bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genome of the river water buffalo
Authors: Mintoo Abdul Awal , Zhang Hailin , Chen Chunhai , Moniruzzaman Mohammad , Deng Tingxian , Anam Mahbub , Emdadul Huque Quazi Mohammad , Guang Xuanmin , Wang Ping , Zhong Zhen , Han Pengfei , Khatun Asma , Awal Tabith M. , Gao Qiang , Liang Xianwei 
Published: February 2019

AbstractWater buffalo (Bubalus bubalis), a large‐sized member of the Bovidae family, is considered as an important livestock species throughout Southeast Asia. In order to better understand the molecular basis of buffalo improvement and breeding, we sequenced and assembled the genome (2n=50) of a river buffalo species Bubalus bubalis from Bangladesh. Its genome size is 2.77 Gb, with a contig N50 of 25 kb and the scaffold N50 of 6.9 Mbp. Based on the assembled genome, we annotated 24,613 genes for future functional genomics studies. Phylogenetic tree analysis of cattle and water buffalo lineages showed that they diverged about 5.8–9.8 million years ago. Our findings provide an insight into the water buffalo genome which will contribute in further research on buffalo such as molecular breeding, understanding complex traits, conservation, and biodiversity.
Soil water vapour isotopes identify missing water source for streamside trees
Authors: Oerter Erik J. , Siebert Griffin , Bowling David R. , Bowen Gabriel 
Published: February 2019

AbstractIn a seminal study, Dawson and Ehleringer used deuterium measurements on water to show that boxelder (Acer negundo) and bigtooth maple (Acer grandidentatum) trees growing directly next to a perennial stream in a mountain meadow did not use the stream water for transpiration, nor could they identify any other potential water source. Since then, similar observations of plant water isotopic signatures that do not match any available water source have been reported from a range of ecosystems worldwide. Here, we use a combination of non‐destructive in situ isotopic soil water sampling along with destructive soil sampling and cryogenic water extraction to demonstrate that isotopically distinct water pools can be identified in soils at the same site as the 1991 study during parts of the summer growing season. Water extracted from xylem tissues shows that streamside boxelder and bigtooth maple at the sites were predominantly using soil water with an isotopic composition similar to that measured by the in situ soil measurement technique. We introduce the use of water vapour probes that were directly attached to intact tree roots in situ to measure the isotopic composition of root xylem water and how it varies through the growing season and evaluate their potential and utility.
Spatial Architecture of Modified Carbon Nanotubes/Electrochemically Reduced Graphene Oxide Nanomaterial for Fast Electron Transfer. Application in Glucose Biosensor
Authors: Jakubow‐Piotrowska Katarzyna , Kowalewska Barbara 
Published: February 2019

AbstractElectron transfer (ET) reactions in bioelectrocatalysis of enzymes at electrode surfaces require not only the efficient immobilization, but also highly conductive nanostructured platform, which allows for retaining its bioactivity and structural conformation. The novel architecture of spatially separated electrochemically reduced graphene oxide (ERGO) by multi‐walled carbon nanotubes functionalized with 4‐(pyrrole‐1‐yl) benzoic acid (MWCNT/PyBA) with the accurate porous structure could be an alternative for earlier approaches to the construction of bioelectrocatalytic systems with rapid diffusion of reagents from the solution to the enzyme molecule. The formation of ERGO/MWCNT/PyBA system was confirmed by electrochemical, spectroscopic and microscopic methods. The cyclic voltammetry experiments revealed that the presence of ERGO in the conductive material affects the electronic communication between the enzyme molecule and modified electrode surface greatly improving its ET properties resulting in a double increase of the heterogeneous ET rate constant value (ks=6.5 s−1). The fabricated glucose oxidase based biosensor sensitively detects glucose, therefore, ERGO/MWCNT/PyBA architecture could provide a novel and efficient platform for immobilization of redox enzymes.
Applications of magnetic materials separation in biological nanomedicine
Authors: Ma Yuanyuan , Chen Tianxiang , Iqbal Muhammad Zubair , Yang Fang , Hampp Norbert , Wu Aiguo , Luo Liqiang 
Published: February 2019

AbstractAs a result of their advantages for superparamagnetic properties, good biocompatibility, and high binding capacity, functionalized magnetic materials became widely popular over the past couple of decades, being applied on large scale in various processes of sample preparation for biomedicine. In this work, we perform an in‐depth review on the current progress in the field of magnetic bead separation, discussing in detail the physical basis of this process, various synthesis methods and surface modification strategies. We place special focus of attention as well on the latest applications of magnetic polymer microspheres in cell separation, protein purification, immobilized enzyme, nucleic acid separation, and extraction of bioactive compounds with low molecular weight. Existing problems are highlighted and possible trends of magnetic separation techniques for biomedicine in the future are proposed.
Flexible antenna design on PDMS substrate for implantable bioelectronics applications
Authors: Fu Yusheng , Lei Jianmin , Zou Xiao , Guo Jiuchuan 
Published: February 2019

AbstractIn the current field of biomedical engineering, the research on implanted antennas has attracted more and more attention. This paper presents a flexible terrestrial radiating antenna with circular polarization characteristics that satisfy various requirements for biomedical implantable antennas. The new type of flexible material is adopted and a novel model is proposed. The square ground with small gap is implemented in the proposed antenna. The passive components can match the impedance and meet the requirements of the circular polarization wave. Simulation is carried out in a single layer tissue model to estimate the performance of the antenna and compared with multilayer tissue model. In addition, the flexible circularly polarized antenna has low profile characteristics and a wide axial ratio bandwidth of 250 MHz, ranging from 2.28 to 2.53 GHz. This paper uses pork to simulate single‐layer and multi‐layer tissue model. The flexible circular polarized antenna prototype is placed in the organization model for performance simulation test, and the measurement impedance bandwidth of 500 MHz is realized in the industrial scientific medical frequency band of 2.4–2.48 GHz.
Large roots dominate the contribution of trees to slope stability
Authors: Giadrossich Filippo , Cohen Denis , Schwarz Massimiliano , Ganga Antonio , Marrosu Roberto , Pirastru Mario , Capra Gian Franco 
Published: February 2019

AbstractTree roots provide surface erosion protection and improve slope stability through highly complex interactions with the soil due to the nature of root systems. Root reinforcement estimation is usually performed by in situ pullout tests, in which roots are pulled out of the soil to reliably estimate the root strength of compact soils. However, this test is not suitable for the scenario where a soil progressively fails in a series of slump blocks – for example, in unsupported soils near streambanks and road cuts where the soil has no compressive resistance at the base of the hillslope. The scenario where a soil is unsupported on its downslope extent and progressively deforms at a slow strain rate has received little attention, and we are unaware of any study on root reinforcement that estimates the additional strength provided by roots in this situation. We therefore designed two complementary laboratory experiments to compare the force required to pull the root out. The results indicate that the force required to pull out roots is reduced by up to 50% when the soil fails as slump blocks compared to pullout tests. We also found that, for slump block failure, roots had a higher tendency to slip than to break, showing the importance of active earth pressure on root reinforcement behaviour, which contributes to reduced friction between soil and roots. These results were then scaled up to a full tree and tree stand using the root bundle and field‐measured spatial distributions of root density. Although effects on the force mobilized in small roots can be relevant, small roots have virtually no effect on root reinforcement at the tree or stand scale on hillslopes. When root distribution has a wide range of diameters, the root reinforcement results are controlled by large roots, which hold much more force than small roots. © 2019 John Wiley & Sons, Ltd.
pH-Dependent Uptake and Sublethal Effects of Antihistamines in Zebrafish (Danio rerio) Embryos
Authors: Bittner Lisa , Teixidó Elisabet , Keddi Isabel , Escher Beate I. , Klüver Nils 
Published: February 2019

Abstract
Reported off-target effects of antihistamines in humans draw interest in ecotoxicity testing of first- and second-generation antihistamines, the latter of which have fewer reported side effects in humans. Because antihistamines are ionizable compounds, the pH influences uptake and toxicity and thus is highly relevant when conducting toxicity experiments. Zebrafish embryo toxicity tests were performed with the 3 first-generation antihistamines ketotifen, doxylamine, and dimethindene and the 2 second-generation antihistamines cetirizine and levocabastine at pH 5.5, 7.0, and 8.0. We detected effects on survival, phenotype, swimming activity, and heart rate for 4 antihistamines with the exception of levocabastine, which did not show any lethal or sublethal effects. When compared to lethal concentrations, effect concentrations neither of phenotype malformation nor of swimming activity or heart rate deviated by more than a factor of 10 from lethal concentrations, indicating that all sublethal effects were fairly nonspecific. First-generation antihistamines are weak bases and showed decreasing external effect concentrations with increasing neutral fraction, accompanied by increased uptake in the fish embryo. As a result, internal effect concentrations were independent from external pH. The pH-dependent toxicity originates from speciation-dependent uptake, with neutral species taken up in higher amounts than the corresponding ionic species. Cetirizine, which shifts from a zwitterionic to an anionic state in the measured pH range, did not show any pH-dependent uptake or toxicity. Environ Toxicol Chem 2019;00:1–11. © 2019 SETAC
Mitochondrial Toxicity of Selected Micropollutants, Their Mixtures, and Surface Water Samples Measured by the Oxygen Consumption Rate in Cells
Authors: Müller Maximilian E. , Vikstrom Sofia , König Maria , Schlichting Rita , Zarfl Christiane , Zwiener Christian , Escher Beate I. 
Published: February 2019

Abstract
Some environmental pollutants impair mitochondria, which are of vital importance as energy factories in eukaryotic cells. Mitochondrial toxicity was quantified by measuring the change of the oxygen consumption rate (OCR) of HepG2 cells with the Agilent Seahorse XFe96 Analyzer. Various mechanisms of mitochondrial toxicity, including inhibition of the electron transport chain or adenosine triphosphate (ATP) synthase as well as uncoupling of oxidative phosphorylation, were differentiated by dosing the sample in parallel with reference compounds following the OCR over time. These time–OCR traces were used to derive effect concentrations for 10% inhibition of the electron transport chain or 10% of uncoupling. The low effect level of 10% was necessary because environmental mixtures contain thousands of chemicals; only few of them interfere with mitochondria, but the others cause cytotoxicity. The OCR bioassay was validated with environmental pollutants of known mechanism of mitochondrial toxicity. Binary mixtures of uncouplers or inhibitors acted according to the mixture model of concentration addition. Uncoupling and/or inhibitory effects were detected in extracts of river water samples without apparent cytotoxicity. Uncoupling effects could only be quantified in water samples if inhibitory effects occurred at lower concentrations because no uncoupling can be detected without an appreciable membrane potential built up. The OCR bioassay can thus complement chemical analysis and in vitro bioassays for monitoring micropollutants in water. Environ Toxicol Chem 2019;00:1–12. © 2019 SETAC
Abstract
Mitochondrial toxicity in water extracts measured by the oxygen consumption rate (OCR) in cells. Agents that uncouple the oxidative phosphorylation (e.g., bromoxynil) increase the cellular OCR and those that inhibit the electron transport chain (e.g., azoxystrobin) decrease OCR.
Trading volume and prediction of stock return reversals: Conditioning on investor types' trading
Authors: Ülkü Numan , Onishchenko Olena 
Published: February 2019

AbstractWe show that contrasting results on trading volume's predictive role for short‐horizon reversals in stock returns can be reconciled by conditioning on different investor types' trading. Using unique trading data by investor type from Korea, we provide explicit evidence of three distinct mechanisms leading to contrasting outcomes: (i) informed buying—price increases accompanied by high institutional buying volume are less likely to reverse; (ii) liquidity selling—price declines accompanied by high institutional selling volume in institutional investor habitat are more likely to reverse; (iii) attention‐driven speculative buying—price increases accompanied by high individual buying‐volume in individual investor habitat are more likely to reverse. Our approach to predict which mechanism will prevail improves reversal forecasts following return shocks: An augmented contrarian strategy utilizing our ex ante formulation increases short‐horizon reversal strategy profitability by 40–70% in the US and Korean stock markets.
A recurrent clonally distinct Burkitt lymphoma case highlights genetic key events contributing to oncogenesis
Authors: Penther Dominique , Viailly Pierre‐Julien , Latour Sylvain , Etancelin Pascaline , Bohers Elodie , Vellemans Hélène , Camus Vincent , Menard Anne Lise , Coutant Sophie , Lanic Hélène , Lemasle Emilie , Drieux Fanny , Veresezan Liana , Ruminy Philippe , Raimbault Anna , Soulier Jean , Frebourg Thierry , Tilly Hervé , Jardin Fabrice 
Published: February 2019

AbstractBurkitt lymphoma (BL) is characterized by a translocation of the MYC oncogene that leads to the upregulation of MYC expression, cell growth and proliferation. It is well‐established that MYC translocation is not a sufficient genetic event to cause BL. Next‐generation sequencing has recently provided a comprehensive analysis of the landscape of additional genetic events that contribute to BL lymphomagenesis. Refractory BL or relapsing BL are almost always incurable as a result of the selection of a highly chemoresistant clonally related cell population. Conversely, a few BL recurrence cases arising from clonally distinct tumors have been reported and were associated with a favorable outcome similar to that reported for first‐line treatment. Here, we used an unusual case of recurrent but clonally distinct EBV+ BL to highlight the key genetic events that drive BL lymphomagenesis. By whole exome sequencing, we established that ID3 gene was targeted by distinct mutations in the two clonally unrelated diseases, highlighting the crucial role of this gene during lymphomagenesis. We also detected a heterozygous E1021K PIK3CD mutation, thus increasing the spectrum of somatic mutations altering the PI3K signaling pathway in BL. Interestingly, this mutation is known to be associated with activated phosphoinositide 3‐kinase delta syndrome (APDS). Finally, we also identified an inherited heterozygous truncating c.5791CT FANCM mutation that may contribute to the unusual recurrence of BL.
Gene–environment interactions related to blood pressure traits in two community‐based Korean cohorts
Authors: Lim Ji Eun , Kim Hye Ok , Rhee Sang Youl , Kim Mi Kyung , Kim Yeon‐Jung , Oh Bermseok 
Published: February 2019

AbstractHypertension is a complex disorder caused by genetic and environmental risk factors. Recently, genome‐wide association studies (GWASs) identified more than 100 genetic variants for blood pressure traits and hypertension. However, the interactions between these genetic variants and environmental factors have not been systematically investigated. Therefore, we examined the interaction between genetic and environmental risk factors in blood pressure traits using the genetic risk score (GRS). Two Korean community‐based cohorts, Cohort I (KARE; N = 8,840) and Cohort II (CAVAS; N = 9,599), were used for this study, and GRSs were calculated from 42 GWAS single‐nucleotide polymorphisms (SNPs) that were validated for their association in these cohorts. We calculated GRSs in both ways by considering the effect sizes of each SNP (weighted GRS) and not considering the effect sizes (unweighted GRS). The unweighted GRS was strongly associated with systolic blood pressure, diastolic blood pressure, and hypertension (p = 9.03 × 10
–47, p = 9.41 × 10
–48, and p = 3.22 × 10
–55 by meta‐analysis, respectively) and the weighted GRS showed the similar results. The environmental factors of body mass index, waist circumference, and drinking status were significantly associated with blood pressure traits, and the interaction between these factors and GRSs were examined. However, no interactions were found with either the GRS or the individual SNPs considered for the GRS. Our findings show that it is challenging to find GRS–environment interactions regarding blood pressure traits.
The current status of orogenesis in the Central Indian Tectonic Zone: A view from its Southern Margin
Authors: Bhowmik Santanu Kumar 
Published: February 2019

The Central Indian Tectonic Zone, because of its critical position in the tectonic framework of East Gondwanaland, holds insights into our understanding of the assembly and dispersal of Columbia and Rodinia supercontinents through the growth of the Greater Indian Landmass. The tectonic zone, which is now a collage of different supracrustal and granulite‐gneiss belts, bears testimony to a multistage orogenic evolution from Late Palaeoproterozoic to Early Neoproterozoic time. In this contribution, the current status of orogenic evolution in the Central Indian Tectonic Zone has been reviewed using petrological and geochronological constraints from the Sausar Mobile Belt, its southernmost constituent. It reveals a three‐stage evolution leading to the growth of the Greater Indian Landmass: (a) c. 1.6–1.5‐Ga accretionary orogenesis produced the first nucleus of Greater India through the assembly of arc, back arc, and continental margins; (b) a phase of Middle Proterzoic extension led to the disintegration of the Proto‐Greater India; and (c) classical Himalayan‐style continental collision between 1.06 and 0.93 Ga finally stitched the North and South India blocks to produce the final configuration of the Greater Indian Landmass. It is argued that the Late Palaeoproterozoic to Early Mesoproterozoic orogenesis in India and former Gondwanaland and Laurentian fragments is a globally significant amalgamation event separate from the Columbia Supercontinent assembly.
Early Cretaceous potassic volcanic rocks from the northern margin of the Sulu orogenic belt, Shandong Province, eastern China: Constraints on petrogenesis and crust–mantle interaction
Authors: Cao Guang‐Yue , Xue Huai‐Min , Liu Zhe 
Published: February 2019

A major and trace element, Sr–Nd–Hf isotope, and zircon U–Pb geochronology study was conducted on Early Cretaceous volcanic rocks from the northern margin of the Sulu orogenic belt in Shandong Province, eastern China. These results constrain the petrogenesis of the volcanic rocks and provide important insights into the significance of crust–mantle interaction. The rocks comprise high‐K basaltic andesite, shoshonites, latites, high‐K dacites, and high‐K rhyolites. U–Pb zircon dating of four representative samples of latite, two high‐K dacites, and high‐K rhyolite indicates that these rocks formed from 126 to 122 Ma. The volcanic rocks are characterized by high K2O (2.04–6.70 wt.%) and total alkalis (Na2O + K2O; 5.3–10.9 wt.%) that plot within the field for shoshonitic rocks. All the rocks are enriched in light rare earth and large‐ion lithophile elements (e.g., Rb, Th, U, and K) and are depleted in high‐field‐strength elements (e.g., Nb, Ta, and Ti). The rocks have high initial 87Sr/86Sr ratios (0.706760–0.708898), low εNd(t) values (−19.5 to −12.5), and negative εHf(t) values (−31.3 to −19.7), similar to the Early Cretaceous Jiaodong mafic dikes and intermediate–mafic volcanic rocks. These geochemical and isotopic characteristics indicate that the volcanic rocks formed through simultaneous fractional crystallization and crustal assimilation of a basaltic magma derived from metasomatized mantle. The metasomatized mantle source might have been produced by the recycling of subducted Yangtze Craton crust into the ancient lithospheric mantle of the North China Craton.
White matter tracts lesions and decline of verbal fluency after deep brain stimulation in Parkinson's disease
Authors: Costentin Guillaume , Derrey Stéphane , Gérardin Emmanuel , Cruypeninck Yohann , Pressat‐Laffouilhere Thibaut , Anouar Youssef , Wallon David , Le Goff Floriane , Welter Marie‐Laure , Maltête David 
Published: February 2019

AbstractDecline of verbal fluency (VF) performance is one of the most systematically reported neuropsychological adverse effects after subthalamic nucleus deep brain stimulation (STN‐DBS). It has been suggested that this worsening of VF may be related to a microlesion due to the electrode trajectories. We describe the disruption of surrounding white matter tracts following electrode implantation in Parkinson's disease (PD) patients with STN‐DBS and assess whether damage of fiber pathways is associated with VF impairment after surgery. We retrospectively analyzed 48 PD patients undergoing bilateral STN DBS. The lesion mask along the electrode trajectory transformed into the MNI 152 coordinate system, was compared with white matter tract atlas in Tractotron software, which provides a probability and proportion of fibers disconnection. Combining tract‐ and atlas‐based analysis reveals that the trajectory of the electrodes intersected successively with the frontal aslant tract, anterior segment of arcuate tract, the long segment of arcuate tract, the inferior longitudinal fasciculus, the superior longitudinal fasciculus, the anterior thalamic radiation, and the fronto striatal tract. We found no association between the proportion fiber disconnection and the severity of VF impairment 6 months after surgery. Our findings demonstrated that microstructural injury associated with electrode trajectories involved white matter bundles implicated in VF networks.