bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of segregation structures in Hafnarhraun pāhoehoe lobe, SW Iceland: a window into crystal–melt separation in basaltic magma
Authors: Nikkola Paavo , Thordarson Thorvaldur , Rämö O. Tapani , Heikkilä Pasi 
Published: November 2019

AbstractTo gain insights into crystal–melt separation processes during basalt differentiation, we have studied an 8-m-thick pāhoehoe lava lobe from the Hafnarhraun lava flow field in SW Iceland. The lobe has abundant melt segregations, porous cylindrical and sheet-like structures, generally interpreted as separated residual melts of a lava lobe. We divide these melt segregations into three types based on morphology and composition: vesicle cylinders (VC), type 1 horizontal vesicle sheets (HVS1), and type 2 horizontal vesicle sheets (HVS2). Remarkably, the studied VC are not simple residual melts generated by fractional crystallization, but their composition points to removal of plagioclase from the parental lava. HVS1 resemble VC, but have fractionated more olivine (ol) + plagioclase (plg) ± augite and have lost most, if not all, of their olivine phenocrysts. HVS2 are Fe-rich and evolved, corresponding to residual melts after 50–60% fractional crystallization of the lobe. We suggest that the Hafnarhraun VC formed in a two-stage process. Firstly, VC forming residual melt and vapor detached as rising diapirs from ol+plg+melt+vapor mush near the lava base, and later, these VC diapirs accumulated ol phenocrysts and minor plg microphenocrysts in the lava core. HVS1 represent accumulations of VC to the viscous base of the solidifying upper crust of the lobe, and HVS2 formed as evolved vapor-saturated residual melts seeped into voids within the upper crust. Such vapor-aided differentiation, here documented for the Hafnarhraun lava, may also apply to shallow crustal magma storage zones, contributing to the formation of evolved basalts.
Evaluating additive versus interactive effects of copper and cadmium on Daphnia pulex life history
Authors: Sadeq Shlair A. , Beckerman Andrew P. 
Published: November 2019

AbstractA key challenge of standard ecotoxicological risk assessment is to predict the sub-lethal risk of multiple contaminants on aquatic organisms. Our study assessed the sub-lethal mixture toxicity of copper (Cu) and cadmium (Cd) on Daphnia pulex and included manipulations of food level and assessment of three genotypes. We investigated the interaction between essential (Cu) and non-essential (Cd) metals on ingestion rate, reproduction, maturation time, size at maturity and somatic growth rate of three D. pulex genotypes, over 21 days and under standard and high food conditions. We explored the potential interaction of the metals on ingestion and life history by implementing a response surface experimental design combining control and two levels of Cu and Cd and their combinations. Overall, both metals reduced ingestion rates, reduced reproduction, delayed maturation, reduced body size at maturity and lowered somatic growth rate. Our results further indicated pervasive interactions between the metals; numerous instances where the effects of each metal were non-linear; the effect of a metal varied by D. pulex food levels (ingestion rate and size at maturity), and the effect of a metal varied by genotypes (reproduction). Apart from the maturation time and somatic growth rate, our results suggest that life history traits are affected in non-additive ways by three factors that are often discussed and rarely estimated together: mixtures of metals, genotypes and resource levels. Our data that are derived from exposing daphnids to two metals highlight how metals interact with each other and the context of food resource and genetic variation. While interactions make it harder to generate predictions, and ultimately water quality regulations about the effects of metals, those detected in this study appear to be tractable.
XPO1 Gene Therapy Attenuates Cardiac Dysfunction in Rats with Chronic Induced Myocardial Infarction
Authors: García-Manzanares María , Tarazón Estefanía , Ortega Ana , Gil-Cayuela Carolina , Martínez-Dolz Luis , González-Juanatey José Ramón , Lago Francisca , Portolés Manuel , Roselló-Lletí Esther , Rivera Miguel 
Published: November 2019

AbstractTranscriptomic signature of XPO1 was highly expressed and inversely related to left ventricular function in ischemic cardiomyopathy patients. We hypothesized that treatment with AAV9-shXPO1 attenuates left ventricular dysfunction and remodeling in a myocardial infarction rat model. We induced myocardial infarction by coronary ligation in Sprague-Dawley rats (n = 10), which received AAV9-shXPO1 (n = 5) or placebo AAV9-scramble (n = 5) treatment. Serial echocardiographic assessment was performed throughout the study. After myocardial infarction, AAV9-shXPO1-treated rats showed partial recovery of left ventricular fractional shortening (16.8 ± 2.8 vs 24.6 ± 4.1%, P < 0.05) and a maintained left ventricular dimension (6.17 ± 0.95 vs 4.70 ± 0.93 mm, P < 0.05), which was not observed in non-treated rats. Furthermore, lower levels of EXP-1 (P < 0.05) and lower collagen fibers and fibrosis in cardiac tissue were observed. However, no differences were found in the IL-6 or TNFR1 plasma levels of the myocardium of AAV9-shXPO1 rats. AAV9-shXPO1 administration attenuates cardiac dysfunction and remodeling in rats after myocardial infarction, producing the gene silencing of XPO1.
Effects from usage of pre-trip information and passenger scheduling strategies on waiting times in public transport: an empirical survey based on a dedicated smartphone application
Authors: Berggren Ulrik , Brundell-Freij Karin , Svensson Helena , Wretstrand Anders 
Published: November 2019

AbstractWaiting times are important indicators of the degree of travel time optimisation and other behavioural traits among public transport (PT) passengers. As previous studies have shown, the level and usage of pre-trip information regarding schedule or real-time departures are important factors that influence the potential to realise travel time savings by enabling PT passengers to optimise waiting times. Most empirical evidence regarding the revealed PT travel behaviour concerning information levels is based on manual interviews or traditional travel surveys, in which there is a risk that the actual context of where and when the choice of departure time was made is not taken into account. This paper reports the results of a travel survey based on a dedicated smartphone application applied in a field study in a Swedish mid-size urban and regional context. Context-aware notification prompting was used to allow respondents to state their use of pre-trip information as well as whether they had pre-planned their trip and how contingent planning aids were used for time optimisation. The implications on passenger waiting times of the use of information regarding departure times by passengers were emphasised during analyses of the resulting data, along with personal characteristics, in which auxiliary sources such as timetable data and Automatic Vehicle Location were utilised to determine ground truth trip trajectories and trip-contextual factors. The results indicate the significance of having access to pre-trip information, especially for long trips above one hour’s duration, in order to pre-plan and thereby optimise waiting times. In addition, the use and source of pre-trip information differ among age and gender groups. Trip purpose and time of day to some extent determine waiting times and choice of trip optimisation strategy (arrival or departure time).
Identification of Sugarcane with NDVI Time Series Based on HJ-1 CCD and MODIS Fusion
Authors: Chen Yanli , Feng Liping , Mo Jianfei , Mo Weihua , Ding Meihua , Liu Zhiping 
Published: November 2019

Abstract
It is currently difficult to acquire the clear-sky data with high spatial resolutions in spring and summer in the southern region of China, making it impossible to carry out timely and fine monitoring of sugarcane planting information. Thus, Fusui, a sugarcane producing county in Guangxi, was selected in this paper to analyze the NDVI characteristics and change rules during the whole growth period of sugarcane based on MODIS and HJ-1 CCD remote sensing data, which were fused into 30 m resolution NDVI time series data with high accuracy by using the spatial and temporal fusion model of multi-source remote sensing data ESTRAFM. In addition, the NDVI change rate and sample automatic training threshold were used to construct the sugarcane planting information identification model. The results showed that the fused images showed a high similarity with the observed images, indicating good fusion quality. Moreover, the correlation coefficients in the sugarcane planting area reached 0.953, and AD, AAD and SD were 0.033, 0.019 and 0.007, respectively. The NDVI change rate model was used to identify the sugarcane planting information in different time phases of 113 d, 129 d, 145 d, 193 d and 209 d in spring and summer, and the overall accuracy was 92.17%, 92.58%, 91.78%, 90.52% and 91.17%, respectively. The established model also achieved good results in 2017 with the overall accuracies are 88.44%, 87.79%, 89.79%, 88.34% for 113 d, 145 d, 193 d and 209 d.
Use of maximum likelihood sparse spike inversion and probabilistic neural network for reservoir characterization: a study from F-3 block, the Netherlands
Authors: Kushwaha Prabodh Kumar , Maurya S. P. , Singh N. P. , Rai Piyush 
Published: November 2019

AbstractMaximum likelihood sparse spike inversion (MLSSI) method is commonly used in the seismic industry to estimate petrophysical parameters in inter-well region. In present study, maximum likelihood sparse spike inversion technique is applied to the processed 3D post-stack seismic data from the F-3 block, the Netherlands, for estimation of acoustic impedance in the region between the wells. The analysis shows that the impedance varies from 2500 to 6200 m/s/*g/cc in the region which is relatively low and indicates the presence of loose formation in the area. The correlation between synthetic seismic trace and original seismic trace is found to be 0.93 and the synthetic relative error as 0.369, which indicate good performance of the algorithm. The analysis also shows low-impedance anomaly in between 600 and 700 ms time interval which may be due to the presence of sand formation. Thereafter, the probabilistic neural network analysis is performed to predict porosity along with multi-attribute transform analysis to estimate P-wave velocity and porosity in inter-well region. These parameters strengthen the seismic data interpretation which is very crucial step of any exploration and production project. The method is first applied to the composite traces near to well locations, and results are compared with well log data. After getting reasonable results, the whole seismic section is inverted for the P-wave velocity and porosity volume. The analysis shows anomaly in between 600 and 700 ms time interval which corroborates well with the low-impedance zone which may correspond to the reservoir. This is preliminarily interpretation; however to confirm a reservoir, there is need for more petrophysical parameters to be studied.
The Translational Status of Cancer Liquid Biopsies
Authors: Bratulic Sinisa , Gatto Francesco , Nielsen Jens 
Published: November 2019

Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.

Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
HOW PUBLIC OPINION SHAPES TAIWAN'S SUNFLOWER MOVEMENT
Authors: Wu Charles K.S. 
Published: November 2019

AbstractThe 2014 Sunflower Movement succeeded in blocking Taiwan's Congress from ratifying the Cross-Strait Services Trade Agreement (CSSTA), a bill that proposed to liberalize trade with China. Since most of the participants in this movement were students and NGO members, they had limited economic and political resources to influence policy change, which makes their success in stopping a trade deal remarkable. Many attribute this important success to an elite alliance with politicians inside the government, fueled by a personal rivalry between political elites. However, I argue that changing public opinion is the more important force behind the creation of the alliance. With original data from interviews with political elites, their staff members, and activists in Taiwan, in addition to secondary information, I confirm public opinion to be the major reason for the political alliance. This case illustrates that in some circumstances, public opinion outweighs the importance of elite rivalry in influencing political elite decision-making, and it could represent a key mechanism of democratic policy-making.
Gain of Chromosome 1q is associated with early progression in multiple myeloma patients treated with lenalidomide, bortezomib, and dexamethasone
Authors: Schmidt Timothy M. , Barwick Benjamin G. , Joseph Nisha , Heffner Leonard T. , Hofmeister Craig C. , Bernal Leon , Dhodapkar Madhav V. , Gupta Vikas A. , Jaye David L. , Wu Jiayi , Goyal Subir , Chen Zhengjia , Boise Lawrence H. , Lonial Sagar , Nooka Ajay K. , Kaufman Jonathan L. 
Published: November 2019

AbstractGain of chromosome 1q (+1q) is commonly identified in multiple myeloma and has been associated with inferior outcomes. However, the prognostic implication of +1q has not been evaluated in the setting of standard triplet regimens. We retrospectively analyzed 201 consecutive patients with newly diagnosed myeloma who received induction with lenalidomide, bortezomib, and dexamethasone (RVD) and were tested for +1q at diagnosis by fluorescent in-situ hybridization. Patients with +1q (n = 94), compared to those without +1q (n = 107), had shorter median progression-free survival (PFS) (41.9 months vs 65.1 months, p = 0.002, HR = 1.90) and overall survival (median not reached (NR) for either arm, p = 0.003, HR 2.69). In subgroup analyses, patients with co-occurring +1q and t(4;14), t(14;16) or del(17p) or with 4 or more copies of 1q had significantly worse PFS (25.1 months and 34.6 months, p < 0.001 and p = 0.0063, respectively), whereas patients with three copies and no other high-risk cytogenetic abnormalities had no significant difference in PFS. These data suggest that when treated with RVD induction, patients with +1q should be considered at very high risk for early progression in multiple myeloma when ≥4 copies are detected or in the context of other high-risk cytogenetic abnormalities.
Polymorphic cobalt diselenide as extremely stable electrocatalyst in acidic media via a phase-mixing strategy
Authors: Zhang Xiao-Long , Hu Shao-Jin , Zheng Ya-Rong , Wu Rui , Gao Fei-Yue , Yang Peng-Peng , Niu Zhuang-Zhuang , Gu Chao , Yu Xingxing , Zheng Xu-Sheng , Ma Cheng , Zheng Xiao , Zhu Jun-Fa , Gao Min-Rui , Yu Shu-Hong 
Published: November 2019

AbstractMany platinum group metal-free inorganic catalysts have demonstrated high intrinsic activity for diverse important electrode reactions, but their practical use often suffers from undesirable structural degradation and hence poor stability, especially in acidic media. We report here an alkali-heating synthesis to achieve phase-mixed cobalt diselenide material with nearly homogeneous distribution of cubic and orthorhombic phases. Using water electroreduction as a model reaction, we observe that the phase-mixed cobalt diselenide reaches the current density of 10 milliamperes per square centimeter at overpotential of mere 124 millivolts in acidic electrolyte. The catalyst shows no sign of deactivation after more than 400 h of continuous operation and the polarization curve is well retained after 50,000 potential cycles. Experimental and computational investigations uncover a boosted covalency between Co and Se atoms resulting from the phase mixture, which substantially enhances the lattice robustness and thereby the material stability. The findings provide promising design strategy for long-lived catalysts in acid through crystal phase engineering.
Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes
Authors: Zhang Yibo , Liu Wei , Li Zihang , Kumar Vinay , Alvarez-Cabrera Ana L. , Leibovitch Emily C. , Cui Yanxiang , Mei Ye , Bi Guo-Qiang , Jacobson Steve , Zhou Z. Hong 
Published: November 2019

AbstractHuman herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 “VΛ”-shaped CATCs are observed in HHV-6B, distinguishing from the 255 “Λ”-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 “Δ”-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC’s binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.
Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk
Authors: Vijayakrishnan Jayaram , Qian Maoxiang , Studd James B. , Yang Wenjian , Kinnersley Ben , Law Philip J. , Broderick Peter , Raetz Elizabeth A. , Allan James , Pui Ching-Hon , Vora Ajay , Evans William E. , Moorman Anthony , Yeoh Allen , Yang Wentao , Li Chunliang , Bartram Claus R. , Mullighan Charles G. , Zimmerman Martin , Hunger Stephen P. , Schrappe Martin , Relling Mary V. , Stanulla Martin , Loh Mignon L. , Houlston Richard S. , Yang Jun J. 
Published: November 2019

AbstractThere is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697,P = 2.11 × 10−8), for high-hyperdiploid ALL at 5q31.1 (rs886285,P = 1.56 × 10−8) and 6p21.31 (rs210143 inBAK1,P = 2.21 × 10−8), andETV6-RUNX1ALL at 17q21.32 (rs10853104 inIGF2BP1,P = 1.82 × 10−8). Particularly notable are the pleiotropic effects of theBAK1variant on multiple haematological malignancies and specific effects ofIGF2BP1onETV6-RUNX1ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.
JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
Authors: Albig Christian , Wang Chao , Dann Geoffrey P. , Wojcik Felix , Schauer Tamás , Krause Silke , Maenner Sylvain , Cai Weili , Li Yeran , Girton Jack , Muir Tom W. , Johansen Jørgen , Johansen Kristen M. , Becker Peter B. , Regnard Catherine 
Published: November 2019

AbstractIn flies, the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, such as dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1’s targeting to chromatin depends on a PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). JASPer-JIL-1 (JJ)-complex is the major form of kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes, to modulate transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identify interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation but also coordinates chromatin-based regulation in the transcribed part of the genome.
Chemotactic behaviour of Escherichia coli at high cell density
Authors: Colin Remy , Drescher Knut , Sourjik Victor 
Published: November 2019

AbstractAt high cell density, swimming bacteria exhibit collective motility patterns, self-organized through physical interactions of a however still debated nature. Although high-density behaviours are frequent in natural situations, it remained unknown how collective motion affects chemotaxis, the main physiological function of motility, which enables bacteria to follow environmental gradients in their habitats. Here, we systematically investigate this question in the model organism Escherichia coli, varying cell density, cell length, and suspension confinement. The characteristics of the collective motion indicate that hydrodynamic interactions between swimmers made the primary contribution to its emergence. We observe that the chemotactic drift is moderately enhanced at intermediate cell densities, peaks, and is then strongly suppressed at higher densities. Numerical simulations reveal that this suppression occurs because the collective motion disturbs the choreography necessary for chemotactic sensing. We suggest that this physical hindrance imposes a fundamental constraint on high-density behaviours of motile bacteria, including swarming and the formation of multicellular aggregates and biofilms.