bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Bioinformatics To Identify Potential Cytokines ALPL /TNAP In Children With Spastic Cerebral Palsy
Authors: Wang Xiaokun , Gao Chao , Zhong Hequan , Kong Xiangyu , Qiao Rui , Zhang Huichun , Yang Dongmei , Gao Yang , Li Bing 
Published: November 2021

Abstract
Background: Several published studies have shown the significance of neuroinflammation in the pathophysiological development of cerebral palsy (CP). However, the underlying molecular mechanisms by which neuroinflammation is associated with brain injury in CP remain poorly understood. Spastic CP is the most common form of CP, comprising 80% of all cases. Therefore, identifying patterns of inflammatory and related biomarkers would serve to understand the etiology of spastic CP.Methods: Related clinical parameters were assessed in 18 children with spastic CP and 20 age-matched healthy individuals. Blood samples of children with spastic CP and controls were analyzed with integrated transcriptomics and proteomics profiling to detect common differentially expressed mRNAs and proteins. Hypoxic ischemic encephalopathy was induced in postnatal day 7 rat pups. Behavioral testing was performed postinjury, and then, the differentially expressed markers and inflammatory cytokines were verified in the peripheral blood and cerebral cortex of the CP model rats by ELISA and Western blot. Independent sample t-tests, one-way analysis of variance and the Pearson correlation were used for statistical analysis.Results: Through proteomic and transcriptome analysis, we identified common differentially expressed genes. Among them, ALPL, encoding tissue nonspecific alkaline phosphatase (TNAP), was downregulated in spastic CP. In addition, compared with those of the corresponding controls, significantly lower mRNA and protein levels of TNAP were found in children with CP and the CP model rats. In contrast, compared with the control rats, the model rats demonstrated a significant increase in osteopontin and proinflammatory biomarkers, such as interleukin (IL)-6, IL-17, and C-reactive protein (CRP), in both the plasma and cerebral cortex, while serum 25 hydroxyvitamin D and anti-inflammatory cytokines such as IL-10 were significantly decreased. Additionally, the level of serum TNAP was correlated with the content of serum CRP and IL-10 in model rats.Conclusion: These results suggest that TNAP, the gene expression product of ALPL, is closely related to the pathogenesis and development of spastic CP, particularly in the upregulation of proinflammatory cytokines and the downregulation of anti-inflammatory cytokines, which contribute to the occurrence of inflammation in the progression of spastic CP.
Discovering Novel Genes in Non-Model Fly Accessory Glands Using De Novo Nanopore Transcriptomics
Authors: Mrinalini Mrinalini , Puniamoorthy Nalini 
Published: November 2021

Abstract
BackgroundOxford Nanopore Technologies (ONT) long-read transcriptomes offer many advantages including long reads (>10kbp), end-to-end transcripts, structural variants, isoform-level resolution of genes and expression. However, uptake of ONT transcriptomics is still low, largely due to high error rates (2 to 13%) and reliance on reference databases that are unavailable for many non-model species. Additionally, bioinformatics tools and pipelines for de novo ONT transcriptomics are still in early stages of development. ResultsHere, we use de novo ONT GridION transcriptomics to discover novel genes from the male accessory glands (AG) of a widespread, non-model dung fly, Sepsis punctum. Insect AGs are of particular interest for this as they are hotspots for rapid evolution of novel reproductive genes, and they synthesize seminal fluid proteins that lack homology to any other known proteins. We implement a completely de novo ONT GridION transcriptome pipeline, incorporating quality-filtering and rigorous error-correction procedures, to characterize this novel gene set and to quantify their expression. Specifically, we compare these ONT genes and their expression against de novo lllumina HiSeq transcriptome data. We find 40 high-quality and high-confidence ONT genes that cross-verify against Illumina genes; twenty-six of which are novel and specific to S. punctum. Read count based expression quantification in ONT samples is highly congruent with Illumina’s Transcript per Million (TPM), both in overall pattern and within functional categories. Novel genes account for an average of 81% of total gene expression underscoring their functional importance in S. punctum AGs. Eighty percentage of these genes are secretory in nature, responsible for 74% total gene expression. Notably, median sequence similarities of ONT nucleotide and protein sequences match within-Illumina sequence similarities indicating that our de novo ONT transcriptome pipeline successfully mitigated sequencing errors. ConclusionsThis is the first study to adapt ONT transcriptomics for completely de novo characterization of novel genes in animals. Our study demonstrates that ONT long-reads, constituting a quarter of the number of bases sequenced at less than a third the cost of Illumina reads, can be a resource-friendly and cost-effective solution for end-to-end sequencing of unknown genes even in the absence of a reference database.
Knowledge and Oral Health Related Behaviour Among Visually Impared Subjects in Addis Ababa, Ethiopia
Authors: Fantaye Wondwossen , Nur Abdela , Kifle Getachew , Engida Fasikawit 
Published: November 2021

Abstract
Background: Oral health is a global issue. It has an enormous impact on the overall health and well-being of an individual. In addition, many studies indicate visual impairment as one of the constraints for proper maintenance of oral hygiene. However, little is known about visually impaired individuals' oral health knowledge and behavior in Ethiopia, Specifically in Addis Ababa. Therefore, this study is conducted to assess the oral health knowledge and related behaviors among participants with visual impairment in Addis Ababa, Ethiopia. Methods: The study was carried out at the Ethiopian National Association for the blind, located in Addis Ababa, the capital city of Ethiopia. Convenience sampling was used from the visually impaired library attendees' in the blind association. Sixty-five individuals, of which 46 males and 19 females, agreed to take part in the study. Of these, 30.8% had partial and 69.2% total visual impairment.Results: 61.3% with totally and 72% with partially visually impaired scored high in the knowledge of caries causes respectively. The use of tooth brushing was confirmed by 42.2% with totally and 25% with partially visually impaired. The use of Traditional chewing sticks was confirmed by 57.7% with totally and 30% with partially visually impaired individuals. Moreover, both (Toothbrush & Traditional chewing stick) was used by 35.5% totally and 55% partially visually impaired individuals, respectively.Conclusions: The study showed the awareness about the causes of Dental Caries among the visually impaired was high. However, the majority of them had a significant misconception about the causes of dental caries.
Implementing Implementation Science; A Bibliometric Study of Qualitative Research in Clinical Artificial Intelligence
Authors: Hogg Henry David Jeffry , Al-Zubaidy Mohaimen , Keane Pearse A , Beyer Fiona R , Maniatopoulos Gregory 
Published: November 2021

Abstract
Background

Implementation science is a pragmatic and multidisciplinary field, centred on the application of a wide range of theoretical approaches to close ‘know-do’ gaps in healthcare. The implementation science community is made of individuals on a continuum between academia and practice, but it is unclear to what extent the theoretical deliberations of implementation academics are translated into the work of implementation practitioners and on to patient benefit. This bibliometric study aims to use the field of clinical artificial intelligence(AI) implementation to sample the prevalence and character of theoretically informed implementation practices.
Methods

Qualitative research of key stakeholder perspectives on clinical AI published between 2014-2021 was systematically identified. Following title, abstract and full-text screening eligible articles were characterised in terms of their publication, AI tool and context studied, the theoretical approach if any and the research methods and quality. Descriptive, comparative and regression statistics were applied.
Results

One-hundred-and-eleven studies met the eligibility criteria, with monthly eligible publication rate increasing from 0.7-4.0 between 2014-2021. Eligible studies represented 23 different nations and 25 different clinical specialities. A theoretical approach was explicitly employed in 39(35.1%) studies though 6 of these described novel theoretical approaches(15.1%) and the most frequently used theoretical approach was only used 3 times. There was no statistically significant trend in the prevalence of theoretically informed research within the study period. Of the 25 theoretically informed studies conducted in Europe or North America 19(76%) used theories that originated in the same continent.
Conclusions

The theoretical approaches which characterise implementation science are not being put to use as often as they could, and the means by which they are selected also seems suboptimal. The field may facilitate a greater synergy between theory and practice if the focus shifts from unifying implementation theories on to unifying and expanding the implementation community. By making more theoretical approaches accessible to practitioners and supporting their selection and application, theory could be more effectively harnessed to close healthcare’s ‘know-do gaps’.
Protocol registration
PROSPERO ID 248025
Logics of Involutive Stone Algebras
Authors: Marcelino Sérgio , Rivieccio Umberto 
Published: November 2021

Abstract
An involutive Stone algebra (IS-algebra) is a structure that is simultaneously a De Morgan algebra and a Stone algebra (i.e. a pseudo-complemented distributive lattice satisfying the well-known Stone identity, ∼ x ∨ ∼ ∼ x ≈ 1). IS-algebras have been studied algebraically and topologically since the 1980’s, but a corresponding logic (here denoted IS ≤ ) has been introduced only very recently. The logic IS ≤ is the departing point for the present study, which we then extend to a wide family of previously unknown logics defined from IS-algebras. We show that IS ≤ is a conservative expansion of the Belnap-Dunn four-valued logic (i.e. the order-preserving logic of the variety of De Morgan algebras), and we give a finite Hilbert-style axiomatization for it. More generally, we introduce a method for expanding conservatively every super-Belnap logic so as to obtain an extension of IS ≤ . We show that every logic thus defined can be axiomatized by adding a fixed finite set of rule schemata to the corresponding super-Belnap base logic. We also consider a few sample extensions of IS ≤ that cannot be obtained in the above- described way, but can nevertheless be axiomatized finitely by other methods. Most of our axiomatization results are obtained in two steps: through a multiple-conclusion calculus first, which we then reduce to a traditional one. The multiple-conclusion axiomatizations introduced in this process, being analytic, are of independent interest from a proof-theoretic standpoint. Our results entail that the lattice of super-Belnap logics (which is known to be uncountable) embeds into the lattice of extensions of IS ≤ . Indeed, as in the super-Belnap case, we establish that the finitary extensions of IS ≤ are already uncountably many.
RPL34 regulates osteosarcoma cells proliferation through c-Myc/RPL34 signaling axis
Authors: Huang Piwei , Wei Minghui , Ji Shufan , Fowdur Mitra , he maolin 
Published: November 2021

Abstract
BackgroundRibosomal protein L34 (RPL34) is a member of the L34E ribosomal protein family containing zinc finger domains. This protein plays a key role in regulating the apoptosis, cell cycle progression and proliferation of various cancer including osteosarcoma (OS). The purpose of this study is to clarify the expression of RPL34 in osteosarcoma cells and its molecular mechanism of regulating osteosarcoma cells. MethodsThe expression levels of c-Myc and RPL34 were detected by qRT-PCR and Western blot. Luciferase reporter assays and chromatin immunoprecipitation (ChIP) were used to analyse the binding site of c-Myc and RPL34. ResultsThe results showed that c-Myc binds to the E-box region in the RPL34 promoter to regulate RPL34 expression. The results indicated that RPL34 regulates osteosarcoma cells proliferation through c-Myc/RPL34 signaling axis. This research may provide new ideas for targeted therapy of OS. Conclusion RPL34 regulates osteosarcoma cells proliferation through c-Myc/RPL34 signaling axis.
Suspension array platform based on aptamer for high-throughput detection of five environmental hormones
Authors: Yao Ziyi , Yao Zi-yi , Jia Xue-xia , Ren Shu-yue , Yang Shi-ping , Gao Zhi-xian 
Published: November 2021

Abstract
Background

As a common small molecule substance, environmental hormones widely exist in nature, especially water sources, which have a profound effects in humans. Highly efficient and sensitive method for estrogens in the environment are essential.
Results

In this paper, a novel high-throughput platform was established based on five small hormones molecules specificity aptamer and magnetic beads (MBs). The results showed that the sensitivity of the proposed method are greatly improved. The limit of detection(LOD) of this method for atrazine(Atz), profenofos, bisphenolA(BPA), estradiol(E2), and polychlorinated biphenyls(PCBs) were 9.46, 20.75, 23.81, 8.97, 6.27 pg/mL, respectively. The Recovery rate of the diluted environmental hormones spiked in the samples of Haihe river were in the range of 87.5-111.02% with relative standard deviations (RSDs) lower than 28.44%.
Conclusion

This platform based on new complementary strand fragments can simultaneously rapid detection five environmental hormones. The whole procedure completed within 1.5h including sample treatment, incubation and detection, greatly improving the detection efficiency.
Impaired Diffusion Capacity and Pulmonary Fibrosis after Recovery from COVID-19: A Systematic Review and Meta-Analysis
Authors: Lee Jong Hyuk , Yim Jae-Joon , Park Jimyung 
Published: November 2021

Abstract
Background: The medium- to long-term pulmonary consequences of coronavirus disease 2019 (COVID-19) after recovery from acute infection remain unclear. Several studies have examined this issue and reported heterogeneous results. Methods: We conducted a systematic review and meta-analysis using a random-effects model to estimate the pooled prevalence of pulmonary sequelae after COVID-19, namely impaired diffusion capacity and pulmonary fibrosis, at least 1 month after the initial infection. PubMed, Embase, and Cochrane Library were searched from January 1, 2020, to February 15, 2021 to identify related studies. We also assessed whether the initial severity of infection was associated with impaired diffusion capacity in the recovery phase. Results: Of the 8159 studies identified, 29 met our eligibility criteria. Among these studies, 25 and 20 had data on follow-up pulmonary function testing and chest computed tomography (CT), respectively. Impaired diffusion capacity (<80% of predicted values or lower limit of normal) was the most common pulmonary abnormality (pooled prevalence 34%, 95% CI 27%–41%). When classified according to the severity of index infection, patients with severe COVID-19 were more likely to display impaired diffusion capacity than those with non-severe COVID-19 (pooled odds ratio 2.97, 95% CI 2.10–4.20). On follow-up chest CT, pulmonary fibrosis was found in 26% (95% CI 17%–36%) of the patients. Conclusions: A substantial number of patients recovering from COVID-19 displayed impaired diffusion capacity and pulmonary fibrosis. The severity of index COVID-19 was associated with impaired diffusion capacity, highlighting the importance of respiratory follow-up in patients recovering from severe COVID-19.Systematic review registration number: PROSPERO CRD42021234357
Characteristics of Oral Mucosal Lesions and Their Association with Socioeconomic Status and Systemic Health in A Remote Rural Area in China: A Cross-Sectional Study of 146 Cases
Authors: Yao Hui , Zhang Qiongyue , Song Qianqian , Liu Mingshan , Tang Guoyao 
Published: November 2021

Abstract
Background: Epidemiological data of oral mucosal lesions (OMLs) are required to develop practical oral care policies. However, limited data are available for rural areas in China. We aimed to estimate the spectrum and prevalence of OMLs and to identify their associated socioeconomic status (SES) and systemic health in a remote rural area in Yunnan, China. Methods: We screened patients for OMLs in an oral medicine clinic in rural Yuannan, China, from August 2020 to February 2021. OMLs were documented. SES, including the highest education level achieved and the previous month’s household income, as well as the patient’s systemic health, including a history of smoking, alcohol use, and chronic disease, were obtained from the Medical History/Health Questionnaire Form and patient medical records. Results: A total of 146 patients were found to have OMLs. The most frequent OML was aphthous ulcer (n = 41, 28.1%), followed by burning mouth syndrome (BMS) (n = 16, 11.0%), viral ulcer (n = 14, 9.6%), and oral lichen planus (OLP) (n = 9, 6.2%). In these patients, the most common chronic diseases were sleep apnea (n = 35, 24.0%), hypertension (n = 23, 15.8%), bronchitis (n = 16, 11.0%), reflux (including gastroesophageal reflux disease) (n = 12, 8.2%), and arthritis (n = 11, 7.5%). On adjusted regression, the patients without chronic diseases had a lower risk of BMS than those with chronic diseases (odds ratio [OR], 0.2; 95% confidence interval [CI], 0.03–0.9). Age was an independent protective factor for viral ulcers (OR, 1.0; 95% CI, 0.9–1.0). Patients with low-income levels had a lower risk of OLP than those with high-income levels (OR, 0.2; 95% CI, 0.05–0.9). Conclusions: In rural Yunnan in China, the most frequent OML was aphthous ulcer, which was followed by BMS, viral ulcer, and OLP. Chronic diseases were associated with BMS. Age was an independent protective factor for oral viral ulcers. A high-income level was associated with the presence of OLP. Oral care policies should be prioritized among patients with aphthous ulcer. Preventive strategy of BMS should be targeted to people with chronic disease for health equalities.
Metagenomic Analysis of The Effects of Salinity On Microbial Diversity and Functional Gene Diversity in Kongsfjorden Estuary
Authors: Lin Lidong , Wang Nengfei , Han Wenbing , Zhang Botao , Zang Jiaye , Li Qinxin , Qin Yiling , Wang Long , Fang Long , Liu Jie 
Published: November 2021

Abstract
Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the salinity of Kongsfjorden increases from the estuary to the interior of the fjord. Our goal was to determine which bacterial taxa and metabolism-related gene abundance were affected by changes in salinity, and whether salinity is correlated with genes related to nitrogen and sulfur cycling in fjord ecosystem using metagenomic analysis. Our data indicate that changes in salinity may affect some bacterial taxa, such as the relative abundance of Alphaproteobacteria and Deltaproteobacteria is higher at high salinity sites, while the relative abundance of Gammaproteobacteria and Betaproteobacteria is more dominant at low salinity sites. In addition, the relative abundance of some bacteria at the high and low salinity sites was different at the family level. For example, Rhodobacteraceae, Pseudoalteromonadaceae, Flavobacteriaceae, Vibrionaceae at the high salinity site Colwelliaceae, Chromatiaceae and Alteromonadaceae at the low salinity site are affected by salinity. In terms of functional gene diversity, our study proved that salinity could affect the relative abundance of related genes by affecting the metabolic mechanism of microorganisms. In addition to salinity, functional attributes of microorganisms themselves were also important factors affecting the relative abundance of metabolism-related genes. In addition, salinity has a certain effect on the relative abundance of genes related to nitrogen and sulfur cycling.
Professors Want to Share: Preliminary Survey Results on Establishing Open Source Endowed Professorships
Authors: Pearce Joshua , Pascaris Alexis S. , Schelly Chelsea 
Published: November 2021

Abstract
This study proposes a novel policy to provide incentives for open science: to offer open source (OS) endowed professorships. To hold an open source endowed chair, in addition to demonstrated excellence in their field, professors would need to agree to: 1) ensuring all of their writing is distributed via open access in some way, and 2) releasing all of their intellectual property in the public domain or under appropriate open source licenses. The results of this survey study of university professors in the U.S. show that a super majority (86.7%) of faculty respondents indicated willingness to accept an OS endowed professorship, while only 13.3% of respondents would not be willing to accept the terms of an OS endowed professorship. The terms of accepting an OS endowed professorship that were the most popular among respondents were increased salary, annual discretionary budget, as a term of tenure and annual RA or TA lines. Although it should be pointed out that more than a quarter of respondents would require no additional compensation. The results demonstrate a clear willingness of academics to expand open access to science, which would hasten scientific progress while also making science more just and inclusive. It is clear that science funders have a large opportunity to move towards open science by offering open source endowed chairs.
Intravitreal Fasudil Monotherapy for Treatment of Refractory Diabetic Macular Edema: a Prospective, Interventional Case-series
Authors: Nourinia Ramin , Abtahi Seyed-Hossein , Nouri Hosein , Eslamipour Jamil , Gerami Ebrahim , Ahmadieh Hamid 
Published: November 2021

Abstract
Purpose: To evaluate the effect of three monthly intravitreal injections of a Rho-associated protein kinase (ROCK) inhibitor (Fasudil, Asahi Kasei Pharma Corporation, Tokyo, Japan) on refractory diabetic macular edema (DME).Study design: Prospective – clinical Methods: This interventional case series included 10 eyes of 10 patients with DME unresponsive to at least six previous intravitreal bevacizumab (IVB) injections. Eligible eyes underwent intravitreal injection of 0.025 mg/0.05 ml Fasudil. Best-corrected visual acuity (BCVA) and central macular thickness (CMT) were evaluated as functional and anatomical response indicators, respectively. Results: Mean age was 60.1±5.1 (range, 53-68) years. Five cases responded to treatment; two with both anatomical and functional response (reduction of CMT from 521 to 395 and from 390 to 301microns and improvement of BCVA from 0.3 to 0.1 LogMAR and 0.6 to 0.4 LogMAR, respectively) and three with only functional improvement (0.7 to 0.4; 0.7 to 0.4; and 0.3 to 0.1 LogMAR). Of note, cases with no significant CMT change had morphologic improvement of retinal microstructure to some extent. No adverse event was observed during the study period.Conclusion: Monotherapy with intravitreal injection of ROCK inhibitors seems to have moderate visual benefits in eyes with DME refractory to IVB. Such effects may be functionally significant without obvious anatomical improvement.