bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass spectral characterization of the CWC‐related isomeric dialkyl alkylphosphonothiolates/alkylphosphonothionates under gas chromatography/mass spectrometry conditions
Authors: Karthikraj R. , Sridhar L. , Prabhakar S. , Raju N. Prasada , Murty M. R. V. S. , Vairamani M. 
Published: May 2013

RATIONALEThe isomeric dialkyl alkylphosphonothiolates and dialkyl alkylphosphonothionates are listed as scheduled chemicals of the Chemical Weapons Convention (CWC) implemented by the OPCW. The P–S and P–R bond connectivity has to be correctly identified for the verification of the CWC. The present study demonstrates successful identification of the target isomers by selective fragmentation under electron ionization (EI) or chemical ionization (CI) conditions.METHODSAll the studied isomeric compounds (27 in total) were synthesized in our laboratory using established methods, then analyzed by EI and CI gas chromatography/mass spectrometry (GC/MS) using an Agilent 6890 gas chromatograph equipped with a HP‐5MS capillary column and interfaced to a 5973 N mass‐selective detector. The retention index (RI) values of all the compounds were calculated using Van den Dool's formula. GC/MS/MS and GC/HRMS experiments were also performed using a VG‐Autospec (magnetic sector) and JEOL‐AccuToF (time‐of‐flight) mass spectrometer, respectively.RESULTSThe EI mass spectra of all the compounds had an abundant molecular ion at m/z 182, except in the case of a few selected butyl‐substituted compounds, where this ion was of low abundance. The EI fragmentation pathways include α‐cleavage, McLafferty rearrangement, McLafferty + 1 rearrangement, O/S‐alkyl radical loss, and an alkene loss with a hydrogen shift. The characteristic fragment ions and their relative abundances are significant in elucidating the alkyl group attached to the P/S/O‐atoms as well as the P–S/P = S bond connectivity. The EI and CI mass spectra together with RI values enable unambiguous identification of all the studied isomeric compounds.CONCLUSIONSThe present study highlights the structural characterization of the isomeric phosphonothiolates and phosphonothionates based on their selective EI fragmentation. The assigned fragmentation pathway helps in the assignment of P–S and P–alkyl connectivity in phosphonothiolates and phosphonothionates, consequently the structure of the unknown compounds. The EI mass spectra (27 compounds) of isomeric compounds are immensely useful in the OPCW official proficiency tests and for off‐site analysis. Copyright © 2013 John Wiley & Sons, Ltd.
Peptide dissociation patterns in secondary ion mass spectrometry under large argon cluster ion bombardment
Authors: Gnaser Hubert , Fujii Makiko , Nakagawa Shunichirou , Seki Toshio , Aoki Takaaki , Matsuo Jiro 
Published: May 2013

RATIONALEThe analysis of organic and biological substances by secondary ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three‐dimensional (3D) imaging of such systems became feasible. Large Arn+ cluster ions may constitute a further improvement in this direction.METHODSTo explore this option, large Arn+ cluster ions (with n ~1500 Ar atoms per cluster) were used to investigate the emission of positive secondary ions from two peptide specimens (angiotensin I and bradykinin) by orthogonal time‐of‐flight SIMS using bombarding energies 6, 10 and 14 keV.RESULTSFor both peptides, the protonated molecular ion is observed in the mass spectra. In addition, distinct fragmentation patterns were observed; these indicate that fragment ions under Ar cluster irradiation form primarily via cleavage of bonds along the peptide backbone whereas the rapture of side chains occurs much less frequently. These features appear to be similar to low‐energy collision‐induced dissociation pathways.CONCLUSIONSTentatively, these findings can then be ascribed to the concerted action of the large number of Ar atoms in the impact zone of cluster at the surface: these low‐energy Ar species (with an average energy of few eV) may effect the cleavage of the peptide bonds and lead, eventually, to the emission of the fragment ions. Copyright © 2013 John Wiley & Sons, Ltd.
Minimally invasive fetal therapy for hydropic lung masses: three different approaches and review of the literature
Authors: Baud D. , Windrim R. , Kachura J. R. , Jefferies A. , Pantazi S. , Shah P. , Langer J. C. , Forsey J. , Chaturvedi R. R. , Jaeggi E. , Keating S. , Chiu P. , Ryan G. 
Published: May 2013

ABSTRACTObjectiveTo report three different antenatal therapeutic approaches for fetal lung masses associated with hydrops.MethodsThree prospectively followed cases are described, and all 30 previously published minimally invasive cases of fetal therapy for hydropic lung masses are reviewed.ResultsThree hydropic fetuses with large intrathoracic lung masses presented at 17, 25 and 21 weeks of gestation, respectively. An aortic feeding vessel was identified in each case and thus a bronchopulmonary sequestration (BPS) was suspected. Under ultrasound guidance, the feeding vessel was successfully occluded with interstitial laser (Case 1), radiofrequency ablation (RFA) (Case 2) and thrombogenic coil embolization (Case 3). Complete (Cases 1 and 2) or partial (Case 3) resolution of the lung mass and hydrops was observed. A healthy infant was born at term after laser therapy (Case 1), and the involved lung lobe was resected on day 2 of postnatal life. In Case 2, hydrops resolved completely following RFA, but an iatrogenic congenital diaphragmatic hernia and abdominal wall defect became apparent 4 weeks later. The neonate died from sepsis following spontaneous preterm labor at 33 weeks. In Case 3, despite technical success in complete vascular occlusion with coils, a stillbirth ensued 2 days after embolization.ConclusionsThe prognosis of large microcystic or echogenic fetal chest masses associated with hydrops is dismal. This has prompted attempts at treatment by open fetal surgery, with mixed results, high risk of premature labor and consequences for future pregnancies. We have demonstrated the possibility of improved outcome following ultrasound‐guided laser ablation of the systemic arterial supply. Despite technical success, RFA and coil embolization led to procedure‐related complications and need further evaluation. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.
Exploring 6D origins of 5D supergravities with Chern-Simons terms
Authors: Bonetti Federico , Grimm Thomas W. , Hohenegger Stefan 
Published: May 2013

AbstractWe consider five-dimensional supergravity theories with eight or sixteen supercharges with Abelian vector fields and ungauged scalars. We address the question under which conditions these theories can be interpreted as effective low energy descriptions of circle reductions of anomaly free six-dimensional theories with (1,0) or (2,0) supersymmetry. We argue that classical and one-loop gauge- and gravitational Chern-Simons terms are instrumental for this question.
Viscoelastic melt rheology and time–temperature superposition of polycarbonate–multi-walled carbon nanotube nanocomposites
Authors: Choong Gabriel Y. H. , De Focatiis Davide S. A. , Hassell David G. 
Published: May 2013

AbstractThis work investigates the linear and non-linear viscoelastic melt rheology of four grades of polycarbonate melt compounded with 3 wt% Nanocyl NC7000 multi-walled carbon nanotubes and of the matching matrix polymers. Amplitude sweeps reveal an earlier onset of non-linearity and a strain overshoot in the nanocomposites. Mastercurves are constructed from isothermal frequency sweeps using vertical and horizontal shifting. Although all nanocomposites exhibit a second plateau at ∼105Pa, the relaxation times estimated from the peak in loss tangent are not statistically different from those of pure melts estimated from cross-over frequencies: all relaxation timescales scale with molar mass in the same way, evidence that the relaxation of the polymer network is the dominant mechanism in both filled and unfilled materials. Non-linear rheology is also measured in large amplitude oscillatory shear. A comparison of the responses from frequency and amplitude sweep experiments reveals the importance of strain and temperature history on the response of such nanocomposites.
Incidental Findings from Clinical Genome‐Wide Sequencing: A Review
Authors: Lohn Z. , Adam S. , Birch P. H. , Friedman J. M. 
Published: May 2013

AbstractThere are several unresolved challenges associated with the clinical application of genome‐wide sequencing technologies. One of the most discussed issues is incidental findings (IF), which are defined as discoveries made as a result of genetic testing that are unrelated to the indication for the test. The discussion surrounding IF began in the context of research, which we have used to frame consideration of IF in the clinical context. There is growing consensus that analytically valid and medically actionable IF should be offered to patients, but whether and to what extent clinicians should disclose other kinds of IF is debated. While others have systematically reviewed the literature concerning genetic IF, previous reviews focus on ethical and research‐related issues and do not consider the implications for the genetic counseling profession specifically. This review discusses the practical considerations, ethical concerns and genetic counseling issues related to IF, with a particular focus on clinical genome‐wide sequencing. To date, the bulk of the literature with respect to IF in the clinical context consists of commentaries, reviews and case reports. There is a need for more empirical studies to provide a foundation for institutional protocols and evidence‐based clinical practice standards.
Effect of a Hydrophilic Head Group on Krafft Temperature, Surface Activities and Rheological Behaviors of Erucyl Amidobetaines
Authors: Wang Yuejiao , Zhang Yongmin , Liu Xingli , Wang Jiyu , Wei Limin , Feng Yujun 
Published: May 2013

AbstractUltra‐long‐chain amidobetaine surfactants have become one of the hot topics recently, but the influence of the hydrophilic head group on the aggregation behaviors and the correlation between surface activities and thickening ability have been less documented. In this work, comparative studies on the effect of the hydrophilic group on Krafft temperature (TK), surface activities and rheological behaviors of erucyl amidobetaines with sulfonate, hydroxyl‐sulfonate or carboxylate were examined. Compared to the sulfobetaines, the carboxybetaine is more water‐soluble; the addition of an hydroxyl group onto the head group of sulfobetaine increases water‐solubility leading to a lower TK. Unexpectedly, the nature of the head groups has little effect on the critical micelle concentration and thickening ability of these surfactants. The packing parameter prediction verifies the formation of wormlike micelles which accounts for the strong thickening ability of the surfactant aqueous solutions.
Effects of Storage Temperature, Atmosphere and Light on Chemical Stability of Astaxanthin Nanodispersions
Authors: Anarjan Navideh , Tan Chin Ping 
Published: May 2013

AbstractAstaxanthin, as a functional lipid, can be incorporated easily into different water‐based food formulations in the form of a nanodispersion. In this study, astaxanthin nanodispersions were produced using different stabilizer systems, namely, polysorbate 20 (PS20), sodium caseinate (SC), gum arabic (GA) and an optimum combination of these three stabilizers (OPT). Since astaxanthin is sensitive to oxidative damage, its degradations kinetics in the prepared nanodispersion systems were investigated as a function of storage temperature, atmosphere and light. The results showed that astaxanthin degradation followed a first‐order kinetic and, in most cases, astaxanthin was more stable in optimum‐formulated three‐component‐stabilized nanodispersions as compared to nanodispersion systems stabilized by individual stabilizers. In addition, high storage temperature and intense illumination significantly (P < 0.05) increased the degradation of astaxanthin, while oxygen‐free conditions significantly (P < 0.05) reduced the astaxanthin degradation rate.
Cortical phase changes in Alzheimer's disease at 7T MRI: A novel imaging marker
Authors: van Rooden Sanneke , Versluis Maarten J. , Liem Michael K. , Milles Julien , Maier Andrea B. , Oleksik Ania M. , Webb Andrew G. , van Buchem Mark A. , van der Grond Jeroen 
Published: May 2013

AbstractBackgroundPostmortem studies have indicated the potential of high‐field magnetic resonance imaging (MRI) to visualize amyloid depositions in the cerebral cortex. The aim of this study is to test this hypothesis in patients with Alzheimer's disease (AD).MethodsT2*‐weighted MRI was performed in 16 AD patients and 15 control subjects. All magnetic resonance images were scored qualitatively by visual assessment, and quantitatively by measuring phase shifts in the cortical gray matter and hippocampus. Statistical analysis was performed to assess differences between groups.ResultsPatients with AD demonstrated an increased phase shift in the cortex in the temporoparietal, frontal, and parietal regions (P < .005), and this was associated with individual Mini‐Mental State Examination scores (r = −0.54, P < .05).ConclusionIncreased cortical phase shift in AD patients demonstrated on 7‐tesla T2*‐weighted MRI is a potential new biomarker for AD, which may reflect amyloid pathology in the early stages.
Effect of APOE genotype status on targeted clinical trials outcomes and efficiency in dementia and mild cognitive impairment resulting from Alzheimer's disease
Authors: Kennedy Richard E. , Cutter Gary R. , Schneider Lon S. 
Published: May 2013

AbstractBackgroundThe apolipoprotein E (APOE) ε4 genotype has been recommended as a potential inclusion or exclusion criterion in targeted clinical trials for Alzheimer's disease (AD) and mild cognitive impairment (MCI) resulting from AD, and has been implemented in trials of immunotherapeutic agents.MethodsWe tested this recommendation with clinical trial simulations using participants from a meta‐database of 19 studies to create trial samples with APOE ε4 proportions ranging from 0% (all noncarriers) to 100% (all carriers). For each percentage of APOE ε4 carriers, we resampled the database randomly for 1000 trials for each trial scenario, planning for 18‐ or 24‐month trials with samples from 50 to 400 patients per treatment or placebo group, up to 40% dropouts, and outcomes on the Alzheimer's Disease Assessment Scale, cognitive subscale (ADAS‐cog) with effect sizes from 0.15 to 0.75, and calculated statistical power.ResultsEnrichment of clinical trial participants based on APOE ε4 carrier status resulted in minimal increases in power compared with enrolling participants with the APOE ε3 genotype only or enrolling patients without regard to APOE genotype. Increased screening requirements to enhance the sample would offset gains in power.ConclusionsAlthough samples enriched for APOE ε4 carriers in AD or MCI clinical trials showed slightly more cognitive impairment and greater decline using the number APOE ε4 alleles as an inclusion criterion most likely would not result in more efficient trials, and trials would take longer because fewer patients would be available. The APOE ε4/εX (where X = 2, 3 or 4) genotype could be useful, however, as an explanatory variable or covariate if warranted by a drug's action.
Predictability of the simple technical trading rules: An out‐of‐sample test
Authors: Fang Jiali , Jacobsen Ben , Qin Yafeng 
Published: May 2013

AbstractIn a true out‐of‐sample test based on fresh data we find no evidence that several well‐known technical trading strategies predict stock markets over the period of 1987 to 2011. Our test safeguards against sample selection bias, data mining, hindsight bias, and other usual biases that may affect results in our field. We use the exact same technical trading rules thatBrock, Lakonishok, and LeBaron (1992)showed to work best in their historical sample. Further analysis shows that this poor out‐of‐sample performance most likely is not due to the market becoming more efficient – instantaneously or gradually over time – but probably a result of bias.
Nontransformed, GM-CSF–dependent macrophage lines are a unique model to study tissue macrophage functions
Authors: Fejer György , Wegner Mareike Dorothee , Györy Ildiko , Cohen Idan , Engelhard Peggy , Voronov Elena , Manke Thomas , Ruzsics Zsolt , Dölken Lars , Prazeres da Costa Olivia , Branzk Nora , Huber Michael , Prasse Antje , Schneider Robert , Apte Ron N. , Galanos Chris , Freudenberg Marina A. 
Published: May 2013

SignificanceMacrophages—cells crucially involved in defense against infections—exhibit, depending on their anatomical location, distinct biological properties. Studies of the underlying mechanisms are of scientific and clinical interest, but are hampered by the difficulty of obtaining primary tissue macrophages in sufficient numbers and purity. Here, we report the generation of nontransformed murine macrophages, which are similar to alveolar macrophages and can be grown continuously without change of phenotype and in unlimited amounts. Such macrophages helped us to recognize several innate immune properties of alveolar macrophages that are involved in the pathogenesis of infectious lung inflammation.
viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
Authors: Watson Mick , Schnettler Esther , Kohl Alain 
Published: May 2013

Abstract
Summary: RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports.
Availability and implementation: viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome.
Contact: mick.watson@roslin.ed.ac.uk
PIUS: peptide identification by unbiased search
Authors: Costa Eduardo P. , Menschaert Gerben , Luyten Walter , De Grave Kurt , Ramon Jan 
Published: May 2013

Abstract
Summary: We present PIUS, a tool that identifies peptides from tandem mass spectrometry data by analyzing the six-frame translation of a complete genome. It differs from earlier studies that have performed such a genomic search in two ways: (i) it considers a larger search space and (ii) it is designed for natural peptide identification rather than proteomics. Differently from other peptidomics tools designed for genome-wide searches, PIUS does not limit the analysis to a set of sequences that match a list of de novo reconstructions.
Availability: Source code, executables and a detailed technical report are freely available at http://dtai.cs.kuleuven.be/ml/systems/pius.
Contact: eduardo.costa@cs.kuleuven.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
Authors: Hon Jiří , Martínek Tomáš , Rajdl Kamil , Lexa Matej 
Published: May 2013

Abstract
Motivation: Upgrade and integration of triplex software into the R/Bioconductor framework.
Results: We combined a previously published implementation of a triplex DNA search algorithm with visualization to create a versatile R/Bioconductor package ‘triplex’. The new package provides functions that can be used to search Bioconductor genomes and other DNA sequence data for occurrence of nucleotide patterns capable of forming intramolecular triplexes (H-DNA). Functions producing 2D and 3D diagrams of the identified triplexes allow instant visualization of the search results. Leveraging the power of Biostrings and GRanges classes, the results get fully integrated into the existing Bioconductor framework, allowing their passage to other Genome visualization and annotation packages, such as GenomeGraphs, rtracklayer or Gviz.
Availability: R package ‘triplex’ is available from Bioconductor (bioconductor.org).
Contact: lexa@fi.muni.cz
Supplementary information: Supplementary data are available at Bioinformatics online.
Abscisic Acid Mediates a Divergence in the Drought Response of Two Conifers
Authors: Brodribb Timothy J. , McAdam Scott A.M. 
Published: May 2013

Abstract
During water stress, stomatal closure occurs as water tension and levels of abscisic acid (ABA) increase in the leaf, but the interaction between these two drivers of stomatal aperture is poorly understood. We investigate the dynamics of water potential, ABA, and stomatal conductance during the imposition of water stress on two drought-tolerant conifer species with contrasting stomatal behavior. Rapid rehydration of excised shoots was used as a means of differentiating the direct influences of ABA and water potential on stomatal closure. Pinus radiata (Pinaceae) was found to exhibit ABA-driven stomatal closure during water stress, resulting in strongly isohydric regulation of water loss. By contrast, stomatal closure in Callitris rhomboidea (Cupressaceae) was initiated by elevated foliar ABA, but sustained water stress saw a marked decline in ABA levels and a shift to water potential-driven stomatal closure. The transition from ABA to water potential as the primary driver of stomatal aperture allowed C. rhomboidea to rapidly recover gas exchange after water-stressed plants were rewatered, and was associated with a strongly anisohydric regulation of water loss. These two contrasting mechanisms of stomatal regulation function in combination with xylem vulnerability to produce highly divergent strategies of water management. Species-specific ABA dynamics are proposed as a central component of drought survival and ecology.
A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins
Authors: Campos Bruna Medéia , Sforça Mauricio Luis , Ambrosio Andre Luis Berteli , Domingues Mariane Noronha , Brasil de Souza Tatiana de Arruda Campos , Barbosa João Alexandre Ribeiro Gonçalvez , Leme Adriana Franco Paes , Perez Carlos Alberto , Whittaker Sara Britt-Marie , Murakami Mario Tyago , Zeri Ana Carolina de Matos , Benedetti Celso Eduardo 
Published: May 2013

AbstractThe citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.