bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the chromatin interactome of microRNA genes
Authors: Chen Dijun , Fu Liang-Yu , Zhang Zhao , Li Guoliang , Zhang Hang , Jiang Li , Harrison Andrew P. , Shanahan Hugh P. , Klukas Christian , Zhang Hong-Yu , Ruan Yijun , Chen Ling-Ling , Chen Ming 
Published: December 2013

AbstractOur knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II–associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA–target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR–MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
Diverge from the norm
Authors: Li Zhen , Qin Anjun 
Published: December 2013

Abstract
It has been a general belief that luminophore aggregation normally quenches light emission. The conceptualization of ‘aggregation-induced emission’ (AIE) breaks this ‘common law’ and provides a new stage for the exploration of practically useful light-­emitting materials. The booming development in this emerging area of research has recently been showcased at the First International Symposium on Aggregation-Induced Emission (ISAIE) held in Wuhan, China.
Past, present and future of the carbon cycle
Authors: Xie Zhenghui , Zeng Ning , Wang Huijun , Lin Zheng , Tian Xiangjun , Jia Binghao 
Published: December 2013

AbstractThe recent Ninth International Carbon Dioxide Conference (ICDC9) held in Beijing highlighted the importance and urgency of global carbon management, research challenges, and recent efforts made by Chinese scientists in this area.
Use of a Novel Laparoscopic Gastrostomy Technique in Children With Severe Epidermolysis Bullosa
Authors: Patel Kamlesh , Wells Jonathan , Jones Rosie , Browne Fiona , Moss Celia , Parikh Dakshesh 
Published: December 2013

ABSTRACTObjective:Supplementing nutrition in children with severe epidermolysis bullosa (EB) is challenging because of skin and mucosal fragility. Percutaneous endoscopic gastrostomy is contraindicated in EB, whereas more invasive open surgical gastrostomy placement can be complicated by chronic leakage. The aim of the study was to review the efficacy and acceptability, in children with severe EB, of our modified 2‐port laparoscopic approach using the Seldinger technique with serial dilatation and tube insertion through a peel‐away sheath.Methods:Retrospective review of children with EB who underwent laparoscopic feeding gastrostomy at our centre since 2009.Results:Seven children (6 severe generalised recessive dystrophic EB, 1 non‐Herlitz junctional EB; 2 girls, 5 boys) underwent modified laparoscopic gastrostomy placement at median age 4.85 years (range 1.0–8.8), with fundoplication for gastro‐oesophageal reflux in 1 case, with follow‐up for 0.3 to 3.9 years. The procedure was well tolerated with oral feeds usually given after 4 hours and whole protein gastrostomy feeds within 24 hours in 6 patients. Improved growth was reflected in mean weight and height z scores: −1.36 (range −2.6 to 0.5) to −0.61 (range −2.34 to 2.0) and −1.09 (range −2.42 to 1.0) to 0.71 (range −1.86 to 1.0), respectively. Postoperatively, 5 patients experienced minor local complications: minimal leakage without skin damage in 3 and transient peristomal granulation rapidly responsive to topical treatment in 2; this followed acute gastrostomy site infection in 1. There was no leakage after the immediate postoperative period.Conclusions:We conclude that our less‐invasive laparoscopic gastrostomy technique is effective and better tolerated in children with severe EB, at least in the medium term, than open gastrostomy placement. Longer follow‐up is required.
Fecal Transplant for Recurrent Clostridium difficile Infection in Children With and Without Inflammatory Bowel Disease
Authors: Russell George H. , Kaplan Jess L. , Youngster Ilan , Baril‐Dore Mariah , Schindelar Lili , Hohmann Elizabeth , Winter Harland S. 
Published: December 2013

ABSTRACTTen children at our institution received single‐infusion fecal microbiome transplant (FMT) using healthy, related screened donor stool to treat recurrent Clostridium difficile infection (RCDI) via nasogastric tube (2 patients) or colonoscopic delivery. Nine of the 10 (90%) children had resolution of their symptoms after a single‐infusion FMT with follow‐up of 1 month to 4 years. No concerning related adverse events were recognized during short‐ or long‐term follow‐up. Three of these children had concomitant inflammatory bowel disease and 2 of these 3 (66%) patients cleared RCDI with no clinical change in their underlying inflammatory bowel disease clinical activity as assessed by Physician's Global Assessment. All of the patients who had clinical improvement of gastrointestinal symptoms of RCDI while treated with antibiotics had lasting return of baseline health after FMT.
Variability of Resting Energy Expenditure in Infants and Young Children With Intestinal Failure–Associated Liver Disease
Authors: Duro Debora , Mitchell Paul D. , Mehta Nilesh M. , Bechard Lori J. , Yu Yong‐Ming , Jaksic Tom , Duggan Christopher 
Published: December 2013

ABSTRACTObjective:The aim of the study was to determine, in a cohort of young children with intestinal failure (IF), whether the estimates of basal metabolic rate (BMR) by standard equations can approximate measured resting energy expenditure (REE) by indirect calorimetry (IC).Methods:IC was performed using the dilutional canopy technique. REE measurements were compared with standard, age‐based estimation equations (World Health Organization) for BMR. Subjects were classified as hypermetabolic (REE > 110% BMR), hypometabolic (REE < 90% BMR), or normal (REE = 90%–110% BMR).Results:Twenty‐eight IF patients (11 girls, 17 boys) had an underlying diagnosis of necrotizing enterocolitis (n = 10) or a congenital gastrointestinal defect (n = 18). Median age was 5.3 months. Median interquartile range (IQR) REE was 46 (42–58) kcal · kg−1 · day−1. Median (IQR) total energy intake provided 209% (172%–257%) of REE, with parenteral nutrition providing 76% (23%) of total energy intake. REE was variable, with 39% (n = 11) of measurements hypermetabolic, 39% (n = 11) hypometabolic, and the remaining 21% (n = 6) normal. Although REE was well correlated with estimated BMR (r = 0.82, P < 0.0001), estimated BMR was not consistently an adequate predictor of REE. BMR over‐ or underestimated REE by >10 kcal · kg−1 · day−1 in 15 of 28 (54%) patients. REE was not significantly correlated with severity of liver disease, nutritional status, total energy intake, or gestational age.Conclusions:Energy expenditure is variable among children with IF and IF‐associated liver disease, with approximately 80% of our cohort exhibiting either hypo‐ or hypermetabolism. Standard estimation equations frequently do not correctly predict individual REE. Longitudinal studies of energy expenditure and body composition may be needed to guide provision of nutrition regimens.
RNA Structure Refinement using the ERRASER-Phenix pipeline
Authors: Chou Fang-Chieh , Echols Nathaniel , Terwilliger Thomas C. , Das Rhiju 
Published: December 2013

SummaryThe final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by Rfree). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).
Analyses of Tomato Fruit Brightness Mutants Uncover Both Cutin-Deficient and Cutin-Abundant Mutants and a New Hypomorphic Allele of GDSL Lipase
Authors: Petit Johann , Bres Cécile , Just Daniel , Garcia Virginie , Mauxion Jean-Philippe , Marion Didier , Bakan Bénédicte , Joubès Jérôme , Domergue Frédéric , Rothan Christophe 
Published: December 2013

Abstract
The cuticle is a protective layer synthesized by epidermal cells of the plants and consisting of cutin covered and filled by waxes. In tomato (Solanum lycopersicum) fruit, the thick cuticle embedding epidermal cells has crucial roles in the control of pathogens, water loss, cracking, postharvest shelf-life, and brightness. To identify tomato mutants with modified cuticle composition and architecture and to further decipher the relationships between fruit brightness and cuticle in tomato, we screened an ethyl methanesulfonate mutant collection in the miniature tomato cultivar Micro-Tom for mutants with altered fruit brightness. Our screen resulted in the isolation of 16 glossy and 8 dull mutants displaying changes in the amount and/or composition of wax and cutin, cuticle thickness, and surface aspect of the fruit as characterized by optical and environmental scanning electron microscopy. The main conclusions on the relationships between fruit brightness and cuticle features were as follows: (1) screening for fruit brightness is an effective way to identify tomato cuticle mutants; (2) fruit brightness is independent from wax load variations; (3) glossy mutants show either reduced or increased cutin load; and (4) dull mutants display alterations in epidermal cell number and shape. Cuticle composition analyses further allowed the identification of groups of mutants displaying remarkable cuticle changes, such as mutants with increased dicarboxylic acids in cutin. Using genetic mapping of a strong cutin-deficient mutation, we discovered a novel hypomorphic allele of GDSL lipase carrying a splice junction mutation, thus highlighting the potential of tomato brightness mutants for advancing our understanding of cuticle formation in plants.
Epidemiology of pemphigus vulgaris in the Northeast China: A 10‐year retrospective study
Authors: Zhu Xiaoling , Pan Jisheng , Yu Zhiming , Wang Yanhua , Cai Limin , Zheng Shuyun 
Published: December 2013

AbstractThe aim of the present study was to evaluate the incidence, epidemiological, clinical and therapeutic features of patients with pemphigus vulgaris in China. We retrospectively investigated a total of 221 patients with pemphigus vulgaris. The parameters including age at diagnosis/onset, sex, diagnostic methods, hospitalizations, side‐effects with different treatments, pemphigus vulgaris‐associated diseases, the therapeutic features and duration of follow up were evaluated. The male : female ratio was 1:1.40. The incidence rate was obviously higher in two age groups, 31–40 years and 41–50 years. The mean age at onset was 44.19 ± 21.45 years. The majority of patients (56.56%) presented the mucocutaneous type. In addition, we found that various doses of corticosteroids (including the mean initial dose, maximum control dose, total dose before reducing and hospitalized total dose) exhibited statistical differences between only corticosteroids and corticosteroids–immunosuppressant groups in mild, moderate and severe pemphigus vulgaris (P < 0.05). Our survey suggested that pemphigus vulgaris most frequently occurred in the 41–50‐year age group in China and the majority of patients manifested mucocutaneous lesions. Importantly, the incidence rate in females was higher than in males. The patients who needed combined immunosuppressant treatment, usually needed higher doses of corticosteroids initially, to control the disease and over the total course of treatment.
Regression and classification methods for nasolabial folds: A possible paradigm for computer‐aided diagnosis of skin diseases
Authors: Lluncor David E. , Belongie Serge , Rullan Peter , Morhenn Vera 
Published: December 2013

AbstractClassification of facial features, for example, nasolabial folds, still relies mainly on clinical assessment, resulting in significant costs because of high intra‐ and interrater variability. Further, diagnosing skin diseases, for example, malignant melanoma, also can present challenges. In an attempt to reduce cost of medical care in future, we determined the utility of methods in image processing and statistical analysis to automatically quantify, for example, the structure of nasolabial folds. To the best of our knowledge, this is the first report of the application of computer technology to grading of nasolabial folds. When classifying severity of wrinkles on a scale of 1–5, the computer achieved an accuracy of 87% compared to the dermatologist, taken as the gold standard. Further, the computer program's capacity to sort the order of wrinkles from least to most wrinkled was 98% as accurate as the clinician(s). We conclude that by using computer technology, nasolabial folds can be categorized almost as accurately as by using grading by dermatologists, suggesting that computer technology may be a useful tool to grade nasolabial folds because a computer is always consistent. We hypothesize that, after additional studies, this technology also may be a useful tool to aid in diagnosing skin diseases.
Evaluation of chimeric DNA vaccines consisting of premembrane and envelope genes of Japanese encephalitis and dengue viruses as a strategy for reducing induction of dengue virus infection‐enhancing antibody response
Authors: Sjatha Fithriyah , Kuwahara Miwa , Sudiro T. Mirawati , Kameoka Masanori , Konishi Eiji 
Published: December 2013

ABSTRACTNeutralizing antibodies induced by dengue virus (DENV) infection show viral infection‐enhancing activities at sub‐neutralizing doses. On the other hand, preimmunity against Japanese encephalitis virus (JEV), a congener of DENV, does not increase the severity of DENV infection. Several studies have demonstrated that neutralizing epitopes in the genus Flavivirus are mainly located in domain III (DIII) of the envelope (E) protein. In this study, chimeric premembrane and envelope (prM‐E) gene‐based expression plasmids of JEV and DENV1 with DIII substitution of each virus were constructed for use as DNA vaccines and their immunogenicity evaluated. Sera from C3H/He and ICR mice immunized with a chimeric gene containing DENV1 DIII on a JEV prM‐E gene backbone showed high neutralizing antibody titers with less DENV infection‐enhancing activity. Our results confirm the applicability of this approach as a new dengue vaccine development strategy.
Architecture, Economic Imaginaries and Urban Politics: The Office Tower as Socially Classifying Device
Authors: Grubbauer Monika 
Published: December 2013

AbstractIn recent studies on the role of architecture in urban restructuring, city marketing and the related struggles for meaning, there has been a focus on high‐profile architects and iconic architecture. In this article I wish to examine architecture and building types as ‘socially signifying devices’, in order to take more everyday buildings and their images into account as well. UsingVienna as a case study, I explore how the commercial office tower is utilized to represent the internationalization of the local economy and render new urban political‐economic strategies socially meaningful. This is done by examining recent shifts in urban policy, and the means, channels and practices of discursive and visual representation of the local office architecture. Connecting the concept of economic imaginaries from cultural political economy (CPE) with a sociological approach to building types, I argue that economic imaginaries gain in plausibility if they are discursively and visually anchored in urban space. However, it is also shown that this kind of spatialization of new economic imaginaries is constructed on a selective visual representation of buildings: the assignment of international economic activities to local office towers is revealed to be only partially true in the case ofVienna.
Protecting Sydney's Peri‐Urban Agriculture: Moving beyond a Housing/Farming Dichotomy
Authors: JAMES SARAH W. 
Published: December 2013

AbstractIn Australia, as in other Western countries, peri‐urban farmland is increasingly being considered a public good, contributing to urban sustainability and climate change mitigation. To retain local food production, advocates have called for the implementation of farmland protection policies that restrict urban development, such as exclusion zoning. Many such policies have been abandoned due to protests, often from the very people the policies are ostensibly intended to protect – farmers. Examining the failure of Sydney's latest ‘green zones’ through a political ecology lens, this paper challenges the prevailing narrative that these protests indicate a lack of community support for the ideal of farmland protection. The failure of the green zones was one of political process, specifically the lack of consultation with Sydney's culturally and linguistically diverse small‐scale farmers, rather than community rejection of the principle of protection. Interview responses from farmers suggest that a bottom‐up approach to policy‐making would have yielded alternative and more successful approaches to maintaining farming on the fringe. This paper concludes that ensuring small‐scale farmers have access to and agency in the environmental decision‐making process generates options for farmland protection policy that move beyond a housing‐versus‐farming dichotomy.
Coupling Hydrotoponymy and GIS Cartography: A Case Study of Hydrohistorical Issues in Urban Groundwater Systems, Porto, NW Portugal
Authors: FREITAS LILIANA , AFONSO MARIA JOSÉ , DEVY‐VARETA NICOLE , MARQUES JOSÉ MANUEL , GOMES ALBERTO , CHAMINÉ HELDER I. 
Published: December 2013

AbstractThe aim of this multidisciplinary study is to retrospectively examine hydrohistorical issues, namely hydrogeographic, hydrotoponymical and hydrogeological features, in order to assess the evolution of the Porto urban groundwater system (NW Portugal). To achieve these goals, the comparison of two main field inventories in a large urban region was performed by (i) historical mapping of sources and groundwater data from scientific reports spanning the late 17th century to the early 20th; and (ii) hydrogeologic and hydrotoponymical field inventory performed under current conditions. These field inventories permitted the location of springs, dug wells, fountains, public washing places and underground water galleries, which collected groundwater to supply the population of Porto until the early 20th century. This study also allowed the development of a hydrotoponymical classification for urban areas and a field hydrotoponymical inventory data sheet. This research integrated several techniques based on historical hydrogeography, hydrogeology and urban geosciences. The results of the field inventories were combined into both a database and a Geographical Information System (GIS) platform. This unified methodology allowed a cross‐check and analysis of several levels of information, namely hydrotoponymy, hydroclimatology, hydrogeology, structural geology and geomorphology. This perspective led to an assessment of the evolution of the quality of water resources in large urban areas over time. In addition, the role of hydrotoponymical features is presented in order to support the hydrogeological conceptual model for large urbanised areas.
Directions in Reshaping Accountability Mechanisms in Multilateral Development Banks and Other Organizations
Authors: Nanwani Suresh 
Published: December 2013

AbstractThis article focuses on directions in reshaping accountability mechanisms in multilateral development banks and other organizations. The term ‘accountability mechanisms’ refers to avenues for private individuals and groups to file claims against the institution for redress of their grievance on poorly designed and/or implemented projects. Since 1993, accountability mechanisms have, over the years, been revised, updated or replaced. This article highlights the salient developments in reshaping accountability mechanisms and concludes with the directions taken and their impact on other institutions and development financiers in adopting similar mechanisms.
Reasons behind Greek problem drug users' decisions to quit using drugs and engage in treatment of their own volition: sense of self and the Greek filotimo
Authors: Fotopoulou Maria 
Published: December 2013

AbstractAimsThe aim of this study was to explore Greek problem drug users' perceptions of the reasons that led them to quit using drugs and engage in treatment of their own volition.DesignQualitative semi‐structured in‐depth interviews.SettingTwo state drug agencies in Thessaloniki, Greece.ParticipantsA total of 40 adult problem drug‐using men and women participated in the study.MeasurementsParticipants were asked to reflect on their decisions to wean themselves from drugs and enter treatment.FindingsParticipants reported that their decisions centred on the re‐conceptualization of the drug‐using community and their membership in it, the desire to restore aspects of identities that were deemed to be spoiled, and finally memories of their drug‐free selves. The importance of the distinctively Greek notion of filotimo in this discussion is highlighted.ConclusionsPrimarily in relation to filotimo (a concept that represents a complex array of virtues that regulates behaviour towards one's family), the desire to restore one's spoiled identity plays a pivotal role in Greek problem drug users' decisions to cease drug use and engage in treatment.