bluuebunny/crossref_metadata_2025_split huggingface dataset:
The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis
Authors: Rostami Mahboubeh R. , Bradic Martina 
Published: June 2021

Abstract
Background
Transposable elements (TEs) are repetitive sequences of viral origin that compose almost half of the human genome. These elements are tightly controlled within cells, and if activated, they can cause changes in both gene regulation and immune viral responses that have been associated with several chronic inflammatory diseases in humans. As oxidants are potent activators of TEs, and because oxidative injury is a major risk factor in relation to idiopathic pulmonary fibrosis (IPF), we hypothesized that TEs might be involved in the regulation of gene expression and so contribute to inflammation in cases of IPF. IPF is a fatal lung disease that involves the gradual replacement of the alveolar tissue with fibrotic scars as well as the accumulation of inflammatory cells in the lower respiratory tract. Although IPF is known to occur as a result of the complex interaction between age, environmental risk factors (i.e., oxidative stress) and genetics, the relative contributions of these factors to the disease remain unclear. To determine whether TEs are associated with IPF, we compared the transcriptional profiles of the genes and TEs of lung cells obtained from both healthy donors and IPF patients.

Results
We quantified TE and gene expression levels using a published bulk RNA-seq dataset containing 24 subjects (16 donors and eight IPF patients), including three lung-cell types per subject, as well as an scRNA-seq dataset concerning 16 subjects (eight donors and eight IPF patients).
We found evidence of TE dysregulation in the alveolar type II lung cells and alveolar macrophages of the IPF patients. In addition, the activation of the LINE1 family of elements in IPF is associated with the increased expression of TE cellular regulators (MOV10, IFI16, SAMHD1, and APOBECG3), interferon-stimulating genes (ISG15, IFI6, IFI27, IFI44, and OAS1), chemokines (CX3CL1 and CXCL9), and interleukins (IL15RA). We also propose that TE derepression might be involved in the regulation of previously reported IPF candidate genes (MUC5B, CHL1, SPP1, and MMP7).

Conclusion
Based on our findings, we propose that TE derepression plays an important role in the regulation of gene expression and can also prompt both the recruitment of inflammatory processes and the disruption of the immunological balance, which can lead to chronic inflammation in IPF.
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment
Authors: Zhou Yadi , Xu Jielin , Hou Yuan , Leverenz James B. , Kallianpur Asha , Mehra Reena , Liu Yunlong , Yu Haiyuan , Pieper Andrew A. , Jehi Lara , Cheng Feixiong 
Published: June 2021

AbstractBackgroundDementia-like cognitive impairment is an increasingly reported complication of SARS-CoV-2 infection. However, the underlying mechanisms responsible for this complication remain unclear. A better understanding of causative processes by which COVID-19 may lead to cognitive impairment is essential for developing preventive and therapeutic interventions.MethodsIn this study, we conducted a network-based, multimodal omics comparison of COVID-19 and neurologic complications. We constructed the SARS-CoV-2 virus-host interactome from protein-protein interaction assay and CRISPR-Cas9-based genetic assay results and compared network-based relationships therein with those of known neurological manifestations using network proximity measures. We also investigated the transcriptomic profiles (including single-cell/nuclei RNA-sequencing) of Alzheimer’s disease (AD) marker genes from patients infected with COVID-19, as well as the prevalence of SARS-CoV-2 entry factors in the brains of AD patients not infected with SARS-CoV-2.ResultsWe found significant network-based relationships between COVID-19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in AD. We also detected aberrant expression of AD biomarkers in the cerebrospinal fluid and blood of patients with COVID-19. While transcriptomic analyses showed relatively low expression of SARS-CoV-2 entry factors in human brain, neuroinflammatory changes were pronounced. In addition, single-nucleus transcriptomic analyses showed that expression of SARS-CoV-2 host factors (BSGandFURIN) and antiviral defense genes (LY6E,IFITM2,IFITM3, andIFNAR1) was elevated in brain endothelial cells of AD patients and healthy controls relative to neurons and other cell types, suggesting a possible role for brain microvascular injury in COVID-19-mediated cognitive impairment. Overall, individuals with the AD risk alleleAPOEE4/E4 displayed reduced expression of antiviral defense genes compared toAPOEE3/E3 individuals.ConclusionOur results suggest significant mechanistic overlap between AD and COVID-19, centered on neuroinflammation and microvascular injury. These results help improve our understanding of COVID-19-associated neurological manifestations and provide guidance for future development of preventive or treatment interventions, although causal relationship and mechanistic pathways between COVID-19 and AD need future investigations.
Healthcare provider characteristics that influence the implementation of individual-level patient-centered outcome measure (PROM) and patient-reported experience measure (PREM) data across practice settings: a protocol for a mixed methods systematic review with a narrative synthesis
Authors: Wolff Angela C. , Dresselhuis Andrea , Hejazi Samar , Dixon Duncan , Gibson Deborah , Howard A. Fuchsia , Liva Sarah , Astle Barbara , Reimer-Kirkham Sheryl , Noonan Vanessa K. , Edwards Lisa 
Published: June 2021

Abstract
Background
Substantial literature has highlighted the importance of patient-reported outcome and experience measures (PROMs and PREMs, respectively) to collect clinically relevant information to better understand and address what matters to patients. The purpose of this systematic review is to synthesize the evidence about how healthcare providers implement individual-level PROMs and PREMs data into daily practice.

Methods
This mixed methods systematic review protocol describes the design of our synthesis of the peer-reviewed research evidence (i.e., qualitative, quantitative, and mixed methods), systematic reviews, organizational implementation projects, expert opinion, and grey literature. Keyword synonyms for “PROMs,” PREMs,” and “implementation” will be used to search eight databases (i.e., MEDLINE, CINAHL, PsycINFO, Web of Science, Embase, SPORTDiscus, Evidence-based Medicine Reviews, and ProQuest (Dissertation and Theses)) with limiters of English from 2009 onwards. Study selection criteria include implementation at the point-of-care by healthcare providers in any practice setting. Eligible studies will be critically appraised using validated tools (e.g., Joanna Briggs Institute). Guided by the review questions, data extraction and synthesis will occur simultaneously to identify biographical information and methodological characteristics as well as classify study findings related to implementation processes and strategies. As part of the narrative synthesis approach, two frameworks will be utilized: (a) Consolidated Framework for Implementation Research (CFIR) to identify influential factors of PROMs and PREMs implementation and (b) Expert Recommendations for Implementing Change (ERIC) to illicit strategies. Data management will be undertaken using NVivo 12TM.

Discussion
Data from PROMs and PREMs are critical to adopt a person-centered approach to healthcare. Findings from this review will guide subsequent phases of a larger project that includes interviews and a consensus-building forum with end users to create guidelines for implementing PROMs and PREMs at the point of care.

Systematic review registration
PROSPERO CRD42020182904.
Post-abortion family planning use, method preference, and its determinant factors in Eastern Africa: a systematic review and meta-analysis
Authors: Bizuneh Asmamaw Demis , Azeze Getnet Gedefaw 
Published: June 2021

AbstractBackgroundUtilization of post-abortion family planning is very critical to reduce high levels of unintended pregnancy, which is the root cause of induced abortion. In Eastern Africa, it is estimated that as many as 95% of unintended pregnancies occurred among women who do not practice contraception at all. Therefore, this meta-analysis aimed to assess post-abortion family planning utilization and its determinant factors in Eastern Africa.MethodsPublished papers from Scopus, HINARI, PubMed, Google Scholar, and Web of Science electronic databases and grey literature repository were searched from database inception to January 30, 2020, with no restriction by design and date of publishing. We screened records, extracted data, and assessed risk of bias in duplicate. Cochrane I2statistics were used to check the heterogeneity of the studies. Publication bias was assessed by Egger and Biggs test with a funnel plot. A random-effects model was calculated to estimate the pooled prevalence of post-abortion family planning utilization.ResultsA total of twenty-nine cross-sectional studies with 70,037 study participants were included. The overall pooled prevalence of post-abortion family planning utilization was 67.86% (95% CI 63.59–72.12). The most widely utilized post-abortion family methods were injectable 33.23% (95% CI 22.12–44.34), followed by implants 24.71% (95% CI 13.53–35.89) and oral contraceptive pills 23.42% (95% CI 19.95–26.89). Married marital status (AOR=3.20; 95% CI 2.02–5.05), multiparity (AOR=3.84; 95% CI 1.43–10.33), having a history of abortion (AOR=2.33; 95% CI 1.44–3.75), getting counselling on post-abortion family planning (AOR=4.63; 95% CI 3.27–6.56), and ever use of contraceptives (AOR=4.63; 95% CI 2.27–5.21) were factors associated with post-abortion family planning utilization in Eastern Africa.ConclusionsThis study revealed that the marital status of the women, multiparity, having a history of abortion, getting counselling on post-abortion family planning, and ever used contraceptives were found to be significantly associated with post-abortion family planning utilization.
On interpolative F-contractions with shrink map
Authors: Alansari Monairah , Ali Muhammad Usman 
Published: June 2021

AbstractIn this article, we introduce two notions of interpolative F-contractions with shrink map and F-contractions with shrink map. We also study the existence of E-fixed points by using these notations on a metric space endowed with a binary relation. As an application and consequence of the main results, we also get some other interesting results like a common fixed point result, an E-fixed point result on a metric space equipped with graph, and an existence theorem for a solution of integral equations.
First-order impulsive differential systems: sufficient and necessary conditions for oscillatory or asymptotic behavior
Authors: Santra Shyam Sundar , Baleanu Dumitru , Khedher Khaled Mohamed , Moaaz Osama 
Published: June 2021

AbstractIn this paper, we study the oscillatory and asymptotic behavior of a class of first-order neutral delay impulsive differential systems and establish some new sufficient conditions for oscillation and sufficient and necessary conditions for the asymptotic behavior of the same impulsive differential system. To prove the necessary part of the theorem for asymptotic behavior, we use the Banach fixed point theorem and the Knaster–Tarski fixed point theorem. In the conclusion section, we mention the future scope of this study. Finally, two examples are provided to show the defectiveness and feasibility of the main results.
The impact of tropical land-use change on downstream riverine and estuarine water properties and biogeochemical cycles: a review
Authors: Tanaka Yasuaki , Minggat Elizerberth , Roseli Wardina 
Published: June 2021

AbstractTropical primary forests have been disappearing quickly to make use of the land for commercial purposes. Land-use change has an impact on downstream aquatic processes, but those impacts have mainly been studied in temperate climate regions. The present article reviews the impacts of various tropical land-use changes caused by human activities on downstream riverine and estuarine water properties and biogeochemical cycles, focusing especially on the behaviors of nitrogen (N) and phosphorus (P). Logging of tropical primary forests, subsequent establishment of pasture lands, and occasional wildfire or intentional burning have decreased terrestrial N fixation and increased the discharge of P combined with soils, which has lowered the N:P ratio of dissolved inorganic nutrients in the adjacent stream waters and downstream rivers. Agricultural fertilizers and aquacultural practices basically cause nutrient enrichment in downstream riverine and estuarine waters, changing the N:P ratio depending on the source. Finally, urbanization causes eutrophication in many tropical estuaries, where a halocline forms easily because of a warm temperature throughout the year and the water at the bottom of the estuary tends to become hypoxic or anoxic. Overall, the impact of land-use change on aquatic processes may be more serious in tropical regions than in temperate or cold climate regions because of (1) a higher biomass and nutrient stock in original tropical forests; (2) higher precipitation, more frequent episodic flooding, and warmer temperatures in tropical regions; and (3) certain practices that are rapidly expanding in tropical regions such as land-based aquaculture. Various land-use changes are causing downstream nutrient enrichment or disturbance of the nutrient balance at tropical land-sea interfaces, and the overall N:P ratios in the aquatic ecosystem seem to be declining. Nonetheless, if proper management is conducted and the discharge of nutrients and soils ceases, tropical aquatic systems may have the potential to recover faster than those in other climate regions because of their abundant precipitation and warm temperature. Long-term monitoring and more attention to elemental stoichiometry are important areas for future research.
Natural nasal–esophageal fiberscopy in the COVID-19 pandemic—preventing sneezing without anesthesia: a case report
Authors: Tsunoda Koichi , Hentona Ko , Yamanobe Yoshiharu 
Published: June 2021

Abstract
Background
We are laryngologists. We observe natural phonatory and swallowing functions in clinical examinations with a trans-nasal laryngeal fiberscope (TNLF). Before each observation, we use epinephrine to enlarge and smooth the common nasal meatus (bottom of nostril) and then insert a wet swab inside the nose, as in taking a swab culture in the nasopharynx. During the current COVID-19 pandemic situation, this careful technique prevents any complications, including nasal bleeding, painfulness, and induced sneezing. Here, we introduce our routine to observe esophageal movement in swallowing in a natural (sitting) position without anesthesia.

Case presentation
The case was a 70-year-old female who complained that something was stuck in her esophagus; there was a strange sensation below the larynx and pharynx. After enlarging and smoothing the common nasal meatus, we inserted the TNLF (slim type ⌀2.9 mm fiberscope, VNL8-J10, PENTAX Medical, Tokyo, Japan.) in the normal way. We then observed the phonatory and swallowing movements of the vocal folds. As usual, to not interfere with natural movements, we used no anesthesia. We found no pathological condition in the pyriform sinus. We asked the patient to swallow the fiberscope. During the swallow, we pushed the TNLF and inserted the tip a bit deeper, which made the fiberscope easily enter the esophagus, like in the insertion of a nasogastric tube. We then asked the patient to swallow a sip of water or saliva to clear and enlarge the lumen of the esophagus. This made it possible to observe the esophagus easily without any air supply. With tone enhancement scan, the esophagus was found to be completely normal except for glycogenic acanthosis.

Conclusions
The advantage of this examination is that it is easily able to perform without anesthesia and with the patient in sitting position. It is quick and minimally invasive, enabling observation the physiologically natural swallowing. It is also possible to observe without anesthesia down to the level of the esophagogastric junction using with a thin type flexible bronchoscope. In the future, gastric fiberscopes might be thinner, even with narrow band imaging (NBI) function. Before that time, physicians should remember to just insert along the bottom of the nose.
Exploring alternatives for adolescent anorexia nervosa: adolescent and parent treatment (APT) as a novel intervention prospect
Authors: Ganci Maria , Atkins Linsey , Roberts Marion E. 
Published: June 2021

AbstractRecovery and remission rates of adolescent anorexia nervosa (AN) following Family Based Treatment (FBT) have seen a relative decline over recent years. While reasonably successful in achieving physical recovery (i.e. weight restoration), both empirical and anecdotal accounts highlight a lack of attention to the psychological recovery of the adolescent within manualised FBT. As such, there is a need for innovation to explore treatment variations and alternatives for the proportion of adolescents with AN who do not respond favourably to this first-line treatment. This paper introduces a new treatment framework to the field for clinical consideration and empirical assessment. Adolescent and Parent Treatment (APT) for adolescent AN draws from both family-based and individual treatment models, applying a developmental lens. APT attends to physical and psychological recovery simultaneously and from the start of treatment, with capacity to tailor individual psychological modules to the adolescent formulation. While clearly in its infancy, APT provides an exciting new avenue for exploration within the field, as we seek new avenues to support young people and their families to effectively combat this deadly illness.
Binge eating symptoms are associated with the severity of premenstrual symptoms among university students, cross sectional study from Palestine
Authors: Badrasawi Manal M. , Zidan Souzan J. , Natour Nihal , Sharif Israa , Atrash Shahd , Abueid Ghada , Al-Jounde Saeda 
Published: June 2021

Abstract
Background
Premenstrual syndrome (PMS) is considered one of the most prevailing disorders among childbearing age women that could considerably interfere with daily living activities life. PMS is underrecognized in Palestine. It is reported that binge eating symptoms are significantly related to premenstrual syndrome. In this regard, the study aimed to determine factors linked with premenstrual symptoms and to explore whether binge eating symptoms are linked with premenstrual syndrome.

Methods
This descriptive study was performed among female undergraduates at Palestine Polytechnic University, using a cross-sectional design. A self-administrated questionnaire was used in order to collect data. Moreover, participants’ nutritional status was assessed using anthropometric measurements. Descriptive statistics, independent t-test and Chi-square were performed.

Results
A sum of 289 undergraduate females were involved in the final analysis. The results indicated that nearly half of undergraduates (47.8%) were classified as having binge eating symptoms. The most frequently noted premenstrual symptoms were lethargy, anger feelings, lack of interest, and anxiety. Chi-square analysis showed that moderate and severe psychological symptoms were significantly more prevalent among females with binge eating symptoms. Besides it was found that moderate and severe physical symptoms were significantly more prevalent among females with binge eating symptoms. Moreover, participants who reported no premenstrual syndrome symptoms were significantly less prevalent among females with binge eating symptoms. The findings also reveal that sociodemographic characteristics was not significantly correlated with premenstrual syndrome symptoms. In multiple adjusted models, both smoking (p < 0.05) and binge eating (p < 0.0001) were significantly related to PMS.

Conclusion
Findings reveals that moderate and severe psychological and physical symptoms were significantly more prevalent among females with binge eating symptoms. The current research also reported that the severity of PMS was not significantly related to sociodemographic variables.
Spatial variations of school-level determinants of reading achievement in Italy
Authors: Sacco Chiara , Falzetti Patrizia 
Published: June 2021

AbstractThe study of the territorial difference in educational achievement is a widely debated topic, in particular in Italy for the presence of the well-known strong regional disparities. National and international large scale assessments confirmed that the main characteristic of the Italian school system is the geographical cleavage between North and South. Policymakers have pressing needs to find solutions to reduce geographical disparities. In this study, we investigate the spatial disparities of academic achievement from a new perspective, assuming that the relationship between academic achievement and predictors varies across Italy. Our aim is to examine the extent of the spatial disparities in the relationship between academic achievement and some school-level factors related to inequalities in educational outcomes, moving beyond the regional administrative confines, in order to identify new spatial patterns. We exploited the reading standardized tests administered by INVALSI in 2018–2019 focusing on the 8th-grade students. Crucial to our contribution is the use of the geographically weighted regression and the k-mean clustering, which allows studying the spatial variability of the impact of the school-level factors on academic achievement and to gather schools in new spatial clusters. The findings of this paper demonstrate the necessity to design a more specific education policy and support the identification of the main critical factors for different geographical areas.
A distributed Content-Based Video Retrieval system for large datasets
Authors: Saoudi El Mehdi , Jai-Andaloussi Said 
Published: June 2021

AbstractWith the rapid growth in the amount of video data, efficient video indexing and retrieval methods have become one of the most critical challenges in multimedia management. For this purpose, Content-Based Video Retrieval (CBVR) is nowadays an active area of research. In this article, a CBVR system providing similar videos from a large multimedia dataset based on query video has been proposed. This approach uses vector motion-based signatures to describe the visual content and uses machine learning techniques to extract key frames for rapid browsing and efficient video indexing. The proposed method has been implemented on both single machine and real-time distributed cluster to evaluate the real-time performance aspect, especially when the number and size of videos are large. Experiments were performed using various benchmark action and activity recognition datasets and the results reveal the effectiveness of the proposed method in both accuracy and processing time compared to previous studies.