bluuebunny/crossref_metadata_2025_split huggingface dataset:
Succession and potential role of bacterial communities duringPleurotus ostreatusproduction
Authors: Bánfi Renáta , Pohner Zsuzsanna , Szabó Attila , Herczeg Gábor , Kovács Gábor M , Nagy Adrienn , Márialigeti Károly , Vajna Balázs 
Published: September 2021

ABSTRACTThere is an increasing interest in studying bacterial-fungal interactions (BFIs), also the interactions of Pleurotus ostreatus, a model white-rot fungus and important cultivated mushroom. In Europe, P. ostreatus is produced on a wheat straw-based substrate with a characteristic bacterial community, where P. ostreatus is exposed to the microbiome during substrate colonisation. This study investigated how the bacterial community structure was affected by the introduction of P. ostreatus into the mature substrate. Based on the results obtained, the effect of the presence and absence of this microbiome on P. ostreatus production in an experimental cultivation setup was determined. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and amplicon sequencing revealed a definite succession of the microbiome during substrate colonisation and fruiting body production: a sharp decrease in relative abundance of Thermus spp. and Actinobacteria, and the increasing dominance of Bacillales and Halomonas spp. The introduced experimental cultivation setup proved the protective role of the microbial community against competing fungi without affecting P. ostreatus growth. We could also demonstrate that this effect could be attributed to both living microbes and their secreted metabolites. These findings highlight the importance of bacterial-fungal interactions during mushroom production.
Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps
Authors: Burrows Ryan M , van de Kamp Jodie , Bodrossy Levente , Venarsky Michael , Coates-Marnane Jack , Rees Gavin , Jumppanen Paavo , Kennard Mark J 
Published: September 2021

ABSTRACTMethane availability in freshwaters is usually associated with spatial-temporal variation in methanogenesis. Unusually, however, natural gas macro-seeps occur along the Condamine River in eastern Australia which elevate ambient water-column methane concentrations more than 3,000 times. We quantified the spatial-temporal variation in methane oxidation rates and the total microbial and methanotroph community composition (through the amplification and sequencing of 16S rRNA and particulate methane monooxygenase (pmoA) genes), and the factors mediating this variation, in reaches with and without macro-seeps. Sediment methane oxidation rates were, on average, 29 times greater, and the abundance of methanotrophs significantly higher, in the vicinity of methane macro-seeps compared to non-seep sites. Methylocystis was the most abundant methanotroph group at all sites, but type Ib methanotrophs showed the steepest increase in abundance at seep sites. pmoA gene analysis identified these as clade 501, while 16S rRNA gene analysis identified these as the closely related genus Methylocaldum. Sediment methane oxidation rates and the relative abundance and composition of benthic microbial communities were primarily influenced by methane availability which was in turn related to variation in river discharge. Methane-derived carbon may be an important energy source for the aquatic food webs in reaches affected by natural gas macro-seeps.
Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress
Authors: Anast Justin M , Schmitz-Esser Stephan 
Published: September 2021

Abstract
Listeria monocytogenes is the causative agent of the highly fatal foodborne disease listeriosis and can persist in food production environments. Recent research highlights the involvement of L. monocytogenes plasmids in different stress response mechanisms, which contribute to its survival in food production facilities. Ultraviolet (UV) light in the UVC spectrum (200–280 nm) is used in food production to control microbial contamination. Although plasmid-encoded UV resistance mechanisms have been described in other bacteria, no research indicates that L. monocytogenes plasmids contribute to the UV stress response. The plasmids of L. monocytogenes strains 6179, 4KSM and R479a are genetically distinct and were utilized to study the roles of plasmids in the UV response. Wild-type and plasmid-cured variant cells were grown to logarithmic or late-stationary phase, plated on agar plates and exposed to UVC for 60 or 90 s, and colony-forming units (CFUs) were determined. CFUs of 6179 and 4KSM, bearing pLM6179 and p4KSM, respectively, were significantly (P-value &lt; 0.05) higher than those of the plasmid-cured strains in both logarithmic and stationary phases. No difference in survival was observed for the R479a strain. Our data show for the first time that certain L. monocytogenes plasmids contribute to the survival of UVC light stress.
Adaptation strategies for spruce forests—economic potential of bark beetle management and Douglas fir cultivation in future tree species portfolios
Authors: Fuchs Jasper M , Hittenbeck Anika , Brandl Susanne , Schmidt Matthias , Paul Carola 
Published: September 2021

Abstract
Productive Norway spruce forests in mountainous growing areas are expected to be affected by increasing climate-driven disturbances, which will most likely result in a reduction of their economic performance. This study seeks to compare the potential of currently discussed management options aiming to maintain the economic performance on typical sites of spruce under a changing climate. For this purpose, we used a combined approach of tree mortality simulation and portfolio optimization to assess the management options: (1) including a deciduous species, (2) establishing mixed stands, (3) shortening the rotation periods, (4) forest protection measures focusing on bark beetles and (5) introducing another highly productive species. As a novel feature, we also compared the effect of combined management strategies on the return and risk of stand management. In our simulation and optimization approach, the inclusion of an alternative, highly productive tree species, such as Douglas fir, into the tree species portfolio outcompeted the forest protection measure of intensive bark beetle monitoring with timely sanitation fellings in terms of balancing risks and returns. The adaptation gain of introducing Douglas fir was further enhanced when combined with additional management options such as adapted rotation periods. The resulting synergies were able to overcompensate for the adverse economic effects of climate change. On the contrary, including beech did not only reduce the risks but also the return in a magnitude which was clearly outcompeted by Douglas fir, even with the assumption of high mortality risks for Douglas fir. These results prove the importance of a proactive tree species selection in relation to more reactive forest protection measures for climate change adaptation. They also advise a careful consideration of expected market demands when selecting an additional species for the portfolio.
A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
Authors: Sætre Camilla Lo Cascio , Eroukhmanoff Fabrice , Rönkä Katja , Kluen Edward , Thorogood Rose , Torrance James , Tracey Alan , Chow William , Pelan Sarah , Howe Kerstin , Jakobsen Kjetill S , Tørresen Ole K 
Published: September 2021

AbstractThe reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.
The Spiritual Experience of Dementia From the Health Care Provider Perspective: Implications for Intervention
Authors: Palmer Jennifer A , Hilgeman Michelle , Balboni Tracy , Paasche-Orlow Sara , Sullivan Jennifer L 
Published: September 2021

AbstractBackground and ObjectivesSpiritual care aims to counter negative outcomes from spiritual distress and is beneficial to persons living with dementia. Such care needs dementia-appropriate customization. We explored the salient spiritual needs in dementia to inform future intervention development. Health care providers are well situated to observe the nature of spiritual needs across and within medical conditions.Research Design and MethodsWe conducted semistructured qualitative interviews with providers. We sampled purposively by discipline (chaplains, nursing staff, social workers, activities professionals) and religious tradition (for chaplains). Our interview guide inquired about, for example, the nature of spiritual needs in dementia and stakeholders’ roles in addressing them. Inductive/deductive thematic analysis was employed.Results24 providers participated. The thematic structure consisted of 2 themes: (a) spiritual experience in dementia differs from that in other medical conditions (subthemes: fear, profound loss of self, progressive and incurable nature, and impacted ability to access faith) and (b) the need for spiritual intervention at the mild stage of dementia (subthemes: awareness in mild dementia and its influence on spiritual distress, and a window of opportunity).Discussion and ImplicationsWe learned about the potential “what” of spiritual needs and “who” and “when” of implementing spiritual care. Implications included the imperative for dementia-specific spiritual assessment tools, interventions targeting fear and loss of self early in symptom progression, and stakeholder training. Researchers should study additionally the “how” of dementia-appropriate spiritual care. Conjointly, these efforts could promote spiritual well-being in persons living with dementia worldwide.
Analysis of S waves singularity points in porous rock with two orthogonal sets of mesoscale fractures
Authors: Pang Shuo , Stovas Alexey , Xing Huilin 
Published: September 2021

SUMMARY
The shear waves phase velocity surfaces in orthorhombic (ORT) and lower symmetry anisotropic models touch each other in one or more points resulting in so called singularity points or acoustic axes. These singularity points result in dramatic changes of velocities, amplitudes and polarizations creating problems in seismic data processing and analysis. Considering the frequency-dependent anisotropy due to mesoscale fractures in Chapman's model, we describe the singularity points in porous rock with two orthogonal sets of mesoscale fractures. First, we give the equations for frequency-dependent phase velocities of P, S1 and S2 waves in this anelastic ORT media. Then, we derive the expressions for frequency-dependent singularity points within the symmetry planes and discuss the conditions to detect the existence of singularity point. Finally, the influences of frequency, porosity, fracture density, fracture scale and saturating fluid style on the positions of singularity points within the symmetry plane are investigated.
Scaling laws for stagnant-lid convection with a buoyant crust
Authors: Batra Kyle , Foley Bradford 
Published: September 2021

SUMMARY
Stagnant-lid convection, where subduction and surface plate motion is absent, is common among the rocky planets and moons in our solar system, and likely among rocky exoplanets as well. How stagnant-lid planets thermally evolve is an important issue, dictating not just their interior evolution but also the evolution of their atmospheres via volcanic degassing. On stagnant-lid planets, the crust is not recycled by subduction and can potentially grow thick enough to significantly impact convection beneath the stagnant lid. We perform numerical models of stagnant-lid convection to determine new scaling laws for convective heat flux that specifically account for the presence of a buoyant crustal layer. We systematically vary the crustal layer thickness, crustal layer density, Rayleigh number and Frank–Kamenetskii parameter for viscosity to map out system behaviour and determine the new scaling laws. We find two end-member regimes of behaviour: a ‘thin crust limit’, where convection is largely unaffected by the presence of the crust, and the thickness of the lithosphere is approximately the same as it would be if the crust were absent; and a ‘thick crust limit’, where the crustal thickness itself determines the lithospheric thickness and heat flux. Scaling laws for both limits are developed and fit the numerical model results well. Applying these scaling laws to rocky stagnant-lid planets, we find that the crustal thickness needed for convection to enter the thick crust limit decreases with increasing mantle temperature and decreasing mantle reference viscosity. Moreover, if crustal thickness is limited by the formation of dense eclogite, and foundering of this dense lower crust, then smaller planets are more likely to enter the thick crust limit because their crusts can grow thicker before reaching the pressure where eclogite forms. When convection is in the thick crust limit, mantle heat flux is suppressed. As a result, mantle temperatures can be elevated by 100 s of degrees K for up to a few Gyr in comparison to a planet with a thin crust. Whether convection enters the thick crust limit during a planet’s thermal evolution also depends on the initial mantle temperature, so a thick, buoyant crust additionally acts to preserve the influence of initial conditions on stagnant-lid planets for far longer than previous thermal evolution models, which ignore the effects of a thick crust, have found.
Cultural adaptation in HPV vaccine intervention among racial and ethical minority population: a systematic literature review
Authors: Zhang Xueying , Tang Lu 
Published: September 2021

Abstract
Racial and ethnic minorities in the United States face higher risks of human papillomavirus (HPV) and are less likely to benefit from HPV vaccines. Effective HPV vaccine promotion efforts need to acknowledge and adapt to the cultural characteristics of these minority groups. This systematic review examines and evaluates the cultural adaptations in the HPV vaccine intervention studies conducted in racial and ethnic minority communities in the United States. We searched five databases and identified 26 peer-reviewed English-language journal articles published between 2010 and 2019. These articles were analyzed using Healey et al.’s (2017) cultural adaptation framework for community health interventions. Almost all of these interventions involved some cultural adaptation. However, there is a lack of use of theories in guiding intervention design, lack of systematic, planned cultural adaptations and insufficient in-depth understanding of the targeted population’s cultural characteristics associated with their HPV-related attitudes, beliefs and behaviors. Future intervention studies should identify specific cultural characteristics related to vaccine attitudes and behaviors to create more targeted cultural adaptations in HPV vaccine promotion.
Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans
Authors: Van Bergen Nicole J , Bell Katrina M , Carey Kirsty , Gear Russell , Massey Sean , Murrell Edward K , Gallacher Lyndon , Pope Kate , Lockhart Paul J , Kornberg Andrew , Pais Lynn , Walkiewicz Marzena , Simons Cas ,   MCRI Rare Diseases Flagship, Wickramasinghe Vihandha O , White Susan M , Christodoulou John 
Published: September 2021

Abstract
The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here, we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings’ neurological disorder.
Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative
Authors: Little Amarise , Hu Yao , Sun Quan , Jain Deepti , Broome Jai , Chen Ming-Huei , Thibord Florian , McHugh Caitlin , Surendran Praveen , Blackwell Thomas W , Brody Jennifer A , Bhan Arunoday , Chami Nathalie , de Vries Paul S , Ekunwe Lynette , Heard-Costa Nancy , Hobbs Brian D , Manichaikul Ani , Moon Jee-Young , Preuss Michael H , Ryan Kathleen , Wang Zhe , Wheeler Marsha , Yanek Lisa R , Abecasis Goncalo R , Almasy Laura , Beaty Terri H , Becker Lewis C , Blangero John , Boerwinkle Eric , Butterworth Adam S , Choquet Hélène , Correa Adolfo , Curran Joanne E , Faraday Nauder , Fornage Myriam , Glahn David C , Hou Lifang , Jorgenson Eric , Kooperberg Charles , Lewis Joshua P , Lloyd-Jones Donald M , Loos Ruth J F , Min Yuan-I , Mitchell Braxton D , Morrison Alanna C , Nickerson Deborah A , North Kari E , O'Connell Jeffrey R , Pankratz Nathan , Psaty Bruce M , Vasan Ramachandran S , Rich Stephen S , Rotter Jerome I , Smith Albert V , Smith Nicholas L , Tang Hua , Tracy Russell P , Conomos Matthew P , Laurie Cecelia A , Mathias Rasika A , Li Yun , Auer Paul L ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Thornton Timothy , Reiner Alexander P , Johnson Andrew D , Raffield Laura M 
Published: September 2021

Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI’s Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
Distinct functional classes of PDGFRB pathogenic variants in primary familial brain calcification
Authors: Lenglez Sandrine , Sablon Ariane , Fénelon Gilles , Boland Anne , Deleuze Jean-François , Boutoleau-Bretonnière Claire , Nicolas Gaël , Demoulin Jean-Baptiste 
Published: September 2021

Abstract
Platelet-derived growth factor receptor beta (PDGFRB) is one of the genes associated with primary familial brain calcification (PFBC), an inherited neurological disease (OMIM:173410). Genetic analysis of patients and families revealed at least 13 PDGFRB heterozygous missense variants, including two novel ones described in the present report. Limited experimental data published on five of these variants had suggested that they decrease the receptor activity. No functional information was available on the impact of variants located within the receptor extracellular domains. Here, we performed a comprehensive molecular analysis of PDGFRB variants linked to PFBC. Mutated receptors were transfected in various cell lines to monitor receptor expression, signaling, mitogenic activity and ligand binding. Four mutants caused a complete loss of tyrosine kinase activity in multiple assays. One of the novel variants, p.Pro154Ser, decreased the receptor expression and abolished binding of platelet-derived growth factor (PDGF-BB). Others showed a partial loss of function related to reduced expression or signaling. Combining clinical, genetic and molecular data, we consider nine variants as pathogenic or likely pathogenic, three as benign or likely benign and one as a variant of unknown significance. We discuss the possible relationship between the variant residual activity, incomplete penetrance, brain calcification and neurological symptoms. In conclusion, we identified distinct molecular mechanisms whereby PDGFRB variants may result in a receptor loss of function. This work will facilitate genetic counseling in PFBC.