bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ozone Production in the Soberanes Smoke Haze: Implications for Air Quality in the San Joaquin Valley During the California Baseline Ozone Transport Study
Authors: Langford Andrew O. , Alvarez Raul J. , Brioude J. , Caputi Dani , Conley Stephen A. , Evan S. , Faloona Ian C. , Iraci Laura T. , Kirgis Guillaume , Marrero Josette E. , Ryoo Ju‐Mee , Senff Christoph J. , Yates Emma L. 
Published: April 2020

AbstractThe Soberanes Fire burned 53,470 ha (132,127 acres) along the central California coast between 22 July and 12 October 2016, generating dense smoke and a variety of gaseous compounds that drifted eastward into the San Joaquin Valley Air Basin (SJVAB), an “extreme” nonattainment area for ozone (O3). These gases included nitrogen oxides (NOx) and volatile organic compounds, the photochemical precursors of O3. The fire started during the California Baseline Ozone Transport Study, a field campaign that brought aircraft, surface, and remote sensing measurements of O3 and related species to central California. In this paper, we use the California Baseline Ozone Transport Study measurements to assess the impact of the Soberanes Fire on ozone and particulate air quality in the SJVAB. We focus our analysis on 27 July to 2 August when the smoke haze was heaviest and the highest O3 concentrations in the SJVAB during 2016 were recorded. Our analyses suggest that while 40 to 60 ppbv of fire‐generated O3 was transported to the eastern SJVAB in the 1‐ to 3‐km‐altitude range, relatively little smoke or fire‐generated O3 reached the surface in the Visalia area.
Surface Radiative Flux Bias Reduction Through Regionally Varying Cloud Fraction Parameter Nudging in a Global Coupled Forecast System
Authors: Ridout James A. , Barton Neil P. , Janiga Matthew A. , Reynolds Carolyn A. , May Jackie C. , Rowley Clark , Bishop Craig H. 
Published: April 2020

AbstractA simple parameter nudging procedure is described that systematically reduces near‐analysis time errors in the surface net shortwave flux in the Navy ESPC (Earth System Prediction Capability) system, a global coupled forecast system that is the product of a continuing development effort at the U. S. Naval Research Laboratory. The procedure generates geographically varying perturbations to one of the cloud fraction parameters in the atmospheric model component of the system during the data assimilation cycle, resulting in large improvements in near‐analysis time surface net shortwave flux biases. After a several week spin‐up period, the global RMSE of the succeeding 10‐day mean bias computed for lead times of 6–12 hours is reduced by 40 percent. Results from application of the approach in a series of 45‐day integrations show that improvements are realized at longer forecast lead times as well. The global RMSE of the surface net shortwave flux averaged over these integrations improves by 37 percent for lead times from 1–5 days, decreasing to 18 percent for lead times from 31–45 days. The corresponding longwave flux errors are slightly degraded, ranging from a 2 percent increase for lead times from 1–5 days to a 0.5 percent increase for lead times from 31–45 days. Global‐mean reductions in ground and sea surface temperature errors are obtained through most of the 45‐day integration period due to improvements over ocean and polar regions. Potential steps for extension and operational application of the method are discussed.
Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis
Authors: Tsukui Tatsuya , Sun Kai-Hui , Wetter Joseph B. , Wilson-Kanamori John R. , Hazelwood Lisa A. , Henderson Neil C. , Adams Taylor S. , Schupp Jonas C. , Poli Sergio D. , Rosas Ivan O. , Kaminski Naftali , Matthay Michael A. , Wolters Paul J. , Sheppard Dean 
Published: April 2020

AbstractCollagen-producing cells maintain the complex architecture of the lung and drive pathologic scarring in pulmonary fibrosis. Here we perform single-cell RNA-sequencing to identify all collagen-producing cells in normal and fibrotic lungs. We characterize multiple collagen-producing subpopulations with distinct anatomical localizations in different compartments of murine lungs. One subpopulation, characterized by expression of Cthrc1 (collagen triple helix repeat containing 1), emerges in fibrotic lungs and expresses the highest levels of collagens. Single-cell RNA-sequencing of human lungs, including those from idiopathic pulmonary fibrosis and scleroderma patients, demonstrate similar heterogeneity and CTHRC1-expressing fibroblasts present uniquely in fibrotic lungs. Immunostaining and in situ hybridization show that these cells are concentrated within fibroblastic foci. We purify collagen-producing subpopulations and find disease-relevant phenotypes of Cthrc1-expressing fibroblasts in in vitro and adoptive transfer experiments. Our atlas of collagen-producing cells provides a roadmap for studying the roles of these unique populations in homeostasis and pathologic fibrosis.
Timing the initiation of multiple myeloma
Authors: Rustad Even H. , Yellapantula Venkata , Leongamornlert Daniel , Bolli Niccolò , Ledergor Guy , Nadeu Ferran , Angelopoulos Nicos , Dawson Kevin J. , Mitchell Thomas J. , Osborne Robert J. , Ziccheddu Bachisio , Carniti Cristiana , Montefusco Vittorio , Corradini Paolo , Anderson Kenneth C. , Moreau Philippe , Papaemmanuil Elli , Alexandrov Ludmil B. , Puente Xose S. , Campo Elias , Siebert Reiner , Avet-Loiseau Herve , Landgren Ola , Munshi Nikhil , Campbell Peter J. , Maura Francesco 
Published: April 2020

AbstractThe evolution and progression of multiple myeloma and its precursors over time is poorly understood. Here, we investigate the landscape and timing of mutational processes shaping multiple myeloma evolution in a large cohort of 89 whole genomes and 973 exomes. We identify eight processes, including a mutational signature caused by exposure to melphalan. Reconstructing the chronological activity of each mutational signature, we estimate that the initial transformation of a germinal center B-cell usually occurred during the first 2nd-3rd decades of life. We define four main patterns of activation-induced deaminase (AID) and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) mutagenesis over time, including a subset of patients with evidence of prolonged AID activity during the pre-malignant phase, indicating antigen-responsiveness and germinal center reentry. Our findings provide a framework to study the etiology of multiple myeloma and explore strategies for prevention and early detection.
Nitrogen enrichment increases greenhouse gas emissions from emerged intertidal sandflats
Authors: Hamilton Dallas J. , Bulmer Richard H. , Schwendenmann Luitgard , Lundquist Carolyn J. 
Published: April 2020

AbstractUnvegetated, intertidal sandflats play a critical role in estuarine carbon and nutrient dynamics. However, these ecosystems are under increasing threat from anthropogenic stressors, especially nitrogen enrichment. While research in this area typically focuses on sediment-water exchanges of carbon and nutrients during tidal inundation, there remain significant gaps in our understanding of GHG (Greenhouse Gas) fluxes during tidal emergence. Here we use in situ benthic chambers to quantify GHG fluxes during tidal emergence and investigate the impact of nitrogen enrichment on these fluxes. Our results demonstrate significant differences in magnitude and direction of GHG fluxes between emerged and submerged flats, demonstrating the importance of considering tidal state when estimating GHG emissions from intertidal flats. These responses were related to differences in microphytobenthic and macrofaunal activity, illustrating the important role of ecology in mediating fluxes from intertidal flats. Our results further demonstrate that nitrogen enrichment of 600 gN m−2 was associated with, on average, a 1.65x increase in CO2 uptake under light (photosynthetically active) conditions and a 1.35x increase in CO2 emission under dark conditions, a 3.8x increase in CH4 emission and a 15x increase in N2O emission overall. This is particularly significant given the large area intertidal flats cover globally, and their increasing exposure to anthropogenic stressors.
Comparison of subjective quality of life after endoscopic submucosal resection or surgery for early gastric cancer
Authors: Tae Chung Hyun , Shim Ki-Nam , Kim Byung-Wook , Kim Jie-Hyun , Hong Su Jin , Baik Gwang Ho , Song Hyun Joo , Kim Yong Sung , Jang Seung-Ho , Jung Hye-Kyung 
Published: April 2020

AbstractQuality of life (QoL) has become an important issue after early gastric cancer (EGC) treatment. We aimed to compare the QoL of EGC survivors after ESD (n = 241) or laparoscopic subtotal gastrectomy (n = 241) without recurrence and to evaluate the QoL over the 5-year period after adjusting for various confounding factors related to QoL. QoL related to the gastric cancer subscale (GCS) was significantly higher in the ESD group than surgery group (p < 0.001). After adjusting for all possible confounding factors, survivors who underwent ESD still had higher QoL related to CSG than those who underwent surgery. On the analysis of interaction effects for all QoL subscales, higher QoL related to GCS of ESD group than those of surgery group has been kept over time (p = 0.983). Therefore, we concluded that EGC survivors who undergo ESD have significantly better QoL related to GCS over a 5-year period after treatment than those who undergo surgery. This may be a useful consideration when selecting treatment modalities for patients with EGC.
The blue mussel inside: 3D visualization and description of the vascular-related anatomy of Mytilus edulis to unravel hemolymph extraction
Authors: Eggermont Mieke , Cornillie Pieter , Dierick Manuel , Adriaens Dominique , Nevejan Nancy , Bossier Peter , Van den Broeck Wim , Sorgeloos Patrick , Defoirdt Tom , Declercq Annelies Maria 
Published: April 2020

AbstractThe blue mussel Mytilus edulis is an intensely studied bivalve in biomonitoring programs worldwide. The lack of detailed descriptions of hemolymph-withdrawal protocols, particularly with regard to the place from where hemolymph could be perfused from, raises questions regarding the exact composition of aspirated hemolymph and does not exclude the possibility of contamination with other body-fluids. This study demonstrates the use of high resolution X-ray computed tomography and histology combined with 3D-reconstruction using AMIRA-software to visualize some important vascular-related anatomic structures of Mytilus edulis. Based on these images, different hemolymph extraction sites used in bivalve research were visualized and described, leading to new insights into hemolymph collection. Results show that hemolymph withdrawn from the posterior adductor muscle could be extracted from small spaces and fissures between the muscle fibers that are connected to at least one hemolymph supplying artery, more specifically the left posterior gastro-intestinal artery. Furthermore, 3D-reconstructions indicate that puncturing hemolymph from the pericard, anterior aorta, atria and ventricle in a non-invasive way should be possible. Hemolymph withdrawal from the heart is less straightforward and more prone to contamination from the pallial cavity. This study resulted simultaneously in a detailed description and visualization of the vascular-related anatomy of Mytilus edulis.
Increased static dielectric constant in ZnMnO and ZnCoO thin films with bound magnetic polarons
Authors: Vegesna Sahitya V. , Bhat Vinayak J. , Bürger Danilo , Dellith Jan , Skorupa Ilona , Schmidt Oliver G. , Schmidt Heidemarie 
Published: April 2020

AbstractA novel small signal equivalent circuit model is proposed in the inversion regime of metal/(ZnO, ZnMnO, and ZnCoO) semiconductor/Si3N4 insulator/p-Si semiconductor (MSIS) structures to describe the distinctive nonlinear frequency dependent capacitance (C-F) and conductance (G-F) behaviour in the frequency range from 50 Hz to 1 MHz. We modelled the fully depleted ZnO thin films to extract the static dielectric constant (εr) of ZnO, ZnMnO, and ZnCoO. The extracted enhancement of static dielectric constant in magnetic n-type conducting ZnCoO (εr ≥ 13.0) and ZnMnO (εr ≥ 25.8) in comparison to unmagnetic ZnO (εr = 8.3–9.3) is related to the electrical polarizability of donor-type bound magnetic polarons (BMP) in the several hundred GHz range (120 GHz for CdMnTe). The formation of donor-BMP is enabled in n-type conducting, magnetic ZnO by the s-d exchange interaction between the electron spin of positively charged oxygen vacancies $${V}_{o}^{+}$$Vo+ in the BMP center and the electron spins of substitutional Mn2+ and Co2+ ions in ZnMnO and ZnCoO, respectively. The BMP radius scales with the Bohr radius which is proportional to the static dielectric constant. Here we show how BMP overlap can be realized in magnetic n-ZnO by increasing its static dielectric constant and guide researchers in the field of transparent spintronics towards ferromagnetism in magnetic, n-ZnO.
Mediators of the association between low socioeconomic status and poor glycemic control among type 2 diabetics in Bangladesh
Authors: Rahman Mosiur , Nakamura Keiko , Hasan S. M. Mahmudul , Seino Kaoruko , Mostofa Golam 
Published: April 2020

AbstractAlthough low socioeconomic status (SES) is related to poor glycemic control, the underlying mechanisms remain unclear. We examined potentially modifiable factors involved in the association between low SES and poor glycemic control using data from the baseline survey of a multicenter, prospective cohort study. Five hundred adult type 2 diabetes patients were recruited from three diabetes centers. Glycemic control was poorer in diabetic individuals with low SES than in those with higher SES. Adverse health-related behaviors, such as non-adherence to medication (adjusted odds ratio [AOR] = 1.07, 95% confidence interval [CI] 1.04–1.13) and diet (AOR = 1.04, 95% CI 1.02–1.06); existing comorbidities, such as depressive symptoms (AOR = 1.05, 95% CI 1.04–1.09); and non-adherence to essential health service-related practices concerning diabetes care, such as irregular scheduled clinic visits (AOR = 1.04, 95% CI 1.03–1.06) and not practicing self-monitoring of blood glucose (AOR = 1.05, 95% CI 1.03–1.07), mediated the relationship between social adversity and poor glycemic control specially in urban areas of Bangladesh. Those identified factors provide useful information for developing interventions to mitigate socioeconomic disparities in glycemic control.
Climatic and societal impacts of a “forgotten” cluster of volcanic eruptions in 1108-1110 CE
Authors: Guillet Sébastien , Corona Christophe , Ludlow Francis , Oppenheimer Clive , Stoffel Markus 
Published: April 2020

AbstractRecently revised ice core chronologies for Greenland have newly identified one of the largest sulfate deposition signals of the last millennium as occurring between 1108 and 1113 CE. Long considered the product of the 1104 CE Hekla (Iceland) eruption, this event can now be associated with substantial deposition seen in Antarctica under a similarly revised chronology. This newly recognized bipolar deposition episode has consequently been deemed to reveal a previously unknown major tropical eruption in 1108 CE. Here we show that a unique medieval observation of a “dark” total lunar eclipse attests to a dust veil over Europe in May 1110 CE, corroborating the revised ice-core chronologies. Furthermore, careful evaluation of ice core records points to the occurrence of several closely spaced volcanic eruptions between 1108 and 1110 CE. The sources of these eruptions remain unknown, but we propose that Mt. Asama, whose largest Holocene eruption occurred in August 1108 CE and is credibly documented by a contemporary Japanese observer, is a plausible contributor to the elevated sulfate in Greenland. Dendroclimatology and historical documentation both attest, moreover, to severe climatic anomalies following the proposed eruptions, likely providing the environmental preconditions for subsistence crises experienced in Western Europe between 1109 and 1111 CE.
Construction of higher-order cellular microstructures by a self-wrapping co-culture strategy using a redox-responsive hydrogel
Authors: Ramadhan Wahyu , Kagawa Genki , Moriyama Kousuke , Wakabayashi Rie , Minamihata Kosuke , Goto Masahiro , Kamiya Noriho 
Published: April 2020

AbstractIn this report, a strategy for constructing three-dimensional (3D) cellular architectures comprising viable cells is presented. The strategy uses a redox-responsive hydrogel that degrades under mild reductive conditions, and a confluent monolayer of cells (i.e., cell sheet) cultured on the hydrogel surface peels off and self-folds to wrap other cells. As a proof-of-concept, the self-folding of fibroblast cell sheet was triggered by immersion in aqueous cysteine, and this folding process was controlled by the cysteine concentration. Such folding enabled the wrapping of human hepatocellular carcinoma (HepG2) spheroids, human umbilical vein endothelial cells and collagen beads, and this process improved cell viability, the secretion of metabolites and the proliferation rate of the HepG2 cells when compared with a two-dimensional culture under the same conditions. A key concept of this study is the ability to interact with other neighbouring cells, providing a new, simple and fast method to generate higher-order cellular aggregates wherein different types of cellular components are added. We designated the method of using a cell sheet to wrap another cellular aggregate the ‘cellular Furoshiki’. The simple self-wrapping Furoshiki technique provides an alternative approach to co-culture cells by microplate-based systems, especially for constructing heterogeneous 3D cellular microstructures.
α-synuclein inclusions are abundant in non-neuronal cells in the anterior olfactory nucleus of the Parkinson’s disease olfactory bulb
Authors: Stevenson Taylor J. , Murray Helen C. , Turner Clinton , Faull Richard L. M. , Dieriks Birger V. , Curtis Maurice A. 
Published: April 2020

AbstractReduced olfactory function (hyposmia) is one of the most common non-motor symptoms experienced by those living with Parkinson’s disease (PD), however, the underlying pathology of the dysfunction is unclear. Recent evidence indicates that α-synuclein (α-syn) pathology accumulates in the anterior olfactory nucleus of the olfactory bulb years before the motor symptoms are present. It is well established that neuronal cells in the olfactory bulb are affected by α-syn, but the involvement of other non-neuronal cell types is unknown. The occurrence of intracellular α-syn inclusions were quantified in four non-neuronal cell types – microglia, pericytes, astrocytes and oligodendrocytes as well as neurons in the anterior olfactory nucleus of post-mortem human PD olfactory bulbs (n = 11) and normal olfactory bulbs (n = 11). In the anterior olfactory nucleus, α-syn inclusions were confirmed to be intracellular in three of the four non-neuronal cell types, where 7.78% of microglia, 3.14% of pericytes and 1.97% of astrocytes were affected. Neurons containing α-syn inclusions comprised 8.60% of the total neuron population. Oligodendrocytes did not contain α-syn. The data provides evidence that non-neuronal cells in the PD olfactory bulb contain α-syn inclusions, suggesting that they may play an important role in the progression of PD.
Retinal phototoxicity and the evaluation of the blue light hazard of a new solid-state lighting technology
Authors: Jaadane Imene , Villalpando Rodriguez Gloria , Boulenguez Pierre , Carré Samuel , Dassieni Irene , Lebon Cecile , Chahory Sabine , Behar-Cohen Francine , Martinsons Christophe , Torriglia Alicia 
Published: April 2020

AbstractExposure Limit Values (ELV) for artificial lighting were defined in order to prevent light-induced damage to the retina. The evaluation of the lighting devices include the correction of their spectra by the B(λ) function or blue light hazard function, representing the relative spectral sensitivity of the human eye to the blue light. This weighting function peaks between 435 and 440 nm. In this study we evaluate a new generation of light emitting diode (LED), the GaN-on-GaN (gallium nitride on gallium nitride) LED, that present an emission peak in the purple part of the spectrum. Wistar rats were exposed to GaN-on-GaN and conventional diodes at different retinal doses (from 2.2 to 0.5 J/cm2). We show that GaN-on-GaN diodes are more toxic than conventional LED for the rat neural retina and the rat retinal pigment epithelium, indicating that the BLH (blue light hazard) weighting is not adapted to this type of diodes. One of the reasons of this increased toxicity is the effects of shorter wavelengths on mitochondria polarization. We also show that the threshold of phototoxic retinal dose in the rat (fixed at 11 J/cm2, BLH weighted) is overestimated, suggesting that the values used for regulations, calculated in primates using the same methods than in rats, should be revised.
Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15
Authors: Fernandez-Garcia Maria Dolores , Simon-Loriere Etienne , Kebe Ousmane , Sakuntabhai A. , Ndiaye Kader 
Published: April 2020

AbstractUsing a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15.
Data-driven segmentation of audiometric phenotypes across a large clinical cohort
Authors: Parthasarathy Aravindakshan , Romero Pinto Sandra , Lewis Rebecca M. , Goedicke William , Polley Daniel B. 
Published: April 2020

AbstractPure tone audiograms are used to assess the degree and underlying source of hearing loss. Audiograms are typically categorized into a few canonical types, each thought to reflect distinct pathologies of the ear. Here, we analyzed 116,400 patient records from our clinic collected over a 24-year period and found that standard categorization left 46% of patient records unclassified. To better account for the full spectrum of hearing loss profiles, we used a Gaussian Mixture Model (GMM) to segment audiograms without any assumptions about frequency relationships, interaural symmetry or etiology. The GMM converged on ten types, featuring varying degrees of high-frequency hearing loss, flat loss, mixed loss, and notched profiles, with predictable relationships to patient age and sex. A separate GMM clustering of 15,380 audiograms from the National Health and Nutrition Examination Survey (NHANES) identified six similar types, that only lacked the more extreme hearing loss configurations observed in our patient cohort. Whereas traditional approaches distill hearing loss configurations down to a few canonical types by disregarding much of the underlying variability, an objective probabilistic model that accounted for all of the data identified an organized, but more heterogenous set of audiogram types that was consistent across two large clinical databases.