bluuebunny/crossref_metadata_2025_split huggingface dataset:
Petroleum crude oil analysis using low‐temperature plasma mass spectrometry
Authors: Benassi Mario , Berisha Arton , Romão Wanderson , Babayev Elbay , Römpp Andreas , Spengler Bernhard 
Published: March 2013

RATIONALEThe analysis of crude oil is a challenging task due to sample complexity. In mass spectrometry, several ionization techniques can be used to perform this task. Herein, we report the use of an atmospheric pressure low‐temperature plasma (LTP) probe to desorb and ionize compounds of petroleum crude oil from different sources and residual fuel oil standard reference materials (SRMs). LTP is used to perform rapid screening of low molecular weight and relatively volatile components enabling characterization and differentiation of crude oil samples relying solely on mass spectrometric data.METHODSCrude oil samples were analyzed without sample preparation or dilution directly from sampling surfaces of different materials such as polytetrafluorethylene, glass and polyethylene. Analyses were performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS) with high mass accuracy and high resolving power of 400 000 at m/z 400 to estimate the elemental composition of the ions produced by LTP. Principal components analysis (PCA) was performed on the LTP data for statistical analysis.RESULTSLTP was found to generate positive ions of lower mass compounds of low to moderate polarity. Three‐dimensional PCA plots efficiently differentiated between SRMs and Azerbaijan crude oil samples. Standards of alkanes, nitrogen heterocycles, sulfur heterocycles, hydrocarbon polycyclic aromatics and saturated acids were investigated for their behavior in LTP ionization. Alkanes were found to form oxidized products to some extent. The LTP probe worked particularly well in the characterization of sulfur compounds.CONCLUSIONSLTP ionization of crude oils was found to advantageously complement analysis by electrospray ionization. The LTP probe in combination with miniaturized mass spectrometers has the potential to provide direct composition analysis and source identification of crude oil contaminations in the future. Copyright © 2013 John Wiley & Sons, Ltd.
Gauge threshold corrections for $ \mathcal{N}=2 $ heterotic local models with flux, and mock modular forms
Authors: Carlevaro Luca , Israël Dan 
Published: March 2013

AbstractWe determine threshold corrections to the gauge couplings in local models of$ \mathcal{N}=2 $smooth heterotic compactifications with torsion, given by the direct product of a warped Eguchi-Hanson space and a two-torus, together with a line bundle. Using the worldsheet cft description previously found and by suitably regularising the infinite target space volume divergence, we show that threshold corrections to the various gauge factors are governed by the non-holomorphic completion of the Appell-Lerch sum. While its holomorphic Mock-modular component captures the contribution of states that localise on the blown-up two-cycle, the non-holomorphic correction originates from non-localised bulk states. We infer from this analysis universality properties for$ \mathcal{N}=2 $heterotic local models with flux, based on target space modular invariance and the presence of such non-localised states. We finally determine the explicit dependence of these one-loop gauge threshold corrections on the moduli of the two-torus, and by S-duality we extract the corresponding string-loop and E1-instanton corrections to the Kähler potential and gauge kinetic functions of the dual type i model. In both cases, the presence of non-localised bulk states brings about novel perturbative and non-perturbative corrections, some features of which can be interpreted in the light of analogous corrections to the effective theory in compact models.
On the tuning and the mass of the composite Higgs
Authors: Panico Giuliano , Redi Michele , Tesi Andrea , Wulzer Andrea 
Published: March 2013

Abstract

We analyze quantitatively the tuning of composite Higgs models with partial compositeness and its interplay with the predicted Higgs mass. In this respect we identify three classes of models, characterized by different quantum numbers of the fermionic colored resonances associated with the top quark, the so-called top partners. The main result of this classification is that in all models with moderate tuning a light Higgs, of 125 GeV mass, requires the presence of light top partners, around 1 TeV. The minimal tuning is comparable to the one of the most attractive supersymmetric models in particular the ones realizing Natural SUSY. This gives further support to an extensive program of top partners searches at the LHC that can already probe the natural region of composite Higgs models.
Investigation of the bacterial retting community of kenaf (Hibiscus cannabinus) under different conditions using next-generation semiconductor sequencing
Authors: Visi David K , D’Souza Nandika , Ayre Brian G , Webber III Charles L , Allen Michael S 
Published: March 2013

Abstract
The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 h from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources and having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria established themselves and in addition their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.
Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus
Authors: Chung Daehwan , Farkas Joel , Westpheling Janet 
Published: March 2013

Abstract
We show that a previously annotated hypothetical protein is the transposase of a new and active IS element, ISCahy1, widespread in Caldicellulosiruptor species. Transposition generated an 11-bp direct repeat at the insertion site in Caldicellulosiruptor hydrothermalis, suggesting a cut-and-paste mechanism. The discovery of an active insertion sequence in Caldicellulosiruptor species led to a survey of potential IS elements in the genome sequences of eight Caldicellulosiruptor species that identified several new elements, including one novel to this genus.
Sexual and reproductive health and HIV services: Integrating HIV/AIDS and cervical cancer prevention and control
Authors: Belhadj Hedia , Rasanathan Jennifer J.K. , Denny Lynette , Broutet Nathalie 
Published: March 2013

AbstractPeople living with HIV are at an increased risk of acquiring HPV and of developing evolutive cervical cancers (women) and penile and anal cancers (men). Low‐cost screening—visual inspection with acetic acid, HPV DNA diagnostics and primary care level treatment, cryotherapy for cervical intraepithelial neoplasia (CIN 2), and primary prevention through HPV vaccination of girls aged 9–13 years—makes the goal of eliminating cervical cancer possible in the long term. Integration of cervical cancer screening and treatment into a sexual and reproductive health service package raises programmatic questions and calls for a continuum of care. The latter is only possible when adequate cytopathology skills and treatment for advanced cancer conditions are available. The present paper highlights the role of member societies of the International Federation of Gynecology and Obstetrics (FIGO) in developing the base for an integrated package that responds to women's sexual and reproductive health needs.
Dual decentralization in China's transitional economy: Welfare regionalism and policy implications for central–local relationship
Authors: Mok Ka Ho , Wu Xiao Fang 
Published: March 2013

Abstract
In the last three decades, China has experienced dual decentralization in transforming its economy, resulting in decentralization and deconcentration in public administration and social service delivery. Under the policy framework of decentralization, particularly when welfare financing has been decentralized to local governments, the emergence of welfare regionalism is evident in China. This paper sets out against this policy context to examine how three local governments in eastern coastal areas in China handle changing labour welfare needs by institutionalizing social and labour protection measures to meet the local needs instead of implementing central policy. With particular reference to examine why regional variations exist in welfare provision even though the socio-economic development status is similar in these areas, this paper shows how different forms of capitals, government's governance style and diversity of industries have affected welfare arrangements for labour in China.
High-resolution metabolic mapping of cell types in plant roots
Authors: Moussaieff Arieh , Rogachev Ilana , Brodsky Leonid , Malitsky Sergey , Toal Ted W. , Belcher Heather , Yativ Merav , Brady Siobhan M. , Benfey Philip N. , Aharoni Asaph 
Published: March 2013

Significance
Analyzing metabolite composition offers a powerful tool for understanding gene function and regulatory processes. Here, we present nontargeted metabolomics assays of five Arabidopsis GFP-tagged lines representing core cell types in the plant root, providing a metabolic map of an organ, composed of its different cell types. Fifty metabolites were putatively identified. The most prominent groups were glucosinolates, phenylpropanoids, and dipeptides. Metabolites were differentially abundant across root cell types and in many cases, this abundance did not correlate with transcript expression, suggesting non–cell-autonomous mechanisms responsible for their targeted localization.
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
Authors: Grove Laurie E. , Hall David R. , Beglov Dmitri , Vajda Sandor , Kozakov Dima 
Published: March 2013

Abstract
Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted.
Availability: FTFlex is freely available as a web-based server at http://ftflex.bu.edu/.
Contact: vajda@bu.edu or midas@bu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PLncDB: plant long non-coding RNA database
Authors: Jin Jingjing , Liu Jun , Wang Huan , Wong Limsoon , Chua Nam-Hai 
Published: March 2013

Abstract
Summary: Plant long non-coding RNA database (PLncDB) attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. Currently, our PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community. This database will be regularly updated with new plant genome when available so as to greatly facilitate future investigations on plant lncRNAs.
Availability: PLncDB is freely accessible at http://chualab.rockefeller.edu/gbrowse2/homepage.html and all results can be downloaded for free at the website.
Contact: chua@rockefeller.edu
Specificity and affinity quantification of protein–protein interactions
Authors: Yan Zhiqiang , Guo Liyong , Hu Liang , Wang Jin 
Published: March 2013

AbstractMotivation: Most biological processes are mediated by the protein–protein interactions. Determination of the protein–protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein–protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein–protein complexes. The scoring function of protein–protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein–protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein–protein complex against competitive ones.Results: We developed a scoring function (named as SPA-PP, specificity and affinity of the protein–protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein–protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein–protein structure and affinity.Availability: The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.Contact: jin.wang.1@stonybrook.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Clinical utility and prognostic value of left atrial volume assessment by cardiovascular magnetic resonance in non‐ischaemic dilated cardiomyopathy
Authors: Gulati Ankur , Ismail Tevfik F. , Jabbour Andrew , Ismail Nizar A. , Morarji Kishen , Ali Aamir , Raza Sadaf , Khwaja Jahanzaib , Brown Tristan D.H. , Liodakis Emmanouil , Baksi Arun J. , Shakur Rameen , Guha Kaushik , Roughton Michael , Wage Ricardo , Cook Stuart A. , Alpendurada Francisco , Assomull Ravi G. , Mohiaddin Raad H. , Cowie Martin R. , Pennell Dudley J. , Prasad Sanjay K. 
Published: March 2013

AimsEchocardiographic studies have shown that left atrial volume (LAV) predicts adverse outcome in small heart failure (HF) cohorts of mixed aetiology. However, the prognostic value of LAV in non‐ischaemic dilated cardiomyopathy (DCM) is unknown. Cardiovascular magnetic resonance (CMR) allows accurate and reproducible measurement of LAV. We sought to determine the long‐term prognostic significance of LAV assessed by CMR in DCM.Methods and resultsWe measured LAV indexed to body surface area (LAVi) in 483 consecutive DCM patients referred for CMR. Patients were prospectively followed up for a primary endpoint of all‐cause mortality or cardiac transplantation. During a median follow‐up of 5.3 years, 75 patients died and 9 underwent cardiac transplantation. After adjustment for established risk factors, LAVi was an independent predictor of the primary endpoint [hazard ratio (HR) per 10 mL/m2 1.08; 95% confidence interval (CI) 1.01–1.15; P = 0.022]. LAVi was also independently associated with the secondary composite endpoints of cardiovascular mortality or cardiac transplantation (HR per 10 mL/m2 1.11; 95% CI 1.04–1.19; P = 0.003), and HF death, HF hospitalization, or cardiac transplantation (HR per 10 mL/m2 1.11; 95% CI 1.04–1.18; P = 0.001). The optimal LAVi cut‐off value for predicting the primary endpoint was 72 mL/m2. Patients with LAVi >72 mL/m2 had a three‐fold elevated risk of death or transplantation (HR 3.00; 95% CI 1.92–4.70; P < 0.001). LAVi provided incremental prognostic value for the prediction of transplant‐free survival (net reclassification improvement 0.17; 95% CI 0.05–0.29; P = 0.002).ConclusionsLAVi is a powerful independent predictor of transplant‐free survival and HF outcomes in DCM. Assessment of LAV improves risk stratification in DCM and should be incorporated into routine CMR examination.
Fluid loss, venous congestion, and worsening renal function in acute decompensated heart failure
Authors: Aronson Doron , Abassi Zaid , Allon Eyal , Burger Andrew J. 
Published: March 2013

AimsTo investigate the relationship between decongestion, central venous pressure, and risk of worsening renal function (WRF) in patients with acute decompensated heart failure (ADHF).Methods and resultsWe studied 475 patients with ADHF, of whom 238 underwent right heart catheterization. Right atrial pressure (RAP) was measured at baseline and at 24 h. Net fluid loss was recorded in the first 24 h. WRF was defined as a >0.3 mg/dL increase in serum creatinine above baseline. WRF occurred in 84 catheterized patients (35.3%). There was a weak correlation between baseline RAP and baseline estimated glomerular filtration rate (r = –0.17, P = 0.009). The amount of fluid removed during the first 24 h did not correlate with the magnitude of RAP reduction (r = 0.06, P = 0.35). No association was observed between WRF and baseline RAP [odds ratio (OR) 1.06, 95% confidence interval (CI) 0.80–1.41, P = 0.68 per 6.6 mmHg] or the decrease in RAP (adjusted OR 1.13, 95% CI 0.85–1.49, P = 0.40 per 5.3 mmHg reduction in RAP). In contrast, smaller net fluid loss was strongly associated with increased WRF risk. Compared with the first net fluid loss tertile, the adjusted OR was 1.85 (95% CI 0.90–3.80, P = 0.10) and 2.58 (95% CI 1.27–5.25; P = 0.009) for the second and third tertile, respectively (P for trend <0.0001).ConclusionSmaller early net fluid loss is associated with increased risk for WRF. RAP is not a reliable surrogate of the magnitude of decongestion and risk of WRF. Future research is necessary to determine if targeting congestion may help prevent WRF.
Physical conditions of the gas in an ALMA [C ii]-identified submillimetre galaxy at z = 4.44
Authors: Huynh M. T. , Norris R. P. , Coppin K. E. K. , Emonts B. H. C. , Ivison R. J. , Seymour N. , Smail Ian , Smolčić V. , Swinbank A. M. , Brandt W. N. , Chapman S. C. , Dannerbauer H. , De Breuck C. , Greve T. R. , Hodge J. A. , Karim A. , Knudsen K. K. , Menten K. M. , van der Werf P. P. , Walter F. , Weiss A. 
Published: March 2013

Abstract
We present 12CO(2–1) observations of the submillimetre galaxy ALESS65.1 performed with the Australia Telescope Compact Array (ATCA) at 42.3 GHz. A previous Atacama Large Millimeter Array study of submillimetre galaxies (SMGs) in the Extended Chandra Deep Field South detected [C ii] 157.74 μm emission from this galaxy at a redshift of z = 4.44. No 12CO(2–1) emission was detected but we derive a firm upper limit to the cold gas mass in ALESS65.1 of $M_{\rm gas} &lt; 1.7 \times 10^{10} {\rm M}_{{\odot }}$. The estimated gas depletion time-scale is &lt;50 Myr, which is similar to other high-redshift SMGs, and consistent with z &gt; 4 SMGs being the likely progenitors of massive red-and-dead galaxies at z &gt; 2. The ratio of the [C ii], 12CO and far-infrared luminosities implies a strong far-ultraviolet field of G0 ≳ 103, as seen in Galactic star-forming regions or local ultraluminous infrared galaxies (ULIRGs). The observed $L_{\rm [C {\small {II}}]}/L_{\rm FIR} = 2.3 \times 10^{-3}$ is high compared to local ULIRGs and, combined with $L_{\rm [C {\small {II}}]}/L_{\rm CO} \gtrsim 2700$, it is consistent with ALESS65.1 either having an extended (several kpc) [C ii] emitting region or lower than solar metallicity.
Supernova 2012ec: identification of the progenitor and early monitoring with PESSTO
Authors: Maund J. R. , Fraser M. , Smartt S. J. , Botticella M. T. , Barbarino C. , Childress M. , Gal-Yam A. , Inserra C. , Pignata G. , Reichart D. , Schmidt B. , Sollerman J. , Taddia F. , Tomasella L. , Valenti S. , Yaron O. 
Published: March 2013

Abstract
We present the identification of the progenitor of the Type IIP SN 2012ec in archival pre-explosion Hubble Space Telescope Wide Field Planetary Camera 2 (WFPC2) and Advanced Camera for Surveys Wide Field Channel F814W images. The properties of the progenitor are further constrained by non-detections in pre-explosion WFPC2 F450W and F606W images. We report a series of early photometric and spectroscopic observations of SN 2012ec. The r′-band light curve shows a plateau with $M_{r^{\prime }}=-17.0$. The early spectrum is similar to the Type IIP SN 1999em, with the expansion velocity measured at Hα absorption minimum of −11 700 km s−1 (at 1 d post-discovery). The photometric and spectroscopic evolution of SN 2012ec shows it to be a Type IIP SN, discovered only a few days post-explosion (&lt;6 d). We derive a luminosity for the progenitor, in comparison with MARCS model spectral energy distributions, of $\log {L/\text{L}}_{\odot } = 5.15\pm 0.19$, from which we infer an initial mass range of 14–22 M⊙. This is the first SN with an identified progenitor to be followed by the Public ESO Spectroscopic Survey of Transient Objects (PESSTO).
Dynamics of gas and dust clouds in active galactic nuclei
Authors: Plewa P. M. , Schartmann M. , Burkert A. 
Published: March 2013

Abstract
We analyse the motion of single optically thick clouds in the potential of a central mass under the influence of an anisotropic radiation field ∼|cos (θ)|, a model applicable to the inner region of active galactic nuclei. Resulting orbits are analytically soluble for constant cloud column densities. All stable orbits are closed, although they have non-trivial shapes. Furthermore, there exists a stability criterion in the form of a critical inclination, which depends on the luminosity of the central source and the column density of the cloud.