bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seven Interactional Benefits of Physical Tasks for People with Intellectual Disability
Authors: Antaki Charles 
Published: August 2012

Abstract
People with intellectual disability can be supported by staff encouraging their skills in communication and in physical tasks. In a qualitative study, I used video evidence from a residential home and from 2 garden therapy services to argue that physical tasks are structurally more likely to result in successful performance (and corresponding positive assessment), whereas verbal tasks tend to result in failure (and corresponding correction and unsatisfactory interaction). I suggested 7 distinguishing characteristics of the 2 kinds of task and briefly discussed the policy implications for supporting people with intellectual disability.
A Longitudinal Study of Narrative Development in Children and Adolescents with Down Syndrome
Authors: Cleave Patricia , Bird Elizabeth Kay-Raining , Czutrin Rachael , Smith Lindsey 
Published: August 2012

Abstract
The present study examined narrative development in children and adolescents with Down syndrome longitudinally. Narratives were collected from 32 children and adolescents with Down syndrome three times over a 1-year period. Both micro- and macrolevel analyses were conducted. Significant growth over the 1-year period was seen in semantic complexity and narrative structure. However, there was no evidence of growth in syntactic complexity or narrative length. Mental age and comprehension skills at Time 1 predicted scores in all 4 areas at Time 3. Expressive language skills added further to the prediction of syntactic complexity and story length.
Measuring Physical Activity with Pedometers in Older Adults with Intellectual Disability: Reactivity and Number of Days
Authors: Hilgenkamp Thessa , Van Wijck Ruud , Evenhuis Heleen 
Published: August 2012

Abstract
The minimum number of days of pedometer monitoring needed to estimate valid average weekly step counts and reactivity was investigated for older adults with intellectual disability. Participants (N  =  268) with borderline to severe intellectual disability ages 50 years and older were instructed to wear a pedometer for 14 days. The outcome measure was steps per day. Reactivity was investigated with repeated measures analysis of variance, and monitoring frame was assessed by comparing combinations of days with average weekly step counts (with intraclass correlation coefficients [ICCs] and regression analyses). No reactivity was present. Any combination of 4 days resulted in ICCs of 0.96 or higher and 90% of explained variance. The study concludes that any 4 days of wearing a pedometer is sufficient to validly measure physical activity in older adults with intellectual disability.
Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea maysL.)
Authors: Rincent R , Laloë D , Nicolas S , Altmann T , Brunel D , Revilla P , Rodríguez V M , Moreno-Gonzalez J , Melchinger A , Bauer E , Schoen C-C , Meyer N , Giauffret C , Bauland C , Jamin P , Laborde J , Monod H , Flament P , Charcosset A , Moreau L 
Published: August 2012

AbstractGenomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix–best linear unbiased predictions model (RA–BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request.
Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion
Authors: Lukić Sergio , Hey Jody 
Published: August 2012

Abstract
We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yield comparable results, although the polynomial-based approach is the most accurate in the weak-migration limit. Also, the economical use of memory attained by the polynomial expansions makes the study of models with four populations possible for the first time. The method was applied to a four-population model of the human expansion out of Africa and the peopling of the Americas, using the Environmental Genome Project (EGP) SNP database. Although our confidence intervals largely overlapped previous analyses of these data, some were significantly different. In particular, estimates of migration among African, European, and Asian populations were considerably lower than those in a previous study and the estimated time of migration out of Africa was earlier. The estimated time of founding of a human population outside of Africa was 52,000 years (95% confidence interval: 36,000–80,800 years).
An Indel Polymorphism in the Hybrid Incompatibility Gene Lethal Hybrid Rescue of Drosophila Is Functionally Relevant
Authors: Maheshwari Shamoni , Barbash Daniel A 
Published: August 2012

Abstract
Hybrid incompatibility (HI) genes are frequently observed to be rapidly evolving under selection. This observation has led to the attractive conjecture that selection-derived protein-sequence divergence is culpable for incompatibilities in hybrids. The Drosophila simulans HI gene Lethal hybrid rescue (Lhr) is an intriguing case, because despite having experienced rapid sequence evolution, its HI properties are a shared function inherited from the ancestral state. Using an unusual D. simulans Lhr hybrid rescue allele, Lhr2, we here identify a conserved stretch of 10 amino acids in the C terminus of LHR that is critical for causing hybrid incompatibility. Altering these 10 amino acids weakens or abolishes the ability of Lhr to suppress the hybrid rescue alleles Lhr1 or Hmr1, respectively. Besides single-amino-acid substitutions, Lhr orthologs differ by a 16-aa indel polymorphism, with the ancestral deletion state fixed in D. melanogaster and the derived insertion state at very high frequency in D. simulans. Lhr2 is a rare D. simulans allele that has the ancestral deletion state of the 16-aa polymorphism. Through a series of transgenic constructs we demonstrate that the ancestral deletion state contributes to the rescue activity of Lhr2. This indel is thus a polymorphism that can affect the HI function of Lhr.
Multiple Pathways of Duplication Formation with and Without Recombination (RecA) in Salmonella enterica
Authors: Reams Andrew B , Kofoid Eric , Kugelberg Elisabeth , Roth John R 
Published: August 2012

Abstract
Duplications are often attributed to “unequal recombination” between separated, directly repeated sequence elements (&gt;100 bp), events that leave a recombinant element at the duplication junction. However, in the bacterial chromosome, duplications form at high rates (10−3–10−5/cell/division) even without recombination (RecA). Here we describe 1800 spontaneous lac duplications trapped nonselectively on the low-copy F′128 plasmid, where lac is flanked by direct repeats of the transposable element IS3 (1258 bp) and by numerous quasipalindromic REP elements (30 bp). Duplications form at a high rate (10−4/cell/division) that is reduced only about 11-fold in the absence of RecA. With and without RecA, most duplications arise by recombination between IS3 elements (97%). Formation of these duplications is stimulated by IS3 transposase (Tnp) and plasmid transfer functions (TraI). Three duplication pathways are proposed. First, plasmid dimers form at a high rate stimulated by RecA and are then modified by deletions between IS3 elements (resolution) that leave a monomeric plasmid with an IS3-flanked lac duplication. Second, without RecA, duplications occur by single-strand annealing of DNA ends generated in different sister chromosomes after transposase nicks DNA near participating IS3 elements. The absence of RecA may stimulate annealing by allowing chromosome breaks to persist. Third, a minority of lac duplications (3%) have short (0–36 bp) junction sequences (SJ), some of which are located within REP elements. These duplication types form without RecA, Tnp, or Tra by a pathway in which the palindromic junctions of a tandem inversion duplication (TID) may stimulate deletions that leave the final duplication.
The Chromosomal Passenger Complex Is Required for Meiotic Acentrosomal Spindle Assembly and Chromosome Biorientation
Authors: Radford Sarah J , Jang Janet K , McKim Kim S 
Published: August 2012

Abstract
DURING meiosis in the females of many species, spindle assembly occurs in the absence of the microtubule-organizing centers called centrosomes. In the absence of centrosomes, the nature of the chromosome-based signal that recruits microtubules to promote spindle assembly as well as how spindle bipolarity is established and the chromosomes orient correctly toward the poles is not known. To address these questions, we focused on the chromosomal passenger complex (CPC). We have found that the CPC localizes in a ring around the meiotic chromosomes that is aligned with the axis of the spindle at all stages. Using new methods that dramatically increase the effectiveness of RNA interference in the germline, we show that the CPC interacts with Drosophila oocyte chromosomes and is required for the assembly of spindle microtubules. Furthermore, chromosome biorientation and the localization of the central spindle kinesin-6 protein Subito, which is required for spindle bipolarity, depend on the CPC components Aurora B and Incenp. Based on these data we propose that the ring of CPC around the chromosomes regulates multiple aspects of meiotic cell division including spindle assembly, the establishment of bipolarity, the recruitment of important spindle organization factors, and the biorientation of homologous chromosomes.
Microtubule-Depolymerizing Kinesin KLP10A Restricts the Length of the Acentrosomal Meiotic Spindle in Drosophila Females
Authors: Radford Sarah J , Harrison Andrew M , McKim Kim S 
Published: August 2012

Abstract
During cell division, a bipolar array of microtubules forms the spindle through which the forces required for chromosome segregation are transmitted. Interestingly, the spindle as a whole is stable enough to support these forces even though it is composed of dynamic microtubules, which are constantly undergoing periods of growth and shrinkage. Indeed, the regulation of microtubule dynamics is essential to the integrity and function of the spindle. We show here that a member of an important class of microtubule-depolymerizing kinesins, KLP10A, is required for the proper organization of the acentrosomal meiotic spindle in Drosophila melanogaster oocytes. In the absence of KLP10A, microtubule length is not controlled, resulting in extraordinarily long and disorganized spindles. In addition, the interactions between chromosomes and spindle microtubules are disturbed and can result in the loss of contact. These results indicate that the regulation of microtubule dynamics through KLP10A plays a critical role in restricting the length and maintaining bipolarity of the acentrosomal meiotic spindle and in promoting the contacts that the chromosomes make with microtubules required for meiosis I segregation.
The Relation of Codon Bias to Tissue-Specific Gene Expression inArabidopsis thaliana
Authors: Camiolo Salvatore , Farina Lorenzo , Porceddu Andrea 
Published: August 2012

AbstractThe codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.
Bark beetle effects on fuel profiles across a range of stand structures in Douglas‐fir forests of Greater Yellowstone
Authors: Donato Daniel C. , Harvey Brian J. , Romme William H. , Simard Martin , Turner Monica G. 
Published: August 2012

Consequences of bark beetle outbreaks for forest wildfire potential are receiving heightened attention, but little research has considered ecosystems with mixed‐severity fire regimes. Such forests are widespread, variable in stand structure, and often fuel limited, suggesting that beetle outbreaks could substantially alter fire potentials. We studied canopy and surface fuels in interior Douglas‐fir (Pseudotsuga menziesiiv.glauca) forests in Greater Yellowstone, Wyoming, USA, to determine how fuel characteristics varied with time since outbreak of the Douglas‐fir beetle (Dendroctonus pseudotsugae). We sampled five stands in each of four outbreak stages, validated for pre‐outbreak similarity: green (undisturbed), red (1–3 yr), gray (4–14 yr), and silver (25–30 yr). General linear models were used to compare variation in fuel profiles associated with outbreak to variation associated with the range of stand structures (dense mesic forest to open xeric parkland) characteristic of interior Douglas‐fir forest.Beetle outbreak killed 38–83% of basal area within stands, generating a mix of live trees and snags over several years. Canopy fuel load and bulk density began declining in the red stage via needle drop and decreased by ∼50% by the silver stage. The dead portion of available canopy fuels peaked in the red stage at 41%. After accounting for background variation, there was little effect of beetle outbreak on surface fuels, with differences mainly in herbaceous biomass (50% greater in red stands) and coarse woody fuels (doubled in silver stands). Within‐stand spatial heterogeneity of fuels increased with time since outbreak, and surface‐to‐crown continuity decreased and remained low because of slow/sparse regeneration. Collectively, results suggest reduced fire potentials in post‐outbreak stands, particularly for crown fire after the red stage, although abundant coarse fuels in silver stands may increase burn residence time and heat release. Outbreak effects on fuels were comparable to background variation in stand structure. The net effect of beetle outbreak was to shift the structure of mesic closed‐canopy stands toward that of parklands, and to shift xeric parklands toward very sparse woodlands. This study highlights the importance of evaluating outbreak effects in the context of the wide structural variation inherent to many forest types in the absence of beetle disturbance.
Amortized Cost for Operating Lease Assets
Authors: Jennings Ross , Marques Ana 
Published: August 2012

SYNOPSIS:
A proposed accounting standard issued jointly by the Financial Accounting Standards Board (FASB) and the International Accounting Standards Board (IASB) would require firms to recognize many more lease assets than are currently required and to amortize those assets on a straight-line basis. A number of respondents to the exposure draft argue that the “front-loading” of lease expense resulting from straight-line amortization would not reflect the economics of the lease assets. This study compares straight-line amortization with the most-often cited alternative, present value amortization. First, we illustrate by example that under stylized conditions, present value amortization provides information that more faithfully represents the future cash flows of lease assets than straight-line amortization. Second, for a large subset of firms that are more likely to conform to the stylized conditions in our example, we find that investors value those firms as though the lease assets are capitalized and amortized on a present value basis. Finally, we find that financial ratio comparability is substantially increased when operating leases are constructively capitalized and amortized using straight-line amortization, and further increased when using present value amortization. Taken together, these results provide no evidence for favoring straight-line amortization over present value amortization as the default method for amortizing capitalized operating leases.
Data Availability: Data used in this paper are publicly available.
On pulse pressure loading of plates with holes
Authors: Schleyer Graham , Underwood Nicholas. , Do Hyung , Paik Jeom , Kim Bong 
Published: August 2012

Abstract
This paper reports the application of an energy solution to a complex problem involving large inelastic deformation in thin, clamped ductile square plates with either square or circular holes under the action of transverse pulse pressure loading. The work is part of a collaborative project to study blast loading of steel plates with penetrations as used for deck plating or bulkheads that may be required to resist loading far in excess of their design limit due to the effects of an accidental explosion. A novel differential pressure loading device was used to impart dynamic loading to 1/8 scaled 0.5 m, 1.1 mm thick, clamped mild steel square plates with a central aperture up to 4% of the plate area. This data was used to validate the energy approach that considers both plastic hinge formation and extensional effects. Accounting for strain rate, scaling and dynamic effects in the tests gave more than acceptable results when compared with final deflections in the tested plates. It is concluded that the energy approach together with small-scale test validation paves the way for a versatile robust design methodology which can be used to advantage for screening purposes and/or early stage conceptual design studies.
Functional Exhaustion of CD4+ T Lymphocytes during Primary Cytomegalovirus Infection
Authors: Antoine Pierre , Olislagers Véronique , Huygens Ariane , Lecomte Sandra , Liesnard Corinne , Donner Catherine , Marchant Arnaud 
Published: August 2012

Abstract
Human CMV establishes lifelong persistence after primary infection. Chronic CMV infection is associated with intermittent viral reactivation inducing high frequencies of CD4+ T lymphocytes with potent antiviral and helper properties. Primary CMV infection is characterized by an intense viral replication lasting for several months. The impact of this prolonged exposure to high Ag loads on the functionality of CD4+ T cells remains incompletely understood. In pregnant women with primary CMV infection, we observed that CMV-specific CD4+ T lymphocytes had a decreased capacity to proliferate and to produce IL-2. A very large proportion of CMV-specific CD4+ T cells had downregulated the expression of CD28, a costimulatory molecule centrally involved in the production of IL-2. Unexpectedly, both CD28− and CD28+CD4+ T cells produced low levels of IL-2. This defective production of IL-2 was part of a larger downregulation of cytokine production. Indeed, CMV-specific CD4+ T cells produced lower amounts of IFN-γ and TNF-α and showed lower functional avidity during primary as compared with chronic infection. Increased programmed death-1 expression was observed in CD28+ CMV-specific CD4+ T cells, and programmed death-1 inhibition increased proliferative responses. These results indicate that primary CMV infection is associated with the exhaustion of CMV-specific CD4+ T cells displaying low functional avidity for viral Ags.
Noncovalent Assembly of Anti-Dendritic Cell Antibodies and Antigens for Evoking Immune Responses In Vitro and In Vivo
Authors: Flamar Anne-Laure , Zurawski Sandra , Scholz Felix , Gayet Ingrid , Ni Ling , Li Xiao-Hua , Klechevsky Eynav , Quinn John , Oh SangKon , Kaplan Daniel H. , Banchereau Jacques , Zurawski Gerard 
Published: August 2012

AbstractTargeting of Ags directly to dendritic cells (DCs) through anti-DC receptor Ab fused to Ag proteins is a promising approach to vaccine development. However, not all Ags can be expressed as a rAb directly fused to a protein Ag. In this study, we show that noncovalent assembly of Ab–Ag complexes, mediated by interaction between dockerin and cohesin domains from cellulose-degrading bacteria, can greatly expand the range of Ags for this DC-targeting vaccine technology. rAbs with a dockerin domain fused to the rAb H chain C terminus are efficiently secreted by mammalian cells, and many Ags not secreted as rAb fusion proteins are readily expressed as cohesin directly fused to Ag either via secretion from mammalian cells or as soluble cytoplasmic Escherichia coli products. These form very stable and homogeneous complexes with rAb fused to dockerin. In vitro, these complexes can efficiently bind to human DC receptors followed by presentation to Ag-specific CD4+ and CD8+ T cells. Low doses of the HA1 subunit of influenza hemagglutinin conjugated through this means to anti-Langerin rAbs elicited Flu HA1-specific Ab and T cell responses in mice. Thus, the noncovalent assembly of rAb and Ag through dockerin and cohesin interaction provides a useful modular strategy for development and testing of prototype vaccines for elicitation of Ag-specific T and B cell responses, particularly when direct rAb fusions to Ag cannot be expressed.