bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing microglial signaling dynamics during inflammation using single-cell mass cytometry
Authors: Kumar Sushanth , Kahle August D. , Keeler Austin B. , Zunder Eli R. , Deppmann Christopher D. 
Published: July 2024

AbstractMicroglia play a critical role in maintaining central nervous system (CNS) homeostasis and display remarkable plasticity in their response to inflammatory stimuli. However, the specific signaling profiles that microglia adopt during such challenges remain incompletely understood. Traditional transcriptomic approaches provide valuable insights, but fail to capture dynamic post-translational changes. In this study, we utilized time-resolved single-cell mass cytometry (CyTOF) to measure distinct signaling pathways activated in microglia upon exposure to bacterial and viral mimetics—lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (Poly(I:C)), respectively. Furthermore, we evaluated the immunomodulatory role of astrocytes on microglial signaling in mixed cultures. Microglia or mixed cultures derived from neonatal mice were treated with LPS or Poly(I:C) for 48 hrs. Cultures were stained with a panel of 33 metal-conjugated antibodies targeting signaling and identity markers. High-dimensional clustering analysis was used to identify emergent signaling modules. We found that LPS treatment led to more robust early activation of pp38, pERK, pRSK, and pCREB compared to Poly(I:C). Despite these differences, both LPS and Poly(I:C) upregulated the classical activation markers CD40 and CD86 at later time-points. Strikingly, the presence of astrocytes significantly blunted microglial responses to both stimuli, particularly dampening CD40 upregulation. Our studies demonstrate that single-cell mass cytometry effectively captures the dynamic signaling landscape of microglia under pro-inflammatory conditions. This approach may pave the way for targeted therapeutic investigations of various neuroinflammatory disorders. Moreover, our findings underscore the necessity of considering cellular context, such as astrocyte presence, in interpreting microglial behavior during inflammation.Main PointsTime-resolved single cell mass cytometry delineates microglial signaling pathways following LPS or Poly(I:C) treatment. Astrocyte presence led to selective reduction of key microglial signaling nodes along with terminal inflammatory profiles.
Active Learning-Assisted Directed Evolution
Authors: Yang Jason , Lal Ravi G. , Bowden James C. , Astudillo Raul , Hameedi Mikhail A. , Kaur Sukhvinder , Hill Matthew , Yue Yisong , Arnold Frances H. 
Published: July 2024

ABSTRACTDirected evolution (DE) is a powerful tool to optimize protein fitness for a specific application. However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior. Here, we present Active Learning-assisted Directed Evolution (ALDE), an iterative machine learning-assisted DE workflow that leverages uncertainty quantification to explore the search space of proteins more efficiently than current DE methods. We apply ALDE to an engineering landscape that is challenging for DE: optimization of five epistatic residues in the active site of an enzyme. In three rounds of wet-lab experimentation, we improve the yield of a desired product of a non-native cyclopropanation reaction from 12% to 93%. We also perform computational simulations on existing protein sequence-fitness datasets to support our argument that ALDE can be more effective than DE. Overall, ALDE is a practical and broadly applicable strategy to unlock improved protein engineering outcomes.
Disentangling the mutational effects on protein stability and interaction of human MLH1
Authors: Larsen-Ledet Sven , Panfilova Aleksandra , Stein Amelie 
Published: July 2024

AbstractMissense mutations can have diverse effects on proteins, depending on their location within the protein and the specific amino acid substitution. Mutations in the DNA mismatch repair geneMLH1are associated with Lynch syndrome, yet the underlying mechanism of most disease-causing mutations remains elusive. To address this gap, we aim to disentangle the mutational effects on two essential properties for MLH1 function: protein stability and protein-protein interaction. We systematically examine the cellular abundance and interaction with PMS2 of 4839 (94%) MLH1 variants in the C-terminal domain. Our combined data shows that most MLH1 variants lose interaction with PMS2 due to reduced cellular abundance. However, substitutions to charged residues in the canonical interface lead to reduced interaction with PMS2. Unexpectedly, we also identify a distal region in the C-terminal domain of MLH1 where substitutions cause both decreased and increased binding with PMS2, and propose a region in PMS2 as the binding site. Our data successfully distinguish benign from pathogenic MLH1 variants and correlate with thermodynamic stability predictions and evolutionary conservation. This work provides mechanistic insights into variant consequences and may help interpret MLH1 variants.Author SummaryMutations in proteins, including single amino acid substitutions, can disrupt normal cellular function and lead to diseases. Hence, there is great interest in understanding their consequences from both basic science and clinical genetics perspectives. Loss-of-function variants in the human mismatch repair protein MLH1 are associated with Lynch syndrome, a hereditary condition that significantly increases the risk of certain cancers. Detailed insights into the molecular consequences of MLH1 variants are essential for understanding the mechanisms underlying Lynch syndrome. In this study, we use high-throughput experimental approaches to test how missense mutations affect the cellular abundance of MLH1 and the interaction with its partner, PMS2. We find that many variants disrupting the interaction with PMS2 also lead to reduced cellular abundance levels, suggesting a strong relationship between protein stability and interaction in MLH1. Additionally, we identify a potential novel interaction site between MLH1 and PMS2, where mutations in MLH1 either increase or decrease interaction without affecting abundance. Our datasets are in line with the classification of clinically annotated MLH1 variants and may aid in interpreting variants of uncertain significance, while also providing new insights into the molecular details of the interaction with PMS2.
Cognitive sequences in obsessive-compulsive disorder are supported by frontal cortex ramping activity and mediated by symptom severity
Authors: Doyle Hannah , Garnaat Sarah , McLaughlin Nicole , Desrochers Theresa M. 
Published: July 2024

AbstractCompleting sequences is part of everyday life. Many such sequences can be considered abstract – that is, defined by a rule that governs the order but not the identity of individual steps (e.g., getting dressed for work). Over-engagement in ritualistic and repetitive behaviors seen in obsessive-compulsive disorder (OCD) suggests that abstract sequences may be disrupted in this disorder. Previous work has shown the necessity of the rostrolateral prefrontal cortex (RLPFC) for abstract sequence processing and that neural activity increases (ramps) in this region across sequences (Desrochers et al., 2015, 2019). Neurobiological models of the cortico-striatal-thalamo-cortical (CSTC) loops describe prefrontal circuitry connected to RLPFC and that is believed to be dysfunctional in OCD. As a potential extension of these models, we hypothesized that neural dynamics of RLPFC could be disrupted in OCD during abstract sequence engagement. We found that neural dynamics in RLPFC did not differ between OCD and healthy controls (HCs), but that increased ramping in pregenual anterior cingulate cortex (rACC), and superior frontal sulcus (SFS) dissociates these two groups in an abstract sequence paradigm.Further, we found that anxiety and depressive symptoms mediated the relationship between observed neural activity and behavioral differences observed in the task. This study highlights the importance of investigating ramping as a relevant neural dynamic during sequences and suggests expansion of current neurobiological models to include regions that support sequential behavior in OCD. Further, our results may point to novel regions to consider for neuromodulatory treatments of OCD in the future.Significance StatementCompleting sequences of tasks is crucial for functional day-to-day living. The possible disruption of this cognitive process in obsessive-compulsive disorder (OCD) urges the investigation of such behavior and its neural underpinnings in this disorder. Our findings elucidate novel cortical regions that support abstract sequential behavior in OCD, highlighting the potential contribution of ramping dynamics to pathology. Further, our results may refine models of dysfunctional neural circuits in OCD, which could inform future treatments and diagnostic criteria.
Genetic Deletion of Skeletal Muscle Inositol Polyphosphate Multikinase Disrupts Glucose Homeostasis and Impairs Exercise Tolerance
Authors: Lee Ji-Hyun , Jung Ik-Rak , Tu-Sekine Becky , Jin Sunghee , Anokye-Danso Frederick , Ahima Rexford S. , Kim Sangwon F. 
Published: July 2024

AbstractInositol phosphates are critical signaling messengers involved in a wide range of biological pathways in which inositol polyphosphate multikinase (IPMK) functions as a rate-limiting enzyme for inositol polyphosphate metabolism. IPMK has been implicated in cellular metabolism, but its function at the systemic level is still poorly understood. Since skeletal muscle is a major contributor to energy homeostasis, we have developed a mouse model in which skeletal muscle IPMK is specifically deleted and examined how a loss of IPMK affects whole-body metabolism. Here, we report that mice in which IPMK knockout is deleted, specifically in the skeletal muscle, displayed an increased body weight, disrupted glucose tolerance, and reduced exercise tolerance under the normal diet. Moreover, these changes were associated with an increased accumulation of triglyceride in skeletal muscle. Furthermore, we have confirmed that a loss of IPMK led to reduced beta-oxidation, increased triglyceride accumulation, and impaired insulin response in IPMK-deficient muscle cells. Thus, our results suggest that IPMK mediates the whole-body metabolism via regulating muscle metabolism and may be potentially targeted for the treatment of metabolic syndromes.
CUT&Tag for high-resolution epigenomic profiling from a low amount ofArabidopsistissue
Authors: Fu Yixuan , Schmid Marc W. , Simonini Sara 
Published: July 2024

AbstractBackgroundThe genome-wide profiling of chromatin states that are defined by different histone post-translational modifications, known as epigenomic profiling, is crucial for understanding the epigenetic regulations of gene expression, both in animal and plant systems. CUT&Tag (Cleavage Under Targets and Tagmentation, [1]) is a novel enzyme-tethering method for epigenomic profiling, initially developed for mammalian cells. CUT&Tag has several advantages compared to the most commonly used epigenomic profiling methods such as Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-seq). CUT&Tag allows epigenenomic profiling from a much less amount of starting material compared to ChIP-seq. CUT&Tag is based on thein situcleavage of DNA by enzymes tethered to antibodies, while in ChIP-seq, the cleavage is done by a nearly random fragmentation step. In theory, this difference in the way of cleaving DNA allows CUT&Tag to reach a higher resolution compared to ChIP-seq. Therefore, CUT&Tag holds the potential to profile the genome-wide distribution at a high resolution even from a small amount of plant tissues.ResultsWe profiled the genome-wide distribution of three histone modifications, H3K27me3, H3K4me3 and H3K27Ac, from a few seedlings ofArabidopsisthat weighed around 0.01 grams. By comparing the H3K27me3 profiles generated from ChIP-seq and CUT&Tag, we showed that CUT&Tag and ChIP-seq capture the same broad lines of the epigenomes, but they also revealed different sets of peaks. Analysis using the CUT&Tag datasets for the three histone modifications revealed their genomic locations and their relationship with the gene expression level, which are consistent with the expected effect of these histone marks on gene transcription. By comparing to the nucleosome occupancy data, we show that CUT&Tag reached nucleosomal resolution, a much higher resolution than ChIP-seq. In the end, we presented that the increased resolution of CUT&Tag could better reveal the exon enrichment of histone modifications and the epigenetic states of the +1 nucleosome, showing benefits and advantages that this technique could bring to the field of plant epigenetics and chromatin study in general.ConclusionCUT&Tag is a valid, easy-to-perform, cost-effective, and reliable approach for efficient epigenomic profiling inArabidopsis, even with limited amount of starting material and provides a higher resolution compared to ChIP-seq. Because the CUT&Tag protocol starting input is isolated nuclei, it is also applicable to other model and non-model plants.
The connectional diaschisis and normalization of cortical language network dynamics after basal ganglia and thalamus stroke
Authors: Chen Qingwen , Guo Xiaolin , Zhong Tao , Yang Junjie , Gao Xiaowei , Hu Zhe , Li Junjing , Liu Jiaxuan , Wang Yaling , Qu Zhiheng , Li Wanchun , Li Zhongqi , Li Wanjing , Huang Yien , Chen Jiali , Wen Hao , Zhang Ye , Yuan Binke , Gao Han 
Published: July 2024

AbstractStroke affecting the basal ganglia and thalamus can lead to language deficits. In addition to the lesion’s direct impact on language processing, connectional diaschisis involving cortical-subcortical interactions also plays a critical role. This study investigated connectional diaschisis using the “dynamic meta-networking framework of language” in patients with basal ganglia and thalamus stroke, analyzing longitudinal resting-state fMRI data collected at 2 weeks (n = 32), 3 months (n = 19), and one year post-stroke (n = 23). As expected, we observed dynamic cortico-subcortical interactions between cortical language regions and subcortical regions in healthy controls (HC, n = 25). The cortical language network exhibited dynamic domain-segregation patterns in HCs, severely disrupted in the acute phase following stroke. The connectional diaschisis manifested as dual effects characterized by both hypo- and hyper-connectivity, which positively and negatively correlated with language deficits, respectively. State-specific changes in nodal and topological properties were also identified. Throughout language recovery, cortical language network dynamics gradually normalized toward sub-optimal domain-segregation patterns, accompanied by the normalization of nodal and topological properties. These findings underscore the crucial role of cortico-subcortical interactions in language processing.
Economic growth and deviations from the equilibrium exchange rate: a panel ARDL and panel NARDL approach
Authors: Ramos-Herrera Maria Del Carmen 
Published: July 2024

Purpose
The purpose of this study is to provide empirical evidence on the impact of deviations from the long-run sustainable real exchange rate (RER) equilibrium on real economic growth rate applying panel autoregressive distributed lag model (ARDL) (Pooled Mean Group, Mean Group and Dynamic Fixed Effects estimators) in a dynamic heterogeneous panel setting and panel NARDL for the largest database covering 104 countries during 1995–2022 period developed by Couharde et al. (2017).

Design/methodology/approach
The EQCHANGE database makes available not only the equilibrium RER but also misalignments according to the Behavioral Equilibrium Exchange Rate approach for each country. One of the main objectives is to examine whether undervaluation or overvaluation RER can imply different responses on economic performance trying to differentiate between short and long run effects. Additionally, the authors consider the World Bank (WB)’s income classifications to compare the asymmetries attending to high-income, upper-middle-income, lower-middle-income and low-income levels.

Findings
Applying the panel ARDL technique, the results suggest that the RER misalignments have a negative but not significant effect on the short-run, nevertheless a negative and highly significant impact on real economic growth rate is detected on the long-run. Considering the panel NARDL, the asymmetric relationship between RER misalignment and economic growth rate is supported considering all countries in the long-run (in the short-term is not significant). In the long run is detected that undervaluation can promote economic growth rate, rather than overvaluation which can harm the economic performance. Additionally, the WB and the International Monetary Fund (IMF) income’s classifications have been applied and the long-run symmetry test is strongly rejected regardless of income group.

Originality/value
To the best of the author knowledge, this is the first time the non-linear panel ARDL methodology has been applied for analyzing the impact of deviations from the long-run sustainable RER equilibrium on real economic growth. This allows us to see the asymmetric effect not seen before. The panel ARDL estimation can efficiently performed regardless of the integration level of the variables, additionally, it is consistent even in the presence of endogeneity. Besides, another advantage of this method is that it is possible to reflect not only the short but also the long-run dynamics. Moreover, this analysis offers a comparison between linear panel ARDL and non-linear to compare the advantages from the former. Additionally, this study covers the largest database, in particular, 104 countries during the 1995–2022 period implemented with the Couharde et al. (2017) EQCHANGE database. Finally, it is compared the asymmetries attending to different income classifications.
Customer-oriented front-line employees' voice behaviours in the hospitality industry: a comprehensive literature review
Authors: Memon Khalid Rasheed , Ghani Bilqees , Han Heesup 
Published: July 2024

PurposeUsing employee voice to advocate for customers' requirements, improves hospitality service. Organizations must understand what motivates or deters employee customer-oriented voice behaviour (COVB) to achieve its goals and enhance performance. This research investigates the predictors and outcomes of COVB of front-line employees (FLEs) in the hotel industry.Design/methodology/approachThe study used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to steer the article search, screening, and inclusion. The research identified the extant studies conducted in both, high/low power distance countries that met the search criteria using the databases of SCOPUS, Web of Science, EBSCOHost and through snowballing of references.FindingsThe content analysis of 55 selected studies identified four themes that explain FLEs’ COVB in the hospitality industry. These four themes include customer-related, employee-related, organizational and leadership factors. Moreover, it was found that theoretical frameworks of the most of published studies are dominated by social exchange and conservation resource theories.Practical implicationsThis study suggests hospitality firms to develop management strategies to foster FLEs COVB especially long-term personality trainings for FLEs is suggested for innovative and novel ideas.Originality/valueThis is the first study, as per our knowledge, on the hospitality industry that has been conducted to analyse and synthesize the literature related to FLEs’ COVB.
Integration through education: utilizing project ECHO to mitigate fragmentation and support adaptive expert care in HIV Psychiatry
Authors: Chaukos Deanna , Genus Sandalia , Guimond Timothy , Mylopoulos Maria 
Published: July 2024

PurposeCare of complex patients requires collaboration across hospital and community settings. Yet there is little recognition of the capabilities that healthcare workers need to effectively implement integrated care. An adaptive expertise theoretical framework can inform educational efforts that aim to give providers the abilities to navigate complexity and ambiguity in the healthcare system, including across hospital and community settings. Prior education research in the HIV sector has demonstrated that adaptive expert skills can be cultivated through education that emphasizes perspective exchange, inviting uncertainty in practice and integration of diverse perspectives on care.Design/methodology/approachThese principles informed the creation of an Extension for Community Healthcare Outcomes (ECHO) in HIV Psychiatry – the first ECHO directed at a non-clinical, community health worker (CHW) audience. The goal was to improve informal collaborations across hospitals and communities.FindingsParticipation in the ECHO was robust, with significant on-camera engagement. Participants attributed success of the ECHO to key themes: explicit value placed on all kinds of knowledge (not simply clinical knowledge), emphasis on approaches for navigating ambiguity and complexity and engagement in perspective exchange for provision of integrated, team-based care. Future cycles of ECHO HIV Psychiatry are being pursued, with a focus on the development of adaptive expert capabilities and the impact on integration of care between community and hospital services.Originality/valueTo our knowledge, this is the only ECHO that is specifically aimed at frontline CHWs.
Heritage yet contemporary: an aesthetic cultural precept explaining diasporic consumer aesthetic appreciation for package design
Authors: Buschgens Mark , Figueiredo Bernardo , Blijlevens Janneke 
Published: July 2024

Purpose
This paper aims to examine how visual elements used in packaging design relate to diasporic consumer identity and influence aesthetic appreciation.

Design/methodology/approach
Drawing on social identity theory, research on aesthetic principles and using a mixed methods approach, two studies are conducted. Study 1 involves a qualitative exploration of the nature of diasporic consumer identity and its relation with visual design in packaging. Study 2 involves quantitative testing and calibration of this relationship and its subsequent influence on aesthetic appreciation.

Findings
Diasporic consumers from the Middle East appreciate hybrid visual designs and prefer packaging that strikes an optimum balance of visual elements (colour, shapes, patterns) from the heritage aspects of their ancestral homeland and more contemporary aspects from their culture of living. Preference for balance elicits an overall positive diasporic identity feeling that mediates the relationship with aesthetic appreciation of visual design in packaging.

Research limitations/implications
These findings offer new knowledge about the role of visual design in packaging in delivering symbolic value to diasporic consumers, evidencing how diasporic consumers’ dual identities shape aesthetic appreciation and preferences for hybrid visual designs.

Practical implications
Provides marketing practitioners and packaging designers with a concise and contextual directive for creating visual designs that appeal to a growing segment of diasporic consumers.

Originality/value
This research draws on social identity theory to uncover an aesthetic cultural precept – heritage, yet contemporary – that can inform the development of packaging designs targeting diasporic consumers.