bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA secondary structure diagrams for very large molecules: RNAfdl
Authors: Hecker Nikolai , Wiegels Tim , Torda Andrew E. 
Published: August 2013

Abstract
Summary: There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 103 bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and produces output in common formats.
Availability and implementation: Source code is available under the GNU General Public License v3.0 at http://sourceforge.net/projects/rnafdl for Linux and similar systems or Windows using MinGW. RNAfdl is implemented in C, uses the Cairo 2D graphics library and offers both command line and graphical user interfaces.
Contact: hecker@rth.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of BRASSINOSTEROID INSENSITIVE1 inArabidopsis
Authors: Di Rubbo Simone , Irani Niloufer G. , Kim Soo Youn , Xu Zheng-Yi , Gadeyne Astrid , Dejonghe Wim , Vanhoutte Isabelle , Persiau Geert , Eeckhout Dominique , Simon Sibu , Song Kyungyoung , Kleine-Vehn Jürgen , Friml Jiří , De Jaeger Geert , Van Damme Daniël , Hwang Inhwan , Russinova Eugenia 
Published: August 2013

AbstractClathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptor-mediated endocytosis.
The value of life and its regional difference in China
Authors: Qin Xuezheng , Li Lixing , Liu Yangyang 
Published: August 2013

PurposeThe purpose of this paper is to estimate the value of a statistical life (VSL) in China using the hedonic wage model, and to explore the regional difference in VSL within the country.Design/methodology/approachUsing the hedonic wage regression, this paper estimates the compensating wage differential for incremental job mortality risk among Chinese workers. The implied VSL is derived for China and its different regions. The data is from the 2005 China inter‐census population survey, consisting of 1.3 million urban and rural workers. The authors also made important improvement in the model specification to explicitly address the missing variable issue in the previous studies.FindingsThe paper results indicate that the industry mortality risk has a significant impact on the wage rate. The implied VSL is 1.81 million RMB, a value substantially higher than previous estimates. The results also suggest a sizable urban‐rural difference, with the urban VSL being 4.3 times higher than the rural estimate. The strong urban‐rural inequality of income could be attributed to the segregation between the urban and rural labor markets.Practical implicationsThe paper findings indicate the importance of reforming the current workers' compensation standard and improving the institutional environment, as well as enhancing the labor protection in the rural labor market.Originality/valueThis paper is the first attempt to estimate the value of life in China using the census based data. The paper results contribute to the growing literature in obtaining comparable VSL estimates in the developing countries.
Plenty of attitude: evaluating measures of attitude toward the site
Authors: Boostrom Robert , Balasubramanian Siva K. , Summey John H. 
Published: August 2013

PurposeResearchers often attempt to assess how different features and content will improve the experience of web site users. One assessment technique is to measure the attitude toward the site. A common version of this measure is the Chen and Wells attitude toward the site scale. The purpose of this paper is to determine if there is a difference in performance between that scale and the less used Bruner and Kumar scale so that researchers might use the better of the two related, but different, published scales.Design/methodology/approachAnalysis is done on survey data from an experiment utilizing three different experimental groups that all completed surveys with both the Chen and Wells and the Bruner and Kumar attitude toward the site scales. Scales are assessed for loading and reliability, as well as measures compared for equivalence within groups and used within partial least squares (PLS) models to compare overall model fit.FindingsIn all tests, the Bruner and Kumar scale is better than, or equivalent to, the Chen and Wells scale in each comparison.Research limitations/implicationsThe research implication is that the Bruner and Kumar scale would be a better choice when selecting scales for future research projects.Originality/valueAlthough Bruner and Kumar had previously performed comparisons of the two scales, in a follow‐up article, this is the first paper to compare the two scales between three different groups and demonstrate how the two different scales would perform within the same conceptual model using PLS structural equation modeling. It will help researchers select the best scale for attitude toward the site.
What are the relationships among Web 2.0, market orientation and innovativeness?
Authors: Palacios‐Marques Daniel , Zegarra Saldaña Alejandro , Enrique Vila Jose 
Published: August 2013

PurposeFirms are adopting Web 2.0 technologies to improve collaboration, participation and communication; however there are few empirical studies testing the impact of this adoption. The purpose of this article is to analyze if there is a linkage amongst market orientation, Web 2.0 adoption and innovativeness.Design/methodology/approachStructural equation modeling was used to test the relationships amongst the variables. A sample of 244 firms of the hospitality industry was used. The theoretical approach is based on the market orientation and innovativeness, concepts, which have been studied by various authors in the literature.FindingsA positive relationship was found between market orientation and Web 2.0 adoption and between Web 2.0 adoption and innovativeness.Research limitations/implicationsThe study was developed in one industry, so in order to generalize the findings, additional testing in other industries should be developed. In addition a longitudinal study is encouraged.Practical implicationsManagers are advised to adopt Web 2.0 technologies to strengthen market orientation behaviors and innovativeness.Originality/valueThis article empirically tested the relationship between market orientation and Web 2.0 adoption and the impact of Web 2.0 adoption on innovativeness. Although some managers and researchers have reported some positive impacts of Web 2.0 on different aspects of the organization, there are still few empirical studies, and the authors contributed to fill this void.
Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade
Authors: Sharma Adrian K. , Becker Jamie W. , Ottesen Elizabeth A. , Bryant Jessica A. , Duhamel Solange , Karl David M. , Cordero Otto X. , Repeta Daniel J. , DeLong Edward F. 
Published: August 2013

SummaryA considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high‐molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.
Vertical partitioning of nitrogen‐loss processes across the oxic‐anoxic interface of an oceanic oxygen minimum zone
Authors: De Brabandere Loreto , Canfield Don E. , Dalsgaard Tage , Friederich Gernot E. , Revsbech Niels Peter , Ulloa Osvaldo , Thamdrup Bo 
Published: August 2013

SummaryWe investigated anammox, denitrification and dissimilatory reduction of nitrite to ammonium (DNRA) activity in the Eastern Tropical South Pacific oxygen minimum zone (OMZ) off northern Chile, at high‐depth resolution through the oxycline into the anoxic OMZ core. This was accompanied by high‐resolution nutrient and oxygen profiles to link changes in nitrogen transformation rates to physicochemical characteristics of the water column. Denitrification was detected at most depths, but anammox was the most active N2‐producing process, while DNRA was not detectable. Anammox and denitrification were mainly active in the anoxic OMZ core while activity was low to not detectable in the oxycline, except in association with an intrusion of OMZ core water. This indicates that continuous exposure to even submicromolar oxygen levels inhibits the processes either directly or through nitrite limitation. Anammox activity did not peak at the oxic‐anoxic boundary but 20–50 m below matching the salinity maximum of the Equatorial Subsurface Water. This suggests that water history plays a major role for anammox activity possibly due to slow growth of anammox bacteria. Denitrification peaked deeper than anammox, likely reflecting a shift in the balance between this process and nitrate reduction to nitrite, governed by the relative availability of nitrate and nitrite.
Pyrosequencing‐based profiling of archaeal and bacterial 16S rRNA genes identifies a novel archaeon associated with black band disease in corals
Authors: Sato Yui , Willis Bette L. , Bourne David G. 
Published: August 2013

SummaryBlack band disease (BBD) is a microbial consortium that creates anoxic, sulfide‐rich microenvironments and kills underlying coral tissues as it rapidly migrates across colonies. Although bacterial communities associated with BBD have been studied extensively, the presence and roles of archaea are unexplored. Using amplicon‐pyrosequencing of 16S ribosomal RNA genes, we investigated the community structure of both archaea and bacteria within microbial lesions of BBD and the less‐virulent precursor stage, ‘cyanobacterial patches’ (CP), affecting the coral Montipora hispida. We detected characteristic shifts in microbial communities during the development of BBD from CP, reflecting microenvironmental changes within lesions. Archaeal profiles in CP suggested a diverse assemblage affiliated with the Thaumarchaeota and Euryarchaeota, similar to communities described for oxic marine environments. In contrast, a novel ribotype, distantly affiliated to the Euryarchaeota, dominated up to 94% of archaeal sequences retrieved from BBD. The physiological characteristics of this dominant archaeal ribotype are unknown because of the novelty of its 16S ribosomal RNA gene sequences; however, their prominent associations with BBD lesions suggest the ability to thrive in the organic‐ and sulfide‐rich anoxic microenvironment characteristic of BBD lesions. Discovery of this novel archaeal ribotype provides new insights into the microbial ecology and aetiology of BBD.
Swimming behaviour and magnetotaxis function of the marine bacterium strain MO‐1
Authors: Zhang Sheng‐Da , Petersen Nikolai , Zhang Wei‐Jia , Cargou Sébastien , Ruan Juanfang , Murat Dorothée , Santini Claire‐Lise , Song Tao , Kato Takayuki , Notareschi Philippe , Li Ying , Namba Keiichi , Gué Anne‐Marie , Wu Long‐Fei 
Published: August 2013

SummaryMagnetotactic bacteria (MTB) have the unique capacity to align and swim along the geomagnetic field lines downward to the oxic–anoxic interface in chemically stratified water columns and sediments. They are most abundant within the first few centimetres of sediments below the water–sediment interface. It is unknown how MTB penetrate into the sediment layer and swim in the pocket water, while their movements are restricted by the alignment along the magnetic field lines. Here we characterized the swimming behaviour of the marine fast‐swimming magnetotactic ovoid bacterium MO‐1.We found that it rotates around and translates along its short body axis to the magnetic north (northward). MO‐1 cells swim forward constantly for a minimum of 1770 μm without apparent stopping. When encountering obstacles, MO‐1 cells squeeze through or swim southward to circumvent the obstacles. The distance of southward swimming is short and inversely proportional to the magnetic field strength. Using a magnetic shielding device, we provide direct evidence that magnetotaxis is beneficial to MO‐1 growth and becomes essential at low cell density. Environmental implications of the fast‐swimming magnetotactic behaviour of magnetococci are discussed.
Glycolytic fast‐twitch muscle fiber restoration counters adverse age‐related changes in body composition and metabolism
Authors: Akasaki Yuichi , Ouchi Noriyuki , Izumiya Yasuhiro , Bernardo Barbara L. , LeBrasseur Nathan K. , Walsh Kenneth 
Published: August 2013

SummaryAging is associated with the development of insulin resistance, increased adiposity, and accumulation of ectopic lipid deposits in tissues and organs. Starting in mid‐life there is a progressive decline in lean muscle mass associated with the preferential loss of glycolytic, fast‐twitch myofibers. However, it is not known to what extent muscle loss and metabolic dysfunction are causally related or whether they are independent epiphenomena of the aging process. Here, we utilized a skeletal‐muscle‐specific, conditional transgenic mouse expressing a constitutively active form of Akt1 to examine the consequences of glycolytic, fast‐twitch muscle growth in young vs. middle‐aged animals fed standard low‐fat chow diets. Activation of the Akt1 transgene led to selective skeletal muscle hypertrophy, reversing the loss of lean muscle mass observed upon aging. The Akt1‐mediated increase in muscle mass led to reductions in fat mass and hepatic steatosis in older animals, and corrected age‐associated impairments in glucose metabolism. These results indicate that the loss of lean muscle mass is a significant contributor to the development of age‐related metabolic dysfunction and that interventions that preserve or restore fast/glycolytic muscle may delay the onset of metabolic disease.
Phenotypic and genetic trends of patellar luxation inDutchFlat‐CoatedRetrievers
Authors: Lavrijsen I. C. M. , Heuven H. C. M. , Breur G. J. , Leegwater P. A. J. , Meutstege F. J. , Hazewinkel H. A. W. 
Published: August 2013

SummaryCanine patellar luxation has been described in various dog breeds, with high prevalence especially in smaller dogs. Most dogs suffer from medial displacement of the patella, although in larger dogs lateral displacement is also seen. A sex predisposition has been described for females. Patellar luxation is considered a polygenic, multifactorial disorder. From 1990 to 2007, in total 3834 Flat‐Coated Retrievers were screened; 23.6% of those animals were affected with patellar luxation. Lateral displacement of the patella was most common in this breed (61% of cases), whereas medial (31% of cases) and lateral and medial (8% of cases) were less common. Unilateral involvement (51% of cases) was just as often observed as was bilateral involvement (49% of cases). Females were more often affected with patellar luxation (30% of all tested females) than were males (17% of all tested males). The heritability of patellar luxation was 0.17 ± 0.03 in this population, and breeding with one affected parent increased the prevalence of patellar luxation in offspring by 45% compared to that with two unaffected parents. Since the start of the screening program, there was an initial decrease from 28% to 18% in incidence, but this stagnated thereafter. The annual average estimated breeding values followed the same pattern. With approximately one quarter of the Dutch Flat‐Coated Retrievers being affected with patellar luxation, this population shows unusually high prevalence compared with reports in other large‐breed dogs. The heritability for patellar luxation in this population was moderate (0.17), indicating that environmental factors play a large role in the manifestation of the disorder. A screening program reduced the prevalence of patellar luxation in this breed, but improvement has recently stagnated. Inclusion of breeding values in the screening program could improve its effectiveness.
Recognition of Similar Objects Using Simulated Prosthetic Vision
Authors: Hu Jie , Xia Peng , Gu Chaochen , Qi Jin , Li Sheng , Peng Yinghong 
Published: August 2013

AbstractDue to the limitations of existing techniques, even the most advanced visual prostheses, using several hundred electrodes to transmit signals to the visual pathway, restrict sensory function and visual information. To identify the bottlenecks and guide prosthesis designing, psychophysics simulations of a visual prosthesis in normally sighted individuals are desirable. In this study, psychophysical experiments of discriminating objects with similar profiles were used to test the effects of phosphene array parameters (spatial resolution, gray scale, distortion, and dropout rate) on visual information using simulated prosthetic vision. The results showed that the increase in spatial resolution and number of gray levels and the decrease in phosphene distortion and dropout rate improved recognition performance, and the accuracy is 78.5% under the optimum condition (resolution: 32 × 32, gray level: 8, distortion: k = 0, dropout: 0%). In combined parameter tests, significant facial recognition accuracy was achieved for all the images with k = 0.1 distortion and 10% dropout. Compared with other experiments, we find that different objects do not show specific sensitivity to the changes of parameters and visual information is not nearly enough even under the optimum condition. The results suggests that higher spatial resolution and more gray levels are required for visual prosthetic devices and further research on image processing strategies to improve prosthetic vision is necessary, especially when the wearers have to accomplish more than simple visual tasks.
Gemtuzumab ozogamicin for treatment of newly diagnosed acute myeloid leukaemia: a systematic review and meta‐analysis
Authors: Kharfan‐Dabaja Mohamed A. , Hamadani Mehdi , Reljic Tea , Pyngolil Rachel , Komrokji Rami S. , Lancet Jeffrey E. , Fernandez Hugo F. , Djulbegovic Benjamin , Kumar Ambuj 
Published: August 2013

SummaryEvidence regarding the efficacy of gemtuzumab ozogamicin (GO) addition to standard induction chemotherapy in newly diagnosed acute myeloid leukaemia (AML) is conflicting. This systematic review aimed to identify and summarize all evidence regarding the benefits and harms of adding GO to conventional chemotherapy for induction treatment of AML. A comprehensive literature search of two databases (PUBMED and Cochrane) from inception up to November 22, 2012, and 4 years of proceedings from four major haematology/oncology conferences was undertaken. Endpoints included benefits (complete remission, relapse‐free, event‐free, and overall survival), and harms (early mortality and incidence of hepatic veno‐occlusive disease/sinusoidal obstructive syndrome). Seven trials (3942 patients) met all inclusion criteria. Addition of GO showed improved relapse‐free [Hazard Ratio (HR) = 0·84 (95% confidence interval (CI) 0·71–0·99)] and event‐free survival [HR = 0·59 (95%CI 0·48–0·74)] but not overall survival [HR = 0·95 (95%CI 0·83–1·08)]. Addition of GO resulted in higher rate of early mortality [Risk Ratio = 1·60 (95%CI 1·07–2·39)]. Improved overall survival was observed in studies using a lower cumulative GO dose (<6 mg/m2) [HR = 0·89 (95%CI 0·81–0·99)]. Addition of GO to conventional chemotherapy as induction therapy may improve relapse‐free and event‐free survival, but does not impact overall survival and significantly increases early mortality in AML.
Mammalian target of rapamycin (mTOR) inhibitor‐associated non‐infectious pneumonitis in patients with renal cell cancer: predictors, management, and outcomes
Authors: Atkinson Bradley J. , Cauley Diana H. , Ng Chaan , Millikan Randall E. , Xiao Lianchun , Corn Paul , Jonasch Eric , Tannir Nizar M. 
Published: August 2013

Objective
To characterise the incidence, onset, management, predictors, and clinical impact of mammalian target of rapamycin (mTOR) inhibitor‐associated non‐infectious pneumonitis (NIP) on patients with metastatic renal cell carcinoma (mRCC).
Patients and Methods
Retrospective review of 310 patients with mRCC who received temsirolimus and/or everolimus between June 2007 and October 2010.
Clinical correlations were made with serial radiological imaging.
Fisher's exact, Wilcoxon rank‐sum, and logistic regression analyses were used to evaluate the association of NIP with demographic or clinical factors.
Log‐rank and Cox proportional hazards regression analyses were used for the time‐to‐event analysis.
Results
NIP occurred in 6% of temsirolimus‐treated and 23% of everolimus‐treated patients. Symptoms included cough, dyspnoea, and fever (median of two and three symptoms per patient, respectively). The median National Cancer Institute Common Toxicity Criteria for Adverse Events pneumonitis grade was 2 for both groups.
Older age and everolimus treatment were predictive of NIP.
Patients who developed NIP had a significantly longer time on treatment (median 4.1 vs 2 months) and overall survival (OS) (median 15.4 vs 7.4 months).
NIP was a predictor of improved OS by multivariate analysis.
Conclusions
There was an increased incidence of NIP in everolimus‐treated patients.
Improved OS in patients who developed NIP is an intriguing finding and should be further investigated. Given the incidence, morbidity, and outcomes seen in patients on everolimus who develop NIP, management should include proactive monitoring and treatment of NIP with the goal of preserving mTOR inhibitor therapy.