Miracle-dz/UniFAR-FTUs huggingface dataset:
Source and acquisition of rhizosphere microbes in Antarctic vascular plants

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.
Dependence of the global dayside reconnection rate on interplanetary magnetic field By and the earth’s dipole tilt

In the recent years, significant attention has been given to the combined effect of Interplanetary Magnetic Field (IMF) duskward component (By) and dipole tilt on the global magnetosphere-ionosphere system response. Numerous studies have pointed out that when the Earth’s magnetic dipole is tilted away from the Sun (negative dipole tilt during northern winter), and IMF has a positive By component, the effects on ionospheric currents, particle precipitation, ionospheric convection, and average size of the auroral oval, is significantly more enhanced, compared to when IMF By is negative. Furthermore, this IMF By polarity effect reverses when Earth’s dipole is tilted in the opposite direction. The underlying cause has remained unclear. Our analysis shows that substorms tend to be stronger during the same IMF By and dipole tilt polarity combination. Taken together with earlier results showing also more frequent substorms during the same conditions, our observations suggests that when IMF By and dipole tilt have opposite signs, there is a more efficient global dayside reconnection rate. We also show analysis of the occurrence frequency of periods of Steady Magnetospheric Convection, substorm onset latitude, and the isotropic boundary of proton precipitation, that are all consistent with our conclusion that the combination of IMF By and dipole tilt polarity affect the global dayside reconnection rate.
Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study

Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.
Factors influencing microgame adoption among secondary school mathematics teachers supported by structural equation modelling-based research

Microgames are rapidly gaining increased attention and are highly being considered because of the technology-based media that enhances students’ learning interests and educational activities. Therefore, this study aims to develop a new construct through confirmatory factor analysis, to comprehensively understand the factors influencing the use of microgames in mathematics class. Participants of the study were the secondary school teachers in West Java, Indonesia, which had a 1-year training in microgames development. We applied a quantitative approach to collect the data via online questionnaires through google form. Structural Equation Modelling (SEM) with AMOS software was used to analyze the proposed model. Empirical results confirmed the perceived easy to use and subjective norm influence (PEU and SN) relationship with teachers’ microgame usage behaviors and intentions. In this condition, SN was found to have the initial significant influence on behavioral intention (BI), as attitude, BI, and facilitating conditions also correlated with the actual use of microgames. Furthermore, the largest influential factor was BI, with the results subsequently showing that TPACK had no significant influence on the actual use of microgames. This report is expected to help bridge the gap across several previous studies, as well as contribute to the explanation and prediction of the factors influencing the teachers’ mathematical utilization of the study’s program. Besides this, it also helps to increase the use of microgames in teaching and learning activities.
The learning-relative hemodynamic modulation of cortical plasticity induced by a force-control motor training

Background Novel motor skills are generally acquired through repetitive practices which are believed to be strongly related to neural plasticity mechanisms. This study aimed to investigate the learning-relative hemodynamic modulation of cortical plasticity induced by long-term motor training. Methods An 8-day participation-control program was conducted. Eighteen right-handed healthy participants were recruited and randomly assigned into the training (12) and control groups (6). The training group were arranged to undergo the 8-day block-designed motor training which required to repeat a visuomotor force-control task. The functional near-infrared spectroscopy (fNIRS) was used to continuously monitor the cortical hemodynamic response during training. Two transcranial magnetic stimulation (TMS) measurements were performed before and after training to evaluate the cortical excitability changes. The transfer effects of learning were also investigated. Results The behavior performance was quantified via score execution accuracy to illustrate the fast/slow learning stages as experience cumulated. The cortical hemodynamic activations mapped by fNIRS exhibited a temporal evolution trends that agreed the expansion–renormalization model, which assumed the brain modulation against skill acquisition includes complex mechanisms of neural expansion, selection, and renormalization. Functional connectivity (FC) analysis showed the FC strength was maintained, while the measured homodynamic activation returned to baseline after certain level of skill acquisition. Furthermore, the TMS results demonstrated a significant increase of motor evoked potential (MEP) on the targeted muscle for the trained participants, who significantly outperformed the untrained subjects in learning transfer investigation. Conclusion The study illustrated the expansion–renormalization trends during continuous motor training, and relative analysis showed the functional connectivity enhancement may be maintained after amplitude renormalization of cortical hemodynamic activations. The TMS findings further gave an implication of neural facilitations on the descending motor pathway when brain activation returned to renormalization status after certain level of learning stages was achieved, and the learning can transfer to enhance the performance while encountering similar tasks.
Association between social capital and self-rated health among community-dwelling older adults

Background It is less known about whether the association of social capital with self-rated health (SRH) varies by the presence of health conditions and how social capital, together with other variables, is linked to self-rated health in later life. Objectives This article aimed to explore the association of social capital with self-rated health and to examine whether the association varies among older people with and without health conditions, with a special focus on how social capital and relevant factors have an effect on self-rated health among community-dwelling older adults. Methods Cross-sectional data were obtained from a survey that commenced from July to September 2017 in Anhui Province. Data on socio-demographic information, social capital (six dimensions), and self-rated health were analyzed. Binary logistic regression and classification and regression tree (CART) models were used to estimate the association. Results Based on the findings, we found that social capital regarding less social support (adjusted odds ratio (AOR) = 1.57, 95% CI: 1.21–2.04), and less reciprocity (AOR = 1.73, 95% CI: 1.29–2.31) were associated with self-rated health among general older adults. Social capital as measured by less social participation (AOR = 1.55, 95% CI: 1.06–2.27), less cohesion (AOR = 0.63, 95% CI: 0.42–0.94), and less reciprocity (AOR =1.77, 95% CI: 1.17–2.68) were linked to self-rated health among older people with health conditions. While social capital regarding less social support (AOR = 2.15, 95% CI: 1.39–3.33) was related to self-rated health among older people without health conditions. We observed the interacting effect of social capital in the CART model, an implication that much focus should be geared toward vulnerable subgroups, especially depressed and lonely older people, as they have low reciprocity and little cohesion. Conclusion This work demonstrates that social capital may be relevant in devising programs and measures to improve self-rated health among community-dwelling older adults with comorbidity.
Association of body mass index and its classifications with gray matter volume in individuals with a wide range of body mass index group: A whole-brain magnetic resonance imaging study

Aim To examine the association of body mass index (BMI) [kg/m2] and its classifications (underweight [BMI < 18.5], normal [18.5 ≤ BMI < 25], overweight [25 ≤ BMI < 30], and obese [BMI ≥ 30]) with brain structure in individuals with a wide range of BMI group. Materials and methods The participants included 382 right-handed individuals (mean age: 46.9 ± 14.3 years, 142 men and 240 women). The intelligence quotient was assessed using the Japanese Adult Reading Test. Voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) were performed to analyze the association of BMI and its classifications with gray and white matter structures, respectively. Results According to VBM, BMI was significantly and negatively correlated with the bilateral cerebellum exterior volumes. In group comparisons, the right cerebellum exterior volume was significantly lower in the overweight or obese group than in the underweight or normal group, while the bilateral cuneus and calcarine cortex, left cuneus, and left precuneus volume was significantly lower in the underweight group than in the non-underweight group. Sex-related stratification analyses for VBM revealed that BMI was significantly and negatively correlated with the bilateral cerebellum exterior volumes only in women. In group comparisons, the left cerebellum exterior volume was significantly lower in obese women than in non-obese women. The left thalamus proper and the right cerebellum exterior volumes were significantly lower in overweight or obese group than in underweight or normal group in men and women, respectively. The bilateral cuneus and calcarine cortex, left cuneus and carcarine cortex, and bilateral cuneus volume was significantly lower in underweight men than in non-underweight men. In contrast, there were no notable findings on DTI. Conclusion Our results suggest association of continuous BMI, being overweight or obese, and being underweight with decreased gray matter volume in individuals with a wide range of BMI group. Furthermore, sex-related differences are seen in the association of BMI and its classifications with regional gray matter volume reductions. Abnormally high or low BMIs may have a negative influence on regional gray matter volumes.
The association of Carbohydrate Quality Index with cardiovascular disease risk factors among women with overweight and obesity: A cross-sectional study

Purpose Diet is one of the most important factors influencing cardiovascular disease (CVD). The negative relationship between carbohydrate intake with lipid profiles and body weight has been previously investigated. However, this is the first study seeking to assess the association of carbohydrate quality index (CQI) with CVD risk factors. Methods This cross-sectional study was conducted on 291 Iranian overweight and obese women, with a body mass index (BMI) ranging between 25 and 40 kg/m2, and aged 18–48 years. CQI scores were calculated by using a validated 168-item semi-quantitative food frequency questionnaire (FFQ). Biochemical and anthropometric measures were assessed using standard methods, and bioelectrical impedance was used to measure body composition. Results We observed that fruits (P < 0.001), vegetables (P < 0.001), and protein (P = 0.002) intake were higher in participants with a higher score of the CQI. When we adjusted for potential confounders, we observed that the CQI was negatively related to systolic blood pressure (SBP) (β = −6.10; 95% CI = −10.11, −2.10; P = 0.003) and DBP (β = −3.11; 95% CI = −6.15, −0.08; P = 0.04). Also, greater adherence to a high CQI dietary pattern, compared to the reference group, was negatively related to HOMA-IR (β = −0.53; 95% CI = −0.94, −0.12) (P for trend = 0.01), WC (β = −3.18; 95% CI = −6.26, −0.10) (P for trend = 0.04), BMI (β = −1.21; 95% CI = −2.50, 0.07) (P for trend = 0.06), and BF (β = −2.06; 95% CI = −3.82, −0.30) (P for trend = 0.02). Conclusion In line with previous studies, the CQI was inversely associated with blood pressure, WC, BMI, and BF. Further prospective and clinical trial studies are suggested to confirm these data.
Characteristics of the immune microenvironment and their clinical significance in non-small cell lung cancer patients with ALK-rearranged mutation

Background Although immune checkpoint inhibitors (ICIs) are one of the most important treatments for advanced-stage non-small-cell lung cancer (NSCLC), NSCLC patients with ALK-rearranged usually don’t obtain a clinical benefit. The reason may be related to the unique tumor microenvironment (TME). We evaluated the characteristics of immune biomarkers of the TME and their prognostic value in ALK-rearranged NSCLC. Methods Tumor samples from patients with ALK-rearranged (N = 39) and EGFR- (N = 40)/KRAS- (N = 30) mutated NSCLC were collected. Immunohistochemistry (IHC) was used to assess the expression of 9 tumor immune markers as well as 6 immune markers of tumor-infiltrating cells. To research the TME of ALK-rearranged NSCLC, EGFR/KRAS-positive patients were used as controls. Furthermore, the correlation between the efficacy and prognosis of patients with advanced-stage (IIIC-IV) ALK rearrangements treated with targeted drugs was analyzed in terms of the TME. Results The proportion of PD-L1+ tumors was lower in ALK-positive NSCLC than in KRAS-positive NSCLC. Besides, the proportion of T cells expressing TIM-3-CD8+ (15.38%), CTLA4-CD8+ (12.82%), LAG3-CD8+ (33.33%) and PD-1-CD8+ (2.56%) in ALK-positive NSCLC was lower than that in EGFR/KRAS-positive NSCLC. The expression of CD3, CD8 T cells and CD20 B cells was lower in ALK-positive NSCLC than in KRAS-positive NSCLC (p < 0.0001, < 0.005, and < 0.001, respectively). Nevertheless, the level of CD4 helper T cells was higher in ALK-positive NSCLC than in EGFR/KRAS-positive NSCLC (p < 0.0001 and p < 0.05, respectively). The repression of TIM3 was higher in ALK-positive NSCLC than in KRAS-positive NSCLC (p < 0.001). In addition, our data showed that high expression of PD-L1 (HR = 0.177, 95% CI 0.038–0.852, p = 0.027) and CTLA4 (HR = 0.196, 95% CI 0.041–0.947, p = 0.043) was related to lower OS in advanced-stage ALK- rearranged NSCLC patients treated with ALK tyrosine kinase inhibitors (TKIs). Conclusions Immunosuppressive status was characteristic of the TME in patients with ALK-positive NSCLC compared with EGFR/KRAS-positive NSCLC. High expression of PD-L1 and CTLA4 was an adverse prognostic factor in advanced-stage ALK-rearranged NSCLC patients treated with ALK-TKIs. Immunotherapy for ALK-rearranged patients requires further exploration and validation by clinical trials.
Inhibition of macrophage migration inhibitory factor (MIF) suppresses apoptosis signal-regulating kinase 1 to protect against liver ischemia/reperfusion injury

Background: Hepatic ischemia–reperfusion (I/R) injury is a major complication leading to surgical failures in liver resection, transplantation, and hemorrhagic shock. The role of cytokine macrophage migration inhibitory factor (MIF) in hepatic I/R injury is unclear. Methods: We examined changes of MIF expression in mice after hepatic I/R surgery and hepatocytes challenged with hypoxia–reoxygenation (H/R) insult. Subsequently, MIF global knock-out mice and mice with adeno-associated-virus (AAV)-delivered MIF overexpression were subjected to hepatic I/R injury. Hepatic histology, the inflammatory response, apoptosis and oxidative stress were monitored to assess liver damage. The molecular mechanisms of MIF function were explored in vivo and in vitro. Results: MIF was significantly upregulated in the serum whereas decreased in liver tissues of mice after hepatic I/R injury. MIF knock-out effectively attenuated I/R -induced liver inflammation, apoptosis and oxidative stress in vivo and in vitro, whereas MIF overexpression significantly aggravated liver injury. Via RNA-seq analysis, we found a significant decreased trend of MAPK pathway in MIF knock-out mice subjected hepatic I/R surgery. Using the apoptosis signal-regulating kinase 1 (ASK1) inhibitor NQDI-1 we determined that, mechanistically, the protective effect of MIF deficiency on hepatic I/R injury was dependent on the suppressing of the ASK1-JNK/P38 signaling pathway. Moreover, we found MIF inhibitor ISO-1 alleviate hepatic I/R injury in mice. Conclusion: Our results confirm that MIF deficiency suppresses the ASK1-JNK/P38 pathway and protects the liver from I/R -induced injury. Our findings suggest MIF as a novel biomarker and therapeutic target for the diagnosis and treatment of hepatic I/R injury.
Duality and Perturbation Methods in Critical Point Theory

1. Lipschitz and smooth perturbed minimization principles 2. Linear and plurisubharmonic perturbed minimization principles 3. The classical min-max theorem 4. A strong form of the min-max principle 5. Relaxed boundary conditions in the presence of a dual set 6. The critical set in the mountain pass theorem 7. Group actions and multiplicity of critical points 8. The Palais-Smale condition around a dual set - examples 9. Morse indices of min-max critical points - the non-degenerate case 10. Morse indices of min-max critical points - the degenerate case 11. Morse-type information on Palais-Smale sequences Appendix References Index.
Quantification of Behavioral Deficits in Developing Mice With Dystonic Behaviors

Converging evidence from structural imaging studies in patients, the function of dystonia-causing genes, and the comorbidity of neuronal and behavioral defects all suggest that pediatric-onset dystonia is a neurodevelopmental disorder. However, to fully appreciate the contribution of altered development to dystonia, a mechanistic understanding of how networks become dysfunctional is required for early-onset dystonia. One current hurdle is that many dystonia animal models are ideally suited for studying adult phenotypes, as the neurodevelopmental features can be subtle or are complicated by broad developmental deficits. Furthermore, most assays that are used to measure dystonia are not suited for developing postnatal mice. Here, we characterize the early-onset dystonia in Ptf1a Cre ;Vglut2 fl/fl mice, which is caused by the absence of neurotransmission from inferior olive neurons onto cerebellar Purkinje cells. We investigate motor control with two paradigms that examine how altered neural function impacts key neurodevelopmental milestones seen in postnatal pups (postnatal day 7–11). We find that Ptf1a Cre ;Vglut2 fl/fl mice have poor performance on the negative geotaxis assay and the surface righting reflex. Interestingly, we also find that Ptf1a Cre ;Vglut2 fl/fl mice make fewer ultrasonic calls when socially isolated from their nests. Ultrasonic calls are often impaired in rodent models of autism spectrum disorders, a condition that can be comorbid with dystonia. Together, we show that these assays can serve as useful quantitative tools for investigating how neural dysfunction during development influences neonatal behaviors in a dystonia mouse model. Our data implicate a shared cerebellar circuit mechanism underlying dystonia-related motor signs and social impairments in mice.