bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole‐Genome Amplification of Single‐Cell Genomes for Next‐Generation Sequencing
Authors: Korfhage Christian , Fisch Evelyn , Fricke Evelyn , Baedker Silke , Loeffert Dirk 
Published: October 2013

AbstractDNA sequence analysis and genotyping of biological samples using next‐generation sequencing (NGS), microarrays, or real‐time PCR is often limited by the small amount of sample available. A single cell contains only one to four copies of the genomic DNA, depending on the organism (haploid or diploid organism) and the cell‐cycle phase. The DNA content of a single cell ranges from a few femtograms in bacteria to picograms in mammalia. In contrast, a deep analysis of the genome currently requires a few hundred nanograms up to micrograms of genomic DNA for library formation necessary for NGS sequencing or labeling protocols (e.g., microarrays). Consequently, accurate whole‐genome amplification (WGA) of single‐cell DNA is required for reliable genetic analysis (e.g., NGS) and is particularly important when genomic DNA is limited. The use of single‐cell WGA has enabled the analysis of genomic heterogeneity of individual cells (e.g., somatic genomic variation in tumor cells). This unit describes how the genome of single cells can be used for WGA for further genomic studies, such as NGS. Recommendations for isolation of single cells are given and common sources of errors are discussed. Curr. Protoc. Mol. Biol. 104:7.14.1‐7.14.11. © 2013 by John Wiley & Sons, Inc.
Pyrosequencing: Powerful and Quantitative Sequencing Technology
Authors: Kreutz Martin , Hochstein Norbert , Kaiser Julia , Narz Frank , Peist Ralf 
Published: October 2013

AbstractPyrosequencing is a sequencing‐by‐synthesis method for DNA analysis that has emerged as a platform not only for de novo sequencing applications, but also for quantitative analysis of genomic methylation, single‐nucleotide polymorphisms, and allele quantification. In this unit, we describe a complete workflow from sample to result that is suitable for each of these applications. As cytosine conversion is a key element of successful methylation analysis using pyrosequencing, a support protocol for bisulfite treatment is also included. Curr. Protoc. Mol. Biol. 104:7.15.1‐7.15.23. © 2013 by John Wiley & Sons, Inc.
Nailing down the slip rate of the Altyn Tagh fault
Authors: He Jiankun , Vernant Philippe , Chéry Jean , Wang Weimin , Lu Shuangjiang , Ku Wenfei , Xia Wenhai , Bilham Roger 
Published: October 2013

AbstractPrevious estimates of the geodetic and geologic slip rates of the 1500 km long Altyn Tagh fault bordering the northern edge of the Tibetan plateau vary by a factor of five. Proposed reasons for these discrepancies include poor GPS geometry, interpretative errors in terrace morphology, and changes in fault slip rate over time. Here we present results from a new dense GPS array orthogonal to the fault at ~86.2°E that indicates a velocity of 9.0−3.2/+4.4 mm/yr, in close agreement with geomorphologic estimates at the same location. Our estimated geodetic slip rate is consistent with recent geological slip rates based on terrace offsets. The resulting mean combined geological and geodetic slip rate (9.0 ± 4.0 mm/yr) is remarkably uniform for the central ~800 km of the Altyn Tagh fault, significantly lower than early kinematic estimates and consistent with deformation elsewhere in Tibet and central Asia.
Tasman Leakage of intermediate waters as inferred from Argo floats
Authors: Rosell‐Fieschi Miquel , Rintoul Stephen R. , Gourrion Jeröme , Pelegrí Josep L. 
Published: October 2013

AbstractWe use Argo float trajectories to infer ocean current velocity at the sea surface and 1000 dbar near Australia. The East Australian Current flows southward along the east coast of Australia at both surface and intermediate levels, but only the intermediate waters leak round the southern tip of Tasmania and cross the Great Australian Bight. We calculate the transport of Antarctic Intermediate Water (AAIW) between the southern Australian coast and the Antarctic Circumpolar Current (ACC) as the velocity at 1000 dbar times the layer thickness. Between March 2006 and December 2012, the Eulerian AAIW transport through 147°E ranges between 0 and 12.0 sverdrup (Sv). The mean Tasman Leakage of intermediate waters from the Pacific Ocean into the Indian Ocean, obtained using all Argo data until March 2013, is 3.8 ± 1.3 Sv. The mean intermediate water transport into the Indian Ocean through 115°E increases to 5.2 ± 1.8 Sv due to contributions from the westward recirculation of ACC waters.
Tide‐induced microseismicity in the Mertz glacier grounding area, East Antarctica
Authors: Barruol Guilhem , Cordier Emmanuel , Bascou Jérôme , Fontaine Fabrice R. , Legrésy Benoit , Lescarmontier Lydie 
Published: October 2013

AbstractThe deployment of a seismic network along the Adélie and George V coasts in East Antarctica during the period 2009–2012 provides the opportunity to monitor cryoseismic activity and to obtain new insights on the relationship between tidal cycles and coastal glacier dynamics. Here we focus on records from a seismometer located on a rocky outcrop in the vicinity of the grounding line of the 35 km broad Mertz glacier, a major outflow of this region. We detect numerous icequakes (50,000 events within 10 months and up to 100 events/h) and demonstrate their clear tidal modulation. We suggest that they result from ice friction and fracturing around the rocky peak and from the glacier flexure in response to the falling and rising tides at its grounding area. We propose that such icequake monitoring could be used as a climate proxy since grounding lines are subject to migrate with sea level changes.
Natural aerosol–climate feedbacks suppressed by anthropogenic aerosol
Authors: Spracklen D. V. , Rap A. 
Published: October 2013

AbstractThe natural environment is an important source of atmospheric aerosol such as dust, sea spray, and wildfire smoke. Climate controls many of these natural aerosol sources, which, in turn, can alter climate through changing the properties of clouds and the Earth's radiative balance. However, the Earth's atmosphere is now heavily modified by anthropogenic pollution aerosol, but how this pollution may alter these natural aerosol–climate feedbacks has not been previously explored. Here we use a global aerosol microphysics model to analyze how anthropogenic aerosol alters one link within these feedbacks, namely, the sensitivity of cloud albedo to changes in natural aerosol. We demonstrate that anthropogenic aerosol in the Northern Hemisphere has halved the hemispheric mean cloud albedo radiative effect that occurs due to changes in natural aerosol emissions. Such a suppression has not occurred in the more pristine Southern Hemisphere.
Lightning attachment process involving connection of the downward negative leader to the lateral surface of the upward connecting leader
Authors: Lu Weitao , Chen Luwen , Ma Ying , Rakov V. A. , Gao Yan , Zhang Yang , Yin Qiyuan , Zhang Yijun 
Published: October 2013

AbstractHigh‐speed video camera records, with a temporal resolution of 20 µs and a spatial resolution of 2.4 m per pixel, of a downward negative lightning flash that terminated on a 440 m high building are examined. The attachment process in this flash exhibited an unexpected behavior in that the downward leader tip connected to the lateral surface of the ~400 m upward connecting leader (UCL) below its tip. It appears that the effect of the downward leader on the UCL is significant, while the effect of the UCL on the downward leader is negligible, except for the final 80 µs preceding the beginning of the first return stroke. The ratio of speeds of the downward leader and the UCL tends to decrease with time, ranging from 1.8 to 0.12, although the lower 80–100 m or so of the UCL were too faint to allow speed measurements.
Local time, seasonal, and solar cycle dependency of longitudinal variations of TEC along the crest of EIA over India
Authors: Sunda Surendra , Vyas B. M. 
Published: October 2013

AbstractThe global wave number 4 structure in the Indian longitudinal region spanning from ~70 to 95°E forming the upward slope of the peak in the total electron content (TEC) are reported along the crest of equatorial ionization anomaly (EIA). The continuous and simultaneous measurements from five GPS stations of GPS Aided Geo Augmented Navigation (GAGAN) network are used in this study. The long‐term database (2004–2012) is utilized for examining the local time, seasonal, and solar cycle dependency on the longitudinal variations of TEC. Our results confirm the existence of longitudinal variations of TEC in accordance with wave number 4 longitudinal structure including its strength. The results suggest that these variations, in general, start to develop at ~09 LT, achieve maximum strength at 12–15 LT, and decay thereafter, the decay rate depending on the season. They are more pronounced in equinoctial season followed by summer and winter. The longitudinal variations persist beyond midnight in equinox seasons, whereas in winter, they are conspicuously absent. Interestingly, they also exhibit significant solar cycle dependence in the solstices, whereas in the equinoxes, they are independent of solar activity. The comparison of crest‐to‐trough ratio (CTR) in the eastern (92°E) and western (72°E) extreme longitudes reveals higher CTR on the eastern side than over the western extreme, suggesting the role of nonmigrating tides in modulating the ExB vertical drift and the consequential EIA crest formation.
Empirical modeling of plasma sheet pressure and three‐dimensional force‐balanced magnetospheric magnetic field structure: 2. Modeling
Authors: Yue Chao , Wang Chih‐Ping , Zaharia Sorin G. , Xing Xiaoyan , Lyons Larry 
Published: October 2013

AbstractThe magnetic field configuration is crucial to plasma sheet dynamics and magnetosphere‐ionosphere coupling. In this study we established 3‐D force‐balanced magnetic fields and investigated configuration changes with Kp and solar wind dynamic pressure (PSW). Pressure distributions from the empirical model developed in Wang et al. (2013) were used for obtaining the force‐balanced field. Based on our model results, we found that (1) higher PSW mainly enhances pressure in the tail plasma sheet, while larger convection during higher Kp drives plasma sheet further earthward, resulting in a pressure increase closer to the Earth; (2) comparing with the magnetic field changes due to increasing PSW, the Kp associated pressure enhancement causes the azimuthal current density (Jϕ) peak and field‐aligned currents (FACs) to move deeper earthward, the magnetic field to decrease further near Earth but increase more in the tail, and field lines to stretch more significantly; (3) as Kp and PSW change, the whole plasma sheet remains stable to interchange instability but may be ballooning unstable in the midnight region at X between −15 and −10 RE; (4) the force‐balanced configurations are characteristically different from the non‐force‐balanced Tsyganenko 89 (T89) magnetic field. A region of positive dBz/dz in the near‐Earth region, which has been observed, is seen in our field but not in T89. On the other hand, a local equatorial Bz minimum is predicted by T89 but not by our model. Jφ bifurcation appears in the near‐Earth region as a result of our Jφ configuration being approximately aligned with field lines, while the T89 Jφ everywhere decreases monotonically with increasing Z by construction.
Suppression of slip and rupture velocity increased by thermal pressurization: Effect of dilatancy
Authors: Urata Yumi , Kuge Keiko , Kase Yuko 
Published: October 2013

AbstractWe investigated the effect of dilatancy on dynamic rupture propagation on a fault where thermal pressurization (TP) is in effect, taking into account permeability varying with porosity; the study is based on three‐dimensional (3‐D) numerical simulations of spontaneous ruptures obeying a slip‐weakening friction law and Coulomb failure criterion. The effects of dilatancy on dynamic ruptures interacting with TP have been often investigated in one‐ or two‐dimensional numerical simulations. The sole 3‐D numerical simulation gave attention only to the behavior at a single point on a fault. Moreover, with the sole exception based on a single‐degree‐freedom spring‐slider model, the previous simulations including dilatancy and TP have not considered changes in hydraulic diffusivity. However, the hydraulic diffusivity, which strongly affects TP, can vary as a power of porosity. In this study, we apply a power law relationship between permeability and porosity. We consider both reversible and irreversible changes in porosity, assuming that the irreversible change is proportional to the slip rate and dilatancy coefficient ɛ. Our numerical simulations suggest that the effects of dilatancy can suppress slip and rupture velocity increased by TP. The results reveal that the amount of slip on the fault decreases with increasing ɛ or exponent of the power law, and the rupture velocity is predominantly suppressed by ɛ. This was observed regardless of whether the applied stresses were high or low. The deficit of the final slip in relation to ɛ can be smaller as the fault size is larger.
Long‐term trends of biogenic sulfur aerosol and its relationship with sea surface temperature in Arctic Finland
Authors: Laing James R. , Hopke Philip K. , Hopke Eleanor F. , Husain Liaquat , Dutkiewicz Vincent A. , Paatero Jussi , Viisanen Yrjö 
Published: October 2013

AbstractForty‐seven years of week‐long total suspended particle samples from Kevo Finland were analyzed for methane sulfonic acid (MSA) and sulfate. Kevo is located 350 km north of the Arctic Circle. MSA and non‐sea‐salt sulfate (NSS‐SO4) showed clear seasonal trends. MSA peaks from May to July, coinciding with warmer waters and increased biogenic activity in the surrounding seas. NSS‐SO4 peaks in March with a minimum during the summer, the typical pattern for Arctic haze. MSA concentrations were found to be positively correlated (p < 0.001) with sea surface temperature anomalies in the surrounding seas. MSA showed a trend of 0.405 ng/m3/yr (0.680%/yr) for June and July. NSS‐SO4 concentrations at Kevo declined dramatically in the early 1990s, probably as a result of the collapse of the Soviet Union. The decline has continued since the mid‐1990s.
Present Role of Positron Emission Tomography in the Diagnosis and Monitoring of Peripheral Inflammatory Arthritis: A Systematic Review
Authors: Bruijnen S. T. G. , Gent Y. Y. J. , Voskuyl A. E. , Hoekstra O. S. , van der Laken C. J. 
Published: October 2013

ObjectiveTo determine the current status of positron emission tomography (PET) as a tool for diagnosis and monitoring of peripheral inflammatory arthritis (IA).MethodsFor conducting this systematic review, the PubMed (Medline), Embase, and Cochrane Library databases were searched until December 31, 2012. Studies of PET for diagnosis and/or therapy monitoring of peripheral IA were included. Data were summarized qualitatively using best evidence synthesis.ResultsEighteen articles met our inclusion criteria. The majority of studies were feasibility studies with varying methods applied. All studies demonstrated that PET visualized IA with high sensitivity, corresponding to clinical assessments. PET outcome of clinically active IA also matched that of ultrasound and magnetic resonance imaging. PET differentiates from other modalities by (quantitative) imaging of molecular sites in the synovium. The first studies reporting on the potential clinical applications of PET to image subclinical synovitis in preclinical RA and during therapy have been published. The results are promising, but the number and study populations of these studies are still limited.ConclusionThus far, a limited number of PET studies addressing IA imaging have been published. The PET modality seems to offer highly sensitive and potentially specific imaging of IA at the (quantitative) molecular level. Clinical application studies for early diagnostics and therapy monitoring are arising, but these topics should be further explored in future studies with larger cohorts. For integration in clinical practice, aspects such as radiation burden and cost‐effectiveness should also be taken into account.
Cost‐Effectiveness of Total Knee Replacement: A Prospective Cohort Study
Authors: Waimann Christian A. , Fernandez‐Mazarambroz Rodrigo J. , Cantor Scott B. , Lopez‐Olivo Maria A. , Zhang Hong , Landon Glenn C. , Siff Sherwin J. , Suarez‐Almazor Maria E. 
Published: October 2013

ObjectiveTotal knee replacement (TKR) rates have significantly increased in the past decade. While the procedure itself might be costly, the cost‐effectiveness and potential offset costs from patient and societal benefits have not been clearly established. The objective of this study was to perform an economic evaluation of TKR in patients with knee osteoarthritis (OA).MethodsWe conducted a 6‐month prospective cohort study of 212 patients with knee OA who underwent TKR at a single hospital in Houston, Texas. We included patient‐level data from hospital billing databases and the patients' self‐reported direct and indirect costs. The clinical outcome measure was pain and function measured by the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) questionnaire; we used the minimum clinically important difference (MCID; ≥20‐point change) and the WOMAC 20% (WOMAC20), 50% (WOMAC50), and 70% (WOMAC70) relative improvement criteria. Incremental cost‐effectiveness ratios were estimated using direct and indirect costs and WOMAC improvement. A societal perspective was used and multiple sensitivity analyses were performed to assess the robustness of the principal analysis.ResultsThe total incremental cost per TKR was $20,133. The incremental cost‐effectiveness ratios (ICERs) for improvement at 6 months were $33,345, $25,255, $35,274, and $56,908 for the MCID, WOMAC20, WOMAC50, and WOMAC70, respectively. Best‐ and worst‐case scenario sensitivity analyses did not have a significant impact on the ICERs. Patient time lost was the most influential variable in the multiway sensitivity analysis.ConclusionTKR is an effective intervention in reducing pain and improving functional status among patients with knee OA and is cost effective at both low and high levels of improvement.
Who Makes It to the Base? Selection Procedure for a Physical Activity Trial Targeting People With Rheumatoid Arthritis
Authors: Nordgren Birgitta , Fridén Cecilia , Demmelmaier Ingrid , Opava Christina H. 
Published: October 2013

ObjectiveTo compare those who were finally included in a large well‐defined sample of individuals with rheumatoid arthritis (RA) at target for a physical activity (PA) trial with those who were not.MethodsIn total, 3,152 individuals answered questionnaires on sociodemographic, disease‐related, and psychosocial factors and PA levels. The differences between individuals making it to the baseline assessments and those who did not were analyzed in 3 steps.ResultsIn a first step, 1,932 individuals were eligible for the trial if they were interested in participating, not physically active enough, and fluent in Swedish and if they were not participating in any other study. The participants were mainly younger women, had higher education and income, were more likely to live with children, and had better support for exercise and had higher outcome expectations of PA than the 1,208 ineligible individuals. In a second step, the 286 individuals accepting participation had higher income and education, more support for exercise, less fear‐avoidance beliefs, and higher outcome expectations of PA than the 1,646 individuals declining participation. In a third step, the 244 individuals assessed at baseline reported less fatigue than the 42 withdrawing before assessment.ConclusionTo our knowledge, this is the first study describing the entire selection procedure, from a target sample for a PA trial to the sample assessed at baseline, in individuals with RA. Factors other than those related to the disease seemed to mainly determine participation and largely resembled determinants in the general population. Sociodemographic and psychosocial factors should be recognized as important for PA in people with RA.
A Convenient and General Reduction of Amides to Amines with Low‐Valent Titanium
Authors: Zhang Tongxin , Zhang Yan , Zhang Weixi , Luo Meiming 
Published: October 2013

AbstractLow‐valent titanium readily prepared in situ from TiCl4 and Mg powder in THF is found to be an active agent for the reduction of amides which were previously considered to be inert towards low‐valent titanium. The reaction proceeds under very mild conditions, and is applicable to all types of amides, primary, secondary and tertiary, to produce the corresponding amines in good to excellent yields. This new finding provides a practical, convenient and general method for the important transformation of amides to amines. A plausible reaction mechanism is proposed.magnified image
Copper‐Catalyzed Domino Route to Natural Nostoclides and Analogues: A Total Synthesis of Nostoclides I and II
Authors: Ngi Samuel Inack , Petrignet Julien , Duwald Romain , El Hilali El Mostafa , Abarbri Mohamed , Duchêne Alain , Thibonnet Jérôme 
Published: October 2013

AbstractAn original and convenient domino route to natural nostoclides I and II has been developed using a two‐step sequence consisting of a copper‐catalyzed tandem reaction associated with Suzuki cross‐coupling. The methodology employed for this total synthesis appeared to be an interesting and sufficiently flexible tool to allow the synthesis of numerous analogues of these nostoclides.magnified image
Hydromagnesite as an Efficient Recyclable Heterogeneous Solid Base Catalyst for the Synthesis of Flavanones, Flavonols and 1,4‐Dihydropyridines in Water
Authors: Rajesh U. Chinna , Manohar Sunny , Rawat Diwan S. 
Published: October 2013

AbstractA form of hydromagnesite (HM) with flower‐like thin‐sheet morphology was synthesized by an environmentally benign approach using simple conventional heating at moderate temperature without using any template in water as medium. The versatility of this HM catalyst was studied in the synthesis of flavanones, flavonols and the multicomponent synthesis of 1,4‐dihydropyridines in water. The recyclability of catalyst was studied for six times and there was no appreciable loss in its catalytic activity.magnified image
Palladium‐Catalysed Dehydrogenative Generation of Imines from Amines. A Nature‐Inspired Route to Indoles via Cross‐Couplings of Amines with Arylhydrazines
Authors: Taddei Maurizio , Mura Manuel G. , Rajamäki Suvi , Luca Lidia De , Porcheddu Andrea 
Published: October 2013

AbstractH‐substituted imines are elusive compounds formed when aldehydes or ketones are mixed with ammonia. However, this class of molecules can be prepared through selective removal of a hydrogen molecule from a primary amine using a transition metal catalyst. This biomimetic transformation, previously employed for the N‐alkylation of anilines, is applied here to a domino preparation of differently substituted indoles from aliphatic primary amines and arylhydrazines. Several different linear and branched aliphatic primary amines are oxidized with reusable palladium on charcoal to the corresponding primary imines entrapped as arylhydrazones that can be isolated as such. Arylhydrazones can be further converted into N‐alkylindole derivatives via an acid‐mediated indolisation reaction. The one‐pot domino hydrogen transfer Fischer indole synthesis under heterogeneous catalysis is also possible, giving access to diverse substituted indoles, including NH indoles obtained after deprotection of the corresponding benzyl compounds. The truly heterogeneous nature of the catalyst was demonstrated by recycling the catalyst in the same reaction, and in other palladium‐catalysed transformations.magnified image