Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis C virus infection enhances TNFα‐induced cell death via suppression of NF‐κB

Hepatitis C virus (HCV) infection results in liver injury and long‐term complications, such as liver cirrhosis and hepatocellular carcinoma. Liver injury in HCV infection is believed to be caused by host immune responses, not by viral cytopathic effects. Tumor necrosis factor‐alpha (TNF‐α) plays a pivotal role in the inflammatory processes of hepatitis C. TNF‐α induces cell death that can be ameliorated by nuclear factor kappaB (NF‐κB) activation. We investigated the regulation of TNF‐α signal transduction in HCV‐infected cells and identified HCV proteins responsible for sensitization to TNF‐α‐induced cell death. We studied the effect of HCV infection on TNF‐α signal transduction using an in vitro HCV infection model (JFH‐1, genotype 2a) with Huh‐7 and Huh‐7.5 cells. We found that TNF‐α‐induced cell death significantly increased in HCV‐infected cells. HCV infection diminished TNF‐α‐induced phosphorylation of IκB kinase (IKK) and inhibitor of NF‐κB (IκB), which are upstream regulators of NF‐κB activation. HCV infection also inhibited nuclear translocation of NF‐κB and expression of NF‐κB‐dependent anti‐apoptotic proteins, such as B‐cell lymphoma—extra large (Bcl‐xL), X‐linked inhibitor of apoptosis protein (XIAP), and the long form of cellular‐FLICE inhibitory protein (c‐FLIP). Decreased levels of Bcl‐xL, XIAP, and c‐FLIP messenger RNA and protein were also observed in livers with chronic hepatitis C. Transfection with plasmids encoding each HCV protein revealed that core, nonstructural protein (NS)4B, and NS5B attenuated TNF‐α‐induced NF‐κB activation and enhanced TNF‐α‐induced cell death. Conclusion: HCV infection enhances TNF‐α‐induced cell death by suppressing NF‐κB activation through the action of core, NS4B, and NS5B. This mechanism may contribute to immune‐mediated liver injury in HCV infection. (HEPATOLOGY 2012;56:831–840)
Correlation of ABH blood group antigens secretion with Helicobacter pylori infection in Pakistani patients

A and B blood group antigens are fucosylated carbohydrate present on human erythrocytes and body secretions. Their presence in body secretions depends on the expression of a dominant allele of secretor gene FUT2 and is correlated with susceptibility to various infectious and non‐infectious diseases. We investigated the correlation of blood group and ABH antigen secretion with Helicobacter pylori infection and gastroduodenal symptoms and analysed the distribution of babA gene among ABH secretors and non‐secretors.
Microindentation Hardness of Protein Crystals under Controlled Relative Humidity

Vickers microindentation hardness of protein crystals was investigated on the (110) habit plane of tetragonal hen egg-white lysozyme crystals containing intracrystalline water at controlled relative humidity. The time evolution of the hardness of the crystals exposed to air with different humidities exhibits three stages such as the incubation, transition, and saturation stages. The hardness in the incubation stage keeps a constant value of 16 MPa, which is independent of the humidity. The incubation hardness can correspond to the intrinsic one in the wet condition. The increase of the hardness in the transition and saturation stages is well fitted with the single exponential curve, and is correlated with the reduction of water content in the crystal by the evaporation. The saturated maximum hardness also strongly depends on the water content equilibrated with the humidity. The slip traces corresponding to the (11 0)[110] slip system around the indentation marks are observed in not only incubation but also saturation stages. It is suggested that the plastic deformation in protein crystals by the indentation can be attributed to dislocation multiplication and motion inducing the slip. The indentation hardness in protein crystals is discussed in light of dislocation mechanism with Peierls stress and intracrystalline water.
Analysis of Deformation in Disordered Materials: Connecting Atomistic Simulations and Rheological Measurements to Continuum Theory

Central to the description of plasticity in disordered solids is the development of constitutive laws capable of encoding the necessary atomistic processes responsible for deformation within continuum-level field theories. Recently considerations of non-equilibrium thermodynamics have shown that an effective temperature may be essential in describing the degree of disorder of the evolving amorphous structure under an imposed shear. This thesis presents theoretical and computational analyses of the deformation of two distinct glassy materials. In the case of a simple yield stress fluid undergoing Couette shear, an effective-temperature model for transient shear-band formation is presented and quantitatively compared with the results of rheological experiments. Then molecular dynamics simulations of a metallic glass are used to propose a methodology for coarse-graining discrete, atomic energies into an effective-temperature field. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. The statistics of the potential energy are used to define a signal-to-noise ratio as a metric to assess the influence of the coarse-graining ii
Characteristics of Decomposition Powers of L-Band Multi-Polarimetric SAR in Assessing Tree Growth of Industrial Plantation Forests in the Tropics

A decomposition scheme was applied to ALOS/PALSAR data obtained from a fast-growing tree plantation in Sumatra, Indonesia to extract tree stem information and then estimate the forest stand volume. The scattering power decomposition of the polarimetric SAR data was performed both with and without a rotation matrix and compared to the following field-measured forest biometric parameters: tree diameter, tree height and stand volume. The analytical results involving the rotation matrix correlated better than those without the rotation matrix even for natural scattering surfaces within the forests. Our primary finding was that all of the decomposition powers from the rotated matrix correlated significantly to the forest biometric parameters when divided by the total power. The surface scattering ratio of the total power markedly decreased with the forest growth, whereas the canopy and double-bounce scattering ratios increased. The observations of the decomposition powers were consistent with the tree growth characteristics. Consequently, we found a significant logarithmic relationship between the decomposition powers and the forest biometric parameters that can potentially be used to estimate the forest stand volume.
Mapping Cycles and Trees on Wrap-Around Butterfly Graphs

We give a new algebraic representation for the wrap-around butterfly interconnection network. This new representation is based on the direct product of groups and finite fields and allows an algebraic expression of the network connectivity. The abstract algebraic tools may then be employed to explore the structural properties of the butterfly. In this paper we exploit this model to map guest graphs on the butterfly. In particular, we provide designs of unit dilation mappings of all possible length cycles on butterflies. We also map the largest possible binary trees on butterfly networks with a dilation 2 if the network degree is less than 16, 3 if it is less than 32, and 4 if it is less than 64. This is a great improvement over previous results.
The Human Circadian System Has a Dominating Role in Causing the Morning/Evening Difference in Diet‐Induced Thermogenesis

Diet‐induced thermogenesis (DIT) is lower in the evening and at night than in the morning. This may help explain why meal timing affects body weight regulation and why shift work is a risk factor for obesity. The separate effects of the endogenous circadian system—independent of behavioral cycles—and of circadian misalignment on DIT are unknown.
Thermodynamic and Differential Entropy under a Change of Variables

The differential Shannon entropy of information theory can change under a change of variables (coordinates), but the thermodynamic entropy of a physical system must be invariant under such a change. This difference is puzzling, because the Shannon and Gibbs entropies have the same functional form. We show that a canonical change of variables can, indeed, alter the spatial component of the thermodynamic entropy just as it alters the differential Shannon entropy. However, there is also a momentum part of the entropy, which turns out to undergo an equal and opposite change when the coordinates are transformed, so that the total thermodynamic entropy remains invariant. We furthermore show how one may correctly write the change in total entropy for an isothermal physical process in any set of spatial coordinates.
Effect of Apical Preparation Size and Taper on Irrigant Penetration in Apical Third of Root Canal using Two Different Endodontic Needles: An In Vivo Study

Introduction: Many in vitro studies have debated over the appropriate apical preparation size and taper for the irrigant to reach the apical third of root canals; however little is known about irrigant penetration in vivo. Aim: The purpose of this in vivo study was to determine the effect of apical preparation size and taper using two different needles on the irrigant penetration into the apical part of root canals. Materials and Methods: A 120 human mandibular teeth indicated for root canal treatment was selected for the study. The study was done in two phases. The first phase aimed to determine the smaller apical size that will allow irrigant penetration to working length. Disto buccal canal of with mandibular 1st molar was selected for study and was sequentially instrumented to 30/0.04 and 35/0.04. All patients were randomly divided into two groups for irrigation: Group A (n=30) 30G flat open ended needle and Group B (n=30) 30G side vented needle. The second phase of the study aimed to determine the taper that will allow irrigant penetration to working length. Teeth were instrumented to 30/0.04 and 30/0.06 and for irrigation patients were randomly divided into group A and B (n=30). Diatrizoate sodium contrast medium was used to measure irrigant penetration with digital radiograph. A blinded observer measured the distance between the working length and maximum irrigant penetration. Results: In both groups A and B, increasing the preparation size of the DB canal from 30 to 35 increased irrigant penetration which was statistically insignificant (p>0.05). But irrigant penetration in 6% taper of DB canal was significantly better than 4% (p<0.001) for both the groups. Flat open ended needles performed significantly better than side vented needles in both phase I and II of the study (p<0.001). Conclusion: Within the limitations of the study it can be concluded that an apical preparation size of 30 and 6% preparation taper in DB canal of mandibular molars allow adequate irrigation penetration in the apical third with flat open ended needles performing better than side vented needles.
Effect of heat loss on performance of thin film thermoelectric; a mathematical model

To produce a higher electrical power in thin film thermoelectric legs, one way is to conduct the heat flow in-plane parallel to the surface of thin films. One important advantage of using the thermoelectric element in-plane is that, due to high thermal resistance of the thermoelectric leg, there is no need for an efficient heat sink at cold side. A comprehensive mathematical model for analyzing performance of a ZnSb based thermoelectric thin film is proposed based on one dimensional (1D) steady state analysis. Finite element method is employed to solve governing equations, and effects of temperature dependency of thermoelectric material are considered in the model. The modeling study is carried out by a comparison between the ideal case, where there is no heat loss from the thin film, and the case that the heat loss accrues from lateral surfaces of the thin film to the ambient. By taking side surface heat transfer into account for both vertical and horizontal placement of the thin film, two different nonlinear temperature distributions along the thin film length are obtained, and variation of matched power output versus different thermal boundary conditions is shown. The results show that convective heat transfer to the ambient reduces thermoelectric power output, especially at higher temperature difference between the hot and cold sides of the leg. Furthermore, different parameters such as Seebeck coefficient, temperature, generated Seebeck voltage, heat loss, thermoelectric voltage and current at peak power point are evaluated for vertical and horizontal thin film configurations.
Mutation scanning‐based analysis of Theileria orientalis populations in cattle following an outbreak

Bovine theileriosis is a tick‐borne disease caused by one or more hemoprotozoan parasites of the genus Theileria. In the past, Theileria infection in cattle in Australia was largely asymptomatic and recognized to be associated with Theileria buffeli. However, outbreaks of theileriosis have occurred in beef and dairy cattle in subtropical climatic regions (New South Wales) of Australia. There is also one published report of a recent theileriosis outbreak in a beef farm near Seymour in the southeastern state of Victoria. In order to gain an improved insight into the genetic composition of Theileria populations following this outbreak, we undertook herein an integrated PCR‐coupled mutation scanning‐sequencing‐phylogenetic analysis of sequence variation in part of the major piroplasm surface protein (MPSP) gene within and among samples from cattle involved in the outbreak. Theileria DNA was detected in 89.4% of 94 cattle in the Seymour farm; the genetic analysis showed that the ikeda and chitose genotypes representing the Theileria orientalis complex were detected in 75 and 4.8% of 84 infected cattle, respectively, and that mixed populations of these two genotypes were found in 20.2% of infected cattle. Given unpublished reports of a significant increase in the number of outbreaks in Victoria, future investigations should focus sharply on elucidating the epidemiology of Theileria to subvert the economic impact on the cattle industry in this state. Although used here to explore genetic variation within the T. orientalis complex in Australia, a mutation scanning‐based approach has broad applicability to other species of Theileria in other countries.
Lung function by impulse oscillometry at age 5–7 years after bronchiolitis at age 0–6 months

Viral bronchiolitis in infancy has been associated with increased bronchial reactivity and reduced lung function in later childhood and even in adulthood. However, lung function at preschool age is less studied, mainly due to technical difficulties. The purpose of the study was to evaluate lung function and bronchial reactivity at preschool age in children who were hospitalized for bronchiolitis in early infancy.
Epidemiology of a tick‐borne viral infection: theoretical insights and practical implications for public health

The morbidity of tick‐borne encephalitis (TBE) varies yearly by as much as 10‐fold among the people of Western Siberia. This long‐term variation is dependent on many factors such as the density of the tick populations, the prevalence of TBE virus (TBEV) among sub‐adult ticks, the yearly virulence of the TBEV, and prophylactic measures. Here we highlight the role of small mammal hosts in the circulation of TBEV through the ecosystem. Refining classical models of non‐viremic horizontal transmission, we emphasize the recently understood fact that the physiological and immunological status of the small mammal hosts affects the tick and virus‐host interactions. In addition to its theoretical interest, our approach may lead to some practical improvements in the precision of epidemiological forecasts and perhaps in forestalling the severity of outbreaks of TBE, or, at least, in forewarning medical authorities and the general public of impending TBE outbreaks.
Antiretroviral drug toxicity in relation to pharmacokinetics, metabolic profile and pharmacogenetics

Introduction: Besides therapeutic effectiveness, drug tolerability is a key issue for treatments that must be taken indefinitely. Given the high prevalence of toxicity in HIV therapy, the factors implicated in drug-induced morbidities should be identified in order to improve the safety, tolerability and adherence to the treatments. Current approaches have focused almost exclusively on parent drug concentrations; whereas recent evidence suggests that drug metabolites resulting from complex genetic and environmental influences can also contribute to treatment outcome. Pharmacogenetic variations have shown to play a relevant role in the variability observed in antiretroviral drug exposure, clinical response and sometimes toxicity. The integration of pharmacokinetic, pharmacogenetic and metabolic determinants will more probably address current therapeutic needs in patients. Areas covered: This review offers a concise description of three classes of antiretroviral drugs. The review looks at the metabolic profile of these drugs and gives a comprehensive summary of the existing literature on the influence of pharmacogenetics on their pharmacokinetics and metabolic pathways, and the associated drug or metabolite toxicity. Expert opinion: Due to the high prevalence of toxicity and the related risk of low adherence to the treatments, association of kinetic, genetic and metabolic markers predictive of therapeutic or toxicity outcomes could represent a more complete approach for optimizing antiretroviral therapy.
Heart rate variability assessment with fingertip photoplethysmography and polar RS800cx as compared with electrocardiography in obese adolescents

Aim: This study investigated the accuracy and reliability of short-term resting heart rate variability (HRV) assessment by fingertip photoplethysmography (PPG) and using a cardiofrequencimeter (Polar RS800cx) in obese adolescents. Obesity in adolescents may be related to autonomic dysfunction due to insulin resistance and/or increased central fat. This fact may affect the accuracy and reliability of the evaluation of autonomic activity at rest. Methods: Fourteen adolescents (15±2 years) classified as obese and exhibiting insulin resistance underwent the following procedures: (a) anthropometric measurements, and (b) two 25-min HRV recordings in a supine position conducted simultaneously using ECG, PPG, and Polar RS800cx. Results: The results showed significant correlations between HRV markers obtained using Polar RS800cx and PPG and those obtained from ECG, with coefficients of determination (R2) and intraclass correlation coefficients ranging from 0.60 to 0.98 (P-value ranging from 0.03 to 0.05) and 0.70 to 0.99 (P-value ranging from 0.01 to 0.05), respectively. The technical error of measurement and intraclass correlation coefficients for test–retest reliability ranged from 8.9 to 45.8% and 0.38 to 0.68 for ECG, 8.0 to 30.5% and 0.29 to 0.61 for Polar RS800cx, and 7.2 to 54.6% and 0.45 to 0.64 for PPG, respectively. Conclusion: HRV indices calculated by Polar RS800cx and PPG appear to be as accurate and reproducible as data from ECG when evaluating the autonomic control of heart rate at rest in obese adolescents.
The limits and possibilities of combining Description Logics and Datalog

Description Logics are currently the most used formalisms for building ontologies, and have been proposed as standard languages for the specification of ontologies in the Semantic Web. The problem of adding rules to Description Logics is currently a hot research topic, due to the interest of Semantic Web applications towards the integration of rule-based systems with ontologies. Most of the approaches in this field concern the study of description logic knowledge bases augmented with rules expressed in Datalog and its nonmonotonic extensions. In this talk we present a set of computational results which identify, from the viewpoint of the expressive abilities of the two formalisms, minimal combinations of Description Logics and (nonmonotonic) Datalog in which reasoning is undecidable. Then, based on the above results, we briefly survey some recent proposals for overcoming such expressive limitations
Predictive modelling of the MR of subgrade cohesive soils incorporating CPT-related parameters through a soft-computing approach

Performance of pavements is significantly influenced by the characteristics and behaviour, e.g. compaction and deformation, of their underlying layer as subjected to different loadings. This can be experimentally or theoretically estimated through the subgrade soil resilient modulus (MR) parameter. The MR found by laboratory tests does not completely describe the actual in situ conditions of subgrade soils. Additionally, almost all of the predictive models proposed in the literature relate the MR parameter to lab-related soil indices and conditions of stresses applied in laboratory tests. This study explores the feasibility of producing a new MR equation using key soil lab and in situ related parameters for the pavements subgrade cohesive soils through gene expression programing (GEP) approach. A database comprising several experimental data acquired by conducting cone penetration test and corresponding resilient moduli tests on various cohesive subgrade soils is employed for modelling of the pertinent MR factor and a new empirical mode is suggested. In order to examine the proposed model from both precision and engineering perspectives, various validation and verification analyses are done. The results present that the strength of GEP approach and the proposed formula for indirect estimation of the MR of pavements subgrade soils.
Rotavirus virus‐like particles (RV‐VLPs) vaccines: An update

Rotaviruses (RVs) cause over 0.2 million deaths annually and are reported to be the foremost cause of gastroenteritis in infants and children worldwide. Vaccination against RVs is the most successful and unsurpassed strategy to combat infection to date. Although the 2 current vaccines, Rotarix and RotaTeq, have dramatically reduced the disease burden, still there is a need for new vaccines. In this context, RV virus‐like particles (RV‐VLPs) represent potential vaccine candidates as they are noninfectious and effective nonreplicating immunogens that may reduce the risk of side effects related to the conventional vaccines. VLPs being conformationally similar to the parent virus are highly immunogenic and hence provide enhanced protection and better serotype coverage. In this review, we have highlighted the various advantages and the implications of RV‐VLPs, discussed the general strategies employed for their production, and talked about the recent developments made in this regard. Overall, the review emphasizes the probable utility of RV‐VLPs in eradicating the highly widespread RVs.