Miracle-dz/UniFAR-FTUs huggingface dataset:
Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii

Solventogenic clostridia are anaerobic bacteria that can produce butanol, ethanol, and acetone, which can be used as biofuels or building block chemicals. Here, we show that AdhR, a σ54-dependent transcriptional activator, senses the intracellular redox status and controls alcohol synthesis in Clostridium beijerinckii. AdhR provides a new example of a GAF domain coordinating a mononuclear non-heme iron to sense and transduce the redox signal. Our study reveals a previously unrecognized functional role of σ54 in control of cellular redox balance and provides new insights into redox signaling and regulation in clostridia. Our results reveal AdhR as a novel engineering target for improving solvent production by C. beijerinckii and other solventogenic clostridia. ABSTRACT The AdhR regulatory protein is an activator of σ54-dependent transcription of adhA1 and adhA2 genes, which are required for alcohol synthesis in Clostridium beijerinckii. Here, we identified the signal perceived by AdhR and determined the regulatory mechanism of AdhR activity. By assaying the activity of AdhR in N-terminally truncated forms, a negative control mechanism of AdhR activity was identified in which the central AAA+ domain is subject to repression by the N-terminal GAF and PAS domains. Binding of Fe2+ to the GAF domain was found to relieve intramolecular repression and stimulate the ATPase activity of AdhR, allowing the AdhR to activate transcription. This control mechanism enables AdhR to regulate transcription of adhA1 and adhA2 in response to cellular redox status. The mutants deficient in AdhR or σ54 showed large shifts in intracellular redox state indicated by the NADH/NAD+ ratio under conditions of increased electron availability or oxidative stress. We demonstrated that the Fe2+-activated transcriptional regulator AdhR and σ54 control alcohol synthesis to maintain redox homeostasis in clostridial cells. Expression of N-terminally truncated forms of AdhR resulted in improved solvent production by C. beijerinckii. IMPORTANCE Solventogenic clostridia are anaerobic bacteria that can produce butanol, ethanol, and acetone, which can be used as biofuels or building block chemicals. Here, we show that AdhR, a σ54-dependent transcriptional activator, senses the intracellular redox status and controls alcohol synthesis in Clostridium beijerinckii. AdhR provides a new example of a GAF domain coordinating a mononuclear non-heme iron to sense and transduce the redox signal. Our study reveals a previously unrecognized functional role of σ54 in control of cellular redox balance and provides new insights into redox signaling and regulation in clostridia. Our results reveal AdhR as a novel engineering target for improving solvent production by C. beijerinckii and other solventogenic clostridia.
Reactive oxygen species-mediated cytoplasmic stiffening impairs the phagocytic ability of the macrophage

ABSTRACT The phagocytic ability of macrophages empowers them to enforce innate immunity. RAW264.7, THP-1 and peripheral blood mononuclear cell-derived macrophages display considerable variability with regards to their phagocytic ability. We identify the underlying causes that attenuate the phagocytic abilities of a macrophage. Deformability of the cytoplasm and cortex influences the macrophage's phagocytic ability, and macrophages use the large cell-to-cell variability of their cytoplasmic stiffness to modulate their phagocytic ability. We find that the more-deformable macrophages have a higher phagocytic ability than those that are less deformable. Further, the subcellular spatial variability of cortex stiffness gives rise to more-deformable subdomains on the membrane for pathogen ingestion. We report a previously unknown negative-feedback loop that is triggered by the phagocytic oxidative burst. Macrophages utilize the excess reactive oxygen species to stiffen the cytoplasm, reducing their phagocytic propensity. In organisms, ageing or pathological conditions impair the phagocytic ability of macrophages. Our findings identify the targets that could potentially be utilized for restoring the phagocytic ability of the defunct macrophages. Summary: Here, we explore how the deformability of macrophages impact their phagocytic ability and report a ROS-dependent cytoplasmic stiffening that reduces their phagocytic ability.
Statins reduce new-onset atrial fibrillation after acute myocardial infarction

Abstract Atrial fibrillation (AF) is an important complication of acute myocardial infarction (AMI). The association between AF and serum lipid profile is unclear and statin use for lowering the incidence of new-onset AF remains controversial. The objective of this study was to investigate whether statins confer a beneficial effect on AF after AMI. Data available in the Taiwan National Health Insurance Research Database on 32886 AMI patients between 2008 and 2011 were retrospectively analyzed. Total 27553 (83.8%) had complete 1-yr follow-up data. Cardiovascular outcomes were analyzed based on the baseline characteristics and AF type (existing, new-onset, or non-AF). AF groups had significantly higher incidence of heart failure (HF), stroke, all-cause death, and major adverse cardiac and cerebrovascular event (MACCE) after index AMI (all P < .05). In contrast, myocardial re-infarction (re-MI) was not significantly different among the three groups (P = .95). Statin use tended to be associated with lower risk of new-onset AF after AMI (HR: 0.935; 95% confidence interval (CI): 0.877–0.998; P = . 0427). Existing AF and new-onset AF subgroups had similar cardiovascular outcomes after AMI and were both inferior to the non-AF group. Statin tended to reduce new-onset AF after AMI.
Mindfulness-Based Cognitive Therapy for Improving Subjective Well-Being Among Healthy Individuals: Protocol for a Randomized Controlled Trial

Background Previous studies have indicated that higher subjective well-being works as a protective factor for health. Some studies have already shown the effects of mindfulness-based interventions on improving subjective well-being. However, these studies targeted specific populations rather than the general public. Furthermore, they assessed either life evaluation or affective aspects of subjective well-being rather than the concept as a whole, including the eudemonic aspect of well-being. Objective This study aims to investigate the effectiveness and cost-effectiveness of mindfulness-based cognitive therapy (MBCT) for improving the wholistic aspects of subjective well-being in healthy individuals. Methods This study was an 8-week, randomized, parallel-group, superiority trial with a 2-month follow-up. Healthy individuals aged 20-65 years with scores lower than 25 on the Satisfaction With Life Scale (SWLS) were eligible to participate and randomly allocated to the MBCT group or the wait-list control group. The intervention program was developed by modifying an MBCT program to improve the well-being of a nonclinical population. The primary outcome was the difference between the two groups in mean change scores from the baseline on the SWLS. The secondary outcomes included scores on the Flourishing Scale and the Scale of Positive and Negative Experience as well as the incremental cost-effectiveness ratio. Results This study began recruiting participants in July 2018 and recruitment was completed at the end of September 2019. Data collection and dataset construction was completed by the end of March 2020. Conclusions This study is unique in that it investigates MBCT’s effects on the three different aspects of subjective well-being: life evaluation, affect, and eudemonia. It is limited, as the specific effect attributable to MBCT cannot be detected because of the lack of an active control group. Trial Registration University Hospital Medical Information Network Clinical Trials Registry (UMIN-CTR) UMIN000031885; https://upload.umin. ac.jp/cgi-open-bin/ctr_e/ctr_view. cgi? recptno=R000036376 International Registered Report Identifier (IRRID) DERR1-10.2196/15892
Demarcation of Sepsis-Induced Peripheral and Central Acidosis with pH (Low) Insertion Cycle Peptide

Acidosis is a key driver for many diseases, including cancer, sepsis, and stroke. The spatiotemporal dynamics of dysregulated pH across disease remain elusive, and current diagnostic strategies do not provide localization of pH alterations. We sought to explore if PET imaging using hydrophobic cyclic peptides that partition into the cellular membrane at low extracellular pH (denoted as pH [low] insertion cycles, or pHLIC) can permit accurate in vivo visualization of acidosis. Methods: Acid-sensitive cyclic peptide c[E4W5C] pHLIC was conjugated to bifunctional maleimide-NO2A and radiolabeled with 64Cu (half-life, 12.7 h). C57BL/6J mice were administered lipopolysaccharide (15 mg/kg) or saline (vehicle) and serially imaged with [64Cu]Cu-c[E4W5C] over 24 h. Ex vivo autoradiography was performed on resected brain slices and subsequently stained with cresyl violet to enable high-resolution spatial analysis of tracer accumulation. A non–pH-sensitive cell-penetrating control peptide (c[R4W5C]) was used to confirm specificity of [64Cu]Cu-c[E4W5C]. CD11b (macrophage/microglia) and TMEM119 (microglia) immunostaining was performed to correlate extent of neuroinflammation with [64Cu]Cu-c[E4W5C] PET signal. Results: [64Cu]Cu-c[E4W5C] radiochemical yield and purity were more than 95% and more than 99%, respectively, with molar activity of more than 0.925 MBq/nmol. Significantly increased [64Cu]Cu-c[E4W5C] uptake was observed in lipopolysaccharide-treated mice (vs. vehicle) within peripheral tissues, including blood, lungs, liver, and small intestines (P < 0.001–0.05). Additionally, there was significantly increased [64Cu]Cu-c[E4W5C] uptake in the brains of lipopolysaccharide-treated animals. Autoradiography confirmed increased uptake in the cerebellum, cortex, hippocampus, striatum, and hypothalamus of lipopolysaccharide-treated mice (vs. vehicle). Immunohistochemical analysis revealed microglial or macrophage infiltration, suggesting activation in brain regions containing increased tracer uptake. [64Cu]Cu-c[R4W5C] demonstrated significantly reduced uptake in the brain and periphery of lipopolysaccharide mice compared with the acid-mediated [64Cu]Cu-c[E4W5C] tracer. Conclusion: Here, we demonstrate that a pH-sensitive PET tracer specifically detects acidosis in regions associated with sepsis-driven proinflammatory responses. This study suggests that [64Cu]Cu-pHLIC is a valuable tool to noninvasively assess acidosis associated with both central and peripheral innate immune activation.
Aerobic fitness and academic achievement: A systematic review and meta-analysis

ABSTRACT This study aims to quantify the association between aerobic fitness and academic achievement, and determine how different aerobic fitness tests and individual demographic characteristics may modify this association. It includes 41 cross-sectional and 7 longitudinal studies focusing on children and adolescents, from MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Cochrane Database and Web of Science. Pooled effect sizes (ES) were estimated for the association between aerobic fitness and specific domains of academic achievement. Subgroup analyses and meta-regressions were based on aerobic fitness tests and demographic characteristics. The ES for the association between aerobic fitness with language/reading-skills, mathematics-related skills and composite scores, were 0.23 (95% CI: 0.12; 0.34); 0.27 (95% CI: 0.19; 0.36) and 0.28 (95% CI: 0.12; 0.45), respectively. Subgroup analyses by aerobic fitness test modified these associations; additionally, analyses by sex or age showed differences between boys and girls as well as between children and adolescents. Finally, meta-regressions revealed a slight effect of body mass index on these associations. Cardiorespiratory fitness is positively associated with academic achievement. Associations were dependent on demographic and aerobic fitness test characteristics, being stronger in boys than in girls, and in children than in adolescents. Systematic review registration: PROSPERO CRD42017069677
Increased Iron Status during a Feeding Trial of Iron-Biofortified Beans Increases Physical Work Efficiency in Rwandan Women

ABSTRACT Background Iron-biofortified staple foods can improve iron status and resolve iron deficiency. However, whether improved iron status from iron biofortification can improve physical performance remains unclear. Objective This study aimed to examine whether changes in iron status from an iron-biofortified bean intervention affect work efficiency. Methods A total of 125 iron-depleted (ferritin <20 μg/L) female Rwandan university students (18–26 y) were selected from a larger sample randomly assigned to consume iron-biofortified beans (Fe-Bean; 86.1 mg Fe/kg) or conventional beans (control: 50.6 mg Fe/kg) twice daily for 18 wk (average of 314 g beans consumed/d). Blood biomarkers of iron status (primary outcome) and physical work efficiency (secondary outcome) were measured before and after the intervention. Work performed was assessed during 5-min steady-state periods at 0-, 25-, and 40-W workloads using a mechanically braked cycle ergometer. Work efficiency was calculated at 25 W and 40 W as the work accomplished divided by the energy expended at that workload above that expended at 0 W. General linear models were used to evaluate the relation between changes in iron status biomarkers and work efficiency. Results The Fe-Bean intervention had significant positive effects on hemoglobin, serum ferritin, and body iron stores but did not affect work efficiency. However, 18-wk change in hemoglobin was positively related to work efficiency at 40 W in the full sample (n = 119; estimate: 0.24 g/L; 95% CI: 0.01, 0.48 g/L; P = 0.044) and among women who were anemic (hemoglobin <120 g/L) at baseline (n = 43; estimate: 0.64 g/L; 95% CI: 0.05, 1.23 g/L; P = 0.036). Among women who were nonanemic at baseline, change in serum ferritin was positively related to change in work efficiency at 40 W (n = 60; estimate: 0.50 μg/L; 95% CI: 0.06, 0.95 μg/L; P = 0.027). Conclusions Increasing iron status during an iron-biofortified bean feeding trial improves work efficiency in iron-depleted, sedentary women. This trial was registered at clinicaltrials.gov as NCT01594359.
Computational study of substituent effect on the electronic properties of ferrocylidene acetophenones complexes

In this study, the substituent effect on the electronic, spectroscopic properties and thermodynamic parameters of neutral and oxidized states of ferrocylidene acetophenone complexes was investigated by adopting the hybrid meta exchange-correlation functional of M06-2X. The frontier orbitals and the highest occupied molecular orbitals–lowest unoccupied molecular orbitals gaps of the substituted compounds were determined. Ionization potential (IP), electron affinity, and reorganization energy values of these molecules were estimated. The thermodynamic parameters (free energy and enthalpy) of the oxidation reaction of the studied complexes were calculated. Also, a variation on the wavenumber of carbonyl group in both states was revealed. Correlations between the evaluated properties and Hammett's constant were explored.
A QUANTITATIVE ANALYSIS OF THE DRAINAGE CHARACTERISTICS OF PART OF THE SON RIVER BASIN

An attempt has been made for quantitative analysis of the study area through morphometric parameters. Quantitative morphometric analysis has been carried out for linear, relief, and areal aspects of drainage basin. 16 morphometric parameters have been calculated and analysed for the present study. The results reveal that trunk stream Son is sixth order stream and lower streams orders mostly dominate the basin. Development of stream segments is affected by slope, local relief and geological structures. The bifurcation ratio indicates that the drainage pattern influenced by geological structures and the study area lying in late juvenile stage. The shape parameters reveal less elongation and nearly square shape of the basin. Low to moderate drainage density, moderate drainage frequency and coarse drainage textures are mainly dominated in the study area.
The Georgefischeriales : a phylogenetic hypothesis 1

To obtain an understanding of the phylogenetic relationships among the Georgefischeriales, septation, cellular interactions, teliospores, basidia, cultures and nucleotide sequences from the 5« terminal domain of the nuclear large subunit rRNA gene were studied. Analyses of both morphological and molecular characters yield similar phylogenetic conclusions. The Georgefischeriales are divided into three groups, corresponding to the Eballistraceae, Georgefischeriaceae, and Tilletiariaceae. The basal dichotomy is between the Eballistraceae and the branch uniting the Georgefischeriaceae and Tilletiariaceae. The Tilletiariaceae are phragmobasidiate, whereas the Eballistraceae and the Georgefischeriaceae are holobasidiate. The Eballistraceae differ from the Georgefischeriaceae and Tilletiariaceae in the lack of the ballistospore mechanism. The systematic position of Tilletiopsis minor is unclear. The Eballistraceae, Eballistra and Phragmotaenium are proposed as new taxa. The descriptions of the Tilletiariaceae and Jamesdicksonia are emended. Except for Entyloma majus, E. parvum, Georgefischeria, Jamesdicksonia brunkii, J. obesa, Tilletiaria anomala, and Tolyposporella chrysopognis, the teleomorphic species of the Georgefischeriales are presented as new combinations.
ANALYSIS OF REPRESENTATION ALTERNATIVES FOR A MULTIPLE-OBJECTIVE FLOATING BOUND SCHEDULING PROBLEM OF A NUCLEAR POWER PLANT SAFETY SYSTEM

The simultaneous optimization of Test Intervals and Test Strategies considered in the Surveillance Requirements for Nuclear Power Plants is a multiple-objective scheduling problem which has been tackled only recently [7-8]. The formulation of this class of problems presents dependence between the current values of some variables and the allowed upper values of others, defining a domain composed by a set of disjoint subsets. In this paper we propose and study different alternatives for representing and solve the problem using multiple-objective genetic algorithms. Additionally, the concepts of ε-dominance and εapproximate Pareto set were employed to post-process and compare the outcomes. As a result, the introduced percentage representation showed the best performance.
Interaction effect of leader-member exchange and stress mindset on challenge stressor and job performance relationship

Purpose - This study integrated job demands-resources model and concept of stress mindset to examine a three-way interaction model. Testing the effect of challenge stressor, leader-member exchange and positive stress mindset on job performance. Methodology - Research data were collected from four hundred eighty-seven employees during different business in Taiwan. Hierarchical regression analysis was conducted, and results supported the three-way moderation effect. Findings- The findings suggested that when supervisors’ social support resources were strong, positive stress mindset can better improve employee’s job performance. Conclusion- There is a three-way interaction moderation effect of challenge stressors, leader-member exchange and positive stress mindset on job performance. A contribution of the present study to research is that we linked job demands-resources model and stress mindset theory to explain a boundary condition effect in stress issue.
FFT-based Identification of Data Loss Models

Recently measurement data loss has been of greater interest, due to the spread of sensor networks and the idea of Internet of things. A procedure is proposed that is able to identify the most frequently employed data loss models. It is assumed that the communication protocol provides information about data loss, i.e. the so-called data availability indicator function is known. The power spectral density (PSD) of the indicator function is representative for the model, and can be used for identification. Spectral estimation is carried out by Fast Fourier Transform (FFT) based techniques. The paper introduces the identification procedure for random independent, random block-based and a Markov model-based data loss patterns. The efficiency of the proposed method is demonstrated by simulation and measurement results. Keywords— data loss; measurement; FFT; PSD; system identification
An investigation of the effect of the covariates on survival time of Breast Cancer patients in Saudi Arabia

Breast cancer is the most common type of cancer in Saudi women, according to the Saudi Cancer Registry in King Faisal Specialist Hospital and Research Centre (KFSH and RC). Around 930 new cases is diagnosed per year, which means that 19.5% of women in Saudi Arabia (Saudi and non-Saudi). The primary objective of this work is to investigate the effect of the covariates on survival time of Breast cancer patients in Saudi Arabia in order to estimate the survival probability of the different patients with different covariate combinations. We fit the Cox proportional hazards model and predict the lifetime of any patient given her covariates. The survival data for this project will consist of a study of 8312 (8172) females and about 140 males (1.68%) patients with advanced breast cancer with thirteen covariates collected for 9-years (2004 to 2013). [Refah Alotaibi. An investigation of the effect of the covariates on survival time of Breast Cancer patients in Saudi Arabia. Cancer Biology 2017;7(2):48-54]. ISSN: 2150-1041 (print); ISSN: 2150-105X (online). http://www.cancerbio. net. 7. doi:10.7537/marscbj070217.07.
The "Grey Area": Towards a Computational Approach for Modeling the Zone of Proximal Development.

In this paper, we propose a computational approach to modeling the Zone of Proximal Development of students who learn using a natural language tutoring system for physics. We employ a student model that predicts students’ performance based on their prior knowledge and their activity when using a dialogue tutor to practice with conceptual, reflection questions about high-school physics. Furthermore, we introduce the concept of the “Grey Area”, the area in which the student model cannot predict with acceptable accuracy whether a student has mastered the knowledge components or skills present in a particular step. We envision that our approach will contribute to the way we design learning content for ITSs and the way we author dialogues for natural-language tutoring systems. We further discuss the impact of our approach on student modeling and discuss future work in systematically and rigorously evaluating the approach.
The Effect of Profitability to the Disclosure of Corporate Social Responsibility (Csr Disclosure) on Mining Companies Listed on Indonesian Stock Exchange (Bei) in the Year 2010-2012

The main objective of this study was to analyze the effect of profitability on the disclosure of Corporate Social Responsibility (CSR Disclosure). The ratio of profitability is proxied by the ROA, ROE, and net profit margin. This study was conducted by examining the effect of profitability as the independent variable on the disclosure of CSR as the dependent variable.The sample of this study was the annual report mining company listed on the Stock Exchange in the period 2010-2012. Samples were selected using purposive sampling method and acquired 63 mining companies that have met the criteria of the sample. Data were analyzed using multiple regression methods. The results of this study find that there are significant effects on profitability through ROA, ROE, and NPM on the disclosure of CSR. ROA and NPM have positive effects on the disclosure of CSR, while ROE negatively affects CSR disclosure.