bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing ENSO Prediction Skill by Combining Model‐Analog and Linear Inverse Models (MA‐LIM)
Authors: Shin Jihoon , Park Sungsu , Shin Sang‐Ik , Newman Matthew , Alexander Michael A. 
Published: December 2019

AbstractTo enhance El Niño–Southern Oscillation (ENSO) forecast skill, we devise a model analog (MA)‐linear inverse model (LIM) by nudging sea surface temperature and sea surface height anomalies forecasted by the LIM into the MA. The performances of the LIM, MA, and MA‐LIM are compared to general circulation model simulations and observations. At short (long) lead month
, the LIM (MA) predicts the Niño 3.4 SST anomalies better than the MA (LIM). On the other hand, the MA‐LIM shows the best performance at all
. At
, the MA performs better than the LIM in the eastern equatorial Pacific and Indian Oceans but worse in other regions. The MA‐LIM substantially remedies the undesirable aspects of the MA. The success of the MA‐LIM appears to come from the use of more accurate initial conditions than the MA and an ad hoc implementation of seasonal cycle and nonlinearities into the LIM through nudging to the MA.
Emission of Electrostatic Whistler Waves Associated With Weak Electron‐Beam Excited Langmuir Waves: The 2‐D Particle‐in‐Cell Simulations
Authors: Sun Haomin , Sun Jicheng 
Published: December 2019

AbstractIn this paper, we perform two‐dimensional (2‐D) electrostatic particle‐in‐cell simulations to investigate the emission of electrostatic whistler waves (EWWs) associated with the weak electron‐beam excited Langmuir waves. Both the linear theory and simulations have shown that quasi‐parallel Langmuir waves can be generated during the linear stage of the beam‐plasma interaction process. The 2‐D particle‐in‐cell simulations further demonstrated that when the background magnetic field is strong (Ωe/ωpe > 1, where Ωe and ωpe are electron gyrofrequency and electron plasma frequency, respectively), EWWs will be generated in weak electron‐beam excited Langmuir waves during the nonlinear stage of wave growth, leading to the increment of perpendicular electric field. When the background magnetic field is weak (Ωe/ωpe < 1), EWWs cannot be generated during the nonlinear stage and the perpendicular electric field has no obvious nonlinear increment. In addition, the influences of the electron beam density and the electron beam velocity on the generation of EWWs are also analyzed in this paper. The simulation results may also account for observations in the Earth's Auroral region.
Nutraceuticals, antioxidant pigments, and phytochemicals in the leaves of Amaranthus spinosus and Amaranthus viridis weedy species
Authors: Sarker Umakanta , Oba Shinya 
Published: December 2019

AbstractSix selected weedy Amaranthus genotypes (three accessions from each species of A. viridis and A. spinosus) were evaluated in terms of nutrients, minerals, antioxidant constituents and antioxidant activity for the possibilities of weedy species as a vegetable cultivar in a randomized complete block design with three replications. As leafy vegetable, Weedy Amaranthus has remarkable protein, dietary fiber, carbohydrates, Ca, K, Mg, P, S, Fe, Mn, Cu, Zn, Na, Mo, B, chlorophylls, β-cyanins, β-xanthins, betalains, β-carotene, vitamin C, TPC, TFC, and TAC (DPPH and ABTS+) compared to any cultivated species. The A. viridis genotype WAV7 and A. spinosus genotype WAS13 had the highest nutrients, pigments, vitamins, phenolics, flavonoids, and antioxidant. Hence, these two weedy accessions could be used as an antioxidant profile enriched cultivar with high nutritional and antioxidant activity. Pigments, β-carotene, vitamin C, phenolics, and flavonoids had strong antioxidant activity and played a vital role in the antioxidant activity of weedy Amaranthus genotypes. Weedy species are an excellent source of phenolics, flavonoids, and antioxidants that have many pharmacological and medicinal effects of their traditional applications and detoxify ROS and offered huge prospects for feeding the antioxidant-deficient community to cope with the hidden hunger and attaining nutritional and antioxidant sufficiency.
Peculiarities of pseudogap in Y0.95Pr0.05Ba2Cu3O7−δ single crystals under pressure up to 1.7 GPa
Authors: Solovjov A. L. , Omelchenko L. V. , Petrenko E. V. , Vovk R. V. , Khotkevych V. V. , Chroneos A. 
Published: December 2019

AbstractThe effect of hydrostatic pressure up to P = 1.7 GPa on the fluctuation conductivity σ′(T) and pseudogap ∆*(T) in Y0.95Pr0.05Ba2Cu3O7−δ single crystal with critical temperature Тс = 85.2 K (at P = 0) was investigated. The application of pressure leads to the increase in Tc with dTc/dP = +1.82 K∙GPa−1 while the resistance decreases as dlnρ(100 K)/dP = −(10.5 ± 0.2) %∙GPa−1. Regardless of the pressure, in the temperature interval from Tc to T0 (~88 K at P = 0) the behaviour of σ′(T) is well described by the Aslamazov – Larkin (AL – 3D) fluctuation theory, and above the T0 by the Lawrence – Doniach theory (LD). The Maki-Thompson (MT – 2D) fluctuation contribution is not observed. This indicates the presence of structural defects in the sample induced by Pr. Here it is determined for the first time that when the pressure is applied to the Y1−xPrxBa2Cu3O7−δ single crystal, the pseudogap increases as dlnΔ*/dP = 0.17 GPa–1.
High heritability of coral calcification rates and evolutionary potential under ocean acidification
Authors: Jury Christopher P. , Delano Mia N. , Toonen Robert J. 
Published: December 2019

AbstractEstimates of heritability inform evolutionary potential and the likely outcome of many management actions, but such estimates remain scarce for marine organisms. Here, we report high heritability of calcification rate among the eight most dominant Hawaiian coral species under reduced pH simulating future ocean conditions. Coral colonies were sampled from up to six locations across a natural mosaic in seawater chemistry throughout Hawaiʻi and fragmented into clonal replicates maintained under both ambient and high pCO2 conditions. Broad sense heritability of calcification rates was high among all eight species, ranging from a low of 0.32 in Porites evermanni to a high of 0.61 in Porites compressa. The overall results were inconsistent with short-term acclimatization to the local environment or adaptation to the mean or ideal conditions. Similarly, in ‘local vs. foreign’ and ‘home vs. away’ tests there was no clear signature of local adaptation. Instead, the data are most consistent with a protected polymorphism as the mechanism which maintains differential pH tolerance within the populations. Substantial individual variation, coupled with high heritability and large population sizes, imply considerable scope for natural selection and adaptive capacity, which has major implications for evolutionary potential and management of corals in response to climate change.
Risk of yellow fever virus importation into the United States from Brazil, outbreak years 2016–2017 and 2017–2018
Authors: Dorigatti Ilaria , Morrison Stephanie , Donnelly Christl A. , Garske Tini , Bowden Sarah , Grills Ardath 
Published: December 2019

AbstractSoutheast Brazil has experienced two large yellow fever (YF) outbreaks since 2016. While the 2016–2017 outbreak mainly affected the states of Espírito Santo and Minas Gerais, the 2017–2018 YF outbreak primarily involved the states of Minas Gerais, São Paulo, and Rio de Janeiro, the latter two of which are highly populated and popular destinations for international travelers. This analysis quantifies the risk of YF virus (YFV) infected travelers arriving in the United States via air travel from Brazil, including both incoming Brazilian travelers and returning US travelers. We assumed that US travelers were subject to the same daily risk of YF infection as Brazilian residents. During both YF outbreaks in Southeast Brazil, three international airports—Miami, New York-John F. Kennedy, and Orlando—had the highest risk of receiving a traveler infected with YFV. Most of the risk was observed among incoming Brazilian travelers. Overall, we found low risk of YFV introduction into the United States during the 2016–2017 and 2017–2018 outbreaks. Decision makers can use these results to employ the most efficient and least restrictive actions and interventions.
Effects of Chikungunya virus immunity on Mayaro virus disease and epidemic potential
Authors: Webb Emily M. , Azar Sasha R. , Haller Sherry L. , Langsjoen Rose M. , Cuthbert Candace E. , Ramjag Anushka T. , Luo Huanle , Plante Kenneth , Wang Tian , Simmons Graham , Carrington Christine V. F. , Weaver Scott C. , Rossi Shannan L. , Auguste Albert J. 
Published: December 2019

AbstractMayaro virus (MAYV) causes an acute febrile illness similar to that produced by chikungunya virus (CHIKV), an evolutionary relative in the Semliki Forest virus complex of alphaviruses. MAYV emergence is typically sporadic, but recent isolations and outbreaks indicate that the virus remains a public health concern. Given the close phylogenetic and antigenic relationship between CHIKV and MAYV, and widespread distribution of CHIKV, we hypothesized that prior CHIKV immunity may affect MAYV pathogenesis and/or influence its emergence potential. We pre-exposed immunocompetent C57BL/6 and immunocompromised A129 or IFNAR mice to wild-type CHIKV, two CHIKV vaccines, or a live-attenuated MAYV vaccine, and challenged with MAYV. We observed strong cross-protection against MAYV for mice pre-exposed to wild-type CHIKV, and moderately but significantly reduced cross-protection from CHIKV-vaccinated animals. Immunity to other alphavirus or flavivirus controls provided no protection against MAYV disease or viremia. Mechanistic studies suggested that neutralizing antibodies alone can mediate this protection, with T-cells having no significant effect on diminishing disease. Finally, human sera obtained from naturally acquired CHIKV infection cross-neutralized MAYV at high titersin vitro. Altogether, our data suggest that CHIKV infection can confer cross-protective effects against MAYV, and the resultant reduction in viremia may limit the emergence potential of MAYV.
Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications
Authors: Song Yun , Zhang Yongjiang , Xu Jin , Li Weimin , Li MingFu 
Published: December 2019

AbstractThe pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.
Molecular Geometry Prediction using a Deep Generative Graph Neural Network
Authors: Mansimov Elman , Mahmood Omar , Kang Seokho , Cho Kyunghyun 
Published: December 2019

AbstractA molecule’s geometry, also known as conformation, is one of a molecule’s most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional conformation generation methods minimize hand-designed molecular force field energy functions that are often not well correlated with the true energy function of a molecule observed in nature. They generate geometrically diverse sets of conformations, some of which are very similar to the lowest-energy conformations and others of which are very different. In this paper, we propose a conditional deep generative graph neural network that learns an energy function by directly learning to generate molecular conformations that are energetically favorable and more likely to be observed experimentally in data-driven manner. On three large-scale datasets containing small molecules, we show that our method generates a set of conformations that on average is far more likely to be close to the corresponding reference conformations than are those obtained from conventional force field methods. Our method maintains geometrical diversity by generating conformations that are not too similar to each other, and is also computationally faster. We also show that our method can be used to provide initial coordinates for conventional force field methods. On one of the evaluated datasets we show that this combination allows us to combine the best of both methods, yielding generated conformations that are on average close to reference conformations with some very similar to reference conformations.
Screening history and FIGO-stages among Danish women with cervical cancer in 2012–2014: a register-based study
Authors: Bchtawi Abir Khalil , Saritas Sinem , Schledermann Doris , Christensen René dePont , Jochumsen Kirsten Marie 
Published: December 2019

AbstractThe objective was to examine whether attendance in the mass cervical screening programme has implications for the prognosis when cervical cancer is diagnosed. We performed a retrospective analysis of all cases of cervical cancer between 1st of January 2012 and 31st of December 2014 in the Region of Southern Denmark. The cases were retrieved from the Danish National Pathology Registry, PatoBank. Odds ratios (OR) with confidence intervals (95% CI) were calculated for attendees versus non-attendees of the screening programme by using χ2-test. 216 patients were included in the study. 61.6% of the study population had not attended the screening programme. Patients who had attended the programme were characterised by disease in low stage (OR = 3.14, 95% CI; 1.66 to 5.92), treatment with surgery alone (OR = 2.63, 95% CI; 1.49 to 4.64) and a lower risk of death (OR = 0.36, 95% CI; 0.15 to 0.87). Adenocarcinomas were more often detected among attendees of the programme compared to squamous cell carcinomas (OR = 4.06, 95% CI; 2.03 to 8.14). Statistically significant results regarding relapse of cancer (OR = 0.62, 95% CI; 0.23 to 1.68, p = 0.47) and lymph node metastases (OR = 0.62, 95% CI; 0.32 to 1.21, p = 0.19) were not found. Cervical cancer detected in women who had attended the mass cervical screening programme prior to the diagnosis, was shown to have a statistically significant lower FIGO stage (p = 0.0004) and was therefore linked to less extensive treatment options. Continued focus on increasing the participation rate of the programme is of importance, as the nonattendance rate continues to be high.
Modification of an aggressive model of Alport Syndrome reveals early differences in disease pathogenesis due to genetic background
Authors: Falcone Sara , Wisby Laura , Nicol Thomas , Blease Andrew , Starbuck Becky , Parker Andrew , Sanderson Jeremy , Brown Steve D. M. , Scudamore Cheryl L. , Pusey Charles D. , Tam Frederick W. K. , Potter Paul K. 
Published: December 2019

AbstractThe link between mutations in collagen genes and the development of Alport Syndrome has been clearly established and a number of animal models, including knock-out mouse lines, have been developed that mirror disease observed in patients. However, it is clear from both patients and animal models that the progression of disease can vary greatly and can be modified genetically. We have identified a point mutation in Col4a4 in mice where disease is modified by strain background, providing further evidence of the genetic modification of disease symptoms. Our results indicate that C57BL/6J is a protective background and postpones end stage renal failure from 7 weeks, as seen on a C3H background, to several months. We have identified early differences in disease progression, including expression of podocyte-specific genes and podocyte morphology. In C57BL/6J mice podocyte effacement is delayed, prolonging normal renal function. The slower disease progression has allowed us to begin dissecting the pathogenesis of murine Alport Syndrome in detail. We find that there is evidence of differential gene expression during disease on the two genetic backgrounds, and that disease diverges by 4 weeks of age. We also show that an inflammatory response with increasing MCP-1 and KIM-1 levels precedes loss of renal function.
Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12
Authors: Shimada Tomohiro , Yokoyama Yui , Anzai Takumi , Yamamoto Kaneyoshi , Ishihama Akira 
Published: December 2019

AbstractOutside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization).
The chick pallium displays divergent expression patterns of chick orthologues of mammalian neocortical deep layer-specific genes
Authors: Fujita Toshiyuki , Aoki Naoya , Fujita Eiko , Matsushima Toshiya , Homma Koichi J. , Yamaguchi Shinji 
Published: December 2019

AbstractThe avian pallium is organised into clusters of neurons and does not have layered structures such as those seen in the mammalian neocortex. The evolutionary relationship between sub-regions of avian pallium and layers of mammalian neocortex remains unclear. One hypothesis, based on the similarities in neural connections of the motor output neurons that project to sub-pallial targets, proposed the cell-type homology between brainstem projection neurons in neocortex layers 5 or 6 (L5/6) and those in the avian arcopallium. Recent studies have suggested that gene expression patterns are associated with neural connection patterns, which supports the cell-type homology hypothesis. However, a limited number of genes were used in these studies. Here, we showed that chick orthologues of mammalian L5/6-specific genes, nuclear receptor subfamily 4 group A member 2 and connective tissue growth factor, were strongly expressed in the arcopallium. However, other chick orthologues of L5/6-specific genes were primarily expressed in regions other than the arcopallium. Our results do not fully support the cell-type homology hypothesis. This suggests that the cell types of brainstem projection neurons are not conserved between the avian arcopallium and the mammalian neocortex L5/6. Our findings may help understand the evolution of pallium between birds and mammals.
Ginsenoside Rb1 exerts antiarrhythmic effects by inhibiting INa and ICaL in rabbit ventricular myocytes
Authors: Liu Zhipei , Song Lv , Zhang Peipei , Cao Zhenzhen , Hao Jie , Tian Youjia , Luo Antao , Zhang Peihua , Ma Jihua 
Published: December 2019

AbstractGinsenoside Rb1 exerts its pharmacological action by regulating sodium, potassium and calcium ion channels in the membranes of nerve cells. These ion channels are also present in cardiomyocytes, but no studies have been reported to date regarding the effects of Rb1 on cardiac sodium currents (INa), L-type calcium currents (ICaL) and action potentials (APs). Additionally, the antiarrhythmic potential of Rb1 has not been assessed. In this study, we used a whole-cell patch clamp technique to assess the effect of Rb1 on these ion channels. The results showed that Rb1 inhibited INa and ICaL, reduced the action potential amplitude (APA) and maximum upstroke velocity (Vmax), and shortened the action potential duration (APD) in a concentration-dependent manner but had no effect on the inward rectifier potassium current (IK1), delayed rectifier potassium current (IK) or resting membrane potential (RMP). We also designed a pathological model at the cellular and organ level to verify the role of Rb1. The results showed that Rb1 abolished high calcium-induced delayed afterdepolarizations (DADs), depressed the increase in intracellular calcium ([Ca2+]i), relieved calcium overload and protected cardiomyocytes. Rb1 can also reduce the occurrence of ventricular premature beats (VPBs) and ventricular tachycardia (VT) in ischemia-reperfusion (I-R) injury.
Physical parameters of selected Gaia mass asteroids
Authors: Podlewska-Gaca E. , Marciniak A. , Alí-Lagoa V. , Bartczak P. , Müller T. G. , Szakáts R. , Duffard R. , Molnár L. , Pál A. , Butkiewicz-Bąk M. , Dudziński G. , Dziadura K. , Antonini P. , Asenjo V. , Audejean M. , Benkhaldoun Z. , Behrend R. , Bernasconi L. , Bosch J. M. , Chapman A. , Dintinjana B. , Farkas A. , Ferrais M. , Geier S. , Grice J. , Hirsh R. , Jacquinot H. , Jehin E. , Jones A. , Molina D. , Morales N. , Parley N. , Poncy R. , Roy R. , Santana-Ros T. , Seli B. , Sobkowiak K. , Verebélyi E. , Żukowski K. 
Published: December 2019

Context. Thanks to the Gaia mission, it will be possible to determine the masses of approximately hundreds of large main belt asteroids with very good precision. We currently have diameter estimates for all of them that can be used to compute their volume and hence their density. However, some of those diameters are still based on simple thermal models, which can occasionally lead to volume uncertainties as high as 20–30%.
Aims. The aim of this paper is to determine the 3D shape models and compute the volumes for 13 main belt asteroids that were selected from those targets for which Gaia will provide the mass with an accuracy of better than 10%.
Methods. We used the genetic Shaping Asteroids with Genetic Evolution (SAGE) algorithm to fit disk-integrated, dense photometric lightcurves and obtain detailed asteroid shape models. These models were scaled by fitting them to available stellar occultation and/or thermal infrared observations.
Results. We determine the spin and shape models for 13 main belt asteroids using the SAGE algorithm. Occultation fitting enables us to confirm main shape features and the spin state, while thermophysical modeling leads to more precise diameters as well as estimates of thermal inertia values.
Conclusions. We calculated the volume of our sample of main-belt asteroids for which the Gaia satellite will provide precise mass determinations. From our volumes, it will then be possible to more accurately compute the bulk density, which is a fundamental physical property needed to understand the formation and evolution processes of small Solar System bodies.