bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imprint of tree species mycorrhizal association on microbial‐mediated enzyme activity and stoichiometry
Authors: Zheng Haifeng , Phillips Richard P. , Rousk Johannes , Yue Kai , Schmidt Inger Kappel , Peng Yan , Wang Senhao , Vesterdal Lars 
Published: March 2023

Abstract

Understanding the effects of tree species and their mycorrhizal association on soil processes is critical for predicting the ecosystem consequences of species shifts owing to global change and forest management decisions. While it is well established that forests dominated by different mycorrhizal types can vary in how they cycle carbon (C), nitrogen (N) and phosphorus (P), the degree to which these patterns are driven by microbial‐mediated enzyme activity (EA) and ecoenzymatic stoichiometry (ES) remains elusive.

Here, we synthesized the effects of mycorrhizal association on seven soil enzymes involved in microbial C, N and P acquisition and ES using data from 56 peer‐reviewed papers.

We found that relative to soil in ectomycorrhizal (EcM) trees, soil in arbuscular mycorrhizal (AM) trees exhibited greater activity of some C acquisition enzymes (e.g. beta‐glucosidase; BG) and higher ecoenzymatic ratios of BG/NAG (N‐acetyl‐glucosaminidase) and BG/AP (acid phosphatase). These results supported that AM trees had rapid C and nutrient turnover rates, inorganic nutrient economics and high soil microbial C limitation. We also found evidence for an organic nutrient economy and greater soil microbial demand for nutrients in EcM trees compared to AM trees. In addition, the effect of mycorrhizal association on the activity of certain soil enzymes and enzymatic stoichiometry (i.e. BG and BG/NAG ratio) appeared to be associated with the differences in soil pH, phylogenetic group (i.e. conifers and broadleaves) and leaf habit (i.e. evergreen and deciduous) between AM and EcM trees.

The results from the global meta‐analysis suggested that soil EA and ES appear to play critical roles in shaping the differences in the nutrient economy between AM and EcM tree species, but leaf morphology and soil conditions should be considered in evaluations of soil processes in forests of different mycorrhizal associations. Given that most of the studies in the database were from the temperate and subtropical regions, further research in other biomes is needed to elucidate the underlying mechanisms driving the mycorrhizal effect at the global scale.

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Mercury isotope clocks predict coastal residency and migration timing of hammerhead sharks
Authors: Besnard Lucien , Lucca Brandyn M. , Shipley Oliver N. , Le Croizier Gaël , Martínez‐Rincón Raúl O. , Sonke Jeroen E. , Point David , Galván‐Magaña Felipe , Kraffe Edouard , Kwon Sae Yun , Schaal Gauthier 
Published: March 2023

Abstract

The management of migratory taxa relies on the knowledge of their movements. Among them, ontogenetic habitat shift, from nurseries to adult habitats, is a behavioural trait shared across marine taxa allowing resource partitioning between life stages and reducing predation risk. As this movement is consistent over time, characterizing its timing is critical to implement efficient management plans, notably in coastal areas to mitigate the impact of fisheries on juvenile stocks.

In the Mexican Pacific, habitat use of the smooth hammerhead shark (Sphyrna zygaena) is poorly described, while the species is heavily harvested. Given the large uncertainties associated with the timing of out‐migration from coastal nursery grounds to offshore waters prior to reproductive maturity, a more precise assessment of smooth hammerhead shark movements is needed.

Photochemical degradation of mercury imparts mass‐independent isotope fractionation (Δ199Hg) which can be used to discriminate between neonate coastal shallow habitats and the offshore deep foraging patterns of late juveniles. Here, we present the application of muscle Δ199Hg as molecular clocks to predict the timing of ontogenetic habitat shifts by smooth hammerhead sharks, based on their isotopic compositions at the initial and arrival habitats and on muscle isotopic turnover rate.

We observed decreases in Δ199Hg values with shark body length, reflecting increasing reliance on offshore mesopelagic prey with age. Coastal residency estimates indicated that smooth hammerhead sharks utilize coastal resources for 2 years prior to offshore migration, suggesting a prolonged residency in these ecosystems.

Policy implications. This study demonstrates how mercury stable isotopes and isotopic clocks can be implemented as a complementary tool for stock management by predicting the timing of animal migration—a key aspect in the conservation of marine taxa. In the Mexican Pacific, fishing pressure on shark species occurs in coastal habitats depleting juvenile stocks. Consequently, management decision support tools are imperative for effectively maintaining early life stage population levels over time. The finding that smooth hammerhead sharks extensively rely on highly fished habitats for 2 years after parturition supports the relevance of establishing a size limit in coastal fisheries and demonstrates how the current temporal shark fishing closure could lack efficiency for the species.
Chemoreceptors from the commensal gut Roseburia rectibacter bind to mucin and trigger chemotaxis
Authors: Chen Hong‐He , Wang Yu‐Xin , Li De‐Feng , Liu Chang , Bi Shuang‐Yu , Jiang Cheng‐Ying , Liu Shuang‐Jiang 
Published: March 2023

AbstractChemotaxis is crucial for bacterial adherence and colonization of the host gastrointestinal tract. Previous studies have demonstrated that chemotaxis affects the virulence of causative pathogens and the infection in the host. However, the chemotactic abilities of non‐pathogenic and commensal gut bacteria have rarely been explored. We observed that Roseburia rectibacter NSJ‐69 exhibited flagella‐dependent motility and chemotaxis to a variety of molecules, including mucin and propionate. A genome‐wide analysis revealed that NSJ‐69 has 28 putative chemoreceptors, 15 of which have periplasmic ligand‐binding domains (LBDs). These LBD‐coding genes were chemically synthesized and expressed heterologously in Escherichia coli. Intensive screening of ligands revealed four chemoreceptors bound to mucin and two bound to propionate. When expressed in Comamonas testosteroni or E. coli, these chemoreceptors elicited chemotaxis toward mucin and propionate. Hybrid chemoreceptors were constructed, and results showed that the chemotactic responses to mucin and propionate were dependent on the LBDs of R. rectibacter chemoreceptors. Our study identified and characterized R. rectibacter chemoreceptors. These results will facilitate further investigations on the involvement of microbial chemotaxis in host colonization.
Diagnosis or prognosis? An umbrella review of mid‐trimester cervical length and spontaneous preterm birth
Authors: Hughes Kelly , Ford Heather , Thangaratinam Shakila , Brennecke Shaun , Mol Ben W. , Wang Rui 
Published: March 2023

AbstractBackgroundCervical length is widely used to assess a woman's risk of spontaneous preterm birth (SPTB).ObjectivesTo summarise and critically appraise the evidence from systematic reviews on the prognostic capacity of transvaginal sonographic cervical length in the second trimester in asymptomatic women with singleton or twin pregnancy.Search strategySearches were performed in Medline, Embase, CINAHL and grey literature from 1 January 1995 to 6 July 2021, including keywords ‘cervical length’, ‘preterm birth’, ‘obstetric labour, premature’, ‘review’ and others, without language restriction.Selection criteriaWe included systematic reviews including women who did not receive treatments to reduce SPTB risk.Data collection and analysisFrom 2472 articles, 14 systematic reviews were included. Summary statistics were independently extracted by two reviewers, tabulated and analysed descriptively. The ROBIS tool was used to evaluate risk of bias of included systematic reviews.Main resultsTwelve reviews performed meta‐analyses: two were reported as systematic reviews of prognostic factor studies, ten used diagnostic test accuracy methodology. Ten systematic reviews were at high or unclear risk of bias. Meta‐analyses reported up to 80 combinations of cervical length, gestational age at measurement and definition of preterm birth. Cervical length was consistently associated with SPTB, with a likelihood ratio for a positive test of 1.70–142.ConclusionsThe ability of cervical length to predict SPTB is a prognostic research question; systematic reviews typically analysed diagnostic test accuracy. Individual participant data meta‐analysis using prognostic factor research methods is recommended to better quantify how well transvaginal ultrasonographic cervical length can predict SPTB.
Functional and physicochemical properties of protein from giant squid (Dosidicus gigas) extracted using foam‐aided pH‐shift processing
Authors: López‐Medina Francisco Antonio , Dublán‐García Octavio , Morachis‐Valdez Ana Gabriela , Gómez‐Oliván Leobardo Manuel , Islas‐Flores Hariz , Hernández‐Navarro María Dolores 
Published: March 2023

AbstractJumbo squid (Dosidicus gigas) is a commercially valuable mollusk in Mexico; 80% of its body is edible. Despite the high protein content (∼18%) and low cholesterol content of this species, its high proteolytic activity (microbial and endogenous enzymes) induces protein degradation and consequent reduction in functional properties from a structural viewpoint. Gelation capacity (texture profile of the gels obtained), solubility, water holding capacity, foaming capacity, emulsification capacity, and emulsion stability were evaluated in protein concentrates obtained by foam‐aided pH‐shift processing: (A) myofibrillar protein extraction with distilled water and no pH‐shifting; (B) alkaline solubilization and isoelectric precipitation; (C) acidic solubilization and isoelectric precipitation; and (D) process A and isoelectric precipitation. Process B showed superior gelation capacity, D had high emulsion stability across a wide range of pH values (4.0–8.0) and C lower plate counts of aerobic mesophilic. Therefore, all three alternative extraction processes showed techno‐functional advantages.Practical ApplicationJumbo squid is an abundant protein source in México, most of which is exported. Functional and physicochemical properties of muscle protein were improved by pH‐shift processing. The recovered protein showed modifications of technological properties, using one of the methods described can lead to produce a protein extract with the most desirable attributes, such as foaming, emulsifying, or gelling capacities. The functional and physicochemical properties of protein from squid can be enhanced by selecting a certain pH‐shift processing, depending on the desirable use. There is a broad perspective on the use of these protein extracts as ingredients or additives.
Come hybrid or high water: Making the case for a Green–Gray approach toward resilient urban stormwater management
Authors: Hendricks Marccus D. , Dowtin Asia L. 
Published: March 2023

Abstract120 years or more of unsustainable urban development has damaged the natural environment and disrupted essential ways to stabilize water body overflow and even mitigate pluvial flooding. In light of catastrophic flooding that has occurred globally, a renewed commitment to transforming built surfaces and incorporating more green infrastructures (GIs) has emerged. In fact, one could argue that an overcommitment to GI is being touted in the literature, but largely disconnected from more real‐world possibilities, considering all things. In this commentary, we make the case that as cities transition from development patterns of the past and even considering climate‐induced storm characteristics of the future, a hybridized solution (e.g., Green–Gray) should be considered. Smaller approaches to urban greening have been implemented in areas that need larger‐scale restorations, thus proving to be insufficient. Likewise, the uncertainty surrounding rainfall and storm events has forced us to be more strategically balanced in our efforts to achieve resilience in our stormwater infrastructure. Hybridized solutions that include a diverse set of systems, anchored in local conditions, position us best for effective urban stormwater management. In the absence of such solutions, runoff volumes will continue to rise, flooding will prevail, and disenfranchised communities will remain disproportionately impacted by these impacts of urbanization.
The need for constructing endangered fish habitats that conform to climate‐driven flow changes in a western U.S. river
Authors: Valdez Richard A. , Cunningham Colleen , Effati Ali , Freeman Deborah L. 
Published: March 2023

AbstractWarmwater fish habitat in the San Juan River of the southwestern United States has been reduced by over 30% as a result of water depletion, reservoir inundation, and cold‐water dam releases combined with drought‐related changes in hydrology. This reduction and a suite of other factors have contributed to declines in native fish populations including the federally endangered Colorado Pikeminnow (Ptychocheilus lucius) and Razorback Sucker (Xyrauchen texanus). Conservation efforts for these species include determining flow needs; protecting, managing, and augmenting habitats; and stocking hatchery fish. But the young of stocked fish have low survival due largely to a paucity of nursery habitat not being reformed and maintained under current conditions. Flow recommendations for Navajo Dam releases designed to mimic the river's natural hydrograph have not been met due to water shortages, and the desired outcomes of increased channel complexity and enhanced fish habitat have not been observed. Forecasted hydrology that includes ongoing drought shows that achieving the flow targets through further dam reoperations is unlikely. Mechanical construction of early life‐stage habitats is a highly recommended complement to flow management for offsetting the effects of flow reduction and habitat loss. Habitats with features that are effective and resilient under a range of flows are important in counterbalancing the effects of climate change.
Mucolipidosis: A mimicker of juvenile idiopathic arthritis
Authors: Chopra Sanya , Maheshwari Anu , Verma Anju , Kannepalli Ashok , Mahto Deonath 
Published: March 2023

AbstractJuvenile idiopathic arthritis is the most common form of chronic arthritis in children and at times misdiagnosed in those presenting with arthropathy secondary to non‐inflammatory causes. The overlap of symptoms often pose a diagnostic challenge for clinicians. This mostly results in a delayed diagnosis subjecting children to unnecessary use of long‐term immunosuppressants and disease‐modifying drugs. We present the case of a 9‐year‐old boy who was previously misdiagnosed as a case of juvenile idiopathic arthritis. Detailed evaluation later led to the diagnosis of mucolipidosis (type III) which was confirmed on genetic testing. Emphasis on detailed history and clinical examination including the subtle hints like lack of signs of inflammation, family history, no morning stiffness and normal inflammatory markers should be picked up to make a timely diagnosis. In today's era of genetic testing and diagnosis, it is prudent to offer these tests for such patients to make an accurate diagnosis and prognosticate them for the long‐term outcome.
Pain in individuals with idiopathic inflammatory myopathies, other systemic autoimmune rheumatic diseases, and without rheumatic diseases: A report from the COVAD study
Authors: Shinjo Samuel Katsuyuki , Kim Minchul , Hoff Leonardo Santos , Missé Rafael Giovani , Sen Parikshit , Naveen R. , Day Jessica , Cordeiro Rafael Alves , Júnior Jucier Gonçalves , Chatterjee Tulika , Lilleker James B. , Agarwal Vishwesh , Kardes Sinan , Milchert Marcin , Gheita Tamer , Salim Babur , Velikova Tsvetelina , Gracia‐Ramos Abraham Edgar , Parodis Ioannis , O'Callaghan Albert Selva , Nikiphorou Elena , Makol Ashima , Tan Ai Lyn , Cavagna Lorenzo , Saavedra Miguel A. , Ziade Nelly , Knitza Johannes , Kuwana Masataka , Nune Arvind , Distler Oliver , Chinoy Hector , Agarwal Vikas , Aggarwal Rohit , Gupta Latika ,   COVAD Study Group
Published: March 2023

AbstractObjectivesTo compare pain intensity among individuals with idiopathic inflammatory myopathies (IIMs), other systemic autoimmune rheumatic diseases (AIRDs), and without rheumatic disease (wAIDs).MethodsData were collected from the COVID‐19 Vaccination in Autoimmune Diseases (COVAD) study, an international cross‐sectional online survey, from December 2020 to August 2021. Pain experienced in the preceding week was assessed using numeral rating scale (NRS). We performed a negative binomial regression analysis to assess pain in IIMs subtypes and whether demographics, disease activity, general health status, and physical function had an impact on pain scores.ResultsOf 6988 participants included, 15.1% had IIMs, 27.9% had other AIRDs, and 57.0% were wAIDs. The median pain NRS in patients with IIMs, other AIRDs, and wAIDs were 2.0 (interquartile range [IQR] = 1.0–5.0), 3.0 (IQR = 1.0–6.0), and 1.0 (IQR = 0–2.0), respectively (P < 0.001). Regression analysis adjusted for gender, age, and ethnicity revealed that overlap myositis and antisynthetase syndrome had the highest pain (NRS = 4.0, 95% CI = 3.5–4.5, and NRS = 3.6, 95% CI = 3.1–4.1, respectively). An additional association between pain and poor functional status was observed in all groups. Female gender was associated with higher pain scores in almost all scenarios. Increasing age was associated with higher pain NRS scores in some scenarios of disease activity, and Asian and Hispanic ethnicities had reduced pain scores in some functional status scenarios.ConclusionPatients with IIMs reported higher pain levels than wAIDs, but less than patients with other AIRDs. Pain is a disabling manifestation of IIMs and is associated with a poor functional status.
MitoGeneExtractor: Efficient extraction of mitochondrial genes from next‐generation sequencing libraries
Authors: Brasseur Marie V. , Astrin Jonas J. , Geiger Matthias F. , Mayer Christoph 
Published: March 2023

Abstract

Mitochondrial DNA (mtDNA) sequences are often found as byproducts in next‐generation sequencing (NGS) datasets that were originally created to capture genomic or transcriptomic information of an organism. These mtDNA sequences are often discarded, wasting this valuable sequencing information.

We developed MitoGeneExtractor, an innovative tool which allows to extract mitochondrial protein coding genes (PCGs) of interest from NGS libraries through multiple sequence alignments of sequencing reads to amino acid references. General references, for example on order level are sufficient for mining mitochondrial PCGs. In a case study, we applied MitoGeneExtractor to recently published genomic datasets of 1993 birds and were able to extract complete or nearly complete sequences for all 13 mitochondrial PCGs for a large proportion of libraries. Compared to an existing assembly guided sequence reconstruction algorithm, MitoGeneExtractor was faster and substantially more sensitive.

We compared COI sequences mined with MitoGeneExtractor to COI databases. Mined sequences show a high sequence similarity and correct taxonomic assignment between the recovered sequence and the assigned morphospecies in most samples. In some cases of incongruent taxonomic assignments, we found evidence for contamination in NGS libraries.

MitoGeneExtractor allows a fast extraction of mitochondrial PCGs from a wide range of NGS datasets. We recommend to routinely harvest and curate mitochondrial sequence information from genomic resources. MitoGeneExtractor output can be used to identify contaminated NGS libraries and to validate the species identity of the sequenced animal based on the extracted COI sequences.
Personalized risk communication and opioid prescribing in association with nonprescribed opioid use: A secondary analysis of a randomized controlled trial
Authors: Nguemeni Tiako Max Jordan , Shofer Frances , Dolan Abby , Goldberg Erica B. , Rhodes Karin V. , Hess Erik P. , Bellamkonda Venkatesh R. , Perrone Jeanmarie , Cannuscio Carolyn C. , Becker Lance , Rodgers Melissa A. , Zyla Michael M. , Bell Jeffrey J. , McCollum Sharon , Engel‐Rebitzer Eden , Schapira Marilyn M. , Meisel Zachary F. 
Published: March 2023

AbstractBackgroundTo determine the impact of personalized risk communication and opioid prescribing on nonprescribed opioid use, we conducted a secondary analysis of randomized controlled trial participants followed prospectively for 90 days after an emergency department (ED) visit for acute back or kidney stone pain.MethodsA total of 1301 individuals were randomized during an encounter at four academic EDs into a probabilistic risk tool (PRT) arm, a narrative‐enhanced PRT arm, or a general risk information arm (control). In this secondary analysis, both risk tool arms were combined and compared with the control arm. We used logistic regressions to determine associations between receiving personalized risk information, receiving an opioid prescription in the ED, and nonprescribed opioid use in general and by race.ResultsComplete follow‐up data were available for 851 participants; 23.3% (n = 198) were prescribed opioids (34.2% of White vs. 11.6% of Black participants, p < 0.001). Fifty‐six (6.6%) participants used nonprescribed opioids. Participants in the personalized risk communication arms had lower nonprescribed opioid use odds (adjusted odds ratio [aOR] 0.58, 95% confidence interval [CI] 0.4–0.83). Black versus White participants had greater nonprescribed opioid use odds (aOR 3.47, 95% CI 2.05–5.87, p < 0.001). Black participants who were prescribed opioids had a lower marginal probability of using nonprescribed opioids versus those who were not (0.06, 95% CI 0.04–0.08, p < 0.001 vs. 0.10, 95% CI 0.08–0.11, p < 0.001). The absolute risk difference in nonprescribed opioid use for Black and White participants, respectively, in the risk communication versus the control arm, was 9.7% and 0.1% (relative risk ratio 0.43 vs. 0.95).ConclusionsAmong Black but not White participants, personalized opioid risk communication and opioid prescribing were associated with lower odds of nonprescribed opioid use. Our findings suggest that racial disparities in opioid prescribing—which have been previously described within the context of this trial—may paradoxically increase nonprescribed opioid use. Personalized risk communication may effectively reduce nonprescribed opioid use, and future research should be designed specifically to explore this possibility in a larger cohort.