bluuebunny/crossref_metadata_2025 huggingface dataset:
A Cost Analysis of Rethink the Strip
Authors: Spees Lisa P. , Young Laura A. , Rees Jennifer , Mottus Kathleen , Leeman Jennifer , Boynton Marcella H. , Richman Erica , Vu Maihan B. , Donahue Katrina E.
Published: November 2023

Background:

Routine self-monitoring of blood glucose is a low-value practice that provides limited benefit for patients with non–insulin-treated type 2 diabetes mellitus.

Objectives:

We estimated the costs of Rethink the Strip (RTS), a multistrategy approach to the de-implementation of self-monitoring of blood glucose in primary care.

Research Design:

RTS was conducted among 20 primary care clinics in North Carolina. We estimated the non–site-based and site-based costs of the 5 RTS strategies (practice facilitation, audit and feedback, provider champions, educational meetings, and educational materials) from the analytic perspective of an integrated health care system for 12 and 27-month time horizons. Material costs were tracked through project records, and personnel costs were assessed using activity-based costing. We used nationally based wage estimates.

Results:

Total RTS costs equaled $68,941 for 12 months. Specifically, non–site-based costs comprised $16,560. Most non–site-based costs ($11,822) were from the foundational programming and coding updates to the electronic health record data to develop the audit and feedback reports. The non–site-based costs of educational meetings, practice facilitation, and educational materials were substantially lower, ranging between ~$400 and $1000. Total 12-month site-based costs equaled $2569 for a single clinic (or $52,381 for 20 clinics). Educational meetings were the most expensive strategy, averaging $1401 per clinic. The site-based costs for the 4 other implementation strategies were markedly lower, ranging between $51 for educational materials and $555 for practice facilitation per clinic.

Conclusions:

This study provides detailed cost information for implementation strategies used to support evidence-based programs in primary care clinics.
μ opioid receptor carboxyl terminal-derived peptide alleviates morphine tolerance by inhibiting β-arrestin2
Authors: Zhang Meng , Zhang Yanling , Li Jian , Li Junliang , Ji Junwei , Wang Zhongshan
Published: November 2023

The interaction between the μ opioid receptor (MOR) and β-arrestin2 serves as a model for addressing morphine tolerance. A peptide was designed to alleviate morphine tolerance through interfering with the interaction of MOR and β-arrestin2. We developed a peptide derived from MOR. The MOR-TAT-pep peptide was expressed in E. coli Bl21(DE3) and purified. The effects of MOR-TAT-pep in alleviating morphine tolerance was examined through behavior tests. The potential mechanism was detected by Western blotting, Mammalian Two-Hybrid and other techniques. The pretreatment with MOR-TAT-pep prior to morphine usage led to an enhanced analgesic effectiveness of morphine and a significant reduction in the development of morphine tolerance. The peptide directly interacted with β-arrestin2 during morphine treatment and deceased the membrane recruitment of β-arrestin2. MOR-TAT-pep effectively suppressed the increase of β-arrestin2 induced by morphine. The MOR-TAT-pep could alleviate morphine tolerance through inhibition of β-arrestin2.
Macrophages are scavengers for injured myelin in a rabbit model of acute inflammatory demyelinating polyneuropathy
Authors: Xu Jie , Yuki Nobuhiro , Kokubun Norito , Gao Feng , Shan Fangzhen , Shi Qiguang , Wang Yuzhong
Published: November 2023

In acute inflammatory demyelinating polyneuropathy (AIDP), myelin vesiculation mediated by complement activation contributes to nerve injury. Macrophage infiltration of the spinal roots has been demonstrated in AIDP, but its pathological significance remains uncertain. The present study aimed to investigate the role of macrophages in the pathogenic sequence of AIDP. A rabbit model of AIDP was induced by immunization with galactocerebroside. Immunostaining was performed to localize the macrophages and myelin injury. The rabbit developed tetraparesis with electrophysiological and pathological features of peripheral nerve demyelination. Immunostaining demonstrated colocalization of IgG antibodies, complement deposition and myelin injury apart from macrophages. Immunostaining and electron microscopy showed myelin injury preceded macrophage infiltration. There was significant disruption of voltage-gated sodium channel clusters at the nodes of Ranvier in the spinal roots. Macrophages acted may as scavengers to remove myelin debris following complement activation-mediated demyelination in the AIDP rabbit. Lesions at the node of Ranvier contribute to conduction failure and muscle weakness.
Exploratory analysis of cortical thickness in low- and high-fit young adults
Authors: Wang Yi Ran , Boré Arnaud , Tremblay Jonathan , Descoteaux Maxime , Champoux François , Théoret Hugo
Published: November 2023

Objective

Studies have shown changes in the human brain associated with physical activity and cardiorespiratory fitness (CRF). The effects of CRF on cortical thickness have been well-described in older adults, where a positive association between CRF and cortical thickness has been reported, but the impact of sustained aerobic activity in young adults remains poorly described. Here, exploratory analysis was performed on cortical thickness data that was collected in groups of fit and sedentary young adults.

Methods

Twenty healthy sedentary individuals (<2 h/week physical activity) were compared to 20 active individuals (>6 h/week physical activity) and cortical thickness was measured in 34 cortical areas. Cortical thickness values were compared between groups, and correlations between cortical thickness and VO2 max were tested.

Results

Cardiorespiratory fitness was significantly higher in active individuals compared to sedentary individuals. Cortical thickness was lower in regions of the left (lateral and medial orbitofrontal cortex, pars orbitalis, pars triangularis, rostral anterior cingulate cortex, superior temporal cortex and frontal pole) and right (lateral and medial orbitofrontal cortex and pars opercularis) hemispheres. Only the left frontal pole and right lateral orbitofrontal cortical thickness remained significant after false discovery rate correction. Negative correlations were observed between VO2 max and cortical thickness in the left (frontal pole) and right (caudal anterior cingulate and medial orbitofrontal cortex) hemispheres.

Conclusion

The present exploratory analysis supports previous findings suggesting that neuroplastic effects of cardiorespiratory fitness may be attenuated in young compared with older individuals, underscoring a moderating effect of age on the relationship between fitness and cortical thickness.
Magnetic cortical oscillations associated with subjective auditory coolness during paired comparison of time-varying HVAC sounds
Authors: Yano Hajime , Takiguchi Tetsuya , Nakagawa Seiji
Published: November 2023

The impressions of heating, ventilation, and air conditioning (HVAC) sounds are important for the comfort people experience in their living spaces. Revealing neural substrates of the impressions induced by HVAC sounds can help to develop neurophysiological indices of the comfort of HVAC sounds. There have been numerous studies on the brain activities associated with the pleasantness of sounds, but few on the brain activities associated with the thermal impressions of HVAC sounds. Seven time-varying HVAC sounds were synthesized as stimuli using amplitude modulation. Six participants took part in subjective evaluation tests and MEG measurements. Subjective coolness of the HVAC sounds was measured using the paired comparison method. Magnetoencephalographic (MEG) measurements were carried out while participants listened to and compared the time-varying HVAC sounds. Time-frequency analysis and cluster-based analysis were performed on the MEG data. The subjective evaluation tests showed that the subjective coolness of the amplitude-modulated HVAC sounds was affected by the modulation frequency, and that there was individual difference in subjective coolness. A cluster-based analysis of the MEG data revealed that the brain activities of two participants significantly differed when they listened to cooler or less cool HVAC sounds. The frontal low-theta (4–5 Hz) and the temporal alpha (8–13 Hz) activities were observed. The frontal low-theta and the temporal alpha activities may be associated with the coolness of HVAC sound. This result suggests that the comfort level of HVAC sound can be evaluated and individually designed using neurophysiological measurements.
Acupuncture with specific mode electro-stimulation effectively and transiently opens the BBB through Shh signaling pathway
Authors: Lin Yubo , Gan Lin , Ren Li , Ma Congcong , Dai Mengyuan , Qian Kecheng , Ye Qinyu , Lin Xianming
Published: November 2023

To explore a new method that patients with brain diseases such as stroke sequelae are hindered by blood-brain barrier (BBB) in clinical treatment. Research preliminarily found that acupuncture with specific mode electro-stimulation (EA) to open BBB-assisted drug delivery may be is an effective means to improve the clinical efficacy of brain disease patients. So here we further explore the features and mechanism. Middle cerebral artery occlusion/R recovery rats were employed as the animal model. Laser Doppler monitoring cerebral blood flow decreased to 45 ± 10% of the baseline value as modeling criteria and TTC staining observed infarcted areas of brain tissue. The permeability of FITC-Dextran and EB in the frontal lobe of rats was observed by microscope. After that, Western blot and Immunofluorescence staining for the detection of the shh and Gli1 signal molecule, Claudin-5 Occludin ZO-1 tight junction (TJ) proteins. EA can open the BBB stably and effectively, and has the characteristics of starting to close soon after the end of EA; EA inhibits the Shh-Gli1 signaling pathway, and downregulates Occludin ZO-1 TJ proteins. These results suggest that EA is safe and reversible in opening the BBB, and its mechanism is related to the inhibition of Shh signaling pathway to down-regulate the expression of TJ proteins.
Improving the quality of self-management in discharged patients with multiple sclerosis: a best practice implementation project
Authors: Xu Yafang , Lizarondo Lucylynn , Zhao Yan , Quan Chao , Cao Yanpei
Published: November 2023

Objectives:

This project determined current compliance with best practice recommendations for self-management in patients with multiple sclerosis (MS) and used a web-based intervention to implement strategies to improve the quality of self-management in discharged patients with MS.

Methods:

Guided by the JBI Evidence-based Model of Health care, this project applied the 7 phases of the JBI Evidence Implementation Framework to improve the quality of self-management in MS patients.

Results:

After implementation, compliance significantly improved across all criteria compared with the baseline audit. All patients were assessed to determine their ability to self-manage (Criterion 1). All health care providers were trained to facilitate self-management and behavioral change (Criterion 2). All patients had self-management goals and action plans that were set together by both health care providers and patients (Criteria 3, 5, 6, 7). All patients received education through online patient education courses and were given an education handbook (Criterion 4). The agreed action plan was documented (Criterion 8). All members of the multidisciplinary team coordinated the services required by the patients (Criterion 9) and provided appropriate support to help patients achieve their goals and solve problems through a WeChat group and the communication module on the self-management online platform (Criterion 10).

Conclusion:

This implementation project effectively promoted practice change by enhancing patients’ knowledge of self-management and staff awareness of delivering self-management support to MS patients.
Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress
Authors: Fu Taoran , Gifford Danna R. , Knight Christopher G. , Brockhurst Michael A.
Published: November 2023

Within-host environments are likely to present a challenging and stressful environment for opportunistic pathogenic bacteria colonizing from the external environment. How populations of pathogenic bacteria respond to such environmental challenges and how this varies between strains is not well understood. Oxidative stress is one of the defences adopted by the human immune system to confront invading bacteria. In this study, we show that strains of the opportunistic pathogenic bacterium

Pseudomonas aeruginosa

vary in their eco-evolutionary responses to hydrogen peroxide stress. By quantifying their 24 h growth kinetics across hydrogen peroxide gradients we show that a transmissible epidemic strain isolated from a chronic airway infection of a cystic fibrosis patient, LESB58, is much more susceptible to hydrogen peroxide than either of the reference strains, PA14 or PAO1, with PAO1 showing the lowest susceptibility. Using a 12 day serial passaging experiment combined with a mathematical model, we then show that short-term susceptibility controls the longer-term survival of populations exposed to subinhibitory levels of hydrogen peroxide, but that phenotypic evolutionary responses can delay population extinction. Our model further suggests that hydrogen peroxide driven extinctions are more likely with higher rates of population turnover. Together, these findings suggest that hydrogen peroxide is likely to be an effective defence in host niches where there is high population turnover, which may explain the counter-intuitively high susceptibility of a strain isolated from chronic lung infection, where such ecological dynamics may be slower.
Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals genetic diversity which correlates with colonization and persistence in vivo
Authors: McDaniel Melissa S. , Sumpter Nicholas A. , Lindgren Natalie R. , Billiot Caitlin E. , Swords W. Edward
Published: November 2023

Stenotrophomonas maltophilia

is a Gram-negative emerging opportunistic pathogen often present in people with respiratory diseases such as cystic fibrosis (CF). People with CF (pwCF) experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that

Pseudomonas aeruginosa

promotes persistence of

S. maltophilia

in mouse respiratory infections. As is typical for environmental opportunistic pathogens,

S. maltophilia

has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of S. maltophilia, combining short and long read sequencing to construct nearly complete genomes of 10 clinical isolates. The genomes of these isolates were then compared with all publicly available

S. maltophilia

genome assemblies, and each isolate was then evaluated for colonization/persistence in vivo, both alone and in coinfection with

P. aeruginosa

. We found that while the overall genome size and GC content were fairly consistent between strains, there was considerable variability in both genome structure and gene content. Similarly, there was significant variability in

S. maltophilia

colonization and persistence in experimental mouse respiratory infections in the presence or absence of

P. aeruginosa

. Ultimately, this study gives us a greater understanding of the genomic diversity of clinical

S. maltophilia

isolates, and how this genomic diversity relates to both interactions with other pulmonary pathogens and to host disease progression. Identifying the molecular determinants of infection with

S. maltophilia

can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.
Epistasis regulates genetic control of cardiac hypertrophy
Authors: Wang Qianru , Tang Tiffany M. , Youlton Nathan , Weldy Chad S. , Kenney Ana M. , Ronen Omer , Weston Hughes J. , Chin Elizabeth T. , Sutton Shirley C. , Agarwal Abhineet , Li Xiao , Behr Merle , Kumbier Karl , Moravec Christine S. , Wilson Tang W. H. , Margulies Kenneth B. , Cappola Thomas P. , Butte Atul J. , Arnaout Rima , Brown James B. , Priest James R. , Parikh Victoria N. , Yu Bin , Ashley Euan A.
Published: November 2023

The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close toCCDC141,IGF1R,TTN, andTNKS.Several loci where variants were deemed insignificant in univariate genome-wide association analyses are identified. Functional genomic and integrative enrichment analyses reveal a complex gene regulatory network in which genes mapped from these loci share biological processes and myogenic regulatory factors. Through a network analysis of transcriptomic data from 313 explanted human hearts, we found strong gene co-expression correlations between these statistical epistasis contributors in healthy hearts and a significant connectivity decrease in failing hearts. We assess causality of epistatic effects via RNA silencing of gene-gene interactions in human induced pluripotent stem cell-derived cardiomyocytes. Finally, single-cell morphology analysis using a novel high-throughput microfluidic system shows that cardiomyocyte hypertrophy is non-additively modifiable by specific pairwise interactions betweenCCDC141and bothTTNandIGF1R. Our results expand the scope of genetic regulation of cardiac structure to epistasis.
Glucose-6-phosphate dehydrogenase deficiency accelerates pancreatic acinar-to-ductal metaplasia
Authors: Radyk Megan D. , Nelson Barbara S. , Halbrook Christopher J. , Wood Alexander , Lavoie Brooke , Salvatore Lucie , Corfas Gabriel , Colacino Justin A. , Shah Yatrik M. , Crawford Howard C. , Lyssiotis Costas A.
Published: November 2023

Activating mutations inKRASextensively reprogram cellular metabolism to support the continuous growth, proliferation, and survival of pancreatic tumors. Targeting these metabolic dependencies are promising approaches for the treatment of established tumors. However, metabolic reprogramming is required early during tumorigenesis to provide transformed cells selective advantage towards malignancy. Acinar cells can give rise to pancreatic tumors through acinar-to-ductal metaplasia (ADM). Dysregulation of pathways that maintain acinar homeostasis accelerate tumorigenesis. During ADM, acinar cells transdifferentiate to duct-like cells, a process driven by oncogenicKRAS. The metabolic reprogramming that is required for the transdifferentiation in ADM is unclear. We performed transcriptomic analysis on mouse acinar cells undergoing ADM and found metabolic programs are globally enhanced, consistent with the transition of a specialized cell to a less differentiated phenotype with proliferative potential. Indeed, we and others have demonstrated how inhibiting metabolic pathways necessary for ADM can prevent transdifferentiation and tumorigenesis. Here, we also find NRF2-target genes are differentially expressed during ADM. Among these, we focused on the increase in the gene coding for NADPH-producing enzyme, Glucose-6-phosphate dehydrogenase (G6PD). Using established mouse models ofKrasG12D-driven pancreatic tumorigenesis and G6PD-deficiency, we find that mutantG6pdaccelerates ADM and pancreatic intraepithelial neoplasia. Acceleration of cancer initiation with G6PD-deficiency is dependent on its NADPH-generating function in reactive oxygen species (ROS) management, as opposed to other outputs of the pentose phosphate pathway. Together, this work provides new insights into the function of metabolic pathways during early tumorigenesis.
Antagonistic functions of CTL1 and SUH1 mediate cell wall assembly inArabidopsis
Authors: Thuy Nguyen Thi , Kim Hyun-Jung , Hong Suk-Whan
Published: November 2023

Plant genomes contain numerous genes encoding chitinase-like (CTL) proteins, which have a similar protein structure to chitinase but lack the chitinolytic activity to cleave theβ-1,4-glycosidic bond in chitins, polymers ofN-acetylglucosamine. Mutations inCTL1in rice andArabidopsishave been found to cause pleiotropic developmental defects, including altered cell wall composition and decreased abiotic stress tolerance, likely due to a reduction in cellulose content. In this study, we identifiedsuppressor of hot2-1(suh1) as a genetic suppressor of thectl1hot2-1mutation inArabidopsis. The mutation inSUH1restored almost allctl1hot2-1defects examined to nearly wild-type levels, with the exception of partial recovery of cellulose content inctl1hot2-1mutants.SUH1encodes a Golgi-located type II membrane protein with glycosyltransferase (GT) activity, and its mutations lead to reduction in cellulose content and hypersensitivity to cellulose biosynthesis inhibitors, although to a lesser extent thanctl1hot2-1mutation. TheSUH1promoter fused with the GUS reporter gene exhibited GUS activity in interfascicular fibers and xylem in stems, and this activity was significantly increased by thectl1hot2-1mutation. Our findings provide genetic and molecular evidence that the antagonistic activities of CTL1 and SUH1 play an essential role in cell wall assembly inArabidopsis.

Highlight

This study reports mutations insuppressor of hot2-1(SUH1) gene that rescues the defects caused by mutations inCTL1, which are characterized by stunted growth due to decreased cellulose levels.
Arousal as a universal embedding for spatiotemporal brain dynamics
Authors: Raut Ryan V. , Rosenthal Zachary P. , Wang Xiaodan , Miao Hanyang , Zhang Zhanqi , Lee Jin-Moo , Raichle Marcus E. , Bauer Adam Q. , Brunton Steven L. , Brunton Bingni W. , Kutz J. Nathan
Published: November 2023

Neural activity in awake organisms shows widespread and spatiotemporally diverse correlations with behavioral and physiological measurements. We propose that this covariation reflects in part the dynamics of a unified, multidimensional arousal-related process that regulates brain-wide physiology on the timescale of seconds. By framing this interpretation within dynamical systems theory, we arrive at a surprising prediction: that a single, scalar measurement of arousal (e.g., pupil diameter) should suffice to reconstruct the continuous evolution of multidimensional, spatiotemporal measurements of large-scale brain physiology. To test this hypothesis, we perform multimodal, cortex-wide optical imaging and behavioral monitoring in awake mice. We demonstrate that spatiotemporal measurements of neuronal calcium, metabolism, and brain blood-oxygen can be accurately and parsimoniously modeled from a low-dimensional state-space reconstructed from the time history of pupil diameter. Extending this framework to behavioral and electrophysiological measurements from the Allen Brain Observatory, we demonstrate the ability to integrate diverse experimental data into a unified generative model via mappings from an intrinsic arousal manifold. Our results support the hypothesis that spontaneous, spatially structured fluctuations in brain-wide physiology—widely interpreted to reflect regionally-specific neural communication—are in large part reflections of an arousal-related process. This enriched view of arousal dynamics has broad implications for interpreting observations of brain, body, and behavior as measured across modalities, contexts, and scales.
Bacterial Diversity and Chemical Ecology of Natural Product-Producing Bacteria from Great Salt Lake Sediment
Authors: Bring Horvath Elijah R. , Brazelton William J. , Kim Min Cheol , Cullum Reiko , Mulvey Matthew A. , Fenical William , Winter Jaclyn M.
Published: November 2023

Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the United States. While the average salinity of seawater is ∼3.3%, the salinity in GSL ranges between 5-28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalogue bacteria found in GSL, the Lake’s microbiome is largely unexplored, and little-to-no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of a newSaccharomonosporaspecies, and provide the first survey of the natural product potential of GSL bacteria.
Fast-slow traits predict competition network structure and its response to resources and enemies
Authors: Daniel Caroline , Allan Eric , Saiz Hugo , Godoy Oscar
Published: November 2023

Plants interact in complex networks but how their structure depends on resources, natural enemies and species resource-use strategy remains poorly understood. Here, we quantified competition networks among 18 plants varying in fast-slow strategy, by testing how increased nutrient availability and reduced foliar pathogens affected intra- and inter-specific interactions. Our results show that nitrogen and pathogens altered several aspects of network structure, often in unexpected ways due to fast and slow growing species responding differently. Nitrogen addition increased competition asymmetry in slow growing networks, as expected, but decreased it in fast growing networks. Pathogen reduction made networks more even and less skewed because pathogens targeted weaker competitors. Surprisingly, pathogens and nitrogen dampened each other’s effect. Our results show that plant growth strategy is key to understand how competition respond to resources and enemies, a prediction from classic theories which has rarely been tested by linking functional traits to competition networks.
OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data
Authors: Dora Tortarolo , Simone Pernice , Clapero Fabiana , Valdembri Donatella , Serini Guido , Riccardo Federica , Tarone Lidia , Bena Chiara Enrico , Bosia Carla , Contaldo Sandro Gepiro , Marco Beccuti , Pennisi Marzio , Francesca Cordero
Published: November 2023

Open science and reproducibility are two key pillars of modern scientific research. Open science is making scientific research and data accessible and transparent to the broader scientific community and the public. Reproducibility, on the other hand, is the ability to replicate and confirm research results by following the same methods and procedures. Reproducibility is thus crucial because it ensures the reliability and validity of scientific findings. The relationship between open science and reproducibility is intertwined; indeed open science practices, such as sharing raw data, detailed methodologies, and code, greatly facilitate the reproducibility of research. In recent years, concerns about the reproducibility of scientific research have gained prominence, and indeed scientists still lament the lack of details in the methods sections of published papers and the unavailability of raw data from the authors. To assist cellular biologists and immunologists and to promote a more transparent, open and reproducible research practice, we developedOmniReproducibleCellAnalysis(ORCA), a new Shiny Application based in R, for the semi-automated analysis of Western Blot (WB), Reverse Transcription-quantitative PCR (RT-qPCR), Enzyme-Linked ImmunoSorbent Assay (ELISA), Endocytosis and Cytotoxicity experiments.ORCAis open-source and approachable by scientists without advanced R language knowledge. Our application automatically compiles a report containing the finalized data analysis and all its preliminary and intermediate steps, ensuring data analysis standardization and reproducibility. Furthermore,ORCAallows to upload raw data and results directly on the data repository Harvard Dataverse, a valuable tool for promoting transparency and data accessibility in scientific research. By employingORCA, scientists will cut down analysis time and human-dependent errors, while taking a step towards a research practice compliant with Open Science and FAIR principle.
X-ray-driven chemistry and conformational heterogeneity in atomic resolution crystal structures of bacterial dihydrofolate reductases
Authors: Smith Nathan , Horswill Alexander R. , Wilson Mark A.
Published: November 2023

Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. Bacterial DHFRs are targets of several important antibiotics as well as model enzymes for the role of protein conformational dynamics in enzyme catalysis. We collected 0.93 Å resolution X-ray diffraction data from bothBacillus subtilis(Bs) andE. coli(Ec) DHFRs bound to folate and NADP+. These oxidized ternary complexes should not be able to perform chemistry, however electron density maps suggest hydride transfer is occurring in both enzymes. Comparison of low- and high-dose EcDHFR datasets show that X-rays drive partial production of tetrahydrofolate. Hydride transfer causes the nicotinamide moiety of NADP+to move towards the folate as well as correlated shifts in nearby residues. Higher radiation dose also changes the conformational heterogeneity of Met20 in EcDHFR, supporting a solvent gating role during catalysis. BsDHFR has a different pattern of conformational heterogeneity and an unexpected disulfide bond, illustrating important differences between bacterial DHFRs. This work demonstrates that X-rays can drive hydride transfer similar to the native DHFR reaction and that X-ray photoreduction can be used to interrogate catalytically relevant enzyme dynamics in favorable cases.
Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles
Authors: Andronov Leonid , Han Mengting , Zhu Yanyu , Balaji Ashwin , Roy Anish R. , Barentine Andrew E. S. , Patel Puja , Garhyan Jaishree , Qi Lei S. , Moerner W.E.
Published: November 2023

The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.
Evaluation of Prompts to Simplify Cardiovascular Disease Information Using a Large Language Model
Authors: Mishra Vishala , Sarraju Ashish , Kalwani Neil M. , Dexter Joseph P.
Published: November 2023

AI chatbots powered by large language models (LLMs) are emerging as an important source of public-facing medical information. Generative models hold promise for producing tailored guidance at scale, which could advance health literacy and mitigate well-known disparities in the accessibility of health-protective information. In this study, we highlight an important limitation of basic approaches to AI-powered text simplification: when given a zero-shot or one-shot simplification prompt, GPT-4 often responds by omitting critical details. To address this limitation, we developed a new prompting strategy, which we term rubric prompting. Rubric prompts involve a combination of a zero-shot simplification prompt with brief reminders about important topics to address. Using rubric prompts, we generate recommendations about cardiovascular disease prevention that are more complete, more readable, and have lower syntactic complexity than baseline responses produced without prompt engineering. This analysis provides a blueprint for rigorous evaluation of AI model outputs in medicine.
Reach and public health implications of proposed new food marketing regulation in Germany: an updated analysis
Authors: Leibinger Anna , Holliday Nicole , Huizinga Oliver , von Philipsborn Peter
Published: November 2023

Introduction

Advertising of unhealthy foods to children is a key public health concern as exposure to such advertising has been shown to adversely affect children’s food preferences, choices, purchases and intake. The proposed Children’s Food Advertising Act (Kinder-Lebensmittel-Werbegesetz or KLWG) in Germany aims to regulate such marketing by using an adapted version of the World Health Organization Regional Office for Europe Nutrient Profile Model (WHO NPM). Since the first announcement of the proposed new legislation in February 2023, several revisions to the proposed law have been made. In the present study, we evaluate the reach and public health implications of the planned law’s latest draft proposed in June 2023, updating a previously published analysis of the initial proposal.

Methods

Our analysis is based on a dataset from the open-source online database Open Food Facts, comprising 660 food products randomly selected from the German market. We assigned these products to the 22 food and beverage categories covered the WHO NPM. We then applied the nutrient and ingredient thresholds of the the June 2023 version of the KLWG to this sample to assess the share of products permitted for marketing to children under the proposed legislation.

Results

Applying the adjustments from the June 2023 KLWG version increased the proportion of products allowed for marketing to children in three product categories, namely plant-based milks (from 70% to 73%), yogurt and cream (from 13% to 73%) and fresh and frozen meat, fish and eggs (from 93% to 100%). Overall, this raised the median share of products across all 22 product categories permitted for marketing to children from 38% to 55%, with an interquartile range of 11%-73%.

Conclusion

Our previous study found the use of the WHO NPM, as part of the KLWG, to be feasible in the German context and suggested additional threshold adjustments. The latest draft of the KLWG from June 2023 incorporated several of these, substantially increasing the proportion of products allowed for marketing to children. This analysis provides an updated perspective on the evolving debate and its implications for public health.
East-West mortality disparities during the COVID-19 pandemic widen the historical longevity divide in Europe: an international comparative study
Authors: Shkolnikov Vladimir M. , Timonin Sergey , Jdanov Dmitry , Medina-Jaudes Naomi , Islam Nazrul , Leon David A.
Published: November 2023

Introduction

For over half a century, life expectancy in the former communist countries of Eastern Europe has been noticeably lower than in Western Europe. Since 2000 this gap has narrowed. We examined the impact of the COVID-19 pandemic on these long-term mortality trends and differences.

Methods

Nationally reported mortality data were used to estimate East-West differences in excess mortality and life expectancy losses. Regression and decomposition methods were employed to examine the contribution of vaccination, trust in government, regulatory enforcement, and air connectivity between populations to these differences.

Results

During the pandemic, the East-West life expectancy gap widened to its highest level in more than two decades. Moreover, the trajectory of excess mortality during the pandemic differed between East and West, with levels of excess mortality in the East being minimal until autumn 2020. Cumulative excess mortality in weeks 10-18 of 2020 was correlated with an index of air connectivity, which was appreciably lower in Eastern compared to Western European countries in the immediate pre-pandemic period. From October 2020 onwards, the East suffered greater losses in life expectancy, especially in 2021. This could not be explained by greater frailty of the Eastern European populations, as indicated by higher pre-pandemic mortality levels. Half of the difference between East and West in 2021 was jointly explained by COVID-19 vaccination levels and trust in government.

Conclusions

East-West contrasts in the timing and magnitude of life expectancy losses during the COVID-19 pandemic appear to have their ultimate origins in differences between societies that were established during the Cold War. These include differences in the connectivity of populations, levels of trust in science and authorities and the related capacity of Eastern countries to mount effective vaccination campaigns.
SPATEs promote the survival ofShigellato the plasma complement system upon local hemorrhage and bacteremia
Authors: Debande Lorine , Sabbah Ahmad , Kuhn Laurianne , Ngondo Patryk , André Antonin C , Roche Béatrice , Laborde Matthieu , Cantalapiedra-Mateo Victoria , Thahouly Tamou , Milinski Ana , Bianchetti Laurent , Allmang-Cura Christine , Frugier Magali , Marteyn Benoit S
Published: November 2023

Shigellaspp. are the causative agents of shigellosis, which remains a leading cause of death in children under the age of five. Shigellosis is characterized by fever and results in hemorrhagic diarrhea; in more severe cases,Shigellabacteremia has been reported. These clinical features strongly suggest thatShigellasurvive exposure to plasma, although this has not yet been studied at the molecular level. In this report, we confirmed in a guinea pig model of shigellosis that local hemorrhages were induced byS. flexneri5a andS. sonnei, and we demonstrated thatShigellareached mucosal CD31+/CD34+ blood vessels during the late stages of infection and further disseminated in the bloodstream. These results confirmed the exposure ofShigellato plasma components within the hemorrhagic colonic mucosa and in the bloodstream. We demonstrated that all the testedShigellastrains survived plasma exposurein vitro, and we showed that Serine Protease Autotransporters of Enterobacteriaceae (SPATEs) are essential forShigelladissemination within the colonic mucosa. We have confirmed that SPATEs are expressed and secreted in poorly oxygenated environments encountered byShigellafrom hypoxic foci of infection to the bloodstream. We further demonstrated that SPATEs promotedShigellasurvival in plasma, by cleaving complement component 3 (C3), thereby impairing complement system activation. We have shown here that the ability ofShigellato survive plasma exposure is a key factor in its virulence, both within primary foci and systemically.

Significance Statement

In this study we aimed to better understand the significance of the ability ofShigellato survive plasma exposure, as we observed that non-pathogenicE. colirapidly lysed upon exposure. Indeed, we reported thatShigellawas already exposed to plasma components within the colonic mucosa, as we reported in a guinea pig model of shigellosis that hemorrhages were induced, that were associated with local diffusion of plasma components in the infected colonic mucosa.Shigellawas obviously exposed to plasma during bacteremia. The ability ofShigellato survive in plasma has not been previously reported. Here we have shown, first, thatShigellawas able to divide and grow in the presence of human plasma, and second, we found that SPATEs played a central role in this process by impairing with the activation of the complement system.
Evolutionary constraint genes implicated in autism spectrum disorder across 2,054 nonhuman primate genomes
Authors: Kikuchi Yukiko , Uddin Mohammed , Veltman Joris A. , Wells Sara , Woodbury-Smith Marc
Published: November 2023

Background

Significant progress has been made in elucidating the genetic underpinning of Autism Spectrum Disorder (ASD). This childhood-onset chronic disorder of cognition, communication and behaviour ranks among the most severe from a public health perspective, and it is therefore hoped that new discoveries will lead to better therapeutic options. However, there are still significant gaps in our understanding of the link between genomics, neurobiology and clinical phenotype in scientific discovery. New models are therefore needed to address these gaps. Rhesus macaques (Macaca mulatta) have been extensively used for preclinical neurobiological research because of remarkable similarities to humans across biology and behaviour that cannot be captured by other experimental animals.

Methods

We used the macaque Genotype and Phenotype (mGAP) resource (v2.0) consisting of 2,054 macaque genomes to examine patterns of evolutionary constraint in known human neurodevelopmental genes. Residual variation intolerance scores (RVIS) were calculated for all annotated autosomal genes (N = 18,168) and Gene Set Enrichment Analysis (GSEA) was used to examine patterns of constraint across ASD genes and related neurodevelopmental genes.

Results

We demonstrated that patterns of constraint across autosomal genes are correlated in humans and macaques, and that ASD-implicated genes exhibit significant constraint in macaques (p= 9.4 x 10-27). Among macaques, many key ASD genes were observed to harbour predicted damaging mutations. A small number of key ASD genes that are highly intolerant to mutation in humans, however, showed no evidence of similar intolerance in macaques (CACNA1D,CNTNAP2,MBD5,AUTS2andNRXN1). Constraint was also observed across genes implicated in intellectual disability (p= 1.1 x 10-46), epilepsy (p= 2.1 x 10-33) and schizophrenia (p= 4.2 x 10-45), and for an overlapping neurodevelopmental gene set (p= 4.0 x 10-10)

Limitations

The lack of behavioural phenotypes among the macaques whose genotypes were studied means that we are unable to further investigate whether genetic variants have similar phenotypic consequences among nonhuman primates.

Conclusion

The presence of pathological mutations in ASD genes among macaques, and the evidence of similar constraints in these genes to humans, provide a strong rationale for further investigation of genotype-phenotype relationships in nonhuman primates. This highlights the importance of identifying phenotypic behaviours associated with clinical symptoms, elucidating the neurobiological underpinnings of ASD, and developing primate models for translational research to advance approaches for precision medicine and therapeutic interventions.
Combinatorial CRISPR screen revealsFYNandKDM4as targets for synergistic drug combination for treating triple negative breast cancer
Authors: Kim Tackhoon , Park Byung-Sun , Heo Soobeen , Jeon Heeju , Kim Jaeyeal , Kim Donghwa , Lee Sang Kook , Jung So-Youn , Kong Sun-Young , Lu Timothy K.
Published: November 2023

Tyrosine kinases play a crucial role in cell proliferation and survival and are extensively investigated as targets for cancer treatment. However, the efficacy of most tyrosine kinase inhibitors (TKIs) in cancer therapy is limited due to resistance. In this study, we identify a synergistic combination therapy involving TKIs for the treatment of triple negative breast cancer. By employing pairwise tyrosine kinase knockout CRISPR screens, we identifyFYNandKDM4as critical targets whose inhibition enhances the effectiveness of TKIs, such as NVP-ADW742 (IGF-1R inhibitor), gefitinib (EGFR inhibitor), and imatinib (ABL inhibitor) bothin vitroandin vivo. Mechanistically, treatment with TKIs upregulates the transcription ofKDM4, which in turn demethylates H3K9me3 atFYNenhancer forFYNtranscription. This compensatory activation ofFYNandKDM4contributes to the resistance against TKIs.FYNexpression is associated with therapy resistance and persistence by demonstrating its upregulation in various experimental models of drug-tolerant persisters and residual disease following targeted therapy, chemotherapy, and radiotherapy. Collectively, our study provides novel targets and mechanistic insights that can guide the development of effective combinatorial targeted therapies, thus maximizing the therapeutic benefits of TKIs.
Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks
Authors: Phipps Jamie , Toulouze Mathias , Ducrot Cécile , Costa Rafaël , Brocas Clémentine , Dubrana Karine
Published: November 2023

DNA double-strand breaks (DSB) must be repaired to ensure genome stability. Crucially, DSB ends must be kept together for timely repair. InSaccharomyces cerevisiae, two poorly understood pathways mediate DSB end-tethering. One employs the Mre11-Rad50-Xrs2 (MRX) complex to physically bridge DSB ends. Another requires the conversion of DSB ends into single-strand DNA (ssDNA) by Exo1, but the bridging proteins are unknown. We uncover that cohesin, its loader and Smc5/6 act with Exo1 to tether DSB ends. Remarkably, cohesin specifically impaired in oligomerization fails to tether DSB ends, revealing a new function for cohesin oligomerization. In addition to the known importance of sister chromatid cohesion, microscopy-based microfluidic experiments unveil a new role for cohesin in repair by ensuring DSB end-tethering. Altogether, our findings demonstrate that oligomerization of cohesin prevents DSB end separation and promotes DSB repair, revealing a novel mode of action and role for cohesin in safeguarding genome integrity.
A BCG Skin Challenge Model for Assessing TB Vaccines
Authors: Krishnan Nitya , Priestman Miles , Uhía Iria , Charitakis Natalie , Glegola-Madejska Izabella T , Baer Thomas M. , Tranberg Albin , Faraj Alan , Simonsson Ulrika SH , Robertson Brian D.
Published: November 2023

Controlled Human infection models (CHIM) are valuable tools for assessing relevant biological activity in vaccine candidates, with the potential to accelerate Tuberculosis vaccine development into the clinic. Tuberculosis infection poses significant constraints on the design of a CHIM using the causative agentMycobacterium tuberculosis. As a safer alternative, we propose a challenge model using the attenuated vaccine agentMycobacterium bovisBCG as a surrogate forMycobacterium tuberculosis,and intradermal (skin) challenge as an alternative to pulmonary infection. We have developed a unique non-invasive imaging system based on fluorescent reporters to quantitatively measure bacterial load over time, thereby determining a relevant biological vaccine effect. We assessed the utility of this model to measure the effectiveness of two TB vaccines: the currently licenced BCG and a novel subunit vaccine candidate. To assess the efficacy of the skin challenge model a pharmacometric model was built describing the decline of fluorescence over time. The results show that vaccination is a statistically significant factor which reduced the fluorescence readout of both fluorophores. The higher decline in vaccinated mice correlated with bacterial burden in the lungs. This supports the fluorescence output from the skin as a reflection of vaccine induced functional pulmonary immune responses. This novel non-invasive approach allows for repeated measurements from the challenge site, providing a dynamic readout of vaccine induced responses over time. This BCG skin challenge model represents an important contribution to the ongoing development of controlled challenge models for Tuberculosis.