bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid reinfection with SARS-CoV-2 variant-of-concern Alpha detected in a nurse during an outbreak at a non-covid inpatient ward: lessons learned
Authors: Koopsen Jelle , Dekker Mireille , Thung Philip , Jonges Marcel , Vennema Harry , Leenstra Tjalling , Eggink Dirk , Welkers Matthijs R. A. , Struijs Peter A. A. , Reusken Chantal , van Mansfeld Rosa , de Jong Menno D. , Schinkel Janke , Spijkerman Ingrid J. B. 
Published: September 2021

AbstractWe describe the lessons learned during a SARS-CoV-2 variant-of-concern Alpha outbreak investigation at a normal care unit in a university hospital in Amsterdam in December 2020. The outbreak consisted of nine nurses and two roomed-in patient family members. (attack rate 18%). One nurse tested positive with a phylogenetically distinct variant, after a documented infection 83 days prior. Three key points were taken from this investigation. First, it was controlled by adherence to existing guidelines, despite increased transmissibility of the variant. Second, viral sequencing can inform transmission cluster inference, but the epidemiological context is essential to draw appropriate conclusions. Third, reinfections with Alpha variants can occur rapidly after primary infection.
Pneumomediastinum complicating COVID-19: a case series
Authors: Damous Sérgio Henrique Bastos , dos Santos Junior Jones Pessoa , Pezzano Álvaro Vicente Alvarez , Chams Mohamad Abdul Majid , Haritov Nathaly , Waksman Ricardo , Lima Helber Vidal Gadelha , dos Santos Miranda Jocielle , Rasslan Roberto , Utiyama Edivaldo Massazo 
Published: September 2021

Abstract
Background
Pneumomediastinum is a rare complication of COVID-19 pneumonia, which may or may not be associated with invasive ventilatory support. Therefore, the report and findings associated with its evolution can be of great contribution in the management of this unknown disease.

Case presentation
Here, we present a series of four patients with severe pneumomediastinum requiring intensive care unit. These patients developed pneumomediastinum before or during orotracheal intubation (OTI) or without OTI. The four patients were three men and one woman with a mean age of 60.5 years (48–74 years). No patients had a known history of lung disease or traumatic events, except for one patient who had a history of smoking, but who was without parenchymal disease. All intubations were performed without complications. No cases of pneumomediastinum occurred after tracheostomy, and none of the patients had tomographic or bronchoscopic evidence of tracheal injury. Although the pneumomediastinum observed in our cases was apparently not related to a violation of the aerodigestive track, this complication was associated with a worse prognosis.

Conclusion
Pneumomediastinum is a rare complication of COVID-19 pneumonia, and the most likely etiopathogenesis is severe pulmonary involvement, which may or may not be associated with invasive ventilatory support. Future studies with a greater number of cases should elucidate the relationship of pneumomediastinum to a probable prognostic factor.
NR4A3 and CCL20 clusters dominate the genetic networks in CD146+ blood cells during acute myocardial infarction in humans
Authors: Wang Yan-hui , Li Chen-xin , Stephenson Jessica M. , Marrelli Sean P. , Kou Yan-ming , Meng Da-zhi , Wu Ting 
Published: September 2021

Abstract
Background
CD146 is a tight junction-associated molecule involved in maintaining endothelial barrier, and balancing immune–inflammation response, in cardiovascular disease. Notably, peripheral CD146+ cells significantly upsurge under vessel dyshomeostasis such as acute myocardial injury (AMI), appearing to be a promising therapeutic target. In this study, with a new view of gene correlation, we aim at deciphering the complex underlying mechanism of CD146+ cells’ impact in the development of AMI.

Methods
Transcription dataset GSE 66,360 of CD146+ blood cells from clinical subjects was downloaded from NCBI. Pearson networks were constructed and the clustering coefficients were calculated to disclose the differential connectivity genes (DCGs). Analysis of gene connectivity and gene expression were performed to reveal the hub genes and hub gene clusters followed by gene enrichment analysis.

Results and conclusions
Among the total 23,520 genes, 27 genes out of 126 differential expression genes were identified as DCGs. These DCGs were found in the periphery of the networks under normal condition, but transferred to the functional center after AMI. Moreover, it was revealed that DCGs spontaneously crowded together into two functional models, CCL20 cluster and NR4A3 cluster, influencing the CD146-mediated signaling pathways during the pathology of AMI for the first time.
Role of fatty liver in coronavirus disease 2019 patients’ disease severity and hospitalization length: a case–control study
Authors: Ziaee Arash , Azarkar Ghodsiyeh , Ziaee Masood 
Published: September 2021

AbstractBackground and purposeFatty liver is one of the most common pre-existing illnesses; it can cause liver injury, leading to further complications in coronavirus disease 2019 patients. Our goal is to determine if pre-existing fatty liver is more prevalent in hospitalized COVID-19 patients compared to patients admitted before the SARS-CoV-2 pandemic and determine the disease severity among fatty liver patients.Experimental approachThis retrospective study involves a case and a control group consisting of 1162 patients; the case group contains hospitalized COVID-19 patients with positive PCR tests and available chest CT-scan; the control group contains patients with available chest CT-scan previous to the COVID-19 pandemic. Patients’ data such as liver Hounsfield unit, hospitalization length, number of affected lobes, and total lungs involvement score were extracted and compared between the patients.ResultsThe findings indicate that 37.9% of hospitalized COVID-19 patients have a pre-existing fatty liver, which is significantly higher (P < 0.001) than the prevalence of pre-existing fatty liver in control group patients (9.02%). In comparison to hospitalized non-fatty liver COVID-19 patients, data from hospitalized COVID-19 patients with fatty liver indicate a longer hospitalization length (6.81 ± 4.76P = 0.02), a higher total lungs involvement score (8.73 ± 5.28P < 0.001), and an increased number of affected lobes (4.42 ± 1.2P < 0.001).ConclusionThe statistical analysis shows fatty liver is significantly more prevalent among COVID-19 against non-COVID-19 patients, and they develop more severe disease and tend to be hospitalized for more extended periods.
Dense core vesicle markers in CSF and cortical tissues of patients with Alzheimer’s disease
Authors: Barranco Neus , Plá Virginia , Alcolea Daniel , Sánchez-Domínguez Irene , Fischer-Colbrie Reiner , Ferrer Isidro , Lleó Alberto , Aguado Fernando 
Published: September 2021

Abstract
Background
New fluid biomarkers for Alzheimer's disease (AD) that reveal synaptic and neural network dysfunctions are needed for clinical practice and therapeutic trial design. Dense core vesicle (DCV) cargos are promising cerebrospinal fluid (CSF) indicators of synaptic failure in AD patients. However, their value as biomarkers has not yet been determined.

Methods
Immunoassays were performed to analyze the secretory proteins prohormone convertases PC1/3 and PC2, carboxypeptidase E (CPE), secretogranins SgIII and SgII, and Cystatin C in the cerebral cortex (n = 45, provided by Bellvitge University Hospital) and CSF samples (n = 66, provided by The Sant Pau Initiative on Neurodegeneration cohort) from AD patients (n = 56) and age-matched controls (n = 55).

Results
In AD tissues, most DCV proteins were aberrantly accumulated in dystrophic neurites and activated astrocytes, whereas PC1/3, PC2 and CPE were also specifically accumulated in hippocampal granulovacuolar degeneration bodies. AD individuals displayed an overall decline of secretory proteins in the CSF. Interestingly, in AD patients, the CSF levels of prohormone convertases strongly correlated inversely with those of neurodegeneration markers and directly with cognitive impairment status.

Conclusions
These results demonstrate marked alterations of neuronal-specific prohormone convertases in CSF and cortical tissues of AD patients. The neuronal DCV cargos are biomarker candidates for synaptic dysfunction and neurodegeneration in AD.
mGWAS identification of six novel single nucleotide polymorphism loci with strong correlation to gastric cancer
Authors: Yang Shuangfeng , Wang Yuan-Liang , Lyu Yanping , Jiang Yu , Xiang Jianjun , Ji Shumi , Kang Shuling , Lyu Xuejie , He Chenzhou , Li Peixin , Liu Baoying , Wu Chuancheng 
Published: September 2021

Abstract
Background
Metabolite genome-wide association studies (mGWAS) are key for understanding the genetic regulation of metabolites in complex diseases including cancers. Although mGWAS has revealed hundreds of metabolomics quantitative trait loci (mQTLs) in the general population, data relating to gastric cancer (GC) are still incomplete.

Methods
We identified mQTLs associated with GC by analyzing genome-wide and metabolome-wide datasets generated from 233 GC patients and 233 healthy controls.

Results
Twenty-two metabolites were statistically different between GC cases and healthy controls, and all of them were associated with the risk of gastric cancer. mGWAS analyses further revealed that 9 single nucleotide polymorphisms (SNPs) were significantly associated with 3 metabolites. Of these 9 SNPs, 6 loci were never reported in the previous mGWAS studies. Surprisingly, 4 of 9 SNPs were significantly enriched in genes involved in the T cell receptor signaling pathway.

Conclusions
Our study unveiled several novel GC metabolite and genetic biomarkers, which may be implicated in the prevention and diagnosis of gastric cancer.
Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines
Authors: Leeuwenburgh V. C. , Urzúa-Traslaviña C. G. , Bhattacharya A. , Walvoort M. T. C. , Jalving M. , de Jong S. , Fehrmann R. S. N. 
Published: September 2021

Abstract
Background
Patient-derived bulk expression profiles of cancers can provide insight into the transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus independent component analyses (c-ICA) can capture statistically independent transcriptional footprints of both subtle and more pronounced metabolic processes.

Methods
We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify the transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs was determined in all samples to create a metabolic transcriptional landscape.

Results
A set of 555 mTCs was identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore the associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment.

Conclusions
To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal (www.themetaboliclandscapeofcancer.com). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.
Relationship between eating disorders and internalized problems in chilean adolescents
Authors: Caqueo-Urízar Alejandra , Urzúa Alfonso , Flores Jerome , Acevedo Daniel , Lorca Jessica Herrera , Casanova Jenifer 
Published: September 2021

AbstractBackgroundEating disorders (ED) are associated with internalized problems (INTP), such as depression and anxiety. Evidence shows that ED and INTP are associated with comorbidities. The relationship between these variables has not been the focus of studies on young people from Northern Chile. Children and adolescents are considered as an at-risk group, since they have been found to experience greater vulnerability to psychological problems than other age groups within the population and given the scarcity of studies in Chile, it is necessary to study the relationship between these variables.MethodsThis study analyzed the relationship between ED and INTP in Chilean high school students aged 12 to 18 years using Pearson's correlation. This is a non-experimental and transactional correlational study. We included 2277 students belonging to the public, government-subsidized, and private educational establishments in Northern Chile. The Child and Adolescent Evaluation System [Sistema de Evaluación de Niños y Adolescentes (SENA)] was used to detect a range of INTP, as well as ED. The Brief Self-Control Scale was used in this study.ResultsA strong and direct correlation of the eating disorder variable with depression and anxiety was found. Additionally, significant differences were observed with sex, highlighting females with a higher presence of INTP and ED.ConclusionsThere is a need to establish strategies in the school setting for detecting frequent symptomatology in adolescents with INTP and ED to achieve a timely and accessible intervention.Plain English SummarySince the symptomatology of ED is more prevalent in adolescents, this research evaluated relationships between ED and INTP in young people from Northern Chile. This research is relevant because the evidence on this topic in Chile is scarce and the relationships found could be the first research on the subject and serve to design an intervention plan at the school level in the medium and long terms. It is a non-experimental and transactional correlational study because all variables were measured at a single moment, and it sought to establish relationships between variables without assuming causality. The sample of secondary school students consisted of 2277 students, belonging to the public, subsidized, and private schools. Strong relationships were observed between INTP and ED, the strongest correlations being with the variables depression and anxiety. In addition, female participants presented greater problems in ED and INTP.
Inpatients experiences about the impact of traumatic stress on eating behaviors: an exploratory focus group study
Authors: Roer Grethe Emilie , Solbakken Heidi Hurlen , Abebe Dawit Shawel , Aaseth Jan Olav , Bolstad Ingeborg , Lien Lars 
Published: September 2021

Abstract
Background
Unhealthy changes in eating behavior among people experiencing trauma have been observed. There is, however, a lack of in-depth knowledge regarding the impact of the after effects of traumatic life experiences on eating behavior. Because eating behavior represents important components for promotion and maintenance of good health throughout life, this study aimed to explore inpatients’ lived experiences of the impact of traumatic stress on eating behavior.

Method
Thirteen female and two male inpatients (age range 28–62 years), recruited from a psychiatric clinic in Norway, participated in this qualitative explorative focus group study. The data analysis was performed using systematic text condensation.

Results
The results in the present study describe the participants’ experiences about the impact of traumatic stress on their eating behavior. Their discussions and descriptions disclosed problems that could be summarized into four main themes: “experiencing eating behaviors as coping strategies”; “experiencing being addicted to food and sweets”; “experiencing eating behaviors controlled by stress and emotions”; and “experiencing lack of appetite and reduced capacity to plan and prepare meals”.

Conclusion
Traumatic stress can impact eating behavior in several complex ways that over time may cause adverse health consequences. The results add to an important understanding of changes in eating behavior that might appear in people struggling to cope with the after effects of traumatic life experiences to the existing literature. To better understand the complexity of how traumatic experiences may impact eating behavior, this knowledge is important and useful for health professionals offering support to those who experience struggling with eating behavior after traumatic experiences.
Absence of Apolipoprotein E is associated with exacerbation of prion pathology and promotes microglial neurodegenerative phenotype
Authors: Pankiewicz Joanna E. , Lizińczyk Anita M. , Franco Leor A. , Diaz Jenny R. , Martá-Ariza Mitchell , Sadowski Martin J. 
Published: September 2021

AbstractPrion diseases or prionoses are a group of rapidly progressing and invariably fatal neurodegenerative diseases. The pathogenesis of prionoses is associated with self-replication and connectomal spread of PrPSc, a disease specific conformer of the prion protein. Microglia undergo activation early in the course of prion pathogenesis and exert opposing roles in PrPSc mediated neurodegeneration. While clearance of PrPSc and apoptotic neurons have disease-limiting effect, microglia-driven neuroinflammation bears deleterious consequences to neuronal networks. Apolipoprotein (apo) E is a lipid transporting protein with pleiotropic functions, which include controlling of the phagocytic and inflammatory characteristics of activated microglia in neurodegenerative diseases. Despite the significance of microglia in prion pathogenesis, the role of apoE in prionoses has not been established. We showed here that infection of wild type mice with 22L mouse adapted scrapie strain is associated with significant increase in the total brain apoE protein and mRNA levels and also with a conspicuous cell-type shift in the apoE expression. There is reduced expression of apoE in activated astrocytes and marked upregulation of apoE expression by activated microglia. We also showed apoE ablation exaggerates PrPSc mediated neurodegeneration. Apoe−/− mice have shorter disease incubation period, increased load of spongiform lesion, pronounced neuronal loss, and exaggerated astro and microgliosis. Astrocytes of Apoe−/− mice display salient upregulation of transcriptomic markers defining A1 neurotoxic astrocytes while microglia show upregulation of transcriptomic markers characteristic for microglial neurodegenerative phenotype. There is impaired clearance of PrPSc and dying neurons by microglia in Apoe−/− mice along with increased level of proinflammatory cytokines. Our work indicates that apoE absence renders clearance of PrPSc and dying neurons by microglia inefficient, while the excess of neuronal debris promotes microglial neurodegenerative phenotype aggravating the vicious cycle of neuronal death and neuroinflammation.
Generation of human chronic wasting disease in transgenic mice
Authors: Wang Zerui , Qin Kefeng , Camacho Manuel V. , Cali Ignazio , Yuan Jue , Shen Pingping , Greenlee Justin , Kong Qingzhong , Mastrianni James A. , Zou Wen-Quan 
Published: September 2021

AbstractChronic wasting disease (CWD) is a cervid prion disease caused by the accumulation of an infectious misfolded conformer (PrPSc) of cellular prion protein (PrPC). It has been spreading rapidly in North America and also found in Asia and Europe. Although bovine spongiform encephalopathy (i.e. mad cow disease) is the only animal prion disease known to be zoonotic, the transmissibility of CWD to humans remains uncertain. Here we report the generation of the first CWD-derived infectious human PrPSc by elk CWD PrPSc-seeded conversion of PrPC in normal human brain homogenates using in vitro protein misfolding cyclic amplification (PMCA). Western blotting with human PrP selective antibody confirmed that the PMCA-generated protease-resistant PrPSc was derived from the human PrPC substrate. Two lines of humanized transgenic mice expressing human PrP with either Val or Met at the polymorphic codon 129 developed clinical prion disease following intracerebral inoculation with the PMCA-generated CWD-derived human PrPSc. Diseased mice exhibited distinct PrPSc patterns and neuropathological changes in the brain. Our study, using PMCA and animal bioassays, provides the first evidence that CWD PrPSc can cross the species barrier to convert human PrPC into infectious PrPSc that can produce bona fide prion disease when inoculated into humanized transgenic mice.
Exploring spatiotemporal changes in cities and villages through remote sensing using multibranch networks
Authors: Mengqi Zhao , Yan Tian 
Published: September 2021

Abstract
With the rapid development of the social economy, monumental changes have taken place in the urban and rural environments. Urban and rural areas play a vital role in the interactions between humans and society. Traditional machine learning methods are used to perceive the massive changes in the urban and rural areas, though it is easy to overlook the detailed information about the changes made to the intentional target. As a result, the perception accuracy needs to be improved. Therefore, based on a deep neural network, this paper proposes a method to perceive the spatiotemporal changes in urban and rural intentional connotations through the perspective of remote sensing. The framework first uses multibranch DenseNet to model the multiscale spatiotemporal information of the intentional target and realizes the interaction of high-level semantics and low-level details in the physical appearance. Second, a multibranch and cross-channel attention module is designed to refine and converge multilevel and multiscale temporal and spatial semantics to perceive the subtle changes in the urban and rural intentional targets through the semantics and physical appearance. Finally, the experimental results show that the multibranch perception framework proposed in this paper has the best performance on the two baseline datasets A and B, and its F-Score values are 88.04% and 53.72%, respectively.
The prediction of impacted versus spontaneously erupted mandibular third molars
Authors: De Sousa Amanda Silva , Neto José Valladares - , Normando David 
Published: September 2021

Abstract
Background
To evaluate the predictive capacity of orthodontists and oral maxillofacial surgeons (OMFSs) in anticipating the process of impaction or eruption of lower third molars (L3Ms) through the examination of serial panoramic radiographs.

Methods
Sixty-eight lower third molars (L3Ms) were analyzed in 34 orthodontically treated patients without extraction. Twenty-seven OMFSs and 27 orthodontists were randomized in order to analyze the radiographs. Initially, the evaluators issued the prognosis for the L3Ms in XR1, a posterior for the XR1 + XR2. Concordance of the diagnosis was examined using Kappa statistics, and the differences between the groups of evaluators were examined using the chi-square test at p<0.05.

Results
When examining XR1 in cases where the teeth erupted spontaneously, the prognostic accuracy rate for OMFSs and orthodontists was similar, 63 and 65.7%, respectively (p=0.19). When evaluating XR1 + XR2, the accuracy among orthodontists (60%) was similar to that reported for XR1 (p=0.19), while OMFSs presented a reduction in the accuracy (55.3%, p<0.0001). When the L3Ms remained impacted, accuracy in XR1 was lower than in spontaneously erupting L3Ms, although similar between OMFSs (50.1%) and orthodontists (49.1%). Furthermore, for impacted L3Ms, when examining XR1 + XR2, the OMFSs presented a significant higher accuracy (71.8%, p <0.0001).

Conclusions
Orthodontists and OMFSs seem unable to predict spontaneous eruption or impaction of the lower third molars from single or longitudinal x-rays. When adding a second longitudinal x-ray, orthodontists and more significantly OMFSs tend to indicate more extractions.