bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new approach to upscaling fracture network models while preserving geostatistical and geomechanical characteristics
Authors: Lei Qinghua , Latham John‐Paul , Tsang Chin‐Fu , Xiang Jiansheng , Lang Philipp 
Published: June 2015

AbstractA new approach to upscaling two‐dimensional fracture network models is proposed for preserving geostatistical and geomechanical characteristics of a smaller‐scale “source” fracture pattern. First, the scaling properties of an outcrop system are examined in terms of spatial organization, lengths, connectivity, and normal/shear displacements using fractal geometry and power law relations. The fracture pattern is observed to be nonfractal with the fractal dimension D ≈ 2, while its length distribution tends to follow a power law with the exponent 2 < a < 3. To introduce a realistic distribution of fracture aperture and shear displacement, a geomechanical model using the combined finite‐discrete element method captures the response of a fractured rock sample with a domain size L = 2 m under in situ stresses. Next, a novel scheme accommodating discrete‐time random walks in recursive self‐referencing lattices is developed to nucleate and propagate fractures together with their stress‐ and scale‐dependent attributes into larger domains of up to 54 m × 54 m. The advantages of this approach include preserving the nonplanarity of natural cracks, capturing the existence of long fractures, retaining the realism of variable apertures, and respecting the stress dependency of displacement‐length correlations. Hydraulic behavior of multiscale growth realizations is modeled by single‐phase flow simulation, where distinct permeability scaling trends are observed for different geomechanical scenarios. A transition zone is identified where flow structure shifts from extremely channeled to distributed as the network scale increases. The results of this paper have implications for upscaling network characteristics for reservoir simulation.
Vegetation persistence and carbon storage: Implications for environmental water management for Phragmites australis
Authors: Whitaker Kai , Rogers Kerrylee , Saintilan Neil , Mazumder Debashish , Wen Li , Morrison R. J. 
Published: June 2015

AbstractEnvironmental water allocations are used to improve the ecological health of wetlands. There is now increasing demand for allocations to improve ecosystem productivity and respiration, and enhance carbon sequestration. Despite global recognition of wetlands as carbon sinks, information regarding carbon dynamics is lacking. This is the first study estimating carbon sequestration for semiarid Phragmites australis reedbeds. The study combined aboveground biomass assessments with stable isotope analyses of soils and modeling of biomass using Normalized Digital Vegetation Index (NDVI) to investigate the capacity of environmental water allocations to improve carbon storage. The study considered relationships between soil organic carbon (SOC), carbon sources, and reedbed persistence in the Macquarie Marshes, a regulated semiarid floodplain of the Murray‐Darling Basin, Australia. SOC storage levels to 1 m soil depth were higher in persistent reedbeds (167 Mg ha−1) than ephemeral reedbeds (116–138 Mg ha−1). In situ P. australis was the predominant source of surface SOC at persistent reedbeds; mixed sources of surface SOC were proposed for ephemeral reedbeds. 13C enrichment with increasing soil depth occurred in persistent and ephemeral reedbeds and may not relate to flow characteristics. Despite high SOC at persistent reedbeds, differences in the rate of accretion contributed to significantly higher rates of carbon sequestration at ephemeral reedbeds (approximately 554 and 465 g m−2 yr−1) compared to persistent reedbeds (5.17 g m−2 yr−1). However, under current water regimes, rapid accretion at ephemeral reedbeds cannot be maintained. Effective management of persistent P. australis reedbeds may enhance carbon sequestration in the Macquarie Marshes and floodplain wetlands more generally.
Spaceborne GNSS reflectometry for ocean winds: First results from the UK TechDemoSat‐1 mission
Authors: Foti Giuseppe , Gommenginger Christine , Jales Philip , Unwin Martin , Shaw Andrew , Robertson Colette , Roselló Josep 
Published: June 2015

AbstractFirst results are presented for ocean surface wind speed retrieval from reflected GPS signals measured by the low Earth orbiting UK TechDemoSat‐1 satellite (TDS‐1). Launched in July 2014, TDS‐1 provides the first new spaceborne Global Navigation Satellite System‐Reflectometry (GNSS‐R) data since the pioneering UK‐Disaster Monitoring Mission (UK‐DMC) experiment in 2003. Examples of onboard‐processed delay‐Doppler maps reveal excellent data quality for winds up to 27.9 m/s. Collocated Advanced Scatterometer (ASCAT) winds are used to develop and evaluate a wind speed algorithm based on signal‐to‐noise ratio (SNR) and the bistatic radar equation. For SNRs greater than 3 dB, wind speed is retrieved without bias and a precision around 2.2 m/s between 3 and 18 m/s even without calibration. Exploiting lower SNR signals, however, requires good knowledge of the antenna beam, platform attitude, and instrument gain setting. This study demonstrates the capabilities of low‐cost, low‐mass, and low‐power GNSS‐R receivers ahead of their launch on the NASA Cyclone GNSS (CYGNSS) constellation in 2016.
Present‐day crustal thinning in the southern and northern Tibetan Plateau revealed by GPS measurements
Authors: Ge Wei‐Peng , Molnar Peter , Shen Zheng‐Kang , Li Qiang 
Published: June 2015

AbstractGPS measurements from sites within the Tibetan Plateau show not only east‐southeast‐west‐northwest extension but also, more importantly, horizontal dilation throughout the interior of the plateau. Assuming conservation of volume, vertical (thinning) strain rates equal horizontal dilation rates, and they, 8.9 ± 0.8 nanostrain a−1 and 7.4 ± 1.2 nanostrain a−1 in northern and southern Tibet, and 12.0 ± 3.2 nanostrain a−1 in its southwestern part, suggest no measureable difference. Principal extensional strain rates also are similar in magnitude and orientation. If crustal thinning began at 10–15 Ma and the current rates of horizontal dilation applied both to the entire crust and to that period, the crust should have thinned by 5.5–8.5 km. If isostatic equilibrium applied, the mean elevation of the plateau would have dropped ~1 km. The similar rates for northern, southern, and southwestern Tibet suggest that the processes dictating crustal extension, normal faulting, and crustal thinning in the three regions differ little from one another.
P wave tomography and anisotropy beneath Southeast Asia: Insight into mantle dynamics
Authors: Huang Zhouchuan , Zhao Dapeng , Wang Liangshu 
Published: June 2015

AbstractSoutheast Asia is surrounded by subduction zones resulting from the interactions of several lithospheric plates. Its evolution has been also influenced by active tectonics due to the Indo‐Asian collision in the Cenozoic. In this study, we use a large number of arrival‐time data of local and regional earthquakes to determine 3‐D P wave tomography and azimuthal anisotropy in the mantle beneath SE Asia. High‐velocity (high‐V) anomalies representing the subducting slabs are clearly visible in the upper mantle and the mantle transition zone (MTZ). Low‐velocity (low‐V) zones with trench‐normal anisotropy are revealed in the uppermost mantle, which indicate back‐arc spreading or secondary mantle‐wedge flow induced by the slab subduction. In contrast, trench‐parallel anisotropy dominates in the deep upper mantle and reflects structures either in the subducting slab or in the upper mantle surrounding the slab. The trench‐parallel anisotropy is also significant in the lower MTZ, which may contribute to shear wave splitting observations. A low‐V body extending down to the lower mantle is visible under the Hainan volcano far away from the plate boundaries, suggesting that Hainan is a hot spot fed by a lower‐mantle plume. The low‐V body under Hainan is connected with low‐V zones in the upper mantle under SE Tibet and Vietnam. Our P wave anisotropy results reflect significant mantle flow existing in the asthenosphere from SE Tibet to Hainan and further southwestward to Vietnam. The present study, especially the 3‐D P wave anisotropy results, provides important new insight into mantle dynamics in SE Asia.
Phytochemicals determination and classification in purple and red fleshed potato tubers by analytical methods and near infrared spectroscopy
Authors: Tierno Roberto , López Ainara , Riga Patrick , Arazuri Silvia , Jarén Carmen , Benedicto Leire , Ruiz de Galarreta José I 
Published: June 2015

AbstractBACKGROUNDOver the last two decades, the attractive colours and shapes of pigmented tubers and the increasing concern about the relationship between nutrition and health have contributed to the expansion of their consumption and a specialty market. Thus, we have quantified the concentration of health promoting compounds such as soluble phenolics, monomeric anthocyanins, carotenoids, vitamin C, and hydrophilic antioxidant capacity, in a collection of 18 purple‐ and red‐fleshed potato accessions.RESULTSCultivars and breeding lines high in vitamin C, such as Blue Congo, Morada and Kasta, have been identified. Deep purple cultivars Violet Queen, Purple Peruvian and Vitelotte showed high levels of soluble phenolics, monomeric anthocyanins, and hydrophilic antioxidant capacity, whereas relatively high carotenoid concentrations were found in partially yellow coloured tubers, such as Morada, Highland Burgundy Red, and Violet Queen.CONCLUSIONThe present characterisation of cultivars and breeding lines with high concentrations of phytochemicals is an important step both to support the consideration of specialty potatoes as a source of healthy compounds, and to obtain new cultivars with positive nutritional characteristics. Moreover, by using near infrared spectroscopy a non‐destructive identification and classification of samples with different levels of phytochemicals is achieved, offering an unquestionable contribution to the potato industry for future automatic discrimination of varieties. © 2015 Society of Chemical Industry
Performance of prenatal diagnosis in esophageal atresia
Authors: Spaggiari Emmanuel , Faure Giuliana , Rousseau Veronique , Sonigo Pascale , Millischer‐Bellaiche Anne‐Elodie , Kermorvant‐Duchemin Elsa , Muller Francoise , Czerkiewicz Isabelle , Ville Yves , Salomon Laurent J. 
Published: June 2015

AbstractObjectiveThe aim of this study was to evaluate the performance of prenatal diagnosis of esophageal atresia (EA) and its associated abnormalities.MethodsWe conducted a retrospective study from a pediatric database of EA managed postnatally in a single center. Prenatal data included ultrasound and magnetic resonance imaging parameters including amniotic fluid (AF) volume, stomach visualization, AF biochemistry, and associated malformations. Postnatal data included type of EA, mortality, and postnatal diagnosis of associated malformations.ResultsOne hundred twenty‐two cases were included. The diagnosis was suspected prenatally in 39/122 (32%) cases. Polyhydramnios was noted in 64/122 (52.4%), and the stomach was not visualized or small in 39 (32%). There was 14 (11.5%), 2 (1.6%), 101 (82.8%), 5 (4.1%), and 0 (0%) types I, II, III, IV, and V, respectively. EA was suspected prenatally in 12/14 (85.7%) in type I and in 27/108 (25%) in cases with tracheoesophageal fistula (II + III + IV + V). Magnetic resonance imaging was performed in 28 cases, which confirmed EA in 19/28 (sensitivity 67.8%). AF biochemistry was performed in 17 cases, which confirmed EA in 15/17 (sensitivity 88.2%) cases. Of the 69 syndromic associations, 41/69 (59.4%) cases were detected prenatally. Associated malformation was a strong predictor of postnatal death [19/69 vs 3/53, odds ratio 6.33 (1.76; 22.75), p < 0.01].ConclusionPrenatal diagnosis of EA remains challenging. MRI and AF biochemistry may prove useful in the diagnosis of EA. Prenatal ultrasound and MRI examination should also focus on associated anomalies. © 2015 John Wiley & Sons, Ltd.
Phasing of single DNA molecules by massively parallel barcoding
Authors: Borgström Erik , Redin David , Lundin Sverker , Berglund Emelie , Andersson Anders F. , Ahmadian Afshin 
Published: June 2015

AbstractHigh-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.
A fast 3D reconstruction system with a low-cost camera accessory
Authors: Zhang Yiwei , Gibson Graham M. , Hay Rebecca , Bowman Richard W. , Padgett Miles J. , Edgar Matthew P. 
Published: June 2015

AbstractPhotometric stereo is a three dimensional (3D) imaging technique that uses multiple 2D images, obtained from a fixed camera perspective, with different illumination directions. Compared to other 3D imaging methods such as geometry modeling and 3D-scanning, it comes with a number of advantages, such as having a simple and efficient reconstruction routine. In this work, we describe a low-cost accessory to a commercial digital single-lens reflex (DSLR) camera system allowing fast reconstruction of 3D objects using photometric stereo. The accessory consists of four white LED lights fixed to the lens of a commercial DSLR camera and a USB programmable controller board to sequentially control the illumination. 3D images are derived for different objects with varying geometric complexity and results are presented, showing a typical height error of <3 mm for a 50 mm sized object.
A computational study of diffusion in a glass-forming metallic liquid
Authors: Wang T. , Zhang F. , Yang L. , Fang X. W. , Zhou S. H. , Kramer M. J. , Wang C. Z. , Ho K. M. , Napolitano R. E. 
Published: June 2015

AbstractLiquid phase diffusion plays a critical role in phase transformations (e.g. glass transformation and devitrification) observed in marginal glass forming systems such as Al-Sm. Controlling transformation pathways in such cases requires a comprehensive description of diffusivity, including the associated composition and temperature dependencies. In the computational study reported here, we examine atomic diffusion in Al-Sm liquids using ab initio molecular dynamics (AIMD) and determine the diffusivities of Al and Sm for selected alloy compositions. Non-Arrhenius diffusion behavior is observed in the undercooled liquids with an enhanced local structural ordering. Through assessment of our AIMD result, we construct a general formulation for Al-Sm liquid, involving a diffusion mobility database that includes composition and temperature dependence. A Volmer-Fulcher-Tammann (VFT) equation is adopted for describing the non-Arrhenius behavior observed in the undercooled liquid. The composition dependence of diffusivity is found quite strong, even for the Al-rich region contrary to the sole previous report on this binary system. The model is used in combination with the available thermodynamic database to predict specific diffusivities and compares well with reported experimental data for 0.6 at.% and 5.6 at.% Sm in Al-Sm alloys.
Hagfish: Champions of CO2 tolerance question the origins of vertebrate gill function
Authors: Baker Daniel W. , Sardella Brian , Rummer Jodie L. , Sackville Michael , Brauner Colin J. 
Published: June 2015

AbstractThe gill is widely accepted to have played a key role in the adaptive radiation of early vertebrates by supplanting the skin as the dominant site of gas exchange. However, in the most basal extant craniates, the hagfishes, gills play only a minor role in gas exchange. In contrast, we found hagfish gills to be associated with a tremendous capacity for acid-base regulation. Indeed, Pacific hagfish exposed acutely to severe sustained hypercarbia tolerated among the most severe blood acidoses ever reported (1.2 pH unit reduction) and subsequently exhibited the greatest degree of acid-base compensation ever observed in an aquatic chordate. This was accomplished through an unprecedented increase in plasma [HCO3−] (>75 mM) in exchange for [Cl−]. We thus propose that the first physiological function of the ancestral gill was acid-base regulation and that the gill was later co-opted for its central role in gas exchange in more derived aquatic vertebrates.
Folic acid inhibits COLO-205 colon cancer cell proliferation through activating the FRα/c-SRC/ERK1/2/NFκB/TP53 pathway: in vitro and in vivo studies
Authors: Kuo Chun-Ting , Chang Chieh , Lee Wen-Sen 
Published: June 2015

AbstractTo investigate the molecular mechanism underlying folic acid (FA)-induced anti-colon caner activity, we showed that FA caused G0/G1 arrest in COLO-205. FA activated the proto-oncogene tyrosine-protein kinase Src (c-SRC)-mediated signaling pathway to enhance nuclear factor of kappa light polypeptide gene enhancer in B-cells (NFκB) nuclear translocation and binding onto the tumor protein p53 (TP53) gene promoter and up-regulated expressions of TP53, cyclin-dependent kinase inhibitor 1A (CDKN1A) and cyclin-dependent kinase inhibitor 1B (CDKN1B). Knock-down of TP53 abolished FA-induced increases in the levels of CDKN1A and CDKN1B protein and G0/G1 arrest in COLO-205. Knock-down of folate receptor alpha (FRα) abolished FA-induced activations in the c-SRC-mediated pathway and increases in the levels of CDKN1A, CDKN1B and TP53 protein. These data suggest that FA inhibited COLO-205 proliferation through activating the FRα/c-SRC/mitogen-activated protein kinase 3/1 (ERK1/2)/NFκB/TP53 pathway-mediated up-regulations of CDKN1A and CDKN1B protein. In vivo studies demonstrated that daily i.p. injections of FA led to profound regression of the COLO-205 tumors and prolong the lifespan. In these tumors, the levels of CDKN1A, CDKN1B and TP53 protein were increased and von willebrand factor (VWF) protein levels were decreased. These findings suggest that FA inhibits COLO-205 colon cancer growth through anti-cancer cell proliferation and anti-angiogenesis.
The physical demands of Super League rugby: Experiences of a newly promoted franchise
Authors: Evans S. D. , Brewer C. , Haigh J. D. , Lake M. , Morton J. P. , Close G. L. 
Published: June 2015

AbstractThe physical match demands for a newly promoted European Super League (ESL) squad were analysed over a full season using global positioning systems. Players were classified into four positional groups: outside backs (OB), pivots (PIV), middle unit forwards (MUF) and wide running forwards (WRF). MUF covered less total distance (4318 ± 570 m) than WRF (6408 ± 629 m), PIV (6549 ± 853) and OB (7246 ± 333 m) (P < 0.05) and less sprint distance (185 ± 58 m) than WRF (296 ± 82 m), PIV (306 ± 108) and OB (421 ± 89 m; P < 0.05), likely attributable to less playing time by MUF (47.8 ± 6.6 min) compared with WRF (77.0 ± 9.0 min), PIV (72.8 ± 10.6 min) and OB (86.7 ± 3.4 min; P < 0.05). Metres per minute were greater for MUF (90.8 ± 2.2 m.min–1) compared with OB (83.6 ± 2.8 m.min–1) and WRF (83.4 ± 2.4 m.min–1; P = 0.001) although not different from PIV (90.2 ± 3.3 m.min–1; P > 0.05). WRF (36 ± 5) and MUF (35 ± 6) were involved in more collisions than OB (20 ± 3) and PIV (23 ± 3; P < 0.05). The high‐speed running and collision demands observed here were greater than that previously reported in the ESL, which may reflect increased demands placed on the lower ranked teams. The present data may be used to inform coaches if training provides the physical stimulus to adequately prepare their players for competition which may be especially pertinent for newly promoted franchises.
GeIST: a pipeline for mapping integrated DNA elements
Authors: LaFave Matthew C. , Varshney Gaurav K. , Burgess Shawn M. 
Published: June 2015

Abstract
Summary: There are several experimental contexts in which it is important to identify DNA integration sites, such as insertional mutagenesis screens, gene and enhancer trap applications, and gene therapy. We previously developed an assay to identify millions of integrations in multiplexed barcoded samples at base-pair resolution. The sheer amount of data produced by this approach makes the mapping of individual sites non-trivial without bioinformatics support. This article presents the Genomic Integration Site Tracker (GeIST), a command-line pipeline designed to map the integration sites produced by this assay and identify the samples from which they came. GeIST version 2.1.0, a more adaptable version of our original pipeline, can identify integrations of murine leukemia virus, adeno-associated virus, Tol2 transposons or Ac/Ds transposons, and can be adapted for other inserted elements. It has been tested on experimental data for each of these delivery vectors and fine-tuned to account for sequencing and cloning artifacts.
Availability and implementation: GeIST uses a combination of Bash shell scripting and Perl. GeIST is available at http://research.nhgri.nih.gov/software/GeIST/.
Contact: burgess@mail.nih.gov
The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework
Authors: Patel Vishal R. , Ceglia Nicholas , Zeller Michael , Eckel-Mahan Kristin , Sassone-Corsi Paolo , Baldi Pierre 
Published: June 2015

Abstract
Motivation: Circadian oscillations have been observed in animals, plants, fungi and cyanobacteria and play a fundamental role in coordinating the homeostasis and behavior of biological systems. Genetically encoded molecular clocks found in nearly every cell, based on negative transcription/translation feedback loops and involving only a dozen genes, play a central role in maintaining these oscillations. However, high-throughput gene expression experiments reveal that in a typical tissue, a much larger fraction (∼10%) of all transcripts oscillate with the day–night cycle and the oscillating species vary with tissue type suggesting that perhaps a much larger fraction of all transcripts, and perhaps also other molecular species, may bear the potential for circadian oscillations.
Results: To better quantify the pervasiveness and plasticity of circadian oscillations, we conduct the first large-scale analysis aggregating the results of 18 circadian transcriptomic studies and 10 circadian metabolomic studies conducted in mice using different tissues and under different conditions. We find that over half of protein coding genes in the cell can produce transcripts that are circadian in at least one set of conditions and similarly for measured metabolites. Genetic or environmental perturbations can disrupt existing oscillations by changing their amplitudes and phases, suppressing them or giving rise to novel circadian oscillations. The oscillating species and their oscillations provide a characteristic signature of the physiological state of the corresponding cell/tissue. Molecular networks comprise many oscillator loops that have been sculpted by evolution over two trillion day–night cycles to have intrinsic circadian frequency. These oscillating loops are coupled by shared nodes in a large network of coupled circadian oscillators where the clock genes form a major hub. Cells can program and re-program their circadian repertoire through epigenetic and other mechanisms.
Availability and implementation: High-resolution and tissue/condition specific circadian data and networks available at http://circadiomics.igb.uci.edu.
Contact: pfbaldi@ics.uci.edu
Supplementary information: Supplementary data are available at Bioinformatics online.