bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of common signature genes and pathways underlying the pathogenesis association between nonalcoholic fatty liver disease and atherosclerosis
Authors: Mo Shuangyang , Wang Yingwei , Yuan Xin , Wu Wenhong , Zhao Huaying , Wei Haixiao , Qin Haiyan , Jiang Haixing , Qin Shanyu 
Published: March 2023

BackgroundAtherosclerosis (AS) is one of the leading causes of the cardio-cerebral vascular incident. The constantly emerging evidence indicates a close association between nonalcoholic fatty liver disease (NAFLD) and AS. However, the exact molecular mechanisms underlying the correlation between these two diseases remain unclear. This study proposed exploring the common signature genes, pathways, and immune cells among AS and NAFLD.MethodsThe common differentially expressed genes (co-DEGs) with a consistent trend were identified via bioinformatic analyses of the Gene Expression Omnibus (GEO) datasets GSE28829 and GSE49541, respectively. Further, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. We utilized machine learning algorithms of lasso and random forest (RF) to identify the common signature genes. Then the diagnostic nomogram models and receiver operator characteristic curve (ROC) analyses were constructed and validated with external verification datasets. The gene interaction network was established via the GeneMANIA database. Additionally, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and immune infiltration analysis were performed to explore the co-regulated pathways and immune cells.ResultsA total of 11 co-DEGs were identified. GO and KEGG analyses revealed that co-DEGs were mainly enriched in lipid catabolic process, calcium ion transport, and regulation of cytokine. Moreover, three common signature genes (PLCXD3, CCL19, and PKD2) were defined. Based on these genes, we constructed the efficiently predictable diagnostic models for advanced AS and NAFLD with the nomograms, evaluated with the ROC curves (AUC = 0.995 for advanced AS, 95% CI 0.971–1.0; AUC = 0.973 for advanced NAFLD, 95% CI 0.938–0.998). In addition, the AUC of the verification datasets had a similar trend. The NOD-like receptors (NLRs) signaling pathway might be the most crucial co-regulated pathway, and activated CD4 T cells and central memory CD4 T cells were significantly excessive infiltration in advanced NAFLD and AS.ConclusionWe identified three common signature genes (PLCXD3, CCL19, and PKD2), co-regulated pathways, and shared immune features of NAFLD and AS, which might provide novel insights into the molecular mechanism of NAFLD complicated with AS.
Automated observation of physical snowpack properties in Ny-Ålesund
Authors: Scoto Federico , Pappaccogli Gianluca , Mazzola Mauro , Donateo Antonio , Salzano Roberto , Monzali Matteo , de Blasi Fabrizio , Larose Catherine , Gallet Jean-Charles , Decesari Stefano , Spolaor Andrea 
Published: March 2023

The snow season in the Svalbard archipelago generally lasts 6–10 months a year and significantly impacts the regional climate, glaciers mass balance, permafrost thermal regime and ecology. Due to the lack of long-term continuous snowpack physical data, it is still challenging for the numerical snow physics models to simulate multi-layer snowpack evolution, especially for remote Arctic areas. To fill this gap, in November 2020, an automated nivometric station (ANS) was installed ∼1 km Southwest from the settlement of Ny-Ålesund (Spitzbergen, Svalbard), in a flat area over the lowland tundra. It automatically provides continuous snow data, including NIR images of the fractional snow-cover area (fSCA), snow depth (SD), internal snow temperature and liquid water content (LWC) profiles at different depths with a 10 min time resolution. Here we present the first-year record of automatic snow preliminary measurements collected between November 2020 and July 2021 together with weekly manual observations for comparison. The snow season at the ANS site lasted for 225 days with an annual net accumulation of 117 cm (392 mm of water equivalent). The LWC in the snowpack was generally low (&lt;4%) during wintertime, nevertheless, we observed three snow-melting events between November and February 2021 and one in June 2021, connected with positive temperature and rain on snow events (ROS). In view of the foreseen future developments, the ANS is the first automated, comprehensive snowpack monitoring system in Ny-Ålesund measuring key essential climate variables needed to understand the seasonal evolution of the snow cover on land.
Students’ basic psychological needs in blended teacher learning groups
Authors: De Vocht Ann , Vrieling-Teunter Emmy , Sins Patrick , Vermeulen Marjan 
Published: March 2023

IntroductionStudent teachers (henceforth: students) in higher education often experience feelings of emotional loneliness that negatively impact upon their well-being and motivation to learn. Consequently, the importance of social learning for students has gained increased prominence, with Teacher Learning Groups (TLGs), that is, social configurations in which students, in-service teachers, and teacher educators, sometimes supplemented by researchers and/or experts, collaboratively learn through social interactions, being introduced in teacher training institutes. Ordinarily, TLGs organized their meetings face-to-face; however, due to COVID-19 measures, they had to rapidly transition to blended meetings, which in turn impacted upon students’ basic psychological needs.MethodsIn the present study, a convergent parallel mixed-methods design was utilized. The variables Social Configurations (Practice integration, Long-term orientation and goals; Shared identity and equal relationships) and Basic Psychological Needs (Competence, Autonomy, Relatedness) were assessed through the use of qualitative interviews and by administering two online quantitative surveys: the “Dimensions of Social Learning Questionnaire” and the “Basic Psychological Need Satisfaction and Frustration Scale”. Seventy students completed the questionnaires, while 14 students were interviewed. The students were recruited from four teacher training institutes.ResultsThe analyses reveal that the more students perceive Shared identity and equal relationships in blended TLGs, the greater the fulfillment of Basic Psychological Needs they experience. Moreover, the more students experience the fulfillment of the need for Competence, the more students perceive TLGs’ Social Configurations.DiscussionBased on the findings, we conclude that, although in-depth learning is more challenging during distance learning, blended TLGs are valuable for students’ Basic Psychological Needs during unpredictable times.
How urban development affects green development efficiency in China: Taking the city cluster of Yangtze river economic belt as an example
Authors: Huang Jing , Shangguan Ziheng , Gui Tiantian , Liu Jianping 
Published: March 2023

Introduction: In order to change the long-term economic development model which is at the expense of the environment, China proposed a series of new energy development and environmental intervention policies. However, there is no evidence to support the impact of urban development on the green development efficiency (GDE) under China’s macroeconomic policies at present. In order to answer this research question and help the government to improve the GDE, this study takes the Yangtze River Economic Belt (YREB) city cluster (41 cities) in China as an example to conduct an empirical study.Methods: We first measure the GDE of these cities by Slack Based Model (SBM). Then, the Tobit model is used to measure the impact of urban development elements, namely population urbanization, land urbanization, and urban industrial development, on GDE.Results and Discussion: The analysis of the data leads to the following conclusions and suggestions: 1) The GDE of the city cluster in the YREB has generally been improved driven by policies. But compared to policy interventions, the level of science, technology and management are the primary drivers of long-term improvement in GDE. 2) In order to avoid the economic development and environmental capacity failure to afford the increase in energy consumption and pollution discharge caused by population urbanization and land urbanization, local governments need to promote energy transformation, increase environmental protection efforts and attract top-tier talent. 3) The improvement of GDE by industrial upgrading is a dynamic and slow process, and blindly pushing industrial restructuring will lead to a decline in GDE. Therefore, the Chinese government needs to provide an ecologically suitable environment for local industrial development, which needs to avoid “pulling out the seedlings” and “one-size-fits-all” approach.
Integration analysis based on fatty acid metabolism robustly predicts prognosis, dissecting immunity microenvironment and aiding immunotherapy for soft tissue sarcoma
Authors: Liu Binfeng , He Shasha , Li Chenbei , Feng Chengyao , Wang Hua , Zhang Haixia , Tu Chao , Li Zhihong 
Published: March 2023

Background: Soft tissue sarcoma (STS) is a highly malignant tumor with a dismal prognosis. Presently, the dysregulation of fatty acid metabolism has received increasing attention in tumor research, but fewer reports are relevant to STS.Methods: Based on fatty acid metabolism-related genes (FRGs), a novel risk score for STS was developed utilizing univariate analysis and least absolute shrinkage selection operator (LASSO) Cox regression analyses in the STS cohort, which were further validated using the external validation cohort from other databases. Furthermore, independent prognostic analysis, C-index, ROC curves, and nomogram were carried out to investigate the predictive performance of fatty acid-related risk scores. We also analysed the differences in enrichment pathways, the immune microenvironment, gene mutations, and immunotherapy response between the two distinct fatty acid score groups. Moreover, the real-time quantitative polymerase chain reaction (RT-qPCR) was used to further verify the expression of FRGs in STS.Results: A total of 153 FRGs were retrieved in our study. Next, a novel fatty acid metabolism-related risk score (FAS) was constructed based on 18 FRGs. The predictive performance of FAS was also verified in external cohorts. In addition, the independent analysis, C-index, ROC curve, and nomograph also revealed that FAS could serve as an independent prognostic factor for the STS patients. Meanwhile, our results demonstrated that the STS cohort in two distinct FAS groups had different copy number variations, immune cell infiltration, and immunotherapy responses. Finally, the in vitro validation results demonstrated that several FRGs included in the FAS exhibited abnormal expression in STS.Conclusion: Altogether, our work comprehensively and systematically clarifies fatty acid metabolism’s potential roles and clinical significance in STS. The novel individualized score based on fatty acid metabolism may be provided as a potential marker and treatment strategy in STS.
Choice of a family planning outlet in urban areas: The role of distance and quality of services in Kenya and Uganda
Authors: Winston Jennifer , Calhoun Lisa M. , Guilkey David , Macharia Peter M. , Speizer Ilene S. 
Published: March 2023

IntroductionQuality of care and physical access to health facilities affect facility choice for family planning (FP). These factors may disproportionately impact young contraceptive users. Understanding which components of service quality drive facility choice among contraceptive users of all ages can inform strategies to strengthen FP programming for all potential users of FP.MethodsThis study uses data from Population Services International's Consumer's Market for Family Planning (CM4FP) project, to examine drivers of facility choice among female FP users. The data collected from female contraceptive users, the outlet where they obtained their contraceptive method, and the complete set of alternative outlets in select urban areas of Kenya and Uganda were used. We use a mixed logit model, with inverse probability weights to correct for selection into categories of nonuse and missing facility data. We consider results separately for youth (18–24) and women aged 25–49 in both countries.ResultsWe find that in both countries and across age groups, users were willing to travel further to public outlets and to outlets offering more methods. Other outlet attributes, including signage, pharmacy, stockouts, and provider training, were important to women in certain age groups or country.DiscussionThese results shed light on what components of service quality drive outlet choice among young and older users and can inform strategies to strengthen FP programming for all potential users of FP in urban settings.
Vertical plants: Plant design of Living walls – evaluation of 34 perennials in a textile based Living wall over a three years experiment
Authors: Stollberg Maren , von Birgelen Alexander 
Published: March 2023

IntroductionUrban green can be complemented by Living walls (LW). Knowledge of LW, including technique or their cooling effects, is well discussed, but little published data on plant diversity, design and development in LWs exists. The plants themselves determine whether LWs achieve their intended benefits. However, LW plants are exposed to extreme conditions such as temperature or drought stress.Material and methodsTherefore, we observed plant development in a textile-based LW (mat) over a three-year experiment under a temperate oceanic climate in the south west of Germany. The aim was to establish higher plant diversity for use in LWs. We chose 34 perennials (shrubs, ferns, grasses, and geophytes) that require high soil moisture. The mat was soil-free and had to be overwatered with a nutrient solution. The perennials were grouped in the plant module “cascade” (tall, hanging plants) and “ground cover” (low-spreading plants). We created four experimental walls exposed to the south, north, west, and east and adapted the plant modules to the lighting conditions of the experiment wall. The modules were pre-cultivated and attached to the experimental walls in a randomised design and repetition of four. We determined the visual attractiveness and additional parameters of individual plants.ResultsWe observed that Tellima grandiflora ‘Rubra’, Waldsteinia ternata, Pachysandra terminalis, and Heuchera Hybride ‘Purple Petticoats’ were the most attractive all year. Ajuga tenorii ‘Mauro’, Alchemilla caucasica, Hosta sieboldii ‘Harry van Trier’, Glechoma hederacea, and Geum coccineum ‘Carlskaer’ showed a nice ornamental effect and flowering during summer. The ferns and Waldsteinia ternata showed delayed growth but nice leaf texture gradually.Discussion and conclusionWe saw differences in winter survival rates depending on minimum temperature in winter. The tested plants developed a special vertical growth form and height. We observed various results at different expositions but found suitable species for each exposition. With these results, we derived a table of plants along with their suitability for LWs and determining conditions.
Added value of including waves into a coupled atmosphere–ocean model system within the North Sea area
Authors: Grayek Sebastian , Wiese Anne , Ho-Hagemann Ha Thi Minh , Staneva Joanna 
Published: March 2023

In this study, the effects of fully coupling the atmosphere, waves, and ocean compared with two-way-coupled simulations of either atmosphere and waves or atmosphere and ocean are analyzed. Two-year-long simulations (2017 and 2018) are conducted using the atmosphere–ocean–wave (AOW) coupled system consisting of the atmosphere model CCLM, the wave model WAM, and the ocean model NEMO. Furthermore, simulations with either CCLM and WAM or CCLM and NEMO are done in order to estimate the impacts of including waves or the ocean into the system. For the North Sea area, it is assessed whether the influence of the coupling of waves and ocean on the atmosphere varies throughout the year and whether the waves or the ocean have the dominant effect on the atmospheric model. It is found that the effects of adding the waves into the system already consisting of atmosphere and ocean model or adding the ocean to the system of atmosphere and wave model vary throughout the year. Which component has a dominant effect and whether the effects enhance or diminish each other depends on the season and variable considered. For the wind speed, during the storm season, adding the waves has the dominant effect on the atmosphere, whereas during summer, adding the ocean has a larger impact. In summer, the waves and the ocean have similar influences on mean sea level pressure (MSLP). However, during the winter months, they have the opposite effect. For the air temperature at 2 m height (T_2m), adding the ocean impacts the atmosphere all year around, whereas adding the waves mainly influences the atmosphere during summer. This influence, however, is not a straight feedback by the waves to the atmosphere, but the waves affect the ocean surface temperature, which then also feedbacks to the atmosphere. Therefore, in this study we identified a season where the atmosphere is affected by the interaction between the waves and the ocean. Hence, in the AOW-coupled simulation with all three components involved, processes can be represented that uncoupled models or model systems consisting of only two models cannot depict.
Palestinian physicians’ self-reported practice regarding antibiotic use for upper respiratory tract infections in primary healthcare
Authors: Maraqa Bessan , Nazzal Zaher , Hamshari Suha , Matani Nardine , Assi Yasmeen , Aabed Mousa , Alameri Furqan 
Published: March 2023

BackgroundThe main objective of this study was to evaluate the antimicrobial therapy knowledge, attitudes, and practices of primary care physicians in the West Bank and Gaza.MethodsBetween January and April 2021, this cross-sectional survey was conducted. A link to the online survey was sent via confidential email lists to 336 primary care physicians who treated patients in Ministry of Health clinics. The survey questions scoring system was devised in order to evaluate the physicians’ practice, knowledge, and attitudes. Our scoring system identified favorable (good) and unfavorable (average and poor) antibiotic practices. In addition to independent t-test, the Chi-square test was used to compare the two groups of physicians’ knowledge, attitudes, and practices with their background characteristics. A multivariate analysis was performed to identify potential confounding variables having significant relationships.ResultsOf the 336 distributed questionnaires, 316 were completed, with a response rate of 94%. More than half (54.7%) were males, half (51.6%) were between 30 and 45 years of age, and most were general practitioners (74.1%). The overall good knowledge and attitude scores were 125 (39.6%) and 194 (61.4%), respectively. More than half (58.2%) had good antibiotic prescription practices. Females reported significantly more favorable practices than males, as did family medicine specialists compared with general practitioners. Finally, knowledge about antibiotic prescriptions had a substantial impact on changing their practices. However, physicians’ attitudes toward antibiotic prescriptions did not have a significant role in shaping their practices.ConclusionOveruse of antibiotics is a significant health issue in Palestine and worldwide. Most physicians know that improper antibiotic usage can cause antimicrobial resistance. More than two-thirds avoided needless antimicrobial prescriptions. In practicing antimicrobial stewardship, most prescribed fewer antibiotics and did not prescribe because of patient pressure. Family medicine specialists, female doctors, and those with high knowledge scores regardless of caseload were more likely to have good practices.
Volumetric measurement of paranasal sinuses and its clinical significance in pituitary neuroendocrine tumors operated using an endoscopic endonasal approach
Authors: Nakaya Masato , Tamura Ryota , Takahara Kento , Senuma Takumi , Yoshida Keisuke , Kitamura Yohei , Ueda Ryo , Toda Masahiro 
Published: March 2023

ObjectiveEndoscopic endonasal surgery (EES) for deep intracranial lesions has gained popularity following recent developments in endoscopic technology. The operability of invasive pituitary neuroendocrine tumors (PitNETs) depends on the anatomy of the nasal cavity and paranasal sinus. This study aimed to establish a simple volume reconstruction algorithm of the nasal cavity and paranasal sinus. Additionally, this is the first study to demonstrate the relationship between the segmentation method and the clinical significance in patients with PitNET.MethodsPre-and postoperative tumor volumes were analyzed in 106 patients with primary (new-onset) PitNETs (80 nonfunctioning and 26 functioning) who underwent EES. The efficiency and accuracy of the semiautomatic segmentation with manual adjustments (SSMA) method was compared with other established segmentation methods for volumetric analysis in the nasal cavity and paranasal sinuses. Correlations between the measured nasal cavity and paranasal sinus volumes and the extent of tumor removal were evaluated.ResultsThe SSMA method yielded accurate and time-saving results following the volumetric analyses of nasal cavity and paranasal sinuses with complex structures. Alternatively, the manual and semiautomatic segmentation methods proved time-consuming and inaccurate, respectively. The sphenoid sinus volume measured by SSMA was significantly correlated with the extent of tumor removal in patients with nonfunctioning Knosp grade 3 and 4 PitNET (r = 0.318; p = 0.015).ConclusionThe volume of sphenoid sinus potentially could predict the extent of resection due to better visualization of the tumor for PitNETs with CS invasion.
Metagenomics by next-generation sequencing (mNGS) in the etiological characterization of neonatal and pediatric sepsis: A systematic review
Authors: Agudelo-Pérez Sergio , Fernández-Sarmiento Jaime , Rivera León Diana , Peláez Ronald Guillermo 
Published: March 2023

IntroductionPediatric and neonatal sepsis is one of the main causes of mortality and morbidity in these age groups. Accurate and early etiological identification is essential for guiding antibiotic treatment, improving survival, and reducing complications and sequelae. Currently, the identification is based on culture-dependent methods, which has many limitations for its use in clinical practice, and obtaining its results is delayed. Next-generation sequencing enables rapid, accurate, and unbiased identification of multiple microorganisms in biological samples at the same time. The objective of this study was to characterize the etiology of neonatal and pediatric sepsis by metagenomic techniques.MethodsA systematic review of the literature was carried out using the PRISMA-2020 guide. Observational, descriptive, and case report studies on pediatric patients were included, with a diagnostic evaluation by clinical criteria of sepsis based on the systemic inflammatory response, in sterile and non-sterile biofluid samples. The risk of bias assessment of the observational studies was carried out with the STROBE-metagenomics instrument and the CARE checklist for case reports.Results and DiscussionFive studies with a total of 462 patients were included. Due to the data obtained from the studies, it was not possible to perform a quantitative synthesis (meta-analysis). Based on the data from the included studies, the result identified that mNGS improves the etiological identification in neonatal and pediatric sepsis, especially in the context of negative cultures and in the identification of unusual microorganisms (bacteria that are difficult to grow in culture, viruses, fungi, and parasites). The number of investigations is currently limited, and the studies are at high risk of bias. Further research using this technology would have the potential to improve the rational use of antibiotics.