bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmission dynamics of drug-resistant tuberculosis in Ningbo, China: an epidemiological and genomic analysis
Authors: Che Yang , Li Xiangchen , Chen Tong , Lu Yewei , Sang Guoxin , Gao Junli , Gao Junshun , Liu Zhengwei , He Tianfeng , Chen Yi 
Published: February 2024

BackgroundTuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a significant public health concern in Ningbo, China. Understanding its molecular epidemiology and spatial distribution is paramount for effective control.MethodsFrom December 24, 2020, to March 12, 2023, we collected clinical Mycobacterium tuberculosis (MTB) strains in Ningbo, with whole-genome sequencing performed on 130 MTB strains. We analyzed DR-related gene mutations, conducted phylogenetic and phylodynamic analyses, identified recent transmission clusters, and assessed spatial distribution.ResultsAmong 130 DR-TB cases, 41% were MDR-TB, 36% pre-XDR-TB, 19% RR-TB, and 3% HR-TB. The phylogenetic tree showed that 90% of strains were Lineage 2 (Beijing genotype), while remaining 10% were Lineage 4 (Euro-American genotype). The spatial analysis identified hotspots of DR-TB in Ningbo’s northern region, particularly in traditional urban centers. 31 (24%) of the DR-TB cases were grouped into 7 recent transmission clusters with a large outbreak cluster containing 15 pre-XDR-TB patients. Epidemiological analyses suggested a higher risk of recent DR-TB transmission among young adult patients who frequently visited Internet cafes, game rooms, and factories.ConclusionOur study provides comprehensive insights into the epidemiology and genetics of DR-TB in Ningbo. The presence of genomic clusters highlights recent transmission events, indicating the need for targeted interventions. These findings are vital for informing TB control strategies in Ningbo and similar settings.
Researching educational barriers in participatory real-world labs: vocational training of refugees in rural counties in Germany
Authors: Thomas Stefan , Albrecht Pauline , Korntheuer Annette , Bucher Judith 
Published: February 2024

IntroductionAs a result of the large-scale arrivals of refugees and migrants, Germany is facing the challenge of providing inclusive education pathways not at least for a successful integration into the labor market. In our research project laeneAs (Ländliche Bildugnsumwelten junger Geflüchteter in der beruflichen Ausbildung/The Rural Educational Environments of Young Refugees in Vocational Training), we focus on educational barriers and good practices within the vocational education and training system (VET) for refugees in rural counties. In particular, racism and discrimination are significant barriers to refugee participation in society and education. Our contribution addresses the following research question: How is educational inclusion discussed and defined in and through real-world labs among stakeholders in four rural districts: social workers, educators, policymakers, administration, and young refugees?.MethodsWe initiated real-world labs as a space for collaborative research, reflection, and development to promote inclusive pathways for young refugees in vocational education and training in four research sites. We used futures labs as a method to identify key challenges and develop action plans as an activating method with stakeholders and refugee trainees. Our data consisted of audio recordings of group discussions in the real-world future labs, which were analyzed using deductive content analysis.ResultsThe analysis identified the following areas as important barriers to education and for practice transformation: (1) infrastructural and cultural barriers; (2) day-to-day problems in vocational schools and companies (3) restrictive immigration policies and regulations.DiscussionEducational barriers are imbedded in a contradictory immigration regime with reciprocal effects so that refugee trainees have difficulties in completing their education and further their social inclusion. On the other side of this contradictory immigration regime, social work and social networks provide fundamental support in obtaining a vocational qualification.
Learning and institutional support for youth in higher education institutions during the COVID-19 pandemic in South Africa
Authors: Dukhi Natisha , Sewpaul Ronel , Zungu Nompumelelo P. , Mokhele Tholang , Sifunda Sibusiso 
Published: February 2024

IntroductionAs higher education institutions (HEIs) moved from in-person to online learning during the COVID-19 pandemic, various challenges were presented. Using a large online survey conducted during the pandemic, this paper investigates the impact of COVID-19 on learning and institutional support offered to students in HEIs in South Africa.MethodsThe study utilized a closed-ended questionnaire on a data-free online platform. The study sample included South African youth aged 18–35 years who were enrolled for some type of educational training or in higher education institutions (including private colleges). Data was benchmarked to the 2019 estimates of the youth population in educational institutions. Descriptive statistics are presented.ResultsAmong the 7011 student participants, the main challenges experienced during lockdown were loss of study time (57.9%), insufficient money for essential personal items for studying (55.8%), loss of social contact (42.2%) and insufficient money for food (40.1%). Overall, 47.0% of students reported having free access to the internet, 49.5% used personal internet or paid for internet access and 3.5% indicated having no access to internet. The majority rated their institution’s eLearning portal as good or excellent, and 23.4% thought their eLearning portal was of poor quality. Significantly fewer (38.1%) technical and vocational education and training (TVET) college students indicated that their institution provided the capacity to conduct virtual learning compared to those enrolled at other types of institutions. Almost two thirds of students (66.2%) from TVET colleges experienced difficulty in communicating with their institutions. Half of the students (49.9%) reported that they had a suitable place to study during lockdown, while 78.6% had regular access to electricity during lockdown. Significantly more TVET and University of Technology students received transport to return home and fee refunds.ConclusionWhile it was encouraging that most HEIs had capacity for online learning and made provision of internet access for students, it was concerning that students who are enrolled at TVET colleges faced more learning challenges during the lockdown. This highlights the inequality in learning support at different types of institutions, and that effective support from HEIs to students during the COVID-19 pandemic was not fully implemented.
People and Data: solving planetary challenges together
Authors: Vanalli Chiara , Howerton Emily , Yang Fuhan , Tran Thu Nguyen-Anh , Hu Weiming 
Published: February 2024

The advancement of computing and information collection technologies has created vast amounts of data describing the world surrounding us. Yet, our planet continues to face unprecedented challenges, including climate change and biodiversity loss. How do we effectively use this information in an open and collaborative way to tackle these planetary-scale issues? We propose a stronger synergistic integration between people and data as we work toward a healthy planet: crowd empowerment in the collection and analysis of data as well as in the identification and implementation of actionable solutions. We use our unique experience as a diverse winning team of the EY Better Working World 2022 global data challenge to illustrate the great potential and current limitations of such an approach. With the objective of fighting biodiversity loss, we were asked to develop a predictive frog multi-species distribution model using occurrence data, gathered from the FrogID app, and environmental conditions. Despite the great potential of global data challenges focused on planetary health, they comprise about 6% of all challenges in the last 5 years. Moreover, though open in principle, in practice, pre-existing disparities limit the inclusion of a diverse crowd. To address existing gaps, we propose practical guidelines to realize the “People and Data” vision: fostering collaboration, seeking funding, enhancing diversity, and ensuring long-term sustainability. In this way, we can tackle the great challenges our world is facing.
Immune cell infiltrates in peritoneal metastases from colorectal cancer
Authors: Sundström Patrik , Hogg Stephen , Quiding Järbrink Marianne , Bexe Lindskog Elinor 
Published: February 2024

BackgroundThe presence of peritoneal metastases (PMs) in patients with colorectal cancer (CRC) confers a poor prognosis and only a minority of patients will benefit from the available treatment options. In primary CRC tumors, it is well established that a high infiltration of CD8+ effector T cells correlates to a favorable patient outcome. In contrast, the immune response induced in PMs from CRC and how it relates to patient survival is still unknown. In this study, we characterized the immune infiltrates and the distribution of immune checkpoint receptors on T cells from PMs from CRC, in order to evaluate the potential benefit of checkpoint blockade immunotherapy for this patient group.MethodsSurgically resected PM tissue from CRC patients (n=22) and synchronous primary tumors (n=8) were processed fresh to single cell suspensions using enzymatic digestion. Surface markers and cytokine production were analyzed using flow cytometry.ResultsT cells dominated the leukocyte infiltrate in the PM specimens analyzed, followed by monocytes and B cells. Comparing two different PMs from the same patient usually showed a similar distribution of immune cells in both samples. The T cell infiltrate was characterized by an activated phenotype and markers of exhaustion were enriched compared with matched circulating T cells, in particular the checkpoint receptors PD-1 and TIGIT. In functional assays most cytotoxic and helper T cells produced INF-γ and TNF following polyclonal stimulation, while few produced IL-17, indicating a dominance of Th1-type responses in the microenvironment of PMs.ConclusionImmune cells were present in all PMs from CRC examined. Although infiltrating T cells express markers of exhaustion, they produce Th1-type cytokines when stimulated. These results indicate the possibility to augment tumor-specific immune responses within PMs using checkpoint blockade inhibitors.
Configuring the field of global marine biodiversity conservation
Authors: Campbell Lisa M. , Gruby Rebecca , Gray Noella J. 
Published: February 2024

IntroductionThe article describes and analyzes the emergence of the field of global marine biodiversity conservation over the past fifteen years. We draw on collaborative research at international meetings, which we position as ‘field’ sites, places where diverse actors come together to negotiate the meaning and terms of global environmental governance and where that work is accessible and visible to researchers.MethodsBased on Collaborative Event Ethnography (CEE), a method developed to facilitate study of large meetings, we mobilize research from seven meetings since 2008 to describe the field of global marine biodiversity conservation, but more importantly to specifying how that field has been configured.ResultsWe identify practices of orchestration, narrative, performance, alliance, social objects, devices, and technologies, formal outcomes, and formal procedures, and their use at three phases of field configuration: building, framing, and bounding.DiscussionThe results: 1) enhance our understanding of the role of international conferences in global environmental governance generally, and for marine biodiversity conservation specifically; 2) demonstrate the relevance of field and field configuration theory; 3) contribute to theory on institutional fields by specifying practices of field configuration.
Detection of centroblast cells in H&E stained whole slide image based on object detection
Authors: Yuenyong Sumeth , Boonsakan Paisarn , Sripodok Supasan , Thuwajit Peti , Charngkaew Komgrid , Pongpaibul Ananya , Angkathunyakul Napat , Hnoohom Narit , Thuwajit Chanitra 
Published: February 2024

IntroductionDetection and counting of Centroblast cells (CB) in hematoxylin &amp; eosin (H&amp;E) stained whole slide image (WSI) is an important workflow in grading Lymphoma. Each high power field (HPF) patch of a WSI is inspected for the number of CB cells and compared with the World Health Organization (WHO) guideline that organizes lymphoma into 3 grades. Spotting and counting CBs is time-consuming and labor intensive. Moreover, there is often disagreement between different readers, and even a single reader may not be able to perform consistently due to many factors.MethodWe propose an artificial intelligence system that can scan patches from a WSI and detect CBs automatically. The AI system works on the principle of object detection, where the CB is the single class of object of interest. We trained the AI model on 1,669 example instances of CBs that originate from WSI of 5 different patients. The data was split 80%/20% for training and validation respectively.ResultThe best performance was from YOLOv5x6 model that used the preprocessed CB dataset achieved precision of 0.808, recall of 0.776, mAP at 0.5 IoU of 0.800 and overall mAP of 0.647.DiscussionThe results show that centroblast cells can be detected in WSI with relatively high precision and recall.
Influence of weeding methods on rhizosphere soil and root endophytic microbial communities in tea plants
Authors: Yan Yuxiao , Wang Conglian , Wan Renyuan , Li Shuang , Yang Yanfen , Lv Caiyou , Li Yongmei , Yang Guangrong 
Published: February 2024

IntroductionPolyethylene mulch is a kind of inorganic mulch widely used in agriculture. The effects of plastic mulch debris on the structure of plant soil and root growth have been fully studied, but their effects on endophytic microbial communities have not been explored to a large extent.MethodsIn this study, High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences were used to analyze microbial community structure and composition in rhizosphere soil and root endophytic of tea plant under three different weeding methods: polyethylene mulching, hand weeding and no weeding (CK).ResultsThe results showed that the weeding methods had no significant effect on the rhizosphere and root endophytic microbial abundance, but the rhizosphere bacterial structure covered by polyethylene mulch was significantly different than hand weeding and CK. The rhizosphere fungal diversity was also significantly higher than the other two analyzed treatments. The community abundance of rhizosphere microorganisms Acidobacteria, Candidatus Rokubacteria and Aspergillus covered by polyethylene mulch decreased significantly, whereas Bradyrhizobium, Solirubrobacterales and Alphaproteobacteria increased significantly. The abundance of bacteria Ktedonobacter, Reticulibacter, Ktedonosporobacter and Dictyobacter communities covered by polyethylene mulch was significantly changed, and the abundance of Fusarium and Nitrobacteraceae was significantly increased. Rhizosphere dominant bacteria were negatively correlated with soil available nitrogen content, while dominant fungi were significantly correlated with soil pH, total nitrogen and total potassium.DiscussionPolyethylene mulch forms an independent micro-ecological environment. At the same time, the soil nutrient environment was enriched by affecting the nitrogen cycle, and the composition of microbial community was affected. This study elucidated the effects of polyethylene mulch on soil microbial community in tea garden and provided a new theoretical understanding for weed management.
Serum proteomic biomarker investigation of vascular depression using data-independent acquisition: a pilot study
Authors: Lan Liuyi , Peng Sisi , Zhang Ran , He Haoying , Yang Yong , Xi Bing , Zhang Junjian 
Published: February 2024

BackgroundVascular depression (VaD) is a depressive disorder closely associated with cerebrovascular disease and vascular risk factors. It remains underestimated owing to challenging diagnostics and limited information regarding the pathophysiological mechanisms of VaD. The purpose of this study was to analyze the proteomic signatures and identify the potential biomarkers with diagnostic significance in VaD.MethodsDeep profiling of the serum proteome of 35 patients with VaD and 36 controls was performed using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Functional enrichment analysis of the quantified proteins was based on Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Reactome databases. Machine learning algorithms were used to screen candidate proteins and develop a protein-based model to effectively distinguish patients with VaD.ResultsThere were 29 up-regulated and 31 down-regulated proteins in the VaD group compared to the controls (|log2FC| ≥ 0.26, p ≤ 0.05). Enrichment pathways analyses showed that neurobiological processes related to synaptic vesicle cycle and axon guidance may be dysregulated in VaD. Extrinsic component of synaptic vesicle membrane was the most enriched term in the cellular components (CC) terms. 19 candidate proteins were filtered for further modeling. A nomogram was developed with the combination of HECT domain E3 ubiquitin protein ligase 3 (HECTD3), Nidogen-2 (NID2), FTO alpha-ketoglutarate-dependent dioxygenase (FTO), Golgi membrane protein 1 (GOLM1), and N-acetylneuraminate lyase (NPL), which could be used to predict VaD risk with favorable efficacy.ConclusionThis study offers a comprehensive and integrated view of serum proteomics and contributes to a valuable proteomics-based diagnostic model for VaD.
Neurological involvement among non-hospitalized adolescents and young adults 6 months after acute COVID-19
Authors: Havdal Lise Beier , Selvakumar Joel , Lund Berven Lise , Stiansen-Sonerud Tonje , Zetterberg Henrik , Blennow Kaj , Holmøy Trygve , Wyller Vegard Bruun Bratholm 
Published: February 2024

IntroductionThe post-COVID-19 condition (PCC) is characterized by debilitating persistent symptoms, including symptoms suggesting neurological aberrations such as concentration difficulties, impaired memory, pain, and sleep disturbances. The underlying mechanisms remain elusive. This study aimed to investigate brain injury biomarkers, neurocognitive test performance, and self-reported neurological and neuropsychological symptoms in young people with PCC.MethodsA total of 404 non-hospitalized adolescents and young adults aged 12–25 years who tested positive for SARS-CoV-2, along with 105 matched SARS-CoV-2 negative individuals, were prospectively enrolled and followed-up for 6 months (Clinical Trials ID: NCT04686734). All participants underwent comprehensive assessment encompassing clinical examinations, questionnaires, neurocognitive testing and blood sampling. Serum samples were immunoassayed for the brain injury biomarkers neurofilament light chain (Nfl) and glial fibrillary acidic protein (GFAp). At 6 months, cross-sectional analyses of serum Nfl/GFAp, neurocognitive test results and symptom scores were performed across groups based on adherence to PCC criteria as well as initial SARS-CoV-2 test results. Also, associations between Nfl/GFAp, neurocognitive test results, and symptom scores were explored.ResultsA total of 381 SARS-CoV-2 positive and 85 SARS-CoV-2 negative were included in the final analysis at 6 months, of whom 48% and 47%, respectively, adhered to the PCC criteria. Serum levels of Nfl and GFAp were almost equal across groups and did not differ from reference values in healthy populations. Also, neurocognitive test results were not different across groups, whereas symptom scores were significantly higher in patients fulfilling PCC criteria (independent of initial SARS-CoV-2 status). No significant associations between Nfl/GFAp, neurocognitive test results, and symptom scores were found.ConclusionNormal brain injury biomarkers and neurocognitive performance 6 months after mild COVID-19 implies that the persistent symptoms associated with PCC are not concurrent with ongoing central nervous system damage or permanent disruption of cognitive functions. This finding contradicts the notion of neuroinflammation as a likely explanation for the persistent symptoms.
Monitoring health and nutrition claims on food labels in Brazil
Authors: Kikuta Carolina , Borges Camila Aparecida , Duran Ana Clara 
Published: February 2024

IntroductionThe monitoring of nutrition and health claims on food and beverage labels has been proposed by international and national organizations because it can collaborate with the development of public policies to regulate food labeling and marketing strategies. One way of carrying out this monitoring is by using data collected by private companies.ObjectiveTo compare information on nutrition and health claims available in a commercial database of a private company that monitors the launch of new foods and beverages in Brazilian food retailers with information on those same claims manually coded by trained research assistants.MethodsThis is a cross-sectional observational study using a data sample of newly launched food and beverages available at a commercial database from 2018 to 2021. We compared the information on health and nutrition claims available on the commercial dataset with reliable information on the same nutrition and health claims manually coded by trained research assistants using a tested taxonomy to classify such claims. We used Gwet’s Kappa AC1 with 95% CI and percentage agreement to compare both data sources and calculated sensitivity and specificity of the compared data.ResultsA total of 6,722 foods and beverages were analyzed. Mintel-GNPD presented 36.28% (n = 2,439) of nutrition claims, while in the trained researchers’ coding, it was 33.73% (n = 2,267). We found a prevalence of 5.4% (n = 362) for health claims in Mintel-GNPD and 10.8% (n = 723) in the researchers’ coding. All subcategories of nutrition and health claims showed high agreement (Kappa &gt;0.81). Health claims presented kappa = 0.89 with 33.7% sensitivity and 98.0% specificity while nutrition claims showed kappa = 0.86 with 92.9% sensitivity and 92.5% specificity.ConclusionNutrition and health claims showed high agreement, with great results in nutrition claims, indicating that Mintel-GPND is suitable for monitoring such claims on food and beverage packaging in Brazil. Additionally, our findings show a high prevalence of nutrition and health claims on food packages launched in the Brazilian food retail, highlighting the need to monitor these to develop public policies to regulate food marketing on packaging in Brazil.