bluuebunny/crossref_metadata_2025_split huggingface dataset:
An evolutionary perspective on genetic load in small, isolated populations as informed by whole genome resequencing and forward-time simulations
Authors: Mathur Samarth , Tomeček John M , Tarango-Arámbula Luis A , Perez Robert M , DeWoody J Andrew 
Published: March 2023

AbstractSmall populations are vulnerable to increased genetic load and drift that can lead to reductions in fitness and adaptive potential. By analyzing 66 individual whole genomes of Montezuma Quail (Cyrtonyx montezumae) from multiple populations, we illustrate how genetic load is dynamic over evolutionary time. We show that Montezuma Quail are evolving like a ring species, where the terminal extant populations from Arizona and Texas have been separated for ~16,500 years. The Texas populations have remained small but stable since the separation, whereas the Arizona population is much larger today but has been contracting for thousands of years. Most deleterious mutations across the genome are young and segregating privately in each population and a greater number of deleterious alleles are present in the larger population. Our data indicate that ancestral load is purged during strong bottlenecks, but the reduced efficiency of selection in small populations means that segregating deleterious mutations are more likely to rise in frequency over time. Forward-time simulations indicate that severe population declines in historically large populations is more detrimental to individual fitness, whereas long-term small populations are more at risk for reduced adaptive potential and population-level fitness. Our study highlights the intimate connections among evolutionary history, historical demography, genetic load, and evolutionary potential in wild populations.
A novel method for jointly modeling the evolution of discrete and continuous traits
Authors: Boyko James D , O’Meara Brian C , Beaulieu Jeremy M 
Published: March 2023

AbstractThe correlated evolution of multiple characters is a crucial aspect of evolutionary change. If change in a particular character influences the evolution of a separate trait, then modeling these features independently can mislead our understanding of the evolutionary process. Progress toward jointly modeling several characters has involved modeling multivariate evolution of the same class of character, but there are far fewer options when jointly modeling traits when one character is discrete and the other is continuous. Here, we develop such a framework to explicitly estimate the joint likelihood for discrete and continuous characters. Specifically, our model combines the probability of observing the continuous character under a generalized OU process with the probability of the discrete character under a hidden Markov model, linked by a shared underlying regime. We use simulation studies to demonstrate that this approach, hOUwie, can accurately evaluate parameter values across a broad set of models. We then apply our model to test whether fleshy and dry fruits of Ericaceae lineages are correlated with their climatic niche evolution as represented by the aridity index. Consistent with expectations, we find that the climatic niche of lineages with fleshy fruits is more conserved while lineages with dry fruits have higher rates of climatic niche evolution and a more humid climatic optimum.
The “comfort timing” strategy: a potential pathway for the cultivation of uncultured microorganisms and a possible adaptation for environmental colonisation
Authors: Laugier Jamie 
Published: March 2023

AbstractEfforts to isolate uncultured microorganisms over the last century and a half, as well as the advanced ‘omics’ technologies developed over the last three decades, have greatly increased the knowledge and resources of microbiology. However, many cellular functions such as growth remain unknown in most of the microbial diversity identified through genomic sequences from environmental samples, as evidenced by the increasingly precise observations of the phenomenon known as the ‘great plate count anomaly’. Faced with the many microbial cells recalcitrant to cultivation present in environmental samples, Epstein proposed the ‘scout’ model, characterised by a dominance of dormant cells whose awakening would be strictly stochastic. Unfortunately, this hypothesis leaves few exploitable possibilities for microbial cultivation. This review proposes that many microorganisms follow the ‘comfort timing’ strategy, characterised by an exit from dormancy responding to a set of environmental conditions close to optimal for growth. This ‘comfort timing’ strategy offers the possibility of designing culture processes that could isolate a larger proportion of uncultured microorganisms. Two methods are briefly proposed in this article. In addition, the advantages of dormancy, of the ‘scout’ model and of the ‘comfort timing’ strategy for survival under difficult conditions, but also for colonisation of environments, are discussed.
Adults Older Than Age 55 Engage in Less Diverse Activities Than Those 18 Years Ago
Authors: Lee Soomi , Koffer Rachel , Drewelies Johanna 
Published: March 2023

AbstractObjectivesLife-span perspectives have long acknowledged that individual functioning is shaped by historical and sociocultural contexts. Secular increases favoring recent cohorts are widely documented. However, little is known about secular trends in day-to-day activities and whether historical changes have occurred in younger and older adults alike.MethodsWe compared data from 2 independent cohort samples of the daily diary portion of the Midlife in the United States Study obtained 18 years apart (1995/1996 cohort: n = 1,499 vs 2013/2014 cohort: n = 782) and identified case-matched cohorts (n = 757 per cohort) based on age, gender, education, and race. An activity diversity score was calculated based on 7 common daily activities, using Shannon’s entropy method. We additionally examined the roles of age and other sociodemographic and health characteristics in cohort differences in activity diversity.ResultsResults revealed that the 2013/2014 cohort experienced lower daily activity diversity than the 1995/1996 cohort. Age was positively associated with activity diversity in the 1995/1996 cohort, whereas age was negatively associated with activity diversity in the 2013/2014 cohort. These associations were significant for those who were older than age 55. Cohorts also differed in the types of most dominant activities and average time spent on those activities.DiscussionFindings show changes in the lifestyles and daily activities of U.S. adults across 2 decades. Contrasting to the common belief that today’s adults may be healthier and more active, they seem engaging in less diverse daily activities, which can be a risk for future health outcomes.
Minimum-phase property and reconstruction of elastodynamic dereverberation matrix operators
Authors: Reinicke Christian , Dukalski Marcin , Wapenaar Kees 
Published: March 2023

SUMMARY
Minimum-phase properties are well-understood for scalar functions where they can be used as physical constraint for phase reconstruction. Existing scalar applications of the latter in geophysics include, for example the reconstruction of transmission from acoustic reflection data, or multiple elimination via the augmented acoustic Marchenko method. We review scalar minimum-phase reconstruction via the conventional Kolmogorov relation, as well as a less-known factorization method. Motivated to solve practice-relevant problems beyond the scalar case, we investigate (1) the properties and (2) the reconstruction of minimum-phase matrix functions. We consider a simple but non-trivial case of 2 × 2 matrix response functions associated with elastodynamic wavefields. Compared to the scalar acoustic case, matrix functions possess additional freedoms. Nonetheless, the minimum-phase property is still defined via a scalar function, that is a matrix possesses a minimum-phase property if its determinant does. We review and modify a matrix factorization method such that it can accurately reconstruct a 2 × 2 minimum-phase matrix function related to the elastodynamic Marchenko method. However, the reconstruction is limited to cases with sufficiently small differences between P- and S-wave traveltimes, which we illustrate with a synthetic example. Moreover, we show that the minimum-phase reconstruction method by factorization shares similarities with the Marchenko method in terms of the algorithm and its limitations. Our results reveal so-far unexplored matrix properties of geophysical responses that open the door towards novel data processing tools. Last but not least, it appears that minimum-phase matrix functions possess additional, still-hidden properties that remain to be exploited, for example for phase reconstruction.
Human norovirus contamination challenge in fresh produce: a global prevalence and meta-analytic assessment
Authors: Ekundayo Temitope C , Ijabadeniyi Oluwatosin A 
Published: March 2023

AbstractAimsAmong fresh produce (FP)-associated foodborne infections, human noroviruses (HNoV) are the leading causative agent. The present study aimed to assess the prevalence of HNoV in FP.Methods and ResultsFP-associated HNoV records mined from 5 repositories until 25/05/2022 according to PRISMA standards were appraised, fitted to a generalized linear mixed-effects model and subgroup analysed by sample type, genogroup, and geographical location. Further, heterogeneity was assessed in the model coupled with a leave-one-out-cross-validation. The overall prevalence of HNoV in FP was 9.3% (95% confidence interval [CI] 3.7–21.7. HNoV prevalence was higher in fruits (9.8%[3.7–23.5]) than vegetables (9.4%[3.1–25.3]). Regarding geographical distribution, FP-associated HNoV prevalence varied from Africa (25.8%, 5.7–66.7), Asia (23.2%[4.6–65.0]), Europe (5.6%[0.7–33.9]), North America (12.4%[1.8–52.7]) to South America (7.5%[0.0–100.0]). HNoV GI overall prevalence in FP was 5.3% (2.5–11.1) and varied by sample type (fruits: 4.9%[1.7–13.2]; vegetables: 5.8%[1.6–18.8]). While the occurrence of GII in FP was 1.7% (0.7–3.9) and varied by sample type (fruits: 2.5%[1.0–6.5]; vegetables: 0.9%[0.2–4.9]), GIGII (detection of both GI and GII) was 0.3% (0.1–1.0) with 0.4% (0.1–2.2) and 0.2% (0.0–1.5) in fruits and vegetables, respectively. In all cases, the test for sample/regional prevalence differences were not significantly different with the exception of GII regional prevalence differences (p = 0.03).ConclusionsThis study suggests that FP represents a critical vehicle for HNoV dissemination, a global and a high risk for public health.
Investigation of some endophytic fungi from five medicinal plants with growth promoting ability on maize (Zea maysL.)
Authors: Hatamzadeh Sareh , Rahnama Kamran , White James Francis , Oghaz Nima Akbari , Nasrollahnejad Saeed , Hemmati Khodayar 
Published: March 2023

ABSTRACTAimsThis study aimed to identify endophytic fungi from Anthemis altissima, Matricaria parthenium, Cichorium intybus, Achillea millefolium, and A. filipendulina with plant-promoting ability on the ZP684 maize hybrid-cultivar.Methods and resultsPlants were collected from northeast-Iran and endophytic fungi were isolated and identified using partial large subunit nrDNA, internal transcribed spacer, translation elongation factor, and β-tubulin genetic markers. Endophytic fungi that improved seed germination were studied under greenhouse conditions. Ninety-seven endophytic fungi were identified. Preussia africana, Bjerkandera adusta, Schizophyllum commune, Alternaria embellisia, Trichaptum biforme, Septoria malagutii, A. consortiale, Verticillium dahliae, Fusarium avenacearum, and Trametes versicolor significantly improved seed-germination. Alternaria consortiale produced the highest level of indole-3-acetic acid-like compounds and maize growth-promoting.ConclusionsPlant fungal colonization frequency increased with orthometric height. Sampling location Chahar Bagh at 2230 m contained the most endophytic fungi. Fusarium and Alternaria were the most frequently isolated endophytic genera. Therefore, medicinal plants are potential hosts for endophytic fungi that may be suitable biofertilizer agents in agriculture.Significance and impact of the studyThis study helps to better understand the ecosystem functions by investigating of endophytic fungi distribution under different ecological conditions. Finding effective isolates among these microorganisms with a suitable plant-promoting ability on crops may help to reduce the use of chemical fertilizers in an agroecosystem.
Culture ofMycobacterium aviumsubsp.paratuberculosis: challenges, limitations and future prospects
Authors: Dane Hannah , Stewart Linda D , Grant Irene R 
Published: March 2023

ABSTRACTMycobacterium avium subsp. paratuberculosis (MAP) causes paratuberculosis (Johne's disease) in ruminants and is suspected to be involved in the development of Crohn's disease and several autoimmune disorders. As such, sensitive and specific MAP detection methods are required to confirm infection in animals and identify potential sources of animal and human exposure. Despite recent developments in immunological and nucleic acid-based detection methods, culture-based detection of MAP remains the ‘gold standard’ against which the sensitivity and specificity of other detection methods are measured. However, not all culture-based approaches are equivalent in terms of detection capability, which can lead to errors in the evaluation of other detection methods. This review will provide an overview of the chronological development of culture methods for MAP, and will consider the unique growth requirements of MAP, the merits of solid versus liquid culture media, the relative performance of the commonly used MAP culture media, and sample preparation/decontamination protocols for different sample types. The limitations of current MAP culture methods and prospects for improvements are discussed.
Bacterial interactions with the mycelium of the cultivated edible mushroomsAgaricus bisporusandPleurotus ostreatus
Authors: Shamugam Shivaghami , Kertesz Michael A 
Published: March 2023

AbstractThe cultivated edible mushrooms Agaricus bisporus and Pleurotus ostreatus are valuable food crops and an important source of human nutrition. Agaricus bisporus is the dominant cultivated species in the western hemisphere and in Australia, while in Asian countries P. ostreatus is more prevalent. These two mushroom species are grown on fermented-pasteurized substrates, and bacteria and fungi play an important role in converting feedstocks into a selective medium for the mushroom mycelium. The mushrooms are usually introduced to the substrate as grain spawn, and the actively growing hyphae form a range of direct interactions with the diverse bacterial community in the substrate. Of these interactions, the most well studied is the removal of inhibitory volatile C8 compounds and ethylene by pseudomonads, which promotes mycelium growth and stimulates primordia formation of both A. bisporus and P. ostreatus. Bacterial biomass in the substrate is a significant nutrition source for the A. bisporus mycelium, both directly through bacteriolytic enzymes produced by A. bisporus, and indirectly through the action of extracellular bacterial enzymes, but this is less well studied for P. ostreatus. Apart from their role as a food source for the growing mycelium, bacteria also form extensive interactions with the mycelium of A. bisporus and P. ostreatus, by means other than those of the removal of inhibitory compounds. Although several of these interactions have been observed to promote mycelial growth, the proposed mechanisms of growth promotion by specific bacterial strains remain largely uncertain, and at times conflicting. Bacterial interactions also elicit varying growth-inhibitory responses from A. bisporus and P. ostreatus. This review explores characterized interactions involving bacteria and A. bisporus, and to a lesser degree P.ostreatus, and whilst doing so identifies existing research gaps and emphasizes directions for future work.
Bioremediation of hexavalent chromium by transformation ofEscherichia coliDH5α with chromate reductase (ChrR) genes ofPseudomonas putidaisolated from tannery effluent
Authors: Sundarraj Shenbagamoorthy , Sudarmani D N P , Samuel Ponpandian , Sevarkodiyone S P 
Published: March 2023

AbstractAimsHexavalent chromium (Cr(VI)), a toxic heavy metal, is a serious pollutant from tannery effluent, and its accumulation in soil and water causes severe environmental concerns and increasing public health issues. The present study focuses on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Ps. putida and transferred to Escherichia coli DH5α for further studies.Methods and ResultsThe bacterial cultures were kept under controlled conditions for 72 h to observe the growth rates and bacterial resistance to chromium. When strains wild-type and transformant E. coli DH5α were grown in chromium-supplemented media, they revealed significant growth, but strains cured type Ps. putida and E. coli DH5α recorded minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5α and wild Ps. putida was 42.52 ± 1.48% and 44.46 ± 0.55%, respectively. The culture supernatant of the wild Ps. putida and transformant E. coli DH5α showed an increased reduction of Cr(VI) compared with cell extract supernatant and cell debris due to the extracellular activity of chromium reductase being responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Ps. putida and transformant E. coli DH5α.ConclusionsTransformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.Significance and Impact of StudyHigh Cr(VI) concentration resistance and high Cr(VI) reducing the strain's ability make it suitable for bioremediation. These possible horizontal gene transfer events indicated in this study may have enabled transformant E. coli DH5α as a good candidate for reducing the heavy metal pollution.
Changes of lipids composition in different ontogenetic stages ofThecaphora frezii: expression of key enzymes for lipid biosynthetic pathways
Authors: Díaz María S , Figueroa Ana C , Alasino Valeria R , Turco Mauricio , Fernández Andrea , Marino Bibiana , Soria Néstor W , Beltramo Dante M 
Published: March 2023

AbstractAimsIt is known that Thecaphora frezii produces peanut smut that generates numerous economic losses. For this reason, it is a priority to search for control strategies. In this sense, we investigated the lipid profile of this pathogen, as possible antifungal targets, regarding polar lipid composition, fatty acid profile, and transcriptional regulation of genes involved in each stage of the development.Method and ResultsLipids from T. frezii teliospores, basidiospores, and hyphae were analyzed by HPLC/CAD and CG/FID. We found differences in the unsaturation levels as well as in the long-chain fatty acids along the stages. Phosphatidylcholine was the main component in the three development stages, followed by cardiolipins. Phosphatidylinositol, phosphatidylethanolamine, and lyso-phosphatidylethanolamine were found in similar amounts in all stages. Although ergosterol was not detected, we found two unsaponifiable lipids. In addition, we found transcripts that encode 28 enzymes involved in the biosynthesis of three lipids by RNA-Seq.ConclusionsThecaphora frezii shows changes in the composition of membrane lipids in different ontogenetic stages as well as in the expression of transcripts for enzymes involved in lipid biosynthesis.
The mechanism of Qingwen Gupi decoction on pulmonary fibrosis based on metabolomics and intestinal flora
Authors: Gao Chen , Chang Hong , Wang Zixuan , Jia Min , Li Qian , Li Xiang , Shi Songli , Bu He 
Published: March 2023

AbstractAimsTo evaluate the effects of the Qingwen Gupi decoction (QGT) in a rat model of bleomycin-induced pulmonary fibrosis (PF), and explore the underlying mechanisms by integrating UPLC-Q-TOF/MS metabolomics and 16S rDNA sequencing of gut microbiota.Methods and ResultsThe animals were randomly divided into the control, PF model, pirfenidone-treated, and low-, medium-, and high-dose QGT groups. The lung tissues were examined and the expression of TGF-β, SMAD-3, and SMAD-7 mRNAs in the lung tissues were analyzed. Metabolomic profiles were analyzed by UPLC-QTOF/MS, and the intestinal flora were examined by prokaryotic 16 rDNA sequencing. Pathological examination and biochemical indices revealed that QGT treatment improved the symptoms of PF by varying degrees. Furthermore, QGT significantly downregulated TGF-β1 and Smad-3 mRNAs and increased the expression levels of Smad-7. QGT-L in particular increased the levels of 18 key metabolic biomarkers that were associated with nine gut microbial species and may exert antifibrosis effects through arachidonic acid metabolism, glycerophospholipid metabolism, and phenylalanine metabolism.ConclusionsQGT alleviated PF in a rat model through its anti-inflammatory, antioxidant, and anti-fibrotic effects, and by reversing bleomycin-induced gut dysbiosis.This study lays the foundation for further research on the pathological mechanisms of PF and the development of new drug candidates.
Soil bacterial community dynamics in plots managed with cover crops and no-till farming in the Lower Mississippi Alluvial Valley, USA
Authors: Firth A G , Brooks J P , Locke M A , Morin D J , Brown A , Baker B H 
Published: March 2023

AbstractAimsAssess bacterial community changes over time in soybean (Glycine max) crop fields following cover crop (CC) and no-till (NT) implementation under natural abiotic stressors.Method and resultsSoil bacterial community composition was obtained by amplifying, sequencing, and analysing the V4 region of the 16S rRNA gene. Generalized linear mixed models were used to assess the effects of tillage, CC, and time on bacterial community response. The most abundant phyla present were Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Bacterial diversity increased in periods with abundant water. Reduced tillage (RT) increased overall bacterial diversity, but NT with a CC was not significantly different than RT treatments under drought conditions. CCs shifted abundances of Firmicutes and Bacteroidetes depending on abiotic conditions.ConclusionsIn the Lower Mississippi Alluvial Valley (LMAV), USA, NT practices lower diversity and influence long-term community changes while cover crops enact a seasonal response to environmental conditions. NT and RT management affect soil bacterial communities differently than found in other regions of the country.