Miracle-dz/UniFAR-FTUs huggingface dataset:
Human papillomavirus type 16 E7 oncoprotein mediates CCNA1 promoter methylation

Human papillomavirus (HPV) oncoproteins drive distinctive promoter methylation patterns in cancer. However, the underlying mechanism remains to be elucidated. Cyclin A1 (CCNA1) promoter methylation is strongly associated with HPV‐associated cancer. CCNA1 methylation is found in HPV‐associated cervical cancers, as well as in head and neck squamous cell cancer. Numerous pieces of evidence suggest that E7 may drive CCNA1 methylation. First, the CCNA1 promoter is methylated in HPV‐positive epithelial lesions after transformation. Second, the CCNA1 promoter is methylated at a high level when HPV is integrated into the human genome. Finally, E7 has been shown to interact with DNA methyltransferase 1 (Dnmt1). Here, we sought to determine the mechanism by which E7 increases methylation in cervical cancer by using CCNA1 as a gene model. We investigated whether E7 induces CCNA1 promoter methylation, resulting in the loss of expression. Using both E7 knockdown and overexpression approaches in SiHa and C33a cells, our data showed that CCNA1 promoter methylation decreases with a corresponding increase in expression in E7 siRNA‐transfected cells. By contrast, CCNA1 promoter methylation was augmented with a corresponding reduction in expression in E7‐overexpressing cells. To confirm whether the binding of the E7–Dnmt1 complex to the CCNA1 promoter induced methylation and loss of expression, ChIP assays were carried out in E7‐, del CR3‐E7 and vector control‐overexpressing C33a cells. The data showed that E7 induced CCNA1 methylation by forming a complex with Dnmt1 at the CCNA1 promoter, resulting in the subsequent reduction of expression in cancers. It is interesting to further explore the genome‐wide mechanism of E7 oncoprotein‐mediated DNA methylation.
Using longitudinal data to define the perimenopause by menstrual cycle characteristics.

OBJECTIVES To determine which aspects of menstrual change best predict time to postmenopause. METHODS A total of 250 Australian-born women aged 45-55 years were divided into five menstrual status categories: Group I reported no change in menstrual flow or frequency; Group II reported change in flow; Group III reported change in frequency; Group IV reported change in both frequency and flow; and Group V reported between 3 and 11 months of amenorrhea. Menstrual status groups were compared on baseline data for age, hormone levels, hot flushes and self-rated menopausal status. The proportion of women moving to postmenopause in subsequent years was compared using 4 years of follow-up data. RESULTS Women in Group V were older, had lower estradiol and inhibin levels, higher follicle stimulating hormone levels, and were more likely to report hot flushes, and to self-rate themselves as having started the menopausal transition, compared with the women who had menstruated in the last 3 months (Groups I-IV). Groups I and II were similar in age and hormonal status, as were Groups III and IV. The proportion of women who had moved to postmenopausal status in the 4 years after baseline were 12%, 14%, 58%, 53% and 94% for Groups I-V, respectively. CONCLUSIONS Amenorrhea is the best predictor of future menopause followed by changes in menstrual frequency. Change in flow only was not predictive of future menopause. A two-stage classification scheme is suggested for defining the perimenopause. 'Early perimenopause' is defined as the self-reporting of changes in menstrual frequency over the last year, and 'late perimenopause' is defined as the self-report of 3-11 months of amenorrhea.
F , D 1 ) , D 3 ) Bound State , S-Duality and Noncommutative Open String / Yang-Mills Theory

We study decoupling limits and S-dualities for noncommutative open string/ Yang-Mills theory in a gravity setup by considering an SL(2, Z) invariant supergravity solutions of the form ((F, D1), D3) bound state of type IIB string theory. This configuration can be regarded as D3-brane solution with both electric and magnetic fields turned on along one of the spatial directions of the brane and preserves half of the space-time supersymmetries of the string theory. Our study indicates that there exists a decoupling limit for which the resulting theory is an open string theory defined in a geometry with noncommutativity in both spacetime and space-space directions. We study S-duality of this noncommutative open string (NCOS) and find that the same decoupling limit in the S-dual description gives rise to a space-space noncommutative Yang-Mills theory (NCYM). We also discuss independently the decoupling limit for NCYM in this D3 brane background. Here we find that S-duality of NCYM theory does not always give a NCOS theory. Instead, it can give an ordinary Yang-Mills with singular metric and infinitely large coupling. We also find that the open string coupling relation between the two S-duality related theories is modified such that S-duality of a strongly coupled open-string/Yang-Mills theory does not necessarily give a weakly coupled theory. The relevant gravity dual descriptions of NCOS/NCYM are also given.
Creative identity theft: issues for artists in collaborative online environments

This paper discusses the qualities of online activity in relation to what is 'new' in 'new media', and examines both the continued use of the technologies by artists to simply redress long standing disputes with the distribution models and editorial practices of 'old media' and the tensions created by encounters with the characteristics of the Internet as a new space for art. It then seeks to identify the features of new technologies that distinguish them from 'old media', principally the opportunities for interaction in real time, for collaboration, of skill sharing, of a wider audience that encounters work for reasons other than the contemplation of artistic work and the nature of proprietary technologies in themselves. These latter have rarely been developed specifically for artists, and often reflect the values and aims of the companies that generate them, presenting ethical and creative problems for artists who use them. The paper draws on research at the Visualisation Research Unit (VRU) at the School of Art, Birmingham City University, and its collaboration with Eastside Projects, a new gallery located in Birmingham, on the Arts Council funded project 'EP:VV' (Eastside Projects: Virtual & Visualized).
Assessing the Carbonation Behavior of Cementitious Materials

The carbonation behavior of six cementitious materials was examined (CSA Type 10 cement, CSA Type 30 cement, fly ash, ground granulated blast furnace (GGBF) slag, electric arc furnace (EAF) slag, and hydrated lime) for applicability to C O2 sequestration applications. No-slump press-formed compacts and loose powders were subjected to 100% C O2 at a constant pressure of 5 bar for 2 h . The C O2 contents of the as-received and the carbonated materials were measured. It was found that the cements, fly ash, and electric arc furnace slag could each show C O2 uptake on the order of 12%, while the lime achieved nearly 40%. The blast furnace slag managed 7% uptake. The carbon uptakes achieved were significantly lower than the theoretical maximum as determined by chemistry. The 2 h carbonation produced high early age strength in cements and hydrated lime, which can be used as structural materials. The strength gain in fly ash, EAF slag, and GGBF slag was nevertheless not sufficient. X-ray diffraction analysis dete.
Transcatheter closure of patent ductus arteriosus with a self-expanding platinum-coated nitinol device.

BACKGROUND An occluding device for closure of patent ductus arteriosus (PDA) was developed from meshed nitinol wires coated with platinum for prevention of nickel release after implantation. OBJECTIVES Our purpose was to assess the immediate and short-term results of transcatheter PDA closure with this device. METHODS Sixty patients (13 males and 47 females) underwent catheter-based PDA closure. The age ranged from 9 months to 65 years, with a median age of 4 years. The weight ranged from 4.2-65 kg, with a median of 15.2 kg. The mean PDA diameter at the narrowest segment was 4.7 +/- 2.2 mm, with a range of 2.0-15.1 mm. Eighteen cases had serial blood samples for serum nickel analysis taken before and at 1, 3 and 30 days after device implantation. RESULTS The devices were successfully deployed in all 60 patients. There were no serious procedural complications. Color Doppler demonstrated complete occlusion rate of 78.3%, 90.0% and 100% at 1 day, 1 month and 1 year after implantation, respectively. There was no statistical difference in serum nickel concentrations between pre- and post-implantation. CONCLUSION Transcatheter PDA closure using a platinum-coated nitinol device can be performed safely and successfully. There was no evidence of nickel release or nickel reaction after device implantation. This device model may be an alternative for PDA closure, especially in patients with potential nickel allergy.
Is controlling phosphorus by decreasing dietary protein intake beneficial or harmful in persons with chronic kidney disease?

BACKGROUND Dietary restrictions to control serum phosphorus, which are routinely recommended to persons with chronic kidney disease, are usually associated with a reduction in protein intake. This may lead to protein-energy wasting and poor survival. OBJECTIVE We aimed to ascertain whether a decline in serum phosphorus and a concomitant decline in protein intake are associated with an increase in the risk of death. DESIGN In a 3-y study (7/2001-6/2004) of 30 075 prevalent maintenance hemodialysis (MHD) patients, we examined changes in serum phosphorus and in normalized protein nitrogen appearance (nPNA), a surrogate of dietary protein intake, during the first 6 mo and the subsequent mortality. Four groups of MHD patients were defined on the basis of the direction of the changes in serum phosphorus and nPNA. RESULTS Baseline phosphorus had a J-shaped association with mortality, whereas higher baseline nPNA was linearly associated with greater survival. Compared with MHD patients whose serum phosphorus and nPNA both rose over 6 mo, those whose serum phosphorus decreased but whose nPNA increased had greater survival, with a case mix-adjusted death risk ratio of 0.90 (95% confidence limits: 0.86, 0.95; P < 0.001), whereas those whose phosphorus increased but whose nPNA decreased or those whose phosphorus and nPNA both decreased had worse mortality with a risk ratio of 1.11 (1.05,1.17; P < 0.001) and 1.06 (1.01,1.12; P = 0.02), respectively. CONCLUSIONS The risk of controlling serum phosphorus by restricting dietary protein intake may outweigh the benefit of controlled phosphorus and may lead to greater mortality. Additional studies including randomized controlled trials should examine whether nondietary control of phosphorus or restriction of nonprotein sources of phosphorus is safer and more effective.
Fast Generation for Convolutional Autoregressive Models

Convolutional autoregressive models have recently demonstrated state-of-the-art performance on a number of generation tasks. While fast, parallel training methods have been crucial for their success, generation is typically implemented in a naive fashion where redundant computations are unnecessarily repeated. This results in slow generation, making such models infeasible for production environments. In this work, we describe a method to speed up generation in convolutional autoregressive models. The key idea is to cache hidden states to avoid redundant computation. We apply our fast generation method to the Wavenet and PixelCNN++ models and achieve up to $21\times$ and $183\times$ speedups respectively.
Electrical microstimulation thresholds for behavioral detection and saccades in monkey frontal eye fields

The frontal eye field (FEF) is involved in the transformation of visual signals into saccadic eye movements. Although it is often considered an oculomotor structure, several lines of evidence suggest that the FEF also contributes to visual perception and attention. To better understand the range of behaviors to which the FEF can contribute, we tested whether monkeys could detect activation of their FEF by electrical microstimulation with currents below those that cause eye movements. We found that stimulation of FEF neurons could almost always be detected at levels below those needed to generate saccades and that the electrical current needed for detection was highly correlated with that needed to generate a saccade. This relationship between detection and saccade thresholds can be explained if FEF neurons represent preparation to make particular saccades and subjects can be aware of such preparations without acting on them when the representation is not strong.
3D Shape Recovery and Tracking from Multi-Camera Video Sequences via Surface Deformation

This paper addresses 3D reconstruction and modeling of time-varying real objects using multicamera video. The work consists of two phases. In the first phase, the initial shape of the object is recovered from its silhouettes using a surface deformation model. The same deformation model is also employed in the second phase to track the recovered initial shape through the time-varying silhouette information by surface evolution. The surface deformation/evolution model allows us to construct a spatially and temporally smooth surface mesh representation having fixed connectivity. This eventually leads to an overall space-time representation that preserves the semantics of the underlying motion and that is much more efficient to process, to visualize, to store and to transmit
Early enteral nutrition support in patients undergoing liver transplantation.

BACKGROUND The purpose of this study was to determine the effects of early postoperative tube feeding on outcomes of liver transplant recipients. METHODS Fifty transplant patients were randomized prospectively to receive enteral formula via nasointestinal feeding tubes (tube-feeding [TF] group) or maintenance i.v. fluid until oral diets were initiated (control group). Thirty-one patients completed the study. Resting energy expenditure, nitrogen balance, and grip strength were measured on days 2, 4, 7, and 12 after liver transplantation. Calorie and protein intakes were calculated for 12 days posttransplant. RESULTS Tube feeding was tolerated in the TF group (n = 14). The TF patients had greater cumulative 12-day nutrient intakes (22,464 +/- 3554 kcal, 927 +/- 122 g protein) than did the control patients (15,474 +/- 5265 kcal, 637 +/- 248 g protein) (p < .002). Nitrogen balance was better in the TF group on posttransplant day 4 than in the control group (p < .03). There was a rise in the overall mean resting energy expenditure in the first two posttransplant weeks from 1487 +/- 338 to 1990 +/- 367 kcal (p = .0002). Viral infections occurred in 17.7% of control patients compared with 0% of TF patients (p = .05). Although other infections tended to occur more frequently in the control group vs the TF group (bacterial, 29.4% vs 14.3%; overall infections, 47.1% vs 21.4%), these differences were not statistically significant. Early posttransplant tube feeding did not influence hospitalization costs, hours on the ventilator, lengths of stay in the intensive care unit and hospital, rehospitalizations, or rejection during the first 21 posttransplant days. CONCLUSIONS Early posttransplant tube feeding was tolerated and promoted improvements in some outcomes and should be considered for all liver transplant patients.
Mining student data to assess the impact of moodle activities and prior knowledge on programming course success

In this paper, Educational Data Mining and Learning Analytics are used in order to find out what impacts Programming 1 success most, since increase in the passing rate has been detected. The research is conducted on the dataset compounded of two parts: the first part is extracted from the Learning Management System (LMS) Moodle logs, while the second part is related to prior knowledge and students' preparation for the study. Classification methods are used to detect connections between prior knowledge and Moodle course activity in relation to final grades.
DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly.

Site‐specific DNA inversion by the Hin recombinase requires the formation of a multicomponent nucleo‐protein structure called an invertasome. In this structure, the two recombination sites bound by Hin are assembled together at the Fis‐bound recombinational enhancer with the requisite looping of the intervening DNA segments. We have analyzed the role of the HU protein in invertasome assembly when the enhancer is located at variable positions close to one of the recombination sites. In the absence of HU in vitro and in hupA hupB mutant cells in vivo, invertasome assembly is very inefficient when there is < 104 bp of DNA between the enhancer and recombination site. Invertasome assembly in the presence of HU in vitro or in vivo displayed a periodicity beginning with 60 bp of intervening DNA that reflected its helical repeat. The average helical repeat for this DNA region was calculated by autocorrelation and Fourier transformation to be 11.2 bp per turn for supercoiled DNA both in the presence of HU in vitro and in hup+ cells in vivo. HU is the only protein in Escherichia coli that can promote invertasome formation with short DNA lengths between the enhancer and recombination sites. However, the presence of certain polyamines and a protein activity present in HeLa nuclear extracts can efficiently substitute for HU in invertasome assembly. These data support a model in which HU binds non‐specifically to the DNA between the enhancer and recombination site to facilitate DNA looping.
Pressures Delivered By Nasal High Flow Oxygen During All Phases of the Respiratory Cycle

BACKGROUND: Nasal high flow (NHF) oxygen therapy and CPAP are modes of noninvasive respiratory support used to improve respiratory function in multiple patient groups. Both therapies provide positive pressure, although this varies during the respiratory cycle. The purpose of this study was to measure and compare the airway pressure generated during different phases of the respiratory cycle in patients receiving NHF at various gas flows. METHODS: Patients scheduled for elective cardiac surgery were invited to participate. Nasopharyngeal pressure measurements were performed using NHF with gas flows of 30, 40, and 50 L/min. All measurements were performed in random order, with the subject breathing with mouth closed. RESULTS: During NHF the mean ± SD nasopharyngeal airway pressures were 1.5 ± 0.6, 2.2 ± 0.8, and 3.1 ± 1.2 at 30, 40, and 50 L/min using NHF. Analyses also determined the mean peak expiratory and mean expiratory plateau pressures. CONCLUSIONS: The expiratory pressure during NHF was higher than the mean pressure previously reported for NHF. This may account in part for the disproportional clinical effects seen with NHF. (Australian Clinical Trials Registry www.anzctr.org.au ACTRN12609000305224).
The Spread of Fecally Transmitted Parasites in Socially-Structured Populations

Mammals are infected by a wide array of gastrointestinal parasites, including parasites that also infect humans and domesticated animals. Many of these parasites are acquired through contact with infectious stages present in soil, feces or vegetation, suggesting that ranging behavior will have a major impact on their spread. We developed an individual-based spatial simulation model to investigate how range use intensity, home range overlap, and defecation rate impact the spread of fecally transmitted parasites in a population composed of social groups (i.e., a socially structured population). We also investigated the effects of epidemiological parameters involving host and parasite mortality rates, transmissibility, disease–related mortality, and group size. The model was spatially explicit and involved the spillover of a gastrointestinal parasite from a reservoir population along the edge of a simulated reserve, which was designed to mimic the introduction pathogens into protected areas. Animals ranged randomly within a “core” area, with biased movement toward the range center when outside the core. We systematically varied model parameters using a Latin hypercube sampling design. Analyses of simulation output revealed a strong positive association between range use intensity and the prevalence of infection. Moreover, the effects of range use intensity were similar in magnitude to effects of group size, mortality rates, and the per-contact probability of transmission. Defecation rate covaried positively with gastrointestinal parasite prevalence. Greater home range overlap had no positive effects on prevalence, with a smaller core resulting in less range overlap yet more intensive use of the home range and higher prevalence. Collectively, our results reveal that parasites with fecal-oral transmission spread effectively in socially structured populations. Future application should focus on parameterizing the model with empirically derived ranging behavior for different species or populations and data on transmission characteristics of different infectious organisms.
Infections after reconstructions of anterior cruciate ligament.

INTRODUCTION Infections after anterior cruciate ligament reconstructions are rare, but, on the other hand, they are difficult to be treated. The aim of this study was to analyze causes of infections, risk factors, diagnostics, and possibilities of their prevention. MATERIAL AND METHODS Seventeen deep infections (1.2%) were found in 1425 patients who had undergone anterior cruciate ligament reconstructions. Fifteen patients were males and two were females. Out of 475 professional athletes nine (1.9%) had this postoperative complication. Eleven patients with septic arthritis were allergic to penicillin. Three of them had immunosuppressive diseases. RESULTS Staphylococcus aureus was isolated in eleven cases (65%), other Staphylococcus and Streptococcus groups were found in four and three patients, respectively; while one patient had infection although the punctate was negative. Out of 965 patients with the patellar tendon grafts, ten (1.03%) had this complication, while the incidence was 1.52% (7/460) in those with the hamstring grafts. Fifteen infections were acute with obvious symptoms within 14 days after surgery. Severe pain, limited range of motion, swelling of the knee joint and fever were the most common symptoms, while rubor and pus developed rarely. The infection was three times more frequent in the patients who had undergone surgery lasting more than 1.5 hour. DISCUSSION AND CONCLUSION The following population groups are at risk of developing septic arthritis after anterior cruciate ligament reconstructions: professional athletes, those who are allergic to penicillin, and those with immunosuppressive diseases. Staphyllococus aureus is the most common cause of infection. The patients with the hamstring autografts have a higher risk than those with the patellar tendon grafts. Preventive measures that should be performed include aseptic conditions in operative rooms, irrigation of the graft before its placement into the bone tunnels, experience of surgeon and proper antibiotics.