Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyruvate Formate-lyase and Its Activation by Pyruvate Formate-lyase Activating Enzyme*

Background: PFL is a glycyl radical enzyme (GRE) activated by a radical AdoMet-activating enzyme (PFL-AE). Results: Equilibrium constants for PFL-AE binding to PFL and AdoMet are determined, and the effects of substrates on activation are quantified. Conclusion: In vivo, PFL-AE exists largely in complex with PFL and AdoMet. Significance: GREs play key roles in anaerobic metabolism, but their activation is poorly understood. The activation of pyruvate formate-lyase (PFL) by pyruvate formate-lyase activating enzyme (PFL-AE) involves formation of a specific glycyl radical on PFL by the PFL-AE in a reaction requiring S-adenosylmethionine (AdoMet). Surface plasmon resonance experiments were performed under anaerobic conditions on the oxygen-sensitive PFL-AE to determine the kinetics and equilibrium constant for its interaction with PFL. These experiments show that the interaction is very slow and rate-limited by large conformational changes. A novel AdoMet binding assay was used to accurately determine the equilibrium constants for AdoMet binding to PFL-AE alone and in complex with PFL. The PFL-AE bound AdoMet with the same affinity (∼6 μm) regardless of the presence or absence of PFL. Activation of PFL in the presence of its substrate pyruvate or the analog oxamate resulted in stoichiometric conversion of the [4Fe-4S]1+ cluster to the glycyl radical on PFL; however, 3.7-fold less activation was achieved in the absence of these small molecules, demonstrating that pyruvate or oxamate are required for optimal activation. Finally, in vivo concentrations of the entire PFL system were calculated to estimate the amount of bound protein in the cell. PFL, PFL-AE, and AdoMet are essentially fully bound in vivo, whereas electron donor proteins are partially bound.
Sgs1's roles in DNA end resection, HJ dissolution, and crossover suppression require a two-step SUMO regulation dependent on Smc5/6

In this study, Bermudez-Lopez et al. investigated the molecular regulation of the RecQ helicase (Bloom/Sgs1), which plays critical roles during DNA repair by homologous recombination. The authors provide new insights into the regulation of recruitment and activation of Sgs1 at damaged sites by showing that the Sgs1 is recruited and activated at sites of DNA damage by the Smc5/6 complex through SUMOylation.
1918 pandemic influenza virus and Streptococcus pneumoniae co‐infection results in activation of coagulation and widespread pulmonary thrombosis in mice and humans

To study bacterial co‐infection following 1918 H1N1 influenza virus infection, mice were inoculated with the 1918 influenza virus, followed by Streptococcus pneumoniae (SP) 72 h later. Co‐infected mice exhibited markedly more severe disease, shortened survival time and more severe lung pathology, including widespread thrombi. Transcriptional profiling revealed activation of coagulation only in co‐infected mice, consistent with the extensive thrombogenesis observed. Immunohistochemistry showed extensive expression of tissue factor (F3) and prominent deposition of neutrophil elastase on endothelial and epithelial cells in co‐infected mice. Lung sections of SP‐positive 1918 autopsy cases showed extensive thrombi and prominent staining for F3 in alveolar macrophages, monocytes, neutrophils, endothelial and epithelial cells, in contrast to co‐infection‐positive 2009 pandemic H1N1 autopsy cases. This study reveals that a distinctive feature of 1918 influenza virus and SP co‐infection in mice and humans is extensive expression of tissue factor and activation of the extrinsic coagulation pathway leading to widespread pulmonary thrombosis. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Prevalence of nontuberculous mycobacterial lung disease in U.S. Medicare beneficiaries.

RATIONALE Pulmonary nontuberculous mycobacteria (PNTM) are an important cause of morbidity among older adults in the United States, but national prevalence estimates are lacking. OBJECTIVES To describe the prevalence and trends of PNTM disease among adults aged 65 years or older throughout the United States. METHODS A nationally representative 5% sample of Medicare Part B beneficiaries was analyzed from 1997 to 2007. Demographic and medical claims data were compiled and prevalence estimates for PNTM and selected comorbidities were calculated and trends over time evaluated. Logistic regression was used to identify demographic and geographic factors associated with PNTM. MEASUREMENTS AND MAIN RESULTS From 1997 to 2007, the annual prevalence significantly increased from 20 to 47 cases/100,000 persons, or 8.2% per year. The period prevalence was 112 cases/100,000 persons, although prevalence was twofold higher among Asians/Pacific Islanders than among whites (228 vs. 116 cases/100,000 persons). Western states had the highest period prevalence at 149 cases/100,000 persons, with Hawaii having the highest prevalence at 396 cases/100,000 persons, followed by southeastern states, which had a period prevalence of 131 cases/100,000 persons. PNTM cases had more comorbid conditions than noncases and were 40% more likely to die than noncases. Women were 1.4 times more likely to be a PNTM case than men. Relative to whites, Asians/Pacific Islanders were twice as likely to be a case, whereas blacks were half as likely. CONCLUSIONS The prevalence of PNTM is increasing across all regions of the United States and among both men and women. Significant racial/ethnic and geographic differences suggest important gene-environment interactions.
Microvesicular Fatty Liver in Rats with Resembling Reye's Syndrome Induced by 4‐Pentenoic Acid

To produce an animal model of Reye's syndrome (RS), 20 adult male Wistar rats were given 10 repeated i.p. injections of 50 mg/kg 4‐pentenoic acid (PA) each separated by an 8‐h interval. Then, 90min after the tenth dose, they were given a final i.p. injection of 150 mg/kg PA. Thirteen control animals were injected with vehicle only using the same time schedule. More than half the animals in each group were fed a common diet, but the others were fasted during the terminal 10‐h stage. All rats were sacrificed 30 min after the last injection. At the terminal stage, in comparison with the vehicle‐injected controls, hypolipemia, hypoglycemia and high titers of serum ammonia and urea N were estimated significantly in the PA treated rats fed throughout the whole period. Hypolipemia and hypoglycemia were more prominent in the terminally fasted group than the group fed continuously. Only in the PA‐treated rats fed throughout the whole period moderate morphological signs of microvesicular fatty liver were exhibited. Ultracytochemical findings and biochemical determinations showed that the major lipids in the microvesicular fatty livers were triglycerides. Morphometric analysis revealed distinct hepatic mitochondrial swelling in the PA‐treated rats. Therefore, the above treatment with PA was able to induce microvesicular fatty liver in rats with resembling RS, which were fed throughout the treatment procedure, but not in the terminally fasted rats.
Brand equity in a tourism destination: a case study of domestic tourists in Hoi An city, Vietnam

Purpose This paper aims to propose and investigate the relationships among the components of brand equity, and examining the effects of these components on overall destination brand equity in Hoi An tourism destination, Vietnam, from the perspective of domestic tourists. Design/methodology/approach Questionnaire data were collected from 319 domestic tourists who have visited Hoi An city. The results of empirical tests using a structural equation model support the research hypotheses. Findings The results indicate that destination brand awareness has significant, positive effects on destination brand image and destination perceived quality; destination brand image has positive influences on destination perceived quality and destination brand loyalty; destination perceived quality has significant, positive impacts on destination brand loyalty; except for destination brand image, the remaining dimensions have positive and direct impacts on overall destination brand equity. Originality/value An integrated model of destination brand equity dimensions and overall destination brand equity was tested in a tourism city in the context of a developing economy. Moreover, relevant implications are provided for destination marketers as to how to improve destination brand equity in the tourism industry.
Potential implications of endogenous aldehydes in β‐amyloid misfolding, oligomerization and fibrillogenesis

Aldehydes are capable of inducing protein cross‐linkage. An increase in aldehydes has been found in Alzheimer's disease. Formaldehyde and methylglyoxal are produced via deamination of, respectively, methylamine and aminoacetone catalyzed by semicarbazide‐sensitive amine oxidase (SSAO, EC 1.4. 3.6. The enzyme is located on the outer surface of the vasculature, where amyloidosis is often initiated. A high SSAO level has been identified as a risk factor for vascular disorders. Serum SSAO activity has been found to be increased in Alzheimer's patients. Malondialdehyde and 4‐hydroxynonenal are derived from lipid peroxidation under oxidative stress, which is also associated with Alzheimer's disease. Aldehydes may potentially play roles in β‐amyloid aggregation related to the pathology of Alzheimer's disease. In the present study, thioflavin‐T fluorometry, dynamic light scattering, circular dichroism spectroscopy and atomic force microscopy were employed to reveal the effect of endogenous aldehydes on β‐amyloid at different stages, i.e. β‐sheet formation, oligomerization and fibrillogenesis. Formaldehyde, methylglyoxal and malondialdehyde and, to a lesser extent, 4‐hydroxynonenal are not only capable of enhancing the rate of formation of β‐amyloid β‐sheets, oligomers and protofibrils but also of increasing the size of the aggregates. The possible relevance to Alzheimer's disease of the effects of these aldehydes on β‐amyloid deposition is discussed.
Family Firm Reputation and Humanization: Consumers and the Trust Advantage of Family Firms Under Different Conditions of Brand Familiarity

Pioneering conceptual and empirical work ascribe a trust advantage to family firms compared with their nonfamily analogies. But it remains unknown if this trust advantage persists with varying degrees of consumers’ brand familiarity. Furthermore, the underlying cognitive mechanisms in the minds of consumers that trigger the trust advantage remain unexplored. Using mixed methods, four studies indicate that family firms’ trust advantage does prevail in the context of real and familiar brands, and the strength of consumers’ perception of an organization as a human being (i.e., humanization) explains higher levels of benevolence and trust attributed to family firms.
Differences in the metabolic properties of gluteus medius and superficial digital flexor muscles and the effect of water treadmill training in the horse.

REASONS FOR PERFORMING STUDY Flexor tendon injury may be due to flexor muscle fatigue, contributing to fetlock joint hyperextension and tendon damage. A water treadmill provides resistance training on flexor tendon muscles, which might reduce the risk of tendon injury. OBJECTIVE To determine the effect of water treadmill training on the properties of the gluteal and superficial digital flexor (SDF) muscles and on cardiocirculatory response to a standardised exercise test. METHODS Five healthy unfit horses were trained on a water treadmill for 5 days/week for 4 weeks, starting with 5 min/day increasing to 20 min/day. Before and after the water treadmill training, an incremental SET was performed on a land treadmill to determine velocity at a heart rate 200 beats/min (V(200)) and resting gluteal and SDF muscle biopsies were obtained for biochemical analyses. RESULTS There was no measurable difference in resting concentrations of gluteal or SDF muscle glycogen, lactate, ATP or glucose-6-phosphate (G6P), or activities of citrate synthase (CS), 3-hydroxyacyl CoA dehydrogenase (HAD) and lactate dehydrogenase (LDH) after training and no change in V(200), Lactate, glycogen, G6P and ATP concentrations were 50% lower and type 1 fibres 30% higher in SDF compared to gluteal muscles. CS and HAD activities were similar between SDF and gluteal, while LDH was lower in the SDF muscle. CONCLUSIONS A more strenuous water treadmill conditioning protocol may be needed to induce a training effect in gluteal and SDF muscle and heart rate response. The low substrate concentrations and oxidative capacity of SDF may predispose this muscle to catastrophic fatigue during maximal exercise.
Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture

In earlier studies, the pathway of toluene and m- and p-xylene degradation (TOL pathway) in Pseudomonas putida (pWW0) was found to be subject to catabolite repression when the strain was grown at the maximal rate on glucose or succinate in the presence of an inducer. This report describes catabolite repression of the TOL pathway by succinate in chemostat cultures run at a low dilution rate (D = 0.05 h-1) under different conditions of inorganic-nutrient limitation. The activity of benzylalcohol dehydrogenase (BADH) in cell extracts was used as a measure of the expression of the TOL upper pathway. When cells were grown in the presence of 10 to 15 mM succinate under conditions of phosphate or sulfate limitation, the BADH activity in response to the nonmetabolizable inducer o-xylene was less than 2% of that of cells grown under conditions of succinate limitation. Less repression was found under conditions of ammonium or oxygen limitation (2 to 10% and 20 to 35%, respectively, of the BADH levels under succinate limitation). The BADH expression levels determined under the different growth conditions appeared to correlate well with the mRNA transcript levels from the upper pathway promoter (Pu), which indicates that repression was due to a blockage at the transcriptional level. The meta-cleavage pathway was found to be less susceptible to catabolite repression. The results obtained suggest that the occurrence of catabolite repression is related to a high-energy status of the cells rather than to a high growth rate or directly to the presence of growth-saturating concentrations of a primary carbon and energy source.
Rapid prototyping of digital controllers for microgrid inverters

A rapid prototyping methodology for digital controllers is presented in this paper. Its main application is in the development, debugging and test of microgrid inverter controllers. To fulfill the application requirements, these systems are characterized by complex multilayer architectures, extending from PWM and current control loops up to global optimization and high level communication functions. The complexity and the wide variability of the different layer implementations make digital control mandatory. However, developing so complex digital controllers on conventional hardware platforms, like DSPs or even FPGAs, is not the most practical choice. The paper shows how multi-platform control devices, where software configurable DSP functions and programmable logic circuits are efficiently combined, represent the optimal solution for this field of application. Furthermore, the paper proposes hardware in the loop real time simulation as an effective means of developing and debugging complex hardware and software co-designed controllers. A case study is presented and used to illustrate the different design and test phases, from initial concept and numerical simulation to final experimental verification.
Sharpened Error Bound for Random Sampling Based ℓ2 Regression

Given a data matrix $X \in R^{n\times d}$ and a response vector $y \in R^{n}$, suppose $n>d$, it costs $O(n d^2)$ time and $O(n d)$ space to solve the least squares regression (LSR) problem. When $n$ and $d$ are both large, exactly solving the LSR problem is very expensive. When $n \gg d$, one feasible approach to speeding up LSR is to randomly embed $y$ and all columns of $X$ into a smaller subspace $R^c$; the induced LSR problem has the same number of columns but much fewer number of rows, and it can be solved in $O(c d^2)$ time and $O(c d)$ space. We discuss in this paper two random sampling based methods for solving LSR more efficiently. Previous work showed that the leverage scores based sampling based LSR achieves $1+\epsilon$ accuracy when $c \geq O(d \epsilon^{-2} \log d)$. In this paper we sharpen this error bound, showing that $c = O(d \log d + d \epsilon^{-1})$ is enough for achieving $1+\epsilon$ accuracy. We also show that when $c \geq O(\mu d \epsilon^{-2} \log d)$, the uniform sampling based LSR attains a $2+\epsilon$ bound with positive probability.
Electrotonic architecture of type-identified alpha-motoneurons in the cat spinal cord.

1. Measurements of input resistance (RN), time constant (tau 0), and electrotonic length (Lpeel) were derived from intracellular voltage changes produced by injection of current pulses in six type-identified triceps surae alpha-motoneurons. The motoneurons were labeled with horseradish peroxidase and subsequently reconstructed and measured from serial sections. These quantitative morphological and physiological data were incorporated into detailed computer models of the motoneurons. 2. Steady-state and dynamic models were used to determine values for specific membrane resistivity (Rm) that matched the experimental estimates of RN, tau 0, and Lpeel for each motoneurons. The models were based on the following assumptions 1) the membrane was electrically passive, 2) cytoplasmic resistivity (Ri) was 70 omega-cm, and 3) "sealed-end" boundary conditions were present at dendritic terminations. We also considered the nature and magnitude of possible errors introduced by using linear (passive) computer models to match responses from motoneurons with nonlinear (i.e., voltage-dependent) conductances. 3. If we assume that the experimental measurements of RN and tau 0 were correct, uniform Rm values that reproduced the experimentally measured RN required widely varying values of Cm (1.4-8.6 microF/cm2) to match the experimental tau 0. Furthermore, the electrotonic distance to dendritic terminals was generally much greater than expected from physiological estimates of Lpeel. However, if we assumed that the RN measurements could have been underestimated by as much as 30% and that Cm = 1.0 microF/cm2, it was possible to choose spatially uniform Rm that matched the observed tau 0 in three of six cases. 4. Relaxing the assumption of spatially uniform membrane resistivity permitted us to reconcile the anatomical and physiological characteristics of all six motoneurons. Two qualitatively different models of Rm nonuniformity gave equally good fits to the experimental results 1) a step-wise increase in Rm from a low value at the soma to a much higher but uniform value over the entire dendritic tree, and 2) a monotonic increase in Rm from soma to distal dendrites as a sigmoidal function of path distance along the dendrites. The step and sigmoidal models of the spatial distribution of Rm generated different electrotonic architectures in motoneuron dendritic trees, but both gave essentially identical electrical responses at the soma. (ABSTRACT TRUNCATED AT 400 WORDS)
Effects of domestic worker legislation reform in Brazil

"In Brazil, approximately 16 per cent of women with professional occupations (more than 6 million people) held jobs as domestic workers in 2014. This occupation is historically associated with poor working conditions, such as lack of legal registration (informality), low wages and high weekly working hours. It is also a unique occupation because, until 2015, it was not governed by the same labour rules as all other private occupations. Other private occupations are subject to the Consolidated Labour Laws from 1943. Instead, labour rules for paid domestic work were set by a specific law (Law No. 5,859) in 1972 and by the 1988 Federal Constitution. The reason for this distinct treatment is the nature of the job performed by domestic workers, usually at the employers home and very close to their family". (? )
Characterization, Antimicrobial Activity and Antibiotic Susceptibility of Lactic Acid Bacteria Isolated from Food Samples

Lactic Acid Bacteria is the most important group of acid producing bacteria in food industry. The industrial importance of the LAB is proved by their generally recognized as safe (GRAS) status, because of their contribution to the healthy microflora found in human mucosal surfaces (Patil et al., 2010). They generally contains the genera in the order Lactobacillales, which includes Lactobacillus, Leuconostoc, Lactococcus,Pediococcus and Streptococcus ,
Measuring dwell time percentage from head-mounted eye-tracking data – comparison of a frame-by-frame and a fixation-by-fixation analysis

Although analysing software for eye-tracking data has significantly improved in the past decades, the analysis of gaze behaviour recorded with head-mounted devices is still challenging and time-consuming. Therefore, new methods have to be tested to reduce the analysis workload while maintaining accuracy and reliability. In this article, dwell time percentages to six areas of interest (AOIs), of six participants cycling on four different roads, were analysed both frame-by-frame and in a ‘fixation-by-fixation’ manner. The fixation-based method is similar to the classic frame-by-frame method but instead of assigning frames, fixations are assigned to one of the AOIs. Although some considerable differences were found between the two methods, a Pearson correlation of 0.930 points out a good validity of the fixation-by-fixation method. For the analysis of gaze behaviour over an extended period of time, the fixation-based approach is a valuable and time-saving alternative for the classic frame-by-frame analysis. Practitioner Summary: A fixation-by-fixation analysis is compared with a frame-by-frame method to analyse dwell time percentage. Although some considerable differences were found between the two methods, a high correlation indicates that the results are very similar. Therefore the fixation-by-fixation method could be a valuable and time-saving alternative for the frame-by-frame analysis.
Molecular cloning and functional analysis of a human cDNA encoding an Escherichia coli AlkB homolog, a protein involved in DNA alkylation damage repair.

The Escherichia coli AlkB protein is involved in protecting cells against mutation and cell death induced specifically by SN2-type alkylating agents such as methyl methanesulfonate (MMS). A human cDNA encoding a polypeptide homologous to E.coli AlkB was discovered by searching a database of expressed sequence tags (ESTs) derived from high throughput cDNA sequencing. The full-length human AlkB homolog (hABH) cDNA clone contains a 924 bp open reading frame encoding a 34 kDa protein which is 52% similar and 23% identical to E.coli AlkB. The hABH gene, which maps to chromosome 14q24, was ubiquitously expressed in 16 human tissues examined. When hABH was expressed in E.coli alkB mutant cells partial rescue of the cells from MMS-induced cell death occurred. Under the conditions used expression of hABH in skin fibroblasts was not regulated by treatment with MMS. Our findings show that the AlkB protein is structurally and functionally conserved from bacteria to human, but its regulation may have diverged during evolution.