bluuebunny/crossref_metadata_2025 huggingface dataset:
Nemo knows: clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a potential adaptive radiation in the clownfish-hosting sea anemones
Authors: Chiodo Tommaso , De Jode Aurélien , Quattrini Andrea , Gibson Miranda K. , Froehlich Catheline Y. M. , Huang Danwei , Fujii Takuma , Yanagi Kensuke , Reimer James D. , Scott Anna , Rodríguez Estefanía , Titus Benjamin M.
Published: November 2024

The symbiosis between clownfishes (or anemonefishes) and their host sea anemones ranks among the most recognizable animal interactions on the planet. Found on coral reef habitats across the Indian and Pacific Oceans, 28 recognized species of clownfishes adaptively radiated from a common ancestor to live obligately with only 10 nominal species of host sea anemones. Are the host sea anemones truly less diverse than clownfishes? Did the symbiosis with clownfishes trigger a reciprocal adaptive radiation in sea anemones, or minimally, a co-evolutionary response to the mutualism? To address these questions, we combined fine- and broad-scale biogeographic sampling with multiple independent genomic datasets for the bubble-tip sea anemone,Entacmaea quadricolor—the most common clownfish host anemone throughout the Indo-West Pacific. Fine-scale sampling and restriction site associated DNA sequencing (RADseq) throughout the Japanese Archipelago revealed three highly divergent cryptic species: two of which co-occur throughout the Ryukyu Islands and can be differentiated by the clownfish species they host. Remarkably, broader biogeographic sampling and bait-capture sequencing reveals that this pattern is not simply the result of local ecological processes unique to Japan, but part of a deeper evolutionary signal where some species ofE. quadricolorserve as host to the generalist clownfish speciesAmphiprion clarkiiand others serve as host to the specialist clownfishA. frenatus. In total, we delimit at least five cryptic species inE. quadricolorthat have diversified within the last five million years. The rapid diversification ofE. quadricolorcombined with functional ecological and phenotypic differentiation supports the hypothesis that this may represent an adaptive radiation in response to mutualism with clownfishes. Our data indicate that clownfishes are not merely settling in locally available hosts but recruiting to specialized host lineages with which they have co-evolved. These findings have important implications for understanding how the clownfish-sea anemone symbiosis has evolved and will shape future research agendas on this iconic model system.
On the Mkv Model with Among-Character Rate Variation
Authors: Capobianco Alessio , Höhna Sebastian
Published: November 2024

Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model— which introduces an acquisition bias correction for sampling only characters that are observed to be variable—and for models of among-character rate variation (ACRV), routinely applied by researchers to relax the equal-rates assumption of Mkv. However, the interaction between variable character acquisition bias and ACRV has never been explored before. We demonstrate that there are two distinct approaches to condition the likelihood on variable characters when there is ACRV, and we call them joint and marginal acquisition bias. Far from being just a trivial mathematical detail, we show that the way in which the variable character conditional likelihood is calculated results in different assumptions about how rate variation is distributed in morphological datasets. Simulations demonstrate that tree length and amount of ACRV in the data are systematically biased when conditioning on variable characters differently from how the data was simulated. Moreover, an empirical case study with extant and extinct taxa reveals a potential impact not only on the estimation of branch lengths, but also of phylogenetic relationships. We recommend the use of the marginal acquisition bias approach for morphological datasets modeled with ACRV. Finally, we urge developers of phylogenetic software to clarify which acquisition bias correction is implemented for both estimation and simulation, and we discuss the implications of our findings on modeling variable characters for the future of morphological phylogenetics.
Predicting Prognostic Bidirectional Molecular Signatures Associating Myocardial Infarction and Lung Cancer: AnIn-SilicoPerspective
Authors: Nandi Dhruva , Janardhanan Rajiv , Agrawal Piyush
Published: November 2024

Myocardial Infarction (MI) and lung cancers substantially contributors to morbidity and mortality. They share common risk factors such as smoking, and hypertension. There is a pressing need to identify bidirectional molecular signatures linking MI and lung cancer relationship to create a unique triage to improve the clinical outcomes of the patient. In the current work, we extracted the common differentially expressed genes (DEGs) between MI and lung cancer and identified 2339 upregulated and 2973 downregulated genes in MI datasets; 952 upregulated and 653 downregulated genes in LUAD; 1466 upregulated and 2816 downregulated genes in LUSC. Among these, 27 genes (11 upregulated and 16 downregulated) were common across MI, LUAD, and LUSC. Functional enrichment analysis revealed shared biological processes, such as inflammatory response, and cell differentiation. KEGG pathway analysis highlighted common pathways such as B cell receptor signaling, TNF signaling. A protein-protein interaction study with STRING revealed a variety of interaction partners; miRNA-mRNA network analysis characterizes conserved binding sites for 6 genes while overall survival analysis for lung cancer patients shows a significant association with prognosis. In addition, machine learning models built using the Support Vector Machine and Random Forest algorithms demonstrated high AUROC values of 0.79 and 0.81 respectively on balanced dataset in the classifying MI patients from non-MI patients. Lastly, based on drug repurposing analysis, we proposed FDA-approved drugs such as Venetoclax, Lomitapide, Regorafenib that could potentially target these genes, indicating novel therapeutic options for the co-occurring conditions of MI and lung cancer. Our findings highlight the similarities in molecular makeup between lung cancer and MI, providing information for future investigations and therapeutic approaches.
Mutagenic impact and evolutionary influence of radiotherapy in hematologic malignancies
Authors: Diamond Benjamin , Chahar Dhanvantri , Jain Michael D. , Poos Alexandra M. , Durante Michael , Ziccheddu Bachisio , Kaddoura Marcella , Papadimitriou Marios , Maclachlan Kylee , Jelinek Tomas , Davies Faith , Figura Nicholas B , Morgan Gareth , Mai Elias , Weisel Katja C. , Fenk Roland , Raab Marc S. , Usmani Saad , Landgren Ola , Locke Frederick L. , Goldschmidt Hartmut , Schatz Jonathan H. , Weinhold Niels , Maura Francesco
Published: November 2024

Ionizing radiotherapy (RT) is a widely used palliative and curative treatment strategy for malignancies. In solid tumors, RT-induced double strand breaks lead to the accumulation of indels, and their repair by non-homologous end-joining has been linked to the ID8 mutational signature in resistant cells. However, the extent of RT-induced DNA damage in hematologic malignancies and its impact on their evolution and interplay with commonly used chemotherapies has not yet been explored. Here, we interrogated 580 whole genome sequencing (WGS) from patients with large B-cell lymphoma, multiple myeloma, and myeloid neoplasms and identified ID8 only in relapsed disease. Yet, it was detected after exposure to both RT and mutagenic chemotherapy (i.e., platinum). Using WGS of single-cell colonies derived from treated lymphoma cells, we revealed a dose-response relationship between RT and platinum and ID8. Finally, using ID8 as a genomic barcode we demonstrate that a single RT-resistant cell may seed systemic relapse.
Single-cell epigenetic profiling reveals an interferon response-high program associated withBAP1deficiency in kidney cancer
Authors: Camp Sabrina Y. , He Meng Xiao , Cuoco Michael S. , Saad Eddy , Pimenta Erica , Meli Kevin , Bakouny Ziad , Labaki Chris , Titchen Breanna M. , Kang Yun Jee , Horst Jack , Trowbridge Rachel , Shannon Erin , Helvie Karla , Thorner Aaron R. , Vigneau Sébastien , Mayorga Angie , Kodali Jahnavi , Lachmayr Hannah , Bemus Meredith , Park Jihye , Choueiri Toni , Bi Kevin , Van Allen Eliezer M.
Published: November 2024

Renal cell carcinoma (RCC) is characterized by recurrent somatic mutations in epigenetic regulators, which stratify patients into clinically significant subgroups with distinct prognoses and treatment responses. However, the cell type-specific epigenetic landscape of RCC—broadly and in the context of these mutations—is incompletely understood. To investigate these open questions, we integrated single nucleus ATAC sequencing data from RCC tumors across four independent cohorts. In clear cell RCC tumors, we identified four shared malignant epigenetic programs related to angiogenesis, proximal tubule-like features, interferon (IFN) signaling, and one that lacked distinct genomic regions with increased accessibility. Among the mutated epigenetic regulators,BAP1mutation exhibited the most significant impact on chromatin accessibility in tumor cells, and the associated epigenetic changes were linked to IFN response. We identify multiple potential sources of elevated IFN signaling in these lesions, such as increased immune infiltration and increased accessibility and expression of an IFN-associated ERV, ERV3-16A3_LTR. We find that the expression of ERV3-16A3_LTR may itself be a negative prognostic biomarker in ccRCC. Our findings highlight the convergence of malignant epigenetic programs across ccRCC tumors and suggest thatBAP1loss, potentially through ERV3-16A3_LTR dysregulation, is associated with an IFN response-high epigenetic program.
Comparison of Gene Expression between Chronic Rhinosinusitis with Nasal Polyposis and without Nasal Polyposis
Authors: Kasem Mahmoud Fawzy , Helal Mohamed Lotfy , Elsfafey Ola Hamdy
Published: November 2024

Objectives

We aimed to compare the gene expression between chronic sinusitis with nasal polyposis and chronic rhinosinusitis without nasal polyposis either eosinophilic or not.

Background

Chronic rhinosinusitis (CRS) is a disease characterized by chronic inflammation of the nasal cavity and sinus mucosa. CRS mainly presents as phenotypes, namely, CRS without nasal polyps (CRSsNP) and CRS with nasal polyps (CRSwNP), based on whether it is accompanied by polyps or not. Micro-array analyses investigating the immune endo-types and pathogenesis of CRSwNP typically rely on invasive nasal biopsies.

Methods

This prospective randomized study was conducted on 150 patients with chronic nasal obstruction (more than 3 months). These group of patients consisted of four groups as CRSwNP patients (including eosinophilic CRSwNP [ECRSwNP] and non-eosinophilic CRSwNP [NECRSwNP]) and CRSsNP patients including eosinophilic CRSwNP [ECRSwNP] and non-eosinophilic CRSwNP [NECRSwNP]) for protein quantification by COLOC platform and gene expression evaluation by RNA-sequencing. Spearman’s analysis was performed to detect correlations between protein expression levels and clinical assessment variables.

Results

There were female predominance in eosinophilic CRS plus higher CT score in ECRSwNP than NECRSwNP. There was also higher SNOT-22 score in ECRSwNP than NECRSwNP. There were significant differences in all items of SNOT-22 scale after nasal polypectomy. The prevalence of the condition/disease is assumed to be 0.1. The sensitivity of 0.1 with 90% power, the specificity was 85%.

Conclusion

Our study revealed that there are higher recurrence, rate of manifestations for the patients with genetic predisposition of CCL18 and CCL13 more than others.
Long-term balancing selection maintains cryptic color polymorphism in frogs
Authors: Goutte Sandra , Boissinot Stéphane
Published: November 2024

Color polymorphism can influence the evolutionary fate of cryptic species because it increases populations’ chances of survival in heterogenous or variable environments. Yet, little is known about the molecular and evolutionary mechanisms underlying the persistence of cryptic color polymorphisms, or the impact these polymorphisms have on the macro-evolutionary dynamics of lineages. Here, we examine the evolutionary history of the most widespread cryptic color polymorphism in anurans, involving green and brown morphs. Using an order-scale comparative analysis, we show that these morphs can co-exist within species over long periods of evolutionary time and that polymorphic lineages switch habitat more frequently and have greater diversification rates than other groups. We then identify the locus responsible for the green/brown polymorphism in a group of African grass frogs, and demonstrate that this genomic region is evolving under long-term balancing selection, resulting in trans-specific polymorphism. These results provide a micro-evolutionary mechanism for the long-term persistence of color polymorphism observed at a macro-evolutionary scale. This study highlights the importance of cryptic color polymorphism in the ecology and evolution of anurans, and provides a framework for future research on the genetic architecture and selective forces underlying cryptic traits.
Real-world epilepsy monitoring with ultra long-term subcutaneous EEG: a 15-month prospective study
Authors: Viana Pedro F. , Duun-Henriksen Jonas , Biondi Andrea , Winston Joel S. , Freestone Dean R. , Schulze-Bonhage Andreas , Brinkmann Benjamin H. , Richardson Mark P.
Published: November 2024

Objective

Novel subcutaneous electroencephalography (sqEEG) systems enable prolonged, near-continuous cerebral monitoring in real-world conditions. Nevertheless, the feasibility, acceptability and overall clinical utility of these systems remains unclear. We report on the longest observational study using ultra long-term sqEEG to date.

Methods

We conducted a 15-month prospective, observational study including ten adult people with treatment-resistant epilepsy. After device implantation, patients were asked to record sqEEG, to use an electronic seizure diary and to complete acceptability and usability questionnaires. sqEEG seizures were annotated visually, aided by automated detection. Seizure clustering was assessed via Fano Factor analysis and seizure periodicity at multiple timescales was investigated through circular statistics.

Results

Over a median duration of 438 days, ten patients recorded a median 18.8 hours/day, totalling 71,984 hours of real-world sqEEG data. Adherence and acceptability remained high throughout the study. While 754 sqEEG seizures were recorded across patients, over half (52%) of these were not reported in the patient diary. Of the 140 (27%) diary reports not associated with an identifiable sqEEG seizure, the majority (68%) were reported as seizures with preserved awareness. The sqEEG to diary F1 agreement score was highly variable, ranging from 0.06 to 0.97. Patient-specific patterns of seizure clustering and seizure periodicity were observed at multiple (circadian and multidien) timescales.

Interpretation

We demonstrate feasibility and high acceptability of ultra long-term (months-years) sqEEG monitoring. These systems help provide real-world, more objective seizure counting compared to patient diaries. It is possible to monitor individual temporal fluctuations of seizure occurrence, including seizure cycles.

Summary for Social Media if Published

[I do not have a X/Twitter handle]

People with epilepsy may suffer from severe injuries or sudden death due to uncontrolled seizures. Many seizures remain unnoticed by people and unreported to doctors, despite these potentially catastrophic consequences. There is an urgent need to detect seizures more objectively. Our study used a novel device placed under the skin to monitor brainwave activity continuously, at home, for many months, in people with treatment-resistant epilepsy. By monitoring epilepsy from home, we detected many seizures unreported by patients, and we also found predictable patterns (cycles) of seizure occurrence over time. In the future, this type of monitoring could revolutionize epilepsy care, by improving safety, treatment management and reducing uncertainty in patients’ daily lives.
Bias in control selection associated with the use of rapid tests in influenza vaccine effectiveness studies
Authors: Poukka Eero , Murphy Caitriona , Mak Loretta , Cheng Samuel M. S. , Peiris Malik , Tsang Tim K. , Sullivan Sheena G. , Cowling Benjamin J.
Published: November 2024

In test-negative design studies that use rapid tests to estimate influenza vaccine effectiveness (VE) a common concern is case/control misclassification due to imperfect test sensitivity and specificity. However, an imperfect test can also fail to exclude from the control group people that do not represent the source population, including people infected with other influenza types or other vaccine-preventable respiratory viruses for which vaccination status is correlated. We investigated these biases by comparing the effectiveness of seasonal 2023/24 influenza vaccination against influenza A and B based on PCR versus rapid test results, excluding controls who tested positive for SARS-CoV-2 or the other type of influenza. By PCR, VE against influenza A was 49% (95%CI 26–65%) after exclusion of PCR-confirmed influenza B and SARS-CoV-2 controls. Corresponding VE against influenza B was 65% (95%CI 35–81%). VE estimated by adjusting for COVID-19 vaccination status yielded similar estimates to the scenario that excluded SARS-CoV-2-positive controls. When case/control status and exclusions from test-negative controls were determined by rapid test, VE was reduced by 5–15 percentage points. Bias correction methods were able to reduce these discrepancies. When estimating VE from a test-negative study using rapid test results, methods to correct misclassification bias are recommended.
CB1 and CB2 receptors differentially modulate the cognitive impact of maternal immune activation and perinatal cannabinoid exposure
Authors: Chen Han-Ting , Mackie Ken
Published: November 2024

Maternal immune activation (MIA) commonly arises in response to an infection during pregnancy. MIA elevates cytokine levels, triggering an inflammatory cascade, which may be detrimental to the developing nervous system. Similarly, cannabis use and exposure of the fetus to cannabinoids during pregnancy (PCE) may elicit neuroinflammation and lead to detrimental behavioral outcomes. This is particularly concerning as there has been a notable rise in cannabis use during pregnancy. This study endeavors to examine the interaction between MIA and PCE and elucidate the role of CB1 and CB2 receptors in MIA and PCE outcomes. To this end, we compared the impact of MIA, PCE and MIA+PCE in wildtype, CB1, and CB2 cannabinoid receptor knockout mice of both sexes. PCE was modeled by daily 3 mg/kg THC administration from gestational day 5 (GD5) to postnatal day 10. MIA was modeled by intravenous Poly (I:C) injection at GD16.5. Subsequently, we assessed emotional and cognitive behaviors of adult offspring. Adult male offspring of dams exposed to PCE or MIA were impaired in novel object recognition and the delayed alternation working memory tasks. Interestingly, these behavioral impairments were absent when MIA and PCE were combined. Cannabinoid receptor knockout studies found that CB1 receptors mediated behavioral deficits after PCE. In contrast CB2 receptors were necessary for full expression of MIA-induced behavioral impairments. Although females showed more modest behavioral changes after MIA or PCE, CB1 receptors were required for the PCE deficit and CB2 receptors were required for the MIA deficit also in females. Notably, lack of CB2 receptors in males prevented the “protection” following combined MIA + PCE, while CB1 knockout mice remained protected. Taken together, these results suggest a complex interplay between PCE, MIA and CB1 and CB2 cannabinoid receptors.

Highlights

Both PCE and MIA impair cognitive behaviors.

Combined PCE and MIA did not affect the cognitive behaviors examined.

CB1 receptors are required for deficits after prenatal cannabis exposure.

CB2 receptors are required for deficits after maternal immune activation.

CB2 receptors are necessary for protection from deficits by combined PCE and MIA.
Assessing the helical stability of polyXYs at the boundaries of Intrinsically Disordered Regions with MD simulations
Authors: Gonçalves-Kulik Mariane , Baptista Luis A. , Schmid Friederike , Andrade-Navarro Miguel A.
Published: November 2024

Intrinsically disordered regions (IDRs) in proteins lack stable structure. By carrying many hydrophilic and charged residues, it prevents them from forming globular domains and contributes to their flexibility and accessibility. Naturally, regions with reduced amino acid composition (low complexity regions; LCRs) occur within IDRs. Disorder and low complexity in protein sequences are linked to various biological functions including phase separation, regulation, and molecular interactions, and mutations in these regions can contribute to several diseases including cancer. Understanding these biological properties requires examination of the structural properties of IDRs and the LCRs within, but their inherently dynamic nature requires specific approaches combining sequence analyses, structure predictions and molecular dynamics (MD) simulations. Here, we leverage our previous work where we identified that some types of LCRs combining two residues (polyXY) are frequent within IDRs and confer them with propensity to form helical conformation. We identify a significant accumulation of such polyXYs at the ends of IDRs following alpha-helices that start outside the IDR and may extend through the polyXY into the IDR, particularly from the N-terminal end of the IDR. MD simulations support the dynamic nature of such helical conformations. Our results suggest a mechanism by which evolutionary emergence of LCRs at IDR ends could provide proteins with flexible regions for fold-upon-binding.
An animal model for autoinflammation with infantile enterocolitis
Authors: Wang Yuhang , Gao Joyce Z. , Gurung Prajwal , Short Sarah P. , Xiong Yiqin , Kang Zizhen
Published: November 2024

Inflammasomes, particularly NLRC4, play a crucial role in immune responses to intracellular bacterial infections. However, gain-of-function mutations of NLRC4 are linked to severe autoinflammatory diseases, including autoinflammation with infantile enterocolitis (AIFEC). Existing mouse models do not adequately replicate the chronic, unprovoked inflammation observed in AIFEC patients. In this study, we developed a loxP-flanked NLRC4 V341A knock-in (KI) mouse model. Our global NLRC4 V341A KI mice exhibited symptoms closely mirroring those of human AIFEC. These mice demonstrated severe infantile enterocolitis, characterized by heightened intestinal inflammation, compromised intestinal barrier integrity, disrupted gut epithelium, and severe diarrhea, with high mortality within 10 days postnatally. Additionally, they displayed systemic autoinflammation marked by elevated levels of IL-1β, IL-18, and IL-6, alongside cytopenia and hemophagocytosis. In contrast, adult NLRC4 conditional KI mice exhibited autoinflammation with only mild enterocolitis. Since AIFEC is characterized by life-threatening enterocolitis in infancy and recurrent severe autoinflammation throughout life, our conditional NLRC4 KI model effectively recapitulates the clinical features of human AIFEC. Moreover, the NLRC4 V341A-mediated monogenic infantile enterocolitis observed in our model resembles infantile-onset inflammatory bowel disease (IBD), positioning it as a valuable platform for research on very early-onset IBD.
VNC-Dist: A machine learning-based tool for quantification of neuronal positioning in the ventral nerve cord ofC. elegans
Authors: Saharkhiz Saber , Petite Mearhyn , Roenspies Tony , Perkins Theodore , Colavita Antonio
Published: November 2024

The ventral nerve cord (VNC) of newly hatchedC. eleganscontains 22 motoneurons organized into three distinct classes: DD, DA, and DB, that show stereotypical positioning and arrangement along its length. The VNC represents a genetically tractable model to investigate mechanisms involved in neuron sorting and positioning. However, accurately and efficiently mapping and quantifying all motoneuron positions within large datasets is a major challenge. Here, we introduce VNC-Dist, a semi-automated software toolbox designed to overcome the limitations of subjective motoneuron positioning analysis in microscopy. VNC-Dist uses an annotator for neuron localization and an automated contour-based method for measuring the relative distances of neurons along the VNC based on deep learning and numerical analysis. To demonstrate the robustness and versatility of VNC-Dist, we applied it to multiple genetic mutants known to disrupt neuron positioning in the VNC. This toolbox will enable the acquisition and analysis of large datasets on neuronal positioning, thereby advancing investigations into the cellular and molecular mechanisms that control neuron positioning and arrangement in the VNC.
Criterial Learning and Feedback Delay: Insights from Computational Models and Behavioral Experiments
Authors: Crossley Matthew J. , Pelzer Benjamin O. , Ashby F. Gregory
Published: November 2024

The notion of a response criterion is ubiquitous in psychology, yet its cognitive and neural underpinnings remain poorly understood. To address this shortcoming, three computational models that capture different hypotheses about criterial learning were developed and tested. The time-dependent drift model assumes the criterion is stored in working memory and that its value drifts over time. The delay-sensitive learning model assumes that the magnitude of criterial learning is temporally discounted by feedback delay. The reinforcement-learning model assumes that criterial learning emerges from stimulus-response association learning without an explicit representation of the criterion, with learning rate also temporally discounted by feedback delay. The performance of these models was investigated under varying feedback delay and intertrial interval (ITI) durations. The time-dependent drift model predicted that long ITIs and feedback delays both impair criterial learning. In contrast, the delay-sensitive and reinforcement-learning models predicted impairments only with feedback delays. Two behavioral experiments, which tested these predictions, showed that human criterial learning is impaired by delayed feedback but not by long ITIs. These results support the delay-sensitive and reinforcement-learning models, and suggest that even in tasks that appear to rely on explicit, rule-based reasoning, criterial learning may have strong associative underpinnings.
A Qualitative Exploration of the use Social Media for Learning by Emergency Medicine Doctors
Authors: Edwards Sarah , Mayat Nabilah
Published: November 2024

Background

The use of social media for learning amongst emergency medicine doctors has been increasing in recent years. However, the role of social media as a learning modality in emergency medicine is not fully understood. This study aims to understand why and how emergency medicine doctors use social media for learning. Through this understanding this study aims to promote thought into design of future resources of learning on social media.

Methods

Emergency Medicine doctors of all grades were recruited, from a single tertiary University Hospital in the United Kingdom. These participants were interviewed by semi structured interview following the principles of a Critical Incident Technique. Recordings were professionally transcribed. Transcriptions were then thematically analysed and coded to understand participant’s perspectives. Ethics was granted by Cardiff University, Wales.

Results

20 emergency medicine doctors from Foundation Year 1 through to consultants were interviewed. Twitter (X) was the most popular platform; infographics were the most popular resource and 80% spent less than 3 hours per week on SM for learning. Key themes from the thematic analysis as to why emergency medicine doctors used social media for their learning included wanting to keep up to date ease of access, discussion around topics, bench marking current practice, community, and recommendations. Only 10% used social media as part of their continued professional development and 65% stated social media had influenced their clinical practice.

Conclusions

This unique qualitative explorative piece of work explores the use of social media for learning by emergency medicine doctors and how it is changing clinical practice.

With the rapid growth and uptake in social media use for educational purposes. It is vital that all educators fully understand how it is being currently used as well as views of learners on this form of learning. This will allow us to further grow and develop this exciting area and maximise the educational impact on its users.

What is already known about the subject?

The use of social media for learning is popular amongst emergency medicine doctors

The term FOAMed was first created following an Emergency Medicine Conference in 2012.

There are increasing amounts of FOAMed resources produced each year related to emergency medicine.

What this study adds?

-

X (Twitter) is a popular social media platform used by doctors

-

Information learnt from social media is being applied to clinical practice

-

Social media is being used for many reasons including to keep up to date, discussion around topics and bench marking of current practice with others

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Learning through social media is being increasingly recognised as a form of Continued Professional Development (CPD) yet commonly not reported by learners as such.
Enhancing Recovery and Reducing Inflammation: The Impact of Enhanced Recovery After Surgery Recommendations on Inflammatory Markers in Laparoscopic Surgery – a Scoping review
Authors: Bersot Carlos Darcy Alves , Gomes Pereira Lucas Ferreira , Vieira Goncho Victor Gabriel , Guimaraes Pereira José Eduardo , Falcão Luiz Fernando dos Reis
Published: November 2024

Introduction

The relationship between the Enhanced Recovery After Surgery (ERAS) guidelines and inflammatory markers in laparoscopic surgery has garnered increasing attention. These recommendations are designed to minimize surgical stress and potentially improve recovery outcomes by modifying perioperative care.

Objective

This scoping review aims to evaluate the impact of ERAS recommendations on inflammatory markers in patients undergoing laparoscopic surgeries, identifying current research gaps and consolidating findings from existing studies.

Methods

Guided by the Cochrane Handbook for Systematic Reviews and adhering to the PRISMA-ScR guidelines, this review analyzed studies from databases like PubMed, Scopus, and Cochrane Library. We included both randomized controlled trials and observational studies that assessed inflammatory markers such as C-reactive protein (CRP), white blood cells (WBC), and Interleukin-6 (IL-6) in laparoscopic surgery patients managed with ERAS recommendations.

Results

Out of 64 initial studies, 7 met the inclusion criteria, involving a total of 2,047 patients. Most of the studies focused on laparoscopic colorectal surgeries. Commonly assessed markers were CRP and WBC. The findings consistently showed that ERAS guideline could mitigate the inflammatory response, evidenced by reduced levels of CRP and IL-6, which correlated with fewer postoperative complications and expedited recovery.

Conclusion

ERAS recommendations appear to beneficially modulate inflammatory responses in laparoscopic surgery, which suggests a potential for enhanced recovery outcomes. However, the evidence is currently limited by the small number of studies and inherent methodological biases. Further robust RCTs are required to strengthen the evidence base and refine these protocols for broader clinical application.
Representational learning by optimization of neural manifolds in an olfactory memory network
Authors: Hu Bo , Temiz Nesibe Z. , Chou Chi-Ning , Rupprecht Peter , Meissner-Bernard Claire , Titze Benjamin , Chung SueYeon , Friedrich Rainer W.
Published: November 2024

Higher brain functions depend on experience-dependent representations of relevant information that may be organized by attractor dynamics or by geometrical modifications of continuous “neural manifolds”. To explore these scenarios we analyzed odor-evoked activity in telencephalic area pDp of juvenile and adult zebrafish, the homolog of piriform cortex. No obvious signatures of attractor dynamics were detected. Rather, olfactory discrimination training selectively enhanced the separation of neural manifolds representing task-relevant odors from other representations, consistent with predictions of autoassociative network models endowed with precise synaptic balance. Analytical approaches using the framework ofmanifold capacityrevealed multiple geometrical modifications of representational manifolds that supported the classification of task-relevant sensory information. Manifold capacity predicted odor discrimination across individuals, indicating a close link between manifold geometry and behavior. Hence, pDp and possibly related recurrent networks store information in the geometry of representational manifolds, resulting in joint sensory and semantic maps that may support distributed learning processes.
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
Authors: Patinios Constantinos , Gupta Darshana , Bassett Harris V. , Collins Scott P. , Kamm Charlotte , Kibe Anuja , Wang Yanyan , Zhao Chengsong , Vollen Katie , Toussaint Christophe , Polkoff Kathryn M. , Nguyen Thuan , Calvin Irene , Migur Angela , Al’Abri Ibrahim S. , Achmedov Tatjana , Del Re Alessandro , Saliba Antoine-Emmanuel , Crook Nathan , Stepanova Anna N. , Alonso Jose M. , Beisel Chase L.
Published: November 2024

Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here, we harness the bacterial anti-phage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes. Fusing an attenuated DarT2 to a Cas9 nickase, we program site-specific ADP-ribosylation of thymines within a target DNA sequence. In tested bacteria, targeting drives efficient homologous recombination in tested bacteria, offering flexible and scar-free genome editing without base replacement nor counterselection. In tested eukaryotes including yeast, plants and human cells, targeting drives substitution of the modified thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions, offering edits inaccessible to current base editors. Altogether, our approach, called append editing, leverages the addition of a chemical moiety to DNA to expand current modalities for precision gene editing.
Mitochondria Regulate the Cell Fate Decisions of Megakaryocyte-Erythroid Progenitors
Authors: Sung Eunkyu , Murakami Shohei , Morita Masanobu , Ida Tomoaki , Akaike Takaaki , Motohashi Hozumi
Published: November 2024

Recent studies highlight the critical role of mitochondria in hematopoiesis, especially in stem cell function and erythroid maturation. To explore mitochondrial contributions to cell lineage commitment of hematopoietic progenitors, we utilizedCars2mutant mice, an ideal model for this purpose. CARS2, a mitochondrial isoform of cysteinyl-tRNA synthetase, has cysteine persulfide synthase (CPERS) activity. Our new mouse model, with reduced CPERS activity, showed that theCars2mutation led to mitochondrial inhibition and anemia by suppressing erythroid commitment in megakaryocyte-erythroid progenitors (MEPs). This suppression was reproduced using mitochondrial electron transport chain inhibitors. We identified two distinct MEP populations based on the mitochondrial content: mitochondria-rich MEPs favored erythroid differentiation, while the mitochondria-poor MEPs favored megakaryocyte differentiation. These findings reveal critical contributions of mitochondria to the MEP lineage selection, acting as a “mitochondrial navigation” for lineage commitment.
Chemical disorder effects on Gilbert damping of FeCo alloys
Authors: Lu Zhiwei , Miranda I. P. , Streib Simon , Xu Qichen , Cheenikundil Rajgowrav , Pereiro Manuel , Sjöqvist Erik , Eriksson Olle , Bergman Anders , Thonig Danny , Delin Anna
Published: November 2024

The impact of the local chemical environment on the Gilbert damping in the binary alloy Fe100−xCox is investigated, using computations based on density functional theory. By varying the alloy composition x as well as Fe-Co atom positions we reveal that the effective damping of the alloy is highly sensitive to the nearest-neighbor environment, especially to the amount of Co and the average distance between Co-Co atoms at nearest-neighbor sites. Both lead to a significant local increase (up to an order of magnitude) of the effective Gilbert damping, originating mainly from variations of the density of states at the Fermi energy. In a global perspective (i.e., making a configuration average for a real material), those differences in damping are masked by statistical averages. When low-temperature explicit atomistic dynamics simulations are performed, the impact of short-range disorder on local dynamics is observed to also alter the overall relaxation rate. Our results illustrate the possibility of local chemical engineering of the Gilbert damping, which may stimulate the study of new ways to tune and control materials aiming for spintronics applications.

Published by the American Physical Society
2024
Dispersion-induced
Q
-factor enhancement in waveguide-coupled surface lattice resonances
Authors: Kelavuori Jussi , Panahpour Ali , Huttunen Mikko J.
Published: November 2024

Diffractively coupled nanoparticle arrays are promising candidates for helping to flatten many photonic devices such as lasers, lenses, and metrology instruments. Their performance, however, is directly linked with the size of the metasurfaces, limiting their applicability in nanophotonic applications. Here, we dramatically reduce array sizes of high-Q factor metasurfaces by utilizing strongly dispersive media. The effect is demonstrated by theoretically and numerically studying periodic arrays of plasmonic nanoparticles embedded inside Bragg-reflector waveguides. We demonstrate array dimensions reduction up to two orders of magnitude while still achieving ultrahigh-Q factors in excess of 104.

Published by the American Physical Society
2024
Thermoelectric cooling of a finite reservoir coupled to a quantum dot
Authors: Matern Stephanie , Moreira Saulo V. , Samuelsson Peter , Leijnse Martin
Published: November 2024

We investigate nonequilibrium transport of charge and heat through an interacting quantum dot coupled to a finite electron reservoir. Both the quantum dot and the finite reservoir are coupled to conventional electric contacts, i.e., infinite electron reservoirs, between which a bias voltage can be applied. We develop a phenomenological description of the system, combining a rate equation for transport through the quantum dot with standard expressions for bulk transport between the finite and infinite reservoirs. The finite reservoir is assumed to be in a quasiequilibrium state with a time-dependent chemical potential and temperature which we solve for self-consistently. We show that the finite reservoir can have a large impact on the stationary state transport properties, including a shift and broadening of the Coulomb diamond edges. We also demonstrate that there is a region around the conductance lines where a heat current flows out of the finite reservoir. Our results reveal the dependence of the temperature that can be reached by this thermoelectric cooling on the system parameters, in particular the coupling between the finite and infinite reservoirs and additional heat currents induced by electron-phonon couplings, and can thus serve as a guide for experiments on quantum-dot-enabled thermoelectric cooling of finite electron reservoirs. Finally, we study the full dynamics of the system, with a particular focus on the timescales involved in the thermoelectric cooling.

Published by the American Physical Society
2024
Charmoniumlike states with the exotic quantum number
JPC=3−+
Authors: Xi Hong-Zhou , Chen Hua-Xing , Chen Wei , Steele T. G. , Zhang Yong , Zhou Dan
Published: November 2024

We apply the method of quantum chromodynamics (QCD) sum rules to study the qcq¯c¯ tetraquark states with the exotic quantum number JPC=3−+, and extract the mass of the lowest-lying state to be 4.49−0.41+0.45  GeV. To construct the relevant tetraquark currents we need to explicitly add the covariant derivative operator. Our systematic analysis of these interpolating currents indicates that: (a) this state readily decays into the P-wave [ρJ/ψ]/[ωJ/ψ] channel but not into the [ρχc2]/[ωχc2]/[J/ψf2(1270)] channels, and (b) it readily decays into the [D*D¯2*] channel but not into the P-wave [D*D¯*] channel.

Published by the American Physical Society
2024
Perturbative QCD meets phase quenching: The pressure of cold quark matter
Authors: Navarrete Pablo , Paatelainen Risto , Seppänen Kaapo
Published: November 2024

Nonperturbative inequalities constrain the thermodynamic pressure of quantum chromodynamics (QCD) with its phase-quenched version, a sign-problem-free theory amenable to lattice treatment. In the perturbative regime with a small QCD coupling constant αs, one of these inequalities manifests as an O(αs3) difference between the phase-quenched and QCD pressures at large baryon chemical potential. In this work, we generalize state-of-the-art algorithmic techniques used in collider physics to address large-scale multiloop computations at finite chemical potential, by direct numerical integration of Feynman diagrams in momentum space. Using this novel approach, we evaluate this O(αs3) difference and show that it is a gauge-independent and small positive number compared to the known perturbative coefficients at this order. This implies that at high baryon densities, phase-quenched lattice simulations can provide a complementary nonperturbative method for accurately determining the pressure of cold quark matter at O(αs3).

Published by the American Physical Society
2024
Contact interaction treatment of
V→Pγ
for light-quark mesons
Authors: Xu Yehan , Sultan M. Atif , Raya Khépani , Chang Lei
Published: November 2024

The V→Pγ and η(η′)→γγ decays are evaluated within a Dyson-Schwinger and Bethe-Salpeter equations framework (here V={ρ±,K⋆±,ϕ} and

P

=

{

π

±

,

K

±

,

η

,

η

′

}

). The so-called impulse approximation (IA) is employed in the computation of the decay constants involved and decay widths, and so in the estimation of the associated charge and interaction radii. For their part, the required propagators and vertices stem from a contact interaction model, embedded within a beyond rainbow-ladder (RL) truncation that accounts for the typical ladder exchanges, quark anomalous magnetic moment, as well as the non-Abelian anomaly. While the examined transitions produce decay widths plainly compatible with the available experimental data, those processes involving the η−η′ mesons highlight the incompleteness of the IA when considering beyond RL effects in the interaction kernels.

Published by the American Physical Society
2024
Gravitationally misaligned ultralight dark matter and implications for neutron stars
Authors: Davoudiasl Hooman
Published: November 2024

We examine the possibility that dark matter (DM) may be an ultralight scalar that was misaligned via nonminimal coupling to gravity, in the early Universe. For a certain regime of scalar masses, gravitational effects in neutron stars could place interesting bounds on the viable parameter space of the model, even in the absence of nongravitational interactions between DM and ordinary matter.

Published by the American Physical Society
2024
Lorentz-violating Yukawa theory at finite temperature
Authors: Cabral D. S. , Evangelista L. A. S. , de Souza J. C. R. , Ferreira L. H. A. R. , Santos A. F.
Published: November 2024

This paper addresses Yukawa theory, focusing on the scattering between two identical fermions mediated by an intermediate scalar boson, considering the effects of thermal contributions and Lorentz symmetry breaking. Temperature is introduced into the theory through the thermofield dynamics formalism, while Lorentz violation arises from a background tensor coupled to the kinetic part of the Klein-Gordon Lagrangian. Two important quantities are calculated: the cross section for the scattering process and the modified Yukawa potential. The main results obtained in this work demonstrate that considering Lorentz symmetry breaking has several implications for changes in symmetries and physical states, while the presence of temperature is strongly related to the strength of the interaction. This interplay between symmetry breaking and temperature effects provides deeper insights into the behavior of the Yukawa theory under different conditions.

Published by the American Physical Society
2024
Comparative analysis of
C
moments using different phenomenological models
Authors: James Jinu , Aggarwal R. , Kaur M.
Published: November 2024

Analysis of normalized C moments of multiplicity distribution calculated from the different phenomenological models, the Bialas-Praszalowics (BP) model, modified negative binomial and the superposed shifted Gompertz distribution at different center of mass (cms) energies is presented. The analysis covers a range of energies (200–900 GeV) of p¯p collisions in restricted phase space slices. A comparison of different models to the experimental data on charged particle multiplicity spectra from the p¯p annihilation in five pseudorapidity windows is reported. The comparison shows that the two approaches other than the BP model are in better agreement to the data. Results on variation of moments with pseudorapidity window size and with center of mass energy and observations from such a study in p¯p annihilation and pp interactions at the same center-of-mass energy are also presented.

Published by the American Physical Society
2024
Light-cone sum rules study on the purely nonfactorizable
Λc+→Ξ0K+
decay
Authors: Shi Yu-Ji , Zhao Zhen-Xing
Published: November 2024

We investigate the purely nonfactorizable Λc+→Ξ0K+ decay using light-cone sum rules. To extract the decay amplitudes, a three-point correlation function is defined and calculated at hadron and quark-gluon level, respectively. Both the W-exchange and the W-inward emission diagrams are considered in the quark-gluon level calculation, where the two-particle light-cone distribution amplitudes (LCDAs) of kaon are used as nonperturbative input. We obtain the decay amplitudes contributed from the twist-2 and twist-3 kaon LCDAs, respectively. The obtained P-wave amplitude is consistent with those predicted in the literature, while the S-wave one is much smaller. This significant difference between the S- and P -wave amplitudes leads to small up-down spin asymmetry, close to the experimental measurement.

Published by the American Physical Society
2024