Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal Peptidase Complex Subunit 1 Participates in the Assembly of Hepatitis C Virus through an Interaction with E2 and NS2

Hepatitis C virus (HCV) nonstructural protein 2 (NS2) is a hydrophobic, transmembrane protein that is required not only for NS2-NS3 cleavage, but also for infectious virus production. To identify cellular factors that interact with NS2 and are important for HCV propagation, we screened a human liver cDNA library by split-ubiquitin membrane yeast two-hybrid assay using full-length NS2 as a bait, and identified signal peptidase complex subunit 1 (SPCS1), which is a component of the microsomal signal peptidase complex. Silencing of endogenous SPCS1 resulted in markedly reduced production of infectious HCV, whereas neither processing of structural proteins, cell entry, RNA replication, nor release of virus from the cells was impaired. Propagation of Japanese encephalitis virus was not affected by knockdown of SPCS1, suggesting that SPCS1 does not widely modulate the viral lifecycles of the Flaviviridae family. SPCS1 was found to interact with both NS2 and E2. A complex of NS2, E2, and SPCS1 was formed in cells as demonstrated by co-immunoprecipitation assays. Knockdown of SPCS1 impaired interaction of NS2 with E2. Our findings suggest that SPCS1 plays a key role in the formation of the membrane-associated NS2-E2 complex via its interaction with NS2 and E2, which leads to a coordinating interaction between the structural and non-structural proteins and facilitates the early step of assembly of infectious particles.
Comparing the effects of waste engine and cooking oil on the properties of asphalt concrete containing reclaimed asphalt pavement (RAP)

The effects of using waste engine oil (WEO) and waste cooking oil (WCO) as rejuvenators on some engineering properties of asphalt concrete containing reclaimed asphalt pavement (RAP) have been studied. 10% (by the weight of total binder) of the rejuvenators has been added to asphalt concrete containing 25%, 50% and 75% (by the weight of aggregate) of RAP, and the Marshall properties, indirect tensile strength (ITS), permanent deformation and fatigue properties of the mixtures have been evaluated. The effect of rejuvenators on Marshall properties depends on RAP content and type of rejuvenator, with higher values for the mixtures containing WEO. The ITS of the mixtures increase with increasing RAP content, and decreases with increasing rejuvenators content. Addition of WEO results in lower accumulated strain in the mixtures than adding WCO. In addition, the accumulated strain in the mixtures containing 50% of RAP is higher than that in the mixtures containing 25% and 75% of RAP. The fatigue life of the mixtures was found to increase with increasing RAP content and decrease by addition of rejuvenator with a higher reduction for the WCO. In general, it is concluded that using the rejuvenators enables using higher RAP content in recycled asphaltic mixtures.
A novel robotic tactile mass detector with application in clinical breast examination

Abstract This paper presents a novel tactile sensing robot designed to detect breast lesions with minimum invasiveness to the tissue while providing exact documentation to make therapeutic and surgical decisions. The robot named “Robotic Tactile Breast Mass Identifier (Robo-Tac-BMI) consists of an indentation probe controlled by a robotic system and a visualization interface to manipulate the end-effecter. Geometrical maps of the test points with related tension-relaxation curves are provided during clinical examinations. Utilizing the curves, three functional stiffness parameters are extracted locally for each test point. These parameters are employed to provide objective information to facilitate the surgeon's task in the diagnostic procedure. Computational analysis is proposed for a real breast tissue model to study the capability of artificial tactile sensing in the mass detection. Indications of the mass existence are determined and employed as the basis of the Robo-Tac-BMI design and construction. Clinical trials are executed by the Robo-Tac-BMI on 161 cases. The results show that the robot has the potential to provide tissue mechanical properties unlike the conventional screening modalities carried out either by the surgeon or the imaging techniques which are not quantitative and lack documentation. Sonography with and without mammography is chosen as the “gold standard” tests.
Adenovirus-mediated small interfering RNA against matrix metalloproteinase-2 suppresses tumor growth and lung metastasis in mice

Matrix metalloproteinases (MMP) are a group of proteinases that have normal physiologic roles degrading and remodeling the extracellular matrix. They also have multiple roles in different stages of tumor progression. Elevated levels of MMPs have been observed in many tumors; these increases have a strong association with the invasive phenotype. MMP-2 and MMP-9 are particularly involved in cancer invasion and metastasis. MMP inhibitors are currently being tested as therapeutic agents for a number of cancers in both preclinical models and in clinical trials. To date, clinical trials using this strategy have had limited efficacy. A major concern is the lack of specificity of commercially available MMP inhibitors. An adenoviral vector expressing small interfering RNA against the MMP-2 gene (Ad-MMP-2) was constructed to specifically inhibit MMP-2 expression. The effect of Ad-MMP-2 on invasion, angiogenesis, tumor growth, and metastasis of A549 lung cancer cell was evaluated. Ad-MMP-2 infection of lung cancer cells showed specific down-regulation of MMP-2 protein, activity, and transcription as determined by Western blotting, gelatin zymography, and reverse transcription-PCR. Ad-MMP-2 inhibition also mitigated lung cancer invasion and migration, and reduced tumor cell–induced angiogenesis in vitro. In an experimental metastatic lung tumor model, treatment of established tumors by Ad-MMP-2 inhibited s.c. tumor growth and formation of lung nodules in mice. Adenoviral-mediated RNA interference against MMP-2 has significant therapeutic potential for lung cancer and exerts some of this effect by inhibiting angiogenesis. [Mol Cancer Ther 2006;5(9):2289–99]
Association Between Sedentary Behavior, Physical Activity, and Obesity: Inactivity Among Active Kids

Introduction Sedentary behavior and physical activity are not mutually exclusive behaviors. The relative risk of overweight for adolescents who are highly sedentary and highly physically active is unclear. A better understanding of the relationship between sedentary behaviors, physical activity, and body mass index (BMI) would provide insight for developing interventions to prevent or reduce overweight. Methods Using the physical activity module of the School Health Action, Planning and Evaluation System (SHAPES), we collected data from 25,060 students in grades 9 through 12 from 76 secondary schools in Ontario, Canada. Sex-specific logistic regression analyses were performed to examine how BMI, weight perceptions, social influences, team sports participation, and smoking behavior were associated with being 1) high active-high sedentary, 2) low active-low sedentary, and 3) low active-high sedentary. Results Low active-high sedentary boys were more likely to be overweight than high active-low sedentary boys (adjusted odds ratio [AOR], 1.60; 95% confidence interval [CI], 1.01-2.58). When compared with high active-low sedentary girls, girls who were low active-high sedentary (OR, 2.24; 95% CI, 1.23-4.09) or high active-high sedentary (OR, 1.91; 95% CI, 1.01-3.61) were more likely to be overweight. Conclusion Sedentary behavior may moderate the relationship between physical activity and overweight. Developing a better understanding of sedentary behavior in relation to physical activity and overweight is critical for preventing and reducing overweight among youth.
Bayesian inference in genetic parameter estimation of visual scores in Nellore beef-cattle

The aim of this study was to estimate the components of variance and genetic parameters for the visual scores which constitute the Morphological Evaluation System (MES), such as body structure (S), precocity (P) and musculature (M) in Nellore beef-cattle at the weaning and yearling stages, by using threshold Bayesian models. The information used for this was gleaned from visual scores of 5,407 animals evaluated at the weaning and 2,649 at the yearling stages. The genetic parameters for visual score traits were estimated through two-trait analysis, using the threshold animal model, with Bayesian statistics methodology and MTGSAM (Multiple Trait Gibbs Sampler for Animal Models) threshold software. Heritability estimates for S, P and M were 0.68, 0.65 and 0.62 (at weaning) and 0.44, 0.38 and 0.32 (at the yearling stage), respectively. Heritability estimates for S, P and M were found to be high, and so it is expected that these traits should respond favorably to direct selection. The visual scores evaluated at the weaning and yearling stages might be used in the composition of new selection indexes, as they presented sufficient genetic variability to promote genetic progress in such morphological traits.
Copper Deficiency Leads to Anemia, Duodenal Hypoxia, Upregulation of HIF-2α and Altered Expression of Iron Absorption Genes in Mice

Iron and copper are essential trace metals, actively absorbed from the proximal gut in a regulated fashion. Depletion of either metal can lead to anemia. In the gut, copper deficiency can affect iron absorption through modulating the activity of hephaestin - a multi-copper oxidase required for optimal iron export from enterocytes. How systemic copper status regulates iron absorption is unknown. Mice were subjected to a nutritional copper deficiency-induced anemia regime from birth and injected with copper sulphate intraperitoneally to correct the anemia. Copper deficiency resulted in anemia, increased duodenal hypoxia and Hypoxia inducible factor 2α (HIF-2α) levels, a regulator of iron absorption. HIF-2α upregulation in copper deficiency appeared to be independent of duodenal iron or copper levels and correlated with the expression of iron transporters (Ferroportin - Fpn, Divalent Metal transporter – Dmt1) and ferric reductase – Dcytb. Alleviation of copper-dependent anemia with intraperitoneal copper injection resulted in down regulation of HIF-2α-regulated iron absorption genes in the gut. Our work identifies HIF-2α as an important regulator of iron transport machinery in copper deficiency.
Primates Decline Rapidly in Unprotected Forests: Evidence from a Monitoring Program with Data Constraints

Growing threats to primates in tropical forests make robust and long-term population abundance assessments increasingly important for conservation. Concomitantly, monitoring becomes particularly relevant in countries with primate habitat. Yet monitoring schemes in these countries often suffer from logistic constraints and/or poor rigor in data collection, and a lack of consideration of sources of bias in analysis. To address the need for feasible monitoring schemes and flexible analytical tools for robust trend estimates, we analyzed data collected by local technicians on abundance of three species of arboreal monkey in the Udzungwa Mountains of Tanzania (two Colobus species and one Cercopithecus), an area of international importance for primate endemism and conservation. We counted primate social groups along eight line transects in two forest blocks in the area, one protected and one unprotected, over a span of 11 years. We applied a recently proposed open metapopulation model to estimate abundance trends while controlling for confounding effects of observer, site, and season. Primate populations were stable in the protected forest, while the colobines, including the endemic Udzungwa red colobus, declined severely in the unprotected forest. Targeted hunting pressure at this second site is the most plausible explanation for the trend observed. The unexplained variability in detection probability among transects was greater than the variability due to observers, indicating consistency in data collection among observers. There were no significant differences in both primate abundance and detectability between wet and dry seasons, supporting the choice of sampling during the dry season only based on minimizing practical constraints. Results show that simple monitoring routines implemented by trained local technicians can effectively detect changes in primate populations in tropical countries. The hierarchical Bayesian model formulation adopted provides a flexible tool to determine temporal trends with full account for any imbalance in the data set and for imperfect detection.
Far Out: Predicting Long-Term Human Mobility

Much work has been done on predicting where is one going to be in the immediate future, typically within the next hour. By contrast, we address the open problem of predicting human mobility far into the future, a scale of months and years. We propose an efficient nonparametric method that extracts significant and robust patterns in location data, learns their associations with contextual features (such as day of week), and subsequently leverages this information to predict the most likely location at any given time in the future. The entire process is formulated in a principled way as an eigendecomposition problem. Evaluation on a massive dataset with more than 32,000 days worth of GPS data across 703 diverse subjects shows that our model predicts the correct location with high accuracy, even years into the future. This result opens a number of interesting avenues for future research and applications.
Long-term use of ticagrelor in patients with prior myocardial infarction.

BACKGROUND The potential benefit of dual antiplatelet therapy beyond 1 year after a myocardial infarction has not been established. We investigated the efficacy and safety of ticagrelor, a P2Y12 receptor antagonist with established efficacy after an acute coronary syndrome, in this context. METHODS We randomly assigned, in a double-blind 1:1:1 fashion, 21,162 patients who had had a myocardial infarction 1 to 3 years earlier to ticagrelor at a dose of 90 mg twice daily, ticagrelor at a dose of 60 mg twice daily, or placebo. All the patients were to receive low-dose aspirin and were followed for a median of 33 months. The primary efficacy end point was the composite of cardiovascular death, myocardial infarction, or stroke. The primary safety end point was Thrombolysis in Myocardial Infarction (TIMI) major bleeding. RESULTS The two ticagrelor doses each reduced, as compared with placebo, the rate of the primary efficacy end point, with Kaplan-Meier rates at 3 years of 7.85% in the group that received 90 mg of ticagrelor twice daily, 7.77% in the group that received 60 mg of ticagrelor twice daily, and 9.04% in the placebo group (hazard ratio for 90 mg of ticagrelor vs. placebo, 0.85; 95% confidence interval [CI], 0.75 to 0.96; P=0.008; hazard ratio for 60 mg of ticagrelor vs. placebo, 0.84; 95% CI, 0.74 to 0.95; P=0.004). Rates of TIMI major bleeding were higher with ticagrelor (2.60% with 90 mg and 2.30% with 60 mg) than with placebo (1.06%) (P<0.001 for each dose vs. placebo); the rates of intracranial hemorrhage or fatal bleeding in the three groups were 0.63%, 0.71%, and 0.60%, respectively. CONCLUSIONS In patients with a myocardial infarction more than 1 year previously, treatment with ticagrelor significantly reduced the risk of cardiovascular death, myocardial infarction, or stroke and increased the risk of major bleeding. (Funded by AstraZeneca; PEGASUS-TIMI 54 ClinicalTrials.gov number, NCT01225562.).
Effect of Radial Neck Length on Joint Loading

Introduction: Load transfer across the radiocapitellar joint of the elbow is poorly understood both in the setting of the native radial head and following radial head arthroplasty. The purpose of this in vitro study was to determine the effects of radial neck length, arm position, and lateral collateral ligament (LCL) repair on radial load.Methods: A uniaxial load cell was implanted into the radial neck of 8 cadaveric specimens that were mounted on an in vitro motion-control simulator and tested (in dependent, varus, and valgus arm orientations) with the native radial neck length and then −4 to +4 mm lengths. Testing was performed with the LCL intact and after sectioning and repair.Results: There was no significant difference between the 2 LCL states (P = .82), and LCL state was not protective of proximal radius overlengthening. Radial loads increased with increasing radial length (P < .001). Discussion and Conclusion: Overlengthening the radial neck resulted in higher compression forces, and underlengthening produced tensile forces, demonstrating that restoration of correct radial length during radial head arthroplasty is important to restore physiologic loading. In the varus position, tensile loading occurred, which may explain clinical problems with ingrowth of uncemented radial head implant stems and dissociation of bipolar implants.
Time Series Based Link Prediction

Link prediction is a task in Social Network Analysis that consists of predicting connections that are most likely to appear considering previous observed links in a social network. The majority of works in this area only performs the task by exploring the state of the network at a specific moment to make the prediction of new links, without considering the behavior of links as time goes by. In this light, we investigate if temporal information can bring any performance gain to the link prediction task. A traditional approach for link prediction uses a chosen topological similarity metric on non-connected pairs of nodes of the network at present time to obtain a score that is going to be used by an unsupervised or a supervised method for link prediction. Our approach initially consists of building time series for each pair of non-connected nodes by computing their similarity scores at different past times. Then, we deploy a forecasting model on these time series and use their forecasts as the final scores of the pairs. Our preliminary results using two link prediction methods (unsupervised and supervised) on co-authorship networks revealed satisfactory results when temporal information was considered.
Advances in Viral Vector-Based TRAIL Gene Therapy for Cancer

Numerous biologic approaches are being investigated as anti-cancer therapies in an attempt to induce tumor regression while circumventing the toxic side effects associated with standard chemo- or radiotherapies. Among these, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has shown particular promise in pre-clinical and early clinical trials, due to its preferential ability to induce apoptotic cell death in cancer cells and its minimal toxicity. One limitation of TRAIL use is the fact that many tumor types display an inherent resistance to TRAIL-induced apoptosis. To circumvent this problem, researchers have explored a number of strategies to optimize TRAIL delivery and to improve its efficacy via co-administration with other anti-cancer agents. In this review, we will focus on TRAIL-based gene therapy approaches for the treatment of malignancies. We will discuss the main viral vectors that are being used for TRAIL gene therapy and the strategies that are currently being attempted to improve the efficacy of TRAIL as an anti-cancer therapeutic.
Parameterization of Centimeter-Scale Sea Ice Surface Roughness Using Terrestrial LiDAR

Microwave scattering from sea ice is partially controlled by the ice surface roughness. In this paper, we propose a technique for calculating 2-D centimeter-scale surface roughness parameters, including the rms height, correlation length, and form of autocorrelation function, from 3-D terrestrial light detection and ranging data. We demonstrate that a single scale of roughness can be extracted from complex sea ice surfaces, incorporating multiple scales of topography, after sophisticated 2-D detrending, and calculate roughness parameters for a wide range of artificial and natural sea ice surface types. The 2-D technique is shown to be considerably more precise than standard 1-D profiling techniques and can therefore characterize surface roughness as a stationary single-scale process, which a 1-D technique typically cannot do. Sea ice surfaces are generally found to have strongly anisotropic correlation lengths, indicating that microwave scattering models for sea ice should include surface spectra that vary as a function of the azimuthal angle of incident radiation. However, our results demonstrate that there is no fundamental relationship between the rms height and correlation length for sea ice surfaces if the sampling area is above a threshold minimum size.
Vector field models of inflation and dark energy

We consider several new classes of viable vector field alternatives to the inflaton and quintessence scalar fields. Spatial vector fields are shown to be compatible with the cosmological anisotropy bounds if only slightly displaced from the potential minimum while dominant, or if driving an anisotropic expansion with nearly vanishing quadrupole today. The Bianchi I model with a spatial field and an isotropic fluid is studied as a dynamical system, and scaling solutions of several types are found. On the other hand, time-like fields are automatically compatible with large-scale isotropy. We show that they can be dynamically important if non-minimal gravity couplings are taken into account. We reconstruct as an example a vector–Gauss–Bonnet model which generates the concordance model acceleration at late times and supports an inflationary epoch at high curvatures. The evolution of the vortical perturbations in such models is computed.
Experimental and modeled UV erythemal irradiance under overcast conditions: the role of cloud optical depth

This paper evaluates the relationship between the cloud modification factor (CMF) in the ultraviolet erythe- mal range and the cloud optical depth (COD) retrieved from the Aerosol Robotic Network (AERONET) "cloud mode" al- gorithm under overcast cloudy conditions (confirmed with sky images) at Granada, Spain, mainly for non-precipitating, overcast and relatively homogenous water clouds. Empiri- cal CMF showed a clear exponential dependence on experi- mental COD values, decreasing approximately from 0.7 for COD= 10 to 0.25 for COD= 50. In addition, these COD measurements were used as input in the LibRadtran radia- tive transfer code allowing the simulation of CMF values for the selected overcast cases. The modeled CMF exhib- ited a dependence on COD similar to the empirical CMF, but modeled values present a strong underestimation with re- spect to the empirical factors (mean bias of 22 %). To ex- plain this high bias, an exhaustive comparison between mod- eled and experimental UV erythemal irradiance (UVER) data was performed. The comparison revealed that the radiative transfer simulations were 8 % higher than the observations for clear-sky conditions. The rest of the bias ( 14 %) may be attributed to the substantial underestimation of modeled UVER with respect to experimental UVER under overcast conditions, although the correlation between both dataset was high (R 2 0.93). A sensitive test showed that the main reason responsible for that underestimation is the experimen- tal AERONET COD used as input in the simulations, which has been retrieved from zenith radiances in the visible range. In this sense, effective COD in the erythemal interval were derived from an iteration procedure based on searching the best match between modeled and experimental UVER values for each selected overcast case. These effective COD values were smaller than AERONET COD data in about 80 % of the overcast cases with a mean relative difference of 22 %.