bluuebunny/crossref_metadata_2025_split huggingface dataset:
"Boom" and "Bust" cycles in virus growth suggest multiple selective forces in influenza a evolution
Authors: Thangavel Rajagowthamee R , Reed Aisha , Norcross Erin W , Dixon Sherrina N , Marquart Mary E , Stray Stephen J 
Published: April 2011

AbstractBackgroundInfluenza A virus evolution in humans is driven at least in part by mutations allowing the virus to escape antibody neutralization. Little is known about the evolution of influenza in birds, a major reservoir of influenza A.MethodsNeutralizing polyclonal antiserum was raised in chicken against reassortant influenza virus, CalX, bearing the hemagglutinin (HA) and neuraminidase (NA) of A/California/7/2004 [H3N2]. CalX was serially passaged in the presence of anti-CalX polyclonal IgY to derive viruses capable of growth in the presence of antibody.ResultsPolyclonal chicken antibody neutralized both HA activity and infection by CalX, but had no effect on a strain bearing an earlier human H3 and an irrelevant neuraminidase (A/Memphis/71-Bellamy/42 [H3N1]). Surprisingly, most of the antibody-resistant viruses were still at least partially sensitive to neutralization of HA activity and viral infection. Although mutant HA genes bearing changes that might affect antibody neutralization were identified, the vast majority of HA sequences obtained were identical to wild type, and no individual mutant sequence was found in more than one passage, suggesting that those mutations that were observed did not confer sufficient selective advantage to come to dominate the population. Different passages yielded infectious foci of varying size and plaques of varying size and morphology. Yields of infectious virus and relative frequency of different morphologies changed markedly from passage to passage. Sequences of bulk, uncloned PCR products from antibody-resistant passages indicated changes in the PB2 and PA proteins with respect to the wild type virus.ConclusionsEach antibody-selected passage consisted of a variety of different cocirculating populations, rather than pure populations of virus able to escape antibody by changes in antibody epitopes. The ability to escape antibody is apparently due to changes in genes encoding the viral polymerase complex, probably resulting in more robust viral replication, allowing the few virus particles not completely neutralized by antibody to rapidly produce large numbers of progeny. Our data suggest that the relative success of an individual variant may depend on both its own gain and loss of fitness, as well as that of its cocirculating variants.
Melatonin reduces the severity of experimental amoebiasis
Authors: França-Botelho Aline C , França Juliana L , Oliveira Fabrício MS , Franca Eduardo L , Honório-França Adenilda C , Caliari Marcelo V , Gomes Maria A 
Published: April 2011

AbstractBackgroundMelatonin has immunomodulatory effects but very little is known about its influence in protozoan infections, such asEntamoeba histolytica, which causes amoebiasis, a disease with significant morbidity and mortality. In this study, we evaluated the effects of exogenous melatonin interference in experimental amoebiasis and on interactions between human blood cells andE. histolyticatrophozoites.MethodsThe effect of melatonin was investigated in models of experimental amoebiasis in hamsters and rats by evaluating the area of necrosis induced byE. histolytica. The activity of melatonin on the interactions between leukocytes and amoebae was determined by examining leukophagocytosis. Forin vitrotests, polymorphonuclear and mononuclear human blood leucocytes were incubated withE. histolyticatrophozoites.ResultsThe areas of amoebic necrosis were significantly reduced in animals treated with melatonin. Melatonin treatment increased leukophagocytosis but was associated with a greater number of dead amoebae.ConclusionsThese results suggest that melatonin may play a beneficial role in the control of amoebic lesions, raising the possibility that this drug may be used as an adjuvant in anti-amoebic therapy.
Silibinin induces apoptosis via calpain-dependent AIF nuclear translocation in U87MG human glioma cell death
Authors: Jeong Ji C , Shin Won Y , Kim Thae H , Kwon Chae H , Kim Jae H , Kim Yong K , Kim Ki H 
Published: April 2011

Abstract

Background
Silibinin, a natural polyphenolic flavonoid, has been reported to induce cell death in various cancer cell types. However, the molecular mechanism is not clearly defined. Our previous study showed that silibinin induces glioma cell death and its effect was effectively prevented by calpain inhibitor. The present study was therefore undertaken to examine the role of calpain in the silibinin-induced glioma cell death.

Methods
U87MG cells were grown on well tissue culture plates and cell viability was measured by MTT assay. ROS generation and △ψm were estimated using the fluorescence dyes. PKC activation and Bax expression were measured by Western blot analysis. AIF nuclear translocation was determined by Western blot and immunocytochemistry.

Results
Silibinin induced activation of calpain, which was blocked by EGTA and the calpain inhibitor Z-Leu-Leu-CHO. Silibinin caused ROS generation and its effect was inhibited by calpain inhibitor, the general PKC inhibitor GF 109203X, the specific PKCδ inhibitor rottlerin, and catalase. Silibinin-induce cell death was blocked by calpain inhibitor and PKC inhibitors. Silibinin-induced PKCδ activation and disruption of △ψm were prevented by the calpain inhibitor. Silibinin induced AIF nuclear translocation and its effect was prevented by calpain inhibitor. Transfection of vector expressing microRNA of AIF prevented the silibinin-induced cell death.

Conclusions
Silibinin induces apoptotic cell death through a calpain-dependent mechanism involving PKC, ROS, and AIF nuclear translocation in U87MG human glioma cells.
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Authors: Kubicek Christian P , Herrera-Estrella Alfredo , Seidl-Seiboth Verena , Martinez Diego A , Druzhinina Irina S , Thon Michael , Zeilinger Susanne , Casas-Flores Sergio , Horwitz Benjamin A , Mukherjee Prasun K , Mukherjee Mala , Kredics László , Alcaraz Luis D , Aerts Andrea , Antal Zsuzsanna , Atanasova Lea , Cervantes-Badillo Mayte G , Challacombe Jean , Chertkov Olga , McCluskey Kevin , Coulpier Fanny , Deshpande Nandan , von Döhren Hans , Ebbole Daniel J , Esquivel-Naranjo Edgardo U , Fekete Erzsébet , Flipphi Michel , Glaser Fabian , Gómez-Rodríguez Elida Y , Gruber Sabine , Han Cliff , Henrissat Bernard , Hermosa Rosa , Hernández-Oñate Miguel , Karaffa Levente , Kosti Idit , Le Crom Stéphane , Lindquist Erika , Lucas Susan , Lübeck Mette , Lübeck Peter S , Margeot Antoine , Metz Benjamin , Misra Monica , Nevalainen Helena , Omann Markus , Packer Nicolle , Perrone Giancarlo , Uresti-Rivera Edith E , Salamov Asaf , Schmoll Monika , Seiboth Bernhard , Shapiro Harris , Sukno Serenella , Tamayo-Ramos Juan Antonio , Tisch Doris , Wiest Aric , Wilkinson Heather H , Zhang Michael , Coutinho Pedro M , Kenerley Charles M , Monte Enrique , Baker Scott E , Grigoriev Igor V 
Published: April 2011

AbstractBackgroundMycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genusHypocrea/Trichoderma.ResultsHere we report an analysis of the genome sequences of the two biocontrol speciesTrichoderma atroviride(teleomorphHypocrea atroviridis) andTrichoderma virens(formerlyGliocladium virens, teleomorphHypocrea virens), and a comparison withTrichoderma reesei(teleomorphHypocrea jecorina). These threeTrichodermaspecies display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative toT. reeseior other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows thatT. reeseiandT. virensare derived relative toT. atroviride. The mycoparasitism-specific genes thus arose in a commonTrichodermaancestor but were subsequently lost inT. reesei.ConclusionsThe data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
Respiratory-gated 18F-FDG PET imaging in lung cancer: effects on sensitivity and specificity
Authors: Daouk Joël , Leloire Marie , Fin Loïc , Bailly Pascal , Morvan Julie , El Esper Isabelle , Saidi Lazhar , Moullart Véronique , François Géraldine , Jounieaux Vincent , Meyer Marc-Etienne 
Published: April 2011

Background Respiratory motion is known to deteriorate positron emission tomography (PET) images and may lead to potential diagnostic errors when a standardized uptake value (SUV) cut-off threshold is used to discriminate between benign and malignant lesions. Purpose To evaluate and compare ungated and respiratory-gated 18F-fluorodeoxyglucose PET/computed tomography (CT) methods for the characterization of pulmonary nodules. Material and Methods The list-mode acquisition during respiratory-gated PET was combined with a short breath-hold CT scan to form the CT-based images. We studied 48 lesions in 43 patients. PET images were analyzed in terms of the maximum SUV (SUVmax) and the lesion location. Results Using receiver-operating characteristic (ROC) curves, the optimal SUV cut-off thresholds for the ungated and CT-based methods were calculated to be 2.0 and 2.2, respectively. The corresponding sensitivity values were 83% and 92%, respectively, with a specificity of 67% for both methods. The two methods gave equivalent performance levels for the upper and middle lobes (sensitivity 93%, specificity 62%). They differed for the lower lobes, where the CT-based method outperformed the ungated method (sensitivity values of 90% and 70%, respectively, and a specificity of 73% with both methods) – especially for lesions smaller than 15 mm. Conclusion The CT-based method increased sensitivity and did not diminish specificity, compared with the ungated method. It was more efficient than the ungated method for imaging the lower lobes and smallest lesions, which are most affected by respiratory motion.
Optimal Housing, Consumption, and Investment Decisions over the Life Cycle
Authors: Kraft Holger , Munk Claus 
Published: April 2011

We derive explicit solutions to life-cycle utility maximization problems involving stock and bond investment, perishable consumption, and the rental and ownership of residential real estate. Prices of houses, stocks and bonds, and labor income are correlated. Because of a positive correlation between house prices and labor income, young individuals want little exposure to house price risk and tend to rent their home. Later in life the desired housing investment increases and will eventually reach and exceed the desired consumption, suggesting that the individual should buy his home—and either additional housing units (for renting out) or house price–linked financial assets. In the final years, preferences shift back to home rental. The derived strategies are still useful if housing positions are only reset infrequently. Our results suggest that markets for real estate investment trusts or other house price–linked contracts lead to nonnegligible welfare gains. This paper was accepted by Wei Xiong, finance.
Performance Analysis of Queueing Networks via Robust Optimization
Authors: Bertsimas Dimitris , Gamarnik David , Rikun Alexander Anatoliy 
Published: April 2011

Performance analysis of queueing networks is one of the most challenging areas of queueing theory. Barring very specialized models such as product-form type queueing networks, there exist very few results that provide provable nonasymptotic upper and lower bounds on key performance measures. In this paper we propose a new performance analysis method, which is based on the robust optimization. The basic premise of our approach is as follows: rather than assuming that the stochastic primitives of a queueing model satisfy certain probability laws—such as i.i.d. interarrival and service times distributions—we assume that the underlying primitives are deterministic and satisfy the implications of such probability laws. These implications take the form of simple linear constraints, namely, those motivated by the law of the iterated logarithm (LIL). Using this approach we are able to obtain performance bounds on some key performance measures. Furthermore, these performance bounds imply similar bounds in the underlying stochastic queueing models. We demonstrate our approach on two types of queueing networks: (a) tandem single-class queueing network and (b) multiclass single-server queueing network. In both cases, using the proposed robust optimization approach, we are able to obtain explicit upper bounds on some steady-state performance measures. For example, for the case of TSC system we obtain a bound of the form C(1 − ρ)−1 ln ln((1 − ρ)−1) on the expected steady-state sojourn time, where C is an explicit constant and ρ is the bottleneck traffic intensity. This qualitatively agrees with the correct heavy traffic scaling of this performance measure up to the ln ln((1 − ρ)−1) correction factor.
Dual-Monoclonal, Sandwich Immunoassay Specific for Glucose-Dependent Insulinotropic Peptide1-42, the Active Form of the Incretin Hormone
Authors: Troutt Jason S , Siegel Robert W , Chen Jinbiao , Sloan John H , Deeg Mark A , Cao Guoqing , Konrad Robert J 
Published: April 2011

BACKGROUND
Glucose-dependent insulinotropic peptide (GIP) is an incretin peptide secreted by intestinal K cells that stimulates insulin secretion in a glucose-dependent manner. It is secreted as an active, intact 42–amino acid peptide GIP1-42, which is rapidly degraded by dipeptidyl peptidase 4 to GIP3-42, which is inactive. There is currently no described monoclonal antibody–based sandwich immunoassay to quantify concentrations of GIP1-42, the active form of the peptide.

METHODS
To create a sandwich ELISA for GIP1-42, we generated a monoclonal antibody specific for the intact N-terminus of the peptide, which was further optimized to increase its affinity. We used this antibody as a conjugate antibody in a sandwich ELISA and paired it with an anti–total GIP capture monoclonal antibody to create a dual monoclonal sandwich ELISA for GIP1-42.

RESULTS
The sandwich ELISA was highly specific for GIP1-42 and did not recognize GIP3-42. The ELISA demonstrated a broad dynamic range and a lower limit of quantification of 5 ng/L. Using the ELISA, we were able to show that GIP1-42 concentrations in healthy volunteers increased dramatically in the postprandial state compared to the fasting state. GIP1-42 values were correlated with total GIP values overall; however, there was substantial interindividual variation.

CONCLUSIONS
The use of an N-terminal–specific monoclonal antibody in a sandwich ELISA format provides a robust and convenient method for measuring concentrations of GIP1-42, the active form of the incretin hormone. This ELISA should help to improve our understanding of the role of GIP1-42 in regulating glucose-dependent insulin secretion.
Modeling Vertical Subcooled Boiling Flows at Low Pressures
Authors: Yeoh G. H. , Cheung S. C. P. , Tu J. Y. , Ho M. K. M 
Published: April 2011

Abstract
An improved wall heat flux partitioning model at the heated surface was developed by Yeoh et al. This model, coupled with a three-dimensional two-fluid model and Multiple Size Group model, has led to satisfactory agreement being achieved between the model predictions and experimental measurements. Nevertheless, one shortcoming is the reliance on empirical correlations for the active nucleation site density in the wall heat flux partitioning model. This discrepancy brings about uncertainties, especially in appropriately evaluating the vapor generation rate, which greatly influences the model prediction on the axial and radial void fraction profiles within the bulk fluid flow. By considering the fractal model with the aforementioned subcooled boiling flow model in the absence of empirical correlations for the active nucleation site density, a comprehensive mechanistic model to predict vertically oriented subcooled boiling flows is developed. The proposed model is assessed against the experimental data of axial measurements of Zeitoun and Shoukri and the radial measurements of Yun et al. and Lee et al. for vertical subcooled boiling flows within annular channels. Improved model predictions are obtained when the model is compared against typically applied empirical correlations for active nucleation site density. Discussions on the agreement of other two-phase flow parameters are also presented.
Outcomes Associated with Influenza Vaccination in the First Year after Kidney Transplantation
Authors: Hurst Frank P. , Lee Jessica J. , Jindal Rahul M. , Agodoa Lawrence Y. , Abbott Kevin C. 
Published: April 2011

Summary

Background and objectives
Influenza vaccination is recommended in all renal transplant recipients. However, immunosuppression in the early period post-transplant may attenuate the immunologic response to the vaccine. Additionally, it has been theorized that vaccination can induce an immune response that could trigger rejection episodes.

Design, setting, participants, & measurements
In a retrospective cohort of 51,730 adult Medicare primary patients who were first transplanted from January 2000 to July 2006 and followed through October 2006, we assessed Medicare claims for influenza vaccination and influenza infections, respectively. Outcomes included allograft loss and death.

Results
There were 9678 (18.7%) patients with claims for influenza vaccination in the first year post-transplant. Factors associated with vaccination included older age, diabetes, later year of transplant, and tacrolimus or mycophenolate at discharge. Vaccinations were less frequent among men, African Americans, highly sensitized patients, or those receiving induction immunosuppression or expanded criteria donor kidneys. Vaccination in the first year after transplant was associated with lower risk of subsequent allograft loss and death. Claims for influenza infection were reported in 310 (0.6%) patients and were not significantly associated with graft loss, although there was a trend toward death.

Conclusions
In the first year after renal transplantation, influenza vaccination was associated with a lower risk of subsequent allograft loss and death. Although this study cannot comment on formation of protective antibodies after vaccination, these data do not support withholding vaccination on the basis of concerns of adversely affecting allograft function.
Modeled Urea Distribution Volume and Mortality in the HEMO Study
Authors: Daugirdas John T. , Greene Tom , Depner Thomas A. , Levin Nathan W. , Chertow Glenn M. 
Published: April 2011

Summary

Background and objectives
In the Hemodialysis (HEMO) Study, observed small decreases in achieved equilibrated Kt/Vurea were noncausally associated with markedly increased mortality. Here we examine the association of mortality with modeled volume (Vm), the denominator of equilibrated Kt/Vurea.

Design, setting, participants, & measurements
Parameters derived from modeled urea kinetics (including Vm) and blood pressure (BP) were obtained monthly in 1846 patients. Case mix–adjusted time-dependent Cox regressions were used to relate the relative mortality hazard at each time point to Vm and to the change in Vm over the preceding 6 months. Mixed effects models were used to relate Vm to changes in intradialytic systolic BP and to other factors at each follow-up visit.

Results
Mortality was associated with Vm and change in Vm over the preceding 6 months. The association between change in Vm and mortality was independent of vascular access complications. In contrast, mortality was inversely associated with V calculated from anthropometric measurements (Vant). In case mix–adjusted analysis using Vm as a time-dependent covariate, the association of mortality with Vm strengthened after statistical adjustment for Vant. After adjustment for Vant, higher Vm was associated with slightly smaller reductions in intradialytic systolic BP and with risk factors for mortality including recent hospitalization and reductions in serum albumin concentration and body weight.

Conclusions
An increase in Vm is a marker for illness and mortality risk in hemodialysis patients.
Chronic Kidney Disease in Octogenarians
Authors: Shastri Shani , Tighiouart Hocine , Katz Ronit , Rifkin Dena E. , Fried Linda F. , Shlipak Michael G. , Newman Anne B. , Sarnak Mark J. 
Published: April 2011

Summary

Background and objectives
There are limited data on the prevalence of chronic kidney disease (CKD) and its clinical importance in the very old. We examined the prevalence of CKD in octogenarians and its association with cardiovascular disease (CVD).

Design, setting, participants, & measurements
In a cross-sectional analysis of 1028 participants from the Cardiovascular Health Study All Stars, we evaluated association of prevalent CKD with CVD using multivariable logistic regression. CKD was defined as eGFR of <60 ml/min per 1.73 m2. GFR was estimated using CKD-Epi creatinine and cystatin C equations that incorporate coefficients for age, gender, and race (eGFREPI, eGFRCYS3var) and the one-variable cystatin C equation (eGFRCYS1var). Prevalent CVD was defined as a composite of coronary heart disease, heart failure, and stroke.

Results
Mean age was 86 years, 64% were women, 86% were Caucasians, 14% had diabetes, and 39% had prevalent CVD. Mean eGFREPI, eGFRCYS3var, and eGFRCYS1var were 59, 62, and 70 ml/min per 1.73 m2, and 51%, 46%, and 33% had CKD, respectively. Associations of CKD with CVD varied by equation in adjusted analyses: CKDEPI (OR, 1.53; 95% CI, 1.15 to 2.03), CKDCYS3var (OR, 1.67; 95% CI, 1.25, 2.23), and CKDCYS1var (OR, 2.09; 95% CI, 1.55, 2.83).

Conclusions
Reduced eGFR is highly prevalent in octogenarians, and the eGFRCYS1var equation yielded the lowest prevalence of CKD but the strongest association with prevalent CVD. Because there are no validated estimating equations in the elderly, estimation of kidney function on the basis of on any one equation should be interpreted with caution.