bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germ banks affect the inference of past demographic events
Authors: Živković Daniel , Tellier Aurélien 
Published: October 2012

AbstractContinuous progress in empirical population genetics based on the whole‐genome polymorphism data requires the theoretical analysis of refined models in order to interpret the evolutionary history of populations with adequate accuracy. Recent studies focus prevalently on the aspects of demography and adaptation, whereas age structure (for example, in plants via the maintenance of seed banks) has attracted less attention. Germ banking, that is, seed or egg dormancy, is a prevalent and important life‐history trait in plants and invertebrates, which buffers against environmental variability and modulates species extinction in fragmented habitats. Within this study, we investigate the combined effect of germ banking and time‐varying population size on the neutral coalescent and particularly derive the allele frequency spectrum under some simplifying assumptions. We then perform anABCanalysis using two simple demographic scenarios—a population expansion and an instantaneous decline. We demonstrate the appreciable influence of seed banks on the estimation of demographic parameters depending on the germination rate with biases scaled by the square of the germination rate. In the more complex case of a population bottleneck, which comprises an instantaneous decline and an expansion phase, ignoring information on the germination rate denies reliable estimates of the bottleneck parameters via the allelic spectrum. In particular, when seeds remain in the bank over several generations, recent expansions may remain invisible in the frequency spectrum, whereas ancient declines leave signatures much longer than in the absence of seed bank.
High prevalence of food sensitisation in young children with liver disease: a clue to food allergy pathogenesis?
Authors: Brown Chrysothemis , Haringman Natasha , Davies Charlotte , Gore Claudia , Hussain Munther , Mieli‐Vergani Giorgina , Vergani Diego , Warner John O. , Marks Stephen D. , Boyle Robert J. 
Published: October 2012

AbstractBackgroundThe pathogenesis of food allergy is not completely understood – animal models suggest hepatic mechanisms may be important for immune tolerance to orally ingested antigens, but there is little direct evidence for this in humans.ObjectivesWe investigated whether there is an association between liver dysfunction or transplantation in young children and IgE sensitisation to food.MethodsWe evaluated paired pre‐ and post‐ liver transplant sera from children aged 0–36 months treated at a single centre during 2001–2008. Sera were assayed for total IgE and cow's milk, egg and peanut‐specific IgE. We quantified hepatic dysfunction pre‐transplant using the Paediatric End‐stage Liver Disease (PELD) score. We also assessed 70 children after renal transplant to establish whether any association between liver transplant and food sensitisation was organ specific.ResultsPaired sera were available from 50 of 94 children who had a liver transplant during the study period. 35 of 50 (70%) had IgE sensitisation (≥0.35 kUa/l) to ≥1 food pre‐transplant and 18 (36%) post‐transplant (p = 0.001). Ten (20%) children had food‐specific IgE levels that carry high probability of challenge‐confirmed food allergy pre‐transplant. Food sensitisation pre‐transplant was associated with severity of liver dysfunction [mean (s.d.) pre‐transplant PELD score 1.52 (0.13) in food sensitised, 0.77 (0.22) in non‐sensitised children p = 0.004]. Total IgE level was raised in 34/42 (81%) pre‐transplant and fell significantly post‐transplant. Interview assessment of the parents of 40 children revealed that 13 (33%) had a history consistent with food allergy. These findings were not replicated in the renal transplant group.ConclusionsYoung children with severe liver dysfunction appear to have a high prevalence of food sensitisation. Hepatic mechanisms may therefore be important for establishing immune tolerance to dietary antigens in humans.
Leaf responses to drought stress in Mediterranean accessions of Solanum lycopersicum: anatomical adaptations in relation to gas exchange parameters
Authors: GALMÉS JERONI , OCHOGAVÍA JOAN MANUEL , GAGO JORGE , ROLDÁN EMILIO JOSÉ , CIFRE JOSEP , CONESA MIQUEL ÀNGEL 
Published: October 2012

ABSTRACTIn a previous study, important acclimation to water stress was observed in the Ramellet tomato cultivar (TR) from the Balearic Islands, related to an increase in the water‐use efficiency through modifications in both stomatal (gs) and mesophyll conductances (gm). In the present work, the comparison of physiological and morphological traits between TR accessions grown with and without water stress confirmed that variability in the photosynthetic capacity was mostly explained by differences in the diffusion of CO2 through stomata and leaf mesophyll. Maximization of gm under both treatments was mainly achieved through adjustments in the mesophyll thickness and porosity and the surface area of chloroplasts exposed to intercellular airspace (Sc). In addition, the lower gm/Sc ratio for a given porosity in drought‐acclimated plants suggests that the decrease in gm was due to an increased cell wall thickness. Stomatal conductance was also affected by drought‐associated changes in the morphological properties of stomata, in an accession and treatment‐dependent manner. The results confirm the presence of advantageous physiological traits in the response to drought stress in Mediterranean accessions of tomato, and relate them to particular changes in the leaf anatomical properties, suggesting specific adaptive processes operating at the leaf anatomical level.
Concept of “awake venovenous extracorporeal membrane oxygenation” in pediatric patients awaiting lung transplantation
Authors: Schmidt F. , Sasse M. , Boehne M. , Mueller C. , Bertram H. , Kuehn C. , Warnecke G. , Ono M. , Seidemann K. , Jack T. , Koeditz H. 
Published: October 2012

AbstractIn patients awaiting LuTx, MV and ECMO are often the last ways to create a bridge to LuTx. Both interventions are associated with a poor posttransplant outcome and survival rate. To improve the results of these patients, new “bridging‐strategies” are necessary. Recent reports demonstrate promising results for the concept of “awake ECMO” in adult patients. To date, no data on this approach in pediatric patients have been available. We therefore describe the use of VV‐ECMO as a treatment strategy for RF in awake pediatric patients. It presents our experiences with the first three children treated using this new concept. Mean amount of time on ECMO was 44 days (range, 11.5–109 days). Two patients were successfully bridged to their LuTx. Both are still alive without any recurrences (24 and three months following LuTx). One patient died before a further LuTx after 109 days on ECMO due to adenoviral infection. Although reintubation was necessary in two patients, and total time being awake while on ECMO was <50%, we conclude that the concept of “awake VV‐ECMO” is feasible for the treatment of RF and can be used as a “bridging therapy” to LuTx.
Impact of Demographic Change, Socioeconomics, and Health Care Resources on Life Expectancy in Cambodia, Laos, and Myanmar
Authors: Chan Moon Fai , Taylor Beverly Joan 
Published: October 2012

AbstractObjectivesDemographic and socioeconomic changes and the availability of health care resources were collected to examine the impacts on life expectancy in Cambodia, Laos, and Myanmar.Design and SampleAn ecological design collecting 29 years (1980–2008) data for three Southeast Asian countries.MeasuresLife expectancy, demographics, socioeconomic status, and health care resources were collected.ResultsThe structural equation model indicates that more available health care resources and socioeconomic advantages were more likely to increase life expectancy. By contrast, demographic change was more likely to increase life expectancy by way of health care resources.ConclusionsResults show that factors that had direct impacts on life expectancy in all three countries were socioeconomic status and health care resources. Demographic changes had an indirect influence on life expectancy via health care resources. These findings suggest that policymakers should be focusing on how to remove the barriers that impede access to health care services during economic downturns. In addition, how to increase preventive care for the populations that have less access to health care in communities.
The linkage principle for restricted critical level representations of affine Kac–Moody algebras
Authors: Arakawa Tomoyuki , Fiebig Peter 
Published: October 2012

AbstractWe study the restricted category 𝒪 for an affine Kac–Moody algebra at the critical level. In particular, we prove the first part of the Feigin–Frenkel conjecture: the linkage principle for restricted Verma modules. Moreover, we prove a version of the Bernstein–Gelfand–Gelfand-reciprocity principle and we determine the block decomposition of the restricted category 𝒪. For the proofs, we need a deformed version of the classical structures, so we mostly work in a relative setting.
New Immunoenzymatic Strategy for Rapid and Selective Growth of Salmonella
Authors: Ponsard Isabelle , Soumillion Patrice 
Published: October 2012

ABSTRACT

We demonstrated that an exogenous conjugate consisting of a β-lactamase and a monoclonal antibody against a surface antigen of
Salmonella
is capable of conferring selective penicillin resistance on bacteria. This immunoenzymatic approach allows the rapid growth and detection of specific bacteria and may find other applications when temporary and nongenetic antibiotic resistance is required.
Pneumococci Can Persistently Colonize Adult Patients with Chronic Respiratory Disease
Authors: Domenech A. , Ardanuy C. , Balsalobre L. , Marti S. , Calatayud L. , De la Campa A. G. , Brueggemann A. B. , Liñares J. 
Published: October 2012

ABSTRACT

Streptococcus pneumoniae
plays an important role in causing acute exacerbations in patients with chronic respiratory disease. However, few data are available regarding pneumococcal persistence in adult patients with chronic respiratory diseases. Fifty pneumococci recovered from sputum samples (1995 to 2010) from 13 adult patients with ≥3 episodes of acute exacerbation or pneumonia, with the same serotype and pulsed-field gel electrophoresis (PFGE) pattern, were studied. Multilocus sequence typing (MLST) loci, penicillin-binding protein (PBP) genes (
pbp
2
x
,
pbp1a
,
pbp2b
), and the quinolone-resistant determining regions (QRDRs) of
parC
,
parE
, and
gyrA
were PCR amplified and sequenced. The average time between the first and last episode was 582 days (standard deviation [SD], ±362). All but two patients received multiple courses of β-lactam treatment, and all persistent strains were resistant to penicillin; however, the PBP sequences were stable over time apart from one variable nucleotide in
pbp
2
x
, observed among pneumococci isolated from three patients. In contrast, 7/11 patients treated with fluoroquinolones had fluoroquinolone-resistant pneumococci. In three patients, the initially fluoroquinolone-susceptible strain developed resistance after fluoroquinolone therapy, and in the remaining four patients, the persistent strain was fluoroquinolone resistant from the first episode. QRDR changes involved in fluoroquinolone resistance were frequently observed in persistent strains after fluoroquinolone treatment; however, the PBP sequences and MLST genotypes of these strains were stable over time.
Allele-Specific PCR for Determination of IL28B Genotype
Authors: Cook Linda , Diem Kurt , Kim Woo , Scott John D. , Jerome Keith R. 
Published: October 2012

ABSTRACT
The IL28B genotype is a critical determinant of interferon response in patients infected with hepatitis C virus genotype 1. We describe an allele-specific PCR assay for the IL28B genotype. The assay is simple and robust, uses commonly available real-time PCR instrumentation, and is well suited for clinical laboratories offering IL28B genotyping.
Bacterial Coinfections in Travelers with Malaria: Rationale for Antibiotic Therapy
Authors: Sandlund Johanna , Naucler Pontus , Dashti Saduddin , Shokri Akhar , Eriksson Sara , Hjertqvist Marika , Karlsson Lillemor , Capraru Teodor , Färnert Anna 
Published: October 2012

ABSTRACT

Malaria predisposes children in areas where malaria is endemic to concurrent bacteremia, often with severe outcomes. The importance of bacterial coinfections in patients diagnosed with malaria in nonendemic settings has, however, not been reported. A retrospective analysis of microbiology data was performed in 755 travelers diagnosed with malaria in Sweden. Bacterial cultures from blood and other locations were correlated to clinical outcome and antibiotic treatment. Blood cultures were drawn from 417 (55%) patients (88% of whom were >15 years old), and bacterial isolates of clinical relevance (
Salmonella enterica
serovar Enteritidis and
Escherichia coli
) were detected in 2 patients (0.3%). Cultures from other locations (mainly urine, nasopharyngeal, and fecal samples) were obtained from 44% of the patients with 4.9% positivity. Of the 38 patients given antibiotics, 47% had neither severe malaria nor positive cultures and/or radiology signs indicative of treatment. C-reactive protein levels were associated with bacterial infections but had only a fair predictive value. Bacterial coinfections are uncommon among travelers with malaria. These data suggest a weaker association between malaria and bacteremia than previously described in endemic settings and might indicate different patient populations with different pathophysiological mechanisms and microbial environments. The study supports a restrictive antibiotic policy in returning travelers with malaria.
Genotypic Characterization of Streptococcus infantarius subsp.
coli
Isolates from Sea Otters with Infective Endocarditis and/or Septicemia and from Environmental Mussel Samples
Authors: Counihan-Edgar Katrina L. , Gill Verena A. , Doroff Angela M. , Burek Kathleen A. , Miller Woutrina A. , Shewmaker Patricia L. , Jang Spencer , Goertz Caroline E. C. , Tuomi Pamela A. , Miller Melissa A. , Jessup David A. , Byrne Barbara A. 
Published: October 2012

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) was used to type 128
Streptococcus infantarius
subsp.
coli
isolates from sea otters and mussels. Six SmaI PFGE groups were detected, with one predominant group representing 57% of the isolates collected over a wide geographic region. Several sea otter and mussel isolates were highly related, suggesting that an environmental infection source is possible.
Short-Term Stability of Pathogen-Specific Nucleic Acid Targets in Clinical Samples
Authors: Hasan Mohammad R. , Tan Rusung , Al-Rawahi Ghada N. , Thomas Eva , Tilley Peter 
Published: October 2012

ABSTRACT

The stability of pathogen-specific DNA or RNA amplification targets in clinical samples following short-term storage at room temperature, 4°C, and −80°C was assessed by real-time PCR. In purified nucleic acid extracts, both DNA and RNA targets were stable for up to 30 days, irrespective of storage temperature. In unextracted samples, temperature-dependent loss of targets (
P
< 0.05) was observed in serum and cerebrospinal fluid specimens, while no changes were observed for EDTA blood samples.
Cellular Protein HAX1 Interacts with the Influenza A Virus PA Polymerase Subunit and Impedes Its Nuclear Translocation
Authors: Hsu Wei-Bin , Shih Jia-Ling , Shih Jie-Ru , Du Jia-Ling , Teng Shu-Chun , Huang Li-Min , Wang Won-Bo 
Published: October 2012

ABSTRACTTranscription and replication of the influenza A virus RNA genome occur in the nucleus through the viral RNA-dependent RNA polymerase consisting of PB1, PB2, and PA. Cellular factors that associate with the viral polymerase complex play important roles in these processes. To look for cellular factors that could associate with influenza A virus PA protein, we have carried out a yeast two-hybrid screen using a HeLa cell cDNA library. We identified six cellular proteins that may interact with PA. We focused our study on one of the new PA-interacting proteins, HAX1, a protein with antiapoptotic function. By using glutathioneS-transferase pulldown and coimmunoprecipitation assays, we demonstrate that HAX1 specifically interacts with PAin vitroandin vivoand that HAX1 interacts with the nuclear localization signal domain of PA. Nuclear accumulation of PA was increased in HAX1-knockdown cells, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can impede nuclear transport of PA. As a consequence, knockdown of HAX1 resulted in a significant increase in virus yield and polymerase activity in a minigenome assay, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can inhibit influenza A virus propagation. Together, these results not only provide insight into the mechanism underlying nuclear transport of PA but also identify an intrinsic host factor that restricts influenza A virus infection.
Inhibition of Alpha Interferon (IFN-α)-Induced MicroRNA-122 Negatively Affects the Anti-Hepatitis B Virus Efficiency of IFN-α
Authors: Hao Junli , Jin Wensong , Li Xinghui , Wang Saifeng , Zhang Xiaojun , Fan Hongxia , Li Changfei , Chen Lizhao , Gao Bin , Liu Guangze , Meng Songdong 
Published: October 2012

ABSTRACT
Alpha interferon (IFN-α)-based therapy can effectively treat chronic hepatitis B virus (HBV) infection, which causes life-threatening complications. Responses to IFN-α therapy vary greatly in chronic hepatitis B (CHB) patients, but underlying mechanisms are almost unknown. In this study, we found that IFN-α treatment induced a marked decrease of microRNA-122 (miR-122) expression in hepatocytes. We next showed that IFN-α-induced miR-122 downregulation was only partly due to transcriptional suppression. One IFN-stimulated gene (ISG), NT5C3, which was identified as a miR-122 target, efficiently inhibited miR-122 by binding and sequestering miR-122 with its mRNA 3′-untranslated region (3′-UTR), indicating that this ISG is involved in IFN-α-mediated miR-122 suppression. Notably, the inhibitory effect of IFN-α on miR-122 was completely abolished by blocking IFN-α-induced upregulation of NT5C3 mRNA expression by RNA interference (RNAi). Meanwhile, we observed that miR-122 dramatically inhibited HBV expression and replication. Finally, we showed that IFN-α-mediated HBV-inhibitory effects could be enhanced significantly by blocking IFN-α-induced downregulation of miR-122. We therefore concluded that IFN-α-induced inhibition of miR-122 may negatively affect the anti-HBV function of IFN-α. These data provide valuable insights for a better understanding of the antiviral mechanism of IFN-α and raise further potential interest in enhancing its anti-HBV efficacy.
Distinct Evolutionary Pressures Underlie Diversity in Simian Immunodeficiency Virus and Human Immunodeficiency Virus Lineages
Authors: Fischer Will , Apetrei Cristian , Santiago Mario L. , Li Yingying , Gautam Rajeev , Pandrea Ivona , Shaw George M. , Hahn Beatrice H. , Letvin Norman L. , Nabel Gary J. , Korber Bette T. 
Published: October 2012

ABSTRACT
Simian immunodeficiency virus (SIV) infection of rhesus macaques causes immune depletion and disease closely resembling human AIDS and is well recognized as the most relevant animal model for the human disease. Experimental investigations of viral pathogenesis and vaccine protection primarily involve a limited set of related viruses originating in sooty mangabeys (SIVsmm). The diversity of human immunodeficiency virus type 1 (HIV-1) has evolved in humans in about a century; in contrast, SIV isolates used in the macaque model evolved in sooty mangabeys over millennia. To investigate the possible consequences of such different evolutionary histories for selection pressures and observed diversity in SIVsmm and HIV-1, we isolated, sequenced, and analyzed 20 independent isolates of SIVsmm, including representatives of 7 distinct clades of viruses isolated from natural infection. We found SIVsmm diversity to be lower overall than HIV-1 M group diversity. Reduced positive selection (i.e., less diversifying evolution) was evident in extended regions of SIVsmm proteins, most notably in Gag p27 and Env gp120. In addition, the relative diversities of proteins in the two lineages were distinct: SIVsmm Env and Gag were much less diverse than their HIV-1 counterparts. This may be explained by lower SIV-directed immune activity in mangabeys relative to HIV-1-directed immunity in humans. These findings add an additional layer of complexity to the interpretation and, potentially, to the predictive utility of the SIV/macaque model, and they highlight the unique features of human and simian lentiviral evolution that inform studies of pathogenesis and strategies for AIDS vaccine design.
Diversity and Distribution of Hantaviruses in South America
Authors: Firth Cadhla , Tokarz Rafal , Simith Darlene B. , Nunes Marcio R. T. , Bhat Meera , Rosa Elizabeth S. T. , Medeiros Daniele B. A. , Palacios Gustavo , Vasconcelos Pedro F. C. , Lipkin W. Ian 
Published: October 2012

ABSTRACTHantaviruses are important contributors to disease burden in the New World, yet many aspects of their distribution and dynamics remain uncharacterized. To examine the patterns and processes that influence the diversity and geographic distribution of hantaviruses in South America, we performed genetic and phylogeographic analyses of all available South American hantavirus sequences. We sequenced multiple novel and previously described viruses (Anajatuba, Laguna Negra-like, two genotypes of Castelo dos Sonhos, and two genotypes of Rio Mamore) from BrazilianOligoryzomysrodents and hantavirus pulmonary syndrome cases and identified a previously uncharacterized species ofOligoryzomysassociated with a new genotype of Rio Mamore virus. Our analysis indicates that the majority of South American hantaviruses fall into three phylogenetic clades, corresponding to Andes and Andes-like viruses, Laguna Negra and Laguna Negra-like viruses, and Rio Mamore and Rio Mamore-like viruses. In addition, the dynamics and distribution of these viruses appear to be shaped by both the geographic proximity and phylogenetic relatedness of their rodent hosts. The current system of nomenclature used in the hantavirus community is a significant impediment to understanding the ecology and evolutionary history of hantaviruses; here, we suggest strict adherence to a modified taxonomic system, with species and strain designations resembling the numerical system of the enterovirus genus.