bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant DNA methylation of uveal melanoma drivers as an excellent prognostic tool
Authors: Soltysova Andrea , Dvorska Dana , Kajabova Viera Horvathova , Pecimonova Martina , Cepcekova Klaudia , Ficek Andrej , Demkova Lucia , Buocikova Verona , Babal Pavel , Juras Ivan , Janikova Katarina , Kasubova Ivana , Samec Marek , Brany Dusan , Lyskova Darina , Dankova Zuzana , Smolkova Bozena , Furdova Alena 
Published: January 2023

Abstract
Background: Despite outstanding advances in understanding the genetic background of uveal melanoma (UM) development and prognosis, the role of DNA methylation reprogramming remains elusive. This study aims to clarify the extent of DNA methylation deregulation in the context of gene expression changes and its utility as a reliable prognostic biomarker.
Methods: Transcriptomic and DNA methylation landscapes in 25 high- and low-risk UMs were interrogated by Agilent SurePrint G3 Human Gene Expression 8×60K v2 Microarray and Human Infinium Methylation EPIC Bead Chip array, respectively. DNA methylation and gene expression of the nine top discriminatory genes, selected by the integrative analysis, were validated by pyrosequencing and qPCR in 58 tissues.
Results: Among 2,262 differentially expressed genes discovered in UM samples differing in metastatic risk, 60 were epigenetic regulators, mostly histone modifiers and chromatin remodelers. 44,398 CpGs were differentially methylated, 27,810 hypomethylated, and 16,588 hypermethylated in high-risk tumors, with Δβ values ranging between -0.78 and 0.79. By integrative analysis, 944 differentially expressed DNA methylation-regulated genes were revealed, 635 hypomethylated/upregulated, and 309 hypermethylated/downregulated. Aberrant DNA methylation in high-risk tumors was associated with the deregulation of key oncogenic pathways such as EGFR tyrosine kinase inhibitor resistance, focal adhesion, proteoglycans in cancer, PI3K-Akt signaling, or ECM-receptor interaction. Notably, DNA methylation values of nine genes, HTR2B, AHNAK2, CALHM2, SLC25A38, EDNRB, TLR1, RNF43, IL12RB2, and MEGF10, validated by pyrosequencing, demonstrated excellent risk group prediction accuracies (AUC ranging between 0.870 and 0.956). Moreover, CALHM2 hypomethylation and MEGF10, TLR1 hypermethylation, as well as two three-gene methylation signatures, Signature 1 combining AHNAK2, CALHM2, and IL12RB and Signature 2 AHNAK2, CALHM2, and SLC25A38genes, correlated with shorter overall survival (HR = 4.38, 95% CI 1.30-16.41, HR = 5.59, 95% CI 1.30-16.41; HR = 3.43, 95% CI 1.30-16.41, HR = 4.61, 95% CI 1.30-16.41 and HR = 4.95, 95% CI 1.39-17.58, respectively).
Conclusions: Our results demonstrate a significant role of DNA methylation aberrancy in UM progression. The advantages of DNA as a biological material and excellent prediction accuracies of methylation markers open the perspective for their more extensive clinical use.
Implementation and Review of the Care Ecosystem in an Integrated Healthcare System
Authors: Rosenbloom Michael , Kashyap Bhavani , Diaz-Ochoa Ana , Karrmann Jan , Svitak Aleta , Finstad Jennifer , Brombach Ann , Sprandel Ann , Hanson Leah , Dulaney Sarah , Possin Katherine 
Published: January 2023

Abstract
Background and Objectives
The University of California, San Francisco Memory and Aging Center (UCSF-MAC) led the development and tested a collaborative care model delivered by lay care team navigators (CTNs) with support from a multidisciplinary team known as the Care Ecosystem (CE). We report the results from the application of the CE within a non-academic healthcare system.
Research Design and Methods
The CE team at HealthPartners consisted of two CTNs, a social worker, an RN, a program coordinator, and a behavioral neurologist. Intake forms were developed to collect demographic, baseline, and annual longitudinal data at one year related to dementia severity and care partner status. Experience surveys were completed every 6 months by participating care partners. All data was entered into REDCap.
Results
A total of 570 PWD-caregiver dyads were recruited into the CE: 53% PWDs female, average age 75.2 ± 9.43, 19% living within rural communities. Of the 173 dyads assessed at one year, 58% of care partners responded to surveys, and 67% of those provided data about their CE experience through survey data. At one year, PWDs progressed in disease severity and functional impairment, although care partner burden and mood remained unchanged. We observed a significant reduction in care partner reported emotional challenges associated with caregiving, sleep problems, and obtaining care partner help at one year. Eighty-six percent of care partners reported feeling supported by their CTN nearly always or quite frequently, and 88% rated the CTN as highly responsive to what was important to them.
Discussion and Implications
The CE was feasible and well-received within a non-academic healthcare system.
Dynamic Evaluation of a Nine-Story Timber-Concrete Hybrid Building during construction
Authors: Larsson Carl , Abeljaber Osama , Dorn Michael 
Published: January 2023

Abstract
Timber-concrete hybrid buildings are an innovative solution to increase the amount of timber materials used in modern buildings. This study presents a dynamic evaluation of a nine-story timber-concrete hybrid residential building during construction. The building consists of a seven-story structure in cross-laminated timber (CLT) on top of two stories in concrete. Ambient vibration tests were conducted seven times during the 13-month construction period, including tests with only the structural elements in place and tests of the finished building with the façade, non-structural walls, and other internal finishing. The results show a clear decrease in the natural frequencies of the building as the building gets higher and more elements are installed. However, a slight increase in the natural frequency was observed following the installation of the non-structural walls in the final construction stage. A corresponding finite element analysis is presented for each test, providing additional insights into the parameters typically used in the structural design process. The study demonstrates the importance of properly selecting reduction factors for CLT elements in a dynamic finite element analysis. It also shows the importance of considering non-structural walls, both regarding weight and stiffness, even in buildings where the number of non-structural walls is relatively small compared to structural walls.
Anatomy of the tsunami and Lamb waves-induced ionospheric signatures generated by the 2022 Hunga Tonga volcanic eruption
Authors: Munaibari Edhah , Rolland Lucie , Sladen Anthony , Delouis Bertrand 
Published: January 2023

Abstract
As tsunamis propagate across open oceans, they remain largely unseen due to the lack of adequate sensors. To address this fundamental limitation of existing tsunami warnings, we investigate Global Navigation Satellites Systems (GNSS) data to monitor the ionosphere Total Electron Content (TEC) for Traveling Ionospheric Disturbances (TIDs) created by tsunami-induced internal gravity waves (IGWs). The approach has been applied to regular tsunamis generated by earthquakes, while the case of undersea volcanic eruptions injecting energy into both the ocean and the atmosphere remains mostly unexplored. With both a regular tsunami and air-sea waves, the large 2022 Hunga Tonga-Hunga Ha’apai volcanic eruption is a challenge. Here, we show that even in near-field regions (1000-1500km), despite the complex wavefield, we can isolate the regular tsunami signature. We also highlight that the eruption-generated Lamb wave induces an ionospheric disturbance with a similar waveform and an amplitude spatial pattern consistent with IGW origin but with a quasi-constant propagation speed (~ 315m/s). These results imply that when GNSS-TEC measurements are registered near an ocean bottom pressure sensor, they can help discriminating the regular tsunami from the initial air-sea waves appearing in the sensor observations.
The catE gene of Bacillus licheniformis M2-7 is essential for growth in Benzopyrene and its expression is regulated by the Csr system
Authors: Blancas Yamilet Morales , Terán José Daniel Reyna , Eligio José Alberto Hernández , Pineda Carlos Ortuño , Jiménez Jeiry Toribio , Barrera Miguel Ángel Rodríguez , Hernández Erubiel Toledo , Ramírez Yanet Romero 
Published: January 2023

Abstract
Benzopyrene is a high molecular weight polycyclic aromatic hydrocarbon with highly recalcitrant and develops carcinogenic effects. CsrA is a conserved regulatory protein, which controls the translation and stability of its target transcripts, having negative or positive effects depending on the target mRNAs. It is known that Bacillus licheniformis M2-7 has the ability to grow and survive in concentrations of hydrocarbons as benzopyrene, which prompted in part by CsrA, as it occurs in the presence of gasoline. However, there are a few studies that reveal the genes involved in that process. In order to know the involved genes in the Bacillus licheniformis M2-7 degradation pathway, the plasmid pCAT-sp containing a mutation in the catEgen was constructed and used to transform B. licheniformis M2-7 and generate the CAT1 strain. We determined the capacity of the mutant B. licheniformis(CAT1) to grow in the presence of glucose and benzopyrene as a carbon source. We observed that CAT1 strain presented an increase in growth in the presence of glucose, but a statistically considerable decrease in the presence of benzopyrene with respect to the wild strain M2-7. Also we demonstrated that the Csr system regulates its expression positively since it was observed that the expression of the gene in the mutant strain LYA12 (M2-7 csrA:: Sp, SpR) decreased considerably with respect to the wild strain. This allowed to characterize the metabolic pathway that Bacillus licheniformis M2-7 implements in the presence of benzopyrene.
An ocular Th1 immune response promotes corneal nerve damage independently of the development of corneal epitheliopathy
Authors: Vereertbrugghen Alexia , Pizzano Manuela , Sabbione Florencia , Keitelman Irene Angelica , Shiromizu Carolina Maiumi , Aguilar Douglas Vera , Fuentes Federico , de Paiva Cintia S , Giordano Mirta , Trevani Analía , Galletti Jeremías G 
Published: January 2023

Abstract
Proper sight is not possible without a smooth, transparent cornea, which is highly exposed to environmental threats. The abundant corneal nerves are interspersed with epithelial cells in the anterior corneal surface and are instrumental to corneal integrity and immunoregulation. Conversely, corneal neuropathy is commonly observed in some immune-mediated corneal disorders but not in others, and its pathogenesis is poorly understood. Here we hypothesized that the type of adaptive immune response may influence the development of corneal neuropathy. To test this, we first immunized OT-II mice with different adjuvants that favor T helper (Th)1 or Th2 responses. Both Th1-skewed mice (measured by interferon-γproduction) and Th2-skewed (measured by interleukin-4 production) developed comparable ocular surface inflammation and conjunctival CD4+ T cell recruitment but no appreciable corneal epithelial changes upon repeated local antigenic challenge. Th1-skewed mice showed decreased corneal mechanical sensitivity and altered corneal nerve morphology (signs of corneal neuropathy) upon antigenic challenge. However, Th2-skewed mice also developed milder corneal neuropathy immediately after immunization and independently of ocular challenge, suggestive of adjuvant-induced neurotoxicity. All these findings were confirmed in wild-type mice. To circumvent unwanted neurotoxicity, CD4+ T cells from immunized mice were adoptively transferred to T cell-deficient mice. In this setup, only Th1-transferred mice developed corneal neuropathy upon antigenic challenge. To further delineate the contribution of each profile, CD4+ T cells were polarized in vitro to either Th1, Th2, or Th17 cells and transferred to T cell-deficient mice. Upon local antigenic challenge, all groups had commensurate conjunctival CD4+ T cell recruitment and macroscopic ocular inflammation. However, none of the groups developed corneal epithelial changes and only Th1-transferred mice showed signs of corneal neuropathy. Altogether the data show that corneal nerves, as opposed to corneal epithelial cells, are sensitive to immune-driven damage mediated by Th1 CD4+ T cells in the absence of other pathogenic factors. These findings have potential therapeutic implications for ocular surface disorders.
Tuberculosis Detection Using Chest X-Ray Image Classification by Deep Learning
Authors: Guia Sana Sahar , Laouid Abdelkader , Kara Mostefa , Hammoudeh Mohammad 
Published: January 2023

Abstract
Tuberculosis is a serious and widespread lung disease, not all patients are usually detected. After the availability of high-resolution chest x-rays, deep learning can now provide solutions for the successful detection of this malignant disease and other possible applications in the health sector. In this manuscript, a new deep learning model for Tuberculosis detection using chest x-ray image classification, employing a mixture of two popular pre-trained vgg16 and vgg19 utilizing the ImageNet dataset, and block attention module in order to obtain spatial data. We validate the presented method through experiments on four popular datasets. After evaluating the model on the test set, we achieve a score of 0.9992 for all metrics (accuracy, precision, recall, f1-score).
Pilot Implementation of Community Health Advocacy Teams to Improve the Effectiveness of Long-Lasting Insecticide Net Distribution through both Campaigns and Continuous Channels in Ghana: A Qualitative Study of Opportunities and Barriers to Implementation
Authors: Dako-Gyeke Phyllis , Hornuvo Ruby , Glozah Franklin N. , Asampong Emmanuel , Tabong Philip Teg-Nefaah , Nwameme Adanna , Chandi Gloria. M. , Peprah Nana Yaw , Gittelman David , Adongo Philip B. 
Published: January 2023

Abstract

Introduction

In Ghana, the National Malaria Control Programme (NMCP) distributes Long-Lasting Insecticide Net (LLIN) to households for free through the periodic Point Mass Distribution (PMD) campaign and continuous distribution to populations most vulnerable to malaria. It is known that the existence of effective and functional community-based groups could influence positive behaviours regarding health interventions promoted through health campaigns. However, there is no evidence of functional community-based groups that aim to improve the effectiveness of LLIN Distribution Campaigns through transitioning into primary healthcare delivery. The aim of this study was to explore the opportunities and barriers to the pilot implementation of co-created community health advocacy teams (CHAT) to improve the effectiveness of LLIN distribution through both campaigns and continuous channels in Ghana.

Methods

A qualitative research approach was used among 43 CHAT members across six communities in the Eastern and Volta regions of Ghana. The CHAT constitutes significant community actors whose roles are centered on key elements of community/social mobilization and capacity building, all nested in social and behaviour change communication strategies. The CHATs were pilot implemented in all study communities for four months after which we identified opportunities and barriers during implementation. CHAT members participated in six Focus Group Discussions which were audio recorded, transcribed verbatim, and analyzed thematically using the NVivo 13.

Results

CHATs were instrumental in sensitizing community members through social and behaviour change communication strategies. Also, there were changes in the behaviour of community members who were receptive towards, and participated in CHAT activities. Community members were accurately informed about malaria (e.g., causes, preventive measures). However, the CHAT experienced barriers during implementation, including lack of financial support to aid in transportation, organization of meetings, and outreach activities. Additionally, level of participation by CHAT members in activities, as well as medium of communication among members were key areas of concern.

Conclusion

The CHATs would be instrumental in promoting LLINs use during and after PMD campaigns through community outreaches. It is therefore necessary to provide resources to support their operations and good network to address communication barriers. Finally, continuous capacity strengthening of CHAT members by the NMCP is important.
Identifying the intermittent flow sub-regimes using pressure drop time series fluctuations
Authors: Arabi Abderraouf , salhi Yacine , Zenati Youcef , Si-Ahmed El-Khider , Legrand Jack 
Published: January 2023

Abstract
From a literature survey, it has been noticed a lack of objective methods to identify and distinct between the intermittent flow sub-regimes. Thus, the aim of this study is to analyze pressure drop fluctuations using statistical methods in order to propose simple tools to characterize the sub-regimes of the intermittent flow. The pressure drop time series were collected from experiments carried out using air-water mixture and 30 mm ID pipe. The utilization of transparent pipes allowed to identify three sub-regimes which are Plug flow, Less Aerated Slug flow (LAS flow), and Highly Aerated Slug flow (HAS flow). It was found that the PDF displayed a unimodal distribution in all cases studied. Meanwhile, the representation of the base width and maximum values of PDF as function of the gas-to-liquid superficial velocities ratio and the mixture Froude number, respectively, showed that the points for each sub-regime are clustered in the same zone. So, these two feature spaces can be used to identify the sub-regimes. A third feature space, based on the statistical parameters standard deviation and kurtosis, was also proposed as a tool to distinguish between the three sub-regimes.
Subsolidus breakdown of armalcolite: Constraints on thermal effects during shock lithification of lunar regolith
Authors: Du Tian-Ran Trina , Zhang Ai-Cheng , Chen Jia-Ni , Wen Yuan-Yun 
Published: January 2023

Abstract
Shock lithification of regolith breccias is a ubiquitous process on the surfaces of airless planetary bodies and may induce thermal effects, including melting on regolith breccia minerals. However, potential thermal effects on lithic and mineral clasts in regolith breccias have seldom been quantitatively constrained. Here, we report two types of micro-textures of armalcolite [(Mg,Fe2+)Ti2O5] in an Mg-suite lithic clast from lunar regolith breccia meteorite Northwest Africa 8182. One type of armalcolite contains oriented fine-grained ilmenite grains; the other occurs as an aggregate of ilmenite, rutile, spinel, and loveringite. We propose that the two types of micro-textures formed through subsolidus breakdown of armalcolite by different processes. The formation of ilmenite inclusions in armalcolite is related to slow cooling after the solidification of its source rock, whereas the ilmenite-rutile-spinel-loveringite aggregates probably formed during the shock lithification event of NWA 8182. The results indicate that the temperature at the margin of lithic clasts could be raised up to at least 600 °C during strong shock lithification of lunar regolith and has profound thermal effects on the mineralogical and isotopic behaviors of lithic and mineral fragments in lunar regolith breccias.
Peri-urban schools of Kinshasa before and during COVID-19: an evaluation of water, handwashing facilities, and girl students’ hand hygiene practices
Authors: Mukiese Nlunda Jean-Marie , Ndungidi Matumona Tatiana , Konde Nkiama Numbi Joël , Yamba Yamba Kapenga Marc , Kiyombo Mbela Guillaume 
Published: January 2023

AbstractThe COVID-19 pandemic has led communities, including Kinshasa peri-urban schools, to reinforce WASH-related practices as a key component in preventing the spread of COVID-19. This study aimed to determine the institutional and behavioural changes in adolescent girl students’ handwashing practices before and during the COVID-19 pandemic. A cross-sectional study was performed, observing the hand hygiene of adolescent girl students, and assessing WASH facilities at schools, chosen from a sample previously selected in the study area. The results indicate significant increases in the prevalence of water points in schools from 10.9 to 22.5%, of handwashing facilities from 43 to 60.1% of schools with an average number of handwashing facilities from one to two, and the prevalence of school WASH brigades from 4.8 to 11.8% of schools. There was also a significant increase in schools receiving funds, and other support for WASH, respectively, from 24.9 to 70.3%, and from 17 to 45.9%, while the proportion of adolescent girl students washing their hands after using the toilet and before eating significantly increased from 6 to 28.4%. However, to improve the current WASH picture, and succeed in curtailing the spread of COVID-19 and related impacts, additional efforts to enhance handwashing practice and WASH items’ coverage are expected.
Microplastics in wastewater treatment plants: Sources, properties, removal efficiency, removal mechanisms, and interactions with pollutants
Authors: Acarer Seren 
Published: January 2023

Abstract
Since wastewater treatment plants (WWTPs) cannot completely remove microplastics (MPs) from wastewater, WWTPs are responsible for the release of millions of MPs into the environment even in 1 day. Therefore, knowing the sources, properties, removal efficiencies and removal mechanisms of MPs in WWTPs is of great importance for the management of MPs. In this paper, firstly the sources of MPs in WWTPs and the quantities and properties (polymer type, shape, size, and color) of MPs in influents, effluents, and sludges of WWTPs are presented. Following this, the MP removal efficiency of different treatment units (primary settling, flotation, biological treatment, secondary settling, filtration-based treatment technologies, and coagulation) in WWTPs is discussed. In the next section, details about MP removal mechanisms in critical treatment units (settling and flotation tanks, bioreactors, sand filters, membrane filters, and coagulation units) in WWTPs are given. In the last section, the mechanisms and factors that are effective in adsorbing organic–inorganic pollutants in wastewater to MPs are presented. Finally, the current situation and research gap in these areas are identified and suggestions are provided for topics that need further research in the future.