bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design‐Based Inference in a Mixture Model for Ordinal Variables for a Two Stage Stratified Design
Authors: Gambacorta R. , Iannario M. , Valliant R. 
Published: June 2014

SummaryIn this paper we present methods for inference on data selected by a complex sampling design for a class of statistical models for the analysis of ordinal variables. Specifically, assuming that the sampling scheme is not ignorable, we derive for the class ofcubmodels (Combination of discrete Uniform and shifted Binomial distributions) variance estimates for a complex two stage stratified sample. Both Taylor linearization and repeated replication variance estimators are presented. We also provide design‐based test diagnostics and goodness‐of‐fit measures. We illustrate by means of real data analysis the differences between survey‐weighted and unweighted point estimates and inferences forcubmodel parameters.
Small intestinal permeability is increased in diarrhoea predominant IBS, while alterations in gastroduodenal permeability in all IBS subtypes are largely attributable to confounders
Authors: Mujagic Z. , Ludidi S. , Keszthelyi D. , Hesselink M. A. M. , Kruimel J. W. , Lenaerts K. , Hanssen N. M. J. , Conchillo J. M. , Jonkers D. M. A. E. , Masclee A. A. M. 
Published: June 2014

SummaryBackgroundIntestinal permeability has been studied in small groups of IBS patients with contrasting findings.AimsTo assess intestinal permeability at different sites of the GI tract in different subtypes of well‐characterised IBS patients and healthy controls (HC), and to assess potential confounding factors.MethodsIBS patients and HC underwent a multi‐sugar test to assess site‐specific intestinal permeability. Sucrose excretion and lactulose/rhamnose ratio in 0–5 h urine indicated gastroduodenal and small intestinal permeability, respectively. Sucralose/erythritol ratio in 0–24 h and 5–24 h urine indicated whole gut and colonic permeability, respectively. Linear regression analysis was used to assess the association between IBS groups and intestinal permeability and to adjust for age, sex, BMI, anxiety or depression, smoking, alcohol intake and use of medication.ResultsNinety‐one IBS patients, i.e. 37% IBS‐D, 23% IBS‐C, 33% IBS‐M and 7% IBS‐U and 94 HC were enrolled. Urinary sucrose excretion was significantly increased in the total IBS group [μmol, median (Q1;Q3): 5.26 (1.82;11.03) vs. 2.44 (0.91;5.85), P < 0.05], as well as in IBS‐C and IBS‐D vs. HC. However, differences attenuated when adjusting for confounders. The lactulose/rhamnose ratio was increased in IBS‐D vs. HC [0.023 (0.013;0.038) vs. 0.014 (0.008;0.025), P < 0.05], which remained significant after adjustment for confounders. No difference was found in 0–24 and 5–24 h sucralose/erythritol ratio between groups.ConclusionsSmall intestinal permeability is increased in patients with IBS‐D compared to healthy controls, irrespective of confounding factors. Adjustment for confounders is necessary when studying intestinal permeability, especially in a heterogeneous disorder such as IBS.
An improved nonparametric lower bound of species richness via a modified good–turing frequency formula
Authors: Chiu Chun‐Huo , Wang Yi‐Ting , Walther Bruno A. , Chao Anne 
Published: June 2014

SummaryIt is difficult to accurately estimate species richness if there are many almost undetectable species in a hyper‐diverse community. Practically, an accurate lower bound for species richness is preferable to an inaccurate point estimator. The traditional nonparametric lower bound developed by Chao (1984, Scandinavian Journal of Statistics 11, 265–270) for individual‐based abundance data uses only the information on the rarest species (the numbers of singletons and doubletons) to estimate the number of undetected species in samples. Applying a modified Good–Turing frequency formula, we derive an approximate formula for the first‐order bias of this traditional lower bound. The approximate bias is estimated by using additional information (namely, the numbers of tripletons and quadrupletons). This approximate bias can be corrected, and an improved lower bound is thus obtained. The proposed lower bound is nonparametric in the sense that it is universally valid for any species abundance distribution. A similar type of improved lower bound can be derived for incidence data. We test our proposed lower bounds on simulated data sets generated from various species abundance models. Simulation results show that the proposed lower bounds always reduce bias over the traditional lower bounds and improve accuracy (as measured by mean squared error) when the heterogeneity of species abundances is relatively high. We also apply the proposed new lower bounds to real data for illustration and for comparisons with previously developed estimators.
Individual prediction regions for multivariate longitudinal data with small samples
Authors: Concordet D. , Servien R. 
Published: June 2014

SummaryFollow‐up is more and more used in medicine/doping control to identify abnormal results in an individual. Currently, follow‐ups are mostly carried out variable by variable using “reference intervals” that contain the values observable in% of healthy/undoped individuals. Observations of the evolution of the variables over time in a sample ofNhealthy/undoped individuals, allows these reference intervals to be individualized by taking into account the possible effect of covariables and some previous observations of these variables obtained when the individual was healthy/undoped. For each variable these individualized intervals should contain% of observable values compatible with previous observed values in this individual. General methods to build these intervals are available, but they allow only a variable by variable follow‐up whatever the possible correlations over time between them. In this article, we propose a general method to jointly follow‐up several correlated variables over time. This methodology relies on a multivariate linear mixed effects model. We first provide a method to estimate the model's parameters. In an asymptotic framework (Nlarge enough), we then derive aindividualized prediction region. Sometimes, the sample sizeNis not large enough for the asymptotic framework to give a reasonable prediction region. It is for this reason, we propose and compare three different prediction regions that should behave better for smallN. Finally, the whole methodology is illustrated by the follow‐up of kidney insufficiency in cats.
Scaffolding strategies for wiki‐based collaboration: Action research in a multicultural Japanese language program
Authors: Jung Insung , Suzuki Yoko 
Published: June 2014

AbstractWikis can be used to encourage and support collaborative constructivist learning. However, their effectiveness depends upon the use of scaffolding strategies to guide the students in their use. This action research investigated three scaffolding strategies for wiki‐based multicultural Japanese language learning: worked examples, grouping and peer assessment. It was found that the use of a template explaining the learning objectives and expected learning process was more effective than detailed worked examples. It was also found that heterogeneous grouping and internal and external peer review were important factors and that wiki‐based collaborative learning can be culture laden and in conflict with traditional teaching and learning.
SL‐401 and SL‐501, targeted therapeutics directed at the interleukin‐3 receptor, inhibit the growth of leukaemic cells and stem cells in advanced phase chronic myeloid leukaemia
Authors: Frolova Olga , Benito Juliana , Brooks Chris , Wang Rui‐Yu , Korchin Borys , Rowinsky Eric K. , Cortes Jorge , Kantarjian Hagop , Andreeff Michael , Frankel Arthur E. , Konopleva Marina 
Published: June 2014

SummaryWhile imatinib and other tyrosine kinase inhibitors (TKIs) are highly efficacious in the treatment of chronic myeloid leukaemia (CML), some patients become refractory to these therapies. After confirming that interleukin‐3 receptor (IL3R, CD123) is highly expressed on CD34+/CD38− BCR‐ABL1+ CML stem cells, we investigated whether targeting IL3R with diphtheria toxin (DT)‐IL3 fusion proteins SL‐401 (DT388‐IL3) and SL‐501 (DT388‐IL3[K116W]) could eradicate these stem cells. SL‐401 and SL‐501 inhibited cell growth and induced apoptosis in the KBM5 cell line and its TKI‐resistant KBM5‐STI subline. Combinations of imatinib with these agents increased apoptosis in KBM5 and in primary CML cells. In six primary CML samples, including CML cells harbouring the ABL1 T315I mutation, SL‐401 and SL‐501 decreased the absolute numbers of viable CD34+/CD38−/CD123+ CML progenitor cells by inducing apoptosis. IL3‐targeting agents reduced clonogenic growth and diminished the fraction of primitive long‐term culture‐initiating cells in samples from patients with advanced phase CML that were resistant to TKIs or harboured an ABL1 mutation. Survival was also extended in a mouse model of primary TKI‐resistant CML blast crisis. These data suggest that the DT‐IL3 fusion proteins, SL‐401 and SL‐501, deplete CML stem cells and may increase the effectiveness of current CML treatment, which principally targets tumour bulk.
The Fibrotic Scar in Neurological Disorders
Authors: Fernández‐Klett Francisco , Priller Josef 
Published: June 2014

AbstractTissue fibrosis, or scar formation, is a common response to damage in most organs of the body. The central nervous system (CNS) is special in that fibrogenic cells are restricted to vascular and meningeal niches. However, disruption of the blood–brain barrier and inflammation can unleash stromal cells and trigger scar formation. Astroglia segregate from the inflammatory lesion core, and the so‐called “glial scar” composed of hypertrophic astrocytes seals off the intact neural tissue from damage. In the lesion core, a second type of “fibrotic scar” develops, which is sensitive to inflammatory mediators. Genetic fate mapping studies suggest that pericytes and perivascular fibroblasts are activated, but other precursor cells may also be involved in generating a transient fibrous extracellular matrix in the CNS. The stromal cells sense inflammation and attract immune cells, which in turn drive myofibroblast transdifferentiation. We believe that the fibrotic scar represents a major barrier to CNS regeneration. Targeting of fibrosis may therefore prove to be a valuable therapeutic strategy for neurological disorders such as stroke, spinal cord injury and multiple sclerosis.
Callosal alterations in pyridoxine‐dependent epilepsy
Authors: Friedman Seth D , Ishak Gisele E , Poliachik Sandra L , Poliakov Andrew V , Otto Randolph K , Shaw Dennis W W , Willemsen Michèl A , Bok Levinus A , Gospe Sidney M 
Published: June 2014

AimWhile there have been isolated reports of callosal morphology differences in pyridoxine‐dependent epilepsy (PDE), a rare autosomal disorder caused by ALDH7A1 gene mutations, no study has systematically evaluated callosal features in a large sample of patients. This study sought to overcome this knowledge gap.MethodSpanning a wide age range from birth to 48 years, corpus callosum morphology and cross‐sectional cerebral area were measured in 30 individuals with PDE (12 males, 18 females, median age 3.92y; 25th centile 0.27, 75th centile 15.25) compared to 30 age‐matched comparison individuals (11 males, 19 females, median age 3.85y; 25th centile 0.26, 75th centile 16.00). Individuals with PDE were also divided into age groups to evaluate findings across development. As delay to treatment may modulate clinical severity, groups were stratified by treatment delay (less than or greater than 2wks from birth).ResultsMarkedly reduced callosal area expressed as a ratio of mid‐sagittal cerebral area was observed for the entire group with PDE (p<0.001). Stratifying by age (<1y, 1–10y, >10y) demonstrated posterior abnormalities to be a consistent feature, with anterior regions increasingly involved across the developmental trajectory. Splitting the PDE group by treatment lag did not reveal overall or sub‐region callosal differences.InterpretationCallosal abnormalities are a common feature of PDE not explained by treatment lag. Future work utilizing tract‐based approaches to understand inter‐ and intra‐hemispheric connectivity patterns will help in the better understanding the structural aspects of this disease.
Induced tree response to herbivory influences the foraging preference and performance of a conifer‐defoliating sawfly
Authors: Johns Rob C. , Leggo Jonathan J. 
Published: June 2014

AbstractHerbivory often alters the growth and development of woody plants and can thereby render hosts less susceptible to subsequent herbivores. We carried out field surveys and experiments to investigate how previous herbivory influences adult egg lay, larval feeding preference, and associated survival of the yellowheaded spruce sawfly, Pikonema alaskensis (Rohwer) (Hymenoptera: Tenthredinidae), within crowns of black spruce, Picea mariana (Mill.) Britton et al. (Pinaceae). Pikonema alaskensis females laid nearly twice as many eggs, and late‐instar larvae consumed nearly twice as much foliar biomass, on undefoliated vs. defoliated branches. The major factor driving the lower incidence of egg lay on defoliated branches was a significant reduction in the availability of preferred size classes of shoots. In general, adult females preferred medium‐sized shoots, whereas late instars preferred large shoots; previous defoliation generally decreased the availability of medium and large shoots. In a field bioassay, late‐instar survival generally declined with increasing defoliation, which again corresponded to significant reductions in shoot length on defoliated branches. The tendency of P. alaskensis to avoid shoots on severely defoliated branches is likely to increase the time lag between herbivory and the feedback effects of induction and could thus contribute to fluctuations in sawfly population density during outbreak. Our results differ from numerous past studies of closely related diprionid sawflies in conifers, most of which have reported weak or positive effects of previous herbivory on host susceptibility; we attribute the observed responses of spruce to the unusual sawfly feeding preference of P. alaskensis for developing conifer foliage.
Vestibular compensation in cerebellar stroke patients
Authors: Baier B. , Müller N. , Rhode F. , Dieterich M. 
Published: June 2014

Background and purposeThere is little evidence about the site where compensatory vestibular mechanisms in patients with cerebellar strokes take place.MethodsTo determine whether the location of a cerebellar lesion might be a crucial variable in vestibular compensation a sample of 22 patients with cerebellar stroke were tested for graviceptive function in the acute and chronic stage.ResultsOur statistical anatomical lesion analysis indicated that mainly lesions of the cerebellar hemispheres (lobule V, VI, VIIa) hinder vestibular compensation and might lead to an overcompensation.ConclusionsOvercompensation‐induced dysfunction can be explained by the absence of cerebellar inhibitory signals.
Statistical characterization of the geometric properties of particles in 7075‐T6 aluminium alloy
Authors: Haden C. V. , Harlow D. G. 
Published: June 2014

ABSTRACTCorrosion in aluminium alloys is initiated and sustained at constituent particles within the metal matrix via a localized galvanic process. These particles are also known to play a critical role in fatigue crack initiation and growth. Consequently, statistical characterization of particle geometrical features is critical when modelling corrosion and fatigue. A key statistic is particle size distribution, which was extensively modelled here via imaging of unstressed and fatigued 7075‐T6 aluminium alloys. Fatigued samples were obtained from the outer wing panels of teardown specimens from retired military aircraft. The purpose of this effort was therefore to analyse extensive sets of particle geometry data obtained via microscopy using advanced multimodal statistical modelling and to appropriately characterize the properties of constituent particles and fatigue cracks found in these specimens. The resulting distribution functions for the underlying modes are assumed to be three‐parameter Weibull distribution functions.
Ecological consequences of amphibian larvae and their native and alien predators on the community structure of temporary ponds
Authors: Arribas Rosa , Díaz‐Paniagua Carmen , Gomez‐Mestre Ivan 
Published: June 2014

Summary

Connections between consumers and resources in food webs are complex and affect the structure and functioning of ecosystems. We assessed the influence of amphibians as consumers on the structure and functioning of temporary ponds, determining their impact on macrophyte abundance, zooplankton diversity and water chemistry.
The effect of amphibians may be modulated by interactions with predators or competitors that alter tadpole density or behaviour. Therefore, we also investigated the consumptive and non‐consumptive effects of native and invasive predators on amphibian larvae and pond ecosystems.
High amphibian density decreased macrophyte biomass and zooplankton diversity and increased water turbidity and nutrient content. These effects were largely attributable to tadpoles of the largest herbivorous species, spadefoot toads (Pelobates cultripes). In the absence of spadefoot toads, amphibians unexpectedly affected plant biomass positively.
Invasive crayfish (Procambarus clarkii) altered community structure in similar ways to high densities of amphibians and caused greater mortality of amphibian larvae than did native predators.
The high herbivorous impact of spadefoot toads and invasive crayfish carried over to the following hydrological cycle.
Temporal evolution of biochar's impact on soil nitrogen processes – a15N tracing study
Authors: Nelissen Victoria , Rütting Tobias , Huygens Dries , Ruysschaert Greet , Boeckx Pascal 
Published: June 2014

AbstractBiochar addition to soils has been proposed as a means to increase soil fertility and carbon sequestration. However, its effect on soil nitrogen (N) cycling and N availability is poorly understood. To gain better insight into the temporal variability of the impact of biochar on gross soil N dynamics, two15N tracing experiments, in combination with numerical data analysis, were conducted with soil from a biochar field trial, 1 day and 1 year after application of a woody biochar type. The results showed accelerated soil N cycling immediately following biochar addition, with increased gross N mineralization (+34%), nitrification (+13%) and ammonium (NH4+) and nitrate (NO3−) immobilization rates (+4500% and +511%, respectively). One year after biochar application, the biochar acted as an inert substance with respect to N cycling. In the short term, biochar's labile C fraction and a pH increase can explain stimulated microbial activity, while in the longer term, when the labile C fraction has been mineralized and the pH effect has faded, the accelerating effect of biochar on N cycling ceases. In conclusion, biochar accelerates soil N transformations in the short‐term through stimulating soil microbial activity, thereby increasing N bio‐availability. This effect is, however, temporary.
Selected elements of cultural landscape structure in Wielkopolska region of Poland as habitats for the parasitoid hymenoptera Pimplinae (Hymenoptera, Ichneumonidae)
Authors: Piekarska‐Boniecka Hanna , Mazur Robert , Wagner Aleksandra , Trzciński PaweŁ 
Published: June 2014

Abstract

The studies included cultural landscapes of simple (agricultural land) and complex (forest) structure in Wielkopolska.

The goal of the studies was to define biocoenotic function of marginal habitats such as – shrubs, field border, road borders, and forest edges – structural elements of agricultural landscape making suitable habitats for parasitoid hymenoptera of subfamily Pimplinae (Hymenoptera, Ichneumonidae)

The authors wanted to establish:

which of marginal habitats are most attractive for Pimplinae;
which of these habitats are similar to forest habitats, due to the qualitative and quantitative structure of parasitoid hymenoptera communities living there; and
whether linear marginal habitats (like road sides) can fulfil the function of ecological corridors for parasitoid hymenoptera, between agricultural and forest habitats.

The species diversity of Pimplinae in all the habitats of agricultural landscape and forest environment (national park) was similar.

On the forest edges (high heterogeneity landscape), the communities of Pimplinae were most numerous. In the low heterogeneity landscape, the greatest species diversity occurred in shrubs. The majority of Pimplinae populations living in agricultural landscape and forest showed great similarity in their qualitative structure and less similarity in their quantitative structure.

The conclusion can be made that marginal habitats of agricultural landscape make attractive environment for parasitoids of Pimplinae and that vegetation alongside roads can make function as ecological corridors.
Use of a dissolved oxygen microsensor for assessing the viability and thickness of microbial biofilm on root surfaces
Authors: Tomazinho F. S. F. , Sousa‐Neto M. D. , Pécora J. D. , Lamon A. W. , Gonzalez B. C. , Silva‐Sousa Y. T. C. 
Published: June 2014

AbstractAimTo evaluate the use of a dissolved oxygen microsensor (DOMS) for assessing the viability and thickness of microbial biofilms on the apical external surface of contaminated human tooth roots.MethodologyApical biofilm formation was evaluated in 15 roots contaminated in vitro with a polymicrobial mixture of Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa and Candida albicans for 7, 21 and 60 days and in three freshly extracted roots with associated radiographically visible periapical lesions. In each root, the thickness and viability (measured by the amount of dissolved oxygen) of biofilm formed on the apical 2 mm were examined with the DOMS. Scanning electron microscopy (SEM) was used as an auxiliary analysis to confirm the existence of the biofilms detected by the DOMS.ResultsThe DOMS detected dissolved oxygen on the biofilms formed on the three residual roots up to thickness of 375 μm, 480 μm and 1650 μm. In the 15 roots contaminated in vitro, the DOMS detected dissolved oxygen in six specimens up to thicknesses from 75 to 250 μm, and the intensity of the metabolic activity (biofilm thickness) was directly proportional to the contamination time. SEM confirmed the presence of biofilm in all roots.ConclusionThe dissolved oxygen microsensor allowed the measurement of the amount of dissolved oxygen in the biofilm, which is indicative of the intensity of the microbial metabolic activity (viability), correlating the results with biofilm thickness. The DOMS was effective in freshly extracted roots, but had limitations in roots contaminated in vitro after short periods (7 and 21 days) of contamination.