bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional networks driving enhancer function in the CFTR gene
Authors: Kerschner Jenny L. , Harris Ann 
Published: June 2012

A critical cis-regulatory element for the CFTR (cystic fibrosis transmembrane conductance regulator) gene is located in intron 11, 100 kb distal to the promoter, with which it interacts. This sequence contains an intestine-selective enhancer and associates with enhancer signature proteins, such as p300, in addition to tissue-specific TFs (transcription factors). In the present study we identify critical TFs that are recruited to this element and demonstrate their importance in regulating CFTR expression. In vitro DNase I footprinting and EMSAs (electrophoretic mobility-shift assays) identified four cell-type-selective regions that bound TFs in vitro. ChIP (chromatin immunoprecipitation) identified FOXA1/A2 (forkhead box A1/A2), HNF1 (hepatocyte nuclear factor 1) and CDX2 (caudal-type homeobox 2) as in vivo trans-interacting factors. Mutation of their binding sites in the intron 11 core compromised its enhancer activity when measured by reporter gene assay. Moreover, siRNA (small interfering RNA)-mediated knockdown of CDX2 caused a significant reduction in endogenous CFTR transcription in intestinal cells, suggesting that this factor is critical for the maintenance of high levels of CFTR expression in these cells. The ChIP data also demonstrate that these TFs interact with multiple cis-regulatory elements across the CFTR locus, implicating a more global role in intestinal expression of the gene.
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion
Authors: Zhang Chao , Knyazev Denis G. , Vereshaga Yana A. , Ippoliti Emiliano , Nguyen Trung Hai , Carloni Paolo , Pohl Peter 
Published: June 2012

Fast lateral proton migration along membranes is of vital importance for cellular energy homeostasis and various proton-coupled transport processes. It can only occur if attractive forces keep the proton at the interface. How to reconcile this high affinity to the membrane surface with high proton mobility is unclear. Here, we tested whether a minimalistic model interface between an apolar hydrophobic phase (
n
-decane) and an aqueous phase mimics the biological pathway for lateral proton migration. The observed diffusion span, on the order of tens of micrometers, and the high proton mobility were both similar to the values previously reported for lipid bilayers. Extensive ab initio simulations on the same water/
n
-decane interface reproduced the experimentally derived free energy barrier for the excess proton. The free energy profile
G

H
+

adopts the shape of a well at the interface, having a width of two water molecules and a depth of 6 ± 2
RT
. The hydroniums in direct contact with
n
-decane have a reduced mobility. However, the hydroniums in the second layer of water molecules are mobile. Their in silico diffusion coefficient matches that derived from our in vitro experiments, (5.7 ± 0.7) × 10
-5
cm
2
s
-1
. Conceivably, these are the protons that allow for fast diffusion along biological membranes.
Plasma decay in air and O2 after a high-voltage nanosecond discharge
Authors: Aleksandrov N L , Anokhin E M , Kindysheva S V , Kirpichnikov A A , Kosarev I N , Nudnova M M , Starikovskaia S M , Starikovskii A Yu 
Published: June 2012

Abstract
This paper presents the results of experimental and theoretical studies of an afterglow in room temperature air and O2 excited by a high-voltage nanosecond discharge for pressures between 1 and 10 Torr. We measured time-resolved electron density by a microwave interferometer for initial electron densities in the range (2–3) × 1012 cm−3. Discharge uniformity was investigated by optical methods. The balance equations for charged particles and electron temperature were numerically solved to describe the temporal evolution of the densities of electrons and ions in the discharge afterglow. It was shown that the loss of electrons is governed by dissociative and three-body electron recombination with

ions under the conditions considered. Good agreement between the calculated and measured electron density histories could be obtained only when the rate of three-body recombination was increased by an order of magnitude and when the dependence of the recombination rate on electron temperature was changed. This could testify that the well-understood mechanism of three-body electron recombination with atomic ions could be noticeably modified in the case of molecular ions.
Liver–intestine cadherin induction by epidermal growth factor receptor is associated with intestinal differentiation of gastric cancer
Authors: Sakamoto Naoya , Oue Naohide , Sentani Kazuhiro , Anami Katsuhiro , Uraoka Naohiro , Naito Yutaka , Oo Htoo Zarni , Hinoi Takao , Ohdan Hideki , Yanagihara Kazuyoshi , Aoyagi Kazuhiko , Sasaki Hiroki , Yasui Wataru 
Published: June 2012

Gastric cancer (GC) is one of the most common malignancies worldwide. The epidermal growth factor receptor (EGFR) molecule is very important in GC progression. To examine the correlation between EGFR and GC‐related genes, we analyzed gene expression profiles of HT‐29 cells treated with EGFR ligands and identified six genes upregulated by epidermal growth factor (EGF) and transforming growth factor (TGF)‐α treatment. Among these, we focused on cadherin 17 (CDH17) encoding liver–intestine cadherin (LI‐cadherin). Expression of LI‐cadherin was induced by both EGF and TGF‐α, as detected by quantitative RT‐PCR and Western blot analysis. A luciferase assay showed that LI‐cadherin promoter activity was enhanced by EGF or TGF‐α in both HT‐29 cells and MKN‐74 GC cells. Immunohistochemical analysis of 152 GC cases showed that out of 58 LI‐cadherin‐positive cases, 24 (41%) cases were also positive for EGFR, whereas out of 94 LI‐cadherin‐negative cases, only 9 (10%) cases were positive for EGFR (P < 0.0001). Double‐immunofluorescence staining revealed that EGFR and LI‐cadherin were coexpressed. Significant correlation was found between LI‐cadherin expression and advanced T grade and N grade. Both EGFR and LI‐cadherin expression were more frequently found in GC cases with an intestinal mucin phenotype than in cases with a gastric mucin phenotype. These results indicate that, in addition to the known intestinal transcription factor caudal type homeobox 2, EGFR activation induces LI‐cadherin expression and participates in intestinal differentiation of GC.
Can abundant colloid exclude oncocytic (Hürthle cell) carcinoma in thyroid fine needle aspiration? Cytohistological correlation of 127 oncocytic (Hürthle cell) lesions
Authors: Yang G. C. H. , Schreiner A. M. , Sun W. 
Published: June 2012

Objective: The objective of the present study was to find out whether the presence or absence of certain cytological features can exclude oncocytic (Hürthle cell) carcinoma in thyroid fine needle aspiration (FNA) to minimize unnecessary surgery.Methods: Over a 17‐year period, 127 hypercellular, oncocyte‐exclusive, lymphocyte‐absent aspirates obtained via ultrasound‐guided FNA with on‐site assessment had histology slides for review. The presence or absence of six cytological features (microfollicular arrangement, discohesive single cells, small cell dysplasia, large cell dysplasia, transgressing blood vessels and colloid) and one histological feature (macrofollicular component) were determined for each case independently by two cytopathologists.Results: Histology showed 12 (9.4%) cases of Hashimoto thyroiditis, 23 (18.1%) oncocytic adenomatoid nodules in nodular goitre, 66 (52.0%) oncocytic adenomas and 26 (20.5%) oncocytic carcinomas (13 minimally invasive without angioinvasion, six minimally invasive with angioinvasion, seven widely invasive). Histologically, a macrofollicular component was present in seven of 26 (26.9%) oncocytic carcinomas, including one case with abundant thin colloid. A microfollicular arrangement, discohesive single cells, small cell dysplasia, large cell dysplasia and transgressing vessels were present in oncocytic carcinoma, oncocytic adenoma and oncocytic adenomatoid nodules in nodular goitre.Conclusions: A macrofollicular component is frequently present in oncocytic carcinoma, oncocytic adenoma and oncocytic adenomatoid nodules in nodular goitre. None of the cytological features studied, including abundant colloid, can exclude oncocytic carcinoma. Oncocytic carcinoma can only be excluded by thorough histological examination of thyroidectomy specimens. A molecular marker is needed to triage oncocytic lesions in thyroid FNA.
A Land System representation for global assessments and land‐use modeling
Authors: van Asselen Sanneke , Verburg Peter H. 
Published: June 2012

AbstractCurrent global scale land‐change models used for integrated assessments and climate modeling are based on classifications of land cover. However, land‐use management intensity and livestock keeping are also important aspects of land use, and are an integrated part of land systems. This article aims to classify, map, and to characterize Land Systems (LS) at a global scale and analyze the spatial determinants of these systems. Besides proposing such a classification, the article tests if global assessments can be based on globally uniform allocation rules. Land cover, livestock, and agricultural intensity data are used to map LS using a hierarchical classification method. Logistic regressions are used to analyze variation in spatial determinants of LS. The analysis of the spatial determinants of LS indicates strong associations between LS and a range of socioeconomic and biophysical indicators of human‐environment interactions. The set of identified spatial determinants of a LS differs among regions and scales, especially for (mosaic) cropland systems, grassland systems with livestock, and settlements. (Semi‐)Natural LS have more similar spatial determinants across regions and scales. Using LS in global models is expected to result in a more accurate representation of land use capturing important aspects of land systems and land architecture: the variation in land cover and the link between land‐use intensity and landscape composition. Because the set of most important spatial determinants of LS varies among regions and scales, land‐change models that include the human drivers of land change are best parameterized at sub‐global level, where similar biophysical, socioeconomic and cultural conditions prevail in the specific regions.
Proximal sensing of the seasonal variability of pasture nutritive value using multispectral radiometry
Authors: Pullanagari R. R. , Yule I. J. , Tuohy M. P. , Hedley M. J. , Dynes R. A. , King W. M. 
Published: June 2012

AbstractThe nutritive value of pasture is an important determinant of the performance of grazing livestock. Proximal sensing of in situ pasture is a potential technique for rapid prediction of nutritive value. In this study, multispectral radiometry was used to obtain pasture spectral reflectance during different seasons (autumn, spring and summer) in 2009–2010 from commercial farms throughout New Zealand. The analytical data set (n = 420) was analysed to develop season‐specific and combined models for predicting pasture nutritive‐value parameters. The predicted parameters included crude protein (CP), acid detergent fibre (ADF), neutral detergent fibre (NDF), ash, lignin, lipid, metabolizable energy (ME) and organic matter digestibility (OMD) using a partial least squares regression analysis. The calibration models were tested by internal and external validation. The results suggested that the global models can predict the pasture nutritive value parameters (CP, ADF, NDF, lignin, ME and OMD) with moderate accuracy (0·64 ≤ r2 ≤ 0·70) while ash and lipid are poorly predicted (0·33 ≤ r2 ≤ 0·40). However, the season‐specific models improved the prediction accuracy, in autumn (0·73 ≤ r2 ≤ 0·83) for CP, ADF, NDF and lignin; in spring (0·61 ≤ r2 ≤ 0·78) for CP and ash; in summer (0·77 ≤ r2 ≤ 0·80) for CP and ash, indicating a seasonal impact on spectral response.
The emergence of shared understanding: applying functional pragmatics to study the requirements development process
Authors: Corvera Charaf Marianne , Rosenkranz Christoph , Holten Roland 
Published: June 2012

AbstractWhile the importance of social interactions and especially communication is generally acknowledged in information systems development and requirements development, there are few studies that investigate communication. Departing from the conceptualisation of information systems development as a language development and formalisation process, we focus on linguistic communication and the development of language‐based shared understanding of requirements. We investigate and analyse the semantic alignment process by which stakeholders achieve shared understanding in requirements development. We adopt Functional Pragmatics and examine how linguistic communication is shaped and regulated during requirements development in an actual project. By developing a pattern for semantic alignment and its use as an analytical lens, we enable a systematic and insightful understanding of communication in information systems development.
Consumer trophic diversity as a fundamental mechanism linking predation and ecosystem functioning
Authors: Hines Jes , Gessner Mark O. 
Published: June 2012

Summary1. Primary production and decomposition, two fundamental processes determining the functioning of ecosystems, may be sensitive to changes in biodiversity and food web interactions.2. The impacts of food web interactions on ecosystem functioning are generally quantified by experimentally decoupling these linked processes and examining either primary production‐based (green) or decomposition‐based (brown) food webs in isolation. This decoupling may strongly limit our ability to assess the importance of food web interactions on ecosystem processes.3. To evaluate how consumer trophic diversity mediates predator effects on ecosystem functioning, we conducted a mesocosm experiment and a field study using an assemblage of invertebrates that naturally co‐occur on North Atlantic coastal saltmarshes. We measured the indirect impact of predation on primary production and leaf decomposition as a result of prey communities composed of herbivores alone, detritivores alone or both prey in combination.4. We find that primary consumers can influence ecosystem process rates not only within, but also across green and brown sub‐webs. Moreover, by feeding on a functionally diverse consumer assemblage comprised of both herbivores and detritivores, generalist predators can diffuse consumer effects on decomposition, primary production and feedbacks between the two processes.5. These results indicate that maintaining functional diversity among primary consumers can alter the consequences of traditional trophic cascades, and they emphasize the role of the detritus‐based sub‐web when seeking key biotic drivers of plant production. Clearly, traditional compartmentalization of empirical food webs can limit our ability to predict the influence of food web interactions on ecosystem functioning.
Development and validation of the Family Meaning of Nursing‐Home Visits Scale
Authors: Tsai Hsiu‐Hsin , Tsai Yun‐Fang , Huang Tzu‐Shin 
Published: June 2012

Aims and objectives.  The purpose of this study was to develop and test a Family Meaning of Nursing‐Home Visits Scale that can be used to assess and document family members’ rationale for visiting nursing home residents.Background.  Understanding the meaning ascribed by families for visiting nursing home residents is necessary to develop intervention programmes that facilitate the quality of families’ nursing home visits. No valid and reliable instrument is available in Taiwan or elsewhere to accurately document the meaning of family visits to nursing home residents.Design.  A cross‐sectional design was used to collect survey data from family members of nursing home residents as the quantitative component of a mixed‐methods study. Items were developed based on qualitative data from our previous research and that of others. This initial pool of items was used to develop and validate the scale.Methods.  The validity of the scale was confirmed by exploratory factor analysis and criterion‐related validity testing. Internal consistency reliability was assessed by Cronbach’s alphas.Results.  Factor analysis yielded a six‐factor final solution (32 items), accounting for 66·76% of the variance. For criterion‐related validity, ‘responsibility for care quality’ was negatively correlated with satisfaction with nursing home caregiving (r = −0·23, p < 0·01) and nursing home rehabilitation activities (r = −0·17, p < 0·05). Cronbach’s α for each subscale ranged from 0·68–0·98, and Cronbach’s α for the total scale was 0·83.Conclusions.  The Family Meaning of Nursing‐Home Visits Scale has acceptable internal consistency reliability, good content validity and acceptable construct validity.Relevance to clinical practice.  The Family Meaning of Nursing‐Home Visits Scale provides nurses and healthcare providers an objective and consistent method to explore the priority of meanings family members assign to nursing home visits. Based on this priority for visiting, interventions could be designed to increase the quality of visits, thus promoting families’ continued incentive to visit in person.
Siblings of individuals with Smith–Magenis syndrome: an investigation of the correlates of positive and negative behavioural traits
Authors: Moshier M. S. , York T. P. , Silberg J. L. , Elsea S. H. 
Published: June 2012

AbstractBackground  Smith–Magenis syndrome (SMS) is a neurodevelopmental disorder that affects approximately one out of 25 000 births worldwide. To date, no research has been conducted to investigate how having an individual with SMS in a family is a positive or negative influence on siblings.Methods  To investigate this question we conducted a study involving 79 siblings and 60 parents of individuals with SMS to assess perceptions of how having a sibling with SMS positively and negative influence siblings' behavioural traits.Results  Our findings show that age of siblings of individuals with SMS was associated with a significant increase in positive behavioural traits and a significant decrease in negative behavioural traits. Additionally, siblings who perceive benefits from having a sibling with SMS demonstrate significantly more positive behavioural traits and significantly fewer negative behavioural traits. Parents accurately assess the changes in sibling behavioural traits with age, and parents who perceive their child as having experienced benefits from the sibling relationship report that siblings demonstrate significantly more positive behavioural traits and significantly fewer negative behavioural traits.Conclusions  Our research shows that although individuals experience difficulties as a result of having a sibling with SMS, overall, siblings tend to fare well and parents appreciate both the positive and negative behavioural effects that result from having a sibling with SMS.
Evaluation of imperfections in silica and chalcogenide glass microspheres using focussed ion beam milling and imaging
Authors: KANE D.M. , CHATER R.J. , MCPHAIL D.S. 
Published: June 2012

AbstractMicrospheres made from optical glasses such as silica and chalcogenide are used as both passive and active optical elements in micro‐optics systems and devices. The homogeneity of the microspheres is crucial to their optical quality and performance in such devices and so it is essential, in optimizing such systems, that techniques with nanometer scale resolution are developed to measure the internal structure and homogeneity of such spheres. In this work an analytical protocol based on focussed ion beam milling, combined with secondary ion and secondary electron imaging, has been developed to study the internal homogeneity of glass microspheres. The results have shown that silica microspheres with diameters of three to five microns, fabricated by a sol–gel method, have internal inhomogeneities and voids that will lead to non‐uniform optical properties. The FIB milling and imaging technique developed has been found to be a very useful method of studying such inhomogeneities, which have been proposed, but never previously observed, in glass microspheres. The FIB based technique has also been used on larger chalcogenide glass (Ga2S3:La2S3) microspheres (diameter of order 70 microns) but no inhomogeneities have been observed at the spatial resolution of a few microns so far achieved for these larger microspheres. This study suggests that the FIB based milling and imaging technique may have potential for quantitative use in the measurement of morphological variations in such systems as well as in the study of aging processes in micron‐sized glass spheres.
Apparent zinc absorption and zinc status of weanling rats fed moderately zinc‐deficient diets enriched with beef tallow or sunflower oil
Authors: Weigand E. , Boesch‐Saadatmandi C. 
Published: June 2012

SummaryThe aim of the study was to compare apparent Zn absorption and Zn status of weanling rats fed diets that differed in Zn level, fat level and fat source. Semi‐synthetic diets, which were about isoenergetic and contained 3% soyabean oil, were supplemented with 7 or 100 mg Zn/kg to create a mild Zn deficiency (LZ) or a high Zn supply (HZ) and with 0 (LF), 22% beef tallow (BT) or 22% sunflower oil (SF) according to a 2 × 3 factorial design of treatments. They were fed ad libitum to 6 × 8 rats for 28 days. Energy intake and growth rates were comparable among the HZ groups. Weight gains in the LZ‐LF, LZ‐BT and LZ‐SF groups averaged 5.54, 4.95 and 4.15 g/day, and apparent Zn absorption averaged 79.4, 60.3 and 48.0 μg Zn/day, respectively, whereas faecal Zn excretion was comparable among these groups. Apparent Zn absorption, and plasma and femur Zn concentrations were lower in the high‐fat groups than in the LF group, possibly due to the high cellulose content of the BT and SF diets. Plasma Zn concentrations were higher in the animals fed the BT‐based than in the SF‐based diets, whereas femur and soft tissue Zn concentrations were comparable among these groups. The differences between the LZ‐BT and LZ‐SF groups in growth rate, Zn absorption rate and Zn status were confirmed in a second experiment. The results indicate that moderately Zn‐deficient diets enriched with SF in relation to BT affect Zn metabolism of weanling rats by a yet unknown mechanism.
Cytokines in human milk and late‐onset breast milk jaundice
Authors: Apaydin Kader , Ermis Bahri , Arasli Mehmet , Tekin Ishak , Ankarali Handan 
Published: June 2012

AbstractBackground:  Maternal milk plays an important role in the development of late‐onset breast milk jaundice (BMJ), possibly due to the unique characteristics of breast milk. The aim of this study was to investigate whether there is a relation between cytokine concentrations in the milk of nursing mothers and BMJ.Methods:  Breast milk samples were collected from breast‐feeding mothers of healthy full‐term neonates, 40 with BMJ and 40 without jaundice. Milk samples were taken between the second and the fourth postpartum week. The concentrations of interleukin (IL)‐1 β, IL‐6, IL‐8, IL‐10, and tumor necrosis factor‐α were measured by flow cytometric bead array.Results:  There were significant differences between the study groups in terms of IL‐1 β concentrations (P= 0.013). Not statistically significant but similar trends were also seen for IL‐10 (P= 0.067) and tumor necrosis factor‐α (P= 0.053) concentrations. However, no significant differences were noted in IL‐6 (P= 0.174) and IL‐8 (P= 0.285) concentrations.Conclusions:  IL‐1 β concentration seems to be increased in milk of mothers whose infants had BMJ. Although the effect of these cytokines on BMJ is unknown, it may cause prolonged jaundice via hepatic uptake, hepatic excretion, conjugation and intestinal absorption.