bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics of Indium Phosphide Epitaxial Growth Using Metal Organic Precursors
Authors: Masi M. , Cavallotti C. , Radaelli G. , Carrà S. 
Published: January 2007

AbstractThe deposition kinetics of InP using metal‐organic precursors is presented. The proposed chemical mechanism involves both gas phase and surface reactions. The fundamental hypothesis adopted in deriving the mechanism was a dual site dissociative adsorption of the precursors on the growing surface. In any case, all the rate constants either were taken from the literature or estimated through thermochemical methods. In addition, the deposition reactor was simulated by means of a monodimensional model that accounts for the main reactor features through the boundary layer theory.
The Lipopolysaccharide of Sinorhizobium meliloti Suppresses Defense-Associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula
Authors: Tellström Verena , Usadel Björn , Thimm Oliver , Stitt Mark , Küster Helge , Niehaus Karsten 
Published: January 2007

Abstract
In the establishment of symbiosis between Medicago truncatula and the nitrogen-fixing bacterium Sinorhizobium meliloti, the lipopolysaccharide (LPS) of the microsymbiont plays an important role as a signal molecule. It has been shown in cell cultures that the LPS is able to suppress an elicitor-induced oxidative burst. To investigate the effect of S. meliloti LPS on defense-associated gene expression, a microarray experiment was performed. For evaluation of the M. truncatula microarray datasets, the software tool MapMan, which was initially developed for the visualization of Arabidopsis (Arabidopsis thaliana) datasets, was adapted by assigning Medicago genes to the ontology originally created for Arabidopsis. This allowed functional visualization of gene expression of M. truncatula suspension-cultured cells treated with invertase as an elicitor. A gene expression pattern characteristic of a defense response was observed. Concomitant treatment of M. truncatula suspension-cultured cells with invertase and S. meliloti LPS leads to a lower level of induction of defense-associated genes compared to induction rates in cells treated with invertase alone. This suppression of defense-associated transcriptional rearrangement affects genes induced as well as repressed by elicitation and acts on transcripts connected to virtually all kinds of cellular processes. This indicates that LPS of the symbiont not only suppresses fast defense responses as the oxidative burst, but also exerts long-term influences, including transcriptional adjustment to pathogen attack. These data indicate a role for LPS during infection of the plant by its symbiotic partner.
Plant Gene and Alternatively Spliced Variant Annotator. A Plant Genome Annotation Pipeline for Rice Gene and Alternatively Spliced Variant Identification with Cross-Species Expressed Sequence Tag Conservation from Seven Plant Species
Authors: Chen Feng-Chi , Wang Sheng-Shun , Chaw Shu-Miaw , Huang Yao-Ting , Chuang Trees-Juen 
Published: January 2007

Abstract
The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are important markers in evolutionary studies. The data and the Web-based interface, RiceViewer, are available for public access at http://RiceViewer.genomics.sinica.edu.tw/.
Recent Proliferation and Translocation of Pollen Group 1 Allergen Genes in the Maize Genome
Authors: Valdivia Elene R. , Sampedro Javier , Lamb Jonathan C. , Chopra Surinder , Cosgrove Daniel J. 
Published: January 2007

AbstractThe dominant allergenic components of grass pollen are known by immunologists as group 1 allergens. These constitute a set of closely related proteins from the β-expansin family and have been shown to have cell wall-loosening activity. Group 1 allergens may facilitate the penetration of pollen tubes through the grass stigma and style. In maize (Zea mays), group 1 allergens are divided into two classes, A and B. We have identified 15 genes encoding group 1 allergens in maize, 11 genes in class A and four genes in class B, as well as seven pseudogenes. The genes in class A can be divided by sequence relatedness into two complexes, whereas the genes in class B constitute a single complex. Most of the genes identified are represented in pollen-specific expressed sequence tag libraries and are under purifying selection, despite the presence of multiple copies that are nearly identical. Group 1 allergen genes are clustered in at least six different genomic locations. The single class B location and one of the class A locations show synteny with the rice (Oryza sativa) regions where orthologous genes are found. Both classes are expressed at high levels in mature pollen but at low levels in immature flowers. The set of genes encoding maize group 1 allergens is more complex than originally anticipated. If this situation is common in grasses, it may account for the large number of protein variants, or group 1 isoallergens, identified previously in turf grass pollen by immunologists.
The Arabidopsis Aleurone Layer Responds to Nitric Oxide, Gibberellin, and Abscisic Acid and Is Sufficient and Necessary for Seed Dormancy
Authors: Bethke Paul C. , Libourel Igor G.L. , Aoyama Natsuyo , Chung Yong-Yoon , Still David W. , Jones Russell L. 
Published: January 2007

AbstractSeed dormancy is a common phase of the plant life cycle, and several parts of the seed can contribute to dormancy. Whole seeds, seeds lacking the testa, embryos, and isolated aleurone layers of Arabidopsis (Arabidopsis thaliana) were used in experiments designed to identify components of the Arabidopsis seed that contribute to seed dormancy and to learn more about how dormancy and germination are regulated in this species. The aleurone layer was found to be the primary determinant of seed dormancy. Embryos from dormant seeds, however, had a lesser growth potential than those from nondormant seeds. Arabidopsis aleurone cells were examined by light and electron microscopy, and cell ultrastructure was similar to that of cereal aleurone cells. Arabidopsis aleurone cells responded to nitric oxide (NO), gibberellin (GA), and abscisic acid, with NO being upstream of GA in a signaling pathway that leads to vacuolation of protein storage vacuoles and abscisic acid inhibiting vacuolation. Molecular changes that occurred in embryos and aleurone layers prior to germination were measured, and these data show that both the aleurone layer and the embryo expressed the NO-associated gene AtNOS1, but only the embryo expressed genes for the GA biosynthetic enzyme GA3 oxidase.
Methylation of Gibberellins by Arabidopsis GAMT1 and GAMT2
Authors: Varbanova Marina , Yamaguchi Shinjiro , Yang Yue , McKelvey Katherine , Hanada Atsushi , Borochov Roy , Yu Fei , Jikumaru Yusuke , Ross Jeannine , Cortes Diego , Ma Choong Je , Noel Joseph P. , Mander Lew , Shulaev Vladimir , Kamiya Yuji , Rodermel Steve , Weiss David , Pichersky Eran 
Published: January 2007

Abstract
Arabidopsis thaliana GAMT1 and GAMT2 encode enzymes that catalyze formation of the methyl esters of gibberellins (GAs). Ectopic expression of GAMT1 or GAMT2 in Arabidopsis, tobacco (Nicotiana tabacum), and petunia (Petunia hybrida) resulted in plants with GA deficiency and typical GA deficiency phenotypes, such as dwarfism and reduced fertility. GAMT1 and GAMT2 are both expressed mainly in whole siliques (including seeds), with peak transcript levels from the middle until the end of silique development. Within whole siliques, GAMT2 was previously shown to be expressed mostly in developing seeds, and we show here that GAMT1 expression is also localized mostly to seed, suggesting a role in seed development. Siliques of null single GAMT1 and GAMT2 mutants accumulated high levels of various GAs, with particularly high levels of GA1 in the double mutant. Methylated GAs were not detected in wild-type siliques, suggesting that methylation of GAs by GAMT1 and GAMT2 serves to deactivate GAs and initiate their degradation as the seeds mature. Seeds of homozygous GAMT1 and GAMT2 null mutants showed reduced inhibition of germination, compared with the wild type, when placed on plates containing the GA biosynthesis inhibitor ancymidol, with the double mutant showing the least inhibition. These results suggest that the mature mutant seeds contained higher levels of active GAs than wild-type seeds.
The PEROXIN11 Protein Family Controls Peroxisome Proliferation inArabidopsis
Authors: Orth Travis , Reumann Sigrun , Zhang Xinchun , Fan Jilian , Wenzel Dirk , Quan Sheng , Hu Jianping 
Published: January 2007

AbstractPEROXIN11 (PEX11) is a peroxisomal membrane protein in fungi and mammals and was proposed to play a major role in peroxisome proliferation. To begin understanding how peroxisomes proliferate in plants and how changes in peroxisome abundance affect plant development, we characterized the extended Arabidopsis thaliana PEX11 protein family, consisting of the three phylogenetically distinct subfamilies PEX11a, PEX11b, and PEX11c to PEX11e. All five Arabidopsis PEX11 proteins target to peroxisomes, as demonstrated for endogenous and cyan fluorescent protein fusion proteins by fluorescence microscopy and immunobiochemical analysis using highly purified leaf peroxisomes. PEX11a and PEX11c to PEX11e behave as integral proteins of the peroxisome membrane. Overexpression of At PEX11 genes in Arabidopsis induced peroxisome proliferation, whereas reduction in gene expression decreased peroxisome abundance. PEX11c and PEX11e, but not PEX11a, PEX11b, and PEX11d, complemented to significant degrees the growth phenotype of the Saccharomyces cerevisiae pex11 null mutant on oleic acid. Heterologous expression of PEX11e in the yeast mutant increased the number and reduced the size of the peroxisomes. We conclude that all five Arabidopsis PEX11 proteins promote peroxisome proliferation and that individual family members play specific roles in distinct peroxisomal subtypes and environmental conditions and possibly in different steps of peroxisome proliferation.
The Kinesin ATK5 Functions in Early Spindle Assembly inArabidopsis
Authors: Ambrose J. Christian , Cyr Richard 
Published: January 2007

AbstractDuring cell division, the mitotic spindle partitions chromosomes into daughter nuclei. In higher plants, the molecular mechanisms governing spindle assembly and function remain largely unexplored. Here, live cell imaging of mitosis in Arabidopsis thaliana plants lacking a kinesin-14 (ATK5) reveals defects during early spindle formation. Beginning during prophase and lasting until late prometaphase, spindles of atk5-1 plants become abnormally elongated, are frequently bent, and have splayed poles by prometaphase. The period of spindle elongation during prophase and prometaphase is prolonged in atk5-1 cells. Time-lapse imaging of yellow fluorescent protein:ATK5 reveals colocalization with perinuclear microtubules before nuclear envelope breakdown, after which it congresses inward from the poles to the midzone, where it becomes progressively enriched at regions of overlap between antiparallel microtubules. In vitro microtubule motility assays demonstrate that in the presence of ATK5, two microtubules encountering one another at an angle can interact and coalign, forming a linear bundle. These data indicate that ATK5 participates in the search and capture of antiparallel interpolar microtubules, where it aids in generating force to coalign microtubules, thereby affecting spindle length, width, and integrity.
Physical Properties of Extruded Products as Affected by Cheese Whey
Authors: ONWULATA C.I. , KONSTANCE R.P. , SMITH P.W. , HOLSINGER V.H. 
Published: January 2007

ABSTRACTCorn, rice and potato flour were extruded with sweet whey solids (SWS) or whey protein concentrate (WPC) using low and high shear extrusion processing conditions. WPC added at product content of 25% had minimal effect on the texture of extruded products. Expansion and breaking strength were improved in some processes through changes in extrusion shear and moisture. Whey product incorporation resulted in reduced specific mechanical energy input to the process. Increasing whey product concentration beyond 25% reduced expansion and water absorption indices significantly, affecting textural hardness. Product quality characteristics were directly related to the whey product content.
Physical Properties of Low‐fat Sour Cream Containing Exopolysaccharide Producing Lactic Acid
Authors: ADAPA S. , SCHMIDT K.A. 
Published: January 2007

ABSTRACTSyneresis, color, apparent viscosity, and texture of three treatments of low‐fat (6%) sour cream were compared. Samples were made using SC 801 (commercial sour cream culture with 3 m exopolysaccharide capsule) alone, or + S‐3 (Streptococcus thermophilus with 2 m capsule) at 75:25 (v/v), or + S‐4 (Streptococcus thermophilus with no capsule) at 75:25 (v/v).Treatments S‐4 and S‐3 resulted in higher syneresis. No differences were found among color ‘L*’,‘a*’, and ‘b*’ values but S‐3 had higher viscosity than S‐4. No differences in cohesiveness occurred but SC 801 had higher adhesiveness than did S‐4. SC 801 had the highest gumminess and S‐4 the lowest.
A concept analysis of self‐monitoring
Authors: Wilde Mary H. , Garvin Suzanne 
Published: January 2007

AbstractTitle. A concept analysis of self‐monitoringAim. This paper reports a concept analysis delineating and clarifying the concept of self‐monitoring to facilitate development and evaluation of interventions to enhance self‐monitoring.Background. The concepts of self‐monitoring, self‐management, self‐care and symptom management are often used in similar or interchangeable ways. Clarification of the concept of self‐monitoring is needed for research and theory development.Method. Rodgers and Knafl's evolutionary concept analysis process was used to delineate and clarify the concept. The PubMed and CINAHL databases were searched using keywords ‘self‐monitoring’, ‘self‐management’ and ‘self‐care’ (with and without the hyphen) for the years 1998–2005, to update a previous study (not published). Later, searching was refined and the keyword ‘self‐monitoring’ was paired with ‘awareness’ and ‘self‐regulation’ was added. Approximately half the papers were from nursing (n = 34) and half from other disciplines (n = 32). The sample from 1998 to 2005 was further stratified by chronic condition. Definition, exemplars, usage, attributes, antecedents/consequences and implications for further study were identified.Findings. Self‐monitoring was composed of two complementary components (attributes): (1) awareness of bodily symptoms, sensations, daily activities, and cognitive processes and (2) measurements, recordings and observations that inform cognition or provide information for independent action or consultation with care providers.Conclusion. Self‐monitoring may be an important concept for understanding how people self‐manage chronic conditions. This concept analysis may be useful for researchers who wish to measure this dimension and to develop nursing theory in this area.
Globalization and the cultural safety of an immigrant Muslim community
Authors: Baker Cynthia 
Published: January 2007

Abstract Title. Globalization and the cultural safety of an immigrant Muslim community Aim.  This paper reports a study the aim of which was to further understanding of cultural safety by focusing on the social health of a small immigrant community of Muslims in a relatively homogeneous region of Canada following the terror attacks on 11 September 2001 (9/11).Background.  The aftermath of 9/11 negatively affected Muslims living in many centers of Western Europe and North America. Little is known about the social health of Muslims in smaller areas with little cultural diversity. Developed by Maori nurses, the cultural safety concept captures the negative health effects of inequities experienced by the indigenous people of New Zealand. Nurses in Canada have used the concept to understand the health of Aboriginal peoples. It has also been used to investigate the nursing care of immigrants in a Canadian metropolitan centre. Findings indicated, however, that the dichotomy between culturally safe and unsafe groups was blurred.Method.  The methodology was qualitative, based on the constructivist paradigm. A purposive sample of 26 Muslims of Middle Eastern, Indian or Pakistani origin and residing in the province of New Brunswick, Canada were interviewed in 2002–2003.Findings.  Participants experienced a sudden transition from cultural safety to cultural risk following 9/11. Their experience of cultural safety included a sense of social integration in the community and invisibility as a minority. Cultural risk stemmed from being in the spotlight of an international media and becoming a visible minority.Conclusion.  Cultural risk is not necessarily rooted in historical events and may be generated by outside forces rather than by longstanding inequities in relationships between groups within the community. Nurses need to think about the cultural safety of their practices when caring for members of socially disadvantaged cultural minority groups as this may affect the health services delivered to them.
Obstructive sleep apnoea syndrome – patients' perceptions of their sleep and its effects on their life situation
Authors: Broström Anders , Johansson Peter , Strömberg Anna , Albers Jan , Mårtensson Jan , Svanborg Eva 
Published: January 2007

Abstract Title. Obstructive sleep apnoea syndrome – patients' perceptions of their sleep and its effects on their life situation Aim.  This paper reports a descriptive study of how untreated patients with obstructive sleep apnoea syndrome perceived their sleep situation and how the syndrome affected their life situation.Background.  Obstructive sleep apnoea syndrome is a prevalent problem independently associated with an increased risk for hypertension, cardiovascular disease, chronic heart failure and mortality. Increased consumption of healthcare resources can often be seen among patients over a long period of time since many have been undiagnosed and untreated.Methods.  A phenomenographic approach was employed. Data were collected by interviews during 2005 with 20 purposively selected participants with untreated obstructive sleep apnoea syndrome.Findings.  Participants described loud snoring, frequent awakenings, dyspnoea, frustration over nocturia, fear of dying during sleep and partners’ anxiety about the apnoea, as being night‐time effects of obstructive sleep apnoea syndrome. They described dry and sore throats, tiredness and daytime sleepiness, shame about falling asleep and snoring, thoughts about complications and depressed mood as daytime effects. Needs, such as increased alertness, improved ability to concentrate, improved relationship, adequate information as well as effective treatment, were described. Participants tried self‐care strategies such as information‐seeking about sleep disturbances and treatment, adapted sleeping routines, change of bedroom arrangements, adapted daily schedules, hyperactivity and avoidance of difficult situations.Conclusion.  The perceived effects and needs, as well as tried self‐care actions by the patients with obstructive sleep apnoea syndrome in this study, could be used to identify and evaluate concerns of other patients with obstructive sleep apnoea syndrome waiting for treatment.
Factors influencing the development of evidence‐based practice: a research tool
Authors: Gerrish Kate , Ashworth Peter , Lacey Anne , Bailey Jeff , Cooke Jo , Kendall Sally , McNeilly Elaine 
Published: January 2007

Abstract Title. Factors influencing the development of evidence‐based practice: a research tool Aim.  The paper reports a study to develop and test a tool for assessing a range of factors influencing the development of evidence‐based practice among clinical nurses.Background.  Achieving evidence‐based practice is a goal in nursing frequently cited by the profession and in government health policy directives. Assessing factors influencing the achievement of this goal, however, is complex. Consideration needs to be given to a range of factors, including different types of evidence used to inform practice, barriers to achieving evidence‐based practice, and the skills required by nurses to implement evidence‐based care.Methods.  Measurement scales currently available to investigate the use of evidence in nursing practice focus on nurses’ sources of knowledge and on barriers to the use of research evidence. A new, wider ranging Developing Evidence‐Based Practice questionnaire was developed and tested for its measurement properties in two studies. In study 1, a sample of 598 nurses working at two hospitals in one strategic health authority in northern England was surveyed. In study 2, a slightly expanded version of the questionnaire was employed in a survey of 689 community nurses in 12 primary care organizations in two strategic health authorities, one in northern England and the other in southern England.Findings.  The measurement characteristics of the new questionnaire were shown to be acceptable. Ten significant, and readily interpretable, factors were seen to underlie nurses’ relation to evidence‐based practice.Conclusion.  Strategies to promote evidence‐based practice need to take account of the differing needs of nurses and focus on a range of sources of evidence. The Developing Evidence‐Based Practice questionnaire can assist in assessing the specific ‘evidencing’ tendencies of any given group of nurses.