bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying the best PCR enzyme for library amplification in NGS
Authors: Quail Michael A , Corton Craig , Uphill James , Keane Jacqueline , Gu Yong
Published: November 2022

Background

PCR amplification is a necessary step in many next generation sequencing (NGS) library preparation methods[1] [2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimised NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short read Illumina library preparation and long fragment amplification ahead of long-read sequencing.

Results

We tested over 20 different Hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) “Equinox” and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR free datasets. We also test a range of enzymes for long read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4kb respectively.

Conclusion

The enzymes of choice for short read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) “Equinox” and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long read sequencing.
Chronological aging impacts abundance, function and microRNA content of extracellular vesicles produced by human epidermal keratinocytes
Authors: Nedachi Taku , Bonod Christelle , Rorteau Julie , Chinoune Wafae , Ishiuchi Yuri , Hughes Sandrine , Gillet Benjamin , Sigaudo-Roussel Dominique , Lamartine Jérôme
Published: November 2022

The disturbance of intercellular communication is one of the hallmarks of aging. The goal of this study is to clarify the impact of chronological aging on extracellular vesicles (EVs), a key mode of communication in mammalian tissues. We focused on epidermal keratinocytes, the main cells of the outer protective layer of the skin which is strongly impaired in the skin of elderly. EVs were purified from conditioned medium of primary keratinocytes isolated from infant or aged adult skin. A significant increase of the relative number of EVs released from aged keratinocytes was observed whereas their size distribution was not modified. By small RNA sequencing, we described a specific microRNA (miRNA) signature of aged EVs with an increase abundance of miR-30a, a key regulator of barrier function in human epidermis. EVs from aged keratinocytes were found to be able to reduce the proliferation of young keratinocytes, to impact their organogenesis properties in a reconstructed epidermis model and to slow down the early steps of skin wound healing in mice, three features observed in aged epidermis. This work reveals that intercellular communication mediated by EVs is modulated during aging process in keratinocytes and might be involved in the functional defects observed in aged skin.
Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data
Authors: Popp Niclas , Stock Marco , Fiorentino Jonathan , Scialdone Antonio
Published: November 2022

In recent years, many algorithms for inferring gene regulatory networks from single-cell transcriptomic data have been published. Several studies have evaluated their accuracy in estimating the presence of an interaction between pairs of genes. However, these benchmarking analyses do not quantify the algorithms’ ability to capture structural properties of networks, which are fundamental, for example, for studying the robustness of a gene network to external perturbations. Here, we devise a three-step benchmarking pipeline called STREAMLINE that quantifies the ability of algorithms to capture topological properties of networks and identify hubs. To this aim, we use data simulated from different types of networks as well as experimental data from three different organisms. We apply our benchmarking pipeline to four algorithms and provide guidance on which algorithm should be used depending on the global network property of interest.
Genomics and Phenomics Enabled Prebreeding Improved Early-Season Chilling Tolerance in Sorghum
Authors: Marla Sandeep , Felderhoff Terry , Hayes Chad , Perumal Ramasamy , Wang Xu , Poland Jesse , Morris Geoffrey P.
Published: November 2022

In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index (NDVI) values from the chilling nested association mapping population detected CT QTL that colocialized with manual phenotyping CT QTL. Two of the four first-generation KASP molecular markers, generated using the peak QTL SNPs, failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomicFSTanalysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from two independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13–24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.
A secreted protease-like protein inZymoseptoria triticiis responsible for avirulence onStb9resistance gene in wheat
Authors: Amezrou Reda , Audéon Colette , compain Jérôme , Gélisse Sandrine , Ducasse Aurélie , Saintenac Cyrille , Lapalu Nicolas , Louet Clémentine , Orford Simon , Croll Daniel , Amselem Joëlle , Fillinger Sabine , Marcel Thierry C
Published: November 2022

Zymoseptoria triticiis the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factorAvrStb9using association mapping and functional validation approaches. PathotypingAvrStb9transgenic strains onStb9cultivars, near isogenic lines and wheat mapping populations, showed thatAvrStb9interacts withStb9resistance gene, triggering an immune response.AvrStb9encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector.AvrStb9is also conserved among a globalZ. triticipopulation and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.

Author Summary

Fungal avirulence (Avr) genes are involved in gene-for-gene relationships with host resistance genes.Avrgenes may at the same time target host defenses to allow infection and be recognized by a host resistance gene triggering a defense response. The fungusZymoseptoria triticicauses Septoria tritici blotch, a major disease of wheat worldwide.Z. triticipopulations rapidly adapt to selection pressures such as host resistance, leading to resistance breakdown. We report the identification of the avirulence geneAvrStb9based on genetic mapping, sequence polymorphisms and allele swapping.AvrStb9is involved in the interaction withStb9resistance gene following the gene-for-gene model, and its recognition hinders disease symptoms in hosts carrying the corresponding resistance gene. Unlike other knownZ. tritici Avreffectors,AvrStb9encodes for an unusually large Avr protein with a predicted protease S41 domain conserved among diverse ascomycete lineages. We also highlight several gene mutations likely involved in escapingStb9-mediated recognition.
Lysergic Acid Diethylamide Alters the Effects of Brain Stimulation in Rodents
Authors: Dwiel Lucas , Henricks Angela , Bragg Elise , Nicol Jeff , Gui Jiang , Doucette Wilder
Published: November 2022

Background

Psychedelic drugs have resurged in neuroscience and psychiatry with promising success in psychedelic-assisted therapy for the treatment of anxiety, depression, and addiction. At the cellular level, psychedelic drugs elicit neuroplastic processes 24 hours after administration, priming neural circuits for change. The acute effects of psychedelic drugs are well characterized with functional imaging and neural oscillations showing an increase in the entropy of spontaneous cortical activity.

Hypotheses

We hypothesized that cortical-striatal oscillations recorded in rats would confirm the effects of psychedelic drugs. We also hypothesized that brain stimulation delivered 24 hours after LSD administration would lead to different effects than brain stimulation alone.

Methods

We recorded local field potential (LFP) oscillations from rats following lysergic acid diethylamide (LSD) or saline administration and determined if exposure to these treatments altered the effect of a targeted intervention (brain stimulation) 24 hours later.

Results

We confirmed acutely decreased low frequency power across the brain when rats are given LSD. We also demonstrated these altered states return to baseline after 24 hours. Brain stimulation applied in the previously reported window of heightened neuroplasticity produced distinct shifts in brain state compared to brain stimulation applied 24 hours after saline.

Conclusions

Despite the acute effects of LSD disappearing after 24 hours, there are still latent effects that interact with brain stimulation to create larger and distinct changes in brain activity compared to brain stimulation alone. Our proof-of-concept findings are the first to suggest that psychedelic drugs could work in combination with brain stimulation to achieve enhanced effects on brain activity and future work will assess impacts on stimulation induced changes in behavior.
Learning the shape of protein micro-environments with a holographic convolutional neural network
Authors: Pun Michael N. , Ivanov Andrew , Bellamy Quinn , Montague Zachary , LaMont Colin , Bradley Philip , Otwinowski Jakub , Nourmohammad Armita
Published: November 2022

Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from structure remains a major challenge. Here, we introduce Holographic Convolutional Neural Network (H-CNN) for proteins, which is a physically motivated machine learning approach to model amino acid preferences in protein structures. H-CNN reflects physical interactions in a protein structure and recapitulates the functional information stored in evolutionary data. H-CNN accurately predicts the impact of mutations on protein function, including stability and binding of protein complexes. Our interpretable computational model for protein structure-function maps could guide design of novel proteins with desired function.
mRNA bivalent booster enhances neutralization against BA.2.75.2 and BQ.1.1
Authors: Davis-Gardner Meredith E. , Lai Lilin , Wali Bushra , Samaha Hady , Solis Daniel , Lee Matthew , Porter-Morrison Andrea , Hentenaar Ian Thomas , Yamamoto Fumiko , Godbole Sucheta , Douek Daniel C. , Lee Frances Eun-Hyung , Rouphael Nadine , Moreno Alberto , Pinsky Benjamin A. , Suthar Mehul S.
Published: November 2022

The emergence of the highly divergent SARS-CoV-2 Omicron variant has jeopardized the efficacy of vaccines based on the ancestral spike. The bivalent COVID-19 mRNA booster vaccine within the United States is comprised of the ancestral and the Omicron BA.5 spike. Since its approval and distribution, additional Omicron subvariants have been identified with key mutations within the spike protein receptor binding domain that are predicted to escape vaccine sera. Of particular concern is the R346T mutation which has arisen in multiple subvariants, including BA.2.75.2 and BQ.1.1. Using a live virus neutralization assay, we evaluated serum samples from individuals who had received either one or two monovalent boosters or the bivalent booster to determine neutralizing activity against wild-type (WA1/2020) virus and Omicron subvariants BA.1, BA.5, BA.2.75.2, and BQ.1.1. In the one monovalent booster cohort, relative to WA1/2020, we observed a reduction in neutralization titers of 9-15-fold against BA.1 and BA.5 and 28-39-fold against BA.2.75.2 and BQ.1.1. In the BA.5-containing bivalent booster cohort, the neutralizing activity improved against all the Omicron subvariants. Relative to WA1/2020, we observed a reduction in neutralization titers of 3.7- and 4-fold against BA.1 and BA.5, respectively, and 11.5- and 21-fold against BA.2.75.2 and BQ.1.1, respectively. These data suggest that the bivalent mRNA booster vaccine broadens humoral immunity against the Omicron subvariants.
Neurofluid Coupling during Sleep and Wake States
Authors: Nair Vidhya Vijayakrishnan , Kish Brianna R , Chong Pearlynne L H , Yang Ho-Ching (Shawn) , Wu Yu-Chien , Tong Yunjie , Schwichtenberg A. J.
Published: November 2022

Low-frequency changes in cerebral hemodynamics have recently been shown to drive cerebrospinal fluid (CSF) movement in the human brain during non-rapid eye movement (NREM) sleep and resting state wakefulness. However, whether the coupling strength between these neurofluids varies between wake and sleep states is not known. In addition, the principal origin (i.e., neuronal vs. systemic) of these slow cerebral hemodynamic oscillations in either state also remains unexplored. To investigate this, a wake/sleep study was conducted on eight young, healthy volunteers, concurrently acquiring neurofluid dynamics using functional Magnetic Resonance Imaging, neural activity using Electroencephalography, and non-neuronal systemic physiology with peripheral functional Near-Infrared Spectroscopy. Our results reveal that low-frequency cerebral hemodynamics and CSF movements are strongly coupled regardless of whether participants were awake or in light NREM sleep. Furthermore, it was also found that, while autonomic neural contributions are present only during light NREM sleep, non-neuronal systemic physiology influences neurofluid low-frquency oscillations in a significant way across both wake and sleep states. These results further our understanding regarding the low-frequency hemodynamic drivers of CSF movement in the human brain and could help inform the development of therapies for enhancing CSF circulation.
Mapping the literature of internal auditing in Europe: a systematic review and agenda for future research
Authors: Hazaea Saddam A. , Zhu Jinyu , Khatib Saleh F.A. , Elamer Ahmed A.
Published: November 2022

Purpose

Although many firms are investing considerable resources in building and designing strong and effective internal auditing (IA) to improve corporate governance and internal control processes, IA literature is still relatively fragmented. Therefore, this paper aims to provide a systematic review of studies on IA in 27 European countries and the UK.

Design/methodology/approach

Based on the Scopus database, 142 papers published between 1987 and 2022 were analyzed. This study focused on evaluating and analyzing the characteristics of literature and the themes investigated with a focus on four key aspects: governance, the effectiveness of IA, the relationship between internal auditors and other parties and risk management to provide directions for future research.

Findings

This study found that IA literature did not provide the integrated knowledge of internal audit functions (IAFs) and the factors that could contribute to their implementation as required. The results showed that the UK, Greece and Italy dominate the published literature in terms of the number of studies. There are a few studies that investigate IA in private institutions and nonprofit organizations. Interestingly, a vast majority of studies are not based on theoretical grounds. The results also showed that there is an absence of studies that discuss the impact of cultural and political systems as well as the demographic characteristics of auditors on the implementation of IAFs.

Originality/value

This study is useful for researchers, organizations and regulators because it contributes to the literature by highlighting the intellectual development of IA in the European countries and the UK, providing several directions for future studies. To the best of the authors’ knowledge, this research is the first study to use a systematic review approach in evaluating the intellectual development of IA research in European countries, identifying areas and elements that received less attention in previous studies and providing a roadmap for future studies.
Regulatory influence on sustainability reporting: evidence from Murray–Darling Basin Authority in Australia
Authors: Hossain Md Moazzem , Rana Tarek , Nahar Shamsun , Rahman Md Jahidur , Lema Aklema Choudhury
Published: November 2022

Purpose

The purpose of this study is to explore the sustainability reporting of a public sector organisation (PSO). This study focuses on socio-environmental practices of a major agro-economic platform in Australia – the Murray–Darling Basin Authority (MDBA) to provide a unique perspective on water resource management and sustainability.

Design/methodology/approach

This longitudinal qualitative case study collects published data from the MDBA’s annual reports over 21 years (1998–2018) and considers economic, social and environmental dimensions of sustainability using legitimacy and institutional theory.

Findings

This study finds that the MDBA’s sustainability reporting is influenced by its response to the Water Act 2007 and the Basin Plan 2012 regulations and to maintain its legitimacy with stakeholders. The MDBA wished to pursue sustainability through integrating these regulations complemented by stakeholder expectations. Although all categories increased in reporting, the environment category has the highest primacy in achieving a healthy basin through sustainable water management for the long-term benefit of the stakeholders.

Research limitations/implications

This study contributes to the PSOs sustainability reporting literature. Particularly, this study provides insights of sustainability reporting patterns and practices over a long period through a longitudinal study. This study contributes new knowledge on the awareness of PSOs sustainability practice which has implications for governments, regulators, policymakers, managers and other stakeholders.

Originality/value

The Australian PSOs setting is under-researched from the perspective of a regulatory framework. The MDBA case provides unique insights on water resource management and sustainability which has value for many countries around the world.
From talk to action: the effects of the non-financial reporting directive on ESG performance
Authors: Aluchna Maria , Roszkowska-Menkes Maria , Kamiński Bogumił
Published: November 2022

Purpose

Non-financial reporting (NFR) is viewed as a major step towards organisational transparency and accountability. While the number of non-financial reports published every year has been growing exponentially over the last two decades, their quality and effectiveness in managing environmental, social and governance (ESG) performance have been questioned. Addressing these concerns, several jurisdictions, including EU Member States, introduced mandatory NFR regimes. However, the evidence on whether such regulation truly translates into enhanced ESG performance remains scarce. This paper aims to fill this gap in the literature by investigating the impact of the EU’s Directive 2014/95/EU (Non-financial Reporting Directive, NFRD) on the ESG scores of Polish companies.

Design/methodology/approach

Drawing upon institutional and strategic perspectives on legitimacy theory, the authors test the relationship between the introduction of the NFRD and the ESG scores derived from the Refinitiv database, using a sample of all those companies listed on the Warsaw Stock Exchange whose disclosure allows for measuring ESG performance (yielding 171 firm-year observations from 43 companies).

Findings

This study’s findings show an improvement of ESG performance following the introduction of the NFRD. The difference-in-differences approach indicates that the improvement is larger for companies that are subject to the legislation when it comes to overall ESG performance, particularly for environmental and social performance. Nonetheless, to the best of the authors’ knowledge, no significant effect is found for performance in the governance dimension.

Originality/value

This study investigates the role of transnational mandatory reporting regulation in the first years of its enactment. The evidence offers insights into the effects of disclosure legislation in the context of an underdeveloped institutional environment.
Do you see what I see? Enhancement of rigour in qualitative approaches to inquiry: a systematic review of evidence
Authors: Patterson Eira Wyn , Ball Kerry , Corkish Jessica , Whittick Isabella May
Published: November 2022

Purpose

The purpose of this paper is to synthesise current literature on the conceptualisation of rigour within qualitative studies and to identify factors which contribute to the enhancement of rigour for the practical implementation of qualitative research.

Design/methodology/approach

This paper presents an interpretivist stance in line with a qualitative approach to research. A systematic review method was adopted to provide a structured and rigorous selection of relevant literature. Data was analysed using a thematic synthesis method, as outlined by Thomas and Harden (2008).

Findings

The results of the thematic synthesis identified seven descriptive themes in the literature: conceptualising rigour, conceptualising truth and value in knowledge generation, participant trust and communication of truth, rigour in research design and implementation, subjectivity, reflexivity and researcher identity, reader confidence and transparency and strategies for enhancing rigour. These descriptive themes were further developed into three analytical themes: ethical co-construction, methodological alignment and multi-perspective interpretation.

Originality/value

This paper presents an interdisciplinary exploration of the concept of rigour in qualitative research. The themes identified are applicable across fields and provide an original application of thematic synthesis.
Investigation of Nagashima‐type palmoplantar keratoderma in China: A cross‐sectional study of 234 patients
Authors: Liu Juan , Chen Zhiming , Hu Linghan , Song Zhongya , Mo Ran , Tsang Lemuel Shui‐Lun , Liu Yihe , Huang Xin , Gong Zhuoqing , Lin Zhimiao , Yang Yong
Published: November 2022

Nagashima‐type palmoplantar keratoderma (NPPK) is the most prevalent hereditary palmoplantar keratoderma (PPK) in China, but there is a paucity of epidemiological data on the Chinese population. To explore the clinical and genetic characteristics, evaluate the demographic distribution, and estimate the burden of disease of NPPK. A total of 234 Chinese patients with NPPK were enrolled from two medical centers and an online PPK support group. Next‐generation sequencing and Sanger sequencing were performed to screen out and confirm pathogenic mutations in SERPINB7. Clinical features and quality of life (QOL) were evaluated using self‐completed questionnaires. In total, 14 pathogenic mutations were identified in SERPINB7 from the cohort. The top four recurrent mutations were c.796C>T (355, 75.9%), c.522dupT (66, 14.1%), c.650_653delCTGT (24, 5.1%), and c.455G>T (12, 2.6%), accounting for 97.6% of Chinese NPPK patients. Other mutations (11, 2.4%) include c.455‐1G>T, c.336+2T>G, c.635delG and seven novel mutations c.2T>C, c.434delG, c.455‐16A>G, c.656T>C, c.745‐553T>G, c.832C>T, c.1036G>T. The estimated prevalence of NPPK in China was found to be 0.975/10 000 based on Chinese databases. Clinically, there were no apparent genotype–phenotype correlations in NPPK patients. Pediatric patients mainly presented with palmoplantar peeling, while adults presented with scale (p < 0.001). The most common comorbidities in NPPK patients were onychomycosis (40.0%), eczema (36.8%), and tinea pedis (30.3%). As for burden of disease, NPPK patients' QOL was decreased by a moderate degree. In this study, pathogenic mutations' allele frequencies in SERPINB7 were updated, and prevalence of NPPK in China was estimated. This large‐scale cohort study provides evidence‐based recommendations for patient management. Identification of new mutations are important for timely diagnosis of NPPK. Palmoplantar peeling in children can be used as a hallmark for early recognition of NPPK.
High accuracy of single‐molecule real‐time sequencing in detecting a rare α‐globin fusion gene in carrier screening population
Authors: Zhou Qiao‐Miao , Jiang Fan , Xu Jing , Lin Dan , Huang Ren‐Liang , Zhou Jian‐Ying , Qu Yan‐Xia , Li Dong‐Zhi
Published: November 2022

Introduction

The α‐globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0‐thalassemia (α0‐thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α‐thal diagnosis.

Methods

In this study, we used the single‐molecule real‐time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next‐generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and β thalassemia were utilized.

Results

According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α‐thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two “pure” heterozygotes: one was compound heterozygote with anti‐3.7 triplication, and the other was homozygote.

Conclusion

Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one‐step properties.
Identifying the culprit artery via 12‐lead electrocardiogram in inferior wall ST‐segment elevation myocardial infarction: A meta‐analysis
Authors: Zhou Peng , Wu Yingying , Wang Meng , Zhao Yikai , Yu Yangjie , Waresi Maieryemu , Li Huiyang , Jin Bo , Luo Xinping , Li Jian
Published: November 2022

Background

Inferior wall ST‐segment elevation myocardial infarction (STEMI) is mostly caused by acute occlusion of right coronary artery (RCA) and left circumflex artery (LCX). Several methods and algorithms using 12‐lead ECG were developed to localize the lesion in inferior wall STEMI. However, the diagnostic properties of these methods remain under‐recognized.

Aims

The aim of this meta‐analysis is to compare the diagnostic properties among the methods of identifying culprit artery in inferior wall STEMI using 12‐lead ECG.

Methods

We performed a meta‐analysis to calculate the pooled sensitive, specificity, area under the curve (AUC) and diagnostic odds ratio (DOR) of each method.

Results

Thirty‐three studies with 4414 participants were included in the analysis. Methods using double leads had better diagnostic properties, especially ST‐segment elevation (STE) in III > II [with pooled sensitivity 0.89 (0.84–0.93), specificity 0.68 (0.57–0.79), DOR 17 (9–32), AUC 0.88 (0.85–0.91)], ST‐segment depression (STD) in aVL > I [with pooled sensitivity 0.82 (0.72–0.90), specificity 0.69 (0.48–0.86), DOR 11 (4–29), AUC 0.85 (0.81–0.88)], and STD V3/STE III ≤1.2 [with pooled sensitivity 0.88 (0.78–0.95), specificity 0.59 (0.42–0.75), DOR 12 (5–27), AUC 0.82 (0.78–0.85)]. Diagnostic algorithms, including Jim score[pooled sensitivity 0.70 (0.55–0.85), specificity 0.88 (0.75–0.96)], Fiol's algorithm [pooled sensitivity 0.54 (0.44–0.62), specificity 0.92 (0.88–0.96)] and Tierala's algorithm [pooled sensitivity 0.60 (0.49–0.71), specificity 0.91 (0.86–0.96)], were not superior to these simple methods.

Conclusions

Our meta‐analysis indicated that diagnostic methods using double leads had better properties. STE in III > II together with STD in aVL > I may be the most ideal method, for its accuracy and convenience.
Drivers of support for citizen science across state wildlife management agencies in the United States
Authors: Van Buskirk Amanda N. , Boley Bertram Bynum , Killmaster Charlie H. , Johannsen Kristina L. , D'Angelo Gino J.
Published: November 2022

Citizen science (CS) is gaining recognition as a valuable approach to meet data needs for environmental projects while fostering collaboration between scientists and members of the public. Despite increasing implementation of CS by natural resource entities, organizations’ motivations for engaging in CS remain poorly understood. We examined the utility of the theory of planned behavior (TPB) and social exchange theory (SET) in identifying factors influencing support of CS by scientific organizations. To test predictions of the TPB and SET theories, we surveyed (quantitative, web based) state wildlife agency staff in the United States on their perceptions of organizational engagement in CS. We divided questions that measured TPB items into individual and organizational components to address the influence of personal‐ and organization‐level decision‐making on staff perceptions and attitudes. We used structural equation modeling to identify key constructs that influence staff support of CS in state wildlife agencies. The survey yielded 627 responses across 44 states. Both TPB and SET constructs accurately predicted staff support of CS; however, measures from SET (e.g., public engagement benefits and costs of CS to scientific credibility) were most influential (i.e., TPB constructs had less impact). Our findings indicate that organizational support for CS is primarily influenced by assessment of trade‐offs among perceived costs and benefits. Indicators of support for CS were further elucidated by including measures from the TPB model. Based on our results, we suggest that natural resource entities give careful consideration to CS project design, develop thorough communication and data management plans, and practice iterative evaluation of CS project productivity.
Application of decision tools to ethical analysis in biodiversity conservation
Authors: Biasetti Pierfrancesco , Hildebrandt Thomas B. , Göritz Frank , Hermes Robert , Holtze Susanne , Stejskal Jan , Galli Cesare , Pollastri Ilaria , Muzzo Alessia , Lekolool Isaac , Ndereeh David , Omondi Patrick , Kariuki Linus , Mijele Domnic , Mutisya Samuel , Ngulu Stephen , de Mori Barbara
Published: November 2022

Achieving ethically responsible decisions is crucial for the success of biodiversity conservation projects. We adapted the ethical matrix, decision tree, and Bateson's cube to assist in the ethical analysis of complex conservation scenarios by structuring these tools so that they can implement the different value dimensions (environmental, social, and animal welfare) involved in conservation ethics. We then applied them to a case study relative to the decision‐making process regarding whether or not to continue collecting biomaterial on the oldest of the two remaining northern white rhinoceroses (Ceratotherium simum cottoni), a functionally extinct subspecies of the white rhinoceros. We used the ethical matrix to gather ethical pros and cons and as a starting point for a participatory approach to ethical decision‐making. We used decision trees to compare the different options at stake on the basis of a set of ethical desiderata. We used Bateson's cube to establish a threshold of ethical acceptability and model the results of a simple survey. The application of these tools proved to be pivotal in structuring the decision‐making process and in helping reach a shared, reasoned, and transparent decision on the best option from an ethical point of view among those available.
Ranking species based on sensitivity to perturbations under non‐equilibrium community dynamics
Authors: Medeiros Lucas P. , Allesina Stefano , Dakos Vasilis , Sugihara George , Saavedra Serguei
Published: November 2022

Managing ecological communities requires fast detection of species that are sensitive to perturbations. Yet, the focus on recovery to equilibrium has prevented us from assessing species responses to perturbations when abundances fluctuate over time. Here, we introduce two data‐driven approaches (expected sensitivity and eigenvector rankings) based on the time‐varying Jacobian matrix to rank species over time according to their sensitivity to perturbations on abundances. Using several population dynamics models, we demonstrate that we can infer these rankings from time‐series data to predict the order of species sensitivities. We find that the most sensitive species are not always the ones with the most rapidly changing or lowest abundance, which are typical criteria used to monitor populations. Finally, using two empirical time series, we show that sensitive species tend to be harder to forecast. Our results suggest that incorporating information on species interactions can improve how we manage communities out of equilibrium.
Seizure outcome of pediatric magnetic resonance‐guided laser interstitial thermal therapy versus open surgery: A matched noninferiority cohort study
Authors: Yossofzai Omar , Stone Scellig , Madsen Joseph , Moineddin Rahim , Wang Shelly , Ragheb John , Mohamed Ismail , Bollo Robert , Clarke Dave , Perry M. Scott , Weil Alexander G. , Raskin Jeffrey , Pindrik Jonathan , Ahmed Raheel , Lam Sandi , Fallah Aria , Maniquis Cassia , Andrade Andrea , Ibrahim George M. , Drake James , Rutka James , Tailor Jignesh , Mitsakakis Nicholas , Puka Klajdi , Widjaja Elysa
Published: November 2022

Objective

Minimally invasive magnetic resonance‐guided laser interstitial thermal therapy (MRgLITT) has been proposed as an alternative to open epilepsy surgery, to address concerns regarding the risk of open surgery. Our primary hypothesis was that seizure freedom at 1 year after MRgLITT is noninferior to open surgery in children with drug‐resistant epilepsy (DRE). The secondary hypothesis was that MRgLITT has fewer complications and shorter hospitalization than surgery. The primary objective was to compare seizure outcome of MRgLITT to open surgery in children with DRE. The secondary objective was to compare complications and length of hospitalization of the two treatments.

Methods

This retrospective multicenter cohort study included children with DRE treated with MRgLITT or open surgery with 1‐year follow‐up. Exclusion criteria were corpus callosotomy, neurostimulation, multilobar or hemispheric surgery, and lesion with maximal dimension > 60 mm. MRgLITT patients were propensity matched to open surgery patients. The primary outcome was seizure freedom at 1 year posttreatment. The difference in seizure freedom was compared using noninferiority test, with noninferiority margin of −10%. The secondary outcomes were complications and length of hospitalization.

Results

One hundred eighty‐five MRgLITT patients were matched to 185 open surgery patients. Seizure freedom at 1 year follow‐up was observed in 89 of 185 (48.1%) MRgLITT and 114 of 185 (61.6%) open surgery patients (difference = −13.5%, one‐sided 97.5% confidence interval = −23.8% to ∞, pNoninferiority = .79). The lower confidence interval boundary of −23.8% was below the prespecified noninferiority margin of −10%. Overall complications were lower in MRgLITT compared to open surgery (10.8% vs. 29.2%, respectively, p < .001). Hospitalization was shorter for MRgLITT than open surgery (3.1 ± 2.9 vs. 7.2 ± 6.1 days, p < .001).

Significance

Seizure outcome of MRgLITT at 1 year posttreatment was inferior to open surgery. However, MRgLITT has the advantage of better safety profile and shorter hospitalization. The findings will help counsel children and parents on the benefits and risks of MRgLITT and contribute to informed decision‐making on treatment options.
Somatic symptoms and related disorders in a large cohort of people with epilepsy: A cohort study
Authors: Shen Sisi , Dong Zaiquan , Sander Josemir W. , Zhou Dong , Li Jinmei
Published: November 2022

Objective

This study was undertaken to characterize somatic symptoms and related disorders (SSD) in epilepsy.

Methods

Adults with epilepsy under active follow‐up at a tertiary epilepsy center were consecutively enrolled. The diagnosis of SSD was performed by an experienced psychologist based on the structured clinical interview for Statistical Manual of Mental Disorders, 5th edition. Detailed social/demographic data, epilepsy features, psychiatric features, life quality, disability, and economic burden were collected and compared between people with SSD and those without. Bodily distress syndrome checklist, Somatic Symptom Disorder–B Criteria Scale, Patient Health Questionnaire‐9, and Generalized Anxiety Disorder seven‐item scale (GAD‐7) were used to evaluate SSD individuals' somatic symptoms, symptom‐related psychological distress, and depressive and anxious symptoms. Quality of life and disability were assessed by Quality of Life in Epilepsy Inventory 31 (QOLIE‐31) and World Health Organization Disability Assessment Schedule V.2.0 (WHO DAS 2.0). A risk prediction nomogram was generated using least absolute shrinkage and selection operator (LASSO) analysis and validated.

Results

One hundred fifty of 631 participants (24%) were diagnosed with SSD. In people with SSD, the top three most common somatic symptoms were memory impairment, headache, and dizziness (85%, 80%, and 78%, respectively), and multiple systems were involved in most (82%) people with SSD. Compared with people without SSD, those with SSD had lower QOLIE‐31 total scores, and higher WHO DAS 2.0 scores and disease economic burdens. LASSO analysis suggested that a history of severe traumatic brain injury, hippocampal sclerosis, low seizure worry and medication effects scores on QOLIE‐31, multiple systems affected by somatic symptoms, and a high GAD‐7 score were risk factors of SSD. The nomogram was validated for good accuracy in the training and testing cohorts.

Significance

SSD are likely to be a common comorbidity in epilepsy and harm epilepsy prognosis. Our risk prediction nomogram was successfully developed but needs further validation in larger cohorts.
Medical decision‐making for adolescents with depression: A bibliometric study and visualization analysis via CiteSpace
Authors: Hua Nan , Tan Xiangmin , He Yuqing , Sun Mei , Wang Xiuhua
Published: November 2022

This study focussed on evaluating the status of recent research on medical decision‐making for adolescents with depression and identifying research hotspots and frontiers via CiteSpace. We extracted studies that were concerned with medical decision‐making for adolescents with depression from the Web of Science Core Collection (WoSCC), covering the period from 1 January 1999 to 20 September 2022. We used CiteSpace to generate online maps of worldwide cooperation among countries, institutions, and authors. Hotspots and frontiers were systematically summarized. A total of 368 papers related to medical decision‐making for adolescents with depression were obtained from WoSCC. The most prolific author was Nick Midgley (seven papers). The United States and University College London were the leading country and institution in this research area, with 177 and 17 papers, respectively. Countries, institutions, and authors all actively collaborated. Main recent research trends include the preference or attitude towards medical treatment in adolescents with depression; approaches for adolescents with depression to seeking medical help; and the key role of parent, family, and primary care in medical decision‐making for adolescents. Thus, further attention should be paid to determining how to promote the role of parents, families, and primary care in the decision‐making process and create appropriate online help‐seeking tools and decision aids to facilitate shared decision‐making in the future.
A highly sensitive turn‐off fluorescent probe based on 2D Eu(III)‐MOFs nanosheets for glutathione in vitro and living cells
Authors: Zhu Mengmeng , Liu Yunpeng , Xia Chao , Zeng Hairong , Hu Song , Jiang Danyu , Zhou Guohong , Li Huili
Published: November 2022

Glutathione (GSH) is generally used as an effective and sensitive tumor marker because its abnormal levels are associated with high free radical level in tumor. In this work, GSH could be easily detected by a kind of designed Eu‐based metal–organic frameworks (Eu‐MOFs, named Eu(DTBA)) fluorescent sensor. Due to the “antenna effect” of 4,4′‐dithiobenzoic acid (4,4′‐DTBA) ligands on Eu3+, Eu(DTBA) emits the strong characteristic red light of Eu3+ under ultraviolet excitation. Moreover, the emission intensity strongly depends on GSH concentrations. Thus, Eu(DTBA) can serve as a turn‐off fluorescent switch of GSH because its framework structure can easily be destroyed by GSH that leads to the fluorescence quenching. Remarkably, during sensing GSH, Eu(DTBA) has shown many appealing performances, such as broad a response window (0–20 mM), fast response (3 min), high sensitivity (LOD = 0.35 µM), and excellent anti‐interference ability. The real bioimaging application has demonstrated that the reported Eu(DTBA) can be used as an excellent bioimaging agent to successfully distinguish tumor cells from normal cells in clinical diagnosis.
Resilience, self‐efficacy and diabetes distress on self‐management behaviours in patients newly diagnosed with type 2 diabetes: A moderated mediation analysis
Authors: Wang Ruey‐Hsia , Chen Shi‐Yu , Lee Chun‐Ming , Lu Chieh‐Hua , Hsu Hui‐Chun
Published: November 2022

Aim

To examine (1) the mediating role of self‐efficacy between resilience and self‐management behaviours and (2) the moderating role of diabetes distress on the relationship between self‐efficacy and self‐management behaviours in patients newly diagnosed with type 2 diabetes.

Design

Cross‐sectional design.

Methods

Totally, 195 patients newly diagnosed with type 2 diabetes for more than 5 months but less than 18 months were recruited from three endocrine clinics in Taiwan through convenience sampling. Self‐reported questionnaires including demographic and disease characteristics, resilience, self‐efficacy and self‐management behaviours were used to collect data from October 2020 to May 2021. Moderated mediation analysis was performed by Hayes's PROCESS macro.

Result

According to bootstrapping results, the indirect effect of resilience on self‐management was significant, although the direct effect of resilience on self‐management was not. Participants were categorized into with and without diabetes distress groups. The results of moderated mediation analysis indicated self‐efficacy significantly correlated with self‐management behaviours in participants without diabetes distress, although self‐efficacy did not significantly correlate with self‐management in participants with diabetes distress.

Conclusion

The association of resilience with self‐management behaviours was fully mediated through self‐efficacy with diabetes distress moderating the relationship between self‐efficacy and self‐management behaviours in patients newly diagnosed with type 2 diabetes.

Impact

Improving resilience could enhance self‐efficacy leading to possible improvement in self‐management behaviour, although improving self‐efficacy might not benefit self‐management behaviours for those with high levels of diabetes distress. Healthcare providers need to first assess and address the diabetes distress before intervening to improve self‐efficacy to enhance self‐management behaviours in patients newly diagnosed with type 2 diabetes.

Patient or Public Contribution

When designing this study, two patients newly diagnosed with diabetes were consulted about the importance of self‐management behaviours for them personally.
Cost‐effective approaches for acrylamide mitigation in high‐temperature‐processed tuber snacks
Authors: Varma Kavya , John Jenny Ann
Published: November 2022

Acrylamide is a potential carcinogen produced at higher temperatures while frying, roasting and baking. Starch‐rich foods like potatoes are known to produce acrylamide in increasing concentrations than other kinds of foods. This study focuses on mitigation of acrylamide in sweet potato, taro and cassava samples subjected to various heat‐treatment processes like oil frying, air frying and baking. Dipping of tuber slices in solutions of garlic, green tea, sodium chloride, yeast, distilled water, whey and blanching prior to frying the tubers were found to be effective pre‐treatment methods. However, the effect of the treatments depended on the sample and mode of processing. Yeast was found to produce a significant reduction in the acrylamide production in taro (98.64%) and garlic pretreatment reduced acrylamide in deep fat fried cassava samples up to 95.62%. Similarly, air fried taro samples dipped in distilled water was found to significantly reduce the browning reaction up to 96.51%; primarily due to the fact that distilled water was found to block the reaction between precursors like asparagine and reducing sugars, thereby preventing the formation of acrylamide. Influence of reducing sugar on the formation of acrylamide, when fried at different temperatures was analyzed using Response Surface Methodology (RSM), clearly indicating that the amount of reducing sugars decreased at higher temperatures with increase in acrylamide content. The attempts in the study clearly shows that simple and cost effective pretreatments can be successful applied to produce healthy tuber products with reduced concentration of acrylamide.

Practical applications

Fried foods are popular among all age groups. However, the acrylamide produced during its processing is a carcinogen of serious concern. Mitigation of this component is an urgent need. The tested simple and cost‐effective pre‐treatment methods can be applied for acrylamide mitigation in ready‐to‐eat food processing sector. Moreover these can be practically used by street‐food vendors to prepare healthier and safer processed snack foods.