bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic differentiation and diversity of sugarbeet germplasm resistant to the sugarbeet root maggot
Authors: Fugate Karen K. , Campbell Larry G. , Covarrubias-Pazaran Giovanny , Rodriguez-Bonilla Lorraine , Zalapa Juan 
Published: November 2019

AbstractGermplasm lines with resistance to the sugarbeet root maggot (SBRM) have been developed and released to the public, providing a means to generate hybrids with resistance against the most devastating insect pest of sugarbeet in North America. Effective use of this germplasm, however, requires knowledge of relative strengths of SBRM resistance between lines and knowledge of the diversity and genetic relationships between germplasm. Therefore, field studies comparing SBRM resistance of four released SBRM-resistant germplasm lines (F1015, F1016, F1024 and F1043), a SBRM-resistant parent (PI 179180) and an unreleased SBRM-resistant population (F1055) were performed, and genetic analysis of the diversity and relationships between SBRM-resistant germplasm and their available parents was conducted using simple sequence repeat (SSR) markers. Under natural SBRM infestations, resistant germplasm exhibited significantly less SBRM damage than a susceptible control, with similar, high levels of resistance in F1016, F1024, F1043, F1055 and PI 179180 and lower resistance in F1015. SSR analysis revealed genetic similarities between F1016, F1024 and F1055, while F1015 and F1043 were genetically distinct from these lines. Among resistant genotypes, F1015 and F1043 exhibited greatest and least within-line genetic diversity, indicating greater and lesser inbreeding for F1043 and F1015, respectively. Similarities in damage ratings and genetics for F1016, F1024 and F1055 indicate that these lines are likely to be equally effective at introducing SBRM resistance into elite populations and in combining ability. In contrast, F1043, with its unique parentage and genetic dissimilarity from other resistant lines, provides a genetically distinct, but similarly effective, source of SBRM resistance.
An encapsulated fruit, vegetable and berry juice powder concentrate increases plasma values of specific carotenoids and vitamins
Authors: Dams Sebastian , Holasek Sandra , Tsiountsioura Melina , Malliga Daniela-Eugenia , Meier-Allard Nathalie , Poncza Brigitte , Lackner Sonja , Jansenberger Yvonne , Lamprecht Manfred 
Published: November 2019

Abstract. Vitamins and carotenoids are organic compounds that are important for vital functions of the human organism. Since the human body is not able to synthesize most of these micronutrients, they need to be supplied by the intake of food or supplements. The aim of this study was to analyze whether a whole food based, encapsulated fruit, berry, and vegetable juice powder concentrate provides bioavailable carotenoids and vitamins A (all-trans retinol), E and C. Eighteen healthy subjects received 6 capsules a day for 8 weeks, which provided 2.91 mg β-carotene, 490 μg vitamin A, 18.7 mg vitamin E, 159 mg vitamin C, 6.1 mg lutein and 1 mg lycopene. Plasma concentrations of several carotenoids and vitamins before and after supplementation were measured. After 8 weeks of supplementation, the plasma concentration of the following carotenoids increased significantly: α-carotene increased from 59.6 ± 22.4 nmol/L to 85.7 ± 24.2 nmol/L (p = 0.002), β-cryptoxanthin from 106.7 ± 39.8 nmol/L to 151.9 ± 57.9 nmol/L (p = 0.017), and lycopene from 1.2 ± 0.5 μmol/L to 1.7 ± 0.5 μmol/L (p = 0.005). Significant increases were also observed for plasma concentrations of vitamin C from 70 ± 20 μmol/L to 90 ± 10 μmol/L (p < 0.001), all-trans retinol from 1.99 ± 0.24 μmol/L to 2.30 ± 0.66 μmol/L (p = 0.015), and α-tocopherol from 27 ± 6 μmol/L to 32 ± 6 μmol/L (p = 0.008). For those micronutrients with accepted plasma reference ranges, all observed increases levelled off around the upper limit of the individual reference range. The data demonstrate that the investigated supplement is able to increase plasma concentrations of certain carotenoids and vitamins of healthy subjects within 8 weeks.
The Accommodation of the South Flank's Motion by the Koa‘e Fault System, Kīlauea, Hawai‘i: Insights From the June 2012 Earthquake Sequence
Authors: Ge Shuangyu , Lin Guoqing , Amelung Falk , Okubo Paul G. , Swanson Donald A. , Yunjun Zhang 
Published: November 2019

AbstractThe Koa‘e fault system is a prominent and complex structural element of Kīlauea Volcano, Hawai‘i. On 5 June 2012, a sequence of shallow earthquakes occurred in the central part of the Koa‘e fault system. The Interferometric Synthetic Aperture Radar (InSAR) data from multiple satellites spanning the time of the earthquake occurrence indicate a maximum of ~10‐cm surface displacement above the seismic events in the Koa‘e. The Global Positioning System (GPS) data from multiple stations show that there was a slow slip event in the south flank in late May 2012. Field visits to the fault after the earthquakes revealed ground cracks. In this study, we combine the seismic, InSAR, GPS data, and field observations to investigate the characteristics of the Koa‘e fault system. We relocate the seismic events in the central part of the Koa‘e fault system, compute the focal mechanisms for the events in the June 2012 earthquake sequence, invert for a two‐fault model based on the surface deformation, and discuss their relationships with the 2012 slow slip event. Based on our Coulomb stress‐change calculation, we infer that the 2012 slow slip event may have triggered both the seismic events and the surface deformation and played a major role in the evolution of the Koa‘e fault system and the accommodation of the south flank's motion. Our integrated analyses are helpful to constrain the fault geometry in the Koa‘e system and to shed light on the role of Koa‘e in the structural evolution of Kīlauea.
Frequency‐Dependent P Wave Polarization and Its Subwavelength Near‐Surface Depth Sensitivity
Authors: Park Sunyoung , Tsai Victor C. , Ishii Miaki 
Published: November 2019

AbstractNear‐surface structure is crucial to assessing seismic hazards and understanding earthquakes and surface processes yet is a major challenge to robustly image. Recently, an approach based on body‐wave polarization was introduced for constraining shallow seismic structure, but the depth sensitivity of the polarization measurement has remained unclear. Using waveform simulations based on a layer over a half space, we find that the depth sensitivity of P wave polarization peaks at the surface and decreases abruptly over a depth range shorter than its wavelength. A strong frequency dependence provides constraints on local 1‐D structure, with frequencies between 0.1 and 10 Hz illuminating structure at depths of 10 m to several kilometers. Applying these results to teleseismic recordings in Japan provides constraints on structure at about 120 to 750 m, including a distinctive weak zone along the Median Tectonic Line in the Kii peninsula and Awaji Island.
Tibetan Plateau's Lake Level and Volume Changes From NASA's ICESat/ICESat‐2 and Landsat Missions
Authors: Zhang Guoqing , Chen Wenfeng , Xie Hongjie 
Published: November 2019

AbstractLake level change is an effective indicator of climate change, because it reflects the dynamic balance of water input and loss. Here we provide a first look of Ice, Cloud, and land Elevation Satellite‐2 (ICESat‐2) on the lakes of the Tibetan Plateau. ICESat‐2 doubles the number of lakes observed using predecessor ICESat data. The ICESat/ICESat‐2 altimetry data between 2003 and 2018 are in excellent agreement with in situ measurements from Qinghai Lake (R2 = 0.95, root‐mean‐square error = 0.10 m) and with gauge observations made on 3 December 2018 (< 2 cm). The 62 lakes examined show a mean rate of water level change of 0.28 ± 0.03 m/year in 2003–2018, with 58 lakes increasing (mean rate 0.30 ± 0.03 m/year), and 4 lakes decreasing (mean rate −0.12 ± 0.06 m/year). A total change of lake water storage of ~14 Gt/year is estimated. The results suggest that ICESat‐2 data will be an important tool for future lake level change studies.
Early Dynamics of the Lunar Core
Authors: Ćuk Matija , Hamilton Douglas P. , Stewart Sarah T. 
Published: November 2019

AbstractThe Moon is known to have a small liquid core, and it is thought that in the distant past the core may have produced strong magnetic fields recorded in lunar samples. Here we implement a numerical model of lunar orbital and rotational dynamics that includes the effects of a liquid core. In agreement with previous work, we find that the lunar core is dynamically decoupled from the lunar mantle and that this decoupling happened very early in lunar history. Our model predicts that the lunar core rotates subsynchronously, and the difference between the core and the mantle rotational rates was significant when the Moon had a high forced obliquity during and after the Cassini State transition. We find that the presence of the lunar liquid core further destabilizes synchronous rotation of the mantle for a wide range of semimajor axes centered around the Cassini State transition. Core‐mantle boundary torques make it even more likely that the Moon experienced large‐scale inclination damping during the Cassini State transition. We present estimates for the mutual core‐mantle obliquity as a function of Earth‐Moon distance, and we discuss plausible absolute time lines for this evolution. We conclude that our results are consistent with the hypothesis of a precession‐driven early lunar dynamo and may explain the variability of the inferred orientation of the past lunar dynamo.
MarsWRF Convective Vortex and Dust Devil Predictions for Gale Crater Over 3 Mars Years and Comparison With MSL‐REMS Observations
Authors: Newman C. E. , Kahanpää H. , Richardson M. I. , Martínez G. M. , Vicente‐Retortillo A. , Lemmon M. T. 
Published: November 2019

Key Points

MarsWRF output combined with thermodynamic theory is used to predict spatiotemporal trends of dust devil activity (DDA) in Gale Crater
Both modeled DDA and number of observed vortex pressure drops are greatest in local summer, peaking ~13:00–14:00, and smallest in winter
Stronger sensible heat fluxes and winds drive a rise in DDA as MSL climbs, but vortex numbers rise faster, unless a threshold DDA is used
MT1G serves as a tumor suppressor in hepatocellular carcinoma by interacting with p53
Authors: Wang Yingchao , Wang Gaoxiong , Tan Xionghong , Ke Kun , Zhao Bixing , Cheng Niangmei , Dang Yuan , Liao Naishun , Wang Fei , Zheng Xiaoyuan , Li Qin , Liu Xiaolong , Liu Jingfeng 
Published: November 2019

AbstractPoor prognosis of hepatocellular carcinoma (HCC) patients is frequently associated with rapid tumor growth, recurrence and drug resistance. MT1G is a low-molecular weight protein with high affinity for zinc ions. In the present study, we investigated the expression of MT1G, analyzed clinical significance of MT1G, and we observed the effects of MT1G overexpression on proliferation and apoptosis of HCC cell lines in vitro and in vivo. Our results revealed that MT1G was significantly downregulated in tumor tissues, and could inhibit the proliferation as well as enhance the apoptosis of HCC cells. The mechanism study suggested that MT1G increased the stability of p53 by inhibiting the expression of its ubiquitination factor, MDM2. Furthermore, MT1G also could enhance the transcriptional activity of p53 through direct interacting with p53 and providing appropriate zinc ions to p53. The modulation of MT1G on p53 resulted in upregulation of p21 and Bax, which leads cell cycle arrest and apoptosis, respectively. Our in vivo assay further confirmed that MT1G could suppress HCC tumor growth in nude mice. Overall, this is the first report on the interaction between MT1G and p53, and adequately uncover a new HCC suppressor which might have therapeutic values by diminishing the aggressiveness of HCC cells.
Androgen receptor expression and response to chemotherapy in breast cancer patients treated in the neoadjuvant TECHNO and PREPARE trial
Authors: Witzel Isabell , Loibl Sibylle , Wirtz Ralph , Fasching Peter A. , Denkert Carsten , Weber Karsten , Lück Hans-Joachim , Huober Jens , Karn Thomas , Mackelenbergh Marion von , Marmé Frederik , Schem Christian , Stickeler Elmar , Untch Michael , Müller Volkmar 
Published: November 2019

Abstract
Background
The androgen receptor (AR) is discussed as a prognostic and/or predictive marker in breast cancer patients.

Methods
AR mRNA expression was analysed by RT-qPCR in breast cancer patients treated in the neoadjuvant TECHNO (n  =  118, HER2-positive) and PREPARE trial (n  =  321, HER2-positive and -negative). In addition, mRNA expression of the AR transcript variants 1 (AR1) and 2 (AR2) was measured.

Results
Regarding subtypes, high AR mRNA levels were frequent in HER2-positive (61.3%, 92/150) and luminal tumours (60.0%, 96/160) but almost absent in triple-negative tumours (4.3%, 3/69) (p < 0.0001). Overall, high AR mRNA levels were found to be associated with lower pathological complete remission (pCR) rates (OR 0.77 per unit, 95% CI 0.67–0.88, p  =  0.0002) but also with better prognosis in terms of longer disease-free survival (DFS) (HR 0.57, 95% CI 0.39–0.85, p  =  0.0054) and overall survival (OS) (HR 0.43, 95% CI, 0.26–0.71, p  =  0.0011). In the PREPARE trial, a survival difference for patients with high and low AR1 mRNA levels could only be seen in the standard chemotherapy arm but not in the dose-dense treatment arm (OS: HR 0.41; 95% CI 0.22–0.74 vs. HR 1.05; 95% CI 0.52–2.13; p  =  0.0459).

Conclusions
We provide evidence that AR mRNA predicts response to chemotherapy in breast cancer patients.
Duplication and transcriptional divergence of three Kunitz protease inhibitor genes that modulate insect and pathogen defenses in tea plant (Camellia sinensis)
Authors: Zhu Junyan , He Yaxian , Yan Xiaomei , Liu Lu , Guo Rui , Xia Xiaobo , Cheng Daojie , Mi Xiaozeng , Samarina Lidiia , Liu Shenrui , Xia Enhua , Wei Chaoling 
Published: November 2019

AbstractKunitz protease inhibitors (KPIs) are ubiquitous in plants and act as crucial compounds in defense responses against insect attack and pathogen infection. However, the influence of gene duplication on the postdivergence of theCsKPIgenes involved in biotic stresses in tea plant is not well known. Here, we identified threeCsKPIgenes from tea plant (Camellia sinensis) and characterized their expression and evolutionary patterns among plant species. We found thatCsKPI1,CsKPI2, andCsKPI3diverged from their common ancestor 72.94 million years ago (MYA), and the tandem duplication ofCsKPI2andCsKPI3occurred 26.78 MYA. An in vitro protein assay showed that the three CsKPI proteins were functional and inhibited the production ofp-nitroanilide (PNA) from an artificial substrate. The three CsKPI-GFP fusion proteins localized to the cytoplasm. We showed that salicylic acid (SA) and transcripts ofCsKPI2andCsKPI3significantly accumulated after infection withGlomerella cingulata. The application of exogenous SA stimulated the high expression of bothCsKPI2andCsKPI3by activatingcis-elements within their promoters. UnderEctropis obliqueattack,CsKPI1expression and jasmonic acid (JA) levels were more abundant in both insect-damaged leaf tissues and undamaged neighboring leaves. The application of jasmonic acid methyl ester elicited high expression levels ofCsKPI1, suggesting thatCsKPI1accumulation requires JA production in tea plant. The overall findings suggest that the transcriptional divergence of KPI genes after duplication led to the specialized role ofCsKPI1in the physiological response to insect stress; the functional conservation betweenCsKPI2andCsKPI3confers resistance to pathogen infection in tea plant.
Adaptive prospective optical gating enables day-long 3D time-lapse imaging of the beating embryonic zebrafish heart
Authors: Taylor Jonathan M. , Nelson Carl J. , Bruton Finnius A. , Kaveh Aryan , Buckley Charlotte , Tucker Carl S. , Rossi Adriano G. , Mullins John J. , Denvir Martin A. 
Published: November 2019

AbstractThree-dimensional fluorescence time-lapse imaging of the beating heart is extremely challenging, due to the heart’s constant motion and a need to avoid pharmacological or phototoxic damage. Although real-time triggered imaging can computationally “freeze” the heart for 3D imaging, no previous algorithm has been able to maintain phase-lock across developmental timescales. We report a new algorithm capable of maintaining day-long phase-lock, permitting routine acquisition of synchronised 3D + time video time-lapse datasets of the beating zebrafish heart. This approach has enabled us for the first time to directly observe detailed developmental and cellular processes in the beating heart, revealing the dynamics of the immune response to injury and witnessing intriguing proliferative events that challenge the established literature on cardiac trabeculation. Our approach opens up exciting new opportunities for direct time-lapse imaging studies over a 24-hour time course, to understand the cellular mechanisms underlying cardiac development, repair and regeneration.
Genetic variants of calcium and vitamin D metabolism in kidney stone disease
Authors: Howles Sarah A. , Wiberg Akira , Goldsworthy Michelle , Bayliss Asha L. , Gluck Anna K. , Ng Michael , Grout Emily , Tanikawa Chizu , Kamatani Yoichiro , Terao Chikashi , Takahashi Atsushi , Kubo Michiaki , Matsuda Koichi , Thakker Rajesh V. , Turney Benjamin W. , Furniss Dominic 
Published: November 2019

AbstractKidney stone disease (nephrolithiasis) is a major clinical and economic health burden with a heritability of ~45–60%. We present genome-wide association studies in British and Japanese populations and a trans-ethnic meta-analysis that include 12,123 cases and 417,378 controls, and identify 20 nephrolithiasis-associated loci, seven of which are previously unreported. A CYP24A1 locus is predicted to affect vitamin D metabolism and five loci, DGKD, DGKH, WDR72, GPIC1, and BCR, are predicted to influence calcium-sensing receptor (CaSR) signaling. In a validation cohort of only nephrolithiasis patients, the CYP24A1-associated locus correlates with serum calcium concentration and a number of nephrolithiasis episodes while the DGKD-associated locus correlates with urinary calcium excretion. In vitro, DGKD knockdown impairs CaSR-signal transduction, an effect rectified with the calcimimetic cinacalcet. Our findings indicate that studies of genotype-guided precision-medicine approaches, including withholding vitamin D supplementation and targeting vitamin D activation or CaSR-signaling pathways in patients with recurrent kidney stones, are warranted.
Quantum chemistry as a benchmark for near-term quantum computers
Authors: McCaskey Alexander J. , Parks Zachary P. , Jakowski Jacek , Moore Shirley V. , Morris Titus D. , Humble Travis S. , Pooser Raphael C. 
Published: November 2019

AbstractWe present a quantum chemistry benchmark for noisy intermediate-scale quantum computers that leverages the variational quantum eigensolver, active-space reduction, a reduced unitary coupled cluster ansatz, and reduced density purification as error mitigation. We demonstrate this benchmark using 4 of the available qubits on the 20-qubit IBM Tokyo and 16-qubit Rigetti Aspen processors via the simulation of alkali metal hydrides (NaH, KH, RbH), with accuracy of the computed ground state energy serving as the primary benchmark metric. We further parameterize this benchmark suite on the trial circuit type, the level of symmetry reduction, and error mitigation strategies. Our results demonstrate the characteristically high noise level present in near-term superconducting hardware, but provide a relevant baseline for future improvement of the underlying hardware, and a means for comparison across near-term hardware types. We also demonstrate how to reduce the noise in post processing with specific error mitigation techniques. Particularly, the adaptation of McWeeny purification of noisy density matrices dramatically improves accuracy of quantum computations, which, along with adjustable active space, significantly extends the range of accessible molecular systems. We demonstrate that for specific benchmark settings and a selected range of problems, the accuracy metric can reach chemical accuracy when computing over the cloud on certain quantum computers.
CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network
Authors: Lee Kanggeun , Jeong Hyoung-oh , Lee Semin , Jeong Won-Ki 
Published: November 2019

AbstractWith recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy.
Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients
Authors: Laheij Alexa M. G. A. , Raber-Durlacher Judith E. , Koppelmans Renée G. A. , Huysmans Marie-Charlotte D. N. J. M. , Potting Carin , van Leeuwen Stephanie J. M. , Hazenberg Mette D. , Brennan Michael T. , von Bültzingslöwen Inger , Johansson Jan-Erik , de Soet Johannes J. , Haverman Thijs M. , Buijs Mark J. , Brandt Bernd W. , Rozema Frederik R. , Blijlevens Nicole M. A. , Zaura Egija 
Published: November 2019

AbstractThe aim of this prospective, two center study was to investigate the dynamics of the microbial changes in relation to the development of ulcerative oral mucositis in autologous SCT (autoSCT) recipients. Fifty-one patients were diagnosed with multiple myeloma and treated with high-dose melphalan followed by autoSCT. They were evaluated before, three times weekly during hospitalization, and three months after autoSCT. At each time point an oral rinse was collected and the presence or absence of ulcerative oral mucositis (UOM) was scored (WHO scale). Oral microbiome was determined by using 16S rRNA amplicon sequencing and fungal load by qPCR. Twenty patients (39%) developed UOM. The oral microbiome changed significantly after autoSCT and returned to pre-autoSCT composition after three months. However, changes in microbial diversity and similarity were more pronounced and rapid in patients who developed UOM compared to patients who did not. Already before autoSCT, different taxa discriminated between the 2 groups, suggesting microbially-driven risk factors. Samples with high fungal load (>0.1%) had a significantly different microbial profile from samples without fungi. In conclusion, autoSCT induced significant and reversible changes in the oral microbiome, while patients who did not develop ulcerative oral mucositis had a more resilient microbial ecosystem.