bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian inference on a microstructural, hyperelastic model of tendon deformation
Authors: Haughton James , Cotter Simon L. , Parnell William J. , Shearer Tom
Published: May 2022

Microstructural models of soft-tissue deformation are important in applications including artificial tissue design and surgical planning. The basis of these models, and their advantage over their phenomenological counterparts, is that they incorporate parameters that are directly linked to the tissue’s microscale structure and constitutive behaviour and can therefore be used to predict the effects of structural changes to the tissue. Although studies have attempted to determine such parameters using diverse, state-of-the-art, experimental techniques, values ranging over several orders of magnitude have been reported, leading to uncertainty in the true parameter values and creating a need for models that can handle such uncertainty. We derive a new microstructural, hyperelastic model for transversely isotropic soft tissues and use it to model the mechanical behaviour of tendons. To account for parameter uncertainty, we employ a Bayesian approach and apply an adaptive Markov chain Monte Carlo algorithm to determine posterior probability distributions for the model parameters. The obtained posterior distributions are consistent with parameter measurements previously reported and enable us to quantify the uncertainty in their values for each tendon sample that was modelled. This approach could serve as a prototype for quantifying parameter uncertainty in other soft tissues.
The Föppl–von Kármán equations of elastic plates with initial stress
Authors: Ciarletta P. , Pozzi G. , Riccobelli D.
Published: May 2022

Initially, stressed plates are widely used in modern fabrication techniques, such as additive manufacturing and UV lithography, for their tunable morphology by application of external stimuli. In this work, we propose a formal asymptotic derivation of the Föppl–von Kármán equations for an elastic plate with initial stresses, using the constitutive theory of nonlinear elastic solids with initial stresses under the assumptions of incompressibility and material isotropy. Compared to existing works, our approach allows us to determine the morphological transitions of the elastic plate without prescribing the underlying target metric of the unstressed state of the elastic body. We explicitly solve the derived FvK equations in some physical problems of engineering interest, discussing how the initial stress distribution drives the emergence of spontaneous curvatures within the deformed plate. The proposed mathematical framework can be used to tailor shape on demand, with applications in several engineering fields ranging from soft robotics to four-dimensional printing.
Overcoming a ‘forbidden phenotype’: the parrot's head supports, propels and powers tripedal locomotion
Authors: Young Melody W. , Dickinson Edwin , Flaim Nicholas D. , Granatosky Michael C.
Published: May 2022

No vertebrate, living or extinct, is known to have possessed an odd number of limbs. Despite this ‘forbidden phenotype’, gaits that use odd numbers of limbs (e.g. tripedalism or pentapedalism) have evolved in both avian and mammalian lineages. Tripedal locomotion is commonly employed by parrots during climbing, who use their beaks as an additional support. However, it is unclear whether the beak functions simply as a stabilizing hook, or as a propulsive limb. Here, we present data on kinetics of tripedal climbing in six rosy-faced lovebirds (Agapornis roseicollis). Our findings demonstrate that parrots use cyclical tripedal gaits when climbing and the beak and hindlimbs generate comparable propulsive and tangential substrate reaction forces and power. Propulsive and tangential forces generated by the beak are of magnitudes equal to or greater than those forces generated by the forelimbs of humans and non-human primates during vertical climbing. We conclude that the feeding apparatus and neck flexors of parrots have been co-opted to function biomechanically as a propulsive third limb during vertical climbing. We hypothesize that this exaptation required substantive alterations to the neuromuscular system including enhanced force-generating capabilities of the neck flexors and modifications to locomotor central pattern generators.
Cellulitis and transient bacteremia by Capnocytophaga canis after a cat scratch in an immunocompetent patient
Authors: Fernández Vecilla Domingo , Ugalde Zarraga Estíbaliz , Urrutikoechea-Gutiérrez Mikel Joseba , Renzi Francesco , Díaz de Tuesta del Arco José Luis
Published: May 2022

Capnocytophaga canis

is still a rare cause of infection. We present a case of an immunocompetent patient admited in the hospital with functional impotence, pain and erythema in his left leg after suffering two scratches from his cat 48 h ago. After obtaining blood and wound cultures, broad-spectrum antimicrobial therapy with intravenous amoxicillin clavulanate was initiated. After 1 day and with a clear improvement of the symptoms the patient was discharged from the hospital with cellulitis and transient bacteremia as diagnosis and completing 1 week of antimicrobial therapy orally. After 80 and 92 h of incubation, both anaerobic flasks were positive. In the Gram-stain Gram-negative rod-shaped bacteria could be observed. Despite subculturing in brucella blood agar, tripticase soy agar with 5 % of sheep blood and chocolate agar, in both anaerobic and microaerophilic conditions, the strain could not be recovered. However, these Gram-negative rods could be identified as

C. canis

by 16S rRNA sequencing, Capsular typing was performed to study the strain, but none of the studied capsule-types tested positive.

C. canis

is still a rare cause of human infection, but it must be considered in the differential diagnosis of infections related to bites, scratches and licks from dogs or cats.
Feasibility analysis and mechanism exploration of Rhei Radix et Rhizome−Schisandrae Sphenantherae Fructus (RS) against COVID-19
Authors: Qi Jian-hong , Dong Fang-xu , Wang Ke , Zhang Shan-yu , Liu Zi-ming , Wang Wen-jing , Sun Feng-zhi , Zhang Hui-min , Wang Xiao-long
Published: May 2022

Introduction. As a novel global epidemic, corona virus disease 2019 (COVID-19) caused by SARS-CoV-2 brought great suffering and disaster to mankind. Recently, although significant progress has been made in vaccines against SARS-CoV-2, there are still no drugs for treating COVID-19. It is well known that traditional Chinese medicine (TCM) has achieved excellent efficacy in the treatment of COVID-19 in China. As a treasure-house of natural drugs, Chinese herbs offer a promising prospect for discovering anti-COVID-19 drugs.

Hypothesis/Gap Statement. We proposed that Rhei Radix et Rhizome−Schisandrae Sphenantherae Fructus (RS) may have potential value in the treatment of COVID-19 patients by regulating immune response, protecting the cardiovascular system, inhibiting the production of inflammatory factors, and blocking virus invasion and replication processes.

Aim. We aimed to explore the feasibility and molecular mechanisms of RS against COVID-19, to provide a reference for basic research and clinical applications.

Methodology. Through literature mining, it is found that a Chinese herbal pair, RS, has potential anti-COVID-19 activity. In this study, we analysed the feasibility of RS against COVID-19 by high-throughput molecular docking and molecular dynamics simulations. Furthermore, we predicted the molecular mechanisms of RS against COVID-19 based on network pharmacology.

Results. We proved the feasibility of RS anti-COVID-19 by literature mining, virtual docking and molecular dynamics simulations, and found that angiotensin converting enzyme 2 (ACE2) and 3C-like protease (3 CL pro) were also two critical targets for RS against COVID-19. In addition, we predicted the molecular mechanisms of RS in the treatment of COVID-19, and identified 29 main ingredients, 21 potential targets and 16 signalling pathways. Rhein, eupatin, (-)-catechin, aloe-emodin may be important active ingredients in RS. ALB, ESR1, EGFR, HMOX1, CTSL, and RHOA may be important targets against COVID-19. Platelet activation, renin secretion, ras signalling pathway, chemokine signalling pathway, and human cytomegalovirus infection may be important signalling pathways against COVID-19.

Conclusion. RS plays a key role in the treatment of COVID-19, which may be closely related to immune regulation, cardiovascular protection, anti-inflammation, virus invasion and replication processes.
MICNet: Prediction of antibiotic susceptibility from microscopic images using transfer learning
Authors: Viehweger Adrian , Hölzer Martin , Brandt Christian
Published: May 2022

Rapid susceptibility testing of bacterial isolates is crucial for anti-infective therapy, especially in critical cases such as bacteriaemia and sepsis. Nevertheless, empiric therapy is often initiated immediately and without testing because two days and more pass between a positive blood culture and a susceptibility profile, so in the meantime, the most likely pathogens are treated. However, current empiric recommendations are very generic. They often remain unmodified even in light of incoming, early data specific to a patient’s case, such as positive blood culture microscopy. Part of the hesitancy to change treatments presumably stems from a lack of systematic integration of early information beyond expert intuition. To enable targeted antimicrobial therapy earlier in a case’s progression, we developed a method to predict antimicrobial susceptibility from microscopy images of bacteria alone. Our proof-of-concept MICNet combines two neural nets in a new chimerical architecture. It is pre-trained on about 100 thousand antibiograms and fine-tuned with only five thousand microscopic images through transfer learning. Predicting susceptibility profiles of four representative species, we show high predictive performance with a mean F-score of nearly 85%. In addition, several qualitative assessments show that our chimerical net has learned substantial expert knowledge. Therefore, MICNet is the first step towards personalized empiric therapy, combining prior pathogen probabilities with patient-specific data.
Immune response to 2-dose BNT162b2 vaccination and risk of SARS-CoV-2 breakthrough infection: The Shieldvacc-2 study
Authors: Seekircher Lisa , Bánki Zoltán , Kimpel Janine , Rössler Annika , Schäfer Helena , Falkensammer Barbara , Bante David , Forer Lukas , Schönherr Sebastian , Harthaller Teresa , Sacher Magdalena , Ower Cornelia , Tschiderer Lena , Ulmer Hanno , Krammer Florian , Laer Dorothee von , Borena Wegene , Willeit Peter
Published: May 2022

It is uncertain to which extent antibody and T-cell responses after vaccination against SARS-CoV-2 are associated with reduced risk of breakthrough infection and whether their measurement enhances risk prediction. We conducted a phase-4 open-label clinical trial in the pre-omicron era, enrolling 2,760 individuals aged ≥16 years 35±8 days after having received the second dose of BNT162b2 (baseline 15-21 May 2021). Over a median 5.9-month of follow-up, we identified incident SARS-CoV-2 breakthrough infections using weekly antigen tests, a confirmatory PCR test, and/or serological evidence for incident infection. We quantified relative risks adjusted for age, sex, and prior SARS-CoV-2 infection for different immunological parameters and assessed improvements in risk discrimination. In contrast to the T-cell response, higher plasma levels of binding antibodies and antibodies in a surrogate neutralization assay were associated with reduced risk of breakthrough infection. Furthermore, assessment of anti-spike IgG levels enhanced prediction of breakthrough infection and may therefore be a suitable measurable correlate of protection in practice.
SLCO5A1 and synaptic assembly genes contribute to impulsivity in juvenile myoclonic epilepsy
Authors: Panjwani Naim , Shakeshaft Amy , Roshandel Delnaz , Lin Fan , Collingwood Amber , Hall Anna , Keenan Katherine , Deneubourg Celine , Mirabella Filippo , Topp Simon , Zarubova Jana , Thomas Rhys H. , Talvik Inga , Syvertsen Marte , Striano Pasquale , Smith Anna B. , Selmer Kaja K. , Rubboli Guido , Orsini Alessandro , Ng Ching Ching , Møller Rikke S. , Lim Kheng Seang , Hamandi Khalid , Greenberg David A. , Gesche Joanna , Gardella Elena , Fong Choong Yi , Beier Christoph P. , Andrade Danielle M. , Jungbluth Heinz , Richardson Mark P. , Pastore Annalisa , Fanto Manolis , Pal Deb K. , Strug Lisa J.
Published: May 2022

Introductory Paragraph

Elevated impulsivity is a key component of attention-deficit hyperactivity disorder (ADHD), bipolar disorder and epilepsy1-5. We performed a genome-wide association, colocalization and pathway analysis of impulsivity in juvenile myoclonic epilepsy (JME). We identify genome-wide associated SNPs at 8q13.3 (p=7.5 × 10−9) and 10p11.21 (p=3.6 × 10−8). The 8q13.3 locus colocalizes with SLCO5A1 expression quantitative trait loci in cerebral cortex (p=9.5 × 10−3). SLCO5A1 codes for a membrane-bound organic anion transporter6 and upregulates synapse assembly/organisation genes7. Pathway analysis also demonstrates 9.3-fold enrichment for synaptic assembly genes (p=0.03) including NRXN1, NLGN1 and PTPRD. RNAi knockdown of Oatp30B, the Drosophila homolog of SLCO5A1, causes both over-reactive startling behaviour (p=8.7 × 10−3) and increased seizure-like events (p=6.8 × 10−7). Polygenic risk score for ADHD correlates with impulsivity scores (p=1.60 × 10−3), demonstrating shared genetic contributions. SLCO5A1 loss-of-function represents a novel impulsivity and seizure mechanism. Synaptic assembly genes may inform the aetiology of impulsivity in health and disease.
Diabetes and neuroaxonal damage in Parkinson’s disease
Authors: Vijiaratnam Nirosen , Lawton Michael , Real Raquel , Heslegrave Amanda J , Guo Tong , Athauda Dilan , Gandhi Sonia , Girges Christine , Ben-Shlomo Yoav , Zetterberg Henrik , Grosset Donald G , Morris Huw R , Foltynie Thomas ,   PRoBaND clinical consortium
Published: May 2022

Patient’s with Parkinson’s disease (PD) with coexistent type 2 diabetes (T2DM) can manifest with more severe motor and cognitive phenotypes. The precise reasons for this remain unclear though underlying pathophysiological differences are increasingly implicated. More severe neuroaxonal injury in PD patients with T2DM was recently proposed as a potential mechanism for this. We explored this in the tracking Parkinson’s study and confirmed these findings. Cases with T2DM had higher serum neurofilament light levels and this remained significant after correction for age and vascular risk factor burden. Disentangling the underlying mechanism for more rapid axonal damage will be important in the development of disease modifying therapies for PD.
Reporting of patient involvement: A mixed-methods analysis of current practice in health research publications
Authors: Weschke Sarah , Franzen Delwen Louise , Sierawska Anna Karolina , Bonde Lea-Sophie , Strech Daniel , Schorr Susanne Gabriele
Published: May 2022

Objectives

To evaluate the extent and quality of patient involvement reporting in examples of current practice in health research.

Design

Mixed-methods study. We used a targeted search strategy across three cohorts to identify health research publications that reported patient involvement: publications published in The BMJ, publications listed in the PCORI database, and publications citing the GRIPP2 reporting checklist for patient involvement or a critical appraisal guideline for user involvement. Publications were coded according to three coding schemes: “Phase of involvement”, the GRIPP2-SF reporting checklist, and the critical appraisal guideline.

Outcome measures

The phase of the study in which patients were actively involved. For the BMJ sample, the proportion of publications that reported patient involvement. The quality of reporting based on the GRIPP2 short form reporting guideline. The quality of patient involvement based on the critical appraisal guideline. Quantitative and qualitative results are reported.

Results

We included 87 publications that reported patient involvement. Patients were most frequently involved in study design (90% of publications, n=78), followed by study conduct (70%, n=61), and dissemination (40%, n=35). Reporting of patient involvement was often incomplete, e.g., only 39% of publications (n=34) reported the aim of patient involvement. While the methods (56%, n=49) and results (59%, n=51) of involvement were reported more frequently, qualitative analyses showed that reporting was often unspecific and the influence of patients’ input remained vague. Therefore, a systematic assessment of the quality and impact of patient involvement according to the critical appraisal guideline was not feasible across samples.

Conclusions

As patient involvement is increasingly seen as an integral part of the research process and requested by funding bodies, it is essential that researchers receive specific guidance on how to report patient involvement activities. Complete reporting builds the foundation for assessing the quality of patient involvement and its impact on research.

PROTOCOL

The protocol was published on the Open Science Framework: https://osf.io/vntgu/

STRENGTHS AND LIMITATIONS

A targeted search strategy was used to identify examples of patient involvement reporting in a variety of publication types and study designs in health research

A mixed-methods approach allowed for an analysis of both the completeness and quality of patient involvement reporting

In this study, we coded statements reporting on patient involvement in 87 health research publications that may be adapted for further use

Reporting of patient involvement was insufficiently detailed to allow for a systematic assessment of the quality of patient involvement
Optical coherence tomography assessment of axonal and neuronal damage of the retina in patients with familial and sporadic multiple sclerosis
Authors: Grudziecka Pyrek M , Selmaj K
Published: May 2022

Objective

Optical coherence tomography (OCT) assessment of axonal and neuronal damage of the retina in patients with familial and sporadic multiple sclerosis.

Methods

45 patients with familial MS (fMS), 58 patients with sporadic MS (sMS) and 35 healthy controls were included in the study. OCT was performed with the spectral domain optical coherence tomography (SD-OCT, Heidelberg Engineering, Germany). The retinal nerve fiber layer (RNFL) thickness and macular volume (MV) were measured.

Results

A significant thinning of the global RNFL thickness was detected in both forms of MS compared to control group, (86,61 (+/- 14,74) µm in sMS, 85,8 (+/- 12,7) µm in fMS, 97,96 (+/- 7,6) µm in control group; p <0,001). There was no significant difference in the global RNFL thickness between sMS and fMS. A significant reduction of the MV was shown in sMS and fMS compared to control group (8,12 (+/- 1,14) mm3 in sMS, 8,1 (+/- 1,12) mm3 in fMS, and 8,81 (+/- 0,31) mm3 in control group; p = 0,003). No difference in MV between sMS and fMS was found. However, in eyes with history of optic neuritis (ON) MV was significantly reduced in sMS versus fMS (8,12 (+/- 2,87) mm3 vs. 8,42 (+/- 0,54) mm3; p=0,05).

Conclusion

We confirmed the presence of axonal and neuronal damage of the retina in sMS and fMS. ON induced a significantly greater reduction of MV in sMS compared to fMS, indicating a stronger neuronal damage in ON eyes in sMS than in fMS.

KEY MESSAGES

The familial MS accounts for a significant proportion of MS patients and there is still ongoing discussion on the distinction between familial (fMS) and sporadic (sMS) forms of this disease. Using OCT, we confirmed the presence of axonal and neuronal damage in the retina in both forms of MS. We found that optic neuritis (ON) induced a greater retinal neuronal damage in sMS than in fMS. These results support the conclusion that there are some discrete differences in pathological processes occurring in the retina in sMS and fMS.
Accuracy of US CDC COVID-19 Forecasting Models
Authors: Chharia Aviral , Jeevan Govind , Jha Rajat Aayush , Liu Meng , Berman Jonathan M , Glorioso Christin
Published: May 2022

Accurate predictive modeling of pandemics is essential for optimally distributing resources and setting policy. Dozens of case predictions models have been proposed but their accuracy over time and by model type remains unclear. In this study, we analyze all US CDC COVID-19 forecasting models, by first categorizing them and then calculating their mean absolute percent error, both wave-wise and on the complete timeline. We compare their estimates to government-reported case numbers, one another, as well as two baseline models wherein case counts remain static or follow a simple linear trend. The comparison reveals that more than one-third of models fail to outperform a simple static case baseline and two-thirds fail to outperform a simple linear trend forecast. A wave-by-wave comparison of models revealed that no overall modeling approach was superior to others, including ensemble models, and error in modeling has increased over time during the pandemic. This study raises concerns about hosting these models on official public platforms of health organizations including the US-CDC which risks giving them an official imprimatur and further raising concerns if utilized to formulate policy. By offering a universal evaluation method for pandemic forecasting models, we expect this work to serve as the starting point towards the development of more accurate models.
Single-cell mapping of tumor heterogeneity in pediatric rhabdomyosarcoma reveals developmental signatures with therapeutic relevance
Authors: Danielli Sara G , Porpiglia Ermelinda , De Micheli Andrea J , Navarro Natalia , Zellinger Michael J , Bechtold Ingrid , Kisele Samanta , Volken Larissa , Marques Joana G , Kasper Stephanie , Bode Peter K , Henssen Anton G , Gürgen Dennis , Roma Josep , Bühlmann Peter , Blau Helen M , Wachtel Marco , Schäfer Beat W
Published: May 2022

Rhabdomyosarcoma (RMS) is an aggressive human pediatric cancer. Despite robust expression of myogenic regulatory factors, RMS cells are blocked in a proliferative state and do not terminally differentiate. The extent to which the skeletal muscle lineage is represented in RMS tumors and the mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing (scRNAseq), mass cytometry (CyTOF) and high-content imaging to resolve RMS heterogeneity. ScRNAseq and CyTOF analysis of a total of 17 patient-derived primary cultures and three cell lines uncovered plastic myogenic subpopulations that delineate a branched trajectory. The less aggressive embryonal RMS (eRMS) harbor primarily muscle stem cell (MuSC)-like cells and exhibit sparse commitment to differentiation. The more aggressive alveolar RMS (aRMS) comprise primarily actively cycling committed progenitors with a paucity of differentiated cells. The oncogenic fusion protein PAX3:FOXO1 sustains aRMS cells in the cycling trajectory loop, which we show can re-wired towards differentiation upon its downregulation or by dual pharmacological RAF and MEK inhibition. Our findings provide insights into the developmental states and trajectories underlying RMS progression and identify the RAS pathway as a promising target of differentiation therapy for human aRMS.

STATEMENT OF SIGNIFICANCE

We present the first comprehensive single-cell transcriptomic and proteomic atlas of pediatric rhabdomyosarcoma (RMS), in which we identify impaired myogenic trajectories with prognostic value. We demonstrate that RAS pathway inhibitors disrupt the oncogenic trajectory and induce terminal differentiation, revealing novel therapeutic targets for the aggressive alveolar RMS subtype.
Whole genome sequencing suggests that “non-pathogenicity on banana (NPB)” is the ancestral state of the Ralstonia solanacearum IIB-4 lineage
Authors: Beutler Jonathan , Holden Samuel , Georgoulis Stratton , Williams Darrielle , Norman David J. , Lowe-Power Tiffany M.
Published: May 2022

The bacterial wilt pathogens in the Ralstonia solanacearum species complex (RSSC) have broad but finite host ranges. Population genetic surveys of RSSC pathogens show that many sequevars (subspecies groups) are predominantly recovered from wilting solanaceous plants. In contrast, strains in the IIB-4 sequevar have been isolated from plants in over a dozen families. Certain IIB-4 lineages have been classified as banana-virulent or “not pathogenic to banana (NPB)”. Prior analysis suggested that the NPB lineage has diverged from the banana-virulent IIB-4 strains. To test this model, we analyzed the phenotypes and phylogeny of a diverse collection of 19 IIB-4 isolates. We used Illumina sequencing to assemble draft genomes of 12 new strains. Based on whole genome phylogenetic analysis, these IIB-4 strains clustered into five subclades. We quantified virulence of each strain on tomato, banana, melon, and impatiens plants. Overall, the virulence patterns correlated with phylogeny. Banana virulence was restricted to the 4/4 IIB-4D subclade (N=4/4 strains) and IIB-4E subclade (N=1/2 strains). Subclades IIB-4D and IIB-4E are sister subclades and their closest relative, the IIB-4A-C subclade, lacked virulence on banana. Our data support a revised model in which banana virulence is an innovation within the IIB4D/E subclades.

Data Summary

Illumina sequencing and genome assembly data are available as NCBI BioProject PRJNA826884, and Table S1 lists the accession numbers for assemblies in GenBank and raw sequencing data in SRA. To enable future meta-analyses that identify genetic factors that drive host-range, the raw virulence data is included as Table S2.
A Hybrid Method for Ultrasound-Based Tracking of Skeletal Muscle Architecture
Authors: Verheul Jasper , Yeo Sang-Hoon
Published: May 2022

Tracking skeletal muscle architecture using B-mode ultra-sound is a widely used method in the field of human movement science and biomechanics. Sequential methods based on optical flow algorithms allow for smooth and coherent muscle tracking but are known to drift over time. Non-sequential feature detection methods on the other hand, do not suffer from drift, but are limited to tracking only lower-dimensional features. They are also known to be sensitive to image noise, and therefore often result in highly irregular tracking patterns. Building on the complimentary nature of both approaches, we present a novel fully automated hybrid muscle tracking approach that combines a sequential feature-point tracking method and a non-sequential method based on Hough transform. Tibialis anterior fascicle pennation angle and length, and central aponeurosis displacement, were measured in five healthy individuals during isometric contractions at five different ankle angles. Our hybrid method was demonstrated to significantly (p < 0.001) reduce drift compared to two sequential methods, and curve irregularity was significantly (p < 0.001) decreased compared to a non-sequential method. These findings suggest that the proposed hybrid approach can uniquely mitigate drift and irregularity limitation of individual methods used for tracking skeletal muscle architecture. Fully automated muscle tracking allows for convenient analysis of large datasets, whereas automatic drift correction opens the door for tracking muscle architecture in long ultrasound recordings during common movements, such as walking, running, and jumping without the need for manual intervention.
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
Authors: Çilingir F.G. , A’Bear L. , Hansen D. , Davis L.R. , Bunbury N. , Ozgul A. , Croll D. , Grossen C.
Published: May 2022

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources forA. giganteaare lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-levelde novogenome assembly ofA. giganteausing PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome forA. giganteais one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.
Macrophages undergo necroptosis during severe influenza A infection and contribute to virus-associated cytokine storm
Authors: Ferreira André C. , Sacramento Carolina Q. , Pereira-Dutra Filipe S. , Fintelman-Rodrigues Natália , Silva Priscila P. , Mattos Mayara , de Freitas Caroline S. , Marttorelli Andressa , de Melo Gabrielle R. , Macedo Mariana C. , Azevedo-Quintanilha Isaclaudia G. , Carlos Aluana S. , Emídio João Vitor , Garcia Cristiana C. , Bozza Patrícia T. , Bozza Fernando A. , Souza Thiago M. L.
Published: May 2022

Influenza A virus (IAV) causes a major public health concern, because it is one of the leading causes of respiratory tract infections and hospitalization. Severe influenza has been associated with the cytokine storm, and IAV productive infection cell death in airway epithelial cells may contribute to the exacerbation of this proinflammatory event. On the other hand, IAV replication in macrophages is non-permissive and whether this immune cell may contribute to severe influenza physiopathology requires more details. Here, we investigated IAV-induced macrophage death, along with potential therapeutic intervention. We found that IAV or simply its surface glycoprotein hemagglutinin (HA) triggers necroptosis in human and murine macrophages in a Toll-like receptor-4 (TLR4) and TNF-dependent manner. Anti-TNF treatment, with the clinically approved drug etanercept, prevented the engagement of the necroptotic loop and mice mortality. impaired IAV-induced pro-inflammatory cytokine storm and lung injury. Our results implicate macrophage necroptosis with severe influenza in experimental models and potentially repurpose a clinically available therapy.

Author Summary

Various fates of cell death have an integral role in the influenza A virus (IAV) pathogenesis and lung/respiratory dysfunction. IAV physiopathology is not restricted to airway epithelial cells, where this virus actively replicated. Macrophages should support both viral clearance and priming of adaptative immune response in patients that adequately control influenza. However, during severe IAV infection, macrophages – which are unable to support a permissive viral replication - undergo disruptive cell death and contribute to the exacerbated production of proinflammatory cytokines/chemokines. We characterized this process by showing that IAV or just its surface glycoprotein hemagglutinin (HA) trigger necroptosis, a disruptive and TNF-dependent cells death. Since TNF is a hallmark of pro-inflammatory cell death, we blocked this mediator with a repurposed biomedicine etanercept, which prevented the severe IAV infection in the experimental model. The present work improves the knowledge of influenza pathophysiology by highlighting the importance of macrophage cell death during severe infection.
Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants
Authors: Arruda Hiam R. S. , Lima Tulio M. , Alvim Renata G. F. , Victorio Fernanda B. A. , Abreu Daniel P. B. , Marsili Federico F. , Cruz Karen D. , Sosa-Acosta Patricia , Quinones-Vega Mauricio , Guedes Jéssica de S. , Nogueira Fábio C. S. , Silva Jerson L. , Castilho Leda R. , de Oliveira Guilherme A. P.
Published: May 2022

The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.
Associations between physical activity and cognitive dysfunction in older companion dogs: Results from the Dog Aging Project
Authors: Bray Emily E. , Raichlen David A. , Forsyth Kiersten K. , Promislow Daniel E.L. , Alexander Gene E. , MacLean Evan L. ,   Dog Aging Project Consortium
Published: May 2022

Canine Cognitive Dysfunction (CCD) is a form of dementia that shares many similarities with Alzheimer’s disease. Given that physical activity is believed to reduce risk of Alzheimer’s disease in humans, we explored the association between physical activity and cognitive health in a cohort of companion dogs, aged 6-18 years. We hypothesized that higher levels of physical activity would be associated with lower (i.e., better) scores on a cognitive dysfunction rating instrument and lower prevalence of dementia, and that this association would be robust when controlling for age, comorbidities, and other potential confounders. Our sample included 11,574 companion dogs enrolled through the Dog Aging Project, of whom 287 had scores over the clinical threshold for CCD. In this observational, cross-sectional study, we used owner-reported questionnaire data to quantify dog cognitive health (via a validated scale), physical activity levels, health conditions, training history, and dietary supplements. We fit regression models with measures of cognitive health as the outcome, and physical activity—with several important covariates—as predictors. We found a significant negative relationship between physical activity and current severity of cognitive dysfunction symptoms (estimate = -0.10, 95% CI: -0.11 to - 0.08, p < 0.001), extent of symptom worsening over a 6-month interval (estimate = -0.07, 95% CI: -0.09 to -0.05, p <0.001), and whether a dog reached a clinical level of CCD (odds ratio = 0.53, 95% CI: 0.45 to 0.63, p <0.001). Physical activity was robustly associated with better cognitive outcomes in dogs. Our findings illustrate the value of companion dogs as a model for investigating relationships between physical activity and cognitive aging, including aspects of dementia that may have translational potential for Alzheimer’s disease. While the current study represents an important first step in identifying a relationship between physical activity and cognitive function, it cannot determine causality. Future studies are needed to rule out reverse causation by following the same dogs prospectively over time, and to evaluate causality by administering physical-activity interventions.
Investigating the antioxidant effects of Aloe vera: Possible role in regulating lipid profile and liver function in high fat and fructose diet (HFFD) fed mice
Authors: Abubakar Abdullahi Mukhtar , Dibal Nathan Isaac , Attah Martha Orendu Oche , Chiroma Samaila Musa
Published: May 2022

Fat rich diets are believed to induce obesity and contributes to the development of diabetes and cardiovascular disease while high fructose diet was reported to increase gut surface area and enhance nutrient uptake resulting in weight gain. The study investigate the role of Aloe vera supplementation on lipid profiles, oxidative stress as well as liver and hear histology in high fat and fructose diet fed mice. Twenty mice were distributed into four groups (n=5). The groups received regular diet, high fat and fructose died (HFFD), HFFD plus 10% Aloe vera (HFFD+AV1) and HFFD plus 20% Aloe vera (HFFD+AV2) respectively for 10 weeks. The cholesterol level of HFFD+AV treated mice were significantly lower compared to HFFD treated mice. The ALT level was significantly increased in HFFD treated mice relative to the control. Aloe vera significantly improve albumin level as well as Catalase and superoxide dismutase activities of HFFD treated mice. The liver tissues of control and HFFD+AV2 treated mice showed normal hepatocytes. The study suggest that Aloe vera supplementation could protect against HFFD induced oxidative stress and hyperlipidemia. These findings might be used for further research on food supplementation for the control of metabolic disorders.
Glutamatergic projections from ventral hippocampus to nucleus accumbens cholinergic neurons are altered in a mouse model of depression
Authors: Medrihan Lucian , Knudsen Margarete , Ferraro Tatiana , Vasques Pedro Del Cioppo , Romin Yevgeniy , Fujisawa Sho , Greengard Paul , Milosevic Ana
Published: May 2022

The cholinergic interneurons (ChATs) of the nucleus accumbens (NAc) have a critical role in the activity of this region, specifically in the context of major depressive disorder. To understand the circuitry regulating this behavior we sought to determine the areas that directly project to these cells/interneurons by utilizing the monosynaptic cell-specific tracing technique. Mapping showed monosynaptic projections that are exclusive to NAc ChATs. To determine if some of these projections are altered in a depression mouse model, we used mice that do not express the calcium binding protein p11 specifically in ChATs (ChAT-p11 cKO) and display a depressive-like phenotype. Our data demonstrated that while the overall projection areas remain similar between wild type and in ChAT-p11 cKO mice, the number of projections coming from the ventral hippocampus (vHIP) is significantly reduced in the ChAT-p11 cKO mice. Furthermore, using optogenetics and electrophysiology we showed that glutamatergic projections from vHIP to NAc ChATs are severely altered in mutant mice. These results show that specific alterations in the circuitry of the accumbal ChAT interneurons could play an important role in the regulation of depressive-like behavior, reward seeking behavior in addictions, or psychiatric symptoms in neurodegenerative diseases.
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence
Authors: Belk Julia A. , Yao Winnie , Ly Nghi , Freitas Katherine A. , Chen Yan-Ting , Shi Quanming , Valencia Alfredo M. , Shifrut Eric , Kale Nupura , Yost Kathryn E. , Duffy Connor V. , Hwee Madeline A. , Miao Zhuang , Ashworth Alan , Mackall Crystal L. , Marson Alexander , Carnevale Julia , Vardhana Santosh A. , Satpathy Ansuman T.
Published: May 2022

T cell exhaustion limits anti-tumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic antigen stimulation assay, we performed genome-wide CRISPR/Cas9 screens to systematically discover genetic regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of several epigenetic regulators, including members of the INO80 and BAF chromatin remodeling complexes, improved T cell persistence in tumors. In vivo paired CRISPR perturbation and single-cell RNA sequencing revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of terminal exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a-depletion limited the global acquisition of chromatin accessibility associated with T cell exhaustion and led to improved anti-tumor immunity after adoptive cell therapy. In summary, we provide a comprehensive atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of the epigenetic state of T cell exhaustion can improve T cell responses in cancer immunotherapy.
The licorice metabolite enoxolone attenuates Clostridioides difficile pathophysiology by corrupting its metabolic and toxin production networks
Authors: Marreddy Ravi K. R. , Picker Jonathan , Phelps Gregory A. , Powell Reid , Cherian Philip T. , Bowling John J. , Stephan Clifford C. , Lee Richard E. , Hurdle Julian G.
Published: May 2022

Toxins TcdA and TcdB are the main virulence factors of Clostridioides difficile, a leading cause of hospital-acquired diarrhea. We investigated the therapeutic potential of inhibiting the biosynthesis of TcdA and TcdB. Accordingly, screening of structurally diverse phytochemicals with medicinal properties identified 18β-glycyrrhetinic acid (enoxolone) as an inhibitor of TcdA and TcdB biosynthesis. Enoxolone also inhibited sporulation. In a CDI colitis model, enoxolone when combined with vancomycin protected mice from becoming moribund and the combination was more effective than vancomycin alone, a standard of care antibiotic for CDI. While enoxolone alone reduced the in vivo load of toxins, the monotherapy did not protect mice from CDI. Affinity based proteomics identified ATP synthase subunit alpha (AtpA) and adenine deaminase (Ade) as possible molecular targets for enoxolone. Silencing of mRNA for Ade and AtpA also reduced toxin biosynthesis, while molecular interaction analysis showed that enoxolone directly bound to Ade. Ade converts adenine to hypoxanthine as an early step in the purine salvage pathway. Metabolomics revealed enoxolone caused cells to accumulate adenosine and deplete hypoxanthine and ATP. Accordingly, supplementation with hypoxanthine partly restored toxin production. Enoxolone also impacted phosphate metabolism by reducing the amounts of cellular phosphate. Thus, supplementation with triethyl phosphate as a source of phosphate also partly restored toxin production. When hypoxanthine and triethyl phosphate were combined, toxin production was fully restored in the presence of enoxolone. Taken together, studies with enoxolone revealed metabolic pathways that affect C. difficile toxin production and could represent potential anti-virulence drug targets.

IMPORTANCE

Clostridioides difficile, a leading cause of hospital-acquired diarrhea, produces two co-regulated toxins (TcdA and TcdB) that are the focus of most anti-virulence discovery efforts for C. difficile infection (CDI). Exploration of an alternate anti-virulence strategy led to the discovery that the licorice metabolite enoxolone inhibits C. difficile virulence by blocking the cellular biosynthesis of TcdA and TcdB. Blockage of toxin production by enoxolone was associated with multiple effects on cells, including inhibiting adenine deaminase and ATP synthase leading to disruption of purine biosynthesis and phosphate metabolism. In mice infected with C. difficile, the efficacy of enoxolone in combination with vancomycin was superior to vancomycin alone. These findings contribute to establishing toxin biosynthesis inhibition as a newer therapeutic concept for CDI.
A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteraemia
Authors: Giulieri Stefano G. , Guérillot Romain , Holmes Natasha E. , Baines Sarah L. , Hachani Abderrahman , Daniel Diane S. , Seemann Torsten , Davis Joshua S. , Van Hal Sebastiaan , Tong Steve Y. C. , Stinear Timothy P. , Howden Benjamin P.
Published: May 2022

Outcomes for patients with severe bacterial infections are determined by the interplay between host, pathogen, and treatments. Most notably, patient age and antibiotic resistance contributes significantly to poor outcomes. While human genomics studies have provided insights into the host genetic factors impacting outcomes of Staphylococcus aureus infections, comparatively little is known about S. aureus genotypes and disease severity. Building on the idea that bacterial pathoadaptation is a key driver of clinical outcomes, we develop a new genome-wide association study (GWAS) framework to identify adaptive bacterial mutations associated with clinical treatment failure and mortality in three large and independent S. aureus bacteraemia cohorts, comprising 1358 episodes. We discovered S. aureus loci with previously undescribed convergent mutations linked to both poorer infection outcomes and reduced susceptibility to vancomycin. Our research highlights the potential of vancomycin-selected mutations and vancomycin MIC as key explanatory variables to predict SAB severity. The contribution of bacterial variation was much lower for clinical outcomes (heritability < 5%), however, GWAS allowed us to identify additional, MIC-independent candidate pathogenesis loci. Using supervised machine-learning, we were able to quantify the predictive potential of these adaptive S. aureus signatures, along with host determinants of bacteraemia outcomes. The statistical genomics framework we have developed is a powerful means to capture adaptive mutations and find bacterial factors that influence and predict severe infections. Our findings underscore the importance of systematically collected, rich clinical and microbiological data to understand bacterial mechanisms promoting treatment failure.