bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metformin regulates expression of DNA methyltransferases through the miR-148/-152 family in non-small lung cancer cells
Authors: Lee Bo Bin , Kim Dongho , Kim Yujin , Han Joungho , Shim Young Mog , Kim Duk-Hwan 
Published: March 2023

Abstract
Background
To understand the molecular mechanisms involved in regulation of DNA methyltransferases (DNMTs) by metformin in non-small cell lung cancer (NSCLC) cells.

Methods
Expression levels of DNMTs in response to metformin were analyzed in NSCLC cells. MicroRNAs regulating expression of DNMTs at the post-transcriptional level were searched using miRNA-target databases (miRDB and miRTarBase), TCGA RNASeqV2 lung cancer data, and miRNA-seq.

Results
Metformin dose-dependently downregulated expression of DNMT1 and DNMT3a at the post-transcriptional level and expression of DNMT3b at the transcriptional level in A549 lung cancer cells. Activity of DNMTs was reduced by about 2.6-fold in A549 cells treated with 10 mM metformin for 72 h. miR-148/-152 family members (miR-148a, miR-148b, and miR-152) targeting the 3′UTR of DNMTs were associated with post-transcriptional regulation of DNMTs by metformin. Metformin upregulated expression of miR-148a, miR-148b, and miR-152 in A549 and H1650 cells. Transfection with an miR-148b plasmid or a mimic suppressed expression of DNMT1 and DNMT3b in A549 cells. Transfection with the miR-148a mimic in A549 and H1650 cells decreased the luciferase activity of DNMT1 3′UTR. A combination of metformin and cisplatin synergistically increased expression levels of miR-148/-152 family members but decreased expression of DNMTs in A549 cells. Low expression of miR-148b was associated with poor overall survival (HR = 2.56, 95% CI 1.09—6.47; P = 0.04) but not with recurrence-free survival.

Conclusions
The present study suggests that metformin inhibits expression of DNMTs by upregulating miR-148/-152 family members in NSCLC cells.
Clusters of co-abundant proteins in the brain cortex associated with fronto-temporal lobar degeneration
Authors: Bridel Claire , van Gils Juami H. M. , Miedema Suzanne S. M. , Hoozemans Jeroen J. M. , Pijnenburg Yolande A. L. , Smit August B. , Rozemuller Annemieke J. M. , Abeln Sanne , Teunissen Charlotte E. 
Published: March 2023

Abstract
Background
Frontotemporal lobar degeneration (FTLD) is characterized pathologically by neuronal and glial inclusions of hyperphosphorylated tau or by neuronal cytoplasmic inclusions of TDP43. This study aimed at deciphering the molecular mechanisms leading to these distinct pathological subtypes.

Methods
To this end, we performed an unbiased mass spectrometry-based proteomic and systems-level analysis of the middle frontal gyrus cortices of FTLD-tau (n = 6), FTLD-TDP (n = 15), and control patients (n = 5). We validated these results in an independent patient cohort (total n = 24).

Results
The middle frontal gyrus cortex proteome was most significantly altered in FTLD-tau compared to controls (294 differentially expressed proteins at FDR = 0.05). The proteomic modifications in FTLD-TDP were more heterogeneous (49 differentially expressed proteins at FDR = 0.1). Weighted co-expression network analysis revealed 17 modules of co-regulated proteins, 13 of which were dysregulated in FTLD-tau. These modules included proteins associated with oxidative phosphorylation, scavenger mechanisms, chromatin regulation, and clathrin-mediated transport in both the frontal and temporal cortex of FTLD-tau. The most strongly dysregulated subnetworks identified cyclin-dependent kinase 5 (CDK5) and polypyrimidine tract-binding protein 1 (PTBP1) as key players in the disease process. Dysregulation of 9 of these modules was confirmed in independent validation data sets of FLTD-tau and control temporal and frontal cortex (total n = 24). Dysregulated modules were primarily associated with changes in astrocyte and endothelial cell protein abundance levels, indicating pathological changes in FTD are not limited to neurons.

Conclusions
Using this innovative workflow and zooming in on the most strongly dysregulated proteins of the identified modules, we were able to identify disease-associated mechanisms in FTLD-tau with high potential as biomarkers and/or therapeutic targets.
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES
Authors: Joeres Roman , Bojar Daniel , Kalinina Olga V. 
Published: March 2023

AbstractGlycans are important polysaccharides on cellular surfaces that are bound to glycoproteins and glycolipids. These are one of the most common post-translational modifications of proteins in eukaryotic cells. They play important roles in protein folding, cell-cell interactions, and other extracellular processes. Changes in glycan structures may influence the course of different diseases, such as infections or cancer. Glycans are commonly represented using the IUPAC-condensed notation. IUPAC-condensed is a textual representation of glycans operating on the same topological level as the Symbol Nomenclature for Glycans (SNFG) that assigns colored, geometrical shapes to the main monomers. These symbols are then connected in tree-like structures, visualizing the glycan structure on a topological level. Yet for a representation on the atomic level, notations such as SMILES should be used. To our knowledge, there is no easy-to-use, general, open-source, and offline tool to convert the IUPAC-condensed notation to SMILES. Here, we present the open-access Python package GlyLES for the generalizable generation of SMILES representations out of IUPAC-condensed representations. GlyLES uses a grammar to read in the monomer tree from the IUPAC-condensed notation. From this tree, the tool can compute the atomic structures of each monomer based on their IUPAC-condensed descriptions. In the last step, it merges all monomers into the atomic structure of a glycan in the SMILES notation. GlyLES is the first package that allows conversion from the IUPAC-condensed notation of glycans to SMILES strings. This may have multiple applications, including straightforward visualization, substructure search, molecular modeling and docking, and a new featurization strategy for machine-learning algorithms. GlyLES is available at https://github.com/kalininalab/GlyLES.
Production of gathering spaces in post-disaster recovery scenarios: case studies from the Great East Japan Earthquake and Tsunami-2011
Authors: Ghezelloo Yegane , Hokugo Akihiko , Tsukihashi Osamu 
Published: March 2023

AbstractGathering and public spaces, along with infrastructure and houses, are demolished because of disasters, which weakens the community ties. Different approaches, such as government-led and community-driven, to recovery initiate the recovery of gatherings and public spaces, and the long-term impact of each recovery approach on community recovery may not be overseen. This study attempts to determine incorporation of community participation in different recovery approaches and its corresponding result in the production of gathering spaces, based on two main background theories: Arnstein’s ladder of citizen participation and Henri Lefebvre’s production of space triad. We attempted to determine the results by reviewing case studies with different recovery processes after the Great East Japan Earthquake and Tsunami-2011 and through interviews and questionnaire surveys. The results showed that the production of gathering spaces may be associated with the recovery scenario in each case study. In community-driven cases, the main gathering spaces are small open spaces, evenly superimposed and accessible, and diverse in spatial configuration, provide services for the users at a good level, and are in a sync with other gathering spaces. By contrast, in government-led cases, gathering spaces contain primary and secondary spaces that lack connections with each other. These main gathering spaces are centralized near disaster public housing sites, are highly accessible to disaster public housing residents, provide a high range of leisure-based activities, and provide services to users from inside and outside of the communities. These main gathering spaces are extended by inclusive open space (Hiroba) and this spatial planning is closer to the concept of public spaces compared to others.
Acute myocarditis during adjuvant therapies for breast cancer: a case report
Authors: Ushiyama Yumiko , Horimoto Yoshiya , Uomori Toshitaka , Ishizuka Yumiko , Okazaki Misato , Onagi Hiroko , Hayashi Takuo , Watanabe Junichiro , Saito Mitsue 
Published: March 2023

Abstract
Background
With the improvement of optimal perioperative drug therapy for breast cancer patients, physicians now have to treat the adverse effects and comorbidities associated with long-term treatments. We report a case who suffered cardiac arrest due to acute myocarditis developed after initiation of adjuvant treatment.

Case presentation
After completing preoperative chemotherapy and undergoing curative surgery for right breast cancer, a 46-year-old female patient started adjuvant tamoxifen and resumed trastuzumab. Two months later, she complained fever and dyspnea. Blood tests showed a marked increase in hepatic enzymes, and the patient was rushed to our emergency room on suspicion of drug-induced liver injury. In the emergency room, the patient went into cardiac arrest shortly after tachycardia with ST-segment elevation appeared on the monitored electrocardiogram. Resuscitation was started immediately and tracheal intubation, intra-aortic balloon pumping, and extracorporeal membrane oxygenation were started. Coronary angiography results were negative for ischemic heart disease. A diagnosis of fulminant myocarditis was made and steroid pulse therapy and immunoglobulin therapy were started. After the start of treatment, the symptoms of heart failure improved steadily and the patient was discharged on the 28th day. Histological findings of the myocardial biopsy revealed degeneration and necrosis of myocardial cells with marked lymphocytic infiltration, consistent with the histology of lymphocytic myocarditis. Serum cytomegalovirus, coxsackie B virus and adenovirus antibodies were all elevated and these findings were consistent with acute viral myocarditis.

Conclusions
We report a case with strong indications for therapy-induced liver damage, who was ultimately diagnosed with acute viral myocarditis and successfully treated with multidisciplinary therapy. We believe that our findings would be useful for other clinicians in managing similar patients.
Designing a generic, adaptive protocol resource for the measurement of health impact in cash transfer pilot and feasibility studies and trials in high-income countries
Authors: Johnson Elliott Aidan , Johnson Matthew Thomas , Kypridemos Christodoulos , Villadsen Aase , Pickett Kate E. 
Published: March 2023

AbstractIntroductionIn the context of the COVID-19 pandemic, upstream interventions that tackle social determinants of health inequalities have never been more important. Evaluations of upstream cash transfer trials have failed to capture comprehensively the impacts that such systems might have on population health through inadequate design of the interventions themselves and failure to implement consistent, thorough research measures that can be used in microsimulations to model long-term impact. In this article, we describe the process of developing a generic, adaptive protocol resource to address this issue and the challenges involved in that process. The resource is designed for use in high-income countries (HIC) but draws on examples from a UK context to illustrate means of development and deployment. The resource is capable of further adaptation for use in low- and middle-income countries (LMIC). It has particular application for trials of Universal Basic Income but can be adapted to those covering other kinds of cash transfer and welfare system changes.MethodsWe outline two types of prospective intervention based on pilots and trials currently under discussion. In developing the remainder of the resource, we establish six key principles, implement a modular approach based on types of measure and their prospective resource intensity, and source (validated where possible) measures and baseline data primarily from routine collection and large, longitudinal cohort studies. Through these measures, we seek to cover all areas of health impact identified in our theoretical model for use in pilot and feasibility studies.ResultsWe find that, in general, self-reported measures alongside routinely collected linked respondent data may provide a feasible means of producing data capable of demonstrating comprehensive health impact. However, we also suggest that, where possible, physiological measures should be included to elucidate underlying biological effects that may not be accurately captured through self-reporting alone and can enable modelling of long-term health outcomes. In addition, accurate self-reported objective income data remains a challenge and requires further development and testing. A process of development and implementation of the resource in pilot and feasibility studies will support assessment of whether or not our proposed health outcome measures are acceptable, feasible and can be used with validity and reliability in the target population.DiscussionWe suggest that while Open Access evaluation instruments are available and usable to measure most constructs of interest, there remain some areas for which further development is necessary. This includes self-reported wellbeing measures that require paid licences but are used in a range of nationally important longitudinal studies instead of Open Access alternatives.
Development and pilot testing of the 2019 Canadian Abortion Provider Survey
Authors: Renner Regina M. , Ennis Madeleine , Maazi Mahan , Dunn Sheila , Norman Wendy V. , Kaczorowski Janusz , Guilbert Edith 
Published: March 2023

Abstract
Background
Substantial changes in abortion care regulations, available medications and national clinical practice guidelines have occurred since a 2012 national Canadian Abortion Provider Survey (CAPS). We developed and piloted the CAPS 2019 survey instrument to explore changes of the abortion provider workforce, their clinical care as well as experiences with stigma and harassment.

Methods
We undertook development and piloting in three phases: (1) development of the preliminary survey sections and questions based on the 2012 survey instrument, (2) content validation and feasibility of including certain content aspects via a modified Delphi Method with panels of clinical and research experts, and (3) pilot testing of the draft survey for face validity and clarity of language; assessing usability of the web-based Research Electronic Data Capture platform including the feasibility of complex skip pattern functionality. We performed content analysis of phase 2 results and used a general inductive approach to identify necessary survey modifications.

Results
In phase 1, we generated a survey draft that reflected the changes in Canadian abortion care regulations and guidelines and included questions for clinicians and administrators providing first and second trimester surgical and medical abortion. In phase 2, we held 6 expert panel meetings of 5–8 participants each representing clinicians, administrators and researchers to provide feedback on the initial survey draft. Due to the complexity of certain identified aspects, such as interdisciplinary collaboration and interprovincial care delivery differences, we revised the survey sections through an iterative process of meetings and revisions until we reached consensus on constructs and questions to include versus exclude for not being feasible. In phase 3, we made minor revisions based on pilot testing of the bilingual, web-based survey among additional experts chosen to be widely representative of the study population. Demonstrating its feasibility, we included complex branching and skip pattern logic so each respondent only viewed applicable questions based on their prior responses.

Conclusions
We developed and piloted the CAPS 2019 survey instrument suitable to explore characteristics of a complex multidisciplinary workforce, their care and experience with stigma on a national level, and that can be adapted to other countries.
“Crossing borders, connecting cultures”: an introduction to the special issue
Authors: Nienaber Birte , Holzapfel-Mantin Nicole , Budach Gabriele 
Published: March 2023

AbstractThis special issue of Comparative Migration Studies on the occasion of the IMISCOE 2021 Conference with the theme “Crossing borders, connecting cultures” features five invited contributions by several conference speakers as well as an article by the host university.
A case–control study of drinking beverages and the risk of multiple sclerosis in Iran
Authors: Dastoorpoor Maryam , Nabavi Seyed Massood , Majdinasab Nastaran , Zare Javid Ahmad , Ahmadi Angali Kambiz , Seyedtabib Maryam 
Published: March 2023

Abstract
Background
There is no study in the world on the relationship between consuming black and green tea as beverages containing polyphenols and the risk of MS. This study aimed to determine the association between the consumption of green and black tea, coffee, non-alcoholic beer, milk, fruit juices and carbonated beverages with the risk of MS.

Methods and materials
This case–control study was performed on 150 patients with MS and 300 healthy individuals as a control group among patients who were referred to the ophthalmology ward of a referral hospital in Ahvaz with the groups matching for age. The data collection tool was a researcher-made questionnaire including demographic information and beverage consumption. Analysis was performed using univariate and multiple logistic regression models.

Results
The mean age of patients at the time of diagnosis was 38.55 ± 8.88 years. The results showed that drinking milk (OR = 5.46), natural juice (OR = 2.49), and carbonated beverages (OR = 16.17) were associated with an increased chance of developing MS. However, drinking non-alcoholic beer (OR = 0.48), black tea (OR = 0.20), green tea (OR = 0.29) and coffee (OR = 0.07) were associated with a reduced chance of developing MS.

Conclusion
The results show that drinking black and green tea, non-alcoholic beer, and coffee are associated with a decrease in the chance of developing MS. The results of this study can be used to design interventional research and to change people's lifestyles to prevent MS.
A novel post-fire method to estimate individual tree crown scorch height and volume using simple RPAS-derived data
Authors: Arkin Jeremy , Coops Nicholas C. , Daniels Lori D. , Plowright Andrew 
Published: March 2023

Abstract
Background
An accurate understanding of wildfire impacts is critical to the success of any post-fire management framework. Fire severity maps are typically created from satellite-derived imagery that are capable of mapping fires across large spatial extents, but cannot detect damage to individual trees. In recent years, higher resolution fire severity maps have been created from orthomosaics collected from remotely piloted aerial systems (RPAS). Digital aerial photogrammetric (DAP) point clouds can be derived from these same systems, allowing for spectral and structural features to be collected concurrently. In this note, a methodology was developed to analyze fire impacts within individual trees using these two synergistic data types. The novel methodology presented here uses RPAS-acquired orthomosaics to classify trees based on a binary presence of fire damage. Crown scorch heights and volumes are then extracted from fire-damaged trees using RPAS-acquired DAP point clouds. Such an analysis allows for crown scorch heights and volumes to be estimated across much broader spatial scales than is possible from field data.

Results
There was a distinct difference in the spectral values for burned and unburned trees, which allowed the developed methodology to correctly classify 92.1% of trees as either burned or unburned. Following a correct classification, the crown scorch heights of burned trees were extracted at high accuracies that when regressed against field-measured heights yielded a slope of 0.85, an R-squared value of 0.78, and an RMSE value of 2.2 m. When converted to crown volume scorched, 83.3% of the DAP-derived values were within ± 10% of field-measured values.

Conclusion
This research presents a novel post-fire methodology that utilizes cost-effective RPAS-acquired data to accurately characterize individual tree-level fire severity through an estimation of crown scorch heights and volumes. Though the results were favorable, improvements can be made. Specifically, through the addition of processing steps that would remove shadows and better calibrate the spectral data used in this study. Additionally, the utility of this approach would be made more apparent through a detailed cost analysis comparing these methods with more conventional field-based approaches.
Cognitive internet of things-based framework for efficient consumption of electrical energy in public higher learning institutions
Authors: Kalinga Ellen A. , Bazila Simon , Ibwe Kwame , Abdalla Abdi T. 
Published: March 2023

AbstractElectric energy is widely used to power homes, businesses, industries, and Higher Learning Institutions. However, the behavioral trend of using electricity poses challenges in saving energy. Most HLIs electricity users do not switch-off electrical appliances such as lights, fans, and air conditioners when not in use, resulting in high electricity bills and a shorter equipment life span. The literature indicates that misuse of electrical power is more of a behavioral matter, which can be challenging to control. In such scenarios, technological intervention is needed to minimize human interaction. Therefore, this work developed a Cognitive Internet of Things (CIoT)-based framework for efficient consumption of electrical energy in HLIs. CIoT has been applied in the context of saving electrical energy. The proposed framework uses the Linear Regression model for training to monitor air conditioners, fans, and light bulbs. The model compared measured values with established thresholds to perform the necessary actions. Training results from the Linear Regression model show that the air conditioning model achieved an of 97.5%, a chi-square, R2, value of 0.450, a standard error of 0.524, and a "t" value of − 4.638% accuracy. The model for fans scored 97.5% accuracy with a chi-square, R2, of 0.314, a standard error of 8.58 × 10–11, and a "t" value of 5.229. On the other hand, the lighting model scored an accuracy of 97.5% with a chi-square, R2, of 0.298, a standard error of 0.396, and a "t" value of 0.311. All scenarios for testing the model using real data were successfully achieved 100%.