bluuebunny/crossref_metadata_2025_split huggingface dataset:
Below-ground secondary succession in tropical forests of Borneo
Authors: Brearley Francis Q. 
Published: May 2011

Abstract:As the destruction and severe disturbance of primary tropical forest continues, it is important to understand how these forests may recover from perturbations. Considerable work has been done on above-ground recovery but below-ground processes are less well understood. To determine changes in root mass during tropical secondary succession in lowland forests of Central Borneo, samples were taken from stands of increasing ages since abandonment of agriculture (1, 3, 14 and 31 y) with a primary forest control (six plots from 1-y-old stands and three from all other ages). Root mass and elemental concentrations were determined and soils were chemically analysed. There was no increase in root mass with stand age for fine-root (< 2 mm diameter) or small-root (< 5 mm diameter) mass but there was a trend for coarse-root mass (5–10 mm diameter) to increase with stand age. Negative correlations were shown between root mass and soil nutrient status. Fine-root C concentrations increased with stand age but there was no clear effect of stand age on fine-root N or P. Fine-root mass did not increase significantly with stand age suggesting a rapid recovery; instead, soil nutrient status appeared to be the most important factor controlling root mass. Of the soil nutrients measured in this study, N had a stronger control over root mass than P suggesting that this element may be limiting during secondary succession in tropical lowland forests of Borneo.
ADAM SMITH’S ESSENTIALS: ON TRUST, FAITH, AND FREE MARKETS
Authors: EVENSKY JERRY 
Published: May 2011

When trust is shaken, individuals pull back and the market system contracts. Where trust grows, individual energy and creativity are unleashed and the system grows. In Adam Smith’s vision of humankind’s progress, trust is the central theme.The Great Recession represents a classic case of a crisis of trust. Looking back to the work of Smith offers insight into the role of citizens and the State in creating an fruitful market environment based on trust, and the challenge of this process, given the human frailty of individuals (unfortunately, we are not angels) and the potential for State power to be captured and abused.
Script Generation of Activities of Daily Living in HIV-Associated Neurocognitive Disorders
Authors: Cobb Scott J. , Woods Steven Paul , Vigil Ofilio , Heaton Robert K. , Grant Igor , Ellis Ronald J. , Marcotte Thomas D. ,   the HIV Neurobehavioral Research Programs (HNRP) Group
Published: June 2011

AbstractScript generation describes one's ability to produce complex, sequential action plans derived from mental representations of everyday activities. The aim of this study was to assess the effect of human immunodeficiency virus (HIV) infection on script generation performance. Sixty HIV+ individuals (48% of whom had HIV-associated neurocognitive disorders [HAND]) and 26 demographically comparable HIV- participants were administered a novel, standardized test of script generation, which required participants to verbally generate and organize the necessary steps for completing six daily activities. HAND participants evidenced significantly more total errors, intrusions, and script boundary errors compared to the HIV- sample, indicating difficulties inhibiting irrelevant actions and staying within the prescribed boundaries of scripts, but had adequate knowledge of the relevant actions required for each script. These findings are generally consistent with the executive dysfunction and slowing common in HAND and suggest that script generation may play a role in everyday functioning problems in HIV. (JINS, 2011, 17, 740–745)
Can Community-Based Interventions on Aspirations Raise Young People's Attainment?
Authors: Lupton Ruth , Kintrea Keith 
Published: June 2011

Against the background of the ‘Inspiring Communities’ programme to raise ‘community-level’ educational aspirations in England, this article considers whether the existing evidence about place and aspirations suggests that it will be beneficial.We address three questions: Do neighbourhoods have an influence on educational attainment? Are ‘community level’ aspirations a mechanism by which neighbourhoods affect individual aspirations? Is there evidence that aspirations are lower in poor neighbourhoods?The article suggests that the available evidence does not lead to firm conclusions; a key problem is that few studies have measured aspirations at a neighbourhood level. It suggests that limited spending on a pilot is a reasonable response. However, aspirations are shaped by a wide range of other influences. This suggests that any interventions on ‘community’ aspirations’ should be conjoined with other programmes to support schools and to address inequalities between neighbourhoods.
Computerized Administration and Scoring of the Dichotic Nonsense Syllable Test
Authors: Lundeen Conrad 
Published: June 2011

Purpose
A user-friendly computer program was designed to administer the dichotic nonsense syllable test (DNST). Computer automation makes it easier for listeners to perform the response task appropriately and for audiologists to administer and accurately score the test.

Method
The program presents test stimuli in a user-controlled, self-paced sequence; provides an easy-to-use client interface to collect listener responses; verifies that appropriate responses are recorded before proceeding with the test; scores responses automatically; and stores the information in an electronic format that is easy to analyze and archive.

Results
The automated DNST protocol is described. Verification tests confirm the accuracy of stimulus sequencing, response recording, and test scoring.

Conclusions
Computer automation makes administering the DNST easier, ensures the accuracy of test scoring, and simplifies the analysis and archiving of results. These refinements may make the DNST more useful to clinicians. Further research is required to establish normative data for this version of the DNST.
Services for Children With Central Auditory Processing Disorder in the Republic of Ireland: Current and Future Service Provision
Authors: Logue-Kennedy Maria , Lyons Rena , Carroll Clare , Byrne Mary , Dignan Eilis , O'Hagan Lucy 
Published: June 2011

Purpose
An interdisciplinary research group was established to investigate current and future service provision for children with central auditory processing disorder ([C]APD) in the Republic of Ireland. The aim of Phase 1 was to identify current awareness and knowledge of (C)APD among the relevant professionals in Ireland, including level of service provision, if any, available for children with (C)APD. The aim of Phase 2 was to explore the initial steps required to develop an integrated service for children presenting with (C)APD.

Method
A quantitative design was used in Phase 1, and 520 surveys were distributed to speech and language therapists, audiologic scientists, and educational psychologists. A qualitative participative design was used in Phase 2.

Results
There was a 53% response rate to the survey. The main findings from Phase 1 were that all professional groups considered themselves to be inadequately informed and lacking in skills for (C)APD assessment or intervention. In Phase 2, 98 participants with backgrounds in speech and language therapy, audiologic science, educational psychology, and occupational therapy engaged in interdisciplinary discussions to identify the first steps required to develop a (C)APD service.

Conclusion
All professional groups considered that they were inadequately informed about (C)APD, and the first steps required to develop services in Ireland include the promotion and development of interdisciplinary teamwork and education, a need for additional resources, a clearer understanding of the definition of (C)APD, and evidence-based assessment and management of this condition.
One-dimensional polaritons with size-tunable and enhanced coupling strengths in semiconductor nanowires
Authors: van Vugt Lambert K. , Piccione Brian , Cho Chang-Hee , Nukala Pavan , Agarwal Ritesh 
Published: June 2011

Strong coupling of light with excitons in direct bandgap semiconductors leads to the formation of composite photonic-electronic quasi-particles (polaritons), in which energy oscillates coherently between the photonic and excitonic states with the vacuum Rabi frequency. The light-matter coherence is maintained until the oscillator dephases or the photon escapes. Exciton-polariton formation has enabled the observation of Bose-Einstein condensation in the solid-state, low-threshold polariton lasing and is also useful for terahertz and slow-light applications. However, maintaining coherence for higher carrier concentration and temperature applications still requires increased coupling strengths. Here, we report on size-tunable, exceptionally high exciton-polariton coupling strengths characterized by a vacuum Rabi splitting of up to 200 meV as well as a reduction in group velocity, in surface-passivated, self-assembled semiconductor nanowire cavities. These experiments represent systematic investigations on light-matter coupling in one-dimensional optical nanocavities, demonstrating the ability to engineer light-matter coupling strengths at the nanoscale, even in non-quantum-confined systems, to values much higher than in bulk.
Principles of opioid titration
Authors: Fallon Marie , McConnell Sandra 
Published: May 2011

AbstractThere is great variation in the dose of opioid required by individual patients. Doses must be tailored to the individual’s need and should start low and then be adjusted (titrated) according to response-up or down. Short acting opioids should be used during the initial titration period and then converted to longer acting formulations when the required dose to achieve pain control is reached. Opioids are useful for neuropathic pain. Adjuvants have an important role in controlling some types of pain where opioids give insufficient analgesia or where adverse effects become intolerable.
Corticosteroid Exposure Not Associated With Long‐term Bone Mineral Density in Pediatric Liver Transplantation
Authors: Nightingale Scott , McEwan‐Jackson Fiona D. , Hawker Gillian A. , Macarthur Colin , Khambalia Amina Z. , Lo Lisha , Fecteau Annie , Ng Vicky L. 
Published: June 2011

ABSTRACTObjectives:The aim of the study was to examine the association of corticosteroid exposure and other skeletal risk factors with bone mineral density (BMD) and fractures following pediatric liver transplantation (LT) at a large single center.Patients and Methods:Lumbar spine BMD, measured using dual‐energy x‐ray absorptiometry (DXA), was corrected for bone age in 52 ambulatory children ages 4 to 18 years, at least 1 year post‐LT. Potential risk factors for skeletal health such as corticosteroid exposure, dietary and lifestyle factors, and growth and fracture occurrence, were related to BMD using univariate and multivariate regression analyses.Results:The prevalence of low BMD (z score <−2) and post‐LT fractures was 3 of 52 (5.8%) and 11 of 52 (21%), respectively. Univariate analysis revealed age >10 years at LT and body mass index (BMI) <85th percentile at time of DXA were significantly associated with BMD (both P = 0.02). BMD did not correlate with corticosteroid dosage in the first year post‐LT, the year before DXA or cumulative lifetime exposure. A cholestatic primary LT indication, acute rejection episodes, and fractures post‐LT were not associated with BMD. Extracurricular physical activity, vitamin D, and calcium intake were not associated with BMD or fractures. Multivariate linear regression revealed increased time post‐LT (P = 0.04) and higher BMI z score at time of DXA (P = 0.02) as the strongest independent variables associated with greater BMD.Conclusions:Neither corticosteroid exposure nor a cholestatic primary indication for LT influenced BMD, which was largely normal in this ambulatory group. Children and adolescents undergoing LT after the age of 10 years and those with low BMI post‐LT may be at greatest risk of poor skeletal health later in life, and thus a potential target patient population to benefit from preventive interventions.
From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT Standardized Keywords: For Immunoglobulins (IG), T Cell Receptors (TR), and Conventional Genes
Authors: Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT standardized keywords have been defined for the identification of immunoglobulins (IG) and T cell receptors (TR) and conventional genes. These keywords are based on the concepts of identification, generated from the IDENTIFICATION axiom of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope that postulates that any molecule, cell, tissue, organ, organism, or population, any process and any relation, has to be identified. Most of the IMGT standardized keywords used for the identification of sequences and structures are names of IMGT-ONTOLOGY leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity). IMGT standardized keywords have been essential for the data entries into the IMGT databases and tools, and particularly into IMGT/LIGM-DB, the first and the largest IMGT database that contains IG and TR nucleotide sequences and the translation of annotated sequences. IMGT standardized keywords for IG, TR, and conventional genes are defined in the context of the IMGT-ONTOLOGY concepts of identification.
IMGT Unique Numbering for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF
Authors: Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONThe “IMGT unique numbering” (or “IMGT_unique_numbering”) concept is a major concept of numerotation (generated from the NUMEROTATION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. The “IMGT unique numbering” concept, described here, allows one to number domain types that are characteristic of protein superfamilies, whatever the species, the molecule type or the chain type. Three leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity) have been defined, respectively, for the variable (V) domain and constant (C) domain of the immunoglobulin superfamily (IgSF) and for the groove (G) domain of the major histocompatibility (MH) superfamily (MhSF). The IMGT unique numbering concept has been a great breakthrough in immunogenetics and systems biology in allowing, for the first time, the bridging of the gap between amino acid (and nucleotide) sequences of any V, C, or G domain and their two-dimensional (2D) and three-dimensional (3D) structures. The IMGT unique numbering concept has been fundamental in the creation of the IMGT Collier de Perles and in the standardization of the description of mutations, amino acid changes, polymorphisms, and contact analysis in the IMGT databases, tools, and web resources.
iTRAQ-Labeled Yeast Peptide Clean-Up Using a Reversed-Phase Column
Authors: Simon Eric S. 
Published: June 2011

INTRODUCTIONA commercial reagent, known as the isobaric tag for relative and absolute quantification (iTRAQ), makes it possible to analyze multiple samples simultaneously. The ability of iTRAQ to compare relative protein abundances across as many as eight samples is a significant advantage over other stable isotope strategies, such as stable isotope labeling by amino acids in cell culture (SILAC) and isotope-coded affinity tag (ICAT). The iTRAQ protocol set compares the proteome of Saccharomyces cerevisiae under two different metabolic states (fermentation versus respiration) with the goal of determining the proteins involved in each of the activated pathways by measuring their relative abundances using iTRAQ. Before using isoelectric focusing (IEF) to fractionate the iTRAQ-labeled peptides, the sample needs to be cleaned up because it contains a high concentration of buffer (500 mM triethylammonium bicarbonate), excess reagents from the reduction and alkylation of the proteins, and degradation products of the iTRAQ reagents. All of these are incompatible with IEF. To remove them, the sample is passed over a reversed-phase C18 column. This protocol describes this procedure.
Isoelectric Focusing of iTRAQ-Labeled Yeast
Authors: Simon Eric S. 
Published: June 2011

INTRODUCTIONA commercial reagent, known as the isobaric tag for relative and absolute quantification (iTRAQ), makes it possible to analyze multiple samples simultaneously. The ability of iTRAQ to compare relative protein abundances across as many as eight samples is a significant advantage over other stable isotope strategies, such as stable isotope labeling by amino acids in cell culture (SILAC) and isotope-coded affinity tag (ICAT). The iTRAQ protocol set compares the proteome of Saccharomyces cerevisiae under two different metabolic states (fermentation versus respiration) with the goal of determining the proteins involved in each of the activated pathways by measuring their relative abundances using iTRAQ. This protocol describes fractionation of the iTRAQ-labeled proteins by isoelectric focusing (IEF) on immobilized pH gradient (IPG) strips using an OFFGEL Fractionator.
IMGT/V-QUEST: IMGT Standardized Analysis of the Immunoglobulin (IG) and T Cell Receptor (TR) Nucleotide Sequences
Authors: Giudicelli Véronique , Brochet Xavier , Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT/V-QUEST is the integrated online IMGT tool for the standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) rearranged nucleotide sequences. The analysis of these antigen receptors represents a crucial challenge for the study of the adaptative immune response in normal and disease-related situations. The expressed IG and TR repertoires represent a potential of 1012 IG and 1012 TR per individual. This huge diversity results from mechanisms that occur at the DNA level during IG molecular synthesis, including the combinatorial rearrangement of the variable (V), diversity (D), and joining (J) genes, the N diversity (V, D, and J exonuclease trimming and addition at random of nucleotides by the terminal deoxynucleotidyl transferase during the V-(D)-J rearrangement) and, for IG, somatic hypermutations. IMGT/V-QUEST, as described here, identifies the V, D, J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. The tool describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions and IMGT/Automat for a complete sequence annotation of the sequences, and provides IMGT Collier de Perles.
Arabidopsis Pht1;5 Mobilizes Phosphate between Source and Sink Organs and Influences the Interaction between Phosphate Homeostasis and Ethylene Signaling
Authors: Nagarajan Vinay K. , Jain Ajay , Poling Michael D. , Lewis Anthony J. , Raghothama Kashchandra G. , Smith Aaron P. 
Published: June 2011

Abstract
Phosphorus (P) remobilization in plants is required for continuous growth and development. The Arabidopsis (Arabidopsis thaliana) inorganic phosphate (Pi) transporter Pht1;5 has been implicated in mobilizing stored Pi out of older leaves. In this study, we used a reverse genetics approach to study the role of Pht1;5 in Pi homeostasis. Under low-Pi conditions, Pht1;5 loss of function (pht1;5-1) resulted in reduced P allocation to shoots and elevated transcript levels for several Pi starvation-response genes. Under Pi-replete conditions, pht1;5-1 had higher shoot P content compared with the wild type but had reduced P content in roots. Constitutive overexpression of Pht1;5 had the opposite effect on P distribution: namely, lower P levels in shoots compared with the wild type but higher P content in roots. Pht1;5 overexpression also resulted in altered Pi remobilization, as evidenced by a greater than 2-fold increase in the accumulation of Pi in siliques, premature senescence, and an increase in transcript levels of genes involved in Pi scavenging. Furthermore, Pht1;5 overexpressors exhibited increased root hair formation and reduced primary root growth that could be rescued by the application of silver nitrate (ethylene perception inhibitor) or aminoethoxyvinylglycine (ethylene biosynthesis inhibitor), respectively. Together, these data indicate that Pht1;5 plays a critical role in mobilizing Pi from P source to sink organs in accordance with developmental cues and P status. The study also provides evidence for a link between Pi and ethylene signaling pathways.
The Pepper E3 Ubiquitin Ligase RING1 Gene,CaRING1, Is Required for Cell Death and the Salicylic Acid-Dependent Defense Response
Authors: Lee Dong Hyuk , Choi Hyong Woo , Hwang Byung Kook 
Published: June 2011

AbstractUbiquitination is essential for ubiquitin/proteasome-mediated protein degradation in plant development and defense. Here, we identified a novel E3 ubiquitin ligase RING1 gene, CaRING1, from pepper (Capsicum annuum). In pepper, CaRING1 expression is induced by avirulent Xanthomonas campestris pv vesicatoria infection. CaRING1 contains an amino-terminal transmembrane domain and a carboxyl-terminal RING domain. In addition, it displays in vitro E3 ubiquitin ligase activity, and the RING domain is essential for E3 ubiquitin ligase activity in CaRING1. CaRING1 also localizes to the plasma membrane. In pepper plants, virus-induced gene silencing of CaRING1 confers enhanced susceptibility to avirulent X. campestris pv vesicatoria infection, which is accompanied by compromised hypersensitive cell death, reduced expression of PATHOGENESIS-RELATED1, and lowered salicylic acid levels in leaves. Transient expression of CaRING1 in pepper leaves induces cell death and the defense response that requires the E3 ubiquitin ligase activity of CaRING1. By contrast, overexpression of CaRING1 in Arabidopsis (Arabidopsis thaliana) confers enhanced resistance to hemibiotrophic Pseudomonas syringae pv tomato and biotrophic Hyaloperonospora arabidopsidis infections. Taken together, these results suggest that CaRING1 is involved in the induction of cell death and the regulation of ubiquitination during the defense response to microbial pathogens.
Global research neglect of population‐based approaches to smoking cessation: time for a more rigorous science of population health interventions
Authors: Lawrence David , Mitrou Francis , Zubrick Stephen R. 
Published: June 2011

ABSTRACTIt has been argued that the preponderance of studies into individual smoking cessation therapies seems grossly out of proportion to the number of people who use these therapies to quit smoking, and that this imbalance is due to factors such as the role of the pharmaceutical industry in funding research and a general bias towards individual‐ rather than population‐based approaches to medical and health problems. We believe that there are other significant factors that affect the balance of research in smoking cessation, such as the higher standards of evidence required to justify the implementation of individual medical therapies compared with population‐based interventions. We argue that research practitioners in the area of population tobacco control are well placed to address this imbalance by setting more rigorous standards of evidence for population health interventions. This could be achieved by setting aside a small proportion of funds from population health and advocacy activities to invest in studying their effectiveness. We believe that this would potentially return information of sufficient value to justify increasing overall population investment beyond the cost of the additional research component. Additional benefits would be gained from increased research in this area, such as better understanding of how to translate tobacco control initiatives to developing countries with high smoking rates, and how to target disadvantaged and marginalized populations more effectively in developed countries that continue to have high rates of smoking and low rates of smoking cessation, despite the existence of broad population‐based strategies.