bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF)
Authors: Ehrenmann François , Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT/DomainGapAlign is the IMGT online tool for the analysis of amino acid (AA) sequences and two-dimensional (2D) structures of domains. The use of this tool is described here. Three domain types can be analyzed: the variable (V) and constant (C) domains of the immunoglobulins (IG) and T cell receptors (TR) and other immunoglobulin superfamily (IgSF) proteins, and the groove (G) domain of major histocompatibility (MH) and other MH superfamily (MhSF) proteins. IMGT/DomainGapAlign creates gaps in the user amino acid sequences and delimits, for the V and C domains, the framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT), and, for the G domains, the strands and helix, according to the IMGT unique numbering. The tool provides alignments with the closest sequences from the IMGT domain directory of IMGT/DomainDisplay. For the IG and TR V domains that result from V-(D)-J rearrangement, the tool provides alignments with the translation of the IMGT/GENE-DB germline V and joining (J) genes. IMGT/DomainGapAlign displays the amino acid changes, highlights them in IMGT Colliers de Perles, and provides tables with their detailed description, according to the IMGT rules. Several amino acid sequences can be analyzed simultaneously, provided that they belong to the same domain type.
IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA)
Authors: Ehrenmann François , Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of (1) antigen receptors that comprise immunoglobulins (IG) or antibodies and T cell receptors (TR), (2) major histocompatibility (MH) proteins of class I (MH1) and class II (MH2), (3) peptide/MH (pMH) complexes (pMH1, pMH2), (4) antigen receptor/antigen complexes (IG/Ag, TR/pMH), and (5) related proteins of the immune system (RPI) belonging to the immunoglobulin and MH superfamilies (IgSF and MhSF, respectively) and found in complexes with IG, TR, or MH. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY axioms and concepts. The use of IMGT/3Dstructure-DB is described here. It provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), and amino acid (AA) positions according to the IMGT unique numbering (NUMEROTATION). IMGT/3Dstructure-DB provides the closest genes and alleles that are expressed in the AA sequences of the 3D structures, by aligning these sequences with the IMGT domain reference directory.
Engineering Light-Regulated Ion Channels: Figure 1.
Authors: Fortin Doris L. , Dunn Timothy W. , Kramer Richard H. 
Published: June 2011

INTRODUCTIONOptical regulation provides unrivaled spatial and temporal precision for the control of protein function. We describe a strategy to engineer photosensitivity onto ion channels based on small photoisomerizable molecules. Photosensitivity is targeted to the ion channel of interest by combining the photoisomerizable moiety with a specific agonist or antagonist. Inclusion of a cysteine-reactive maleimide group enables covalent attachment of the photoswitch to a genetically engineered cysteine on the surface of the ion channel. Exposure to different wavelengths of light triggers changes in the properties of the photoswitch that enable control of protein function.
Optical Projection Tomography of Vertebrate Embryo Development
Authors: Quintana Laura , Sharpe James 
Published: June 2011

INTRODUCTIONThis article includes a brief introduction to optical projection tomography (OPT) as a method for imaging whole vertebrate embryos. To place OPT in its proper context within the field of three-dimensional (3D) embryo imaging, the article starts with a brief overview of the previously existing techniques, both destructive and nondestructive. Next is a description of how OPT works and its advantages over other approaches. Two practical sections are then presented that consider the applications of OPT and how to get the best results from OPT in terms of specimen preparation and imaging modes.
Perturbation of spermine synthase Gene Expression and Transcript Profiling Provide New Insights on the Role of the Tetraamine Spermine in Arabidopsis Defense against Pseudomonas viridiflava
Authors: Gonzalez María Elisa , Marco Francisco , Minguet Eugenio Gómez , Carrasco-Sorli Pedro , Blázquez Miguel Angel , Carbonell Juan , Ruiz Oscar Adolfo , Pieckenstain Fernando Luis 
Published: June 2011

Abstract
The role of the tetraamine spermine in plant defense against pathogens was investigated by using the Arabidopsis (Arabidopsis thaliana)-Pseudomonas viridiflava pathosystem. The effects of perturbations of plant spermine levels on susceptibility to bacterial infection were evaluated in transgenic plants (35S::spermine synthase [SPMS]) that overexpressed the SPMS gene and accumulated spermine, as well as in spms mutants with low spermine levels. The former exhibited higher resistance to P. viridiflava than wild-type plants, while the latter were more susceptible. Exogenous supply of spermine to wild-type plants also increased disease resistance. Increased resistance provided by spermine was partly counteracted by the polyamine oxidase inhibitor SL-11061, demonstrating that the protective effect of spermine partly depends on its oxidation. In addition, global changes in gene expression resulting from perturbations of spermine levels were analyzed by transcript profiling 35S::SPMS-9 and spms-2 plants. Overexpression of 602 genes was detected in 35S::SPMS-9 plants, while 312 genes were down-regulated, as compared to the wild type. In the spms-2 line, 211 and 158 genes were up- and down-regulated, respectively. Analysis of gene ontology term enrichment demonstrated that many genes overexpressed only in 35S::SPMS-9 participate in pathogen perception and defense responses. Notably, several families of disease resistance genes, transcription factors, kinases, and nucleotide- and DNA/RNA-binding proteins were overexpressed in this line. Thus, a number of spermine-responsive genes potentially involved in resistance to P. viridiflava were identified. The obtained results support the idea that spermine contributes to plant resistance to P. viridiflava.
Novel alternative splicing by exon skipping in KIT associated with whole‐body roan in an intercrossed population of Landrace and Korean Native pigs
Authors: Lim H. T. , Zhong T. , Cho I. C. , Seo B. Y. , Kim J. H. , Lee S. S. , Ko M. S. , Park H. B. , Kim B. W. , Lee J. H. , Jeon J. T. 
Published: June 2011

SummaryThe KIT locus has been suggested to be a strong candidate region linked with whole‐body roan in the F2 population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the IRn allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U26 repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base‐pairing‐mediated looping‐out of introns 4 and 5, which may mediate the exon 5‐skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U26 repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.
An international collaborative study comparing Swedish and Japanese nurses’ reactions to elder abuse
Authors: Erlingsson Christen , Ono Mitsu , Sasaki Akiko , Saveman Britt‐Inger 
Published: June 2011

erlingsson c., ono m., sasaki a. & saveman b.‐I. (2012) An international collaborative study comparing Swedish and Japanese nurses’ reactions to elder abuse. Journal of Advanced Nursing68(1), 56–68.AbstractAim. This paper reports an analysis of aggregated data from two national studies on Swedish community‐based nurses’ and Japanese Public Health Nurses’ responses to hypothetical elder abuse cases.Background. Elder abuse is an under‐researched area despite being globally recognized as a serious and escalating problem. Yet research, adding needed socio‐cultural perspectives to current knowledge has been limited.Methods. Eighty‐one community‐based nurses in Sweden and 124 Public Health Nurses in Japan responded to a questionnaire based on three hypothetical elder abuse cases. Swedish and Japanese results (data collection 2006–2007) were combined and the aggregated data were analysed using manifest and qualitative content analyses.Results. Nurses’ response patterns in the aggregated data were similar across all three hypothetical cases and within themes Awareness, Assessment and Intervention. However, there were also noteworthy differences between Swedish and Japanese responses, e.g. Swedish responses were generally practical, action oriented and involved increased levels of suspicion and personal intervention to achieve increased control; whereas Japanese responses concerned better understanding that involved the family members and their situation, focusing on interventions grounded in collaboration.Conclusion. Despite cultural differences, responses of Swedish and Japanese nurses were very similar which points to a global ‘humanness’ of the problem of, and nurses’ responses to, elder abuse. Results endorse the value of international collaborations that give information and inspiration to nursing colleagues across cultural boundaries. Results also give hope that global tools for elder abuse assessment and intervention can be developed.
The impact of a pathogenic bacterium on a social carnivore population
Authors: Höner Oliver P. , Wachter Bettina , Goller Katja V. , Hofer Heribert , Runyoro Victor , Thierer Dagmar , Fyumagwa Robert D. , Müller Thomas , East Marion L. 
Published: June 2011

Summary1. The long‐term ecological impact of pathogens on group‐living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium,Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyenaCrocuta crocutapopulation in the Ngorongoro Crater, Tanzania.2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent (‘outbreak’) and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rateR0of the bacterium.3. During the five pre‐outbreak years, the mean annual hyena mortality rate was 0·088, and annual population growth was relatively high (13·6%). During the outbreak, mortality increased by 78% to a rate of 0·156, resulting in an annual population decline of 4·3%. After the outbreak, population size increased moderately (5·1%) during the first three post‐outbreak years before resuming a growth similar to pre‐outbreak levels (13·9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors.4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females – the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimatedR0for the bacterium to be 2·7, indicating relatively fast transmission.5. Our results suggest that the short‐term ‘top–down’ impact ofS. equi ruminatorumduring the outbreak was driven by ‘bottom–up’ effects on nutritionally disadvantaged age–sex classes, whereas the longer‐term post‐outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent poor recruitment of breeding females. These results suggest synergistic effects of ‘bottom–up’ and ‘top–down’ processes on host population dynamics.
Exploring risk factors for depression among older men residing in Macau
Authors: Chan Moon Fai , Zeng Wen 
Published: June 2011

Aim.  To determine the prevalence of depression level of older men in Macau and identify factors that predict depression.Background.  Studies have revealed the contribution of psychosocial factors such as stress, dissatisfaction at work and stressful life events to older men and the mental health burdens pose a grave threat to their quality of life.Design.  A descriptive survey.Method. The study was conducted from July–August 2004 in six parishes in Macau; 839 older men aged 60+ completed a structured questionnaire.Outcome measures.  Predisposing characteristics, social and daily activities, health history and need/behaviours and depression level were collected. Multiple logistic regression models were used to identify factors to predict older men who will have depression.Results.  The prevalence rate of depression of older men was 8·6%. It showed that a history of stroke (p = 0·039), insomnia (p < 0·001), palpitations (p = 0·014), poor social network (p = 0·005) and self‐perceived health status (p = 0·001) and perceived low ability to meet living costs (p < 0·001) were significant risk factors for depression.Conclusion.  We should focus on older men by reducing their burden to meet living costs, improving their sleep quality and helping them to expand their social network. These should help in both prevention and recognition of the onset of depression. Those with the low social network scores could be targeted for more intensive support from the beginning.Relevance to clinical practice.  It is important to screen regularly for depression status among older men in the community. Attention to poor perceived health and not enough on the ability to meet living costs were needed and important to follow up.
The emotional sequelae of whistleblowing: findings from a qualitative study
Authors: Peters Kath , Luck Lauretta , Hutchinson Marie , Wilkes Lesley , Andrew Sharon , Jackson Debra 
Published: June 2011

Aims and objectives.  To highlight and illuminate the emotional sequelae of whistleblowing from whistleblowers and subjects of whistleblowing complaints.Background.  Whistleblowing has the potential to have a negative impact on individuals’ physical and emotional well‐being. However, few empirical studies have been conducted using qualitative methods to provide an in‐depth exploration of the emotional consequences for those involved in whistleblowing incidents.Design.  Qualitative narrative inquiry design.Method.  Purposive sampling was used to recruit participants who had been involved in whistleblowing incidents. During interviews participants’ accounts were digitally recorded and then transcribed verbatim. Data were then analysed by two researchers until consensus was reached.Results.  Findings revealed that participants’ emotional health was considerably compromised as a result of the whistleblowing incident. Analysis of the data revealed the following dominant themes: ‘I felt sad and depressed’: overwhelming and persistent distress; ‘I was having panic attacks and hyperventilating’: acute anxiety; and, ‘I had all this playing on my mind’: nightmares, flashbacks and intrusive thoughts.Conclusions.  While it has been previously acknowledged that whistleblowing has the potential to have a negative impact on all aspects of an individual’s life, this study notably highlights the intensity of emotional symptoms suffered by participants as well as the extended duration of time these symptoms were apparent.Relevance to clinical practice.  As professionals, nurses, as well as organisations, have a responsibility to identify those who may be suffering the emotional trauma of whistleblowing and ensure they have access to appropriate resources.
Attitude and practice of the health care professionals towards the clinical practice guidelines in King Khalid University Hospital in Saudi Arabia
Authors: Wahabi Hayfaa A. , Alzeidan Rasmieh A. , Fayed Amel A. , Esmaeil Samia A. , Al Aseri Zohair A. 
Published: June 2011

AbstractRationale, aims and objectives  To explore the opinion and practice of the health care providers in King Khalid University Hospital (KKUH) towards clinical practice guidelines (CPGs).Methods  A cross‐sectional self‐reported anonymous survey was distributed to 2225 health care professionals working in KKUH clinical departments.Results  The response rate was 56.5%. The respondents had a positive attitude towards CPGs; 90% thought that CPG unify patients' care and 96% agreed that CPGs improve the quality of services provided. The respondents' practice in using CPGs concurred with their attitude and opinion. A total of 86.3% agreed that CPGs changed the way they manage their patients and 71.8% agreed with the statement that they have already used CPGs in the management of the patients. Compared to nurses, physicians were significantly less likely to use CPGs in practice (P < 0.05); moreover, the practice of using guidelines differs significantly according to the years of experience, with 71% of respondents with experience of 15 years or more using CPGs in the management of their patients, compared to 60% among respondents with less years of experience (P < 0.05).Conclusion  The health care providers at KKUH have positive practice and attitude towards CPGs in general, which could positively influence the future introduction and implementation of evidence‐based CPGs.
EIN2 regulates salt stress response and interacts with a MA3 domain‐containing protein ECIP1 in Arabidopsis
Authors: LEI GANG , SHEN MING , LI ZHI‐GANG , ZHANG BO , DUAN KAI‐XUAN , WANG NING , CAO YANG‐RONG , ZHANG WAN‐KE , MA BIAO , LING HONG‐QING , CHEN SHOU‐YI , ZHANG JIN‐SONG 
Published: June 2011

ABSTRACTEthylene signalling regulates plant growth and development. However, its roles in salt stress response are less known. Here we studied functions of EIN2, a central membrane protein of ethylene signalling, and its interacting protein ECIP1 in salt stress responses. Mutation of EIN2 led to extreme salt sensitivity as revealed by phenotypic and physiological changes, and overexpression of C‐terminus of EIN2 suppressed salt sensitivity in ein2‐5, indicating that EIN2 is required for salt tolerance. Downstream components EIN3 and EIL1 are also essential for salt tolerance because ein3‐1eil1‐1 double mutant showed extreme salt‐sensitive phenotype. A MA3 domain‐containing protein ECIP1 was further identified to interact with EIN2 in yeast two‐hybrid assay and GST pull‐down assay. Loss‐of‐function of ECIP1 resulted in enhanced ethylene response but altered salt response during seed germination and plant growth. Double mutant analysis revealed that ein2‐1 was epistatic to ecip1, and ecip1 mutation partially suppressed ethylene‐insensitivity of etr2‐1 and ein4‐1. These studies strengthen that interactions between ECIP1 and EIN2 or ethylene receptors regulate ethylene response and stress response.
Carbonic anhydrase and the molecular evolution of C4 photosynthesis
Authors: LUDWIG MARTHA 
Published: June 2011

ABSTRACTC4 photosynthesis, a biochemical CO2‐concentrating mechanism (CCM), evolved more than 60 times within the angiosperms from C3 ancestors. The genus Flaveria, which contains species demonstrating C3, C3–C4, C4‐like or C4 photosynthesis, is a model for examining the molecular evolution of the C4 pathway. Work with carbonic anhydrase (CA), and C3 and C4Flaveria congeners has added significantly to the understanding of this process. The C4 form of CA3, a β‐CA, which catalyses the first reaction in the C4 pathway by hydrating atmospheric CO2 to bicarbonate in the cytosol of mesophyll cells (mcs), evolved from a chloroplastic C3 ancestor. The molecular modifications to the ancestral CA3 gene included the loss of the sequence encoding the chloroplast transit peptide, and mutations in regulatory regions that resulted in high levels of expression in the C4 mesophyll. Analyses of the CA3 proteins and regulatory elements from Flaveria photosynthetic intermediates indicated C4 biochemistry very likely evolved in a specific, stepwise manner in this genus. The details of the mechanisms involved in the molecular evolution of other C4 plant β‐CAs are unknown; however, comparative genetics indicate gene duplication and neofunctionalization played significant roles as they did in Flaveria.
Identification of a homolog of Arabidopsis DSP4 (SEX4) in chestnut: its induction and accumulation in stem amyloplasts during winter or in response to the cold
Authors: BERROCAL‐LOBO MARTA , IBAÑEZ CRISTIAN , ACEBO PALOMA , RAMOS ALBERTO , PEREZ‐SOLIS ESTEFANIA , COLLADA CARMEN , CASADO ROSA , ARAGONCILLO CIPRIANO , ALLONA ISABEL 
Published: June 2011

ABSTRACTOligosaccharide synthesis is an important cryoprotection strategy used by woody plants during winter dormancy. At the onset of autumn, starch stored in the stem and buds is broken down in response to the shorter days and lower temperatures resulting in the buildup of oligosaccharides. Given that the enzyme DSP4 is necessary for diurnal starch degradation in Arabidopsis leaves, this study was designed to address the role of DSP4 in this seasonal process in Castanea sativa Mill. The expression pattern of the CsDSP4 gene in cells of the chestnut stem was found to parallel starch catabolism. In this organ, DSP4 protein levels started to rise at the start of autumn and elevated levels persisted until the onset of spring. In addition, exposure of chestnut plantlets to 4 °C induced the expression of the CsDSP4 gene. In dormant trees or cold‐stressed plantlets, the CsDSP4 protein was immunolocalized both in the amyloplast stroma and nucleus of stem cells, whereas in the conditions of vegetative growth, immunofluorescence was only detected in the nucleus. The studies indicate a potential role for DSP4 in starch degradation and cold acclimation following low temperature exposure during activity–dormancy transition.