bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding advances agricultural invertebrate biomonitoring by enhancing resolution, increasing throughput and facilitating network inference
Authors: Hawthorne Ben S. J. , Cuff Jordan P. , Collins Larissa E. , Evans Darren M. 
Published: May 2024

Abstract
Biomonitoring of agriculturally important insects is increasingly vital given our need to understand: (a) the severity of impacts by pests and pathogens on crop yield and health and (b) the impact of environmental change and land management on insects, in line with sustainable development and global conservation targets.
Traditional entomological traps remain an important part of the biomonitoring toolbox, but sample processing is laborious and introduces latency, and accuracy can be variable. The integration of molecular techniques such as environmental DNA and DNA metabarcoding into insect biomonitoring has gained increasing attention, but the advantages of doing so, the kind of data this can generate, and how easily and effectively molecular analyses can be integrated with the diverse types of entomological traps currently used remains relatively unclear.
In this review, we examine how combining DNA metabarcoding with a range of conventional and unconventional entomological sampling techniques can advance biomonitoring in a way that is useful to researchers and practitioners. We highlight some of the key challenges and how to mitigate them, using examples of its integration with different sampling methods from the literature (e.g., interception, pitfall and sticky traps) to demonstrate efficacy and suitability.
We discuss how metabarcoding data can be used to infer ecological networks, emphasizing the importance of this as a framework for understanding species interactions and ecosystem functioning for more effective and descriptive biomonitoring.
Finally, future advances in biomonitoring are highlighted, alongside recommendations of best practice for researchers both new to and experienced in invertebrate biomonitoring with metabarcoding.
Dynamic linkages in agricultural and energy markets: A quantile impulse response approach
Authors: Wang Linjie , Chavas Jean‐Paul , Li Jian 
Published: May 2024

AbstractThis article investigates the dynamic linkages between agricultural and energy markets, with a focus on an econometric analysis of multivariate stochastic dynamics based on the joint distribution of state variables. The analysis relies on a quantile approach followed by the evaluation of a copula. Applied to nonlinear price dynamics, the approach is flexible and supports a general evaluation of impulse response functions representing how prices adjust over time and across markets in response to a given shock. The analysis allows for arbitrary distribution functions; it captures own‐price and cross‐price dynamics that can depend on the nature of shocks; and it also allows current changes to affect all moments of the future price distributions. The usefulness of the approach is illustrated in an econometric investigation of dynamic linkages in US corn, ethanol, and crude oil markets. We show how price adjustments can vary across quantiles, reflecting different speeds of adjustments depending on market conditions. We find evidence of nonlinear dynamics specific to the tails of the price distributions. We uncover evidence of positive contemporaneous codependence, especially tail dependence. We show how price shocks affect mean, variance, skewness as well as kurtosis of future price distributions. These results stress the importance of going beyond a standard mean‐variance analysis. They also shed new light on the deep linkages existing in the food‐fuel nexus.
Genetic predictors for bacterial vaginosis in women living with and at risk for HIV infection
Authors: Murphy Kerry , Shi Quihu , Hoover Donald R. , Adimora Adaora A. , Alcaide Maria L. , Brockmann Susan , Daubert Elizabeth , Duggal Priya , Merenstein Daniel , Dionne Jodie A. , Sheth Anandi N. , Keller Marla J. , Herold Betsy C. , Anastos Kathryn , Aouizerat Bradley 
Published: May 2024

AbstractProblemBacterial vaginosis (BV) disproportionally impacts Black and Hispanic women, placing them at risk for HIV, sexually transmitted infections and preterm birth. It is unknown whether there are differences by genetic ancestry in BV risk or whether polymorphisms associated with BV risk differ by ancestry.MethodsWomen's Interagency HIV Study (WIHS) participants with longitudinal Nugent scores were dichotomized as having (n = 319, Nugent 7–10) or not having BV (n = 367, Nugent 0–3). Genetic ancestry was defined by clustering of principal components from ancestry informative markers and further stratified by BV status. 627 single nucleotide polymorphisms (SNPs) across 41 genes important in mucosal defense were identified in the WIHS GWAS. A logistic regression analysis was adjusted for nongenetic predictors of BV and self‐reported race/ethnicity to assess associations between genetic ancestry and genotype.ResultsSelf‐reported race and genetic ancestry were associated with BV risk after adjustment for behavioral factors. Polymorphisms in mucosal defense genes including syndecans, cytokines and toll‐like receptors (TLRs) were associated with BV in all ancestral groups.ConclusionsThe common association of syndecan, cytokine and TLR genes and the importance of immune function and inflammatory pathways in BV, suggests these should be targeted for further research on BV pathogenesis and therapeutics.
Longitudinal peanut and Ara h 2 specific‐IgE, ‐IgG4, and ‐IgG4/‐IgE ratios are associated with the natural resolution of peanut allergy in childhood
Authors: Parker Kayla M. , Dang Thanh D. , Wijesuriya Rushani , Soriano Victoria X. , Lowe Adrian J. , Dharmage Shyamali C. , Loke Paxton , Tang Mimi L. K. , Allen Katie J. , Koplin Jennifer J. , Perrett Kirsten P. , Peters Rachel L. 
Published: May 2024

AbstractBackgroundThere are no studies of longitudinal immunoglobulin measurements in a population‐based cohort alongside challenge‐confirmed peanut allergy outcomes. Little is known about biomarkers for identifying naturally resolving peanut allergy during childhood.ObjectivesTo measure longitudinal trends in whole peanut and component Ara h 2 sIgE and sIgG4 in the first 10 years of life, in a population cohort of children with challenge‐confirmed peanut allergy, and to determine whether peanut‐specific immunoglobulin levels or trends are associated with peanut allergy persistence or resolution by 10 years of age.MethodsOne‐year‐old infants with challenge‐confirmed peanut allergy (n = 156) from the HealthNuts study (n = 5276) were prospectively followed at ages 4, 6, and 10 years with questionnaires, skin prick tests, oral food challenges, and plasma total‐IgE, sIgE and sIgG4 to peanut and Ara h 2.ResultsPeanut allergy resolved in 33.9% (95% CI = 25.3%, 43.3%) of children by 10 years old with most resolving (97.4%, 95% CI = 86.5%, 99.9%) by 6 years old. Decreasing Ara h 2 sIgE (p = .01) and increasing peanut sIgG4 (p < .001), Ara h 2 sIgG4 (p = .01), peanut sIgG4/sIgE (p < .001) and Ara h 2 sIgG4/sIgE (p < .001) from 1 to 10 years of age were associated with peanut allergy resolution. Peanut sIgE measured at 1 year old had the greatest prognostic value (AUC = 0.75 [95% CI = 0.66, 0.82]); however, no single threshold produced both high sensitivity and specificity.ConclusionOne third of infant peanut allergy resolved by 10 years of age. Decreasing sIgE and sIgG4 to peanut and Ara h 2 over time were associated with natural resolution of peanut allergy. However, biomarker levels at diagnosis were not strongly associated with the natural history of peanut allergy.
Quality of life following laparoscopic totally extraperitoneal repair of a unilateral reducible inguinal hernia
Authors: Chuah Jun Sen , Siow Sze Li , Bujang Mohamad Adam 
Published: May 2024

AbstractBackgroundLaparoscopic totally extraperitoneal (TEP) inguinal hernia repair has become increasingly favored over open Lichtenstein tension‐free mesh repair owing to its associated benefits, including reduced postoperative pain, early return to normal activities, and a comparable recurrence rate. In recent years, emphasis has been placed on patient‐reported outcomes, particularly health‐related quality of life (QOL), as a critical metric for evaluating surgical success. This study aimed to evaluate the overall QOL following laparoscopic TEP repair of unilateral inguinal hernia.MethodsThis prospective study enrolled patients aged 18 years or older who underwent elective laparoscopic TEP hernia repair for unilateral inguinal hernia from April 2020 to March 2022. Data collected include demographic details, hernia characteristics, postoperative complications, and postoperative QOL assessment. The Short Form 36 Health Survey Version 2 (SF‐36v2), a validated general QoL questionnaire, was administered preoperatively and at 1 month, 6 months, and 1 year postoperatively. Statistical analysis utilized paired t‐tests for comparisons, with significance set at a p‐value <.05.ResultsA cohort of 49 patients, with a mean (standard deviation) age of 56.7 (14.0) years, predominantly comprising 47 men, was available for evaluation. Complications were observed in three (6.1%) of cases, with seroma/hematoma occurring in two patients and a wound infection necessitating antibiotic treatment in one patient. Notably, there were no instances of recurrence during the study period. Postoperative assessments revealed significant improvements in both physical and mental health at 1 month, with continued improvement noted up to 12 months.ConclusionLaparoscopic TEP inguinal hernia repair has been shown to improve both physical and mental health in patients with unilateral reducible inguinal hernia, with the majority of the improvement typically occurring within the initial month following surgery. It is crucial to communicate these improvement trends to patients undergoing hernia repair to help manage their expectations effectively.
A fine‐scale genetic map of the Japanese population
Authors: Takayama Jun , Makino Satoshi , Funayama Takamitsu , Ueki Masao , Narita Akira , Murakami Keiko , Orui Masatsugu , Ishikuro Mami , Obara Taku ,   the Tohoku Medical Megabank Project Study Group, Kuriyama Shinichi , Yamamoto Masayuki , Tamiya Gen 
Published: May 2024

AbstractGenetic maps are fundamental resources for linkage and association studies. A fine‐scale genetic map can be constructed by inferring historical recombination events from the genome‐wide structure of linkage disequilibrium—a non‐random association of alleles among loci—by using population‐scale sequencing data. We constructed a fine‐scale genetic map and identified recombination hotspots from 10 092 551 bi‐allelic high‐quality autosomal markers segregating among 150 unrelated Japanese individuals whose genotypes were determined by high‐coverage (30×) whole‐genome sequencing, and the genotype quality was carefully controlled by using their parents' and offspring's genotypes. The pedigree information was also utilized for haplotype phasing. The resulting genome‐wide recombination rate profiles were concordant with those of the worldwide population on a broad scale, and the resolution was much improved. We identified 9487 recombination hotspots and confirmed the enrichment of previously known motifs in the hotspots. Moreover, we demonstrated that the Japanese genetic map improved the haplotype phasing and genotype imputation accuracy for the Japanese population. The construction of a population‐specific genetic map will help make genetics research more accurate.
Accuracy of digital and conventional implant‐level impression techniques for maxillary full‐arch screw‐retained prosthesis: A crossover randomized trial
Authors: Jasim Ammar Ghanim , Abo Elezz Mona Galal , Altonbary Gilan Y. , Elsyad Moustafa Abdou 
Published: May 2024

AbstractObjectivesThis study aimed to compare the accuracy of implant‐level conventional and digital impressions for atrophied maxillary ridges.Materials and MethodsTwelve participants with atrophied edentulous maxillary ridges received six implants. Six months later and after soft tissue maturation around healing abutments, a control cast was constructed using the final passive restoration for each patient. Two types of implant‐level impression techniques were carried out for each patient: (1) conventional (splinted open‐tray) impression technique and (2) digital impression technique. For both techniques, scan bodies were labeled from the most distal implant on the left side (A, B, C, D, E, and F) and scanning was made. Accuracy of both techniques was measured using in vitro (two‐dimensional and three‐dimensional) and in vivo (clinical) methods. Two‐dimensional methods include measurement of the difference in linear distances AB, AC AD, AE, and AF. Geomagic software was used to assess the three‐dimensional deviation between the two impression techniques using the superimposition of standard tessellation language files. The incidence and percentage of nonpassive frameworks and framework misfits of final restorations for both types of impression techniques were assessed using the single screw test.ResultsFor all distances, digital impressions recorded significantly higher deviation from control measurements than conventional impressions. The highest two‐dimensional linear deviation was noted for AF distance and the lowest difference was noted for AB distance. For all scan bodies, digital impressions recorded significantly higher three‐dimensional deviation than conventional impressions. The highest three‐dimensional deviation was noted with scan bodies C and D. Digital impressions recorded a significantly higher incidence of nonpassive frameworks and framework misfits than conventional impressions. [Correction added on 11 June 2024, after first online publication: In the preceding sentence, “digital impressions” was changed to “conventional impressions” in this version.]ConclusionWithin the limitations of this study, it could be concluded that the conventional implant‐level impression technique showed greater in vitro and in vivo accuracy than the digital impression technique when used for full‐arch maxillary fixed restorations on inclined implants.
An 18F‐FDG‐PET/CT‐based radiomics signature for estimating malignance probability of solitary pulmonary nodule
Authors: Zheng Jingchi , Hao Yue , Guo Yan , Du Ming , Wang Pengyuan , Xin Jun 
Published: May 2024

AbstractBackgroundSome solitary pulmonary nodules (SPNs) as early manifestations of lung cancer, it is difficult to determine its nature, which brings great trouble to clinical diagnosis and treatment. Radiomics can deeply explore the essence of images and provide clinical decision support for clinicians. The purpose of our study was to explore the effect of positron emission tomography (PET) with 2‐deoxy‐2‐[fluorine‐18] fluoro‐d‐glucose integrated with computed tomography (CT; 18F‐FDG‐PET/CT) combined with radiomics for predicting probability of malignancy of SPNs.MethodsWe retrospectively enrolled 190 patients with SPNs confirmed by pathology from January 2013 to December 2019 in our hospital. SPNs were benign in 69 patients and malignant in 121 patients. Patients were randomly divided into a training or testing group at a ratio of 7:3. Three‐dimensional regions of interest (ROIs) were manually outlined on PET and CT images, and radiomics features were extracted. Synthetic minority oversampling technique (SMOTE) method was used to balance benign and malignant samples to a ratio of 1:1. In the training group, least absolute shrinkage and selection operator (LASSO) regression analyses and Spearman correlation analyses were used to select the strongest radiomics features. Three models including PET model, CT model, and joint model were constructed using multivariate logistic regression analysis. Receiver operating characteristic (ROC) curves, calibration curves, and decision curves were plotted to evaluate diagnostic efficiency, calibration degree, and clinical usefulness of all models in training and testing groups.ResultsThe estimative effectiveness of the joint model was superior to the CT or PET model alone in the training and testing groups. For the joint model, CT model, and PET model, area under the ROC curve was 0.929, 0.819, 0.833 in the training group, and 0.844, 0.759, 0.748 in the testing group, respectively. Calibration and decision curves showed good fit and clinical usefulness for the joint model in both training and testing groups.ConclusionRadiomics models constructed by combining PET and CT radiomics features are valuable for distinguishing benign and malignant SPNs. The combined effect is superior to qualitative diagnoses with CT or PET radiomics models alone.
Risk and prognosis of secondary lung cancer after radiation therapy for thoracic malignancies
Authors: Chen Kang , Liu Chong , Li Xueman , Chen Tianyou , Liu Shan , Xiong Fei , Zhang Zhou 
Published: May 2024

AbstractObjectiveRadiation therapy (RT) may increase the risk of second cancer. This study aimed to determine the association between exposure to radiotherapy for the treatment of thoracic cancer (TC) and subsequent secondary lung cancer (SLC).Materials and MethodsThe Surveillance, Epidemiology, and End Results (SEER) database (from 1975 to 2015) was queried for TC. Univariate Cox regression analyses and multiple primary standardized incidence ratios (SIRs) were used to assess the risk of SLC. Subgroup analyses of patients stratified by latency time since TC diagnosis, age at TC diagnosis, and calendar year of TC diagnosis stage were also performed. Overall survival and SLC‐related death were compared among the RT and no radiation therapy (NRT) groups by using Kaplan–Meier analysis and competitive risk analysis.ResultsIn a total of 329 129 observations, 147 847 of whom had been treated with RT. And 6799 patients developed SLC. Receiving radiotherapy was related to a higher risk of developing SLC for TC patients (adjusted HR, 1.25; 95% CI, 1.19–1.32; P < 0.001). The cumulative incidence of developing SLC in TC patients with RT (3.8%) was higher than the cumulative incidence (2.9%) in TC patients with NRT(P). The incidence risk of SLC in TC patients who received radiotherapy was significantly higher than the US general population (SIR, 1.19; 95% CI, 1.14–1.23; P < 0.050).ConclusionsRadiotherapy for TC was associated with higher risks of developing SLC compared with patients unexposed to radiotherapy.
Listening to the response of bat and bush‐cricket communities to management regimes of powerline clearings
Authors: Thibault Martin , Garnier Lisa K. M. , Kauffmann Cyprian , Bas Yves , Kerbiriou Christian 
Published: May 2024

AbstractLinear transportation infrastructures (LTIs) are established drivers of habitat fragmentation and barrier effects. Yet, they represent an increasing surface of managed seminatural habitats where increased consideration of biodiversity outputs is needed in an era of global biodiversity decline. A combined effort by both scientists and stakeholders is, therefore, needed to evaluate the promises and limits of these alternatives so that they best achieve their conservation potential. Our study explores the effects of forest powerline clearings on biodiversity, as well as the potential benefits of integrated vegetation management (IVM) as alternatives to clear‐cuts. We recorded the acoustic activity at 35 pairs of forest/clearing stations in two forested regions of France in 2021. Our results suggest that powerline clearings represent increased movement opportunities for bats and, most particularly, edge‐foraging species. They also provide suitable habitats for bush‐cricket species, particularly species requiring thermophilic conditions. We detected no direct benefit from IVM on bat communities. However, bush‐cricket communities appeared richer, more acoustically active, and statistically different from adjacent forests in clearings favoring secondary vegetation compared with clear‐cut ones. This collaborative study provides data on understudied taxa in the context of LTIs and sheds light on conservation promises and limits associated with their management.
Management of loperamide‐related opioid use disorder with buprenorphine within an Australian context: A case report
Authors: Dunn Andrew , Wu Nicholas , Cordaro Frank 
Published: May 2024

AbstractLoperamide is an over‐the‐counter peripheral mu‐opioid agonist commonly used to manage diarrhoea. When taken in an excessive dose, loperamide's penetration of the central nervous system increases, leading to euphoria, respiratory depression and other opioid effects. A health warning was released in the United States in 2016 with increased reports of excessive loperamide use leading to cardiac conduction abnormalities such as ventricular tachycardia, prolonged QTc and Torsades des Pointes. The growing number of cases is likely due to the increased restrictions on other opioids. Loperamide use disorder has been managed effectively in the United States and the United Kingdom using buprenorphine. In Australia, there have been recent opioid restrictions limiting easy access to opioids. We describe the case of a 28‐year‐old male who was admitted to hospital on multiple occasions with symptoms relating to loperamide use disorder. Buprenorphine was used to manage withdrawal symptoms in the hospital and maintain abstinence from loperamide in the community through an opioid agonist treatment program. To our knowledge, this is the first case study to describe the successful management of loperamide use disorder with buprenorphine within Australia. Our findings suggest that buprenorphine can be used to manage patients with loperamide associated withdrawal and help them remain abstinent upon discharge. Extramedical use of over‐the‐counter opioid medication may be becoming an emerging trend in Australia, and increased monitoring is warranted to prevent detrimental health outcomes.