Miracle-dz/UniFAR-FTUs huggingface dataset:
CD137 Expression Is Induced by Epstein-Barr Virus Infection through LMP1 in T or NK Cells and Mediates Survival Promoting Signals

To clarify the mechanism for development of Epstein-Barr virus (EBV)-positive T- or NK-cell neoplasms, we focused on the costimulatory receptor CD137. We detected high expression of CD137 gene and its protein on EBV-positive T- or NK-cell lines as compared with EBV-negative cell lines. EBV-positive cells from EBV-positive T- or NK-cell lymphoproliferative disorders (EBV-T/NK-LPDs) patients also had significantly higher CD137 gene expression than control cells from healthy donors. In the presence of IL-2, whose concentration in the serum of EBV-T/NK-LPDs was higher than that of healthy donors, CD137 protein expression was upregulated in the patients' cells whereas not in control cells from healthy donors. In vitro EBV infection of MOLT4 cells resulted in induction of endogenous CD137 expression. Transient expression of LMP1, which was enhanced by IL-2 in EBV-T/NK-LPDs cells, induced endogenous CD137 gene expression in T and NK-cell lines. In order to examine in vivo CD137 expression, we used EBV-T/NK-LPDs xenograft models generated by intravenous injection of patients' cells. We identified EBV-positive and CD8-positive T cells, as well as CD137 ligand-positive cells, in their tissue lesions. In addition, we detected CD137 expression on the EBV infected cells from the lesions of the models by immune-fluorescent staining. Finally, CD137 stimulation suppressed etoposide-induced cell death not only in the EBV-positive T- or NK-cell lines, but also in the patients' cells. These results indicate that upregulation of CD137 expression through LMP1 by EBV promotes cell survival in T or NK cells leading to development of EBV-positive T/NK-cell neoplasms.
"Sitation" distributions and Bradford's law in a closed Web space

The study looks at how well the distribution of “sitations” (inlinks received by Web spaces) fits either a power law (of the Lotka type) or a bibliometric distribution for printed publications (of the Bradford type). The experimental sample examines the sitations found in a closed generic environment of thematically‐related Web sites – the case of Extremadura (Spain). Two sets of data, varying several parameters, were used. The sitation distributions found were coherent with those described in previous experiments of this type, including in the exponent. The plots of accumulated clusters of sitations and targets, however, did not fit the typical Bradford distribution.
Wireless network simplification: Beyond diamond networks

We consider an arbitrary layered Gaussian relay network with L layers of N relays each, from which we select subnetworks with K relays per layer. We prove that: (i) For arbitrary L;N and K = 1, there always exists a subnetwork that approximately achieves 2/(L-1)N+4 (resp. 2/LN+2) of the network capacity for odd L (resp. even L), (ii) For L = 2; N = 3; K = 2, there always exists a subnetwork that approximately achieves 1/2 of the network capacity. We also provide example networks where even the best subnetworks achieve exactly these fractions (up to additive gaps). Along the way, we derive some results on MIMO antenna selection and capacity decomposition that may also be of independent interest.
Evaluation of Test Day Milk Yield in Iranian Primiparous Holstein Using Different Random Regression Models

Several functions were used to model fixed and random part of the lactation curve in Iranian primiparous Holstein cows using random regression analysis. Legendre polynomials of orders three and four as well as parametric lactation curve for the random part of the first lactation milk production were compared to find the best model. The models differed in fixed regression lactation curve part and residual variance assumed heterogeneous during lactation. Based on eigenvalue, associated eigenfunction and residual variance, third order polynomial Quadratic form for random effects and Ali and Schaefer model for fixed part AS33 model is optimal and make parsimonious less parameters for adjustment of test day milk yield records. The maximum residual and permanent environmental variances were obtained at the beginning and at the end of lactation respectively. The greatest additive genetic variance was in the middle of lactation and residual variance decreased during lactation. The highest heritability observed in middle of lactation (170 to 205 d) and ranged from 0.06 to 0.40. The genetic, permanent environmental and phenotypic correlation between extreme parts of lactation was 0.519, 0.317 and 0.240, respectively.
The dislocation density, flow stress and stored energy in deformed polycrystalline copper

Abstract The relationships between the dislocation density, flow stress and stored energy in polycrystalline copper have been determined experimentally. The stored energy can be predicted from the observed density and distribution of dislocations. The flow stress–stored energy and flow stress–dislocation density relationships can be accounted for if the flow stress is attributed either to the stress required for a dislocation to penetrate the forest of dislocations, or to the stress required to move jogged dislocations.
Prediction of Treatment Week Eight Response & Sustained Virologic Response in Patients Treated with Boceprevir Plus Peginterferon Alfa and Ribavirin

Aim Sustained virologic response (SVR) can be attained with boceprevir plus peginterferon alfa and ribavirin (PR) in up to 68% of patients, and short duration therapy is possible if plasma HCV RNA levels are undetectable at treatment week 8 (TW8 response). We have developed predictive models for SVR, and TW8 response using data from boceprevir clinical trials. Methods Regression models were built to predict TW8 response and SVR. Separate models were built for TW8 and SVR using baseline variables only, and compared to models with baseline variables plus HCV RNA change after 4 weeks of PR (TW4 delta). Predictive accuracy was assessed by c-statistics, calibration curves, and decision curve analyses. Nomograms were developed to create clinical decision support tools. Models were externally validated using independent data. Results The models that included TW4 delta produced the best discrimination ability. The predictive factors for TW8 response (n = 856) were TW4 delta, race, platelet count and ALT. The predictive factors for SVR (n = 522) were TW4 delta, HCV-subtype, gender, BMI, RBV dose and platelet count. The discrimination abilities of these models were excellent (C-statistics = 0.88, 0.80 respectively). Baseline models for TW8 response (n = 444) and SVR (n = 197) had weaker discrimination ability (C-statistic = 0.76, 0.69). External validation confirmed the predictive accuracy of the week 4 models. Conclusions Models incorporating baseline and treatment week 4 data provide excellent prediction of TW8 response and SVR, and support the clinical utility of the lead-in phase of PR. The nomograms are suitable for point-of-care use to inform individual patient and physician decision-making.
Public Housing Relocation and Its Effect on Residents' Self-esteem and Self-efficacy

In 2008, Atlanta was the first city in the United States to completely eliminate its highrise public housing projects. Georgia State University professors Drs. Ruel, Oakley, and Reid undertook a three-year study to determine the health, behavior, and attitudes of residents both before and after relocation. This study sought to determine whether residents’ self-esteem and self-efficacy improved after relocation into areas that have lower levels of social disorder and poor housing conditions. Overall, results show that while housing conditions, social disorder, and fear of crime had little or no significant effect on changes in residents’ self-esteem, an improvement in these indicators in residents’ new neighborhoods had a significant effect on selfefficacy. The significance of decreased social disorder and poor housing conditions, as well as fear of crime on residents’ self-efficacy (but not self-esteem) has important implications for future research regarding neighborhood and housing effects as well as public housing relocation. INDEX WORDS: Public housing, Self-esteem, Self-efficacy, Neighborhood effects, Social disorder, Housing conditions, Relocation PUBLIC HOUSING RELOCATION AND ITS EFFECT ON RESIDENTS’ SELF-ESTEEM AND SELF-EFFICACY
Whole-body scintigraphy in melanoma patients: comparison of 99Tcm-tetrofosmin and 201Tl

The aim of this study was to determine the diagnostic value of 99Tcm-tetrofosmin whole-body imaging in comparison to 201Tl scintigraphy in patients with metastatic melanoma. In 27 patients with known or suspected melanoma metastases we performed 201Tl scintigraphy and 99Tcm-tetrofosmin scintigraphy using a 1-day protocol. In five patients with known locoregional metastasis the in vivo uptake kinetics of both radiotracers were compared. The final diagnosis was confirmed by surgical histology in 39 lesions (group I) and computed tomography (CT) and clinical course in 14 lesions (group II). In group I, containing mainly locoregional metastases, 201Tl scintigraphy correctly identified 36 of 39 metastases and 99Tcm-tetrofosmin 35 of 39 resulting in a sensitivity of 92% and 90% respectively. The T/B ratios of 201Tl (1.4-4.0, mean 2.15) were statistically significantly higher in comparison to tetrofosmin (1.3-3.0, mean 1.88). However, both radiotracers showed similar uptake and washout kinetics with a maximum of tracer uptake between 1 and 5 min p.i. In group II, containing mainly cerebral and pulmonary metastases, both methods correctly identified six of 14 metastases resulting in a sensitivity of only 43%. We conclude that the uptake of 99Tcm-tetrofosmin and 201Tl in melanoma metastases is very similar. The T/B ratios with 99Tcm-tetrofosmin are significantly lower than with 201Tl. In locoregional melanoma metastases the sensitivity of tetrofosmin scintigraphy is identical with 201Tl imaging and amounts to 90%. In cerebral and lung metastases the sensitivity of both methods is limited when using whole-body scintigraphy.
Simvastatin Reduces the Association of NMDA Receptors to Lipid Rafts: A Cholesterol-Mediated Effect in Neuroprotection

Background and Purpose— Excess brain extracellular glutamate induced by cerebral ischemia leads to neuronal death, mainly through overactivation of N-methyl-d-aspartate (NMDA) receptors. The cholesterol-lowering drugs statins have been reported to protect from NMDA-induced neuronal death but, so far, the mechanism underlying this protection remains unclear. Because NMDA receptors have been reported to be associated with the cholesterol-rich membrane domains known as lipid rafts, we have investigated the effect of treatments that deplete cholesterol levels on excitotoxicity and on association of NMDA receptors to lipid rafts. Methods— Primary neuronal cultures were pretreated with inhibitors of cholesterol synthesis and cholesterol, and NMDA-induced cell death was determined by measuring release of lactate dehydrogenase. Lipid raft fractions were isolated and Western blots were performed. Results— Treatment with the inhibitors of cholesterol synthesis simvastatin, which inhibits the first step of cholesterol synthesis, or AY9944, which inhibits the last step of cholesterol synthesis, protected neurons from NMDA-induced neuronal death by 70% and 54%, respectively. Treatment with these compounds reduced neuronal cholesterol levels by 35% and 13%, respectively. Simvastatin and AY9944 reduced the association of the subunit 1 of NMDA receptors (NMDAR1) to lipid rafts by 42% and 21%, respectively, and did not change total expression of NMDAR1. Addition of cholesterol reduced neuroprotection by statins and AY9944, and partially reverted the effect of simvastatin on the association of NMDAR1 to lipid rafts. Conclusions— These data demonstrate that reduction of cholesterol levels protects from NMDA-induced neuronal damage probably by reducing the association of NMDA receptors to lipid rafts.
Rendering Rough Opaque Materials with Interfaced Lambertian Microfacets

Specular microfacet distributions have been successfully employed by many authors for representing glossiness of materials. They are generally combined with a Lambertian term to account for the colored aspect. These representations make use of the Fresnel reflectance factor at the interface, but the transmission factor at the interface should also be managed. One solution is to employ a multi-layered model with a single layer for the rough interface, which requires a numerical simulation for handling the multiple reflections of light between the substrate and the interface. In this paper, we propose rather to use a representation corresponding to a Fresnel interface lying on a Lambertian substrate, for which the multiple reflections of light between the interface and the substrate can be expressed analytically. With this interfaced Lambertian model, we show how Fresnel transmission affects the material appearance for flat and rough surfaces with isotropic and anisotropic distributions, that produce light backscattering effects. We also propose a methodology for using such materials in any physically based Monte Carlo rendering system, as well as an approximate representation, suitable for GPU applications or measured data fitting. Our approach generalizes several previous models, including flat Lambertian materials as well as specular and Lambertian microfacets. Our results illustrate the wide range of materials that can be rendered with this representation.
Genome-Wide Inference of Ancestral Recombination Graphs

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the “ancestral recombination graph” (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of chromosomes conditional on an ARG of chromosomes, an operation we call “threading. ” Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps.
Different Implications of Paternal and Maternal Atopy for Perinatal IgE Production and Asthma Development

Asthma is a hereditary disease associated with IgE-mediated reaction. Whether maternal atopy and paternal atopy have different impacts on perinatal IgE production and asthma development remains unclear. This paper reviews and summarizes the effects of maternal and paternal atopy on the developmental aspects of IgE production and asthma. Maternal atopy affects both pre- and postnatal IgE production, whereas paternal atopy mainly affects the latter. Maternally transmitted genes GSTP1 and FceRI-beta are associated with lung function and allergic sensitization, respectively. In IgE production and asthma development, the maternal influence on gene-environment interaction is greater than paternal influence. Maternal, paternal, and/or postnatal environmental modulation of allergic responses have been linked to epigenetic mechanisms, which may be good targets for early prevention of asthma.
Foxg1 regulates retinal axon pathfinding by repressing an ipsilateral program in nasal retina and by causing optic chiasm cells to exert a net axonal growth-promoting activity

Mammalian binocular vision relies on the divergence of retinal ganglion cell axons at the optic chiasm, with strictly controlled numbers projecting contralaterally and ipsilaterally. In mouse, contralateral projections arise from the entire retina, whereas ipsilateral projections arise from ventrotemporal retina. We investigate how development of these patterns of projection is regulated by the contralateral determinant Foxg1, a forkhead box transcription factor expressed in nasal retina and at the chiasm. In nasal retina, loss of Foxg1 causes increased numbers of ipsilateral projections and ectopic expression of the ipsilateral determinants Zic2, Ephb1 and Foxd1, indicating that nasal retina is competent to express an ipsilateral program that is normally suppressed by Foxg1. Using co-cultures that combine Foxg1-expressing with Foxg1-null retinal explants and chiasm cells, we provide functional evidence that Foxg1 promotes contralateral projections through actions in nasal retina, and that in chiasm cells, Foxg1 is required for the generation of a hitherto unrecognized activity supporting RGC axon growth.
Comparison of two‐dimensional and three‐dimensional simulations of dense nonaqueous phase liquids (DNAPLs): Migration and entrapment in a nonuniform permeability field

The influence of reduced dimensionality (two‐dimensional (2‐D) versus 3‐D) on predictions of dense nonaqueous phase liquid (DNAPL) infiltration and entrapment in statistically homogeneous, nonuniform permeability fields was investigated using the University of Texas Chemical Compositional Simulator (UTCHEM), a 3‐D numerical multiphase simulator. Hysteretic capillary pressure–saturation and relative permeability relationships implemented in UTCHEM were benchmarked against those of another lab‐tested simulator, the Michigan‐Vertical and Lateral Organic Redistribution (M‐VALOR). Simulation of a tetrachloroethene spill in 16 field‐scale aquifer realizations generated DNAPL saturation distributions with approximately equivalent distribution metrics in two and three dimensions, with 2‐D simulations generally resulting in slightly higher maximum saturations and increased vertical spreading. Variability in 2‐D and 3‐D distribution metrics across the set of realizations was shown to be correlated at a significance level of 95–99%. Neither spill volume nor release rate appeared to affect these conclusions. Variability in the permeability field did affect spreading metrics by increasing the horizontal spreading in 3‐D more than in 2‐D in more heterogeneous media simulations. The assumption of isotropic horizontal spatial statistics resulted, on average, in symmetric 3‐D saturation distribution metrics in the horizontal directions. The practical implication of this study is that for statistically homogeneous, nonuniform aquifers, 2‐D simulations of saturation distributions are good approximations to those obtained in 3‐D. However, additional work will be needed to explore the influence of dimensionality on simulated DNAPL dissolution.
Berberine – a novel approach to cholesterol lowering

Although low-density lipoprotein (LDL)-cholesterol lowering with the statins reduces the mortality and morbidity associated with coronary artery disease, considerable mortality and morbidity remains. Berberine upregulates the LDL receptor (LDLR) by a mechanism distinct from that of the statins, which involves stabilising the LDLR mRNA. In hamsters fed a high-fat and high-cholesterol diet for 2 weeks, the oral administration of berberine 100 mg/kg for 10 days reduced total serum cholesterol from ∼ 4.8 to 2.7 mmol/l, and LDL-cholesterol from ∼ 2.5 to 1.4 mmol/l. In subjects with hypercholesterolaemia, berberine hydrochloride (0.5 g b.i.d. for 3 months) reduced LDL-cholesterol (from 3.2 to 2.4 mmol/l) without any effect on high-density lipoprotein-cholesterol. Berberine also caused a reduction in triglyceride levels from 2.3 to 1.5 mmol/l. As berberine and statins both upregulate LDLR, their lipid-lowering profiles are similar. Thus, this mechanism is unlikely to make berberine an attractive alternative to statins for lipid lowering in most circumstances. However, the other effects of berberine (antihypertensive, inotropic and class III antiarrhythmic properties) may make it a useful agent in the treatment of cardiovascular disease.
Binding of mannose-binding protein to Klebsiella O3 lipopolysaccharide possessing the mannose homopolysaccharide as the O-specific polysaccharide and its relation to complement activation

Lipopolysaccharide from Klebsiella pneumoniae O3, which possesses the mannose homopolysaccharide as the O-specific polysaccharide, exhibits an extraordinarily high ability to activate the human complement system. We isolated the mannose-binding protein with a Klebsiella O3 lipopolysaccharide affinity column. The protein isolated had a molecular mass of much higher than 200 kDa, and it consisted of subunits with an apparent molecular mass of 32 kDa. The NH2-terminal sequence of the 32-kDa subunits was completely consistent with a part of the amino acid sequence of human serum mannose-binding protein. In immunoblotting, an anti-mannose-binding protein monoclonal antibody was definitely reactive with the isolated protein with the higher molecular mass. The protein isolated was bound exclusively to lipopolysaccharides possessing the mannose homopolysaccharide, not to lipopolysaccharide possessing the heteropolysaccharides. Klebsiella O3 lipopolysaccharide did not exhibit a high anticomplement activity in the serum from which the mannose-binding protein was depleted. It was concluded that the serum factor that bound to Klebsiella O3 lipopolysaccharide may be mannose-binding protein and that it may play a crucial role in the strong complement activation by Klebsiella O3 lipopolysaccharide.
Design Optimization and Fabrication of a Novel Structural SOI Piezoresistive Pressure Sensor with High Accuracy

This paper presents a novel structural piezoresistive pressure sensor with four-grooved membrane combined with rood beam to measure low pressure. In this investigation, the design, optimization, fabrication, and measurements of the sensor are involved. By analyzing the stress distribution and deflection of sensitive elements using finite element method, a novel structure featuring high concentrated stress profile (HCSP) and locally stiffened membrane (LSM) is built. Curve fittings of the mechanical stress and deflection based on FEM simulation results are performed to establish the relationship between mechanical performance and structure dimension. A combination of FEM and curve fitting method is carried out to determine the structural dimensions. The optimized sensor chip is fabricated on a SOI wafer by traditional MEMS bulk-micromachining and anodic bonding technology. When the applied pressure is 1 psi, the sensor achieves a sensitivity of 30.9 mV/V/psi, a pressure nonlinearity of 0.21% FSS and an accuracy of 0.30%, and thereby the contradiction between sensitivity and linearity is alleviated. In terms of size, accuracy and high temperature characteristic, the proposed sensor is a proper choice for measuring pressure of less than 1 psi.