bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptoms and Subtypes in Pediatric Functional Dyspepsia: Relation to Mucosal Inflammation and Psychological Functioning
Authors: Schurman Jennifer V , Singh Meenal , Singh Vivekanand , Neilan Nancy , Friesen Craig A 
Published: May 2010

ABSTRACTObjectives:The aim of the present study was to explore relations between antral or duodenal inflammatory cells and aspects of psychological functioning with clinical symptom presentation in children with functional dyspepsia (FD), as well as to determine whether histologic inflammation and/or psychopathology are differentially associated with FD subtypes as defined by the Rome II and Rome III criteria.Patients and Methods:One hundred pediatric patients with dyspepsia completed a standardized history and physical examination at initial evaluation. Patients and parents also completed a measure of psychological functioning. Subsequently, 63 of these patients underwent upper endoscopy with biopsy (4 patients excluded from analysis because of mucosal disease). Inflammatory cells in the mucosa of stomach and duodenum were enumerated. Associations between specific symptoms and FD subtypes with inflammatory cell densities and anxiety, depression, and somatization scores were examined.Results:Rome III subtypes were more robustly related to differences in mast cell densities and scores on psychologic subscales than was true for Rome II subtypes. At the individual symptom level, having pain wake the patient from sleep was associated with higher duodenal mast cell density. Bloating was associated with lower levels of general antral inflammation, as well as higher self‐reported levels of anxiety and somatization. Early satiety and bothersome postprandial fullness also were associated with higher levels of self‐reported anxiety and depression.Conclusions:The present study provides preliminary evidence for a relation between clinical presentation, specific types of inflammatory cell infiltrates, and aspects of psychological functioning in children with FD. Rome III subtyping, adopted for adult dyspepsia, may be relevant to the pediatric population.
Obesity in Pediatric Celiac Disease
Authors: Venkatasubramani Narayanan , Telega Grzegorz , Werlin Steven L 
Published: May 2010

ABSTRACTBackground and Aim:Celiac disease (CD) is a T cell–mediated chronic autoimmune enteropathy occurring in genetically susceptible individuals, and manifested by a permanent intolerance to gluten‐containing products. CD commonly presents in children as failure to thrive and malabsorption or after screening high‐risk groups such as people with diabetes. Almost half of adult patients with CD have a body mass index (BMI) >25 at diagnosis. Classic symptoms like diarrhea are less common in obese patients. Few children have been reported with CD and obesity. Because many children with newly diagnosed CD are identified by screening high‐risk groups, obesity is more common than previously suspected. The aim of the study was to estimate the prevalence of obesity at diagnosis in children with CD and to describe the clinical characteristics of this group.Patients and Methods:This is a retrospective study of 143 patients with CD diagnosed between 1986 and 2003 at Children's Hospital of Wisconsin. Data collected included patient's age, sex, ethnicity, presenting signs and symptoms, BMI, celiac antibody titers, small‐intestinal biopsy results, and follow‐up weight 1 year after initiating a gluten‐free diet (GFD).Results:Seven of the 143 (5%) patients had BMI >95th percentile. The most common presenting symptoms among obese patients were abdominal pain, diabetes, and diarrhea. Symptoms improved in all of the patients on a GFD. BMI decreased in 4 (50%), increased in 2 (25%), and was not available in 1 patient at 1 year after starting on GFD.Conclusions:Obesity is more common in children with CD than previously recognized. In the appropriate clinical setting, CD must be considered even in obese children.
Effects of Zinc Exposure on Zinc Transporter Expression in Human Intestinal Cells of Varying Maturity
Authors: Jou Ming‐Yu , Philipps Anthony F , Kelleher Shannon L , Lönnerdal Bo 
Published: May 2010

ABSTRACTObjectives:Zinc (Zn) homeostasis in adults is achieved principally through a balance between intestinal absorption and excretion involving adaptive mechanisms programmed by levels of dietary Zn. Zn absorption in infants is not as tightly regulated as that in adults, which may induce potential toxicity in infants due to the relatively high capacity of Zn absorption. We hypothesized that intestinal Zn homeostasis is developmentally regulated and depends on intestinal maturation, which in turn affects Zn transporter regulation.Materials and Methods:Cultured human fetal (FHs 74 Int, F) and adult (Caco‐2: undifferentiated, U; differentiated, D) intestinal cells were used to determine developmental differences in Zn uptake and effects of Zn exposure on Zn transporters.Results:Zn uptake rates in F and U cells were higher compared with D cells (F, 9‐fold; U, 3‐fold). F cells were more intolerant to Zn exposure than were U or D cells (LD50 = 67.9 ± 5.3; 117.0 ± 5.2; 224.4 ± 3.7 μmol/L, respectively). Two mechanisms were involved in developmental regulation of Zn homeostasis: differential Zn transporter expression and differential response to Zn exposure. In F cells, zinc‐regulated transporter (ZRT)/iron‐regulated transporter (IRT)–like protein (Zip)4 expression was undetectable; Zn (50 μmol/L) increased levels of Zn transporter (ZnT)1, ZnT2, and metallothionein‐1 mRNA and ZnT1 protein. U and D cells had higher mRNA expression of ZnT1 (U: 5‐fold; D: 7‐fold, respectively) and ZnT2 (U: 2‐fold; D: 9‐fold, respectively) than F cells, and D cells also had higher Zip4 expression (3‐fold) than U cells. In U cells, Zn exposure increased Zip4 protein level, but not membrane‐associated abundance. However, in D cells, Zn exposure decreased both the Zip4 protein level and membrane‐associated abundance.Conclusions:Zn absorption is developmentally regulated through intestinal Zn efflux and sequestration and import mechanisms, which may be responsible for differences in Zn absorption observed between infants and adults.
Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae
Authors: Carretero-Paulet Lorenzo , Galstyan Anahit , Roig-Villanova Irma , Martínez-García Jaime F. , Bilbao-Castro Jose R. , Robertson David L. 
Published: May 2010

Abstract
Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.
Overexpression of the Arabidopsis Gene UPRIGHT ROSETTE Reveals a Homeostatic Control for Indole-3-Acetic Acid
Authors: Sun Yue , Yang Yang , Yuan Zheng , Müller Jutta Ludwig , Yu Chen , Xu Yanfei , Shao Xinghua , Li Xiaofang , Decker Eva L. , Reski Ralf , Huang Hai 
Published: May 2010

Abstract
Auxins are phytohormones that are essential for many aspects of plant growth and development. The main auxin produced by plants is indole-3-acetic acid (IAA). IAA exists in free and conjugated forms, corresponding to the bioactive and stored hormones, respectively. Free IAA levels, which are crucial for various physiological activities, are maintained through a complex network of environmentally and developmentally responsive pathways including IAA biosynthesis, transport, degradation, conjugation, and conjugate hydrolysis. Among conjugated IAA forms, ester- and amide-type conjugates are the most common. Here we identify a new gene, UPRIGHT ROSETTE (URO), the overexpression of which alters IAA homeostasis in Arabidopsis (Arabidopsis thaliana). We previously identified a semidominant mutant, uro, which had multiple auxin-related phenotypes. We show here that compared to wild-type plants, the uro plants contain increased levels of free and ester-conjugated IAA, and decreased levels of amino-conjugated IAA. uro plants carrying the pDR5:β-glucuronidase (GUS) construct have strong GUS staining in cotyledons and stem, and their cotyledons are able to generate roots on auxin-free medium, further confirming that this mutant contains higher levels of free IAA. The URO gene encodes a C2H2 zinc-finger protein that belongs to a plant-specific gene family. The response to URO overexpression is evolutionarily conserved among plants, as GUS activity that may reflect free IAA levels was increased markedly in transgenic p35S:URO/pGH3:GUS/Physcomitrella patens and pNOS:URO/pGH3:GUS/P. patens plants.
Modeling Lignin Polymerization. I. Simulation Model of Dehydrogenation Polymers
Authors: van Parijs Frederik R.D. , Morreel Kris , Ralph John , Boerjan Wout , Merks Roeland M.H. 
Published: May 2010

Abstract
Lignin is a heteropolymer that is thought to form in the cell wall by combinatorial radical coupling of monolignols. Here, we present a simulation model of in vitro lignin polymerization, based on the combinatorial coupling theory, which allows us to predict the reaction conditions controlling the primary structure of lignin polymers. Our model predicts two controlling factors for the β-O-4 content of syringyl-guaiacyl lignins: the supply rate of monolignols and the relative amount of supplied sinapyl alcohol monomers. We have analyzed the in silico degradability of the resulting lignin polymers by cutting the resulting lignin polymers at β-O-4 bonds. These are cleaved in analytical methods used to study lignin composition, namely thioacidolysis and derivatization followed by reductive cleavage, under pulping conditions, and in some lignocellulosic biomass pretreatments.
Stomatal Responses to Flooding of the Intercellular Air Spaces Suggest a Vapor-Phase Signal Between the Mesophyll and the Guard Cells
Authors: Sibbernsen Erik , Mott Keith A. 
Published: May 2010

Abstract
Flooding the intercellular air spaces of leaves with water was shown to cause rapid closure of stomata in Tradescantia pallida, Lactuca serriola, Helianthus annuus, and Oenothera caespitosa. The response occurred when water was injected into the intercellular spaces, vacuum infiltrated into the intercellular spaces, or forced into the intercellular spaces by pressurizing the xylem. Injecting 50 mm KCl or silicone oil into the intercellular spaces also caused stomata to close, but the response was slower than with distilled water. Epidermis-mesophyll grafts for T. pallida were created by placing the epidermis of one leaf onto the exposed mesophyll of another leaf. Stomata in these grafts opened under light but closed rapidly when water was allowed to wick between epidermis and the mesophyll. When epidermis-mesophyll grafts were constructed with a thin hydrophobic filter between the mesophyll and epidermis stomata responded normally to light and CO2. These data, when taken together, suggest that the effect of water on stomata is caused partly by dilution of K+ in the guard cell and partly by the existence of a vapor-phase signal that originates in the mesophyll and causes stomata to open in the light.
cis-Regulatory Elements and Chromatin State Coordinately Control Temporal and Spatial Expression ofFLOWERING LOCUS TinArabidopsis
Authors: Adrian Jessika , Farrona Sara , Reimer Julia J. , Albani Maria C. , Coupland George , Turck Franziska 
Published: May 2010

AbstractFlowering time of summer annual Arabidopsis thaliana accessions is largely determined by the timing of FLOWERING LOCUS T (FT) expression in the leaf vasculature. To understand the complex interplay between activating and repressive inputs controlling flowering through FT, cis-regulatory sequences of FT were identified in this study. A proximal and an ∼5-kb upstream promoter region containing highly conserved sequence blocks were found to be essential for FT activation by CONSTANS (CO). Chromatin-associated protein complexes add another layer to FT regulation. In plants constitutively overexpressing CO, changes in chromatin status, such as a decrease in binding of LIKE HETEROCHROMATIN PROTEIN1 (LHP1) and increased acetylation of H3K9 and K14, were observed throughout the FT locus, although these changes appear to be a consequence of FT upregulation and not a prerequisite for activation. Binding of LHP1 was required to repress enhancer elements located between the CO-controlled regions. By contrast, the distal and proximal promoter sequences required for FT activation coincide with locally LHP1 and H3K27me3 depleted chromatin, indicating that chromatin status facilitates the accessibility of transcription factors to FT. Therefore, distant regulatory regions are required for FT transcription, reflecting the complexity of its control and differences in chromatin status delimit functionally important cis-regulatory regions.
High-resolution X-ray crystal structure of bovine H-protein at 0.88 Å resolution
Authors: Higashiura Akifumi , Kurakane Takeshi , Matsuda Makoto , Suzuki Mamoru , Inaka Koji , Sato Masaru , Kobayashi Tomoyuki , Tanaka Tetsuo , Tanaka Hiroaki , Fujiwara Kazuko , Nakagawa Atsushi 
Published: May 2010

Recent technical improvements in macromolecular X-ray crystallography have significantly improved the resolution limit of protein structures. However, examples of high-resolution structure determination are still limited. In this study, the X-ray crystal structure of bovine H-protein, a component of the glycine cleavage system, was determined at 0.88 Å resolution. This is the first ultrahigh-resolution structure of an H-protein. The data were collected using synchrotron radiation. Because of limitations of the hardware, especially the dynamic range of the CCD detector, three data sets (high-, medium- and low-resolution data sets) were measured in order to obtain a complete set of data. To improve the quality of the merged data, the reference data set was optimized for merging and the merged data were assessed by comparing merging statistics andRfactors against the final model and the number of visualized H atoms. In addition, the advantages of merging three data sets were evaluated. The omission of low-resolution reflections had an adverse effect on visualization of H atoms in hydrogen-omit maps. Visualization of hydrogen electron density is a good indicator for assessing the quality of high-resolution X-ray diffraction data.
Quantifying instrument errors in macromolecular X-ray data sets
Authors: Diederichs Kay 
Published: May 2010

An indicator which is calculated after the data reduction of a test data set may be used to estimate the (systematic) instrument error at a macromolecular X-ray source. The numerical value of the indicator is the highest signal-to-noise [I/σ(I)] value that the experimental setup can produce and its reciprocal is related to the lower limit of the mergingRfactor. In the context of this study, the stability of the experimental setup is influenced and characterized by the properties of the X-ray beam, shutter, goniometer, cryostream and detector, and also by the exposure time and spindle speed. Typical values of the indicator are given for data sets from the JCSG archive. Some sources of error are explored with the help of test calculations usingSIM_MX[Diederichs (2009),Acta Cryst.D65, 535–542]. One conclusion is that the accuracy of data at low resolution is usually limited by the experimental setup rather than by the crystal. It is also shown that the influence of vibrations and fluctuations may be mitigated by a reduction in spindle speed accompanied by stronger attenuation.
Interest‐based bargaining: achieving improved relationships through collaboration
Authors: Hargrove Scott 
Published: May 2010

PurposeThe purpose of this paper is to evaluate the use of interest‐based bargaining as opposed to traditional adversarial bargaining when negotiating collective agreements in unionized libraries.Design/methodology/approachThis paper explores existing theory, research and practice on the use of interest‐based bargaining in labor negotiations. It accomplishes this goal through a review of relevant literature and case studies, concentrating on practical application in a typical library labor environment. Two specific implementation models are described and the benefits and limitations of interest‐based bargaining are presented, supported by evidence from multiple examples.FindingsInterest‐based bargaining offers significant benefits to organizations that adopt this approach when negotiating collective agreements, including improved working relationships between management and workers and longer term solutions to problems and issues. Library managers in unionized libraries could realize these benefits by implementing interest‐based bargaining strategies in coordination with a supportive union.Research limitations/implicationsThere is very little literature dealing with interest‐based bargaining in a library environment, so extrapolations from other industry examples have been used to illustrate the strengths of this approach.Practical implicationsGiven the potential benefits of using collaborative negotiation approaches, and the increasing adoption rate in other labor industries including comparable public sector organizations, libraries have much to gain by investigating this option as either an alternative or an adjunct to traditional adversarial collective bargaining.Originality/valueThe paper presents a solid case for exploring the use of interest‐based bargaining in a library context.
Relationship among leadership style, organizational culture and employee commitment in university libraries
Authors: Rafiq Awan Muhammad , Mahmood Khalid 
Published: May 2010

PurposeThe purpose of this paper is to explore leadership style, organizational culture and job commitment in university libraries of Pakistan and the relationships among them.Design/methodology/approachA structured questionnaire was developed and self administered to 115 professional librarians. Hypotheses were tested through t‐test, Pearson chi‐square and ANOVA.FindingsThe results show that the library professionals were not very sensitive about any relationship among these three variables at their workplace. A majority of the professionals perceived that their chief librarians had an autocratic style of leadership and libraries tend to adopt an achievement and bureaucratic culture. Most of the library professionals seemed to be highly committed with their organizations. It means that they favored result‐oriented culture.Research limitationsThe research was limited to university libraries in Pakistan's province of Punjab and federal capital Islamabad.Originality/valueThe study is useful to understand leadership style, organizational culture and job commitment in university libraries.
Conducting focus groups with library staff: best practices and participant perceptions
Authors: Mellinger Margaret , Chau May 
Published: May 2010

PurposeThe purpose of this paper is to describe a process of designing a focus group study for library staff, and to present a method for analyzing and interpreting focus group data. In addition, the paper aims to report on participants' perceptions of the focus group experience.Design/methodology/approachFocus group methodology was used to gather staff responses. An online survey was used to gauge staff perceptions of the focus groups.FindingsFocus groups with library staff are a productive way to gather issues and trends for library management to address. In addition, it seems from the follow up survey that participating in focus groups benefits staff morale and engagement, if best practices are employed.Originality/valueWhile there are many articles about using focus groups to understand library users and their needs, there are few articles about employing this methodology with library staff. This paper fills some of the gaps.
Change is a constant requiring a coach
Authors: Rolfe Jo 
Published: May 2010

PurposeThe purpose of this paper is to assess individualized and team coaching as a tool for empowering library employees to respond to the constantly changing needs of customers.Design/methodology/approachThe paper documents a variety of strategic models and approaches to coaching that can be adapted for practical implementation with the aim of promoting positive change in employee skills and behaviors.FindingsTo remain competitive libraries must cultivate intrinsically motivated, high‐performance employees inspired by a culture that puts people first. Coaching is a methodology that can generate passion for the organizational vision and goals.Research limitations/implicationsAnalysis of the theoretical premise for implementing a coaching program at the public library branch level is largely derived from referenced literature from the corporate domain. Evaluation of coaching goals should be conducted using qualitative and quantitative research methods decided upon during strategic planning for the coaching program.Originality/valueThe paper highlights that coaching has a multiplicity of benefits that address a renewed sense of urgency for library staff development, retention and succession management.