bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Critical Biomarkers Identification of Insulin Signaling Involved in Initiating cAMP Signaling Mediated Salivary Secretion in Sjogren Syndrome: Transcriptome Sequencing in NOD Mice Model
Authors: Chen Bo , Zhou Jiannan , Mao Tianjiao , Cao Tingting , Hu Shilin , Zhang Wenqi , Li Xueyang , Qin Xiuni , Liu Xintong , Watanabe Nobumoto , Li Jiang 
Published: December 2022

Abstract
Background
Sjogren’s syndrome (SS) is an autoimmune disorder characterized by the destruction of exocrine glands, resulting in dry mouth and eyes. Currently, there is no effective treatment for SS, and the mechanisms associated with inadequate salivary secretion are poorly understood.

Methods
In this study, we used NOD mice model to monitor changes in mice’s salivary secretion and water consumption. Tissue morphology of the submandibular glands was examined by H&E staining, and Immunohistochemical detected the expression of AQP5 (an essential protein in salivary secretion). Global gene expression profiling was performed on submandibular gland tissue of extracted NOD mice model using RNA-seq. Subsequently, a series of bioinformatics analyses of transcriptome sequencing was performed, including differentially expressed genes (DEGs) identification, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, PPI network construction, hub gene identification, and the validity of diagnostic indicators using the dataset GSE40611. Finally, IFN-γ was used to treat the cells, the submandibular gland tissue of NOD mice model was extracted, and RT-qPCR was applied to verify the expression of hub genes.

Results
We found that NOD mice model had reduced salivary secretion and increased water consumption. H&E staining suggests acinar destruction and basement membrane changes in glandular tissue. Immunohistochemistry detects a decrease in AQP5 immunostaining within acinar. In transcriptome sequencing, 42 overlapping DEGs were identified, and hub genes (REN, A2M, SNCA, KLK3, TTR, and AZGP1) were identified as initiating targets for insulin signaling. In addition, insulin signaling and cAMP signaling are potential pathways for regulating salivary secretion and constructing a regulatory relationship between target-cAMP signaling-salivary secretion.

Conclusion
The new potential targets and signal axes for regulating salivary secretion provide a strategy for SS therapy in a clinical setting.
Analysis of differentially expressed long non-coding RNAs in LPS-induced human HMC3 microglial cells
Authors: Baek Mina , Chai Jin Choul , Choi Hae In , Yoo Eunyoung , Binas Bert , Lee Young Seek , Jung Kyoung Hwa , Chai Young Gyu 
Published: December 2022

Abstract
Background
Long non-coding RNAs (lncRNAs) are emerging as key modulators of inflammatory gene expression, but their roles in neuroinflammation are poorly understood. Here, we identified the inflammation-related lncRNAs and correlated mRNAs of the lipopolysaccharide (LPS)-treated human microglial cell line HMC3. We explored their potential roles and interactions using bioinformatics tools such as gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG), and weighted gene co-expression network analysis (WGCNA).

Results
We identified 5 differentially expressed (DE) lncRNAs, 4 of which (AC083837.1, IRF1-AS1, LINC02605, and MIR3142HG) are novel for microglia. The DElncRNAs with their correlated DEmRNAs (99 total) fell into two network modules that both were enriched with inflammation-related RNAs. However, treatment with the anti-inflammatory agent JQ1, an inhibitor of the bromodomain and extra-terminal (BET) protein BRD4, neutralized the LPS effect in only one module, showing little or even enhancing effect on the other.

Conclusions
These results provide insight into, and a resource for studying, the regulation of microglia-mediated neuroinflammation and its potential therapy by small-molecule BET inhibitors.
OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics
Authors: Roder Thomas , Oberhänsli Simone , Shani Noam , Bruggmann Rémy 
Published: December 2022

AbstractBackgroundAs the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.ResultsOpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available atopengenomebrowser.github.ioand a demo server is freely accessible atopengenomebrowser.bioinformatics.unibe.ch.ConclusionsTo our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration.
Carotenoid biosynthesis is associated with low-temperature adaptation in Rhodosporidium kratochvilovae
Authors: Guo Rui , Liu Tao , Guo Caina , Chen Gongshui , Fan Jingdie , Zhang Qi 
Published: December 2022

Abstract
Background
Low temperatures greatly limit the growth of microorganisms. Low-temperature adaptation in microorganisms involves multiple mechanisms. Carotenoids are naturally occurring lipid-soluble pigments that act as antioxidants and protect cells and tissues from the harmful effects of free radicals and singlet oxygen. However, studies on the regulation of carotenoid biosynthesis at low temperatures in microorganisms are limited. In this study, we investigated the correlation between carotenoids and low-temperature adaptation in the cold-adapted strain of Rhodosporidium kratochvilovae YM25235.

Results
Carotenoid biosynthesis in YM25235 was inhibited by knocking out the bifunctional lycopene cyclase/phytoene synthase gene (RKCrtYB) using the established CRISPR/Cas9 gene-editing system based on endogenous U6 promoters. The carotenoids were extracted with acetone, and the content and composition of the carotenoids were analyzed by spectrophotometry and HPLC. Then, the levels of reactive oxygen species (ROS) and the growth rate in YM25235 were determined at a low temperature. The results indicated that the carotenoid biosynthesis and ROS levels were increased in the YM25235 strain at a low temperature and inhibition of carotenoid biosynthesis was associated with higher ROS levels and a significant decrease in the growth rate of YM25235 at a low temperature.

Conclusions
The regulation of carotenoid biosynthesis was associated with low-temperature adaptation in YM25235. Our findings provided a strong foundation for conducting further studies on the mechanism by which YM25235 can adapt to low-temperature stress.
Gender differences in brain response to infant emotional faces
Authors: Zhang Kaihua , Du Xiaoyu , Liu Xianling , Su Wei , Sun Zhenhua , Wang Mengxing , Du Xiaoxia 
Published: December 2022

AbstractInfant emotional stimuli can preferentially engage adults’ attention and provide valuable information essential for successful interaction between adults and infants. Exploring the neural processes of recognizing infant stimuli promotes better understandings of the mother-infant attachment mechanisms. Here, combining task-functional magnetic resonance imaging (Task-fMRI) and resting-state fMRI (rs-fMRI), we investigated the effects of infants’ faces on the brain activity of adults. Two groups including 26 women and 25 men were recruited to participate in the current study. During the task-fMRI, subjects were exposed to images of infant emotional faces (including happy, neutral, and sad) randomly. We found that the brains of women and men reacted differently to infants’ faces, and these differential areas are in facial processing, attention, and empathetic networks. The rs-fMRI further showed that the connectivity of the default-mode network-related regions increased in women than in men. Additionally, brain activations in regions related to emotional networks were associated with the empathetic abilities of women. These differences in women might facilitate them to more effective and quick adjustments in behaviors and emotions during the nurturing infant period. The findings provide special implications and insights for understanding the neural processing of reacting to infant cues in adults.
A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize
Authors: Guo Jianfei , Ma Zhigang , Deng Ce , Ding Junqiang , Chang Yuxiao 
Published: December 2022

AbstractLysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected withPuccinia polysora(P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response toP. polysorainfection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.
Influential factors and transcriptome analyses of immature diploid embryo anthocyanin accumulation in maize
Authors: Chen Chen , Zhang Yuling , Fu Xiuyi , Chen Chuanyong , Wu Shanshan , Zhang Chunyuan , Zhang Huasheng , Chang Yiyao , Chen Shaojiang , Zhao Jiuran , Liu Chenxu , Wang Yuandong 
Published: December 2022

Abstract
Background
Anthocyanins are widely applied as a marker for haploid identification after haploid induction in maize. However, the factors affecting anthocyanin biosynthesis in immature embryos and the genes regulating this process remain unclear.

Results
In this study, we analyzed the influence of genetic background of the male and female parents, embryo age and light exposure on anthocyanin accumulation in embryos. The results showed that light exposure was the most crucial factor enhancing the pigmentation of immature embryos. The identification accuracy of haploid embryos reached 96.4% after light exposure, but was only 11.0% following dark treatment. The total anthocyanin content was 7-fold higher in immature embryos cultured for 24 h under light conditions compared to embryos cultured in the dark. Transcriptome analysis revealed that the differentially expressed genes between immature embryos cultured for 24 h in dark and light chambers were significantly enriched in the pathways of flavonoid, flavone, flavonol and anthocyanin biosynthesis. Among the genes involved in anthocyanin biosynthesis, five up-regulated genes were identified: F3H, DFR, ANS, F3′H and the MYB transcription factor-encoding gene C1. The expression patterns of 14 selected genes were confirmed using quantitative reverse transcription-polymerase chain reaction.

Conclusion
Light is the most important factor facilitating anthocyanin accumulation in immature embryos. After 24 h of exposure to light, the expression levels of the structural genes F3H, DFR, ANS, F3′H and transcription factor gene C1 were significantly up-regulated. This study provides new insight into the factors and key genes regulating anthocyanin biosynthesis in immature embryos, and supports improved efficiency of immature haploid embryo selection during doubled haploid breeding of maize.
Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales)
Authors: Yang Zhen , Ma Wenxu , Yang Xiaohong , Wang Lujun , Zhao Tiantian , Liang Lisong , Wang Guixi , Ma Qinghua 
Published: December 2022

Abstract
Background
Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae.

Results
All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution.

Conclusions
Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
Understanding the primary health care experiences of individuals who are homeless in non-traditional clinic settings
Authors: Ramirez Jahanett , Petruzzi Liana J. , Mercer Timothy , Gulbas Lauren E. , Sebastian Katherine R. , Jacobs Elizabeth A. 
Published: December 2022

Abstract
Background
Despite the widespread implementation of Health Care for the Homeless programs that focus on comprehensive, integrated delivery systems of health care for people experiencing homelessness, engaging and retaining people experiencing homelessness in primary care remains a challenge. Few studies have looked at the primary care delivery model in non-traditional health care settings to understand the facilitators and barriers to engagement in care. The objective of our study was to explore the clinic encounters of individuals experiencing homelessness receiving care at two different sites served under a single Health Care for the Homeless program.

Methods
Semi-structured interviews were conducted with people experiencing homelessness for an explorative qualitative study. We used convenience sampling to recruit participants who were engaged in primary care at one of two sites: a shelter clinic, n = 16, and a mobile clinic located in a church, n = 15. We then used an iterative, thematic approach to identify emergent themes and further mapped these onto the Capability-Opportunity-Motivation model.

Results
Care accessibility, quality and integration were themes that were often identified by participants as being important facilitators to care. Psychological capability and capacity became important barriers to care in instances when patients had issues with memory or difficulty with perceiving psychological safety in healthcare settings. Motivation for engaging and continuing in care often came from a team of health care providers using shared decision-making with the patient to facilitate change.

Conclusion
To optimize health care for people experiencing homelessness, clinical interventions should: (1) utilize shared-decision making during the visit, (2) foster a sense of trust, compassion, and acceptance, (3) emphasize continuity of care, including consistent providers and staff, and (4) integrate social services into Health Care for the Homeless sites.
(The shift to) online delivery of a rural faculty development program in research skills: lessons learned
Authors: Asghari Shabnam , Price Jonathan , Anaraki Nahid Rahimipour , Mariathas Hensley Hubert , Bethune Cheri , Graham Wendy , Graham Andrew 
Published: December 2022

AbstractBackgroundWhile rural physicians are the ideal candidates to investigate health and healthcare issues in rural communities, they often lack the required skills, competencies, and resources. As a result, research skills development programs are crucial to help ensure communities receive the quality of care they deserve. Memorial University of Newfoundland created a research skills development program called 6for6 to empower and enable rural physicians to research solutions to community-specific health needs. 6for6 program delivery was exclusively in-person until 2019. However, with limitations introduced due to the COVID-19 pandemic, organizations around the globe needed to respond quickly. As we work to return to a post-pandemic environment, program administrators and educators worldwide are unsure whether to retain or remove the changes made to programs to adapt to the pandemic restrictions. Therefore, this work addresses the impact of the online delivery model in two areas: 1) attainment of competencies (specifically research skills, knowledge, and attitudes); and 2) participant experiences, defined as the ease of attendance, the capacity to interact with team members and peers, and challenges or barriers associated with navigating program resources.MethodsWe compared the effect of an online delivery model pivoted to adapt pandemic restrictions with the original model (primarily face-to-face) on the acquisition of learning competencies and participant experience using a mixed-methods study. Various data collection methods, such as a pre-post program survey, post-program focus group, and structured observation, were utilized.ResultsFrom 2014 to 2021, 35 physicians attended the program (30 face-to-face and five online). The Wilcoxon-sign-rank test did not show any significant differences in the participants’ median change of research competency scores who attended face-to-face and online learning, respectively: knowledge (32.6, 26.8), attitudes (3.8, 3.5), and skills (32.4, 20.0). Flexibility and accessibility were key aspects of participants’ experiences during the online model. Comparison with previous years demonstrated no significant challenges with the virtual delivery model, yet participants struggled with mentorship challenges and learning-life balance.ConclusionsAlthough presenting some unique challenges, the online model did not negatively affect learner competencies. Likewise, it provided opportunities for rural physicians to attend learning sessions and interact with experts and peers while remaining in their communities.
Smoking quit rates among patients receiving pharmacotherapy who received general practitioner counselling versus intensive counselling: a retrospective cohort study
Authors: Yehoshua Ilan , Adler Limor , Hermoni Sharon Alon , Mizrahi Reuveni Miri , Bilitzky Avital , Oren Keren , Zacay Galia 
Published: December 2022

Abstract
Background
Behavioral treatments can augment the success of pharmacotherapy in smoking cessation. The aim of this study was to compare smoking quit rates between patients receiving individual counseling with their general practitioner during office visits or intensive counselling with behavioral support, both augmented by varenicline.

Methods
A nationwide retrospective cohort study conducted in a large Healthcare Maintenance Organization in Israel. We selected randomly patients who filled a prescription for varenicline and received either individual consulting by their general practitioner or intensive counselling with behavioural support, and asked them to answer a questionnaire. The outcome variables were smoking cessation 26–52 weeks following the beginning of treatment and satisfaction with the process.

Results
870 patients were contacted and 604 agreed to participate (a response rate of 69%); 301 patients in the general practitioner group, 300 in the intensive counselling group and 3 were excluded due to missing date. The quit rate was 36.5% in the general practitioner group and 42.3% in the intensive counselling group (P = 0.147). In a logistic regression analysis, controlling for age, gender, socioeconomic status, ischemic heart disease, chronic obstructive pulmonary disease, pack years and duration of varenicline consumption, the adjusted OR for quitting in the general practitioner group was 0.79 (95% CI 0.56,1.13). The adjusted OR was higher in the group with the highest socioeconomic status at 2.06 (1.39,3.07) and a longer period of varenicline consumption at 1.30 (1.15,1.47). Age, gender and cigarette pack-years were not associated with quit rate. In the general practitioner group 68% were satisfied with the process, while 19% were not. In the intensive counselling group 64% were satisfied and 14% were not (P = 0.007).

Conclusion
We did not detect a statistically significant difference in smoking quit rates, though there was a trend towards higher quit rates with intensive counselling.