bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of timely metadata curation to the global surveillance of genetic diversity
Authors: Crandall Eric D. , Toczydlowski Rachel H. , Liggins Libby , Holmes Ann E. , Ghoojaei Maryam , Gaither Michelle R. , Wham Briana E. , Pritt Andrea L. , Noble Cory , Anderson Tanner J. , Barton Randi L. , Berg Justin T. , Beskid Sofia G. , Delgado Alonso , Farrell Emily , Himmelsbach Nan , Queeno Samantha R. , Trinh Thienthanh , Weyand Courtney , Bentley Andrew , Deck John , Riginos Cynthia , Bradburd Gideon S. , Toonen Robert J. 
Published: January 2023

AbstractGenetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data‐sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
Blind spots and spotlights in bureaucratic politics: An analysis of policy co‐production in environmental governance dynamics in Indonesia
Authors: Sahide Muhammad Alif K. , Fisher Micah R. , Sirimorok Nurhady , Faturachmat Fatwa , Dhiaulhaq Ahmad , Maryudi Ahmad , Batiran Karno B. , Supratman Supratman 
Published: January 2023

SummaryMotivationThere has been growing interest in recent years in a better understanding of knowledge/science and policy co‐production in environmental governance.PurposeWe aim to shed more light on the politics among the numerous actors shaping ideas that drive environmental policy in Indonesia. We focus our theoretical engagement on a framing of bureaucratic politics, which is a research tradition that has made various strides in explaining the formal and non‐formal processes that influence environmental governance outcomes.Methods and approachBuilding from a wide range of case studies drawn from deep engagement of participatory research in policy‐making in Indonesia, we established a simple typology that helps explain eight categories that emerge when bureaucracies, knowledge institutions, and publics come together to shape environmental governance outcomes.FindingsThe bureaucratic politics specifically clarified the features of cases that have clear fragmentation of bureaucracy but clear explanation variables from the formal and informal interest of bureaucracy. Potential uncovered by bureaucratic politics framing means that, if the metapolitical works alter, the bureaucracy works smoothly or makes it impossible for bureaucracy to operationalize their formal and informal interest in capturing the dynamics of macro and micro politics. In terms of form of knowledge, knowledge produced “from below” can also be used in policy co‐production. It can be produced by non‐expert actors, or from dialogue among them and sympathetic experts that occur below the bureaucracy's radar (people‐driven).Policy implicationsOur ideal policy co‐production implication is where the three actors have a strong foundation of “common consciousness” and interact equally to address a particular environmental policy agenda, with enough working space to jointly commit to creating the knowledge base to shape policy.
Lipids uniquely alter the secondary structure and toxicity of amyloid beta 1–42 aggregates
Authors: Zhaliazka Kiryl , Matveyenka Mikhail , Kurouski Dmitry 
Published: January 2023

Abrupt aggregation of amyloid β1‐42 (Aβ) peptide is a hallmark of Alzheimer's disease (AD), a severe pathology that affects more than 44 million people worldwide. A growing body of evidence suggests that lipids can uniquely alter rates of Aβ1‐42 aggregation. However, it remains unclear whether lipids only alter rates of protein aggregation or also uniquely modify the secondary structure and toxicity of Aβ1‐42 oligomers and fibrils. In this study, we investigated the effect of phosphatidylcholine (PC), cardiolipin (CL), and cholesterol (Chol) on Aβ1‐42 aggregation. We found that PC, CL and Chol strongly accelerated the rate of fibril formation compared to the rate of Aβ1‐42 aggregation in the lipid‐free environment. Furthermore, anionic CL enabled the strongest acceleration of Aβ1‐42 aggregation compared to zwitterionic PC and uncharged Chol. We also found that PC, CL and Chol uniquely altered the secondary structure of early‐, middle‐ and late‐stage Aβ1‐42 aggregates. Specifically, CL and Chol drastically increased the amount of parallel β‐sheet in Aβ1‐42 oligomers and fibrils grown in the presence of these lipids. This caused a significant increase in the toxicity of Aβ : CL and Aβ : Chol compared to the toxicity of Aβ : PC and Aβ1‐42 aggregates formed in the lipid‐free environment. These results demonstrate that toxicity of Aβ aggregates correlates with the amount of their β‐sheet content, which, in turn, is determined by the chemical structure of lipids present at the stage of Aβ1‐42 aggregation.
Drought‐induced increase in tree mortality and corresponding decrease in the carbon sink capacity of Canada's boreal forests from 1970 to 2020
Authors: Liu Qiuyu , Peng Changhui , Schneider Robert , Cyr Dominic , McDowell Nate G. , Kneeshaw Daniel 
Published: January 2023

AbstractCanada's boreal forests, which occupy approximately 30% of boreal forests worldwide, play an important role in the global carbon budget. However, there is little quantitative information available regarding the spatiotemporal changes in the drought‐induced tree mortality of Canada's boreal forests overall and their associated impacts on biomass carbon dynamics. Here, we develop spatiotemporally explicit estimates of drought‐induced tree mortality and corresponding biomass carbon sink capacity changes in Canada's boreal forests from 1970 to 2020. We show that the average annual tree mortality rate is approximately 2.7%. Approximately 43% of Canada's boreal forests have experienced significantly increasing tree mortality trends (71% of which are located in the western region of the country), and these trends have accelerated since 2002. This increase in tree mortality has resulted in significant biomass carbon losses at an approximate rate of 1.51 ± 0.29 MgC ha−1 year−1 (95% confidence interval) with an approximate total loss of 0.46 ± 0.09 PgC year−1 (95% confidence interval). Under the drought condition increases predicted for this century, the capacity of Canada's boreal forests to act as a carbon sink will be further reduced, potentially leading to a significant positive climate feedback effect.
Migraine, inflammatory bowel disease and celiac disease: A Mendelian randomization study
Authors: Welander Nike Zoe , Rukh Gull , Rask‐Andersen Mathias , Harder Aster V. E. ,   The International Headache Genetics Consortium, van den Maagdenberg Arn M. J. M. , Schiöth Helgi Birgir , Mwinyi Jessica 
Published: January 2023

AbstractObjectiveTo assess whether migraine may be genetically and/or causally associated with inflammatory bowel disease (IBD) or celiac disease.BackgroundMigraine has been linked to IBD and celiac disease in observational studies, but whether this link may be explained by a shared genetic basis or could be causal has not been established. The presence of a causal association could be clinically relevant, as treating one of these medical conditions might mitigate the symptoms of a causally linked condition.MethodsLinkage disequilibrium score regression and two‐sample bidirectional Mendelian randomization analyses were performed using summary statistics from cohort‐based genome‐wide association studies of migraine (59,674 cases; 316,078 controls), IBD (25,042 cases; 34,915 controls) and celiac disease (11,812 or 4533 cases; 11,837 or 10,750 controls). Migraine with and without aura were analyzed separately, as were the two IBD subtypes Crohn's disease and ulcerative colitis. Positive control analyses and conventional Mendelian randomization sensitivity analyses were performed.ResultsMigraine was not genetically correlated with IBD or celiac disease. No evidence was observed for IBD (odds ratio [OR] 1.00, 95% confidence interval [CI] 0.99–1.02, p = 0.703) or celiac disease (OR 1.00, 95% CI 0.99–1.02, p = 0.912) causing migraine or migraine causing either IBD (OR 1.08, 95% CI 0.96–1.22, p = 0.181) or celiac disease (OR 1.08, 95% CI 0.79–1.48, p = 0.614) when all participants with migraine were analyzed jointly. There was some indication of a causal association between celiac disease and migraine with aura (OR 1.04, 95% CI 1.00–1.08, p = 0.045), between celiac disease and migraine without aura (OR 0.95, 95% CI 0.92–0.99, p = 0.006), as well as between migraine without aura and ulcerative colitis (OR 1.15, 95% CI 1.02–1.29, p = 0.025). However, the results were not significant after multiple testing correction.ConclusionsWe found no evidence of a shared genetic basis or of a causal association between migraine and either IBD or celiac disease, although we obtained some indications of causal associations with migraine subtypes.
A synthesis of Eurasian Curlew (Numenius arquata arquata) demography and population viability to inform its management
Authors: Viana Duarte S. , Santoro Simone , Soriguer Ramón C. , Figuerola Jordi 
Published: January 2023

The European population of Eurasian Curlew Numenius arquata arquata, a near‐threatened wader subspecies, has undergone pronounced population declines over the past 30 years. To assess the demography and viability of its global population, we surveyed studies quantifying demographic rates (productivity and survival) and complemented this review with new estimates of survival probability at the flyway scale. Then, using a demographic model, we estimated population growth rates while accounting for the range of variation of demographic parameters, and compared these estimates (expected based on demographic rates) with those observed based on population censuses. Both observed and expected average growth rates were negative but the observed rates were higher than estimates from demographic models (λ = 0.98–0.99 compared with 0.85–0.95). This discrepancy implies that there is geographical variation in the demography of different populations that is not fully covered by current demographic data, namely unstudied regions with higher productivity. According to our calculations, at the flyway scale, productivity is currently c. 0.57 fledglings per pair per year, higher than the average reported productivity of 0.29, but lower than the 0.68 needed to achieve a stable global population size (λ = 1). Adult survival, estimated at 0.90, was the most sensitive parameter determining population growth rates, but the low productivity levels over the last few decades seems to be the most probable cause of population declines. The negative population growth rates require immediate conservation actions to preserve adult survival and increase the extremely low productivity in western and northern European populations to values above 0.68 fledglings per pair per year. We hope our synthesis on the demographic status of Curlew in Europe will encourage the collection of more demographic data and allow concrete management goals at the flyway scale to be established in order to recover the global population of this iconic species.
Comparison of the characteristics and factors influencing hospital visits among children with nocturnal enuresis in Japan: The Hirakata–Urayasu population‐based cohort study
Authors: Nishizaki Naoto , Tsuji Shoji , Akagawa Shohei , Hirano Daishi , Takahashi Ken , Shimizu Toshiaki , Kaneko Kazunari 
Published: January 2023

ObjectivesThe aim of this study was to compare the demographic characteristics of school‐aged children with nocturnal enuresis and factors influencing hospital visits between two regions in Japan.MethodsA cross‐sectional survey was conducted in Hirakata City, Osaka Prefecture, and Urayasu City, Chiba Prefecture. An anonymous online questionnaire was administered to all public elementary and junior high school students (aged 6–16 years) or their guardians. Questions included age, gender, perinatal history, frequency of nocturnal enuresis, frequency of bowel movements, comorbidities, and hospital visits for nocturnal enuresis.ResultsThe survey response rates were 15.4% in Hirakata City and 37.0% in Urayasu City. In total, 426 children with nocturnal enuresis in Hirakata City and 270 in Urayasu City were included in the final analysis. In both cities, the boy–girl ratio was approximately 2:1, and the prevalence of nocturnal enuresis gradually decreased with age. Multivariate analysis revealed that children aged ≥11 years had a significantly higher proportion of hospital visits (OR, 2.61; 95% CI: 1.49–4.56; p = 0.001; OR, 2.72; 95% CI: 1.12–6.64; p = 0.027, respectively). However, the frequency of nocturnal enuresis did not affect hospital visits.ConclusionsThe findings of this study suggest that parents with school‐aged children have low awareness that nocturnal enuresis is a health problem and therefore subject to medical consultation. Although the proportion of hospital visits increases for children aged ≥11 years, children and families suffering from nocturnal enuresis should be encouraged to see a doctor instead of adopting a “wait and see attitude,” even at a young age.
Silencing of the immune gene BmPGRP‐L4 in the midgut affects the growth of silkworm (Bombyx mori) larvae
Authors: Liang Yebin , Wang Tao , Yang Weiyi , Chen Zemin , Li Qingrong , Swevers Luc , Liu Jisheng 
Published: January 2023

AbstractPeptidoglycan recognition proteins (PGRPs) are one of the receptors in insects' immune pathways, essential for insects to recognize the exogenous pathogens in order to activate the Toll and immune deficiency (IMD) pathway. In the silkworm Bombyx mori, previous studies focused on the short PGRPs and less is known about the long PGRPs. In this study, a long PGRP in silkworm BmPGRP‐L4 was cloned and its expression and function were analysed. The results showed that BmPGRP‐L4 contains a transmembrane region, a conserved PGRP domain, and an amidase‐2 domain. The expression profile demonstrated that BmPGRP‐L4 existed in diverse tissues including epidermis, fat body, midgut, and silk glands, with remarkably high expression in the midgut in the 5th instar. Oral infection with Escherichia coli and Staphylococcus aureus significantly induced BmPGRP‐L4 in the midgut and epidermis, as well as in the fat body and silk glands. Peptidoglycan also induced the expression of BmPGRP‐L4 in midgut tissue ex vivo and BmN4 cells in vitro. RNAi of BmPGRP‐L4 was effective in the midgut and epidermis, while the efficiency in the fat body was transient. RNAi‐mediated knock‐down of BmPGRP‐L4 reduced the weight and growth of the silkworm, possibly due to its participation in the immune response and the regulation of the microbiota in the midgut lumen of the silkworm larvae.
Systemic immune mediators reflect tumour‐infiltrating lymphocyte intensity and predict therapeutic response in triple‐negative breast cancer
Authors: Lopes Ananda D. , Galdino Nayane A. L. , Figueiredo Amanda B. , Brianese Rafael C. , Morais Katia L. P. , De Brot Marina , Osório Cynthia A. B. T. , Teixeira‐Carvalho Andrea , Calsavara Vinicius F. , Evangelista Guilherme F. B. , Alves Natalia S. , Makdissi Fabiana B. , Sanches Solange M. , Cordeiro de Lima Vladmir C. , Carraro Dirce M. , Gollob Kenneth J. 
Published: January 2023

AbstractTriple‐negative breast cancer (TNBC) is an aggressive form of breast cancer (BC). Neoadjuvant chemotherapy has proven efficacy in its treatment, and a pathological complete response (pCR) to therapy is predictive of improved long‐term survival. The immune response is key to successful neoadjuvant chemotherapy, as indicated by the relation between the percentage of stromal tumour‐infiltrating lymphocytes (TILs) in pre‐treated tumour tissue samples and the likelihood of achieving pCR. Here we studied systemic immune mediators from volunteer TNBC patients before undergoing neoadjuvant chemotherapy to determine the systemic response association with TIL intensity, treatment response and survival. Patients were classified into pCR responder or non‐responder at time of surgery. We found higher levels of immune mediators before treatment began in patients that went on to be pCR responders versus non‐pCR, with area under the curve (AUC) values of 0.64–0.80. We also observed a positive correlation between inflammatory systemic immune mediators and the percentage of TILs in pCR responder patients. Combining TILs and systemic immune mediator levels provided stronger AUC values (range of 0.72–0.82). Last, performing a progression‐free survival analysis with several of the systemic cytokines that predict pCR, segregated the patients into long‐ and short‐survival groups based on high and low production of the cytokines, respectively. Our study demonstrates that circulating cytokines, before treatment begins, predict pCR in TNBC patients treated with neoadjuvant chemotherapy. Moreover, they may act as a surrogate marker of high TILs or together with TILs to better predict pCR and survival.
Online reach correction in 6‐ and 11‐month‐old infants
Authors: Verhaar Erik , Medendorp W. Pieter , Hunnius Sabine , Stapel Janny C. 
Published: January 2023

AbstractThe current study investigated the development of online reach control. Six‐ and 11‐month‐old infants reached for a toy while their hand position was tracked. The toy either remained stationary (baseline trials) or unexpectedly displaced left‐ or rightward during the reach (perturbation trials). To obtain a measure of online reach correction, we compared reaches in the perturbation trials to reaches in baseline trials using autoregression analysis. Infants of both age groups adjusted their reach trajectories in the direction of the displacement. Moreover, we divided the reaching movements into movement units, defined as the submovements of a reach between local minima in hand speed. Eleven‐month‐old infants adjusted their reach within the span of a single movement unit; corrections in 6‐month‐olds spanned multiple movement units. These results suggest that the reach control system has a rudimentary replanning capacity by 6 months of age, which, with age, further develops to a more sophisticated online control mechanism for ongoing reaches.
Family income modifies the association between frequent sugar intake and dental caries
Authors: Lima Laura Jordana Santos , da Consolação Soares Maria Eliza , Moreira Luana Viviam , Ramos‐Jorge Joana , Ramos‐Jorge Maria Letícia , Marques Leandro Silva , Fernandes Izabella Barbosa 
Published: January 2023

AbstractAimThe aim of this cross‐sectional study was to investigate whether family income modifies associations between dental caries and sex, age, mother's education, type of preschool, sugar intake, and toothbrushing.BackgroundDental caries is a multifactorial dyanamic disease primarily mediated by biofilm and sugar.DesignA randomly selected sample of 308 Brazilian preschool children aged 1–3 years underwent a clinical oral examination for the assessment of moderate/extensive dental caries using codes 3–6 of the International Caries Detection and Assessment System. Mothers were asked to fill out a form addressing the child's demographic and socioeconomic characteristics as well as the frequency of sugar intake. Statistical analysis involved descriptive statistics, the chi‐squared test, and Poisson regression models.ResultsThe prevalence of moderate/extensive dental caries was 42.5%. The adjusted model revealed that within low‐income families (<2 times the monthly minimum wage), the prevalence of dental caries was higher among children with a high frequency of sugar intake (≥ twice per day) than in those with a low frequency of sugar intake (< twice a day) (RR = 1.79; CI: 1.38–2.33). In families with higher income (≥2 times the monthly wage), no significant association between sugar intake and dental caries was, however, found.ConclusionsIn conclusion, monthly family income can modify the association between the high frequency of sugar intake and dental caries.
Evolution of female colours in birds: The role of female cost of reproduction and paternal care
Authors: Fargevieille Amélie , Grégoire Arnaud , Gomez Doris , Doutrelant Claire 
Published: January 2023

Abstract
Female ornamentation is frequently observed in animal species and is sometimes found as more evolutionary labile than male ornamentation. A complex array of factors may explain its presence and variation. Here we assessed the role of female cost of reproduction and paternal care. Both factors have been pinpointed as important by theoretical studies but have not been investigated yet in details at the interspecific level. We worked on 133 species of North temperate Passeriformes bird species for which both the clutch volume – here taken as the proxy of female cost of reproduction – and amount of paternal care are relatively well known. Using spectrometry, we measured the whole-body coloured plumage patches and quantified three metrics corresponding to brightness (i.e. achromatic component), colour chromaticity (i.e. intensity) and colour volume (i.e. diversity). We found a strong association between male and female colour metrics. Controlling for this association, we found additional small but detectable effects of both cost of reproduction and paternal care. First, females of species with more paternal care were slightly brighter. Second, the interaction between the level of paternal care and egg volume was correlated with female colour intensity: females with more paternal care were more chromatic, with this association mostly present when their investment in reproduction was low. Together these results suggest that female cost of reproduction and paternal care are part of the multiple factors explaining variation of female coloration, besides the strong covariation between male and female coloration.
Abstract
To a lesser extent than male conspicuous plumage, female plumage colouration may also vary across bird species. This study explores the role of egg production and male parental care in the evolution of female plumage colouration, using 133 species of songbirds. Pictures were provided by Justine Le Vaillant, David López-Idiáquez and Matthew Silk.