Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of 4-Nitrophenol Oxidation in Rhodococcus sp. Strain PN1: Characterization of the Two-Component 4-Nitrophenol Hydroxylase and Regulation of Its Expression

ABSTRACT 4-Nitrophenol (4-NP) is a toxic product of the hydrolysis of organophosphorus pesticides such as parathion in soil. Rhodococcus sp. strain PN1 degrades 4-NP via 4-nitrocatechol (4-NC) for use as the sole carbon, nitrogen, and energy source. A 5-kb EcoRI DNA fragment previously cloned from PN1 contained a gene cluster (nphRA1A2) involved in 4-NP oxidation. From sequence analysis, this gene cluster is expected to encode an AraC/XylS family regulatory protein (NphR) and a two-component 4-NP hydroxylase (NphA1 and NphA2). A transcriptional assay in a Rhodococcus strain revealed that the transcription of nphA1 is induced by only 4-NP (of several phenolic compounds tested) in the presence of nphR, which is constitutively expressed. Disruption of nphR abolished transcriptional activity, suggesting that nphR encodes a positive regulatory protein. The two proteins of the 4-NP hydroxylase, NphA1 and NphA2, were independently expressed in Escherichia coli and purified by ion-exchange chromatography or affinity chromatography. The purified NphA2 reduced flavin adenine dinucleotide (FAD) with the concomitant oxidation of NADH, while the purified NphA1 oxidized 4-NP into 4-NC almost quantitatively in the presence of FAD, NADH, and NphA2. This functional analysis, in addition to the sequence analysis, revealed that this enzyme system belongs to the two-component flavin-diffusible monooxygenase family. The 4-NP hydroxylase showed comparable oxidation activities for phenol and 4-chlorophenol to that for 4-NP and weaker activities for 3-NP and 4-NC.
Apoptosis Induced by Manganese on Neuronal SK-N-MC Cell Line: Endoplasmic Reticulum (ER) Stress and Mitochondria Dysfunction

Objectives Manganese chloride (MnCl2) is one of heavy metals for causing neurogenerative dysfunction like Manganism. The purpose of this study was to determine the acute toxicity of MnCl2 using different times and various concentrations including whether manganese toxicity may involve in two intrinsic pathways, endoplasmic reticulum (ER) stress and mitochondria dysfunction and lead to neuronal apoptosis mediated by organelle disorders in neuroblastoma cell line SK-N-MC. Methods In the acute toxicity test, five concentrations (200, 400, 600, 800, 1,000 uM) of MnCl2 with 3, 6, 12, 24, 48 hours exposure were selected to analyze cell viability. In addition, to better understand their toxicity, acute toxicity was examined with 1,000 uM MnCl2 for 24 hours exposure via reactive oxygen species (ROS), mitochondria membrane potential, western blotting and mitochondrial complex activities. Results Our results showed that both increments of dose and time prompt the increments in the number of dead cells. Cells treated by 1,000 µM MnCl2 activated 265% (±8.1) caspase-3 compared to control cell. MnCl2 induced intracellular ROS produced 168% (±2.3%) compared to that of the control cells and MnCl2 induced neurotoxicity significantly dissipated 48.9% of mitochondria membrane potential compared to the control cells. Conclusions This study indicated that MnCl2 induced apoptosis via ER stress and mitochondria dysfunction. In addition, MnCl2 affected only complex I except complex II, III or IV activities.
Recognition of harmonic sounds in polyphonic audio using a missing feature approach

A method based on local spectral features and missing feature techniques is proposed for the recognition of harmonic sounds in mixture signals. A mask estimation algorithm is proposed for identifying spectral regions that contain reliable information for each sound source and then bounded marginalization is employed to treat the feature vector elements that are determined as unreliable. The proposed method is tested on musical instrument sounds due to the extensive availability of data but it can be applied on other sounds (i.e. animal sounds, environmental sounds), whenever these are harmonic. In simulations the proposed method clearly outperformed a baseline method for mixture signals.
Bisphenol A Exposure In Utero Disrupts Early Oogenesis in the Mouse

Estrogen plays an essential role in the growth and maturation of the mammalian oocyte, and recent studies suggest that it also influences follicle formation in the neonatal ovary. In the course of studies designed to assess the effect of the estrogenic chemical bisphenol A (BPA) on mammalian oogenesis, we uncovered an estrogenic effect at an even earlier stage of oocyte development—at the onset of meiosis in the fetal ovary. Pregnant mice were treated with low, environmentally relevant doses of BPA during mid-gestation to assess the effect of BPA on the developing ovary. Oocytes from exposed female fetuses displayed gross aberrations in meiotic prophase, including synaptic defects and increased levels of recombination. In the mature female, these aberrations were translated into an increase in aneuploid eggs and embryos. Surprisingly, we observed the same constellation of meiotic defects in fetal ovaries of mice homozygous for a targeted disruption of ERβ, one of the two known estrogen receptors. This, coupled with the finding that BPA exposure elicited no additional effects in ERβ null females, suggests that BPA exerts its effect on the early oocyte by interfering with the actions of ERβ. Together, our results show that BPA can influence early meiotic events and, importantly, indicate that the oocyte itself may be directly responsive to estrogen during early oogenesis. This raises concern that brief exposures during fetal development to substances that mimic or antagonize the effects of estrogen may adversely influence oocyte development in the exposed female fetus.
Selectin Ligands Sialyl-Lewis a and Sialyl-Lewis x in Gastrointestinal Cancers

The tetrasaccharide structures Siaα2,3Galβ1,3(Fucα1,4)GlcNAc and Siaα2,3Galβ1,4(Fucα1,3)GlcNAc constitute the epitopes of the carbohydrate antigens sialyl-Lewis a (sLea) and sialyl-Lewis x (sLex), respectively, and are the minimal requirement for selectin binding to their counter-receptors. Interaction of sLex expressed on the cell surface of leucocytes with E-selectin on endothelial cells allows their arrest and promotes their extravasation. Similarly, the rolling of cancer cells ectopically expressing the selectin ligands on endothelial cells is potentially a crucial step favoring the metastatic process. In this review, we focus on the biosynthetic steps giving rise to selectin ligand expression in cell lines and native tissues of gastrointestinal origin, trying to understand whether and how they are deregulated in cancer. We also discuss the use of such molecules in the diagnosis of gastrointestinal cancers, particularly in light of recent data questioning the ability of colon cancers to express sLea and the possible use of circulating sLex in the early detection of pancreatic cancer. Finally, we reviewed the data dealing with the mechanisms that link selectin ligand expression in gastrointestinal cells to cancer malignancy. This promising research field seems to require additional data on native patient tissues to reach more definitive conclusions.
Application of the premature chromosome condensation assay in simulated partial-body radiation exposures: evaluation of the use of an automated metaphase-finder.

The premature chromosome condensation (PCC) assay has been proposed as a useful and rapid end point for biological dosimetry following accidental high-dose radiation overexposures. A major benefit of the PCC assay is that it does not require cells to divide for evaluation of cytogenetic damage. The PCC assay was performed on isolated human peripheral lymphocytes exposed in vitro to doses from 1 to 9 Gy of 250 kVp x-rays. The dose-response relationships of the frequency distribution and the yield of PCC fragments in cells were determined after one day of repair at 37 degrees C. A Qpcc approach, which involves the analysis of the yield of excess PCC fragments in damaged cells, was used to establish a dose-response calibration curve. This method is identical in concept to the Qdr technique introduced by Sasaki for partial-body exposure dose-estimates using asymmetrical chromosome aberrations (i.e., dicentrics and rings) in metaphase spreads of human lymphocytes. A simulated in vitro test of a partial-body exposure to a 6-Gy dose was performed. The results from this test provided dose estimates of 5.3 +/- 0.6, 4.7 +/- 0.6, 5.0 +/- 0.6 and 4.7 +/- 0.8 Gy for the 20, 30, 50 and 75 percent component of 6-Gy irradiated cells, respectively. An automated metaphase-finding system was evaluated for use with the PCC assay. This system helped to locate PCC spreads among the mitotic inducer Chinese hamster ovary (CHO) metaphase spreads, thereby facilitating rapid scoring of samples. (ABSTRACT TRUNCATED AT 250 WORDS)
Memes in Digital Culture

In December 2012, the exuberant video "Gangnam Style" became the first YouTube clip to be viewed more than one billion times. Thousands of its viewers responded by creating and posting their own variations of the video--"Mitt Romney Style," "NASA Johnson Style," "Egyptian Style," and many others. "Gangnam Style" (and its attendant parodies, imitations, and derivations) is one of the most famous examples of an Internet meme: a piece of digital content that spreads quickly around the web in various iterations and becomes a shared cultural experience. In this book, Limor Shifman investigates Internet memes and what they tell us about digital culture. Shifman discusses a series of well-known Internet memes -- including "Leave Britney Alone," the pepper-spraying cop, LOLCats, Scumbag Steve, and Occupy Wall Street's "We Are the 99 Percent. " She offers a novel definition of Internet memes: digital content units with common characteristics, created with awareness of each other, and circulated, imitated, and transformed via the Internet by many users. She differentiates memes from virals; analyzes what makes memes and virals successful; describes popular meme genres; discusses memes as new modes of political participation in democratic and nondemocratic regimes; and examines memes as agents of globalization. Memes, Shifman argues, encapsulate some of the most fundamental aspects of the Internet in general and of the participatory Web 2.0 culture in particular. Internet memes may be entertaining, but in this book Limor Shifman makes a compelling argument for taking them seriously.
Challenges and Solutions in Battery Fuel Gauging

In recent years, the purpose of battery gas gauging has changed from providing warnings of low state of charge (SOC) to servicing applications with information needed to make critical decisions. These increasing demands have been met with improvements in measurement precision and incremental correction of existing run-time calculation methods. However, the need to provide some applications with run-time information with an error below 1% for all operational conditions calls for a radical new solution based on deep understanding of the physics governing battery response to load and its dependence on parameters such as battery age, temperature, load profile, and others.
Vector Field Based Texture Mapping of Animated Implicit Objects

This paper shows that an adequate use of vectorfields can solve most inconsistencies related to texture mapping that appear in current animation and rendering systems based on implicit objects. The method used is based on the concept of a virtual skin. A skin with its own texture mapping is spread over an implicit object and is constrained to stick to the deformation of the implicit object. A vectorfield is used to compute the relationship between the motion of the skin and the deformation of the object. Visual and implementation issues are discussed with respect to typical applications of implicit objects in computer graphics.
Functional Characterization of Recombinant Chloroplast Signal Recognition Particle*

The signal recognition particle (SRP) is a ubiquitous system for the targeting of membrane and secreted proteins. The chloroplast SRP (cpSRP) is unique among SRPs in that it possesses no RNA and is functional in post-translational as well as co-translational targeting. We have expressed and purified the two components of the Arabidopsis thaliana chloroplast signal recognition particle (cpSRP) involved in post-translational transport: cpSRP54 and the chloroplast-specific protein, cpSRP43. Recombinant cpSRP supports the efficient in vitro insertion of pea preLhcb1 into isolated thylakoid membranes. Recombinant cpSRP is a stable heterodimer with a molecular mass of ∼100 kDa as determined by analytical ultracentrifugation, gel filtration analysis, and dynamic light scattering. The interactions of the components of the recombinant heterodimer and pea preLhcb1 were probed using an immobilized peptide library (pepscan) approach. These data confirm two previously reported interactions with the L18 region and the third transmembrane helix of Lhcb1 and suggest that the interface of the cpSRP43 and cpSRP54 proteins is involved in substrate binding. Additionally, cpSRP components are shown to recognize peptides from the cleavable, N-terminal chloroplast transit peptide of preLhcb1. The interaction of cpSRP43 with cpSRP54 was probed in a similar experiment with a peptide library representing cpSPR54. The C terminus of cpSRP54 is essential for the formation of the stable cpSRP complex and cpSPR43 interacts with distinct regions of the M domain of cpSRP54.
Patterns of Self-Employment: An Empirical Comparison of Young People’s Entrepreneurial Pursuits in Poland and Ireland

This article analyses the phenomenon of self-employment and entrepreneurship among the 20-35-year-olds in the two country contexts; Poland and Ireland, and the capital cities of Warsaw and Dublin, respectively, in 2005. It seeks to compare motivations driving the choice of an autonomous style of work; role of social capital both for decisions to start up as well as for subsequent economic performance; the value of an institutional environment for entrepreneurial efforts. It examines such aspects through the prism of the economic and socio-cultural characteristics of the countries in question. By this, the article draws a broad picture of findings that may inform individual as well as macro-related characteristics of entrepreneurship.
Women in senior management positions : an exploration of how they balance their roles.

The research explored how women from the University of KwaZulu-Natal balanced both their personal and professional roles in order to advance into senior management positions. The study used a qualitative research methodology in which semistructured interviews were conducted on nine participants. The data were then analysed using Qualitative Thematic Analysis. The findings of this study revealed that although the participants faced various challenges, which were related to their gender they did manage to advance into senior management positions. What facilitated their advancement was that these women learned how to balance their dual roles through observing and imitating positive role models, which is supported by Bandura’s Social Learning Theory. The findings of the study were both confirmed and disconfirmed by the literature. However what this study does show is that women are managing to advance into positions of senior management despite challenges that they may face and thus indicting that the glass ceiling is cracking. Management should therefore be prepared to manage this new breed of managers in their echelons.
NF-κB/Rel: agonist and antagonist roles in HIV-1 latency

Purpose of reviewTo discuss recent advances in our understanding of the diverse roles of NF-κB/Rel family members in HIV-1 latency. Recent findingsVarious NF-κB/Rel family members can reinforce maintenance of HIV-1 latency. For example, p50 recruits histone deacetylase 1 to the HIV-1 long terminal repeat promoting chromatin condensation and reduced RNA Pol II recruitment. Low-level NF-κB activation during homeostatic proliferation of memory CD4 T cells induced by IL-7 and TCR signaling or OX40 action promotes expression of antiapoptotic gene targets such as BCL2 and BCLXL. Additionally, the IκB kinase phosphorylates FOXO3a transcription factor, blocking its induction of proapoptotic genes. These combined effects promote memory CD4 T-cell survival, thus maintaining the latent reservoir. Conversely, when the nontumorigenic phorbol ester prostratin is combined with histone deacetylase inhibitors, potent synergistic activation of latent HIV-1 occurs involving nuclear expression of NF-κB. SummaryThese recent findings highlight both the antagonistic and agonistic effects of the NF-κB signaling pathway on HIV-1 latency. Synergistic inducers might be useful for flushing of latent virus from reservoirs in infected patients. The ultimate, albeit lofty, goal is to achieve full viral eradication. However, a more reasonable goal might be a functional cure where patients experience a drug-free remission.
Novel Recommendation of User-based Collaborative Filtering

Recommendation system has been widely used in various types of e-commerce sites. One of the most successful examples is the collaborative filtering algorithm. However, the traditional algorithms only aim at accuracy and ignore these factors closely related with customer satisfaction, such as novelty etc. In this paper, we defined novelty of item from the perspective of the users, designed the corresponding offline experiment scheme and evaluation metrics. The dissimilarity and the time-popularity were embedded in the traditional collaborative filtering algorithm, the ability of predicting user's future needs and coverage of recommended list were obviously improved, and the ability of recommended long tail items were also enhanced. Subject Categories and Descriptors H.2. 8 (Database Applications) Data Mining; H.5. 3 (Group and Organization Interfaces) Collaborative Computing
Bird Richness and Abundance in Response to Urban Form in a Latin American City: Valdivia, Chile as a Case Study

There is mounting evidence that urban areas influence biodiversity. Generalizations however require that multiple urban areas on multiple continents be examined. Here we evaluated the role of urban areas on avian diversity for a South American city, allowing us to examine the effects of urban features common worldwide, using the city of Valdivia, Chile as case study. We assessed the number of birds and their relative abundance in 152 grid cells of equal size (250 m2) distributed across the city. We estimated nine independent variables: land cover diversity (DC), building density (BD), impervious surface (IS),municipal green space (MG),non-municipal green space (NG), domestic garden space (DG), distance to the periphery (DP), social welfare index (SW), and vegetation diversity (RV). Impervious surface represent 41.8% of the study area, while municipal green, non-municipal green and domestic garden represent 11.6%, 23.6% and 16% of the non- man made surface. Exotic vegetation species represent 74.6% of the total species identified across the city. We found 32 bird species, all native with the exception of House Sparrow and Rock Pigeon. The most common species were House Sparrow and Chilean Swallow. Total bird richness responds negatively to IS and MG, while native bird richness responds positively to NG and negatively to BD, IS DG and, RV. Total abundance increase in areas with higher values of DC and BD, and decrease in areas of higher values of IS, SW and VR. Native bird abundance responds positively to NG and negatively to BD, IS MG, DG and RV. Our results suggest that not all the general patterns described in previous studies, conducted mainly in the USA, Europe, and Australia, can be applied to Latin American cities, having important implications for urban planning. Conservation efforts should focus on non-municipal areas, which harbor higher bird diversity, while municipal green areas need to be improved to include elements that can enhance habitat quality for birds and other species. These findings are relevant for urban planning in where both types of green space need to be considered, especially non-municipal green areas, which includes wetlands, today critically threatened by urban development.
CpG Oligodeoxynucleotides as Vaccine Adjuvants in Primates1

Synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG motifs act as immune adjuvants in mice, boosting the humoral and cellular response to coadministered Ags. CpG ODN that stimulate human PBMC are only weakly active in mice. Thus, alternative animal models are needed to monitor the activity and safety of “human” CpG ODN in vivo. This work demonstrates that rhesus macaques recognize and respond to the same CpG motifs that trigger human immune cells. Coadministering CpG ODN with heat-killed Leishmania vaccine provided significantly increased protection of macaques against cutaneous Leishmania infection. These findings indicate that rhesus macaques provide a useful model for studying the in vivo activity of human CpG motifs, and that ODN expressing these motifs act as strong immune adjuvants.
Multi-Objective control through evolutionary neuro-controller for interactive mobile robot manipulator

Effective control of autonomous robots evolving in dynamic and unpredictable environments is a hard problem. The challenging issue is to achieve this control while the robot is performing a constrained and an interactive task. Namely, our aim is endow a mobile manipulator by controllers allowing safe and effective interactions with humans. This multi criteria optimization problem includes the coordination of two or more behaviors, in order to reach global goal. We propose in this paper a new concept to achieve multi-behaviors of catching objects and avoiding moving obstacles simultaneously for autonomous mobile robot arm. The mobile robot is equipped with an arm of 7 DOF. The robot's learns to avoid obstacles by moving (translation and rotation) its base while its arm tries to catch a given target. Multi-behaviors are controlled by a combination of Continuous Time Recurrent Neural Networks (CTRNN) and Multi-Objectives Genetic Algorithms (MOGA). Furthermore, the Multi-Objective optimization helps to use one genotype for both behaviors to evaluate the CTRNN's circuit parameters. The results we obtained show that the best individual has a good fitness, meaning that the robot can catch the target with the arm and avoid moving obstacle with the base simultaneously.
Endothelial Dysfunction: Clinical Implications in Cardiovascular Disease and Therapeutic Approaches

Atherosclerosis is a chronic progressive vascular disease. It starts early in life, has a long asymptomatic phase, and a progression accelerated by various cardiovascular risk factors. The endothelium is an active inner layer of the blood vessel. It generates many factors that regulate vascular tone, the adhesion of circulating blood cells, smooth muscle proliferation, and inflammation, which are the key mechanisms of atherosclerosis and can contribute to the development of cardiovascular events. There is growing evidence that functional impairment of the endothelium is one of the first recognizable signs of development of atherosclerosis and is present long before the occurrence of atherosclerotic cardiovascular disease. Therefore, understanding the endothelium's central role provides not only insights into pathophysiology, but also a possible clinical opportunity to detect early disease, stratify cardiovascular risk, and assess response to treatments. In the present review, we will discuss the clinical implications of endothelial function as well as the therapeutic issues for endothelial dysfunction in cardiovascular disease as primary and secondary endothelial therapy. Graphical Abstract
Self-directed learning skills in air-traffic control training; An eye-tracking approach

Van Meeuwen, L. W. , Brand-Gruwel, S. , De Bock, J. J. P. R. , Kirschner, P. A. , & Van Merrienboer, J. J. G. (2010, September). Self-directed Learning Skills in Air-traffic Control Training; An Eye-tracking Approach. Paper presented at the European Association for Aviation Psychology, Budapest.