Miracle-dz/UniFAR-FTUs huggingface dataset:
CTCF Prevents the Epigenetic Drift of EBV Latency Promoter Qp

The establishment and maintenance of Epstein-Barr Virus (EBV) latent infection requires distinct viral gene expression programs. These gene expression programs, termed latency types, are determined largely by promoter selection, and controlled through the interplay between cell-type specific transcription factors, chromatin structure, and epigenetic modifications. We used a genome-wide chromatin-immunoprecipitation (ChIP) assay to identify epigenetic modifications that correlate with different latency types. We found that the chromatin insulator protein CTCF binds at several key regulatory nodes in the EBV genome and may compartmentalize epigenetic modifications across the viral genome. Highly enriched CTCF binding sites were identified at the promoter regions upstream of Cp, Wp, EBERs, and Qp. Since Qp is essential for long-term maintenance of viral genomes in type I latency and epithelial cell infections, we focused on the role of CTCF in regulating Qp. Purified CTCF bound ∼40 bp upstream of the EBNA1 binding sites located at +10 bp relative to the transcriptional initiation site at Qp. Mutagenesis of the CTCF binding site in EBV bacmids resulted in a decrease in the recovery of stable hygromycin-resistant episomes in 293 cells. EBV lacking the Qp CTCF site showed a decrease in Qp transcription initiation and a corresponding increase in Cp and Fp promoter utilization at 8 weeks post-transfection. However, by 16 weeks post-transfection, bacmids lacking CTCF sites had no detectable Qp transcription and showed high levels of histone H3 K9 methylation and CpG DNA methylation at the Qp initiation site. These findings provide direct genetic evidence that CTCF functions as a chromatin insulator that prevents the promiscuous transcription of surrounding genes and blocks the epigenetic silencing of an essential promoter, Qp, during EBV latent infection.
Effect of Firefighter Masks on Monocular and Binocular Peripheral Vision

Peripheral vision can impact essential job functions of firefighters and other workers who use Self-Contained Breathing Apparatus and other full face masks. It is important for physicians to know how these masks alter peripheral vision. Also, one must understand the effect of monocular vision on peripheral vision. Using the Goldman Perimeter Machine we measured peripheral vision in the monocular and binocular state, with and without two different types of masks. The results show that monocularity causes an average loss of 23° in the nasal meridian. The use of the masks did not affect this difference. Also, the masks caused an average loss of 28° of peripheral vision in the inferior meridian. How these losses affect the ability of the users of the masks to perform their essential job functions still needs to be researched.
Vasoinhibin, an N-terminal Prolactin Fragment, Directly Inhibits Cardiac Angiogenesis in Three-dimensional Heart Culture

Vasoinhibins (Vi) are fragments of the growth hormone/prolactin (PRL) family and have antiangiogenic functions in many species. It is considered that Vi derived from PRL are involved in the pathogenesis of peripartum cardiomyopathy (PPCM). However, the pathogenic mechanism of PPCM, as well as heart angiogenesis, is not yet clear. Therefore, the aim of the present study is to clarify whether Vi act directly on angiogenesis inhibition in heart blood vessels. Endothelial cell viability was decreased by Vi treatment in a culture experiment. Furthermore, expression of proangiogenic genes, such as vascular endothelial growth factor, endothelial nitric oxide synthase, and VE-cadherin, were decreased. On the other hand, apoptotic factor gene, caspase 3, and inflammatory factor genes, tumor necrosis factor α and interleukin 6, were increased by Vi treatment. In three-dimensional left ventricular wall angiogenesis assay in mice, Vi treatment also inhibited cell migration, neovessel sprouting, and growth toward collagen gel. These data demonstrate that Vi treatment directly suppresses angiogenesis of the heart and support the hypothesis that Vi induce PPCM.
Aberrant T cell immunity triggered by human Respiratory Syncytial Virus and human Metapneumovirus infection

ABSTRACT Human Respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) are the two major etiological viral agents of lower respiratory tract diseases, affecting mainly infants, young children and the elderly. Although the infection of both viruses trigger an antiviral immune response that mediate viral clearance and disease resolution in immunocompetent individuals, the promotion of long-term immunity appears to be deficient and reinfection are common throughout life. A possible explanation for this phenomenon is that hRSV and hMPV, can induce aberrant T cell responses, which leads to exacerbated lung inflammation and poor T and B cell memory immunity. The modulation of immune response exerted by both viruses include different strategies such as, impairment of immunological synapse mediated by viral proteins or soluble factors, and the induction of pro-inflammatory cytokines by epithelial cells, among others. All these viral strategies contribute to the alteration of the adaptive immunity in order to increase the susceptibility to reinfections. In this review, we discuss current research related to the mechanisms underlying the impairment of T and B cell immune responses induced by hRSV and hMPV infection. In addition, we described the role each virulence factor involved in immune modulation caused by these viruses.
International Journal of Behavioral Nutrition and Physical Activity Parental Influences on Adolescents' Physical Activity and Sedentary Behavior: Longitudinal Findings from Project Eat-ii

Background: The long-term role that parental encouragement and attitudes about fitness and exercise play in adolescents' physical activity and sedentary behavior habits remains unclear. This paper aims to longitudinally examine how parental encouragement to be physically active and parental concern about staying fit are associated with adolescents' physical activity and sedentary behavior habits five years later.
Diffuse dermal angiomatosis of the breast: a series of 22 cases from a single institution.

BACKGROUND Diffuse dermal angiomatosis (DDA) is a rare cutaneous disorder that can affect the breast. A total of nine cases of breast involvement have been described in the literature, but there is currently no consensus in the best therapeutic approach. The objective of this study was to examine patient outcomes with such therapies in women diagnosed with DDA of the breast. METHODS Consecutive cases of DDA of the breast were retrospectively reviewed including patient demographic variables, diagnostic criteria and type of therapies. A successful outcome was defined as complete healing of chronic open breast wounds and absence of disease recurrence after cessation of therapy. RESULTS Twenty-two women (mean age, 48.4 years) diagnosed with DDA of the breast were identified between 2004 and 2012. The diagnosis was confirmed with skin biopsy in 12 patients and clinical diagnosis in the remaining ten patients. The majority of patients were obese [68.2% (15/22), average body mass index (BMI), 36.9 kg/m(2)] and at the time of diagnosis, 27.3% of patients were active smokers (6/22). Only two patients (9.1%) received isotretinoin, neither had full recovery and both patients showed recurrence when taken off of therapy. Other medical therapies showed less to no improvement. Two patients underwent successful surgical treatment. One patient had a successful outcome following breast reduction, although her postoperative course was complicated with delayed wound healing. The other patient presented with recurrence of DDA following breast reduction, and was successfully managed with bilateral simple mastectomies. CONCLUSIONS Our findings suggest that DDA of the breast is associated with macromastia, obesity and tobacco use. Isotretinoin therapy is published as having favorable outcomes to other therapies, but in this series only appears to reduce symptoms rather than eradicate DDA. Our findings indicate that other medical therapies have been attempted with limited success. Surgical management of DDA of the breast may provide definitive treatment.
Assessment of demographic and clinical data related to dental implants in a group of Turkish patients treated at a university clinic

PURPOSE This retrospective study analyzed the distribution of the dental implants with regards to age and gender of the patients and type of indication for the implant therapy, as well as the location, dimension and type of the implants. MATERIALS AND METHODS The data of demographics (age and gender), type of indication for implant therapy, anatomical location, dimensions (length and diameter) and type (bone and tissue level) of 1616 implants were recorded from patient charts between January 2000 and January 2010. Descriptive statistics were analyzed using a chi-squared test for demographic parameters, type of indication, tooth position, anatomical location, implant dimensions and type (α=.05). RESULTS The patient pool comprised of 350 women and 266 men, with a mean age of 52.12 ± 13.79 years. The difference in n% of the implants of the age groups was statistically significant between the types of indications. The difference in the position of the implants was statistically significant between the n% of the implants of all age groups. Gender did not significantly vary, except that the diameter of the implants was significantly higher for the standard diameter implants in males. The difference between the implant positions was statistically significant when considered according to indication. The relationship between implant length and anatomical location was statistically significant. CONCLUSION The indication for dental implant use is age dependent and the type and size of the implant seems to be strongly related to the location of the implant.
Up-regulation of MicroRNA-155 in Macrophages Contributes to Increased Tumor Necrosis Factor α (TNFα) Production via Increased mRNA Half-life in Alcoholic Liver Disease*

Activation of Kupffer cells (KCs) by gut-derived lipopolysaccharide (LPS) and Toll-Like Receptors 4 (TLR4)-LPS-mediated increase in TNFα production has a central role in the pathogenesis of alcoholic liver disease. Micro-RNA (miR)-125b, miR-146a, and miR-155 can regulate inflammatory responses to LPS. Here we evaluated the involvement of miRs in alcohol-induced macrophage activation. Chronic alcohol treatment in vitro resulted in a time-dependent increase in miR-155 but not miR-125b or miR-146a levels in RAW 264.7 macrophages. Furthermore, alcohol pretreatment augmented LPS-induced miR-155 expression in macrophages. We found a linear correlation between alcohol-induced increase in miR-155 and TNFα induction. In a mouse model of alcoholic liver disease, we found a significant increase in both miR-155 levels and TNFα production in isolated KCs when compared with pair-fed controls. The mechanistic role of miR-155 in TNFα regulation was indicated by decreased TNFα levels in alcohol-treated macrophages after inhibition of miR-155 and by increased TNFα production after miR-155 overexpression, respectively. We found that miR-155 affected TNFα mRNA stability because miR-155 inhibition decreased whereas miR-155 overexpression increased TNFα mRNA half-life. Using the NF-κB inhibitors, MG-132 or Bay11-7082, we demonstrated that NF-κB activation mediated the up-regulation of miR-155 by alcohol in KCs. In conclusion, our novel data demonstrate that chronic alcohol consumption increases miR-155 in macrophages via NF-κB and the increased miR-155 contributes to alcohol-induced elevation in TNFα production via increased mRNA stability.
Effect of Surface Treatment and Resin Cement on Microtensile Bond Strength of Zirconia to Dentin

To evaluate the effect of three surface treatments and two resin cements on microtensile bond strength of zirconia to dentin. Sixty human molars were embedded in acrylic resin and sectioned 3 mm below the occlusal plane. Teeth specimens and sixty zirconia specimens were randomized into 3 groups according to the following surface treatments (n=20): no treatment (control), sandblasting and silane application (SB+SI), sandblasting then silica coating and silane application (SB+SC+SI). In each group, half of the ceramic-tooth assemblies were cemented with PanaviaTM F (Kurary Dental), the rest with RelyX Unicem (3M ESPE). All specimens were cut into microtensile sticks that were loaded in tension until failure. Data were analyzed using two-way ANOVA and Tukey’s HSD test (α=0.05). The SB+SC+SC group presented higher values than SB+SI and the control group (P<0.05). Bond strength in PanaviaTM F groups were significantly higher than those in RelyX Unicem regardless of the surface treatment (P<0.05). Data indicated that both surface treatment and resin cement have significant effects on bond strength of zirconia to dentin.
Clustering-based Image Segmentation using Automatic GrabCut

GrabCut is one of the most powerful semi-automatic segmentation techniques. One main drawback of GrabCut is the need for user interaction in order to initialize the segmentation process. User interaction involves dragging a rectangle around the object of interest in the image to extract it. This restricts GrabCut for binary-label segmentation, where the image cannot be segmented into more than two; foreground and background segments. Unsupervised clustering is a powerful automatic tool for dividing images into a specified number of regions based on defined image features. The authors had introduced the SOFM clustering technique for GrabCut automation as a replacement to the user interaction. In this paper, K-means and Fuzzy C-means are introduced as new clustering techniques to automate GrabCut and improve the segmentation accuracy. Experimental results and comparisons with the previous results are carried out to test the efficiency of the proposed techniques in terms of segmentation quality and accuracy.
Characterization of three novel mechanosensitive channel activities in Escherichia coli

Mechanosensitive channels sense elevated membrane tension that arises from rapid water influx occurring when cells move from high to low osmolarity environments (hypoosmotic shock). These non-specific channels in the cytoplasmic membrane release osmotically-active solutes and ions. The two major mechanosensitive channels in Escherichia coli are MscL and MscS. Deletion of both proteins severely compromises survival of hypoosmotic shock. However, like many bacteria, E. coli cells possess other MscS-type genes (kefA, ybdG, ybiO, yjeP and ynaI). Two homologs, MscK (kefA) and YbdG, have been characterized as mechanosensitive channels that play minor roles in maintaining cell integrity. Additional channel openings are occasionally observed in patches derived from mutants lacking MscS, MscK and MscL. Due to their rare occurrence, little is known about these extra pressure-induced currents or their genetic origins. Here we complete the identification of the remaining E. coli mechanosensitive channels YnaI, YbiO and YjeP. The latter is the major component of the previously described MscM activity (~300 pS), while YnaI (~100 pS) and YbiO (~1000 pS) were previously unknown. Expression of native YbiO is NaCl-specific and RpoS-dependent. A Δ7 strain was created with all seven E. coli mechanosensitive channel genes deleted. High level expression of YnaI, YbiO or YjeP proteins from a multicopy plasmid in the Δ7 strain (MJFGH) leads to substantial protection against hypoosmotic shock. Purified homologs exhibit high molecular masses that are consistent with heptameric assemblies. This work reveals novel mechanosensitive channels and discusses the regulation of their expression in the context of possible additional functions.
In situ hybridization and immunohistochemistry of bone sialoprotein and secreted phosphoprotein 1 (osteopontin) in the developing mouse mandibular condylar cartilage compared with limb bud cartilage

Mandibular condylar cartilage is often classified as a secondary cartilage, differing from the primary cartilaginous skeleton in its rapid progress from progenitor cells to hypertrophic chondrocytes. In this study we used in situ hybridization and immunohistochemistry to investigate whether the formation of primary (tibial) and secondary (condylar) cartilage also differs with respect to the expression of two major non‐collagenous glycoproteins of bone matrix, bone sialoprotein (BSP) and secreted phosphoprotein 1 (Spp1, osteopontin). The mRNAs for both molecules were never expressed until hypertrophic chondrocytes appeared. In the tibial cartilage, hypertrophic chondrocytes first appeared at E14 and the expression of BSP and Spp1 mRNAs was detected in the lower hypertrophic cell zone, but the expression of BSP mRNA was very weak. In the condylar cartilage, hypertrophic chondrocytes appeared at E15 as soon as cartilage tissue appeared. The mRNAs for both molecules were expressed in the newly formed condylar cartilage, although the proteins were not detected by immunostaining; BSP mRNA in the condylar cartilage was more extensively expressed than that in the tibial cartilage at the corresponding stage (first appearance of hypertrophic cell zone). Endochondral bone formation started at E15 in the tibial cartilage and at E16 in the condylar cartilage. At this stage (first appearance of endochondral bone formation), BSP mRNA was also more extensively expressed in the condylar cartilage than in the tibial cartilage. The hypertrophic cell zone in the condylar cartilage rapidly extended during E15–16. These results indicate that the formation process of the mandibular condylar cartilage differs from that of limb bud cartilage with respect to the extensive expression of BSP mRNA and the rapid extension of the hypertrophic cell zone at early stages of cartilage formation. Furthermore, these results support the hypothesis that, in vivo, BSP promotes the initiation of mineralization.
Inhibition Ability of Food Cues between Successful and Unsuccessful Restrained Eaters: A Two-Choice Oddball Task

Background Previous studies have presented mixed findings on the inhibition ability in restrained eaters (REs) due to the limited amount of neural evidence and limitations of behavioral measures. The current study explores the neural correlations of the specific inhibition ability among successful restrained eaters (S-REs), unsuccessful restrained eaters (US-REs), and unrestrained eaters (UREs). Methodology and Principal Findings Three groups of females (with 13 participants in each group) completed a two-choice Oddball task, while the event-related potentials (ERPs) are recorded synchronously. Results indicate that S-REs showed inhibition deficit in processing high-energy food cues whereas US-REs show inhibition deficit in processing both low- and high-energy food cues. Conclusion Results indicate that S-REs and US-REs differ in terms of specific inhibition ability and that enhanced inhibition is essential to a successful diet.
Nitrogen in Insects: Implications for Trophic Complexity and Species Diversification

Disparities in nutrient content (nitrogen and phosphorus) between herbivores and their plant resources have lately proven to have major consequences for herbivore success, consumer‐driven nutrient cycling, and the fate of primary production in ecosystems. Here we extend these findings by examining patterns of nutrient content between animals at higher trophic levels, specifically between insect herbivores and predators. Using a recently compiled database on insect nutrient content, we found that predators exhibit on average 15% greater nitrogen content than herbivores. This difference persists after accounting for variation from phylogeny and allometry. Among herbivorous insects, we also found evidence that recently derived lineages (e.g., herbivorous Diptera and Lepidoptera) have, on a relative basis, 15%–25% less body nitrogen than more ancient herbivore lineages (e.g., herbivorous Orthoptera and Hemiptera). We elaborate several testable hypotheses for the origin of differences in nitrogen content between trophic levels and among phylogenetic lineages. For example, interspecific variation in insect nitrogen content may be directly traceable to differences in dietary nitrogen (including dilution by gut contents), selected for directly in response to the differential scarcity of dietary nitrogen, or an indirect consequence of adaptation to different feeding habits. From some functional perspectives, the magnitude rather than the source of the interspecific differences in nitrogen content may be most critical. We conclude by discussing the implications of the observed patterns for both the trophic complexity of food webs and the evolutionary radiation of herbivorous insects.
Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon1[C][W][OPEN]

The temperate grass, Brachypodium distachyon, is a useful model for studying gene networks controlling flowering. Timing of flowering is key to the reproductive success of many plants. In temperate climates, flowering is often coordinated with seasonal environmental cues such as temperature and photoperiod. Vernalization is an example of temperature influencing the timing of flowering and is defined as the process by which a prolonged exposure to the cold of winter results in competence to flower during the following spring. In cereals, three genes (VERNALIZATION1 [VRN1], VRN2, and FLOWERING LOCUS T [FT]) have been identified that influence the vernalization requirement and are thought to form a regulatory loop to control the timing of flowering. Here, we characterize natural variation in the vernalization and photoperiod responses in Brachypodium distachyon, a small temperate grass related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Brachypodium spp. accessions display a wide range of flowering responses to different photoperiods and lengths of vernalization. In addition, we characterize the expression patterns of the closest homologs of VRN1, VRN2 (VRN2-like [BdVRN2L]), and FT before, during, and after cold exposure as well as in different photoperiods. FT messenger RNA levels generally correlate with flowering time among accessions grown in different photoperiods, and FT is more highly expressed in vernalized plants after cold. VRN1 is induced by cold in leaves and remains high following vernalization. Plants overexpressing VRN1 or FT flower rapidly in the absence of vernalization, and plants overexpressing VRN1 exhibit lower BdVRN2L levels. Interestingly, BdVRN2L is induced during cold, which is a difference in the behavior of BdVRN2L compared with wheat VRN2 during cold.
Speech-Based Interactive Information Guidance System using Question-Answering Technique

This paper addresses an interactive framework for information navigation based on document knowledge base. In conventional audio guidance systems, such as those deployed in museums, the information flow is one-way and the content is fixed. In order to make an interactive guidance system, we propose the application of question-answering (QA) techniques. Since users tend to use anaphoric expressions in successive questions, we investigate appropriate handling of contextual information based on topic detection, together with the effect of using N-best information in ASR output. Moreover, we apply the QA technique to generation of system-initiative information recommendation. A navigation system on Kyoto city information was implemented. Effectiveness of the proposed techniques was confirmed through a field trial by a number of real novice users.
Epidemiology of Chronic Dialysis Patients in the Intensive Care Unit

The incidence and prevalence of end-stage renal disease (ESRD) is rising worldwide, in part due to increasing rates of diabetes, hypertension and an ageing population [1,2]. Incidence rates of patients commencing renal replacement therapy (RRT) are estimated at 109 and 354 per million population (pmp) per year in the UK and US respectively [1,2], with the highest incidence seen in patients over 75 years of age.