bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 infection unevenly impacts metabolism in the coronal periphery of the lungs
Authors: Laro Jarrod , Xue Biyun , Zheng Jian , Ness Monica , Perlman Stanley , McCall Laura-Isobel 
Published: May 2024

SummaryHighlightsCOVID-19 significantly decreases amino acids, fatty acids, and most eicosanoidsSARS-CoV-2 preferentially localizes to central lung tissueMetabolic disturbance is highest in peripheral tissue, not central like viral loadSpatial metabolomics allows detection of metabolites not altered overallSARS-CoV-2, the virus responsible for COVID-19, is a highly contagious virus that can lead to hospitalization and death. COVID-19 is characterized by its involvement in the lungs, particularly the lower lobes. To improve patient outcomes and treatment options, a better understanding of how SARS-CoV-2 impacts the body, particularly the lower respiratory system, is required. In this study, we sought to understand the spatial impact of COVID-19 on the lungs of mice infected with mouse-adapted SARS2-N501YMA30. Overall, infection caused a decrease in fatty acids, amino acids, and most eicosanoids. When analyzed by segment, viral loads were highest in central lung tissue, while metabolic disturbance was highest in peripheral tissue. Infected peripheral lung tissue was characterized by lower levels of fatty acids and amino acids when compared to central lung tissue. This study highlights the spatial impacts of SARS-CoV-2 and helps explain why peripheral lung tissue is most damaged by COVID-19.
One probe fits all: a highly customizable modular RNAin situhybridization platform expanding the application of SABER DNA probes
Authors: Ustyantsev Kirill , Stranges Mattia , Volpe Filippo Giovanni , Mouton Stijn , Berezikov Eugene 
Published: May 2024

ABSTRACTIn situhybridization (ISH) of RNA is a key method to visualize gene expression patterns in complex biological samples. The technique is indispensable for biological research related to e.g. development, disease, gene function, and the validation of novel cell types identified by single-cell sequencing methods. Especially in non-mammalian models lacking accessibility to a broad spectrum of antibodies, ISH remains a major research tool. Diverse available ISH protocols require different custom hybridization probe types, design, and/or proprietary signal detection chemistry. This makes it hard to navigate for a beginner and increases the research costs when multiple methods need to be applied. Here, we describe OneSABER – a unified open platform connecting commonly used canonical and recently developed single- and multiplex, colorimetric, and fluorescent ISH approaches. This platform uses a single type of ISH DNA probes adapted from the signal amplification by exchange reaction (SABER) method. We demonstrate applications of the proposed ISH framework in whole-mount samples of the regenerative flatwormMacrostomum lignano, advancing this animal as a powerful model for stem cell and regeneration research.
Diabetes and Stroke: Does an Excess Risk of Hemodynamic Cerebral Ischemia Exist?
Authors: Petitjean Christian , Labreuche Julien 
Published: May 2024

ABSTRACTBACKGROUNDDiabetes is an independent risk factor for ischemic stroke. This study was undertaken to determine whether hemodynamic cerebral ischemia (HCI), which increases stroke severity, is more frequent in diabetic patients.METHODSBetween 01/01/1990 and 30/06/2019, we revascularized 4117 carotid bifurcations in 3739 patients (2683 men and 1056 women; mean age: 71 (range: 28–97) years; 940 (25.1%) diabetics and 2799 (74.9%) nondiabetics). HCI was diagnosed clinically, under regional anesthesia, when a shunt needed to be inserted.RESULTSThe HCI rate during carotid-clamping, requiring shunt placement, was 11.0% (114/1034) for diabetics and 7.1% (219/3083) for nondiabetics (odds ratio,1.62 [95% CI, 1.27–2.05];P<0.0001).CONCLUSIONSDiabetes was associated with increased HCI risk in our patients with carotid stenosis. This HCI-associated excess risk might explain, in part, stroke severity in diabetics and heightened surgical risk. It might be prevented by HCI detection and modification of therapeutic management.
Factors Associated With Chronic Arthropathy And Rheumatological Diseases After Chikungunya Infection in Colombia: A Case-Control Study
Authors: Luna Guillermo Alejandro Ramírez , Paz Fabian Méndez 
Published: May 2024

AbstractObjectiveTo identify the factors associated with the development of chronic arthropathy and rheumatological conditions in individuals who presented with clinical chikungunya infection.MethodsA case-control study was carried out among individuals with a clinical diagnosis of chikungunya treated at a Colombian Health Provider Institution between 2014 and 2015. Two logistic regression models were constructed: one excluding the variables with more than 50% of the missing data, and another with all the variables but with the imputed data.ResultsIn total 133 cases and 216 controls were obtained (349 individuals). In both models, female gender was a risk factor (OR: 2.27, CI95: 1.03 - 4.97, p = 0.04, and OR: 2.37, CI95: 1.09 - 5.17, p = 0.029, respectively), while acute involvement of the wrists was a protective factor (OR: 0.44, CI95: 0.20 - 0.95, p < 0.037; and OR: 0.29, CI95: 0.13 - 0.65, p = 0.003 respectively). Arthralgia duration was a risk factor in the imputed data model (OR: 1.03, CI95: 1.00 - 1.06, p = 0.02).ConclusionFemale gender and the duration of joint symptoms in the acute phase were the main risk factors for the development of chronic chikungunya arthropathy or rheumatological pathology. Wrist involvement was a protective factor. Only rheumatoid arthritis was found to be a rheumatological disease associated with chikungunya infections. Finally, this study suggests that the interaction between usual cardiovascular factors could enhance the probability of developing chronic symptoms.
Predictive Biophysical Neural Network Modeling of a Compendium ofin vivoTranscription Factor DNA Binding Profiles forEscherichia coli
Authors: Lally Patrick , Gómez-Romero Laura , Tierrafría Víctor H. , Aquino Patricia , Rioualen Claire , Zhang Xiaoman , Kim Sunyoung , Baniulyte Gabriele , Plitnick Jonathan , Smith Carol , Babu Mohan , Collado-Vides Julio , Wade Joseph T. , Galagan James E. 
Published: May 2024

AbstractThe DNA binding of mostEscherichia coliTranscription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping ofin vivoDNA binding for 139E. coliTFs using ChIP-Seq. We used these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We used BoltzNet to quantitatively design novel binding sites, which we validated with biophysical experiments on purified protein. We have generated models for 125 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.
Initiation of Lumen Formation from Junctions via Differential Actomyosin Contractility Regulated by Dynamic Recruitment of Rasip1
Authors: Yin Jianmin , Schellinx Niels , Maggi Ludovico , Gundel Kathrin , Wiesner Cora , Kotini Maria Paraskevi , Lee Minkyoung , Phng Li-Kun , Belting Heinz-Georg , Affolter Markus 
Published: May 2024

AbstractVascular lumens are essential for the dispersal of nutrients, oxygen, and immune cells throughout the body.De novolumen formation necessitates the precise segregation of junctional proteins from apical surfaces. Direct visualization of this process and a comprehensive understanding on how the apical and junctional compartments are segregated and established remain elusive, due to the lack of visualizable systems, proper reporters and manipulative tools. Using zebrafish as an experimental model, we have established a wealth of molecular reporters, photo-convertible and optogenetic tools and combined them with genetic analyses to study the establishment of apical domains from pre-apical junctional complexes. Our study identified Rasip1 as one of the earliest apical proteins recruited, peripheralizing cortical contractility at the junctional patches by inhibiting NMII at the center, thereby initiating the outward flow of junctional complexes. After the establishment of the apical compartments, Rasip1 shuttles between junctions and the apical compartments to the high-tension sites and tunes down the local hyper contractility, restricting Cdh5 to junctions by suppressing apical contractility. Above all, the formation ofde novolumens and maintenance of junctional integrity depend on the precise control of contractility within the apical compartments and junctions, orchestrated by the dynamic recruitment of Rasip1.
AMH protects the ovary from doxorubicin by regulating cell fate and the response to DNA damage
Authors: Nguyen Ngoc Minh Phuong , Chang Eun Mi , Chauvin Maeva , Sicher Natalie , Kashiwagi Aki , Nagykery Nicholas , Chow Christina , May Phoebe , Mermin-Bunnel Alana , Cleverdon Josephine , Duong Thy , Meinsohn Marie-Charlotte , Gao Dadi , Donahoe Patricia K. , Pepin David 
Published: May 2024

SummaryAnti-Müllerian hormone (AMH) protects the ovarian reserve from chemotherapy, and this effect is most pronounced with Doxorubicin (DOX). However, the mechanisms of DOX toxicity and AMH rescue in the ovary remain unclear. Herein, we characterize these mechanisms in various ovarian cell types using scRNAseq. In the mesenchyme, DOX activates the intrinsic apoptotic signaling pathway through p53 class mediators, particularly affecting theca progenitors, while co-treament with AMH halts theca differentiation and reduces apoptotic gene expression. In preantral granulosa cells, DOX upregulates the cell cycle inhibitorCdkn1aand dysregulates Wnt signaling, which are ameliorated by AMH co-treatment. Finally, in follicles, AMH inducesId3, a protein involved in DNA repair, which is necessary to prevent the accumulation of DNA lesions marked by γ-H2AX in granulosa cells. Altogether this study characterizes cell, and follicle stage-specific mechanisms of AMH protection of the ovary, offering promising new avenues for fertility preservation in cancer patients undergoing chemotherapy.HighlightsDoxorubicin treatment induces DNA damage that activates the p53 pathway in stromal and follicular cells of the ovary.AMH inhibits the proliferation and differentiation of theca and granulosa cells and promotes follicle survival following Doxorubicin insult.AMH treatment mitigates Doxorubicin-induced DNA damage in the ovary by preventing the accumulation of γ-H2AX-positive unresolved foci, through increased expression of ID3, a protein involved in DNA repair.Graphical Abstract
Mapping Large-scale Spatiotemporal Dynamics of Synaptic Plasticity and LTP for Memory Encoding in the Hippocampal Network
Authors: Khanzada Shahrukh , Hu Xin , Emery Brett Addison , Średniawa Władysław , Wójcik Daniel K , Kempermann Gerd , Amin Hayder 
Published: May 2024

AbstractUnderstanding memory formation requires elucidating the intricate dynamics of neuronal networks in the hippocampus, where information is encoded and processed through specific activity patterns and synaptic plasticity. Here, we introduce “EVOX,” an advanced network electrophysiology platform equipped with high-density microelectrode arrays to capture critical network-level synaptic dynamics integral to learning and memory. This platform surpasses traditional methods by enabling label-free, high-order mapping of neural interactions, providing unprecedented insights into network Long-Term Potentiation (LTP) and evoked synaptic transmission within the hippocampal network. Utilizing EVOX, we demonstrate that high-frequency stimulation induces network-wide LTP, revealing enhanced synaptic efficacy in previously inactive cell assemblies in hippocampal layers. Our platform enables the real-time observation of network synaptic transmission, capturing the intricate patterns of connectivity and plasticity that underpin memory encoding. Advanced computational techniques further elucidate the mesoscale transmembrane generators and the dynamic processes that govern network-level memory encoding mechanisms. These findings uncover the complex dynamics that underlie learning and memory, showcasing EVOX’s potential to explore synaptic and cellular phenomena in aging circuits. EVOX not only advances our understanding of hippocampal memory mechanisms but also serves as a powerful tool to investigate the broader scope of neural plasticity and network interactions in healthy and diseased states.
A dorsal versus ventral network for understanding others in the developing brain
Authors: Schüler Clara , Berger Philipp , Wiesmann Charlotte Grosse 
Published: May 2024

AbstractYoung children strongly depend on others, and learning to understand their mental states (referred to as Theory of Mind, ToM) is a key challenge of early cognitive development. Traditionally, ToM is thought to emerge around the age of 4 years. Yet, in non-verbal tasks, preverbal infants already seem to consider others’ mental states when predicting their actions. These early non-verbal capacities, however, seem fragile and distinct from later-developing verbal ToM. So far, little is known about the nature of these early capacities and the neural networks supporting them. To identify these networks, we investigated the maturation of nerve fiber connections associated with children’s correct non-verbal action prediction and compared them with connections supporting verbal ToM reasoning in 3- to 4-year-old children, that is, before and after their breakthrough in verbal ToM. This revealed a ventral network for non-verbal action prediction versus a dorsal network for verbal ToM. Non-verbal capacities were associated with maturational indices in ventral fiber tracts connecting regions of the salience network, involved in bottom-up social attention processes. In contrast, verbal ToM performance correlated with maturational indices of the arcuate fascicle and cingulum, which dorsally connect regions of the default network, involved in higher-order social cognitive processes including ToM in adults. As non-verbal tasks were linked to connections of the salience network, young children may make use of salient perceptual social cues to predict others’ actions, questioning theories of mature ToM before 4 years.SignificanceAs highly social beings, humans frequently reason about other people’s thoughts, termed Theory of Mind (ToM). While ToM is traditionally assumed not to emerge before 4 years, preverbal infants already seem to consider others’ thoughts when predicting their actions non-verbally. This raises the question of when ToM develops and what explains this discrepancy. We show that young children’s success in non-verbal tasks is related to different neural networks than those involved in mature verbal ToM. While verbal ToM was linked to ToM network connections, younger children’s non-verbal capacities were associated with the maturation of connections of the salience network. This indicates that, instead of mature ToM, young children might utilize salient social cues to predict others’ actions.
TRIM46 is not required for axon specification or axon initial segment formationin vivo
Authors: Melton Allison J. , Palfini Victoria L. , Ogawa Yuki , Rasband Matthew N. 
Published: May 2024

ABSTRACTVertebrate nervous systems use the axon initial segment (AIS) to initiate action potentials and maintain neuronal polarity. The microtubule-associated protein tripartite motif containing 46 (TRIM46) was reported to regulate axon specification, AIS assembly, and neuronal polarity through the bundling of microtubules in the proximal axon. However, these claims are based on TRIM46 knockdown in cultured neurons. To investigate TRIM46 functionin vivo, we examined TRIM46 knockout mice. Contrary to previous reports, we find that TRIM46 is dispensable for AIS formation and maintenance, and axon specification. TRIM46 knockout mice are viable, have normal behavior, and have normal brain structure. Thus, TRIM46 is not required for AIS formation, axon specification, or nervous system function. We also show TRIM46 enrichment in the first ∼100 μm of axon occurs independently of ankyrinG (AnkG), although AnkG is required to restrict TRIM46 only to the AIS. Our results suggest an unidentified protein may compensate for loss of TRIM46in vivoand highlight the need for further investigation of the mechanisms by which the AIS and microtubules interact to shape neuronal structure and function.SIGNIFICANCE STATEMENTA healthy nervous system requires the polarization of neurons into structurally and functionally distinct compartments, which depends on both the axon initial segment (AIS) and the microtubule cytoskeleton. In contrast to previous reports, we show that the microtubule-associated protein TRIM46 is not required for axon specification or AIS formation in mice. Our results emphasize the need for further investigation of the mechanisms by which the AIS and microtubules interact to shape neuronal structure and function.
Proteomic analysis of the TDP-43-associated insoluble fraction from NEFH-TDP-43 mouse brain suggests sustained stress granule formation, CLUH granule recruitment and impaired mitochondrial metabolism
Authors: Dunlop Felicity , Mason Shaun , Tsitkanou Stavroula , Russell Aaron P. 
Published: May 2024

AbstractCytoplasmic accumulation and aggregation of TDP-43 is a hallmark of ∼97% of ALS cases. Formation of TDP-43 insoluble aggregates is suggested to either directly or indirectly cause motor neuron loss and progressive neuromuscular degeneration, although how this occurs is not precisely understood. Cytoplasmic TDP-43 is observed in stress granules (SG). SGs are ribonucleoprotein (RNP) complexes formed during stress conditions, consisting of mRNAs and RNA-binding proteins (RNPs). Chronic TDP-43/SG formation may play a role in neuromuscular degeneration in ALS. The composition ofin vivoTDP-43-asscociated SGs in ALS not known. This knowledge may provide insights into the molecular pathways impaired by TDP-43-associated SGs and suggest disease modifying mechanisms. The aim of this study was to isolate and analyse the proteome of the insoluble TDP-43-associated SG fraction from brain tissue of end-stage TDP-43ΔNLS mice. Proteomic analysis identified 134 enriched and 17 depleted proteins in the TDP-43ΔNLS mice, when compared to the control mice. Bioinformatics analyses of the impacted proteins from the SG preparation suggested that brain tissue from end-stage NEFH-TDP-43ΔNLS mice have sustained SG formation, CLUH granule recruitment and impaired mitochondrial metabolism. This is the first time that CLUH granule recruitment has been demonstrated in ALS and the known role of CLUH suggests that cell starvation is a potential mechanism of motor neuron loss that could be targeted in ALS.HighlightsWe present a detailed a protocol for the extraction of cross-linked TDP containing stress granules from brain tissue.We present proteomics data from the insoluble fraction from brain tissue of an ALS mouse model.We identify the mitochondrial mRNA transport protein CLUH and CLUH targets trapped in insoluble SG fraction of brain.Reanalysing proteomics data from axonal soluble fraction supports a link between proteins trapped in the brain and depleted from the axons.Propose a model where metabolic mitochondrial enzymes trapped in the insoluble fraction from the brain via a CLUH dependent mechanism results in motor neuron death by starvation in ALS.
2D Label-free Prediction of Multiple Organelles Across Different Transmitted-light Microscopy Images with Bag-of-Experts
Authors: Zhou Yu , Zhao Shuo , Sonneck Justin , Chen Jianxu 
Published: May 2024

ABSTRACTLabel-free prediction has emerged as a significant application of artificial intelligence (AI) in the field of bioimaging, which aims to predict the localization of specific organelles directly from readily-accessible transmitted-light images, thereby alleviating the need for acquiring fluorescent images. Despite the existence of numerous research, in practice, the high variability in imaging conditions, modalities, and resolutions poses a challenge to the final prediction. In this study, we propose a “Bag-of-Experts” strategy, targeting at different organelles, with self-supervised pre-training. The comprehensive experimentation showcases that our model is agnostic to the transmitted-light image modalities and the imaging conditions, to certain extent, indicating considerable generalizability. The code is released at:https://github.com/MMV-Lab/LightMyCells
Transfer pricing, earnings management and corporate governance among listed firms: Evidence from Ghana
Authors: Duho King Carl Tornam , Asare Emmanuel Tetteh , Glover Abraham , Duho Divine Mensah 
Published: May 2024

Purpose
This study aims to examine the prevalence of transfer pricing and earnings management activities, and how they are impacted by corporate governance mechanisms.

Design/methodology/approach
Using the political cost theory, the study provides insights into how opportunistic managerial behaviours which have a strong link to profit shifting and tax evasion are driven by corporate governance using data from 16 listed firms for the period 2008–2020.

Findings
The results reveal that the transaction-based transfer pricing model is better than the index-based model and the accrual-based earnings management model suits the political cost theory more than the real earnings management metric. Board size and female CEO increase transfer pricing aggressiveness but board independence, CEO tenure, CEO nationality and female Board Chairwomanship reduce transfer pricing aggressiveness. The findings also reveal the role of multinational enterprise status, private ownership, industry type, firm size, financial leverage, asset tangibility and firm age. For accrual-based earnings management, board independence, CEO tenure, and female Board Chairwomanship significantly decrease earnings management. Other factors include private ownership, firm size, and firm age.

Practical implications
The findings of the study are relevant for shaping industry-level policies on earning management, transfer pricing and related-party transactions. Since these opportunistic managerial behaviours are the foremost drivers of tax avoidance and profit shifting, the findings of this study provide relevant insights for practitioners, tax and other regulatory authorities, policymakers and the academic community alike.

Originality/value
This is among the premier studies on the transfer pricing and earnings management nexus with corporate governance factors using the political cost theory, especially in the developing country context. It also reveals the significant impact of gender and suggests the need for gender diversity in corporate management.