Miracle-dz/UniFAR-FTUs huggingface dataset:
Stromal Cell-derived Factor-1 and its Receptor CXCR4 are Upregulated Expression in Degenerated Intervertebral Discs

Background: Although chemokine stromal cell-derived factor 1 (SDF-1) and its receptor CXCR4 induce degradation of articular cartilage in rheumatoid arthritis (RA) and osteoarthritis (OA), the association between the SDF-1/CXCR4 pathway and degradation of the cartilaginous endplate and nucleus pulposus has not been thoroughly clarified. We investigated the expression of SDF-1 and CXCR4 in intervertebral discs (IVDs). Methods: SDF-1 and CXCR4 levels in human IVDs and the rat L5/6 motion segment were quantified by enzyme-linked immunosorbent assay. SDF-1 staining was quantified using a microscope and Image-Pro Plus software. Integrated optical density (IOD) served as the measurement parameter. The number of CXCR4 immunoreactive cells was expressed as a percentage of the total number of cells. Results: SDF-1 and CXCR4 were both expressed in IVDs, and the levels of SDF-1 and CXCR4 were both significantly higher in the degeneration group than in the normal group of human (or rat) discs. Both nucleus pulposus cells and cartilaginous endplate cells expressed the CXCR4 protein. Furthermore, a positive correlation was observed between the SDF-1 IOD value and the percentage of CXCR4-positive disc cells in the nucleus pulposus and cartilaginous endplate. The SDF-1 IOD values were significantly higher in the outer annular fibrosus and bone/endplate junction region than in the nucleus pulposus and cartilaginous endplate in the rat specimens. Conclusions: Our findings suggest upregulated expression of SDF-1 and its receptor CXCR4 in degenerated IVD.
A novel frequency-hopping spread-spectrum multiple-access network using M-ary orthogonal Walsh sequence keying

A novel frequency-hop spread-spectrum multiple-access network employing M-ary orthogonal Walsh sequence keying with noncoherent demodulation is proposed. The transmitted Walsh sequence is overlaid by a user-specific pseudonoise sequence to reduce the effect of multiple-access hits. Two Gaussian approximations for the multiple-access interference from both the dehopped slot and its neighboring slots are developed and are used to analyze the performance of the proposed network for synchronous and asynchronous hopping under nonfading and Rayleigh fading channels. The effect of imperfect hop timing synchronization at the receiver is also analyzed. It is shown that the proposed network offers significantly improved network throughput compared to networks based on traditional M-ary frequency-shift keying modulation.
Age-related changes in monocytes exacerbate neointimal hyperplasia after vascular injury

Neointimal hyperplasia is the leading cause of restenosis after endovascular interventions. It is characterized by the accumulation of myofibroblast-like cells and extracellular matrix in the innermost layer of the wall and is exacerbated by inflammation. Monocytes from either young or aged rats were applied perivascularly to injured vascular walls of young recipient animals. Monocytes from aged rats, but not young donors, increased neointima thickness. Accordingly, the gene expression profiles of CD11b+ monocytes from aged rats showed significant up-regulation of genes involved in cellular adhesion, lipid degradation, cytotoxicity, differentiation, and inflammation. These included cadherin 13 (Cdh13), colony stimulating factor 1 (Csf1), chemokine C-X-C motif ligand 1 (Cxcl1), endothelial cell-selective adhesion molecule (Esam), and interferon gamma (Ifng). In conclusion, our results suggest that the increased inflammatory and adhesive profile of monocytes contributes to pathological wall remodeling in aged-related vascular diseases.
Identification of a novel tumor necrosis factor α‐responsive region in the NCF2 promoter

The phagocyte reduced nicotinamide adenine dinucleotide phosphate oxidase is a multiprotein enzyme that catalyzes the production of microbicidal oxidants. Although oxidase assembly involves association of several membrane and cytosolic oxidase proteins, one of the cytosolic cofactors, p67phox, appears to play a more prominent role in final activation of the enzyme complex. Based on the importance of p67phox, we investigated transcriptional regulation of the p67phox gene [neutrophil cytosolic factor 2 (NCF2)] and demonstrated previously that activator protein‐1 (AP‐1) was essential for basal transcriptional activity. As p67phox can be up‐regulated by tumor necrosis factor α (TNF‐α), which activates AP‐1, we hypothesized that TNF‐α might regulate NCF2transcription via AP‐1. In support of this hypothesis, we show here that NCF2 promoter‐reporter constructs are up‐regulated by TNF‐α but only when AP‐1 factors were coexpressed. Consistent with this observation, we also demonstrate that NCF2 mRNA and p67phox protein are up‐regulated by TNF‐α in various myeloid cell lines as well as in human monocytes. It was surprising that mutagenesis of the AP‐1 site in NCF2 promoter constructs did not eliminate TNF‐α induction, suggesting additional elements were involved in this response and that AP‐1 might play a more indirect role. Indeed, we used NCF2 promoter‐deletion constructs to map a novel TNF‐α‐responsive region (TRR) located between −56 and −16 bp upstream of the translational start site and demonstrated its importance in vivo using transcription factor decoy analysis. Furthermore, DNase footprinting verified specific binding of factor(s) to the TRR with AP‐1 binding indirectly to this region. Thus, we have identified a novel NCF2 promoter/enhancer domain, which is essential for TNF‐α‐induced up‐regulation of p67phox.
Parenting “YouTube Natives”: The Impact of Pre-Roll Advertising and Text Disclosures on Parental Responses to Sponsored Child Influencer Videos

The Children's Advertising Review Unit's recent press releases involving child influencer unboxing videos expressed concern that they did not appropriately disclose sponsorship. Placement of pre-roll advertising was also cited as contributing to the blurring between content and advertising. This study investigated parents’ understanding of and responses to sponsored child influencer unboxing videos. We conducted a 2 × 3 online experiment among 418 parents that examined the influence of sponsorship text disclosure (present or absent) and sponsor pre-roll (sponsor pre-roll, nonsponsor pre-roll, and no pre-roll) on conceptual persuasion knowledge, perceptions of sponsorship transparency, and several outcome measures. We also tested the potential moderating variable of parental mediation. We found that sponsor pre-roll advertising positively impacted parents’ perceptions of sponsorship transparency, which in turn mediated attitudinal and perceptual outcomes. In addition, high levels of parental mediation conditionally impacted the indirect effect of a sponsor pre-roll advertisement via sponsorship transparency on perceptions of the unboxing video and attitudes toward the sponsor. Based on the findings, we discuss theoretical, managerial, and public policy implications.
Satellite Ecology: The Dearth of Environment Dependence

Using the Sloan Digital Sky Survey (SDSS) galaxy group catalogue of Yang et al. (2007), we study the average colour (representing star formation history) and average concentration (representing mass assembly history) of satellite galaxies as function of (i) their stellar mass, (ii) their group mass, and (iii) their group-centric radius. We find that the colours and concentrations of satellite galaxies are (almost) completely determined by their stellar mass. In particular, at fixed stellar mass, the average colours and concentrations of satellite galaxies are independent of either halo mass or halo-centric radius. We find clear evidence for mass segregation of satellite galaxies in haloes of all masses, and argue that this explains why satellites at smaller halocentric radii are somewhat redder and somewhat more concentrated. In addition, the weak colour and concentration dependence of satellite galaxies on halo mass is simply a reflection of the fact that more massive haloes host, on average, more massive satellites. Combining these results with the fact that satellite galaxies are, on average, redder and somewhat more concentrated than central galaxies of the same stellar mass, the following picture emerges: galaxies become redder and somewhat more concentrated once they fall into a bigger halo (i.e., once they become a satellite galaxy). This is a clear manifestation of environment dependence. However, there is no indication that the magnitude of the transformation (or its timescale) depends on environment; a galaxy undergoes a transition when it becomes a satellite, but it does not matter whether it becomes a satellite of a small (Milky Way sized) halo, or of a massive cluster. We discuss the implication of this ‘dearth’ of environment dependence for the physical processes responsible for transforming satellite galaxies.
Phenotypic and Genetic Heterogeneity in Vibrio cholerae O139 Isolated from Cholera Cases in Delhi, India during 2001–2006

Incidence of epidemic Vibrio cholerae serogroup O139 has declined in cholera endemic countries. However, sporadic cholera caused by V. cholerae O139 with notable genetic changes is still reported from many regions. In the present study, 42 V. cholerae O139 strains isolated from 2001 to 2006 in Delhi, India, were retrospectively analyzed to understand their phenotype and molecular characteristics. The majority of isolates were resistant to ampicillin, furazolidone and nalidixic acid. Though the integrative conjugative element was detected in all the O139 isolates, the 2004–2006 isolates remained susceptible to co-trimoxazole, chloramphenicol, and streptomycin. Cholera toxin genotype 1 was present in the majority of the O139 isolates while few had type 3 or a novel type 4. In the cholera toxin encoding gene (ctx) restriction fragment length polymorphism, the majority of the isolates harbored three copies of CTX element, of which one was truncated. In this study, the ctx was detected for the first time in the small chromosome of V. cholerae O139 and one isolate harbored 5 copies of CTX element, of which 3 were truncated. The ribotype BII pattern was found in most of the O139 isolates. Three V. cholerae O139 isolated in 2001 had a new ribotype BVIII. Pulsed-field gel electrophoresis analysis revealed clonal variation in 2001 isolates compared to the 2004–2006 isolates. Molecular changes in V. cholerae O139 have to be closely monitored as this information may help in understanding the changing genetic features of this pathogen in relation to the epidemiology of cholera.
Gastric adenocarcinoma of the fundic gland (chief cell-predominant type): A review of endoscopic and clinicopathological features

Gastric adenocarcinoma of the fundic gland (chief cell-predominant type, GA-FG-CCP) is a rare variant of well-differentiated adenocarcinoma, and has been proposed to be a novel disease entity. GA-FG-CCP originates from the gastric mucosa of the fundic gland region without chronic gastritis or intestinal metaplasia. The majority of GA-FG-CCPs exhibit either a submucosal tumor-like superficial elevated shape or a flat shape on macroscopic examination. Narrow-band imaging with endoscopic magnification may reveal a regular or an irregular microvascular pattern, depending on the degree of tumor exposure to the mucosal surface. Pathological analysis of GA-FG-CCPs is characterized by a high frequency of submucosal invasion, rare occurrences of lymphatic and venous invasion, and low-grade malignancy. Detection of diffuse positivity for pepsinogen-I by immunohistochemistry is specific for GA-FG-CCP. Careful endoscopic examination and detailed pathological evaluation are essential for early and accurate diagnosis of GA-FG-CCP. Nearly all GA-FG-CCPs are treated by endoscopic resection due to their small tumor size and low risk of recurrence or metastasis.
The Frequency of Culture-Specific Elements in the ELT Coursebooks at Elementary Schools in Turkey.

Providing cultural elements within the textbook contents is crucial for foreign language learners so that they can attain the authentic language appropriately involving some culture specific expressions that are commonly used in communication. Therefore, it is important for Turkish English learners to understand target culture for effective intercultural interactions. However, most of the course materials at elementary education in Turkey avoid including culture specific expressions as most of the course book writers are not native speakers but Turkish. The present paper pins down this issue by figuring out how much the course books focus on the culture specific expressions in foreign language teaching. To do this, three different randomly selected course books from the 6th, 7th and 8th grades at elementary education in Turkey have been evaluated in terms of the culture specific expressions. After analysing the course books the list and percentage of the cultural expressions will be portrayed.
A Hh-driven gene network controls specification, pattern and size of the Drosophila simple eyes

During development, extracellular signaling molecules interact with intracellular gene networks to control the specification, pattern and size of organs. One such signaling molecule is Hedgehog (Hh). Hh is known to act as a morphogen, instructing different fates depending on the distance to its source. However, how Hh, when signaling across a cell field, impacts organ-specific transcriptional networks is still poorly understood. Here, we investigate this issue during the development of the Drosophila ocellar complex. The development of this sensory structure, which is composed of three simple eyes (or ocelli) located at the vertices of a triangular patch of cuticle on the dorsal head, depends on Hh signaling and on the definition of three domains: two areas of eya and so expression – the prospective anterior and posterior ocelli – and the intervening interocellar domain. Our results highlight the role of the homeodomain transcription factor engrailed (en) both as a target and as a transcriptional repressor of hh signaling in the prospective interocellar region. Furthermore, we identify a requirement for the Notch pathway in the establishment of en maintenance in a Hh-independent manner. Therefore, hh signals transiently during the specification of the interocellar domain, with en being required here for hh signaling attenuation. Computational analysis further suggests that this network design confers robustness to signaling noise and constrains phenotypic variation. In summary, using genetics and modeling we have expanded the ocellar gene network to explain how the interaction between the Hh gradient and this gene network results in the generation of stable mutually exclusive gene expression domains. In addition, we discuss some general implications our model may have in some Hh-driven gene networks.
Decentralized control of adaptive sampling in wireless sensor networks

The efficient allocation of the limited energy resources of a wireless sensor network in a way that maximizes the information value of the data collected is a significant research challenge. Within this context, this article concentrates on adaptive sampling as a means of focusing a sensor's energy consumption on obtaining the most important data. Specifically, we develop a principled information metric based upon Fisher information and Gaussian process regression that allows the information content of a sensor's observations to be expressed. We then use this metric to derive three novel decentralized control algorithms for information-based adaptive sampling which represent a trade-off in computational cost and optimality. These algorithms are evaluated in the context of a deployed sensor network in the domain of flood monitoring. The most computationally efficient of the three is shown to increase the value of information gathered by approximately 83%, 27%, and 8% per day compared to benchmarks that sample in a naïve nonadaptive manner, in a uniform nonadaptive manner, and using a state-of-the-art adaptive sampling heuristic (USAC) correspondingly. Moreover, our algorithm collects information whose total value is approximately 75% of the optimal solution (which requires an exponential, and thus impractical, amount of time to compute).
Infrared Light Curves of Mira Variable Stars from COBE DIRBE Data

We have used the COBE DIRBE database to derive near- and mid-infrared light curves for a well-defined sample of 38 infrared-bright Mira variable stars and compared with optical data from the AAVSO. In general the 3.5 and 4.9 μm DIRBE bandpasses provide the light curves with the best signal-to-noise ratio (S/N), with S/N decreasing with wavelength at longer wavelengths. At 25 μm good light curves are only available for ∼10% of our stars, and at wavelengths ≥60 μm extracting high quality light curves is not possible. The amplitude of variability is typically less in the near-infrared than in the optical and less in the mid-infrared than in the near-infrared, with decreasing amplitude with increasing wavelength. On average there are 0.20 ± 0.01 mag variation at 1.25 μm and 0.14 ± 0.01 mag variation at 4.9 μm for each magnitude variation in V. The observed amplitudes are consistent with results of recent theoretical models of circumstellar dust shells around Mira variables. For a few stars in our sample we find clear evidence of time lags between the optical and near-infrared maxima of phase ∼0.05–0.13, with no lags in the minima. For three stars mid-infrared maximum appears to occur slightly before that in the near-infrared, but after optical maximum. We find three examples of secondary maxima in the rising portions of the DIRBE light curves, all of which have optical counterparts in the AAVSO data, supporting the hypothesis that they are due to shocks rather than newly formed dust layers. We find no conclusive evidence for rapid (hours to days) variations in the infrared brightnesses of these stars.
Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering

Homing endonucleases (HEs) cleave long (∼20 bp) DNA target sites with high site specificity to catalyze the lateral transfer of parasitic DNA elements. In order to determine whether comprehensive computational design could be used as a general strategy to engineer new HE target site specificities, we used RosettaDesign (RD) to generate 3200 different variants of the mCreI LAGLIDADG HE towards 16 different base pair positions in the 22 bp mCreI target site. Experimental verification of a range of these designs demonstrated that over 2/3 (24 of 35 designs, 69%) had the intended new site specificity, and that 14 of the 15 attempted specificity shifts (93%) were achieved. These results demonstrate the feasibility of using structure-based computational design to engineer HE variants with novel target site specificities to facilitate genome engineering.
Functional distinctiveness of major plant lineages

Plant traits vary widely across species and underpin differences in ecological strategy. Despite centuries of interest, the contributions of different evolutionary lineages to modern‐day functional diversity remain poorly quantified. Expanding data bases of plant traits plus rapidly improving phylogenies enable for the first time a data‐driven global picture of plant functional diversity across the major clades of higher plants. We mapped five key traits relevant to metabolism, resource competition and reproductive strategy onto a phylogeny across 48324 vascular plant species world‐wide, along with climate and biogeographic data. Using a novel metric, we test whether major plant lineages are functionally distinctive. We then highlight the trait–lineage combinations that are most functionally distinctive within the present‐day spread of ecological strategies. For some trait–clade combinations, knowing the clade of a species conveys little information to neo‐ and palaeo‐ecologists. In other trait–clade combinations, the clade identity can be highly revealing, especially informative clade–trait combinations include Proteaceae, which is highly distinctive, representing the global slow extreme of the leaf economic spectrum. Magnoliidae and Rosidae contribute large leaf sizes and seed masses and have distinctively warm, wet climatic distributions. Synthesis. This analysis provides a shortlist of the most distinctive trait–lineage combinations along with their geographic and climatic context: a global view of extant functional diversity across the tips of the vascular plant phylogeny.
A two-cilia model for vertebrate left-right axis specification.

The mechanisms underlying vertebrate left-right (L-R) axis specification have attracted much interest among developmental biologists (for review, see Burdine and Schier 2000; Capdevila et al. 2000). Of particular interest from a conceptual standpoint is the question of how L-R positional information first originates within the context of a bilaterally symmetric embryo. To achieve the consistent L-R handedness characteristic of the vertebrate body plan, the L-R axis must be reliably oriented with respect to the other two embryonic axes, anteroposterior (A-P) and dorsoventral (D-V; Brown and Wolpert 1990). Understanding how embryos achieve this goal without reference to any external cues represents a formidable challenge for embryologists and theoretical biologists alike. The first breakthrough in understanding the molecular basis of handed asymmetry was the discovery of a cascade of signals produced asymmetrically in the early embryo that was sufficient to direct the orientation of later L-R morphogenetic events (Levin et al. 1995). This, together with subsequent reports identifying additional genes expressed asymmetrically in the early embryo, opened the door to ongoing work directed at understanding how L-R positional information is propagated in the embryo as well as how this information is ultimately translated into morphological manifestations of L-R asymmetry (for review, see Burdine and Schier 2000; Capdevila et al. 2000). Perhaps most important, however, were the general patterns of asymmetric gene expression first reported by Levin et al. (1995)—initial tightly localized domains of asymmetric gene expression at the chick node (ActRIIa, Shh, and then Nodal medially) followed by broad domains of asymmetric gene expression throughout the lateral plate (Nodal in the left lateral plate mesoderm). Significantly, although some of the specific molecular players appear to vary across different species, the node has consistently been the location where the earliest molecular asymmetries are centered, drawing attention to this region as the most likely site for the initial symmetry breaking event responsible for specifying the orientation of the L-R axis (Vogan and Tabin 1999; Capdevila et al. 2000). The precise manner in which asymmetric gene expression might first be established, however, remained a mystery until a second breakthrough discovery documenting the existence of motile monocilia and directional fluid flow at the mouse node (Nonaka et al. 1998).