bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel and Simplified Parameter for Mandible Angle Asymmetry Evaluation in Chinese Females
Authors: Zhong Yehong , Chen Zhewei , Lei Bowen , Sun Tiecheng , Li Binghang , Ma Hengyuan , Yang Bin
Published: March 2023

Aim:

To develop a novel and simplified parameter for mandible angle asymmetry (MAA) evaluation for facial countering surgeries in Chinese females.

Materials and Methods:

A total of 250 craniofacial computer tomography of healthy Chinese individuals were collected in this retrospective study. Mimics 21.0 was applied for 3-dimensional anthropometry. The Frankfort and Green planes were set as referenced vertical and horizontal planes for measuring the distances to gonions. The differences in both orientations were analyzed to verify the symmetry. Mandible angle asymmetry (∠Go-N-ANS, MAA) which comprehensively represented horizontal and vertical placements was defined qas the novel parameter for asymmetric evaluation and quantitative analysis was conducted to generate referenced materials.

Results:

Mandible angle asymmetry was divided into horizontal and vertical asymmetry. No significant differences were found in either horizontal or vertical orientations. The horizontal difference was 3.09±2.52 mm, the reference range was (0.28, 7.54) mm, whereas the±ertical difference was 2.59±2.48 mm, the reference range was (0.12, 6.34) mm. The difference of MAA was 1.74±1.30 degrees, and the reference range was (0.10,4.32）degrees.

Conclusion:

This study provided a novel parameter for asymmetric evaluation in the mandible angle region through quantitative 3-dimensional anthropometry, arousing plastic surgeons’ attention to both aesthetics and symmetry in facial contouring surgery.
Using a Delphi Method Approach to Select Theoretical Underpinnings of Crowdsourcing and Rank Their Application to a Crowdsourcing App
Authors: Clarke Krystina M. , Barari Ahmad , Hogue Andrew , Dubrowski Adam
Published: March 2023

Introduction

Since the catapult of online learning during the COVID-19 pandemic, most simulation laboratories are now completed virtually, leaving a gap in skills training and potential for technical skills decay. Acquiring standard, commercially available simulators is prohibitively expensive, but three-dimensional (3D) printing may provide an alternative. This project aimed to develop the theoretical foundations of a crowdsourcing Web-based application (Web app) to fill the gap in health professions simulation training equipment via community-based 3D printing. We aimed to discover how to effectively leverage crowdsourcing with local 3D printers and use these resources to produce simulators via this Web app accessed through computers or smart devices.

Methods

First, a scoping literature review was conducted to discover the theoretical underpinnings of crowdsourcing. Second, these review results were ranked by consumer (health field) and producer (3D printing field) groups via modified Delphi method surveys to determine suitable community engagement strategies for the Web app. Third, the results informed different app iteration ideas and were then generalized beyond the app to address scenarios entailing environmental changes and demands.

Results

A scoping review revealed 8 crowdsourcing-related theories. Three were deemed most suitable for our context by both participant groups: Motivation Crowding Theory, Social Exchange Theory, and Transaction Cost Theory. Each theory proposed a different crowdsourcing solution that can streamline additive manufacturing within simulation while applicable to multiple contexts.

Conclusions

Results will be aggregated to develop this flexible Web app that adapts to stakeholder needs and ultimately solves this gap by delivering home-based simulation via community mobilization.
FasterRib: A deep learning algorithm to automate identification and characterization of rib fractures on chest computed tomography scans
Authors: Edamadaka Sathya , Brown David W. , Swaroop Roshan , Kolodner Matthew , Spain David A. , Forrester Joseph D. , Choi Jeff
Published: March 2023

OBJECTIVE

Characterizing and enumerating rib fractures are critical to informing clinical decisions, yet in-depth characterization is rarely performed because of the manual burden of annotating these injuries on computed tomography (CT) scans. We hypothesized that our deep learning model, FasterRib, could predict the location and percentage displacement of rib fractures using chest CT scans.

METHODS

The development and internal validation cohort comprised more than 4,700 annotated rib fractures from 500 chest CT scans within the public RibFrac. We trained a convolutional neural network to predict bounding boxes around each fracture per CT slice. Adapting an existing rib segmentation model, FasterRib outputs the three-dimensional locations of each fracture (rib number and laterality). A deterministic formula analyzed cortical contact between bone segments to compute percentage displacements. We externally validated our model on our institution's data set.

RESULTS

FasterRib predicted precise rib fracture locations with 0.95 sensitivity, 0.90 precision, 0.92 f1 score, with an average of 1.3 false-positive fractures per scan. On external validation, FasterRib achieved 0.97 sensitivity, 0.96 precision, and 0.97 f1 score, and 2.24 false-positive fractures per scan. Our publicly available algorithm automatically outputs the location and percent displacement of each predicted rib fracture for multiple input CT scans.

CONCLUSION

We built a deep learning algorithm that automates rib fracture detection and characterization using chest CT scans. FasterRib achieved the highest recall and the second highest precision among known algorithms in literature. Our open source code could facilitate FasterRib's adaptation for similar computer vision tasks and further improvements via large-scale external validation.

LEVEL OF EVIDENCE

Diagnostic Tests/Criteria; Level III.
Multicompartmental traumatic injury induces sex-specific alterations in the gut microbiome
Authors: Munley Jennifer A. , Kelly Lauren S. , Park Gwoncheol , Gillies Gwendolyn S. , Pons Erick E. , Kannan Kolenkode B. , Whitley Elizabeth M. , Bible Letitia E. , Efron Philip A. , Nagpal Ravinder , Mohr Alicia M.
Published: March 2023

BACKGROUND

Previous preclinical studies have demonstrated an altered gut microbiome after traumatic injury; however, the impact of sex on dysbiosis remains unknown. We hypothesized that the “pathobiome” phenotype induced by multicompartmental injuries and chronic stress is host sex specific with unique microbiome signatures.

METHODS

Male and proestrus female Sprague-Dawley rats (n = 8/group) aged 9 weeks to 11 weeks were subjected to either multicompartmental injury (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), PT plus 2 hours daily chronic restraint stress (PT/CS) or naive controls. Fecal microbiome was measured on Days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. Beta-diversity was assessed using principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide binding protein. Histologic evaluation of ileum and colon tissues was scored for injury by a blinded pathologist. Analyses were performed in GraphPad and R, with significance defined as p < 0.05 between males versus females.

RESULTS

At baseline, females had significantly elevated alpha-diversity (Chao1, Shannon indices) compared with males (p < 0.05) which was no longer present 2 days postinjury in PT and PT/CS. Beta-diversity also differed significantly between males and females after PT (p = 0.01). At Day 2, the microbial composition in PT/CS females was dominated by Bifidobacterium, whereas PT males demonstrated elevated levels of Roseburia (p < 0.01). The PT/CS males had significantly elevated ileum injury scores compared with females (p = 0.0002). Plasma occludin was higher in PT males compared with females (p = 0.004); plasma lipopolysaccharide binding protein was elevated in PT/CS males (p = 0.03).

CONCLUSION

Multicompartmental trauma induces significant alterations in microbiome diversity and taxa, but these signatures differ by host sex. These findings suggest that sex is an important biological variable that may influence outcomes after severe trauma and critical illness.
A unique gene expression signature in visceral adipose tissue identifies a high blood pressure group in patients with Cushing’s syndrome
Authors: Stifel Ulrich , Vogel Frederick , Caratti Giorgio , Reincke Martin , Tuckermann Jan
Published: March 2023

Cushing’s syndrome (CS) is a rare disease caused by excess cortisol levels with high cardiovascular morbidity and mortality. Hypertension is a frequent feature of Cushing’s syndrome, promoting hypercortisolism-associated cardiovascular events. Adipose tissue is a highly plastic tissue with most of the major cell types strongly affected in their function by the excess cortisol exposure. We hypothesized that the molecular and cellular changes of visceral adipose tissue (VAT) in response to cortisol excess can impact on systemic blood pressure levels in patients with CS. We, therefore, investigated gene expression signatures in VAT from patients with CS collected during curative adrenal surgery identifying significant alterations. During active CS we observed a strong downregulation of gene programs associated with immunity and inflammation in the VAT. In addition, we observed an clustering of the patients based on VAT gene expression profiles into two groups (CSLowand CSHigh) according to blood pressure levels. The two clusters showed significant differences in gene expression pattens of the renin-angiotensin-aldosterone-system (RAAS). Renin (REN) was the strongest regulated gene compared to control patients and its expression correlated with increased blood pressure observed in our patients while systemic renin plasma levels were suppressed indicative of an abnormal blood pressure and volume status in response to VAT RAAS activation. Here we show for the first time a relevant contribution of the local RAAS system on systemic blood pressure levels in patients with CS. Patients from the CSHighgroup had still a significant increased blood pressure levels 6 months into remission, highlighting the importance of local tissue effects on long-term systemic effects observed in CS.
Management of Risk Factors for Health Care Workers After Initial Contact with Patients Infected with SARS-COV-2 in Niamey, The Center of the Epidemic in Niger
Authors: Ramatoulaye Hamidou Lazoumar , Abdal-Kader Aliou Sanda , Lagare Adamou , Maiga Mahamadou A , Aliane Fakani Aboutalib , Sylviane François Comlan Aida , Issa Idi , Sidikou Bibata Abdou , Oumarou Garda Idé , sidiki Ali , Aouta Zeinabou Abdou , Moussa Amina , Alassan Zeinabou Dioffo , Karidjo Ibrahim , Bachir Goni Alhassan Maman , Djibo Issifou , Moussa Salia , Laminou Ibrahim Maman , Jambou Ronan
Published: March 2023

Background

The covid-19 pandemic is caused by a new corona virus called SARS Cov-2. Health care workers are particularly exposed target.

Aim

this study aims to analyze the risk factors of SARS-Cov-2 infection in health workers who have been in contact with positive patient.

Methods

This is a prospective cohort conducted among health workers from March 2022 to January 2021 in health care facilities in Niamey. A questionnaire was administrated at inclusion. rRT-PCR was performed if clinical signs were present. ELISA testing was performed at baseline, day15 and day 30. The chi-square or Fisher test, Kaplan-Meir survival model, Cow regression and logistic regression were used as statistical test.

Results

259 health workers were included. More than half of the respondents were female. 45.95% of the participants were nurses and 36.68% were physicians. The prevalence of Covid-19 was 28.8%. 56.4% of the participants had positive serology at day 30. The risk factors associated with Covid-19 were professional category (p=0.024). Membership structure (p<0.001) and the chronic liver disease (p=0.034). Hand hygiene (p=0.019) and alcohol-based hand cleaning (p<0.001) protects against the occurrence of SARS-Cov-2 infection. According to the characterization of the preventive measures those who practiced them rarely were associated with a positive rRT-PCR and those who practice them occasionally or most of the time were associated with negative serology and rRT-PCR.

Conclusion

Comorbidities, function and affiliation are the main risk factors for Covid-19 and hand hygiene is a protective factor.
Pilot study of the association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure
Authors: Zeamer Abigail L , Salive Marie-Claire , An Xinming , House Stacey L , Beaudoin Francesca L , Stevens Jennifer S , Zeng Donglin , Neylan Thomas C , Clifford Gari D , Linnstaedt Sarah D , Rauch Scott L , Storrow Alan B , Lewandowski Christopher , Musey Paul I , Hendry Phyllis L , Sheikh Sophia , Jones Christopher W , Punches Brittany E , Swor Robert A , Hudak Lauren A , Pascual Jose L , Seamon Mark J , Harris Erica , Pearson Claire , Peak David A , Merchant Roland C , Domeier Robert M , Rathlev Niels K , O’Neil Brian J , Sergot Paulina , Sanchez Leon D , Bruce Steven E , Kessler Ronald C , Koenen Karestan C , McLean Samuel A , Bucci Vanni , Haran John P
Published: March 2023

Background

Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biologic mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition at the time of trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether baseline the gut microbiomes of trauma-exposed emergency department patients who later develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms.

Methods

We performed metagenomic analysis on stool samples (n=51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and metabolic pathways.

Results

Microbial species, includingFlavonifactor plauttiandRuminococcus gnavus,which are associated with inflammation and poor health outcomes, were found to be important in predicting worse APNS outcomes. Notably, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways.

Conclusions

Pro-inflammatory microbes that are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, which also has been demonstrated in patients with PTSD.
Hip joint space width is causally related to hip osteoarthritis risk via distinct protective and susceptibility mechanisms: findings from a genome-wide association study meta-analysis
Authors: Frysz Monika , Faber Benjamin G. , Boer Cindy G. , Evans Daniel S. , Ebsim Raja , Flynn Kaitlyn A. , Lundberg Mischa , Southam Lorraine , Hartley April , Saunders Fiona R. , Lindner Claudia , Gregory Jennifer S. , Aspden Richard M. , Lane Nancy E. , Harvey Nicholas C. , Evans David M. , Zeggini Eleftheria , Smith George Davey , Cootes Timothy , Van Meurs Joyce , Kemp John P. , Tobias Jonathan H.
Published: March 2023

Objective

Minimum joint space width (mJSW) from 2-dimensional images provides a proxy for cartilage thickness. This study aimed to conduct a genome-wide association study (GWAS) of mJSW to (i) identify new genetic determinants of mJSW and use them to (ii) examine causal effects of mJSW on hip osteoarthritis (HOA) risk.

Methods

GWAS meta-analysis of hip mJSW derived from plain X-rays (four cohorts) or DXA (one cohort) was performed, stratified by sex and adjusted for age and ancestry principal components. Mendelian randomisation (MR) and cluster analyses were used to examine causal effect of mJSW on HOA.

Results

50,745 individuals were included in the meta-analysis. 42 SNPs, which mapped to 39 loci (35 novel), were identified. Mendelian randomisation (MR) revealed little evidence of a causal effect of mJSW on HOA (βIVW-0.01 [95% CI -0.19, 0.17]). However, MR-Clust analysis suggested the null MR estimates reflected the net effect of two distinct causal mechanisms cancelling each other out, one of which was protective, whereas the other increased HOA susceptibility. For the latter mechanism, all loci were positively associated with height, suggesting mechanisms leading to greater height and mJSW increase the risk of HOA in later life.

Conclusions

GWAS and MR analyses suggested one group of mJSW loci reduces HOA risk via increased mJSW, suggesting possible utility as targets for chondroprotective therapies. The second group of mJSW loci increased HOA risk, despite increasing mJSW, but were also positively related to height, suggesting they contribute to mJSW and HOA risk via a growth-related mechanism.
Cerebral blood flow pattern in patients with carotid artery stenosis with low trans-stenotic blood flow
Authors: Zarrinkoob Laleh , Myrnäs Sanne , Wåhlin Anders , Eklund Anders , Malm Jan
Published: March 2023

Background

Compromised cerebral blood flow has been identified as a contributing risk factor for future ischemic events in patients with symptomatic carotid artery disease. Nevertheless, the hemodynamic impact of carotid stenosis is rarely evaluated. The aim of this observational cross-section study was to investigate how a reduced internal carotid artery (ICA) blood flow rate (BFR), rather than stenosis degree, relates to BFR in the cerebral arteries.

Methods

Four-dimensional phase-contrast magnetic resonance imaging (4D-PCMRI) was used to measure cerebral blood flow in 38 patients with symptomatic carotid stenosis (≥50%), being considered for carotid endarterectomy. The BFR in the cerebral arteries was compared between two subgroups that were based on the BFR in the symptomatic (ipsilateral) ICA: I. reduced ICA flow (<160 mL/min) i.e., 2 SD <normal ICA BFR; II. preserved ICA flow (≥160 mL/min). Furthermore, BFR laterality was defined as a difference in the paired ipsilateral-contralateral arteries within the groups.

Results

The degree of stenosis was not significantly different between the two subgroups (72% vs. 80%;P=0.09). In the reduced group compared to the preserved ICA flow group, a reduced BFR was found in the ipsilateral middle cerebral artery (MCA) (108±32 vs. 136±24 mL/min;P<0.01) and anterior cerebral artery (A1 segment) (−6±47 vs. 81±27 mL/min;P<0.001), while the BFR was increased in the contralateral A1 segment (152±79 vs. 82±41 mL/min;P<0.001). There was also a reversed BFR in the posterior communicating artery and ophthalmic artery on the ipsilateral side in the group with reduced ICA flow. BFR laterality was observed in all paired arteries in the reduced ICA flow group (P<0.05), while there was no laterality in the preserved ICA flow group (P>0.05).

Conclusions

4D-PCMRI revealed compromised cerebral blood flow in patients with carotid stenosis, not possible to detect by solely analyzing the stenosis degree. In patients with reduced ICA flow, collateral recruitment was not sufficient to maintain symmetrical BFR distribution to the two hemispheres.
Human synaptic neoteny requires species-specific balancing of SRGAP2-SYNGAP1 cross-inhibition
Authors: Libé-Philippot Baptiste , Iwata Ryohei , Recupero Aleksandra J , Wierda Keimpe , Ditkowska Martyna , Gaspariunaite Vaiva , Vermaercke Ben , Peze-Heidsieck Eugénie , Remans Daan , Charrier Cécile , Polleux Franck , Vanderhaeghen Pierre
Published: March 2023

Human-specific (HS) genes are potential drivers of brain evolution, but their impact on human neuron development and disease remains unclear. Here we studied HS genes SRGAP2B/C in human cortical projection neurons (CPNs) in vivo, using xenotransplantation in the mouse cortex. Downregulation of SRGAP2B/C in human CPNs greatly accelerated synaptic development, indicating their requirement for human-specific synaptic neoteny. SRGAP2B/C acted by downregulating their ancestral paralog SRGAP2A, thereby upregulating postsynaptic levels of SYNGAP1, a major intellectual deficiency/autism spectrum disorder (ID/ASD) gene. Combinatorial genetic invalidation revealed that the tempo of synaptogenesis is set by a balance between SRGAP2A and SYNGAP1, which in human CPNs is tipped towards neoteny by SRGAP2B/C. Our results demonstrate that HS genes can modify the phenotypic expression of ID/ASD mutations through regulation of synaptic neoteny.

One-Sentence Summary

Human-specific genes SRGAP2B/C control human cortical neuron neoteny by regulating the function of neurodevelopmental disorder gene SYNGAP1
Biosynthesis of plant papanridins -A group of novel oligomeric flavonoids
Authors: Zhu Yue , Yuzuak Seyit , Sun Xiaoyan , Xie De-Yu
Published: March 2023

Discovery of novel flavonoids and their biosynthesis are fundamental to understand their roles in plants and benefits to human and animal health. Herein, we report a new polymerization pathway of a group of novel oligomeric flavonoids in plants. We have engineered red cells for discovering genes of interest involved in the flavonoid pathway and identified a gene that encodes a novel flavanol polymerase (FP) localized in the central vacuole. FP catalyzes the polymerization of flavanols, such as epicatechin and catechin, to produce yellowish dimers or oligomers. Structural elucidation show that these compounds are featured with a novel oligomeric flaven-flavan (FF) skeleton linked by interflavan-flaven and interflaven bonds, which are different from proanthocyanidins and dehydrodicatechins. Detailed chemical and physical characterizations further demonstrate that FFs are novel flavonoids. Mechanistic investigations show that FP polymerizes flavan-3-ols and flav-2-en-3-ol carbocation to form dimeric or oligomeric flaven-4→8-flavans, termed as papanridins. Data from transgenic, mutation, metabolic profiling, and phylogenetic analyses demonstrate that the biosynthesis of papanridins is prevalent in cacao, grape, blue berry, corn, rice, Arabidopsis and others in the plant kingdom. Given that these findings are the first report, many questions remain for answers. For instance, what are roles of papanridins in plants and what benefits do they have for human and animal health? We anticipate that these findings will promote investigations across plant, nutritional, and animal sciences to understand papanridins in plants and food products.

Teaser

Plant flavanol polymerase catalyzes the biosynthesis of novel oligomeric flavonoids in the plant kingdom.
Bacterial Form I’ rubisco has smaller carbon isotope fractionation than its Form I counterpart
Authors: Wang Renée Z. , Liu Albert K. , Banda Douglas M. , Fischer Woodward W. , Shih Patrick M.
Published: March 2023

Form I rubiscos evolved in Cyanobacteria ≥2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) that cap both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I’; L8) demonstrates that the enzyme complex assembles without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in13C relative to12C. In Cyanobacteria only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measuredin vitrothe KIEs of Form I’ (CandidatusPromineofilum breve) and Form I (Synechococcus elongatusPCC 6301) rubiscos and found the KIE to be smaller in the L8rubisco (16.25 ± 1.36‰ vs. 22.42 ± 2.37‰ respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.
Cholangiocyte primary cilia transduce a fluid shear signal to increase KLF2 via the actin cytoskeleton
Authors: Wehrkamp Cody J. , Oleksijew Andrew M. , Mansini Adrian P. , Gradilone Sergio A. , Mohr Ashley M. , Mott Justin L.
Published: March 2023

Cholangiocarcinoma is an aggressive solid tumor formed in the bile duct epithelium. Often this tumor obstructs bile flow, known as cholestasis. Normal cholangiocytes detect bile flow in the ductal lumen with an extension of the apical membrane called the primary cilium. However, these sensory organelles are often lost in malignant cells. Krüppel-like factor 2 (KLF2) is an important flow-sensitive transcription factor involved in shear stress response in endothelial cells, and has anti-proliferative, anti-inflammatory, and anti-angiogenic effects. The potential role of KLF2 in cholangiocyte flow detection and in cholangiocarcinoma is unknown. We hypothesized that reduced bile flow contributes to malignant features in cholangiocarcinoma through regulation of KLF2 signaling. We observed that primary cilia were expressed in normal cholangiocytes but were absent in malignant cells. KLF2 expression was higher in normal cells compared to malignant. Depletion of cilia in normal cells led to a decrease in KLF2 expression and increased cilia number was associated with increased KLF2. Enforced KLF2 expression inhibited cell proliferation, migration, and also decreased cell death induction in malignant cells. Applied media flow over cholangiocytes increased KLF2 and cilia depletion completely blocked flow-induced KLF2 expression. Disruption of filamentous actin decreased KLF2 expression, suggesting the cilium may communicate through a cytoskeletal mechanotransduction pathway. Our studies demonstrate that cilia positively regulated KLF2 protein levels and increased fluid flow induced KLF2 expression for the first time in cholangiocytes, emphasizing the importance of reestablishing bile flow in cholestatic cholangiocarcinoma.
Farnesoid X receptor agonism prevents neutrophil extracellular traps via reduced sphingosine-1-phosphate in chronic kidney disease
Authors: Jones Bryce A. , Myakala Komuraiah , Guha Mahilan , Davidson Shania , Adapa Sharmila , Santiago Isabel Lopez , Schaffer Isabel , Yue Yang , Allegood Jeremy , Cowart Lauren A. , Wang Xiaoxin X. , Rosenberg Avi Z. , Levi Moshe
Published: March 2023

Background

Activation of the farnesoid X receptor (FXR) reduces renal inflammation, but the underlying mechanisms remain elusive. Neutrophil extracellular traps (NETs) are webs of DNA formed when neutrophils undergo specialized programmed cell death (NETosis). Sphingosine-1-phosphate (S1P) is a signaling lipid that stimulates NETosis via its receptor on neutrophils. Here, we identify FXR as a negative regulator of kidney NETosis via repressing S1P signaling in male but not female mice.

Methods

We determined the effects of the FXR agonist obeticholic acid (OCA) in mouse models of adenosine phosphoribosyltransferase deficiency and Alport syndrome. We assessed renal NETosis by immunofluorescence in these models and in biopsies from patients with Alport syndrome (6 male, 9 female). We also inhibited de novo sphingosine production in Alport mice to show a causal relationship between S1P signaling and renal NETosis.

Results

Renal FXR activity is greatly reduced in both models, and OCA prevents kidney fibrosis, inflammation, and lipotoxicity. OCA reduces renal neutrophilic inflammation and NETosis in male adenine and Alport mice, but not in female adenine mice. Extensive NETosis was also identified in human Alport kidney biopsies. Kidney sphingosine kinase 1 (Sphk1) expression is increased in mice with kidney disease and reduced by OCA in male but not female mice. Also, Sphk1 expression correlates with NETosis in male but not female mice. Short-term inhibition of sphingosine synthesis reduces neutrophilic inflammation and NETosis.

Conclusion

FXR agonism represses kidney Sphk1 expression in male but not female mice. This inhibits renal S1P signaling, thereby reducing neutrophilic inflammation and NETosis in a sex-dependent manner.
Biophysical Characterization and Interaction study of WhiB6 Protein ofMycobacterium tuberculosiswith Nucleic Acid
Authors: Kumari Sonam , Singh Ruchi , Teena  , Siddhanta Soumik , Deep Shashank
Published: March 2023

Tuberculosis is an intractable disease because of the peculiar nature of the virulent properties ofMycobacterium tuberculosis. The WhiB6 protein, a transcriptional regulator, plays a crucial role in the virulence systems ofMtb. It regulates the expression of genes essential for the virulence pathways by binding to their promoter region;espAis one such gene. Herein, we have used biophysical methods, including steady-state intrinsic fluorescence spectroscopy, circular dichroism spectroscopy, Isothermal titration calorimetry (ITC), and Surface-Enhanced Raman Spectroscopy (SERS) to understand the interaction of WhiB6 protein withespApromoter DNA. For the first time, we report the conformational details and biophysical parameters related to the WhiB6-espApromoter DNA interaction. WhiB6 binds the DNA with moderate affinity, as revealed by ITC. CD and SERS studies suggest subtle perturbation in the secondary conformation of the protein on binding to the DNA. SERS provided detailed structural insights into the WhiB6 protein and the amino acids involved in the interaction, which could be harnessed to find suitable inhibitors of the protein-DNA interaction. Preventing the binding of WhiB6 with promoter DNA of the virulence genes can hinder the functioning ofMtband hence can act as an effective therapeutic intervention for tuberculosis.
Decision-making dynamics are predicted by arousal and uninstructed movements
Authors: Hulsey Daniel , Zumwalt Kevin , Mazzucato Luca , McCormick David A. , Jaramillo Santiago
Published: March 2023

During sensory-guided behavior, an animal’s decision-making dynamics unfold through sequences of distinct performance states, even while stimulus-reward contingencies remain static. Little is known about the factors that underlie these changes in task performance. We hypothesize that these decision-making dynamics can be predicted by externally observable measures, such as uninstructed movements and changes in arousal. Here, combining behavioral experiments in mice with computational modeling, we uncovered lawful relationships between transitions in strategic task performance states and an animal’s arousal and uninstructed movements. Using hidden Markov models applied to behavioral choices during sensory discrimination tasks, we found that animals fluctuate between minutes-long optimal, sub-optimal and disengaged performance states. Optimal state epochs were predicted by intermediate levels, and reduced variability, of pupil diameter, along with reduced variability in face movements and locomotion. Our results demonstrate that externally observable uninstructed behaviors can predict optimal performance states, and suggest mice regulate their arousal during optimal performance.
Isolation of ACE2-dependent and -independent sarbecoviruses from Chinese horseshoe bats
Authors: Guo Hua , Li Ang , Dong Tian-Yi , Si Hao-Rui , Hu Ben , Li Bei , Zhu Yan , Shi Zheng-Li , Letko Michael
Published: March 2023

While the spike proteins from SARS-CoV and SARS-CoV-2 bind to host ACE2 to infect cells, the majority of bat sarbecoviruses cannot use ACE2 from any species. Despite their discovery almost 20 years ago, ACE2-independent sarbecoviruses have never been isolated from field samples, leading to the assumption these viruses pose little risk to humans. We have previously shown how spike proteins from a small group of ACE2-independent bat sarbecoviruses may possess the ability to infect human cells in the presence of exogenous trypsin. Here, we adapted our earlier findings into a virus isolation protocol, and recovered two new ACE2-dependent viruses, RsYN2012 and RsYN2016, as well as an ACE2-independent virus, RsHuB2019. Although our stocks of RsHuB2019 rapidly acquired a tissue-culture adaption that rendered the spike protein resistant to trypsin, trypsin was still required for viral entry, suggesting limitations on the exogenous entry factors that support bat sarbecoviruses. Electron microscopy revealed ACE2-independent sarbecoviruses have a prominent spike corona and share similar morphology to other coronaviruses. Our findings demonstrate a broader zoonotic threat posed by sarbecoviruses and shed light onto the intricacies of coronavirus isolation and propagationin vitro.

SIGNIFICANCE

Several coronaviruses have transmitted from animals to people and 20 years of virus discovery studies have uncovered thousands of new coronavirus sequences in nature. Most of the animal-derived sarbecoviruses have never been isolated in culture due to cell incompatibilities and a poor understanding of thein vitrorequirements for their propagation. Here, we built on our growing body of work characterizing viral entry mechanisms of bat sarbecoviruses in human cells and have developed a virus isolation protocol that allows for exploration of these understudied viruses. Our protocol is robust and practical, leading to successful isolation of more sarbecoviruses than previous approaches and from field samples that had been collected over a 10-year longitudinal study.
Hogs sleep like logs: wild boars reduce the risk of anthropic disturbance by adjusting where they rest
Authors: Fradin Gustave , Chamaillé-Jammes Simon
Published: March 2023

Many animals living in anthropized landscapes try to avoid encountering people by being active at night. By doing so, however, they risk being disturbed while at rest during the day. To mitigate this risk, diurnally resting species may be highly selective about where they rest. Here, we used GPS and activity sensors to study how wild boars (Sus scrofa) adjust their resting site selection and visitation patterns to the risk of disturbance by people. The data was complemented with audio recordings from animal-borne loggers to evaluate the efficacy of wild boars’ resting strategy in reducing the probability of encountering people while at rest. Generally, we found that wild boars did not specifically avoid resting near villages or roads, i.e. where the risk of encountering people is higher, if they could find sites with suitable vegetation cover. Wild boars could actually rest close to villages with very little risk of being disturbed. Resting sites located close to villages were visited more repeatedly that those located further away, suggesting that focusing on a few familiar and quiet resting sites was a successful strategy for resting undisturbed in an anthropized landscape.
White matter properties in fronto-parietal tracts predict maladaptive functional activation and deficient response inhibition in ADHD
Authors: Smullen Daniel , Bagshaw Andrew P. , Shalev Lilach , Tsafrir Shlomit , Kolodny Tamar , Mevorach Carmel
Published: March 2023

Response inhibition, defined as the ability to suppress inappropriate responses, is a key characteristic of adaptive human behaviour. However, in individuals with attention deficit hyperactivity disorder (ADHD) it is often impaired and is linked to broad life outcomes. Previous neuroimaging investigations have indicated a myriad of brain networks in response inhibition, which limit its utility in understanding and overcoming response inhibition difficulties. More recently, it has been suggested that a specific fronto-parietal functional circuitry between the inferior frontal gyrus (IFG) and the intraparietal sulcus (IPS), dictates the recruitment of the IPS in response inhibition in ADHD. To ascertain the critical role of the IFG-IPS functional circuit and its relevance to response inhibition in ADHD, it is crucial to understand the underlying structural architecture of this circuit so that the functional relevance could be interpreted correctly. Here we investigated the white matter pathways connecting the IFG and IPS using seed-based probabilistic tractography on diffusion data in 42 ADHD and 24 neurotypicals and assessed their impact on both the recruitment of IPS in response inhibition scenarios and on response inhibition performance in a Go/No-go task. Our results showed that individual differences in the structural properties of the IPS-IFG circuit, including tract volume and diffusivity, were linked to IPS activation and even predicted response inhibition performance outside the scanner. These findings highlight the structural-functional coupling of the IFG-IPS circuit in response inhibition in ADHD and confirm a structural basis for maladaptive functional top-down control in deficient inhibition in ADHD. Our results also support the notion of ADHD as a continuum and suggest that individual differences in tract-specific functional and structural connectivity could serve as neuromarkers of ADHD.
Patient and cell-type specific hiPSC-modeling of a truncating titin variant associated with atrial fibrillation
Authors: Huang Kate , Ashraf Mishal , Rohani Leili , Luo Yinhan , Sacayanan Ardin , Huang Haojun , Haegert Anne , Volik Stanislav , Sar Funda , LeBihan Stéphane , Liew Janet , Roberts Jason D. , Tibbits Glen F. , Churko Jared M. , Sanatani Shubhayan , Collins Colin , Brunham Liam R. , Laksman Zachary W.
Published: March 2023

Background

Protein truncating mutations in the titin gene are associated with increased risk of atrial fibrillation (AF). However, little is known regarding the underlying pathophysiology.

Methods

We identified a heterozygous titin truncating variant in a patient with unexplained early-onset AF using whole exome sequencing. We used atrial and ventricular patient induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), CRISPR/Cas9 genetic correction, and engineered heart tissue (EHT) constructs to evaluate the impact of the titin truncating variant on electrophysiology, sarcomere structure, contractility, and gene expression.

Results

We generated atrial and ventricular iPSC-CMs from the AF patient with the titin truncating variant and a CRISPR/Cas9 genome corrected isogenic control. We demonstrate that the titin truncating variant increases susceptibility to pacing-induced arrhythmia (prevalence of arrhythmogenic phenotypes, 85.7% versus 14.2%;P= 0.03), promotes sarcomere disorganization (mean ± SEM, 66.3 ± 6.8% versus 88.0 ± 2.9%;P= 0.04) in atrial iPSC-CMs, and reduces contractile force (0.013 ± 0.003 mN versus 0.027 ± 0.004 mN;P< 0.01) in atrial EHTs compared to isogenic controls. In ventricular iPSC-CMs, this variant led to altered electrophysiology (90.0% versus 33.3%;P= 0.02) and sarcomere organization (62.0 ± 3.9% versus 82.9 ± 2.9%;P< 0.01) with no change in EHT contractility compared to isogenic controls. RNA-sequencing revealed an upregulation of cell adhesion and extracellular matrix genes in the presence of the titin truncating variant for both atrial and ventricular EHTs.

Conclusions

In a patient with early-onset unexplained AF and normal ventricular function, iPSC-CMs with a titin truncating variant showed structural and electrophysiological abnormalities in both atrial and ventricular preparations, while only atrial EHTs demonstrated reduced contractility. Whole transcriptome sequencing showed upregulation of genes involved in cell-cell and cell-matrix interactions in both atrial and ventricular EHTs. Together, these findings suggest titin truncating variants promote the development of AF through remodeling of atrial cardiac tissue and provide insight into the chamber-specific effects of titin truncating variants.
In VitroEvolution to Increase the Titers of Difficult Bacteriophages: Rapid Appelmans Protocol
Authors: Kok Danielle N. , Turnbull Joanne , Takeuchi Nobuto , Tsourkas Philippos K. , Hendrickson Heather L.
Published: March 2023

Bacteriophages are becoming increasingly important in the race to find alternatives to antibiotics. Unfortunately, bacteriophages that might otherwise be useful are sometimes discarded due to low titers making them unsuitable for downstream applications. Here, we present two distinct approaches to experimentally evolve novel New ZealandPaenibacillus larvaebacteriophages. The first approach uses the traditional agar-overlay method, whereas the other was a Rapid Appelmans Protocol (RAP) modelled after the established Appelmans Method. Both approaches resulted in an increase in plaque-forming units (PFU/mL). The RAP approach was significantly faster and simpler, and allowed us to evolve a set of bacteriophages in as little as four days, increasing titers 100-1000-fold relative to their ancestors. The resultant titers were sufficient to extract and sequence DNA from these bacteriophages. An analysis of these phage genomes is provided. We also propose a model that describes the parameters that allow the RAP approach to select improvement of bacteriophage titer. The RAP approach is an effective method for experimentally evolving previously intractable bacteriophages in a high-throughput and expeditious manner.
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis
Authors: Baer Lachlan , Barthelson Karissa , Postlethwait John , Adelson David , Pederson Stephen , Lardelli Michael
Published: March 2023

In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show thatchromosomally co-located differentially expressed genes(CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs thatarelikely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
Authors: Munasinghe Manisha , Read Andrew , Stitzer Michelle C. , Song Baoxing , Menard Claire , Ma Kristy Yubo , Brandvain Yaniv , Hirsch Candice N. , Springer Nathan
Published: March 2023

Background

Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated forde-novogenome assemblies of 26 diverse inbred maize lines.

Results

We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both putative insertion and deletion events. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that, genome-wide, deletions of transposable elements account for more structural variation than insertions. These deletions are often large structural variants containing multiple transposable elements.

Conclusions

Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.