Miracle-dz/UniFAR-FTUs huggingface dataset:
Satellite DNA: An Evolving Topic

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
Advances in Treatment Techniques: Stereotactic Body Radiation Therapy and the Spread of Hypofractionation

Radiation therapy (RT) is an essential component of the management of many cancers. Traditionally, a course of external bream RT often involved daily treatments for a duration of 6 weeks or longer in some instances. Now, however, emerging clinical evidence indicates that, for some common cancers, the total length of treatment can be substantially shortened, offering convenience to patients and opportunities for resource utilization efficiencies. This trend toward so-called hypofractionated RT has been supported by hypothesis-driven clinical research guided by a combination of radiobiological and clinical insights and technological enhancements. The present review presents the rationale behind and current status of hypofractionation for prostate, breast, and medically inoperable early stage lung cancer.
Photobactericidal activity of phenothiazinium dyes against methicillin-resistant strains of Staphylococcus aureus.

The photodynamic antibacterial properties of a closely related series of phenothiazinium dyes were tested against several pathogenic strains of Staphylococcus aureus, four of which were methicillin-resistant. Illumination of the photosensitisers at a fluence rate of 1.75 mW cm-2 generally resulted in the enhancement of antibacterial activity in liquid culture and in greater efficacy than the methicillin analogue flucloxacillin. For methylene blue, dimethyl methylene blue and new methylene blue illumination led to increases in bactericidal activity < or = 16-fold, typically 4-fold. In addition dimethyl methylene blue and new methylene blue were active against epidemic strains of methicillin-resistant Staphylococcus aureus at concentrations lower than that of vancomycin (> or = 0.5 microM).
Melatonin As a Free Radical Scavenger: Implications for Aging and Age‐Related Diseases a

Melatonin, ~-acetyl-5-methoxytryptamine, is phylogenetically a very old molecule. Melatonin is known to exist in the dinoflagellate Gonyaulax polyedra, ' and it is perhaps produced by most if not all organisms in the animal kingdom. The conservation of this molecule during evolution may relate to its free radical scavenging ability.2 This recently discovered function of melatonin establishes a role for this indole in every organism, and indeed in every cell, from the most primitive members of the animal kingdom up to and including the was shown to be a hormone produced in and secreted from the mammalian pineal gland. In vertebrates melatonin's production in the pineal exhibits a circadian rhythm with highest blood levels of the hormone being present during the night.6 The circadian rhythm in melatonin production provides important time-of-day and time-of-year information' and, as a result, this hormonal cycle drives other 24-hour rhythms8 as well as seasonal cycles of reproduction, at least in photoperiodic mammal^. ^ Although for years melatonin was thought to be exclusively produced in the pineal gland and to function only as a hormone which acted via membrane receptors located at a few discrete sites in mammals,'O~" it was subsequently learned that in perhaps all vertebrates melatonin is found in a number of other cells and organs. l 2 , l 3 Its likely production outside the pineal gland was strongly reinforced by the observation that melatonin is even produced in unicellular organisms such as the dinoflagellate;' since they obviously lack a pineal gland, or for that matter any other organ, it is clear that individual pineal-unrelated cells can synthesize melatonin. The fact that melatonin is highly lipophilic made some investigators question Melatonin, when discovered slightly over 30 years
High-Q thin-film silicon resonators processed at temperatures below 110/spl deg/C on glass and plastic substrates

This work reports on the fabrication and characterization of thin-film silicon micromachined bridge resonators processed at temperatures below 110/spl deg/C on glass and plastic substrates. The microelectromechanical structures are electrostatically actuated and the resulting deflection is optically monitored as a function of the geometrical dimensions and the measurement pressure. Resonance frequencies in the MHz range are detected. Quality factors up to 5000 are observed in vacuum for the microresonators on glass substrates, while the quality factors for similar bridges on plastic substrates are more than one order of magnitude lower. The elementary energy dissipation processes in hydrogenated amorphous silicon based resonators are discussed.
Inherited Connective Tissue Disorders of Collagens: Lessons from Targeted Mutagenesis

The extracellular matrix (ECM) is the cell structural environment in tissues and organs. The ECM is a dynamic structure that it is constantly remodelled. It contributes to tissue integrity and mechanical properties. It is also essential for maintaining tissue homeostasis, morphogenesis and differentiation, which it does, through specific interactions with cells. The ECM is composed of a mixture of water and macromolecules classified into four main categories: collagens, proteoglycans, elastic proteins, and non-collagenous glycoproteins (also called adhesive glycoproteins). The nature, concentration and ratio of the different ECM components are all important factors in the regulation of the assembly of complex tissue-specific networks tuned to meet mechanical and biological requirements of tissues.
Novel expressions for the Marcum and one dimensional Q-functions

The aim of this work is twofold. Firstly, we derive a novel closed-form representation for the Marcum Q-function, Qm(a, b), which is valid for all values of its order m. Secondly, we propose a novel tight approximation for the one dimensional Q-function, Q(x). The high accuracy of the derived expressions is verified with the aid of computational algorithms as well as through comparisons with existing, yet limited, representations. Importantly, the derived relationships have a relatively simple algebraic form and therefore, they are convenient to handle both analytically and numerically. As a consequence, they may be considered as useful mathematical tools in analytic performance evaluations of digital communications over fading channels.
Affective priming with subliminal auditory stimulus exposure

The primacy hypothesis about affection (Zajonc, 1980) holds that positive and negative affective reactions can be elicited with minimal stimulus input and virtually no cognitive processing. This hypothesis challenges the cognitive appraisal viewpoint (Lazarus, 1982), which maintains that affection cannot emerge without prior cognitive mediation. There have been many studies shown that human emotion could be affected by subliminal visual stimulus, so how about subliminal auditory stimulus (SAS)? In this study two pieces of traditional Chinese music were used as SAS, and the unheard music was played in a continuous loop, which was different from the commonly used priming paradigm. 56 undergraduates were randomly divided into two groups, participants in one group were exposed to the subliminal happy music, and in the other group were exposed to the subliminal sad music. A before-and-after self-paired design was used to assess the emotion of all the subjects. During the experiment their galvanic skin response (GSR) and subjective ratings were recorded. The results showed that SAS caused the obviously change on human's GSR, but there was no change found in their subjective ratings of emotional valence (happy-unhappy). A lot of evidence showed that GSR was more sensitive than subjective ratings for the evaluation to current emotion status. The overall results of our study confirmed this perspective. So, we believed that SAS affected people's emotion, and this kind of affective priming wasn't perceived consciously by people themselves.
Nitrogen fixation in restored eelgrass meadows

Biological nitrogen (N2) fixation is the primary input of new nitrogen (N) to marine systems, and is important in meeting the N demands of primary producers. In this study, we deter- mined whether restoration of the eelgrass Zostera marina L. in a shallow coastal bay facilitated increasing rates of N2 fixation as the meadows aged. Rates of N2 fixation were measured in a system that had been devoid of eelgrass following local extinction in the 1930s until restoration by seeding began in 2001. Restored meadows of different ages were compared to nearby bare sediment sites during summer peak metabolism over 2 yr. Nutrient addition by N2 fixation was enhanced as the meadows aged. Rates of N2 fixation in the older (7 to 8 yr old) meadows were 2.7 times more than the younger (2 to 3 yr old) meadows (average 390 and 146 µmol N m �2 d �1 , respectively), and 28 times more than bare sediments (average 14 µmol N m �2 d �1 ). Heterotrophic epiphyte bacteria fixed approximately 90% of the total N2 in Z. marina meadows of both age classes. Both sediment and epiphyte N2 fixation were strongly related to Z. marina density and sediment organic content, suggesting that shoot density increases the positive feedback of plant presence on N2 fixation through the release of organic carbon exudates into the rhizosphere and phyllosphere, and the build up of sediment organic matter also increases. The N provided through fixation represented a large fraction (20.5 to 30%) of the total N demand to support eelgrass aboveground growth during this period of peak summertime production.
Recurrent axon collaterals of intrinsically photosensitive retinal ganglion cells

Abstract Retinal ganglion cells (RGCs), the output neurons of the retina, have axons that project via the optic nerve to diverse targets in the brain. Typically, RGC axons do not branch before exiting the retina and thus do not provide it with synaptic feedback. Although a small subset of RGCs with intraretinal axon collaterals has been previously observed in human, monkey, cat, and turtle, their function remains unknown. A small, more recently identified population of RGCs expresses the photopigment melanopsin. These intrinsically photosensitive retinal ganglion cells (ipRGCs) transmit an irradiance-coding signal to visual nuclei in the brain, contributing both to image-forming vision and to several nonimage-forming functions, including circadian photoentrainment and the pupillary light reflex. In this study, using melanopsin immunolabeling in monkey and a genetic method to sparsely label the melanopsin cells in mouse, we show that a subgroup of ipRGCs have axons that branch en route to the optic disc, forming intraretinal axon collaterals that terminate in the inner plexiform layer of the retina. The previously described collateral-bearing population identified by intracellular dye injection is anatomically indistinguishable from the collateral-bearing melanopsin cells identified here, suggesting they are a subset of the melanopsin-expressing RGC type and may therefore share its functional properties. Identification of an anatomically distinct subpopulation in mouse, monkey, and human suggests this pathway may be conserved in these and other species (turtle and cat) with intraretinal axon collaterals. We speculate that ipRGC axon collaterals constitute a likely synaptic pathway for feedback of an irradiance signal to modulate retinal light responses.
Adjunctive strategies in the treatment of refractory bipolar depression: clinician options in the absence of a systematic database

Multiple approaches to enhancing antidepressant treatment response in bipolar depression are available and should, in many instances, be explored despite a lack of definitive controlled trial literature supporting their efficacy. Given that the morbidity of depression is three times greater than mania in bipolar illness, a range of treatment approaches to this phase of illness should be pursued. This paper highlights the preliminary evidence of efficacy versus side effects, tolerability, and safety in order to suggest an overall provisional utility grade for each well-studied to highly-experimental option. Given the general paucity of evidence to support efficacy or to sequence different approaches for augmenting treatment of bipolar depression, it is critical that patient and physician adopt a systematic and, preferably, daily rating approach to the assessment of benefit for a given patient of each strategy contemplated. The goal is to achieve and maintain remission of depressive symptoms and associated comorbidities, which is often not accomplished using primary mood stabiliser treatments alone, or in combination; thus, an active clinical approach to augmentation strategies is indicated even when the literature provides only highly preliminary guidance.
Sparse-Grid Quadrature $H_\infty $ Filter for Discrete-Time Systems with Uncertain Noise Statistics

In This paper H<sub>∞</sub> technique is combined with the recently developed sparse-grid quadrature (SGQ) filtering to improve the accuracy and robustness of the state estimation when the noise statistics is not known a priori. The proposed new SGQ H<sub>∞</sub> filter (SGQH<sub>∞</sub>F) is compared with other H<sub>∞</sub> filters via two numerical examples. It is shown that the SGQH<sub>∞</sub>F is more robust and accurate than the extended H<sub>∞</sub> filter, unscented H<sub>∞</sub> filter, and cubature H<sub>∞</sub> filter. In addition it maintains a close performance to the Gauss-Hermite quadrature (GHQ) H<sub>∞</sub> filter but is computationally much more efficient since it uses far fewer quadrature points.
Quadtree and symmetry in FFT computation of digital images

The discrete Fourier transform (DFT) of a real sequence f[x, y] of size N/spl times/N, where N=2/sup n/, can be computed by a two-dimensional (2-D) FFT of size N/4, or smaller if f[x, y] is known to have certain symmetries. This paper presents theorems that identify the symmetry in f[x, y] based on the depth of the quadtree to expedite 2-D FFT computation of coherent digital images. In principle, it establishes that if the quadtree of f[x, y] has maximum depth k<n where K=2/sup n/, then the DFT can be computed by a 2-D FFT of size K/2. An algorithm is given, and its performance analyzed. Finally, applications are considered in transform coding systems and lossy compression of images.
Necessary for IL-12-Mediated Regression of the The CXC Chemokines IP-10 and Mig Are

The role of the non-ELR-containing CXC chemokines IP-10 and Mig in antitumor activity induced by systemic treatment with IL-12 was examined in mice bearing the murine renal adenocarcinoma RENCA. IL-12 treatment produces a potent antitumor effect that is associated with tumor inﬁltration by CD8 1 T lymphocytes. The regression of tumor is associated with the elevated expression of the IFN- g -inducible chemokines IP-10 and Mig within the tumor tissue. IP-10 and Mig have been shown to function as chemoattractants for activated T lymphocytes. In animals treated with rabbit polyclonal Abs speciﬁc for IP-10 and for Mig, the IL-12-induced regression of RENCA tumors was partially abrogated. This effect was associated with a dramatic inhibition of T cell inﬁltration. Thus, it appears that IL-12-dependent, T cell-mediated antitumor activity requires the intermediate expression of IP-10 and Mig to recruit antitumor effector T cells to the tumor site. The Journal of Immunology, 1998, 161: 927–932. shown agarose-formaldehyde gel, and blotted by capillary transfer onto nylon membranes. The blots prehybridized 6 to 18 h at 42°C in 50% formamide, 1% SDS, 5 3 SSC, 1 3 Denhardt’s solution (0.02% Ficoll, 0.02% BSA, and 0.02% polyvinylpyr-rolidine), 0.25 mg/ml denatured salmon sperm DNA, and 50 mM sodium phosphate buffer, pH 6.5. Hybridization was conducted at 42°C for 12 to 18 h with 10 7 cpm of denatured probe. The ﬁlters were washed twice for 15 min each time at 55°C in 0.1% SDS-0.5 3 SSC. The blots were then exposed using XAR-5 x-ray ﬁlm (Eastman Kodak, Rochester, NY) with DuPont (Wilmington, DE) Cronex Lightening Plus intensifying screens at 2 70°C. Expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA was used as an internal control and was applied in all experiments.Semiquantitative RT-PCR analysis of perforin mRNA was conducted as reported previously (6, 25, 32). One microgram of total RNA was ampliﬁed using an oligo(dT) antisense primer and AMV reverse transcriptase at 42°C for 1 h. The RT reaction products were used undiluted or at a 1/10 dilution for PCR ampliﬁcation using 20 mM sense and antisense primers (see be- low) and Taq polymerase. PCR reactions were conducted in a Perkin-Elmer/Cetus DNA Thermal Cycler for 15 cycles (denaturation, 1 min, 94°C; annealing, 1 min, 60°C; ampliﬁcation, 2 min, 72°C). The primer sequences used were as follows: perforin antisense primer, GGTGGAGT GGAGGTTTTTGTACC; and perforin sense primer, CAGAATGCAAG CAGAAGCACAAG (perforin product size, 486 bp). These primers were chosen from separate exons to ensure
Photodegradation of the herbicide penoxsulam in aqueous methanol and acetonitrile

Penoxsulam is a triazolopyrimidine sulfonamide group of rice herbicide. The phototransformation of penoxsulam was studied under UV light (λmax ≥ 290 nm) and sunlight in aqueous methanol and acetonitrile solvent system using TiO2 as sensitizer. The rate of photodegradation of penoxsulam in different solvent systems followed first-order kinetics and calculated half-lives was found to be in the range of 51.89–73.41 h and 62.70–97.09 h for UV light and sunlight respectively in the presence or absence of sensitizer. From this study, a total of six photoproducts were identified and characterized on the basis of Q-Tof micromass spectral data. The plausible mechanism of phototransformation involved were hydrolysis, photo oxidation of the sulfonamide group, breaking of sulfonamide bond, loss of amino and sulfonic acid group.
Angiostatin Diminishes Activation of the Mitogen-Activated Protein Kinases ERK-1 and ERK-2 in Human Dermal Microvascular Endothelial Cells

Angiostatin is an endogenous inhibitor of angiogenesis that was isolated from tumor-bearing mice. It has been established that angiostatin inhibits endothelial cell proliferation; however, the underlying mechanisms remain to be elucidated. Here we report that angiostatin reduces transiently the phosphorylation of the mitogen-activated protein kinases ERK-1 and ERK-2 in human dermal microvascular cells, but not in human vascular smooth muscle cells or human dermal fibroblasts. We demonstrate that angiostatin diminishes ERK activation by basic fibroblast growth factor and vascular endothelial growth factor. Dephosphorylation of ERK and other tyrosine-phosphorylated proteins was blocked by pretreatment of the cells with sodium meta-vanadate, an inhibitor of protein tyrosine phosphatases, indicating that angiostatin signaling may require the activity of a tyrosine phosphatase. Concentrations of angiostatin that inhibited ERK activation also inhibited basic fibroblast growth factor-stimulated collagen gel invasion by endothelial cells, but did not affect endothelial cell proliferation. We thus show that angiostatin inhibits primarily the invasion of endothelial cells and exerts minimal (if any) effects on their proliferation. Invasion is a process that involves proteolysis, adhesion and migration, all of which have been linked to ERK signaling.
Interaction of brefeldin A-inhibited guanine nucleotide-exchange protein (BIG) 1 and kinesin motor protein KIF21A

Brefeldin A-inhibited guanine nucleotide-exchange protein (BIG) 1 activates human ADP-ribosylation factor (ARF) 1 and 3 by accelerating the replacement of ARF-bound GDP with GTP to initiate recruitment of coat proteins for membrane vesicle formation. Liquid chromatography MS/MS analysis of peptides from proteins that co-precipitated with BIG1 antibodies identified “kinesin family member 21A” (KIF21A), a plus-end-directed motor protein that moves cargo on microtubules away from the microtubule-organizing center. Reciprocal immunoprecipitation (IP) of endogenous proteins and microscopically apparent overlap of immunoreactive BIG1 with overexpressed GFP-KIF21A in the perinuclear region were consistent with an interaction of KIF21A–BIG1. Overexpression of full-length KIF21A and BIG1 and their fragments in HEK293 cells followed by reciprocal IP revealed that the C-terminal tail of KIF21A, with seven WD-40 repeats, may interact with structure in the C-terminal region of BIG1. Interfering with cyclic activation and inactivation of ARF1 by overexpressing constitutively active ARF1(Q71L) or dominant inactive ARF1(T31N) altered the distribution of BIG1 as well as its interaction with KIF21A. A requirement for ARF1 was confirmed by its selective depletion with siRNA. Unlike disruption of microtubules with nocodazole, selective inhibition of transport by depletion of KIF21A with specific siRNA altered BIG1 distribution without changing that of intrinsic Golgi membrane proteins. These newly recognized interactions of BIG1 and KIF21A should enable us to understand better the mechanisms through which, acting together, they may integrate local events in membrane trafficking with longer-range transport processes and to relate those processes to the diverse signaling and scaffold functions of BIG1.