Published: September 2024

To enhance the practical application of intestinal organoids, it is imperative to establish standardized guidelines. This proposed standardization outlines a comprehensive framework to ensure consistency and reliability in the development, characterization, and application of intestinal organoids. The recommended guidelines encompass crucial parameters, including culture conditions, critical quality attributes, quality control measures, and functional assessments, aimed at fostering a standardized approach across diverse research initiatives. The implementation of these guidelines is anticipated to significantly contribute to the reproducibility and comparability of results in the burgeoning field of intestinal organoid research.
Southern blue criminology: rethinking ocean harmscapes in a global context
Authors: Hübschle Annette , Berg Julie
Published: September 2024

This paper introduces southern blue criminology, a novel theoretical framework that extends traditional criminological analysis to encompass the environmental harms affecting the world’s oceans, particularly from a Global South perspective. This approach critiques crime-centric analysis and expands upon the concept of “harmscapes” – areas significantly impacted by ecological damage – by integrating socio-economic and cultural contexts often overlooked by prevailing enforcement paradigms developed in the Global North. Through a critical review of existing criminological theories and maritime enforcement practices, this study highlights the inadequacies of current approaches that fail to account for the transnational and complex nature of oceanic harms. Southern blue criminology is proposed through four integrative perspectives: shifting from a crime-centric view to embracing a broader conception of ocean harmscapes; moving beyond state-centric responses to foster whole-of-society involvement including non-state actors; transcending Western-centric governance models in favor of context-dependent strategies that respect local knowledge and practices; and expanding the analytical frame from human-centric approaches to include human–nonhuman assemblages, recognizing the ocean as an active participant in ecological and social interactions. The framework aims to foster more effective and sustainable management of marine environments, proposing a shift from a punitive focus to a more comprehensive, preventive, and restorative approach. The implications of this research are significant, suggesting a transformative shift in policies to better address the intricate web of factors contributing to maritime environmental crimes and to enhance global ecological justice.
Finite element analysis of dental structures: the role of mandibular kinematics and model complexity
Authors: Özcan Canan , Lestriez Philippe , Özcan Mutlu , Josset Yannick
Published: September 2024

Introduction

This study observed the consequences of integrating mandibular kinematics in maxillary and mandibular teeth contact in a finite element analysis (FEA), and investigate the level of simplification of the dental models in FEA. The purpose of this study was to compare the results of finite element analysis obtained from simple to more complex dental models incorporating mandibular motion during loading phase.

Methods

Six models were generated for this study. The simplest models consisted of only the crown of the tooth and an antagonist tooth with either the same properties or rigid body properties while the subsequent models incorporated the root of the study tooth and the surrounding bone. The most complex model involved the hyperelastic ligament and the other anatomical elements of the tooth and surrounding bone. Mandibular movement data recorded with the Modjaw® system (Modjaw-Technologie) were used to bring the teeth into contact and generate the loading in all models where the stresses exerted on tooth structures during the chewing process were evaluated.

Results

von Mises stress and the shear stress obtained in all models, exceeded the ultimate compression strength of the materials, except for the model with the hyperelastic periodontal ligament. The forces applied to the tooth were extremely different depending on the addition or removal of anatomical elements despite the systematic study of the same teeth.

Discussion

The inclusion of mandibular kinematics in the finite element analysis requires the modelling of a complex dental model as simplification generated an overestimation of the forces and stresses on the structures. Finite element dental models allow for the observation and prevention of restorative failures by numerical methods but misinterpretations caused by poorly designed models have clinical implications on estimating performance of dental restorations.
A new perspective on selenium’s impact on renal function: European population-based analysis of plasma proteome-mediated Mendelian randomization study
Authors: Fu Shaojie , Qian Man , Yuan Zishu , Su Sensen , Ma Fuzhe , Li Fan , Xu Zhonggao
Published: September 2024

Background

The relationship between selenium and renal function has always attracted widespread attention. Increased selenium level has been found to cause impaired renal function in our previous study, but the mechanism is not clear. In this study, we evaluate the potential mediating effects of plasma proteome in the association of selenium level and renal function to understand the mechanisms of selenium’s effect on renal function.

Methods

Utilizing two-sample two-step mediating mendelian randomization (MR) methodology to investigate the genetically causal relationship between selenium level and renal function as well as the role of the plasma proteome in mediating them. Additionally, the mediating proteins were enriched and analyzed through bioinformatics to understand the potential mechanisms of selenium effects on renal function.

Results

In the MR analysis, an increase in selenium level was found to decrease estimated glomerular filtration rate (eGFR). Specifically, for each standard deviation (SD) increase in selenium levels, eGFR levels are reduced by 0.003 SD [Beta (95% CI): -0.003 (-0.004 ~ -0.001), P=0.001, with no observed heterogeneity and pleiotropy]. Through mediation analysis, 35 proteins have been determined mediating the genetically causal effects of selenium on the levels of eGFR, including Fibroblast growth factor receptor 4 (FGFR4), Fibulin-1, Cilia- and flagella-associated protein 45, Mothers against decapentaplegic homolog 2 (SMAD2), and E3 ubiquitin-protein ligase ZNRF3, and the mediation effect rates of these proteins ranged from 1.59% to 23.70%. In the enrichment analysis, 13 signal transduction pathways, including FGFR4 mutant receptor activation and Defective SLC5A5 causing thyroid dyshormonogenesis 1, were involved in the effect of selenium on eGFR levels.

Conclusion

Our finding has revealed the underlying mechanism by which increased selenium level lead to deterioration of renal function, effectively guiding the prevention of chronic kidney disease and paving the way for future studies.
Exploring the potential of myo-inositol in thyroid disease management: focus on thyroid cancer diagnosis and therapy
Authors: Razavi S. Adeleh , Kalari Mohadeseh , Haghzad Tahereh , Haddadi Fatemeh , Nasiri Shirzad , Hedayati Mehdi
Published: September 2024

Thyroid cancer (TC) is a malignancy that is increasing in prevalence on a global scale, necessitating the development of innovative approaches for both diagnosis and treatment. Myo-inositol (MI) plays a crucial role in a wide range of physiological and pathological functions within human cells. To date, studies have investigated the function of MI in thyroid physiology as well as its potential therapeutic benefits for hypothyroidism and autoimmune thyroiditis. However, research in the field of TC is very restricted. Metabolomics studies have highlighted the promising diagnostic capabilities of MI, recognizing it as a metabolic biomarker for identifying thyroid tumors. Furthermore, MI can influence therapeutic characteristics by modulating key cellular pathways involved in TC. This review evaluates the potential application of MI as a naturally occurring compound in the management of thyroid diseases, including hypothyroidism, autoimmune thyroiditis, and especially TC. The limited number of studies conducted in the field of TC emphasizes the critical need for future research to comprehend the multifaceted role of MI in TC. A significant amount of research and clinical trials is necessary to understand the role of MI in the pathology of TC, its diagnostic and therapeutic potential, and to pave the way for personalized medicine strategies in managing this intricate disease.
Causal association between 1400 metabolites and dilated cardiomyopathy: a bidirectional two-sample Mendelian randomization analysis
Authors: Zeng Xianghui , Zeng Qingfeng , Wang Xianggui , Li Kening , Wu Jincheng , Luo Jianping
Published: September 2024

Background

Dilated cardiomyopathy (DCM) is a cardiac disease with a poor prognosis of unclear etiology. Previous studies have shown that metabolism is associated with DCM. This study investigates the causal relationship between 1400 metabolites and DCM using a two-sample Mendelian randomization (MR) approach.

Methods

The study utilized data from the OpenGWAS database, comprising 355,381 Europeans, including 1,444 DCM cases. A total of 1,400 metabolites were evaluated for their causal association with DCM. Instrumental variables (IVs) were selected based on genetic variation and used in the MR analysis. The primary analysis method was inverse variance weighting (IVW), supplemented by weighted median-based estimation and sensitivity analyses.

Results

Of the 1,400 metabolites analyzed, 52 were identified as causally associated with DCM. The analysis revealed both positively and negatively correlated metabolites with DCM risk. Notable findings include the positive correlation of Tryptophan betaine and 5-methyluridine (ribothymidine) levels, and an inverse association of Myristoleate and Erythronate levels with DCM.

Conclusions

The study provides significant insights into the metabolites potentially involved in the pathogenesis of DCM. These findings could pave the way for new therapeutic strategies and biomarker identification in DCM management.
An integrated mitigation approach to diffuse agricultural water pollution–a scoping review
Authors: Quill Luke , Ferreira Diogo , Joyce Brian , Coleman Gabriel , Harper Carla , Martins Marta , Hodkinson Trevor , Trimble Daniel , Gill Laurence , O’Connell David W.
Published: September 2024

Non-point source pollution and water eutrophication from agricultural runoff present global challenges that impact ground and surface waters. The search for a feasible and sustainable mitigation strategy to combat this issue remains ongoing. This scoping review aims to explore one potential solution by examining relevant literature on agricultural practices of the past and recent edge-of-field measures, designed to ameliorate the impacts of agricultural runoff on soil and water quality. The study focuses on integrating findings from diverse research fields into a novel myco-phytoremediation approach, which involves the synergistic relationship of plants, arbuscular mycorrhizal fungi, and plant beneficial bacteria within vegetative buffer strips. The implementation of these augmented buffer strips enhances nutrient retention in the soil, reduces runoff volume, promotes biodiversity, and increases plant biomass. This biomass can be converted into biochar, an effective sorbent that can be used to filter dissolved and particulate nutrients from surface waterways. The resulting nutrient-rich biochar can be repurposed as a form of bio-fertiliser, optimizing fertiliser consumption and subsequently reducing the depletion rate of phosphorus, a limited resource. This paper investigates a circular model of abatement of agricultural runoff via maximal nutrient retention and subsequent recycling of nitrogen and phosphorus back into the agricultural system. The key impact lies in its contribution to addressing the issue of non-point source pollution and eutrophication by encouraging multidisciplinary research aimed at solving these complex environmental issues.
A study on the measurement and influencing factors of the urban wastewater treatment efficiency in China based on the superefficiency SBM-Tobit model
Authors: Tao Tingyu , Zhang Hao , Hu Zikun
Published: September 2024

With urbanization acceleration, ensuring urban water use security and sustainable water resource management has become a major global challenge. As a populous country, China faces increasingly severe challenges. Comprehensive and systematic urban wastewater treatment efficiency (UWTE) assessments constitute a prerequisite for addressing this problem. Based on 2011–2021 panel data of 30 Chinese provinces, the superefficiency SBM model was employed for UWTE measurement from national and regional perspectives. ArcGIS software and the Tobit model were adopted to analyse the spatial-temporal patterns and factors influencing UWTE. UWTE in most provinces generally exhibited a fluctuating upward trend, with an uneven east-high and west-low spatial distribution pattern. The decomposition results showed that the low UWTE in the eastern region was mainly constrained by scale efficiency, while in the central region, pure technical efficiency was the primary constraint. The shunt pipeline construction level, load rate, and wastewater treatment scale significantly positively impacted UWTE, while economic scale yielded a negative impact. It is recommended that the Chinese government adjust the outdated construction-without-operation model and implement differentiated wastewater treatment policies. It is necessary to vigorously promote rainwater and wastewater diversion pipeline construction, optimize and upgrade sewer networks and wastewater treatment facilities, and fully utilize scale effects. These findings provide insights for China and countries similar to China to facilitate efficient wastewater management practices.
Identification of cellular senescence-related genes and immune cell infiltration characteristics in intervertebral disc degeneration
Authors: Wang Muyi , Wang Hao , Wang Xin , Shen Yifei , Zhou Dong , Jiang Yuqing
Published: September 2024

Background

Intervertebral disc degeneration (IDD) progression involves multiple factors, including loss of nucleus pulposus cells and extracellular matrix as the basic pathological mechanism of degeneration, and is closely related to cellular senescence and immune cell infiltration. The aim of study was to identify critical cellular senescence-related genes and immune cell infiltration characteristics in IDD.

Methods

Four datasets, including GSE70362, GSE112216, GSE114169, and GSE150408, were downloaded from the Gene Expression Omnibus database. The senescence-related genes were acquired from the CellAge Database and intersected with differentially expressed genes (DEGs) between IDD and control samples for senescence-related DEGs (SRDEGs). Protein-protein interaction (PPI) network analysis was performed to obtain ten hub SRDEGs. A consensus cluster analysis based on these hub genes was performed to divide the patients into clusters. The functional enrichment, and immune infiltration statuses of the clusters were compared. Weighted gene co-expression network analysis was used to identified key gene modules. The overlapping genes from key modules, DEGs of clusters and hub SRDEGs were intersected to obtain potential biomarkers. To verify the expression of potential biomarkers, quantitative polymerase chain reaction (qPCR) and immunohistochemistry were performed by using human intervertebral disc tissues.

Results

In the GSE70362 dataset, a total of 364 DEGs were identified, of which 150 were upregulated and 214 were downregulated, and 35 genes were selected as SRDEGs. PPI analysis revealed ten hub SRDEGs and consensus cluster analysis divided the patients into two clusters. Compared to Cluster 2, Cluster 1 was highly enriched in extracellular matrix organization and various metabolic process. The level of Follicular T helper cells in the Cluster 1 was significantly higher than that in the Cluster 2. IGFBP3 and NQO1 were identified as potential biomarkers. The remaining 3 datasets, and the result of qPCR and immunohistochemistry showed that the expression levels of NQO1 and IGFBP3 in the degenerated group were higher than those in the control or treatment groups.

Conclusion

Senescence-related genes play a key role in the development and occurrence of IDD. IGFBP3 and NQO1 are strongly correlated with immune infiltration in the IDD and could become novel therapeutic targets that prevent the progression of IDD.
Causal effects and metabolites mediators between immune cell and risk of colorectal cancer: a Mendelian randomization study
Authors: Yang Qian , Duan Bixia , Yue Jian , Zhang Donglin , Chen Xueping , Shi Mengjia , Kan Jie , Li Ruochan , Li Hongda , Gan Lin
Published: September 2024

Objective

The involvement of immune cells in colorectal cancer (CRC) and their interplay with metabolic disorders are yet to be fully elucidated. This study examines how peripheral immune cells, inferred genetically, affect CRC and investigates the intermediary roles of metabolites.

Methods

We employed a two-sample bidirectional Mendelian randomization (MR) approach to assess the causal influence of immune cells on CRC. Additionally, a two-step MR strategy was utilized to pinpoint potential metabolites that mediate this effect. Our analysis incorporated data from genome-wide association studies (GWAS), involving 731 immune cell types, 1,400 metabolites, and CRC outcomes. The primary method of analysis was randomized inverse variance weighting (IVW), supported by MR-Egger, weighted median, simple mode, and weighted mode analyses. Sensitivity checks were conducted using Cochran’s Q test, MR-PRESSO test, MR-Egger regression intercept, and leave-one-out analysis.

Results

The study identified 23 immune cell types and 17 metabolites that are causally linked to CRC. Our mediation analysis highlighted that nine metabolites act as intermediaries in the relationship between nine specific immune cells and CRC risk. Notably, The ratios of Adenosine 5’-monophosphate (AMP) to aspartate and Retinol (Vitamin A) to linoleoyl-arachidonoyl-glycerol (18:2 to 20:4) were found to concurrently mediate the promoting effects of Myeloid DC %DC and BAFF-R on B cells in colorectal cancer (CRC). Moreover, iminodiacetate (IDA) was found to mediate the protective effect of CD14+ CD16- monocytes on CRC, contributing 11.8% to this mediation. In contrast, IDA was also seen to decrease the protective effect of IgD+ CD38br %B cells on CRC risk, with a mediation effect proportion of -10.4%.

Conclusion

This study delineates a complex network involving immune cells, metabolites, and CRC, suggesting a multifaceted pathophysiological interaction. The identified causal links and mediation pathways underscore potential therapeutic targets, providing a foundation for interventions aimed at modulating immune responses to manage CRC.
Unlocking sustainable marine economic growth: the role of financial development, innovation, and capital investment in coastal China
Authors: Meng Zhaosu , Pang Mengjiao , Zhang Dingyue , Chen Wenxiang
Published: September 2024

Introduction

As global resource demands and environmental challenges intensify, China's vast marine resources present a significant opportunity for sustainable economic development. This study investigates the impact of financial development on high-quality growth in China's marine economy across 11 coastal regions from 2011 to 2020.

Methods

We examine a mediation and moderation model linking financial development and marine economic quality in China, where the marine economy increasingly relies on financial support. This study proposes marine innovation output and industrial structure upgradation as mediators, with marine capital investment as a moderator.

Results

Our findings reveal that financial development significantly promotes high-quality marine economic growth, albeit with regional heterogeneity. The strongest effect is observed in the Eastern Marine Economic Zone, while the Southern Marine Economic Zone shows the weakest impact. Marine scientific research and industrial structure upgrading serve as key mediating factors, with the former demonstrating a stronger intermediary effect. Notable, marine capital investment positively moderates the relationship between financial development and marine economic growth.

Discussion

This study innovatively combines macro-finance and micro-finance indicators to construct a comprehensive financial development index system. It incorporates a multi-dimensional approach to measuring high-quality development in coastal regions, challenging one-size-fits-all models by highlighting regional variations. By providing insights into specific differences and underlying mechanisms, our study offers valuable guidance for policymakers in crafting region-specific strategies to leverage financial development for sustainable marine economic growth.
Prone positioning ventilation treatment rescuing a patient with chlamydia abortus-induced ARDS diagnosed by next generation sequencing: a case report
Authors: Chen Yi , Lan Pin , Liu Lixue , Zhou Kechun
Published: September 2024

Background

Chlamydia abortus is a pathogen capable of infecting both humans and animals. In most known cases, this pathogen primarily infects pregnant women, leading to miscarriage and preterm birth. However, it is exceedingly rare for this pathogen to cause pneumonia that progresses to severe Acute Respiratory Distress Syndrome (ARDS).

Case introduction

We present a case of a 76-year-old male patient who was clinically diagnosed with Acute Respiratory Distress Syndrome (ARDS) caused by Chlamydia abortus and successfully treated. The patient’s condition rapidly deteriorated over six days, evolving from a lung infection to severe pneumonia, ultimately leading to ARDS and sepsis. Initially, he was admitted to a local hospital for a lung infection where routine etiological examinations failed to identify any significant pathogens, and he received only empirical antimicrobial therapy. However, the lung infection was not controlled, and the patient’s condition rapidly worsened, resulting in severe respiratory distress. This necessitated tracheal intubation and assisted ventilation, after which he was transferred to our hospital for treatment. Due to the patient’s family’s inability to afford the cost of ECMO treatment, we adopted a prone positioning ventilation strategy to improve the patient’s ventilation-perfusion matching. Additionally, we performed metagenomic next-generation sequencing on the patient’s bronchoalveolar lavage fluid, which confirmed the infection with Chlamydia abortus. These measures ultimately led to the successful treatment of the patient.

Conclusion

Chlamydia abortus infection can lead to severe ARDS, necessitating timely diagnosis and active intervention by clinicians. This case highlights the crucial role of metagenomic next-generation sequencing in diagnosing rare pathogens. Timely adoption of prone positioning ventilation can significantly improve ventilation-perfusion matching, effectively treating ARDS caused by Chlamydia abortus. Additionally, the combination of moxifloxacin and piperacillin-tazobactam can treat ARDS caused by Chlamydia abortus.
Transplantation of autologous mesenchymal stromal cells in complete cervical spinal cord injury: a pilot study
Authors: Macêdo Carolina Thé , de Freitas Souza Bruno Solano , Villarreal Cristiane Flora , Silva Daniela Nascimento , da Silva Kátia Nunes , de Souza Clarissa Lima e Moura , da Silva Paixão Daniela , da Rocha Bezerra Milena , da Silva Moura Costa Antônio Olímpio , Brazão Eduardo Santos , Marins Filho Josildo Pereira , Matos André Costa , dos Santos Ricardo Ribeiro , Soares Milena Botelho Pereira
Published: September 2024

Objective

Spinal cord injury (SCI) is a serious condition that can lead to partial or complete paraplegia or tetraplegia. Currently, there are few therapeutic options for these conditions, which are mainly directed toward the acute phase, such as surgical intervention and high-dose steroid administration. Mesenchymal stromal cells (MSC) have been shown to improve neurological function following spinal cord injury. The aim of the study was to evaluate the safety, feasibility, and potential efficacy of MSC transplantation in patients with cervical traumatic SCI.

Methods

We included seven subjects with chronic traumatic SCI (> 1 year) at the cervical level, classified as American Spinal Cord Injury Association impairment scale (AIS) grade A. Subjects received two doses of autologous bone marrow derived MSC, the first by direct injection into the lesion site after hemilaminectomy and the second three months later by intrathecal injection. Neurologic evaluation, spinal magnetic resonance imaging (MRI), urodynamics, and life quality questionnaires were assessed before and after treatment.

Results

Cell transplantation was safe without severe or moderate adverse effects, and the procedures were well tolerated. Neurological evaluation revealed discrete improvements in sensitivity below the lesion level, following treatment. Five subjects showed some degree of bilateral sensory improvement for both superficial and deep mechanical stimuli compared to the pretreatment profile. No significant alterations in bladder function were observed during this study.

Conclusion

Transplantation of autologous MSC in patients with chronic cervical SCI is a safe and feasible procedure. Further studies are required to confirm the efficacy of this therapeutic approach.

Clinical trial registration

https://clinicaltrials.gov/study/NCT02574572, identifier NCT02574572.
Adherence to the antirheumatic drugs: a systematic review and meta-analysis
Authors: Aksoy Nilay , Ozturk Nur , Agh Tamas , Kardas Przemyslaw
Published: September 2024

Introduction

This systematic review and meta-analysis aimed to analyze the adherence rate for conventional and biological disease-modifying antirheumatic drugs (DMARDs) utilizing different assessment measures.

Method

A systematic literature search was performed in four electronic databases, including PubMed, Scopus, Web of Science, and the Cochrane Central Register of Controlled Trials (CENTRAL), covering the time frame from April 1970 to April 2023. Studies that present data on medication adherence among adult patients with rheumatoid arthritis (RA), specifically focusing on DMARDs (conventional or biological), were included in the analysis. The adherence rate for different assessment measures was documented and compared, as well as for conventional and biological DMARDs. A random-effects meta-analysis was performed to assess adherence rates across different adherence assessment measures and drug groups.

Results

The search identified 8,480 studies, out of which 66 were finally included in the analysis. The studies included in this meta-analysis had adherence rates ranging from 12 to 98.6%. Adherence rates varied across several adherent measures and calculation methods. Using the subjective assessment measures yielded the outcomes in terms of adherence rate: 64.0% [0.524, 95% CI 0.374–0.675] for interviews and 60.0% [0.611, 95% CI 0.465–0.758] for self-reported measures (e.g., compliance questionnaires on rheumatology CQR-5), p > 0.05. In contrast, the objective measurements indicated a lower adherence rate of 54.4% when using the medication event monitoring system (p > 0.05). The recorded rate of adherence to biological DMARDs was 45.3% [0.573, 95% CI 0.516–0.631], whereas the adherence rate for conventional DMARDs was 51.5% [0.632, 95% CI 0.537–0.727], p > 0.05. In the meta-regression analysis, the covariate “Country of origin” shows a statistically significant (p = 0.003) negative effect with a point estimate of −0.36, SE (0.12), 95% CI, −0.61 to −0.12.

Discussion

Despite its seemingly insignificant factors that affect the adherence rate, this meta-analysis reveals variation in adherence rate within the types of studies conducted, the methodology used to measure adherence, and for different antirheumatic drugs. Further research is needed to validate the findings of this meta-analysis before applying them to clinical practice and scientific research. In order to secure high reliability of adherence studies, compliance with available reporting guidelines for medication adherence research is more than advisable.
Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis
Authors: Yan Jin , Doublet Benoît , Wiedemann Agnès
Published: September 2024

Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.
Far-red light photoacclimation in a desert Chroococcidiopsis strain with a reduced FaRLiP gene cluster and expression of its chlorophyll f synthase in space-resistant isolates
Authors: di Stefano Giorgia , Battistuzzi Mariano , La Rocca Nicoletta , Selinger Vera M. , Nürnberg Dennis J. , Billi Daniela
Published: September 2024

Introduction

Some cyanobacteria can use far-red light (FRL) to drive oxygenic photosynthesis, a phenomenon known as Far-Red Light Photoacclimation (FaRLiP). It can expand photosynthetically active radiation beyond the visible light (VL) range. Therefore, it holds promise for biotechnological applications and may prove useful for the future human exploration of outer space. Typically, FaRLiP relies on a cluster of ~20 genes, encoding paralogs of the standard photosynthetic machinery. One of them, a highly divergent D1 gene known as chlF (or psbA4), is the synthase responsible for the formation of the FRL-absorbing chlorophyll f (Chl f) that is essential for FaRLiP. The minimum gene set required for this phenotype is unclear. The desert cyanobacterium Chroococcidiopsis sp. CCMEE 010 is unusual in being capable of FaRLiP with a reduced gene cluster (15 genes), and it lacks most of the genes encoding FR-Photosystem I.

Methods

Here we investigated whether the reduced gene cluster of Chroococcidiopsis sp. CCMEE 010 is transcriptionally regulated by FRL and characterized the spectral changes that occur during the FaRLiP response of Chroococcidiopsis sp. CCMEE 010. In addition, the heterologous expression of the Chl f synthase from CCMEE 010 was attempted in three closely related desert strains of Chroococcidiopsis.

Results

All 15 genes of the FaRLiP cluster were preferentially expressed under FRL, accompanied by a progressive red-shift of the photosynthetic absorption spectrum. The Chl f synthase from CCMEE 010 was successfully expressed in two desert strains of Chroococcidiopsis and transformants could be selected in both VL and FRL.

Discussion

In Chroococcidiopsis sp. CCME 010, all the far-red genes of the unusually reduced FaRLiP cluster, are transcriptionally regulated by FRL and two closely related desert strains heterologously expressing the chlF010 gene could grow in FRL. Since the transformation hosts had been reported to survive outer space conditions, such an achievement lays the foundation toward novel cyanobacteria-based technologies to support human space exploration.
Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation
Authors: Ong Chian Teng , Blackall Patrick. J. , Boe-Hansen Gry B. , deWet Sharon , Hayes Ben J. , Indjein Lea , Korolik Victoria , Minchin Catherine , Nguyen Loan To , Nordin Yusralimuna , Siddle Hannah , Turni Conny , Venus Bronwyn , Westman Mark E. , Zhang Zhetao , Tabor Ala E.
Published: September 2024

Introduction

Bovine Genital Campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between C. fetus subsp. venerealis and C. fetus subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between C. fetus subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.

Methods and results

This study reported the complete genomes of four C. fetus subsp. fetus and five C. fetus subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses (n = 25) were conducted, incorporating an additional 16 complete C. fetus genomes from the NCBI database, to investigate the genomic differences between these two closely related C. fetus subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two C. fetus subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the C. fetus subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG “Peptidoglycan Biosynthesis” pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of C. fetus subsp. venerealis and its biovar variant. Verification with 58 annotated C. fetus genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF (Campylobacter fetus subsp. fetus) or CFV/CFVi (Campylobacter fetus subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting C. fetus subspecies using a quantitative PCR assay.

Discussion

Our results highlighted the high genetic stability of C. fetus subspecies. Nevertheless, Campylobacter fetus subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from C. fetus subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of C. fetus subspecies.
Antibiotic-induced dysbiosis in the SCIME™ recapitulates microbial community diversity and metabolites modulation of in vivo disease
Authors: Dalle Vedove Elena , Benvenga Alessia , Nicolai Gianluca , Massimini Marcella , Giordano Maria Veronica , Di Pierro Francesco , Bachetti Benedetta
Published: September 2024

Establishing the context

Intestinal dysbiosis is a significant concern among dog owners, and the gut health of pets is an emerging research field. In this context, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data.

Stating the purpose/introducing the study

The current study presents a further application of this model by using amoxicillin and clavulanic acid to induce dysbiosis, aiming to provoke changes in microbial community and metabolite production, which are well-known markers of the disease in vivo.

Describing methodology

Following the induction of dysbiosis, prebiotic supplementation was tested to investigate the potential for microbiota recovery under different dietary conditions.

Presenting the results

The results showed that antibiotic stimulation in the SCIME™ model can produce significant changes in microbial communities and metabolic activity, including a decrease in microbial richness, a reduction in propionic acid production, and alterations in microbial composition. Additionally, changes in ammonium and butyric acid levels induced by the tested diets were observed.

Discussing the findings

This alteration in microbial community and metabolites production mimicks in vivo canine dysbiosis patterns. A novel dynamic in vitro model simulating canine antibiotic-induced dysbiosis, capable of reproducing microbial and metabolic changes observed in vivo, has been developed and is suitable for testing the effects of nutritional changes.
Microbial landscape of cooked meat products: evaluating quality and safety in vacuum-packaged sausages using culture-dependent and culture-independent methods over 1 year in a sustainable food chain
Authors: Lemos Junior Wilson José Fernandes , Marques Costa Lucas , Alberto Guerra Carlos , Sales de Oliveira Vanessa , Gava Barreto Angela , Alves de Oliveira Fabiano , Paula Breno Pereira de , Esmerino Erick Almeida , Corich Viviana , Giacomini Alessio , Guerra André Fioravante
Published: September 2024

Over the last few decades, advancements in process safety and quality methods have been significantly improved, yet new challenges continue to emerge in the sustainable food supply chain. This study aimed to investigate some physicochemical and microbiological parameters impacting meat products, particularly cooked sausages, within a sustainable supply chain, focusing on quality, spoilage populations, and syneresis formation under vacuum conditions. A comprehensive analysis was conducted on 355 samples collected over four seasons using high-throughput sequencing (16S/ITS) and microbiological and physicochemical [pH and water activity (aw)] assessments. The microbial growth predictor MicroLab_ShelfLife was employed, and multiple factor analysis (MFA) and agglomerative hierarchical clustering (AHC) were utilized to understand how these variables influence the microbiome resilience of these products. Lactic and acetic acids were correlated with the microbiome of the sausages and the liquid coating covering them using metagenomic analyses. The study highlighted that 52% of the evaluated meat industries in southeastern Brazil are implementing effective protocols for sustainable chain production. The results indicated that the durability of vacuum-packaged cooked sausages was primarily influenced by storage temperature (RV coefficient of 0.906), initial microbial load (0.755), and aw (0.624). Average microbial counts were 4.30 log cfu/g (initial), 4.61 (7°C/4 days), 4.90 (7°C/8 days), 6.06 (36°C/4 days), and 6.79 (36°C/8 days). Seasonal durability analysis revealed that winter had the highest average durability of 45.58 days, while summer had the lowest at 26.33 days. Yeast populations, including Trichosporon sp. and Candida sp., were identified as key genera influencing spoilage dynamics. In addition, Bacillus species emerged as dominant spoilage microorganisms, highlighting the need for new critical controls. This study demonstrates the impact of metagenomic approaches, including ITS and 16S amplicon sequencing, in revealing microbial community dynamics, storage temperature, and aw, which are essential for developing targeted interventions to enhance food safety and quality sustainably.
The Schizosaccharomyces pombe ornithine-N5-oxygenase Sib2 interacts with the N5-transacetylase Sib3 in the ferrichrome biosynthetic pathway
Authors: Mbuya Berthy , Plante Samuel , Ammar Farouk , Brault Ariane , Labbé Simon
Published: September 2024

The fission yeast Schizosaccharomyces pombe produces the hydroxamate-type siderophore ferrichrome (Fc). The biosynthesis of Fc requires the Fc synthase Sib1, the ornithine-N5-oxygenase Sib2, and the N5-hydroxyornithine-N5-transacetylase Sib3. In this study, we demonstrate the critical importance of the His248 residue of Sib3 in Fc production. Cells expressing a sib3H248A mutant allele fail to grow in iron-poor media without Fc supplementation. These sib3H248A mutant cells are consistently unable to promote Fc-dependent growth of Saccharomyces cerevisiae cells in cross-feeding experiments. Green fluorescent protein (GFP)-tagged wild-type Sib3 and mutant Sib3H248A exhibit a pancellular distribution. Coimmunoprecipitation assays revealed that both wild-type and Sib3H248A physically interact with Sib2. Further analysis identified a minimal C-terminal region from amino acids 290–334 of Sib3 that is required for interaction with Sib2. Deletion mapping analysis identified two regions of Sib2 as being required for its association with Sib3. The first region encompasses amino acids 1–135, and the second region corresponds to amino acids 281–358 of Sib2. Taken together, these results describe the first example of a physical interaction between an ornithine-N5-oxygenase and an N5-hydroxyornithine-N5-transacetylase controlling the biosynthesis of a hydroxamate-type siderophore.