bluuebunny/crossref_metadata_2025 huggingface dataset:
Reliably quantifying the severity of social symptoms in children with autism using ASDSpeech
Authors: Eni Marina , Ilan Michal , Michaelovski Analya , Golan Hava M. , Meiri Gal , Menashe Idan , Dinstein Ilan , Zigel Yaniv
Published: October 2023

Several studies have demonstrated that the severity of social communication problems, a core symptom of Autism Spectrum Disorder (ASD), is correlated with specific speech characteristics of ASD individuals. This suggests that it may be possible to develop speech analysis algorithms that can quantify ASD symptom severity from speech recordings in a direct and objective manner. Here we demonstrate the utility of a new open-source AI algorithm, ASDSpeech, which can analyze speech recordings of ASD children and reliably quantify their social communication difficulties across multiple developmental timepoints. The algorithm was trained and tested on the largest ASD speech dataset available to date, which contained 99,193 vocalizations from 197 ASD children recorded in 258 Autism Diagnostic Observation Schedule, 2ndedition (ADOS-2) assessments. ASDSpeech was trained with acoustic and conversational features extracted from the speech recordings of 136 children, who participated in a single ADOS-2 assessment, and tested with independent recordings of 61 additional children who completed two ADOS-2 assessments, separated by 1–2 years. Estimated total ADOS-2 scores in the test set were significantly correlated with actual scores when examining either the first (r(59) = 0.544,P< 0.0001) or second (r(59) = 0.605,P< 0.0001) assessment. Separate estimation of social communication and restricted and repetitive behavior symptoms revealed that ASDSpeech was particularly accurate at estimating social communication symptoms (i.e., ADOS-2 social affect scores). These results demonstrate the potential utility of ASDSpeech for enhancing basic and clinical ASD research as well as clinical management. We openly share both algorithm and speech feature dataset for use and further development by the community.
ChineseCVD: first-in-world, web-based, Chinese-specific Cardiovascular Risk Calculator incorporating long COVID, COVID-19 vaccination, SGLT2i and PCSK9i treatment effects
Authors: Chang Carlin , Tse Gary , Lee Quinncy , Chou Oscar Hou In , Lee Teddy Tai Loy , Leung Bosco Kwok-hei , Ngai Amy Lee , Khan Adan , Wong Wing Tak , Wai Abraham Ka Chung , Chen Kang-yin , Liu Tong , Zhou Jiandong
Published: October 2023

Background

Web-based risk prediction tools for cardiovascular diseases are crucial for providing rapid risk estimates for busy clinicians, but there is none available specifically for Chinese subjects. This study developed ChineseCVD, first-in-world web-based Chinese-specific Cardiovascular Risk Calculator incorporating long COVID, COVID-19 vaccination, SGLT2i and PCSK9i treatment effects.

Methods

Adult patients attending government-funded family medicine clinics in Hong Kong between 1stJanuary 2000 and 31stDecember 2003 were included. The primary outcome was major adverse cardiovascular events (MACE) defined as a composite of myocardial infarction, heart failure, transient ischaemic attacks/ischaemic strokes, and cardiovascular mortality.

Results

A total of 155,066 patients were used as the derivation cohort. Over a median follow-up of 16.1 (11.6-17.8) years, 31,061 (20.44%) had MACE. Cox regression identified male gender, age, comorbidities, cardiovascular medications, systolic and diastolic blood pressure, and laboratory test results (neutrophil-lymphocyte ratio, creatinine, ALP, AST, ALT, HbA1c, fasting glucose, triglyceride, LDL and HDL) as significant predictors of the above outcomes. ChineseCVD further incorporates the impact of smoking status, COVID-19 infection, number of COVID-19 vaccination doses, and modifier effects of newest medication classes of PCSK9i and SGLT2i. The calculator enables clinicians to demonstrate to patients how risks vary with different medications.

Conclusions

The ChineseCVD risk calculator enables rapid web-based risk assessment for adverse cardiovascular outcomes, thereby facilitating clinical decision-making at the bedside or in the clinic.
Mental health conditions and COVID-19 vaccine outcomes: a scoping review
Authors: Jia Ru , Coupland Carol , Vinogradova Yana , Qureshi Nadeem , Turner Emma , Vedhara Kavita
Published: October 2023

Background

The COVID-19 pandemic has had a profound impact on the mental health of people worldwide. Mental health also impacts on physical health. In the context of viral illnesses, viral challenge studies have shown that indices of mental health are associated with susceptibility to viral infections, including coronaviruses. Research conducted during the pandemic has shown that people with a history of mental health conditions were at increased risk of infection, hospitalisation, and mortality. However, the relationship between mental health conditions and vaccine outcomes such as vaccine intentions, uptake, and vaccine breakthrough is not yet well-understood.

Methods

We conducted a systematic search on the topics of COVID-19 vaccine intentions, vaccine uptake, and vaccine breakthrough, in relation to mental health conditions, in four databases: PubMed, MEDLINE, SCOPUS, and PsychINFO, as well as the publication lists of Clinical Practice Research Datalink (CPRD), The Health Improvement Network (THIN), OpenSAFELY, and QResearch. Inclusion criteria focus on studies reporting either of the aforementioned COVID-19 vaccine outcomes among people with mental health conditions.

Results

Thirty-three out of 251 publications met our inclusion criteria for this review. Overall, the evidence is inconclusive regarding the level of intention to accept the COVID-19 vaccine among people with mental health conditions. However, people with mental health conditions were more likely to have lower uptake of the COVID-19 vaccine, compared to people without. Common barriers to COVID-19 vaccine uptake include concerns about the safety, effectiveness, and side effects of the vaccines. Limited evidence also suggests that vaccine breakthrough may be a particular risk for those with substance use disorder.

Conclusions

Our findings revealed a possible intention-behaviour gap for receiving the COVID-19 vaccine among people with mental health conditions, yielding interventions to encourage vaccine uptake in this population. There is also the need to enhance our understanding of COVID-19 vaccine breakthrough in people with mental health conditions.
Echocardiographic characterisation in severe Covid-19 with respiratory failure - an observational study
Authors: Isackson Henrik , Larsson Anders , Lipcsey Miklos , Frithiof Robert , Flachskampf Frank A. , Hultström Michael
Published: October 2023

Objective

We aimed to investigate cardiac effects of severe SARS-CoV-2 and the importance of echocardiography-assessment and biomarkers.

Methods

This is an observational study of the first patients admitted to intensive care due to SARS-CoV-2-respiratory failure. Thirty-four underwent echocardiography of which twenty-five were included, compared to forty-four non-echo patients. Exclusion was based on absence of normofrequent sinus rhythm and/or mechanical respiratory support. Biomarkers were analysed on clinical indication.

Results

Mortality was higher in the echo-compared to non-echo group (44 % vs. 16%, p<0.05). Right-sided parameters were not under significant strain. Tricuspid valve regurgitation velocity indicated how increased pulmonary pressure was associated with mortality (survivors: 2.51 ± 0.01 m/s vs. non-survivors: 3.06 ± 0.11 m/s, p<0.05), before multiple comparison-correction. Setting cut-off for pulmonary hypertension to 2.8 m/s generated p<0.01 using frequency distribution testing. Cardiac markers, high sensitivity cardiac troponin I and N-terminal pro brain natriuretic peptide, and D-dimer were higher in the echocardiography group. (hs-TnI (ng/L): echo : 133 ± 45 vs. non-echo: 81.3 ± 45, p<0.01; NT-proBNP (ng/L): echo: 2959 ± 573 vs. non-echo: 1641 ± 420, p<0.001; D-dimer (mg/L): echo: 16.1 ± 3.7 vs. non-echo: 6.1 ± 1.5, p<0.01) and non-survivor group (hs-TnI (ng/L): survivors: 59.1 ± 21 vs. non-survivors: 211 ± 105, p<0.0001; NT-proBNP (ng/L): survivors: 1310 ± 314 vs. non-survivors: 4065 ± 740, p<0.0001; D-dimer (mg/L): survivors: 7.2 ± 1.5 vs. non-survivors: 17.1 ± 4.8, p<0.01). Tricuspid regurgitation velocity was positively correlated with cardiac troponin I (r=0.93, r2=0.74, p<0.001).

Conclusions

These results suggest there is no negative effect on cardiac function in critical SARS-CoV-2. Pulmonary pressure appears higher amongst non-survivors indicating pulmonary disease as the driver of mortality. Echocardiography was more commonly performed in the non-survivor group, and cardiac biomarkers as well as D-dimer was higher in the non-survivor group suggesting they carry negative prognostic values.

Trial registration number

This is an observational study from patients included in “Clinical trialsNCT04316884”

Strength and limitations of this study

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The patient cohort is recruited from consecutive patients admitted to the ICU in need of mechanical respiratory support independent of background which makes it relevant to clinical practice.

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The echocardiographic image acquisition was carried out by hospital assigned agents on clinical indication, which makes the results applicable in a clinical setting.

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Since the image acquisition was carried out on a clinical indication, the results may be skewed towards the false positive if applied to all Covid19 patients.
Allostatic load in early adolescence: gene / environment contributions and relevance for mental health
Authors: Hoffman Kevin W. , Tran Kate T. , Moore Tyler M. , Gataviņš Mārtiņš M. , Visoki Elina , DiDomenico Grace E. , Schultz Laura M. , Almasy Laura , Hayes Matthew R. , Daskalakis Nikolaos P. , Barzilay Ran
Published: October 2023

Background

Allostatic load is the cumulative “wear and tear” on the body due to chronic adversity. We aimed to test poly-environmental (exposomic) and polygenic contributions to allostatic load and their combined contribution to early adolescent mental health.

Methods

We analyzed data on N = 5,035 diverse youth (mean age 12) from the Adolescent Brain Cognitive Development Study (ABCD). Using dimensionality reduction method, we calculated and overall allostatic load score (AL) using body mass index [BMI], waist circumference, blood pressure, blood glycemia, blood cholesterol, and salivary DHEA. Childhood exposomic risk was quantified using multi-level environmental exposures before age 11. Genetic risk was quantified using polygenic risk scores (PRS) for metabolic system susceptibility (type 2 diabetes [T2D]) and stress-related psychiatric disease (major depressive disorder [MDD]). We used linear mixed effects models to test main, additive, and interactive effects of exposomic and polygenic risk (independent variables) on AL (dependent variable). Mediation models tested the mediating role of AL on the pathway from exposomic and polygenic risk to youth mental health. Models adjusted for demographics and genetic principal components.

Results

We observed disparities in AL with non-Hispanic White youth having significantly lower AL compared to Hispanic and Non-Hispanic Black youth. In the diverse sample, childhood exposomic burden was associated with AL in adolescence (beta=0.25, 95%CI 0.22-0.29, P<.001). In European ancestry participants (n=2,928), polygenic risk of both T2D and depression was associated with AL (T2D-PRS beta=0.11, 95%CI 0.07-0.14, P<.001; MDD-PRS beta=0.05, 95%CI 0.02-0.09, P=.003). Both polygenic scores showed significant interaction with exposomic risk such that, with greater polygenic risk, the association between exposome and AL was stronger. AL partly mediated the pathway to youth mental health from exposomic risk and from MDD-PRS, and fully mediated the pathway from T2D-PRS.

Conclusions

AL can be quantified in youth using anthropometric and biological measures and is mapped to exposomic and polygenic risk. Main and interactive environmental and genetic effects support a diathesis-stress model. Findings suggest that both environmental and genetic risk be considered when modeling stress-related health conditions.
The magnitude, determinants, and outcome of shock among pediatric patients: A cross-sectional hospital-based study
Authors: Kidanu Mebrahtu G. , Tazebe Engdaeshet , Birhane Alemseged , Yemane Marta , Kahsay Mebrihit M. , Tedla Mebrahtu G.
Published: October 2023

Background

Pediatric shock, a potentially fatal illness, develops after a systemic circulatory system failure. It appears to be a common emergency in children and produces substantial morbidity and mortality particularly if there is no early identification and therapy. The extent and causes of shock-induced death among children in Ethiopia have not been sufficiently studied.

Objective

This study was conducted to evaluate the severity, determinants, and prognosis of shock in pediatric patients who visited Ayder Comprehensive Specialized Hospital in Tigray, Northern Ethiopia.

Methods

From October 1st, 2020, to July 30th, 2022, an observational cross-sectional study was carried out at Ayder Comprehensive Specialized Hospital. The study included 132 children from the age of 1 month to 18 years. According to pediatric advanced life support guidelines, shock was diagnosed among patients. To gather information, a pretested questionnaire was employed. To examine the relationship between the independent variables and shock outcome, bivariate logistic regression was performed, and statistical significance was defined as a P-value of 0.05 or lower.

Result

The prevalence of shock was 2.2%. This study revealed 70.4 % decompensated stage of shock. Mortality rate of shock was 45.5% (95% CI: 37.1-53.8). A delayed presentation by more than one week with an adjusted odd ratio(AOR) of 16.9 (95% CI:2.3-123), type of shock other than hypovolemic shock with AOR of 8.3 (95% CI: 1.4-48), stage of shock with AOR of 27.8 (95% CI: 2.8-157), requirement of mechanical ventilation with AOR of 11 (95% CI:2.6-53) and length of hospital stay less than three days with AOR of 9 (95% CI: 1.7-48) were identified as a predictor of mortality by shock in children.

Conclusion

According to this study, shock causes a higher rate of child mortality. Independent predictors of mortality included delayed presentation, shock type, shock stage, need for mechanical ventilation, and brief hospital stay (less than three days).
WITHDRAWN: Classification and Treatment of Tibial Tubercle Fractures in Adults
Authors: Yao Xiang , Liu Hongyuan , Hu Minjie , Wang Chong , Miao Han , Tang Jilei
Published: October 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to 1. The paper needs structural changes. 2. Some of the data were found to have errors that need to be corrected after the previous submission. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
On the estimation of beat-to-beat time domain heart rate variability indices from smoothed heart rate time series
Authors: Garcia-Gonzalez Miguel A. , Mohammadpoor-Faskhodi Mahtab , Fernandez-Chimeno Mireya , Ramos-Castro Juan J.
Published: October 2023

This study tests the feasibility of estimating some time-domain heart rate variability indices (the standard deviation of the RR time series, SDNN, and the standard deviation of the differentiated RR time series, or RMSSD) from smoothed and rounded to the nearest beat per minute heart period time series using shallow neural networks. These time series are often stored in wearable devices instead of the beat-to-beat RR time series. Because the algorithm for obtaining the recorded mean heart rate in wearable devices is often not disclosed, this study test different hypothetic sampling strategies and smoothers. Sixteen features extracted from 5 minute smoothed heart period time series were employed to train, validate, and test shallow neural networks in order to provide estimates of the SDNN and RMSSD indices from freely available public databases RR time series. The results show that, using the proposed features, the median relative error (averaged for each database) in the SDNN ranges from 2% to 14% depending on the smoothness, sampling strategy, and database. The RMSSD is harder to estimate, and its median relative error ranges from 6% to 32%. The proposed methodology can be easily extended to other averaged heart rate time series, HRV indices and supervised learning algorithms
Costs, catastrophic out-of-pocket payments and impoverishment related to accessing surgical care among households in rural Ethiopia
Authors: Hailemichael Yohannes , Eshetu Tigist , Timothewos Sewit , Deneke Andualem , Tadesse Amezene , Abdella Ahmed , Bekele Abebe , Leather Andrew , Medhin Girmay , Prince Martin , Hanlon Charlotte
Published: October 2023

Background

The objective of this study was to assess the costs, catastrophic out-of-pocket (OOP) health expenditure, impoverishment and coping mechanisms used to pay for surgical care in a predominantly rural area of Ethiopia.

Methods

We conducted a community-based, cross-sectional household survey of 182 people who had undergone a surgical procedure. Participants were interviewed in their homes at six weeks post-operation. Using a contextually adapted version of the Study of global AGEing and adult health (SAGE) questionnaire, we estimated direct and indirect costs of surgical care from a household perspective. Catastrophic out-of-pocket (OOP) health expenditure was estimated using thresholds of 10% and 25% of annual household consumption expenditure. Impacts of surgical care payments on poverty levels was estimated by comparing pre-and post-operative OOP payments. Analysis of variance, t-test and a logit model were used to assess factors associated with catastrophic OOP health expenditure.

Results

Most surgical patients were women (87.9%), with 65% receiving obstetric surgical care. Direct costs dominated expenditure: direct medical costs Birr 1649.5 (44.6%), direct non-medical costs Birr 1226.5 (33.2%), indirect costs Birr 821.9 (22.2%). Catastrophic OOP surgical care expenditure was experienced by 69.2% households at the 10% threshold and 45.6% at the 25% threshold. The increase in average normalized poverty gap due to OOP surgical care expenditure was higher in non-obstetric (14.1%) compared to obstetric (5.8%) procedures, and for non-emergency (13.3%) compared to emergency care (6.3%). To pay for surgical care, 38% of households had sold assets and 5% had borrowed money.

Conclusions

Due to surgical care, households faced severe financial burdens leading to impoverishment. Households implemented hardship coping strategies to mitigate the financial constraints. Provision of free maternal care reduced but did not eliminate these burdens. There is a pressing need to tailor financial risk protection mechanisms to achieve universal coverage for surgical care.
Olfactory impairment and the risk of major adverse cardiovascular outcomes in older adults
Authors: Chamberlin Keran W. , Yuan Yaqun , Li Chenxi , Luo Zhehui , Reeves Mathew , Kucharska-Newton Anna , Pinto Jayant M. , Ma Jiantao , Simonsick Eleanor M. , Chen Honglei
Published: October 2023

Background

Olfactory impairment is common in older adults and may be associated with adverse cardiovascular health; however, empirical evidence is sparse.

Objective

To examine olfaction and the risk of coronary heart disease (CHD), stroke, and congestive heart failure (CHF).

Methods

This study included 2,537 older adults (aged 75.6±2.8 years) from the Health ABC Study with olfaction assessed by the 12-item Brief Smell Identification Test in 1999-2000, defined as poor (score ≤8), moderate (9-10), or good (11-12). The outcomes were incident CHD, stroke, and CHF.

Results

During up to 12-year follow-up, 353 incident CHD, 258 stroke, and 477 CHF events were identified. Olfaction was associated with incident CHF, but not with CHD or stroke. After adjusting for demographics, the cause-specific hazard ratio (HR) of CHF was 1.35 (95% confidence interval (CI): 1.08, 1.70) for moderate and 1.39 (95%CI: 1.09, 1.76) for poor olfaction. With additional adjustment for lifestyle, chronic diseases, and biomarkers of CHF, the HR was modestly attenuated to 1.32 (95%CI: 1.05, 1.66) for moderate and 1.28 (95%CI: 1.01, 1.64) for poor olfaction. These associations were robust in pre-planned subgroup analyses by age, sex, race, and prevalent CHD/stroke. However, the associations appeared to be evident among participants who reported very-good-to-excellent health (HR=1.47 (95%CI: 1.02, 2.13) for moderate and 1.76, (95%CI: 1.20, 2.57) for poor olfaction). In contrast, null association with CHF was found among those with fair-to-poor self-reported health.

Conclusions

In community-dwelling older adults, a single olfaction test was associated with a long-term risk for incident CHF, particularly among those reporting very-good-to-excellent health.
Transcriptome Profiling and Characterization of Peritoneal Metastasis Ovarian Cancer Xenografts in Humanized Mice
Authors: Kang Sung Wan , Lee Ji-young , Kang Ok-Ju , Kim Yong-Man , Choi Eun Kyung , Lee Shin-Wha
Published: October 2023

Background

Although immunotherapy has not yet been as successful in ovarian cancer (OC), it remains a potential therapeutic strategy. Preclinical models of OC are necessary to evaluate the efficacy of immuno-oncology (IO) drugs targeting human cancer and immune components but have been underutilized. Developing mouse models with a humanized (Hu) immune system can help understand the human immune response to IO drugs, including immune checkpoint inhibitors (ICIs), which have demonstrated limited effectiveness in OC patients.

Methods

We established OC xenograft Hu-mouse models by intraperitoneally injecting luciferase-expressing SKOV-3 Luc and OVCAR-3 Luc OC cells into CD34+Hu-mice. Tumor growth was monitored through bioluminescence imaging (BLI). We assessed the efficacy of PD-1 blockade with pembrolizumab in the SKOV-3 Luc Hu-mouse model. The immune profiles of the tumors were characterized using colorimetric immunostaining and flow cytometry. Additionally, we analyzed RNA-seq data to investigate the gene expression signature of pembrolizumab refractory tumors.

Results

We confirmed tumor development in both OC cell lines within CD34+Hu-mice. In these models, human lymphocyte and myeloid cell subsets were present in the tumors, draining lymph nodes, blood, and spleens. The SKOV-3 Luc tumor-bearing Hu-mice did not respond to pembrolizumab monotherapy. These tumors exhibited a high presence of tumor-infiltrating macrophages. Tumors in Hu-mice unresponsive to pembrolizumab showed a lower abundance of CD8+T-cells, memory B cells, plasma cells, and a higher proportion of naïve M0 macrophages and mast cells compared to the PBS control. Furthermore, we identified 43 significantly enriched gene sets in these tumors. The differentially expressed genes (DEGs) were predominantly enriched in HDAC class I, RB1, KLF1/3, TCF21, MYD88, SMARCE1 target genes, and genes associated with epithelial-mesenchymal transition (EMT) and fibroblasts.

Conclusion

Our xenograft Hu-mouse model of OC provides a valuable tool for investigating the efficacy of IO drugs. The insights gained from this model offer potential avenues to explore mechanisms of resistance to PD-1/PD-L1 blockade in OC.
Docking for molecules that bind in a symmetric stack with SymDOCK
Authors: Smith Matthew S. , Knight Ian S. , Kormos Rian C. , Pepe Joseph G. , Kunach Peter , Diamond Marc I. , Shahmoradian Sarah H. , Irwin John J. , DeGrado William F. , Shoichet Brian K.
Published: October 2023

Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of much current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein’s symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand’s docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in aprospectivestudy SymDOCK predicted the structure of the PET tracer MK-6240 bound in a symmetrical stack to AD PHF tau before that structure was determined; the docked pose was used to determine how MK-6240 fit the cryo-EM density. In proof-of-concept studies, SymDOCK enriched known ligands over property-matched decoys in retrospective screens without sacrificing docking speed, and can address large library screens that seek new symmetrical stackers. Future applications of this approach will be considered.
Cell surface architecture of the cultivated DPANN archaeonNanobdella aerobiophila
Authors: Kato Shingo , Tahara Yuhei O. , Nishimura Yuki , Uemastu Katsuyuki , Arai Takahiro , Nakane Daisuke , Ihara Ayaka , Nishizaka Takayuki , Iwasaki Wataru , Itoh Takashi , Miyata Makoto , Ohkuma Moriya
Published: October 2023

The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of the ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeonNanobdella aerobiophilastrain MJ1Tand its hostMetallosphaera sedulastrain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy (TEM), quick-freeze deep-etch (QFDE) TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1Twere different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1Tgene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1Tand MJ1HA were motile, but sole MJ1Tcells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle ofNanobdella aerobiophila.

Importance

DPANN archaea are widely distributed in a variety of natural and artificial environments, and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon,Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle ofNanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
The proteomic toolbox for identification, quantification, and characterization of polyclonal antibodies
Authors: Tang Weize , Drabovich Andrei P.
Published: October 2023

Recent advances in proteomics and mass spectrometry facilitated the in-depth characterization of monoclonal antibodies and enabled innovative approaches for the quantification of polyclonal antibodies generated against numerous antigens. Human respiratory syncytial virus (RSV) is a contagious respiratory pathogen often manifested as a common cold infection in adults and more serious symptoms in infants and the elderly population. Here, we used a reference IgG1κ monoclonal antibody NISTmAb 8671 and its affinity interaction with an RSV fusion glycoprotein F as a model to develop the proteomic toolbox for identification, quantification, and characterization of polyclonal antibodies. Our toolbox integrated a variety of proteomic and mass spectrometry approaches for accurate mass measurements of antibody fragments, antibody digestion with the complimentary proteases (trypsin, asparaginase, and proalanase), immunoaffinity enrichments, and bottom-up or middle-down proteomics. We measured absolute concentrations of anti-RSV antibody isotypes and subclasses in 69 serum samples of healthy individuals and revealed IgG1 (2,580 ng/mL), IgA1 (280 ng/mL), and IgM (180 ng/mL) as the most abundant isotypes. Interestingly, we also identified the presence of IgG2 (74 ng/ml), IgG4 (4.9 ng/mL) and IgA2 (5.5 ng/mL) antibodies. Interactome measurements detected the consistent co-precipitation of C1q complement complexes. Repertoire profiling of the variable regions of polyclonal antibodies revealed the frequent use of IGHV3 subgroup genes, while IGHV5-51 was the most abundant single gene of the anti-RSV polyclonal antibody response. The presented toolbox will facilitate the in-depth characterization of polyclonal antibodies and pave the way to quantitative approaches in serological studies and precision immunology.
Inhibition ofPseudomonas aeruginosaquorum sensing by chemical induction of the MexEF-oprN efflux pump
Authors: Kristensen Rasmus , Andersen Jens Bo , Rybtke Morten , Jansen Charlotte Uldahl , Fritz Blaine Gabriel , Kiilerich Rikke Overgaard , Uhd Jesper , Bjarnsholt Thomas , Qvortrup Katrine , Tolker-Nielsen Tim , Givskov Michael , Jakobsen Tim Holm
Published: October 2023

The cell-to-cell communication system quorum sensing (QS), used by various pathogenic bacteria to synchronize gene expression and increase host invasion potentials, is studied as a potential target for persistent infection control. To search for novel molecules targeting the QS system in the Gram-negative opportunistic pathogenPseudomonas aeruginosaa chemical library consisting of 3280 small compounds from LifeArc was screened. A series of ten conjugated phenones that have not previously been reported to target bacteria were identified as inhibitors of QS inP. aeruginosa. Two lead compounds (ethylthio enynone and propylthio enynone) were resynthesized for verification of activity and further elucidation of the mode of action. The isomeric pure Z-ethylthio enynone was used for RNA sequencing revealing a strong inhibitor of QS-regulated genes and the QS-regulated virulence factors rhamnolipid and pyocyanin were significantly decreased by treatment with the compounds. A transposon mutagenesis screen performed in a newly constructedlasB-gfpmonitor strain identified the target of Z-ethylthio enynone inP. aeruginosato be the MexEF-OprN efflux pump, which was further established using definedmexknockout mutants. Our data indicate that the QS inhibitory capabilities of Z-ethylthio enynone were caused by the drainage of intracellular signal molecules as a response to chemical-induced stimulation of the MexEF-oprN efflux pump thereby inhibiting the auto-generated positive feedback and its enhanced signal-molecule synthesis.
Spatially resolved distribution of pancreatic hormones proteoforms by MALDI-imaging mass spectrometry
Authors: Sisnande Tháyna , Brum Felipe Lopes , Matias Daiane O. , Ribeiro Fernando de Sá , Moulin Thayana Beninatto , Mohana-Borges Ronaldo , de Magalhães Mariana T. Q. , Lima Luís Maurício T. R.
Published: October 2023

Zinc plays crucial role in the immune system and endocrine processes. Dietary zinc restriction leads to the degeneration of the endocrine pancreas resulting in hormonal imbalance in β-cell. Proteostasis may vary depending on the stage of a pathophysiological process, motivating the development of tools aimed at the direct analysis of biological status. Among proteomics methods, MALDI-ToF-MS can serve as a rapid peptidomics tool from analysis of extracts or by histological imaging. Here we report the optimization of MALDI imaging mass spectrometry analysis of thin histological sections from mouse pancreas, allowing the identification of major islet peptide hormones and major accumulated precursors and/or proteolytic products of peptide hormones. Cross-validation of the identified peptide hormones was performed by LC-ESI-MS from pancreatic islet extracts. Mice fed a zinc-restricted diet had a relatively lower amount of peptide intermediates in comparison with the control group. These data provide evidence for complex modulation of proteostasis by an imbalance of micronutrients, directly accessed by MALDI-MSI.
Computational mechanism underlying switching of motor actions
Authors: Zhong Shan , Pouratian Nader , Christopoulos Vassilios
Published: October 2023

Surviving in a constantly changing environment requires not only the ability to select actions, but also the flexibility to stop and switch actions when necessary. Extensive research has been devoted to understanding how the brain switches actions, yet the computations underlying switching and how it relates to selecting and stopping processes remain elusive. A central question is whether switching is an extension of the stopping process or involves different mechanisms. To address this question, we modeled action regulation tasks with a neurocomputational theory and evaluated its predictions on individuals performing reaches in a dynamic environment. Our findings suggest that, unlike stopping, switching does not necessitate a proactive pause mechanism to delay movement onset. However, switching engages a pause mechanism after movement onset, if the new target location is unknown prior to switch signal. These findings offer a new understanding of the action-switching computations, opening new avenues for future neurophysiological investigations.
Molecular mechanism of NAD+binding to the Nudix homology domains of DBC1
Authors: Ou Liming , Zhao Xuechen , Wu Ivy (Jing) , Xiong Zhiyuan , Ruan Zhi , Zhou Guangyu , Chen Wen
Published: October 2023

DBC1 (deleted in breast cancer 1) is a human nuclear protein that modulates the activities of various proteins. NAD+(oxidized form of nicotinamide adenine dinucleotide) is thought to potentially bind to the Nudix homology domains (NHDs) of DBC1, thereby regulating DBC1-PARP1 [poly (adenosine diphosphate–ribose) polymerase] interactions, the modulation of which may restore DNA repair to protect against cancer, radiation, and aging. Therefore, our study comprehensively employed methods including NMR (Nuclear Magnetic Resonance), ITC (isothermal titration calorimetry), genetic mutation, and computer biology to thoroughly investigate the molecular mechanism of the binding interaction between NAD+and its precursor NMN with the NHD domain of DBC1 (DBC1354-396). The results from NMR and ITC indicate that NAD+likely interacts with DBC1354-396through hydrogen bonding, with a binding affinity nearly twice that of NMN. The key binding sites are primarily E363 and D372. Molecular Docking further revealed the importance of conventional hydrogen bonds and carbon-hydrogen bonds in the binding process. These findings may lead to a better understanding of how NAD+regulates the physiological functions of DBC1, thereby offering guiding principles for the development of targeted therapies and drug research focused on tumor diseases associated with DBC1.
cellPLATO: an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data
Authors: Shannon Michael J. , Eisman Shira E. , Lowe Alan R. , Sloan Tyler , Mace Emily M.
Published: October 2023

Advances in imaging, cell segmentation, and cell tracking now routinely produce microscopy datasets of a size and complexity comparable to transcriptomics or proteomics. New tools are required to process this ‘phenomics’ type data. Cell PLasticity Analysis TOol (cellPLATO) is a Python-based analysis software designed for measurement and classification of diverse cell behaviours based on clustering of parameters of cell morphology and motility. cellPLATO is used after segmentation and tracking of cells from live cell microscopy data. The tool extracts morphological and motility metrics from each cell per timepoint, before being using them to segregate cells into behavioural subtypes with dimensionality reduction. Resultant cell tracks have a ‘behavioural ID’ for each cell per timepoint corresponding to their changing behaviour over time in a sequence. Similarity analysis allows the grouping of behavioural sequences into discrete trajectories with assigned IDs. Trajectories and underlying behaviours generate a phenotypic finger-print for each experimental condition, and representative cells are mathematically identified and graphically displayed for human understanding of each subtype. Here, we use cellPLATO to investigate the role of IL-15 in modulating NK cell migration on ICAM-1 or VCAM-1. We find 8 behavioural subsets of NK cells based on their shape and migration dynamics, and 4 trajectories of behaviour. Therefore, using cellPLATO we show that IL-15 increases plasticity between cell migration behaviours and that different integrin ligands induce different forms of NK cell migration.
A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses
Authors: Laosuntisuk Kanjana , Vennapusa Amaranatha , Somayanda Impa M. , Leman Adam R. , Jagadish SV Krishna , Doherty Colleen J.
Published: October 2023

RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3’ RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
Streamlined DNA template preparation and co-transcriptional 5′ capped RNA synthesis enabled by solid-phase catalysis
Authors: García-Marquina Guillermo , Zhang Aihua , Sproviero Michael , Fang Yi , Gardner Andrew F. , Robb G. Brett , Chan S. Hong , Xu Ming-Qun
Published: October 2023

The success of SARS-CoV-2 mRNA vaccines demonstrated that rapid, large-scale manufacturing of synthetic mRNA is necessary for an effective and timely response to a pandemic. Innovations in areas such as template design and manufacturing processes are being implemented to facilitate more simple, cost-effective and scalable mRNA synthesis. In this study, for the first time, we demonstrate that the enzymatic steps in mRNA production (including DNA template linearization, RNA synthesis, 5′ capping and methylation) can be carried out using enzymes immobilized to a solid support. Specifically, we demonstrate efficient IVT template DNA linearization using immobilized BspQI, where the linearized template DNA can be directly used in IVT without the need of purification. We also showed that immobilized T7 RNA polymerase, Faustovirus RNA capping enzyme (FCE), vaccinia cap 2′-O-methyltransfease (2′OMTase) and a novel FCE::T7RNAP fusion enable efficient enzymatic synthesis of Cap-1 RNA in a one-pot format. This solid-phase enzymatic platform may enable highly efficient, seamless and continuous mRNA synthesis workflows that minimizes sample loss and units of operation in biopharmaceutical manufacturing.
Deciphering the biology and chemistry of the mutualistic partnership betweenBacillus velezensisand the arbuscular mycorrhizal fungusRhizophagus irregularis
Authors: Anckaert Adrien , Stéphane Declerck , Poussart Laure-Anne , Lambert Stéphanie , Catherine Helmus , Boubsi Farah , Steels Sebastien , Arias Anthony Argüelles , Calonne-Salmon Maryline , Ongena Marc
Published: October 2023

Arbuscular mycorrhizal (AM) fungi (e.g.Rhizophagus irregularis) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not yet been investigated especially as it involves bacteria known as strong producers of antifungal compounds such asBacillus velezensis. Here, we show that the soil dwellingB. velezensismigrates along the hyphal network of the AM fungusR. irregularis, forming biofilms and inducing metabolic fluxes that contributes to host plant root colonization by the bacterium. During hyphosphere colonization,R. irregularismodulates the biosynthesis of specific lipopeptides and antimicrobial compounds inB. velezensisas a mechanism toward-off mycoparasitic fungi and bacteria to ensure stable coexistence. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.
Exosomes promote axon outgrowth by engaging the Wnt-Planar Cell Polarity pathway
Authors: Ahmad Samar , Pye Melanie , Narimatsu Masahiro , Song Siyuan , Christova Tania , Wrana Jeffrey L , Attisano Liliana
Published: October 2023

In neurons, the acquisition of a polarized morphology is achieved upon the outgrowth of a single axon from one of several neurites. Exosomes or small extracellular vesicles (sEVs) from diverse sources are known to promote the neurite outgrowth and thus may have therapeutic potential. However, the effect of fibroblast-derived exosomes on axon elongation in neurons of the central nervous system under growth permissive conditions remains unclear. Here, we show that fibroblast-derived sEVs promote axon outgrowth and a polarized neuronal morphology in mouse primary embryonic cortical neurons. Mechanistically, we demonstrate that the sEV-induced increase in axon outgrowth requires endogenous Wnts and core PCP components including Prickle, Vangl, Frizzled and Dishevelled. We demonstrate that sEVs are internalized by neurons, colocalize with Wnt7b and induce relocalization of Vangl2 to the distal axon during axon outgrowth. In contrast, sEVs derived from neurons or astrocytes do not promote axon outgrowth, while sEVs from activated astrocytes inhibit elongation. Thus, our data reveals that fibroblast-derived sEVs promote axon elongation through the Wnt-PCP pathway in a manner that is dependent on endogenous Wnts.
Haematopoietic stem cell numbers are not solely determined by niche availability
Authors: Takeishi Shoichiro , Marchand Tony , Koba Wade R. , Borger Daniel K. , Xu Chunliang , Guha Chandan , Bergman Aviv , Frenette Paul S. , Gritsman Kira , Steidl Ulrich
Published: October 2023

Haematopoietic stem cells (HSCs) reside in specialized microenvironments, also referred to as niches, and it has been widely believed that HSC numbers are determined by the niche size alone1–5. However, the vast excess of the number of niche cells over that of HSCs raises questions about this model. We initially established a mathematical model of niche availability and occupancy, which predicted that HSC numbers are restricted at both systemic and local levels. To address this question experimentally, we developed a femoral bone transplantation system, enabling us to increase the number of available HSC niches. We found that the addition of niches does not alter total HSC numbers in the body, regardless of whether the endogenous (host) niche is intact or defective, suggesting that HSC numbers are limited at the systemic level. Additionally, HSC numbers in transplanted wild-type femurs did not increase beyond physiological levels when HSCs were mobilized from defective endogenous niches to the periphery, indicating that HSC numbers are also constrained at the local level. Our study demonstrates that HSC numbers are not solely determined by niche availability, thereby rewriting the long-standing model for the regulation of HSC numbers.
Comprehensive analysis of the Aquaporin genes inEucalyptus grandissuggests potential targets for drought stress tolerance
Authors: Seidel Dayana S. , Claudino Paulo H. , Sperotto Gabriela , Wendt Simone N. , Shomo Zachery D. , Mural Ravi V. , Dias Henrique M.
Published: October 2023

This study delves into the comprehensive analysis ofAQPgenes inEucalyptus grandis, providing insights into their genomic abundance, diversification, expression patterns across tissues, and responses to drought stress. We identified 53AQPgenes in theEucalyptus grandisgenome, categorized into four subfamilies:AQP-NIP,AQP-SIP,AQP-PIP, andAQP-TIP. This abundance ofAQPgenes is a reflection of gene duplications, both tandem and whole-genome, which have shaped their expansion. The chromosomal distribution of these genes reveals their widespread presence across the genome, with some subfamilies exhibiting more tandem duplications, suggesting distinct roles and evolutionary pressures. Sequence analysis uncovered characteristic motifs specific to different AQP subfamilies, demonstrating the diversification of protein and targeting. The expression profiles ofAQPgenes in various tissues in bothArabidopsis thalianaandEucalyptus grandisshowcased variations, with root tissues showing higher expression levels. Notably,AQP-PIPgenes consistently exhibited robust expression across tissues, highlighting their importance in maintaining water regulation within plants. Furthermore, the study investigated the response ofAQPgenes to drought stress and rehydration, revealing differential expression patterns.EgAQP-NIPandEgAQP-TIPgenes were up-regulated during drought stress, emphasizing their role in osmotic equilibrium and water transport. Conversely,EgAQP-PIPgenes showed down-regulation during drought stress but were up-regulated upon rehydration, indicating their involvement in water movement across cell membranes. Overall, this research contributes to our understanding ofAQPgenes inEucalyptus grandis, shedding light on their genomic evolution, expression patterns, and responses to environmental challenges, particularly drought stress. This information can be valuable for future studies aimed at enhancing the drought resilience of woody perennial plants likeEucalyptus grandis.