bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-medical students’ perceptions of educational environment and their subjective happiness: a comparative study before and after the COVID-19 pandemic
Authors: Lin Yanyan , Kang Ye Ji , Lee Hyo jeong , Kim Do-Hwan 
Published: December 2021

AbstractBackgroundThe COVID-19 pandemic necessarily changed pre-medical students’ educational environment into an online format—and students’ subjective happiness (SH) is highly impacted by their educational environment. This study investigates changes in pre-medical students’ perceptions of their educational environment and their SH before and after the pandemic, as well as explores the predictors related to their SH.MethodsThe Korean version of the Dundee Ready Educational Environment Measure (DREEM) questionnaire and single-item measures of SH and professional identity (PI) were used. The t-test was employed to analyze the differences of the SH, PI, and DREEM subscales scores before and after the onset of COVID-19. Cohen’s d was used as effect size and correlations between SH and different subscales of DREEM were analyzed using Pearson’s correlation. The multiple regression analysis was performed to reveal associations between predictors and SH.ResultsA total of 399 pre-medical students completed the survey both before and after the COVID-19 pandemic. The DREEM scores and all subscales scores significantly increased but each presents a different effect size. Students’ Perceptions of Learning (SPL: Cohen’s d = 0.97), Students’ Perceptions of Teaching (SPT: Cohen’s d = 1.13), and Students’ Perceptions of Atmosphere (SPA: Cohen’s d = 0.89) have large effect sizes. Students’ Academic Self-Perceptions (SASP: Cohen’s d = 0.66) have a medium effect size and Students’ Social Self-Perceptions (SSSP: Cohen’s d = 0.40) have a small effect size. In contrast, no significant change was noted in the SH and PI. Both PI and SSSP impacted SH before COVID-19, but after the pandemic, SH was impacted by SPL, SPA, and SSSP.ConclusionsStudents’ overall perception of their educational environment was more positive after the onset of COVID-19, but their social self-perceptions improved the least. Additionally, SSSP is the only predictor of SH both before and after the pandemic. The findings of this study suggest that educational institutions must pay attention to students’ social relationships when trying to improve their educational environment. Furthermore, so as to increase students’ SH, development of both educational environment and PI is essential.
splatPop: simulating population scale single-cell RNA sequencing data
Authors: Azodi Christina B. , Zappia Luke , Oshlack Alicia , McCarthy Davis J. 
Published: December 2021

AbstractPopulation-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between individuals from different cohorts as well as genetically-driven co-expression.
The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells
Authors: Azevedo Portilho Nathalia , Saini Deepak , Hossain Ishtiaque , Sirois Jacinthe , Moraes Christopher , Pastor William A. 
Published: December 2021

Abstract
Background
DNA methylation plays an important role in regulating gene expression in mammals. The covalent DNMT1 inhibitors 5-azacytidine and decitabine are widely used in research to reduce DNA methylation levels, but they impart severe cytotoxicity which limits their demethylation capability and confounds interpretation of experiments. Recently, a non-covalent inhibitor of DNMT1 called GSK-3484862 was developed by GlaxoSmithKline. We sought to determine whether GSK-3484862 can induce demethylation more effectively than 5-azanucleosides. Murine embryonic stem cells (mESCs) are an ideal cell type in which to conduct such experiments, as they have a high degree of DNA methylation but tolerate dramatic methylation loss.

Results
We determined the cytotoxicity and optimal concentration of GSK-3484862 by treating wild-type (WT) or Dnmt1/3a/3b triple knockout (TKO) mESC with different concentrations of the compound, which was obtained from two commercial sources. Concentrations of 10 µM or below were readily tolerated for 14 days of culture. Known DNA methylation targets such as germline genes and GLN-family transposons were upregulated within 2 days of the start of GSK-3484862 treatment. By contrast, 5-azacytidine and decitabine induced weaker upregulation of methylated genes and extensive cell death. Whole-genome bisulfite sequencing showed that treatment with GSK-3484862 induced dramatic DNA methylation loss, with global CpG methylation levels falling from near 70% in WT mESC to less than 18% after 6 days of treatment with GSK-3484862. The treated cells showed a methylation level and pattern similar to that observed in Dnmt1-deficient mESCs.

Conclusions
GSK-3484862 mediates striking demethylation in mESCs with minimal non-specific toxicity.
Recurrent autoimmune hypophysitis treated with rituximab: a case report
Authors: Kruse Maria , Olesen Thomas Bastholm , Markovic Ljubo , Glintborg Dorte , Andersen Marianne Skovsager 
Published: December 2021

Abstract
Background
Autoimmune hypophysitis is a rare condition that often results in enlargement of the pituitary gland and hypopituitarism due to inflammatory infiltration. Management of autoimmune hypophysitis can include long-term hormonal replacement and close control of the inflammatory pituitary mass. Mass-related symptoms in patients with autoimmune hypophysitis are treated with anti-inflammatory therapy, surgery, and/or radiotherapy.

Case presentation
We present a 25-year-old White man with visual field defects of the right eye, headache, and weight loss. Magnetic resonance imaging showed a sellar mass, and the patient underwent transcranial surgery. Histopathology revealed autoimmune hypophysitis with predominantly CD20 positive B-cell infiltration. Progression of visual field defects necessitated postoperatively anti-inflammatory treatment with prednisolone. Azathioprine was initiated under gradual tapering of prednisolone with stable conditions at first, but relapse followed after dose reduction. Therefore, rituximab treatment was initiated, which resulted in regression of the pituitary mass. Rituximab treatment was discontinued after 25 months. The patient has continuously been in remission for 4 years after rituximab treatment was stopped.

Conclusion
This case illustrates that rituximab might be an effective alternative treatment in B-cell predominant autoimmune hypophysitis.
Idiopathic pulmonary fibrosis diagnosed concomitantly with diffuse squamous cell lung cancer on surgical lung biopsy: a case report
Authors: Niel C. , Ricordel C. , Guy T. , Kerjouan M. , De Latour B. , Chiforeanu D. , Lederlin M. , Jouneau S. 
Published: December 2021

Abstract
Background
Idiopathic pulmonary fibrosis is a disease with a poor prognosis and has been associated with increased lung cancer incidence.

Case presentation
We report the case of a Caucasian 75-year-old woman, a former smoker, hospitalized for breathlessness with a chest computed tomography scan showing an interstitial lung disease. A surgical lung biopsy was performed, confirming a pattern of usual interstitial pneumonia but also numerous disseminated foci of well-differentiated focally invasive squamous cell carcinoma without hypermetabolic lung nodule, mass, or enlarged lymph node visualized on chest computed tomography or positron emission tomography scan. Nintedanib was started for its antifibrotic and antitumor properties, without any other antineoplastic treatment. Three years after initiation of nintedanib, clinical, functional, and computed tomography scan evaluations were stable, and there was no evidence for evolution of the squamous cell carcinoma.

Conclusions
Data are scarce regarding the benefit of nintedanib in patients with idiopathic pulmonary fibrosis-associated lung cancer, and it is unclear whether nintedanib could have a preventive role in lung carcinogenesis in idiopathic pulmonary fibrosis patients. This experience could help the scientific community in case of similar incidental findings.
A novel coconut-malt extract medium increases growth rate of morels in pure culture
Authors: Evangelista Fabiola Rodríguez , Chairez Isaac , Sierra Sigfrido , Leal Lara Hermilo , Martínez-González César Ramiro , Garín Aguilar María Eugenia , Valencia del Toro Gustavo 
Published: December 2021

AbstractMorels are gourmet wild edible mushrooms that can grow on several substrates with significant growth rate variations. Such variations have hindered the development of a standardized culture media to promote morel’s sustainable production. The aim of this study is developing a novel culture media that takes advantage of coconut water as a complementary component of culture media. Coconut water has been extensively used as a growth-promoting component for plant tissue cultures; however, its application as component of fungi cultivation medium has not been fully developed. This study confirms that coconut water can be efficiently used as culture media component for morels using a kinetic characterization. Morchella sp. kinetic growth is evaluated in different cultures: agar, malt extract agar (MEA), lactose, coconut water (15%) and combinations of them. Kinetic growth parameters (lag phase, λ and maximum specific growth rate, µmax) are estimated using primary modeling methods. Among the selected models, the best fit is achieved using Baranyi’s model. A significant increase from 15.8% to 43.4% of the µmax values was observed when culture media (agar, lactose, MEA) is supplemented with coconut water. The largest values of µmax are obtained in MEA-coconut cultures (21.13 ± 0.43–22.57 ± 0.35). Micro-sclerotia and late sclerotia are observed in all cultures containing coconut water justifying the development of a feasible and cost-effective way of culturing morels. The results demonstrate that coconut water can be used for formulation of standard media for morel cultivation leading to a cheap alternative to produce dense mycelium and promote sclerotia formation.
Enhancement of membrane vesicle production by disrupting the degP gene in Meiothermus ruber H328
Authors: Asano Yuki , Onishi Manato , Nishi Kaito , Kawasaki Kazunori , Watanabe Kunihiko 
Published: December 2021

AbstractThe phenomenon of membrane vesicle (MV) production is known to be common to all bacterial cells. Although MVs are expected to be employed in a variety of applications, improving MV productivity is essential for applications. Since the deletion of the degP gene, a periplasmic dual-function protease and chaperone, in Escherichia coli has successfully improved MV production capacity, we tried to enhance MV productivity in the thermophilic M. ruber H328 by deleting the degP gene. One gene (mrH_0331) was selected for degP gene from the H328 genome and we constructed the mutant strain ∆degP by deleting the degP gene of the H328 strain that was replaced with the htk gene showing thermophilic kanamaycin resistance by homologous recombination. The mutant strain ∆degP exhibited smooth growth but a lower level of turbidity at 60 °C although there was no difference in growth at 55 °C between the wild strain and the mutant strain. Finally, we have confirmed that incubation at 60 °C increases MV in the mutant strain ∆degP strain about fivefold by using two fluorescent dyes, DiI and FM4-64, which is followed by TEM analysis. The deletion of the degP gene presumably causes an increase in denatured proteins at 60 °C, leading to enhanced MV production. Meanwhile, the S-layer protein included in the outer membrane of the H328 strain increased in the MV fraction prepared from the mutant cells incubated at 60 °C. This indicates that this method is effective for MV production and that degP deletion enhances it in strain H328.
Derivation of pb(II)-sensing Escherichia coli cell-based biosensors from arsenic responsive genetic systems
Authors: Lee Yejin , Jeon Yangwon , Jang Guepil , Yoon Youngdae 
Published: December 2021

AbstractHeavy metal-responsive operons were used for the generation of Escherichia coli cell-based biosensors. The selectivity and specificity of the biosensors were determined based on the interaction between heavy metals and regulatory proteins; thereby, the modulating target selectivity of biosensors could be achieved by changing target sensing properties of regulatory proteins. The results of this study demonstrated that Pb(II)-sensing biosensors could be generated from an arsenic-responsive genetic system, which was originally used for arsenic-sensing biosensors. The amino acids around to As(III)-binding sites of ArsR were mutated and cysteine residues were relocated to modulate the metal selectivity. In addition, genes encoding metal ion-translocating P-type ATPases, such as copA and zntA, were deleted to enhance the specificity by increasing the intercellular levels of divalent metal ions. Based on the results, channel protein deleted E. coli cells harboring a pair of recombinant genes, engineered ArsR and arsAp::egfp, showed enhanced responses upon Pb exposure and could be used to quantify the amount of Pb(II) in artificially contaminated water and plants grown in media containing Pb(II). Although we focused on generating Pb(II)-specific biosensors in this study, the proposed strategy has a great potential for the generation of diverse heavy metal-sensing biosensors and risk assessment of heavy metals in environmental samples as well as in plants.
Improvement of putrescine production through the arginine decarboxylase pathway in Escherichia coli K-12
Authors: Thongbhubate Kullathida , Irie Kanako , Sakai Yumi , Itoh Akane , Suzuki Hideyuki 
Published: December 2021

AbstractIn the bio-based polymer industry, putrescine is in the spotlight for use as a material. We constructed strains of Escherichia coli to assess its putrescine production capabilities through the arginine decarboxylase pathway in batch fermentation. N-Acetylglutamate (ArgA) synthase is subjected to feedback inhibition by arginine. Therefore, the 19th amino acid residue, Tyr, of argA was substituted with Cys to desensitize the feedback inhibition of arginine, resulting in improved putrescine production. The inefficient initiation codon GTG of argA was substituted with the effective ATG codon, but its replacement did not affect putrescine production. The essential genes for the putrescine production pathway, speA and speB, were cloned into the same plasmid with argAATG Y19C to form an operon. These genes were introduced under different promoters; lacIp, lacIqp, lacIq1p, and T5p. Among these, the T5 promoter demonstrated the best putrescine production. In addition, disruption of the puuA gene encoding enzyme of the first step of putrescine degradation pathway increased the putrescine production. Of note, putrescine production was not affected by the disruption of patA, which encodes putrescine aminotransferase, the initial enzyme of another putrescine utilization pathway. We also report that the strain KT160, which has a genomic mutation of YifEQ100TAG, had the greatest putrescine production. At 48 h of batch fermentation, strain KT160 grown in terrific broth with 0.01 mM IPTG produced 19.8 mM of putrescine.
Sharing reflections and expressing appreciation upon completing a decade as co-editor of the IJHPR
Authors: Rosen Bruce 
Published: December 2021

AbstractThe Israel Journal of Health Policy Research (IJHPR) was launched in January 2012. In December 2021 it will be completing 10 years of continuous publication. I have had the privilege of serving as the journal’s co-editor in chief during this period, and after ten years of service I am now preparing to step down from that role. IJHPR achievements of which I am particularly proud include remaining true to its mission, attracting manuscripts from virtually all the Israeli institutions engaged in health policy research as well as many leading institutions abroad, widening the circle of Israeli professionals who are submitting manuscripts to journals, and helping many established Israeli academics expand their repertoires to include articles with strong policy components. Several people and organizations have helped make editing the IJHPR such a wonderful experience for me. They include IJHPR co-editor Avi Israeli, IJHPR associate editor Steve Schoenbaum, the Israel National Institute for Health Policy Research (which sponsors the journal), BioMed Central (which publishes the journal), the Myers-JDC-Brookdale Institute (my employer), my family (and particularly my wife, Laura Rosen), and the thousands of authors who have chosen to publish with the IJHPR. May the journal’s second decade be even better than its first one!
A platform for the international exchange of ideas: the Israel Journal of Health Policy Research celebrates its first decade
Authors: McKee Martin 
Published: December 2021

AbstractFor ten years the Israel Journal of Health Policy Research has provided a platform for exchange of knowledge and insights on health policy. It is a unique attempt by scholars and practitioners in one small country to share their knowledge with the world and, in turn to learn from experience elsewhere. Never has this role been as important as during the COVID pandemic, a message that is very clear when we look at failings elsewhere.
Antioxidant activity of thymol essential oil and inhibition of polyphenol oxidase enzyme: a case study on the enzymatic browning of harvested longan fruit
Authors: Khan Muhammad Rafiullah , Huang Chongxing , Zhao Hui , Huang Haohe , Ren Liu , Faiq Muhammad , Hashmi Majid Suhail , Li Bo , Zheng Dantong , Xu Yangfan , Su Hongxia , An Jiejie 
Published: December 2021

Abstract
Background
Enzymatic browning and microbial decay are the primary concerns that limit the postharvest life of longan fruit. These factors can be effectively prevented by sulfur dioxide (SO2) fumigation; however, due to the safety and regulatory issues of SO2, other alternatives must be tested. In this study, antioxidant and antimicrobial activities of thymol were determined against the pericarp browning and decay of longan fruit. A simple, cost-effective method was designed for its controlled release. Thymol vapors were obtained from the slurry prepared from 5 g of thymol in 5 mL of distilled water in a 180-mL glass jar, hermetically sealed and allowed for 24 h to accumulate the vapors in the headspace. Fruits were packed in polyethylene packages and fumigated with thymol through a septum. Non-fumigated fruits served as control and all the packages were stored at 25 ± 2 °C for 8 days.

Results
Thymol significantly (P ≤ 0.05) retarded pericarp browning (BI), delayed the decay incidence (DI) and maintained high color values of longan pericarp. Thymol also retained high total phenolic (TPC) and total flavonoid (TFC) contents, inhibited polyphenol oxidase (PPO) and peroxidase (POD) activities than those in control. A high coefficient of correlation of PPO with BI (r = 0.86), L* (r =  − 0.94), weight loss (r = 0.93), TPC (r =  − 0.77), TFC (r =  − 0.80), DI (r = 0.92) and many other quality and color parameters indicated the antioxidant efficacy of thymol. Longer shelf life of 8 days with good quality attributes was obtained in thymol-treated fruits than 6 days in control.

Conclusion
Thymol could be effectively used as a natural antioxidant for a wide range of fruits.

Graphic abstract
Classification of imbalanced cloud image data using deep neural networks: performance improvement through a data science competition
Authors: Matsuoka Daisuke 
Published: December 2021

AbstractImage data classification using machine learning is an effective method for detecting atmospheric phenomena. However, extreme weather events with a small number of cases cause a decrease in classification prediction accuracy owing to the imbalance in data between the target class and the other classes. To build a highly accurate classification model, I held a data analysis competition to determine the best classification performance for two classes of cloud image data, specifically tropical cyclones including precursors and other classes. For the top models in the competition, minority data oversampling, majority data undersampling, ensemble learning, deep layer neural networks, and cost-effective loss functions were used to improve the classification performance of the imbalanced data. In particular, the best model of 209 submissions succeeded in improving the classification capability by 65.4% over similar conventional methods in a measure of the low false alarm ratio.
Applications of Artificial Intelligence in Pediatric Oncology: A Systematic Review
Authors: Ramesh Siddhi , Chokkara Sukarn , Shen Timothy , Major Ajay , Volchenboum Samuel L. , Mayampurath Anoop , Applebaum Mark A. 
Published: December 2021

PURPOSE There is a need for an improved understanding of clinical and biologic risk factors in pediatric cancer to improve patient outcomes. Machine learning (ML) represents the application of computational inference from advanced statistical methods that can be applied to increasing amount of data available for study in pediatric oncology. The goal of this systematic review was to systematically characterize the state of ML in pediatric oncology and highlight advances and opportunities in the field. METHODS We conducted a systematic review of the Embase, Scopus, and MEDLINE databases for applications of ML in pediatric oncology. Query results from all three databases were aggregated and duplicate studies were removed. RESULTS A total of 42 unique articles that examined the applications of ML in pediatric oncology met inclusion criteria for review. We identified 20 studies of CNS tumors, 13 of solid tumors, and nine of leukemia. ML tasks included classification, prediction of treatment response, and dose optimization with a variety of methods being used including neural network, k-nearest neighbor, random forest, naive Bayes, and support vector machines. Strengths of the identified studies included matching or outperforming physician comparators via automated analysis and predicting therapeutic response. Common limitations included significant heterogeneity in reporting standards, clinical applicability, small sample sizes, and missing external validation cohorts. CONCLUSION We identified areas where ML can enhance clinical care in ways that may not otherwise be achievable. Although ML promises enormous potential in improving diagnostics, decision making, and monitoring for children with cancer, the field remains in early stages and future work will be aided by standards and guidelines to ensure rigorous methodologic design and maximizing clinical utility.