Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontogeny of Carbon Monoxide-Related Gene Expression in a Deep-Diving Marine Mammal

Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. The natural turnover of heme by heme oxygenase enzymes (encoded by HMOX1 and HMOX2) produces endogenous carbon monoxide (CO), which is present at high levels in NES blood and has been shown to have cytoprotective effects in laboratory systems exposed to hypoxia. To understand how pathways associated with endogenous CO production and signaling change across ontogeny in diving mammals, we measured muscle CO and baseline expression of 17 CO-related genes in skeletal muscle and whole blood of three age classes of NES. Muscle CO levels approached those of animals exposed to high exogenous CO, increased with age, and were significantly correlated with gene expression levels. Muscle expression of genes associated with CO production and antioxidant defenses (HMOX1, BVR, GPX3, PRDX1) increased with age and was highest in adult females, while that of genes associated with protection from lipid peroxidation (GPX4, PRDX6, PRDX1, SIRT1) was highest in adult males. In contrast, muscle expression of mitochondrial biogenesis regulators (PGC1A, ESRRA, ESRRG) was highest in pups, while genes associated with inflammation (HMOX2, NRF2, IL1B) did not vary with age or sex. Blood expression of genes involved in regulation of inflammation (IL1B, NRF2, BVR, IL10) was highest in pups, while HMOX1, HMOX2 and pro-inflammatory markers (TLR4, CCL4, PRDX1, TNFA) did not vary with age. We propose that ontogenetic upregulation of baseline HMOX1 expression in skeletal muscle of NES may, in part, underlie increases in CO levels and expression of genes encoding antioxidant enzymes. HMOX2, in turn, may play a role in regulating inflammation related to ischemia and reperfusion in muscle and circulating immune cells. Our data suggest putative ontogenetic mechanisms that may enable phocid pups to transition to a deep-diving lifestyle, including high baseline expression of genes associated with mitochondrial biogenesis and immune system activation during postnatal development and increased expression of genes associated with protection from lipid peroxidation in adulthood.
Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility

High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3. OTU tables were rarefied, and differences in α-diversity and β-diversity were tested for different groups in a dataset. Finally, these results were checked for consistency among these example pipelines. Of articles that deposited data, only 57% made all sequencing and metadata available. When processing the datasets, issues were encountered, caused by read characteristics and differences between tools and their defaults in combination with a lack of detail in the methodology of the articles. In general, the four mainstream pipelines provided similar results, but importantly, P-values sometimes differed between pipelines beyond the significance threshold. Our results indicated that for published articles, the description of bioinformatics methods and data deposition should be improved, and regarding reproducibility, that analysis of multiple subsamples is required when using rarefying as library-size normalization method.
Predicting Physical Activity Behavior by Automatic and Reflective Self-Regulatory Processes

In this study, we examined the interaction of automatic (i.e., automatic affective evaluations) and reflective [i.e., reflective intention and executive functions (EFs)] processes on physical activity (PA) behavior based on dual-process theories. We expected main effects as well as significant interaction effects between automatic associations, intention, and EFs on behavior. In particular, a well-controlled implicit-association-test (IAT) was applied to assess automatic affective evaluation. A prospective study with two points of measurement (N=212 students) was conducted. At t1, age, sex, PA behavior (control variables), automatic associations, EFs (shifting, updating, inhibition), and PA intention (predictors and moderators) were assessed with standardized questionnaires and tests. At t2 (4weeks later), PA behavior (dependent variable) was measured with a standardized questionnaire. A hierarchical multiple linear regression analysis including two- and three-way interactions between IAT results, intention, and EFs on PA behavior was conducted. Results showed that the interactions Intention x Shifting and IAT x Intention x Inhibition were significant. Moderation analyses revealed that participants with higher intentions and lower inhibition values (improved inhibition abilities) showed a negative association between IAT and PA, while those with lower intentions and lower inhibition values showed a positive association between IAT and PA, which was documented in a significant slope difference test between these two groups. Thus, both automatic and reflective processes contribute and interact in predicting PA. As well as fostering more positive affective evaluations towards PA, interventions to strengthen PA intentions and to improve EFs could help to increase PA behavior.
Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Tobacco bacterial wilt (TBW) is a devastating soil-borne disease threatening the yield and quality of tobacco. However, its genetic foundations are not fully understood. In this study, we identified 126,602 high-quality single-nucleotide polymorphisms (SNPs) in 94 tobacco accessions using genotyping-by-sequencing (GBS) and a 94.56 KB linkage disequilibrium (LD) decay rate for candidate gene selection. The population structure analysis revealed two subpopulations with 37 and 57 tobacco accessions. Four multi-locus genome-wide association study (ML-GWAS) approaches identified 142 quantitative trait nucleotides (QTNs) in E1–E4 and the best linear unbiased prediction (BLUP), explaining 0.49–22.52% phenotypic variance. Of these, 38 novel stable QTNs were identified across at least two environments/methods, and their alleles showed significant TBW-DI differences. The number of superior alleles associated with TBW resistance for each accession ranged from 4 to 24; eight accessions had more than 18 superior alleles. Based on TBW-resistant alleles, the five best cross combinations were predicted, including MC133 × Ruyuan No. 1 and CO258 × ROX28. We identified 52 candidate genes around 38 QTNs related to TBW resistance based on homologous functional annotation and KEGG enrichment analysis, e.g., CYCD3;2, BSK1, Nitab4. 5_0000641g0050, Nitab4. 5_0000929g0030. To the best of our knowledge, this is the first comprehensive study to identify QTNs, superior alleles, and their candidate genes for breeding TBW-resistant tobacco varieties. The results provide further insight into the genetic architecture, marker-assisted selection, and functional genomics of TBW resistance, improving future breeding efforts to increase crop productivity.
Tri-Ponderal Mass Index as a Screening Tool for Identifying Body Fat and Cardiovascular Risk Factors in Children and Adolescents: A Systematic Review

Because of the limitation of body mass index (BMI) in distinguishing adipose mass from muscle, the tri-ponderal mass index (TMI) has been proposed as a new indicator for better assessing adiposity in children and adolescents. However, it remains unclear whether TMI performs better than BMI or other adiposity indices in predicting obesity status in childhood and obesity-related cardiovascular risk factors (CVRFs) in childhood or adulthood. We searched PubMed, Cochrane Library, and Web of Science for eligible publications until June 15, 2021. A total of 32 eligible studies were included in this systematic review. We found that TMI had a similar or better ability to predict body fat among children and adolescents than BMI. However, most of the included studies suggested that TMI was similar to BMI in identifying metabolic syndrome although TMI was suggested to be a useful tool when used in combination with other indicators (e.g., BMI and waist circumference). In addition, limited evidence showed that TMI did not perform better than BMI for identifying specific CVRFs, including insulin resistance, high blood pressure, dyslipidemia, and inflammation in children and adolescents, as well as CVRFs in adults. Systematic Review Registration https://www.crd. york.ac. uk/prospero, CRD42021260356.
Crustal Anisotropy Beneath the Trans-North China Orogen and its Adjacent Areas From Receiver Functions

As an important segment of the North China Craton, the Trans-North China Orogen (TNCO) has experienced strong tectonic deformation and magmatic activities since the Cenozoic and is characterized by significant seismicity. To understand the mechanism of the crustal deformation and seismic hazards, we determined the crustal thickness (H), Vp/Vs ratio (κ) and crustal anisotropy (the fast polarization direction φ and splitting time τ) beneath the TNCO and its adjacent areas by analyzing receiver function data recorded by a dense seismic array. The (H, κ) and (φ, τ) at a total of 309 stations were measured, respectively. The Moho depth varies from ∼30 km beneath the western margin of the Bohai bay basin to the maximum value of ∼48 km beneath the northern Lüliang Mountain, which shows the positive and negative correlations with the elevation and the Bouguer anomaly. The average φ is roughly parallel to the strikes of the faults, grabens and Mountains in this study area, whereas a rotating distribution is shown around the Datong-Hannuoba volcanic regions. Based on the φ measured from the Moho Ps and SKS/SKKS phases, we propose that the crustal deformation and seismic hazards beneath the TNCO could be due to the counterclockwise rotation of the Ordos block driven by the far-field effects of the India-Eurasian collision.
Genetic Polymorphisms and Clinical Features in Diabetic Patients With Fatty Liver: Results From a Single-Center Experience in Southern Italy

Genetic background may be involved in the promotion and progression of non-alcoholic fatty liver disease (NAFLD). Previous studies have suggested that the single nucleotide polymorphisms (SNPs) may be associated with the specific clinical features in the patients with hepatic steatosis; however, data on the patients with diabetes from Southern Italy are lacking. We enrolled 454 patients and 260 of them had type 2 diabetes. We studied the PNPLA3 rs738409, LPIN1 rs13412852, KLF6 rs3750861, SOD2 rs4880, TM6SF2 rs58542926, and ZNF624 rs12603226 SNPs and their distribution in the study population. Lipid profile, liver stiffness, and kidney function were also studied to understand the potential role of the SNPs in the development of clinical phenotypes. No differences were observed in the distribution of polymorphisms between the diabetic and non-diabetic subjects. Carriers of risk allele G for PNPLA3 rs738409 SNP showed a lower mean value of serum triglycerides and a higher liver stiffness. Risk allele for KLF6 rs3750861 and SOD2 rs4880 polymorphism had a lower estimated glomerular filtration rate (eGFR) value, whereas no differences in the glucose and glycated hemoglobin level were observed in the subgroups by the different genotypes. Genetic polymorphisms are useful to identify the patients at higher risk of development of liver fibrosis and lower eGFR values in the patients with diabetes and NAFLD. Their use in clinical practice may help the clinicians to identify the patients who require a more strict follow-up program.
Protective Effects of Bacillus amyloliquefaciens 40 Against Clostridium perfringens Infection in Mice

This study aimed to investigate the protective effects of Bacillus amyloliquefaciens (BA40) against Clostridium perfringens (C. perfringens) infection in mice. Bacillus subtilis PB6 was utilized as a positive control to compare the protective effects of BA40. In general, a total of 24 5-week-old male C57BL/6 mice were randomly divided into four groups, with six mice each. The BA40 and PB6 groups were orally dosed with resuspension bacteria (1 × 109 CFU/ml) once a day, from day 1 to 13, respectively. In the control and infected groups, the mice were orally pre-treated with phosphate-buffered saline (PBS) (200 μl/day). The mice in the infected groups, PB6 + infected group and BA40 + infected group, were orally challenged with C. perfringens type A (1 × 109 CFU/ml) on day 11, whereas the control group was orally dosed with PBS (200 μl/day). The results showed that the BA40 group ameliorated intestinal structure damage caused by the C. perfringens infection. Furthermore, the inflammatory responses detected in the infected groups which include the concentrations of IL-1β, TNF-α, IL-6, and immunoglobulin G (IgG) in the serum and secretory immunoglobulin (SigA) in the colon, and nitric oxide (NO) production and inducible nitric oxide synthase (iNOS) activity in the jejunum, were also alleviated (P < 0.05) by BA40 treatment. Similarly, cytokines were also detected by quantitative PCR (qPCR) in the messenger RNA (mRNA) levels, and the results were consistent with the enzyme-linked immunosorbent assay (ELISA) kits. Additionally, in the infected group, the mRNA expression of Bax and p53 was increasing and the Bcl-2 expression was decreasing, which was reversed by BA40 and PB6 treatment (P < 0.05). Moreover, the intestinal microbiota imbalance induced by the C. perfringens infection was restored by the BA40 pre-treatment, especially by improving the relative abundance of Verrucomicrobiota (P < 0.05) and decreasing the relative abundance of Bacteroidetes (P < 0.05) in the phyla level, and the infected group increased the relative abundance of some pathogens, such as Bacteroides and Staphylococcus (P < 0.05) in the genus level. The gut microbiota alterations in the BA40 group also influenced the metabolic pathways, and the results were also compared. The purine metabolism, 2-oxocarboxylic acid metabolism, and starch and sucrose metabolism were significantly changed (P < 0.05). In conclusion, our results demonstrated that BA40 can effectively protect mice from C. perfringens infection.
How Do Russians Perceive and Justify the Status Quo: Insights From Adapting the System Justification Scales

This paper aims to adapt the system justification scales (general, political, economic, and gender) for the Russian socio-cultural context and to carry out their psychometric analysis. In Study 1 (N = 450), the original items from four system justification scales on a Russian sample were tested. The results suggested that none of the original scales worked properly in Russia and all of them demonstrated weak fit indices. In Study 2 (N = 553), culturally specific grounds for system justification in the Russian context were highlighted and tested. The results of this study confirmed that all the adapted scales demonstrated a good fit to the data. In Study 3 (N = 1,011), the invariance of system justification scales and the convergent and discriminant validity of the scales was tested. The results confirmed that the general, political, and economic system justification scales demonstrated full invariance, while the gender system justification scale showed partial invariance for multigroup comparison. All the scales convergent and discriminant validity, which leads to consider them as an effective tool for measuring system justification in various types of social relationships in Russia. The role of socio-cultural characteristics in justifying the status quo is discussed.
Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins

GATA transcription factors (TFs) are type IV zinc-finger proteins that have roles in plant development and growth. The 27 GATA TFs identified in the Brachypodium distachyon genome in this study were unevenly distributed across all five chromosomes and classified into four subgroups. Phylogenesis-related GATAs shared similar gene structures and conserved motifs. Expression profiles showed that all BdGATA genes were expressed in leaves and most were induced by PEG treatment. BdGATA13 was predominantly expressed in leaf tissue and phylogenetically close to OsSNFL1, AtGNC, and AtGNL. Its protein was detected in the nucleus by subcellular localization analysis. Overexpression of BdGATA13 in transgenic Arabidopsis resulted in darker green leaves, later flowering, and more importantly, enhanced drought tolerance compared to the wild type. BdGATA13 also promoted primary root development under GA treatment. These results lay a foundation for better understanding the function of GATA genes in B. distachyon and other plants.
Risk of Pneumonitis Associated With Immune Checkpoint Inhibitors in Melanoma: A Systematic Review and Network Meta-Analysis

Background Immune checkpoint inhibitors (ICIs) have dramatically altered the treatment landscape for patients with melanoma. However, their use also generates unique immune-related adverse effects (irAEs). We performed a systematic review and network meta‐analysis to compare the risk of pneumonitis associated with ICIs for patients with advanced or metastatic melanoma. Methods Phase II/III randomized clinical trials (RCTs) with ICIs were identified through comprehensive searches of multiple databases. An NMA was conducted to compare the risk of pneumonitis associated with ICIs and all‐grade (grade 1‐5) and high‐grade (grade 3‐5) immune‐related pneumonitis (IRP) were estimated by odds ratios (ORs). Results A total of 10 randomized clinical trials involving 5,335 patients were enrolled in this study. Conventional chemotherapy was associated with a lower risk of grade 1–5 IRP compared with ICIs monotherapy (OR, 0.14, 95% CI, 0.03 to 0.73) and dual ICIs combination (OR, 0.03, 95% CI, 0.00 to 0.19). In addition, dual ICIs combination showed a noticeably higher risk than ICI monotherapy (OR, 4.45, 95% CI, 2.14 to 9.25) of grade 1–5 IRP. No significant difference in grade 1–5 IRP was observed between cytotoxic T lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1) inhibitors. As to grade 3‐5 IRP, no statistically significant difference was found among different ICIs-based regimens. Conclusion These findings revealed that ICIs could increase the risk of all-grade pneumonitis for patients with advanced melanoma, compared with conventional chemotherapy. Dual ICIs combination could further increase the risk of all-grade pneumonitis than ICIs monotherapy. There was no significant difference in the risk of pneumonia between CTLA-4 and PD-1 inhibitors.
Working Memory and Cross-Frequency Coupling of Neuronal Oscillations

Working memory (WM) is the active retention and processing of information over a few seconds and is considered an essential component of cognitive function. The reduced WM capacity is a common feature in many diseases, such as schizophrenia, attention deficit hyperactivity disorder (ADHD), mild cognitive impairment (MCI), and Alzheimer's disease (AD). The theta-gamma neural code is an essential component of memory representations in the multi-item WM. A large body of studies have examined the association between cross-frequency coupling (CFC) across the cerebral cortices and WM performance; electrophysiological data together with the behavioral results showed the associations between CFC and WM performance. The oscillatory entrainment (sensory, non-invasive electrical/magnetic, and invasive electrical) remains the key method to investigate the causal relationship between CFC and WM. The frequency-tuned non-invasive brain stimulation is a promising way to improve WM performance in healthy and non-healthy patients with cognitive impairment. The WM performance is sensitive to the phase and rhythm of externally applied stimulations. CFC-transcranial-alternating current stimulation (CFC-tACS) is a recent approach in neuroscience that could alter cognitive outcomes. The studies that investigated (1) the association between CFC and WM and (2) the brain stimulation protocols that enhanced WM through modulating CFC by the means of the non-invasive brain stimulation techniques have been included in this review. In principle, this review can guide the researchers to identify the most prominent form of CFC associated with WM processing (e.g., theta/gamma phase-amplitude coupling), and to define the previously published studies that manipulate endogenous CFC externally to improve WM. This in turn will pave the path for future studies aimed at investigating the CFC-tACS effect on WM. The CFC-tACS protocols need to be thoroughly studied before they can be considered as therapeutic tools in patients with WM deficits.
Total Ecosystem Carbon Stocks of Mangroves in Lamu, Kenya; and Their Potential Contributions to the Climate Change Agenda in the Country

Mangroves are carbon-rich ecosystems found in tropical and subtropical areas around the world. However, they are threatened by a combination of natural and human-induced factors. When mangroves are lost or degraded, their co-benefits to human society are greatly diminished along with the ecosystem’s ability to sequester carbon. The current study assessed mangrove cover and cover change, as well as measuring carbon stocks and their emissions levels from the mangroves of Lamu County, Kenya. We sampled above-and below-ground carbon pools, including soil organic carbon (SOC), in 191 plots distributed throughout the study area. Lastly, we evaluated the economics of avoiding mangrove deforestation based on the carbon-offset market. The total carbon stock of mangroves in Lamu was estimated at 20 million Mg C, with an average density of 560.22 ± 79.79 Mg C ha–1. Southern swamps recorded significantly higher carbon densities (p < 0.05) than other mangrove management blocks in Lamu. At least 1,739 ha of mangroves in Lamu were lost between 1990 and 2019 due to anthropogenic activities, representing a decline of 60 ha yr–1. Total emissions from loss and degradation of mangroves in Lamu is estimated at 140.1 Mg C ha–1; which translates to 30,840.1 Mg CO2e yr–1. Assuming an offset price of US$10/Mg CO2e, the estimated costs of avoided emissions in Lamu is US$308,401 yr–1 plus other co-benefits such as fishery functions and shoreline protection. Mainstreaming mangroves and associated blue carbon ecosystems into national development and climate change agenda could accelerate Kenya’s achievements of both Sustainable Development Goals (SDGs) and the Paris Agreement.