bluuebunny/crossref_metadata_2025 huggingface dataset:
The coevolutionary mosaic of bat betacoronavirus emergence risk
Authors: Forero-Muñoz Norma R , Muylaert Renata L , Seifert Stephanie N , Albery Gregory F , Becker Daniel J , Carlson Colin J , Poisot Timothée
Published: December 2023

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus disease 2019 (COVID-19), we examine the global biogeography of bat-origin betacoronaviruses, and find that coevolutionary principles suggest geographies of risk that are distinct from the hotspots and coldspots of host richness. Further, our framework helps explain patterns like a unique pool of merbecoviruses in the Neotropics, a recently discovered lineage of divergent nobecoviruses in Madagascar, and—most importantly—hotspots of diversification in southeast Asia, sub-Saharan Africa, and the Middle East that correspond to the site of previous zoonotic emergence events. Our framework may help identify hotspots of future risk that have also been previously overlooked, like West Africa and the Indian subcontinent, and may more broadly help researchers understand how host ecology shapes the evolution and diversity of pandemic threats.
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway
Authors: Garcia Ignacio , Lee Yunsung , Brynildsrud Ola , Eldholm Vegard , Magnus Per , Blomfeldt Anita , Leegaard Truls M , Müller Fredrik , Dudman Susanne , Caugant Dominique A
Published: December 2023

Vaccination against SARS-CoV-2 has greatly mitigated the impact of the COVID-19 pandemic. However, concerns have been raised about the degree to which vaccination might drive the emergence and selection of immune escape mutations that will hamper the efficacy of the vaccines. In this study, we investigate whether vaccination impacted the micro-scale adaptive evolution of SARS-CoV-2 in the Oslo region of Norway, during the first nine months of 2021, a period in which the population went from near-zero to almost 90 per cent vaccine coverage in the population over 50 years old. Weekly aggregated data stratified by age on vaccine uptake and number of SARS-CoV-2 cases in the area were obtained from the National Immunization Registry and the Norwegian Surveillance System for Communicable Diseases, respectively. A total of 6,438 virus sequences (7.5 per cent of the registered cases) along with metadata were available. We used a causal-driven approach to investigate the relationship between vaccination progress and changes in the frequency of 362 mutations present in at least ten samples, conditioned on the emergence of new lineages, time, and population vaccination coverage. After validating our approach, we identified 21 positive and 12 negative connections between vaccination progress and mutation prevalence, and most of them were outside the Spike protein. We observed a tendency for the mutations that we identified as positively connected with vaccination to decrease as the vaccinated population increased. After modelling the fitness of different competing mutations in a population, we found that our observations could be explained by a clonal interference phenomenon in which high fitness mutations would be outcompeted by the emergence or introduction of other high-fitness mutations.
Sensitivity of Phytophthora nicotianae in Tennessee and North Carolina to Mefenoxam, Oxathiapiprolin, Mandipropamid, and Fluopicolide
Authors: Miller Taylor , Richmond Mitchell , Vann Matthew , Hansen Zachariah
Published: December 2023

Phytophthora nicotianae causes devastating disease in a range of hosts, including tobacco (N. tabacum L.), tomato, citrus, strawberry, and numerous ornamentals. Black shank, caused by P. nicotianae, is the most economically important disease to tobacco production in Tennessee and North Carolina. Black shank management includes the use of resistant cultivars, crop rotation, and fungicides. Fungicide resistance is a concern for black shank management due to the limited number of active ingredients available and the repeated exposure of pathogen populations to these products. In vitro fungicide sensitivity assays were conducted on 155 P. nicotianae isolates collected in Tennessee and North Carolina in 2021 and 2022 to determine their EC50 values for oxathiapiprolin, mandipropamid, and fluopicolide. The P. nicotianae was isolated predominantly from burley, dark, and flue-cured tobacco showing symptoms of black shank as well as tomato with buckeye rot symptoms. A discriminatory dose was used to determine each isolate’s sensitivity to mefenoxam in 2021 and 2022. In 2021, EC50 values were determined for oxathiapiprolin, mandipropamid, and fluopicolide. In 2022, discriminatory doses based on EC75 values were used to determine each isolate’s sensitivity to these fungicides. All isolates from the 2 years were sensitive to mefenoxam, mandipropamid, and fluopicolide. One isolate in 2022 was moderately sensitive to oxathiapiprolin, while all other isolates were sensitive.
Genetic Analysis of the Emerging Citrus Yellow Vein Clearing Virus Reveals a Divergent Virus Population in American Isolates
Authors: Abrahamian Peter , Tian Tongyan , Posis Katie , Guo Ying , Yu Doris , Blomquist Cheryl L. , Wei Gang , Adducci Benjamin , Vidalakis Georgios , Bodaghi Sohrab , Osman Fatima , Roy Avijit , Nunziata Schyler O. , Nakhla Mark , Mavrodieva Vessela , Rivera Yazmín
Published: December 2023

Citrus yellow vein clearing virus is a previously reported citrus virus from Asia with widespread distribution in China. In 2022, the California Department of Food and Agriculture conducted a multipest citrus survey targeting multiple citrus pathogens including citrus yellow vein clearing virus (CYVCV). In March 2022, a lemon tree with symptoms of vein clearing, chlorosis, and mottling in a private garden in the city of Tulare, California, tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and noncitrus species, were collected and tested for CYVCV using conventional reverse transcription polymerase chain reaction, reverse transcription quantitative polymerase chain reaction, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using 17 complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study made up the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, the CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area.
FDA Issues Warning on Ketamine Compounds
Authors: Roush Karen
Published: December 2023

More research is needed on their safe use in psychotherapy.
Descriptive and Inferential Statistics in Nursing Research
Authors: Keeler Courtney , Curtis Alexa Colgrove
Published: December 2023

Editor's note: This is the 19th article in a series on clinical research by nurses. The series is designed to be used as a resource for nurses to understand the concepts and principles essential to research. Each column will present the concepts that underpin evidence-based practice—from research design to data interpretation. To see all the articles in the series, go to https://links.lww.com/AJN/A204.
Small-Volume Blood Collection Tubes May Reduce RBC Transfusions in the ICU
Authors: Rosenberg Karen
Published: December 2023

According to this study:
Tight Blood Glucose Control Doesn't Improve ICU Outcomes
Authors: Rosenberg Karen
Published: December 2023

According to this study:
Running Outperforms Antidepressants in Improving Physical Health Outcomes in Patients with Depression and Anxiety
Authors: Rosenberg Karen
Published: December 2023

According to this study:
Strategies for interpreting arterial blood gases
Authors: Pruitt Bill
Published: December 2023

This article provides a step-by-step guide for nurses to interpret arterial blood gas (ABG) results, focusing on five key components: SaO2, PaO2, pH, PaCO2, and HCO3
-. It explains how to assess a patient's oxygenation status, compensation levels, and determine if there is an acid-base disturbance and if that disturbance is respiratory or metabolic.
From hashtags to headaches
Authors: To Khanh K.
Published: December 2023

A 2022 incident involving a group of labor and delivery nurses who posted a social media video criticizing patients has put a spotlight on the importance of maintaining professional conduct on social media. This article outlines the risks of social media use among nurses, the possible consequences of social media misuse, and the benefits of providing social media guidance in nursing curricula.
Alternative sources of bioactive omega-3 fatty acids: what are the options?
Authors: Baker Ella J.
Published: December 2023

Purpose of review

The very-long chain (VLC) omega-3 polyunsaturated fatty acids (PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) promote optimal development, physiological function and healthy ageing and help to manage disease. EPA and DHA are sourced mainly from fish, which is not sustainable. This review explores alternative sustainable sources.

Recent findings

Recent research confirms that higher intake and status of EPA and DHA are associated with health benefits including lower risk of incident type-2 diabetes and cardiovascular disease mortality. Meta-analyses confirm benefits of intravenous EPA and DHA in hospitalized adults. Algal oils and seed oils from some genetically modified (GM) plants are sources of EPA and DHA. An oil from GM camelina showed equivalence with fish oil in human trials. Ahiflower oil, a source of stearidonic acid, had biological effects in experimental studies that might translate into health benefits. An intravenous lipid emulsion based on Ahiflower oil has been tested in experimental research. Pine nut oil (PNO) is a source of pinolenic acid, which is not an omega-3 PUFA but has similar actions.

Algal oils, oils from GM seed crops, Ahiflower oil and other sources of stearidonic acid, and nonomega-3 oils including PNO, are plant-sourced sustainable alternatives to fish-sourced VLC omega-3 PUFAs.
Quality of Life and Pain in Patients With Chronic Pancreatitis
Authors: Błachnio Klaudia , Szymocha Adrianna , Kovalsky Maryan , Pawlak Andrzej , Juzwiszyn Jan , Chabowski Mariusz
Published: December 2023

Introduction

The quality of life (QoL) of patients with chronic conditions is a function of factors associated with the illness, its natural course, and treatment as well as those related to the patient. Chronic pancreatitis (CP) is a critical public health problem. Chronic pancreatitis patients can experience chronic pain with different mechanisms, malabsorption, diabetes, and cachexia.

Objective

Chronic pancreatitis (CP) is a critical public health problem. CP patients can experience chronic pain with different mechanisms, malabsorption, diabetes, and cachexia. The aim of the study was to assess the Quality of Life (QoL) of patients with CP and identify factors affecting QoL.

Methods

104 patients diagnosed with CP from the hospital in Wrocław, Poland, were included. The study was conducted using our own questionnaire, the World Health Organization Quality of Life-BREF (WHOQOL-BREF) scale, the 36-Item Short Form Health Survey (SF-36), and the Visual Analog Scale (VAS).

Results

The mean total SF-36 score was 47.7, with the highest mean rating for the physical functioning domain. The mean VAS pain score was 5.13. Pain intensity was significantly correlated with impairments in activities of daily living (P = 0.001), the need to reduce their duration (P = 0.001), and the performance of physical activity (P = 0.003). Comorbidities, education, and age have a significant relationship with only some domains of SF-36.

Conclusions

One aspect that has an impact on QoL impairment is pain which perception is governed by the same brain regions in which abnormalities result in depression and anxiety. QoL in CP patients also depends on the patient’s age, comorbidities, and level of education.
Optimizing behavioral and pharmacological smoking cessation interventions among people with HIV
Authors: Himelhoch Seth , Kelly Deana , deFilippi Chris , Taylor Gregory , Bennett Melanie , Medoff Deborah , Li Lan , Christenson Robert , Potts Wendy , Shuter Jonathan
Published: December 2023

Background:

People with HIV/AIDS (PWH) smoke at nearly three times the rate of the general population. Interventions to promote sustained quitting among PWH are urgently needed.

Methods:

Our study used a randomized factorial design to evaluate the effects of varenicline, compared with placebo, and behavioral cessation therapy, positively smoke free (PSF), compared with standard of care (SOC) among PWH who smoke. The study was designed with power to detect a small effect (Cohen's h of 0.28–0.36) with 240 participants. The primary outcome was the 7-day point prevalence abstinence (PPA) confirmed by exhaled carbon monoxide (ECO) less than 10 ppm for both main effects at 36 weeks. The study was conducted from June 2016 to November 2020. During the study's last year, recruitment was halted because of COVID-19.

Results:

The study randomized 184 participants with power to detect a medium effect (Cohen's h of 0.41). Participants were mostly African American (89.7%), men (62.8%) who smoked mentholated cigarettes (96.7%). Nearly all received antiretroviral medication (96.2%). Quit rates for the entire sample were 7.5% at 36 weeks. Compared with those who received placebo, neither those who received varenicline [36 weeks; OR (95% CI), 1.31 (0.33–5.22), P = 0.70] nor PSF [36 weeks; OR (95% CI), 0.26 (0.03–2.44), P = 0.24) were more likely to quit smoking.

Conclusion:

Among an urban living, primarily African American sample of PWH who smoke neither varenicline nor PSF was found to be efficacious at 36 weeks. Our study was not powered to detect small effects sizes. Larger trials are needed to establish tobacco treatment standards for PWH who smoke.
Life course history of physical and sexual abuse is associated with cardiovascular disease risk among women living with and without HIV
Authors: Appleton Allison A. , Kuniholm Mark H. , Vásquez Elizabeth , Cohen Mardge H. , Donohue Jessica , Floris-Moore Michelle , Friedman M. Reuel , Hanna David B. , Mimiaga Matthew J. , Moran Caitlin A. , Plankey Michael W. , Teplin Linda A. , Shitole Sanyog G. , Ware Deanna , Jones Deborah L. , Wise Jenni
Published: December 2023

Objective:

Sexual and physical abuse predict cardiovascular disease (CVD) among women in the general population. Women living with HIV (WLWH) report more abuse and have higher CVD risk compared with other women, yet associations between abuse history and CVD have not been considered among WLWH. This study fills this gap, and describes possible pathways linking abuse to CVD risk among WLWH and women living without HIV (WLWOH).

Methods:

Using 25 years of data from the Women's Interagency HIV Study (WIHS; n = 2734; WLWH n = 1963; WLWOH n = 771), we used longitudinal generalized estimating equations (GEE) to test associations between sexual and physical abuse with CVD risk. Framingham (FRS-H) and the American College of Cardiology/American Heart Association-Pooled Cohort Equation (ACC/AHA-PCE) scores were examined. Analyses were stratified by HIV-serostatus.

Results:

Among WLWH, childhood sexual abuse was associated with higher CVD risk (β
FRS-H = 1.25, SE = 1.08, P = 0.005; β
ACC/AHA-PCE = 1.14, SE = 1.07, P = 0.04) compared with no abuse. Adulthood sexual abuse was associated with higher CVD risk for WLWH (β
FRS-H = 1.39, SE = 1.08, P < 0.0001) and WLWOH (β
FRS-H = 1.58, SE = 1.14, P = 0.0006). Childhood physical abuse was not associated with CVD risk for either group. Adulthood physical abuse was associated with CVD risk for WLWH (β
FRS-H = 1.44, SE = 1.07; P < 0.0001, β
ACC/AHA-PCE = 1.18, SE = 1.06, P = 0.002) and WLWOH (β
FRS-H = 1.68, SE = 1.12, P < 0.0001; β
ACC/AHA-PCE = 1.24, SE = 1.11, P = 0.03). Several pathway factors were significant, including depression, smoking, and hepatitis C infection.

Conclusion:

Life course abuse may increase CVD risk among WLWH and women at high risk of acquiring HIV. Some comorbidities help explain the associations. Assessing abuse experiences in clinical encounters may help contextualize cardiovascular risk among this vulnerable population and inform intervention.
Adverse Events Following SARS-CoV-2 mRNA Vaccination in Adolescents: A Norwegian Nationwide Register-Based Study
Authors: Larsen Vilde Bergstad , Gunnes Nina , Gran Jon Michael , Dahl Jesper , Bøås Håkon , Watle Sara Viksmoen , Berild Jacob Dag , Greve-Isdahl Margrethe , Størdal Ketil , Gulseth Hanne Løvdal , Karlstad Øystein , Ruiz Paz Lopez-Doriga , Tapia German
Published: December 2023

Background

Vaccination of older adolescents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in the spring of 2021 and continued with younger adolescents throughout the summer and fall. We assessed risks of adverse events following immunization (AEFI) in adolescents aged 12–19 years following SARS-CoV-2 vaccination with a messenger RNA (mRNA) vaccine in Norway.

Materials and Methods

The study sample included 496,432 adolescents born in 2002–2009, residing in Norway, and unvaccinated against SARS-CoV-2 at the beginning of the age-specific waves of vaccination in 2021. The exposures under study were first- and second-dose SARS-CoV-2 mRNA vaccinations vs. no dose. We applied Poisson regression and self-controlled case series (SCCS) analysis to estimate incidence rate ratios (IRRs) of 17 preselected outcomes, with associated 95% confidence intervals (CIs), between vaccinated and unvaccinated subjects using predefined post-vaccination risk windows.

Results

Most outcome-specific numbers of cases were low. There were no statistically significant associations between first-dose vaccination and any of the outcomes. In the main Poisson regression, second-dose vaccination was associated with increased risks of anaphylactic reaction (adjusted IRR [aIRR]: 10.05; 95% CI: 1.22–82.74), lymphadenopathy (aIRR: 2.33; 95% CI: 1.46–3.72), and myocarditis and pericarditis (aIRR: 5.27; 95% CI: 1.98–14.05). We also observed increased incidence of acute appendicitis outside the 14-day risk window. When expanding the risk window to 42 days in a post-hoc analysis, there was increased incidence of acute appendicitis following both first-dose vaccination (aIRR: 1.39; 95% CI: 1.09–1.78) and second-dose vaccination (aIRR: 1.43; 95% CI: 1.07–1.91). Results of the SCCS analysis were similar to the Poisson regression.

Conclusions

In general, potential AEFI were rare among adolescents. We found increased risks of anaphylactic reaction, lymphadenopathy, and myocarditis and pericarditis following second-dose vaccination. There were also indications of increased acute appendicitis risk when applying longer risk windows.
Personalized Prediction of Stress-Induced Blood Pressure Spikes in Real Time from FitBit Data using Artificial Intelligence: A Research Protocol
Authors: Kargarandehkordi Ali , Washington Peter
Published: December 2023

Background

Referred to as the “silent killer,” elevated blood pressure often goes unnoticed due to the absence of apparent symptoms, resulting in cumulative harm over time. While various health conditions contribute to hypertension, they collectively account for a minority of cases. Chronic stress has been identified as a significant factor in increased blood pressure, and the heterogeneous nature of stress responses makes it challenging to identify specific deleterious behaviors through traditional clinical interviews.

Objective

We aim to leverage machine learning algorithms for real-time predictions of stress-induced blood pressure spikes using consumer wearable devices such as FitBit, providing actionable insights to both patients and clinicians to improve diagnostics and enable proactive health monitoring.

Methods

The study proposes the development of machine learning algorithms to analyze biosignals obtained from these wearable devices, aiming to make real-time predictions about blood pressure spikes.

Results

We have developed the core study application, named CardioMate. CardioMate will be used to remind participants to initiate blood pressure readings using an Omron HeartGuide wearable monitor. The project described is supported as a pilot project from the Robert C. Perry Fund of the Hawai’i Community Foundation. This protocol was approved by the University of Hawai’i Institutional Review Board (IRB) under protocol #2023-00130.

Conclusions

Personalized machine learning when applied to biosignals is a promising approach to providing the mobile sensing backend support for real-time digital health interventions for chronic stress and its corresponding symptoms.
Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea
Authors: Singh Ajit Pal , Singh Ekampreet , Singh Amit Kumar , Fatima Urooj , Senthil-Kumar Muthappa , Giri Jitender
Published: December 2023

Jasmonates (JAs) form a group of oxylipin-derived phytohormones involved in multiple biotic and abiotic stress responses and regulate plant development. JAs are perceived by the receptor proteins, COI (coronatine insensitive). These JA receptors encoding F-box protein, form SCFCOIubiquitin ligase complex (Skp, Cullin, F-box) and activate JA signaling by facilitating degradation of the transcriptional repressor (JAZ; Jasmonate associated ZIM domain containing) proteins through 26S proteasomal pathway. However, JA signaling is poorly understood in chickpea, a vital legume plant. Here, we first identified two putative chickpea JA receptor named CaCOI1, CaCOI2 and demonstrated CaCOI2 as a functional JA receptor. Further subcellular localization studies revealed that CaCOI2 is localized to extra-nuclear region and move to the nucleus on JA perception to activate JA signaling. Using domain swapping (between CaCOI1 and CaCOI2) experiments, we have demonstrated that the LRR region of JA receptors, which interact with bioactive JA i.e., JA-Ile, also plays a critical role in regulating subcellular localization of CaCOI proteins. We report that an acidic amino acid in F-box region of COI proteins (AtCOI1T29) stabilizes COI-InsP8 (1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6) tetrakisphosphate) interaction. This interaction is found to be critical for COI-JAZ interaction and therefore, their functionality. Our study thus identified a functional JA receptor in chickpea and revealed novel aspects of JA signaling and perception, which might also have implications in other plants.
Neutral evolution of snoRNA Host Gene long non-coding RNA affects cell fate control
Authors: Vietri Rudan Matteo , Sipilä Kalle H. , Philippeos Christina , Gânier Clarisse , Negri Victor A. , Watt Fiona M.
Published: December 2023

A fundamental challenge in molecular biology is to understand how evolving genomes can acquire new functions. Several recent studies have underscored how non-conserved sequences can contribute to organismal diversification in the primate lineage1–3. Actively transcribed, non-coding parts of the genome provide a potential platform for the development of new functional sequences4, but their biological and evolutionary roles remain largely unexplored. Here we show that a set of neutrally evolving long non-coding RNAs (lncRNA) arising from small nucleolar RNA Host Genes (SNHGs) are highly expressed in skin and dysregulated in inflammatory conditions. SNHGs affect cell fate determination and can behave as evolutionary intermediates to develop new functions5. Using SNHG7 and human epidermal keratinocytes as a model, we describe a mechanism by which these lncRNAs can increase self-renewal and inhibit differentiation. SNHG7 lncRNA’s activity has been acquired recently in the primate lineage and depends on a short sequence required for microRNA binding. Taken together, our results highlight the importance of understanding the role of fast-evolving transcripts in normal and diseased epithelia, and inform on how poorly conserved, actively transcribed non-coding sequences can participate in the evolution of genomic functionality.
Uncovering the Dual Role of Mitochondrial and Nuclear DNA Variants in Pediatric Cardiomyopathies
Authors: Temena M. Arda , Erzurumluoglu Gokalp Ebru , Susam Ezgi , Cinar Duygu , Kiztanir Hikmet , Kosger Pelin , Durak Aras Beyhan , Artan Sevilhan , Cilingir Oguz
Published: December 2023

Myocardial defects, originating from disruptions in genes affecting mitochondrial proteins interacting with others, have received limited research attention. In our study involving 27 pediatric cardiomyopathy patients, we explored mitochondrial and nuclear genes for four main cardiomyopathy subtypes. Sequencing cardiomyopathy-associated genes in patients was followed by whole mtDNA sequencing in these individuals, with 31 healthy pediatric controls for the latter part. Our findings uncovered significant pathogenic variants: MYH7 variants in three hypertrophic cardiomyopathy cases, a notable TNNC1 variant inherited interestingly in an autosomal recessive manner in two related restrictive cardiomyopathy patients, and a pathogenic TRDN variant in a left-ventricular non-compaction patient. Both a variant in FOXRED1, functioning in mitochondrial complex I stability, and a MT-CO1 variant were detected in two siblings, influencing early onset together. Additionally, a novel MT-RNR1 variant (m.684T>C) in one case might explain the phenotype. Our study highlights how both mtDNA and nDNA variants could have interconnected roles in understanding cardiomyopathy genetics. This study emphasizes that the functional studies are needed to recognize this dual relationship within bioenergetic pathways in cardiac muscle.
Using Digital Tools in Clinical, Health and Social Care Research: A Mixed-Methods Study of UK Stakeholders
Authors: Clohessy Sophie , Arvanitis Theodoros N. , Rashid Umer , Craddock Carly , Evans Mark , Toro Carla , Elliott Mark T.
Published: December 2023

Objective

The COVID-19 pandemic accelerated changes to clinical research methodology, with clinical studies being carried out via online/remote means. This mixed-methods study aimed to identify which digital tools are currently used across all stages of clinical research by stakeholders in clinical, health and social care research and investigate their experience using digital tools.

Design

Two online surveys followed by semi-structured interviews were conducted. Interviews were audio recorded, transcribed, and analysed thematically.

Setting, Participants

To explore the digital tools used since the pandemic, survey participants [Researchers and Related Staff (n=41), Research and Development staff (n=25)], needed to have worked on clinical, health or social care research studies over the past two years (2020-2022) in an employing organisation based in the West Midlands region of England (due to funding from a regional clinical research network). Survey participants had the opportunity to participate in an online qualitative interview to explore their experiences of digital tools in greater depth (n=8).

Results

Six themes were identified in the qualitative interviews: ‘Definition of a Digital Tool in Clinical Research’;‘Impact of the COVID-19 Pandemic’;‘Perceived Benefits/Drawbacks of Digital Tools’;‘Selection of a Digital Tool’; ‘Barriers and Overcoming Barriers’;and‘Future Digital Tool Use’.The context of each theme is discussed, based on the interview results.

Conclusions

Findings demonstrate how digital tools are becoming embedded in clinical research, as well as the breadth of tools used across different research stages. The majority of participants viewed the tools positively, noting their ability to enhance research efficiency. Several considerations were highlighted; concerns about digital exclusion; need for collaboration with digital expertise/clinical staff, research on tool effectiveness and recommendations to aid future tool selection. There is a need for the development of resources to help optimise the selection and use of appropriate digital tools for clinical research staff and participants.

Article Summary

Strengths and Limitations of the Study

Mixed-method study to explore experiences of utilising digital tools in clinical research, utilising participants from a variety of roles; both Research and Research and Development staff.

Survey and qualitative questions co-designed with an experienced stakeholder group.

It is likely that participants were motivated to participate due to an underlying interest in digital tools, consequently some perspectives may not have been included in this study.

The study was limited to exploring the views of stakeholders employed by organisations based in the West Midlands, United Kingdom.
PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function
Authors: He Hua , Bell Sheila M. , Davis Ashley Kuenzi , Zhao Shuyang , Sridharan Anusha , Na Cheng-Lun , Guo Minzhe , Xu Yan , Snowball John , Swarr Daniel T. , Zacharias William J. , Whitsett Jeffrey A.
Published: December 2023

Differential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion ofPrdm3andPrdm16in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function.Prdm3/16deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. Combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.

Graphical Abstract

Model of the role of PRMD3/16 in alveolar development

PRMD3/16 participate in cell fate specification in the lung by modulating chromatin accessibility (top row) and by partnering with NKX2-1 and partner transcription factors to drive gene expression (second row) via a gene regulatory network required for terminal cell differentiation and surfactant expression in AT2 cells (third row). Loss of PRDM3/16 activity in lung endoderm leads to reduced AT2 quorum, failure of AT2 surfactant function, and transition to an immature AT1 phenotype (bottom panel).
Temperature impacts SARS-CoV-2 spike fusogenicity and evolution
Authors: Dufloo Jérémy , Sanjuán Rafael
Published: December 2023

SARS-CoV-2 infects both the upper and lower respiratory tracts, which are characterized by different temperatures (33°C and 37°C, respectively). In addition, fever is a common COVID-19 symptom. SARS-CoV-2 has been shown to replicate more efficiently at low temperatures but the effect of temperature on different viral proteins remains poorly understood. Here, we investigate how temperature affects the SARS-CoV-2 spike function and evolution. We first observed that rising temperature from 33°C to 37°C or 39°C increased spike-mediated cell-cell fusion. We then experimentally evolved a recombinant vesicular stomatitis virus expressing the SARS-CoV-2 spike at these different temperatures. We found that spike-mediated cell-cell fusion was maintained during evolution at 39°C, but was lost in a high proportion of viruses evolved at 33°C or 37°C. Consistently, sequencing of the spikes evolved at 33°C or 37°C revealed the accumulation of mutations around the furin cleavage site, a region that determines cell-cell fusion, whereas this did not occur in spikes evolved at 39°C. Finally, using site-directed mutagenesis, we found that disruption of the furin cleavage site had a temperature-dependent effect on spike-induced cell-cell fusion and viral fitness. Our results suggest that variations in body temperature may affect the activity and diversification of the SARS-CoV-2 spike.

Importance

When it infects humans, SARS-CoV-2 is exposed to different temperaures (e.g. replication site, fever…). Temperature has been shown to strongly impact SARS-CoV-2 replication but how it affects the activity and evolution of the spike protein remains poorly understood. Here, we first show that high temperatures increase the SARS-CoV-2 spike fusogenicity. Then, we demonstrate that the evolution of the spike activity and variants depends on temperature. Finally, we show that the functional effect of specific spike mutations is temperature-dependent. Overall, our results suggest that temperature may be a factor influencing the activity and adapatation of the SARS-CoV-2 spike in vivo, which will help understanding viral tropism, pathogenesis, and evolution.
Uncertainty Quantification in Acoustic Impedance of Atlantic Salmon Fish Scale using Scanning Acoustic Microscopy
Authors: Agarwal Komal , Ojha Shivam , Dalmo Roy Ambil , Seternes Tore , Shelke Amit , Melandsø Frank , Habib Anowarul
Published: December 2023

Scanning Acoustic Microscopy (SAM) emerges as a versatile label-free imaging technology with broad applications in biomedical imaging, non-destructive testing, and material research. This article presents a framework for the estimation of stochastic impedance through SAM, with a particular focus on its application to the salmon fish scale. The framework leverages uncertain reflectance, marking its pioneering application to uncertainty quantification in the acoustic impedance of fish scales through acoustic responses. The study uses maximal overlap discrete wavelet transform, to decompose acoustic responses effectively and is further processed to predict the acoustic impedance. To establish the effectiveness of the proposed framework, well-known materials like a pair of target medium (polyvinylidene fluoride) and reference medium (polyimide) are employed for impedance characterization. Results demonstrate over 90%accuracy in PVDF impedance estimation, validating the framework. A stochastic impedance map, using Kriging with a Gaussian variogram, offers insights into the complex biomechanics of a fish’s scale.
RCPedia: A global resource for studying and exploring retrocopies in diverse species
Authors: Conceição Helena B. , Mercuri Rafael L. V. , de Castro Matheus P. M. , Ohara Daniel T. , Guardia Gabriela D. A. , Galante Pedro A F
Published: December 2023

Motivation

Gene retrocopies, or processed pseudogenes, arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species.

Results

Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtle, lizard, frog, zebrafish, and drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology and transposable elements. In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species.

Availability

RCPedia is available athttps://www.rcpediadb.org
Minimal vertex model explains how the amnioserosa avoids fluidization duringDrosophiladorsal closure
Authors: Tah Indrajit , Haertter Daniel , Crawford Janice M. , Kiehart Daniel P. , Schmidt Christoph F. , Liu Andrea J.
Published: December 2023

Dorsal closure is a process that occurs during embryogenesis ofDrosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments.

Significance Statement

During embryogenesis, cells in tissues can undergo significant shape changes. Many epithelial tissues fluidize, i.e. cells exchange neighbors, when the average cell shape index increases above a threshold value, consistent with the standard vertex model. During dorsal closure inDrosophila melanogaster, however, the amnioserosa tissue remains solid even as the average cell shape index increases well above threshold. We introduce perimeter polydispersity and allow the preferred cell perimeters, usually held fixed in vertex models, to decrease linearly with time as seen experimentally. With these extensions to the standard vertex model, we capture experimental observations quantitatively. Our results demonstrate that vertex models can describe the behavior of the amnioserosa in dorsal closure by allowing normally fixed parameters to vary with time.
Inhibition of the Rho/MRTF pathway improves the response of BRAF-resistant melanoma to PD1/PDL1 blockade
Authors: Foda Bardees M. , Misek Sean A. , Gallo Kathleen A. , Neubig Richard R.
Published: December 2023

Metastatic cutaneous melanoma is a fatal skin cancer. Resistance to targeted and immune therapies limits the benefits of current treatments. Identifying and adding anti-resistance agents to current treatment protocols can potentially improve clinical responses. Myocardin-related transcription factor (MRTF) is a transcriptional coactivator whose activity is indirectly regulated by actin and the Rho family of GTPases. We previously demonstrated that development of BRAF inhibitor (BRAFi) resistance frequently activates the Rho/MRTF pathway in human and mouse BRAFV600Emelanomas. In clinical trials, pre-treatment with BRAFi reduces the benefit of immune therapies. We aimed to test the efficacy of concurrent treatment with our MRTF pathway inhibitor CCG-257081 and anti-PD1in vivoand to examine its effects on the melanoma immune microenvironment. Because MRTF pathway activation upregulates the expression of immune checkpoint inhibitor genes/proteins, we asked whether CCG-257081 can improve the response to immune checkpoint blockade. CCG-257081 reduced the expression of PDL1 in BRAFi-resistant melanoma cells and decreased surface PDL1 levels on both BRAFi- sensitive and -resistant melanoma cells. Using our recently described murine vemurafenib-resistant melanoma model, we found that CCG-257081, in combination with anti-PD1 immune therapy, reduced tumor growth and increased survival. Moreover, anti-PD1/CCG-257081 co-treatment increased infiltration of CD8+T cells and B cells into the tumor microenvironment and reduced tumor-associated macrophages. Here, we propose CCG-257081 as an anti-resistance and immune therapy-enhancing anti-melanoma agent.

Novelty and Impact

We present a study that provides evidence for a new combined approach for targeting BRAF inhibitor-resistant melanoma. Pharmacological inhibition of the resistance-inducing Rho/MRTF pathway using CCG-257081 enhanced the response to PD1/PDL-1 blockadein vivo. These results indicate a role of the Rho/MRTF pathway in regulating tumor-immune interactions. Thus, CCG-257081 emerges as a potential new anti-resistance agent that can improve the response to immune checkpoint inhibitors in advanced melanoma and, possibly, other cancers.
Unexpected roles for AMPK in the suppression of autophagy and the reactivation of mTORC1 signaling during prolonged amino acid deprivation
Authors: Kazyken Dubek , Dame Sydney G. , Wang Claudia , Wadley Maxwell , Fingar Diane C.
Published: December 2023

AMPK promotes catabolic and suppresses anabolic cell metabolism to promote cell survival during energetic stress, in part by inhibiting mTORC1, an anabolic kinase requiring sufficient levels of amino acids. We found that cells lacking AMPK displayed increased apoptotic cell death during nutrient stress caused by prolonged amino acid deprivation. We presumed that impaired autophagy explained this phenotype, as a prevailing view posits that AMPK initiates autophagy (often a pro-survival response) through phosphorylation of ULK1. Unexpectedly, however, autophagy remained unimpaired in cells lacking AMPK, as monitored by several autophagic readouts in several cell lines. More surprisingly, the absence of AMPK increased ULK1 signaling and LC3b lipidation during amino acid deprivation while AMPK-mediated phosphorylation of ULK1 S555 (a site proposed to initiate autophagy) decreased upon amino acid withdrawal or pharmacological mTORC1 inhibition. In addition, activation of AMPK with compound 991, glucose deprivation, or AICAR blunted autophagy induced by amino acid withdrawal. These results demonstrate that AMPK activation and glucose deprivation suppress autophagy. As AMPK controlled autophagy in an unexpected direction, we examined how AMPK controls mTORC1 signaling. Paradoxically, we observed impaired reactivation of mTORC1 in cells lacking AMPK upon prolonged amino acid deprivation. Together these results oppose established views that AMPK promotes autophagy and inhibits mTORC1 universally. Moreover, they reveal unexpected roles for AMPK in the suppression of autophagy and the support of mTORC1 signaling in the context of prolonged amino acid deprivation. These findings prompt a reevaluation of how AMPK and its control of autophagy and mTORC1 impact health and disease.
The radiation of nodulatedChamaecristaspecies from the rainforest into more diverse habitats has been accompanied by a reduction in growth form and a shift from fixation threads to symbiosomes
Authors: Casaes Patricia Alves , Ferreira dos Santos José Miguel , Silva Verônica Cordeiro , Rhem Mariana Ferreira Kruschewsky , Teixeira Cota Matheus Martins , de Faria Sergio Miana , Rando Juliana Gastaldello , James Euan K. , Gross Eduardo
Published: December 2023

All non-mimosoid nodulated genera in the legume subfamily Caesalpinioideae confine their rhizobial symbionts within cell wall-bound “fixation threads” (FTs). The exception is the large genusChamaecristain which shrubs and subshrubs house their rhizobial bacteroids more intimately within symbiosomes, whereas large trees have FTs. This study aimed to unravel the evolutionary relationships betweenChamaecristagrowth habit, habitat, nodule bacteroid type, and rhizobial genotype. The growth habit, bacteroid anatomy, and rhizobial symbionts of 30 nodulatedChamaecristaspecies native to different biomes in the Brazilian state of Bahia, a major centre of diversity for the genus, was plotted onto an ITS-TrnL-F-derived phylogeny ofChamaecrista. The bacteroids from most of theChamaecristaspecies examined were enclosed in symbiosomes (SYM-type nodules), but those in arborescent species in the sectionApoucouita, at the base of the genus, were enclosed in cell wall material containing homogalacturonan (HG) and cellulose (FT-type nodules). Most symbionts wereBradyrhizobiumgenotypes grouped according to the growth habits of their hosts, but the tree,C. eitenorum,was nodulated byParaburkholderia.Chamaecristahas a range of growth habits that allow it to occupy several different biomes and to co-evolve with a wide range of (mainly) bradyrhizobial symbionts. FTs represent a less intimate symbiosis linked with nodulation losses, so the evolution of SYM-type nodules by mostChamaecristaspecies may have (a) aided the genus-wide retention of nodulation, and (b) assisted in its rapid speciation and radiation out of the rainforest into more diverse and challenging habitats.
Metabolite Fingerprinting for Phenotypic Screening by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry
Authors: Joignant Alena N. , Pu Fan , McLoughlin Shaun M. , Sawicki James W. , Radosevich Andrew J. , Ma Renze , Williams Jon D. , Gopalakrishnan Sujatha M. , Elsen Nathaniel L.
Published: December 2023

The adoption of mass spectrometry for high-throughput screening in drug discovery has become increasingly prevalent and has enabled label-free screening against diverse targets. Cellular assays for phenotypic screening, however, are primarily conducted by microscopy as there remain many challenges associated with conducting phenotypic screens via ultra-high throughput mass spectrometry.

Following a simple on-plate extraction, infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) was employed to directly sample the cell lysate at a speed of one second per sample. A549 cells were treated with compounds identified as hits in literature including a recently reported glutaminase cellular screen. Among the test compounds, there were confirmed glutaminase inhibitors, proposed nuisance compounds, and cell-active but enzyme-inactive compounds. Filtered data were further processed in R for dimensionality reduction and unsupervised clustering.

Though it was observed that all compounds affected the intracellular conversion of glutamine to glutamate, there were clear metabolic differences between the biochemically active compounds and the off-target hits. Moreover, two nuisance compounds were observed to cluster separately from the confirmed glutaminase inhibitors in the observed metabolite fingerprints.

This proof-of-concept work establishes a complete workflow that enables highthroughput mass spectrometry-based phenotypic screening. The methods proposed herein, at the throughput enabled by IR-MALDESI, could offer a new avenue for discovery of novel drugs.