bluuebunny/crossref_metadata_2025_split huggingface dataset:
Notwithstanding Circumstantial Alibis, Cytotoxic T Cells Can Be Major Killers of HIV-1-Infected Cells
Authors: Gadhamsetty Saikrishna , Coorens Tim , de Boer Rob J. 
Published: May 2016

ABSTRACTSeveral experiments suggest that in the chronic phase of human immunodeficiency virus type 1 (HIV-1) infection, CD8+cytotoxic T lymphocytes (CTL) contribute very little to the death of productively infected cells. First, the expected life span of productively infected cells is fairly long, i.e., about 1 day. Second, this life span is hardly affected by the depletion of CD8+T cells. Third, the rate at which mutants escaping a CTL response take over the viral population tends to be slow. Our main result is that all these observations are perfectly compatible with killing rates that are much faster than one per day once we invoke the fact that infected cells proceed through an eclipse phase of about 1 day before they start producing virus. Assuming that the major protective effect of CTL is cytolytic, we demonstrate that mathematical models with an eclipse phase account for the data when the killing is fast and when it varies over the life cycle of infected cells. Considering the steady state corresponding to the chronic phase of the infection, we find that the rate of immune escape and the rate at which the viral load increases following CD8+T cell depletion should reflect the viral replication rate, ρ. A meta-analysis of previous data shows that viral replication rates during chronic infection vary between 0.5 ≤ ρ ≤ 1 day−1. Balancing such fast viral replication requires killing rates that are several times larger than ρ, implying that most productively infected cells would die by cytolytic effects.IMPORTANCEMost current data suggest that cytotoxic T cells (CTL) mediate their control of human immunodeficiency virus type 1 (HIV-1) infection by nonlytic mechanisms; i.e., the data suggest that CTL hardly kill. This interpretation of these data has been based upon the general mathematical model for HIV infection. Because this model ignores the eclipse phase between the infection of a target cell and the start of viral production by that cell, we reanalyze the same data sets with novel models that do account for the eclipse phase. We find that the data are perfectly consistent with lytic control by CTL and predict that most productively infected cells are killed by CTL. Because the killing rate should balance the viral replication rate, we estimate both parameters from a large set of published experiments in which CD8+T cells were depleted in simian immunodeficiency virus (SIV)-infected monkeys. This confirms that the killing rate can be much faster than is currently appreciated.
Deep Sequencing of the HIV-1
env
Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions
Authors: Zhou Shuntai , Bednar Maria M. , Sturdevant Christa B. , Hauser Blake M. , Swanstrom Ronald 
Published: May 2016

ABSTRACT

HIV-1 requires the CD4 receptor and a coreceptor (CCR5 [R5 phenotype] or CXCR4 [X4 phenotype]) to enter cells. Coreceptor tropism can be assessed by either phenotypic or genotypic analysis, the latter using bioinformatics algorithms to predict tropism based on the
env
V3 sequence. We used the Primer ID sequencing strategy with the MiSeq sequencing platform to reveal the structure of viral populations in the V1/V2 and C2/V3 regions of the HIV-1
env
gene in 30 late-stage and 6 early-stage subjects. We also used endpoint dilution PCR followed by cloning of
env
genes to create pseudotyped virus to explore the link between genotypic predictions and phenotypic assessment of coreceptor usage. We found out that the most stringently sequence-based calls of X4 variants (Geno2Pheno false-positive rate [FPR] of ≤2%) formed distinct lineages within the viral population, and these were detected in 24 of 30 late-stage samples (80%), which was significantly higher than what has been seen previously by using other approaches. Non-X4 lineages were not skewed toward lower FPR scores in X4-containing populations. Phenotypic assays showed that variants with an intermediate FPR (2 to 20%) could be either X4/dual-tropic or R5 variants, although the X4 variants made up only about 25% of the lineages with an FPR of <10%, and these variants carried a distinctive sequence change. Phylogenetic analysis of both the V1/V2 and C2/V3 regions showed evidence of recombination within but very little recombination between the X4 and R5 lineages, suggesting that these populations are genetically isolated.

IMPORTANCE
Primer ID sequencing provides a novel approach to study genetic structures of viral populations. X4 variants may be more prevalent than previously reported when assessed by using next-generation sequencing (NGS) and with a greater depth of sampling than single-genome amplification (SGA). Phylogenetic analysis to identify lineages of sequences with intermediate FPR values may provide additional information for accurately predicting X4 variants by using V3 sequences. Limited recombination occurs between X4 and R5 lineages, suggesting that X4 and R5 variants are genetically isolated and may be replicating in different cell types or that X4/R5 recombinants have reduced fitness.
Glutathione Depletion Is Linked with Th2 Polarization in Mice with a Retrovirus-Induced Immunodeficiency Syndrome, Murine AIDS: Role of Proglutathione Molecules as Immunotherapeutics
Authors: Brundu Serena , Palma Linda , Picceri Giusi Giada , Ligi Daniela , Orlandi Chiara , Galluzzi Luca , Chiarantini Laura , Casabianca Anna , Schiavano Giuditta Fiorella , Santi Martina , Mannello Ferdinando , Green Kathy , Smietana Michaël , Magnani Mauro , Fraternale Alessandra 
Published: May 2016

ABSTRACTInjection of the LP-BM5 murine leukemia virus into mice causes murine AIDS, a disease characterized by many dysfunctions of immunocompetent cells. To establish whether the disease is characterized by glutathione imbalance, reduced glutathione (GSH) and cysteine were quantified in different organs. A marked redox imbalance, consisting of GSH and/or cysteine depletion, was found in the lymphoid organs, such as the spleen and lymph nodes. Moreover, a significant decrease in cysteine and GSH levels in the pancreas and brain, respectively, was measured at 5 weeks postinfection. The Th2 immune response was predominant at all times investigated, as revealed by the expression of Th1/Th2 cytokines. Furthermore, investigation of the activation status of peritoneal macrophages showed that the expression of genetic markers of alternative activation, namely, Fizz1, Ym1, and Arginase1, was induced. Conversely, expression of inducible nitric oxide synthase, a marker of classical activation of macrophages, was detected only when Th1 cytokines were expressed at high levels.In vitrostudies revealed that during the very early phases of infection, GSH depletion and the downregulation of interleukin-12 (IL-12) p40 mRNA were correlated with the dose of LP-BM5 used to infect the macrophages. Treatment of LP-BM5-infected mice withN-(N-acetyl-l-cysteinyl)-S-acetylcysteamine (I-152), anN-acetyl-cysteine supplier, restored GSH/cysteine levels in the organs, reduced the expression of alternatively activated macrophage markers, and increased the level of gamma interferon production, while it decreased the levels of Th2 cytokines, such as IL-4 and IL-5. Our findings thus establish a link between GSH deficiency and Th1/Th2 disequilibrium in LP-BM5 infection and indicate that I-152 can be used to restore the GSH level and a balanced Th1/Th2 response in infected mice.IMPORTANCEThe first report of an association between Th2 polarization and alteration of the redox state in LP-BM5 infection is presented. Moreover, it provides evidence that LP-BM5 infection causes a decrease in the thiol content of peritoneal macrophages, which can influence IL-12 production. The restoration of GSH levels by GSH-replenishing molecules can represent a new therapeutic avenue to fight this retroviral infection, as it reestablishes the Th1/Th2 balance. Immunotherapy based on the use of pro-GSH molecules would permit LP-BM5 infection and probably all those viral infections characterized by GSH deficiency and a Th1/Th2 imbalance to be more effectively combated.
MAVS Expressed by Hematopoietic Cells Is Critical for Control of West Nile Virus Infection and Pathogenesis
Authors: Zhao Jincun , Vijay Rahul , Zhao Jingxian , Gale Michael , Diamond Michael S. , Perlman Stanley 
Published: May 2016

ABSTRACT

West Nile virus (WNV) is the most important cause of epidemic encephalitis in North America. Innate immune responses, which are critical for control of WNV infection, are initiated by signaling through pathogen recognition receptors, RIG-I and MDA5, and their downstream adaptor molecule, MAVS. Here, we show that a deficiency of MAVS in hematopoietic cells resulted in increased mortality and delayed WNV clearance from the brain. In
Mavs
−/−
mice, a dysregulated immune response was detected, characterized by a massive influx of macrophages and virus-specific T cells into the infected brain. These T cells were polyfunctional and lysed peptide-pulsed target cells
in vitro
. However, virus-specific T cells in the brains of infected
Mavs
−/−
mice exhibited lower functional avidity than those in wild-type animals, and even virus-specific memory T cells generated by prior immunization could not protect
Mavs
−/−
mice from WNV-induced lethal disease. Concomitant with ineffective virus clearance, macrophage numbers were increased in the
Mavs
−/−
brain, and both macrophages and microglia exhibited an activated phenotype. Microarray analyses of leukocytes in the infected
Mavs
−/−
brain showed a preferential expression of genes associated with activation and inflammation. Together, these results demonstrate a critical role for MAVS in hematopoietic cells in augmenting the kinetics of WNV clearance and thereby preventing a dysregulated and pathogenic immune response.

IMPORTANCE
West Nile virus (WNV) is the most important cause of mosquito-transmitted encephalitis in the United States. The innate immune response is known to be critical for protection in infected mice. Here, we show that expression of MAVS, a key adaptor molecule in the RIG-I-like receptor RNA-sensing pathway, in hematopoietic cells is critical for protection from lethal WNV infection. In the absence of MAVS, there is a massive infiltration of myeloid cells and virus-specific T cells into the brain and overexuberant production of proinflammatory cytokines. These results demonstrate the important role that MAVS expression in hematopoietic cells has in regulating the inflammatory response in the WNV-infected brain.
Critical Role of the PA-X C-Terminal Domain of Influenza A Virus in Its Subcellular Localization and Shutoff Activity
Authors: Hayashi Tsuyoshi , Chaimayo Chutikarn , McGuinness James , Takimoto Toru 
Published: May 2016

ABSTRACT

PA-X is a recently identified influenza virus protein that is composed of the PA N-terminal 191 amino acids and unique C-terminal 41 or 61 residues. We and others showed that PA-X has a strong ability to suppress host protein synthesis via host mRNA decay, which is mediated by endonuclease activity in its N-terminal domain (B. W. Jagger, H. M. Wise, J. C. Kash, K. A. Walters, N. M. Wills, Y. L. Xiao, R. L. Dunfee, L. M. Schwartzman, A. Ozinsky, G. L. Bell, R. M. Dalton, A. Lo, S. Efstathiou, J. F. Atkins, A. E. Firth, J. K. Taubenberger, and P. Digard, 2012, Science
337:
199–204,
http://dx.doi.org/10.1126/science.1222213
, and E. A. Desmet, K. A. Bussey, R. Stone, and T. Takimoto, 2013, J Virol
87:
3108–3118,
http://dx.doi.org/10.1128/JVI.02826-12
). However, the mechanism of host mRNA degradation, especially where and how PA-X targets mRNAs, has not been analyzed. In this study, we determined the localization of PA-X and the role of the C-terminal unique region in shutoff activity. Quantitative subcellular localization analysis revealed that PA-X was located equally in both cytoplasm and nucleus. By characterizing a series of PA-X C-terminal deletion mutants, we found that the first 9 amino acids were sufficient for nuclear localization, but an additional 6 residues were required to induce the maximum shutoff activity observed with intact PA-X. Importantly, forced nuclear localization of the PA-X C-terminal deletion mutant enhanced shutoff activity, highlighting the ability of nuclear PA-X to degrade host mRNAs more efficiently. However, PA-X also inhibited luciferase expression from transfected mRNAs synthesized
in vitro
, suggesting that PA-X also degrades mRNAs in the cytoplasm. Among the basic amino acids in the PA-X C-terminal region, 3 residues, 195K, 198K, and 199R, were identified as key residues for inducing host shutoff and nuclear localization. Overall, our data indicate a critical role for the 15 residues in the PA-X C-terminal domain in degrading mRNAs in both the cytoplasm and nucleus.

IMPORTANCE
Influenza A viruses express PA-X proteins to suppress global host gene expression, including host antiviral genes, to allow efficient viral replication in infected cells. However, little is known about how PA-X induces host shutoff. In this study, we showed that PA-X localized equally in both the cytoplasm and nucleus of the cells, but the nuclear localization of PA-X mediated by its C-terminal region has a significant impact on shutoff activity. Three basic residues at the C-terminal region play a critical role in nuclear localization, but additional basic residues were required for maximum shutoff activity. Our findings indicate that PA-X targets and degrades mRNAs in both the nucleus and cytoplasm, and that the first 15 residues of the PA-X unique C-terminal region play a critical role in shutoff activity.
Informed consent for paediatric clinical trials in Europe
Authors: Lepola Pirkko , Needham Allison , Mendum Jo , Sallabank Peter , Neubauer David , de Wildt Saskia 
Published: May 2016

ObjectivePaediatric clinical trials are often conducted as multinational trials. Informed consent or assent is part of the ethics committee approval for clinical trials. The consent requirements vary between countries due to national laws and regulations, which are not harmonised in Europe. These discrepancies can present challenges for paediatric clinical trials. The aim of this study was to assemble these consent and assent requirements across the European Economic Area. The collated national requirements have not been publicly available before, despite a real need for this data.MethodsNational consent and assent requirements for paediatric clinical trials were analysed and collated for 25 European Union Member States and 2 European Free Trade Association countries until the end of 2014. The data were retrieved from existing databases and through communication with the competent authorities and selected ethics committees. Results from a literature search for international or national guidelines, declarations and conventions and academic societies' publications served as comparison material.ResultsConsent and assent requirements are heterogeneous across these countries. We compiled our findings in ‘The Informed Consent and Assent Tool Kit’, a table including 27 national consent and assent requirements listed by individual country.ConclusionsWide variation in paediatric consents and assents presents challenges for multinational paediatric trials in Europe. The toolkit is available for all those involved in paediatric clinical trials and ethics committees, providing a new platform for proactive feedback on informed consent requirements, and may finally lead to a needed harmonisation process, including uniform standards accepted across Europe.
Development of a brief assessment and algorithm for ascertaining dementia in low-income and middle-income countries: the 10/66 short dementia diagnostic schedule
Authors: Stewart Robert , Guerchet Maëlenn , Prince Martin 
Published: May 2016

ObjectivesTo develop and evaluate a short version of the 10/66 dementia diagnostic schedule for use in low-income and middle-income countries.DesignSplit-half analysis for algorithm development and testing; cross-evaluation of short-schedule and standard-schedule algorithms in 12 community surveys.Settings(1) The 10/66 pilot sample data set of people aged 60 years and over in 25 international centres each recruiting the following samples: (a) dementia; (b) depression, no dementia; (c) no dementia, high education and (d) no dementia, low education. (2) Cross-sectional surveys of people aged 65 years or more from 12 urban and rural sites in 8 countries (Cuba, Dominican Republic, Peru, Mexico, Venezuela, India, China and Puerto Rico).ParticipantsIn the 10/66 pilot samples, the algorithm for the short schedule was developed in 1218 participants and tested in 1211 randomly selected participants; it was evaluated against the algorithm for the standard 10/66 schedule in 16 536 survey participants.Outcome measuresThe short diagnostic schedule was derived from the Community Screening Instrument for Dementia, the CERAD 10-word list recall task and the Euro-D depression screen; it was evaluated against clinically assigned groups in the pilot data and against the standard schedule (using the Geriatric Mental State (GMS) rather than Euro-D) in the surveys.ResultsIn the pilot test sample, the short-schedule algorithm ascertained dementia with 94.2% sensitivity. Specificities were 80.2% in depression, 96.6% in the high-education group and 92.7% in the low-education group. In survey samples, it coincided with standard algorithm dementia classifications with over 95% accuracy in most sites. Estimated dementia prevalences in the survey samples were not consistently higher or lower using the short compared to standard schedule.ConclusionsFor epidemiological studies of dementia in low-income and middle-income settings where the GMS interview (and/or interviewer training required) is not feasible, the short 10/66 schedule and algorithm provide an alternative with acceptable levels of performance.
Examining the pathways for young people with drug and alcohol dependence: a mixed-method design to examine the role of a treatment programme
Authors: Nathan Sally , Rawstorne Patrick , Hayen Andrew , Bryant Joanne , Baldry Eileen , Ferry Mark , Williams Megan , Shanahan Marian , Jayasinha Ranmalie 
Published: May 2016

IntroductionYoung people with drug and alcohol problems are likely to have poorer health and other psychosocial outcomes than other young people. Residential treatment programmes have been shown to lead to improved health and related outcomes for young people in the short term. There is very little robust research showing longer term outcomes or benefits of such programmes. This paper describes an innovative protocol to examine the longer term outcomes and experiences of young people referred to a residential life management and treatment programme in Australia designed to address alcohol and drug issues in a holistic manner.Methods and analysisThis is a mixed-methods study that will retrospectively and prospectively examine young people's pathways into and out of a residential life management programme. The study involves 3 components: (1) retrospective data linkage of programme data to health and criminal justice administrative data sets, (2) prospective cohort (using existing programme baseline data and a follow-up survey) and (3) qualitative in-depth interviews with a subsample of the prospective cohort. The study will compare findings among young people who are referred and (a) stay 30 days or more in the programme (including those who go on to continuing care and those who do not); (b) start, but stay fewer than 30 days in the programme; (c) are assessed, but do not start the programme.Ethics and disseminationEthics approval has been sought from several ethics committees including a university ethics committee, state health departments and an Aboriginal-specific ethics committee. The results of the study will be published in peer-reviewed journals, presented at research conferences, disseminated via a report for the general public and through Facebook communications. The study will inform the field more broadly about the value of different methods in evaluating programmes and examining the pathways and trajectories of vulnerable young people.
Health and social predictors of applications to public housing: a population-based analysis
Authors: Hinds Aynslie M , Bechtel Brian , Distasio Jino , Roos Leslie L , Lix Lisa M 
Published: May 2016

BackgroundResidents of public housing are often in poor health. However, it is unclear whether poor health precedes residency in public housing. We compared the health of people who applied to public housing to people who did not apply and had similar socioeconomic characteristics.MethodsPopulation-based administrative databases from Manitoba, Canada, containing health, housing and income assistance information were used to identify a cohort of individuals who applied to public housing and a matched cohort from the general population. Conditional logistic regression was used to test the association between a public housing application and health status and health service use, after controlling for income.ResultsThere were 10 324 individuals in each of the public housing applicant and matched cohorts; the majority were women, young, urban residents, and received income assistance. A higher per cent of the public housing cohort had physician-diagnosed physical and mental health conditions compared to the matched cohort. Physical health, mental health and health service use were significantly associated with applying to public housing, after controlling for individual and area-level income.ConclusionsApplicants to public housing were in poorer health compared to people of the same income level who did not apply to public housing. These health issues may affect the long-term stability of their tenancy if appropriate services and supports are not provided. Additionally, preventing ill health, better management of mental health and additional supports may reduce the need for public housing, which, in turn, would alleviate the pressure on governments to provide this form of housing.
Germination of leafy spurge (Euphorbia esula L.) seeds under alternating temperatures: the effects of amplitude, midpoint, and imbibition in gibberellic acid
Authors: Foley Michael E. 
Published: May 2016

Germinability of dormant seeds or the capacity to germinate under particular conditions is sometimes enhanced by a diurnal alternating temperature regime relative to a constant temperature. Alternating temperature regimes vary in amplitude (difference between the minimum and maximum) and midpoint (average). The aim of this research was to test the effects of amplitude and midpoint regimes on germination of dormant leafy spurge seed from a Fargo, ND population in water and gibberellic acid (GA3). The optimal regimes for germination in both water and GA3 were 20:30 °C (16 h:8 h) and 20:35 °C (19 h:5 h), which provided amplitudes of 10 °C and 15 °C, respectively, with both conditions having a midpoint temperature of 23.3 °C. However, midpoint temperature of 22 °C to 27 °C were equally effective for germination under the 20:30 °C and 20:35 °C alternating temperature regimes. Additional alternating temperature regimes with amplitudes of 15 °C (15:30 °C and 10:25 °C), 20 °C (10:30 °C), and 25 °C (10:35 °C) generally displayed reduced germination in both water and GA3, which is likely attributable to the low initial alternating temperature (≤15 °C) component of the regime relative to the higher initial temperature of 20 °C for the optimum regimes of 20:30 °C and 20:35 °C. Under the alternating temperature regimes tested, seeds germinated in GA3 generally displayed higher germination (≥80%) compared with seeds in water (30%–50%).