bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenological research based on natural history collections: Practical guidelines and a lepidopteran case study
Authors: Belitz Michael W. , Larsen Elise A. , Shirey Vaughn , Li Daijiang , Guralnick Robert P. 
Published: September 2022

Abstract

Natural history collections (NHCs) have been indispensable to understanding longer‐term trends of the timing of seasonal events. Massive‐scale digitization of specimens promises to further enable phenological research, especially the ability to move towards a deeper understanding of drivers of change and how trait–environment interactions shape phenological sensitivity.

Despite the promise of NHCs to answer fundamental phenology questions, the use of these data resources presents unique and often overlooked challenges requiring specialized workflow steps, such as assembling multisource data, accounting for date imprecision and making decisions about trade‐offs between data density and spatial resolution.

We provide a set of key best practice recommendations and showcase these via a case study that utilizes NHC data to test hypotheses about spatiotemporal trends in adult Lepidoptera (i.e. butterflies and moths) flight timing across North America. Our case study is a worked example of these best practices, helping practitioners recognize and overcome potential pitfalls at each step, from data acquisition and cleaning, to delineating spatial units and proper estimation of phenological metrics and associated uncertainty, to building appropriate models.

We confirm and extend the critical importance of voltinism and diapause strategy, but less‐so daily activity patterns, for predicting Lepidoptera phenology spatiotemporal trends. Our case study also showcases the unique power of NHC data to test existing hypotheses and generate new insights about temporal phenological trends. Specifically, migratory species and species that enter diapause as adults are advancing the start of flight periods in more recent years, even after accounting for climate context. These results highlight the physiological and adaptive differences between species with different overwintering strategies.

We close by noting the value of partnerships between data scientists, museum experts and ecological modellers to fully harness the power of digital data resources to address pressing global change challenges. These partnerships can extend approaches for integrating multiple data types to fully unlock our understanding of the tempo, mode, drivers and outcomes of phenological changes at greater spatial, temporal and taxonomic scales.

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Why are biodiversity—ecosystem functioning relationships so elusive? Trophic interactions may amplify ecosystem function variability
Authors: Wu Dan , Xu Chi , Wang Shaopeng , Zhang Lai , Kortsch Susanne 
Published: September 2022

Abstract

The relationship between biodiversity and ecosystem functions (BEFs) has attracted great interest. Studies on BEF have so far focused on the average trend of ecosystem function as species diversity increases. A tantalizing but rarely addressed question is why large variations in ecosystem functions are often observed across systems with similar species diversity, likely obscuring observed BEFs.

Here we use a multi‐trophic food web model in combination with empirical data to examine the relationships between species richness and the variation in ecosystem functions (VEFs) including biomass, metabolism, decomposition, and primary and secondary production. We then probe the mechanisms underlying these relationships, focusing on the role of trophic interactions.

While our results reinforce the previously documented positive BEF relationships, we found that ecosystem functions exhibit significant variation within each level of species richness and the magnitude of this variation displays a hump‐shaped relationship with species richness. Our analyses demonstrate that VEFs is reduced when consumer diversity increases through elevated nonlinearity in trophic interactions, and/or when the diversity of basal species such as producers and decomposers decreases. This explanation is supported by a 34‐year empirical food web time series from the Gulf of Riga ecosystem.

Our work suggests that biodiversity loss may not only result in ecosystem function decline, but also reduce the predictability of functions by generating greater function variability among ecosystems. It thus helps to reconcile the debate on the generality of positive BEF relationships and to disentangle the drivers of ecosystem stability. The role of trophic interactions and the variation in their strengths mediated by functional responses in shaping ecosystem function variation warrants further investigations and better incorporation into biodiversity—ecosystem functioning research.
Plant characteristics drive ontogenetic changes in herbivory damage in a temperate forest
Authors: Kurokawa Hiroko , Oguro Michio , Takayanagi Sakino , Aiba Masahiro , Shibata Rei , Mimura Makiko , Yoshimaru Hiroshi , Nakashizuka Tohru 
Published: September 2022

Abstract

Understanding ontogenetic differences in plant defenses and herbivory damage is crucial for obtaining a better understanding of plant life‐history strategies, community assembly, and dynamics. Although many studies have compared plant defenses or herbivory damage between ontogenetic stages (e.g. sapling vs. adult), how the effects of plant characteristics on leaf herbivory damage change during plant ontogeny has rarely been examined across species or in a species‐rich natural community.

To elucidate the effects of plant characteristics, we compared the relationships of leaf herbivory by insects with stem density, plant size, and leaf traits between saplings and adults for almost all co‐occurring woody species (56 species, ranging from rare to abundant) in a Japanese temperate forest.

In most species, adults were larger, fewer in number, and had leaf traits that were potentially less favorable to herbivores (e.g. stronger, or with more phenolics). In contrast, we observed species‐specific directions of changes in herbivory damage between adults and saplings with plant phylogeny or density having no clear effect. The relationships between some plant traits and herbivory damage were ontogeny dependent, indicating a shift from chemical to physical defense as plants mature, although most of the species characteristics studied were highly correlated between stages. Such ontogeny‐dependent relationships between plant traits and herbivory damage could cause variation in the ontogenetic changes in herbivory damage among species depending on the value of plant traits. Moreover, the direction and magnitude of the effects of ontogenetic differences in species traits on the ontogenetic differences in herbivory damage varied depending on the traits. Together, these factors could have caused the observed ontogenetic changes in herbivory damage among species.

Synthesis. Our study demonstrated how relationships between plant characteristics and herbivory damage can change ontogenetically across many coexisting woody species in a forest community, suggesting that plant traits may perform different functions related to herbivory at different ontogenetic stages. This has rarely been considered in previous dualistic comparisons of individual traits and herbivory damage between ontogenetic stages, and it is vital for understanding plant life‐history strategies across stages in relationships with herbivores in natural communities.
Histone deacetylase SirE regulates development, DNA damage response and aflatoxin production in Aspergillus flavus
Authors: Wen Meifang , Lan Huahui , Sun Ruilin , Chen Xuan , Zhang Xin , Zhu Zhuo , Tan Can , Yuan Jun , Wang Shihua 
Published: September 2022

AbstractAspergillus flavus is a ubiquitous saprotrophic soil‐borne pathogenic fungus that causes crops contamination with the carcinogen aflatoxins. Although sirtuin E (SirE) is known to be a NAD‐dependent histone deacetylase involved in global transcriptional regulation. Its biological functions in A. flavus are not fully understood. To explore the effects of SirE, we found that SirE was located in the nucleus and increased the level of H3K56 acetylation. The ΔsirE mutant had the most severe growth defect in the sirtuin family. The RNA‐Seq revealed that sirE was crucial for secondary metabolism production as well as genetic information process and oxidation–reduction in A. flavus. Further analysis revealed that the ΔsirE mutant increased aflatoxin production. Both the sirE deletion and H3K56 mutants were highly sensitive to DNA damage and oxidative stresses, indicating that SirE was required for DNA damage and redox reaction by the H3K56 locus. Furthermore, the ΔsirE mutant displayed high sensitivity to osmotic stress and cell wall stress, but they may not be associated with the H3K56. Finally, the catalytic activity site N192 of SirE was required for regulating growth, deacetylase function and aflatoxin production. Together, SirE is essential for histone deacetylation and biological function in A. flavus.
Globalization and the proportion of women in vulnerable employment in sub‐Saharan Africa: The role of economic, social, and political conditions
Authors: Uwajumogu Nkechinyere R. , Nwokoye Ebele S. , Ojike Richard O. , Okere Kingsley I. , Ugwu Joy N. , Ogbuagu Anuli R. 
Published: September 2022

AbstractInvestigating the impacts of globalization on vulnerable employment with a focus on sub‐Saharan African (SSA) women's job experience is in line with efforts towards achieving Sustainable Development Goal 8. We examined the impacts of social, economic, and political globalization, as well as de facto and de jure conditions, in explaining the proportion of women working in vulnerable jobs in SSA. Using the instrumental variable generalized method of moment approach with panel data from 37 SSA countries for the period 2000–2016, we found de facto/de jure globalization conditions to have positive/negative impacts on the proportion of women in vulnerable employment in SSA. Furthermore, estimates from disaggregated globalization indices indicate that both economic de facto and social de facto globalization conditions had negative impacts whereas political globalization had positive impacts on our subject matter. Developing inclusive socioeconomic policies that promote women's welfare in SSA would therefore necessitate political reforms as well as policies that support improvements in women's economic and social conditions.
Risk‐reducing strategies after a product‐harm crisis: The moderating role of controllability attribution
Authors: Zhimei Yuan , Yi Guo 
Published: September 2022

AbstractExtant research on crisis communication underexplored firm responses in terms of risk‐reducing strategies. When a product‐harm crisis occurs, a focal firm can use strategies targeted at repairing the damage that has already happened (i.e., to reduce consequence) or preventing the recurrence of the crisis (i.e., to reduce recurrence likelihood) to mitigate potential damage and assuage public concern. This paper reveals that the effectiveness of risk‐reducing strategies is influenced by consumers' controllability attribution. Controllability attribution refers to whether or not consumers perceive that a focal firm could have prevented an event from happening. Results of the study indicate that consequence‐reducing strategies lead to better attitudes, but not greater worry reduction than likelihood‐reducing strategies when controllability attribution is low. However, likelihood‐reducing strategies result in greater worry reduction, but not better attitudes than consequence‐reducing strategies when controllability attribution is high. Message credibility perceptions fully mediate the effects of risk‐reducing strategies on attitudes and worry reduction in the case of low firm controllability. The results highlight the role of controllability attribution in affecting the relative effectiveness of the two risk‐reducing strategies.
The characterization of disperse dyes in polyester fibers using DART mass spectrometry
Authors: Millbern Zoe , Vinueza Nelson R. 
Published: September 2022

AbstractTextile fibers alone are highly prevalent in our environment, and not only are there a wide variety of fibers, but generally, consumer textiles are colored. Given the variety of crime locations where dyes are encountered and the potential circumstances, a rapid, preparation free analysis of samples is highly beneficial. This study has characterized a collection of commercially available textiles dyes by verifying the chemical structure, collecting reference spectra, and developing a method to analyze dyed fibers via Direct Analysis in Real‐Time (DART) mass spectrometry. A methodology for direct analysis of pieces of fabric and single thread samples of polyester fibers dyed with disperse dyes was developed. The presence of 31 target dyes on fibers whose structures were previously established via high‐resolution mass spectrometry was confirmed. Dyed fabrics containing mixtures of dyes in varying concentrations were also evaluated to determine whether each dye in the composition could be detected. The DART‐MS methodology was sensitive and positively characterized disperse dyes in polyester fibers, allowing for blind identification of mixtures with the assistance of a high‐resolution mass spectrometry database.
Virtual navigation bronchoscopy‐guided intraoperative indocyanine green localization in simultaneous surgery for multiple pulmonary nodules
Authors: Yang Qingjie , Han Kaibao , Lv Shenghua , Li Qingtian , Sun Xiaoyan , Feng Xinhai , Kang Mingqiang 
Published: September 2022

AbstractBackgroundAccurate localization of pulmonary nodules is the main difficulty experienced in wedge resection. Commonly used localization methods have their own advantages and disadvantages. However, clinical work has demonstrated that intraoperative indocyanine green localization under electromagnetic navigation bronchoscopy/virtual navigation bronchoscopy (VNB) is more advantageous than conventional methods for patients with multiple pulmonary nodules undergoing simultaneous surgery, especially for those undergoing bilateral lung surgery.MethodsData of patients undergoing simultaneous surgery for multiple pulmonary nodules with preoperative methylene blue localization by computed tomography (CT)‐guided percutaneous lung puncture (methylene blue group) or intraoperative indocyanine green localization under VNB (virtual navigation group) were retrospectively analyzed. Patient characteristics, pulmonary nodule features, localization time, preoperative location time, location success rate, operation time, complication incidence, visceral pleural staining rate after localization, and pulmonary nodule primary resection success rate were compared between the two groups.ResultsThe methylene blue and virtual navigation groups comprised 39 and 20 patients with 119 and 67 pulmonary nodules resected, respectively. Sex, age, number of pulmonary nodules resected simultaneously, unilateral/bilateral lung surgery, pulmonary nodule size, distance between pulmonary nodules and the visceral pleura, pulmonary nodule consolidation‐to‐tumor ratio, location of pulmonary nodules in the pulmonary lobe, postoperative pathology, visceral pleura staining rate, primary pulmonary nodule resection success rate, and surgical duration did not differ significantly between the groups (p > 0.05). The localization time of the virtual navigation group was significantly shorter than that of the methylene blue group (p < 0.05), regardless of unilateral or bilateral multiple nodules. In the methylene blue group, 25.64% (10/39) of patients presented complications, all of which were pneumothorax, whereas no complications were found in the virtual navigation group.ConclusionsFor patients with multiple pulmonary nodules undergoing simultaneous surgery, indocyanine green injection under VNB can achieve a similar effect on pulmonary nodule localization as classical methylene blue injection under CT‐guided percutaneous lung puncture, with shorter localization time and fewer complications.
Balancing structural complexity with ecological insight in Spatio‐temporal species distribution models
Authors: Laxton Megan R. , Rodríguez de Rivera Óscar , Soriano‐Redondo Andrea , Illian Janine B. 
Published: September 2022

Abstract

The potential for statistical complexity in species distribution models (SDMs) has greatly increased with advances in computational power. Structurally complex models provide the flexibility to analyse intricate ecological systems and realistically messy data, but can be difficult to interpret, reducing their practical impact. Founding model complexity in ecological theory can improve insight gained from SDMs.

Here, we evaluate a marked point process approach, which uses multiple Gaussian random fields to represent population dynamics of the Eurasian crane Grus grus in a spatio‐temporal species distribution model. We discuss the role of model components and their impacts on predictions, in comparison with a simpler binomial presence/absence approach. Inference is carried out using Integrated Nested Laplace Approximation (INLA) with inlabru, an accessible and computationally efficient approach for Bayesian hierarchical modelling, which is not yet widely used in SDMs.

Using the marked point process approach, crane distribution was predicted to be dependent on the density of suitable habitat patches, as well as close to observations of the existing population. This demonstrates the advantage of complex model components in accounting for spatio‐temporal population dynamics (such as habitat preferences and dispersal limitations) that are not explained by environmental variables. However, including an AR1 temporal correlation structure in the models resulted in unrealistic predictions of species distribution; highlighting the need for careful consideration when determining the level of model complexity.

Increasing model complexity, with careful evaluation of the effects of additional model components, can provide a more realistic representation of a system, which is of particular importance for a practical and impact‐focused discipline such as ecology (though these methods extend to applications for a wide range of systems). Founding complexity in contextual theory is not only fundamental to maintaining model interpretability but can be a useful approach to improving insight gained from model outputs.
Migration Mapper: Identifying movement corridors and seasonal ranges for large mammal conservation
Authors: Merkle Jerod A. , Gage Josh , Sawyer Hall , Lowrey Blake , Kauffman Matthew J. 
Published: September 2022

Abstract

Modern tracking technology has facilitated a novel understanding of terrestrial mammal movement while revealing that movements are being truncated and lost. The first step towards conserving mobile animals is identifying movement corridors and key seasonal ranges. Yet, the identification and subsequent mapping of these important areas has remained a challenge due to the analytical skills necessary to conduct such analyses.

Migration Mapper (MM) is a user‐friendly software that provides tools to analyse global positioning system (GPS) collar data to create season‐specific, population‐level polygons representing areas where most of a population moves (i.e. movement corridors) and areas where most of a population spends time (e.g. high‐use areas, seasonal ranges).

MM consists of six standalone modules including data cleaning and review, seasonal movement delineation, movement model application, calculation of population‐level outputs and visualization of results.

Analysis of GPS data using MM can provide the spatial polygons necessary to facilitate conservation and policy planning. New initiatives at the local and global levels are already beginning to use MM to facilitate conservation of large, terrestrial mammals.
The role of the peat seed bank in plant community dynamics of a fire‐prone New Zealand restiad bog
Authors: Wilson Clara Renée , Lusk Christopher H. , Campbell David Ian 
Published: September 2022

AbstractNew Zealand restiad bogs have histories of natural fire, which is reflected in the presence of plant species with adaptations such as serotiny and fire‐stimulated flowering. The possibility of fire‐cued germination has not been investigated in restiad bogs, despite its widespread occurrence in other fire‐prone environments, globally. We performed a glasshouse experiment to assess the role of peat seed banks in post‐fire regeneration at Kopuatai Bog in northern New Zealand. Peat samples collected were either (a) heated until they reached 70 °C, (b) exposed to wood smoke for 30 min, (c) heated and smoked consecutively, or (d) left untreated. The emergence of vascular plants was then monitored for 105 days in a glasshouse. Mean seedling density was highest in the control treatment (7228 ± SE 1040 m−2); it was lowest in the heated samples, suggesting that the heat treatment may have been excessive. Smoke did not significantly increase emergence. Epacris pauciflora accounted for 76.7% of total seedlings, consistent with our hypothesis based on vegetation surveys that this species relies on synchronous post‐fire seed bank germination. E. pauciflora was most abundant in the control, suggesting that emergence is in response to some disturbance‐related cue other than heat or smoke. The restiad Sporadanthus ferrugineus was abundant in the control and smoke treatments. Its emergence following heating was reduced, but still considerable enough to cast doubt on its classification as a fire‐sensitive species. In contrast, the dominant peat‐forming restiad Empodisma robustum showed low levels of emergence. Our overall findings demonstrate that substantial quantities of viable seed are stored in the upper peat layers of a restiad bog and are capable of germinating in response to disturbance‐related environmental changes. These findings contribute to our understanding of restiad peatland plant community dynamics, particularly explaining the mechanism behind increased E. pauciflora dominance post‐fire.
Antimicrobial resistance in patients with endodontic infections: A systematic scoping review of observational studies
Authors: Ardila Carlos‐M. , Bedoya‐García Jader‐Alexander , González‐Arroyave Daniel 
Published: September 2022

AbstractThe aim of this study was to assess the prevalence and proportions of antimicrobial‐resistant species in patients with endodontic infections. A systematic scoping review of scientific evidence was accomplished involving different databases. Nine investigations were selected including 651 patients. Enterococcus faecalis was resistant to tetracycline (30%–70%), clindamycin (100%), erythromycin (10%–20%), ampicillin (9%) and azithromycin (60%). On the contrary, Prevotella spp., Fusobacterium spp., Peptostreptococcus spp. and Streptococcus spp. were resistant to penicillin, tetracycline, doxycycline, ciprofloxacin, amoxicillin, erythromycin, metronidazole and clindamycin in different proportions. Fusobacterium nucleatum showed high resistance to amoxicillin, amoxicillin plus clavulanate and erythromycin. Prevotella oralis presented a predisposition to augment its resistance to clindamycin over time. Tanerella forsythia exhibited resistance to ciprofloxacin and rifampicin. Lactococcus lactis presented robust resistance to cephalosporins, metronidazole, penicillin, amoxicillin and amoxicillin–clavulanic acid. It was observed high levels of resistance to antimicrobials that have been utilised in the local and systemic treatment of oral cavity infections.