bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced Recovery After Cesarean from the Patient Perspective: A Prospective Study of the ERAC Questionnaire (ERAC-Q)
Authors: Meyer Jessica A , Alton Suzanne , Seung Hyunuk , Pahlavan Autusa , Trilling Ariel R , Coghlan Martha , Goetzinger Katherine R , Cojocaru Liviu
Published: June 2023

OBJECTIVE

To evaluate the impact of an Enhanced Recovery After Cesarean (ERAC) protocol on the post-cesarean recovery experience using a validated ten-item questionnaire (ERAC-Q).

METHODS

This is a prospective cohort study of patients completing ERAC quality-of-life questionnaires (ERAC-Q) during inpatient recovery after cesarean delivery (CD) between October 2019 and September 2020, before and after the implementation of our ERAC protocol. Patients with non-Pfannenstiel incision, ICU admission, massive transfusion, bowel injury, existing chronic pain disorders, acute postpartum depression, or neonatal demise were excluded. The ERAC-Q was administered on postoperative day one and day of discharge to the pre– and post-ERAC implementation cohorts, rating aspects of their recovery experience on a scale of 0 (best) to 10 (worst). The primary outcome was ERAC-Q scores. Statistical analysis was performed with SAS software.

RESULTS

There were 196 and 112 patients in the pre– and post-ERAC cohorts, respectively. The post-ERAC group reported significantly lower total ERAC-Q scores compared to the pre-ERAC group, reflecting fewer adverse symptoms and greater perceived recovery on postoperative day one (1.6 [0.7, 2.8] vs. 2.7 [1.6, 4.3]) and day of discharge (0.8 [0.3, 1.5] vs. 1.4 [0.7, 2.2]) (p<0.001). ERAC-Q responses did not predict the time to achieve objective postoperative milestones. However, worse ERAC-Q pain and total scores were associated with higher inpatient opiate use.

CONCLUSIONS

ERAC implementation positively impacts patient recovery experience. The administration of ERAC-Q can provide real-time feedback on patient-perceived recovery quality and how healthcare protocol changes may impact their experience.
A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object
Authors: Niehues Anna , de Visser Casper , Hagenbeek Fiona A. , Kulkarni Purva , Pool Rene , Karu Naama , Kindt Alida S. D. , Singh Gurnoor , Vermeiren Robert R. J. M. , Boomsma Dorret I. , van Dongen Jenny , 't Hoen Peter A. C. , van Gool Alain J.
Published: June 2023

Background. Applying good data management and FAIR data principles (Findable, Accessible, Interoperable, and Reusable) in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines. Practical examples can help promote the adoption of FAIR practices for computational workflows in the research community. We developed a multi-omics data analysis workflow implementing FAIR practices to share it as a FAIR Digital Object. Findings. We conducted a case study investigating shared patterns between multi-omics data and childhood externalizing behavior. The analysis workflow was implemented as a modular pipeline in the workflow manager Nextflow, including containers with software dependencies. We adhered to software development practices like version control, documentation, and licensing. Finally, the workflow was described with rich semantic metadata, packaged as a Research Object Crate, and shared via WorkflowHub. Conclusions. Along with the packaged multi-omics data analysis workflow, we share our experiences adopting various FAIR practices and creating a FAIR Digital Object. We hope our experiences can help other researchers who develop omics data analysis workflows to turn FAIR principles into practice.
Discrete projections from MCH neurons mediate anti-parkinsonian effects of acupuncture
Authors: Oh Ju-Young , Lee Hyowon , Jang Sun-Young , Kim Hyunjin , Park Geunhong , Serikov Almas , Jang Jae-Hwan , Kim Junyeop , Yang Seulkee , Sa Moonsun , Lee Sung Eun , Han Young-Eun , Hwang Tae-Yeon , Kim Hee Young , Lee Seung Eun , Oh Soo-Jin , Kim Jeongjin , Kim Jongpil , Lee C. Justin , Nam Min-Ho , Park Hi-Joon
Published: June 2023

Parkinson’s disease (PD) presents with typical motor dysfunction and non-motor symptoms, including memory loss. Although acupuncture is suggested as an alternative therapy for PD, its neuroanatomical mechanisms remain unclear. We demonstrate that acupuncture ameliorates both motor and memory deficits in PD mice through activation of melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus and zona incerta (LH/ZI)—MCHLH/ZI— via nerve conduction. We identify two distinct subpopulations of MCHLH/ZIprojecting to the substantia nigra and hippocampus, each of which is responsible for controlling motor and memory function. This effect can be attributed to MCH-mediated recovery from dopaminergic neurodegeneration, reactive gliosis, and impaired hippocampal synaptic plasticity. Collectively, MCHLH/ZIconstitutes not only the neuroanatomical basis of acupuncture but also a potential cellular target for treating both motor and non-motor PD symptoms.

One-Sentence Summary

Acupuncture alleviates both motor and non-motor symptoms in Parkinson’s disease by activating two distinct MCH projections.
CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
Authors: Koci Orges , Russell Richard K. , Shaikh M. Guftar , Edwards Christine , Gerasimidis Konstantinos , Ijaz Umer Zeeshan
Published: June 2023

We have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The software provides a single platform to give statistical inference, and employs algorithms, some borrowed from numerical ecology literature to allow exploratory as well as hypothesis driven analyses. The end product is a highly interactive toolkit with multiple document interface, that makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant hypotheses. As a proof-of-concept, we have used CViewer to explore two distinct metagenomics datasets: a dietary intervention study to understand Crohn’s disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean.
Cross-reactivity of antibodies against T cell markers in the Bank vole (Myodes glareolus)
Authors: Magdalena Migalska , Kazimierz Weglarczyk , Renata Mezyk-Kopec , Katarzyna Baliga-Klimczyk , Joanna Homa
Published: June 2023

The bank vole is a common Cricetidae rodent that is a reservoir of several zoonotic pathogens and an emerging model in eco-immunology. Here, we add to a developing immunological toolkit for this species by testing the cross-reactivity of commercially available monoclonal antibodies (mAbs) to the bank vole lymphocyte differentiation molecules and a transcription factor. We show that a combination of mAbs against CD4, CD3, and Foxp3 allows flow cytometric distinction of the main subsets of T cells: putative helper CD4+, cytotoxic CD8+ (as CD3+CD4-) and regulatory CD4+Foxp3+. We also provide a comparative analysis of amino acid sequences of CD4, CD8αβ, CD3εγδ and Fopx3 molecules for a number of commonly studied Cricetidae rodents and discuss mAb cross-reactivity patterns reported so far in this rodent family.
METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OFPNEUMOCYSTISGROWTH MEDIUM
Authors: Nev Olga A. , Zamaraeva Elena , De Oliveira Romain , Duvenage Lucian , Abou-Jaoudé Wassim , Ouattara Djomangan Adama , Hoving Jennifer Claire , Gudelj Ivana , Brown Alistair J. P.
Published: June 2023

Establishing suitablein vitroculture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, includingPneumocystis jirovecii, remain unculturable, hampering research efforts.P. jiroveciiis a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact ofPneumocystison human health, we remain ignorant about the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organismin vitro. We present a comprehensivein silicogenome-scale metabolic model ofPneumocystisgrowth and metabolism, with a view to identifying metabolic requirements and imbalances that hinder growthin vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of thePneumocystisgrowth medium. Our findings offer insights into the biology ofPneumocystisand provide a novel strategy to overcome the longstanding challenge of culturing this pathogenin vitro.
Enteric glial hub cells coordinate intestinal motility
Authors: Scavuzzo Marissa A. , Letai Katherine C. , Maeno-Hikichi Yuka , Wulftange William J. , Shah Isha K. , Rameshbabu Jeyashri S. , Tomar Alka , Shick H. Elizabeth , Shah Aakash K. , Xiong Ying , Cohn Erin F. , Allan Kevin C. , Tesar Paul J.
Published: June 2023

Enteric glia are the predominant cell type in the enteric nervous system yet their identities and roles in gastrointestinal function are not well classified. Using our optimized single nucleus RNA-sequencing method, we identified distinct molecular classes of enteric glia and defined their morphological and spatial diversity. Our findings revealed a functionally specialized biosensor subtype of enteric glia that we call “hub cells.” Deletion of the mechanosensory ion channel PIEZO2 from adult enteric glial hub cells, but not other subtypes of enteric glia, led to defects in intestinal motility and gastric emptying in mice. These results provide insight into the multifaceted functions of different enteric glial cell subtypes in gut health and emphasize that therapies targeting enteric glia could advance the treatment of gastrointestinal diseases.
Modelling protein complexes with crosslinking mass spectrometry and deep learning
Authors: Stahl Kolja , Demann Lorenz , Bremenkamp Rica , Warneke Robert , Hormes Björn , Stülke Jörg , Brock Oliver , Rappsilber Juri
Published: June 2023

Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrated experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially improves modelling performance on challenging targets, by helping to identify interfaces, focusing sampling, and improving model selection. This extends to single crosslinks from whole-cell crosslinking MS, opening the possibility of whole-cell structural investigations driven by experimental data. We demonstrate this by revealing the molecular basis of iron homeostasis inBacillus subtilis.
Intraspecific encounters can induce home-range shifts
Authors: Fagan William F. , Krishnan Ananke , Liao Qianru , Fleming Christen H. , Liao Daisy , Lamb Clayton , Patterson Brent , Wheeldon Tyler , Martinez-Garcia Ricardo , Menezes Jorge F. S. , Noonan Michael J. , Gurarie Eliezer , Calabrese Justin M.
Published: June 2023

Direct encounters, in which two or more individuals are physically close to one another, are a topic of increasing interest as more and better movement data become available. Recent progress, including the development of statistical tools for estimating robust measures of changes in animals’ space use over time, facilitates opportunities to link direct encounters between individuals with the long-term consequences of those encounters. Working with movement data for coyotes (Canis latrans) and grizzly bears (Ursus arctos horribilis), we investigate whether close intraspecific encounters were associated with spatial shifts in the animals’ range distributions, as might be expected if one or both of the individuals involved in an encounter were seeking to reduce or avoid conflict over space. We analyze the movement data of a pair of coyotes in detail, identifying how a shift in home range location resulting from altered movement behavior was apparently a consequence of a close intraspecific encounter. With grizzly bear movement data, we approach the problem from the perspective of a set of encounter pairs within a population. We find support for the hypotheses that 1) close intraspecific encounters between bears are, on average, associated with subsequent shifts in range distributions and 2) encounters defined at finer spatial scales are followed by greater changes in space use. Our results suggest that animals can undertake long-term, large-scale spatial shifts in response to close intraspecific encounters that have the potential for conflict. These results lend support for existing theory on the evolution of territories and space use (e.g., Maynard-Smith’s bourgeois strategy regarding low-conflict coexistence). Overall, we find that analyses of movement data in a pairwise context can 1) identify distances at which individuals’ proximity to one another may alter behavior and 2) facilitate testing of population-level hypotheses concerning the potential for direct encounters to alter individuals’ space use.

Open Research Statement

Movement data for the coyotes and grizzly bears are posted onMovebank.orgas datasets 1614661371 and 1044288582, respectively. Statistical tools for estimating, manipulating, and comparing home ranges from movement data are implemented in the open-source R packagectmm. R scripts used to carry out specific analyses for this study are openly available on GitHub athttps://github.com/anagkrish/encounter_homerangeshift.
Sleep disruption precedes forebrain synaptic Tau burden and contributes to cognitive decline in a sex-dependent manner in the P301S Tau transgenic mouse model
Authors: Martin Shenee C. , Joyce Kathryn K. , Harper Kathryn M. , Nikolova Viktoriya D. , Cohen Todd J. , Moy Sheryl S. , Diering Graham H.
Published: June 2023

Background

Sleep is an essential process that supports brain health and cognitive function in part through the modification of neuronal synapses. Sleep disruption, and impaired synaptic processes, are common features in neurodegenerative diseases, including Alzheimer’s disease (AD). However, the casual role of sleep disruption in disease progression is not clear. Neurofibrillary tangles, made from hyperphosphorylated and aggregated Tau protein, form one of the major hallmark pathologies seen in AD and contribute to cognitive decline, synapse loss and neuronal death.

Tau has been shown to aggregate in synapses which may impair restorative synapse processes occurring during sleep. However, it remains unclear how sleep disruption and synaptic Tau pathology interact to drive cognitive decline. It is also unclear whether the sexes show differential vulnerability to the effects of sleep loss in the context of neurodegeneration.

Methods

We used a piezoelectric home-cage monitoring system to measure sleep behavior in 3-11month-old transgenic hTau P301S Tauopathy model mice (PS19) and littermate controls of both sexes. Subcellular fractionation and Western blot was used to examine Tau pathology in mouse forebrain synapse fractions. To examine the role of sleep disruption in disease progression, mice were exposed to acute or chronic sleep disruption. The Morris water maze test was used to measure spatial learning and memory performance.

Results

PS19 mice exhibited a selective loss of sleep during the dark phase, referred to as hyperarousal, as an early symptom with an onset of 3months in females and 6months in males. At 6months, forebrain synaptic Tau burden did not correlate with sleep measures and was not affected by acute or chronic sleep disruption. Chronic sleep disruption accelerated the onset of decline of hippocampal spatial memory in PS19 males, but not females.

Conclusions

Dark phase hyperarousal is an early symptom in PS19 mice that precedes robust Tau aggregation. We find no evidence that sleep disruption is a direct driver of Tau pathology in the forebrain synapse. However, sleep disruption synergized with Tau pathology to accelerate the onset of cognitive decline in males. Despite the finding that hyperarousal appears earlier in females, female cognition was resilient to the effects of sleep disruption.
Successful placentation in human pregnancy is regulated by reciprocal interactions between maternal uterine NK cells and fetal placental trophoblast
Authors: Li Qian , Sharkey Andrew , Sheridan Megan , Magistrati Elisa , Arutyunyan Anna , Huhn Oisin , Sancho-Serra Carmen , Anderson Holly , McGovern Naomi , Esposito Laura , Fernando Ridma , Gardner Lucy , Vento-Tormo Roser , Turco Margherita Yayoi , Moffett Ashley
Published: June 2023

Fetal growth and development during human pregnancy depends on delivery of adequate maternal oxygen and nutrients to the fetus via the placenta. In humans, the balanced invasion of fetal placental trophoblast cells into the maternal uterine lining, where they interact with uterine natural killer cells (uNK), is thought to be critical for a successful pregnancy but exactly how this influences reproductive outcomes remains undefined. Here, we used our trophoblast organoid model and primary tissue samples to determine how uNK affect placentation. By locating potential interaction axes between primary trophoblast cells and uNK using single cell transcriptomics, andin vitromodelling of these interactions in trophoblast organoids, we identify a uNK-derived cytokine signal that promotes trophoblast differentiation by enhancing epithelial-mesenchymal transition and increasing trophoblast cells at the late stage of the invasive pathway. Moreover, it affects transcriptional programs involved in increasing blood flow, placental access to nutrients, and dampening inflammatory and adaptive immune responses, as well as gene signatures associated with disorders of pregnancy such as pre-eclampsia. Our findings shed new light on how optimal immunological interactions between maternal uNK cells and fetal trophoblast enhance reproductive success.
RETROFIT: REFERENCE-FREE DECONVOLUTION OF CELL-TYPE MIXTURES IN SPATIAL TRANSCRIPTOMICS
Authors: Singh Roopali , He Xi , Park Adam Keebum , Hardison Ross Cameron , Zhu Xiang , Li Qunhua
Published: June 2023

Spatial transcriptomics (ST) profiles gene expression in intact tissues. However, ST data measured at each spatial location may represent gene expression of multiple cell types, making it difficult to identify cell-type-specific transcriptional variation across spatial contexts. Existing cell-type deconvolutions of ST data often require single-cell transcriptomic references, which can be limited by availability, completeness and platform effect of such references. We present RETROFIT, a reference-free Bayesian method that produces sparse and interpretable solutions to deconvolve cell types underlying each location independent of single-cell transcriptomic references. Results from synthetic and real ST datasets acquired by Slide-seq and Visium platforms demonstrate that RETROFIT outperforms existing reference-based and reference-free methods in estimating cell-type composition and reconstructing gene expression. Applying RETROFIT to human intestinal development ST data reveals spatiotemporal patterns of cellular composition and transcriptional specificity. RETROFIT is available athttps://bioconductor.org/packages/release/bioc/html/retrofit.html.
In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss
Authors: Vijayakumar Sarath , DiGuiseppi Joe A. , Dabestani Jila , Ryan William G. , Vielman Quevedo Rene , Li Yuju , Diers Jack , Tu Shu , Fleegel Jonathan , Nguyen Cassidy , Rhoda Lauren M. , Imami Ali Sajid , Hamoud Ali Abdul-Rizaq , Lovas Sándor , McCullumsmith Robert , Zallocchi Marisa , Zuo Jian
Published: June 2023

Noise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 – a potent inhibitor of cyclin dependent kinase 2 – produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL.

Highlights

In silico transcriptome-based drug screens identify pathways and drugs against NIHL.

EGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae.

Afatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish.

Orally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor.
Speckle rheological spectroscopy reveals wideband viscoelastic spectra of biological tissues
Authors: Leartprapun Nichaluk , Zeng Ziqian , Hajjarian Zeinab , Bossuyt Veerle , Nadkarni Seemantini K.
Published: June 2023

Mechanical transformation of tissue is not merely a symptom but a decisive driver in pathological processes. Comprising intricate network of cells, fibrillar proteins, and interstitial fluid, tissues exhibit distinct solid- (elastic) and liquid-like (viscous) behaviours that span a wide band of frequencies. Yet, characterization of wideband viscoelastic behaviour in whole tissue has not been investigated, leaving a vast knowledge gap in the higher frequency range that is linked to fundamental intracellular processes and microstructural dynamics. Here, we present wideband Speckle rHEologicAl spectRoScopy (SHEARS) to address this need. We demonstrate, for the first time, analysis of frequency-dependent elastic and viscous moduli up to the sub-MHz regime in biomimetic scaffolds and tissue specimens of blood clots, breast tumours, and bone. By capturing previously inaccessible viscoelastic behaviour across the wide frequency spectrum, our approach provides distinct and comprehensive mechanical signatures of tissues that may provide new mechanobiological insights and inform novel disease prognostication.
Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets
Authors: Koldobskiy Michael A. , Camacho Oscar , Reddy Pradeep , Izpisua Belmonte Juan Carlos , Feinberg Andrew P.
Published: June 2023

Rejuvenation of tissues in physiologically aging mice can be accomplished by long-term partial reprogramming via expression of reprogramming factors (Oct4, Sox2, Klf4 and c-Myc). To investigate the epigenetic determinants of partial reprogramming-mediated rejuvenation, we used whole genome bisulfite sequencing to carry out unbiased comprehensive profiling of DNA methylation changes in skin from mice subjected to partial reprogramming, as well as young and untreated old controls. We found a striking convergence of age- and rejuvenation-related epigenetic alterations on targets of the Polycomb repressive complex 2 (PRC2). These results are also supported by a likewise prominent enrichment of PRC2 targets in gene expression data, suggesting that PRC2 activity can modulate aging and mediate tissue rejuvenation.
Associating Transcription Factors to Single-Cell Trajectories with DREAMIT
Authors: Maulding Nathan D , Seninge Lucas , Stuart Joshua M.
Published: June 2023

Trajectory methods have enabled the organization of cells into contiguous cellular changes from their transcriptional profiles measured by single cell RNA sequencing. Few methods enable investigating the implied gene regulatory network dynamics from the cell transitions between and along trajectory branches. In particular, there remains an opportunity to develop methods that leverage the predicted “pseudotime” orderings of cells to reveal transcription factor (TF) dynamics. Here we present DREAMIT (DynamicRegulation ofExpressionAcrossModules inInferredTrajectories), a novel framework developed to detect patterns of TF activity along single-cell trajectory branches. It detects significant TF-target associations using a relational enrichment approach. Using a benchmark representing several different tissues, the method was found to have increased tissue-specific sensitivity and specificity over competing approaches. To illustrate the utility of the approach, we apply it to the analysis of a peripheral blood mononucleocyte dataset and discuss several examples of TF networks associated with monocytes and erythrocytes that reveal potential causal relationships among TFs. In summary, DREAMIT provides a useful tool for uncovering potential TF-to-target gene regulatory mechanisms associated with the cell-to-cell transitions predicted by trajectory inference methods.
Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases
Authors: Karlsson Linda , Vogel Jacob , Arvidsson Ida , Åström Kalle , Janelidze Shorena , Blennow Kaj , Palmqvist Sebastian , Stomrud Erik , Mattsson-Carlgren Niklas , Hansson Oskar
Published: June 2023

Cerebrospinal fluid (CSF) biomarkers reflect brain pathophysiology and are used extensively in translational research as well as in clinical practice for diagnosis of neurological diseases, e.g., Alzheimer’s disease (AD). However, CSF biomarker concentrations may be influenced by non-disease related mechanisms which vary between individuals, such as CSF production and clearance rates. Here we use a data-driven approach to demonstrate the existence of inter-individual variability in mean CSF protein levels. We show that these non-disease related differences cause many commonly reported CSF biomarkers to be highly correlated, thereby producing misleading results if not accounted for. To adjust for this inter-individual variability, we identified and evaluated high-performing reference proteins which improved the diagnostic accuracy of key CSF AD biomarkers. Our novel reference protein method attenuates the risk for false positive findings, and improves the sensitivity and specificity of CSF biomarkers, with broad implications for both research and clinical practice.
Subpopulations of corticotropin-releasing factor containing neurons and internal circuits in the chicken central extended amygdala
Authors: Pross Alessandra , Metwalli Alek H. , Abellán Antonio , Desfilis Ester , Medina Loreta
Published: June 2023

In mammals, the central extended amygdala is critical for regulation of the stress response. This regulation is extremely complex, involving multiple subpopulations of GABAergic neurons and complex networks of internal and external connections. Two neuron subpopulations expressing corticotropin-releasing factor (CRF), located in the central amygdala and the lateral bed nucleus of the stria terminalis (BSTL), play key roles in the long-term components of fear learning and in sustained fear responses akin to anxiety. Very little is known on the regulation of stress by the amygdala in non-mammals, hindering efforts for trying to improve animal welfare. In birds, one of the major problems relates to the high evolutionary divergence of the telencephalon, where the amygdala is located. In the present study, we aimed to investigate the presence of CRF neurons of the central extended amygdala in chicken and the local connections within this region. We found two major subpopulations of CRF cells in BSTL and the medial capsular central amygdala of chicken. Based on multiple labeling of CRF mRNA with different developmental transcription factors, all CRF neurons seem to originate within the telencephalon since they express Foxg1, and there are two subtypes with different embryonic origins that express Islet1 or Pax6. In addition, we demonstrated direct projections from Pax6 cells of the capsular central amygdala to BSTL and the oval central amygdala. We also found projections from Islet1 cells of the oval central amygdala to BSTL, which may constitute an indirect pathway for regulation of BSTL output cells. Part of these projections may be mediated by CRF cells, in agreement with expression of CRF receptors in both Ceov and BSTL. Our results show a complex organization of the central extended amygdala in chicken, and open new venues for studying how different cells and circuits regulate stress in these animals.
De novo design of aβ-helix tau protein scaffold: An oligomer-selective vaccine immunogen candidate for Alzheimer’s disease
Authors: Aina Adekunle , Hsueh Shawn C.C. , Gibbs Ebrima , Peng Xubiao , Cashman Neil R. , Plotkin Steven S.
Published: June 2023

Tau pathology is associated with many neurodegenetive disorders, including Alzheimer’s disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope343KLDFK347was scaffolded by designing aβ-helix structure that incorporated multiple instances of the 16-residue tau fragment339VKSEKLDFKDRVQSKI354. Largescale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth 𝒟 showed that the multi-epitope scaffolding approach, employed in designing theβ-helix scaffold, was predicted to better discriminate toxic tau oligomers than other “monovalent” strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of theβ-helix scaffold, along with a C-terminal stabilizingα-helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesizedβ-helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover the strength of binding of these antibodies toin vitrotau oligomers correlated with the strength of binding to theβ-helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.
Overburdened Ferroptotic Stress Impairs Tooth Morphogenesis
Authors: Wang H.S. , Wang X.F. , Huang L.Y. , Wang C.L. , Yu F.Y. , Ye L.
Published: June 2023

The role of regulated cell death (RCD) in organ development, particularly the impact of non-apoptotic cell death, remains largely uncharted. Ferroptosis, a non-apoptotic cell death pathway known for its iron dependence and lethal lipid peroxidation, is currently being rigorously investigated for its pathological functions. The balance between ferroptotic stress (iron and iron-dependent lipid peroxidation) and ferroptosis supervising pathways (anti-lipid peroxidation systems) serves as the key mechanism regulating the activation of ferroptosis. Comparing to other forms of regulated necrotic cell death (RNCD), ferroptosis is critically related to the metabolism of lipid and iron which are also important in organ development. In our study, we examined the role of ferroptosis in organogenesis using anex vivotooth germ culture model, investigating the presence and impact of ferroptotic stress on tooth germ development. Our findings revealed that ferroptotic stress increased during tooth development, while the expression of Gpx4, a crucial anti-lipid peroxidation enzyme, also escalated in dental epithelium/mesenchyme cells. The inhibition of ferroptosis was found to partially rescue erastin-impaired tooth morphogenesis. Our results suggest that while ferroptotic stress is present during tooth organogenesis, its effects are efficaciously controlled by the subsequent upregulation of Gpx4. Notably, an overabundance of ferroptotic stress, as induced by erastin, suppresses tooth morphogenesis.
A novel sorting signal for RNA packaging into small extracellular vesicles
Authors: Oka Yuma , Tanaka Kosei , Kawasaki Yuki
Published: June 2023

Extracellular vesicles (EVs) play a critical role in the transport of functional RNAs to target recipient cells in numerous physiological processes. The RNA profiles present in EVs differed significantly from those in the originating cells, suggesting selective and active loading of specific RNAs into EVs. Small EVs (sEVs) obtained by stepwise ultracentrifugation have been reported to contain non-sEV components. Analysis of sEVs separated from non-sEVs components revealed that microRNAs may not be released by sEVs. This has raised interest in other RNA types, such as mRNA, which may be functional molecules released by sEVs. However, the molecular mechanisms underlying selective loading of mRNA into sEVs remain unclear. Here, we show that the part of 3’ untranslated region (UTR) sequence ofRAB13selectively enriches RNA in sEVs and serves as an RNA signal for loading into sEVs. Our results demonstrate thatRAB13is the most enriched RNA in sEVs, and this enrichment is primarily driven by its 3’UTR sequence. These findings highlight the potential of theRAB133’UTR sequence as an RNA signal that enables the loading of target RNA into sEVs. This technology has the potential to improve EV-based drug delivery and other applications.
Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose
Authors: Hullahalli Karthik , Dailey Katherine G. , Waldor Matthew K.
Published: June 2023

To cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These bottlenecks restrict the inoculum and largely determine whether pathogen exposure results in disease. Infection bottlenecks therefore quantify the effectiveness of immune barriers. Here, using a model ofEscherichia colisystemic infection, we identify bottlenecks that tighten or widen with higher inoculum sizes, revealing that the efficacy of innate immune responses can increase or decrease with pathogen dose. We term this concept “dose scaling”. DuringE. colisystemic infection, dose scaling is tissue specific, dependent on the LPS receptor TLR4, and can be recapitulated by mimicking high doses with killed bacteria. Scaling is therefore due to sensing of pathogen molecules rather than interactions between the host and live bacteria. We propose that dose scaling quantitatively links innate immunity with infection bottlenecks and is a valuable framework for understanding how the inoculum size governs the outcome of pathogen exposure.
Prediction of Heart Disease and Survivability using Support Vector Machine and Naive Bayes Algorithm
Authors: Patel Tanvi S. , Patel Daxesh P. , Sanyal Mallika , Shrivastav Pranav S.
Published: June 2023

Purpose

In the present work, we examined the outcomes and accuracy of the Support vector machine (SVM) and the Naive Bayes algorithms on a dataset, to predict whether the patient has heart disease or not, and the patient’s survival prediction status.

Method

The machine learning procedures were developed using the clinically validated datasets with sixteen attributes from the University of California, Irvine’s Centre for Machine Learning, and Intelligent Systems. Confusion matrix was used to visualise the accuracy, recall, precision, and error of the models. Statistical analysis was done to prove the model accuracy using the receiver operating characteristic (ROC) curve and area under the curve (AUC).

Results

The proposed method of heart disease prediction using Naïve Bayes had 87 % accuracy. The accuracy for heart survivability models using SVM and Naïve Bayes were 88 % and 93 %. The model efficiency for heart survivability using ROC curve with AUC 0.93 for Naïve Bayes and AUC 0.91 for SVM.

Conclusion

Such prediction systems can help the medical sector to save energy, cost, and time by providing more efficient techniques to forecast decisions with high accuracy. This study will enable the statisticians and researchers to select more efficient and accurate machine learning algorithms to achieve better prediction of the “cardiovascular disease”.
Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind the same epitope
Authors: Spoendlin Fabian C. , Abanades Brennan , Raybould Matthew I. J. , Wong Wing Ki , Georges Guy , Deane Charlotte M.
Published: June 2023

The function of an antibody is intrinsically linked to which epitope it engages. Clonal clustering methods, based on sequence identity, are commonly used to group antibodies that will bind the same epitope. However, such methods neglect the fact that antibodies with highly diverse sequences can exhibit similar binding site geometries and engage common epitopes. In a previous study we described SPACE1, a method that structurally clustered antibodies in order to predict their epitopes. This methodology was limited by the inaccuracies and incomplete coverage of template-based modelling. It was also only benchmarked at the level of domain-consistency on one virus class. Here, we present SPACE2, which uses the latest machine learning based structure prediction technology combined with a novel clustering protocol and benchmark it on binding data that has epitope level resolution. On six diverse sets of antigen specific antibodies we demonstrate that SPACE2 accurately clusters antibodies that engage common epitopes and achieves far higher data set coverage than clonal clustering and SPACE1. Furthermore, we show that the functionally consistent structural clusters identified by SPACE2 are even more diverse in sequence, genetic lineage, and species origin than those found by SPACE1. These results reiterate that structural data improves our ability to identify antibodies that bind the same epitope, adding information to sequence-based methods, especially in data sets of antibodies from diverse sources. SPACE2 is openly available on Github (https://github.com/oxpig/SPACE2).
Enhancing the antibacterial function of probioticEscherichia coliNissle: when less is more
Authors: Bartram Emma , Asai Masanori , Gabant Philippe , Wigneshweraraj Sivaramesh
Published: June 2023

Probiotic bacteria confer multiple health benefits, including preventing the growth, colonisation, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probioticEscherichia colistrain Nissle (EcN) the ability to produce McC from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon, whilst ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in aGalleria mellonellainfection model of enterohemorrhagicE. coli, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little to none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic or diagnostic applications.

IMPORTRANCE

Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial ‘probiotic’ bacteria as chassis to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side-effects on the performance of such bacteria and thereby compromise their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic or diagnostic applications.
Using normative models pre-trained on cross-sectional data to evaluate intra-individual longitudinal changes in neuroimaging data
Authors: Rehák Bučková Barbora , Fraza Charlotte , Rehák Rastislav , Kolenič Marián , Beckmann Christian , Španiel Filip , Marquand Andre , Hlinka Jaroslav
Published: June 2023

Longitudinal neuroimaging studies offer valuable insight into intricate dynamics of brain development, ageing, and disease progression over time. However, prevailing analytical approaches rooted in our understanding of population variation are primarily tailored for cross-sectional studies. To fully harness the potential of longitudinal neuroimaging data, we have to develop and refine methodologies that are adapted to longitudinal designs, considering the complex interplay between population variation and individual dynamics.

We build on normative modelling framework, which enables the evaluation of an individual’s position compared to a population standard. We extend this framework to evaluate an individual’s longitudinalchangecompared to the longitudinal change reflected by the (population) standard dynamics. Thus, we exploit the existing normative models pre-trained on over 58,000 individuals and adapt the framework so that they can also be used in the evaluation of longitudinal studies. Specifically, we introduce a quantitative metric termed“z-diff”score, which serves as an indicator of a temporal change of an individual compared to a population standard. Notably, our framework offers advantages such as flexibility in dataset size and ease of implementation.

To illustrate our approach, we applied it to a longitudinal dataset of 98 patients diagnosed with early-stage schizophrenia who underwent MRI examinations shortly after diagnosis and one year later.

Compared to cross-sectional analyses, which showed global thinning of grey matter at the first visit, our method revealed a significant normalisation of grey matter thickness in the frontal lobe over time. Furthermore, this result was not observed when using more traditional methods of longitudinal analysis, making our approach more sensitive to temporal changes.

Overall, our framework presents a flexible and effective methodology for analysing longitudinal neuroimaging data, providing insights into the progression of a disease that would otherwise be missed when using more traditional approaches.
Structural Basis of σ54Displacement and Promoter Escape in Bacterial Transcription
Authors: Gao Forson , Ye Fuzhou , Zhang Bowen , Cronin Nora , Buck Martin , Zhang Xiaodong
Published: June 2023

Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated and in bacteria, transcription initiation is mediated by σ factors, which recruit RNA polymerase (RNAP) to the promoter DNA region and facilitate open complex formation, where double stranded DNA is opening up into a transcription bubble and template strand DNA is in position for initial RNA synthesis. During initial transcription, DNA downstream of the transcription start site is fed into the active site of RNAP, whilst the upstream promoter DNA remains tethered to the RNAP via the σ factor, resulting in a build-up of tension. In order to progress to the processive elongation state, RNAP must escape from the promoter, and displace or dissociate the σ factor. Bacteria s factors can be broadly separated into two classes with the majority belong to the s70 class, represented by the σ70that regulate housekeeping genes. σ54forms a class on its own and regulate stress response genes. Extensive studies on σ70have revealed the molecular mechanisms of σ70promoter escape while how σ54transitions from initial transcription to elongation is unknown. Here we present a series of cryo electron microscopy structures of the σ54factor with progressively longer RNA, revealing the molecular mechanism of σ54displacement and promoter escape. Our data show that the initial instability is driven by DNA scrunching, and the final displacement steps are driven by both RNA extension and DNA scrunching.
Optimisation of sample preparation from primary mouse tissue to maintain RNA integrity for methods examining translational control
Authors: Munro June , Gillen Sarah L. , Mitchell Louise , Laing Sarah , Karim Saadia A. , Rink Curtis , Waldron Joseph A. , Bushell Martin
Published: June 2023

Protein output of different mRNAs can vary by two orders of magnitude therefore it is critical to understand the processes that control gene expression that operate at the level of translation. Translatome-wide techniques such as polysome profiling and ribosome profiling are key methods for determining translations rates occurring on specific mRNAs. These techniques are now widely used in cell lines; however, they are underutilised in tissues and cancer models. Ribonuclease (RNase) expression is often found to be higher in complex primary tissues in comparison to cell lines. Methods used to preserve RNA during lysis often use denaturing conditions which needs to be avoided when requiring to maintain the interaction and position of the ribosome with the mRNA. Here we detail the cell lysis conditions that produce high quality RNA from several different tissues covering a range of endogenous RNase expression levels. We highlight the importance of RNA integrity for accurate determination of the global translation status of the cell as determined by polysome gradients and discuss key aspects to optimise for accurate assessment of the translatome from primary mouse tissue.