bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying Associations Between Child Health and Neighborhood Social Vulnerability: Does the Choice of Index Matter?
Authors: Zolotor Anna , Huang Ro W. , Bhavsar Nrupen A. , Cholera Rushina
Published: June 2023

Importance

Policymakers have increasingly utilized place-based social disadvantage indices to quantify the impacts of place on health and inform equitable resource allocation. Indices vary in design, content, and purpose but are often used interchangeably, potentially resulting in differential assignments of relative disadvantage depending on index choice.

Objective

To compare associations between three commonly used disadvantage indices (Social Vulnerability Index (SVI), Area Deprivation Index (ADI), and Child Opportunity Index (COI)) and two epidemiologically distinct child health outcomes—infant well-child check (WCC) attendance and adolescent obesity.

Design

Cross-sectional analysis of Duke University Health System electronic health record (EHR) data from January 2014 to December 2019.

Participants

Children ≤18 years of age with outpatient encounters between January 2014 and December 2019, and who were Durham County residents were eligible. WCC attendance was assessed for infants ages 0-15 months; obesity was assessed for children ages 11-17 years.

Exposures

2014 Social Vulnerability Index (SVI), 2015 Area Deprivation Index (ADI), and 2015 Child Opportunity Index (COI) 2.0.

Main Outcomes

1) Infant WCC attendance: attending less than the minimum recommended six WCCs in the first 15 months of life, and 2) Adolescent obesity: BMI ≥ the 95th percentile at both the most recent encounter and an encounter within the prior 9-36 months.

Results

Of 10175 patients in the WCC cohort, 20% (n = 2073) had less than six WCCs. Of 14961 patients in the obesity cohort, 20% (n = 2933) had obesity. All three indices were associated with both WCCs (OR for SVI 1.10, 95% CI 1.08-1.12; OR for ADI 1.10, 95% CI 1.08-1.12; OR for COI 1.12, 95% CI 1.10-1.14) and obesity (OR for SVI 1.05, 95% CI 1.04-1.08; OR for ADI 1.08, 95% CI 1.06-1.10; OR for COI 1.07, 95% CI 1.05-1.08).

Conclusions and relevance

Higher social disadvantage as defined by all three indices was similarly associated with both adolescent obesity and decreased infant WCC attendance. While the COI incorporates a broader set of child-specific variables, the SVI and ADI may often be just as suitable for pediatric research. Users should consider population and outcome characteristics when selecting an index.
Prothrombin Knockdown Protects Podocytes and Reduces Proteinuria in Glomerular Disease
Authors: Waller Amanda P. , Wolfgang Katelyn J. , Pruner Iva , Stevenson Zachary S. , Abdelghani Eman , Muralidharan Kaushik , Wilkie Tasha K. , Blissett Angela R. , Calomeni Edward P. , Vetter Tatyana A. , Brodsky Sergey V. , Smoyer William E. , Nieman Marvin T. , Kerlin Bryce A.
Published: June 2023

Chronic kidney disease (CKD) is a leading cause of death, and its progression is driven by glomerular podocyte injury and loss, manifesting as proteinuria. Proteinuria includes urinary loss of coagulation zymogens, cofactors, and inhibitors. Importantly, both CKD and proteinuria significantly increase the risk of thromboembolic disease. Prior studies demonstrated that anticoagulants reduced proteinuria in rats and that thrombin injured cultured podocytes. Herein we aimed to directly determine the influence of circulating prothrombin on glomerular pathobiology. We hypothesized that (pro)thrombin drives podocytopathy, podocytopenia, and proteinuria. Glomerular proteinuria was induced with puromycin aminonucleoside (PAN) in Wistar rats. Circulating prothrombin was either knocked down using a rat-specific antisense oligonucleotide or elevated by serial intravenous infusions of prothrombin protein, which are previously established methods to model hypo- (LoPT) and hyper-prothrombinemia (HiPT), respectively. After 10 days (peak proteinuria in this model) plasma prothrombin levels were determined, kidneys were examined for (pro)thrombin co-localization to podocytes, histology, and electron microscopy. Podocytopathy and podocytopenia were determined and proteinuria, and plasma albumin were measured. LoPT significantly reduced prothrombin colocalization to podocytes, podocytopathy, and proteinuria with improved plasma albumin. In contrast, HiPT significantly increased podocytopathy and proteinuria. Podocytopenia was significantly reduced in LoPT vs. HiPT rats. In summary, prothrombin knockdown ameliorated PAN-induced glomerular disease whereas hyper-prothrombinemia exacerbated disease. Thus, (pro)thrombin antagonism may be a viable strategy to simultaneously provide thromboprophylaxis and prevent podocytopathy-mediated CKD progression.
Sperm production and allocation in response to risk of sperm competition in the black soldier flyHermetia illucens
Authors: Manas Frédéric , Labrousse Carole , Bressac Christophe
Published: June 2023

In polyandrous species, competition between males for offspring paternity goes on after copulation through the competition of their ejaculates for the fertilisation of female’s oocytes. Given that males allocating more spermatozoa are favored, different models of sperm competition predict adaptive plasticity in male sperm production and allocation. These predictions were tested experimentally in the black soldier fly (BSF)Hermetia illucens. In this farmed insect, adult biology is little known despite the economic interest of larvae for bioconversion and as an animal feedstuff. Two sets of experiments were carried out to modify the risk of sperm competition perceived by males. The first consisted of placing adult males alone or in groups of 10 – modifying mean risk of sperm competition – and then measuring their sperm production. The second took place at the beginning of copulation; pairs with males from the two mean risk of sperm competition treatments were transferred to different contexts of immediate risk of sperm competition (empty cages, cages containing 10 males, or cages containing 10 females) and the number of spermatozoa stored by the females was counted. Males reared in groups of 10 showed more spermatozoa in their seminal vesicles than males reared alone. Regarding sperm allocation, females that mated in the presence of conspecifics – either 10 males or 10 females – stored more spermatozoa than those that mated alone. This study shows that sperm production and allocation are dependent on sperm competition risk in BSF, revealing a plasticity of reproduction under socio-sexual situations.
A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq
Authors: Brown Daniel V. , Anttila Casey J.A. , Ling Ling , Grave Patrick , Baldwin Tracey M. , Munnings Ryan , Farchione Anthony J. , Bryant Vanessa L. , Dunstone Amelia , Biben Christine , Taoudi Samir , Weber Tom S. , Naik Shalin H. , Hadla Anthony , Barker Holly E. , Vandenberg Cassandra J. , Dall Genevieve , Scott Clare L. , Moore Zachery , Whittle James R. , Freytag Saskia , Best Sarah A. , Papenfuss Anthony T. , Olechnowicz Sam W.Z. , MacRaild Sarah E. , Wilcox Stephen , Hickey Peter F. , Amann-Zalcenstein Daniela , Bowden Rory
Published: June 2023

Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of sample multiplexing reagents can impact data quality and experimental outcomes. In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across diverse sample types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust toex vivomanipulation but suffered from signal-to-noise issues in more delicate sample types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are critical to optimal performance. We also compared the performance of fixed scRNA-Seq kits and highlight the advantages of the Parse Biosciences kit for fragile samples. Highly multiplexed scRNA-Seq experiments require more sequencing resources, therefore we evaluated CRISPR-based destruction of non-informative genes to enhance sequencing value. Our comprehensive analysis provides insights into the selection of appropriate sample multiplexing reagents and protocols for scRNASeq experiments, facilitating more accurate and cost-effective studies.
Deep learning, data ramping, and uncertainty estimation for detecting artifacts in large, imbalanced databases of MRI images
Authors: Pizarro Ricardo , Assemlal Haz-Edine , Boopathy Jegathambal Sethu K. , Jubault Thomas , Antel Samson , Arnold Douglas , Shmuel Amir
Published: June 2023

Magnetic resonance imaging (MRI) is increasingly being used to delineate morphological changes underlying neurological disorders. Successfully detecting these changes depends on the MRI data quality. Unfortunately, image artifacts frequently compromise the MRI utility, making it critical to screen the data. Currently, quality assessment requires visual inspection, a time-consuming process that suffers from inter-rater variability. Automated methods to detect MRI artifacts could improve the efficiency of the process. Such automated methods have achieved high accuracy using small datasets, with balanced proportions of MRI data with and without artifacts. With the current trend towards big data in neuroimaging, there is a need for automated methods that achieve accurate detection in large and imbalanced datasets. Deep learning (DL) is the ideal MRI artifact detection algorithm for large neuroimaging databases. However, the inference generated by DL does not commonly include a measure of uncertainty. Here, we present the first stochastic DL algorithm to generate automated, high-performing MRI artifact detection implemented on a large and imbalanced neuroimaging database. We implemented Monte Carlo dropout in a 3D AlexNet to generate probabilities and epistemic uncertainties. We then developed a method to handle class imbalance, namely data-ramping to transfer the learning by extending the dataset size and the proportion of the artifact-free data instances. We used a 34,800 scans (98% clean) dataset. At baseline, we obtained 89.3% testing accuracy (F1 = 0.230). Following the transfer learning (with data-ramping), we obtained 94.9% testing accuracy (F1 = 0.357) outperforming focal cross-entropy (92.9% testing accuracy, F1 = 0.304) incorporated for comparison at handling class imbalance. By implementing epistemic uncertainties, we improved the testing accuracy to 99.5% (F1 = 0.834), outperforming the results obtained in previous comparable studies. In addition, we estimated aleatoric uncertainties by incorporating random flips to the MRI volumes, and demonstrated that aleatoric uncertainty can be implemented as part of the pipeline. The methods we introduce enhance the efficiency of managing large databases and the exclusion of artifact images from big data analyses.

Highlights

We address the difficulty in automatically detecting artifacts in a large, imbalanced image database.

We reproduced high accuracy in detecting artifacts in small balanced datasets.

We implemented Monte Carlo (MC) dropout in 3D AlexNet to generate uncertainty metrics.

We transfer the learning from a small balanced dataset to a large imbalanced dataset, outperforming focal loss.

We outperformed artifact detection in previous studies using comparable large imbalanced datasets

The user can select an operating point to consider manual inspection vs. artifact detection error.
p97/VCP targetsToxoplasma gondiivacuoles for parasite restriction in interferon-stimulated human cells
Authors: Clough Barbara , Fisch Daniel , Mize Todd H , Encheva Vesela , Snijders Ambrosius , Frickel Eva-Maria
Published: June 2023

Infection with the parasiteToxoplasma gondiileads to production of interferon gamma (IFNγ) that stimulates cells to upregulate defence proteins targeting the parasite for cell intrinsic elimination or growth restriction. Various host defence mechanisms operate at the parasitophorous vacuole (PV) in different human cell types leading to PV disruption, acidification, or membrane envelopment. Ubiquitin and p62 are players in all human host control mechanisms ofToxoplasma, but other unifying proteins have not been identified. Here, we show that p97/valosin-containing protein (VCP), as well as its associated proteins ANKRD13A and UBXD1 controlToxoplasmainfection while recruited to the PV in IFNγ-stimulated endothelial cells. Convergent deposition of ANKRD13A, p97/VCP and UBXD1 onto the same vacuole is dependent on vacuolar ubiquitination and observed within 2h post-infection. ANKRD13A, p97/VCP and UBXD1 all drive the acidification mechanism of the vacuole, which is the IFNγ-dependent control pathway ofToxoplasmain endothelial cells. We assessed p97/VCP inToxoplasmacontrol in various human cells and demonstrate that p97/VCP is a universal IFNγ-dependent host restriction factor targeting theToxoplasmaPV in epithelial (HeLa) and endothelial cells (HUVEC), fibroblasts (HFF) and macrophages (THP1).
RAS G-domains fine-tune the sorting of phosphatidylserine acyl chains in the plasma membrane
Authors: Arora Neha , Liang Hong , Zhou Yong
Published: June 2023

Mutant RAS are major contributors to cancer and signal from nanoclusters on the plasma membrane (PM), via isoform-specific membrane anchors. However, the same RAS isoform bound to different guanine nucleotides are segregated on the PM. Paradoxically, various segregated RAS nanoclusters all enrich a type of anionic phospholipid, phosphatidylserine (PS). These findings suggest intricate participation of RAS G-domains in their PM distribution, which have not been explored. We now show that wild-types, oncogenic G12V mutants and membrane anchors of isoforms HRAS, KRAS4A and KRAS4B sort distinct PS species. Mechanistically, shifting orientation states of KRAS4B G-domain exposes residues, such as Arg 73, Arg 102 and Arg 135, to the PM, and contributes to PS acyl chain sorting. Oncogenic mutations may shift orientation states of G-domains. We show that G12V, G12D, G12C, G13D and Q61H mutants of KRAS4B sort distinct PS species. Thus, RAS G-domains fine-tune their lateral distribution on the PM.
Tomosyns attenuate SNARE assembly and synaptic depression by binding to VAMP2-containing template complexes
Authors: Meijer Marieke , Öttl Miriam , Yang Jie , Subkhangulova Aygul , Kumar Avinash , Groffen Alexander J. , van Weering Jan R.T. , Zhang Yongli , Verhage Matthijs
Published: June 2023

Tomosyns are soluble SNARE proteins proposed to attenuate membrane fusion by competing with synaptobrevin-2/VAMP2 for SNARE-complex assembly. Here, we present evidence against this scenario using a novel mouse model, energy barrier recordings, and single-molecule force measurements. Tomosyn-1/2 deficiency drastically enhanced the probability that synaptic vesicles fuse at synapses, resulting in stronger synapses with faster depression and slower recovery. While wildtype tomosyn-1m rescued these phenotypes, substitution of its SNARE motif with that of synaptobrevin-2/VAMP2 did not. Force measurements revealed that tomosyn’s SNARE motif cannot substitute synaptobrevin-2/VAMP2 to form template complexes with Munc18-1 and syntaxin-1, an essential intermediate for SNARE assembly. Instead, tomosyns bind synaptobrevin-2/VAMP2-containing template complexes and prevent SNAP-25 association. Structure-function analyses indicate that regions outside the SNARE motif contribute to tomosyn’s inhibitory function. These results reveal that tomosyns regulate synaptic transmission by preventing SNAP-25 binding to template complexes, increasing the energy barrier for synaptic vesicle fusion, and limiting synaptic depression.
Extended correlation functions for spatial analysis of multiplex imaging data
Authors: Bull Joshua A. , Mulholland Eoghan J. , Leedham Simon J. , Byrne Helen M.
Published: June 2023

Imaging platforms for generating highly multiplexed histological images are being continually developed and improved. Significant improvements have also been made in the accuracy of methods for automated cell segmentation and classification. However, less attention has focussed on the quantification and analysis of the resulting point clouds which describe the spatial coordinates of individual cells. We focus here on a particular spatial statistical method, the cross-pair correlation function (cross-PCF), which can identify positive and negative spatial correlation between cells across a range of length scales. However, limitations of the cross-PCF hinder its widespread application to multiplexed histology. For example, it can only consider relations between pairs of cells, and cells must be classified using discrete categorical labels (rather than labelling continuous labels such as stain intensity).

In this paper, we present three extensions to the cross-PCF which address these limitations and permit more detailed analysis of multiplex images: Topographical Correlation Maps (TCMs) can visualise local clustering and exclusion between cells; Neighbourhood Correlation Functions (NCFs) can identify colocalisation of two or more cell types; and weighted-PCFs (wPCFs) describe spatial correlation between points with continuous (rather than discrete) labels. We apply the extended PCFs to synthetic and biological datasets in order to demonstrate the insight that they can generate.

Impact statement

This paper introduces three methods for performing spatial analysis on multiplex digital pathology images. We apply the methods to synthetic datasets and regions of interest from a murine colorectal carcinoma, in order to illustrate their relative strengths and weaknesses. We note that these methods have wider application to marked point pattern data from other sources.
Walking entrains unique oscillations in performance on a visual detection task
Authors: Davidson Matthew J. , Verstraten Frans A.J. , Alais David
Published: June 2023

Walking is among our most frequent and natural of voluntary behaviours, yet the consequences of locomotion upon perceptual and cognitive function remain largely unknown. Recent work has highlighted that although walking feels smooth and continuous, critical phases exist within each step-cycle for the successful coordination of perceptual and motor function. Here, we tested whether these phasic demands impact upon visual perception, by assessing performance in a visual detection task during natural unencumbered walking. We finely sampled visual performance over the stride cycle as participants walked along a smooth linear path at a comfortable speed in a wireless virtual reality environment. At the group-level, accuracy, reaction times, and response likelihood showed strong oscillations, modulating at approximately 2 cycles-per-stride (∼2 Hz) with a marked phase of optimal performance aligned with the swing phase of each step. At the participant level, Bayesian inference of population prevalence revealed highly prevalent oscillations that clustered in two idiosyncratic frequency ranges (2 or 4 cycles per stride), with a strong phase alignment across participants.
Biophysical neural adaptation mechanisms enable artificial neural networks to capture dynamic retinal computation
Authors: Idrees Saad , Manookin Michael B. , Rieke Fred , Field Greg D. , Zylberberg Joel
Published: June 2023

Adaptation is a universal aspect of neural systems that changes circuit computations to match prevailing inputs. These changes facilitate efficient encoding of sensory inputs while avoiding saturation. Conventional artificial neural networks (ANNs) have limited adaptive capabilities, hindering their ability to reliably predict neural output under dynamic input conditions. Can embedding neural adaptive mechanisms in ANNs improve their performance? To answer this question, we develop a new deep learning model of the retina that incorporates the biophysics of photoreceptor adaptation at the front-end of conventional convolutional neural networks (CNNs). These conventional CNNs build on ‘Deep Retina,’ a previously developed model of retinal ganglion cell (RGC) activity. CNNs that include this new photoreceptor layer outperform conventional CNN models at predicting primate and rat RGC responses to naturalistic stimuli that include dynamic local intensity changes and large changes in the ambient illumination. These improved predictions result directly from adaptation within the phototransduction cascade. This research underscores the potential of embedding models of neural adaptation in ANNs and using them to determine how neural circuits manage the complexities of encoding natural inputs that are dynamic and span a large range of light levels.
Tunnelling nanotubules are druggable mediators of cancer-niche crosstalk
Authors: Hockney Sean , Parker Jess , Tzivelekis Babis , Blair Helen , Dalgarno Kenny , Pal Deepali
Published: June 2023

Treatment resistance, conferred onto cancer cells largely by the oncogenic niche, remains a clinically unmet need in leukaemia. Tractable and clinically translatable models that mimic cancer-niche crosstalk remain limited, consequently means of clinically drugging microenvironment-driven cancer treatment resistance remain underexplored. Here we develop a prototype bone marrow (BM) like extracellular matrix (ECM), Vitronectin-Alginate-Laminin (VAL), which comprises animal-free components, displays viscoelastic properties like the human BM, and engrafts a range of patient-derived-xenograft acute lymphoblastic leukaemia (PDX-ALL) samples. We discover that following treatment with oxidative stress-inducing apoptotic therapies, such as dexamethasone, ABT-199 and dexamethasone-ABT-199 combination, PDX-ALL cells reach out to MSC via the formation of tunnelling nanotubes (TNT). Nevertheless, we reveal that ALL-VAL-MSC-TNTs are clinically druggable, as they are absent following treatment with CDH2 antagonist ADH-1, a compound well-tolerated in solid cancer Phase I trials. We ultimately expose a triple drug combination of dexamethasone-ABT-199 and ADH-1, with most synergy area (MSA) scores of >30, that shows high efficacy and disrupts functional cancer-niche-TNTs in 4 different high risk PDX-ALL samples. In summary, here we develop prototype cancer-ECM-niche organoids and using leukaemia as a disease paradigm, we provide proof-of-concept insights enabling the beginning of research into drugging functional cancer cell crosstalk with its surrounding cellular and ECM niche.
Quercetin Suppresses TNBC Cell by Targeting ORM2
Authors: Chen Zhijun
Published: June 2023

Background

Triple-negative breast cancer (TNBC) is known for its aggressive nature, and Quercetin (QUE) has shown potential anti-cancer effects.

Methods

We determined the IC50 of QUE for inhibiting cell viability in multiple TNBC, non-TNBC, and normal breast cell lines. We compared the expression of ORM2 in TNBC clinical samples and normal tissues. Additionally, we measured ORM2 expression in TNBC and normal breast cell lines. We determined the IC50 of QUE for inhibiting cell viability after ORM2 knockdown. An orthotopic implantation mice model was used to evaluate the treatment effect of QUE. We also conducted molecular docking and amino acid exchange validation to model the binding of QUE to ORM2. Furthermore, we performed a protein-protein interaction network analysis and GO enrichment analysis of differentially expressed genes associated with ORM2 in TNBC.

Results

QUE inhibited the viability of both TNBC and non-TNBC cell lines, but it was specifically associated with worse survival in TNBC patients. We observed higher expression of ORM2 in breast cancer cells compared to normal breast cells. Knockdown of ORM2 reduced the viability of TNBC cells. Treatment with QUE inhibited ORM2 expression and decreased viability in TNBC cells. In the animal model, QUE improved survival and downregulated ORM2 expression in tumors. Enrichment analysis provided insights into the potential functions of ORM2.

Conclusion

Our findings indicate that QUE directly inhibits TNBC cell viability through its interaction with ORM2. These results contribute to our understanding of the anti-cancer mechanisms of QUE in TNBC and highlight ORM2 as a potential therapeutic target.
A Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) Binary Classification Platform for Tabular Data
Authors: Nasimian Ahmad , Younus Saleena , Tatli Özge , Hammarlund Emma U. , Pienta Kenneth J. , Rönnstrand Lars , Kazi Julhash U.
Published: June 2023

Therapeutic resistance continues to impede overall survival rates for those affected by cancer. Although driver genes are associated with diverse cancer types, a scarcity of instrumental methods for predicting therapy response or resistance persists. Therefore, the impetus for designing predictive tools for therapeutic response is crucial and tools based on machine learning open new opportunities. Here, we present an easily accessible platform dedicated to Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) yet wholly modifiable binary classification models. Our platform encompasses both unsupervised and supervised feature selection options, hyperparameter search methodologies, under-sampling and over-sampling methods, and normalization methods, along with fifteen machine learning algorithms. The platform furnishes a k-fold receiver operating curve (ROC) - area under the curve (AUC) and accuracy plots, permutation feature importance, SHapley Additive exPlanations (SHAP) plots, and Local Interpretable Model-agnostic Explanations (LIME) plots to interpret the model and individual predictions. We have deployed a unique custom metric for hyperparameter search, which considers both training and validation scores, thus ensuring a check on under or over-fitting. Moreover, we introduce an innovative scoring method, NegLog2RMSL, which incorporates both training and test scores for model evaluation that facilitates the evaluation of models via multiple parameters. In a bid to simplify the user interface, we provide a graphical interface that sidesteps programming expertise and is compatible with both Windows and Mac OS. Platform robustness has been validated using pharmacogenomic data for 23 drugs across four diseases and holds the potential for utilization with any form of tabular data.
Prenatal Methadone Exposure Leads To Disruptions In Adult-Born Dentate Granule Cell Survival And Female Persistent Fear Responding
Authors: Gamble Meredith E. , Diaz Marvin R.
Published: June 2023

Methadone is used for the treatment of opioid use disorder, including in pregnant patients. Research has established several consequences of prenatal exposure to misused opioids, however little work has investigated the effects of prenatal methadone exposure (PME) on the offspring long-term, despite the continued prescription to pregnant individuals. The current study aimed to identify the long-term cognitive impairments arising from PME and assess hippocampal neurogenesis in these adult offspring. Pregnant Sprague Dawley rats were injected with methadone or sterile water twice daily from gestational day 3-20 or were left undisturbed as naïve controls. Adult offspring were tested in one of three behavioral tasks to assess pattern separation, spatial learning and memory, and contextual learning and memory, or were assigned to hippocampal tissue collection. For assessment of neurogenesis, offspring underwent injections of bromodeoxyuridine, and brains were collected at 24hr, 2wks, or 4wks for immunofluorescent staining. Methadone-exposed females, but not males, showed subtle impairments in pattern separation and heightened freezing during the extinction period in the fear conditioning task, and spatial memory in both sexes remained unaffected. Additionally, PME did not alter the rate of dentate granule cell proliferation but did significantly reduce the number of adult-born neuron surviving to a mature phenotype in the PME females at the 4wk timepoint. This work adds to the understanding of PME on offspring long-term and demonstrates female-specific sensitivity to these consequences. Future work is needed to fully investigate the neural disruptions arising from PME, with the goal of better supporting exposed individuals long-term.
A method for storing information in DNA with improved dropout tolerance
Authors: Mortuza Golam , Tobiason Michael D. , Suyehira Kelsey , Hughes William L. , Andersen Tim , Zadegan Reza
Published: June 2023

Storing information in synthetic DNA oligomers is attractive for archival purposes due to the favorable physical density, stability, and energy efficiency of this storage medium. However, issues with this medium sometimes cause dropout (i.e., loss of oligomers) which may prevent the recovery of stored information. Here, an improved information storage method derived from the existing “DNA Fountain” method is reported. In this work we have developed and experimentally tested a robust algorithm to write digital data in pools of DNA strands by applying a rateless erasure code (i.e., fountain code), a Reed Solomon code, and an oligomer mapping code. Our new method includes changes to the fountain code, the oligomer mapping code, and the encoding and decoding processes. We have tested and benchmarked our algorithm vs similar algorithms and found that our method increases robustness to dropout, decreases encoding time, and decreases decoding time. The new method was validatedin-vitroby successfully storing and recovering 105,360 bits of information. The advantages of the new method make it more appropriate for applications where information recovery is critical, where substantial sequence loss is expected, and/or where computational resources are limited. Furthermore, the inclusion of the novel oligomer mapping code enabled us to mitigate errors by restricting sequences of repeated bases and enhance security by eliminating start/stop codons, thus minimizing the risk of interaction with living cells.
Structural basis for recognition of unfolded proteins by the ER stress sensor ERN1/IRE1α
Authors: Simpson Mariska S. , Luca Heidi De , Cauthorn Sarah , Luong Phi , Udeshi Namrata D. , Svinkina Tanya , Schmeider Stefanie S. , Carr Steven A. , Grey Michael J. , Lencer Wayne I.
Published: June 2023

IRE1α is an endoplasmic reticulum sensor that recognizes misfolded proteins to activate the unfolded protein response (UPR). We used cholera toxin (CTx), which activates IRE1α in cells, to understand how unfolded proteins are recognized. In vitro, the A1 subunit of CTx (CTxA1) bound IRE1α lumenal domain (IRE1αLD). Global unfolding was not required. Instead, IRE1αLDrecognized a 7-residue motif within a metastable region of CTxA1 that was also found in microbial and host proteins involved in IRE1α activation. Binding mapped to a pocket on IRE1αLDnormally occupied by a segment of the IRE1α C-terminal flexible loop implicated in IRE1α regulation. Mutation of the recognition motif blocked CTx-induced IRE1α activation in live cells. These findings describe a mechanism for substrate recognition by IRE1α that induces the UPR.
SMART: reference-free deconvolution for spatial transcriptomics using marker-gene-assisted topic models
Authors: Yang C , Sin DD , Ng RT
Published: June 2023

Spatial transcriptomics (ST) offers valuable insights into gene expression patterns within the spatial context of tissue. However, most technologies do not have a single-cell resolution, masking the signal of the individual cell types. Here, we present SMART, a reference-free deconvolution method that simultaneously infers the cell type-specific gene expression profile and the cellular composition at each spot. Unlike most existing methods that rely on having a single-cell RNA-sequencing dataset as the reference, SMART only uses marker gene symbols as the prior knowledge to guide the deconvolution process and outperforms the existing methods in realistic settings when an ideal reference dataset is unavailable. SMART also provides a two-stage approach to enhance its performance on cell subtypes. Allowing the inclusion of covariates, SMART provides condition-specific estimates and enables the identification of cell type-specific differentially expressed genes across conditions, which elucidates biological changes at a single-cell-type resolution.
Putting a new spin on insect jumping performance using 3D modeling and computer simulations of spotted lanternfly nymphs
Authors: Li Chengpei , Xu Aaron J. , Beery Eric , Hsieh S. Tonia , Kane Suzanne Amador
Published: June 2023

How animals jump and land on a variety of surfaces is an ecologically important problem relevant to bioinspired robotics. We investigated this topic in the context of the jumping biomechanics of the planthopperLycorma delicatula(the spotted lanternfly, SLF), an invasive insect in the US that jumps frequently for dispersal, locomotion, and predator evasion. High-speed video was used to analyze jumping by SLF nymphs from take-off to impact on compliant surfaces. These insects used rapid hindleg extensions to achieve high take-off speeds (2.7-3.4 m/s) and accelerations (800-1000 ms-2), with midair trajectories consistent with zero-drag ballistic motion without steering. Despite rotating rapidly (5-45 Hz) in the air about time-varying axes of rotation, they landed successfully in 58.9% of trials; they also attained the most successful impact orientation significantly more often than predicted by chance, consistent with their using attitude control. Notably, these insects were able to land successfully when impacting surfaces at all angles, pointing to the emerging importance of collisional recovery behaviors. To further understand their rotational dynamics, we created realistic 3D rendered models of SLFs and used them to compute their mechanical properties during jumping. Computer simulations based on these models and drag torques estimated from fits to tracked data successfully predicted several features of their measured rotational kinematics. This analysis showed that SLF nymphs are able to use posture changes and drag torques to control their angular velocity, and hence their orientation, thereby facilitating predominately successful landings when jumping.

High-speed video revealed that juvenile spotted lanternflies are adept at landing after tumbling rapidly midair during jumping. We present computer simulations and realistic 3D models to help explain these abilities.
Toward transparent taxonomy: an interactive web-tool for evaluating competing taxonomic arrangements
Authors: Vernygora Oksana V. , Sperling Felix A.H. , Dupuis Julian R.
Published: June 2023

1. Informative and consistent taxonomy above the species level is essential to communication about evolution, biodiversity, and conservation, and yet the practice of taxonomy is considered opaque and subjective by non-taxonomist scientists and the public alike. While various proposals have tried to make the basis for ranking and inclusiveness of taxa more transparent and objective, widespread adoption of these ideas has lagged.

2. Here, we present TaxonomR, an interactive online decision-support tool to evaluate alternative taxonomic classifications. This tool implements an approach that quantifies the criteria commonly used in taxonomic treatments and allows the user to interactively manipulate weightings for different criteria to compare scores for taxonomic groupings under those weights.

3. We use the butterfly taxonArgynnisto demonstrate how different weightings applied to common taxonomic criteria result in fundamentally different genus-level classifications that are predominantly used in different continents and geographic regions. These differences are objectively compared and quantified using TaxonomR to evaluate the kinds of criteria that have been emphasized in earlier classifications, and the nature of the support for current alternative taxonomic arrangements.

4. The main role of TaxonomR is to make taxonomic decisions transparent via an explicit prioritization scheme. TaxonomR is not a prescriptive application. Rather, it aims to be a tool for facilitating our understanding of alternative taxonomic classifications that can, in turn, potentially support global harmony in biodiversity assessments through evidence-based discussion and community-wide resolution of historically entrenched taxonomic tensions.
Decellularisation and characterisation of porcine pleura for lung tissue engineering
Authors: Vikranth Trisha , Dale Tina , Forsyth Nicholas R
Published: June 2023

Decellularisation offers a broad range of biomimetic scaffolds of allogeneic and xenogeneic origins, exhibiting innate tissue-specific characteristics. We explored a physico-chemical method for decellularising porcine pleural membranes (PPM) as potential tissue-engineered surrogates for lung tissue repair. Decellularised PPM (dPPM) was characterised with histology, quantitative assays, mechanical testing, and sterility evaluation. Cytotoxicity and recellularisation assays assessed the biocompatibility of dPPM. Haematoxylin and Eosin staining showed an evident reduction in nuclei in dPPM, confirmed with nuclear staining and analysis (****p < 0.0001). Sulphated glycosaminoglycans (sGAG) and collagen histology demonstrated minimal disruption to the structural assembly of the core extracellular matrix (ECM) in dPPM. Confocal imaging demonstrated realignment of ECM fibres in dPPM against native control. Quantitative analysis defined a significant change in the angular distribution (****p < 0.0001) and coherence of fibre orientations (***p < 0.001) in dPPM versus native ECM. DNA quantification indicated ≥ 85% reduction in native nuclear dsDNA in dPPM (**p < 0.001). Collagen and sGAG quantification indicated reductions of both (**p < 0.001). dPPM displayed increased membrane thickness (*p < 0.05). However, the Youngs modulus (447.8 ± 41.9 kPa) and ultimate tensile strength (5080 ± 2034.5 kPa) of dPPM were comparable with that of native controls at (411.3 ± 8.1 kPa) and (3933.3 ± 1734.5), respectively.In vitrocytotoxicity and scaffold biocompatibility assays demonstrated robust human mesothelial cell line (MeT-5A) attachment and viability. Here, we define a decellularisation protocol for porcine pleura that represents a step forward in their potential application as bioscaffolds in lung tissue engineering.

Impact statement

Design and development of ‘off the shelf’ tissue engineered products can rely on decellularisation of native tissue that can be functionalised with cell ingress from surrounding host microenvironment. We describe a reproducible decellularisation method for porcine pleural membranes. Histology, mechanical testing, and biocompatibility studies demonstrated protocol efficiency in adequate removal of native tissue cellularity and retention of gross microarchitecture and bioactivity in the decellularised pleura. The study represents a step forward in establishing an off the shelf potential of decellularised pleura as site-specific mechanical barriers in curtailing prolonged air leaks and promoting spontaneous tissue regeneration with relevant physiological cues.
A 128-ch area-efficient neurochemical-sensing front-end for FSCV recordings of dopamine
Authors: White Kevin A. , Darroudi Mahdieh , Park Jinwoo , Kim Brian N.
Published: June 2023

Neurochemical recordings rely on electrochemical reactions of electroactive neurotransmitters such as dopamine, serotonin, and norepinephrine. This electrochemical technique allows for highly sensitive monitoring of neurotransmitters in the brain. Traditionally, single-channel carbon-fiber microelectrode recordings have been considered the gold standard method. However, an alternative approach involves the use of a microelectrode array, which enables high spatiotemporal resolution imaging of electroactive neurotransmitters. To enable neurochemical imaging using a microelectrode array, the development of a high-density current-sensing microchip is necessary. Here, a neurochemical microchip is introduced, featuring a 128-channel current sensing front-end capable of supporting 128 parallel neurochemical measurements. The designed amplifier array employs a highly scalable resistive feedback transimpedance amplifier design. This design allows for a large neurochemical dynamic range of ±5µA with a noise performance as low as 0.22nARMS. With the integration of this microchip,in vivoneurochemical imaging of dopamine can be achieved with high spatiotemporal resolution.
Wound induced small-peptide mediated signalling cascade regulated by OsPSKR, dictates balance between growth and defense in rice
Authors: Harshith C.Y. , Pal Avik , Chakraborty Monoswi , Nair Ashwin , Raju Steffi , Shivaprasad P. V.
Published: June 2023

Wounding is a general stress in plants that results from various pest and pathogenic infections in addition to environment induced mechanical damages. Plants have sophisticated molecular mechanisms to recognize and respond to pests and pathogens. Although several molecules such as phytohormones, peptides and receptors have been attributed to wound responses in dicots, such mechanisms for monocots probably having distinct wound responses are less understood. Here, we show the involvement of two distinct categories of temporally separated, endogenously derived peptides, namely, plant elicitor peptides (PEPs) and phytosulfokine (PSK), that mediate wound responses in rice. These peptides trigger a dynamic signal relay in which a novel receptor kinase named OsPSKR played a major role. OsPSKR perceived PSK ligand, acting in association with a co-receptor OsSERK1, to activate downstream responses in a kinase activity-dependent manner. Perturbation of OsPSKR expression in rice led to compromised development and constitutive autoimmune phenotypes. These results suggested that OsPSKR maintains the trade-off between growth and exaggerated defense responses, both during homeostasis and wounding. Collectively, these findings indicate the presence of a stepwise peptide-mediated signal relay that regulates the transition from defense to growth upon wounding in monocots.

One line summary

Endogenous peptide signalling initiated wound responses through a receptor-like kinase OsPSKR to maintain the balance between growth and defense responses.
Striatonigral distribution of a fluorescent reporter following intracerebral delivery of genome editors
Authors: Neuman Samuel S. , Metzger Jeanette M. , Bondarenko Viktoriya , Wang Yuyuan , Felton Jesi , Levine Jon E. , Saha Krishanu , Gong Shaoqin , Emborg Marina E.
Published: June 2023

Introduction

Targeted gene editing is proposed as a therapeutic approach for numerous disorders, including neurological diseases. As the brain is organized into neural networks, it is critical to understand how anatomically connected structures are affected by genome editing. For example, neurons in the substantia nigra pars compacta (SNpc) project to the striatum, and the striatum contains neurons that project to the substantia nigra pars reticulata (SNpr).

Methods

Here, we report the effect of injecting genome editors into the striatum of Ai14 reporter mice, which have a LoxP-flanked stop cassette that prevents expression of the red fluorescent protein tdTomato. Two weeks following intracerebral delivery of either synthetic nanocapsules (NCs) containing CRISPR ribonucleoprotein targeting the tdTomato stop cassette or adeno-associated virus (AAV) vectors expressing Cre recombinase, the brains were collected, and the presence of tdTomato was assessed in both the striatum and SN.

Results

TdTomato expression was observed at the injection site in both the NC- and AAV-treated groups and typically colocalized with the neuronal marker NeuN. In the SN, tdTomato-positive fibers were present in the pars reticulata, and SNpr area expressing tdTomato correlated with the size of the striatal genome edited area.

Conclusion

These results demonstratein vivoanterograde axonal transport of reporter gene protein products to the SNpr following neuronal genome editing in the striatum.
Lack of detectable neoantigen depletion in treatment-naïve cancers
Authors: Slagter Maarten , Fanchi Lorenzo F. , van Buuren Marit M. , Velds Arno , Bounova Gergana , Wessels Lodewyk F.A. , Schumacher Ton N.
Published: June 2023

While neoantigen depletion, a form of immunoediting due to Darwinian pressure exerted by the T cell based immune system during tumor evolution, has been clearly described in murine models, its prevalence in treatment-naive, developing human tumors remains controversial. We developed two novel methodologies to test for depletion of predicted neoantigens in patient cohorts, which both compare patients in terms of their expected number of neoantigens per mutational event. Application of these strategies to TCGA patient cohorts showed that neither basic nor more extensive versions of the methodologies, controlling for confounding factors such as genomic loss of the HLA locus, provided statistically significant evidence for neoantigen depletion. In the subset of analyses that did show a trend towards neoantigen depletion, statistical significance was not reached and depletion was not consistently observed across HLA alleles. Our results challenge the notion that neoantigen depletion is detectable in cohorts of unmatched patient samples using HLA binding prediction-based methodology.
Multimodule imaging of the hierarchical equine hoof wall porosity and structure
Authors: Mahrous Mahmoud A. , Chadha Charul , Robins Pei L. , Bonney Christian , Boateng Kingsley A. , Meyers Marc , Jasiuk Iwona
Published: June 2023

The equine hoof wall has a complex, hierarchical structure that can inspire designs of impact-resistant materials. In this study, we utilized micro-computed tomography (μ-CT) and serial block-face scanning electron microscopy (SBF-SEM) to image the microstructure and nanostructure of the hoof wall. We quantified the morphology of tubular medullary cavities by measuring equivalent diameter, surface area, volume, and sphericity. High-resolution μ-CT revealed that tubules are partially or fully filled with tissue near the exterior surface and become progressively empty towards the inner part of the hoof wall. Thin bridges were detected within the medullary cavity, starting in the middle section of the hoof wall and increasing in density and thickness towards the inner part. Porosity was measured using three-dimensional (3D) μ-CT, two-dimensional (2D) μ-CT, and a helium pycnometer, with the highest porosity obtained using the helium pycnometer (8.07%), followed by 3D (3.47%) and 2D (2.98%) μ-CT. SBF-SEM captured the 3D structure of the hoof wall at the nanoscale, showing that the tubule wall is not solid, but has nano-sized pores, which explains the higher porosity obtained using the helium pycnometer. The results of this investigation provide morphological information on the hoof wall for the future development of hoof-inspired materials and offer a novel perspective on how various measurement methods can influence the quantification of porosity.
The neural basis of resting-state fMRI functional connectivity in fronto-limbic circuits revealed by chemogenetic manipulation
Authors: Elorette Catherine , Fujimoto Atsushi , Stoll Frederic M. , Fujimoto Satoka H. , Fleysher Lazar , Bienkowska Niranjana , Russ Brian E. , Rudebeck Peter H.
Published: June 2023

Measures of fMRI resting-state functional connectivity (rs-FC) are an essential tool for basic and clinical investigations of fronto-limbic circuits. Understanding the relationship between rs-FC and neural activity in these circuits is therefore vital. Here we introduced inhibitory designer receptors exclusively activated by designer drugs (DREADDs) into the macaque amygdala and activated them with a highly selective and potent DREADD agonist, deschloroclozapine. We evaluated the causal effect of activating the DREADD receptors on rs-FC and neural activity within circuits connecting amygdala and frontal cortex. Interestingly, activating the inhibitory DREADD increased rs-FC between amygdala and ventrolateral prefrontal cortex. Neurophysiological recordings revealed that the DREADD-induced increase in fMRI rs-FC was associated with increased local field potential coherency in the alpha band (6.5-14.5Hz) between amygdala and ventrolateral prefrontal cortex. Thus, our multi-disciplinary approach reveals the specific signature of neuronal activity that underlies rs-FC in fronto-limbic circuits.