bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project
Authors: Van Vlierberghe Mick , Di Franco Arnaud , Philippe Hervé , Baurain Denis 
Published: August 2021

Abstract
Objectives
Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps.

Data description
We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.
PRC2: an epigenetic multiprotein complex with a key role in the development of rhabdomyosarcoma carcinogenesis
Authors: Zoroddu Stefano , Marchesi Irene , Bagella Luigi 
Published: August 2021

AbstractSkeletal muscle formation represents a complex of highly organized and specialized systems that are still not fully understood. Epigenetic systems underline embryonic development, maintenance of stemness, and progression of differentiation. Polycomb group proteins play the role of gene silencing of stemness markers that regulate muscle differentiation. Enhancer of Zeste EZH2 is the catalytic subunit of the complex that is able to trimethylate lysine 27 of histone H3 and induce silencing of the involved genes. In embryonal Rhabdomyosarcoma and several other tumors, EZH2 is often deregulated and, in some cases, is associated with tumor malignancy. This review explores the molecular processes underlying the failure of muscle differentiation with a focus on the PRC2 complex. These considerations could open new studies aimed at the development of new cutting-edge therapeutic strategies in the onset of Rhabdomyosarcoma.
Evaluating QualiCO: an ontology to facilitate qualitative methods sharing to support open science
Authors: Hocker Julian , Bipat Taryn , McDonald David W. , Zachry Mark 
Published: August 2021

AbstractQualitative science methods have largely been omitted from discussions of open science. Platforms focused on qualitative science that support open science data and method sharing are rare. Sharing and exchanging coding schemas has great potential for supporting traceability in qualitative research as well as for facilitating the reuse of coding schemas. In this study, we present and evaluate QualiCO, an ontology to describe qualitative coding schemas. Twenty qualitative researchers used QualiCO to complete two coding tasks. In our findings, we present task performance and interview data that focus participants’ attention on the ontology. Participants used QualiCO to complete the coding tasks, decreasing time on task, while improving accuracy, signifying that QualiCO enabled the reuse of qualitative coding schemas. Our discussion elaborates some issues that participants had and highlights how conceptual and prior practice frames their interpretation of how QualiCO can be used.
MRI-detected extramural venous invasion of rectal cancer: Multimodality performance and implications at baseline imaging and after neoadjuvant therapy
Authors: Inoue Akitoshi , Sheedy Shannon P. , Heiken Jay P. , Mohammadinejad Payam , Graham Rondell P. , Lee Hee Eun , Kelley Scott R. , Hansel Stephanie L. , Bruining David H. , Fidler Jeff L. , Fletcher Joel G. 
Published: August 2021

AbstractMRI is routinely used for rectal cancer staging to evaluate tumor extent and to inform decision-making regarding surgical planning and the need for neoadjuvant and adjuvant therapy. Extramural venous invasion (EMVI), which is intravenous tumor extension beyond the rectal wall on histopathology, is a predictor for worse prognosis. T2-weighted images (T2WI) demonstrate EMVI as a nodular-, bead-, or worm-shaped structure of intermediate T2 signal with irregular margins that arises from the primary tumor. Correlative diffusion-weighted images demonstrate intermediate to high signal corresponding to EMVI, and contrast enhanced T1-weighted images demonstrate tumor signal intensity in or around vessels. Diffusion-weighted and post contrast images may increase diagnostic performance but decrease inter-observer agreement. CT may also demonstrate obvious EMVI and is potentially useful in patients with a contraindication for MRI. This article aims to review the spectrum of imaging findings of EMVI of rectal cancer on MRI and CT, to summarize the diagnostic accuracy and inter-observer agreement of imaging modalities for its presence, to review other rectal neoplasms that may cause EMVI, and to discuss the clinical significance and role of MRI-detected EMVI in staging and restaging clinical scenarios.
RETRACTED ARTICLE: Using a new HSPC senescence model in vitro to explore the mechanism of cellular memory in aging HSPCs
Authors: Dong Yongpin , Guo Chunni , Zhou Wuxiong , Li Wenfang , Zhang Lina 
Published: August 2021

Abstract
Background
Age-associated changes attenuate human blood system functionality through the aging of hematopoietic stem and progenitor cells (HSPCs), manifested in human populations an increase in myeloproliferative disease and even leukemia; therefore, study on HSPC senescence bears great significance to treat hematopoietic-associated disease. Furthermore, the mechanism of HSPC aging is lacking, especially the cellular memory mechanism. Here, we not only reported a new HSPC senescence model in vitro, but also propose and verify the cellular memory mechanism of HSPC aging of the Polycomb/Trithorax system.

Methods
HSPCs (Lin−c-kit+ cells) were isolated and purified by magnetic cell sorting (MACS). The proportions and cell cycle distribution of cells were determined by flow cytometry; senescence-related β-galactosidase assay, transmission electron microscope (TEM), and colony-forming unit (CFU)-mix assay were detected for identification of the old HSPC model. Proteomic tests and RNA-seq were applied to analyze differential pathways and genes in the model cells. qPCR, Western blot (WB), and chromatin immunoprecipitation PCR (CHIP-PCR) were used to detect the gene expression of cell memory-related proteins. Knockdown of cell memory-related key genes was performed with shRNA interference.

Results
In the model old HSPCs, β-gal activity, cell cycle, colony-forming ability, aging-related cell morphology, and metabolic pathway were significantly changed compared to the young HSPCs. Furthermore, we found the model HSPCs have more obvious aging manifestations than those of natural mice, and IL3 is the major factor contributing to HSPC aging in the model. We also observed dramatic changes in the expression level of PRC/TrxG complexes. After further exploring the downstream molecules of PRC/TrxG complexes, we found that Uhrf1 and TopII played critical roles in HSPC aging based on the HSPC senescence model.

Conclusions
These findings proposed a new HSPC senescence model in vitro which we forecasted could be used to preliminary screen the drugs of the HSPC aging-related hemopathy and suggested cellular memory mechanism of HSPC aging.
Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans
Authors: Bordel Sergio , van Spanning Rob J. M. , Santos-Beneit Fernando 
Published: August 2021

AbstractPoly(3-hydroxybutyrate) (PHB) granule formation in Paracoccus denitrificans Pd1222 was investigated by laser scanning confocal microscopy (LSCM) and gas chromatography analysis. Cells that had been starved for 2 days were free of PHB granules but resynthesized them within 30 min of growth in fresh medium with succinate. In most cases, the granules were distributed randomly, although in some cases they appeared in a more organized pattern. The rates of growth and PHB accumulation were analyzed within the frame of a Genome-Scale Metabolic Model (GSMM) containing 781 metabolic genes, 1403 reactions and 1503 metabolites. The model was used to obtain quantitative predictions of biomass yields and PHB synthesis during aerobic growth on succinate as sole carbon and energy sources. The results revealed an initial fast stage of PHB accumulation, during which all of the acetyl-CoA originating from succinate was diverted to PHB production. The next stage was characterized by a tenfold lower PHB production rate and the simultaneous onset of exponential growth, during which acetyl-CoA was predominantly drained into the TCA cycle. Previous research has shown that PHB accumulation correlates with cytosolic acetyl-CoA concentration. It has also been shown that PHB accumulation is not transcriptionally regulated. Our results are consistent with the mentioned findings and suggest that, in absence of cell growth, most of the cellular acetyl-CoA is channeled to PHB synthesis, while during exponential growth, it is drained to the TCA cycle, causing a reduction of the cytosolic acetyl-CoA pool and a concomitant decrease of the synthesis of acetoacetyl-CoA (the precursor of PHB synthesis).
Interoperability technology of sports health monitoring equipment based on multi-sensor information fusion
Authors: Zhang Di 
Published: August 2021

AbstractNowadays, the pace of society is accelerating, people’s living standard has been greatly improved compared with the past, and we pay more and more attention to the real-time, flexibility, and intelligence of medical services. Information fusion technology is the study of how to effectively and comprehensively utilize multi-sensor information to overcome information imperfections and uncertainties. In recent years, it has become a hotspot for research, but with the development of communication technology, electronic technology, and computers, the form of information becomes complicated and diverse in science and technology such as technology. In this case, the information obtained by a single sensor is always imperfect, so multiple sensors must be used to detect the target from multiple angles. Obtaining more dimensional information about the target and fusing it to ensure the integrity and accuracy of the information helps to accurately determine the physiological health of the human body. This paper analyzes the multi-sensor information fusion technology in detail, discusses the basic principle of multi-sensor information fusion, fusion process, fusion level, architecture and general fusion algorithm, constructs a sensor information fusion technology and its application model in biomedical detection, from the application framework, control structure of multi-sensor integrated system, information fusion, etc. The current situation of multi-sensor information fusion technology is studied in several aspects. An interoperability technology of sports health monitoring equipment based on multi-sensor information fusion is constructed. The experimental results show that the experimental efficiency is improved by 20% after using the application model in this paper, which has certain practicability.
Effect of carcass contamination on necrophagous invertebrate performance
Authors: Hunting Ellard R. , Schrama Maarten , Rozen Daniel E. , Joenssen Christina , Brun Nadja R. 
Published: August 2021

Abstract
Background
The breakdown of dead organic matter is driven by a diverse array of organisms and is an important process increasingly impacted by a range of contaminants. While many studies have documented how contaminants affect food webs that are fueled by decaying plant litters, much less is known about how contaminants affect organisms that rely on dead animal material. Here, we begin to explore the effects of food contamination—using silver nanoparticles (AgNPs) as a model contaminant—on the carrion beetle Nicrophorus vespilloides that buries carcasses of small vertebrates in soils as food source and larval nursing grounds.

Results
Our data show that a single ingestion of a non-lethal dose of 1 μg mL−1 AgNPs by adult female beetles does not affect overall gut microbial activity but results in shifts in the gut microbial community composition towards pathogens including Alcaligenes, Morganella, and Pseudomonas. While no effects were observed in offspring clutch size, some reductions were visible in clutch weight, number of larvae, and number of eclosing pupae in exposed N. vespilloides in comparison with controls. Repeated ingestion of AgNPs over several weeks led to a decrease in survival of adult beetles, suggesting that more environmentally realistic exposure scenarios can directly affect the success of carcass-feeding animals.

Conclusions
Sub-lethal carcass contamination with a model pollutant can affect the gut microbial composition in female beetles and reduce offspring fitness. This encourages consideration of currently overlooked propagation routes of contaminants through necrophagous food webs and inherent consequences for ecological and evolutionary processes.
Optimization of cerebral organoids: a more qualified model for Alzheimer’s disease research
Authors: Bi Feng-Chen , Yang Xin-He , Cheng Xiao-Yu , Deng Wen-Bin , Guo Xiao-Li , Yang Hui , Wang Yin , Li Juan , Yao Yao 
Published: August 2021

AbstractAlzheimer’s disease (AD) is a neurodegenerative disease that currently cannot be cured by any drug or intervention, due to its complicated pathogenesis. Current animal and cellular models of AD are unable to meet research needs for AD. However, recent three-dimensional (3D) cerebral organoid models derived from human stem cells have provided a new tool to study molecular mechanisms and pharmaceutical developments of AD. In this review, we discuss the advantages and key limitations of the AD cerebral organoid system in comparison to the commonly used AD models, and propose possible solutions, in order to improve their application in AD research. Ethical concerns associated with human cerebral organoids are also discussed. We also summarize future directions of studies that will improve the cerebral organoid system to better model the pathological events observed in AD brains.
Farmer-herder conflicts, tenure insecurity and farmer’s investment decisions in Agogo, Ghana
Authors: Kugbega Selorm Kobla , Aboagye Prince Young 
Published: August 2021

AbstractOwing to climate change, population growth and tenurial changes, the past decade has witnessed high interest among migrant and settler pastoralist groups in the vegetal-rich customary lands of the Agogo Traditional Area. This has resulted in lease grants of large land areas to pastoralists by traditional authorities and usufruct families, for reasons of ensuring optimum use and gaining the highest returns from lands. This paper examines the implications of consequent competing interests over land resources between farmers and herders on indigenous farmer’s agricultural investment decisions. The study uses qualitative methods and empirical evidence is given by primary data from semi-structured interviews and focus group discussions in the case study area. Results indicated that land owners exploit lapses in customary land administration systems to allocate lands in exchange for money, to pastoralists while neglecting indigenous farmers’ land use rights. Thus, indigenous farmers report land tenure insecurity and a sense of deprivation from their customary lands. Despite tenure insecurity concerns, farmer’s agricultural investment decisions remain unchanged because such changes in investment decisions may reduce incomes and compromise their livelihoods. The findings herein contradict theoretical expectations and provide new perspectives for understanding the relationship between tenure (in)security and investment decisions.
Supplemental magnolol or honokiol attenuates adverse effects in broilers infected with Salmonella pullorum by modulating mucosal gene expression and the gut microbiota
Authors: Chen Fang , Zhang Hao , Du Encun , Fan Qiwen , Zhao Na , Jin Feng , Zhang Wei , Guo Wanzheng , Huang Shaowen , Wei Jintao 
Published: August 2021

Abstract
Background
Salmonella pullorum is one of the most harmful pathogens to avian species. Magnolol and honokiol, natural compounds extracted from Magnolia officinalis, exerts anti-inflammatory, anti-oxidant and antibacterial activities. This study was conducted to evaluate the effects of dietary supplemental magnolol and honokiol in broilers infected with S. pullorum. A total of 360 one-day-old broilers were selected and randomly divided into four groups with six replicates: the negative control group (CTL), S. pullorum-infected group (SP), and the S. pullorum-infected group supplemented with 300 mg/kg honokiol (SPH) or magnolol (SPM).

Results
The results showed that challenging with S. pullorum impaired growth performance in broilers, as indicated by the observed decreases in body weight (P < 0.05) and average daily gains (P < 0.05), along with increased spleen (P < 0.01) and bursa of Fabricus weights (P < 0.05), serum globulin contents, and the decreased intestine villus height and villus/crypt ratios (P < 0.05). Notably, supplemental magnolol and honokiol attenuated these adverse changes, and the effects of magnolol were better than those of honokiol. Therefore, we performed RNA-Seq in ileum tissues and 16S rRNA gene sequencing of ileum bacteria. Our analysis revealed that magnolol increased the α-diversity (observed species, Chao1, ACE, and PD whole tree) and β-diversity of the ileum bacteria (P < 0.05). In addition, magnolol supplementation increased the abundance of Lactobacillus (P < 0.01) and decreased unidentified Cyanobacteria (P < 0.05) both at d 14 and d 21. Further study confirmed that differentially expressed genes induced by magnolol and honokiol supplementation enriched in cytokine-cytokine receptor interactions, in the intestinal immune network for IgA production, and in the cell adhesion molecule pathways.

Conclusions
Supplemental magnolol and honokiol alleviated S. pullorum-induced impairments in growth performance, and the effect of magnolol was better than that of honokiol, which could be partially due to magnolol’s ability to improve the intestinal microbial and mucosal barrier.
Contemporary Variables that Impact Sleep and Development in Female Adolescent Swimmers and Gymnasts
Authors: Bartholomew Janine , Gilligan Carrie , Spence Ann 
Published: August 2021

AbstractThe effects of sleep on elite athletes in late adolescence and early adulthood have been well documented in a myriad of sports. However, there is underrepresentation of pre-pubertal and young female adolescent athlete research between the ages of 11–17, and specifically female gymnast and swimmers. Neglecting to understand how high energy demand at a young age relates to sleep and restoration may lead to developmental ramifications for this group, as they display physiological dysfunctions like delayed puberty, amenorrhea and are at risk for the female athlete triad or components of the triad. This review aims to summarize the contemporary variables of blue light emitting screens, social media, and caffeine on quality and quantity of sleep in young athletes while identifying gaps in the literature on how these factors impact the target group of young female swimmers and gymnasts. The implications of this work include sleep hygiene recommendations for increasing duration and quality of sleep, as well as future research with respect to electronic device usage, social media participation, caffeine consumption, and sport engagement in female early adolescent athletes.
Speech-aid prosthesis in velopharyngeal incompetency patient with cleft palate: can speech aids be applicable for adult patient?
Authors: Kang Dong-Cheol , Park Jung-Ho , Seok Hyun , Baek Jin-A , Kim Da-Wa , Ko Seung-O 
Published: August 2021

Abstract
Background
Velopharyngeal incompetence (VPI) therapy for cleft palate (speech therapy alone, speech therapy using speech aids, or combined therapy such as speech therapy using a pharyngeal flap), is more effective in younger patients than in adult patients. Speech therapy is known as very difficult for patients who still have VPI as an adult. Because of the possibility of subsequent speech disorders, the timing of surgery for cleft palate is accelerating. Herein, we present a case of an adult with articulation disorder due to VPI who was treated by speech therapy and a speech-aid prosthesis.

Case presentation
A woman who underwent cleft palate surgery at 8 years of age still had difficulty with articulation due to VPI as a 24-year-old adult because of a lack of continuous speech therapy. We decided to use a speech-aid application using palatal lift, and a reduction program was conducted four times, along with simultaneous speech therapy, over a period of 1 year and 7 months. During the therapy period, she was able to speak normally within a relatively short period of time, and after implementation of the reduction program, the therapy was completed by completely removing the device. Long-term observations have shown normal speech function without recurrence, even after the device was removed.

Conclusion
As seen in this case, speech therapy using speech aids can show a good result for adult patients with cleft palate who missed the usual timing for the treatment of articulation disorders, depending on the situation. Therefore, it is hereby reported as a therapy option worthy of consideration.
FBXW7 gene polymorphism is associated with type 2 diabetes in the Uygur population in Xinjiang, China
Authors: Yan Shi-Qi , Adi Dilare , Liu Cheng , Wang Meng-Meng , Abuzhalihana Jialin , Wu Yun , Fu Zhen-Yan , Yang Yi-Ning , Li Xiao-Mei , Xie Xiang , Liu Fen , Chen Bang-Dang , Ma Yi-Tong 
Published: August 2021

Abstract
Background
FBXW7 gene expression is positively correlated with glycolipid metabolism and is associated with diabetes in animal models. In the current study, we focused on exploring whether genetic variants of the FBXW7 gene were associated with type 2 diabetes (T2DM) and the risk factors for T2DM in Uygur people in Xinjiang, China.

Methods
A total of 2164 Chinese Uygur subjects (673 T2DM patients and 1491 controls) were recruited for our case–control study, and four SNPs (rs10033601, rs2255137, rs2292743 and rs35311955) of the FBXW7 gene were genotyped using the improved multiplex ligation detection reaction (iMLDR) technique.

Results
Our study showed that the genotypes using the overdominant model (GA vs AA + GG) of rs10033601 and using the overdominant model (TA vs TT + AA) of rs2292743 were significantly different between T2DM patients and the controls (P = 0.005 and P = 0.012, respectively). After multivariate adjustments for confounders, the rs10033601 and rs2292743 SNPs were still independent risk factors for T2DM [GA vs AA + GG: odds ratio = 1.35, 95% confidence interval (CI) = 1.12–1.64, P = 0.002; TA vs TT + AA: OR = 1.28, 95% CI = 1.06–1.55, P = 0.011]. Participants within the Chinese Uygur populations and who with the GA genotype of rs10033601 and the TA genotype of rs2292743 were associated with significantly elevated glucose levels.

Conclusions
Our study revealed that both rs10033601 and rs2292743 of the FBXW7 gene were associated with T2DM in the Uygur populations in Xinjiang.