bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropsychological and behavioral profiles of patients with chronic trigeminal neuralgia
Authors: Pashkov Anton , Filimonova Elena , Martirosyan Azniv , Moisak Galina , Rzaev Jamil 
Published: November 2024

AbstractPatients suffering from chronic pain are known to exhibit distinctive personality traits and impaired neuropsychological performance across various cognitive domains. However, there is currently a lack of comprehensive evidence regarding cognitive and behavioral functioning patterns in patients with trigeminal neuralgia. In this study, we aimed to thoroughly characterize a range of psychological and neuropsychological variables in a sample of 80 patients and 34 healthy controls, and to assess their relationship with pain intensity and duration. Our findings revealed that patients with trigeminal pain scored significantly higher on measures of anxiety, depression, perceived stress, alexithymia, pain catastrophizing, harm avoidance and lower on Self-transcendence subscale compared to healthy controls. Additionally, these patients demonstrated lower performance scores on tasks assessing working memory and verbal fluency. These findings may provide valuable insights for the development of personalized treatment plans for patients with trigeminal neuralgia, specifically targeting their unique personality traits and cognitive impairments.
Portable Six-Channel Laser Speckle System for Simultaneous Cerebral Blood Flow and Volume Measurement with Potential Application for Characterization of Brain Injury
Authors: Mahler Simon , Huang Yu Xi , Ismagilov Max , Álvarez-Chou David , Abedi Aidin , Tyszka J. Michael , Lo Yu Tung , Russin Jonathan , Pantera Richard L. , Liu Charles , Yang Changhuei 
Published: November 2024

AbstractIn regional cerebrovascular monitoring, cerebral blood flow (CBF) and cerebral blood volume (CBV) are key metrics. Simultaneous, non-invasive measurement of CBF and CBV at different brain locations would advance cerebrovascular monitoring and pave the way for brain injury detection, as current brain injury diagnostic methods are often constrained by high costs, limited sensitivity, and reliance on subjective symptom reporting. This study’s aim is to develop a multi-channel non-invasive optical system for measuring CBF and CBV at different regions of the brain simultaneously with a cost-effective, reliable, and scalable system capable of detecting potential differences in CBF and CBV across different regions of the brain. The system is based on speckle contrast optical spectroscopy (SCOS) and consists of laser diodes and board cameras which have been both tested and investigated for safe use on the human head. Results on a cohort of five healthy subjects indicated that the dynamics of both CBF and CBV were synchronized and exhibited similar cardiac period waveforms across all six channels. As a preliminary investigation, we also explored the potential use of our six-channel system for detecting the physiological sequela of brain injury, involving a subject with significant structural brain damage compared to another with lesser structural brain damage. The six-point CBF and CBV measurements were compared to MRI scans, revealing that regions with altered blood dynamics closely correlated with the injury sites identified by MRI.
Untangling Empowerment and Contraceptive Use Longitudinally in Five African Settings
Authors: Zimmermann Marita , Myers Cara , Dhar Diva , O’Brien Michelle 
Published: November 2024

AbstractObjectiveEmpowerment impacts reproductive health behaviors profoundly. Similarly, contraceptive access and use result in broader social and economic opportunities. We aimed to quantify the directionality of this cyclical relationship.Study designThis study utilizes data from the Performance Monitoring for Action (PMA) surveys in Kenya, Nigeria (Kano), Burkina Faso, Democratic Republic of Congo (DRC), and Uganda. Using annual longitudinal data (2019-2021), we employed cross-lagged panel models (CLPM) to analyze the bidirectional relationship between women’s empowerment and contraceptive use.ResultsThere was a significant positive impact of contraceptive use on women’s empowerment. In Kenya and Kano, contraceptive use was associated with a 10.1% and 12.0% increase in paid work and 14.5% and 14.8% greater control over wages, respectively. In Kenya, women doing paid work with wage control were 5.2% more likely to use contraception the following year. In Kano, control over partner’s wages increased contraceptive use by 9.6%. Additionally, having savings, financial goals, increased financial autonomy, and knowledge of financial information were associated with higher future contraceptive use.ConclusionsContraceptive use can act as a catalyst for empowerment, while empowerment, particularly decision-making autonomy over finances, enhances contraceptive use. However, these dynamics vary across different settings, emphasizing the need for context-specific strategies.
Genomics and resistance assays inform the management of two tree species being devastated by the invasive myrtle rust pathogen
Authors: Chen Stephanie H , Yap Jia-Yee S , Viler Veronica , Stehn Craig , Sandhu Karanjeet S , Percival Julie , Pegg Geoff S , Menzies Tracey , Jones Ashley , Guo Karina , Giblin Fiona R , Cohen Joel , Edwards Richard J , Rossetto Maurizio , Bragg Jason G 
Published: November 2024

AbstractMyrtle rust is a plant disease caused by the invasive fungal pathogenAustropuccinia psidii(G. Winter) Beenken, which has a global host list of 480 species. It was detected in Australia in 2010 and has caused the rapid decline of native Myrtaceae species, including rainforest treesRhodamnia rubescens(Benth.) Miq. (scrub turpentine) andRhodomyrtus psidioides(G.Don) Benth. (native guava).Ex situcollections of these species have been established, with the goal of preserving remaining genetic variation. Analysis of reduced representation sequencing (DArTseq;n= 444 forR.rubescensandn= 301 forR.psidioides) showed genetic diversity is distributed along a latitudinal gradient across the range of each species. A panel of samples of each species (n= 27 forR.rubescensandn= 37 forR.psidioides) were resequenced at genome scale, revealing large historical e]ective population sizes, and little variation among individuals in inferred levels of deleterious load. InRhodamnia rubescens, experimental assays (n= 297) identified individuals that are putatively resistant to myrtle rust. This highlights two important points: there are tangible pathways to recovery for species that are highly susceptible to rust via a genetically informed breeding program, and there is a critical need to act quickly before more standing diversity is lost.
Genetically based variation in fitness and carbon assimilation among bur oak populations
Authors: Rea L.M.S. , Ostrowsky L. , Mohn R. , Garner M. , Worcester L. , Lapadat C. , McCarthy H.R. , Hipp A.L. , Cavender Bares J. 
Published: November 2024

AbstractOngoing climate change will negatively impact tree populations unless they are able to acclimate to the changes in their local environment. Effective planning for climate adaptation management requires an understanding of the current state of local adaptation and physiological performance to assess whether populations are at risk of local extinction, determine if assisted migration is appropriate, and to select appropriate seed sources if intervention is needed. We established a new reciprocal transplant experiment (ACE, Adaptation to Climate and Environment) across a latitudinal gradient in North America to examine the impacts of warming on three bur oak (Quercus macrocarpa) populations across much of the species range. We established common gardens in Minnesota, Illinois, and Oklahoma with seedlings grown from seeds collected within 50 km of each of those locations from a total of sixty maternal families. We aimed to 1) assess local adaptation in each of the populations using survival and size as fitness metrics, and 2) evaluate physiological responses to different environments along the latitudinal gradient. We found that northern populations are maladapted to hotter climates as evidenced by their low survival, growth, and photosynthetic rates in the warmest common garden. The southernmost population had the highest survival rate, growth rate, and fitness of the three populations in the southernmost garden, providing evidence for local adaptation to the warmest site. However, conditions in the middle garden resulted in the highest fitness and best physiological performance for all populations. Growth and survival were correlated in the middle garden but were decoupled in the northern and southern gardens. This decoupling is likely due to stress associated with the relatively extreme climates in the gardens at the ends of the gradient that led to greater resource allocation to survival than growth. Our results suggest that southern seed sources may perform well in warmer conditions in the north brought on by climate change, which has important implications for managers assisting broadly ranged tree species in adapting to climate change.
PMAIP1-Mediated Glucose Metabolism and its Impact on the Tumor Microenvironment in Breast Cancer: Integration of Multi-Omics Analysis and Experimental Validation
Authors: Zhang Yidong , Han Xuedan , Yu Qiyi , Zheng Lufeng , Xiao Hua 
Published: November 2024

AbstractBackgroundGlucose metabolism in breast cancer has a potential effect on tumor progression and is related to the immune microenvironment. Thus, this study aimed to develop a glucose metabolism– tumor microenvironment score to provide new perspectives on breast cancer treatment.MethodData were acquired from the Gene Expression Omnibus and UCSC Xena databases, and glucose-metabolism-related genes were acquired from the Gene Set Enrichment Analysis database. Genes with significant prognostic value were identified, and immune infiltration analysis was conducted, and a prognostic model was constructed based on the results of these analyses. The results were validated by in vitro experiments with MCF-7 and MCF-10A cell lines, including expression validation, functional experiments, and bulk sequencing. Single-cell analysis was also conducted to explore the role of specific cell clusters in breast cancer, and Bayes deconvolution was used to further investigate the associations between cell clusters and tumor phenotypes of breast cancer.ResultsFour significant prognostic genes (PMAIP1, PGK1, SIRT7, and SORBS1) were identified, and, through immune infiltration analysis, a combined prognostic model based on glucose metabolism and immune infiltration was established. The model was used to classify clinical subtypes of breast cancer, and PMAIP1 was identified as a potential critical gene related to glucose metabolism in breast cancer. Single-cell analysis and Bayes deconvolution jointly confirmed the protective role of the PMAIP1+ luminal cell cluster.
Screening of potential biomarkers using activity-based protein profiling in a rat model of chemotherapy-induced peripheral neuropathy
Authors: Miao He , Ren Yuxuan , Zhou Yile , Miao Mengmeng , Chen Tong , Ni Feng , Chen Xiaowei 
Published: November 2024

AbstractChemotherapy-induced peripheral neuropathy (CIPN) is a debilitating condition affecting cancer patients, often resulting from the use of neurotoxic agents, such as paclitaxel. This study aimed to establish a rat model of CIPN through systemic administration of paclitaxel and to identify potential biomarkers using activity-based protein profiling (ABPP) with a desthiobiotin iodoacetamide (DBIA) probe. Male Sprague-Dawley rats received paclitaxel injections at a dosage of 2 mg/kg on Days 0, 2, 4, and 6. Behavioral assessments revealed significant mechanical and thermal pain hypersensitivity in paclitaxel-treated rats compared to control groups. ABPP analysis identified a total of 2,445 proteins and 6,765 peptides, resulting in the identification of 7 candidate proteins as potential biomarkers for CIPN. Notably, 5 proteins were significantly upregulated, while 2 protein including Q63425 (Prx) demonstrated downregulation in response to paclitaxel. These findings suggest that alterations in candidate protein levels may compromise alterations in the spinal cord in the context of CIPN. This study underscores the utility of ABPP in elucidating the proteomic changes associated with CIPN and highlights the potential of identified biomarkers like Prx for enhancing our understanding of chemotherapy-induced neuropathic pain mechanisms.
High-throughput single molecule microscopy with adaptable spatial resolution using exchangeable oligonucleotide labels
Authors: de Zwaan Klarinda , Huo Ran , Hensgens Myron N.F. , Wienecke Hannah Lena , Tekpinar Miyase , Geertsema Hylkje , Grussmayer Kristin 
Published: November 2024

ABSTRACTSuper-resolution microscopy facilitates the visualization of cellular structures at resolutions approaching the molecular level. Especially, super-resolution techniques based on the localization of single-molecules have relatively modest instrument requirements and are thus good candidates for adoption in bioimaging. However, their low throughput nature hampers their applicability in biomolecular research and screening. Here, we propose a workflow for more efficient data collection, starting with scanning of large areas using fast fluctuation based imaging, followed by single-molecule localization microscopy of selected cells. To achieve this workflow, we exploit the versatility of DNA oligo hybridization kinetics with DNA-PAINT probes to tailor the fluorescent blinking towards high-throughput and high-resolution imaging. Additionally, we employ super-resolution optical fluctuation imaging (SOFI) to analyze statistical fluctuations in the DNA-PAINT binding kinetics, thereby tolerating much denser blinking and facilitating accelerated imaging speeds. Thus, we demonstrate 30-300-fold faster imaging of different cellular structures compared to conventional DNA-PAINT imaging, albeit at a lower resolution. Notably, by tuning image medium and data processing though, we can flexibly switch between high-throughput SOFI (scanning a FOV of 0.65mm× 0.52mmwithin 4 minutes of total acquisition time) and super-resolution DNA-PAINT microscopy and thereby demonstrate that combining DNA-PAINT and SOFI enables to adapt image resolution and acquisition time based to the imaging needs. We envision this approach to be especially powerful when combined with multiplexing and 3D imaging.
Graph-Regularized Optimal Transport for Single-Cell Data Integration
Authors: Wang Zexuan , Zhan Qipeng , Shen Li 
Published: November 2024

AbstractRecent advancements in single-cell omics technologies have enabled comprehensive analyses of cellular processes. However, due to the lack of co-assay sequencing technologies, single-cell omics datasets often comprise unpaired observations with varying feature dimensions. In this study, we present Graph-Regularized Optimal Transport for Single-Cell Data Integration (GROT), a computational method that aligns different multi-omics datasets without requiring correspondence information. GROT achieves global alignment through optimal transport while preserving local structure via graph regularization. We demonstrate its effectiveness on four simulated datasets and two real-world datasets, achieving superior performance compared to current state-of-the-art unsupervised alignment methods. The software is available athttps://github.com/PennShenLab/GROT.
A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs
Authors: Subbanna Mythili S. , Winters Matthew J. , Örd Mihkel , Davey Norman E. , Pryciak Peter M. 
Published: November 2024

ABSTRACTTransient protein-protein interactions play key roles in controlling dynamic cellular responses. Many examples involve globular protein domains that bind to peptide sequences known as Short Linear Motifs (SLiMs), which are enriched in intrinsically disordered regions of proteins. Here we describe a novel functional assay for measuring SLiM binding, called Systematic Intracellular Motif Binding Analysis (SIMBA). In this method, binding of a foreign globular domain to its cognate SLiM peptide allows yeast cells to proliferate by blocking a growth arrest signal. A high-throughput application of the SIMBA method involving competitive growth and deep sequencing provides rapid quantification of the relative binding strength for thousands of SLiM sequence variants, and a comprehensive interrogation of SLiM sequence features that control their recognition and potency. We show that multiple distinct classes of SLiM-binding domains can be analyzed by this method, and that the relative binding strength of peptides in vivo correlates with their biochemical affinities measured in vitro. Deep mutational scanning provides high-resolution definitions of motif recognition determinants and reveals how sequence variations at non-core positions can modulate binding strength. Furthermore, mutational scanning of multiple parent peptides that bind human tankyrase ARC or YAP WW domains identifies distinct binding modes and uncovers context effects in which the preferred residues at one position depend on residues elsewhere. The findings establish SIMBA as a fast and incisive approach for interrogating SLiM recognition via massively parallel quantification of protein-peptide binding strength in vivo.
A mathematical model informs optimal fungicide use against Sclerotinia stem rot to maximize profits in soybean production
Authors: Byer Tanner , Hatfield Tad , Kadelka Claus 
Published: November 2024

AbstractSclerotinia sclerotiorum, the causative agent of stem rot (SR), is a significant yield-limiting disease affecting soybean crops in the temperate climates around the globe. Effective disease management practices rely on fungicides to mitigate the growth and spread of the disease. To infer optimal, profit-maximizing fungicide application rates, this study develops a mathematical model of mold and soybean growth with a requisite profit function. Sensitivity of the optimal fungicide application rate was computed against profit parameters (fungicide cost and soybean bushel price), and model parameters (mold growth rate, maximal SR damage to crops and fungicide efficiency). Expectantly, higher soybean bushel prices, rates of mold growth, and maximal mold damage to crops return elevated optimal fungicide rates. In contrast, higher levels of fungicide efficiency motivate lower optimal fungicide rates. The model also reveals a discontinuity in the optimal fungicide application rates for elevated fungicide costs; in this economic context, it becomes more profitable to apply no fungicide rather than low, ineffectual amounts that still allow mold to reach near-maximal outbreak levels in a finite time period. Future refinements of the model will incorporate variable mold growth rates modeled on annual weather patterns, crop rotation practices, and further exploring the relationships that soybean densities and row spacing have on mold growth, in order to build a more robust system to analyze the long-term effect of disease behavior on soybean crop yield.
Single-cell, spatial, and fate-mapping analyses uncover niche dependent diversity of cochlear myeloid cells
Authors: Chiot Aude , Felgner Max J. , Brownell Dillon , Rott Katherine H. , Bogachuk Alina , Rosmus Dennis-Dominik , Masuda Takahiro , Ching Audrey , Atkinson Patrick J. , Prinz Marco , Sachs Karen , Cheng Alan G. , Wieghofer Peter , Ajami Bahareh 
Published: November 2024

SummaryRecent advances in fate mapping and single-cell technologies have revealed how the dynamics and function of tissue-resident macrophages are shaped by their environment. However, macrophages in sensory organs such as the cochlea where the central nervous system and peripheral nervous system meet remain understudied. Combining single-cell transcriptomics, fate mapping, and parabiosis experiments, we show that five types of myeloid cells including three tissue-resident macrophage subpopulations, coexist in the mouse cochlea. The three macrophage subsets showed different potential functions in relationship with their specific topography across cochlear compartments. Further analysis revealed that they were partially derived from yolk sac progenitors during development, while in adulthood, most cochlear macrophages were long-term resident. Finally, we showed that cochlear macrophage morphology and density changed during aging. Our findings show that cochlea is a microenvironment with a unique heterogeneity of macrophages in terms of gene expression, spatial distribution, ontogeny, and function.
Loss of DOT1L function disrupts neuronal transcription, animal behavior, and leads to a novel neurodevelopmental disorder
Authors: Maroni Marissa J. , Barton Melissa , Lynch Katherine , Deshwar Ashish R. , Campbell Philip , Millard Josephine , Lee Rachel , Cohen Annastelle , Paranjapye Alekh , Faundes Víctor , Repetto Gabriela M. , McKenna Caoimhe , Shillington Amelle L. , Phornphutkul Chanika , Mancini Grazia MS. , Schot Rachel , Barakat Tahsin Stefan , Richmond Christopher M. , Lauzon Julie , Elsayed Ibrahim Ahmed Ibrahim , Benito Daniel Natera-de , Ortez Carlos , Estevez-Arias Berta , Lecoquierre François , Cassinari Kévin , Guerrot Anne-Marie , Levy Jonathan , Latypova Xenia , Verloes Alain , Innes A. Micheil , Yang Xiao-Ru , Banka Siddharth , Vill Katharina , Jacob Maureen , Kruer Michael , Skidmore Peter , Galaz-Montoya Carolina I. , Bakhtiari Somayeh , Mester Jessica L. , Granato Michael , Armache Karim-Jean , Costain Gregory , Korb Erica 
Published: November 2024

ABSTRACTIndividuals with monoallelic pathogenic variants in the histone lysine methyltransferase DOT1L display global developmental delay and varying congenital anomalies. However, the impact of monoallelic loss ofDOT1Lremains unclear. Here, we present a largely female cohort of 11 individuals withDOT1Lvariants with developmental delays and dysmorphic facial features. We found thatDOT1Lvariants include missense variants clustered in the catalytic domain, frameshift, and stop-gain variants. We demonstrate that specific variants cause loss of methyltransferase activity and therefore sought to define the effects of decreased DOT1L function. Using RNA-sequencing of cultured neurons and single nucleus RNA-sequencing of mouse cortical tissue, we found that partialDot1ldepletion causes sex-specific transcriptional responses and disrupts transcription of synaptic genes. Further,Dot1lloss alters neuron branching and expression of synaptic proteins. Lastly using zebrafish and mouse models, we found behavioral disruptions that include sex-specific deficits in mice. Overall, we define how DOT1L loss leads to neurological dysfunction by demonstrating that partialDot1lloss impacts transcription, neuron morphology, and behavior across multiple models and systems.