bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single nucleotide variants in microRNA biosynthesis genes in Mexican individuals
Authors: Juárez-Luis Jesús , Canseco-Ocaña Moisés , Cid-Soto Miguel Angel , Castro-Martínez Xochitl H. , Martínez-Hernández Angélica , Orozco Lorena , Hernández-Zavala Araceli , Córdova Emilio J. 
Published: March 2023

Background: MicroRNAs (miRNAs) are important regulators in a variety of biological processes, and their dysregulation is associated with multiple human diseases. Single nucleotide variants (SNVs) in genes involved in the processing of microRNAs may alter miRNA regulation and could present high allele heterogeneity in populations from different ethnic groups. Thus, the aim of this study was to genotype 15 SNVs in eight genes involved in the miRNA processing pathway in Mexican individuals and compare their frequencies across 21 populations from five continental groups.Methods: Genomic DNA was obtained from 399 healthy Mexican individuals. SNVs in AGO2 (rs2293939 and rs4961280), DGCR8 (rs720012), DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), GEMIN3 (rs197388 and rs197414), GEMIN4 (rs7813, rs2740349, and rs4968104), TNRC6B (rs9611280), and XP05 (rs11077 and rs34324334) were genotyped using TaqMan probes. The minor allele frequency of each SNV was compared to those reported in the 1,000 Genomes database using chi-squared. Sankey plot was created in the SankeyMATIC package to visualize the frequency range of each variant in the different countries analyzed.Results: In Mexican individuals, all 15 SNVs were found in Hardy-Weinberg equilibrium, with frequencies ranging from 0.04 to 0.45. The SNVs rs4961280, rs2740349, rs34324334, and rs720012 in Mexican individuals had the highest minor allele frequencies worldwide, whereas the minor allele frequencies of rs197388, rs10719, rs197414, and rs1107 were among the lowest in Mexican individuals. The variants had high allele heterogeneity among the sub-continental populations, ranging from monomorphic, as was the case for rs9611280 and rs34324334 in African groups, to &gt;0.50, which was the case for variants rs11077 and rs10719 in most of the populations. Importantly, the variants rs197388, rs720012, and rs197414 had FST values &gt; 0.18, indicating a directional selective process. Finally, the SNVs rs13078 and rs10719 significantly correlated with both latitude and longitude.Conclusion: These data indicate the presence of high allelic heterogeneity in the worldwide distribution of the frequency of SNVs located in components of the miRNA processing pathway, which could modify the genetic susceptibility associated with human diseases in populations with different ancestry.
Key genes associated with non-alcoholic fatty liver disease and hepatocellular carcinoma with metabolic risk factors
Authors: Yang Fan , Ni Beibei , Lian Qinghai , Qiu Xiusheng , He Yizhan , Zhang Qi , Zou Xiaoguang , He Fangping , Chen Wenjie 
Published: March 2023

Background: Hepatocellular carcinoma (HCC) has become the world’s primary cause of cancer death. Obesity, hyperglycemia, and dyslipidemia are all illnesses that are part of the metabolic syndrome. In recent years, this risk factor has become increasingly recognized as a contributing factor to HCC. Around the world, non-alcoholic fatty liver disease (NAFLD) is on the rise, especially in western countries. In the past, the exact pathogenesis of NAFLD that progressed to metabolic risk factors (MFRs)-associated HCC has not been fully understood.Methods: Two groups of the GEO dataset (including normal/NAFLD and HCC with MFRs) were used to analyze differential expression. Differentially expressed genes of HCC were verified by overlapping in TCGA. In addition, functional enrichment analysis, modular analysis, Receiver Operating Characteristic (ROC) analysis, LASSO analysis, and Genes with key survival characteristics were analyzed.Results: We identified six hub genes (FABP5, SCD, CCL20, AGPAT9(GPAT3), PLIN1, and IL1RN) that may be closely related to NAFLD and HCC with MFRs. We constructed survival and prognosis gene markers based on FABP5, CCL20, AGPAT9(GPAT3), PLIN1, and IL1RN.This gene signature has shown good diagnostic accuracy in both NAFLD and HCC and in predicting HCC overall survival rates.Conclusion: As a result of the findings of this study, there is some guiding significance for the diagnosis and treatment of liver disease associated with NAFLD progression.
Comparison of mifepristone plus misoprostol with misoprostol alone for first trimester medical abortion: A systematic review and meta-analysis
Authors: Shimels Tariku , Getnet Melsew , Shafie Mensur , Belay Lemi 
Published: March 2023

ObjectiveTo compare mifepristone plus a misoprostol-combined regimen with misoprostol alone in the medical abortion of first trimester pregnancy.MethodsAn internet-based search of available literature was performed using text words contained in titles and abstracts. PubMed/Medline, Cochrane CENTRAL, EMBASE, and Google scholar were used to locate English-based articles published until December 2021. Studies fulfilling the inclusion criteria were selected, appraised, and assessed for methodological quality. The included studies were pooled for meta-analysis, and the results were presented in risk ratio at a 95% confidence interval.FindingsNine studies comprising 2,052 participants (1,035 intervention and 1,017 controls) were considered. Primary endpoints were complete expulsion, incomplete expulsion, missed abortion, and ongoing pregnancy. The intervention was found to more likely induce complete expulsion irrespective of gestational age (RR: 1.19; 95% CI: 1.14–1.25). The administration of misoprostol 800 mcg after 24 h of mifepristone pre-treatment in the intervention group more likely induced complete expulsion (RR: 1.23; 95% CI: 1.17–1.30) than after 48 h. The intervention group was also more likely to experience complete expulsion when misoprostol was used either vaginally (RR: 1.16; 95% CI: 1.09–1.17) or buccally (RR: 1.23; 95% CI: 1.16–1.30). The intervention was more effective in the subgroup with a negative foetal heartbeat at reducing incomplete abortion (RR: 0.45; 95% CI: 0.26–0.78) compared with the control group. The intervention more likely reduced both missed abortion (RR: 0.21; 95% CI: 0.08–0.91) and ongoing pregnancy (RR: 0.12; 95% CI: 0.05–0.26). Fever was less likely to be reported (RR: 0.78; 95% CI: 0.12–0.89), whereas the subjective experience of bleeding was more likely to be encountered (RR: 1.31; 95% CI: 1.13–1.53) by the intervention group.ConclusionThe review strengthened the theory that a combined mifepristone and misoprostol regimen can be an effective medical management for inducing abortions during first trimester pregnancy in all contexts. Specifically, there is a high-level certainty of evidence on complete expulsion during the early stage and its ability to reduce both missed and ongoing pregnancies.Systematic Review Registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42019134213, identifier CRD42019134213.
Immunogenicity against wild-type and Omicron SARS-CoV-2 after a third dose of inactivated COVID-19 vaccine in healthy adolescents
Authors: Leung Daniel , Cohen Carolyn A. , Mu Xiaofeng , Rosa Duque Jaime S. , Cheng Samuel M. S. , Wang Xiwei , Wang Manni , Zhang Wenyue , Zhang Yanmei , Tam Issan Y. S. , Lam Jennifer H. Y. , Chan Sau Man , Chaothai Sara , Kwan Kelvin K. H. , Chan Karl C. K. , Li John K. C. , Luk Leo L. H. , Tsang Leo C. H. , Chu Nym Coco , Wong Wilfred H. S. , Mori Masashi , Leung Wing Hang , Valkenburg Sophie , Peiris Malik , Tu Wenwei , Lau Yu Lung 
Published: March 2023

IntroductionTwo doses of inactivated SARS-CoV-2 vaccine CoronaVac cannot elicit high efficacy against symptomatic COVID-19, especially against the Omicron variant, but that can be improved by a third dose in adults. The use of a third dose of CoronaVac in adolescents may be supported by immunobridging studies in the absence of efficacy data.MethodsWith an immunobridging design, our study (NCT04800133) tested the non-inferiority of the binding and neutralizing antibodies and T cell responses induced by a third dose of CoronaVac in healthy adolescents (N=94, median age 14.2 years, 56% male) compared to adults (N=153, median age 48.1 years, 44% male). Responses against wild-type (WT) and BA.1 SARS-CoV-2 were compared in adolescents. Safety and reactogenicity were also monitored.ResultsA homologous third dose of CoronaVac further enhanced antibody response in adolescents compared to just 2 doses. Adolescents mounted non-inferior antibody and T cell responses compared to adults. Although S IgG and neutralizing antibody responses to BA.1 were lower than to WT, they remained detectable in 96% and 86% of adolescents. T cell responses to peptide pools spanning only the mutations of BA.1 S, N and M in adolescents were preserved, increased, and halved compared to WT respectively. No safety concerns were identified.DiscussionThe primary vaccination series of inactivated SARS-CoV-2 vaccines for adolescents should include 3 doses for improved humoral immunogenicity.
Quantitative and causal analysis for inflammatory genes and the risk of Parkinson’s disease
Authors: Yi Minhan , Li Jiaxin , Jian Shijie , Li Binbin , Huang Zini , Shu Li , Zhang Yuan 
Published: March 2023

BackgroundThe dysfunction of immune system and inflammation contribute to the Parkinson’s disease (PD) pathogenesis. Cytokines, oxidative stress, neurotoxin and metabolism associated enzymes participate in neuroinflammation in PD and the genes involved in them have been reported to be associated with the risk of PD. In our study, we performed a quantitative and causal analysis of the relationship between inflammatory genes and PD risk.MethodsStandard process was performed for quantitative analysis. Allele model (AM) was used as primary outcome analysis and dominant model (DM) and recessive model (RM) were applied to do the secondary analysis. Then, for those genes significantly associated with the risk of PD, we used the published GWAS summary statistics for Mendelian Randomization (MR) to test the causal analysis between them.ResultsWe included 36 variants in 18 genes for final pooled analysis. As a result, IL-6 rs1800795, TNF-α rs1799964, PON1 rs854560, CYP2D6 rs3892097, HLA-DRB rs660895, BST1 rs11931532, CCDC62 rs12817488 polymorphisms were associated with the risk of PD statistically with the ORs ranged from 0.66 to 3.19 while variants in IL-1α, IL-1β, IL-10, MnSOD, NFE2L2, CYP2E1, NOS1, NAT2, ABCB1, HFE and MTHFR were not related to the risk of PD. Besides, we observed that increasing ADP-ribosyl cyclase (coded by BST1) had causal effect on higher PD risk (OR[95%CI] =1.16[1.10-1.22]) while PON1(coded by PON1) shown probably protective effect on PD risk (OR[95%CI] =0.81[0.66-0.99]).ConclusionSeveral polymorphisms from inflammatory genes of IL-6, TNF-α, PON1, CYP2D6, HLA-DRB, BST1, CCDC62 were statistically associated with the susceptibility of PD, and with evidence of causal relationships for ADP-ribosyl cyclase and PON1 on PD risk, which may help understand the mechanisms and pathways underlying PD pathogenesis.
Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: Gene expression of bees performing grooming behavior
Authors: Morfin Nuria , Harpur Brock A. , De la Mora Alvaro , Guzman-Novoa Ernesto 
Published: March 2023

IntroductionSocial organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restrain the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry.MethodsA bidirectional breeding program to select honey bee colonies with low and high V. destructor population growth (LVG and HVG, respectively) was conducted. Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: ‘light groomers’ and ‘intense groomers’. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified.ResultsFour odorant-binding proteins and a gustatory receptor were identified as differentially expressed genes. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the LVG line showed lower levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1/DWV-B), and Deformed wing virus-A (DWV-A) compared to bees of the HVG line. The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways.DiscussionThese results provide new insights on the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic assisted selection to improve breeding programs.
Effects of the visual environment on object localization in posterior cortical atrophy and typical Alzheimer's disease
Authors: Ocal Dilek , McCarthy Ian D. , Poole Teresa , Primativo Silvia , Suzuki Tatsuto , Tyler Nick , Frost Chris , Crutch Sebastian J. , Yong Keir X. X. 
Published: March 2023

IntroductionVisual processing deficits in Alzheimer's disease are associated with diminished functional independence. While environmental adaptations have been proposed to promote independence, recent guidance gives limited consideration to such deficits and offers conflicting recommendations for people with dementia. We evaluated the effects of clutter and color contrasts on performances of everyday actions in posterior cortical atrophy and memory-led typical Alzheimer's disease.Methods15 patients with posterior cortical atrophy, 11 with typical Alzheimer's disease and 16 healthy controls were asked to pick up a visible target object as part of two pilot repeated-measures investigations from a standing or seated position. Participants picked up the target within a controlled real-world setting under varying environmental conditions: with/without clutter, with/without color contrast cue and far/near target position. Task completion time was recorded using a target-mounted inertial measurement unit.ResultsAcross both experiments, difficulties locating a target object were apparent through patient groups taking an estimated 50–90% longer to pick up targets relative to controls. There was no evidence of effects of color contrast when locating objects from standing/seated positions and of any other environmental conditions from a standing position on completion time in any participant group. Locating objects, surrounded by five distractors rather than none, from a seated position was associated with a disproportionately greater effect on completion times in the posterior cortical atrophy group relative to the control or typical Alzheimer's disease groups. Smaller, not statistically significant but directionally consistent, ratios of relative effects were seen for two distractors compared with none.DiscussionFindings are consistent with inefficient object localization in posterior cortical atrophy relative to typical Alzheimer's disease and control groups, particularly with targets presented within reaching distance among visual clutter. Findings may carry implications for considering the adverse effects of visual clutter in developing and implementing environmental modifications to promote functional independence in Alzheimer's disease.
Biofilm formation of two genetically diverse Staphylococcus aureus isolates under beta-lactam antibiotics
Authors: Liang Jinglong , Huang Teng Yi , Mao Yuzhu , Li Xuejie 
Published: March 2023

PurposeOur aim was to evaluate the biofilm formation of 2 genetically diverse Staphylococcus aureus isolates, 10379 and 121940, under different concentrations of beta-lactam antibiotics on biomass content and biofilm viability.MethodsBiofilm formation and methicillin resistance genes were tested using PCR and multiplex PCR. PCR was combined with bioinformatics analysis to detect multilocal sequence typing (MLST) and SCCmec types, to study the genetical correlation between the tested strains. Then, the crystal violet (CV) test and XTT were used to detect biomass content and biofilm activity. Antibiotic susceptibility was tested using a broth dilution method. According to their specific MIC, different concentrations of beta-lactam antibiotics were used to study its effect on biomass content and biofilm viability.ResultsStrain 10379 carried the icaD, icaBC, and MRSA genes, not the icaA, atl, app, and agr genes, and MLST and SCCmec typing was ST45 and IV, respectively. Strain 121940 carried the icaA, icaD, icaBC, atl, and agr genes, not the aap gene, and MLST and SCCmec typed as ST546 and IV, respectively. This suggested that strains 10379 and 121940 were genotypically very different. Two S. aureus isolates, 10379 and 121940, showed resistance to beta-lactam antibiotics, penicillin, ampicillin, meropenem, streptomycin and kanamycin, some of which promoted the formation of biofilm and biofilm viability at low concentrations.ConclusionDespite the large differences in the genetic background of S. aureus 10379 and 121940, some sub-inhibitory concentrations of beta-lactam antibiotics are able to promote biomass and biofilm viability of both two isolates.
Simultaneous silencing of juvenile hormone metabolism genes through RNAi interrupts metamorphosis in the cotton boll weevil
Authors: Vasquez Daniel D. N. , Pinheiro Daniele H. , Teixeira Lays A. , Moreira-Pinto Clidia E. , Macedo Leonardo L. P. , Salles-Filho Alvaro L. O. , Silva Maria C. M. , Lourenço-Tessutti Isabela T. , Morgante Carolina V. , Silva Luciano P. , Grossi-de-Sa Maria F. 
Published: March 2023

The cotton boll weevil (CBW) (Anthonomus grandis) is one of the major insect pests of cotton in Brazil. Currently, CBW control is mainly achieved by insecticide application, which is costly and insufficient to ensure effective crop protection. RNA interference (RNAi) has been used in gene function analysis and the development of insect control methods. However, some insect species respond poorly to RNAi, limiting the widespread application of this approach. Therefore, nanoparticles have been explored as an option to increase RNAi efficiency in recalcitrant insects. Herein, we investigated the potential of chitosan–tripolyphosphate (CS-TPP) and polyethylenimine (PEI) nanoparticles as a dsRNA carrier system to improve RNAi efficiency in the CBW. Different formulations of the nanoparticles with dsRNAs targeting genes associated with juvenile hormone metabolism, such as juvenile hormone diol kinase (JHDK), juvenile hormone epoxide hydrolase (JHEH), and methyl farnesoate hydrolase (MFE), were tested. The formulations were delivered to CBW larvae through injection (0.05–2 µg), and the expression of the target genes was evaluated using RT-qPCR. PEI nanoparticles increased targeted gene silencing compared with naked dsRNAs (up to 80%), whereas CS-TPP-dsRNA nanoparticles decreased gene silencing (0%–20%) or led to the same level of gene silencing as the naked dsRNAs (up to 50%). We next evaluated the effects of targeting a single gene or simultaneously targeting two genes via the injection of naked dsRNAs or dsRNAs complexed with PEI (500 ng) on CBW survival and phenotypes. Overall, the gene expression analysis showed that the treatments with PEI targeting either a single gene or multiple genes induced greater gene silencing than naked dsRNA (∼60%). In addition, the injection of dsJHEH/JHDK, either naked or complexed with PEI, significantly affected CBW survival (18% for PEI nanoparticles and 47% for naked dsRNA) and metamorphosis. Phenotypic alterations, such as uncompleted pupation or malformed pupae, suggested that JHEH and JHDK are involved in developmental regulation. Moreover, CBW larvae treated with dsJHEH/JHDK + PEI (1,000 ng/g) exhibited significantly lower survival rate (55%) than those that were fed the same combination of naked dsRNAs (30%). Our findings demonstrated that PEI nanoparticles can be used as an effective tool for evaluating the biological role of target genes in the CBW as they increase the RNAi response.
Can anxiety-like behavior and spatial memory predict the extremes of skilled walking performance in mice? An exploratory, preliminary study
Authors: Schiavo Aniuska , Martins Lucas Athaydes , Wearick-Silva Luís Eduardo , Orso Rodrigo , Xavier Léder Leal , Mestriner Régis Gemerasca 
Published: March 2023

IntroductionSkilled walking is influenced by memory, stress, and anxiety. While this is evident in cases of neurological disorders, memory, and anxiety traits may predict skilled walking performance even in normal functioning. Here, we address whether spatial memory and anxiety-like behavior can predict skilled walking performance in mice.MethodsA cohort of 60 adult mice underwent a behavioral assessment including general exploration (open field), anxiety-like behavior (elevated plus maze), working and spatial memory (Y-maze and Barnes maze), and skilled walking performance (ladder walking test). Three groups were established based on their skilled walking performance: superior (SP, percentiles ≥75), regular (RP, percentiles 74–26), and inferior (IP, percentiles ≤25) performers.ResultsAnimals from the SP and IP groups spent more time in the elevated plus maze closed arms compared to the RP group. With every second spent in the elevated plus maze closed arms, the probability of the animal exhibiting extreme percentiles in the ladder walking test increased by 1.4%. Moreover, animals that spent 219 s (73% of the total time of the test) or more in those arms were 4.67 times more likely to exhibit either higher or lower percentiles of skilled walking performance.DiscussionWe discuss and conclude anxiety traits may influence skilled walking performance in facility-reared mice.