bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactive transport modelling of an intra-basalt sandstone reservoir, Rosebank, UK
Authors: Sætre C. , Hellevang H. , Dennehy C. , Dypvik H. 
Published: March 2021

AbstractThe Rosebank field, located in the Faroe-Shetland Basin, contains producible hydrocarbons in intra-basaltic siliciclastic reservoirs. The volcanic-reservoir interface is poorly studied and the geochemical system, as a function of distance from the basalt, is largely unknown. The current paper applies a geochemical model coupling mineral dissolution and precipitation with element diffusion to investigate the geochemical system in time and space from the basalt-sandstone interface. Earlier studies indicate few negative effects on reservoir properties despite the proximity to a reactive volcanic lithology. The causes of this minimal impact have not been studied. The numerical simulations in this study expand on the knowledge demonstrating that precipitation of authigenic phases at the basalt-sandstone interface buffer the formation water solution for key elements, which hamper the transport of solutes and subsequent precipitation of secondary minerals within the reservoir. Saturation index values over the simulated period indicate that precipitation of authigenic phases should not extend beyond the basalt-sandstone interface. This shows that diffusion alone is not enough to reduce the reservoir quality due to increased precipitation of secondary phases. The basalt dissolution rate varies according to the silica concentration. The combined effects on silica concentration by diffusional fluxes, mineral precipitation and dissolution, control the basalt dissolution rate, and there are no differences in the results between high and low basalt reactive surface area.
Symptoms and syndromes associated with SARS-CoV-2 infection and severity in pregnant women from two community cohorts
Authors: Molteni Erika , Astley Christina M. , Ma Wenjie , Sudre Carole H. , Magee Laura A. , Murray Benjamin , Fall Tove , Gomez Maria F. , Tsereteli Neli , Franks Paul W. , Brownstein John S. , Davies Richard , Wolf Jonathan , Spector Tim D. , Ourselin Sebastien , Steves Claire J. , Chan Andrew T. , Modat Marc 
Published: March 2021

AbstractWe tested whether pregnant and non-pregnant women differ in COVID-19 symptom profile and severity, and we extended previous investigations on hospitalized pregnant women to those who did not require hospitalization. Two female community-based cohorts (18–44 years) provided longitudinal (smartphone application, N = 1,170,315, n = 79 pregnant tested positive) and cross-sectional (web-based survey, N = 1,344,966, n = 134 pregnant tested positive) data, prospectively collected through self-participatory citizen surveillance in UK, Sweden and USA. Pregnant and non-pregnant were compared for frequencies of events, including SARS-CoV-2 testing, symptoms and hospitalization rates. Multivariable regression was used to investigate symptoms severity and comorbidity effects. Pregnant and non-pregnant women positive for SARS-CoV-2 infection were not different in syndromic severity, except for gastrointestinal symptoms. Pregnant were more likely to have received testing, despite reporting fewer symptoms. Pre-existing lung disease was most closely associated with syndromic severity in pregnant hospitalized. Heart and kidney diseases and diabetes increased risk. The most frequent symptoms among non-hospitalized women were anosmia [63% pregnant, 92% non-pregnant] and headache [72%, 62%]. Cardiopulmonary symptoms, including persistent cough [80%] and chest pain [73%], were more frequent among pregnant who were hospitalized. Consistent with observations in non-pregnant populations, lung disease and diabetes were associated with increased risk of more severe SARS-CoV-2 infection during pregnancy.
Molecular typing and antimicrobial resistance profiling of 33 mastitis-related Staphylococcus aureus isolates from cows in the Comarca Lagunera region of Mexico
Authors: Mora-Hernández Y. , Vera Murguía E. , Stinenbosch J. , Hernández Jauregui P. , van Dijl Jan Maarten , Buist G. 
Published: March 2021

AbstractMastitis in cows is a major cause of economic losses and it is commonly associated with Staphylococcus aureus. Little is known about the S. aureus lineages causing mastitis in Mexican cattle. The aim of this study was to type S. aureus isolates causing mastitis in cows from the Comarca Lagunera region in Mexico in 2015–2016. Multi-locus variable number tandem repeat fingerprinting (MLVF) of 33 S. aureus isolates obtained from 210 milk samples revealed the MLVF clusters A (n = 1), B (n = 26), C (n = 5) and D (n = 1). Spa-typing showed that clusters A and B represent the spa-type t224, cluster C includes spa-types t3196 and t416, and cluster D represents spa-type t114. The different spa-types were mirrored by the masses of protein A bands as detected by Western blotting. Antimicrobial susceptibility testing showed that one isolate was susceptible to all antimicrobials tested, whereas all other strains were resistant only to benzylpenicillin. These findings show that only four S. aureus lineages, susceptible to most antimicrobials, were responsible for causing mastitis at the time of sampling. Lastly, many isolates carried the same small plasmid, designated pSAM1. The high prevalence of pSAM1 amongst the antimicrobial-susceptible isolates suggests an association with bovine colonization or mastitis rather than antimicrobial resistance.
Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches
Authors: Pontes Camila , Andrade Miguel , Fiorote José , Treptow Werner 
Published: March 2021

AbstractThe problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were shown to store the strongest mutual information (MI) signal to discriminate MSA concatenations with the largest fraction of correct pairings. Although that signal might be of practical relevance in the search for an effective heuristic to solve the problem, the number of MSA concatenations with near-native MI is large, imposing severe limitations. Here, a Genetic Algorithm that explores possible MSA concatenations according to a MI maximization criteria is shown to find degenerate solutions with two error sources, arising from mismatches among (i) similar and (ii) non-similar sequences. If mistakes made among similar sequences are disregarded, type-(i) solutions are found to resolve correct pairings at best true positive (TP) rates of 70%—far above the very same estimates in type-(ii) solutions. A machine learning classification algorithm helps to show further that differences between optimized solutions based on TP rates are not artificial and may have biological meaning associated with the three-dimensional distribution of the MI signal. Type-(i) solutions may therefore correspond to reliable results for predictive purposes, found here to be more likely obtained via MI maximization across protein systems having a minimum critical number of amino acid contacts on their interaction surfaces (N > 200).
Social media language of healthcare super-utilizers
Authors: Guntuku Sharath Chandra , Klinger Elissa V. , McCalpin Haley J. , Ungar Lyle H. , Asch David A. , Merchant Raina M. 
Published: March 2021

AbstractAn understanding of healthcare super-utilizers’ online behaviors could better identify experiences to inform interventions. In this retrospective case-control study, we analyzed patients’ social media posts to better understand their day-to-day behaviors and emotions expressed online. Patients included those receiving care in an urban academic emergency department who consented to share access to their historical Facebook posts and electronic health records. Super-utilizers were defined as patients with more than six visits to the Emergency Department (ED) in a year. We compared posts by super-utilizers with a matched group using propensity scoring based on age, gender and Charlson comorbidity index. Super-utilizers were more likely to post about confusion and negativity (D = .65, 95% CI-[.38, .95]), self-reflection (D = .63 [.35, .91]), avoidance (D = .62 [.34, .90]), swearing (D = .52 [.24, .79]), sleep (D = .60 [.32, .88]), seeking help and attention (D = .61 [.33, .89]), psychosomatic symptoms, (D = .49 [.22, .77]), self-agency (D = .56 [.29, .85]), anger (D = .51, [.24, .79]), stress (D = .46, [.19, .73]), and lonely expressions (D = .44, [.17, .71]). Insights from this study can potentially supplement offline community care services with online social support interventions considering the high engagement of super-utilizers on social media.
Neurocognitive modeling of latent memory processes reveals reorganization of hippocampal-cortical circuits underlying learning and efficient strategies
Authors: Supekar Kaustubh , Chang Hyesang , Mistry Percy K. , Iuculano Teresa , Menon Vinod 
Published: March 2021

AbstractEfficient memory-based problem-solving strategies are a cardinal feature of expertise across a wide range of cognitive domains in childhood. However, little is known about the neurocognitive mechanisms that underlie the acquisition of efficient memory-based problem-solving strategies. Here we develop, to the best of our knowledge, a novel neurocognitive process model of latent memory processes to investigate how cognitive training designed to improve children’s problem-solving skills alters brain network organization and leads to increased use and efficiency of memory retrieval-based strategies. We found that training increased both the use and efficiency of memory retrieval. Functional brain network analysis revealed training-induced changes in modular network organization, characterized by increase in network modules and reorganization of hippocampal-cortical circuits. Critically, training-related changes in modular network organization predicted performance gains, with emergent hippocampal, rather than parietal cortex, circuitry driving gains in efficiency of memory retrieval. Our findings elucidate a neurocognitive process model of brain network mechanisms that drive learning and gains in children’s efficient problem-solving strategies.
De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation
Authors: Dwivedy Abhisek , Ashraf Anam , Jha Bhavya , Kumar Deepak , Agarwal Nisheeth , Biswal Bichitra K. 
Published: March 2021

AbstractIntracellular pathogens including Mycobacterium tuberculosis (Mtb) have evolved with strategies to uptake amino acids from host cells to fulfil their metabolic requirements. However, Mtb also possesses de novo biosynthesis pathways for all the amino acids. This raises a pertinent question- how does Mtb meet its histidine requirements within an in vivo infection setting? Here, we present a mechanism in which the host, by up-regulating its histidine catabolizing enzymes through interferon gamma (IFN-γ) mediated signalling, exerts an immune response directed at starving the bacillus of intracellular free histidine. However, the wild-type Mtb evades this host immune response by biosynthesizing histidine de novo, whereas a histidine auxotroph fails to multiply. Notably, in an IFN-γ−/− mouse model, the auxotroph exhibits a similar extent of virulence as that of the wild-type. The results augment the current understanding of host-Mtb interactions and highlight the essentiality of Mtb histidine biosynthesis for its pathogenesis.
Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections
Authors: Pauli Martin , Paul Mila M. , Proppert Sven , Mrestani Achmed , Sharifi Marzieh , Repp Felix , Kürzinger Lydia , Kollmannsberger Philip , Sauer Markus , Heckmann Manfred , Sirén Anna-Leena 
Published: March 2021

AbstractRevealing the molecular organization of anatomically precisely defined brain regions is necessary for refined understanding of synaptic plasticity. Although three-dimensional (3D) single-molecule localization microscopy can provide the required resolution, imaging more than a few micrometers deep into tissue remains challenging. To quantify presynaptic active zones (AZ) of entire, large, conditional detonator hippocampal mossy fiber (MF) boutons with diameters as large as 10 µm, we developed a method for targeted volumetric direct stochastic optical reconstruction microscopy (dSTORM). An optimized protocol for fast repeated axial scanning and efficient sequential labeling of the AZ scaffold Bassoon and membrane bound GFP with Alexa Fluor 647 enabled 3D-dSTORM imaging of 25 µm thick mouse brain sections and assignment of AZs to specific neuronal substructures. Quantitative data analysis revealed large differences in Bassoon cluster size and density for distinct hippocampal regions with largest clusters in MF boutons.
Vitamin D upregulates the macrophage complement receptor immunoglobulin in innate immunity to microbial pathogens
Authors: Small Annabelle G. , Harvey Sarah , Kaur Jaspreet , Putty Trishni , Quach Alex , Munawara Usma , Perveen Khalida , McPhee Andrew , Hii Charles S. , Ferrante Antonio 
Published: March 2021

AbstractVitamin D deficiency remains a global concern. This ‘sunshine’ vitamin is converted through a multistep process to active 1,25-dihydroxyvitamin D3 (1,25D), the final step of which can occur in macrophages. Here we demonstrate a role for vitamin D in innate immunity. The expression of the complement receptor immunoglobulin (CRIg), which plays an important role in innate immunity, is upregulated by 1,25D in human macrophages. Monocytes cultured in 1,25D differentiated into macrophages displaying increased CRIg mRNA, protein and cell surface expression but not in classical complement receptors, CR3 and CR4. This was associated with increases in phagocytosis of complement opsonised Staphylococcus aureus and Candida albicans. Treating macrophages with 1,25D for 24 h also increases CRIg expression. While treating macrophages with 25-hydroxyvitamin D3 does not increase CRIg expression, added together with the toll like receptor 2 agonist, triacylated lipopeptide, Pam3CSK4, which promotes the conversion of 25-hydroxyvitamin D3 to 1,25D, leads to an increase in CRIg expression and increases in CYP27B1 mRNA. These findings suggest that macrophages harbour a vitamin D-primed innate defence mechanism, involving CRIg.
Kindlin-2 mediates mechanotransduction in bone by regulating expression of Sclerostin in osteocytes
Authors: Qin Lei , Fu Xuekun , Ma Jing , Lin Manxia , Zhang Peijun , Wang Yishu , Yan Qinnan , Tao Chu , Liu Wen , Tang Bin , Chen Di , Bai Xiaochun , Cao Huiling , Xiao Guozhi 
Published: March 2021

AbstractOsteocytes act as mechanosensors in bone; however, the underlying mechanism remains poorly understood. Here we report that deleting Kindlin-2 in osteocytes causes severe osteopenia and mechanical property defects in weight-bearing long bones, but not in non-weight-bearing calvariae. Kindlin-2 loss in osteocytes impairs skeletal responses to mechanical stimulation in long bones. Control and cKO mice display similar bone loss induced by unloading. However, unlike control mice, cKO mice fail to restore lost bone after reloading. Osteocyte Kindlin-2 deletion impairs focal adhesion (FA) formation, cytoskeleton organization and cell orientation in vitro and in bone. Fluid shear stress dose-dependently increases Kindlin-2 expression and decreases that of Sclerostin by downregulating Smad2/3 in osteocytes; this latter response is abolished by Kindlin-2 ablation. Kindlin-2-deficient osteocytes express abundant Sclerostin, contributing to bone loss in cKO mice. Collectively, we demonstrate an indispensable novel role of Kindlin-2 in maintaining skeletal responses to mechanical stimulation by inhibiting Sclerostin expression during osteocyte mechanotransduction.
Spin-texture-driven electrical transport in multi-Q antiferromagnets
Authors: Seo Soonbeom , Hayami Satoru , Su Ying , Thomas Sean M. , Ronning Filip , Bauer Eric D. , Thompson Joe D. , Lin Shi-Zeng , Rosa Priscila F. S. 
Published: March 2021

AbstractUnusual magnetic textures can be stabilized inf-electron materials due to the interplay between competing magnetic interactions, complex Fermi surfaces, and crystalline anisotropy. Here we investigate CeAuSb2, anf-electron incommensurate antiferromagnet hosting both single-Qand double-Qspin textures as a function of magnetic fields (H) applied along thecaxis. Experimentally, we map out the field-temperature phase diagram via electrical resistivity and thermal expansion measurements. Supported by calculations of a Kondo lattice model, we attribute the puzzling magnetoresistance enhancement in the double-Qphase to the localization of the electronic wave functions caused by the incommensurate magnetic texture.
What are the traits of a social-ecological system: towards a framework in support of urban sustainability
Authors: Andersson Erik , Haase Dagmar , Anderson Pippin , Cortinovis Chiara , Goodness Julie , Kendal Dave , Lausch Angela , McPhearson Timon , Sikorska Daria , Wellmann Thilo 
Published: March 2021

AbstractTo ensure that cities and urban ecosystems support human wellbeing and overall quality of life we need conceptual frameworks that can connect different scientific disciplines as well as research and practice. In this perspective, we explore the potential of a traits framework for understanding social-ecological patterns, dynamics, interactions, and tipping points in complex urban systems. To do so, we discuss what kind of framing, and what research, that would allow traits to (1) link the sensitivity of a given environmental entity to different globally relevant pressures, such as land conversion or climate change to its social-ecological consequences; (2) connect to human appraisal and diverse bio-cultural sense-making through the different cues and characteristics people use to detect change or articulate value narratives, and (3) examine how and under what conditions this new approach may trigger, inform, and support decision making in land/resources management at different scales.
Fractional crystallization causes the iron isotope contrast between mid-ocean ridge basalts and abyssal peridotites
Authors: Chen Yanhong , Niu Yaoling , Duan Meng , Gong Hongmei , Guo Pengyuan 
Published: March 2021

AbstractThe iron isotope contrast between mid-ocean ridge basalts and abyssal peridotites is far greater than can be explained by mantle melting alone. Here we investigate a suite of mid-ocean ridge magma chamber rocks sampled by the Ocean Drilling Project Hole 735B in the Atlantis Bank of the Indian Ocean. We report major and trace element geochemistry from these rocks and measure their iron isotope compositions to investigate the potential role of fractional crystallization during melt evolution. We observe a large range of δ56Fe that defines a significant inverse curvilinear correlation with bulk rock MgO/FeOT. These data confirm that δ56Fe in the melt increases as fractional crystallization proceeds but, contrary to expectation, δ56Fe continues to increase even when oxides begin to crystallize. We conclude that iron isotope fractionation through fractional crystallization during the evolution of mid-ocean ridge basalts from abyssal peridotites reconciles the disparity in isotopic compositions between these two lithologies.
Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor
Authors: Li Jiyun , Hua Zheng-Shuang , Liu Tao , Wang Chengwen , Li Jie , Bai Ge , Lücker Sebastian , Jetten Mike S M , Zheng Min , Guo Jianhua 
Published: March 2021

Abstract
The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.
Fine-scale sampling unveils diazotroph patchiness in the South Pacific Ocean
Authors: Benavides Mar , Conradt Louis , Bonnet Sophie , Berman-Frank Ilana , Barrillon Stéphanie , Petrenko Anne , Doglioli Andrea 
Published: March 2021

Abstract
Diazotrophs are important contributors to nitrogen availability in the ocean. Oceanographic cruise data accumulated over the past three decades has revealed a heterogeneous distribution of diazotroph species at regional to global scales. However, dynamic fine-scale physical structures likely affect the distribution of diazotrophs at smaller spatiotemporal scales. The interaction between fine-scale ocean dynamics and diazotrophs remains poorly understood due to typically insufficient spatiotemporal sampling resolution and the lack of parallel detailed physical studies. Here we show the distribution of five groups of diazotrophs in the South Pacific at an unprecedented resolution of 7–16 km. We find a patchy distribution of diazotrophs, with each group being differentially affected by parameters describing fine-scale physical structures. The observed variability in species abundance and distribution would be masked by a coarser sampling resolution, highlighting the need to consider fine-scale physics to resolve the distribution of diazotrophs in the ocean.
Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil
Authors: Wilhelm Roland C , DeRito Christopher M , Shapleigh James P , Madsen Eugene L , Buckley Daniel H 
Published: March 2021

Abstract
Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3–13 µmols C g−1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g−1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.