bluuebunny/crossref_metadata_2025 huggingface dataset:
Thrombotic Features as the Primary Cause of SARS-CoV-2 Related Acute Abdomen in Children
Authors: Amoroso Angela , Di Stasio Fabiana , Ranucci Giusy , Betalli Pietro , Cheli Maurizio , Dalla Rosa Davide , D’Anna Carolina , Gaglione Giovanni , Giannotti Giulia , Licini Lisa , Mandato Claudia , Massazza Gabriella , Orlando Francesca , Morotti Denise , Rocco Michele , Sonzogni Aurelio , Tipo Vincenzo , Verdoni Lucio , D’Antiga Lorenzo , Norsa Lorenzo
Published: July 2023

Objectives:

We performed a retrospective case control study to evaluate the histological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive pediatric patients undergoing laparoscopic exploration for acute abdomen symptoms. To our knowledge this is the first study that analyzes histopathological characteristics of abdominal tissues in SARS-CoV-2 children.

Study design:

We enrolled 8 multisystem inflammatory syndrome in children (MIS-C) patients and 4 SARS-CoV-2 positive patients who underwent intestinal resection versus 36 control appendectomies from 2 pediatric tertiary referral centers between March 2020 and July 2021. Surgical resection samples were evaluated on several histological sections focusing on general inflammatory pattern and degree of inflammation. Peculiar histological features (endotheliitis and vascular thrombosis) were semi-quantitatively scored respectively in capillary, veins, and arteries.

Results:

All SARS-CoV-2 related surgical samples showed thrombotic patterns. Those patterns were significantly less frequent in SARS-CoV-2 negative appendectomies (P = 0.004). The semi-quantitative score of thrombosis was significantly higher (P = 0.002) in patients with SARS-CoV-2 related procedures.

Conclusions:

Our results showed that SARS-CoV-2 can cause thrombotic damage in abdominal tissues both in the acute phase of the infection (SARS-CoV-2 related appendectomies) and secondary to cytokine storm (MIS-C).
#PathMastodon: An Up-In-Coming Platform for Pathology Education Among Pathologists, Trainees, and Medical Students
Authors: Schukow Casey , Punjabi Lavisha S. , Gardner Jerad M.
Published: July 2023

Social media use in pathology has continued to grow and become more mainstream among pathologists, trainees, and medical students over the past decade. Twitter has historically been (and still seems to be) a positive platform for the social media pathology community to engage with each other virtually (ie, PathTwitter). However, as a new era of Twitter leadership began to unfold in October 2022, a young platform called “Mastodon” began to gain notice within this community as the hashtag #PathMastodon became prevalent. Founded in 2016 by Eugen Rochko, Mastodon is a decentralized, open-sourced, ads-free platform intended to promote public knowledge in a safe and public manner. When compared with Twitter, however, Mastodon is globally much smaller, and its medical professional server called “Med-Mastodon” is more cumbersome with certain features (eg, tracking analytics and username changes). Nevertheless, this new platform, which looks and feels much like Twitter, has great potential to provide continued medical education and virtual excellence among the social media pathology community. Thus, the purpose of this review is to provide a relevant synopsis of how Mastodon, Med-Mastodon, and #PathMastodon may benefit pathologists, trainees, and medical students who use social media. A qualitative analysis of pertinent peer-reviewed and non–peer-reviewed materials relative to the topic will be performed. In addition, we will provide a comparison of Mastodon and Twitter, provide example figures of #PathMastodon and related posts, and elaborate on the importance this discussion brings to the social media pathology community.
Impact of the COVID-19 Pandemic on a Clinical Trial: A Quantitative Report on Study Engagement and Strategies
Authors: Brown Shaaron E. , Miller Meagan , Darring Jodi , Inamdar Ketaki , Salgaonkar Arya , Burnsed Jennifer C. , Stevenson Richard D. , Shall Mary S. , Harper Amy D. , Hendricks-Munoz Karen D. , Thacker Leroy R. , Hyde Meg , Dusing Stacey C.
Published: July 2023

Introduction:

The COVID-19 pandemic impacted clinical research worldwide potentially altering research findings. The study purpose was to measure the effect of the pandemic on recruitment, retention, assessment, and intervention completion rates.

Methods:

Enrollment and participation data from a clinical trial evaluating efficacy of a physical therapy intervention for high-risk preterm infants were compared across 3 pandemic periods (February 2019 through November 2021).

Results:

Recruitment, retention, assessment, and intervention completion rates were lowest during the peak pandemic period.

Conclusions:

In compliance with the Human Subjects Review Board, and for the participants' and staff safety, transition from in-person to telehealth or hybrid visits was required to continue this longitudinal study. Despite the negative effect of the pandemic, parental resilience and commitment to the study was clear. Flexibility, quick action, dedication, and efficiency of the research team were key elements enabling study continuation with successful transition to telehealth assessments/interventions during the peak pandemic period.
The value of chest radiography after chest tube removal in nonventilated trauma patients: A post hoc analysis of a multicenter prospective cohort study
Authors: Sweet Arthur A.R. , Kobes Tim , Houwert Roderick M. , Leenen Luke P.H. , de Jong Pim A. , Veldhuis Wouter B. , IJpma Frank F.A. , van Baal Mark C.P.M.
Published: July 2023

BACKGROUND

Chest tubes are commonly placed in trauma care to treat life-threatening intrathoracic injuries by evacuating blood or air from the pleural cavity. Currently, it is common practice to routinely obtain chest radiographs between 1 to 8 hours after chest tube removal, while the necessity of it has been questioned. This study describes the “ins-and-outs” of chest tubes and evaluates the value of routine postremoval chest radiography in nonventilated trauma patients.

METHODS

A post hoc analysis of a multicenter observational prospective cohort study was performed in blunt chest trauma patients admitted with multiple rib fractures to two level 1 trauma centers between January 2018 and March 2021 and treated with one or more chest tubes. Exclusion criteria were mechanical ventilation during chest tube removal, missing reports of postremoval chest radiography, transfer to another hospital, or mortality before chest tube removal. Descriptive analyses were performed to calculate the number of findings on postremoval chest radiographs and reinterventions.

RESULTS

A total of 207 patients were included for analysis of whom 14 underwent bilateral chest tube placement, resulting in 221 chest tube removals investigated in this study. The mean ± SD age was 58 ± 17 years, 71% were male, 73% had American Society of Anesthesiologists scores of 1 or 2, and the median Injury Severity Score was 19 (interquartile range, 14–29). In 68 of 221 chest tube removals (31%), postremoval chest radiography showed increased or recurrent intrathoracic pathology (i.e., 13% pneumothorax, 18% pleural fluid, and 8% atelectasis). Only two (3%) of these patients underwent a same-day reintervention based on these findings, of whom one had signs or symptoms of recurrent pathology and one was asymptomatic.

CONCLUSION

It seems safe to omit routine use of postremoval chest radiography in nonventilated blunt chest trauma patients and to selectively use imaging in those patients presenting with clinical signs or symptoms after chest tube removal.

LEVEL OF EVIDENCE

Diagnostic Tests/Criteria; Level IV.
On automated model discovery and a universal material subroutine
Authors: Peirlinck Mathias , Linka Kevin , Hurtado Juan A. , Kuhl Ellen
Published: July 2023

Constitutive modeling is the cornerstone of computational and structural mechanics. In a finite element analysis, the constitutive model is encoded in the material subroutine, a function that maps local strains onto stresses. This function is called within every finite element, at each integration point, within every time step, at each Newton iteration. Today’s finite element packages offer large libraries of material subroutines to choose from. However, the scientific criteria for model selection remain highly subjective and prone to user bias. Here we fully automate the process of model selection, autonomously discover the best model and parameters from experimental data, encode all possible discoverable models into a single material subroutine, and seamlessly integrate this universal material subroutine into a finite element analysis. We prototype this strategy for tension, compression, and shear data from human brain tissue and perform a hyperelastic model discovery from twelve possible terms. These terms feature the first and second invariants, raised to the first and second powers, embedded in the identity, exponential, and logarithmic functions, generating 22×2×3= 4096 models in total. We demonstrate how to integrate these models into a single universal material subroutine that features the classical neo Hooke, Blatz Ko, Mooney Rivlin, Demiray, Gent, and Holzapfel models as special cases. Finite element simulations with our universal material subroutine show that it specializes well to these widely used models, generalizes well to newly discovered models, and agrees excellently with both experimental data and previous simulations. It also performs well within realistic finite element simulations and accurately predicts stress concentrations in the human brain for six different head impact scenarios. We anticipate that integrating automated model discovery into a universal material subroutine will generalize naturally to more complex anisotropic, compressible, and inelastic materials and to other nonlinear finite element platforms. Replacing dozens of individual material subroutines by a single universal material subroutine that is populated directly via automated model discovery—entirely without human interaction—makes finite element analyses more accessible, more robust, and less vulnerable to human error. This could forever change how we simulate materials and structures.
Deciphering the genetic architecture of atrial fibrillation offers insights into disease prediction, pathophysiology and downstream sequelae
Authors: Yuan Shuai , Li Yuying , Wang Lijuan , Xu Fengzhe , Chen Jie , Levin Michael G , Xiong Ying , Voight Benjamin F. , Damrauer Scott M , Gill Dipender , Burgess Stephen , Åkesson Agneta , Michaëlsson Karl , Li Xue , Shen Xia , Larsson Susanna C.
Published: July 2023

Aims

The study aimed to discover novel genetic loci for atrial fibrillation (AF), explore the shared genetic etiologies between AF and other cardiovascular and cardiometabolic traits, and uncover AF pathogenesis using Mendelian randomization analysis.

Methods and results

We conducted a genome-wide association study meta-analysis including 109,787 AF cases and 1,165,920 controls of European ancestry and identified 215 loci, among which 91 were novel. We performed Genomic Structural Equation Modeling analysis between AF and four cardiovascular comorbidities (coronary artery disease, ischemic stroke, heart failure, and vneous thromboembolism) and found 189 loci shared across these diseases as well as a universal genetic locus shared by atherosclerotic outcomes (i.e., rs1537373 nearCDKN2B). Three genetic loci (rs10740129 nearJMJD1C, rs2370982 nearNRXN3, and rs9931494 nearFTO) were associated with AF and cardiometabolic traits. A polygenic risk score derived from this genome-wide meta-analysis was associated with AF risk (odds ratio 2.36, 95% confidence interval 2.31-2.41 per standard deviation increase) in the UK biobank. This score, combined with age, sex, and basic clinical features, predicted AF risk (AUC 0.784, 95% CI 0.781-0.787) in Europeans. Phenome-wide association analysis of the polygenic risk score identified many AF-related comorbidities of the circulatory, endocrine, and respiratory systems. Phenome-wide and multi-omic Mendelian randomization analyses identified associations of blood lipids and pressure, diabetes, insomnia, obesity, short sleep, and smoking, 27 blood proteins, one gut microbe (genus.Catenibacterium), and 11 blood metabolites with risk to AF.

Conclusions

This genome-wide association study and trans-omic Mendelian randomization analysis provides insights into disease risk prediction, pathophysiology and downstream sequelae.
Robust use of phenotypic heterogeneity at drug target genes for mechanistic insights: application ofcis-multivariable Mendelian randomization toGLP1Rgene region
Authors: Patel Ashish , Gill Dipender , Shungin Dmitry , Mantzoros Christos S. , Knudsen Lotte Bjerre , Bowden Jack , Burgess Stephen
Published: July 2023

Phenotypic heterogeneity at genomic loci encoding drug targets can be exploited by multivariable Mendelian randomization to provide insight on the pathways by which pharmacological interventions may affect disease risk. However, statistical inference in such investigations may be poor if overdispersion heterogeneity in measured genetic associations is unaccounted for. In this work, we first develop conditional F-statistics for dimension-reduced genetic associations that enable more accurate measurement of phenotypic heterogeneity. We then develop a novel extension for two-sample multivariable Mendelian randomization that accounts for overdispersion heterogeneity in dimension-reduced genetic associations. Our empirical focus is to use genetic variants in theGLP1Rgene region to understand the mechanism by which GLP1R agonism affects coronary artery disease (CAD) risk. Colocalization analyses indicate that distinct variants in theGLP1Rgene region are associated with body mass index and type 2 diabetes. Multivariable Mendelian randomization analyses that were corrected for overdispersion heterogeneity suggest that bodyweight lowering rather than type 2 diabetes liability lowering effects of GLP1R agonism are more likely contributing to reduced CAD risk. Tissue-specific analyses prioritised brain tissue as the most likely to be relevant for CAD risk, of the tissues considered. We hope the multivariable Mendelian randomization approach illustrated here is widely applicable to better understand mechanisms linking drug targets to diseases outcomes, and hence to guide drug development efforts.
APOE4/4 is linked to damaging lipid droplets in Alzheimer’s microglia
Authors: Haney Michael S. , Pálovics Róbert , Munson Christy Nicole , Long Chris , Johansson Patrik , Yip Oscar , Dong Wentao , Rawat Eshaan , West Elizabeth , Schlachetzki Johannes CM , Tsai Andy , Guldner Ian Hunter , Lamichhane Bhawika S. , Smith Amanda , Schaum Nicholas , Calcuttawala Kruti , Shin Andrew , Wang Yung-Hua , Wang Chengzhong , Koutsodendris Nicole , Serrano Geidy E , Beach Thomas G , Reiman Eric M , Glass Christopher K , Abu-Remaileh Monther , Enejder Annika , Huang Yadong , Wyss-Coray Tony
Published: July 2023

Several genetic risk factors for Alzheimer’s Disease (AD) implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells. However, the relationship between lipid metabolism in glia and AD pathology remains poorly understood. Through single-nucleus RNA-sequencing of AD brain tissue, we have identified a microglial state defined by the expression of the lipid droplet (LD) associated enzymeACSL1with ACSL1-positive microglia most abundant in AD patients with theAPOE4/4genotype. In human iPSC-derived microglia (iMG) fibrillar Aβ (fAβ) inducesACSL1expression, triglyceride synthesis, and LD accumulation in an APOE-dependent manner. Additionally, conditioned media from LD-containing microglia leads to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for AD with microglial LD accumulation and neurotoxic microglial-derived factors, potentially providing novel therapeutic strategies for AD.
Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions
Authors: Perez-Lamarque Benoît , Morlon Hélène
Published: July 2023

Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: “Do closely related hosts interact with closely related symbionts?” and “Do host and symbiont phylogenies mirror one another?”. These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as “cophylogenetic signal”, does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as “phylogenetic congruence”, is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events.

Here we apply a set of methods (ParaFit, PACo, and eMPRess), which significance is often interpreted as evidence for phylogenetic congruence, to simulations under three biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking with frequent cospeciation events. The latter is the only scenario that generates phylogenetic congruence, whereas the first two generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the three scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.
Extracellular release of a disintegrin and metalloproteinases orchestrates periodontal disease severity
Authors: Aljohmani Ahmad , Heinze Hakon , Gharzia Federico Guillermo , Reda Bashar , Abdrabou Ahmed Mohamed Mostafa , Becker Sören , Bischoff Markus , Hannig Matthias , Yildiz Daniela
Published: July 2023

Periodontal diseases are amongst the most common pathologies worldwide with a high risk for the development of systemic complications. Periodontal disease is driven by oral pathogens such asPorphyromonas gingivalisand the release of inflammatory cytokines. These cytokines (e.g. TNF) or their receptors (IL-1R) are substrates of a disintegrin and metalloproteinases (ADAMs). In a comparative approach, we observed an increase of ADAM8 protein expression and activity in the sulcus fluid of periodontal disease patients correlating with the disease stage. In contrast, the induced ADAM10 expression was decreased.In vitromechanistic studies revealed that bothPorphyromonas gingivalisinfection and the resulting cytokine release orchestrated the release of soluble ADAM8 by keratinocytes and neutrophils as soluble ectodomain and on exosomes, respectively. Furthermore, ADAM8 regulated the release of ADAM10 and MMP9, thereby potentially influencing wound healing and tissue destruction. Thus, the dysregulation of the cell-associated and extracellular ADAM proteolytic activity mainly driven by ADAM8 may be an essential regulatory element in periodontal disease onset and progression. This potential as novel local treatment option should be addressed in future translational studies.
Preferential differential gene expression within the WC1.1+γδ T cell compartment in cattle naturally infected withMycobacterium bovis
Authors: Bhat Sajad A. , Elnaggar Mahmoud , Hall Thomas J. , McHugo Gillian P. , Reid Cian , MacHugh David E. , Meade Kieran G.
Published: July 2023

Bovine tuberculosis (bTB), caused by infection withMycobacterium bovis, continues to cause significant issues for the global agriculture industry as well as for human health. An incomplete understanding of the host immune response contributes to the challenges of control and eradication of this zoonotic disease. In this study, high-throughput bulk RNA sequencing (RNA-seq) was used to characterize differential gene expression in γδ T cells – a subgroup of T cells that bridge innate and adaptive immunity and have known anti-mycobacterial response mechanisms. γδ T cell subsets are classified based on expression of a pathogen-recognition receptor known asWorkshop Cluster 1(WC1) and we hypothesised that bTB disease may alter the phenotype and function of specific γδ T cell subsets. Peripheral blood was collected from naturallyM. bovis-infected (positive for single intradermal comparative tuberculin test (SICTT) and IFN-γ ELISA) and age- and sex-matched, non-infected control Holstein-Friesian cattle. γδ T subsets were isolated using fluorescence activated cell sorting (n= 10–12 per group) and high-quality RNA extracted from each purified lymphocyte subset (WC1.1+, WC1.2+, WC1-and γδ-) was used to generate transcriptomes using bulk RNA-seq (n= 6 per group, representing a total of 48 RNA-seq libraries). Relatively low numbers of differentially expressed genes (DEGs) were observed between most cell subsets; however, 189 genes were significantly differentially expressed in theM. bovis-infected compared to the control groups for the WC1.1+γδ T cell compartment (absolute log2FC ≥ 1.5 and FDRPadj.≤ 0.1). The majority of these DEGs (168) were significantly increased in expression in cells from the bTB+ cattle and included genes encoding transcription factors (TBX21andEOMES), chemokine receptors (CCR5andCCR7), granzymes (GZMA, GZMM, andGZMH) and multiple killer cell immunoglobulin-like receptor (KIR) proteins indicating cytotoxic functions. Biological pathway overrepresentation analysis revealed enrichment of genes with multiple immune functions including cell activation, proliferation, chemotaxis, and cytotoxicity of lymphocytes. In conclusion, WC1.1+γδ T cells have been proposed as major regulatory cell subset in cattle, and we provide evidence for preferential differential activation of this specific subset in cattle naturally infected withM. bovis.
isGWAS: ultra-high-throughput, scalable and equitable inference of genetic associations with disease
Authors: Foley Christopher N , Kuncheva Zhana , Marioni Riccardo E. , Runz Heiko , Sun Benjamin B
Published: July 2023

Genome-wide association studies (GWAS) have proven a powerful tool for human geneticists to generate biological insights or hypotheses for drug discovery. Nevertheless, a dependency on sensitive individual-level data together with ever-increasing cohort sample sizes, numbers of variants and phenotypes studied put a strain on existing algorithms, limiting the GWAS approach from maximising potential. Here we present in-silico GWAS (isGWAS), a uniquely scalable algorithm to infer regression parameters in case-control GWAS from cohort-level summary data. For any sample size, isGWAS computes a variant-disease association parameter in ∼1 millisecond, or ∼11m variants in UK-Biobank within ∼4 minutes (∼1500-fold faster than state-of-the-art). Extensive simulations and empirical tests demonstrate that isGWAS results are highly comparable to traditional regression-based approaches. We further introduce a heuristic re-sampling algorithm, leapfrog re-sampler (LRS), to extrapolate association results to semi-virtually enlarged cohorts. Owing to significant computational gains we anticipate a broad use of isGWAS and LRS which are customizable on a web interface.
Exuberantde novodendritic spine growth in mature neurons
Authors: Krüssel Sarah , Deb Ishana , Son Seungkyu , Ewall Gabrielle , Chang Minhyeok , Lee Hey-Kyoung , Heo Won do , Kwon Hyung-Bae
Published: July 2023

Dendritic spines are structural correlates of excitatory synapses maintaining stable synaptic communications. However, this strong spine-synapse relationship was mainly characterized in excitatory pyramidal neurons (PyNs), raising a possibility that inferring synaptic density from dendritic spine number may not be universally applied to all neuronal types. Here we found that the ectopic expression of H-Ras increased dendritic spine numbers regardless of cortical cell types such as layer 2/3 pyramidal neurons (PyNs), parvalbumin (PV)- and vasoactive intestinal peptide (VIP)-positive interneurons (INs) in the primary motor cortex (M1). The probability of detecting dendritic spines was positively correlated with the magnitude of H-Ras activity, suggesting elevated local H-Ras activity is involved in the process of dendritic spine formation. H-Ras overexpression caused high spine turnover rate via adding more spines rather than eliminating them. Two-photon photolysis of glutamate triggeredde novodendritic spine formation in mature neurons, suggesting H-Ras induced spine formation is not restricted to the early development. In PyNs and PV-INs, but not VIP-INs, we observed a shift in average spine neck length towards longer filopodia-like phenotypes. The portion of dendritic spines lacking key excitatory synaptic proteins were significantly increased in H-Ras transfected neurons, suggesting that these increased spines have other distinct functions. High spine density caused by H-Ras did not result in change in the frequency or the amplitude of miniature excitatory postsynaptic currents (mEPSCs). Thus, our results propose that dendritic spines possess more multifaceted functions beyond the morphological proxy of excitatory synapse.
Hummingbirds use wing inertial effects to improve maneuverability
Authors: Haque Mohammad Nasirul , Cheng Bo , Tobalske Bret W. , Luo Haoxiang
Published: July 2023

Hummingbirds outperform other birds in terms of aerial agility at low flight speeds. To reveal the key mechanisms that enable such unparalleled agility, we reconstructed body and wing motion of hummingbird escape maneuvers from high-speed videos; then, we performed computational fluid dynamics modeling and flight mechanics analysis, in which each wingbeat was resolved. We found that the birds utilized the inertia of their wings to achieve peak body rotational acceleration within half a wingbeat before the aerodynamic forces became dominant. The aerodynamic forces instead counteracted the reversed inertial forces in the other half wingbeat, thereby to sustain body rotation, albeit at a lower acceleration. Thus, individual wingbeat cycles that generated body rotations can be split into an agility phase with rapid inertial acceleration, and a stability phase with counteracting aerodynamic and inertial acceleration. This mechanism involving inertial steering enables hummingbirds to generate instantaneous body acceleration at any phase of a wingbeat, and it is likely the key to understanding the unique dexterity distinguishing them from aircraft that solely rely on aerodynamics for maneuvering.
Western diet consumption impairs memory function via dysregulated hippocampus acetylcholine signaling
Authors: Hayes Anna M. R. , Lauer Logan Tierno , Kao Alicia E. , Sun Shan , Klug Molly E. , Tsan Linda , Rea Jessica J. , Subramanian Keshav S. , Gu Cindy , Tanios Natalie , Ahuja Arun , Donohue Kristen N. , Décarie-Spain Léa , Fodor Anthony A. , Kanoski Scott E.
Published: July 2023

Western diet (WD) consumption during development yields long-lasting memory impairments, yet the underlying neurobiological mechanisms remain elusive. Here we developed an early life WD rodent model to evaluate whether dysregulated hippocampus (HPC) acetylcholine (ACh) signaling, a pathology associated with memory impairment in human dementia, is causally-related to WD-induced cognitive impairment. Rats received a cafeteria-style WD (access to various high-fat/high-sugar foods; CAF) or healthy chow (CTL) during the juvenile and adolescent periods (postnatal days 26-56). Behavioral, metabolic, and microbiome assessments were performed both before and after a 30-day healthy diet intervention beginning at early adulthood. Results revealed CAF-induced HPC-dependent contextual episodic memory impairments that persisted despite healthy diet intervention, whereas CAF was not associated with long-term changes in body weight, body composition, glucose tolerance, anxiety-like behavior, or gut microbiome. HPC immunoblot analyses after the healthy diet intervention identified reduced levels of vesicular ACh transporter in CAF vs. CTL rats, indicative of chronically reduced HPC ACh tone. To determine whether these changes were functionally related to memory impairments, we evaluated temporal HPC ACh binding via ACh-sensing fluorescent reporterin vivofiber photometry during memory testing, as well as whether the memory impairments could be rescued pharmacologically. Results revealed dynamic HPC ACh binding during object-contextual novelty recognition was highly predictive of memory performance and was disrupted in CAF vs. CTL rats. Further, HPC alpha-7 nicotinic receptor agonist infusion during consolidation rescued memory deficits in CAF rats. Overall, these findings identify dysregulated HPC ACh signaling as a mechanism underlying early life WD-associated memory impairments.
Injectable microcapillary network hydrogels engineered by liquid-liquid phase separation for stem cell transplantation
Authors: Nishiguchi Akihiro , Ito Shima , Nagasaka Kazuhiro , Komatsu Hiyori , Uto Koichiro , Taguchi Tetsushi
Published: July 2023

Injectable hydrogels are promising carriers for cell delivery in regenerative medicine. However, injectable hydrogels composed of crosslinked polymer networks are often non porous and prevent biological communication with host tissues through signals, nutrients, oxygen, and cells, thereby limiting graft survival and tissue integration. Here we report injectable hydrogels with liquid-liquid phase separation-induced microcapillary networks (µCN) as stem cell-delivering scaffolds. The molecular modification of gelatin with hydrogen bonding moieties induced liquid-liquid phase separation when mixed with unmodified gelatin to form µCN structures in the hydrogels. Through spatiotemporally controlled covalent crosslinking and dissolution processes, porous µCN structures were formed in the hydrogels, which can enhance mass transport and cellular activity. The encapsulation of cells with injectable µCN hydrogels improved cellular adhesion, spreading, migration, and proliferation. Transplantation of mesenchymal stem cells with injectable µCN hydrogels enhanced graft survival and recovered hindlimb ischemia by enhancing material-tissue communication with biological signals and cells through µCN. This facile approach may serve as an advanced scaffold for improving stem cell transplantation therapies in regenerative medicine.
CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry
Authors: Huang Jingjing , Staes An , Impens Francis , Demichev Vadim , Van Breusegem Frank , Gevaert Kris , Willems Patrick
Published: July 2023

Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA within silicopredicted spectral libraries, we quantified an average of 18% cysteine oxidation inArabidopsis thalianaby DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.
Ion selectivity and activation mechanism for kalium channelrhodopsins
Authors: Zhang Mingfeng , Shan Yuanyue , Zhao Liping , Li Xiao , Pei Duanqing
Published: July 2023

Channelrhodopsins harvest the light and convert photons to the cellular ion flow. The ion selectivity and activation mechanism at the atomic level remains unknown. Here we describe cryo-EM structures forH. catenoideskalium channelrhodopsin (HcKCR1), its paralog, sodium selective channelrhodopsin (HcCCR), an open state ofHcKCR1 (C110T), the voltage-dependent inwardly rectifier (D116N) and higher potassium selective channelrhodopsin (B1ChR2) fromBilabrum sp, illuminating the ion selectivity and activation mechanism. Briefly, the hourglass shaped lumen is occupied by the stepwise dehydrated potassium in both intracellular and extracellular side. The aromatic amino acids likely function as partial dehydrated potassium filter in the extracellular lumen, and intracellular dehydrated ion occupying layer chooses the right size of dehydrated ion, thus specifying ion selectivity and the higher dehydration capacity, the higher potassium selectivity. Furthermore, structural comparison ofHcKCR1 and C110T suggested that the conformational changes of retinal triggers the extracellular side of TM6 extension as well as the retinal interaction residues motion, which then leads to ion flow. Our results not only uncovered the ion selectivity mechanism of potassium or sodium selective channelrhodopsins, but also elucidated their activation mechanism. It may provide a framework for designing next generation optogenetic tools.
The dynamics and geometry of choice in premotor cortex
Authors: Genkin Mikhail , Shenoy Krishna V. , Chandrasekaran Chandramouli , Engel Tatiana A.
Published: July 2023

The brain represents sensory variables in the coordinated activity of neural populations, in which tuning curves of single neurons define the geometry of the population code. Whether the same coding principle holds for dynamic cognitive variables remains unknown because internal cognitive processes unfold with a unique time course on single trials observed only in the irregular spiking of heterogeneous neural populations. Here we show the existence of such a population code for the dynamics of choice formation in the primate premotor cortex. We developed an approach to simultaneously infer population dynamics and tuning functions of single neurons to the population state. Applied to spike data recorded during decision-making, our model revealed that populations of neurons encoded the same dynamic variable predicting choices, and heterogeneous firing rates resulted from the diverse tuning of single neurons to this decision variable. The inferred dynamics indicated an attractor mechanism for decision computation. Our results reveal a common geometric principle for neural encoding of sensory and dynamic cognitive variables.
PIEZO1 force sensing controls global lipid homeostasis
Authors: Lichtenstein Laeticia , Cheng Chew W , Evans Elizabeth L , Gaunt Hannah J , Bartoli Fiona , Chuntharpursat-Bon Eulashini , Patel Shaili , Konstantinou Charalampos , Futers T Simon , Reay Melanie , Parsonage Gregory , Bertrand-Michel Justine , Sukumar Piruthivi , Roberts Lee D , Beech David J
Published: July 2023

How cardiovascular activity beneficially regulates lipid homeostasis is unclear. Here we hypothesise a mechanism in which mechanical force sensed by PIEZO1 ion channels in endothelium links blood flow to lipid regulation. We engineered mice for conditional deletion of PIEZO1 in endothelium and determined consequences for lipid regulation. Prominent are upregulated expression of hepaticCyp7a1and intestinalLdlrgenes, which are pivotal in cholesterol catabolism and excretion. Consistent with such regulation is endothelial PIEZO1-dependence of hepatic, intestinal and whole body cholesterol and bile homeostasis. There is organ perfusion-dependent gene regulation via endothelial PIEZO1 and downstream nitric oxide synthase. Endothelial PIEZO1-deleted mice are protected against hyperlipidaemia and ectopic fat deposition. HumanPIEZO1gene variants and a recapitulated humanPIEZO1gain-of-function variant in mice associate with dyslipidaemia. The data suggest lipid-promoting effects of endothelial force sensing and new opportunity for understanding and addressing problems of hyperlipidaemia.
Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model
Authors: Selvakumar Pavitra , Siddharthan Rahul
Published: July 2023

Transcription factor binding sites (TFBS), like other DNA sequence, evolve via mutation and selection relating to their function. Models of nucleotide evolution describe DNA evolution via single-nucleotide mutation. A stationary vector of such a model is the long-term distribution of nucleotides, unchanging under the model. Neutrally evolving sites may have uniform stationary vectors, but one expects that sites within a TFBS instead have stationary vectors reflective of the fitness of various nucleotides at those positions. We introduce “position-specific stationary vectors” (PSSVs), the collection of stationary vectors at each site in a TFBS locus, analogous to the position weight matrix (PWM) commonly used to describe TFBS. We infer PSSVs for human TFs using two evolutionary models (Felsenstein 1981 and Hasegawa-Kishino-Yano 1985). We find that PSSVs reflect the nucleotide distribution from PWMs, but with reduced specificity. We infer ancestral nucleotide distributions at individual positions and calculate “conditional PSSVs” conditioned on specific choices of majority ancestral nucleotide. We find that certain ancestral nucleotides exert a strong evolutionary pressure on neighbouring sequence while others have a negligible effect. Finally, we present a fast likelihood calculation for the F81 model on moderate-sized trees that makes this approach feasible for large-scale studies along these lines.
Repeated Caffeine Intake Suppresses Cerebral Grey Matter Responses to Chronic Sleep Restriction in an A1Adenosine Receptor-Dependent Manner
Authors: Lin Yu-Shiuan , Lange Denise , Baur Diego , Foerges Anna , Chu Congying , Li Changhong , Elmenhorst Eva-Maria , Neumaier Bernd , Bauer Andreas , Aeschbach Daniel , Landolt Hans-Peter , Elmenhorst David
Published: July 2023

Evidence has shown that both sleep loss and daily caffeine intake can induce changes in grey matter (GM). Caffeine is frequently used to combat sleepiness and impaired performance caused by insufficient sleep. It is unclear 1) whetherdailyuse of caffeine could prevent or exacerbate the GM alterations induced bychronicsleep restriction, and 2) whether the potential impact on GM plasticity depends on individual differences in the availability of adenosine receptors, which are involved in mediating effects of caffeine on sleep and waking function. In this double-blind, randomized, controlled study, 36 healthy adults (aged 28.9 ± 5.2 y/o; 15 females; habitual daily caffeine intake < 450 mg; 29 homozygous C/C allele carriers of the A2A adenosine receptor (A2AR) gene variant rs5751876 ofADORA2A) underwent a 9-day laboratory visit consisting of one adaption day, 2 baseline days (BL), 5-day sleep restriction (CSR, 5 h time-in-bed), and a recovery day (REC) after an 8-h sleep opportunity. Nineteen participants received 300 mg caffeine in coffee through the 5 days of CSR (CAFF group), while 17 matched participants received decaffeinated coffee (DECAF group). We measured the GM morphology on the 2ndBL Day, 5thCSR Day, and REC Day. Moreover, we used [18F]-CPFPX PET to quantify the baseline availability of A1adenosine receptors (A1R) and their relation to GM plasticity. The voxel-wise multimodal whole-brain analysis on T1-weighted images controlled for variances of cerebral blood flow indicated a significant interaction between caffeine and CSR in four brain regions: 1) right temporal-occipital region, 2) right thalamus, 3) left dorsolateral, and 4) dorsomedial prefrontal region. The post-hoc analyses indicated increased GM intensity in the DECAF group in all four regions but decreased GM in the thalamus as well as dorsolateral and dorsomedial prefrontal regions in the CAFF group after sleep restriction. Furthermore, lower baseline subcortical A1R availability predicted larger reduction in the CAFF group after CSR of all brain regions except for the caffeine-associated thalamic reduction. In conclusion, our data suggest an adaptive upregulation in GM after 5-day CSR, while concomitant use of caffeine instead leads to a GM reduction. The lack of consistent association with individual A1R availability may suggest that CSR and caffeine affect GM plasticity predominantly by a different mechanism. Future studies on the role of adenosine A2Areceptors (ADORA2A) in CSR-induced GM plasticity are warranted.
Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes
Authors: Khoo Amanda , Govindarajan Meinusha , Qiu Zhuyu , Liu Lydia Y. , Ignatchenko Vladimir , Waas Matthew , Macklin Andrew , Keszei Alexander , Main Brian P. , Yang Lifang , Lance Raymond S. , Downes Michelle R. , Semmes O. John , Vesprini Danny , Liu Stanley K. , Nyalwidhe Julius O. , Boutros Paul C. , Kislinger Thomas
Published: July 2023

Urine is a complex biofluid that reflects both overall physiologic state and the state of the genitourinary tissues through which it passes. It contains both secreted proteins and proteins encapsulated in tissue-derived extracellular vesicles (EVs). To understand the population variability and clinical utility of urine, we quantified the secreted and EV proteomes from 190 men, including a subset with prostate cancer. We demonstrate that a simple protocol enriches prostatic proteins in urine. Secreted and EV proteins arise from different subcellular compartments. Urinary EVs are faithful surrogates of tissue proteomes, but secreted proteins in urine or cell line EVs are not. The urinary proteome is longitudinally stable over several years. It can accurately and non-invasively distinguish malignant from benign prostatic lesions, and can risk-stratify prostate tumors. This resource quantifies the complexity of the urinary proteome, and reveals the synergistic value of secreted and EV proteomes for translational and biomarker studies.
O-GlcNAcylation of Keratin 18 coordinates TCA cycle to promote cholangiocarcinoma progression
Authors: Meng Xiangfeng , Zhou Yue , Xu Lei , Wang Changjiang , Tian Xiao , Zhang Xiang , Hao Yi , Cheng Bo , Wang Lei , Liu Jialin , Xie Ran
Published: July 2023

Glycosylation in human cholangiocarcinoma (CCA) actively contributes to pathophysiological steps of tumor progression. Of note is the dynamic modification of proteins byO-linked β-N-acetyl-glucosamine (O-GlcNAcylation) that modulates various tumor-associated biological activities. By using a cutting-edge chemical proteomic methodology for intact glycopeptide analysis, we show herein thatO-GlcNAcylation of Keratin 18 (K18) coordinates the tricarboxylic acid (TCA) cycle enzymes, namely isocitrate dehydrogenases (IDHs), to promote CCA progression. Mechanistically, site-specificO-GlcNAcylation of K18 on Ser 30 stabilizes K18, which benefits the expression of cell cycle checkpoints to enhance cell cycle progression and cell growth. Interaction with IDHs down-regulates the level of citrate and isocitrate, while up-regulates the level of α-ketoglutarate (α-KG). Our study thus expands the current understanding of proteinO-GlcNAcylation, and adds another dimension of complexity to post-translational control over metabolism and tumorigenesis.
Genetic characterization and dissemination ofStaphylococcus aureusand Staphylococci genus: food and health perspective
Authors: Alkuraythi Dalal M. , Alkhulaifi Manal M. , Binjomah Abdulwahab Z. , Alarawi Mohammed , Aldakhil Hind M , Mujallad Mohammed I. , Alharbi Saleh Ali , Alshomrani Mohammed , Alshahrani Saeed Mastour , Gojobori Takashi , Alajel Sluiman M
Published: July 2023

Hospitals and communities are significant hubs for antibiotic-resistant staphylococcal infections, but recently there have been spread of the Staphylococci to other settings including farms and food chains. This study aimed to compare the methicillin-resistantStaphylococcus aureus(MRSA) isolates from humans and food to understand the genetic characteristics and similarities between the circulating clones across both groups. A total of 250 samples of meat (camel, beef, chicken, fish, and lamb) were collected from different retailers in Riyadh, Saudi Arabia. Culture, and Genomics analysis of the isolates yielded 53S.aureusout of which (42/53; 79%) were methicillin-sensitiveS.aureus(MSSA) and (11/53; 21%) were MRSA in addition to to other Staphylococci. 80 clinically confirmed MRSA isolates were obtained from patients in the same city. The most commonS. aureusclone in patients and retail meat belonged to clonal complex (CC5). In meat, ST6 and ST97 were the most common clones found in (6/11; 54.5%) of MRSA isolates, and ST1153 (9/42; 21.42%), ST672 (7/42; 16.66%) of MSSA isolates. The majority of MRSA isolates in meat carried SCCmectype V, which was observed in (6/11; 54.54%) of isolates. While in patients, ST5 and ST6 were the predominant clones found in (37/80; 46%) of MRSA isolates. The most prevalent SCCmectypes in MRSA isolates from patients were SCCmectype IVa, which was observed in (39/80; 48.7%) of isolates. While there was no MRSA found in beef, camel meat had the highest prevalence of MRSA ST6-t2450 contamination. The other two clones, CC97 and CC361, were the second-most prevalent clones in meat and were relatively common among patients. NovelS. aureuslineages were sequenced and characterized for the first time ST8109 from meat and ST8110 and ST8111 from patients. A structured One Health approach onS. aureusconsidering its dissemination, genetic characterization, antibiotic resistance, and overall impact on food intended for human consumption and its effect on human health is advised.