bluuebunny/crossref_metadata_2025 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

A 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

Environmental 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

First 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

GPS 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

Southeast 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.
Potential for Stem Cell‐Based Periodontal Therapy
Authors: Bassir Seyed Hossein , Wisitrasameewong Wichaya , Raanan Justin , Ghaffarigarakani Sasan , Chung Jamie , Freire Marcelo , Andrada Luciano C. , Intini Giuseppe
Published: June 2015

Periodontal diseases are highly prevalent and are linked to several systemic diseases. The goal of periodontal treatment is to halt the progression of the disease and regenerate the damaged tissue. However, achieving complete and functional periodontal regeneration is challenging because the periodontium is a complex apparatus composed of different tissues, including bone, cementum, and periodontal ligament. Stem cells may represent an effective therapeutic tool for periodontal regeneration due to their plasticity and their ability to regenerate different tissues. This review presents and critically analyzes the available information on stem cell‐based therapy for the regeneration of periodontal tissues and suggests new avenues for the development of more effective therapeutic protocols. J. Cell. Physiol. 230: 50–61, 2016. © 2015 Wiley Periodicals, Inc.
Participation of TNF‐α in Inhibitory Effects of Adipocytes on Osteoblast Differentiation
Authors: Abuna Robrigo P.F. , De Oliveira Fabiola S. , Santos Thiago De S. , Guerra Thais R. , Rosa Adalberto L. , Beloti Marcio M.
Published: June 2015

Mesenchymal stem cells from bone marrow (BM‐MSCs) and adipose tissue (AT‐MSCs) are attractive tools for cell‐based therapies to repair bone tissue. In this study, we investigated the osteogenic and adipogenic potential of BM‐MSCs and AT‐MSCs as well as the effect of crosstalk between osteoblasts and adipocytes on cell phenotype expression. Rat BM‐MSCs and AT‐MSCs were cultured either in growth, osteogenic, or adipogenic medium to evaluate osteoblast and adipocyte differentiation. Additionally, osteoblasts and adipocytes were indirectly co‐cultured to investigate the effect of adipocytes on osteoblast differentiation and vice versa. BM‐MSCs and AT‐MSCs exhibit osteogenic and adipogenic potential under non‐differentiation‐inducing conditions. When exposed to osteogenic medium, BM‐MSCs exhibited higher expression of bone markers compared with AT‐MSCs. Conversely, under adipogenic conditions, AT‐MSCs displayed higher expression of adipose tissue markers compared with BM‐MSCs. The presence of adipocytes as indirect co‐culture repressed the expression of the osteoblast phenotype, whereas osteoblasts did not exert remarkable effect on adipocytes. The inhibitory effect of adipocytes on osteoblasts was due to the release of tumor necrosis factor alpha (TNF‐α) in culture medium by adipocytes. Indeed, the addition of exogenous TNF‐α in culture medium repressed the differentiation of BM‐MSCs into osteoblasts mimicking the indirect co‐culture effect. In conclusion, our study showed that BM‐MSCs are more osteogenic while AT‐MSCs are more adipogenic. Additionally, we demonstrated the key role of TNF‐α secreted by adipocytes on the inhibition of osteoblast differentiation. Thus, we postulate that the higher osteogenic potential of BM‐MSCs makes them the first choice for inducing bone repair in cell‐based therapies. J. Cell. Physiol. 230: 204–214, 2016. © 2015 Wiley Periodicals, Inc.
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

BACKGROUND

Over 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.

RESULTS

Cultivars 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.

CONCLUSION

The 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

Objective

The aim of this study was to evaluate the performance of prenatal diagnosis of esophageal atresia (EA) and its associated abnormalities.

Methods

We 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.

Results

One 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].

Conclusion

Prenatal 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.
Energizing eukaryotic cell‐free protein synthesis with glucose metabolism
Authors: Anderson Mark J. , Stark Jessica C. , Hodgman C. Eric , Jewett Michael C.
Published: June 2015

Eukaryotic cell‐free protein synthesis (CFPS) is limited by the dependence on costly high‐energy phosphate compounds and exogenous enzymes to power protein synthesis (e.g., creatine phosphate and creatine kinase, CrP/CrK). Here, we report the ability to use glucose as a secondary energy substrate to regenerate ATP in a Saccharomyces cerevisiae crude extract CFPS platform. We observed synthesis of 3.64 ± 0.35 μg mL−1 active luciferase in batch reactions with 16 mM glucose and 25 mM phosphate, resulting in a 16% increase in relative protein yield (μg protein/$ reagents) compared to the CrP/CrK system. Our demonstration provides the foundation for development of cost‐effective eukaryotic CFPS platforms.
Identification of nuclear localization signals within the human BCOR protein
Authors: Surapornsawasd Thunyaporn , Ogawa Takuya , Moriyama Keiji
Published: June 2015

Mutations in theBCL‐6 corepressor (BCOR) gene, which encodes a transcriptional corepressor, were described to cause oculofaciocardiodental syndrome (MIM300166). The purpose of this study was to localize the classical nuclear localization signals (NLSs) of the BCOR using reported humanBCOR mutations with comparable phenotypes. The genotype–phenotype correlation among the mutations could not be clearly explained; however, the classical NLSs were identified at two possible sites; RVDRKRKVSGD at aa1131–1141 (NLS1) and LKAKRRRVSK at aa1158–1167 (NLS2). In addition, according to our results, NLS2 displayed a more efficient nuclear import function than NLS1.
Reactive oxygen species induce Cox‐2 expression via TAK1 activation in synovial fibroblast cells
Authors: Onodera Yuta , Teramura Takeshi , Takehara Toshiyuki , Shigi Kanae , Fukuda Kanji
Published: June 2015

Oxidative stress within the arthritis joint has been indicated to be involved in generating mediators for tissue degeneration and inflammation. COX‐2 is a mediator in inflammatory action, pain and some catabolic reactions in inflamed tissues. Here, we demonstrated a direct relationship between oxidative stress and Cox‐2 expression in the bovine synovial fibroblasts. Furthermore, we elucidated a novel mechanism, in which oxidative stress induced phosphorylation of MAPKs and NF‐κB through TAK1 activation and resulted in increased Cox‐2 and prostaglandin E2 expression. Finally, we demonstrated that ROS‐induced Cox‐2 expression was inhibited by supplementation of an antioxidant such as N‐acetyl cysteamine and hyaluronic acidin vitro andin vivo. From these results, we conclude that oxidative stress is an important factor for generation of Cox‐2 in synovial fibroblasts and thus its neutralization may be an effective strategy in palliative therapy for chronic joint diseases.
Grading Hampers Cooperative Information Sharing in Group Problem Solving
Authors: Hayek Anne-Sophie , Toma Claudia , Oberlé Dominique , Butera Fabrizio
Published: June 2015

We hypothesized that individual grading in group work, a widespread practice, hampers information sharing in cooperative problem solving. Experiment 1 showed that a condition in which members’ individual contribution was expected to be visible and graded, as in most graded work, led to less pooling of relevant, unshared information and more pooling of less-relevant, shared information than two control conditions where individual contribution was not graded, but either visible or not. Experiment 2 conceptually replicated this effect: Group members primed with grades pooled less of their unshared information, but more of their shared information, compared to group members primed with neutral concepts. Thus, grading can hinder cooperative work and impair information sharing in groups.
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

High-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

Photometric 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

Liquid 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

The 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

To 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.
Enantioseparation characteristics of tadalafil and its intermediate on chitin derived chiral stationary phases
Authors: Zhang Juan , Wang Zhao-Qun , Wang Xiao-Chen , Zhang Jun-Jun , Bai Zheng-Wu , Chen Wei
Published: June 2015

The enantioseparation of tadalafil and its intermediate was affected by the presence of their diastereoisomers or structural analogues.
Investigating the relationship between changes in collagen fiber orientation during skin aging and collagen/water interactions by polarized-FTIR microimaging
Authors: Eklouh-Molinier Christophe , Happillon Teddy , Bouland Nicole , Fichel Caroline , Diébold Marie-Danièle , Angiboust Jean-François , Manfait Michel , Brassart-Pasco Sylvie , Piot Olivier
Published: June 2015

Polarized-FTIR imaging highlights the importance of bound water in collagen fiber orientation changes during skin aging.
Label-free fluorescence light-up detection of T4 polynucleotide kinase activity using the split-to-intact G-quadruplex strategy by ligation-triggered and toehold-mediated strand displacement release
Authors: Zhou Lu , Shen Xiaoqiang , Sun Na , Wang Kewei , Zhang Yuanyuan , Pei Renjun
Published: June 2015

A label-free, fluorescence light-up detection method for T4 polynucleotide kinase activity has been developed using the split-to-intact G-quadruplex strategy.
Development of a low cost microfluidic sensor for the direct determination of nitrate using chromotropic acid in natural waters
Authors: Cogan Deirdre , Fay Cormac , Boyle David , Osborne Conor , Kent Nigel , Cleary John , Diamond Dermot
Published: June 2015

This study has demonstrated, for the first time, a microfluidic autonomous analyser for the direct determination of nitrate, incorporating a modified version of the chromotropic method resulting in a direct, quick, inexpensive and simple procedure to measure nitratein situ.
Hydration-switchable charge transfer in the first bimetallic assembly based on the [Ni(cyclam)]3+ – magnetic CN-bridged chain {(H3O)[NiIII(cyclam)][FeII(CN)6]·5H2O}n
Authors: Nowicka Beata , Reczyński Mateusz , Rams Michał , Nitek Wojciech , Żukrowski Jan , Kapusta Czesław , Sieklucka Barbara
Published: June 2015

The use of the cyclam complex of nickel in an unusual oxidation state enabled merging interesting redox properties with structural flexibility of the coordination skeleton.
Ugi-derived dehydroalanines as a pivotal template in the diversity oriented synthesis of aza-polyheterocycles
Authors: García-González Ma. Carmen , Hernández-Vázquez Eduardo , Gordillo-Cruz Raúl E. , Miranda Luis D.
Published: June 2015

Various readily available, Ugi-derived dehydroalanines were used as pivotal templates to easily and efficiently assemble diverse pharmacologically important polyheterocyclic systems through cascade palladium-catalyzed C–C bond formation processes.
Complex transition metal hydrides: linear correlation of countercation electronegativity versus T–D bond lengths
Authors: Humphries T. D. , Sheppard D. A. , Buckley C. E.
Published: June 2015

For homoleptic 18-electron complex hydrides, an inverse linear correlation has been established between the T–deuterium bond length and the average electronegativity of the metal countercations.
The synthesis and evaluation of near-infrared probes with barbituric acid acceptors forin vivodetection of amyloid plaques
Authors: Zhou Kaixiang , Fu Hualong , Feng Liang , Cui Mengchao , Dai Jiapei , Liu Boli
Published: June 2015

A new array of near-infrared probes containing barbituric acid acceptors has been developed as Aβ imaging agents.
Relatively strong intramolecular antiferromagnetic coupling in a neutral CrIII2NbV2heterobimetallic molecular square
Authors: Oliveira Willian X. C. , Pereira Cynthia L. M. , Pinheiro Carlos B. , Cano Joan , Lloret Francesc , Julve Miguel
Published: June 2015

This work features the preparation of a CrIII2Nbv2molecular square exhibiting a relatively large intramolecular antiferromagnetic coupling between the CrIIIions through the diamagnetic –O–Nbv–O– bridge.
Pd(OAc)2 in WERSA: a novel green catalytic system for Suzuki–Miyaura cross-coupling reactions at room temperature
Authors: Boruah Preeti Rekha , Ali Abdul Aziz , Chetia Mitali , Saikia Bishwajit , Sarma Diganta
Published: June 2015

Pd(OAc)2–WERSA as a novel, efficient and recyclable/reusable catalyst system for Suzuki–Miyaura cross-coupling reactions at room temperature. This is a ligand/base/promoter/additive/organic media free protocol.
Reactive simulation of the chemistry behind the condensed-phase ignition of RDX from hot spots
Authors: Joshi Kaushik L. , Chaudhuri Santanu
Published: June 2015

Reactive MD-based chemical model for thermal initiation and spontaneous ignition in condensed-phase RDX crystals.
Computational and experimental evidence for a new TM–N3/C moiety family in non-PGM electrocatalysts
Authors: Kabir Sadia , Artyushkova Kateryna , Kiefer Boris , Atanassov Plamen
Published: June 2015

Our DFT computations predict favourable formation energies for previously unexplored Fe–N3/C defect moieties in carbonaceous catalysts. N 1s core-level shifts were computed from first-principles for XPS fingerprinting.
A microporous lanthanum metal–organic framework as a bi-functional chemosensor for the detection of picric acid and Fe3+ ions
Authors: Zhang Chuanqi , Yan Yan , Pan Qinhe , Sun Libo , He Hongming , Liu Yunling , Liang Zhiqiang , Li Jiyang
Published: June 2015

A novel microporous lanthanum metal–organic framework 1 was synthesized by using the rigid unsymmetrical tricarboxylate ligand H3TPT. This compound exhibits selective detection of picric acid (PA) and Fe3+ ion.
Ruthenium catalysts for water oxidation involving tetradentate polypyridine-type ligands
Authors: Tong Lianpeng , Zong Ruifa , Zhou Rongwei , Kaveevivitchai Nattawut , Zhang Gang , Thummel Randolph P.
Published: June 2015

A series of RuIIcomplexes that behave as water oxidation catalysts were prepared involving a tetradentate equatorial ligand and two 4-substituted pyridines as the axial ligands. Two of these complexes were derived from 2,9-di-(pyrid-2′-yl)-1,10-phenanthroline (dpp) and examine the effect of incorporating electron-donating amino and bulkyt-butyl groups on catalytic activity. A third complex replaced the two distal pyridines withN-methylimidazoles that are more electron-donating than the pyridines of dpp and potentially stabilize higher oxidation states of the metal. The tetradentate ligand 2-(pyrid-2′-yl)-6-(1′′,10′′-phenanthrol-2′′-yl)pyridine (bpy–phen), possessing a bonding cavity similar to dpp, was also prepared. The RuIIcomplex of this ligand does not have two rotatable pyridines in the equatorial plane and thus shows different flexibility from the [Ru(dpp)] complexes. All the complexes showed activity towards water oxidation. Investigation of their catalytic behavior and electrochemical properties suggests that they may follow the same catalytic pathway as the prototype [Ru(dpp)pic2]2+involving a seven-coordinated [RuIV(O)] intermediate. The influence of coordination geometry on catalytic performance is analyzed and discussed.
Amphiphilic zein hydrolysate as a novel nano-delivery vehicle for curcumin
Authors: Wang Yong-Hui , Wang Jin-Mei , Yang Xiao-Quan , Guo Jian , Lin Yuan
Published: June 2015

We developed amphiphilic zein hydrolysate as a novel delivery vehicle, which could be used for preparation of curcumin-loaded nanoparticles (<50 nm). These nanoparticles have a great application potential in nutraceutical-fortified food and clear beverages.
Photopatterned oil-reservoir micromodels with tailored wetting properties
Authors: Lee Hyundo , Lee Seung Goo , Doyle Patrick S.
Published: June 2015

We present a new method to fabricate oil-reservoir micromodels with heterogeneous wetting properties.
Time-dependent evolution of the Bi3.64Mo0.36O6.55/Bi2MoO6 heterostructure for enhanced photocatalytic activity via the interfacial hole migration
Authors: Dai Zan , Qin Fan , Zhao Huiping , Tian Fan , Liu Yunling , Chen Rong
Published: June 2015

Hierarchical Bi3.64Mo0.36O6.55/Bi2MoO6 heterostructures displayed enhanced photocatalytic activity for dye photodegradation due to efficient electron–hole separation and interfacial hole migration from inner Bi3.64Mo0.36O6.55 layer to outer Bi2MoO6 layer.
Copper(ii)-promoted direct conversion of methylarenes into aromatic oximes
Authors: Yu Jiatao , Lu Ming
Published: June 2015

A simple and efficient catalytic system for direct conversion of methylarenes into aromatic oximes has been developed, with Cu(OAc)2 as catalyst, NHPI (N-hydroxyphthalimide) as additive, tert-butyl nitrite (TBN) as both the nitrogen source and the oxidant. The process proceeds under mild conditions, tolerates a wide range of substrates, affording the corresponding aromatic oximes in 63–86% yields.
Design, synthesis and biological evaluation of 5′-C-piperidinyl-5′-O-aminoribosyluridines as potential antibacterial agents
Authors: Nakaya Takeshi , Matsuda Akira , Ichikawa Satoshi
Published: June 2015

Caprazamycin analogues, which were designed and synthesized via an aza-Prins–Ritter reaction, exhibit a good MraY and antibacterial activity without cytotoxicity against human cells.
Copper-catalyzed cross-coupling reactions for C–P bond formation
Authors: Zhang Hui , Zhang Xue-Yan , Dong Dao-Qing , Wang Zu-Li
Published: June 2015

Phosphorus compounds are important compounds in many areas.
The economic, environmental and welfare implications of alternative systems of accommodating dairy cows during the winter months
Authors: French P. , Driscoll K. O. , Horan B. , Shalloo L.
Published: June 2015

Pasture grazed in situ is one of the most competitive and sustainable feeding systems for dairy cows globally because of a low environmental footprint, the potential for excellent animal welfare and the relatively low cost in the production and utilisation of the feed. However, because of seasonal variation in grass production and inclement weather conditions, dairy cattle may have to be accommodated and/or fed off pasture. There are numerous infrastructural options for achieving this and the focus of the present paper was to review the research and discuss the merits of these alternate animal accommodation systems, focussing on the impact that they have on the environment, animal welfare and farm profitability relative to pasture-only systems. Research data showed that dairy cow welfare can be protected in a range of well managed alternative winter accommodation. In a temperate climate, such as that which pertains in Ireland, adequately fed adult cattle will not use extra feed energy to maintain body temperature when accommodated outdoors and exposed to the effects of wind, rain and low temperatures, as the heat produced from the digestion of feed is in excess of the requirement to maintain body temperature. The main welfare challenge of a wintering system in such conditions is to provide suitable lying facilities for cows to express normal lying behaviour and provide adequate feed. The primary economic focus of pasture-based systems should be to maximise the length of the grass-grazing season and, consequently, to minimise the period off paddock. Provided that body condition targets can be met, there will be minimal effect of wintering system on dairy cow productivity and the only economic differences will be in costs. The cost analysis should combine the capital costs of construction financed over its useful life and the annual operating costs, including labour.
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

The 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

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

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.
Fusarium Wilt of Banana
Authors: Ploetz Randy C.
Published: June 2015

Banana (Musa spp.) is one of the world’s most important fruits. In 2011, 145 million metric tons, worth an estimated $44 billion, were produced in over 130 countries. Fusarium wilt (also known as Panama disease) is one of the most destructive diseases of this crop. It devastated the ‘Gros Michel’-based export trades before the mid-1900s, and threatens the Cavendish cultivars that were used to replace it; in total, the latter cultivars are now responsible for approximately 45% of all production. An overview of the disease and its causal agent, Fusarium oxysporum f. sp. cubense, is presented below. Despite a substantial positive literature on biological, chemical, or cultural measures, management is largely restricted to excluding F. oxysporum f. sp. cubense from noninfested areas and using resistant cultivars where the pathogen has established. Resistance to Fusarium wilt is poor in several breeding targets, including important dessert and cooking cultivars. Better resistance to this and other diseases is needed. The history and impact of Fusarium wilt is summarized with an emphasis on tropical race 4 (TR4), a ‘Cavendish’-killing variant of the pathogen that has spread dramatically in the Eastern Hemisphere.
N-terminal pro-B-type Natriuretic Peptides’ Prognostic Utility Is Overestimated in Meta-analyses Using Study-specific Optimal Diagnostic Thresholds
Authors: Potgieter Danielle , Simmers Dale , Ryan Lisa , Biccard Bruce M. , Lurati-Buse Giovanna A. , Cardinale Daniela M. , Chong Carol P. W. , Cnotliwy Miloslaw , Farzi Sylvia I. , Jankovic Radmilo J. , Lim Wen Kwang , Mahla Elisabeth , Manikandan Ramaswamy , Oscarsson Anna , Phy Michael P. , Rajagopalan Sriram , Van Gaal William J. , Waliszek Marek , Rodseth Reitze N.
Published: June 2015

AbstractAbstract

Meta-analysis of studies that made use of a study-specific optimal N-terminal fragment B-type natriuretic peptide threshold resulted in a larger risk point estimate for the prediction of the composite outcome of postoperative mortality and nonfatal myocardial infarction at 30 days after noncardiac surgery compared with using a single threshold across all studies. These data suggest that future biomarker studies should be evaluated as continuous variables rather than making use of post hoc study-specific optimal thresholds, and care should be taken when conducting meta-analysis on studies that have used study-specific optimal thresholds to evaluate biomarker prognostic ability, as it is likely that this methodology will overestimate biomarker predictive performance.

Background:

N-terminal fragment B-type natriuretic peptide (NT-proBNP) prognostic utility is commonly determined post hoc by identifying a single optimal discrimination threshold tailored to the individual study population. The authors aimed to determine how using these study-specific post hoc thresholds impacts meta-analysis results.

Methods:

The authors conducted a systematic review of studies reporting the ability of preoperative NT-proBNP measurements to predict the composite outcome of all-cause mortality and nonfatal myocardial infarction at 30 days after noncardiac surgery. Individual patient-level data NT-proBNP thresholds were determined using two different methodologies. First, a single combined NT-proBNP threshold was determined for the entire cohort of patients, and a meta-analysis conducted using this single threshold. Second, study-specific thresholds were determined for each individual study, with meta-analysis being conducted using these study-specific thresholds.

Results:

The authors obtained individual patient data from 14 studies (n = 2,196). Using a single NT-proBNP cohort threshold, the odds ratio (OR) associated with an increased NT-proBNP measurement was 3.43 (95% CI, 2.08 to 5.64). Using individual study-specific thresholds, the OR associated with an increased NT-proBNP measurement was 6.45 (95% CI, 3.98 to 10.46). In smaller studies (<100 patients) a single cohort threshold was associated with an OR of 5.4 (95% CI, 2.27 to 12.84) as compared with an OR of 14.38 (95% CI, 6.08 to 34.01) for study-specific thresholds.

Conclusions:

Post hoc identification of study-specific prognostic biomarker thresholds artificially maximizes biomarker predictive power, resulting in an amplification or overestimation during meta-analysis of these results. This effect is accentuated in small studies.