bluuebunny/crossref_metadata_2025 huggingface dataset:
On some general characteristics of the spread of the COVID epidemic
Authors: Below Denis , Mairanowski Felix G.
Published: September 2023

An analytical model for calculating the spread of the COVID-19 epidemic is described, and it is shown that the main patterns of epidemic development are determined by three dimensionless complexes representing the ratios of transmission rates, contact limitation due to lockdown, and population vaccination. A comparison of statistical data on the growth of the epidemic in Germany, Berlin and its various neighbourhoods shows that the development of the epidemic depends to a large extent on the ethnic composition of the population. In the same way as it is accepted in some sections of physics, it is proposed to use the methods of similarity theory to investigate the regularities of the emergence and development of the epidemic.
Multi-modal profiling of biostabilized human skin modules reveals a coordinated ecosystem response to injected mRNA-1273 COVID-19 vaccine
Authors: Scholaert Manon , Peries Mathias , Braun Emilie , Martin Jeremy , Serhan Nadine , Loste Alexia , Bruner Audrey , Basso Lilian , Chaput Benoît , Merle Eric , Descargues Pascal , Pagès Emeline , Gaudenzio Nicolas
Published: September 2023

The field of vaccination is witnessing a remarkable surge in the development of innovative strategies. There is a need to develop technological platforms capable of generating human data prior to progressing to clinical trials. Here we introduce VaxSkin, a flexible solution designed for the comprehensive monitoring of the natural human skin ecosystem’s response to vaccines over time. Based on bioengineering to repurpose surgical resections, it allows a comprehensive analysis of the response to vaccines at both organ and single-cell levels. Upon injection of the mRNA-1273 COVID-19 vaccine, we characterized precise sequential molecular events triggered upon detection of the exogenous substance. We also found that the vaccine consistently targets DC/macrophages and mast cells, regardless of the administration route, while promoting specific cell-cell communications in surrounding immune cell subsets. Given its direct translational relevance, VaxSkin provides a multiscale vision of skin vaccination that could pave the way toward the development of new vaccination development strategies.
Topography influences diurnal and seasonal microclimate fluctuations in hilly terrain environments of coastal California
Authors: John Aji , Olden Julian D. , Oldfather Meagan F. , Kling Matthew M , Ackerly David D.
Published: September 2023

Understanding the topographic basis for microclimatic variation remains fundamental to predicting the site level effects of warming air temperatures. Quantifying diurnal fluctuation and seasonal extremes in relation to topography offer insight into the potential relationship between site level conditions and changes in regional climate. The present study investigated an annual understory temperature regime for 50 sites distributed across a topographically diverse area (>12 km2) comprised of mixed evergreen-deciduous woodland vegetation typical of California coastal ranges. We investigated the effect of topography and tree cover on site-to-site variation in near-surface temperatures using a combination of multiple linear regression and multivariate techniques. Sites in topographically depressed areas (e.g., valley bottoms) exhibited larger seasonal and diurnal variation. Elevation (at 10 m resolution) was found to be the primary driver of daily and seasonal variations, in addition to local topographic features that measure how depressed a site is compared to the surrounding area, canopy cover and northness. The elevation effect on seasonal mean temperatures was inverted, reflecting large-scale cold-air pooling in the study region, with elevated minimum and mean temperature at higher elevations. Additionally, several of our sites showed considerable buffering (dampened diurnal and seasonal temperature fluctuations) compared to average regional conditions measured by weather station. Results from this study help inform efforts to extrapolate temperature records across large landscapes and have the potential to improve our ecological understanding of fine-scale seasonal climate variation in coastal range environments.
Guilt and Reproductive Decision Making in Patients Inherited Cardiac Diseases
Authors: Smith Emily , Krishnamoorthy Dhurga , Burke-Martindale Carolyn , Weissler-Snir Adaya
Published: September 2023

Background

A diagnosis of an inherited cardiac condition may cause guilt for having the condition (i.e. personal guilt), for passing it to one’s offspring (i.e. reproductive guilt), and may also impact the reproductive decision-making. We sought to identify factors that are associated with guilt and reproduction decision-making amongst patients with inherited cardiomyopathy and arrhythmia syndromes.

Methods

We used an anonymous web-based survey that included validated measures to assess patients’ perceptions of their illness and quality of life and questions on feeling personal guilt and reproductive guilt, genetic testing results, family planning, and cascade screening.

Results

Of 514 potential participants, 128(24.9%) responded to the survey. Most respondents had cardiomyopathy(66.4%). Thirty-eight(29.6%) respondents were probands and 41 (32.0%) had ICDs. Probands had a more severe perception of illness score compared to non-probands(p<0.01). Thirty-four percent(13/38) of probands and 8.8% (8/90) of non-probands reported reproductive guilt(p<0.001). Reproductive guilt was associated with a more severe perception of illness(p<0.001) and a proband status (p=<0.001). After adjusting for illness perception, being a proband was no longer a predictor for reproductive guilt. Twenty-two participants (17.2%) reported experiencing current or past personal guilt, with a trend of more personal guilt amongst patients with inherited arrhythmia (33.3%vs.15%,p=0.06). Personal guilt was associated with a worse illness perception (p<0.001), a lower quality of life (p=0.01) and proband status (p<0.001), with thirty-four percent (13/38) of probands vs. ten percent of non-probands (9/90) (p<0.001) feeling or having felt personal guilt. After adjusting for quality of life and illness perception proband status did not remain an independent predictor for personal guilt.

Conclusion

Personal and reproductive guilt are common among individuals with inherited cardiac conditions despite having good quality of life. Probands are more prone to feeling guilt due to a worse illness perception. Better opportunities for psychologic and genetic counseling for these patients are warranted.
Causal Inference for Estimation of Vaccine Effects from Time-to-Event Data
Authors: Li Zhouxuan , Zhang Kai , Talebi Yashar , Wu Hulin , Chan Wenyaw , Boerwinkle Eric , Xiong Momiao
Published: September 2023

Vaccine is the most efficient method for controlling of infectious disease. Vaccine effectiveness estimation is extremely important in monitoring vaccine efficacy and controlling disease spreading. To study about the COVID-19 vaccine effectiveness from EHR data, we apply the counterfactual reasoning method with deep neural network for vaccine effectiveness estimation from the time-to-event data which are extracted from Optum EHR dataset. The estimated vaccine effectiveness by the counterfactual reasoning is compared with the Cox regression model and Random survival forest model. The preliminary results show that the proposed model is more unbiased than the Cox regression and Random survival forest models.
Process of Use of Evidence Products by Frontline Maternal, Newborn and Child Health Staff at the Facility Level in Ghana
Authors: Abekah-Nkrumah Gordon , Ottie-Boakye Doris , Owusu Richmond , Ermel Johnson , Issiaka Sombié , Baku Anita Asiwome Adzo
Published: September 2023

Although the use of evidence products has been identified as beneficial in improving reproductive, maternal and child health, very little is known about the processes that facilitate the use of these evidence products by frontline Maternal, Newborn and Child Health and Reproductive and Child Health (RNCH/RCH) practitioners in decision-making on the issues that confront them in their line of work. This study explored the processes that facilitate the use of evidence products in reproductive, maternal and child health service provision in selected healthcare facilities in Ghana. Using a cross-sectional qualitative design, interviews of 24 frontline RNCH/RCH practitioners across 16 healthcare facilities in the Greater Accra, Eastern, and Ashanti regions of Ghana were conducted. The study employed a semi-structured interview guide modelled along the Action Cycle phase of the Knowledge-To-Action (KTA) framework, and the objectives of the study. Themes were built out of the transcribed data. The study revealed that the processes that facilitate the use of evidence products include problem identification activities (such as service evaluation, using accepted benchmarks, inadequate logistics for providing service and client feedback) and, adapting knowledge to their local context. The usual suspects of socio-cultural and health systems-related factors such as resource constraints and human factors were found to hinder the use of evidence products in providing RNCH/RCH services. The study contributes to knowledge by operationaliing the KTA, simplifying the concept of knowledge sustainability and makes it easy for adoption and implementation especially at the frontline. Appropriate interventions that rely on strong education to navigate the societal norms and beliefs that inhibit the uptake of evidence-based care by clients will be essential in improving the use of evidence to inform practice decisions.
Pneumocystis jiroveciipneumonia mortality risk associated with preceding long-term steroid use for the underlying disease: a multicenter, retrospective cohort study
Authors: Miyake Kohei , Senoo Satoru , Shiiba Ritsuya , Itano Junko , Kimura Goro , Kawahara Tatsuyuki , Tamura Tomoki , Kudo Kenichiro , Kawamura Tetsuji , Nakahara Yasuharu , Higo Hisao , Himeji Daisuke , Takigawa Nagio , Miyahara Nobuaki ,   Okayama Respiratory Disease Study Group (ORDSG)
Published: September 2023

Objective

Long-term steroid use increases the risk of developing Pneumocystis pneumonia (PcP), but there are limited reports on the relation of long-term steroid and PcP mortality.

Methods

Retrospective multicenter study to identify risk factors for PcP mortality, including average steroid dose before the first visit for PcP in non-human immunodeficiency virus (HIV)-PcP patients. We generated receiver operating characteristic (ROC) curves for 90-day all-cause mortality and the mean daily steroid dose per unit body weight in the preceding 10 to 90 days in 10-day increments. Patients were dichotomized by 90-day mortality and propensity score-based stabilized inverse probability of treatment weighting (IPTW) adjusted covariates of age, sex, and underlying disease. Multivariate analysis with logistic regression assessed whether long-term corticosteroid use affected outcome.

Results

Of 133 patients with non-HIV-PcP, 37 died within 90 days of initial diagnosis. The area under the ROC curve for 1-40 days was highest, and the optimal cutoff point of median adjunctive corticosteroid dosage was 0.34 mg/kg/day. Past steroid dose, underlying interstitial lung disease and emphysema, lower serum albumin and lower lymphocyte count, higher lactate dehydrogenase, use of therapeutic pentamidine and therapeutic high-dose steroids were all significantly associated with mortality.

Underlying autoimmune disease, past immunosuppressant use, and a longer time from onset to start of treatment, were associated lower mortality. Logistic regression analysis after adjusting for age, sex, and underlying disease with IPTW revealed that steroid dose 1-40 days before the first visit for PcP (per 0.1 mg/kg/day increment, odds ratio 1.36 [95% confidence interval = 1.16-1.66],P<0.001), low lymphocyte counts, and high lactate dehydrogenase revel were independent mortality risk factor, while respiratory failure, early steroid, and sulfamethoxazole/trimethoprim for PcP treatment did not.

Conclusion

A steroid dose before PcP onset was strongly associated with 90-day mortality in non-HIV-PcP patients, emphasizing the importance of appropriate prophylaxis especially in this population.
Acupuncture at Sanyinjiao(SP6) for patients with primary dysmenorrhea: Protocol for a systematic review and meta-analysis
Authors: Wang Xuemei , Yang Jiao , Liu Jing , Yang Yepeng , Zhang Zhiyuan , Xie Ping
Published: September 2023

Background

Primary dysmenorrhea (PD) is a gynecological disease that seriously affects women’s physical and mental health and quality of life. Sanyinjiao (SP6) is the most used acupoint for acupuncture treatment of PD, and acupuncture SP6 is more commonly used in the clinical treatment of PD, but evidence of effectiveness and safety is lacking. The purpose of this systematic review plan is to develop a study protocol that can evaluate the efficacy and safety of acupuncture SP6 in the treatment of PD.

Methods

The upper limit of retrieval time will be set to September 2023. Foreign and Chinese databases will be searched respectively: Cochrane Library, PubMed, EMBASE, Ovid, Korea Med, J-Global, J-Stage databases, and CNKI, CBM, SinoMed, VIP, Wanfang. Randomized controlled trials meeting the inclusion criteria will be screened by two independent reviewers, and data extraction and risk of bias assessment will be carried out. The primary outcome is dysmenorrhea symptoms, and the secondary outcomes include recent clinical cure rate, concomitant symptoms, serum prostaglandins, uterine artery blood flow resistance under ultrasound monitoring, and adverse reactions. Use RevMan V.5.3 software to perform the following operations: data synthesis, subgroup analysis, heterogeneity analysis, and sensitivity analysis. The evidence quality of clinical studies included in this study will be evaluated by the software of “Grading of Recommendations Assessment, Development, and Evaluation”.

Results

This study will provide comprehensive clinical evidence for treating PD with acupuncture SP6.

Conclusion

This systematic review will confirm whether acupuncture SP6 is safe and effective in treating PD clinically.

Registration details

PROSPERO CRD42020171664.
Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike
Authors: Wang Qian , Guo Yicheng , Liu Liyuan , Schwanz Logan T. , Li Zhiteng , Ho Jerren , Zhang Richard M. , Iketani Sho , Yu Jian , Huang Yiming , Qu Yiming , Valdez Riccardo , Lauring Adam S. , Gordon Aubree , Wang Harris H. , Liu Lihong , Ho David D.
Published: September 2023

Although the COVID-19 pandemic has officially ended1, SARS-CoV-2 continues to spread and evolve. Recent infections have been dominated by XBB.1.5 and EG.5.1 subvariants2. A new subvariant designated BA.2.86 has just emerged, spreading to 21 countries in 5 continents3. This virus contains 34 spike mutations compared to its BA.2 predecessor, thereby raising concerns about its propensity to evade existing antibodies. We examined its antigenicity using human sera and monoclonal antibodies (mAbs). Reassuringly, BA.2.86 was not more resistant to human sera than XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from patients who had XBB breakthrough infection exhibited robust neutralizing activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection. The finding that the longer genetic distance of BA.2.86 did not yield a larger antigenic distance was partially explained by the mAb data. While BA.2.86 showed greater resistance to mAbs to subdomain 1 (SD1) and receptor-binding domain (RBD) class 2 and 3 epitopes, it was more sensitive to mAbs to class 1 and 4/1 epitopes in the “inner face” of RBD that is exposed only when this domain is in the “up” position. We also identified six new spike mutations that mediate antibody resistance, including E554K that threatens SD1 mAbs in clinical development. The BA.2.86 spike also had a remarkably high receptor affinity. The ultimate trajectory of this new SARS-CoV-2 variant will soon be revealed by continuing surveillance, but its worldwide spread is worrisome.
The Impact of Intermittent Hypoxemia on Type 1 Retinopathy of Prematurity in Preterm Infants
Authors: Rabienia Haratbar Samaneh , Chen Li , Cheng Qiang , Singh Dara , Fathi Faraneh , Mohtasebi Mehrana , Liu Xuhui , Patwardhan Abhijit , Bhandary Prasad , Bada Henrietta S. , Yu Guoqiang , Abu Jawdeh Elie G.
Published: September 2023

Background

Intermittent hypoxemia (IH) may influence retinopathy of prematurity (ROP) development in preterm infants, however, previous studies had mixed results. This study aims to assess the influence and evaluate the predictive ability of IH measures on Type 1 ROP, a stage beyond which ROP treatment is indicated.

Methods

IH was quantified by continuously monitoring oxygen saturation (SpO2) using high-resolution pulse oximeters during the first 10 weeks of life. Statistical analyses assessed the relationship and predictive ability of weekly and cumulative IH variables for Type 1 ROP development.

Results

Univariate analyses suggested that IH measures are greater in infants with Type 1 ROP and are predictive of Type 1 ROP development. Multivariable logistic regression analyses revealed that cumulative IH of longer duration during certain postnatal periods are associated with Type 1 ROP development after adjusting for gestational age (GA) or birth weight (BW). Although area under the curve (AUC) analyses revealed added predictivity of cumulative IH variables above GA or BW, these increments in AUC were not statistically significant.

Conclusions

The duration of IH events was associated with Type 1 ROP development. Interventions for reducing the duration of IH events may potentially improve ROP outcomes.

Impact

This study investigates the impact of IH on the development of Type 1 ROP in preterm infants.

Univariate analyses revealed that IH measures are greater in infants with Type 1 ROP and are predictive of Type 1 ROP development.

Multivariable logistic regression analyses revealed that cumulative IH events of longer duration are associated with Type 1 ROP development after adjusting for GA or BW.

Interventions for reducing the duration of IH events during critical postnatal periods may potentially improve ROP outcomes.
Antimicrobial susceptibility testing reveals reduced susceptibility to azithromycin and other antibiotics inLegionella pneumophilaserogroup 1 isolates from Portugal
Authors: Minetti Corrado , Barton Rachael , Farley Caitlin , Spiller Owen Brad , Rodrigues Raquel , Gonçalves Paulo
Published: September 2023

Background

Although not fully investigated, studies show thatLegionella pneumophilacan develop antibiotic resistance. As there is limited data available for Portugal, we determined the antibiotic susceptibility profile of PortugueseL. pneumophilaserogroup 1 (LpnSg1) isolates against antibiotics used in the clinical practice in Portugal.

Methods

Minimum inhibitory concentrations (MICs) were determined forLpnSg1clinical (n=100) and related environmental (n=7) isolates, collected between 2006-2022 in the context of the National Legionnaire’s Disease Surveillance Programme, against azithromycin, clarithromycin, erythromycin, levofloxacin, ciprofloxacin, moxifloxacin, rifampicin, doxycycline, tigecycline, and amoxicillin/clavulanic acid, using 3 different assays. Isolates were also PCR-screened for the presence of thelpeABgene.

Results

Twelve isolates had azithromycin MICs above the EUCAST tentative highest WT MIC, 9 of which werelpeABnegative; for erythromycin and clarithromycin, all isolates tested within the susceptible range. The number of isolates with MICs above the tentative highest WT MIC for the remaining antibiotics was: ciprofloxacin: 7; levofloxacin: 17; moxifloxacin: 8; rifampicin: 11; doxycycline: 82; tigecycline: 4. EUCAST breakpoints are not available for amoxicillin/clavulanic acid. We estimated the ECOFFs and one isolate had a MIC 8-fold higher than the E-test ECOFF. Additionally, a clinical isolate generated three colonies growing on the E-test inhibition zone that resulted in MICs 4-fold higher than for the parental isolate.

Conclusions

We report, for the first time, elevated MICs against first-line and other antibiotics (including azithromycin, fluoroquinolones and amoxicillin/clavulanic acid commonly used to treat pneumonia patients in Portugal) in PortugueseL. pneumophilastrains. Results point towards decreased susceptibility in circulating strains, justifying further investigation.
MindWatch: A Smart Cloud-based AI solution for Suicide Ideation Detection leveraging Large Language Models
Authors: Bhaumik Runa , Srivastava Vineet , Jalali Arash , Ghosh Shanta , Chandrasekharan Ranganathan
Published: September 2023

Suicide, a serious public health concern affecting millions of individuals worldwide, refers to the intentional act of ending one’s own life. Mental health issues such as depression, frustration, and hopelessness can directly or indirectly influence the emergence of suicidal thoughts. Early identification of these thoughts is crucial for timely diagnosis. In recent years, advances in artificial intelligence (AI) and natural language processing (NLP) have paved the way for revolutionizing mental health support and education. In this proof-of-concept study, we have created MindWatch, a cutting-edge tool that harnesses the power of AI-driven language models to serve as a valuable computer-aided system for the mental health professions to achieve two important goals such asearly symptom detection, and personalized psychoeducation. We utilized ALBERT and Bio-Clinical BERT language models and fine-tuned them with the Reddit dataset to build the classifiers. We evaluated the performance of bi-LSTM, ALBERT, Bio-Clinical BERT, OpenAI GPT3.5 (via prompt engineering), and an ensembled voting classifier to detect suicide ideation. For personalized psychoeducation, we used the state-of-the-art Llama 2 foundation model leveraging prompt engineering. The tool is developed in the Amazon Web Service environment. All models performed exceptionally well, with accuracy and precision/recall greater than 92%. ALBERT performed better (AUC=.98) compared to the zero-shot classification accuracies obtained from OpenAI GPT3.5 Turbo (ChatGPT) on hidden datasets (AUC=.91). Furthermore, we observed that the inconclusiveness rate of the Llama 2 model is low while tested for few examples. This study emphasizes how transformer models can help provide customized psychoeducation to individuals dealing with mental health issues. By tailoring content to address their unique mental health conditions, treatment choices, and self-help resources, this approach empowers individuals to actively engage in their recovery journey. Additionally, these models have the potential to advance the automated detection of depressive disorders.
MRMCsamplesize: An R Package for Estimating Sample Sizes for Multi-Reader Multi-Case Studies
Authors: Robert Dennis , Sathyamurthy Saigopal , Putha Preetham
Published: September 2023

Multi-Reader Multi-Case (MRMC) studies are typically used to evaluate improvement in diagnostic accuracy of readers (diagnosticians) when they are assisted by a computer-assisted device (CAD) such as, but not limited to, those based on Artificial Intelligence (AI) algorithms. Statistical analysis of MRMC study data is not trivial and these studies can consume a lot of resources. Optimal planning is crucial and estimation of sample size is a significant step during the study planning phase. MRMC sample size estimations require many parameter assumptions and without pilot data this is generally not intuitive. MRMCsamplesize package can help researchers to estimate sample sizes for an MRMC study in the absence of any pilot data. The program outputs the number of cases required for a given number of readers. The package can also estimate sample sizes for scenarios where intra-cluster correlation (ICC) needs to be adjusted.
RADIF(C1orf112)-FIGNL1 Complex Regulates RAD51 Chromatin Association to Promote Viability After Replication Stress
Authors: Tischler Jessica D. , Tsuchida Hiroshi , Oda Tommy T. , Park Ana , Adeyemi Richard O.
Published: September 2023

Homologous recombination (HR) plays critical roles in repairing lesions that arise during DNA replication and is thus essential for viability. RAD51 plays important roles during replication and HR, however, how RAD51 is regulated downstream of nucleofilament formation and how the varied RAD51 functions are regulated is not clear. We have investigated the poorly characterized protein c1orf112/RADIF that previously scored in genome-wide screens for mediators of DNA inter-strand crosslink (ICL) repair. Upon ICL agent exposure, RADIF loss leads to marked cell death, elevated chromosomal instability, increased micronuclei formation, altered cell cycle progression and increased DNA damage signaling. RADIF is recruited to damage foci and forms a complex with FIGNL1. Both proteins have epistatic roles in ICL repair, forming a co-stable complex. Mechanistically, RADIF loss leads to increased RAD51 amounts and foci on chromatin both with or without exogenous DNA damage, defective replication fork progression and reduced HR competency. We posit that RADIF is essential for limiting RAD51 levels on chromatin in the absence of damage and for RAD51 dissociation from nucleofilaments to properly complete HR. Failure to do so leads to replication slowing and inability to complete repair.
Bmp9 regulates Notch signaling and the temporal dynamics of angiogenesis via Lunatic Fringe
Authors: Ristori Tommaso , Thuret Raphael , Hooker Erika , Quicke Peter , Lanthier Kevin , Ntumba Kalonji , Aspalter Irene M. , Uroz Marina , Herbert Shane P. , Chen Christopher S. , Larrivée Bruno , Bentley Katie
Published: September 2023

In brief

The mechanisms regulating the signaling pathways involved in angiogenesis are not fully known. Ristori et al. show that Lunatic Fringe (LFng) mediates the crosstalk between Bone Morphogenic Protein 9 (Bmp9) and Notch signaling, thereby regulating the endothelial cell behavior and temporal dynamics of their identity during sprouting angiogenesis.

Highlights

Bmp9 upregulates the expression of LFng in endothelial cells.

LFng regulates the temporal dynamics of tip/stalk selection and rearrangement.

LFng indicated to play a role in hereditary hemorrhagic telangiectasia.

Bmp9 and LFng mediate the endothelial cell-pericyte crosstalk.

Bone Morphogenic Protein 9 (Bmp9), whose signaling through Activin receptor-like kinase 1 (Alk1) is involved in several diseases, has been shown to independently activate Notch target genes in an additive fashion with canonical Notch signaling. Here, by integrating predictive computational modeling validated with experiments, we uncover that Bmp9 upregulates Lunatic Fringe (LFng) in endothelial cells (ECs), and thereby also regulates Notch activity in an inter-dependent, multiplicative fashion. Specifically, the Bmp9-upregulated LFng enhances Notch receptor activity creating a much stronger effect when Dll4 ligands are also present. During sprouting, this LFng regulation alters vessel branching by modulating the timing of EC phenotype selection and rearrangement. Our results further indicate that LFng can play a role in Bmp9-related diseases and in pericyte-driven vessel stabilization, since we find LFng contributes to Jag1 upregulation in Bmp9-stimulated ECs; thus, Bmp9-upregulated LFng results in not only enhanced EC Dll4-Notch1 activation, but also Jag1-Notch3 activation in pericytes.
Untargeted proteomics identifies plant substrates of the bacterial-derived ADP-ribosyltransferase AvrRpm1
Authors: Kaur Simranjit , Colby Thomas , Thieme Domenika , Proksch Carsten , Matschi Susanne , Matić Ivan , Wirthmueller Lennart
Published: September 2023

One class of enzymes that plant pathogens employ to manipulate innate immunity and physiology of the infected cells are host-targeted ADP-ribosyltransferases. The bacterial pathogenPseudomonas syringaeuses its type III secretion system to inject several effector proteins with ADP-ribosyltransferase activity into plant cells. One of them, AvrRpm1, ADP-ribosylates the plasma membrane-associated RPM1-INTERACTING PROTEIN 4 (RIN4) inGlycine maxandArabidopsis thalianato attenuate targeted secretion of defense-promoting compounds. Substrate identification of host-targeted ADP-ribosyltransferases is complicated by the biochemical lability of the protein modification during plant protein extraction and in several cases required prior knowledge on plant immune signaling pathways that are impaired by the ADP-ribosylating type III effector. Using the AvrRpm1-RIN4 pair as a proof-of-concept, we present an untargeted proteomics workflow for enrichment and detection of ADP-ribosylated proteins and peptides from plant cell extracts that in several cases provides site-resolution for the modification.
Cellular RNA Interacts with MAVS to Promote Antiviral Signaling
Authors: Gokhale Nandan S. , Somfleth Kim , Thompson Matthew G. , Sam Russell K. , Marciniak Daphnée M. , Chu Lan H. , Park Moonhee , Dvorkin Steve , Oberst Andrew , Horner Stacy M. , Ong Shao-En , Gale Michael , Savan Ram
Published: September 2023

Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multi-protein complex organized around the central adaptor protein MAVS. Recent work has shown that protein complex function can be modulated by RNA molecules providing allosteric regulation or acting as molecular guides or scaffolds. Thus, we hypothesized that RNA plays a role in organizing MAVS signaling platforms. Here, we show that MAVS, through its central intrinsically disordered domain, directly interacts with the 3′ untranslated regions of cellular mRNAs. Importantly, elimination of RNA by RNase treatment disrupts the MAVS signalosome, including newly identified regulators of RLR signaling, and inhibits phosphorylation of the transcription factor IRF3. This supports the hypothesis that RNA molecules scaffold proteins in the MAVS signalosome to induce IFNs. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.
Neuroanatomical, electrophysiological, and morphological characterization of melanin-concentrating hormone cells coexpressing cocaine- and amphetamine-regulated transcript
Authors: Miller Persephone A , Williams-Ikhenoba Jesukhogie G , Sankhe Aditi S , Hoffe Brendan H , Chee Melissa J
Published: September 2023

Melanin-concentrating hormone (MCH) cells in the hypothalamus regulate fundamental physiological functions like energy balance, sleep, and reproduction. This diversity may be ascribed to the neurochemical heterogeneity among MCH cells. One prominent subpopulation of MCH cells coexpresses cocaine- and amphetamine-regulated transcript (CART), and as MCH and CART can have opposing actions, MCH/CART+ and MCH/CART− cells may differentially modulate behavioural outcomes. However, it is not known if there are differences in cellular properties underlying their functional differences, thus we compared the neuroanatomical, electrophysiological, and morphological properties of MCH cells in male and femaleMch-cre;L10-Egfpreporter mice. Half of MCH cells expressed CART and were most prominent in the medial hypothalamus. Whole-cell patch-clamp recordings revealed differences in their passive and active membrane properties in a sex-dependent manner. Female MCH/CART+ cells had lower input resistances, but male cells largely differed in their firing properties. All MCH cells increased firing when stimulated, but their firing frequency decreases with sustained stimulation. MCH/CART+ cells showed stronger spike rate adaptation than MCH/CART− cells. The kinetics of excitatory events at MCH cells also differed by cell type, as the rising rate of excitatory events was slower at MCH/CART+ cells. By reconstructing the dendritic arborization of our recorded cells, we found no sex differences, but male MCH/CART+ cells had less dendritic length and fewer branch points. Overall, distinctions in topographical division and cellular properties between MCH cells add to their heterogeneity and help elucidate their response to stimuli or effect on modulating their respective neural networks.
A morphogenic cascade emerges from the co-evolution of spheroid fluidization and fracturing of multicellular barriers
Authors: Wu Selwin K. , Ho Celestine Z. , Sun Fuqiang , Lou Yuting , Huang Christina Bao-Xian , Xiao Jingwei , Shagirov Murat , Yow Ivan , Chin Jasmine Fei Li , Verma Suzie , Yap Alpha S. , Lin Yuan , Hiraiwa Tetsuya , Low Boon Chuan
Published: September 2023

Cell collectives migrate and undergo morphological transitions during development and diseases. How cells collectively invade a tissue barrier and its immediate consequence remains elusive. An outstanding challenge is to achieve a comprehensive understanding of the invasion cascade by integrating and applying principles from material science, biophysics, and cell biology. Using a three-dimensional model system of cancer spheroids invading the mesothelium, we show that collective cell invasion emerges from an interplay between spheroid fluidization and fracturing of the multicellular barrier. We found that mesothelial cell- cell contacts undergo tensile fracturing due to spheroid invasion. At the subcellular level, force transmission via intercellular integrin complexes between spheroid and mesothelial cells induces mesothelial cell apical constriction that leads to fracturing. Concurrently, fluidization and directed spheroid cells motility expand the mesothelial fracture. In response, the deformed mesothelium retards spheroid spreading, leading to spheroid cells crowding with contact inhibition of locomotion and proliferation. Our results demonstrate that collective invasion is a morphogenic cascade, revealing that the multicellular barrier undergoing invasion-induced fracture can subsequently force the invaded cells into a dormant state of reduced proliferative potential. Thus, our conclusion may help explain why cancer cells that have invaded a foreign microenvironment tend to enter dormancy.
Unveiling the ultrastructural landscape of native extracellular matrix via lift-out cryo-FIBSEM and cryo-ET
Authors: Zens Bettina , Fäßler Florian , Hansen Jesse M , Hauschild Robert , Datler Julia , Hodirnau Victor-Valentin , Zheden Vanessa , Alanko Jonna , Sixt Michael , Schur Florian KM
Published: September 2023

The extracellular matrix (ECM) is a highly hydrated, three-dimensional network composed of various macromolecules and signaling factors. It serves as a structural scaffold for cells and plays an essential role in the regulation of numerous cellular processes, including cell migration, adhesion, and proliferation. Despite its importance in metazoans, structural knowledge is rudimentary on how the components of the matrisome are secreted, remodeled, and interact with each other and with surrounding cells. Specifically, the exact molecular assembly of important ECM fibers, such as fibronectin fibrils, fibrillin microfibrils, or Collagen-VI filaments has remained enigmatic. This is largely due to methodological limitations in specimen preparation for conventional room-temperature electron microscopy (EM).

To overcome these limitations, we have developed a cell culture-based 3D-ECM platform compatible with sample thinning by cryo-lift out focused ion beam (FIB) milling and cryo-electron tomography (cryo-ET). Our workflow involves the implementation of cell-derived matrices (CDMs) grown on EM grids, resulting in a highly adaptable and versatile tool to closely mimic ECM environments. This allows us to visualize native ECM and its components for the first time in their fully hydrated, cellular context. Our data reveals an intricate network of ECM fibers and their positioning with respect to matrix-secreting cells. In addition to D-spaced collagen fibers, we visualize previously unresolved fibrous structures, and an amorphous matrix co-assembling in proximity to ECM fibers and delineating the boundary between ECM and empty extra-cellular space. Intra- and extracellular granules presumably represent assembly intermediates of the ECM. Our results add to the structural atlas of the ECM and provide novel insights into ECM secretion, assembly and maintenance.
Automatic learning mechanisms for flexible human locomotion
Authors: Rossi Cristina , Leech Kristan A. , Roemmich Ryan T. , Bastian Amy J.
Published: September 2023

Movement flexibility and automaticity are necessary to successfully navigate different environments. When encountering difficult terrains such as a muddy trail, we can change how we step almost immediately so that we can continue walking. This flexibility comes at a cost since we initially must pay deliberate attention to how we are moving. Gradually, after a few minutes on the trail, stepping becomes automatic so that we do not need to think about our movements. Canonical theory indicates that different adaptive motor learning mechanisms confer these essential properties to movement: explicit control confers rapid flexibility, while forward model recalibration confers automaticity. Here we uncover a distinct mechanism of treadmill walking adaptation – an automatic stimulus-response mapping – that confers both properties to movement. The mechanism is flexible as it learns stepping patterns that can be rapidly changed to suit a range of treadmill configurations. It is also automatic as it can operate without deliberate control or explicit awareness by the participants. Our findings reveal a tandem architecture of forward model recalibration and automatic stimulus-response mapping mechanisms for walking, reconciling different findings of motor adaptation and perceptual realignment.
NatB-dependent acetylation protects procaspase-8 from UBR4-mediated degradation and is required for full induction of the extrinsic apoptosis pathway
Authors: Guedes Joana P. , Boyer Jean Baptiste , Elurbide Jasmine , Carte Beatriz , Redeker Virginie , Sago Laila , Meinnel Thierry , Côrte-Real Manuela , Giglione Carmela , Aldabe Rafael
Published: September 2023

N-terminal acetyltransferase B (NatB) is a major contributor to the N-terminal acetylome and is implicated in several key cellular processes including apoptosis and proteostasis. However, the molecular mechanisms linking NatB-mediated N-terminal acetylation to apoptosis and its relationship with protein homeostasis remain elusive. In this study, we generated mouse embryonic fibroblasts (MEFs) with an inactivated catalytic subunit of NatB (Naa20-/-) to investigate the impact of NatB deficiency on apoptosis regulation. Through quantitative N-terminomics, label-free quantification, and targeted proteomics, we demonstrated that NatB does not influence the proteostasis of all its substrates. Instead, our focus on putative NatB-dependent apoptotic factors revealed that NatB-mediated acetylation serves as a protective shield against UBR4 and UBR1 Arg/N-recognin-mediated degradation. Notably,Naa20-/-MEFs exhibited reduced responsiveness to extrinsic pro-apoptotic stimuli, a phenotype that was partially reversible upon UBR4 Arg/N-recognin silencing and consequent inhibition of procaspase-8 degradation. Collectively, our results shed light on how the interplay between NatB-mediated acetylation and the Arg/N-degron pathway impacts apoptosis regulation, providing new perspectives in the field including in therapeutic interventions.
Nutritional condition drives spatial variation in physiology of Antarctic lipid-storing copepods
Authors: Berger Cory A. , Steinberg Deborah K. , Tarrant Ann M.
Published: September 2023

Lipid-rich copepods form an essential link between primary producers and higher trophic levels in high-latitude oceans. These zooplankton can take advantage of ephemeral phytoplankton blooms to fuel development and reproduction. However, we have limited understanding of how the physiological condition of these animals varies in relation to environmental factors such as food availability. Due to high advection, it is likely that physiological plasticity, rather than local adaptation, is primarily responsible for physiological differences within a region. We use transcriptomics and other physiological metrics to understand how two species of copepods (Calanoides acutusandCalanus propinquus) vary across environmental gradients along the West Antarctic Peninsula. For the primarily herbivorousC. acutus, physiological separation between sampling locations appears to be driven by feeding status, and gene expression differences indicate differential expression of genes regulating lipid metabolism, reproduction, aerobic metabolism, and protein translation. For the more omnivorousC. propinquus,physiology and gene expression did not segregate as clearly by location, showed minimal signs of food deprivation at any location, and had a weaker relationship with chlorophyll compared toC. acutus. By comparing these results with concurrent starvation experiments, we find thatspatial variation in gene expression reflects short-term differences in food availability (particularly forC. acutus,), and we identify genes whose expression indicates recent feeding status. Further examination of the relationships between food availability, copepod physiology, and population dynamics will ultimately improve our capacity to predict how copepod populations will respond to rapidly changing environmental conditions in the West Antarctic Peninsula ecosystem.
Affinity-tagged SMAD1 and SMAD5 mouse lines reveal transcriptional reprogramming mechanisms during early pregnancy
Authors: Liao Zian , Tang Suni , Nozawa Kaori , Shimada Keisuke , Ikawa Masahito , Monsivais Diana , Matzuk Martin M.
Published: September 2023

Endometrial decidualization, a prerequisite for successful pregnancies, relies on transcriptional reprogramming driven by progesterone receptor (PR) and bone morphogenetic protein (BMP)-SMAD1/SMAD5 signaling pathways. Despite their critical roles in early pregnancy, how these pathways intersect in reprogramming the endometrium into a receptive state remains unclear. To define how SMAD1 and/or SMAD5 integrate BMP signaling in the uterus during early pregnancy, we generated two novel transgenic mouse lines with affinity tags inserted into the endogenous SMAD1 and SMAD5 loci (Smad1HA/HAandSmad5PA/PA). By profiling the genome-wide distribution of SMAD1, SMAD5, and PR in the mouse uterus, we demonstrated the unique and shared roles of SMAD1 and SMAD5 during the window of implantation. We also showed the presence of a conserved SMAD1, SMAD5, and PR genomic binding signature in the uterus during early pregnancy. To functionally characterize the translational aspects of our findings, we demonstrated that SMAD1/5 knockdown in human endometrial stromal cells suppressed expressions of canonical decidual markers (IGFBP1, PRL, FOXO1)and PR-responsive genes (RORB,KLF15). Here, our studies provide novel tools to study BMP signaling pathways and highlight the fundamental roles of SMAD1/5 in mediating both BMP signaling pathways and the transcriptional response to progesterone (P4) during early pregnancy.
The grass that built the Central Highland of Madagascar: environmental niches and morphological diversity ofLoudetia simplex
Authors: Almary Tchana O. M. , White Joseph , Rasaminirina Fitiavana , Razanatsoa Jacqueline , Lehmann Caroline , Rakotoarinivo Mijoro , Ralimanana Hélène , Vorontsova Maria S. , Tiley George P.
Published: September 2023

1) Research Aims —Loudetia simplexis a common and dominant species throughout grassland ecosystems in mainland Africa and Madagascar. It is highly polymorphic, often classified as two taxa endemic to Madagascar:L. simplexsubsp.stipoidesandL. madagascariensis. A better understanding of the inter- and intra-specific variation between these taxa and its contributing environmental factors could improve our understanding of the history of Madagascar’s grasslands.

2) Methods — The taxonomic status ofL. simplexsubsp.stipoidesandL. madagascariensiswas evaluated by morphometric analyses of 119 herbarium specimens. Species distribution modelling was used to determine the most important environmental factors underlyingthe L. simplexdistribution in Madagascar versus other African grasslands. We investigated ifL. simplexin Madagascar could be predicted by distributions across mainland Africa with niche overlap analyses.

3) Key Result — African and Malagasy species exhibited variation potentially associated with environment. Specimens from northern and western Madagascar were taller with smaller spikelets than those from Southern Africa and central Madagascar.Loudetia simplextypically occurred in cooler temperatures with high precipitation and pronounced seasonality, but taller populations were found in warmer conditions. Projecting ecological niches of Southern Africa and East Tropical Africa onto Madagascar demonstrates much of the present distribution in the Central Highlands is expected from other natural African grasslands.

4) Key Point — Malagasy and African individuals represent a single species, and the Malagasy species can be considered as a synonym of L. simplex. Distribution models are congruent with pre-human presence of grasslands in Madagascar.

SOCIETAL IMPACT STATEMENT

Understanding dominant species likeLoudetia simplexis necessary to understand the fire-driven grassy ecosystems they create. In Madagascar, grasslands are considered a low-value ecosystem despite their unique biodiversity and crucial importance as zebu rangeland. Only 1.8% of Madagascar’s grasslands are protected despite facing similar threats to forests and biodiversity loss. This study of common grasses will support the management of protected areas by providing information on resource management of vulnerable open ecosystems in Madagascar. Distribution models of common grass species and clear taxonomic classification can help land management stakeholders identify natural grasslands versus degraded forests.