Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA amplification in mixed aqueous-organic media: chemical analysis of leading polymerase chain reaction compositions

PCR amplification of GC-rich regions often leads to low yield and specificity. Addition of PCR-enhancing compounds is employed in order to overcome these obstacles. PCR-enhancing additives are low molecular polar organic compounds that are included as undisclosed co-solvents in commercial PCR buffers. In the interest of transparency and to permit further optimization by researchers of PCR compositions for challenging amplification problems, we studied eight PCR buffers by GC/MS to identify and quantify their co-solvents. Buffer specificity, both rich in water and salified substances, required a suitable sample preparation before injection into the GC/MS system. The aqueous phase of each buffer was replaced by an organic solvent to remove, by precipitation and filtration, salified substances which are detrimental to the GC/MS analysis. This approach has demonstrated the advantage of eliminating both water and salified substances without any loss of co-solvents. The sensitivity of the developed method was demonstrated as the main co-solvents were easily detected, identified and quantified. The methodology for identifying the co-solvents is mainly based on comparison of both library matching of acquired MS spectra with NIST library and experimental mass spectra obtained from authentic chemical standards. For the quantification of each co-solvent, deuterated Internal standards of similar structure to the cosolvents were used to correct the variable recovery caused by sample preparation, matrix effects, and ion source variability. The recovery ratio of the developed method was verified and found to be in the range 90-120 %. We then characterized the effects of specific organic co-solvents identified during PCR amplification -- using DNA melting, polymerase thermostability, polymerase activity and real-time PCR methods -- in order to elucidate their mechanism of action and to permit further optimization of their effects on amplification efficiency and specificity.
DLPFC controls the rapid neural response to visual threat: An ERP and rTMS study

Individuals are faster at detecting threatening stimuli than neutral stimuli. While generally considered a rapid bottom-up response, this threat superiority effect is also modulated by top-down mechanisms known to rely on the dorsolateral prefrontal cortex (DLPFC). What remains unclear is whether the response is modulated only at later stages of processing, or whether rapid attention to threat itself is controlled in a top-down manner. To test this, we used repetitive transcranial magnetic stimulation (rTMS) to inhibit activity in the DLPFC, and measured EEG to index the immediate neural response to threat. Participants attended two sessions where they performed a visual search task with threatening or neutral targets. Prior to this, they received 15 minutes of 1 Hz inhibitory or sham rTMS targeting the right DLPFC. We measured the impact of rTMS on the P1, a rapid visually-evoked potential that is modulated by attention. We found that threatening targets increased the amplitude of the P1 in the sham condition, but inhibition of the DLPFC abolished this increase. These results suggest that the neural signature of rapid attentional detection of threat, even at its earliest stage, is influenced in a top-down fashion by the right DLPFC.
Sequence features of retrotransposons allow for epigenetic variability

Transposable elements (TEs) are mobile genetic elements that make up a large fraction of mammalian genomes. While select TEs have been co-opted in host genomes to have function, the majority of these elements are epigenetically silenced by DNA methylation in somatic cells. However, some TEs in mice, including the Intracisternal A-particle (IAP) subfamily of retrotransposons, have been shown to display interindividual variation in DNA methylation. Recent work has revealed that IAP sequence differences and strain-specific KRAB zinc finger proteins (KZFPs) may influence the methylation state of these IAPs. However, the mechanisms underlying the establishment and maintenance of interindividual variability in DNA methylation still remain unclear. Here we report that sequence content and genomic context influence the likelihood that IAPs become variably methylated. IAPs that differ from consensus IAP sequences have altered KZFP recruitment that can lead to decreased KAP1 recruitment when in proximity of constitutively expressed genes. These variably methylated loci have a high CpG density, similar to CpG islands, and can be bound by ZF-CxxC proteins, providing a potential mechanism to maintain this permissive chromatin environment and protect from DNA methylation. These observations indicate that variably methylated IAPs escape silencing through both attenuation of KZFP binding and recognition by ZF-CxxC proteins to maintain a hypomethylated state.
Maize Genotypes With Different Zinc Efficiency in Response to Low Zinc Stress and Heterogeneous Zinc Supply

All over the world, a common problem in the soil is the low content of available zinc (Zn), which is unevenly distributed and difficult to move. However, information on the foraging strategies of roots in response to heterogeneous Zn supply is still very limited. Few studies have analyzed the adaptability of maize inbred lines with different Zn efficiencies to different low Zn stress time lengths in maize. This study analyzed the effects of different time lengths of low Zn stress on various related traits in different inbred lines. In addition, morphological plasticity of roots and the response of Zn-related important gene iron-regulated transporter-like proteins (ZIPs) were studied via simulating the heterogeneity of Zn nutrition in the soil. In this report, when Zn deficiency stress duration was extended (from 14 to 21 days), under Zn-deficient supply (0.5 μM), Zn efficiency (ZE) based on shoot dry weight of Wu312 displayed no significant difference, and ZE for Ye478 was increased by 92.9%. Under longer-term Zn deficiency, shoot, and root dry weights of Ye478 were 6.5 and 2.1-fold higher than those of Wu312, respectively. Uneven Zn supply strongly inhibited the development of some root traits in the -Zn region. Difference in shoot dry weights between Wu312 and Ye478 was larger in T1 (1.97 times) than in T2 (1.53 times). Under heterogeneous condition of Zn supply, both the –Zn region and the +Zn region upregulated the expressions of ZmZIP3, ZmZIP4, ZmZIP5, ZmZIP7, and ZmZIP8 in the roots of two inbred lines. These results indicate that extended time length of low-Zn stress will enlarge the difference of multiple physiological traits, especially biomass, between Zn-sensitive and Zn-tolerant inbred lines. There were significant genotypic differences of root morphology in response to heterogeneous Zn supply. Compared with split-supply with +Zn/+Zn, the difference of above-ground biomass between Zn-sensitive and Zn-tolerant inbred lines under split-supply with –Zn/+Zn was higher. Under the condition of heterogeneous Zn supply, several ZmZIP genes may play important roles in tolerance to low Zn stress, which can provide a basis for further functional characterization.
Serum LAG-3 Predicts Outcome and Treatment Response in Hepatocellular Carcinoma Patients With Transarterial Chemoembolization

Background Transarterial chemoembolization (TACE) stands for the most commonly utilized therapy for hepatocellular carcinoma (HCC) worldwide. This study was to explore the potential predictive and prognostic roles of LAG-3 and PD-L1 as serum biomarkers in HCC patients underwent TACE treatment. Methods A total of 100 HCC patients receiving TACE as well as 30 healthy controls were enrolled in the study. Serum LAG-3 and PD-L1 levels were determined at baseline and 3 day after TACE using enzyme-linked immunosorbent assay (ELISA). Results We found serum levels of LAG-3 and PD-L1 were significantly elevated in HCC patients compared with healthy controls. Interestingly, patients with low pre-TACE and post-TACE levels of LAG-3 but not PD-L1 had a high probability of achieving an objective response (OR) after TACE treatment. Additionally, high pre-TACE LAG-3 level was correlated with poor disease outcome, and the patients with both high serum LAG-3 and PD-L1 level had the shorter overall survival (OS) than patients who are either PD-L1 or LAG-3 high or both PD-L1 and LAG-3 low. High pre-TACE serum LAG-3 level was positively associated with more cirrhosis pattern, advanced BCLC stage, pre-TACE alanine aminotransferase (ALT) level, and pre-TACE aspartate aminotransferase (AST) level. Furthermore, in 50 patients who underwent TACE, the serum LAG-3 level was significantly decreased at 3 day after TACE. Conclusion Both pre-TACE and post-TACE serum LAG-3 levels could serve as powerful predictors for tumor response of TACE, and high pre-TACE serum LAG-3 level was an indicator for poor prognosis in HCC.
First Detection in West Africa of a Mutation That May Contribute to Artemisinin Resistance Plasmodium falciparum

Background: The spread of drug resistance has seriously impacted the effective treatment of infection with the malaria parasite, Plasmodium falciparum. Continuous monitoring of molecular marker polymorphisms associated with drug resistance in parasites is essential for malaria control and elimination efforts. Our study describes mutations observed in the resistance genes Pfkelch13, Pfcrt, and Pfmdr1 in imported malaria and identifies additional potential drug resistance-associated molecular markers. Methods: Chinese patients infected in Africa with P. falciparum were treated with intravenous (IV) injections of artesunate 240–360 mg for 3–5 days while hospitalized and treated with oral dihydroartemisinin-piperaquine (DHP) for 3 days after hospital discharge. Blood samples were collected and PCR sequencing performed on genes Pfkelch13, Pfcrt, and Pfmdr1 from all isolates. Results: We analyzed a total of 225 patients from Guangxi, China with P. falciparum malaria acquired in Africa between 2016 and 2018. All patients were cured completely after treatment. The F446I mutation of the Pfkelch13 gene was detected for the first time from samples of West African P. falciparum, with a frequency of 1.0%. Five haplotypes of Pfcrt that encode residues 72–76 were found, with the wild-type CVMNK sequence predominating (80.8% of samples), suggesting that the parasites might be chloroquine sensitive. For Pfmdr1, N86Y (13.1%) and Y184F (58.8%) were the most prevalent, suggesting that artemether-lumefantrine may not, in general, be a suitable treatment for the group. Conclusions: For the first time, this study detected the F446I mutation of the Pfkelch13 gene from Africa parasites that lacked clinical evidence of resistance. This study provides the latest data for molecular marker surveillance related to antimalarial drug resistance genes Pfkelch13, Pfcrt, and Pfmdr1 imported from Africa, in Guangxi, China from Chinese migrate workers. Clinical Trial Registration: ChiCTROPC17013106.
Social Support as a Facilitator of Musical Self-Efficacy

Previous research has shown that musical self-efficacy is one of the predictors of academic achievement, but few studies have analyzed the function of social support in the construction of musical self-efficacy. In this study we analyze the relationship between three sources of support perceived by music students – parents, teachers, and peers – and their influence on levels of self-efficacy for learning and for public performance. We analyze three groups of students under the hypothesis that relationships among those variables can vary with age and the level of education. A total of 444 students enrolled in six Spanish music schools, two music universities, and four advanced music schools, completed the Social Support Scale for Music Students, as well as the General Musical Self-Efficacy Scale. Results reveal significant relationships among the aforementioned variables, with considerable variation according to academic level. For the youngest students enrolled in advanced music schools (conservatorios profesionales), the role of parents and teachers was crucial, especially for predicting self-efficacy for learning, which, in turn, is the best predictor of self-efficacy for public performance. For the 16–18-year-olds enrolled in the same advanced music schools, their peers play a particularly relevant role in reinforcing their self-efficacy for learning. Social support had a negligible influence on the self-efficacy of university-level students, but they did experience a strong relationship between self-efficacy for learning, on the one hand, and public performance, on the other. We interpret these results in view of potential long-term careers in music, relating them with a series of different agents.
Alternative Complement Pathway Inhibition Does Not Abrogate Meningococcal Killing by Serum of Vaccinated Individuals

Dysregulation of complement activation causes a number of diseases, including paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome. These conditions can be treated with monoclonal antibodies (mAbs) that bind to the complement component C5 and prevent formation of the membrane attack complex (MAC). While MAC is involved in uncontrolled lysis of erythrocytes in these patients, it is also required for serum bactericidal activity (SBA), i.e. clearance of encapsulated bacteria. Therefore, terminal complement blockage in these patients increases the risk of invasive disease by Neisseria meningitidis more than 1000-fold compared to the general population, despite obligatory vaccination. It is assumed that alternative instead of terminal pathway inhibition reduces the risk of meningococcal disease in vaccinated individuals. To address this, we investigated the SBA with alternative pathway inhibitors. Serum was collected from adults before and after vaccination with a meningococcal serogroup A, C, W, Y capsule conjugate vaccine and tested for meningococcal killing in the presence of factor B and D, C3, C5 and MASP-2 inhibitors. B meningococci were not included in this study since the immune response against protein-based vaccines is more complex. Unsurprisingly, inhibition of C5 abrogated killing of meningococci by all sera. In contrast, both factor B and D inhibitors affected meningococcal killing in sera from individuals with low, but not with high bactericidal anti-capsular titers. While the anti-MASP-2 mAb did not impair SBA, inhibition of C3 impeded meningococcal killing in most, but not in all sera. These data provide evidence that vaccination can provide protection against invasive meningococcal disease in patients treated with alternative pathway inhibitors.
Construction and Validation of a Serum Albumin-to-Alkaline Phosphatase Ratio-Based Nomogram for Predicting Pathological Complete Response in Breast Cancer

Background Breast cancer patients who achieve pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) have favorable outcomes. Reliable predictors for pCR help to identify patients who will benefit most from NAC. The pretreatment serum albumin-to-alkaline phosphatase ratio (AAPR) has been shown to be a prognostic predictor in several malignancies, but its predictive value for pCR in breast cancer is still unknown. This study aims to investigate the predictive role of AAPR in breast cancer patients and develop an AAPR-based nomogram for pCR rate prediction. Methods A total of 780 patients who received anthracycline and taxane-based NAC from January 2012 to March 2018 were retrospectively analyzed. Univariate and multivariate analyses were performed to assess the predictive value of AAPR and other clinicopathological factors. A nomogram was developed and calibrated based on multivariate logistic regression. A validation cohort of 234 patients was utilized to further validate the predictive performance of the model. The C-index, calibration plots and decision curve analysis (DCA) were used to evaluate the discrimination, calibration and clinical value of the model. Results Patients with a lower AAPR (<0.583) had a significantly reduced pCR rate (OR 2.228, 95% CI 1.246-3.986, p=0.007). Tumor size, clinical nodal status, histological grade, PR, Ki67 and AAPR were identified as independent predictors and included in the final model. The nomogram was used as a graphical representation of the model. The nomogram had satisfactory calibration and discrimination in both the training cohort and validation cohort (the C-index was 0.792 in the training cohort and 0.790 in the validation cohort). Furthermore, DCA indicated a clinical net benefit from the nomogram. Conclusions Pretreatment serum AAPR is a potentially valuable predictor for pCR in breast cancer patients who receive NAC. The AAPR-based nomogram is a noninvasive tool with favorable predictive accuracy for pCR, which helps to make individualized treatment strategy decisions.
Synthesis of Ni/NiAlOx Catalysts for Hydrogenation Saturation of Phenanthrene

The saturation of octahydrophenanthrene was the rate-determining step in the hydrogenation process from phenanthrene to perhydrophenanthrene, which was due to the steric hindrance and competitive adsorption of octahydrophenanthrene. In this work, a series of Ni/NiAlOx catalysts with a uniform electron-deficient state of Ni derived from the nickel aluminate structure was synthesized to overcome the disadvantage of noble catalyst and the traditional sulfided catalysts in the saturation hydrogenation process of phenanthrene. Results showed that the catalyst calcinated at 650°C possessed more Ni2+ (∼98%) occupying octahedral sites and exhibited the highest robs (1.53 × 10−3 mol kg−1 s−1) and TOF (14.64 × 10−3 s−1) for phenanthrene hydrogenation. Furthermore, its ability to overcome steric hindrance and promote the rate-determining step was proven by octahydrophenanthrene hydrogenation. Comparing the evolution of hydrogenation activity with the change in the electronic structure of surface Ni sites, it was shown that the increase of metallic electron deficiency hindered the π-back bonding between surface Ni and aromatic rings, which was unfavorable for aromatic adsorption. As a result, the phenanthrene hydrogenation saturation performance can be enhanced by stabilizing the electron-deficient state of surface Ni on an optimal degree.
The Microbiome in Autoimmune Liver Diseases: Metagenomic and Metabolomic Changes

Recent studies have identified the critical role of microbiota in the pathophysiology of autoimmune liver diseases (AILDs), including autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC). Metagenomic studies reveal significant decrease of gut bacterial diversity in AILDs. Although profiles of metagenomic vary widely, Veillonella is commonly enriched in AIH, PBC, and PSC. Apart from gut microbiome, the oral and bile microbiome seem to be associated with these diseases as well. The functional analysis of metagenomics suggests that metabolic pathways changed in the gut microbiome of the patients. Microbial metabolites, including short-chain fatty acids (SCFAs) and microbial bile acid metabolites, have been shown to modulate innate immunity, adaptive immunity, and inflammation. Taken together, the evidence of host–microbiome interactions and in-depth mechanistic studies needs further accumulation, which will offer more possibilities to clarify the mechanisms of AILDs and provide potential molecular targets for the prevention and treatment in the future.
Sociodemographic Analysis of Suicide Rates Among Older Adults Living in Ecuador: 1997–2019

Background: Despite most suicides occurring in low-and-middle-income countries (LAMICs), limited reports on suicide rates in older adults among LAMICs are available. In Ecuador, high suicide rates have been reported among adolescents. Little is known about the epidemiology of suicides among older adults in Ecuador. Aim: To examine the sociodemographic characteristics of suicides among older adults living in Ecuador from 1997 to 2019. Methods: An observational study was conducted using Ecuador's National Institute of Census and Statistics database from 1997 to 2019 in Ecuadorians aged 60 and older. International Classification of Diseases 10th Revision (ICD-10) (X60-X84)-reported suicide deaths were included in addition to deaths of events of undetermined intent (Y21-Y33). Sex, age, ethnicity, educational level, and method of suicide were analyzed. Annual suicide rates were calculated per 100,000 by age, sex, and method. To examine the trends in rates of suicide, Joinpoint analysis using Poisson log-linear regression was used. Results: Suicide rates of female older adults remained relatively stable between 1997 and 2019 with an average annual percentage increase of 2.4%, while the male rates increased between 2002 and 2009, 2014 and 2016, and maintained relatively stable within the past 3 years (2017–2019). The annual age-adjusted male suicide rate was 29.8 per 100,000, while the female suicide rate was 5.26 per 100,000 during the study period. When adding deaths of undetermined intent, the annual male rate was 60.5 per 100,000, while the same rate was 14.3 for women. The most common suicide method was hanging (55.7%) followed by self-poisoning (26.0%). The highest suicide numbers were reported in urban districts, men, and those with lower education status. Conclusion: This study contributes to building the baseline for further studies on suicide rates of older adults in Ecuador. Results highlight priority areas of suicide prevention. By examining suicide trends over 23 years, findings can help inform policy and future interventions targeting suicide prevention.