bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved protocol for measurement of plasma β‐amyloid in longitudinal evaluation of Alzheimer's Disease Neuroimaging Initiative study patients
Authors: Figurski Michal J. , Waligórska Teresa , Toledo Jon , Vanderstichele Hugo , Korecka Magdalena , Lee Virginia M.Y. , Trojanowski John Q. , Shaw Leslie M. 
Published: June 2012

AbstractBackgroundThe interassay variability and inconsistency of plasma β‐amyloid (Aβ) measurements among centers are major factors precluding the interpretation of results and a substantial obstacle in the meta‐analysis across studies of this biomarker. The goal of this investigation was to address these problems by improving the performance of the bioanalytical method.MethodsWe used the Luminex immunoassay platform with a multiplex microsphere‐based reagent kit from Innogenetics. A robotic pipetting system was used to perform crucial steps of the procedure. The performance of this method was evaluated using two kit control samples and two quality control plasma samples from volunteer donors, and by retesting previously assayed patient samples in each run. This setup was applied to process 2454 patient plasma samples from the Alzheimer's Disease Neuroimaging Initiative study biofluid repository. We have additionally evaluated the correlations between our results and cerebrospinal fluid (CSF) biomarker data using mixed‐effects modeling.ResultsThe average precision values of the kit controls were 8.3% for Aβ1‐40 and 4.0% for Aβ1‐42, whereas the values for the plasma quality controls were 6.4% for Aβ1‐40 and 4.8% for Aβ1‐42. From the test–retest evaluation, the average precision was 7.2% for Aβ1‐40 and 4.5% for Aβ1‐42. The range of final plasma results for Alzheimer's Disease Neuroimaging Initiative patients was 13 to 372 pg/mL (median: 164 pg/mL) for Aβ1‐40 and 3.5 to 103 pg/mL (median: 39.3 pg/mL) for Aβ1‐42. We found that sample collection parameters (blood volume and time to freeze) have a small, but significant, influence on the result. No significant difference was found between plasma Aβ levels for patients with Alzheimer's disease and healthy control subjects. We have determined multiple significant correlations of plasma Aβ1‐42 levels with CSF biomarkers. The relatively strongest, although modest, correlation was found between plasma Aβ1‐42 levels and CSF p‐tau181/Aβ1‐42 ratio in patients with mild cognitive impairment. Plasma Aβ1‐40 correlations with CSF biomarkers were weaker and diminished completely when we used longitudinal data. No significant correlations were found for the plasma Aβ1‐42/Aβ1‐40 ratio.ConclusionsThe precision of our robotized method represents a substantial improvement over results reported in the literature. Multiple significant correlations between plasma and CSF biomarkers were found. Although these correlations are not strong enough to support the use of plasma Aβ measurement as a diagnostic screening test, plasma Aβ1‐42 levels are well suited for use as a pharmacodynamic marker.
Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates
Authors: Bowen Jennifer L , Morrison Hilary G , Hobbie John E , Sogin Mitchell L 
Published: June 2012

Abstract
Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.
The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks
Authors: Hawlena Hadas , Rynkiewicz Evelyn , Toh Evelyn , Alfred Andrew , Durden Lance A , Hastriter Michael W , Nelson David E , Rong Ruichen , Munro Daniel , Dong Qunfeng , Fuqua Clay , Clay Keith 
Published: June 2012

Abstract
Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment.
Rhynchosporium commune: a persistent threat to barley cultivation
Authors: Avrova Anna , Knogge Wolfgang 
Published: June 2012

SummaryRhynchosporium commune is a haploid fungus causing scald or leaf blotch on barley, other Hordeum spp. and Bromus diandrus.TaxonomyRhynchosporium commune is an anamorphic Ascomycete closely related to the teleomorph Helotiales genera Oculimacula and Pyrenopeziza.Disease symptomsRhynchosporium commune causes scald‐like lesions on leaves, leaf sheaths and ears. Early symptoms are generally pale grey oval lesions. With time, the lesions acquire a dark brown margin with the centre of the lesion remaining pale green or pale brown. Lesions often merge to form large areas around which leaf yellowing is common. Infection frequently occurs in the leaf axil, which can lead to chlorosis and eventual death of the leaf.Life cycleRhynchosporium commune is seed borne, but the importance of this phase of the disease is not fully understood. Debris from previous crops and volunteers, infected from the stubble from previous crops, are considered to be the most important sources of the disease. Autumn‐sown crops can become infected very soon after sowing. Secondary spread of disease occurs mainly through splash dispersal of conidia from infected leaves. Rainfall at the stem extension growth stage is the major environmental factor in epidemic development.Detection and quantificationRhynchosporium commune produces unique beak‐shaped, one‐septate spores both on leaves and in culture. The development of a specific polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) has allowed the identification of asymptomatic infection in seeds and during the growing season.Disease controlThe main measure for the control of R. commune is the use of fungicides with different modes of action, in combination with the use of resistant cultivars. However, this is constantly under review because of the ability of the pathogen to adapt to host plant resistance and to develop fungicide resistance.
On measures of association among genetic variables
Authors: Gianola Daniel , Manfredi Eduardo , Simianer Henner 
Published: June 2012

SummarySystems involving many variables are important in population and quantitative genetics, for example, in multi‐trait prediction of breeding values and in exploration of multi‐locus associations. We studied departures of the joint distribution of sets of genetic variables from independence. New measures of association based on notions of statistical distance between distributions are presented. These are more general than correlations, which are pairwise measures, and lack a clear interpretation beyond the bivariate normal distribution. Our measures are based on logarithmic (Kullback‐Leibler) and on relative ‘distances’ between distributions. Indexes of association are developed and illustrated for quantitative genetics settings in which the joint distribution of the variables is either multivariate normal or multivariate‐t, and we show how the indexes can be used to study linkage disequilibrium in a two‐locus system with multiple alleles and present applications to systems of correlated beta distributions. Two multivariate beta and multivariate beta‐binomial processes are examined, and new distributions are introduced: the GMS‐Sarmanov multivariate beta and its beta‐binomial counterpart.
Familial short stature and intrauterine growth retardation associated with a novel mutation in the IGF‐I receptor (IGF1R) gene
Authors: Labarta José I. , Barrio Eva , Audí Laura , Fernández‐Cancio Mónica , Andaluz Pilar , de Arriba Antonio , Puga Beatriz , Calvo María T. , Mayayo Esteban , Carrascosa Antonio , Ferrández‐Longás Angel 
Published: June 2012

SummaryContextIGF‐I is essential for normal human growth and mediates its effects through the IGF1R. IGF1R mutations have been associated with varying degrees of intrauterine and postnatal growth retardation.ObjectiveTo identify IGF1R gene mutations in a short‐statured family with intrauterine growth retardation and microcephaly.MethodsDirect DNA sequencing was used to identify IGF1R mutations. Multiplex ligation‐dependent probe amplification analyses were performed for deletions and duplications of all IGF1R exons. Functional studies were conducted to assess mutation pathogenicity.ResultsA novel heterozygous IGF1R missense mutation in exon 7 (c.A1549T, p.Y487F) was identified in a short‐statured girl with severe prenatal growth retardation and microcephaly. The same mutation was also identified in her mother, who presented prenatal and postnatal growth failure, and her short‐statured maternal grandmother, both of whom exhibited microcephaly. The index case showed a partial response to rhGH. Functional studies performed in dermal fibroblasts from the index case and her mother showed normal IGF‐I binding; however, IGF‐I activation of intracellular signalling measured as AKT and extracellular signal–regulated kinase phosphorylation was markedly reduced, with patients' values being lower than those of her mother. IGF‐I stimulation of DNA synthesis was significantly reduced compared with controls.ConclusionOur results show a novel missense mutation in the IGF1R gene (c.A1549T, p.Y487F) associated with prenatal and postnatal growth failure and microcephaly in the context of familial short stature. The functional studies are in line with the inactivation of one copy of the IGF1R gene with variable expression within the same family.
Time constraints and flexibility of growth strategies: geographic variation in catch‐up growth responses in amphibian larvae
Authors: Dahl Emma , Orizaola Germán , Nicieza Alfredo G. , Laurila Anssi 
Published: June 2012

Summary1. As size is tightly associated with fitness, compensatory strategies for growth loss can be vital for restoring individual fitness. However, immediate and delayed costs of compensatory responses may prevent their generalization, and the optimal strategy may depend on environmental conditions. Compensatory responses may be particularly important in high‐latitude habitats with short growing seasons, and thus, high‐latitude organisms might be more efficient at compensating after periods of unfavourable growth conditions than low‐latitude organisms.2. We investigated geographical differences in catch‐up growth strategies of populations of the common frog (Rana temporaria) from southern and northern Sweden in two factorial common garden experiments involving predation risk and two different causes of growth arrest (nutritional stress and low temperatures) to evaluate how the compensatory strategies can be affected by context‐dependent costs of compensation. Larval and metamorphic traits, and post‐metamorphic performance were used as response variables.3. Only northern tadpoles exposed to low food completely caught up in terms of metamorphic size, mainly by extending the larval period. Low food decreased survival and post‐metamorphic jumping performance in southern, but not in northern tadpoles, suggesting that northern tadpoles have a better ability to compensate after periods of restricted food.4. Both northern and southern tadpoles were able to metamorphose at the same size as control tadpoles after being exposed to low temperatures, indicating that consequences of variation in temperature and food availability differed for tadpoles. However, the combination of low temperatures and predation risk reduced survival in both southern and northern tadpoles. Also, predation risk decreased energy storage in both experiments.5. Our results highlight the influence of climatic variation and the type of stressor as selective factors shaping compensatory strategies.
Information content in cortical spike trains during brain state transitions
Authors: ARNOLD MARIA M. , SZCZEPANSKI JANUSZ , MONTEJO NOELIA , AMIGÓ JOSÉ M. , WAJNRYB ELIGIUSZ , SANCHEZ‐VIVES MARIA V. 
Published: June 2012

SummaryEven in the absence of external stimuli there is ongoing activity in the cerebral cortex as a result of recurrent connectivity. This paper attempts to characterize one aspect of this ongoing activity by examining how the information content carried by specific neurons varies as a function of brain state. We recorded from rats chronically implanted with tetrodes in the primary visual cortex during awake and sleep periods. Electro‐encephalogram and spike trains were recorded during 30‐min periods, and 2–4 neuronal spikes were isolated per tetrode off‐line. All the activity included in the analysis was spontaneous, being recorded from the visual cortex in the absence of visual stimuli. The brain state was determined through a combination of behavior evaluation, electroencephalogram and electromyogram analysis. Information in the spike trains was determined by using Lempel–Ziv Complexity. Complexity was used to estimate the entropy of neural discharges and thus the information content (Amigóet al. Neural Comput., 2004, 16: 717–736). The information content in spike trains (range 4–70 bits s−1) was evaluated during different brain states and particularly during the transition periods. Transitions toward states of deeper sleep coincided with a decrease of information, while transitions to the awake state resulted in an increase in information. Changes in both directions were of the same magnitude, about 30%. Information in spike trains showed a high temporal correlation between neurons, reinforcing the idea of the impact of the brain state in the information content of spike trains.
Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist
Authors: WEINER AGNES , AURAHS RALF , KURASAWA ATSUSHI , KITAZATO HIROSHI , KUCERA MICHAL 
Published: June 2012

AbstractA large portion of the surface‐ocean biomass is represented by microscopic unicellular plankton. These organisms are functionally and morphologically diverse, but it remains unclear how their diversity is generated. Species of marine microplankton are widely distributed because of passive transport and lack of barriers in the ocean. How does speciation occur in a system with a seemingly unlimited dispersal potential? Recent studies using planktonic foraminifera as a model showed that even among the cryptic genetic diversity within morphological species, many genetic types are cosmopolitan, lending limited support for speciation by geographical isolation. Here we show that the current two‐dimensional view on the biogeography and potential speciation mechanisms in the microplankton may be misleading. By depth‐stratified sampling, we present evidence that sibling genetic types in a cosmopolitan species of marine microplankton, the planktonic foraminifer Hastigerina pelagica, are consistently separated by depth throughout their global range. Such strong separation between genetically closely related and morphologically inseparable genetic types indicates that niche partitioning in marine heterotrophic microplankton can be maintained in the vertical dimension on a global scale. These observations indicate that speciation along depth (depth‐parapatric speciation) can occur in vertically structured microplankton populations, facilitating diversification without the need for spatial isolation.
Aminoarabinose is essential for lipopolysaccharide export and intrinsic antimicrobial peptide resistance in Burkholderia cenocepacia†
Authors: Hamad Mohamad A. , Di Lorenzo Flaviana , Molinaro Antonio , Valvano Miguel A. 
Published: June 2012

SummaryOne common mechanism of resistance against antimicrobial peptides in Gram‐negative bacteria is the addition of 4‐amino‐4‐deoxy‐l‐arabinose (l‐Ara4N) to the lipopolysaccharide (LPS) molecule. Burkholderia cenocepacia exhibits extraordinary intrinsic resistance to antimicrobial peptides and other antibiotics. We have previously discovered that unlike other bacteria, B. cenocepacia requires l‐Ara4N for viability. Here, we describe the isolation of B. cenocepacia suppressor mutants that remain viable despite the deletion of genes required for l‐Ara4N synthesis and transfer to the LPS. The absence of l‐Ara4N is the only structural difference in the LPS of the mutants compared with that of the parental strain. The mutants also become highly sensitive to polymyxin B and melittin, two different classes of antimicrobial peptides. The suppressor phenotype resulted from a single amino acid replacement (aspartic acid to histidine) at position 31 of LptG, a protein component of the multi‐protein pathway responsible for the export of the LPS molecule from the inner to the outer membrane. We propose that l‐Ara4N modification of LPS provides a molecular signature required for LPS export and proper assembly at the outer membrane of B. cenocepacia, and is the most critical determinant for the intrinsic resistance of this bacterium to antimicrobial peptides.
The Effects of Iodine Deficiency in Pregnancy and Infancy
Authors: Zimmermann Michael B. 
Published: June 2012

AbstractIodine requirements are increased ≥50% during pregnancy. Iodine deficiency during pregnancy can cause maternal and fetal hypothyroidism and impair neurological development of the fetus. The consequences depend upon the timing and severity of the hypothyroidism; the most severe manifestation is cretinism. In moderate‐to‐severely iodine‐deficient areas, controlled studies have demonstrated that iodine supplementation before or during early pregnancy eliminates new cases of cretinism, increases birthweight, reduces rates of perinatal and infant mortality and generally increases developmental scores in young children by 10–20%. Mild maternal iodine deficiency can cause thyroid dysfunction but whether it impairs cognitive and/or neurologic function in the offspring remains uncertain. Two meta‐analyses have estimated that iodine‐deficient populations experience a mean reduction in IQ of 12–13.5 points. In nearly all regions affected by iodine deficiency, salt iodisation is the most cost‐effective way of delivering iodine and improving maternal and infant health.
Vitamin A and Carotenoids During Pregnancy and Maternal, Neonatal and Infant Health Outcomes: a Systematic Review and Meta‐Analysis
Authors: Thorne‐Lyman Andrew L. , Fawzi Wafaie W. 
Published: June 2012

AbstractVitamin A (VA) deficiency during pregnancy is common in low‐income countries and a growing number of intervention trials have examined the effects of supplementation during pregnancy on maternal, perinatal and infant health outcomes. We systematically reviewed the literature to identify trials isolating the effects of VA or carotenoid supplementation during pregnancy on maternal, fetal, neonatal and early infant health outcomes. Meta‐analysis was used to pool effect estimates for outcomes with more than one comparable study. We used GRADE criteria to assess the quality of individual studies and the level of evidence available for each outcome. We identified 23 eligible trials of which 17 had suitable quality for inclusion in meta‐analyses. VA or beta‐carotene (βC) supplementation during pregnancy did not have a significant overall effect on birthweight indicators, preterm birth, stillbirth, miscarriage or fetal loss. Among HIV‐positive women, supplementation was protective against low birthweight (<2.5 kg) [risk ratio (RR) = 0.79 [95% confidence interval (CI) 0.64, 0.99]], but no significant effects on preterm delivery or small‐for‐gestational age were observed. Pooled analysis of the results of three large randomised trials found no effects of VA supplementation on neonatal/infant mortality, or pregnancy‐related maternal mortality (random‐effects RR = 0.86 [0.60, 1.24]) although high heterogeneity was observed in the maternal mortality estimate (I2 = 74%,P = 0.02). VA supplementation during pregnancy was found to improve haemoglobin levels and reduce anaemia risk (<11.0 g/dL) during pregnancy (random‐effects RR = 0.81 [0.69, 0.94]), also with high heterogeneity (I2 = 52%,P = 0.04). We found no effect of VA/βC supplementation on mother‐to‐child HIV transmission in pooled analysis, although some evidence suggests that it may increase transmission. There is little consistent evidence of benefit of maternal supplementation with VA or βC during pregnancy on maternal or infant mortality. While there may be beneficial effects for certain outcomes, there may also be potential for harm through increased HIV transmission in some populations.
Impact of Increasing Inter‐pregnancy Interval on Maternal and Infant Health
Authors: Wendt Amanda , Gibbs Cassandra M. , Peters Stacey , Hogue Carol J. 
Published: June 2012

AbstractShort inter‐pregnancy intervals (IPIs) have been associated with adverse maternal and infant health outcomes in the literature. However, many studies in this area have been lacking in quality and appropriate control for confounders known to be associated with both short IPIs and poor outcomes. The objective of this systematic review was to assess this relationship using more rigorous criteria, based on GRADE (Grading of Recommendations Assessment, Development and Evaluation) methodology. We found too few higher‐quality studies of the impact of IPIs (measured as the time between the birth of a previous child and conception of the next child) on maternal health to reach conclusions about maternal nutrition, morbidity or mortality. However, the evidence for infant effects justified meta‐analyses. We found significant impacts of short IPIs for extreme preterm birth [<6 m adjusted odds ratio (aOR): 1.58 [95% confidence interval (CI) 1.40, 1.78], 6–11 m aOR: 1.23 [1.03, 1.46]], moderate preterm birth (<6 m aOR: 1.41 [1.20, 1.65], 6–11 m aOR: 1.09 [1.01, 1.18]), low birthweight (<6 m aOR: 1.44 [1.30, 1.61], 6–11 m aOR: 1.12 [1.08, 1.17]), stillbirth (aOR: 1.35 [1.07, 1.71] and early neonatal death (aOR: 1.29 [1.02, 1.64]) outcomes largely in high‐ and moderate‐income countries. It is likely these effects would be greater in settings with poorer maternal health and nutrition. Future research in these settings is recommended. This is particularly important in developing countries, where often the pattern is to start childbearing at a young age, have all desired children quickly and then control fertility through permanent contraception, thereby contracting women's fertile years and potentially increasing their exposure to the ill effects of very short IPIs.