We sought to apply natural language processing to the task of automatic risk of bias assessment in preclinical literature, which could speed the process of systematic review, provide information to guide research improvement activity, and support translation from preclinical to clinical research. We use 7840 full‐text publications describing animal experiments with yes/no annotations for five risk of bias items. We implement a series of models including baselines , neural models  and models using BERT with two strategies (document chunk pooling and sentence extraction). We tune hyperparameters to obtain the highest F1 scores for each risk of bias item on the validation set and compare evaluation results on the test set to our previous regular expression approach. The F1 scores of best models on test set are 82.0% for random allocation, 81.6% for blinded assessment of outcome, 82.6% for conflict of interests, 91.4% for compliance with animal welfare regulations and 46.6% for reporting animals excluded from analysis. Our models significantly outperform regular expressions for four risk of bias items. For random allocation, blinded assessment of outcome, conflict of interests and animal exclusions, neural models achieve good performance; for animal welfare regulations, BERT model with a sentence extraction strategy works better. Convolutional neural networks are the overall best models. The tool is publicly available which may contribute to the future monitoring of risk of bias reporting for research improvement activities. Risk of bias assessment is critical to reduce translation issues from preclinical to clinical research.Animal intervention studies vary from clinical trials and automatic tools designed for risk of bias assessment in preclinical literature remain to be developed.We present and implement a series of natural language processing models for the classification of reporting of five preclinical risk of bias items.The open‐source tool provides the possibility for future research improvement activities.1Systematic review is a type of literature review that attempts to collate all empirical evidence relevant to a pre‐specified research question. It uses explicit and systematic methods to minimise bias and provide more reliable findings than narrative review.Systematic reviewers have advocated the use of automated approaches to assist risk of bias assessment, using human effort and machine automation in mutually reinforcing ways.Compared with clinical trials, animal studies are conducted in relatively small teams, are reported in a different style, have been shown to have lower reporting of strategies to reduce risks of bias,Several reporting standards relevant to the design, conduct, analysis and reporting of animal studies have been suggested, including the ARRIVE guidelines2We consider the risk of bias assessment as a typical text classification task. A classification model cannot be trained from the plain text directly and we need to convert text information to analysable data. The core concept is to map each document to a matrix consisting of fixed‐dimension word vectors or embeddings,2.1We use a collection of full‐text publications which our group has annotated for risk of biasThe risk of bias labels are at the document level  and we consider five risk of bias domains: (1) Random Allocation: animals are randomly allocated to treatment or control groups; (2) Blinded Assessment of Outcome: group identity is concealed from the scientist measuring the outcome; (3) Compliance with Animal Welfare Regulations: researchers report that they complied with relevant animal welfare regulations; (4) Conflict of Interests: authors report any relationship which might be perceived to introduce a potential conflict of interests, or the absence of such a relationship; and (5) Animal Exclusions: a statement of whether or not all animals, all data and all outcomes measured are accounted for and presented in the final analysis. The prevalence of reporting of each of these items, and some example sentences indicating the reporting for each risk of bias item are displayed in Table https://www.xpdfreader.com). We converted all text to lower case and used regular expressions to remove references, citations, URLs, digits, non‐ASCII characters and text which precedes the ‘Introduction’ section, because they are irrelevant to the risk of bias reporting. We used Stanford CoreNLPPublications were available in PDF format and we converted them to plain text using Xpdf (2.2We explore three text representation methods in baseline models: (1) bag‐of‐words, (2) word2vec and (3) doc2vec. Bag‐of‐words (bow) uses word frequency within the document to represent its importance. Considering less important words with high frequency such as ‘the’ and ‘a’, TF‐IDF (term frequency‐inverse document frequency) weighting is applied, which normalises the word frequency in a document by multiplying a log‐scale of the inverse of the frequency of documents where the word occurred.We explore three baseline classifiers: support vector machine, logistic regression and random forest. Support vector machine and logistic regression are linear classifiers, which are trained to map the word embeddings to the target risk of bias label to minimise a hinge loss function and log loss function separately.2.3We explore three neural models: CNN, a powerful model for text classification;2.3.1xi:j denote the matrix extracted from row i to row j of the document matrix. For one document matrix x∈ℝs×d and one filter f∈ℝh×d , the convolution layer sequentially extracts a submatrix which has the same dimension as filter f and does the sum operation of the element‐wise product between xi:i−h+1 and f. This generates a summarised feature vector w∈ℝs−h+1 of the document matrix x by filter f with filter size h. For filter size h, multiple filters are used to capture different features.We use the classic one‐layer CNNThe output vectors from the convolutional layer are then passed through an activation function such as ReLU to add non‐linearity, and a pooling layer, which extracts the maximum value of each vector. A dropout layer, which randomly sets some values in the vectors to zero, is applied to prevent over‐fitting. A final linear transformation is applied to map the vector concatenated from the pooling layer into two numeric values, representing separately whether or not the document reported the risk of bias item.2.3.2Recurrent neural network is a type of neural network which builds connections over time steps.∈ℝs×h) is created to learn the importance of each word in the document (similar to the attention mechanism described below for HNNs). The attention module is then added to learn and emphasise the word contributions to the entire document sequence.In the general recurrent structure, the output from the hidden layer is obtained by simply taking the hidden state of the last recurrent cell, which loses some information from other recurrent cells; or averaging hidden states of all recurrent cells, which treats words at different positions equally. However, the same word may play a different role in the decision of the classification when it occurs in different sentences or contexts. A global context matrix  max pooling, (2) average pooling, (3) concatenate output from max pooling and average pooling, (4) use hidden states of the first token, (5) concatenate hidden states of all tokens. After two pooling layers, we explore three head layers  for the downstream classification task. The convolution and LSTM heads use the same architecture as described previously. The linear head cannot handle sequences of different lengths, so we add another pooling layer to obtain the fixed‐dimension output. The pooling methods use the same options applied in the second pooling layer, with the exclusion of ‘concatenate hidden states of all tokens’, which does not generate a fixed‐dimension output.We split documents into text chunks, apply BioBERT to each chunk, and pool the hidden states from different chunks using multiple strategies. This is similar to the structure applied in the classification of clinical notes for patient smoking status,2.4.2k sentences with the highest similarity scores, that is, the most k relevant sentences, to form a new shorter passage. We then fine‐tune the DistilBERTInstead of using the full‐text document as input, we extract the most relevant sentences to the risk of bias description. We first use scispaCy2.5Recall (or Sensitivity) = True Positive/; (2) Precision = True Positive/; (3) F1 score = /; and (4) Specificity = True Negative/. Recall measures the portion of records which are identified as reported among all truly reported records. Precision measures the portion of truly reported records among all records identified reported. Specificity measures the portion of records identified as unreported among all unreported records. F1 is the harmonic mean of recall and precision, and we use this as the main metric for hyperparameter and model selection.To evaluate model performance, we define ‘True Positive’ as the number of records which report the risk of bias item and are predicted as reported; ‘True Negative’ as the number of records which do not report the risk of bias item and are predicted as unreported; ‘False Positive’ as the number of records which do not report the risk of bias item but are predicted as reported; and ‘False Negative’ as the number of records which report the risk of bias item but are predicted as unreported. For all classification models described above, we calculate four metrics of performance, being (1) 3The performance of eight models from three categories  on the validation set are shown in Table We find that neural models are more robust to hyperparameter tuning than baseline models. For random allocation, blinded assessment of outcome and conflict of interests, neural models improve F1 by 14%–30% over baseline models, with little difference among the three neural models. For compliance with animal welfare regulations, neural models have no advantage over baselines, with F1 falling 4%–14%. For animal exclusions, weight balancing strategy and under‐sampling do not effectively address the data imbalance issue, and the training process is prone to over‐fitting.Models using BERT with the two strategies described do not outperform neural models, except the item of compliance of animal welfare regulations, which has 3% improvement. This is expected because in the document chunk pooling (DCP) strategy, we do not take any advantages of BERT structure by freezing all the encoder layers, and multiple pooling strategies do not address this limitation; in the sentence extraction strategy, although we can fine‐tune DistilBERT, we still lose some information by using shorter texts extracted from full publications. We have not been able to evaluate the performance of sentence extraction modules, which requires further sentence‐level annotations.p < 0.05 by the McNemar's testUsing the best model in its optimal setting for four risk of bias items, we evaluate and compare the performance with our previous regular expression approach on the test set . For blinded assessment of outcome, we select the RNN with attention as the optimal model instead of BERT with document chunk pooling (BERT‐DCP) because we do not consider the very small advantage to justify the complexity of pre‐processing in the latter approach. Table Table 4We have shown that different models are optimal for the detection of reporting of different risks of bias. Convolutional neural network is best for conflict of interests and RNN with attention are best for random allocation and blinded assessment of outcome. For compliance with animal welfare regulations, models using BERT with sentence extraction (BERT‐SE) strategy achieve the best performance. For animal exclusions, CNN achieves the best performance on the validation set, but no approach provides reliable performance on the test set. Compared with the previous regular expression approach, the F1 scores for four risk of bias items are between 13% and 36% higher, indicating a substantial improvement. The sentence extraction function can provide potentially relevant sentences as clues for users making the judgement. We can analyse all positive samples and use the RNN with the attention module to output attention scores for tokens in each individual paper, thus we can extract the most important words in the decision of classification task Figure , which mAmong the incorrect records, our models are more likely to conclude that papers report random allocation, blinded assessment of outcome and animal exclusions, and less likely to predict that papers report conflict of interests and animal welfare regulation Figure . To analhttps://github.com/qianyingw/pre-rob. The levels of performance achieved make these tools suitable for research improvement activity where several hundred publications are to be evaluated. For instance, for random allocation in a corpus of 1000 manuscripts, this approach would estimate prevalence within 3% of the true value and for 100 publications, within 10% of the true value . Given that the changes sought in research improvement activities are at least of this magnitude, we consider the performance of these tools in determining the reporting of risk of bias items to be such that they are suitable for deployment in a research improvement context. Similarly, they are suitable for the evaluation of risk of bias in large corpuses such as large preclinical systematic reviews. However, they are not yet at the level where they are appropriate for the evaluation of individual publications.The tool and codes for predicting probabilities of risk of bias reporting in preclinical full texts is available at PLoS One and Nature. This may influence the generalizability of our findings. Second, PDF to text conversion loses document structure and we cannot identify the main sections of publications. This introduces some noise (for instance text from figures and tables) to our training corpus. Tools like GROBID (https://github.com/kermitt2/grobid) can convert PDFs to structured XML but it highly depends on the quality of PDF, and in our experience it does not work well for some preclinical publications. However, enhanced approaches to PDF conversion, and increased availability of publications in XML format, means that this approach may become feasible in the future. Finally, following our own systematic review practice, we considered all publications which did not report measures to reduce risks of bias to be at high risk of bias, with no ‘unclear’ category. Because our models output continuous probability scores ranging from 0 to 1 which can be then used to provide a binary score, it might be possible to identify the ‘unclear’ category as those with intermediate scores; but since these are not labelled in each of our datasets we have not been able to do so.Our work has several limitations. First, our training dataset includes publications drawn from three datasets focusing largely on the neurosciences, as well as two datasets from unselected preclinical studies published in In future work, we will seek to improve performance further, using datasets involving more journals and a wider range of preclinical experiments, and will exploit diseases and texts from structured PubMed XMLs, which may yield better performance. We will continue improving the attribution of animal exclusions to achieve more reliable performance and we will develop approaches for other risk of bias items including sample size calculation and allocation concealment. We will also develop a user‐friendly function embedded in the preclinical systematic review facility SyRF5We explore multiple text classification models, from baselines to recent NLP techniques and demonstrate the advantages of neural models and BERT models for risk of bias assessment in preclinical literature. BERT models work well for animal welfare regulations, while convolutional or RNNs achieve better performance for. We encourage the use of NLP techniques to assist risk of bias assessment and reduce workflow in preclinical systematic reviews. If computational limitations require the implementation of a single tool, we recommend using CNNs, which achieve overall good performance across our five risk of bias items. The performance of these tools is such that they could be deployed in automated approaches to monitor risks of bias reporting as part of institutional research improvement activities.The authors declare that they have no conflict of interests.Qianying Wang and Malcolm Macleod conceived the study. Mirella Lapata was involved in the design of model architecture. Qianying Wang and Jing Liao processed the full‐text data. Qianying Wang implemented the classification models, analysed results and wrote the initial draft of the manuscript. All authors provided comments on preliminary versions and approved the final manuscript.Appendix S1: Supporting informationClick here for additional data file.


This study aims to co‐design an evidence‐ and theory‐based behavioural intervention to reduce the impact of chemotherapy‐induced peripheral neuropathy (CIPN) symptoms on patients' quality of life.Guided by the Medical Research Council Framework for developing and evaluating complex interventions, our intervention development process was guided by (a) findings of systematic reviews, (b) inductive analysis of 39 h of observational fieldwork, 12 patient and 11 clinician interviews, (c) deductive analysis using the Common‐Sense Model to develop a Self‐Regulation Model of CIPN and (d) 17 patients and 18 clinicians co‐designing the intervention.CIPN perception and coping behaviours were highlighted as processes to target when co‐designing an intervention. The processes targeted in our intervention are CIPN perception and coping behaviours, namely, (a) self‐monitoring of symptoms, (b) communicating and early reporting of symptoms to clinicians, (c) participating in making chemotherapy dose reduction decisions with their clinicians and (d) engaging in self‐management and safety strategies to reduce impact of CIPN symptoms. To address these, a behavioural intervention was deemed suitable.We developed a self‐regulation model of CIPN and a logic model for documenting the proposed mechanism of action of our co‐designed behavioural intervention for reducing impact of CIPN symptoms. There is no drug recommended to prevent CIPN symptoms from developing  describe an evidence and theory‐based approach to co‐designing complex interventions, (b) share our experience of using this approach, (c) present a self‐regulation model of CIPN and (d) propose a behavioural intervention for reducing the impact of CIPN symptoms. We use the guidance for reporting intervention development studies in health research (GUIDED) . East Midlands ‐ Leicester South Research Ethics Committee (REC Reference 19/EM/0192) assessed and approved the study.Following ethical and site approval, convenience purposive sampling was used to approach potential patient participants. Adults diagnosed with either breast or colorectal cancer, and who were due to receive or who were actively receiving neurotoxic chemotherapy were invited to participate. Clinicians involved in obtaining consent and/or conducting chemotherapy‐related consultations with patients were recruited. All participants signed written informed consent and had the option to attend one or more of the study activities, that is, interview, observation and workshops (see below).2.1.2Experience data were collected through observations of chemotherapy patient‐clinician consultations, clinician interviews and filmed/audio recorded patient interviews. Inductive analysis of interview and observation data was carried out. Findings have been published elsewhere  , timeline (beliefs related to how long the illness might last), consequences , cause (perceived reason or cause for the development of the illness); controllability and illness coherence (whether the person feels they have a coherent understanding of the illness) , delivery mechanisms (the structures in place to deliver the intervention), mechanisms of impact (our assumptions about how the intervention will produce intended effects) and intended outcomes. Behaviour change techniques (BCT) were specified using the Behaviour Change Taxonomy version 1 .33.1n = 7) were conducted virtually. Follow‐up emails were exchanged between members of the co‐design teams after workshops. Table All participants were given the option of attending one or more study activities. In total, there were 42 EBCD participants across all stages. Five patient participants and five clinicians participated in all stages. Four members of the NCEG attended all workshops. Due to COVID‐19 government restrictions, only three initial small co‐design workshops were conducted face‐to‐face; all subsequent workshops   of Self‐Regulation enhanced our understanding of the complex processes involved in experiences of CIPN and ways to address this condition.3.4Societal factors that contribute to the interpretative process through which the individual formulates their perception of CIPN were highlighted. How individuals coped with CIPN was influenced by the roles they carry out, for example, at home or in the workplace, and what they perceived to be a general societal lack of awareness of CIPN. Early cognitive and emotional representations of CIPN were influenced by the attitudes of clinicians and the information and descriptions given by them, which coincided with information‐overload about the acute and potentially life‐threatening side‐effects of cancer treatments. Individuals were less in favour of reducing chemotherapy dose for controlling symptoms.3.5Attributes of the cognitive representation of CIPN include causal beliefs about symptoms , perceived inevitability of CIPN due to cancer treatment and perceived ability to control the symptoms . Patient's perceived understanding of CIPN symptoms increased when symptoms were experienced and when symptoms affected activities involving their hands or feet. When symptoms become more noticeable and begin to cause problems, patients also report their symptoms.3.6The threatening situation, combined with the cognitive beliefs, can trigger emotional distress and low mood, prompting emotion‐focused coping such as minimisation of the problem (not reporting how severe their symptoms were) or avoidance (not reporting their symptoms or avoiding conversations about CIPN). Patients' perception of CIPN was also influenced by fear of death from cancer.new normal within the context of cancer diagnosis and treatment side‐effects.The most common coping strategies individuals used were information‐seeking, positive reframing, seeking social support, active coping and acceptance of the symptoms. However, reappraisal of coping strategies was not observed during their treatment. Rather, patients viewed CIPN as part of an acceptable Figure 3.7Guided by the CSM, the processes targeted in our intervention are CIPN perception and coping behaviours, namely, (a) self‐monitoring of symptoms, (b) communicating and early reporting of symptoms to clinicians, (c) participating in making chemotherapy dose reduction decisions with their clinicians and (d) engaging in self‐management and safety strategies to reduce impact of CIPN symptoms. We identified potential facilitators of these behaviours and mapped these on to CSM constructs that influence CIPN symptom perception Table . Table 3Reducing the Impact of Chemotherapy Induced Peripheral Neuropathy). The REACT‐CIPN booklet and film are complementary in targeting behavioural processes.To address these behaviours, a behavioural intervention, that is, booklet and film, was deemed suitable. The intervention name agreed by the co‐design team was REACT‐CIPN  and control (treatment), respectively.Behavioural change techniques (BCTs) used in the intervention are (a) information about health consequences, (b) salience of consequences, (c) instruction on how to perform a behaviour and (d) action planning. Proposed BCTs were guided by our findings from the literature reviews  and after chemotherapy cycle 2 (film). A logic model showing details of the REACT‐CIPN intervention components, delivery mechanisms, BCTs  gain detailed insight into the context of CIPN experience and patients' needs  by their clinicians about all potential side‐effects of their chemotherapy treatment. CIPN information provided by clinicians is key to developing CIPN perceptions; thus, timing must be considered. Strategies such as reinforcement of CIPN information at cycle 2 onwards, availability of information in formats preferred by patients and easily accessible CIPN information were suggested.identity) of CIPN, the patient's perception of CIPN will influence interpretation of the cause of the symptoms. This is particularly challenging because the threat of cancer is clearly more important than eliminating the cause of CIPN, that is, the chemotherapy that could save their lives. The consequences of continuing or stopping chemotherapy will be internalised and made part of the person's CIPN representation and resulting behaviours. Further, perceived control of CIPN symptoms will influence reporting or self‐managing behaviours which can affect symptom severity.Aside from recognising the symptoms and impact  and external factors  changes the illness representation over time and further guides the individual's actions in response to the threat (CIPN) (Diefenbach & Leventhal, In addition, a person's ability to change the overall Complementing theory‐ and evidence‐based approaches, the EBCD approach ensured patient needs and perspectives were understood and clinicians' perspectives were accommodated to maximise engagement and future implementation. Although EBCD has been used predominantly for quality improvement (Green et al., We acknowledge limitations of this study. First, combining purposive sampling and the option to engage in chosen study activities may have resulted in a sample that was not representative of the wider population of patients with CIPN. Despite efforts to include interview participants from ethnic minority backgrounds in the co‐design activities, no participants from this group of interviewees consented to participate. This is a common observation in healthcare studies including participatory health research (Roura et al., 5The study showed that the EBCD approach can usefully complement theory‐based and evidence‐based intervention development. It provided ongoing opportunities for patient and clinician participants to work collaboratively in co‐designing a behavioural intervention aimed at reducing the impact of CIPN symptoms. Guided by the newly developed self‐regulation model of CIPN, the two processes targeted in our intervention are CIPN perception and coping behaviours. To address these, a behavioural intervention containing four behaviour change techniques was deemed suitable. We developed an intervention logic model vital for documenting the proposed mechanisms of action of the co‐designed intervention. This model will be refined and tested in a subsequent process evaluation as part of a feasibility trial of the intervention.The authors declare that there is no conflict of interest.Data S1. Supporting InformationClick here for additional data file.


Advances in RNA biology such as RNAi, CRISPR, and the first mRNA vaccine represent the enormous potential of RNA research to address current problems. Additionally, plants are a diverse and undeniably essential resource for life threatened by climate change, loss of arable land, and pollution. Different aspects of RNA such as its processing, modification and structure are intertwined with plant development, physiology and stress response. This report details the findings of researchers around the world during the 23rd Penn State Symposium in Plant Biology with a focus in RNA biology. The advent of the first mRNA vaccines for COVID‐19 shows how invaluable RNA research can be to providing solutions for modern problems. The 23rd Penn State Symposium in Plant Biology was held May 18–20, 2022, at the University Park campus of The Pennsylvania State University. It gathered RNA aficionados to share their exciting, new discoveries in plant RNA biology. This conference featured over 100 participants, and research spanning 20 countries, as well as 24 states within the United States.trans‐kingdom communication utilizing small RNAs (sRNAs).In this meeting report, we describe research that was presented on RNA processing that occurs within the cell, such as alternative splicing, noncanonical RNA caps and RNA editing, RNA turnover, and RNA‐directed regulation of transcription and translation. We delve into new insights regarding short and long noncoding RNAs (ncRNAs) in epigenetic reprograming. Finally, we discuss the RNA‐based tool CRISPR, RNA sensing of environmental responses via RNA modification and structure, and RNA interactions outside the cell through its role in 1.1Arabidopsis thaliana. The two isoforms of SR45, SR45.1 (long) and SR45.2 (short), have been shown to function in different developmental processes including flowering and root growth, respectively  or ABA‐related genes. This suggests the long isoform of SR45 is critical to regulate splicing in salt stress‐related pathways  is a processing step that expands the transcriptome of eukaryotes through the formation of multiple isoforms of a gene, each capable of independent functions. This process has been shown to primarily occur cotranscriptionally in the spliceosome and through recruitment of additional RNA‐binding proteins Reddy, . Dr. AniIn addition to mRNA processing occurring cotranscriptionally, evidence presented by Dr. Artur Jarmolowski  suggested that pri‐miRNAs (the primary transcripts that give rise to microRNAs) are processed cotranscriptionally in Arabidopsis. Dr. Jarmolowski's work utilized “plant native elongating transcripts sequencing” (plaNET‐seq) to show that cotranscriptional processing of pri‐miRNAs occurs within Arabidopsis and that the process relies heavily on R‐loop formation at the transcriptional start site of the miRNA loci. Interestingly, growth conditions may impact whether a transcript is cotranscriptionally or posttranscriptionally processed, potentially due to regulation of R‐loop formation . C‐to‐U conversions are widespread in plant mitochondria and chloroplasts. Dr. Stephane Bentolila  demonstrated the involvement of the RanBP2 zinc finger (RanBP2 Znf) domain in plant organelle RNA intron editing and splicing , have been identified in plants and other eukaryotes  is a eukaryotic mRNA surveillance system that shapes the transcriptome by eliminating mRNAs that contain premature stop codon. Dr. Misato Ohtani  discovered that deficiency of NMD alters tissue‐specific cell redifferentiation. NMD‐deficient mutants formed adventitious roots instead of adventitious shoots, under the shoot induction condition of tissue culture  and exonuclease digestion by EXORIBONUCLEASE (XRN4) or 3′ to 5′ degradation via SUPPRESSOR OF VARICOSE (SOV) or the exosome pathway  were solely regulated by decay which supports the idea of transcriptional balance between synthesis and decay. Dr. Sieburth also found a subset of sov mRNAs with shorter half‐lives, or high flux, but moderately increased abundance in comparison with WT. This indicates transcription plays a significant role in determining mRNA abundance. This phenomenon where significant changes in half‐life were measured but no significant changes in abundance were detected is an RNA decay defect feedback pathway known as RNA buffering. One key similarity for transcripts exhibiting RNA buffering is degradation involving mRNA decapping by VCS. These VCS‐dependent, high‐flux RNAs included genes known to function as environmental and developmental signals, which indicates probable regulatory function.mRNA abundance is controlled by the balance of two factors: its synthesis from transcription and its decay. mRNA turnover is also critical in cellular homeostasis. A major pathway in plants known as the cytoplasmic mRNA decay pathway consists of mRNA deadenylation followed by either 5′ to 3′ degradation via the decapping enzyme DCP1‐ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) targets. DNE1 is a cytoplasmic mRNA decay factor known to be involved in mRNA decapping and NMD  presented her group's research on the elucidation of Arabidopsis RNS2, the major RNase in Arabidopsis, autophagy‐related (ATG) genes, and the RNA helicase SKI2. Dr. MacIntosh's group has shown through a rns2‐2 null mutant that more total RNA is present in the cell comparison to WT, RNA accumulates in the vacuoles, and rRNA has an extended half‐life , that ski2‐5 null mutant plants have reduced ability to transport fluorescent RNA to vacuoles  presented his work on the vacuolar RNA salvage pathway through 1.4Eukaryotic organisms have evolved several mechanisms to alter the expression of genetic loci in developmental or stress‐specific manners through sRNA. The symposium featured talks on two major pathways of sRNA‐mediated control: sRNA silencing transposons through the deposition of chromatin modification marks from Dr. Julie Law  and Dr. Zofia Szweykowska‐Kulinska's  work understanding microRNA‐mediated response to abiotic stress in barley.Global DNA methylation patterning has emerged as a critical layer of genetic regulation with the establishment, removal, and regulation of these marks indicative of a complex and highly regulated evolved mechanism in Arabidopsis and other eukaryotes , as a major class of gene expression regulators in the context of drought stress in barley. Her group's tissue‐specific identification of novel miRNAs and their targets through sRNA‐seq and degradome seq target suggest an important involvement of microRNAs in the development and function of floral organs as well as abiotic stress  tackled how plastid DNA is structurally organized  are open reading frames that have start codons contained within the 5′ untranslated region  presented his research on conserved peptide uORFs (CPuORFs), specifically bZIP11's CPuORF function in ribosome stalling in high sucrose concentration leading to lower translation for bZIP11's main ORF  discussed that abundant 24‐nt siRNAs are produced from a small number of “siren” loci in ovules . Dr. Mary Gehring  reported the effects of parental Pol IV activity and the resulting developmental impacts on seed fitness and gene expression within the endosperm of Arabidopsis. Pol IV functions in the RdDM pathway by producing short, noncoding transcripts that are eventually processed into 24‐nt sRNAs. Dr. Gehring's work focused on NRPD1, a subunit of Pol IV, which previous studies have shown to play a major role in endosperm gene expression. Using a series of homozygous and heterozygous 1.8Since the initial discovery of the CRISPR‐Cas9 system, significant advances have been made in manipulating this system for the purposes of genetic engineering. The Cas9 nuclease will bind a single‐guide RNA (sgR) that it uses to scan the genome for the complement in the organism in which it is expressed  reported that the fat mass and obesity‐associated protein FTO, an RNA methylase, is responsible for demethylating m6A long‐interspersed element‐1 (LINE1) ultimately leading to chromatin state alterations and changes in gene expression that affect mouse oocyte/embryonic development  transcript is an example of a riboSNitch possessing a G to A SNP that alters its secondary structure  (riboSNitches) and climatic factors in Arabidopsis. The 1.11trans‐species miRNAs in a plant–plant interaction, and Dr. Hailing Jin  presented findings detailing the mobility and function of sRNAs traveling between organisms of differing taxonomic kingdoms in a plant–pathogen model.Presentations on the role of RNA in plant interactions with other organisms were focused on sRNAs generated in one organism and functioning in another. This phenomenon has been studied in the context of sRNAs traveling between interacting organisms with the outcome of inducing transgene silencing of pathogen and parasite mRNAs and suppressing host immune response  and RDR6‐ (RNA‐DEPENDENT RNA POLYMERASE/SGS2), they measured differential abundance of each siRNA to confirm that parasite Cuscuta‐derived miRNA activity is dependent on host machinery. Target mRNAs included TIR1 (TRANSPORT INHIBITOR RESPONSE 1) and AFB2 (AUXIN SIGNALING F‐BOX 2) involved in bacterial pathogenesis and defense signaling  involved in reducing sap loss after wounding  (Cai et al., 2Contributions from this conference highlight the importance and necessity to further understand RNA properties due to RNA's expansive and diverse impacts within the cell, ability for communication outside the cell and between organisms, and potential for crop improvement. Novel RNA discoveries continue to deepen our understanding of both established and newly discovered pathways and processes. RNA phenomena in plants provide a unique perspective as parallel pathways in animals can differ to varying degrees, as evidenced by the research presented in this report. In turn, the continued development of tools such as CRISPR as illustrated by Dr. Yiping Qi's dual base editing and gene activation system, and RNA‐based crop improvement methods, shown by Dr. Zofia Szweykowska‐Kulinska's work in barley miRNA and Dr. Chuan He′s work in potato and rice through RNA modifications, can be used to address current biological and agricultural problems. The field of RNA biology, especially in plants, remains a research area full of potential discoveries to improve crop systems, reveal novel aspects of established pathways, and identify noncanonical processes.The authors declare no conflict of interest associated with the work described in this manuscript.


Opinion is divided regarding their definition, histological grading, clinical significance and risk of subsequently developing cutaneous melanoma (CM). A recent systematic review by Vuong et al.A retrospective single‐centre cohort study was conducted of cases of histologically confirmed DN reported in the Trust Pathology Database using standardised SNOMED codes between 1 January 2008 and 31 December 2013. All reports were manually verified by a clinician. Cases were analysed for demographics, referral source, anatomical site, procedure type, clearance margins, histological severity grading, re‐excision and development of subsequent CM  with a median (range) age at diagnosis of 44  and median (range) follow‐up period of 75  months. One patient died 2 years before the end of the follow‐up period of an unrelated cause. The majority of specimens (93.55%) were excisional biopsies in keeping with national guidelinesU = 238, p = 0.006). A prior history of CM was significantly associated with the risk of developing a subsequent separate site CM .Six patients developed a separate site CM (two melanoma in situ and four melanoma). A third of these had a prior personal history of CM. Three patients were diagnosed concurrently with a separate site CM on the same day as the diagnosis of DN. The crude incidence rate of subsequent separate site CM in all patients with histologically confirmed DN was 374.73 per 100 000 person years. Indirect age‐standardisation of our cohort using the Northern Ireland Cancer Registry incidence rates of melanoma for 2014–2018This was a retrospective review with inherent limitations. Although a single‐centre study our Healthcare Trust is one of the largest in the United Kingdom with a Pathology Department servicing just under a million people. It provides tertiary dermatology and plastic surgery services, possibly introducing bias in terms of the complexity of cases. We have a small cohort of dedicated reporting Dermatopathologists, however, which may have mitigated against interpathologist reporting variability. Lack of clinical information precluded other risk factor analyses. Finally, the study period predates the introduction of the ‘Tissue pathway for Dermatopathology’ by the Royal College of Pathologists UKTo our knowledge, this is the first follow‐up study reporting clinical outcomes for histologically proven DN in a UK Centre. Our study supports broad opinion that the risk of transformation of an individual DN to CM is low. However, despite the study limitations, given the increased risk of subsequent separate site CM in patients with DN, we add to the growing body of literature that suggests DN should be considered as a surrogate marker for increased skin surveillance, particularly in those with a prior history of CM.The author declares that there is no conflict of interest.


Uterine artery embolisation is well established as a treatment for symptomatic fibroids, however, there remain some uncertainties. We have carried out a focused literature review on three particularly challenging aspects – post-procedure fertility, symptomatic adenomyosis and large volume fibroids and uteri, to enable operators to utilise evidence-based guidance in patient selection, consent, and management.Literature searches were performed of the PubMed/Medline, Google scholar, EMBASE and Cochrane databases.The outcomes of our analysis of studies which recorded fertility rates in women desiring pregnancy following UAE for symptomatic fibroids found an overall mean pregnancy rate of 39.4%, live birth rate of 69.2% and miscarriage rate of 22%. The major confounding factor was patient age with many studies including women over 40 years who already have lower fertility compared to younger cohorts. Miscarriage rates and pregnancy rates in the studies analysed were comparable to the age matched population.Treatment of pure adenomyosis and adenomyosis with co-existing uterine fibroids with UAE has been shown to produce symptomatic improvement with better outcomes in those with combined disease. Although the effectiveness is not as high as it is in pure fibroid disease, UAE provides a viable and safe alternative for patients seeking symptom relief and uterine preservation.Our analysis of studies assessing the outcomes of UAE in patients with large volume uteri and giant fibroids (> 10 cm) demonstrate no significant difference in major complication rates demonstrating that fibroid size should not be a contraindication to UAE.3. It is however clear that the quality of evidence needs to be improved on with an emphasis on well-designed randomised controlled trials addressing all three areas and the consistent use of validated quality of life questionnaires for outcome assessment to enable effective comparison of outcomes in different studies.Our findings suggest uterine artery embolisation can be offered to women desiring pregnancy with fertility and miscarriage rates comparable to that of the age-matched general population. It is also an effective therapeutic option for symptomatic adenomyosis as well as for the treatment of large fibroids > 10 cm in diameter. Caution is advised in those with uterine volumes greater than 1000cmThe online version contains supplementary material available at 10.1186/s42155-023-00353-2. Uterine artery embolisation (UAE) is a safe and effective therapeutic option for symptomatic uterine fibroids   acknowleMany patients with symptomatic adenomyosis also have uterine fibroids, and whilst there are publications outlining the use of UAE to treat these patients with encouraging results  and keywords (for example – ‘uterine artery embolisation’ and ‘fertility’) were utilised with searches performed in turn using each database. The reference list of relevant papers was also reviewed for additional studies. Our Pubmed search strategy is included in Additional file We included clinical studies with ranging levels of evidence– randomised controlled trials (RCT), controlled clinical trials (CCT), comparative studies, prospective/retrospective cohort studies, case-control studies and case series. Populations, interventions and outcomes are outlined in Table Formal ethical/institutional board review is not required for this type of study.Following our literature search and applying our exclusion criteria, a total of 17 studies were included for further analysis, which are summarised in Table Of the studies included in the analysis there were two RCTs which compared outcomes following UAE and myomectomy  and found pregnancy rates of 51%–69%  in the UAE cohort described by McLucas et al.  had prevWe found the most important factor affecting fertility was the variable age of patients with many studies including patients who were over the age of 40. It is well documented that advancing age as an independent factor negatively impacts fertility and increases obstetric complications such as miscarriage. Hirst et al.  describeThe American College of Obstetricians and Gynaecologists report fecundity  in healthy women aged above 40 years as 5%. This improves to between 12.4%–22.1% in women aged 35–40 years and 31.9% in women aged under 35 years  studiedThese findings were similar to a prior study by Kim et al.  which alNijenhuis et al.  evaluateA longer-term, 7-year follow-up study of this same patient cohort was then published by de Bruijn et al. . QualityFollowing this, a systematic review by de Bruijn et al. was published in JVIR in 2017 de Bruijn et al. The authors noted several difficulties related to the data as most studies incurred small sample sizes, relatively few studies used validated questionnaires such as UFS-QOL and there was variation in particles sizes used for embolisation. There were no randomised controlled trials (RCTs) available for inclusion. Of the 30 studies (22 prospective cohorts and 8 retrospective cohorts) included in the systematic review, only 6 studies assessed symptom improvement with a validated quality of life questionnaire. We have summarised these, included an additional study and excluded a paper only available in German in Table Despite the growing evidence for favorable outcomes in UAE for adenomyosis, the lack of randomized controlled trials and Level 1 evidence makes it difficult to extrapolate existing data. The outcomes of the Quality of Life after Embolisation vs Hysterectomy in Adenomyosis (QUESTA) which commenced recruitment in 2015 are currently awaited  particles. Kim et al. It has been theorized that since adenomyosis has a more diffuse and deep distribution throughout the myometrium compared to uterine fibroids, targeting the smaller myometrial arteries results in deeper penetration into the vascular plexus enabling more effective targeting of areas of adenomyosis. In studies to date, the use of medium sized particles such as tris-acryl gelatin microspheres (TAGM) sized at 500–700 um  and larger dominant fibroid volume (> 100 cm3) were associated with an increased risk of major complications  of 81 patients, showed that larger uterine volume  is not associated with reduced symptomatic improvement or higher rate of complications at 12 months  experienced less symptomatic improvement at 1 year but this difference did not persist at 2 years  at 12 months  showed satisfactory imaging outcomes in terms of fibroid volume reduction and infarction rate with no incidence of severe complications at 4 years  or large uterine volumes  and re-interventions  in ‘giant’ uterine fibroids, defined as dominant fibroid diameter > 10 cm +/− uterine volume > 700 cm3. The major complications related to fibroid expulsion, uterine infection and one patient with sexual dysfunction post UAE.Interestingly, the two most recent studies on fibroid size suggest an increased risk of complications in women with greater fibroid burden. A large retrospective case control study reviewed 333 patients with respect to intra-uterine infection post UAE and identified large uterine volume > 1000 cmThe data supports the effectiveness of the technique as a viable treatment option with appropriate counselling in this patient group. The potential for described complications is higher, and more rigorous follow up of patients and closer collaboration with gynaecology colleagues would be recommended to anticipate and deal with potential complications promptly. This includes expedient management of infections and transvaginal resection of devascularised fibroids in an elective manner to avoid the need for emergency surgery  to be less effective and associated with increased complication rates. More recent data is contrasting, confirming that UAE is effective in treating the symptoms of uterine fibroids in large volume uteri. However, there is some evidence to suggest a higher risk of infective complications in patients with a significantly larger fibroid burden (uterine volume > 1000 cm3) as well as a higher rate of reintervention. Therefore, although UAE should not be contraindicated in this group, patients should be counselled appropriately prior to treatment.We found limited early evidence reporting UAE in large fibroids (> 10 cm or uterine volume > 700 cmThe available evidence supports the use of UAE as a viable management option in women seeking to preserve fertility, those with symptomatic adenomyosis and those with large fibroids.However, there remains alack of high-quality robust data addressing these three areas. Whilst well designed randomised controlled trials remain the gold standard of evidence, the consistent use of validated quality of life questionnaires for outcome assessment in studies would enable effective comparison of outcomes from different studies. In the area of adenomyosis, the results of the QUESTA trial are awaited, which may address the issue of lack of RCT data. From a practical perspective, Standards of Practice documents from Interventional Radiology societies should also be updated to reflect the growing role, indications and suitability of UAE in these difficult clinical areas.Additional file 1. Pubmed search terms used for each outcome which were then adapted for each database.


The current standard model of language production involves a sensorimotor dorsal stream connecting areas in the temporo‐parietal junction with those in the inferior frontal gyrus and lateral premotor cortex. These regions have been linked to various aspects of word production such as phonological processing or articulatory programming, primarily through neuropsychological and functional imaging group studies. Most if not all the theoretical descriptions of this model imply that the same network should be identifiable across individual speakers. We tested this hypothesis by quantifying the variability of activation observed across individuals within each dorsal stream anatomical region. This estimate was based on electrical activity recorded directly from the cerebral cortex with millisecond accuracy in awake epileptic patients clinically implanted with intracerebral depth electrodes for pre‐surgical diagnosis. Each region's activity was quantified using two different metrics—intra‐cerebral evoked related potentials and high gamma activity—at the level of the group, the individual and the recording contact. The two metrics show simultaneous activation of parietal and frontal regions during a picture naming task, in line with models that posit interactive processing during word retrieval. They also reveal different levels of between‐patient variability across brain regions, except in core auditory and motor regions. The independence and non‐uniformity of cortical activity estimated through the two metrics push the current model towards sub‐second and sub‐region explorations focused on individualized language speech production. Several hypotheses are considered for this within‐region heterogeneity. Standard models of language processing involve a dorsal stream connecting temporal, parietal and frontal regions, each linked to particular aspects of word production—for example, phonological processing or articulatory programming. Most theories imply that the same network should be identifiable across individuals. This hypothesis was tested by quantifying the variability of activation observed across speakers within each region. Two metrics of brain activity recorded intra‐cerebrally in awake epileptic patients revealed diverse levels of variability. Several hypotheses are considered for this within‐region heterogeneity. AGangular gyrusBABrodmann AreaBOLDblood‐oxygen‐level‐dependentCTcomputed tomographyEEGelectroencephalographyfMRIfunctional magnetic resonance imagingHGAhigh gamma activityiERPintra‐cerebral event‐related potentialIFGinferior frontal gyrusIFSinferior frontal sulcusIPSintra parietal sulcusMEGmagneto‐encephalographicMFGmiddle frontal gyrusMIAMulti‐Patient Intracerebral Data Analysis ToolboxMNIMontreal Neurological InstituteMPRAGEMagnetization Prepared Rapid Acquisition with Gradient EchoMRImagnetic resonance imagingRTresponse timeSEEGstereo‐electro‐encephalographySFGsuperior frontal gyrusSFSsuperior frontal sulcusSLFsuperior longitudinal fasciculusSMAsupra marginal gyrusSTGsuperior temporal gyrus1In human cognitive neuroscience, linking a processing model with single‐case patient data provides a fruitful means to pursue improvements of both the model and the clinical assessment. Constructing ‘typical’ participants from aggregated  data has been the primary focus of research on brain function  signals have a fair spatial resolution and a high temporal resolution, but synthetizing them in a unified spatio‐temporal model of word production has proved to be challenging  that required the implantation of intra‐cerebral depth electrodes. Recordings from these electrodes gave us access to the variability in time‐resolved electrophysiological signals rather than the spatial variability derived from functional magnetic resonance imaging (fMRI) data , and 6 were implanted bilaterally . Patients were invited to participate in a picture naming experiment when their implantation included depth electrodes within the parieto‐frontal networks known as the dorsal language stream Hickok, . All pat3.23.2.1All MRI scans were acquired from a 3T Siemens Skyra scanner . The T1‐weighed Magnetization Prepared Rapid Acquisition with Gradient Echo (MPRAGE) volumetric scan was used for co‐registration with stereo‐computerized tomography (CT).3.2.2Immediately after SEEG implantation, a high‐resolution stereo‐CT was taken to obtain the anatomical location of the implanted electrodes. The post‐implantation CT scan was exported into Curry 7 , and co‐registration with the MPRAGE images was performed using an automated full‐volume registration with maximization of mutual information. The accuracy of the co‐registration was inspected visually and confirmed in all patients by a neurosurgeon (JGM) to ensure accuracy. The location of each electrode contact, determined by the centre of the highest intensity on the CT, was individually labelled and superimposed on the MRI for visualization of its anatomical location.3.2.3Further processing was performed within the software suite SPM12  in MATLAB 2015a  to normalize the locations of the electrodes of interest from all the patients. Three processing steps were performed: (1) co‐registration of the CT to the MRI for each individual patient; (2) normalization of the individual MRI with the Montreal Neurological Institute (MNI) 3D common stereotactic space  was localized to a specific brain region of the Talairach atlas , naming latencies were recorded with a microphone (audio Technica ATR20) placed about 13 cm in front of the patient. In this case, response times (RTs) were automatically recorded in milliseconds by the software's voice key. A trial consisted of a fixation point , followed by the black and white target picture (presented for fixed duration of 1000 ms). Various pseudo‐random orders were created to vary across patients the order of items within a block and the order of the blocks within the experiment.The experiment was controlled by the software E‐Prime v2.0.1 . The pictures were presented on the centre of the screen within a visual angle of 6° × 6°. For a subset of the patients  at a sampling rate of 1000 Hz per channel. During the cognitive task, stimuli and behavioural event data were simultaneously acquired along with the SEEG signal . Evoked potentials and HGA were computed and combined into a group analysis using the Multi‐patient Intracerebral data Analysis toolbox . Epochs starting 1500 ms before stimulus onset and lasting 1500 ms post‐stimulus were created, for a total of 3000 ms per trial. Only the epochs corresponding to correct behavioural responses were kept for the analysis. Epochs containing interictal epileptic activity  were removed manually following visual inspection of all epochs.3.5.1Within‐region variability across contacts and patients for the adopted strategy). In addition, they do not distinguish excitatory from inhibitory currents  were averaged across trials to yield iERP. iERP arises from synaptic activity of large numbers of neurons distributed over a cortical region. They primarily capture low frequency components and are time and phase‐locked to the stimulus. They provide a measure of the synaptic input to, and the local processing within, the area where they are recorded  and finally summed. This procedure was used to compensate for the larger contribution of low frequencies that would otherwise overpower the contribution of higher frequencies, due to the 1/f distribution of signal power , which is characterized as broadband activity measured here between 80 and 120 Hz. To estimate HGA, a bipolar montage was computed in which the activity recorded at adjacent contacts was subtracted to yield bipolar channels . Morlet Wavelet transforms were first performed separately at five consecutive frequencies between 80 and 120 Hz with a 10 Hz step . Then, the five resulting time courses were separately normalized with a 3.5.3t test across trials at each time sample. To address the resulting multiple‐comparison problem in the time domain, a minimum duration threshold T was estimated with a bootstrap procedure. Each step of this procedure involved the random selection of the same number of trials as in the original data set, with resampling, and the identification of periods with significant activity within the baseline window (−800 ms to −50 ms) in that sample. At each iteration, the significant period of maximal duration (p < 0.001) was pooled into a bootstrap surrogate distribution constructed through 1000 iterations of the procedure. For each patient, the significance threshold  was defined as the right‐tail 95% quantile of that bootstrap distribution of durations. This yielded a threshold of significance for each channel , which was used to determine task‐related significant activity. Independently of the statistical analysis, an expert neurophysiologist (CLC) examined the responses for each contact and identified no discrepancies between the detections based on human expertise and the statistical method.Task‐evoked responses were determined to be significant using a The analysis described above was conducted per patient. We also report the time courses of each patient in each region, obtained by averaging together all the contacts of a patient within a region that showed significant activity (any activity on the mask of significance). Finally, a group analysis was performed by computing the grand average of patients' time‐courses per region.3.5.4The variability of neural activities within each region of interest was estimated with a Pearson correlation metric computed from the recorded signal time courses. Specifically, we computed the pair‐wise correlations across all signals within one region, at two different levels: contacts/channels and patients. The signal was first averaged across trials to yield a time course for each contact/channel. These time courses were correlated pairwise, yielding a covariance matrix of correlations whose values were averaged. The resulting value is the ‘correlation across contacts/channel’ in the region. Then, the contacts of each patient were grouped, and their time courses averaged to yield a regional time course for each patient. The correlation matrix of these time courses was computed and averaged, as before, to yield the ‘correlation across patients’ in the region.Importantly, for iERPs, any aggregation of signals from various contacts into a single metric must consider the arbitrary sign of the evoked potentials. Typically, two contacts recording the same dipolar source activity from opposite sides would show signals of opposite polarity, an inversion that can occur within or across patients. Conversely, opposite polarity alone does not warrant a single underlying source, as the two signals may arise from different regional sources. Here, for simplicity, we did not attempt to solve the SEEG inverse problem, which might have clarified this issue but which is very rarely explored in SEEG  when permutating each signal with a signal from any other brain region. The two correlation indexes described above were computed. After 1000 permutations, we obtained surrogate distributions of correlation values  with which significance was established at an alpha level of 0.05.For any region, we preserved the number of patient and number of contacts and the statistics consisted in randomly permutating these signals with those of other anatomical regions.44.1SD 105 ms). Mean accuracy was above 90%. Only trials with correct responses were included in the neural signal analysis.All patients except P‐15 completed the task correctly. This left the data from 16 patients for the analysis. Because of technical issues, RTs could only be recorded in 8 out of 16 patients. In addition, the experimental software we used (E‐Prime 2) detected vocal response onsets automatically based on sound intensity, without generating a recording of the sound wave for offline checking. Such intensity‐based automatic detections are considered suboptimal  for the 447 monopolar contacts revealed 359 contacts for which there was significant post‐stimulus task‐related activity  and 88 contacts without significant response. There was a 100% consistency between the active/inactive classification performed visually (and independently) by the expert neurophysiologist (CLC) and by the automated statistical method. For the HGA, the 447 monopolar contacts were re‐coded as 367 bipolar channels. Among them, 211 revealed significant post‐stimulus task‐related HGA , and 156 contacts were without significant response.Across the 25 sampled regions, there was a strong similarity between the variability of neural responses estimated in terms of correlations between contact averages vs. correlations between patient averages Figure . This suRegions with high correlations  are easily understood as being recruited by the task, and the consistently recorded activity can be described as the signature of the cortical region for this task. For regions exhibiting higher variability of responses, more detailed interpretations  will be considered. Four groups of regions were distinguished based on the significance level of variability observed with each of the two metrics  and motor regions such as central sulcus and sub‐central gyrus. Figure Within‐region variability across contacts and patients). Additionally, the iERP being computed over mono‐polar recordings is more sensitive to distant sources that might be present in one patient but not in others. In contrast with the between‐patient variability in iERPs, HGA was consistent across patients and even across trials. The single‐trial raster plots reveal that IPS activity was linked to stimulus presentation rather than response preparation or execution  and in some regions of the motor network . These activities were linked to the patients' responses (auditory feedback and motor articulation). Interestingly, the activity in central sulcus started before and was sustained throughout the overt response, which is consistent with a motor preparation occurring bilaterally. A good spatial agreement between iERP and HGA in STG and the motor cortex is consistent with previous intracranial studies . This null result extended to the absence or suppression of activity stands in contrast with some studies that showed activation during lexico‐semantic control, syntactic processes and retrieval processes  are generally sensitive to the number of active neurons. Another contributing factor is noise. Activities in high gamma frequencies could have poor signal to noise ratio due to contacts being positioned near the skull, which attenuates signal changes  retrieval tasks, such as verbal fluency or verb generation in functional imaging or word‐production after morphological inflection  although not all patients were recorded in all areas. Future studies based on larger group sizes and focusing on smaller groups of regions of interest should confirm or challenge our conclusions regarding the consistency of activities. As noted in the Section Some technical limitations of our analysis must be acknowledged. First, we explored the variability of neural responses both within and across patients. This was done on a medium size group , which have been linked to semantic processing and word retrieval. Lagging by around 100 ms on the average time courses was the activation of regions more specialized in phonological processing and articulatory preparation, such as Pars Opercularis and the Precentral gyrus. These overall timing properties are suggestive of a temporal overlap between regions dedicated to the different sub‐processes of word production; they are in line with models that posit interactive processing and the concurrent recruitment of brain areas. Nevertheless, the high variability observed across patients in either one or both neurophysiological metrics confirms that they reflect two facets of the cortical activation subserved by distinct neural mechanisms. Gamma oscillations reflect a competition between excitation and inhibition in local cortical areas, whereas iERP represents the post synaptic activity resulting from the firing of nearby neurons along with remote neurons with afferent inputs into a region (Nunez & Srinivasan, Tentative interpretations were provided for some of these variations, based on the fine‐grained spatial location of the recording contacts within each region. They call for sub‐second and sub‐region focused explorations of individualized language maps and for multimodal and individualized language assessments prior to brain surgery involving language cortical areas. Such individualized clinical assessments would benefit from complementing picture naming with alternative experimental tasks designed to maximize the likelihood of activity in the targeted regions.From such clinical standpoint, the results pose a challenge for standard language localization at the individual level using the picture naming task. The results indicate the need for specific paradigms of language testing when evaluating language function in clinical settings. This highlights the importance of individualized interpretations of language mapping results, especially in the essential function of production. Although our report does not resolve the issue of the inter‐individual variability of SEEG signals, it provides a grounding for future developments in neural signal assessment, clinical interpretations and neuroscientific theories.The authors declare they have no conflict of interest.https://publons.com/publon/10.1111/ejn.15807.The peer review history for this article is available at


During the coronavirus pandemic (COVID‐19), healthcare providers confronted risks of disease transmission to themselves and their family members, resulting in physical and psychological burdens. This might affect their decisions to leave their jobs temporarily or permanently, fearing infection and protecting their families. This study examined the factors related to the intention to leave a job among healthcare providers during the COVID‐19 pandemic in Jordan.A cross‐sectional correlational design was used to collect data using a convenience sample of 557 healthcare providers working in different sectors across Jordan. Data were collected using a self‐administered questionnaire about the intention to leave jobs during the pandemic.t = 2.60, p < 0.05), gender , and marital status . Participants with a high risk of exposure to COVID‐19 and who experienced higher workloads had higher scores of intention to leave their job during COVID‐19, while being married had lower scores.The sample included 368 females (63.8%) and 209 males (36.6%) participants. The mean age of participants was 30.8 years (SD = 6.65). Differences found in intention to leave job during COVID‐19 in relation to age (Policy‐makers need to pay attention to young and single healthcare providers during the COVID‐19 pandemic to prevent them leave their job. Crucial guidelines for managing workload during the COVID‐19 pandemic are needed. Policy‐makers during pandemics have to protect healthcare providers who feel they are at high risk of infection. Generally, studies showed that HCPs are 10‐folds at risk of COVID‐19 compared to the general population1.What are the factors associated with HCPs' intention to leave their job seriously?2.What are the factors associated with HCPs' perception of intent to leave their job seriously?The panic public response and the lack of resources and workforce have a significant role in increasing fear and worries among HCPs that may force many of them to leave the job, fearing infection and to look after their families. Before COVID‐19, stressful working conditions, work overload, and burden were factors associated with the intention to leave their job in spite of their feeling of although a safe working environment and sufficient resources.22.1A cross‐sectional correlational study was conducted during the COVID‐19 pandemic using an online survey between October 5 and November 15, 2020.2.2A convenience sampling technique was used to select HCPs caring for patients diagnosed with COVID‐19. The HCPs who provided care directly to patients with COVID‐19 and had internet access and skills to fill out the survey online were included in the study. No exclusion criteria were used to maximize participation.2.3As the nature of the online survey, this study was conducted via a structured questionnaire sent online through a social network and email to accessible HCPs from the Jordanian healthcare sector, including various governmental and teaching hospitals. These hospitals extended over all regions  of Jordan and provided care for the majority of patients in Jordan (67%).2.4Data was collected using an online platform of an Arabic self‐administered survey. WHO guidelines for translation and tool adaptation were used to translate the instruments that are unavailable in Arabic. The instruments have been evaluated for validity using the face and content validity methods through a panel of experts. The WHO guidelines were used and followed to reach the final draft of the translated versions of the survey. The survey in the current study has three parts. The first part is related to socio‐demographic data (six items), including age, gender, marital status, job description, length of experience, and previous experience with patients with serious diseases. The second part consists of two items to assess the serious of HCPs' intention to leave the job. Item 1 was “Looking for another job or considering resigning because of the risk of COVID‐19,” and item 2 was “Considered that should not care for patients with COVID‐19.” Each item has two scores; score “1” if the answer is “yes” and score “0” if the answer is “No.” If participants answered both questions with “Yes,” they would consider leaving the job seriously.The third part is about perceived leaving the job during the COVID‐19 pandemic, which included 32 items. The 32 items were grouped into seven subscales: organizational support (six items), perceived risk of contracting COVID‐19 (seven items), workload and stress (five items), social relationships (four items), emotional support (five items), the perceived fatality of COVID‐19 (three items), and personal protective equipment (two items).2.5The Institutional Review Board at Prince Hamza Hospital has approved this study. The current study followed the Declaration of Helsinki provisions, and all participants provided informed consent. The permission to use and translate copyrighted instruments has been received from the original author. No approval from hospitals was required according to the nature of the online study. The study was conducted following the EQUATOR research reporting checklist; (STROBE checklist) for cross‐sectional research. It was uploaded to the online system.2.6After checking the instruments for reliability and validity, minor changes were performed based on expert panel recommendations. The online pilot survey was then carried out on 25 randomly selected HCPs to assess the survey's clarity, relevance, acceptability, feasibility, and time needed. Improvements were made to facilitate better comprehension and organize the survey items before the last draft. The time needs to complete the survey is less than 15 min. These participants were excluded from the study.The target population was accessed through a URL link posted in a Facebook group established in October 2018, publishing the latest news and regulations about healthcare services and illness statistics updates. The Facebook group includes more than 400 thousand active members of HCPs all over the healthcare institutions in Jordan. In addition, the questionnaire was sent via email. After entering all items into the software, the URL link was sent and opened on October 5 for 15 days. The software password is kept only with the primary author to anonymize participants' confidentiality and information. The participants voluntarily enrolled in this study without offering any monetary incentive.The online informed consent was appended to the survey on the front page. Once the participant receives and clicks the link, it is automatically directed toward the front page. The front page included information to assure the participants of their right to voluntary participation and their right to withdraw at any time. Interested ones were asked to sign the consent letter and then move them directly to the survey included in the first page before the socio‐demographic information. The website views the remaining questions sequentially on an average of 9–10 items per page. Also, to ensure the quality of collected data, a unique number was assigned for each participant to avoid multiple responses from the same person. Furthermore, the identifiable information provided in the socio‐demographic section was separated in analysis from the other variables of the study. Finally, on the platform page was a list including participants' codes, address, time of completion survey, and the device used to answer the items .2.7t‐test were utilized to assess the difference between respondent characteristics and serious consideration of leaving the job. Multivariate logistic regression was conducted to determine the predictive factors associated with HCPs considering leaving the job. The relationship between the perception of HCPs to leave the job and participants' characteristics was assessed using analysis of variance (ANOVA) or t‐test for independent categorical variables and Pearson correlation coefficient for the continuous variables.The IBM‐SPSS (V. 25.0) software was used to analyze the data. Descriptive statistics using the central tendency and dispersion measures were used to describe the study's variables. Frequencies and percentages were used to describe the categorical variables. The chi‐square test and independent 33.1n = 326, 56.5%). Most of the participants  were nurses who were directly involved in providing direct care for patients with COVID‐19. Despite 30.5% of participants having less than 5 years of experience, 64.1% have previously cared for patients with infectious diseases  completed the survey. About 126 surveys were excluded because they were incomplete . The remaining 577 surveys represented the final sample and were included in the analysis. Of 577 HCPs, 368 were females (63.8%), and 209 were males (36.6%). The mean age of participants was 30.8 years (SD = 6.65). More than half of the participants were married  and seriously considering leaving the job . Similarly, marital status was significantly associated with intent to avoid caring for patients with COVID‐19  and seriously considering leaving the job . Moreover, participants' age was related to looking for another job and seriously considering leaving the job . In contrast, the length of experience was related to looking for another job .The item analysis showed that 26.2% of the respondents agree with the statement “I feel that I should not be looking after patients with COVID‐19,” and 36.7% agree with the statement “I am looking for another job or considering resigning because of the risk,” see Table 3.1.2χ2 (15) = 148.74, p < 0.001. Married HCPs have a significantly lower consideration for leaving the job seriously than single HCPs . About the perception of HCPs of leaving the job, those who feel that the job puts them at great risk of COVID‐19  and experience a high workload  were significantly associated with seriously considering leaving the job (p < 0.01). Moreover, HCPs who reported less seriously considering leaving the job perceived that people recently avoided them because of the job. Besides, less appreciation from their organization  and believing that they could die from COVID‐19 more than from cancer  were significant predictors for more considering leaving the job.Factors contributing to leaving the job were assessed using multivariate logistic regression Table . The log3.1.3r = −0.21, p < 0.001), and male participants of HCPs  feel at higher risk of being infected with COVID‐19. Also, male HCPs  and those with long experience  experienced more workload and stress during the COVID‐19 pandemic. Older HCPs  with long experience in the job  and previous experience caring for patients during a pandemic  noted more social relationships during the COVID‐19 pandemic. Also, younger  and married HCPs and those with long professional experience  stated more emotional support than others. Nevertheless, the younger, married HCPs and those without previous experience in caring for patients with infectious diseases reported the possibility of fatality from COVID‐19 more than other illnesses. All socio‐demographic variables were significantly associated with the perception of HCPs about the adequacy of personal protective equipment in their departments.The relationship between the perception of HCPs of leaving the job and socio‐demographic variables is described in Table 4The pandemic of COVID‐19 has affected the mental and psychosocial well‐being of individuals and HCPs, as well; work overload, distress related to COVID‐19, and fear of infection and being a source of infection were the most reported factors that influenced HCPs.Nevertheless, the finding in this study was supporting previous reports that almost equal percentages of nurses had an intention to leave their jobs during the pandemic of COVID‐19.During the COVID‐19 pandemic, other factors are associated with leaving the HCPs their jobs, such as the availability of personal protective equipment. Notably, the low availability of protective equipment probably increased the risk of leaving the HCPs their jobs.COVID‐19 can easily spread to individuals close to HCPs as patients, families, and friends.5The current study may shed light on some clinical practice and leadership implications, such as presenting clear policies that aim to protect HCPs during such pandemics and offering support from leaders. These points could increase their self‐confidence, improve their morale, motivate them, and decrease their intention to leave the job. Offering personal protective measures in healthcare settings will give the HCPs a sense of safety and maximize teamwork that minimizes stress. Promoting psychosocial support for HCPs from their organizations and the public will enhance their satisfaction and minimize their fear, resulting in low intention to leave the job.Considering that participants were enrolled from various public hospitals in the region, this could reflect the strength of the study and thus could support the generalizability of the findings to Jordan. Similarly, the study considered a clustering effect because the data were collected from different regions. However, this study had some limitations related to the use of an online cross‐sectional survey that might affect the attrition rate of the participants. In this regard, many surveys were excluded due to missing data that could introduce potential bias and affect the study's findings. In addition, missing some confounding factors such as the specialty of the physicians, professional level, and daily working hours could all affect the participants' intention to leave job.6This study highlighted that HCPs with a high risk of exposure to COVID‐19 and who experienced more workload were seriously considering leaving their jobs. At the same time, married participants have lower consideration for leaving their jobs. Policy‐makers need to pay attention to young and single HCPs during the COVID‐19 pandemic to prevent them from leaving their job. Clear guidelines for managing workload during the COVID‐19 pandemic are needed. Furthermore, as the global risk of COVID‐19 infection remains high and HCPs in several countries could be confronted with similar challenges, all possible psychosocial and work‐related factors should be urgently identified.Mohammad M. Alnaeem: Conceptualization; formal analysis; methodology; writing–original draft; writing–review and editing. Ayman M. Hamdan‐Mansour: Formal analysis; writing–original draft; writing–review and editing. Abdulqadir J. Nashwan: Writing–original draft; writing–review and editing. Alaa Abuatallah: Data curation; writing–original draft; writing–review and editing. Mahmoud Al‐Hussami: Data curation; writing–original draft; writing–review and editing.The authors declare that they have no competing interests. Abdulqadir J. Nashwan is an Editorial Board member of Health Science Reports and coauthor of this article. He is excluded from editorial decision‐making related to the acceptance of this article for publication in the journal.The Institutional Review Board at Prince Hamza Hospital has approved this study. The current study followed the Declaration of Helsinki provisions, and all participants provided informed consent. The permission to use and translate copyrighted instruments has been received from the original author. No approval from hospitals was required according to the nature of the online study. The study was conducted following the EQUATOR research reporting checklist; (STROBE checklist) for cross‐sectional research. It was uploaded to the online system.The lead author Abdulqadir J. Nashwan affirms that this manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as planned  have been explained.


Dolichonyx oryzivorus) breed in grasslands across northern North America and migrate from their breeding grounds toward the eastern Atlantic Coast and then proceed through the Caribbean to South America. However, a small but regular number of Bobolinks have been recorded on the Galapagos Islands. We collected genetic samples from nine Galapagos Bobolinks and performed double‐digest restriction site‐associated sequencing. We compared them with samples from seven locations across their breeding distribution to determine their population of origin. Galapagos Bobolinks shared the genetic structure of a cluster in the eastern portion of the breeding range that includes New Brunswick and Ontario, Canada, and Vermont, United States. Genetic assignment tests largely corroborated this finding, although slightly different results were obtained for the two methods. All individuals were assigned to the Ontario breeding population using AssignPop, while Rubias assigned six of the migrants to Ontario and three to a Midwest breeding population. Low average relatedness among Galapagos individuals indicates that they are not more related to one another than to individuals within a breeding population and are therefore likely not from a single, small isolated population. Our results do not support the probability hypothesis—that Galapagos Bobolinks originated from the region that includes the greatest proportion of their breeding range (Great Plains)—or the vagrant hypothesis—that migrants are displaced onto Galapagos due to weather events. Instead, our findings support the proximity hypothesis, where migrants originate from the geographically closest‐breeding populations.Little is known about the causes and consequences of alternative pathways flown by long‐distance migratory birds. Bobolinks ( Little is known about the causes and consequences of alternative pathways flown by long‐distance migratory birds. Using population genetic analyses, we compared samples from migratory Bobolinks stopping over in Galapagos with samples from seven locations across their breeding distribution to determine the migrant's breeding population of origin. Galapagos Bobolinks shared the genetic structure of a cluster in the eastern portion of the breeding range in North America that includes New Brunswick, Vermont, and Ontario. For example, morphological traits that favor higher maneuverability can enable individuals to take a less risky but more energetically challenging route  tracked from three populations across their European breeding distribution took detours from the shortest route possible, and the detour extent varied among populations and between spring versus fall migration , a grassland obligate songbird in the blackbird family (Icteridae), migrates between North and South America each year. Its breeding range spans nearly coast to coast in Canada and the United States. Populations from British Columbia to Nova Scotia migrate through the Caribbean and the Llanos of Venezuela and Colombia to and from their wintering grounds in Bolivia and Argentina  The vagrant hypothesis suggests that Bobolinks are in Galapagos as a result of weather events that have displaced them from their usual migration route. Under this hypothesis, we expect that Bobolinks that stop on Galapagos would originate from multiple breeding populations. This hypothesis could also be supported if Galapagos Bobolinks originate from only one region, and by chance, the weather events affect this region only. (3) The proximity hypothesis predicts that Galapagos birds originate from the part of the breeding range that is the shortest orthodromic distance from Galápagos. Under this hypothesis, we expect that Galápagos Bobolinks would originate from the southern part of midwestern or eastern breeding populations. (4) Under the alternate non‐breeding range hypothesis, Bobolinks stopping in the Galápagos Islands are passing through on their way to spend the austral summer in Ecuador, potentially on the islands themselves, in Ecuador west of the Andes, or in Peru (areas outside of their main wintering range).We propose four main hypotheses, not mutually exclusive, to explain why some Bobolinks migrate through Galapagos. (1) Under the Here, we use genetic analyses to examine the breeding origins of Bobolinks that stop in Galápagos during their southbound migration. We assign individuals to their breeding region based on the known genetic population structure of Bobolink across its breeding range  sequencing libraries for the nine Galápagos samples in this study and the 174 Bobolink breeding population samples, following the Peterson et al.  protocolBioinformatic data processing and SNP identification are also described in Renfrew et al. . In summm = 3  and M and n = 5 . We used program Populations in STACKS to group individuals into eight geographic sampling locations , from which we identified polymorphic SNPs. We required an SNP to be present in 70% of individuals and six populations to be called. We also required a minimum minor allele frequency of 0.01 and maximum observed heterozygosity of 0.5 to process a nucleotide site at a locus. Only the first SNP per stack was used to avoid linkage in the dataset. This resulted in a final SNP panel of 3234 SNPs. We tested for conformance to Hardy–Weinberg equilibrium and validated that missing data in our final dataset had no effect on inference of population structure  pipeline to identify SNPs from these filtered sequences. We optimized parameters for the de novo assembly, as described in Renfrew et al. , resulti2.3K value (K = 1–8). We used the LocPrior model . To assess the results of STRUCTURE and determine the best‐supported model, we used a combination of the delta K method  with the Adegenet package in program R as an additional method to assess genetic differentiation among the samples Jombart,  and deteFis values) for each of the seven breeding locations and the nine Galápagos migrants, in the program Populations of STACKS. We calculated pairwise individual relatedness values for each bird using ‐‐realtedness2 function in VCF tools  in fisheries, and it is powerful for estimating mixture proportions and individual assignments in other systems as well . After de novo assembly , we werK method, STRUCTURE analysis supported a k = 3 solution; however, the plateau in the estimated log probability of the data (LnP(D)) suggested a model of k = 4  were similar among all the sampling locations , while Nebraska exhibited the highest value (0.147). Mean pairwise relatedness within populations was low for all sample locations  for the four regional breeding population groups , with all groups having >89% correct assignment Table . Self‐asFor the simulated mixtures in Rubias, the average P of Z was consistently high across regional breeding population simulations , regardless of the method of resampling, ranging from 99% to 100% with the gene copy method and 91%–100% with the full multilocus method  for the analysis with the seven breeding populations matched the results of the assignment testing, with approximately 0.606 proportional assignment to Ontario, 0.315 to Nebraska, and 0–0.019 to the other five populations. Bootstrap correctedproportions were largely similar to the uncorrected mixture proportions, albeit slightly higher to Nebraska and Ontario, thereby further strengthening the evidence for these assignments Table . Uncorre4Using genetic data in conjunction with assignment testing and mixture analysis, we identified the breeding population of origin of individual Bobolinks that use an alternate migratory pathway through the Galápagos Islands. Comparing the genotypes at 3234 SNPs of nine Bobolinks captured in Galápagos during their southbound migration to population genetic data for seven locations in the Bobolink breeding range, we determined that the Galápagos migrants were genetically most similar to Bobolinks from the eastern portion of the breeding range. The two different assignment testing approaches that we used gave largely similar results, however, there were slight discrepancies. The AssignPop method assigned all nine migrants to the Ontario location within the eastern breeding population with high confidence. Rubias assigned six of the migrants to the Ontario population with high confidence and three to Nebraska (in the midwestern breeding group). When mixture analysis was conducted with the four genetically distinct breeding groups, rather than all seven breeding locations, the bootstrap corrected mixing proportions corroborated the AssignPop results, with nearly the full mixture assigned to the eastern population. Taken together, these results best support the eastern breeding population as the origin of most or all of the Galápagos migrants, although it cannot be ruled out that some individuals may have originated in the Midwest.Fis and negative relatedness values for the Galápagos Bobolinks  is the same as the longitude where the Mississippi River divides southern Wisconsin and southern Minnesota, approximately 4900 km from the Galápagos Islands. The Mississippi River basin would therefore be the location that is the shortest orthodromic distance from the Galápagos Islands. If this region of the Midwest is genetically similar to the eastern breeding population (particularly Ontario), it would provide evidence supporting the origin of Galápagos Bobolinks in the Mississippi River basin, thereby supporting the proximity hypothesis. Alternatively, the proximity hypothesis would also be supported if the Galápagos Bobolinks originated from the southeastern portion of the breeding range , although the Bobolinks would have to fly a portion of that route along a declination counter to that of the main route through the Caribbean. Under the vagrant hypothesis, individuals from the eastern part of their breeding distribution could have been forced west by weather events prior to southbound migration and did not correct their migratory declination accordingly. There is support for such a lack of correction: a Bobolink breeding in North Dakota that was experimentally displaced to California prior to migration did not adjust its migration declination, and instead flapped in the direction of the coast of California, toward the Pacific Ocean ; funding acquisition (lead); investigation (lead); methodology ; project administration (lead); resources ; writing – original draft (lead); writing – review and editing (lead). Logan M. Maxwell: Formal analysis ; investigation ; methodology ; visualization (lead); writing – original draft ; writing – review and editing . Adrienne Kovach: Conceptualization ; formal analysis ; funding acquisition ; investigation ; methodology ; resources ; writing – original draft ; writing – review and editing . Patricia Parker: Conceptualization ; writing – original draft ; writing – review and editing . Rosalind B. Renfrew: Conceptualization ; investigation ; writing – original draft ; writing – review and editing .Benefits from this research accrue from the sharing of our data and results on public databases as described above.Appendix S1Click here for additional data file.


The COVID‐19 pandemic has led to temporary changes in human–animal interactions due to changes in human activities. Here, we report on a surge in hedgehog observations during the first COVID‐19 lockdown in Germany in 2020, on the citizen science Web portal “Igel in Bayern” (Hedgehogs in Bavaria) in Germany. This increase in comparison with previous years was attributed to an increase in the number of people reporting hedgehog observations, rather than an increase in the number of hedgehog observations made by each observer. Additionally, in contrast to other studies on the effects of a COVID‐19 lockdown on observations recorded by citizen science projects, the share of observations made in more urbanized areas during the lockdown time was not higher than the change observed in less urbanized areas. This is possibly a result of the differences in COVID‐19 measures between Germany and other countries where preceding studies were carried out, in particular the lack of measures limiting traveling outdoor activities for citizens. A significant increase in Hedgehog observations and people observing hedgehogs can be observed in the first COVID‐19 lockdown in Bavaria, Germany, based on data from the NGO "Landesbund für Vogelschutz." The increase in observations was attributed to the increase in observers. In contrast to other studies on the effect of a COVID‐19 lockdown on observations recorded by citizen science projects, the share of observations made in more urbanized areas was not higher than the change observed in less urbanized areas. In several countries, these lockdowns have increased public interest in urban nature , and entailed restrictions on movement and contacts among people . Observations started in 2015. We use data collected by the portal to ask the following questions:Did the first major lockdown in Germany lead to an increase in the number of hedgehog observations on the LBV app and portal?Is a change in the number of observations due to an increased number of people making observations, or to an increased number of observations made by each observer?Are there differences between urban and nonurban areas in any changes in the number of observations?Here, we report on a COVID‐19 effect on observations of hedgehogs made through a citizen science portal in Germany. The NGO "Landesbund für Vogelschutz" (LBV) in Bavaria uses an app and a Web portal to monitor the occurrence of hedgehogs in Bavaria ; Data curation ; Formal analysis (lead); Investigation (lead); Methodology (lead); Project administration ; Software (lead); Visualization (lead); Writing – original draft (lead); Writing – review & editing . Thomas Rödl: Data curation ; Resources ; Writing – review & editing . Wolfgang Weisser: Conceptualization ; Formal analysis (supporting); Funding acquisition (lead); Methodology (supporting); Resources (lead); Supervision ; Writing – review & editing .The authors declare no conflict of interest.AppendixS1Click here for additional data file.