bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of an Epidemic Driven by Random Transmission Rate: Explaining the Dynamics of COVID-19 in Bogotá
Authors: Ríos-Gutiérrez Andrés , Mubayi Anuj , ARUNACHALAM VISWANATHAN 
Published: November 2022

Abstract
The epidemic disease model is often used to predict an epidemic's characteristics and help plan an effective control strategy. Motivated by recent COVID-19 outbreaks, we develop and mathematically analyze a simple stochastic model that considers random perturbations in transmission rates and shows its validity using data from the Colombian city of Bogota. The stochastic epidemic model is stratified in the Susceptible-Exposed-Infectious-Recovered, \textit{SEIR}, type compartmental model with the randomness depicting the impact of stochastic variations due to external factors such as changes in environmental conditions and human behaviors that may impact the dynamics of an infectious disease. The analysis resulted in derivation of approximate distribution of \textit{eventual extinction of infection state}, \textit{persistence of infection in the mean}, and \textit{the quasi-stationary infectious state}). Finally, we illustrate inferences and model parameters using reported COVID-19 epidemic data from the Colombian city of Bogotá. The outbreak in Bogota is divided into six distinct periods, with transmission rates high during the initiation of the epidemic and even much higher during the last period, potentially due to the rapid spread of the Omicron variant in Colombia still has a low vaccination rate.
Mathematics Subject Classification: 92D30
Bioinformatics analysis of gene expression network regulation in osteogenic differentiation of human bone marrow mesenchymal stem cells RunningTitle: Bioinformatics analysis of osteogenic differentiation
Authors: zhang shuhong , Yao Jingke , Bai Xiaoyuan , Li Lihua , Li Shuang , Xu Xinhui , Sun Yongkun , Xu Chunyang , Zhang Hu , Wang Xianwei 
Published: November 2022

AbstractBackground:Among mesenchymal stem cells (MSCs), bone marrow mesenchymal stem cells (BMSCs) are considered the gold standard treatment for bone tissue regeneration. BMSCs have become an important cell source in bone and cartilage tissue engineering and regenerative medicine. However, the mechanism of osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) remains incompletely understood. In this study, we aimed to analyze the function of key gene in osteogenic differentiation of hBMSCs.Methods:From the Gene Expression Omnibus (GEO) database, we downloaded three microarray data sets: GSE12266, GSE18043 and GSE80614. Differentially expressed genes (DEGs) were screened using the ‘limma’ package, and enrichment analysis was performed. Protein–protein interaction network analysis and visualization analysis were performed in the String website and in Cytoscape software. We construct core gene regulatory network, and a reactome-based Gene Set Enrichment Analysis (GSEA) was performed on the differential genes. Experimental verification of target gene expression, osteogenic differentiation and the related markers was assessed by alkaline phosphatase (ALP) activity detection, calcium content detection, alizarin red (ARS) staining and RT-qPCR, respectively.Results:A total of 11,077 DEGs were identified, including 5296 upregulated genes and 5781 downregulated genes. Functional enrichment pathways of the identified DEGs are related to cell cycle, nuclear division, apoptosis, organelle fission, chromosomal region, centromeric region, ATPase activity, tubulin binding, microtubule blinding, shear stress, TNF signaling, etc. Further functional and correlation analyses of four core genesBRCA1,BIRC5,GMNNandTSC22D3, as well as the followed verification experiments including qPCR, ARS and ALP staining all showed thatTSC22D3andBIRC5were significantly related to the osteogenic differentiation of hBMSCs.Conclusions：This study provides a novel insight into the biological process of osteogenic differentiation of hBMSCs, and identifies novel genes for osteogenic differentiation of MSCs. Meanwhile, the findings in this study also provide potential therapeutic targets for bone tissue engineering.
SMPD1 Expression Profile and Mutation Landscape Help Decipher Genotype–Phenotype Association and Precision Diagnosis for Acid Sphingomyelinase Deficiency
Authors: Wang Ruisong , Qin Ziyi , Huang Long , Luo Huiling , Peng Han , Zhou Xinyu , Zhao Zhixiang , Liu Mingyao , Yang Pinhong , Shi Tieliu 
Published: November 2022

Abstract
Background
Acid sphingomyelinase deficiency (ASMD) disorder, also known as Niemann–Pick disease (NPD) is a rare genetic disease caused by mutations in SMPD1 gene, which encodes sphingomyelin phosphodiesterase (ASM). Except for liver and spleen enlargement and lung disease, two subtypes (Type A and B) of NDP have different onset times, survival times, ASM activities, and neurological abnormalities. To comprehensively explore the genotype-phenotype association and pathophysiological characteristics of NPD, we collected 144 NPD cases with strict quality control through literature mining.
Results
The difference in ASM activity can differentiate NPD type A from other subtypes, with the ratio of ASM activity to the reference values being lower in type A (threshold 0.045 (4.45%)). Severe variations, such as deletion and insertion, can cause complete loss of ASM function, leading to type A, whereas relatively mild missense mutations generally result in type B. Among reported mutations, p.Arg3AlafsX76 mutation is highly prevalent in the Chinese population, and p.R608del mutation is common in Mediterranean countries. The expression profiles of SMPD1 from GTEx and single-cell RNA sequencing data of multiple fetal tissues showed that high expressions of SMPD1 can be observed in the liver, spleen, and brain tissues of adults and in hepatoblasts, hematopoietic stem cells, STC2_TLX1-positive cells, mesothelial cells of the spleen, vascular endothelial cells of the cerebellum and the cerebrum of fetuses, indicating that SMPD1 dysfunction is highly likely to have a significant effect on the function of those cell types during development and the clinicians need pay attention to these organs or tissues as well during diagnosis. In addition, we also predicted 21 new pathogenic mutations in the SMPD1 gene that potentially cause the NPD, signifying that more rare cases will be detected with those mutations in SMPD1.
Conclusions
Our study is the first one to elucidate the effects of SMPD1 mutation on cell types and at the tissue level, which provides new insights into the genotype-phenotype association and can help in the precise diagnosis of NPD.
Codes based on basic algebras
Authors: Yılmaz Damla 
Published: November 2022

Abstract
In this article, we consider basic algebra, a common generalization of an MV-algebra (an algebraic counterpart of the Lukasiewicz many-valued propositional logic) and an orthomodular lattice (an algebraic counterpart of the logic of quantum mechanics). We get some results regarding b-functions and b-subsets by giving the concept of basic-function on a nonempty set V . We also build a basic code W and explore a new order of it. Finally, we prove that the corresponding orders of the basic algebra B and the basic code W generated by B are the same.
Impact of the COVID-19 pandemic on a clinical trial of pneumococcal vaccine scheduling (PVS) in rural Gambia
Authors: Hossain Ilias , Osei Isaac , Lobga Galega , Wutor Baleng M. , Olatunji Yekini , Adefila Williams , Adeshola Banjo , Isa Yasir , Nguyen Cattram , Sonko Kemo , Ceesay Lamin , Baldeh Bubacarr , Barrow Omar , Young Benjamin , Ceesay Saidina , Nyassi Abdoullah , Sarwar Golam , Barjo Ousman , Drammeh Momodou M. , Salaudeen Rasheed , Mackenzie Grant 
Published: November 2022

Abstract
The COVID-19 pandemic represents an unprecedented challenge for clinical research. The Pneumococcal Vaccine Schedules (PVS) study is a non-inferiority, interventional trial in which infants resident in 68 geographic clusters are randomised to two different schedules for pneumococcal vaccination. From September 2019 onwards, all infants resident in the study area became eligible for trial enrolment at all Expanded Programme on Immunisation (EPI) clinics in the study area. Surveillance for clinical endpoints is conducted at all 11 health facilities in the study area. PVS is conducted as a collaboration between the Medical Research Council Unit The Gambia (MRCG) at LSHTM and the Gambian Ministry of Health (MoH). The COVID-19 pandemic caused many disruptions to PVS. MRCG instructed interventional studies that participant enrolment be suspended on 26 March 2020 and a public health emergency was declared in The Gambia on 28 March 2020. Enrolment in PVS restarted on 1 July 2020, was suspended again on 5 August 2020 after The Gambia experienced a sharp increase in COVID-19 cases in late July 2020 and restarted again on 1 September 2020.. During periods of suspended enrolment of infants at EPI clinics PVS continued safety surveillance at health facilities, albeit with disruptions. During the periods of suspended enrolment infants who had been enrolled before 26 March 2020 continued to receive the PCV schedule to which they had been randomly allocated based on their village of residence, whereas all other infants received the standard PCV schedule. Throughout 2020 and 2021 the trial faced numerous technical and operational challenges; disruption to MoH delivery of EPI services and clinical care at health facilities, episodes of staff illness and isolation, disruption of MRCG transport, procurement, communications, human resource management, and also a range of ethical, regulatory, sponsorship, trial monitoring, and financial challenges. In April 2021 a formal review concluded that the pandemic had not compromised the scientific validity of PVS and that the trial should continue as per protocol. The continuing challenges that COVID-19 poses to PVS and other clinical trials will persist for some time.
A Pleistocene origin of the coastal platform (strandflat) in southwestern Scandinavia
Authors: Fossen Haakon 
Published: November 2022

Abstract
An impressively extensive shore platform, the strandflat, is cut 20-50 km into hard crystalline bedrock along most of the Norwegian coastline. Its age and origin have been debated for more than a century, including a model that it represents a weathered, buried and re-exposed Triassic surface. Resolving this issue requires integrated examination of the coastal area, including the offshore Mesozoic rift margin. Here we combine new 3D broadband seismic, bathymetric and onshore elevation data along coastal West Norway and find that the near-horizontal strandflat postdates both the west-sloping onshore “paleic” surface and the offshore Jurassic denudation surface. It also postdates tilted North Sea Neogene sediments. Consistent with low-temperature thermochronologic data, this shows that the strandflat is a Pleistocene geomorphic feature formed through periods of varying climatic conditions, facilitated by mostly rift-related fault and fracture zones. It is not, in general, part of an inherited Mesozoic landscape.
Key genes associated with Alzheimer's disease and periodontitis
Authors: Zhou Kebing , Wang Lijun , Wu Lingbo , Wu Qing , Zhu Lingping , Yang Xuefeng , li duo 
Published: November 2022

Abstract
Background: With increasing research on Alzheimer's disease and periodontitis, many studies suggest a close correlation between Alzheimer's disease and periodontitis, but the underlying pathophysiological mechanisms remain unclear. The aim of this study was to identify potential pivotal genes and pathways associated with both diseases by using a bioinformatics approach.
Materials/Methods: The GEO dataset GSE5281 for Alzheimer's disease patients and normal controls was downloaded from the GEO database. The GSE10334 dataset for periodontitis patients and healthy controls was also obtained. Differentially expressed genes (DEGs) for the Alzheimer's disease and periodontitis datasets were obtained, as well as genes common between them. Further GO and KEGG enrichment analyses were performed on the common genes. To determine the pathogenesis associated with Alzheimer's disease and periodontitis, protein-protein interaction (PPI) networks were constructed. Finally, the diagnostic value of HUB genes in the Alzheimer's disease and periodontitis datasets was analyzed separately using SPSS software.
Results: A total of 16 common genes were obtained for Alzheimer's disease and periodontitis with a P value <0.05. 7 GO entries and 2 KEGG pathways were obtained. In addition, the first 6 central genes (CD4, KDR, CXCR4, CXCL12, JAK2 and PTPN11) were selected with a P<0.05.
Conclusion: The results of this study suggest that some novel genes play an important role in the development and progression of Alzheimer's disease and periodontitis. More experimental studies and clinical trials are needed to validate our results.
Climate Change and Food Security in Sub-Saharan Africa
Authors: Muleta Batru Wolde 
Published: November 2022

Abstract
Climate change affects food security directly through temperature levels and water availability in agriculture and indirectly through its impact on disease vectors and pests. This paper investigates the economic impact of climate change on food security in SSA. Panel data of all SSA countries are used in the analysis, to analyze the impact of temperature and precipitation on food security. Their coefficient of variation is used to analyze their impact on food security. The results from the analysis indicate that the coefficient of variations in both temperature and precipitation affects food security negatively. The climate variables affect food security directly through its impact on food production and indirectly through its impact on other food security indicators. The study recommends ecosystem management and production system improvement. According to the findings, the impact of climate change on food security in the SSA region is damaging. To overcome the impact, the study suggests appropriate land use policy formulation, natural resource conservation, implementing best agronomic practices and maintaining the number of population at an optimum level in the region.
Patterns and predictors of public dental service utilisation among refugees in Victoria, Australia: A latent profile and multilevel analysis
Authors: Veginadu Prabhakar , Masood Mohd , Gussy Mark , Calache Hanny 
Published: November 2022

Abstract
Background
The purpose of the study was to explore, analyse, and describe the patterns of public dental services utilisation among the refugee populations in Victoria, Australia, and determine their predictors at the individual and contextual levels.
Methods
Data on the refugees who attended Victorian public dental services between July 2016 to June 2020 was gathered from the Dental Health Program dataset. Latent profile analysis was used to identify discrete groups among the refugee clientele with similar mean utilisation patterns across six indicator variables describing the attributes of dental services received and the site of care provision, over the study period. Multilevel multinomial logistic regression analysis was performed to examine the individual and contextual level correlates of the identified utilisation patterns.
Results
Six distinct profiles of public dental service utilisation were identified among the study population (n = 25542). The largest group comprised refugees predominantly using restorative services under general course of care (38.10%), followed by extraction services under emergency course of care (23.50%). Only a small proportion were estimated as having a higher mean utilisation of preventive services under general course of care (9.10%). Multilevel analysis revealed that the following variables had a significant association with refugee utilisation pattern: at the individual-level – demographic and ethnic attributes including age, gender, region of birth, preferred language for communication, use of language interpreter services, and type of eligibility card; at the contextual-level – characteristics of refugees’ area of residence including urbanicity, area-based socioeconomic disadvantage, delivery of Refugee Health Program at the community health centres, and spatial accessibility to public dental services via driving and public transit modes of travel.
Conclusions
The study represents a significant step towards the development of an evidence-based knowledge around public dental service utilisation among Victorian refugees. Overall, the study findings reiterate the critical need for targeted strategies to promote the importance of routine dental visits, oral disease prevention, and timely intervention among refugee groups.
The cisplatin-induced acute kidney injury is a novel risk factor for postoperative complications in patients with esophageal cancer: a retrospective cohort study
Authors: Ueno Shuhei , Murashima Miho , Ogawa Ryo , Saito Masaki , Ito Sunao , Hayakawa Shunsuke , Okubo Tomotaka , Sagawa Hiroyuki , Tanaka Tatsuya , Takahashi Hiroki , Matsuo Yoichi , Mitsui Akira , Kimura Masahiro , Hamano Takayuki , Takiguchi Shuji 
Published: November 2022

Abstract
Background
Cisplatin-induced acute kidney injury (AKI) is common during preoperative chemotherapy for esophageal cancer. The purpose of this study was to investigate the association between AKI after preoperative chemotherapy and postoperative complications in patients with esophageal cancer.
Methods
In this retrospective cohort study, we included patients who had received preoperative chemotherapy with cisplatin and underwent surgical resection for esophageal cancer under general anesthesia from January 2017 to February 2022 at an education hospital. A predictor was stage 2 or higher cisplatin-induced AKI (c-AKI) defined by the KDIGO criteria within 10 days after chemotherapy. Outcomes were postoperative complications and length of hospital stays. Associations between c-AKI and outcomes including postoperative complications and length of hospital stays were examined with logistic regression models.
Results
Among 101 subjects, 22 developed c-AKI with full recovery of the estimated glomerular filtration (eGFR) before surgery. Demographics were not significantly different between patients with and without c-AKI. Patients with c-AKI had significantly longer hospital stays than those without c-AKI (mean [95% confidence interval (95%CI)]: 27.6 days [23.3–31.9] and 43.8 days [26.5–61.2], respectively, mean difference [95%CI]: 16.2 days [4.4–28.1]). Those with c-AKI had higher C-reactive protein (CRP) levels and prolonged weight gain after surgery and before the events of interest despite having comparable eGFR trajectories after surgery. c-AKI was significantly associated with anastomotic leakage and postoperative pneumonia (odds ratios [95%CI]: 4.14 [1.30-13.18] and 3.87 [1.35-11.0], respectively). Propensity score adjustment and inverse probability weighing yielded similar results. Mediation analysis showed that a higher incidence of anastomotic leakage in patients with c-AKI was primarily mediated by CRP levels (mediation percentage 45%).
Conclusion
c-AKI after preoperative chemotherapy in esophageal cancer patients was significantly associated with the development of postoperative complications and led to a resultant longer hospital stay. Increased vascular permeability and tissue edema due to prolonged inflammation might explain the mechanisms for the higher incidence of postoperative complications.
Soil physical and biological quality in a peasant agroforestry in Southern Brazil
Authors: Charnobay Aghata C. R. , Neto Pedro H. Weirich , Auler André C. , Gomes Jaime A. , de Souza Natali M. , Hyeda Daiane , Galvão Carolina W. , Gomes Aline L. , Lima Carmen L. R. F. 
Published: November 2022

Abstract
Agroforestry systems bring together social, economic, and environmental services and can be alternatives for promoting development and sustainability in peasant agriculture. This study aimed to evaluate the soil physical and microbiological quality in a four-years peasant agroecological agroforestry intercropped with vegetables, located in Lapa, South Brazil. Treatments included an agroforestry row (AFS-R) managed under no-tillage and cultivated with trees for fruit and wood production; an agroforestry inter-row (AFS-I) managed with conventional tillage and cultivated with vegetables; and an area managed with conventional tillage (CT) for one year and cultivated with landrace maize. Soil physical assessments comprised soil bulk density, total porosity, macroporosity, microporosity, bioporosity, mean weight diameter of aggregates, field capacity, aeration capacity, soil saturated hydraulic conductivity, and the visual evaluation of soil structure. Microbiological indicators included soil microbial biomass, basal respiration, microbial quotient, metabolic quotient, soil organic carbon, and the most probable number of nitrogen-fixing, ammonifying, and nitrite-oxidizing bacteria. The results demonstrated that AFS-R management improved several soil physical and microbiological attributes, highlighting the importance of plants diversity, organic residues input, and no-tillage for soil quality. On the other hand, the tillage practice contributed to structural and microbiological degradation in CT, and more intensively in AFS-I, indicating that more conservationist soil management, like minimum or no-tillage, might be studied as an alternative for the cultivation of vegetable crops in agroforestry systems.
Explaining the Nutritional Behavior of Iranian Pregnant Women with Diabetes: application of Health Action Process Approach model : Across sectional study
Authors: Changizi Maryam , Mohamadian Hooshang , Shojaezadeh Davoud 
Published: November 2022

Abstract
Background: Gestational diabetes mellitus (GDM) is currently the most common medical complication of pregnancy. Evidence suggests that by lifestyle modifications, especially nutritional behaviors, GDM may be preventable. This study aimed to investigate the Health Action Process Approach in predicting behavior and nutrition style in diabetic pregnant mothers referred to health centers under Abadan University of Medical Sciences (southern Iran).
Method: This descriptive cross-sectional study on 82 pregnant women with diabetes referred to an urban health center. The samples were selected using simple random sampling. Data were analyzed using SPSS 25 software through descriptive tests, regression, analysis of variance, and correlation.
Results: Most pregnant mothers (41.5 %) were in the 21-30 age group. 4 3.9% of the subjects were at the moderate economic level. Linear regression test showed among demographic variables, the strongest predictor of HAPA model was income (p<0.01, R=19.9, β=-0.299).The result also showed that none of the model constructs alone predicted nutritional behavior in pregnant women. The HAPA model was able to predict 21% of the variance of the nutritional behavior (p<0.001, r=0.210, β=0.458).
Conclusion: Positive or negative outcomes, pregnant women's behavioral intent, and planning for healthy eating behaviors are effective in educating pregnant women about the prevention and control of diabetes.