bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three‐Dimensional Closure of Field‐Aligned Currents in the Polar Ionosphere
Authors: Yano Yuto , Ebihara Yusuke 
Published: August 2021

AbstractUsing a simplified three‐dimensional Hall‐magnetohydrodynamics simulation, we investigated the current closure of field‐aligned currents (FACs) in the polar ionosphere. Ion‐neutral collision was taken into consideration. To excite a pair of FACs, an electric field perturbation is applied to the upper boundary of the simulation box. The flow shear propagated downward accompanied with the FACs. When the electron density was initially uniform, most of the FACs are connected with the Pedersen current due to electrostatic processes. Some of them are connected with the Hall current due to inductive processes. When the density was initially enhanced in a longitudinally elongated region (high‐density band), overflow of the Hall current takes place near the edge of the high‐density band. Additionally, localized FACs appear to bridge between the Pedersen current layer (high altitude) and the Hall current layer (low altitude). The formation of the additional FACs is closely associated with the field‐aligned gradient of ∇∙E, where E is the electric field. We compared the current lines with those evaluated by the traditional thin‐layer assumption. The current closure obtained by the thin‐layer assumption is fully different from that obtained by the three‐dimensional model. In the full three‐dimensional simulation, a current line flowing in the Hall layer can pass underneath the current flowing in the Pedersen layer. Such “intersection” is not allowed in the thin‐layer assumption. We believe that the three‐dimensional model offers advantages for fully understanding the closure of the FACs together with the current closure on the magnetospheric side.
Deep Relative Geologic Time: A Deep Learning Method for Simultaneously Interpreting 3‐D Seismic Horizons and Faults
Authors: Bi Zhengfa , Wu Xinming , Geng Zhicheng , Li Haishan 
Published: August 2021

AbstractExtracting horizons and detecting faults in a seismic image are basic steps for structural interpretation and important for many seismic processing schemes. A common ground of the two tasks is to analyze seismic structures and they are related to each other. However, previously proposed methods deal with the tasks independently, and challenge remains in each of them. We propose a volume‐to‐volume neural network to estimate a relative geologic time (RGT) volume from a seismic volume, and this RGT volume is further used to simultaneously interpret horizons and faults. The network uses U‐shaped framework with attention mechanism to systematically aggregate multi‐scale information and automatically highlight informative features, and achieves high prediction accuracy with affordable computational costs. To train the network, we build thousands of 3‐D noisy synthetic seismic volumes and corresponding RGT volumes with realistic and various structures. We introduce a loss function based on structure similarity to capture spatial dependencies among seismic samples for better optimizing the network, and use multiple reasonable assessments to evaluate the predicted results. Trained by using synthetic data, our network outperforms the conventional approaches in recognizing structural features in field data examples. Once obtaining an RGT volume, we can not only obtain seismic horizons by simply extracting RGT constant surfaces but also detect faults that are indicated by lateral RGT discontinuities. To be able to deal with large seismic volumes, we further propose a workflow to first estimate sub‐volumes of RGT and merge them to obtain a full RGT volume without boundary artifacts.
Dissolved Cd, Co, Cu, Fe, Mn, Ni, and Zn in the Arctic Ocean
Authors: Gerringa L. J. A. , Rijkenberg M. J. A. , Slagter H. A. , Laan P. , Paffrath R. , Bauch D. , Rutgers van der Loeff M. , Middag R. 
Published: August 2021

AbstractDuring the Polarstern (PS94) expedition, summer 2015, part of the international GEOTRACES program, sources and sinks of dissolved (D) Cd, Co, Cu, Fe, Mn, Ni, and Zn were studied in the central Arctic Ocean. In the Polar Surface Water in which the TransPolar Drift (TPD) is situated, salinity and δ18O derived fractions indicated a distinct riverine source for silicate DCo, DCu, DFe, DMn, and DNi. Linear relationships between DMn and the meteoric fraction depended on source distance, likely due to Mn‐precipitation during transport. In the upper 50 m of the Makarov Basin, outside the TPD core, DCo, DMn, DNi, DCd, and DCu were enriched by Pacific waters, whereas DFe seemed diluted. DCo, DFe, DMn, and DZn were relatively high in the Barents Sea and led to enrichment of Atlantic water flowing into the Nansen Basin. Deep concentrations of all metals were significantly lower in the Makarov Basin compared to the Nansen and Amundsen, the Eurasian, Basins. The Gakkel ridge hydrothermal input and higher continental slope convection are explanations for higher metal concentrations in the Eurasian Basins. Although scavenging rates are lower in the Makarov Basin compared to the Eurasian Basins, the residence time is longer and therefore scavenging can decrease the dissolved concentrations with time. This study provides a baseline to assess future change, and additionally identifies processes driving trace metal distributions. Our results underline the importance of fluvial input as well as shelf sources and internal cycling, notably scavenging, for the distribution of bio‐active metals in the Arctic Ocean.
Niño 4 West (Niño‐4W) Sea Surface Temperature Variability
Authors: Feng Ming , Zhang Ying , Hendon Harry H. , McPhaden Michael J. , Marshall Andrew G. 
Published: August 2021

AbstractSea surface temperature (SST) variability in the western half of the Niño 4 region (Niño‐4W), bounded by 160°E−175°W and 5°S–5°N, has a significant impact on weather and the marine environment of the Indo‐Pacific. It exhibits significant negative skewness, with the strong penetration of the cold tongue into the western Pacific during strong La Niñas but a more muted response during El Niños. Zonal advection plays a dominant role in driving Niño‐4W SST cooling during the strong La Niña events; vertical processes also contribute, with air‐sea heat fluxes providing weak negative feedback. Advection also plays a key role in driving the Niño‐4W SST warming, which is not always in sync with El Niño events. Among the advection terms, the advection of mean temperature by zonal velocity anomalies, or zonal advective feedback, plays a key role during the development phase of the warm and cold events. Strong negative air‐sea heat flux anomalies during the development of warm events are linked to the negative SST skewness in the Niño‐4W region.
Nutrient and Carbon Export From a Tidewater Glacier to the Coastal Ocean in the Canadian Arctic Archipelago
Authors: Williams Patrick L. , Burgess David O. , Waterman Stephanie , Roberts Megan , Bertrand Erin M. , Bhatia Maya P. 
Published: August 2021

AbstractA range of glacially driven processes modify and export freshwater and sediments to the ocean. This glacial runoff may influence biological productivity in coastal ecosystems by supplying essential nutrients and labile carbon. Previous studies of glacial meltwater export to the ocean have primarily been conducted on rivers draining land‐terminating glaciers, or in fjords with large tidewater glaciers. These studies speculate about downstream effects (river studies) or upstream causes (fjord studies) of differing carbon and nutrient availability and biological productivity, but do not measure them. Here, we conduct the first ice‐to‐ocean study at a marine‐terminating glacier in the Canadian Arctic Archipelago (CAA). We characterize the nutrient and carbon content of ice and meltwater collected on the glacier surface, at its margins, and in the near‐shore coastal ocean, all within 1 to 25 km of the glacier terminus. Results demonstrate that while meltwater from a shallow tidewater glacier did not directly increase downstream carbon and nutrient concentrations, it induced upwelling of deeper nutrient‐rich marine water. Although carbon concentrations in meltwater were low, results show that this carbon is potentially more bioavailable than marine carbon. Glacially mediated delivery of labile carbon and upwelling of nutrient‐rich water occurs in summer, when surface waters are nutrient‐limited. Collectively, these processes could benefit surface marine plankton, potentially stimulating production at the base of the food web. Shallow tidewater glaciers are commonly retreating in Arctic regions like the CAA and Svalbard, and understanding how increased meltwater output from these systems impacts marine ecosystems is critical.
Mutational spectrum of SARS-CoV-2 during the global pandemic
Authors: Yi Kijong , Kim Su Yeon , Bleazard Thomas , Kim Taewoo , Youk Jeonghwan , Ju Young Seok 
Published: August 2021

AbstractViruses accumulate mutations under the influence of natural selection and host–virus interactions. Through a systematic comparison of 351,525 full viral genome sequences collected during the recent COVID-19 pandemic, we reveal the spectrum of SARS-CoV-2 mutations. Unlike those of other viruses, the mutational spectrum of SARS-CoV-2 exhibits extreme asymmetry, with a much higher rate of C>U than U>C substitutions, as well as a higher rate of G>U than U>G substitutions. This suggests directional genome sequence evolution during transmission. The substantial asymmetry and directionality of the mutational spectrum enable pseudotemporal tracing of SARS-CoV-2 without prior information about the root sequence, collection time, and sampling region. This shows that the viral genome sequences collected in Asia are similar to the original genome sequence. Adjusted estimation of the dN/dSratio accounting for the asymmetrical mutational spectrum also shows evidence of negative selection on viral genes, consistent with previous reports. Our findings provide deep insights into the mutational processes in SARS-CoV-2 viral infection and advance the understanding of the history and future evolution of the virus.
Pituitary P62 deficiency leads to female infertility by impairing luteinizing hormone production
Authors: Li Xing , Zhou Ling , Peng Guiliang , Liao Mingyu , Zhang Linlin , Hu Hua , Long Ling , Tang Xuefeng , Qu Hua , Shao Jiaqing , Zheng Hongting , Long Min 
Published: August 2021

AbstractP62 is a protein adaptor for various metabolic processes. Mice that lack p62 develop adult-onset obesity. However, investigations on p62 in reproductive dysfunction are rare. In the present study, we explored the effect of p62 on the reproductive system. P62 deficiency-induced reproductive dysfunction occurred at a young age (8 week old). Young systemic p62 knockout (p62-/-) and pituitary-specific p62 knockout (p62flox/flox αGSUcre) mice both presented a normal metabolic state, whereas they displayed infertility phenotypes (attenuated breeding success rates, impaired folliculogenesis and ovulation, etc.) with decreased luteinizing hormone (LH) expression and production. Consistently, in an infertility model of polycystic ovary syndrome (PCOS), pituitary p62 mRNA was positively correlated with LH levels. Mechanistically, p62-/- pituitary RNA sequencing showed a significant downregulation of the mitochondrial oxidative phosphorylation (OXPHOS) pathway. In vitro experiments using the pituitary gonadotroph cell line LβT2 and siRNA/shRNA/plasmid confirmed that p62 modulated LH synthesis and secretion via mitochondrial OXPHOS function, especially Ndufa2, a component molecule of mitochondrial complex I, as verified by Seahorse and rescue tests. After screening OXPHOS markers, Ndufa2 was found to positively regulate LH production in LβT2 cells. Furthermore, the gonadotropin-releasing hormone (GnRH)-stimulating test in p62flox/flox αGSUcre mice and LβT2 cells illustrated that p62 is a modulator of the GnRH-LH axis, which is dependent on intracellular calcium and ATP. These findings demonstrated that p62 deficiency in the pituitary impaired LH production via mitochondrial OXPHOS signaling and led to female infertility, thus providing the GnRH-p62-OXPHOS(Ndufa2)-Ca2+/ATP-LH pathway in gonadotropic cells as a new theoretical basis for investigating female reproductive dysfunction.
Molecular genetics of cocaine use disorders in humans
Authors: Fernàndez-Castillo Noèlia , Cabana-Domínguez Judit , Corominas Roser , Cormand Bru 
Published: August 2021

AbstractDrug addiction, one of the major health problems worldwide, is characterized by the loss of control in drug intake, craving, and withdrawal. At the individual level, drugs of abuse produce serious consequences on health and have a negative impact on the family environment and on interpersonal and work relationships. At a wider scale, they have significant socio-economic and public health consequences and they cause delinquency and citizen insecurity. Cocaine, a psychostimulant substance, is one of the most used illicit drugs, especially in America, Western Europe, and Australia. Cocaine use disorders (CUD) are complex multifactorial conditions driven by both genetic and environmental influences. Importantly, not all people who use cocaine develop CUD, and this is due, at least in part, to biological factors that are encoded in the genome of individuals. Acute and repeated use of cocaine induces epigenetic and gene expression changes responsible for the neuronal adaptations and the remodeling of brain circuits that lead to the transition from use to abuse or dependence. The purpose of this review is to delineate such factors, which should eventually help to understand the inter-individual variability in the susceptibility to cocaine addiction. Heritability estimates for CUD are high and genetic risk factors for cocaine addiction have been investigated by candidate gene association studies (CGAS) and genome-wide association studies (GWAS), reviewed here. Also, the high comorbidity that exists between CUD and several other psychiatric disorders is well known and includes phenotypes like schizophrenia, aggression, antisocial or risk-taking behaviors. Such comorbidities are associated with a worse lifetime trajectory, and here we report shared genetic factors that may contribute to them. Gene expression changes and epigenetic modifications induced by cocaine use and chronic abuse in humans are addressed by reviewing transcriptomic studies performed on neuronal cells and onpostmortembrains. We report some genes which expression is altered by cocaine that also bear genetic risk variants for the disorder. Finally, we have a glance to the pharmacogenetics of CUD treatments, still in early stages. A better understanding of the genetic underpinnings of CUD will foster the search of effective treatments and help to move forward to personalized medicine.
Topoisomerase II is regulated by translationally controlled tumor protein for cell survival during organ growth in Drosophila
Authors: Yang Dae-Wook , Mok Jung-Wan , Telerman Stephanie B. , Amson Robert , Telerman Adam , Choi Kwang-Wook 
Published: August 2021

AbstractRegulation of cell survival is critical for organ development. Translationally controlled tumor protein (TCTP) is a conserved protein family implicated in the control of cell survival during normal development and tumorigenesis. Previously, we have identified a human Topoisomerase II (TOP2) as a TCTP partner, but its role in vivo has been unknown. To determine the significance of this interaction, we examined their roles in developing Drosophila organs. Top2 RNAi in the wing disc leads to tissue reduction and caspase activation, indicating the essential role of Top2 for cell survival. Top2 RNAi in the eye disc also causes loss of eye and head tissues. Tctp RNAi enhances the phenotypes of Top2 RNAi. The depletion of Tctp reduces Top2 levels in the wing disc and vice versa. Wing size is reduced by Top2 overexpression, implying that proper regulation of Top2 level is important for normal organ development. The wing phenotype of Tctp RNAi is partially suppressed by Top2 overexpression. This study suggests that mutual regulation of Tctp and Top2 protein levels is critical for cell survival during organ development.
Extracellular vesicles package dsDNA to aggravate Crohn’s disease by activating the STING pathway
Authors: Zhao Fan , Zheng Tao , Gong Wenbin , Wu Jie , Xie Haohao , Li Weijie , Zhang Rui , Liu Peizhao , Liu Juanhan , Wu Xiuwen , Zhao Yun , Ren Jianan 
Published: August 2021

AbstractCrohn’s disease (CD) is an intestinal immune-dysfunctional disease. Extracellular vesicles (EVs) are membrane-enclosed particles full of functional molecules, e.g., nuclear acids. Recently, EVs have been shown to participate in the development of CD by realizing intercellular communication among intestinal cells. However, the role of EVs carrying double-strand DNA (dsDNA) shed from sites of intestinal inflammation in CD has not been investigated. Here we isolated EVs from the plasma or colon lavage of murine colitis and CD patients. The level of exosomal dsDNA, including mtDNA and nDNA, significantly increased in murine colitis and active human CD, and was positively correlated with the disease activity. Moreover, the activation of the STING pathway was verified in CD. EVs from the plasma of active human CD triggered STING activation in macrophages in vitro. EVs from LPS-damaged colon epithelial cells were also shown to raise inflammation in macrophages via activating the STING pathway, but the effect disappeared after the removal of exosomal dsDNA. These findings were further confirmed in STING-deficient mice and macrophages. STING deficiency significantly ameliorated colitis. Besides, potential therapeutic effects of GW4869, an inhibitor of EVs release were assessed. The application of GW4869 successfully ameliorated murine colitis by inhibiting STING activation. In conclusion, exosomal dsDNA was found to promote intestinal inflammation via activating the STING pathway in macrophages and act as a potential mechanistic biomarker and therapeutic target of CD.
The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding
Authors: Parker Alexandra V. , Mann Daniel , Tzokov Svetomir B. , Hwang Ling C. , Bergeron Julien R. C. 
Published: August 2021

AbstractThe efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with theparSDNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of theVibrio choleraeParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA’s cooperative binding to DNA and the formation of high ParA density regions on the nucleoid.
Stimulus-dependent representational drift in primary visual cortex
Authors: Marks Tyler D. , Goard Michael J. 
Published: August 2021

AbstractTo produce consistent sensory perception, neurons must maintain stable representations of sensory input. However, neurons in many regions exhibit progressive drift across days. Longitudinal studies have found stable responses to artificial stimuli across sessions in visual areas, but it is unclear whether this stability extends to naturalistic stimuli. We performed chronic 2-photon imaging of mouse V1 populations to directly compare the representational stability of artificial versus naturalistic visual stimuli over weeks. Responses to gratings were highly stable across sessions. However, neural responses to naturalistic movies exhibited progressive representational drift across sessions. Differential drift was present across cortical layers, in inhibitory interneurons, and could not be explained by differential response strength or higher order stimulus statistics. However, representational drift was accompanied by similar differential changes in local population correlation structure. These results suggest representational stability in V1 is stimulus-dependent and may relate to differences in preexisting circuit architecture of co-tuned neurons.
International consensus on the prevention of venous and arterial thrombotic events in patients with inflammatory bowel disease
Authors: Olivera Pablo A. , Zuily Stephane , Kotze Paulo G. , Regnault Veronique , Al Awadhi Sameer , Bossuyt Peter , Gearry Richard B. , Ghosh Subrata , Kobayashi Taku , Lacolley Patrick , Louis Edouard , Magro Fernando , Ng Siew C. , Papa Alfredo , Raine Tim , Teixeira Fabio V. , Rubin David T. , Danese Silvio , Peyrin-Biroulet Laurent 
Published: August 2021

AbstractPatients with inflammatory bowel disease (IBD) are at increased risk of thrombotic events. Therapies for IBD have the potential to modulate this risk. The aims of this Evidence-Based Guideline were to summarize available evidence and to provide practical recommendations regarding epidemiological aspects, prevention and drug-related risks of venous and arterial thrombotic events in patients with IBD. A virtual meeting took place in May 2020 involving 14 international IBD experts and 3 thrombosis experts from 12 countries. Proposed statements were voted upon in an anonymous manner. Agreement was defined as at least 75% of participants voting as ‘fully agree’ or ‘mostly agree’ with each statement. For each statement, the level of evidence was graded according to the Scottish Intercollegiate Guidelines Network (SIGN) grading system. Consensus was reached for 19 statements. Patients with IBD harbour an increased risk of venous and arterial thrombotic events. Thromboprophylaxis is indicated during hospitalization of any cause in patients with IBD. Disease activity is a modifiable risk factor in patients with IBD, and physicians should aim to achieve deep remission to reduce the risk. Exposure to steroids should be limited. Antitumour necrosis factor agents might be associated with a reduced risk of thrombotic events.
Pregnancy outcomes in women affected by fetal alpha-thalassemia: a case control study
Authors: Li Jiangheng , Yan Jingli , Huang Yongquan , Wei Jinlu , Xie Bingyan , Zhu Maoling , Jiang Wu 
Published: August 2021

AbstractTo evaluate the possible associations between fetal α-thalassemia and risk of adverse pregnancy outcomes using a provincial woman-child health service information database in China. This was a case control study (N = 438,747) in which we compared all singleton pregnancies of women with or without the α-thalassemia trait from May 2016 to May 2020, and where women with the trait were further allocated to a normal fetal group, a group of fetuses with the α-thalassemia trait, and a fetal group with hemoglobin H (HbH) disease according to the results of fetal DNA analysis. With thalassemic women whose fetuses were normal as the reference, fetuses in the HbH disease group showed a higher increase in the odds of Apgar scores being < 7 at 1 min (adjusted odds ratio [aOR], 2.79; 1.03–7.59) and 5 min (aOR, 4.56; 1.07–19.40). With non-thalassemic women as the reference, these trends were more obvious (aOR, 4.83; 2.55–9.16; aOR, 6.24; 2.75–14.18, respectively); whereas the normal fetal group was more likely to be diagnosed with postpartum hemorrhage (aOR, 1.66; 1.10–2.50). In addition, fetal HbH disease and gestational age were two independent factors influencing low Apgar scores, and their combination reflected medium accuracy in Apgar predictions.