Miracle-dz/UniFAR-FTUs huggingface dataset:
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding regarding the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates originated from polyextremophilic prokaryotes that live in similar habitats as the Cyanidiales and encodes functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the nonexistence of a eukaryotic pan-genome. Therefore, absence of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction underlines the importance of non-endosymbiosis related foreign gene acquisition.
Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy

Abstract With the advent of high-throughput DNA sequencing technologies, traditional methodologies for taxonomic classification of bacteria as DNA–DNA hybridization and 16S rRNA identity analyses are being challenged by the development of a fast-growing number of genomic metrics. The large amount of portable and digitized genome sequences available in public repositories constitutes an invaluable data for bacterial classification. Consequently, several genomic metrics and tools were developed to aid the interpretation of these massive data. Genomic metrics are based on the assumption that higher genome similarities would reflect closer phylogenetic relationships. Different metrics would vary in their methodology of analysis, resolution power, limitations and easiness of use. The aim of this review is to highlight the differences among available genome-based methods and tools to provide a guide for in silico bacterial identification and classification.
Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.
Pressure dependence of the structure of liquid NiTi: a molecular dynamics study

We evaluate the structure of liquid NiTi under various pressures from 0 GPa to 40 GPa in the atomic level using molecular dynamics simulations. The structure factor and radial distribution function are used to investigate the general structural change of the system. Further identification of the local structures is examined by the bond-angle method and bond-angle distribution analysis. From our results, we found that the count of the local structure of fcc, hcp, bcc, and icosahedral short-range order monotonically increase when the pressures increase. We also observed in our results that the size of the local cluster grows as the pressure increases, and the long-range connectivity of the quasi-crystal is achieved at high pressure.
Liposomal integration method for assessing antioxidative activity of water insoluble compounds towards biologically relevant free radicals: example of avarol

Abstract The liposomal integration method, in conjunction with electron paramagnetic resonance (EPR) spectroscopy, has been presented for the investigation of antioxidant activity of selected water-insoluble compound towards biologically relevant free radicals. This method was applied to avarol, a sesquiterpenoid hydroquinone isolated from the marine sponge Dysidea avara. The antioxidant activity of water-insoluble avarol towards •OH, O2•− and NO• radicals was attained by its incorporation into the DPPC liposomes bilayer, and towards ascorbyl radicals in the organic solvent. Avarol’s activity towards •OH, O2•−, NO• and ascorbyl radicals was 86.2%, 50.9%, 23.6% and 61.8%, respectively, showing its significant radical scavenging potential.
Catalytic Activity of Bimetallic (Ruthenium/Palladium) Nano-alloy Decorated Porous Carbons Toward Reduction of Toxic Compounds.

Chicken feathers-derived high surface area porous activated carbon (CFAC) material was prepared using chemical activation. A new composite Chicken feathers-derived high surface area porous activated carbon (CFAC) material was prepared using chemical activation. A new composite composed of Ru-Pd nanoparticles supported on CFAC (Ru-Pd@CFAC) has been prepared by microwave-thermal reduction in the presence of the support. The characterization achieved by XRD, Raman, BET, FESEM/TEM, FT-IR, TGA, XPS, HAADF-STEM-EDS, H2-chemisorption, H2-TPR, and ICP-AES was utilized to scrutinize the catalysts. This catalyst is found to be efficient for the reduction of hexavalent chromium (CrVI), potassium ferricyanide (K3[Fe(CN)6]), 4-nitrophenol (4-NP), and pendimethalin (PDM), under room temperature, and remains stable and even after several repeated runs. Moreover, it showed excellent catalytic activity compared with the mono metallic couterparts.
Involvement of γ protein kinase C in estrogen‐induced neuroprotection against focal brain ischemia through G protein‐coupled estrogen receptor

The neuroprotective effects of estrogen were studied in the ischemic model mice by 90 min transient unilateral middle cerebral artery occlusion (MCAO) followed by 22.5 h reperfusion. The total infarct size in C57BL/6 female mice after MCAO and reperfusion was significantly smaller than that in male mice. Intraperitoneal injection of estrogen after the start of reperfusion significantly reduced the infarct volume in the male mice. However, no significant gender difference was found in total infarct size in γ protein kinase C (PKC)‐knockout mice, suggesting that the neuroprotective effects of estrogen are due to the activation of a specific subtype of PKC, γPKC, a neuron‐specific PKC subtype, in the brain. We demonstrated that exogenous estrogen‐induced neuroprotection was attenuated in γPKC‐knockout mice. Immunocytochemical study showed that γPKC was translocated to nerve fiber‐like structures when observed shortly after MCAO and reperfusion. We also visualized the rapid and reversible translocation of γPKC‐GFP (green fluorescent protein) by estrogen stimulation in living CHO‐K1 cells. These results suggest that the activation of γPKC through the G‐protein‐coupled estrogen receptors on the plasma membrane is involved in the estrogen‐induced neuroprotection against focal brain ischemia.
Second-harmonic generation microscopy analysis reveals proteoglycan decorin is necessary for proper collagen organization in prostate

Abstract. Collagen remodeling occurs in many prostate pathologies; however, the underlying structural architecture in both normal and diseased prostatic tissues is largely unexplored. Here, we use second-harmonic generation (SHG) microscopy to specifically probe the role of the proteoglycan decorin (Dcn) on collagen assembly in a wild type (wt) and Dcn null mouse (Dcn − / − ). Dcn is required for proper organization of collagen fibrils as it regulates size by forming an arch-like structure at the end of the fibril. We have utilized SHG metrics based on emission directionality (forward–backward ratio) and relative conversion efficiency, which are both related to the SHG coherence length, and found more disordered fibril organization in the Dcn − / − . We have also used image analysis readouts based on entropy, multifractal dimension, and wavelet transforms to compare the collagen fibril/fiber architecture in the two models, where all these showed that the Dcn − / − prostate comprised smaller and more disorganized collagen structures. All these SHG metrics are consistent with decreased SHG phase matching in the Dcn − / − and are further consistent with ultrastructural analysis of collagen in this model in other tissues, which show a more random distribution of fibril sizes and their packing into fibers. As Dcn is a known tumor suppressor, this work forms the basis for future studies of collagen remodeling in both malignant and benign prostate disease.
Validity and Reliability of 2-Dimensional Video-Based Assessment to Analyze Foot Strike Pattern and Step Rate During Running: A Systematic Review

Context: Two-dimensional (2D) video-based analysis is often used by clinicians to examine the foot strike pattern (FSP) and step rate in runners. Reliability and validity of 2D video-based analysis have been questioned. Objective: To synthesize the psychometric properties of 2D video-based analysis for assessing runners’ FSP and step rate while running. Data Sources: Medline/PubMed, Science Direct, Embase, EBSCOHost/CINAHL, and Scielo were searched from their inception to August 2018. Study Selection: Studies were included if (1) they were published in English, French, Portuguese or Spanish; (2) they reported at least 1 psychometric property (validity and/or reliability) of 2D video-based analysis to assess running kinematics; and (3) they assessed FSP or step rate during running. Study Design: Systematic review. Level of Evidence: Level 2. Data Extraction: Studies were screened for methodological (MacDermid checklist) and psychometric quality (COSMIN checklist) by 2 independent raters. Results: Eight studies, with a total of 702 participants, were included. Seven studies evaluated the reliability of 2D video to assess FSP and found very good to excellent reliability (0.41 ≤ κ ≤ 1.00). Two studies reported excellent reliability for the calculation of step rate (0.75 ≤ intraclass correlation coefficient [ICC] ≤ 1.00). One study demonstrated excellent concurrent validity between 2D and 3D (gold standard) motion capture systems to determine FSP (Gwet agreement coefficient [AC] > 0.90; ICC > 0.90), and another study found excellent concurrent validity between 2D video and another device to calculate step rate (0.84 ≤ ICC ≤ 0.95). Conclusion: Strong evidence suggests that 2D video-based analysis is a reliable method for assessing FSP and quantifying step rate, regardless of the experience of the assessor. Limited evidence exists on the validity of 2D video-based analysis in determining FSP and calculating step rate during running.
Improving coal mine wireless-communications performance based on MIMO technology

Transmission environment of mine laneway is non-free, wireless communication reliability is reduced by multi-path fading. MIMO can efficiently overcome multi-path fading, but MIMO channels in mine laneways have strong correlation. In this paper, the performances of space-time code in mine laneway are investigated, and the pair wise error probability (PEP) about mine laneway is analyzed. Following that, this paper proposes a novel space-time code construction which could compensate the impact of strong correlation MIMO channels in mine laneway-quasi-orthogonal space-time code. The simulation results show that the orthogonal qualification what every element must be pluralism in transfer matrix is reduced and the qualification of unattached coding is relaxed else. The less SNR is need merely under the satisfying high target bit error rate.
Psychosocial Motivators for Moderate Drinking among Young Asian Flushers in Singapore

Asians are more susceptible to alcohol flush syndrome and its associated health risks because they are genetically predisposed towards it. Guided by the theory of planned behaviour, this research examined the psychosocial factors associated with moderate alcohol consumption, in order to inform the development of a health campaign targeting young Asian “flushers” in Singapore. We employed a mixed-method design comprising an online survey and focus group discussions. The survey results identified perceived behavioural control as the most salient belief associated with moderate drinking intentions, particularly for Asian flushers. Although Asian flushers had more positive attitudes towards, and perceived behavioural control about drinking in moderation, they were more likely to consider that their peers disapprove of such a practice, compared to non-flushers. Additionally, Asian flushers did not consider themselves as having a higher risk of long-term health effects from alcohol consumption than non-Flushers despite their actual high-risk status. Focus group findings suggest that young Asian flushers have poor knowledge of, and skills associated with moderate drinking, in addition to feeling self-imposed social pressure. The study findings provide practical insights into bridging the information gap on Asian flush and promoting Asian flushers’ drinking in moderation.
Variations in Screening Quality in a Federal Colorectal Cancer Screening Program for the Uninsured

Introduction Screening can decrease colorectal cancer incidence and mortality and is recommended in clinical practice guidelines. Poor quality of colorectal cancer screening can negate the benefit of screening. The objective of this study was to assess the quality of screening services provided by the Centers for Disease Control and Prevention’s Colorectal Cancer Control Program from July 2009 through June 2015. Methods We collected data from the program’s 29 grantees, funded to provide colorectal cancer screening and diagnostic services to asymptomatic, low-income, and underinsured or uninsured adults aged 50 to 64. We collected data on the dates and results of all screening and diagnostic tests and, for colonoscopies, on whether the cecum was reached, whether bowel preparation was adequate, and endoscopists’ recommendations for the next test. Results Overall, 82.9% (range among grantees, 50.0%–97.2%) of positive FOBTs/FITs were followed up by colonoscopy; 95.2% of colonoscopies occurred within 180 days of the positive stool test. Cecal intubation rates ranged among grantees from 94.2% to 100%. Adenoma detection rates met recommended threshold levels for almost all grantees. Recommendations for rescreening and surveillance intervals deviated from guidelines in both directions. Of clients with normal colonoscopies, 85.3% (range, 37.7%–99.7%) were told to return in 10 years, as recommended in national guidelines. Of clients with advanced adenomas, 55.2% (range, 20.0%–84.6%) were told to return in 3 years as recommended, 25.4% (range, 3.8%–56.6%) in 5 or more years, and 18.6% (range, 0%–47.2%) in less than 3 years. Conclusion Although overall screening quality was good, it varied considerably. Ongoing monitoring to identify performance problems is essential for all colorectal cancer screening activities, so that efforts designed to improve performance can be targeted to individual clinicians.
Physiological Arousal Quantifying Perception of Safe and Unsafe Virtual Environments by Older and Younger Adults

Physiological arousal has been increasingly applied to monitor exploration (or navigation) of a virtual environment (VE), especially when the VE is designed to evoke an anxiety-related response. The present work aims to evaluate human physiological reactions to safe and unsafe VEs. We compared the effect of the presence of handrails in the VE in two different samples, young and older adults, through self-reports and physiological data: Electrodermal activation (EDA) and electrocardiogram (ECG) sensors. After navigation, self-report questionnaires were administered. We found that the VEs evoked a clearly differentiated perception of safety and unsafety demonstrated through self-reports, with older adults being more discriminative in their responses and reporting a higher sense of presence. In terms of physiological data, the effect of handrails did not provoke significant differences in arousal. Safety was better operationalized by discriminating neutral/non-neutral spaces, where the reaction of older adults was more pronounced than young adults. Results serve as a basis for orienting future experiments in the line of VE and applied physiology usage in the architectural spaces design process. This specific work also provided a basis for the development of applications that integrate virtual reality and applied biofeedback, tapping into mobility and ageing.
Novel Algorithm for Mining ENSO-Oriented Marine Spatial Association Patterns from Raster-Formatted Datasets

The ENSO (El Niño Southern Oscillation) is the dominant inter-annual climate signal on Earth, and its relationships with marine environments constitute a complex interrelated system. As traditional methods face great challenges in analyzing which, how and where marine parameters change when ENSO events occur, we propose an ENSO-oriented marine spatial association pattern (EOMSAP) mining algorithm for dealing with multiple long-term raster-formatted datasets. EOMSAP consists of four key steps. The first quantifies the abnormal variations of marine parameters into three levels using the mean-standard deviation criteria of time series; the second categorizes La Niña events, neutral conditions, or El Niño events using an ENSO index; then, the EOMSAP designs a linking–pruning–generating recursive loop to generate (m + 1)-candidate association patterns from an m-dimensional one by combining a user-specified support with a conditional support; and the fourth generates strong association patterns according to the user-specified evaluation indicators. To demonstrate the feasibility and efficiency of EOMSAP, we present two case studies with real remote sensing datasets from January 1998 to December 2012: one considers performance analysis relative to the ENSO-Apriori and Apriori methods; and the other identifies marine spatial association patterns within the Pacific Ocean.
Factors of importance for reducing fatigue in persons with rheumatoid arthritis: a qualitative interview study

Objective Physical activity plays an important role in the treatment of persons with rheumatoid arthritis (RA) and is the non-pharmacological intervention with the strongest evidence to reduce fatigue. However, physical activity can be challenging for persons who are fatigued. The aim of this study was to investigate factors of importance for reducing fatigue in persons with RA. Design This is a qualitative interview study based on semistructured, indepth individual interviews. Interviews were analysed using qualitative content analysis. Participants Participants were 12 people with RA recruited from a previous randomised controlled trial of a person-centred treatment model focusing on health-enhancing physical activity and daily balance to lessen fatigue in persons with RA. Setting Interviews were conducted in a hospital setting. Results The analysis resulted in one theme: an intellectual and embodied understanding that sustainable physical activity is important to handle fatigue. This included five categories describing barriers and facilitating factors for sustainable physical activity: mentally overcoming the fatigue in order to be active, making exercise easy, reaching for balance, receiving support to be physically active and dealing with RA disease to be physically active. Conclusion The participants in this study expressed that physical activity was important in handling fatigue, but also that this insight could only come from personal experience. The use of a person-centred ethic in physiotherapy coaching for patients with fatigue appears to promote sustainable physical activity behaviours by facilitating patients’ resources to overcome barriers to physical activity.
Short Communication: Asymmetric Dimethylarginine Impairs Angiogenic Progenitor Cell Function in Patients With Coronary Artery Disease Through a MicroRNA-21–Dependent Mechanism

Rationale: The endogenous nitric oxide synthase inhibitor asymmetrical dimethylarginine (ADMA) is increased in patients with coronary artery disease and may regulate function of circulating angiogenic progenitor cells (APCs) by small regulatory RNAs. Objectives: To study the role of microRNAs in ADMA-mediated impairment of APCs. Methods and Results: By using microarray analyses, we established microRNA expression profiles of human APCs. We used ADMA to induce APC dysfunction and found 16 deregulated microRNAs. We focused on miR-21, which was 3-fold upregulated by ADMA treatment. Overexpression of miR-21 in human APCs impaired migratory capacity. To identify regulated miR-21 targets, we used proteome analysis, using difference in-gel electrophoresis followed by mass spectrometric analysis of regulated proteins. We found that transfection of miR-21 precursors significantly repressed superoxide dismutase 2 in APCs, which resulted in increased intracellular reactive oxygen species concentration and impaired nitric oxide bioavailability. MiR-21 further repressed sprouty-2, leading to Erk Map kinase–dependent reactive oxygen species formation and APC migratory defects. Small interference RNA–mediated superoxide dismutase 2 or sprouty-2 reduction also increased reactive oxygen species formation and impaired APC migratory capacity. ADMA-mediated reactive oxygen species formation and APC dysfunction was rescued by miR-21 blockade. APCs from patients with coronary artery disease and high ADMA plasma levels displayed >4-fold elevated miR-21 levels, low superoxide dismutase 2 expression, and impaired migratory capacity, which could be normalized by miR-21 antagonism. Conclusions: We identified a novel miR-21–dependent mechanism of ADMA-mediated APC dysfunction. MiR-21 antagonism therefore emerges as an interesting strategy to improve dysfunctional APCs in patients with coronary artery disease.