Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Human Papillomavirus Types 6 and 11 in Pubic and Perianal Hair from Patients with Genital Warts

ABSTRACT Genital human papillomavirus (HPV) types 6 and 11 are of clinical importance due to their role in the development of anogenital warts. A pilot study was performed to investigate whether DNAs from HPV types 6 and 11 are present in hairs plucked from the pubic and perianal regions and eyebrows of patients with genital warts at present and patients with a recent history of genital warts. Genital HPV DNA was detected in 9 of 25 (36%) pubic hair samples and in 11 of 22 (50%) perianal hair samples by the CPI/CPIIg PCR. After sequencing of 17 of 20 samples, HPV type 6 or 11 was detected in 6 of 25 (24%) hair samples from the pubis and 8 of 22 (36%) hair samples from the perianal region. These types were not detected in plucked eyebrow hairs. In contrast, the HPV types associated with epidermodysplasia verruciformis were detected in similar proportions (62%) in both samples of pubic and eyebrow hairs. Moreover, HPV type 6 and 11 DNAs were detected in pubic hairs plucked from two patients who had been successfully treated and who did not show any lesion at the time of hair collection; this finding is an argument that HPV DNA may persist in this region. The presence of genital HPV types in plucked pubic and perianal hair suggests that there is an endogenous reservoir for HPV which may play a role in the recurrences of genital warts.
Genome macrorestriction analysis of diversity and variability of Pseudomonas aeruginosa strains infecting cystic fibrosis patients

Genome macrorestriction fingerprinting with XbaI and DraI was used to analyze the relatedness of 166 Pseudomonas aeruginosa isolates collected from 31 cystic fibrosis patients over a 1- to 20-month period and to correlate their genotype with patterns of resistance to 14 antimicrobial agents. Quantitative comparison of intra- and interpatient similarities of P. aeruginosa macrorestriction patterns disclosed two discrete ranges that clearly discriminated subclonal variation (> 80% relatedness) and clonal diversity (10 to 70% relatedness). Cloning-derived mutants exhibited up to 20% divergence of genomic macrorestriction patterns during the course of chronic colonization of individual patients. Change of susceptibility to multiple antimicrobial agents developed in 50% of sequential pairs of isolates from individual patients. Only 19% of these susceptibility changes were attributable to strain substitution, while the majority (56%) of resistance changes were associated with minor genomic variations of a persistent strain. Sixty-six percent of patients harbored one strain, and 33% carried two strains. Three common strains colonized 5 (28%) of 18 patients attending a cystic fibrosis clinic, and another two strains colonized two patient pairs (31%) of 13 patients staying at a rehabilitation center, suggesting potential cross-infection in these settings. By indexing regional polymorphisms throughout the chromosome structure, macrorestriction analysis can monitor subclonal evolution of P. aeruginosa and identify isogenic resistance mutants. Quantitative macrorestriction fingerprinting enables discrimination between clonal variants and clones of distinct origins and should therefore provide a reliable tool for investigating the mode of acquisition of P. aeruginosa in cystic fibrosis patients.
Redesign of Choline Acetyltransferase Specificity by Protein Engineering*

Since the development of site-directed mutagenesis techniques over 15 years ago (Zoller, M. J., and Smith, M. (1982) Nucleic Acids Res. 10, 6487–6500), it has been a goal of protein engineering to utilize the procedure to redesign existing enzyme structures to produce proteins with altered or novel catalytic properties. To date, however, the more successful achievements have relied exclusively on the availability of three-dimensional protein structure maps to direct the redesign strategies. Presently, such maps are unavailable for choline acetyltransferase and carnitine acetyltransferase, enzymes that catalyze the reversible transfer of an acetyl group from acetyl-CoA to choline and l-carnitine, respectively. A more empirical approach, based on cross-referencing substrate structure comparisons with protein alignment data, was used to redesign choline acetyltransferase to accommodate l-carnitine as an acceptor of the acetyl group. A mutant choline acetyltransferase that incorporates four amino acid substitutions from wild type, shows a substantial increase in catalytic efficiency (k cat/K m ) towardl-carnitine (1,620-fold) and shifts the catalytic discrimination between choline and l-carnitine by >390,000 in favor of the latter substrate. These dramatic alterations in catalytic function demonstrate that significant success in protein redesign can be achieved in the absence of three-dimensional protein structure data.
Intersection-based Distance and Traffic-Aware Routing (IDTAR) protocol for smart vehicular communication

The Vehicular Ad-hoc Networks (VANET) raises as an emerging technology for smart transport as observed in the recent decade. However, there are some hurdles affect the applications of VANET, the advancement of VANET needed to cope up with the requirement of smart transport in smart cities. The routing is the important factor for having effective communication between smart vehicles, which need to be addressed smartly. Many factors affect the communication between the vehicles such as topology fragmentation which results in the phenomenon of Local-Maximum-Problem that lead to packet delivery failure. The traditional routing schemes failed to address the problem of the trade-off between Packet-Delivery-Ratio and the high cost, in term of End-to-End-Delay, of packet recovery from the failures that occurs frequently because of Local-Maximum-Problem. Therefore, this article works out to analyses the performance of existing position-based routing protocols for Inter-vehicle ad-hoc network and introduced Intersection-based Distance and Traffic-Aware Routing (IDTAR) protocol. IDTAR aims to provide optimal performance in environments of smart transport in smart cities. The experiments evaluate IDTAR against famous position-based routing protocols such as GyTAR, A-STAR-SR and GSR considering several densities of vehicles. Simulation result shows that IDTAR protocol has a fewer End-to-End-Delay and high packet delivery ratio in smart cities circumstances. This concludes that IDTAR can be adaptive for smart transport in smart cities communication with some consideration in terms of its security, compatibility and reliability.
Dynamic Stiffnesses of Active Magnetic Thrust Bearing Including Eddy-Current Effects

The eddy currents induced in a thrust bearing result not only in a power loss of the system but also in phase lag and a decrease in magnitude of the magnetic force. Therefore, an accurate model including eddy-current effects would be highly beneficial at the design stage. We present a linear model including eddy-current effects for a typical active magnetic thrust bearing (AMTB). We define and calculate the dynamic current stiffness and displacement stiffness using both an analytical method and transient finite element (FE) analysis. We present a simple magnetic circuit model including eddy currents from which the two stiffnesses can be derived analytically. Furthermore, by using a transient analysis of the FE model, flux saturation, leakage, and fringing effects can all be taken into account. We show that the two stiffnesses have the same frequency response characteristics, both in the analytical model and from the results of the linear FE analysis, when the leakage and fringing effects are ignored. Even in the more practical case when the flux saturation, leakage and fringing effects are considered, the two stiffnesses can be considered to have the same frequency response characteristics within the 3 dB bandwidth without introducing much error. The open-loop frequency response of the two stiffnesses derived from the analytical model and the FE model agrees well with the experimental results.
An extended procedure of constructing neural networks for supervised dichotomy

K.J. Clos and N. Liu (1992) proposed a neural network generation procedure for supervised two-class discretization based on a continuous ID3 algorithm. The method constructs neural networks consisting of neurons with linear activation functions. We extend the procedure to allow decision boundaries to be any arbitrary function. The advantage of the extension is revealed by the decrease in size of the generated neural networks.
Combination Forecasting of Energy Demand in the UK

In more deregulated markets such as the UK, demand forecasting is vital for the electric industry as it is used to set electricity generation and purchasing, establishing electricity prices, load switching and demand response. In this paper we produce improved short-term forecasts of the demand for energy produced from five different sources in the UK averaging from a set of 6 univariate and multivariate models. The forecasts are averaged using six different weighting functions including Simple Model Averaging (SMA), Granger-Ramanathan Model Averaging (GRMA), Bayesian Model Averaging (BMA), Smoothing Akaike (SAIC), Mallows Weights (MMA) and Jackknife (JMA). Our results show that model averaging gives always a lower Mean Square Forecast Error (MSFE) than the best/optimal models within each class however selected. For example, for Coal, Wind and Hydro generated Electricity forecasts generated with model averaging, we report a MSFE about 12% lower than that obtained using the best selected individual models. Among these, the best individual forecasting models are the Non-Linear Artificial Neural Networks and the Vector Autoregression and that models selected by the Jackknife have often superior performance. However, MMA averaged forecasts almost always beat the predictions obtained from any of the individual models however selected, and those generated by other model averaging techniques.
The Threshold for Thermoregulatory Vasoconstriction During Nitrous Oxide/Sevoflurane Anesthesia Is Reduced in the Elderly

Elderly patients become more hypothermic during surgery, shiver less postoperatively, and take longer to rewarm than younger patients.Similarly, the vasoconstriction threshold (triggering core temperature) is reduced approximately 1 degrees C in elderly patients during nitrous oxide/isoflurane anesthesia. Accordingly, we tested the hypothesis that the vasoconstriction threshold in the elderly is also reduced approximately 1 degrees C during nitrous oxide and sevoflurane anesthesia. Eleven young patients aged 30-50 yr and 14 elderly patients aged 60-80 yr were anesthetized with nitrous oxide (50%) and sevoflurane (1%). Mean skin temperature was calculated from four sites. Fingertip blood flow was estimated using forearm minus fingertip skin-temperature gradients, with a gradient of 0 degrees C identifying onset of vasoconstriction. The distal esophageal temperature triggering onset of vasoconstriction identified the threshold for this thermoregulatory defense. The data from five patients who did not vasoconstrict at minimum core temperatures of 33-34 degrees C were eliminated, leaving 10 patients in each group. The vasoconstriction threshold was significantly less in the elderly (35.0 +/- 0.8 degrees C) than in younger patients (35.8 +/- 0.3 degrees C), despite similar mean skin temperatures (mean +/- SD, P < 0.01, Student's t-test). Age dependence of thermoregulatory vasoconstriction during nitrous oxide/sevoflurane anesthesia is similar to that previously observed during nitrous oxide/isoflurane anesthesia. (Anesth Analg 1997;84:1029-33)
Bovine γ/δ TcR+ T Lymphocytes are Stimulated to Proliferate by Autologous Theileria annulata‐Infected Cells in the Presence of Interleukin‐2

An in vitro model system has been developed in which freshly isolated resting WC1+γ/δTcR+ T cells proliferate in response to cells transformed by the protozoan parasite Theileria annulata, providing a strategy in which the basis of activation of naive γ/δ T cells can be investigated. Irradiated parasite‐transformed cells stimulate the proliferation, but not cytolytic activity, of autologous peripheral blood mononuclear cells (PBMC) from non‐immune animals. The proliferating cells are mainly WC1+γ/δ T cells. The majority of WC1+γ/δ T cells in freshly isolated PBMC express CD25 at a low level that increases when stimulated with T. annulata‐infected cells. Purified WC1+γ/δ T cells fail to proliferate when cultured with irradiated T. annulata‐infected cells and produce a small proliferative response to IL‐2, but proliferate strongly to irradiated or lightly fixed Theileria‐infected cells in combination with IL–2. The Theileria‐infected cells express cytokine transcripts encoding IL‐1α, IL‐1β, IL‐6 and IL‐10, but not IFNγ, IL‐2, IL‐4 and IL–7. Purified WC1+γ/δ T cells stimulated with T. annulata‐infected cells with or without IL‐2 fail to produce IL‐2 transcripts, but do produce those for TNFα. These experiments show that WC1+γ/δ T cells recognize a surface determinant on T. annulata‐infected cells, that together with a second signal, which can be provided by exogenous IL‐2, stimulates their proliferation.
MicroRNA‐196a promotes an oncogenic effect in head and neck cancer cells by suppressing annexin A1 and enhancing radioresistance

Radiotherapy is a major treatment modality for head and neck squamous cell carcinoma (HNSCC). Up to 50% of patients with locally advanced disease relapse after radical treatment and there is therefore a need to develop predictive bomarkers for clinical use that allow the selection of patients who are likely to respond. MicroRNA (miRNA) expression profiling of a panel of HNSCC tumours with and without recurrent disease after surgery and radiotherapy detected miR‐196a as one of the highest upregulated miRNAs in the poor prognostic group. To further study the role of miR‐196a, its expression was determined in eight head and neck cancer cell lines. Overexpression of miR‐196a in HNSCC cells, with low endogenous miR‐196a expression, significantly increased cell proliferation, migration and invasion, and induced epithelial to mesenchymal transition. Conversely, miR‐196a knockdown in cells with high endogenous expression levels significantly reduced oncogenic behaviour. Importantly, overexpression of miR‐196a increased radioresistance of cells as measured by gamma H2AX staining and MTT survival assay. Annexin A1 (ANXA1), a known target of miR‐196a, was found to be directly modulated by miR‐196a as measured by luciferase assay and confirmed by Western blot analysis. ANXA1 knockdown in HNSCC exhibited similar phenotypic effects to miR‐196a overexpression, suggesting the oncogenic effect of miR‐196a may at least be partly regulated through suppression of ANXA1. In conclusion, this study identifies miR‐196a as a potential important biomarker of prognosis and response of HNSCC to radiotherapy. Furthermore, our data suggest that miR‐196a and/or its target gene ANXA1 could represent important therapeutic targets in HNSCC.
Cooperative Regulation of the Cell Division Cycle by the Protein Kinases RAF and AKT

ABSTRACT The RAS-activated RAF→MEK→extracellular signal-regulated kinase (ERK) and phosphatidylinositol 3′-kinase (PI3′-kinase)→PDK1→AKT signaling pathways are believed to cooperate to promote the proliferation of normal cells and the aberrant proliferation of cancer cells. To explore the mechanisms that underlie such cooperation, we have derived cells harboring conditionally active, steroid hormone-regulated forms of RAF and AKT. These cells permit the assessment of the biological and biochemical effects of activation of these protein kinases either alone or in combination with one another. Under conditions where activation of neither RAF nor AKT alone promoted S-phase progression, coactivation of both kinases elicited a robust proliferative response. Moreover, under conditions where high-level activation of RAF induced G1 cell cycle arrest, activation of AKT bypassed the arrest and promoted S-phase progression. At the level of the cell cycle machinery, RAF and AKT cooperated to induce cyclin D1 and repress p27Kip1 expression. Repression of p27Kip1 was accompanied by a dramatic reduction in KIP1 mRNA and was observed in primary mouse embryo fibroblasts derived from mice either lacking SKP2 or expressing a T187A mutated form of p27Kip1. Consistent with these observations, pharmacological inhibition of MEK or PI3′-kinase inhibited the effects of activated RAS on the expression of p27Kip1 in NIH 3T3 fibroblasts and in a panel of bona fide human pancreatic cancer cell lines. Furthermore, we demonstrated that AKT activation led to sustained activation of cyclin/cdk2 complexes that occurred concomitantly with the removal of RAF-induced p21Cip1 from cyclin E/cdk2 complexes. Cumulatively, these data strongly suggest that the RAF→MEK→ERK and PI3′K→PDK→AKT signaling pathways can cooperate to promote G0→G1→S-phase cell cycle progression in both normal and cancer cells.
Wide-input high power density flexible converter topology for dc-dc applications

In this paper a highly flexible 2-phase step-down dc-dc converter topology designed for a wide range of point-of-load (PoL) applications is introduced. The new wide-input flying-capacitor based multi-level converter has smaller overall volume and better power processing efficiency than the conventionally used 2-phase interleaved buck solution, achieved through the reduction of voltage swings across its components. Compared to other multi-level solutions the new topology has much higher flexibility, allowing operating-condition dependent changes of the topology for efficiency optimization. Also, the silicon area required for the implementation of the switches is smaller than that of the other solutions, since all transistors are rated at ½ of the input voltage, further contributing to size reduction and power processing efficiency improvements. The advantages of the new topology have been experimentally verified with a wide input range, 3 V ≤ Vin ≤ 48 V, wide output range, 1 V ≤ Vout ≤ 12 V, output power Pout ≤ 72 W, 800 kilohertz switching frequency discrete experimental prototype. The results show that the introduced topology requires about 33% smaller inductor and 33% smaller output capacitor than the conventional 2-phase interleaved buck, while having higher power processing efficiency over the entire range of operation.
Response to Anti-VEGF-A Treatment of Retinal Pigment Epithelial Cells In Vitro

Purpose The neovascular or wet form of age-related macular degeneration is characterized by the growth of abnormal blood vessels in the retina stimulated by vascular endothelial growth factors (VEGF). In the last decade, several anti-VEGF drugs have been developed for treating neovascular diseases of the eyes. This study was conducted to compare the effects of 2 anti-VEGF-A drugs, ranibizumab and aflibercept, on the expression and secretion of VEGF family members in retinal pigment epithelial cells (RPE) in vitro. Methods ARPE-19 cells were exposed for 24 hours to ranibizumab or aflibercept at clinical dose concentration. Cell viability and expression and secretion of VEGF-A, VEGF-B, VEGF-C, and placental growth factor (PlGF) were evaluated respectively by real-time polymerase chain reaction and enzyme-linked immunosorbent assay. Results Ranibizumab and aflibercept did not affect ARPE-19 cell viability after 24 hours of treatment. Ranibizumab increased expression of VEGF-A and PlGF. On the contrary, expression and secretion of VEGF-C was decreased by ranibizumab. PlGF secretion was not affected by ranibizumab. Aflibercept strongly increased VEGF-A and PlGF expression but reduced their detection on the culture media, and decreased expression and secretion of VEGF-C. No effect on expression and secretion of VEGF-B was observed after exposure to these drugs. Conclusions Ranibizumab and aflibercept exert similar effects on VEGF expression and secretion, leading to establishing an antiangiogenic environment. Increased VEGF-A expression observed in RPE cells treated with these drugs suggests a compensatory response of the cells to the lack of VEGF-A.
Essays on Systemic Risk in European Banking

This thesis makes a contribution to systemic risk literature in the European banking system. The intimate interdependence between the European banking industries and the fragile GIIPS debt market has jeopardized the banking sector in Europe. The threats of unfavourable financial conditions in European bank- ing sufficiently highlight the importance of the dissertation’s distinct focus on systemic risk measurement and on the risk drivers. The outcomes of the three included papers give support to the European authorities to enact comprehen- sive macroprudential regulation schemes.The first paper estimates the systemic risk contributions of GIIPS-block bank- ing on 14 major banking systems in Europe. The CoVaR measure further eval- uates the magnitude of risk using two methods; quantile regression and DCC. Our results indicate a substantial spillover effect of GIIPS banking on the exam- ined banking systems. In other words, the countries’ banking sectors are in part driven by systemic risk in the GIIPS banking system. We also find supporting ev- idence of amplified spillover effects from the GIIPS-block banking sector during the financial crises.The second paper firstly quantifies the sovereign debt spillovers based on daily returns of GIIPS and individual banks’ CDSs over the period of 2007-2015. Then, it examines banks’ financial features and financial markets’ circumstances that determine variations in the banks’ sovereign risk exposures. We find those banks that hold higher assets in times of crisis or work in markets with unfa- vorable profiles, i.e. low returns and high idiosyncratic risks tend to be further susceptible to sovereign risk. However, we do not observe that variations in the risk exposures have been driven by dissimilarities in individual fundamentals such as leverage, debt-to-cash, and market-to-book value of equity ratios.The third paper analyzes the main determinants of systemic contagion from an individual country’s banking sector to the whole banking industry of Europe in 1999-2013. The results show that differences in systemic risk contribution are driven by a combination of balance-sheet characteristics and macroeconomic conditions such as the country-level VaR, crisis episodes, size or total asset, bi- lateral loan, market-to-book ratio, stock market returns, and industry produc- tion index (IPI). Keywords: Systemic Risk, CoVaR, GIIPS, Quantile Regression, DCC, CDS JEL Classification: G01, G21, E43, N24, H63, F30i (Less)