bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular vesicles in bone and periodontal regeneration: current and potential therapeutic applications
Authors: Gholami Leila , Nooshabadi Vajihe Taghdiri , Shahabi Shiva , Jazayeri Marzieh , Tarzemany Rana , Afsartala Zohreh , Khorsandi Khatereh 
Published: January 2021

AbstractOral mesenchymal stem cells (MSCs) and their secretomes are considered important factors in the field of medical tissue engineering and cell free biotherapy due to their ease of access, differentiation potential, and successful therapeutic outcomes. Extracellular vesicles (EVs) and the conditioned medium (CM) from MSCs are gaining more attraction as an alternative to cell-based therapies due to the less ethical issues involved, and their easier acquisition, preservation, long term storage, sterilization, and packaging. Bone and periodontal regenerative ability of EVs and CM have been the focus of some recent studies. In this review, we looked through currently available literature regarding MSCs’ EVs or conditioned medium and their general characteristics, function, and regenerative potentials. We will also review the novel applications in regenerating bone and periodontal defects.
RETRACTED ARTICLE: Research on intelligent medical big data system based on Hadoop and blockchain
Authors: Zhang Xiangfeng , Wang Yanmei 
Published: January 2021

AbstractIn order to improve the intelligence of the medical system, this paper designs and implements a secure medical big data ecosystem on top of the Hadoop big data platform. It is designed against the background of the increasingly serious trend of the current security medical big data ecosystem. In order to improve the efficiency of traditional medical rehabilitation activities and enable patients to maximize their understanding of their treatment status, this paper designs a personalized health information system that allows patient users to understand their treatment and rehabilitation status anytime and anywhere, and all medical health data distributed in different independent medical institutions to ensure that these data are stored independently. As a distributed accounting technology for multi-party maintenance and backup information security, blockchain is a good breakthrough point for innovation in medical data sharing. In this paper, the system realizes the personal health data centre on the Hadoop big data platform, and the original distributed data are stored and analyzed centrally through the data synchronization module and the independent data acquisition system. Utilizing the advantages of the Hadoop big data platform, the personalized health information system for stroke has designed to provide personalized health management services for patients and facilitate the management of patients by medical staff.
Mathematical analysis of nonlinear integral boundary value problem of proportional delay implicit fractional differential equations with impulsive conditions
Authors: Ali Arshad , Shah Kamal , Abdeljawad Thabet , Mahariq Ibrahim , Rashdan Mostafa 
Published: January 2021

AbstractThe current study is devoted to deriving some results about existence and stability analysis for a nonlinear problem of implicit fractional differential equations (FODEs) with impulsive and integral boundary conditions. The concerned problem involves proportional type delay term. By using Schaefer’s fixed point theorem and Banach’s contraction principle, the required conditions are developed. Also, different kinds of Ulam stability results are derived by using nonlinear analysis. Providing a pertinent example, we demonstrate our main results.
Conservational tree growing by smallholder farm households: evidence from Gamo highlands of Southern Ethiopia
Authors: Massa Malebo Mancha , Mosa Abdulaziz 
Published: January 2021

AbstractDeforestation and environmental degradation were identified among the leading factors worsening risk exposure in developing countries. Conservational tree growing was found a permissible option and an awake up policy direction to curve down the problem in Ethiopia. However, the uptake of this practice is far from complete and the art has not been made to a level that could make households self-reliant at least in tree resources, particularly in the highlands. The objective of this study was to identify the decisive factors that influence conservational tree growing behavior of smallholder farm households in Gamo highlands of Southern Ethiopia. The study was based on survey data collected from 11 villages in 2011/2012. A multi-stage sampling technique was used to select 335 farm households. Structured interview questionnaires and observations were used to collect primary data. Descriptive and inferential statistics and logistic regression model were used to analyze the data. The key findings showed that a host of factors significantly influenced smallholders’ decision to practice conservational tree growing. The study found that tree growing experience, farm size, and availability of suitable land area for tree growing and cash income from sales of trees were the significant factors explaining the variation in conservational tree growing behavior of households. We also observed old-aged trees in traditionally protected areas. Among others, funeral and mystical sites host large number of long-lived indigenous tree species than private farms in Gamo highlands of southern Ethiopia. Based on the findings, the study concluded that intra-farmer experience sharing, and support to efficient indigenous institutions and rural tree markets as potential entry points for mitigating deforestation and developing environmentally sustainable agriculture.
Lessons learned from the prenatal microbiome controversy
Authors: Blaser Martin J. , Devkota Suzanne , McCoy Kathy D. , Relman David A. , Yassour Moran , Young Vincent B. 
Published: January 2021

AbstractFor more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid, meconium, and even fetal tissues have challenged the dogma of a sterile womb, and additional reports have emerged that used culture, microscopy, and quantitative PCR to support the presence of a low-biomass microbial community at prenatal sites. Given the substantial implications of prenatal exposure to microbes for the development and health of the host, the findings have gathered substantial interest from academics, high impact journals, the public press, and funding agencies. However, an increasing number of studies have challenged the prenatal microbiome identifying contamination as a major issue, and scientists that remained skeptical have pointed to inconsistencies with in utero colonization, the impact of c-sections on early microbiome assembly, and the ability to generate germ-free mammals. A lively academic controversy has emerged on the existence of the wider importance of prenatal microbial communities. Microbiome has asked experts to discuss these issues and provide their thoughts on the implications. To allow for a broader perspective of this discussion, we have specifically selected scientists, who have a long-standing expertise in microbiome sciences but who have not directly been involved in the debate so far.
Polinton-like viruses are abundant in aquatic ecosystems
Authors: Bellas Christopher M. , Sommaruga Ruben 
Published: January 2021

Abstract
Background
Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they have been found to encode virus capsid genes, suggesting they may actually be integrated viruses; however, an extracellular form has yet to be detected. Recently, circa 25 Polinton-like viruses have been discovered in environmental metagenomes and algal genomes, which shared distantly related genes to both Polintons and virophages (Lavidaviridae). These entities could be the first members of a major class of ancient eukaryotic viruses; however, owing to the lack of available genomes for analysis, information on their global diversity, evolutionary relationships, eukaryotic hosts, and status as free virus particles is limited.

Results
Here, we analysed the metaviromes of an alpine lake to show that Polinton-like virus genome sequences are abundant in the water column. We identify major capsid protein genes belonging to 82 new Polinton-like viruses and use these to interrogate publicly available metagenomic datasets, identifying 543 genomes and a further 16 integrated into eukaryotic genomes. Using an analysis of shared gene content and major capsid protein phylogeny, we define large groups of Polinton-like viruses and link them to diverse eukaryotic hosts, including a new group of viruses, which possess all the core genes of virophages and infect oomycetes and Chrysophyceae.

Conclusions
Our study increased the number of known Polinton-like viruses by 25-fold, identifying five major new groups of eukaryotic viruses, which until now have been hidden in metagenomic datasets. The large enrichment (> 100-fold) of Polinton-like virus sequences in the virus-sized fraction of this alpine lake and the fact that their viral major capsid proteins are found in eukaryotic host transcriptomes support the hypothesis that Polintons in unicellular eukaryotes are viruses. In summary, our data reveals a diverse assemblage of globally distributed viruses, associated with a wide range of unicellular eukaryotic hosts. We anticipate that the methods we have developed for Polinton-like virus detection and the database of over 20,000 genes we present will allow for continued discovery and analysis of these new viral groups.
A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis
Authors: Yan Zhixiang , He Feixiang , Xiao Fei , He Huanhuan , Li Dan , Cong Li , Lin Lu , Zhu Huijin , Wu Yanyan , Yan Ru , Li Xiaofeng , Shan Hong 
Published: January 2021

Abstract
Background
Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn’s disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis.

Results
We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events.

Conclusions
This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance.
Group therapy on in utero colonization: seeking common truths and a way forward
Authors: Silverstein Rachel B. , Mysorekar Indira U. 
Published: January 2021

AbstractThe human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief that a broad understanding of human development, health, physiology, and disease requires understanding of the microbiome along with the genome and epigenome. We are learning daily of the interdependent relationships between microbiome/microbiota and immune responses, mood, cancer progression, response to therapies, aging, obesity, antibiotic usage, and overusage and much more. The next frontier in microbiome field is understanding when does this influence begin? Does the human microbiome initiate at the time of birth or are developing human fetuses already primed with microbes and their products in utero. In this commentary, we reflect on evidence gathered thus far on this question and identify the unknown common truths. We present a way forward to continue understanding our microbial colleagues and our interwoven fates.
High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice
Authors: Serrano Joan , Smith Kathleen R. , Crouch Audra L. , Sharma Vandana , Yi Fanchao , Vargova Veronika , LaMoia Traci E. , Dupont Lydia M. , Serna Vanida , Tang Fenfen , Gomes-Dias Laisa , Blakeslee Joshua J. , Hatzakis Emmanuel , Peterson Scott N. , Anderson Matthew , Pratley Richard E. , Kyriazis George A. 
Published: January 2021

AbstractBackgroundNon-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, some interventional studies in humans and rodents have shown unfavorable changes in glucose homeostasis in response to NCAS consumption. The causative mechanisms are largely unknown, but adverse changes in gut microbiota have been proposed to mediate these effects. These findings have raised concerns about NCAS safety and called into question their broad use, but further physiological and dietary considerations must be first addressed before these results are generalized. We also reasoned that, since NCAS are bona fide ligands for sweet taste receptors (STRs) expressed in the intestine, some metabolic effects associated with NCAS use could be attributed to a common mechanism involving the host.ResultsWe conducted a double-blind, placebo-controlled, parallel arm study exploring the effects of pure saccharin compound on gut microbiota and glucose tolerance in healthy men and women. Participants were randomized to placebo, saccharin, lactisole (STR inhibitor), or saccharin with lactisole administered in capsules twice daily to achieve the maximum acceptable daily intake for 2 weeks. In parallel, we performed a 10-week study administering pure saccharin at a high dose in the drinking water of chow-fed mice with genetic ablation of STRs (T1R2-KO) and wild-type (WT) littermate controls. In humans and mice, none of the interventions affected glucose or hormonal responses to an oral glucose tolerance test (OGTT) or glucose absorption in mice. Similarly, pure saccharin supplementation did not alter microbial diversity or composition at any taxonomic level in humans and mice alike. No treatment effects were also noted in readouts of microbial activity such as fecal metabolites or short-chain fatty acids (SCFA). However, compared to WT, T1R2-KO mice were protected from age-dependent increases in fecal SCFA and the development of glucose intolerance.ConclusionsShort-term saccharin consumption at maximum acceptable levels is not sufficient to alter gut microbiota or induce glucose intolerance in apparently healthy humans and mice.Trial registrationTrial registration numberNCT03032640, registered on January 26, 2017.
The impact of the COVID-19 pandemic on individuals with eating disorders: the role of emotion regulation and exploration of online treatment experiences
Authors: Vuillier L. , May L. , Greville-Harris M. , Surman R. , Moseley R. L. 
Published: January 2021

Abstract
Objective
The Covid-19 pandemic has wrought disruption to everyday life and services, and emerging evidence suggests that those with eating disorders (EDs) are likely to experience marked distress and exacerbation of their symptoms. However, little is known around the most relevant factors to symptom change; whether certain emotion regulation and coping strategies are linked to better outcomes; and how people with EDs are adjusting to psychological interventions moving online.

Method
In a mixed-method design, we collected qualitative and quantitative data from 207 (76 males) self-selected UK residents with self-reported ED, who described and ranked impacts of the pandemic on their symptoms. Regression analysis examined whether emotion regulation strategies were associated with self-reported symptom change, ED symptomatology, and negative emotional states. Thematic analysis explored participants’ experiences of the pandemic, particularly factors affecting their ED, coping strategies used, and experiences of psychological intervention.

Results
Most participants (83.1%) reported worsening of ED symptomatology, though factors affecting symptom change differed between specific EDs. Emotion regulation, such as having fewer strategies, poorer emotional clarity, and non-acceptance of emotions, explained nearly half of the variance in emotional distress during the pandemic. Qualitative findings indicated that difficult emotions (such as fear and uncertainty), changes to routine, and unhelpful social messages were triggering for participants during the pandemic. While some participants described employing positive coping strategies (such as limiting social media exposure), many reported using ED behaviours (among other maladaptive strategies, like alcohol use) to cope with the pandemic. Finally, loss of treatment support, feeling underserving of support and experiencing a ‘detached connection’ online were further exacerbating factors for these participants.

Discussion
While our sample was self-selected and may not represent all people with EDs, our results suggest that people with EDs have been strongly affected by the pandemic. Some aspects of online treatment were found to be beneficial but our findings suggest it also needs some improvement. Our paper discusses implications for online treatment such as taking into account personal circumstances and, in a time where people have limited control over the antecedents of negative emotion, the need to develop skills to manage emotions when they arise.
Seed dispersal in Neuwiedia singapureana: novel evidence for avian endozoochory in the earliest diverging clade in Orchidaceae
Authors: Zhang Yu , Li Yuan-Yuan , Wang Miaomiao , Liu Jia , Luo Fanqiang , Lee Yung-I 
Published: January 2021

Abstract
Background
Seed dispersal allows plants to colonize new habitats that has an significant influence on plant distribution and population dynamics. Orchids produce numerous tiny seeds without endosperm, which are considered to be mainly wind-dispersed. Here, we report avian seed dispersal for an early diverging orchid species, Neuwiedia singapureana, which produces fleshy fruits with hard seed coats in the understory of tropical forests.

Results
Neuwiedia singapureana produced fleshy fruits that turned red in autumn, and birds were confirmed to be the primary seed dispersers. As compared to its sister species, N. veratrifolia with dehiscent capsular fruits, embryos of N. singapureana were larger and enclosed by thickened and lignified seed coats. After passing through the digestive tracts of birds, the seeds still stayed alive, and the walls of seed coat contained several cracks. The germination percentage increased significantly for digested seeds as compared with seeds from intact fruits.

Conclusion
The thickened and lignified seed coat may protect seeds as they passed through the digestive tracts of birds. Taken together with a recent report of insect-mediated seed dispersal system in the subfamily Apostasioideae, the animal-mediated seed dispersal may be an adaptive mechanism promoting the success of colonization in dark understory habitats.
Explore the genetics of weedy traits using rice 3K database
Authors: Lin Yu-Lan , Wu Dong-Hong , Wu Cheng-Chieh , Huang Yung-Fen 
Published: January 2021

AbstractBackgroundWeedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativaL.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP).ResultsBased on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus,indica,temperate japonica,tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close toRcwere particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data.ConclusionsThe genotype of trait-associated SNPs identified in this study, especially those located in or close toRc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.