bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a Cloud Scheme With Prognostic Cloud Fraction and Two Moment Microphysics for ECHAM‐HAM
Authors: Muench Steffen , Lohmann Ulrike 
Published: August 2020

AbstractWe present a new cloud scheme for the ECHAM‐HAM global climate model (GCM) that includes prognostic cloud fraction and allows for subsaturation and supersaturation with respect to ice separately in the cloud‐free and cloudy air. Stratiform clouds form by convective detrainment, turbulent vertical diffusion, and large‐scale ascent. For each process, the corresponding cloud fraction is calculated, and the individual updraft velocities are used to determine cloud droplet/ice crystal number concentrations. Further, convective condensate is always detrained as supercooled cloud droplets at mixed‐phase temperatures (between 235 and 273 K), and convectively detrained ice crystal number concentrations are calculated based on the updraft velocity. Finally, the new scheme explicitly calculates condensation/evaporation and deposition/sublimation rates for phase‐change calculations. The new cloud scheme simulates a reasonable present‐day climate, reduces the previously overestimated cirrus cloud fraction, and in general improves the simulation of ice clouds. The model simulates the observed in‐cloud supersaturation for cirrus clouds, and it allows for a better representation of the tropical to extra‐tropical ratio of the longwave cloud radiative effect. Further, the ice water path, the ice crystal number concentrations, and the supercooled liquid fractions in mixed‐phase clouds agree better with observations in the new model than in the reference model. Ice crystal formation is dominated by the liquid‐origin processes of convective detrainment and homogeneous freezing of cloud droplets. The simulated ice clouds strongly depend on model tuning choices, in particular, the enhancement of the aggregation rate of ice crystals.
TSPAN5 influences serotonin and kynurenine: pharmacogenomic mechanisms related to alcohol use disorder and acamprosate treatment response
Authors: Ho Ming-Fen , Zhang Cheng , Zhang Lingxin , Wei Lixuan , Zhou Ying , Moon Irene , Geske Jennifer R. , Choi Doo-Sup , Biernacka Joanna , Frye Mark , Wen Zhexing , Karpyak Victor M. , Li Hu , Weinshilboum Richard 
Published: August 2020

AbstractWe previously reported that SNPs near TSPAN5 were associated with plasma serotonin (5-HT) concentrations which were themselves associated with selective serotonin reuptake inhibitor treatment outcomes in patients with major depressive disorder (MDD). TSPAN5 SNPs were also associated with alcohol consumption and alcohol use disorder (AUD) risk. The present study was designed to explore the biological function of TSPAN5 with a focus on 5-HT and kynurenine concentrations in the tryptophan pathway. Ethanol treatment resulted in decreased 5-HT concentrations in human induced pluripotent stem cell (iPSC)-derived neuron culture media, and the downregulation of gene expression of TSPAN5, DDC, MAOA, MAOB, TPH1, and TPH2 in those cells. Strikingly, similar observations were made when the cells were treated with acamprosate—an FDA approved drug for AUD therapy. These results were replicated in iPSC-derived astrocytes. Furthermore, TSPAN5 interacted physically with proteins related to clathrin and other vesicle-related proteins, raising the possibility that TSPAN5 might play a role in vesicular function in addition to regulating expression of genes associated with 5-HT biosynthesis and metabolism. Downregulation of TSPAN5 expression by ethanol or acamprosate treatment was also associated with decreased concentrations of kynurenine, a major metabolite of tryptophan that plays a role in neuroinflammation. Knockdown of TSPAN5 also influenced the expression of genes associated with interferon signaling pathways. Finally, we determined that TSPAN5 SNPs were associated with acamprosate treatment outcomes in AUD patients. In conclusion, TSPAN5 can modulate the concentrations of 5-HT and kynurenine. Our data also highlight a potentially novel pharmacogenomic mechanism related to response to acamprosate.
Neohesperidin enhances PGC-1α-mediated mitochondrial biogenesis and alleviates hepatic steatosis in high fat diet fed mice
Authors: Wang Si-wei , Sheng Hao , Bai Yong-feng , Weng Yuan-yuan , Fan Xue-yu , Lou Li-jun , Zhang Feng 
Published: August 2020

AbstractBackgroundsMitochondria plays a critical role in the development and pathogenesis of nonalcoholic fatty liver disease (NAFLD). Neohesperidin (NHP) could lower blood glucose and prevent obesity in mice. However, the direct effect of NHP on hepatic steatosis has not been reported.MethodsMice were fed with either a chow diet or HFD with or without oral gavage of NHP for 12 weeks. A variety of biochemical and histological indicators were examined. In vitro cell culture model was utilized to demonstrate underlying molecular mechanism of the effect induced by NHP treatment.ResultsNHP increases mitochondrial biogenesis, improves hepatic steatosis and systematic insulin resistance in high fat diet (HFD) fed mice. NHP elevates hepatic mitochondrial biogenesis and fatty acid oxidation by increasing PGC-1α expression. Mechanistically, the activation of AMP-activated protein kinase (AMPK) is involved in NHP induced PGC-1α expression.ConclusionsPGC-1α-mediated mitochondrial biogenesis plays a vital role in the mitigation of hepatic steatosis treated by NHP. Our result suggests that NHP is a good candidate to be dietary supplement for the auxiliary treatment of NAFLD.
Electroconvulsive therapy modulates functional interactions between submodules of the emotion regulation network in major depressive disorder
Authors: Xu Jinping , Wei Qiang , Bai Tongjian , Wang Lijie , Li Xuemei , He Zhengyu , Wu Jianhuang , Hu Qingmao , Yang Xun , Wang Chao , Tian Yanghua , Wang Jiaojian , Wang Kai 
Published: August 2020

AbstractAn increasing number of neuroimaging studies have consistently revealed that disrupted functional interactions within the cognitive emotion regulation network (ERN) contribute to the onset of major depressive disorders (MDD). To disentangle the functional reorganization of ERN after electroconvulsive therapy (ECT) in MDD is curial for understanding its neuropathology. Resting-state functional magnetic resonance imaging data was collected from 23 MDD patients before and after ECT, as well as 25 healthy controls. Network modularity analysis was used to identify the submodules and functional connectivity (FC) was used to investigate the functional reorganization of ERN in the MDD patients after ECT. Four submodules of ERN were identified, including emotion response module (ERM), emotion integration module (EIM), emotion generation module (EGM), and emotion execution module (EEM). The increased intra-modular FC of EEM and inter-modular FCs of EEM with EIM\ERM were found in MDD patients after ECT. Modular transition analysis revealed that left ventrolateral prefrontal cortex, supplementary motor area, posterior cingulate cortex, right angular gyrus, and right precentral gyrus were transferred across different submodules across the three groups. Further analyses showed correlations between changed FC and clinical symptoms in the MDD patients after ECT. Finally, we also identified 11 increased connections between nodes belonging to different submodules of ERN in MDD patients after ECT. These results showed that ECT could induce functional reorganization of intra- and inter-modules within the ERN, and the functional changes were related to therapeutic efficacy or memory impairments of ECT in MDD patients.
Phosphorus-rich stars with unusual abundances are challenging theoretical predictions
Authors: Masseron Thomas , García-Hernández D. A. , Santoveña Raúl , Manchado Arturo , Zamora Olga , Manteiga Minia , Dafonte Carlos 
Published: August 2020

AbstractAlmost all chemical elements have been made by nucleosynthetic reactions in various kind of stars and have been accumulated along our cosmic history. Among those elements, the origin of phosphorus is of extreme interest because it is known to be essential for life such as we know on Earth. However, current models of (Galactic) chemical evolution under-predict the phosphorus we observe in our Solar System. Here we report the discovery of 15 phosphorus-rich stars with unusual overabundances of O, Mg, Si, Al, and Ce. Phosphorus-rich stars likely inherit their peculiar chemistry from another nearby stellar source but their intriguing chemical abundance pattern challenge the present stellar nucleosynthesis theoretical predictions. Specific effects such as rotation or advanced nucleosynthesis in convective-reactive regions in massive stars represent the most promising alternatives to explain the existence of phosphorus-rich stars. The phosphorus-rich stars progenitors may significantly contribute to the phosphorus present on Earth today.
Voluntary control of auditory hallucinations: phenomenology to therapeutic implications
Authors: Swyer Ariel , Powers Albert R. 
Published: August 2020

AbstractAuditory verbal hallucinations (AVH) have traditionally been thought to be outside the influence of conscious control. However, recent work with voice hearers makes clear that both treatment-seeking and non-treatment-seeking voice hearers may exert varying degrees of control over their voices. Evidence suggests that this ability may be a key factor in determining health status, but little systematic examination of control in AVH has been carried out. This review provides an overview of the research examining control over AVH in both treatment-seeking and non-treatment-seeking populations. We first examine the relationship between control over AVH and health status as well as the psychosocial factors that may influence control and functioning. We then link control to various cognitive constructs that appear to be important for voice hearing. Finally, we reconcile the possibility of control with the field’s current understanding of the proposed cognitive, computational, and neural underpinnings of hallucinations and perception more broadly. Established relationships between control, health status, and functioning suggest that the development of control over AVH could increase functioning and reduce distress. A more detailed understanding of the discrete types of control, their development, and their neural underpinnings is essential for translating this knowledge into new therapeutic approaches.
A replication-defective Japanese encephalitis virus (JEV) vaccine candidate with NS1 deletion confers dual protection against JEV and West Nile virus in mice
Authors: Li Na , Zhang Zhe-Rui , Zhang Ya-Nan , Liu Jing , Deng Cheng-Lin , Shi Pei-Yong , Yuan Zhi-Ming , Ye Han-Qing , Zhang Bo 
Published: August 2020

AbstractIn our previous study, we have demonstrated in the context of WNV-ΔNS1 vaccine (a replication-defective West Nile virus (WNV) lacking NS1) that the NS1 trans-complementation system may offer a promising platform for the development of safe and efficient flavivirus vaccines only requiring one dose. Here, we produced high titer (107 IU/ml) replication-defective Japanese encephalitis virus (JEV) with NS1 deletion (JEV-ΔNS1) in the BHK-21 cell line stably expressing NS1 (BHKNS1) using the same strategy. JEV-ΔNS1 appeared safe with a remarkable genetic stability and high degrees of attenuation of in vivo neuroinvasiveness and neurovirulence. Meanwhile, it was demonstrated to be highly immunogenic in mice after a single dose, providing similar degrees of protection to SA14-14-2 vaccine (a most widely used live attenuated JEV vaccine), with healthy condition, undetectable viremia and gradually rising body weight. Importantly, we also found JEV-ΔNS1 induced robust cross-protective immune responses against the challenge of heterologous West Nile virus (WNV), another important member in the same JEV serocomplex, accounting for up to 80% survival rate following a single dose of immunization relative to mock-vaccinated mice. These results not only support the identification of the NS1-deleted flavivirus vaccines with a satisfied balance between safety and efficacy, but also demonstrate the potential of the JEV-ΔNS1 as an alternative vaccine candidate against both JEV and WNV challenge.
Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations
Authors: Martin Jacob T. , Cottrell Christopher A. , Antanasijevic Aleksandar , Carnathan Diane G. , Cossette Benjamin J. , Enemuo Chiamaka A. , Gebru Etse H. , Choe Yury , Viviano Federico , Fischinger Stephanie , Tokatlian Talar , Cirelli Kimberly M. , Ueda George , Copps Jeffrey , Schiffner Torben , Menis Sergey , Alter Galit , Schief William R. , Crotty Shane , King Neil P. , Baker David , Silvestri Guido , Ward Andrew B. , Irvine Darrell J. 
Published: August 2020

AbstractFollowing immunization, high-affinity antibody responses develop within germinal centers (GCs), specialized sites within follicles of the lymph node (LN) where B cells proliferate and undergo somatic hypermutation. Antigen availability within GCs is important, as B cells must acquire and present antigen to follicular helper T cells to drive this process. However, recombinant protein immunogens such as soluble human immunodeficiency virus (HIV) envelope (Env) trimers do not efficiently accumulate in follicles following traditional immunization. Here, we demonstrate two strategies to concentrate HIV Env immunogens in follicles, via the formation of immune complexes (ICs) or by employing self-assembling protein nanoparticles for multivalent display of Env antigens. Using rhesus macaques, we show that within a few days following immunization, free trimers were present in a diffuse pattern in draining LNs, while trimer ICs and Env nanoparticles accumulated in B cell follicles. Whole LN imaging strikingly revealed that ICs and trimer nanoparticles concentrated in as many as 500 follicles in a single LN within two days after immunization. Imaging of LNs collected seven days postimmunization showed that Env nanoparticles persisted on follicular dendritic cells in the light zone of nascent GCs. These findings suggest that the form of antigen administered in vaccination can dramatically impact localization in lymphoid tissues and provides a new rationale for the enhanced immune responses observed following immunization with ICs or nanoparticles.
A data resource from concurrent intracranial stimulation and functional MRI of the human brain
Authors: Thompson W. H. , Nair R. , Oya H. , Esteban O. , Shine J. M. , Petkov C. I. , Poldrack R. A. , Howard M. , Adolphs R. 
Published: August 2020

AbstractMapping the causal effects of one brain region on another is a challenging problem in neuroscience that we approached through invasive direct manipulation of brain function together with concurrent whole-brain measurement of the effects produced. Here we establish a unique resource and present data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. We describe the resource, data collection process, preprocessing using the fMRIPrep analysis pipeline and management of artifacts, and provide end-user analyses to visualize distal brain activation produced by site-specific electrical stimulation. The data are organized according to the brain imaging data structure (BIDS) specification, and are available for analysis or future dataset contributions on openneuro.org including both raw and preprocessed data.
Mapping of 30-meter resolution tile-drained croplands using a geospatial modeling approach
Authors: Valayamkunnath Prasanth , Barlage Michael , Chen Fei , Gochis David J. , Franz Kristie J. 
Published: August 2020

AbstractTile drainage is one of the dominant agricultural management practices in the United States and has greatly expanded since the late 1990s. It has proven effects on land surface water balance and quantity and quality of streamflow at the local scale. The effect of tile drainage on crop production, hydrology, and the environment on a regional scale is elusive due to lack of high-resolution, spatially-explicit tile drainage area information for the Contiguous United States (CONUS). We developed a 30-m resolution tile drainage map of the most-likely tile-drained area of the CONUS (AgTile-US) from county-level tile drainage census using a geospatial model that uses soil drainage information and topographic slope as inputs. Validation of AgTile-US with 16000 ground truth points indicated 86.03% accuracy at the CONUS-scale. Over the heavily tile-drained midwestern regions of the U.S., the accuracy ranges from 82.7% to 93.6%. These data can be used to study and model the hydrologic and water quality responses of tile drainage and to enhance streamflow forecasting in tile drainage dominant regions.
SWATH-MS-based quantitative proteomics reveals a uniquely intricate defense response in Cnaphalocrocis medinalis-resistant rice
Authors: Cheah Boon Huat , Lin Hou-Ho , Chien Han-Ju , Liao Chung-Ta , Liu Li-Yu D , Lai Chien-Chen , Lin Ya-Fen , Chuang Wen-Po 
Published: August 2020

AbstractCnaphalocrocis medinalis is a major insect pest of rice in Asia. A few defensive enzymes were reported to show higher activities in a resistant rice line (Qingliu) than in a susceptible rice line (TN1) upon leaffolder infestation. However, the overall molecular regulation of the rice defense response against leaffolder herbivory is unknown. Here, differential proteomic analysis by SWATH-MS was performed to identify differentially expressed proteins between the two rice varieties, Qingliu and TN1, at four time points of leaffolder herbivory, 0, 6, 24, and 72 h. Gene Ontology (GO) enrichment of the differentially expressed proteins indicated overrepresentation of (1) photosynthesis, (2) amino acid and derivative metabolic process, and (3) secondary metabolic process. Phenylalanine ammonia lyase and chalcone synthase, which catalyze flavonoid biosynthesis, and lipoxygenase, which catalyzes jasmonic acid biosynthesis, exhibited higher expression in Qingliu than in TN1 even before insect herbivory. Momentary activation of the light reaction and Calvin cycle was detected in Qingliu at 6 h and 24 h of insect herbivory, respectively. At 72 h of insect herbivory, amino acid biosynthesis and glutathione-mediated antioxidation were activated in Qingliu. A defense response involving jasmonic acid signaling, carbon remobilization, and the production of flavonoids and glutathione could underlie the resistance of Qingliu to leaffolder.
The third dimension in river restoration: how anthropogenic disturbance changes boundary conditions for ecological mitigation
Authors: Guzelj Martin , Hauer Christoph , Egger Gregory 
Published: August 2020

AbstractThe goals of the European Water Framework Directive changed the perspective on rivers from human to ecosystem-based river management. After decades of channelizing and damming rivers, restoration projects are applied with more or less successful outcomes. The anthropogenic influence put on rivers can change their physical parameters and result in a different morphological type of river. Using the Ammer River as an example, a comparison between applied systems of corridor determination based on historical maps and data; calculation of regime width; and the change in parameters and river typology are pointed out. The results showed (a) a change in stream power and morphology (b) great difference between the historical and the predicted river type and (c) that regulated rivers can have a near-natural morphology.
Heterotypic immunity against vaccinia virus in an HLA-B*07:02 transgenic mousepox infection model
Authors: Kumar Amrendra , Suryadevara Naveen Chandra , Wolf Kyle J. , Wilson John T. , Di Paolo Richard J. , Brien James D. , Joyce Sebastian 
Published: August 2020

AbstractVaccination with vaccinia virus (VACV) elicits heterotypic immunity to smallpox, monkeypox, and mousepox, the mechanistic basis for which is poorly understood. It is generally assumed that heterotypic immunity arises from the presentation of a wide array of VACV-derived, CD8+ T cell epitopes that share homology with other poxviruses. Herein this assumption was tested using a large panel of VACV-derived peptides presented by HLA-B*07:02 (B7.2) molecules in a mousepox/ectromelia virus (ECTV)-infection, B7.2 transgenic mouse model. Most dominant epitopes recognized by ECTV- and VACV-reactive CD8+ T cells overlapped significantly without altering immunodominance hierarchy. Further, several epitopes recognized by ECTV-reactive CD8+ T cells were not recognized by VACV-reactive CD8+ T cells, and vice versa. In one instance, the lack of recognition owed to a N72K variation in the ECTV C4R70–78 variant of the dominant VACV B8R70–78 epitope. C4R70–78 does not bind to B7.2 and, hence, it was neither immunogenic nor antigenic. These findings provide a mechanistic basis for VACV vaccination-induced heterotypic immunity which can protect against Variola and Monkeypox disease. The understanding of how cross-reactive responses develop is essential for the rational design of a subunit-based vaccine that would be safe, and effectively protect against heterologous infection.
Contribution to the ecology of the Italian hare (Lepus corsicanus)
Authors: Buglione Maria , Petrelli Simona , de Filippo Gabriele , Troiano Claudia , Rivieccio Eleonora , Notomista Tommaso , Maselli Valeria , di Martino Luciano , Carafa Marco , Gregorio Romano , Latini Roberta , Fortebraccio Mario , Romeo Giorgia , Biliotti Claudia , Fulgione Domenico 
Published: August 2020

AbstractThe Italian hare (Lepus corsicanus) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due to habitat alterations, low density and fragmented populations and ecological competition with the sympatric European hare (Lepus europaeus). Despite this status, only few and local studies have explored its ecological features. We provided some key traits of the ecological niche of the Italian hare as well as its potential distribution in the Italian peninsula. All data derived from genetically validated presences. We generated a habitat suitability model using maximum entropy distribution model for the Italian hare and its main competitor, the European hare. The dietary habits were obtained for the Italian hare with DNA metabarcoding and High-Throughput Sequencing on faecal pellets. The most relevant environmental variables affecting the potential distribution of the Italian hare are shared with the European hare, suggesting a potential competition. The variation in the observed altitudinal distribution is statistically significant between the two species.The diet of the Italian hare all year around includes 344 plant taxa accounted by 62 families. The Fagaceae, Fabaceae, Poaceae, Rosaceae and Solanaceae (counts > 20,000) represented the 90.22% of the total diet. Fabaceae (60.70%) and Fagaceae (67.47%) were the most abundant plant items occurring in the Spring/Summer and Autumn/Winter diets, respectively. The Spring/Summer diet showed richness (N = 266) and diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than the Autumn/Winter diet (N = 199, Shannon: 1.818, Evenness: 0.03096, Equitability: 0.3435). Our contribution adds important information to broaden the knowledge on the environmental (spatial and trophic) requirements of the Italian hare, representing effective support for fitting management actions in conservation planning.