bluuebunny/crossref_metadata_2025_split huggingface dataset:
miaSim: an R/Bioconductor package to easily simulate microbial community dynamics
Authors: Gao Yu , Şimşek Yağmur , Gheysen Emma , Borman Tuomas , Li Yi , Lahti Leo , Faust Karoline , Garza Daniel Rios 
Published: May 2023

Abstract

Microbiomes never stop changing. Their compositions and functions are shaped by the complex interplay of intrinsic and extrinsic drivers, such as growth and migration rates, species interactions, available nutrients and environmental conditions. Mathematical models help us make sense of these complex drivers and intuitively explain how, why and when specific microbiome states are reached while others are not. To make simulations of microbiome dynamics intuitive and accessible, we present miaSim.

miaSim provides users with a wide range of possibilities to match their specific assumptions and scenarios, starting from a core implementation of four widely used models (namely the stochastic logistic model, MacArthur's consumer‐resource model, Hubbell's neutral model and the generalized Lotka‐Volterra model) and several of their derivations. The diverse model implementations share the same data structures and, whenever possible, share state variables, which significantly facilitates cross‐model combinations and comparisons.

We combined and simulated some published examples of microbiome models in miaSim and performed cross‐model comparisons and tested diverse model assumptions. Our examples illustrate the reliability, robustness and user‐friendliness of the package. In addition, miaSim is accompanied by miaSimShiny, which allows users to explore the parameter space of their models in real‐time in an intuitive graphical interface. miaSim is fully compatible with the ‘miaverse’, an R/Bioconductor framework for microbiome data science, allowing users to combine and compare model simulations with microbiome datasets. The stable version of miaSim is available through Bioconductor 3.15, and the version for future development is available at https://github.com/microbiome/miaSim. miaSimShiny is available at https://github.com/gaoyu19920914/miaSimShiny.

We anticipate that miaSim will significantly facilitate the task of simulating microbiome dynamics, highlighting the role of ecological simulations as important tools in microbiome data science.
Identification of multiple symptoms of huanglongbing by electronic nose based on the variability of volatile organic compounds
Authors: Xu Qian , Bai Junwen , Ma Lixin , Li Ziqi , Tan Bin , Sun Li , Cai Jianrong 
Published: May 2023

AbstractHuanglongbing (HLB) is highly contagious and cannot be cured, resulting in a decrease in the commercial value of citrus. Timely detection and removal of diseased trees is an effective way to reduce losses. Complex symptoms of HLB, such as nutrient deficiencies often accompany HLB; as a result effective and accurate identification of HLB remains a challenge. In this study, 175 volatile organic compounds (VOCs) were detected in three categories (healthy, HLB, and Zn‐deficiency) of samples using headspace solid‐phase microextraction gas chromatography–mass spectrometry (HS‐SPME‐GC/MS), highlighting the variability of VOCs present in different categories of samples. In order to simplify the testing steps and reduce the cost in practical agricultural production, a method based on electronic nose technology to collect VOCs from citrus leaves for HLB detection was proposed. Among them, limiting value features and linear discriminant analysis were identified as the best combination of feature extraction and pattern recognition methods. Multiple sets of comparison experiments were set up and the collection conditions of VOCs were optimized. The results showed that the best classification performance was achieved for a 0.2 g sample at a collection time of 20 min when the collection temperature was 40°C and the headspace volume was 200 mL. Four types of samples (healthy, HLB‐positive, Zn‐deficiency, Zn‐deficiency and HLB‐positive) were used for model reliability validation, with an accuracy of 97.79% for HLB samples for multiple symptoms (including HLB‐positive and Zn‐deficiency and HLB‐positive) identification. In addition, the accuracy of samples with a combined effect of Zn‐deficiency and HLB was 96.43%. The results show that the E‐nose‐based HLB detection method is conducive to suppressing the spread of HLB, which can ensure the quality of citrus products and reduce the economic loss to horticulturists, and has good practical value.
Lithic and stone industries of Bahra 1, an Ubaid‐related site in northern Kuwait
Authors: Kozłowski Stefan Karol , Białowarczuk Marcin 
Published: May 2023

AbstractBahra 1 is a large site in the north of the Arabian Peninsula that provided an assemblage of nearly 100,000 lithic artefacts. The whole lithic industry of Bahra 1 represents a set of well‐thought‐out flint, quartz and stone tools for the mass production of shell jewellery, with only a small share of typical household tools. They mostly relate to the Ubaid tradition with Arabian Neolithic influences. However, limited excavations of the oldest occupational layers of the site also revealed an Epipalaeolithic Zarzian tradition. This paper presents a techno‐typological, functional and cultural characteristic of the whole Bahra 1 chipped and ground stone industry identified during the excavations at the site in 2009–2019.
Rabies postexposure prophylaxis: What the U.S. emergency medicine provider needs to know
Authors: Gibbons Kyle , Dvoracek Kyle 
Published: May 2023

AbstractApproximately 55,000 patients per year in the United States are exposed to potentially rabid animals and receive rabies postexposure prophylaxis (PEP) and these patients commonly present to the emergency department (ED) for wound care and PEP. Despite the number of rabies exposures seen in EDs each year, there appears to be a knowledge gap among health care providers with regard to prescribing and administering rabies PEP. The following review aims to bridge that knowledge gap by discussing the importance of obtaining a comprehensive exposure history to determine the category of the encounter, the type of animal, and the location of the bite and of consulting outside expert resources to determine whether the rabies PEP series is indicated. In addition, this article will discuss dosing, administration, and schedule of the rabies vaccine and human rabies immune globulin to ensure patients are fully protected from developing rabies. Lastly, this article discusses the potential cost associated with rabies PEP and provides information on managing this barrier.
Binge drinking alcohol and circadian misalignment in night shift nurses is associated with decreased resiliency to COVID‐19 infection
Authors: Swanson Garth R. , Schwartz Benjamin A. , Joyce Cara , Keshavarzian Ali 
Published: May 2023

AbstractBackgroundNurses and other first responders are at high risk of exposure to the SARS‐CoV2 virus, and many have developed severe COVID‐19 infection. A better understanding of the factors that increase the risk of infection after exposure to the virus could help to address this. Although several risk factors such as obesity, diabetes, and hypertension have been associated with an increased risk of infection, many first responders develop severe COVID‐19 without established risk factors. As inflammation and cytokine storm are the primary mechanisms in severe COVID‐19, other factors that promote an inflammatory state could increase the risk of COVID‐19 in exposed individuals. Alcohol misuse and shift work with subsequent misaligned circadian rhythms are known to promote a pro‐inflammatory state and thus could increase susceptibility to COVID‐19. To test this hypothesis, we conducted a prospective, cross‐sectional observational survey‐based study in nurses using the American Nursing Association network.MethodWe used validated structured questionnaires to assess alcohol consumption (the Alcohol Use Disorders Identification Test) and circadian typology or chronotype (the Munich Chronotype Questionnaire Shift ‐MCTQ‐Shift).ResultsBy latent class analysis (LCA), high‐risk features of alcohol misuse were associated with a later chronotype, and binge drinking was greater in night shift workers. The night shift was associated with more than double the odds of COVID‐19 infection of the standard shift (OR 2.67, 95% CI: 1.18 to 6.07). Binge drinkers had twice the odds of COVID‐19 infection of those with low‐risk features by LCA (OR: 2.08, 95% CI: 0.75 to 5.79).ConclusionWorking night shifts or binge drinking may be risk factors for COVID‐19 infection among nurses. Understanding the mechanisms underlying these risk factors could help to mitigate the impact of COVID‐19 on our at‐risk healthcare workforce.
Early life experience with predators impacts development, behavior, and post‐translocation outcomes in an endangered amphibian
Authors: Hammond T. T. , Jacobs L. E. , Curtis M. J. , Trotman E. M. , Swaisgood R. R. , Shier D. M. 
Published: May 2023

AbstractPre‐release training is becoming a standard practice in conservation breeding and translocation programs for mammals and birds, but is still relatively neglected for herpetofauna, likely stemming from widespread beliefs that amphibians are “hard‐wired” and are thus predicted to benefit little from experiential learning. However, experience during development can drive both morphological and behavioral modifications that could benefit post‐translocation survival. Here, we developed an anti‐predator training program for the endangered mountain yellow‐legged frog Rana muscosa and evaluated its impact on morphometrics, developmental rates, behavior, and post‐release outcomes. Using a controlled, balanced factorial experimental design, we exposed individuals at two developmental stages (tadpoles and post‐metamorphic) to visual and olfactory cues from one of its principal predators, the two‐striped garter snake Thamnophis hammondii. We found that exposure to predators during the tadpole stage impacted tadpole development, morphology, and behavior. However, we found no evidence that post‐metamorphic behavior or post‐release outcomes were influenced by tadpole predator exposure, either on its own or in interaction with post‐metamorphic training treatments. Training of post‐metamorphic frogs, however, yielded evidence of learning, with downstream effects on behavior and apparent survival after release into the wild. Our findings produce novel insights on the value of anti‐predator training in amphibian conservation translocation programs, bolster recent evidence re‐evaluating the importance of learning and developmental experience for amphibian species, and provide guidance for selecting optimal developmental windows for training.
Dirty care in the transfronterizo experience: Walking with Mexicali/Calexico teachers through their youth
Authors: O'Donnell Jennifer Lee 
Published: May 2023

AbstractMany educators living near the United States and Mexico border were transfronterizo students—young people with familial and institutional ties to both countries, who crossed the border each day to attend United States schools. This study is concerned with how these teachers’ identities formed within distinct sociocultural contexts like the Borderlands and how this can serve education institutions invested in teacher identity work.
Effects of land cover changes and forest fragmentation on three species of east African mini‐antelopes
Authors: Said Mohamed K. , Misana Salome B. 
Published: May 2023

AbstractHuman beings have continued to decline and fragment mini‐antelopes habitats. We studied the effects of land cover change on the conservation of the endangered Ader's Duiker (Cephalophus adersi), the Zanzibar blue duiker (Cephalophus monticola sundevalli) and the Suni (Neotragus moschatus zanzibaricus) in Zanzibar, Tanzania. Data were obtained from the 1975, 2009 and 2014 satellite images and geographical information systems, focus group discussions, transect‐walk and observation. We found that the habitat of mini‐antelopes had declined from 87.3% to 58.5% between 1975 and 2014 and become fragmented. The forest fragments increased from 35 to 139 patches while shrubs increased from 41 to 199 patches. Community members had the perception that the decline and fragmentation of the habitat had caused the numbers of mini‐antelopes and their forage to decline. We also found that there were incidences of mini‐antelopes eating crop plants such as cowpeas, yams and tomatoes in the farms during the night as an adaptive mechanism for forage decline. Conclusively, land cover changes from human activities have caused negative effects on the mini‐antelopes. There is, therefore need for the local people, the government and private individuals or corporations to introduce collective conservation initiatives, including the establishment of conservation areas to conserve the mini‐antelopes.
Breeding and demographic aspects of Montemys delectorum, an East African endemic rodent
Authors: Gebrezgiher Genet B. , Meheretu Yonas , Katakweba Abdul A. S. , Sabuni Christopher , Makundi Rhodes H. 
Published: May 2023

AbstractMontemys delectorum is the only member of the genus Montemys within the family Muridae, which is an endemic rodent of the Eastern Africa Highlands. It is a threatened species due to habitat loss, and its current conservation status is uncertain. We studied the breeding pattern and population size of M. delectorum, two of the most important factors in understanding the conservation status of a species. Capture–mark–release studies were conducted from February 2021 to June 2022 in open patchy forests and dense forest habitats. Montemys delectorum showed bimodal breeding seasonality: a low rate for the short interval between December and February and a pronounced rate for May–July, following the high rainfall in April. This shows that rainfall promotes vegetation availability, which stimulates breeding activity and adds offspring to the population, resulting in increased population abundance. The population of M. delectorum is not stable in this landscape, as indicated by the significant differences in population size between the two forest types, with a significantly greater population in the patchy open forest. This indicates that the patchy open forest should be considered an essential refuge for the species.
Deep learning in optical coherence tomography: Where are the gaps?
Authors: Li Dawei , Ran An Ran , Cheung Carol Y. , Prince Jerry L. 
Published: May 2023

AbstractOptical coherence tomography (OCT) is a non‐invasive optical imaging modality, which provides rapid, high‐resolution and cross‐sectional morphology of macular area and optic nerve head for diagnosis and managing of different eye diseases. However, interpreting OCT images requires experts in both OCT images and eye diseases since many factors such as artefacts and concomitant diseases can affect the accuracy of quantitative measurements made by post‐processing algorithms. Currently, there is a growing interest in applying deep learning (DL) methods to analyse OCT images automatically. This review summarises the trends in DL‐based OCT image analysis in ophthalmology, discusses the current gaps, and provides potential research directions. DL in OCT analysis shows promising performance in several tasks: (1) layers and features segmentation and quantification; (2) disease classification; (3) disease progression and prognosis; and (4) referral triage level prediction. Different studies and trends in the development of DL‐based OCT image analysis are described and the following challenges are identified and described: (1) public OCT data are scarce and scattered; (2) models show performance discrepancies in real‐world settings; (3) models lack of transparency; (4) there is a lack of societal acceptance and regulatory standards; and (5) OCT is still not widely available in underprivileged areas. More work is needed to tackle the challenges and gaps, before DL is further applied in OCT image analysis for clinical use.
From dissonant dominance to synchronic sanctity: Relational extraction as counter‐resonance to extractivism
Authors: Woods James E. 
Published: May 2023

AbstractThere is a growing tendency within various disciplines of the humanities to conflate the terms extraction and extractivism. While the first word has many everyday uses—tooth extraction, vanilla “extract”—the latter term was specifically coined to identify a malevolent imaginary that indemnifies the removal of so‐called “resources,” especially when that displacement involves layers of violence and/or looks solely to satisfy a particular economic aim. Given these disparate denotations, the unqualified use of “extraction” synonymously with “extractivism” introduces unnecessary ambiguity, inviting divergent arguments that ultimately diminish an otherwise worthy discussion and losing sight of the grave issues that underlie the conversation's original intent. As such, this essay investigates the biblical origins of this false equivalency and suggests how this usage might be disentangled to properly recenter the malevolence its users are attempting to describe.
Selectivity ofBacillus thuringiensis(Bacillales: Bacillaceae) to the polyphagous predatorCeraeochrysa claveri(Navás, 1911) (Neuroptera: Chrysopidae)
Authors: Daquila Bruno Vinicius , Moi Dieison André , Scudeler Elton Luiz , Oliveira João Arthur dos Santos , Polanczyk Ricardo Antonio , Conte Helio 
Published: May 2023

AbstractBioinsecticides based onBacillus thuringiensis(Bt) are widely used to control agricultural pests. However, there are concerns about their impact on non‐target organisms, with for example, the green lacewingCeraeochrysa claveri, a polyphagous predator with important value in the biological control of insect pests in agroecosystems. This study aimed to analyse the effects of Agree®bioinsecticide (containing Bt serovaraizawaiGC‐91) on the post‐embryonic development ofC. claveri. For this, neonate larvae ofC. claveriwere fed withDiatraea saccharaliseggs contaminated with different concentrations of Agree®(0.62, 1.25, 2.50 and 5.00 g L−1) until their pupation. Samples of the midgut of larvae were collected for histological and ultrastructural analysis. The larval and pupal inviability data were collected at the end of the respective developmental stages. After the emergence of adult insects, were considered inviable those with morphological alterations. To evaluate the reproduction, adult insect couples were formed, and the oviposition was collected. No significant differences in the viability of eggs, larvae, pupae and adults ofC. clavericontaminated with Agree®were reported. Midgut analyses did not reveal cellular damage in the epithelium, indicating a possible lack of insecticidal proteins receptors. The oviposition and their viability were similar between treated and control groups. Our results demonstrated that Agree®bioinsecticide did not affect the post‐embryonic development ofC. claveri. This illustrates that the combined use of Bt andC. claverifor the biological control of arthropod pests can be a sustainable strategy for integrated pest management.
Identification of antibacterial activity of LEAP2 from Antarctic icefish Chionodraco hamatus
Authors: Fei Yueyue , Wang Qin , Lu Jigang , Ouyang Linyue , Li Wei , Hu Ruiqin , Chen Liangbiao 
Published: May 2023

AbstractLiver‐expressed antimicrobial peptide 2 (LEAP2) is a small peptide, which is consisted of signal peptide, pro‐peptide and the bioactive mature peptide. Mature LEAP2 is an antibacterial peptide with four highly conserved cysteines forming two intramolecular disulfide bonds. Chionodraco hamatus, an Antarctic notothenioid fish that lives in the coldest water, has white blood unlike most fish of the world. In this study, the LEAP2 coding sequence was cloned from C. hamatus, including a 29 amino acids signal peptide and mature peptide of 46 amino acids. High levels of LEAP2 mRNA were detected in the skin and liver. Mature peptide was obtained by chemical synthesis in vitro, displayed selective antimicrobial activities against Escherichia coli, Aeromonas hydrophila, Staphylococcus aureus and Streptococcus agalactiae. Liver‐expressed antimicrobial peptide 2 showed bactericidal activity by destroying the cell membrane integrity and robustly combined with bacterial genomic DNA. In addition, overexpression of the Tol‐LEAP2‐EGFP in zebrafish larva showed stronger antimicrobial activity in C. hamatus than in zebrafish, accompanied by lower bacterial load and expression of pro‐inflammatory factors. This is the first demonstration of the antimicrobial activity of LEAP2 from C. hamatus, which is of useful value in improving resistance to pathogens.
Testing a model for person‐centred pain management: A systematic review and synthesis guided by the Fundamentals of Care framework
Authors: Avallin Therese , Muntlin Åsa , Kitson Alison , Jangland Eva 
Published: May 2023

AbstractAimsTo test a model for person‐centred pain management using qualitative evidence in the literature and refine it based on the results.DesignA qualitative systematic review with thematic synthesis using the Fundamentals of Care framework.Methods and Data SourcesA literature search in February 2021 in six scientific databases: CINAHL, PsycInfo, Pubmed, Scopus, Social Science Premium Collection and Web of Science, reported using ENTREQ and PRISMA. Quality assessment was performed for the individual studies. Thematic analysis and the GRADE‐CERQual approach were used in the synthesis including the assessment of confidence in the evidence.ResultsThe model was tested against the evidence in 15 studies appraised with moderate or high quality and found represented in the literature but needed to be expanded. A refined model with a moderate/high confidence level of evidence presents elements to be used in a holistic care process; The nurse is guided to establish a trusting relationship with the patient and enable communication to identify and meet pain management needs using pharmacological and non‐pharmacological management. Nurse leaders are guided to support this process by providing the right contextual conditions.ConclusionsThe strengths of the confidence level in the refined model, and that it is represented from the nurse and patient perspectives in nursing research across countries and cultures, support our recommendation for empirical evaluation.Implications for the Profession and/or Patient CareThe model links the knowledge of pain management elements from individual studies together into actions to be performed in clinical practice. It also outlines the organizational support needed to make this happen. Nurses and nursing leaders are suggested to test the model to implement person‐centred pain management in clinical practice.Patient or Public ContributionNo patient or public contribution.ImpactWhat Problem Did the Study Address? There is a need to transfer available evidence of person‐centred pain management into practice to relieve the patient from pain. What Were the Main Findings? Person‐centred pain management is of high priority for patients and nurses around the world and can be performed in a holistic care process including patient–nurse trust and communication, supported by contextual conditions to deliver timely pharmacological and non‐pharmacological pain management addressing the patient's physical, psychosocial and relational care needs. Where and on Whom will the Research Have an Impact? The model is to be tested and evaluated in clinical practice to guide the providers to relieve the patient from pain.Reporting MethodRelevant EQUATOR guidelines were used to report the study: The Preferred Reporting Items for Systematic Reviews and Meta‐Analyses Statement.