bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcium (II) - and dipicolinic acid mediated-biostimulation of oil-bioremediation under multiple stresses by heat, oil and heavy metals
Authors: Radwan Samir S. , Al-Mailem Dina M. , Kansour Mayada K. 
Published: August 2017

AbstractThe oil-producing Arabian Gulf states have hot summer seasons of about 7-month in length. Therefore, environmental oil spills should be bioremediated by the activity of indigenous, hydrocarbonoclastic (hydrocarbon-degrading) microorganisms with optimum growth at about 50 °C. Soils in such arid countries harbor thermophilic bacteria, whose oil-consumption potential is enhanced by calcium (II) - and dipicolinic acid (DPA)-supplement. Those organisms are, however, subjected to additional stresses including toxic effects of heavy metals that may be associated with the spilled oil. Our study highlighted the resistance of indigenous, thermophilic isolates to the heavy metals, mercury (II), cadmium (II), arsenic (II) and lead (II) at 50 °C. We also detected the uptake of heavy metals by 15 isolates at 50 °C, and identified the merA genes coding for Hg2+-resistance in 4 of the studied Hg2+-resistant isolates. Hg2+ was the most toxic metal and the metal toxicity was commonly higher in the presence of oil. The addition of Ca2+ and DPA enhanced the Hg2+-resistance among most of the isolates at 50 °C. Crude oil consumption at 50 °C by 4 selected isolates was inhibited by the tested heavy metals. However, Ca2+ and DPA limited this inhibition and enhanced oil-consumption, which exceeded by far the values in the control cultures.
DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern
Authors: Steinke Dirk , Bernard Andrea M. , Horn Rebekah L. , Hilton Paul , Hanner Robert , Shivji Mahmood S. 
Published: August 2017

AbstractContinuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or – in two cases – to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories ‘Endangered’ and ‘Vulnerable’, raising further concerns about the impacts of this trade on the sustainability of these low productivity species.
Three-Dimensional Geometric Morphometric Analysis of Fossil Canid Mandibles and Skulls
Authors: Drake Abby Grace , Coquerelle Michael , Kosintsev Pavel A. , Bachura Olga P. , Sablin Mikhail , Gusev Andrei V. , Fleming Lacey S. , Losey Robert J. 
Published: August 2017

AbstractMuch of the fossil record for dogs consists of mandibles. However, can fossil canid mandibles be reliably identified as dogs or wolves? 3D geometric morphometric analysis correctly classifies 99.5% of the modern dog and wolf mandibles. However, only 4 of 26 Ust’-Polui fossil mandibles, a Russian Arctic site occupied from 250BCE to 150CE, were identified as dogs and none of the 20 Ivolgin mandibles, an Iron Age site in southern Russia, were identified as dogs. Three of the Ust’-Polui mandibles and 8 of the Ivolgin mandibles were identified as wolves. In contrast, all 12 Ivolgin skulls and 5 Ust’-Polui skulls were clearly identified as dogs. Only the classification of the UP6571 skull as a dog (Dog Posterior Probability = 1.0) was not supported by the typical probability. Other evidence indicates these canids were domesticated: they were located within human dwellings, remains at both sites have butchery marks indicating that they were consumed, and isotope analysis of canid and human remains from Ust’-Polui demonstrate that both were consuming freshwater protein; indicating that the humans were feeding the canids. Our results demonstrate that the mandible may not evolve as rapidly as the cranium and the mandible is not reliable for identifying early dog fossils.
Tensile properties of millimeter-long multi-walled carbon nanotubes
Authors: Kim Hyung-ick , Wang Mei , Lee Stephanie K. , Kang Junmo , Nam Jae-Do , Ci Lijie , Suhr Jonghwan 
Published: August 2017

AbstractThere have been a number of theoretical and experimental studies on tensile properties of carbon nanotubes (CNT), reporting the Young’s modulus of the individual CNT up to 1 TPa. Although CNT shows the promise to be used as reinforcement in a high modulus/strength composite material, it exhibits quite disappointing in terms of modulus or strength. Along with recent advance in CNT growth technique, we will be able to directly measure tensile properties of millimeter-long MWCNTs. This study firstly tackles the direct measurement of the tensile properties of millimeter-long MWCNTs that can be used as reinforcement in a composite system. A carefully designed tensile testing technique for the MWCNTs is developed, which allows us to obtain more accurate and reliable measured values. The average tensile strength and Young’s modulus of the CNTs investigated in this study are measured to be 0.85 GPa and 34.65 GPa, respectively. Also, this work statistically investigates the effect of the CNT dimensions including length, diameter and volume on the tensile properties. To the best of our knowledge, this is the very first report on the tensile properties of macroscopically long and continuous CNTs.
Preoperative prognostic nutritional index is a powerful predictor of prognosis in patients with stage III ovarian cancer
Authors: Zhang Weiwei , Ye Bin , Liang Weijiang , Ren Yazhou 
Published: August 2017

AbstractMany established inflammation- and nutrition-related factors have been investigated as potential independent prognostic factors in various cancers, including the C-reactive protein/albumin ratio (CAR), lymphocyte/monocyte ratio (LMR), modified Glasgow prognostic score (mGPS), body mass index (BMI), and prognostic nutritional index (PNI). This study was performed to estimate the prognostic value of these factors in predicting survival and platinum resistance in ovarian cancer (OC), especially according to stage. Kaplan-Meier and multivariate analyses were performed to plot the survival curve and determine the independent prognostic factors. Additionally, the area under the receiver operating characteristic curve (AUC) was used to predict platinum resistance and prognosis by comparing the predictive ability of PNI and cancer antigen (CA)-125. In all patients, decreased PNI was significantly associated with platinum resistance and poor overall survival (OS) and progression-free survival (PFS). Regarding tumor stage, decreased PNI was significantly associated with poor PFS and OS only in stage III OC. Furthermore, the PNI also showed a significantly higher AUC value than CA-125 for predicting mortality and platinum resistance in all OC patients, but not in stage III patients. In conclusion, decreased PNI is a powerful predictor of a poor prognosis in OC, and especially for stage III cases.
Pharmacological Inhibition of PTEN Aggravates Acute Kidney Injury
Authors: Zhou Jun , Jia Li , Hu Zhaoyong , Wang Yanlin 
Published: August 2017

AbstractRenal ischemia/reperfusion is a major cause of acute kidney injury. However, the pathogenic mechanisms underlying renal ischemia/reperfusion injury (IRI) are not fully defined. Here, we investigated the role of PTEN, a dual protein/lipid phosphatase, in the development of ischemic AKI in mice. Pharmacological inhibition of PTEN with bpV(HOpic) exacerbated renal dysfunction and promoted tubular damage in mice with IRI compared with vehicle-treated mice with IRI. PTEN inhibition enhanced tubular cell apoptosis in kidneys with IRI, which was associated with excessive caspase-3 activation. Furthermore, PTEN inhibition expanded the infiltration of neutrophils and macrophages into kidneys with IRI, which was accompanied by increased expression of the proinflammatory molecules. These results have demonstrated that PTEN plays a crucial role in the pathogenesis of ischemic acute kidney injury through regulating tubular cell apoptosis and inflammation suggesting PTEN could be a potential therapeutic target for acute kidney injury.
A novel use of etched multi‐mode fibre as magnetic field sensor
Authors: Bhardwaj Vanita , Singh Vinod Kumar 
Published: August 2017

In this study, an optical fibre magnetic field sensor is experimentally demonstrated using chemical etched multimode fibre sandwiched between two single mode fibres. The obtained result of the magnetic field and refractive index response shows that the decreasing fibre diameter in the sensing region plays an important role to enhance the sensitivity of the device. The magnetic field sensing is based on a tunable refractive index (RI) property of magnetic fluid infiltrated into the capillary tube. The sensing system is verified by testing RI of different concentrations of sodium chloride (NaCl) solution before sealing in capillary tube. Experimental results show that the sensor with taper fibre diameter of 45 µm has relatively high magnetic field sensitivity of ∼0.993 dB/mT ranging from 0 to 6 mT. The proposed devices find potential applications in magnetic field sensing.
Heterocyclic Chemistry – Old Science or the Forefront of Chemistry?
Authors: Reiser Oliver 
Published: August 2017

Oliver Reiser studied chemistry at the Universities of Hamburg, Jerusalem and Los Angeles (UCLA) and earned his Ph.D. degree from the University of Hamburg (Prof. Armin de Meijere) in 1989. After postdoctoral stays at IBM Research Center (Dr. Robert D. Miller) and Harvard University (Prof. David A. Evans), he started his independent research in 1992 at the University of Göttingen. In 1996, he moved to the University of Stuttgart as an Associate Professor and in 1997, to the University of Regensburg as Professor of Chemistry. His research group specializes in catalysis starting from renewable resources such as furans and pyrroles toward fine chemicals, natural products and drugs. He is currently serving as President of the International Society of Heterocyclic Chemistry.
High-precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization
Authors: Marquart Gregory D. , Tabor Kathryn M. , Horstick Eric J. , Brown Mary , Geoca Alexandra K. , Polys Nicholas F. , Nogare Damian Dalle , Burgess Harold A. 
Published: August 2017

Abstract
Atlases provide a framework for spatially mapping information from diverse sources into a common reference space. Specifically, brain atlases allow annotation of gene expression, cell morphology, connectivity, and activity. In larval zebrafish, advances in genetics, imaging, and computational methods now allow the collection of such information brain-wide. However, due to technical considerations, disparate datasets may use different references and may not be aligned to the same coordinate space. Two recent larval zebrafish atlases exemplify this problem: Z-Brain, containing gene expression, neural activity, and neuroanatomical segmentations, was acquired using immunohistochemical stains, while the Zebrafish Brain Browser (ZBB) was constructed from live scans of fluorescent reporters in transgenic larvae. Although different references were used, the atlases included several common transgenic patterns that provide potential “bridges” for transforming each into the other's coordinate space. We tested multiple bridging channels and registration algorithms and found that the symmetric diffeomorphic normalization algorithm improved live brain registration precision while better preserving cell morphology than B-spline-based registrations. Symmetric diffeomorphic normalization also corrected for tissue distortion introduced during fixation. Multi-reference channel optimization provided a transformation that enabled Z-Brain and ZBB to be co-aligned with precision of approximately a single cell diameter and minimal perturbation of cell and tissue morphology. Finally, we developed software to visualize brain regions in 3 dimensions, including a virtual reality neuroanatomy explorer. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate reference templates and acquisition protocols, when sufficient information is present for bridging. Increased accuracy and interoperability of zebrafish digital brain atlases will facilitate neurobiological studies.
Bayes Forest: a data-intensive generator of morphological tree clones
Authors: Potapov Ilya , Järvenpää Marko , Åkerblom Markku , Raumonen Pasi , Kaasalainen Mikko 
Published: August 2017

Abstract
Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree “clones” based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research.
De-Constitutionalising Collective Labour Rights: The Case of Greece
Authors: Katsaroumpas Ioannis 
Published: August 2017

Abstract
Since 2010, multiple waves of EU/IMF-imposed legislative reforms have led to extensive deregulation or ‘de-construction’ of Greek collective labour law. While there are many accounts of the Greek reforms, no systematic attention has been devoted to the following paradox: how is such a de-construction possible, in a jurisdiction enjoying a strong domestic constitutionalisation of labour rights, and apparently observing multiple transnational collective labour rights, derived from the CFREU, ECHR, and ILO Conventions? This article sets out to investigate the constitutional dynamics behind the process termed here as ‘de-constitutionalisation’ of collective labour rights. It seeks to add two contributions to the existing literature. Firstly, taking its cue from Eric Tucker’s mapping of multi-level ‘capital’ and ‘labour’ constitutions developed in the Canadian context, it suggests that the Greek case of de-constitutionalisation is the cumulative result of a specific configuration of interactions between ‘aggressive’ EU-IMF conditionality at the level of transnational capital rights, and ‘defensive’ articulation of labour rights at domestic and transnational levels. As will be seen, these interactions disguise an asymmetric clash between a strong constutionalisation of capital rights at transnational level, and a weak constitutionalisation of labour rights at both transnational and domestic levels. Secondly, the article projects the Greek case onto the broader constitutionalisation debate, which questions the desirability of constitutionalising collective labour rights as an effective response to neo-liberal policies and laws. While submitting that the Greek developments support the sceptical side of this debate, in particular by providing a continental European confirmation of Tucker’s thesis, the article offers several new reflections of relevance to the constitutionalisation debate.
The scatter, residual correlations and curvature of the sparc baryonic Tully–Fisher relation
Authors: Desmond Harry 
Published: August 2017

Abstract
In recent work, Lelli et al. argue that the tightness of the baryonic Tully–Fisher relation (BTFR) of the sparc galaxy sample, and the weakness of the correlation of its residuals with effective radius, pose challenges to Λ cold dark matter cosmology. In this Letter, we calculate the statistical significance of these results in the framework of halo abundance matching, which imposes a canonical galaxy–halo connection. Taking full account of sample variance among sparc-like realizations of the parent halo population, we find the scatter in the predicted BTFR to be 3.6σ too high, but the correlation of its residuals with galaxy size to be naturally weak. Further, we find abundance matching to generate BTFR curvature in 3.0σ disagreement with the data, and a fraction of galaxies with non-flat rotation curves somewhat larger than observed.
Stacked Generalization: An Introduction to Super Learning
Authors: Naimi Ashley I. , Balzer Laura B. 
Published: August 2017

AbstractStacked generalization is an ensemble method that allows researchers to combine several different prediction algorithms into one. Since its introduction in the early 1990s, the method has evolved several times into what is now known as “Super Learner”. Super Learner usesV-fold cross-validation to build the optimal weighted combination of predictions from a library of candidate algorithms. Optimality is defined by a user-specified objective function, such as minimizing mean squared error or maximizing the area under the receiver operating characteristic curve. Although relatively simple in nature, use of the Super Learner by epidemiologists has been hampered by limitations in understanding conceptual and technical details. We work step-by-step through two examples to illustrate concepts and address common concerns.
Characterizing a thermostable Cas9 for bacterial genome editing and silencing
Authors: Mougiakos Ioannis , Mohanraju Prarthana , Bosma Elleke F. , Vrouwe Valentijn , Bou Max Finger , Naduthodi Mihris I. S. , Gussak Alexander , Brinkman Rudolf B. L. , Kranenburg Richard van , der Oost John van 
Published: August 2017

AbstractCRISPR-Cas9 based genome engineering tools have revolutionized fundamental research and biotechnological exploitation of both eukaryotes and prokaryotes. However, the mesophilic nature of the established Cas9 systems does not allow for applications that require enhanced stability, including engineering at elevated temperatures. Here, we identify and characterize ThermoCas9: an RNA-guided DNA-endonuclease from the thermophilic bacterium Geobacillus thermodenitrificans T12. We show that ThermoCas9 is active in vitro between 20°C and 70°C, a temperature range much broader than that of the currently used Cas9 orthologues. Additionally, we demonstrate that ThermoCas9 activity at elevated temperatures is strongly associated with the structure of the employed sgRNA. Subsequently, we develop ThermoCas9-based engineering tools for gene deletion and transcriptional silencing at 55°C in Bacillus smithii and for gene deletion at 37°C in Pseudomonas putida. Altogether, our findings provide fundamental insights into a thermophilic CRISPR-Cas family member and establish the first Cas9-based bacterial genome editing and silencing tool with a broad temperature range.
SPIN1 promotes tumorigenesis by blocking the uL18-MDM2-p53 pathway
Authors: Fang Ziling , Liao Jun-Ming , Cao Bo , Deng Jun , Plummer Kevin D , Liao Peng , Liu Tao , Zeng Shelya X. , Xiong Jianping , Lu Hua 
Published: August 2017

AbstractRibosomal proteins (RPs) play important roles in modulating the MDM2-p53 pathway. However, less is known about the upstream regulators of the RPs. Here we identify SPIN1 (Spindlin 1) as a novel binding partner of human RPL5/uL18 that is important for this pathway. SPIN1 ablation activates p53, suppresses cell growth, reduces clonogenic ability, and induces apoptosis of cancer cells by sequestering uL18 in the nucleolus, preventing it from interacting with MDM2, and thereby alleviating uL18-mediated inhibition of MDM2 ubiquitin ligase activity towards p53. SPIN1 deficiency increases ribosome-free uL18 and uL5 (human RPL11), which are required for SPIN1 depletion-induced p53 activation. Analysis of cancer genomic databases suggests that SPIN1 is highly expressed in several human cancers, and its overexpression is positively correlated with poor prognosis in cancer patients. Altogether, our findings reveal that the oncogenic property of SPIN1 is highly attributed to its negative regulation of uL18, leading to p53 inactivation.
BCL-3 enhances β-catenin signalling in colorectal tumour cells promoting a cancer stem cell phenotype
Authors: Legge Danny N , Shephard Alex P , Collard Tracey J , Greenhough Alexander , Chambers Adam C , Clarkson Richard W , Paraskeva Christos , Williams Ann C 
Published: August 2017

AbstractIncreased nuclear BCL-3 (a key regulator of inflammation and NF-κB signalling when associated with p50 or p52 homodimers) has been reported in a subset of colorectal cancers, but its role in colorectal tumorigenesis remains poorly understood. Interestingly, recent studies have highlighted the importance of the interplay between NF-κB signalling and the Wnt/β-catenin pathway in colorectal epithelial cells, reporting that non-stem cells engineered to undergo high levels of Wnt and NF-κB signalling can de-differentiate, initiating tumours in mice. Here we show that BCL-3 is an important co-activator of β-catenin/TCF-mediated transcriptional activity in colorectal cancer cells, increasing expression of Wnt-regulated intestinal stem cell genes. We demonstrate RNAi-mediated BCL-3 suppression reduced β-catenin/TCF-dependent transcription and the expression of intestinal stem cell genes and Wnt targetsLGR5andASCL2. Further we show that BCL-3 promotes the stem cell phenotype in colorectal cancer cells by increasing colorectal spheroid and tumoursphere formation in 3D culture conditions. Our data suggest that targeting BCL-3 may represent an exciting new approach for CRC treatment, particularly as it acts downstream of frequently mutated APC and β-catenin.