bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection
Authors: Bai Yulin , Wang Mei , Zhao Ji , Bai Huaqiang , Zhang Xinyi , Wang Jiaying , Ke Qiaozhen , Qu Ang , Pu Fei , Zheng Weiqiang , Zhou Tao , Xu Peng 
Published: March 2022

Abstract
Background
Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea. Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker.

Results
In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of C. irritans, in this study, by comparing transcriptome data from different tissues of L. crocea, we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of L. crocea gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein–protein interaction (PPI) network analysis identified 3 hub genes including NFKBIA, TNFAIP3 and CEBPB, and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method.

Conclusions
In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of L. crocea post C. irritans and the molecular mechanism of pathogenesis for cryptocaryonosis.

Highlights

Skin and gills are important sources of pro-inflammatory molecules,
and their gene expression patterns are tissue-specific after C. irritans infection.

15 DEGs and 5 DE
lncRNAs were identified as hub regulatory elements after C. irritans infection

The HIF-1 signaling
pathway and the complement and coagulation cascade pathway may be key
tissue-specific regulatory pathways in gills and skin, respectively.
Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis
Authors: Liu Jian , Lindstrom Anders J. , Gong Xun 
Published: March 2022

Abstract
Background
Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections.

Results
All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny.

Conclusions
Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.
Molecular cytogenetics and development of St-chromosome-specific molecular markers of novel stripe rust resistant wheat–Thinopyrum intermedium and wheat–Thinopyrum ponticum substitution lines
Authors: Wang Siwen , Wang Changyou , Feng Xianbo , Zhao Jixin , Deng Pingchuan , Wang Yajuan , Zhang Hong , Liu Xinlun , Li Tingdong , Chen Chunhuan , Wang Baotong , Ji Wanquan 
Published: March 2022

Abstract
Background
Owing to their excellent resistance to abiotic and biotic stress, Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt) and Th. ponticum (2n = 10x = 70) are both widely utilized in wheat germplasm innovation programs. Disomic substitution lines (DSLs) carrying one pair of alien chromosomes are valuable bridge materials for transmission of novel genes, fluorescence in situ hybridization (FISH) karyotype construction and specific molecular marker development.

Results
Six wheat–Thinopyrum DSLs derived from crosses between Abbondanza nullisomic lines (2n = 40) and two octoploid Trititrigia lines (2n = 8x = 56), were characterized by sequential FISH–genome in situ hybridization (GISH), multicolor GISH (mc-GISH), and an analysis of the wheat 15 K SNP array combined with molecular marker selection. ES-9 (DS2St (2A)) and ES-10 (DS3St (3D)) are wheat–Th. ponticum DSLs, while ES-23 (DS2St (2A)), ES-24 (DS3St (3D)), ES-25(DS2St (2B)), and ES-26 (DS2St (2D)) are wheat–Th. intermedium DSLs. ES-9, ES-23, ES-25 and ES-26 conferred high thousand-kernel weight and stripe rust resistance at adult stages, while ES-10 and ES-24 were highly resistant to stripe rust at all stages. Furthermore, cytological analysis showed that the alien chromosomes belonging to the same homoeologous group (2 or 3) derived from different donors carried the same FISH karyotype and could form a bivalent. Based on specific-locus amplified fragment sequencing (SLAF-seq), two 2St-chromosome-specific markers (PTH-005 and PTH-013) and two 3St-chromosome-specific markers (PTH-113 and PTH-135) were developed.

Conclusions
The six wheat–Thinopyrum DSLs conferring stripe rust resistance can be used as bridging parents for transmission of valuable resistance genes. The utility of PTH-113 and PTH-135 in a BC1F2 population showed that the newly developed markers could be useful tools for efficient identification of St chromosomes in a common wheat background.
Trauma triage criteria as predictors of severe injury - a Swedish multicenter cohort study
Authors: Holmberg Lina , Mani Kevin , Thorbjørnsen Knut , Wanhainen Anders , Andréasson Håkan , Juhlin Claes , Linder Fredrik 
Published: March 2022

Abstract
Background
Adequate performance of trauma team activation (TTA) criteria is important in order to accurately triage trauma patients. The Swedish National Trauma Triage Criteria (SNTTC) consists of 29 criteria that trigger either a Trauma Alert, the highest level of TTA, or a Trauma Response. This study aimed to evaluate the SNTTC and its accuracy in predicting a severely injured patient in a multicenter setting.

Methods
A cohort study in Sweden involving six trauma receiving hospitals. Data was collected from the Swedish Trauma Registry. Some 626 patients were analyzed with regard to the specific criteria used to initiate the TTA, injury severity with New Injury Severity Score (NISS) and emergency interventions. Sensitivity, specificity, positive predictive value (PPV) and positive likelihood ratio (LR+) of the criteria were calculated, as well as undertriage and overtriage.

Results
All 29 criteria of SNTTC had a sensitivity > 80% for identifying a severely injured patient. The 16 Trauma Alert Criteria had a lower sensitivity of 62.6% but higher LR+ (3.5 vs all criteria 1.4), specificity (82.3 vs 39.1%) and PPV (55.4 vs 37.6%) and the highest accuracy (AUC 0.724). When using only the six physiological criteria, sensitivity (44.8%) and accuracy (AUC 0.690) decreased while LR+ (6.7), specificity (93.3%) and PPV (70.2%) improved.

Conclusion
SNTTC is efficient in identifying severely injured patients. The current set of criteria exhibits the best sensitivity compared to other examined combinations and no additional criterion was found to improve the protocol enough to promote a change.
Tools for early screening of autism spectrum disorders in primary health care – a scoping review
Authors: Sobieski Mateusz , Sobieska Aleksandra , Sekułowicz Małgorzata , Bujnowska-Fedak Maria Magdalena 
Published: March 2022

Abstract
Background
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that manifests itself in early childhood. Early diagnosis of these disorders allows for the initiation of early therapy, which is crucial for the child's further functioning in society.

Objectives
This review aims to gather and present the existing ASD screening tools that can be used in primary care and adapted to different countries conditions linguistically and culturally.

Eligibility criteria
We searched for English-language publications on ASD screening tools for children aged 0–3 years suitable for use in primary care (i.e. free, requiring no additional training or qualifications).

Sources of evidence
Four databases were explored to find English studies on ASD screening tools intended for the rapid assessment of children aged 0–3.

Charting methods
The information sought (specific features of the questionnaires relevant to primary health care workers, psychometric and diagnostic values of a given cultural adaptation of screening tools, and the linguistic and cultural changes made) were extracted and collected to create profiles of these tools.

Results
We found 81 studies which met inclusion criteria and underwent full data extraction. Three additional data sources were included. These allowed to create 75 profiles of adaptations for 26 different screening tools and collect data on their psychometric values and characteristic features.

Conclusions
The results of our study indicate the availability of several diagnostic tools for early ASD screening in primary care setting concordant culturally and linguistically with a given population. They could be an effective method of accelerating the diagnostic process and starting personalized therapy faster. However, most tools have significant limitations – some are only available for research purposes, while others do not have scientific evidence to prove their effectiveness.
Time-to-positivity of Mycobacterium avium complex in broth culture associates with culture conversion
Authors: Mingora Christina M. , Garcia Bryan A. , Mange Kevin C. , Yuen Dayton W. , Ciesielska Monika , van Ingen Jakko , Flume Patrick A. , Dorman Susan E. 
Published: March 2022

Abstract
Background
Mycobacterial time to positivity (TTP) in liquid culture media has predictive value for longer term outcomes in pulmonary tuberculosis, but has not been thoroughly studied in nontuberculous mycobacterial pulmonary disease. This study sought to evaluate for association between TTP and sputum culture conversion to negative in pulmonary disease caused by Mycobacterium avium complex (MAC).

Methods
Data from the CONVERT trial (NCT02344004) that evaluated efficacy of guideline-based-therapy with or without amikacin liposome inhalation suspension in adults with refractory MAC-PD (Mycobacterium avium complex pulmonary disease) were analyzed. We evaluated TTP measures for sputum obtained prior to study treatment initiation and at monthly visits, assessing reproducibility of measures as well as association of TTP with culture conversion on treatment.

Results
Data from 71 participants with at least one screening visit TTP value were analyzed. For participants who provided more than one sputum sample at a given visit, there was moderate between-sample reliability, with median intraclass correlation coefficient 0.62 (IQR 0.50, 0.70). Median TTP at screening was longer in those participants who subsequently achieved vs. did not achieve culture conversion (10.5 [IQR 9.4] days vs. 4.2 [IQR 2.8] days, p = 0.0002). Individuals with culture conversion by study treatment month 6 were more likely to have a screening TTP > 5 days compared to those who did not achieve culture conversion (OR 15.4, 95% CI 1.9, 716.7, p = 0.0037) and had increasing TTPs over time.

Conclusions
TTP prior to and on treatment is associated with microbiological treatment response in patients with MAC-PD.
Clinical course of neonatal acute kidney injury: multi-center prospective cohort study
Authors: Pantoja-Gómez O. C. , Realpe S. , Cabra-Bautista Ginna , Restrepo J. M. , Prado O. L. , Velasco A. M. , Martínez G. E. , Leal S. , Vallejo A. , Calvache Jose Andrés 
Published: March 2022

AbstractBackgroundNeonatal acute kidney injury (AKI) has been associated with unfavorable outcomes, including increased mortality. We aimed to describe the clinical course and outcomes during the first 7 days after diagnosis in newborns with AKI in three neonatal intensive care units in Popayán-Colombia.MethodsMulti-center prospective cohort study conducted between June 2019 and December 2020 in three NICUs after ethical approval. We included newborns between 2 and 28 days of life, first diagnosed with AKI using the KDIGO classification modified for newborns which consider increased serum creatinine values over baseline values as well as urine output over time in hours or both. Patients with chromosomal abnormalities, major kidney malformations, and complex congenital heart disease were excluded. Patients were followed for up to 7 days after diagnosis and the maximum KDIGO stage, recovery of kidney function, need for renal replacement therapy and cumulative incidence of death were evaluated.ResultsOver the 18 months of the study, 4132 newborns were admitted to the NICUs, and 93 patients (2.25, 95% CI 1.82–2.75%) developed neonatal AKI. 59.1% of the newborns were premature and there were no differences in severity according to gestational age. During follow-up, the maximum KDIGO was 64.5% for AKI-stage 1, 11.8% for AKI-stage 2, and 23.7% for AKI-stage 3. Kidney function recovery was higher in AKI-stage 1 patients vs. AKI-severe (AKI-stage 2 and 3) (95% vs. 48.5%). Five patients (5.4%) received renal replacement therapy and 15 died (16.1%), four in AKI-stage 1 vs. 11 in AKI-severe (6.7% vs 33.3%).ConclusionsNewborns admitted to the NICUs can develop AKI regardless of gestational age, and it is more frequent between the second and ninth days of life. More patients whit AKI-stage 1 recover and die less than those in a severe stage.
The prevalence of barriers to rearing children aged 0–3 years following China’s new three-child policy: a national cross-sectional study
Authors: Kang Liangyu , Jing Wenzhan , Liu Jue , Ma Qiuyue , Zhang Shikun , Liu Min 
Published: March 2022

Abstract
Background
To further optimize birth policy, China implemented a new three-child policy to allow per couple to have up to three children on May 31, 2021.

Methods
A national cross-sectional survey was conducted among 18 to 49-year-old Chinese parents who had at least one child in June 2021. We calculated the prevalence of self-reported childrearing barriers and used univariate logistic regression and multivariate logistic regression to analyze associated factors.

Results
94.7% of the respondents self-reported barriers to rearing children aged 0–3 years, and the biggest barrier included high time cost (39.3%), high parenting cost (36.5%) and high education cost (13.5%). Women (aOR 1.49, 95%CI 1.13,1.96) and people with college degree or above (aOR 3.46, 95%CI 2.08, 5.75) were associated with higher prevalence of childrearing barriers, and people who intended to have a second child (aOR 0.58, 95%CI 0.40, 0.83) and people who intended to have a third child (aOR 0.51,95%CI 0.37, 0.71) were less likely to report childrearing barriers. The biggest barrier was more likely to be high time cost for parents one of whom is only child (aOR1.21, 95%CI 1.03, 1.42) and physical factors for parents both of whom are only child (aOR 1.56,95%CI 1.08, 2.26).

Conclusions
The prevalence of barriers to rearing children aged 0–3 years was high among Chinese people of childbearing age who had children. Full consideration should be given to the barriers of people with different sociodemographic characteristics and people with fertility intention, thus making targeted childrearing policies and supporting measures to reduce the burden on people of childbearing age, encourage suitable couples to have a second or third child and then cope with China’s aging population.
Diffuse large B-cell lymphoma presenting as reversible intrapulmonary arteriovenous shunts with hypoxia, fever and progressive jaundice: a case report and literature review
Authors: Hou Huan , Guo Cuiyan , Que Chengli , Nie Ligong , Zhang Qi , Zhao Hong , Nong Lin , Ma Wei , Wang Qian , Liang Zeyin , Wang Bingjie , Ma Jing , Wang Guangfa 
Published: March 2022

Abstract
Background
Intrapulmonary arteriovenous shunts is rare seen in a patient without lung involvement.

Case presentation
This is the first report of reversible intrapulmonary arteriovenous shunts secondary to extrapulmonary lymphoma as one initial symptom. The patient presented as fever of unknown origin and dyspnea, and examinations of infection were negative. Diagnosis of DLBCL was finally confirmed through bone marrow and splenic biopsies. Intrapulmonary arteriovenous shunts were diagnosed through 100% oxygen inhalation test and transthoracic contrast echocardiography (TTCE). After the treatment of lymphoma, his respiratory failure was relieved. We rechecked the 100% oxygen inhalation test and TTCE, which both indicated that his intrapulmonary arteriovenous shunts had resolved.

Conclusions
We speculated the prominent inflammation from active DLBCL was the most possible mechanism associated with the reversible intrapulmonary shunt in this patient. These findings will assist us to better understand the mechanism of intrapulmonary shunts.
The efficiency of natural wound healing and bacterial biofilm inhibition of Aloe vera and Sodium Chloride toothpaste preparation
Authors: Vajrabhaya La-ongthong , Korsuwannawong Suwanna , Ruangsawasdi Nisarat , Phruksaniyom Chareerut , Srichan Ratchaporn 
Published: March 2022

Abstract
Background
Prevention is a preliminary focus of periodontitis treatment. Rather than giving complicated treatment to a periodontitis patient, a variety of toothpastes have been suggested to prevent periodontal disease progression. Herbal toothpastes containing natural plant components for maintaining or increasing healing might be a treatment modality for improving oral hygiene. Aloe vera is a medicinal plant with active ingredients that have antioxidant and anti-inflammatory effects. Additionally, increased sodium in the environment inhibits microorganism growth. A toothpaste containing salt and aloe vera may be an option to provide good oral hygiene.

Aim
To assess the in vitro cell migration of human gingival fibroblasts and antimicrobial effects of an herbal toothpaste containing A. vera and Sodium chloride.

Methods
The cytotoxicity of 0.02% or 0.2% toothpaste solution on human gingival fibroblast cell line was evaluated using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. The cell migration after treatment with 0.2% (v/v) toothpaste was determined using a Boyden Chamber assay. The effect of the toothpaste on inhibiting Porphylomonas gingivalis planktonic and biofilm growth was compared with Chlohexidine (CHX) using a Disk Diffusion and Biofilm susceptibility test, respectively. The results of the cytotoxicity assay, inhibition zone and percentage of live cells in the biofilm were statistically analyzed with One-way analysis of variance. Cell migration and biofilm inhibition were evaluated using the independent sample t-test and multiple t-test, respectively (p = 0.05).

Results
Neither test concentration of the toothpaste solution was toxic to the target cells. The 0.2% concentration was selected for the cell migration experiment. The herbal toothpaste formulation significantly increased cell migration compared with the control group (culture medium) (p = .02) The antimicrobial effect of this formulation on the P. gingivalis planktonic form was lower compared with 0.12% CHX (positive control group), however, it demonstrated greater P. gingivalis biofilm formation inhibition compared with the 0.12% CHX group.

Conclusions
The alternative use of an herbal toothpaste instead of a non-herbal toothpaste formulation should be considered for promoting oral health care. However, further clinical studies are necessary before it can be considered for patient use.
The effect of implementing mind maps for online learning and assessment on students during COVID-19 pandemic: a cross sectional study
Authors: Alsuraihi Amany A. 
Published: March 2022

AbstractBackgroundIn Saudi Arabia, the sudden shift from conventional (in-person) to online education due to the coronavirus disease 2019 (COVID-19) pandemic affected teaching and assessment methods. This research aimed to assess the effectiveness of mind maps in this regard, measure students’ reactions to certain educational environment-related changes caused by the pandemic, and identify skills that students perceived they gained through mind mapping.MethodsThis study employed a non-intervention (cross sectional) design. Participants were King Abdulaziz University students from two medical physics courses (second and fourth level). Data were collected twice (after the first and last mind mapping assignments), and responses were analyzed using a paired t-test. Overall student results were compared against overall student performance in the previous term using chi-squares test hypothesis testing. The data were collected and analyzed using SPSS software.ResultsThe results of the paired t-test showed no significant differences between students’ mean satisfaction in both surveys. Nevertheless, students’ responses revealed their satisfaction with using mind maps. Moreover, students believed that they gained skills like organizing and planning, decision making, and critical thinking from the mind map assignments. The chi-squares test (Chi-square = 4.29 <$${x}_{\mathrm{0.05,4}}^{2}$$x0.05,42 = 9.48 andp-value = 0.36 > 0.05) showed no differences in students’ grade distribution between the two terms of 2020 (pre- and post-COVID-19 pandemic) despite the change in assessment style post-pandemic commencement.ConclusionsMind mapping can be adapted as an online teaching and assessment method. Additionally, student support and education institution-level effective communication can reduce stress during challenging times.