bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pancreatic Islet Transcriptional Enhancers and Diabetes
Authors: Cebola Inês 
Published: November 2019

Abstract
Purpose of Review
Common genetic variants that associate with type 2 diabetes risk are markedly enriched in pancreatic islet transcriptional enhancers. This review discusses current advances in the annotation of islet enhancer variants and their target genes.

Recent Findings
Recent methodological advances now allow genetic and functional mapping of diabetes causal variants at unprecedented resolution. Mapping of enhancer-promoter interactions in human islets has provided a unique appreciation of the complexity of islet gene regulatory processes and enabled direct association of noncoding diabetes risk variants to their target genes.

Summary
The recently improved human islet enhancer annotations constitute a framework for the interpretation of diabetes genetic signals in the context of pancreatic islet gene regulation. In the future, integration of existing and yet to come regulatory maps with genetic fine-mapping efforts and in-depth functional characterization will foster the discovery of novel diabetes molecular risk mechanisms.
Collagen fingerprinting and the Chumash billfish fishery, Santa Barbara Channel, California, USA
Authors: Rick Torben , Harvey Virginia L. , Buckley Michael 
Published: November 2019

AbstractBillfish from the families Xiphiidae (swordfish) and Istiophoridae (marlins and sailfish) are large, often pelagic fishes that are highly migratory. Although some billfish have been the target of global commercial and sport fisheries for decades, prehistoric billfish foraging is relatively rare, but includes systematic swordfish (Xiphias gladius) and/or striped marlin (Kajikia audax) exploitation in the Santa Barbara Channel region of California, the Gulf of Maine, and the northern coast of Chile. While whole vertebrae, rostra, and other elements can often be identified to species, fragments of these, or other non-diagnostic elements such as fin ray spines, as well as modified bones, are difficult to determine to species-level beyond general identification as billfish or “large fish.” We performed collagen fingerprinting on modern (n = 17) and archaeological (n = 30) billfish and large tuna (Scombridae) remains from museum collections and Chumash archaeological sites in California’s Santa Barbara Channel region to test this method for determining the species of fragmentary remains. These data demonstrate that collagen fingerprinting can distinguish between the families Istiophoridae, Xiphiidae, and Scombridae, although distinguishing between species within Istiophoridae needs additional research. All but one of our archaeological specimens are from swordfish, with just one striped marlin, suggesting that the Chumash were likely encountering or targeting swordfish more frequently than other billfish species. Our study demonstrates that collagen fingerprinting is an important technique for documenting ancient billfish and other fisheries around the world.
Association between thiopurine medication exposure and Alzheimer's disease among a cohort of patients with inflammatory bowel disease
Authors: Sutton S.Scott , Magagnoli Joseph , Cummings Tammy , Hardin James W. 
Published: November 2019

AbstractIntroductionRas‐related C3 botulinum toxin substrate 1 (Rac1), a member of the Rho‐GTPase family of proteins, could be an Alzheimer's disease (AD) triggering co‐factor due to its effect on both amyloid precursor protein (APP) and tau. Thiopurine medications, such as azathioprine and mercaptopurine, are immunosuppressants that suppress Rac1 activation. We hypothesize that due to their ability to suppress Rac1, thiopurines are associated with a lower risk of AD.MethodsTo explore the relationship between thiopurines and incident AD diagnosis, we conducted a national retrospective cohort study among U.S. Veterans with inflammatory bowel disease (IBD), including Crohn's disease (CD) or ulcerative colitis (UC), as well as a non‐IBD control. We created propensity score‐matched cohorts and estimated the hazard ratio via the time‐dependent Cox proportional hazards model.ResultsThe study sample size was 66,312 patients and consisted of 24,057 IBD patients (4354 thiopurine exposed and 19,703 unexposed) and 42,255 patients without IBD or thiopurine exposure. Patients exposed to thiopurines have the lowest rate of AD, and our results demonstrate for each additional year of thiopurine exposure risk of AD is reduced by 8.3%% (adjusted HR = 0.917; 95% CI = [0.851–0.989]).DiscussionOur results support the preclinical findings implicating Rac1 in the AD disease process. A national cohort study demonstrated that Rac1 is associated with the AD process consistent with the preclinical evidence. Further exploration and evaluation of Rac1 inhibition are needed.
A novelMYBPC3c.2737+1 (IVS26) G>T mutation responsible for high-risk hypertrophic cardiomyopathy
Authors: Tong Wuyang , Liu Wei , Guo Hong , Wang Jiang , Yu Shiyong , Zhang Jihang , Liu Chuan , Chen Jia , Zhao Xiaohui 
Published: November 2019

AbstractBackground:Hypertrophic cardiomyopathy is an autosomal dominant hereditary disease characterised by left ventricular asymmetry hypertrophy. However, our knowledge of the genetic background in hypertrophic cardiomyopathy cases is limited. Here, we aimed to evaluate pathogenic gene mutations in a family with high-risk hypertrophic cardiomyopathy and analyse the genotype/phenotype relationships in this family.Methods:The proband, her parents, and her niece underwent whole-exome sequencing, and the genotypes of family members were identified using Sanger sequencing. mRNA expression was detected using reverse transcription sequencing. Structural impairments were predicted by homologous modelling. A family survey was conducted for patients with positive results to obtain information on general clinical symptoms, electrocardiography, ambulatory electrocardiography, echocardiography, and 3.0T cardiac magnetic resonance findings. Regular follow-up was performed for up to 6 months.Results:Five family members, including the proband, carried a cleavage site mutation in theMYBPC3gene (c.2737+1 (IVS26) G>T), causing exon 26 of theMYBPC3gene transcript to be skipped and leading to truncation of cardiac myosin-binding protein C. Family survey showed that the earliest onset age was 13 years old, and three people had died suddenly at less than 40 years old. Three pathogenic gene carriers were diagnosed with hypertrophic cardiomyopathy, and all showed severe ventricular septal hypertrophy.Conclusion:The c.2737+1 (IVS26) G>T mutation in theMYBPC3gene led to exon 26 skipping, thereby affecting the structure and function of cardiac myosin-binding protein C and leading to severe ventricular hypertrophy and sudden death.
Contrasting Hydroclimatic Model‐Data Agreements Over the Nordic‐Arctic Region
Authors: Bring A. , Goldenberg R. , Kalantari Z. , Prieto C. , Ma Y. , Jarsjö J. , Destouni G. 
Published: November 2019

AbstractRapid changes in high‐latitude hydroclimate have important implications for human societies and environment. Previous studies of different regions have indicated better agreement between climate model results and observation data for the thermodynamic variable of surface air temperature (T) than for the water variables of precipitation (P), evapotranspiration (ET), and runoff (R). Here we compare climate model output with observations for 64 Nordic and Arctic hydrological basins of different sizes, and for the whole region combined. We find an unexpectedly high agreement between models and observations for R, about as high as the model‐observation agreement for T and distinctly higher than that for P or ET. Model‐observation agreement for R and T is also consistently higher on the whole‐region scale than individual basin scales. In contrast, model‐observation agreement for P and ET is overall lower, and for some error measures also lower for the whole region than for individual basins of various scales. Region‐specific soil freeze–thaw bias of climate models can at least partly explain the low model‐observation agreement for P and ET, while leaving modeled R relatively unaffected. Thereby, model projections for this region may be similarly reliable and directly useful for large‐scale average conditions of R as of T.
Sound Velocities in Shock‐Synthesized Stishovite to 72 GPa
Authors: Berryman Eleanor J. , Winey J. M. , Gupta Yogendra M. , Duffy Thomas S. 
Published: November 2019

AbstractStishovite (rutile‐type SiO2) is the archetype of dense silicates and may occur in postgarnet eclogitic rocks at lower‐mantle conditions. Sound velocities in stishovite are fundamental to understanding its mechanical and thermodynamic behavior at high pressure and temperature. Here, we use plate‐impact experiments combined with velocity interferometry to determine the stress, density, and longitudinal sound speed in stishovite formed during shock compression of fused silica at 44 GPa and above. The measured sound speeds range from 12.3(8) km/s at 43.8(8) GPa to 9.8(4) km/s at 72.7(11) GPa. The decrease observed at 64 GPa reflects a decrease in the shear modulus of stishovite, likely due to the onset of melting. By 72 GPa, the measured sound speed agrees with the theoretical bulk sound speed indicating loss of all shear stiffness due to complete melting. Our sound velocity results provide direct evidence for shock‐induced melting, in agreement with previous pyrometry data.
Improved Quantification of Global Mean Ocean Mass Change Using GRACE Satellite Gravimetry Measurements
Authors: Chen Jianli , Tapley Byron , Seo Ki‐Weon , Wilson Clark , Ries John 
Published: November 2019

AbstractGlobal mean ocean mass change derived from the Gravity Recovery and Climate Experiment (GRACE) gravity solutions generally agrees well with ocean mass change inferred from satellite altimeter sea surface height and Argo floats observations during the period January 2005 to December 2015. However, there is a systematic annual phase lag (~10°) between GRACE and Altimeter‐Argo estimates. This phase lag is attributed to the enforced mass conservation in GRACE gravity solutions, in which the ΔC00 coefficients (representing changes in total Earth mass) are set to zero. After a correct implementation of global mass conservation by removing global mean atmospheric mass from the GRACE solutions using atmospheric model predictions, the annual phase lag is nearly completely gone, yielding significantly improved agreement between GRACE and Altimeter‐Argo estimates. In addition, retaining GRACE ΔJ2 coefficients provides better GRACE ocean mass estimates at both seasonal and long‐term time scales.
Magnetic Reconnection in Three Dimensions: Modeling and Analysis of Electromagnetic Drift Waves in the Adjacent Current Sheet
Authors: Ergun R. E. , Hoilijoki S. , Ahmadi N. , Schwartz S. J. , Wilder F. D. , Drake J. F. , Hesse M. , Shay M. A. , Ji H. , Yamada M. , Graham D. B. , Cassak P. A. , Swisdak M. , Burch J. L. , Torbert R. B. , Holmes J. C. , Stawarz J. E. , Goodrich K. A. , Eriksson S. , Strangeway R. J. , LeContel O. 
Published: November 2019

AbstractWe present a model of electromagnetic drift waves in the current sheet adjacent to magnetic reconnection at the subsolar magnetopause. These drift waves are potentially important in governing 3‐D structure of subsolar magnetic reconnection and in generating turbulence. The drift waves propagate nearly parallel to the X line and are confined to a thin current sheet. The scale size normal to the current sheet is significantly less than the ion gyroradius and can be less than or on the order of the wavelength. The waves also have a limited extent along the magnetic field (B), making them a three‐dimensional eigenmode structure. In the current sheet, the background magnitudes of B and plasma density change significantly, calling for a treatment that incorporates an inhomogeneous plasma environment. Using detailed examination of Magnetospheric Multiscale observations, we find that the waves are best represented by series of electron vortices, superimposed on a primary electron drift, that propagate along the current sheet (parallel to the X line). The waves displace or corrugate the current sheet, which also potentially displaces the electron diffusion region. The model is based on fluid behavior of electrons, but ion motion must be treated kinetically. The strong electron drift along the X line is likely responsible for wave growth, similar to a lower hybrid drift instability. Contrary to a classical lower hybrid drift instability, however, the strong changes in the background B and no, the normal confinement to the current sheet, and the confinement along B are critical to the wave description.
Jupiter's Dark Polar Region as Observed by the Hubble Space Telescope During the Juno Approach Phase
Authors: Swithenbank‐Harris B. G. , Nichols J. D. , Bunce E. J. 
Published: November 2019

AbstractWe present an analysis of Jupiter's dark polar region, previously described as a crescent‐shaped region devoid of emission along the dawnside poleward of the main oval. Using ultraviolet images obtained by the Hubble Space Telescope between days of year 137 and 176, coupled with interplanetary data captured during the approach phase of the NASA Juno spacecraft, we examine the morphology and variability of the dark polar region and the influence of solar wind conditions on the region. We find that the dark polar region is more variable than previously thought and in particular shows significant variability during compressions of the magnetosphere by the solar wind. Duskward extensions of the dark polar region through the noon sector are often observed during periods of deep rarefaction in the solar wind, while a larger dark polar region width is observed nearer to local noon under solar wind compression. Intensity distributions of the dark polar region reveal a greater probability of lower emission intensity during deep rarefactions. Calculation of the magnetic flux associated with the dark polar region returns lower flux values than previous estimates of the total open flux at Jupiter. This may suggest that either the dark polar region does not account for the entirety of the open flux region, or the magnetotail is not composed of only open flux, as previously suggested.
Strength of Laboratory Synthesized Hydrate‐Bearing Sands and Their Relationship to Natural Hydrate‐Bearing Sediments
Authors: Priest Jeffrey A. , Hayley Jocelyn L. 
Published: November 2019

AbstractThe strength of hydrate‐bearing sediments is an important input parameter for numerical simulations for evaluating the long‐term future gas production from these sediments and the risks associated with such activities on the environment. Studies on laboratory synthesized, and natural, hydrate‐bearing coarse‐grained soils exhibit similar behavior, where increasing hydrate saturation increases specimen strength and stiffness with the corresponding development of peak stress, postpeak strain softening and tendency for sample dilation, which is suppressed with increasing effective stress, although strength is increased. For synthesized specimens, hydrate growth at grain contacts leads to “cementing” behavior and the largest increase in strength, which is subdued when hydrate growth is prevented at these locations. Sample disturbance in natural samples lead to lower strength and stiffness compared to laboratory synthesized samples. Unconfined compression shear tests on natural samples highlight the strong “cementing” effect of gas hydrates on coarse‐grained soils. The strength of natural sediments appears strongly correlated with particle size and clay content, with smaller particle and increasing clay content reducing strength for a given hydrate saturation. The strength parameters, friction angle, and cohesion appear to depend on sample type. For synthesized specimens, friction angle was reasonably independent of hydrate saturation while cohesion increased in an exponential manner, with the largest increase occurring when hydrate growth is at particle contacts. In contrast, friction angle appeared to increase with a corresponding reduction in cohesion for natural hydrate‐bearing sediments. However, these observations may be related to sample disturbance and stress conditions under which the data were acquired.
A Statistical Analysis of the Propagating Quasi 16‐Day Waves at High Latitudes and Their Response to Sudden Stratospheric Warmings From 2005 to 2018
Authors: Gong Yun , Wang Hongling , Ma Zheng , Zhang Shaodong , Zhou Qihou , Huang Chunming , Huang Kaiming 
Published: November 2019

AbstractThis study presents an analysis of the long‐term variations of four propagating quasi 16‐day waves with Wavenumbers 1 and 2 and investigates their association with sudden stratospheric warming (SSW) events. The study is based on the data obtained from Aura Microwave Limb Sounder satellite and Modern‐Era Retrospective Analysis for Research and Applications‐2 reanalysis data in the period from 2004 to 2018. Strong quasi 16‐day waves are found in the winter hemisphere. The propagating waves with Wavenumber 1 are prominent in the Northern Hemisphere and eastward‐propagating waves are dominant in the Southern Hemisphere. By analyzing 14 SSW events, we found that the westward‐propagating quasi 16‐day waves increase rapidly around the onset dates of the major SSWs, which is likely associated with the quickly reduced mean eastward background winds. Based on analysis of geopotential height, Ertel potential vorticity and Eliassen‐Palm flux, the propagating quasi 16‐day waves with Wavenumbers 1 and 2, (mainly from westward‐propagating components) contribute to the formation of the vortex displaced and vortex split SSWs, respectively.
A Scale‐Aware Parameterization for Estimating Subgrid Variability of Downward Solar Radiation Using High‐Resolution Digital Elevation Model Data
Authors: He Siwei , Smirnova Tatiana G. , Benjamin Stanley G. 
Published: November 2019

AbstractSubgrid variability of solar downward radiation at the surface can be important in estimating subgrid variability of other radiation‐driven variables, such as snowmelt and soil temperature. However, this information is ignored in current hydrological and weather prediction models as only the mean downward solar radiation of model grid is used. In this study, a parameterization for estimating subgrid variability of downward solar radiation from the model grid mean using high‐resolution digital elevation model (DEM) data is proposed. This scheme considers aspect and slope effects on the subgrid variability. The advantage of this scheme is that computations are performed at the same resolution as the considered hydrological or weather prediction model, and subgrid topographic properties derived from high‐resolution DEM data are used as static inputs. This proposed scheme has been verified in mountainous and flat areas, respectively. It is found that the scheme can well estimate the subgrid variability of downward solar radiation. Also, effects of the DEM resolution on the calculated subgrid variability and the spatial correlation of downward solar radiation are studied. Results show that modeled subgrid variability highly depends on the resolution of the DEM, while the spatial correlation is negligibly time dependent. The proposed scheme can be used in any hydrological and weather prediction model to estimate subgrid variability of downward solar radiation. For example, it is planned to be tested in future NOAA regional and global weather models to account for the effects of the subgrid variability of downward solar radiation on the snow model of the land‐surface component.
Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
Authors: Rinke Christian , Rubino Francesco , Messer Lauren F , Youssef Noha , Parks Donovan H , Chuvochina Maria , Brown Mark , Jeffries Thomas , Tyson Gene W , Seymour Justin R , Hugenholtz Philip 
Published: November 2019

Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Dual-species, multi-qubit logic primitives for Ca+/Sr+ trapped-ion crystals
Authors: Bruzewicz C. D. , McConnell R. , Stuart J. , Sage J. M. , Chiaverini J. 
Published: November 2019

AbstractWe demonstrate key multi-qubit quantum-logic primitives in a dual-species trapped-ion system based on $${}^{40}$$40Ca$${}^{+}$$+ and $${}^{88}$$88Sr$${}^{+}$$+ ions, using two optical qubits with quantum-logic-control frequencies in the red to near-infrared range. With all ionization, cooling, and control wavelengths in a wavelength band similar for the two species and centered in the visible, and with a favorable mass ratio for sympathetic cooling, this pair is a promising candidate for scalable quantum information processing. Same-species and dual-species two-qubit gates, based on the Mølmer–Sørensen interaction and performed in a cryogenic surface-electrode trap, are characterized via the fidelity of generated entangled states; we achieve fidelities of 98.8(2)% and 97.5(2)% in Ca$${}^{+}$$+–Ca$${}^{+}$$+ and Sr$${}^{+}$$+–Sr$${}^{+}$$+ gates, respectively. For a similar Ca$${}^{+}$$+–Sr$${}^{+}$$+ gate, we achieve a fidelity of 94.3(3)%, and carrying out a Sr$${}^{+}$$+–Sr$${}^{+}$$+ gate performed with a Ca$${}^{+}$$+ sympathetic cooling ion in a Sr$${}^{+}$$+–Ca$${}^{+}$$+–Sr$${}^{+}$$+ crystal configuration, we achieve a fidelity of 95.7(3)%. These primitives form a set of trapped-ion capabilities for logic with sympathetic cooling and ancilla readout or state transfer for general quantum computing and communication applications.
Arbovirus emergence in the temperate city of Córdoba, Argentina, 2009–2018
Authors: Robert Michael A. , Tinunin Daniela T. , Benitez Elisabet M. , Ludueña-Almeida Francisco F. , Romero Moory , Stewart-Ibarra Anna M. , Estallo Elizabet L. 
Published: November 2019

AbstractThe distribution of arbovirus disease transmission is expanding from the tropics and subtropics into temperate regions worldwide. The temperate city of Córdoba, Argentina has been experiencing the emergence of dengue virus, transmitted by the mosquito Aedes aegypti, since 2009, when autochthonous transmission of the virus was first recorded in the city. The aim of this work is to characterize the emergence of dengue and related arboviruses (Zika and chikungunya) in Córdoba since 2009. Herein, we present a data set with all known information about transmission of dengue, Zika, and chikungunya viruses in Córdoba, Argentina from 2009–2018, including what information is known of dengue virus (DENV) serotypes in circulation and origins of imported cases. The data presented in this work will assist researchers in investigating drivers of arbovirus emergence and transmission in Córdoba, Argentina and contribute to a better understanding of the global problem of the expanding distribution of arbovirus disease transmission.