bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decipher: A computational pipeline to extract context-specific mechanistic insights from single-cell profiles
Authors: Basto Edgar , Wajid Bilal , Read James , Armitage Jesse , Waithman Jason , Small Michael , Bosco Anthony 
Published: May 2024

AbstractThe advent of single-cell profiling technologies has revolutionized our understanding of the cellular and molecular states that underpin disease states and response to therapies. However, current computational tools cannot recover both known and novel mechanistic insights at distinct layers of biological regulation in an unbiased manner. Here, we presentDecipher, a novel computational pipeline that builds integrated cell signalling networks from single-cell profiles in a context-specific, data-driven manner and identifies the key cellular and molecular events that drive disease. We benchmarkedDecipheragainst existing tools and found it could recover known, experimentally determined cytokine signalling pathways with high accuracy, whilst maintaining the flexibility to detect novel pathways and context-specific effects. Notably,Decipherreports a manageable set of interactions that can be aggregated into global cell-to-cell signalling maps that are interpretable. In addition, we utilisedDecipherto unveil the cellular and molecular mechanisms driving a novel population of inflammatory monocytes enriched with interferon stimulated genes that is markedly increased in frequency following secondary immunization with the Pfizer-BioNTech COVID-19 mRNA vaccine. Taken together, our findings demonstrate thatDeciphercan decode signalling pathways and report on ligand-receptor mediated transcription factor – target gene networks that underlie processes in homeostasis and disease, as well as cellular responses to therapies. We presentDecipheras an invaluable new tool for the discovery of novel therapeutic targets and the development of new medicines.
When the liver is in poor condition, so is the heart - cardiac remodelling in MASH mouse models
Authors: Bott Sebastian , Lallement Justine , Marino Alice , Daskalopoulos Evangelos P. , Beauloye Christophe , Esfahani Hrag , Dessy Chantal , Leclercq Isabelle Anne 
Published: May 2024

AbstractMetabolic dysfunction-associated steatohepatitis (MASH) confers a risk for cardiovascular diseases in patients. Animal models may help exploring the mechanisms linking liver and heart diseases. Hence, we explored the cardiac phenotype in MASH mouse models.MethodsWe evaluated pathological alterations in liver and heart infoz/fozmice fed a high fat diet for 24 or 60 weeks and in C57BL/6J mice fed a high fat, high fructose diet for 60 weeks. Angiotensin ll (Angll) was used as an additional cardiovascular stressor.ResultsFoz/fozmice with fibrosing MASH developed cardiac hypertrophy with adverse cardiac remodelling not seen in WT similarly fed the high fat diet. Angll caused hypertension and upregulated the expression of genes contributing to pathological cardiac hypertrophy (Nppa,Myh7) more severely so infoz/fozmice than in controls. After 60 weeks of HFD, while liver disease had progressed to burn-out non steatotic MASH with hepatocellular carcinoma in 50% of the animals, the cardiomyopathy did not. In an independent model (C57BL/6J mice fed a high fat, high fructose diet), moderate fibrosing MASH is associated with cardiac fibrosis and dysregulation of genes involved in pathological remodelling (Collal,Col3al,Vim,Myh6,Slc2al).ConclusionAnimals with MASH present consistent adverse structural changes in the heart with no patent alteration of cardiac function even when stressed with exogenous Angll. Liver disease, and not overfeeding or aging alone, is associated with this cardiac phenotype. Our findings confirmfoz/fozmice as suitable for studying links between MASH and heart structural changes ahead of heart failure.
Behavioural evidence of spectral opponent processing in the visual system of stomatopod crustaceans
Authors: Wang Ching-Wen Judy , Marshall Justin 
Published: May 2024

AbstractStomatopods, commonly known as mantis shrimps, possess an intricate colour vision with up to 12 photoreceptor classes organised in four specialised ommatidia rows (rows 1-4 in the midband region of the eye) for colour perception. While 2-4 spectral sensitivities suffice for most visual systems, the mechanism behind stomatopods’ 12-channel colour vision remains unclear. Based on neuroarchitecture, it was initially suggested that rows 1-4 may function as four parallel dichromatic channels allowing fine spectral discrimination and strong colour constancy in narrow spectral zones. Subsequently, unexpectedly low resolution in behavioural experiments indicated that a binning processing system may operate instead of or in addition to the ‘normal’ opponent processing system, categorising information into separate channels to create an activation pattern for rapid colour recognition. Previous anatomical and behavioural studies have speculated on the potential coexistence of these two systems in stomatopods’ colour vision. However, no behavioural study has specifically investigated the potential for colour opponency in their colour vision. Our findings provide the first direct behavioural evidence for spectral opponency in stomatopods’ visual system, showing that rows 1-4 operate, at least some of the time, as multiple dichromatic channels.
Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions
Authors: Lalit Farhaan , Jose Antony M 
Published: May 2024

AbstractProgress in biology has generated numerous lists of genes that share some property. But advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing inC. elegansto illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field was captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Some proteins encoded by these understudied genes are predicted to physically interact with known regulators of RNA silencing, suggesting feedback regulation. Predicted interactions with proteins that act in other processes and the clustering of studied genes among the most frequently perturbed suggest regulatory links connecting RNA silencing to other processes like the cell cycle and asymmetric cell division. Thus, among the gene products altered when a process is perturbed could be regulators of that process acting to restore homeostasis, which provides a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process.
Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs
Authors: Manning Aidan C. , Bashir Mahmoud M. , Jimenez Ariana R. , Upton Heather E. , Collins Kathleen , Lowe Todd M. , Tucker Jessica M. 
Published: May 2024

AbstractTransfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.ImportanceDiverse conditions of infection and cellular stress incite the cleavage of transfer RNAs, leading to the formation of tRNA fragments which can directly regulate gene expression. In our study of gammaherpesviruses, such as the murine herpesvirus 68 and human oncogenic Kaposi Sarcoma associated Herpesvirus, we discovered that transfer RNA regulation and cleavage is a key component of gene reprogramming during infection. We present the first in-depth profile of tRNA fragment generation in response to DNA virus infection, using state-of-the-art sequencing techniques that overcome several challenges with tRNA sequencing. We present several lines of evidence that tRNA fragments are made from newly-transcribed premature tRNAs and propose that this may be a defining characteristic of tRNA cleavage in some contexts. Finally, we show that tRNA splicing machinery is involved with the formation of some MHV68-induced tRNA fragments, with a key regulator of splicing, CLP1, required for maximal viral titer. Together, we posit that tRNA processing may be integral to the elegant shift in gene expression that occurs during viral take-over of the host cell.
The embryo-derived protein PDI is highly conserved among placental mammals and alters the function of the endometrium in species with different implantation strategies
Authors: Tinning Haidee , Taylor Alysha , Wang Dapeng , Pullinger Anna , Oikonomou Georgios , Velazquez Miguel A. , Thompson Paul , Treumann Achim , Ruane Peter T. , O’Connell Mary J , Forde Niamh 
Published: May 2024

ABSTRACTPregnancy establishment in mammals requires a complex sequence of events, including bi-lateral embryo-maternal communication, leading up to implantation. This is the time when most pregnancy loss occurs in mammals (including humans and food production species) and dysregulation in embryo-maternal communication contributes to pregnancy loss. Embryo-derived factors modify the function of the endometrium for pregnancy success. We hypothesise that these previously unexplored conceptus-derived proteins may be involved in altering the function of the endometrium to facilitate early pregnancy events in mammals with different early pregnancy phenotypes. Here, we show that protein disulphide-isomerase (PDI) is a highly conserved protein among mammals, and provide evidence for a species-specific roles for PDI in endometrial function in mammals with different implantation strategies. We show how PDI alters the endometrial transcriptome in human and bovinein vitroin a species-specific manner, and using a microfluidic approach we demonstrate that it alters the secretome capability of the endometrium. We also provide evidence fromin vitroassays using human-derived cells thatMNS1,a transcript commonly downregulated in response to PDI in human and bovine endometrial epithelial cells, may be involved in the attachment (but not invasion) phase of implantation. We propose that the trophoblast-derived protein PDI, is involved in supporting the modulation of the uterine luminal fluid secreted by the endometrium to support conceptus nourishment, and also in the process of embryo attachment to the uterine lumen for pregnancy success in mammals.SIGNIFICANCE STATEMENTWe provide evidence that a highly conserved protein (PDI) alters the endometrial transcriptome in a species- and cell-specific manner. Exposure of endometrial epithelia to PDI altered genes belonging to immune modulatory, pro-inflammatory, and adhesion-pathways. One transcript, MNS1, was commonly downregulated in endometrial epithelia from species with superficial (bovine) and invasive (human) implantation morphologies. Knockdown of MNS1 expression in humans epithelia altered the ability of human trophoblast BeWo spheroids to attach suggesting a mechanism by which PDI affects implantation in human and bovine. In addition, using a microfluidics approach we have shown that PDI alters the secretome in a species-specific manner demonstrating PDI alters a key function of the endometrium in mammals.
Condensin II activation by M18BP1
Authors: Borsellini Alessandro , Conti Duccio , Cutts Erin , Harris Rebecca J. , Walstein Kai , Graziadei Andrea , Cecatiello Valentina , Aarts Tom F. , Xie Ren , Mazouzi Abdelghani , Sen Sushweta , Hoencamp Claire , Pleuger Richard , Ghetti Sabrina , Oberste-Lehn Lina , Pan Dongqing , Bange Tanja , Haarhuis Judith H.I. , Perrakis Anastassis , Brummelkamp Thijn R. , Rowland Benjamin D. , Musacchio Andrea , Vannini Alessandro 
Published: May 2024

ABSTRACTCondensin complexes promote the drastic spatial rearrangement of the genome upon mitotic entry. Condensin II initiates chromosome condensation in early mitosis. To prevent chromosome condensation during interphase, condensin II is inhibited by MCPH1, but the mechanism is unknown. Through genetic and proteomic approaches, we identify M18BP1, a protein previously associated with centromere identity, as a factor required for condensin II localization to chromatin. M18BP1 directly binds condensin II’s CAP-G2 subunit and competes with MCPH1 for binding. Upon mitotic entry, CDK1 mediated phosphorylation may promote a switch from MCPH1 to M18BP1 binding to activate condensin II. Our results identify a fundamental and evolutionarily conserved mechanism of condensin II activation.
High transmission efficiency collection system for laser-accelerated proton beams based on permanent magnet quadrupoles prefocusing
Authors: Yan Yang , Cheng Hao , Li Yuze , Fang Yanlv , Xia Yadong , He Qiangyou , Li Chentong , Li Fangnan , Guo Zhen , Yan Yiting , Huang Mingfeng , Wu Minjian , Wang Kedong , Zhu Kun , Yan Xueqing , Lin Chen 
Published: May 2024

A new high transmission efficiency, easily tunable, and cost-effective beam collection system is proposed for laser-accelerated proton beams with large divergence angles and wide energy spectra. In previous experiments conducted at the compact laser plasma accelerator platform of Peking University, a beamline was initially constructed with a collection system based on an electromagnetic quadrupoles (EMQs) triplet. However, due to the limited acceptance angle, the EMQs exhibited a monoenergetic transmission efficiency of only 10% to 20% for laser accelerated proton beams. Permanent magnet quadrupoles (PMQs), known for their high magnetic field gradients, compact size, and lower expenses, are well suited for integration with other readily adjustable transmission elements like EMQs and solenoids, effectively enhancing the beam collection capabilities of the system. In this paper, we show that by introducing a pair of centimeter-sized PMQs in front of the EMQs for beam prefocusing, the beam’s transverse size is quickly compressed, enabling transmission of highly divergent protons. Experimental results demonstrate that the prefocusing by PMQs increased the system’s transmission efficiency by a factor of 2.44 to 6.01 compared to the original setup, while also enhancing the energy selection based on stronger chromatic effect. This method can be extended to 100 MeV high-energy proton beamlines and is crucial for applications of laser plasma accelerators.

Published by the American Physical Society
2024
Power dynamics in business relationships in a turbulent environment: focus on anticipated power consequences and value creation
Authors: Siemieniako Dariusz 
Published: May 2024

PurposeI aimed to develop a conceptual model of power dynamics focused on an anticipated power consequences in business relationships in a context of high environmental turbulence. I also intended to discuss the theoretical significance of my findings and indicate future research directions.Design/methodology/approachConceptual article indicating future research directions.FindingsThe proposal of the conceptual model of power dynamics focusing on anticipated power consequences in business relationships.Research limitations/implicationsThe limitations of the presented model stem from the critique of the holistic view. My contribution lies in advancing our understanding of power dynamics in business relationships amid significant environmental change. I elucidate how transformative practices relate to power outcomes and value creation in these relationships.Practical implicationsThe model highlights the importance of a mindful approach to managing business relationships in a turbulent environment. It emphasizes considering expected power outcomes from activities and their impact on creating value in these relationships.Social implicationsThe proposed concept resonates with systems theory, which emphasizes how different levels of business relationships are interconnected. It enables the analysis of power dynamics at the individual level, such as employees, consumers and local communities. These groups often include the most vulnerable individuals impacted by relational business structures.Originality/valueThe focus on anticipated power consequences of transformative practices triggered by high environmental turbulences, while considering the impact of power distribution of relationship actors on the sharing of benefits and costs.
Polychronicity fit and turnover intentions in projects: the mediating roles of exhaustion and work overload
Authors: Shah Syed Waqas , Jepsen Denise Mary , Bankins Sarah 
Published: May 2024

PurposeDespite the deployment of state-of-the-art methodologies for project management, employee turnover in projects remains high. Such turnover has significant costs in terms of replacing personnel, potential deadline overruns and financial expenditure. Employee turnover in project contexts may stem from time-related issues associated with multiple parallel projects and short deadlines. Using person–environment fit and time congruence theories, this research examines the relationship between employee turnover intentions and individual–organizational (I–O) polychronicity fit, which captures the degree of match between individuals’ and organizational preferences for focusing on multiple tasks simultaneously.Design/methodology/approachSurvey data were collected from 309 software project employees in Pakistan. Hypotheses were tested using polynomial regressions and response surface modeling.FindingsI–O polychronicity fit is related to turnover intentions. Turnover intentions are lower when I–O polychronicity fit occurs on the lower end of the polychronicity continuum, whereas turnover intentions are higher when fit is observed on the higher end of the polychronicity continuum. The relationship between I–O polychronicity fit and turnover intentions is significantly explained by exhaustion and perceptions of work overload.Practical implicationsThe study’s insights provide recommendations for organizations to optimally manage multitasking to help retain project employees.Originality/valueThese findings extend our understanding of the underlying mechanisms between I–O polychronicity fit and turnover intentions. Furthermore, this research expounds on how employee exhaustion and perceptions of work overload explain the relationship between I–O polychronicity fit and turnover intentions.
Social network group decision-making model considering interactions between trust relationships and opinion evolution
Authors: Ma Jin , Wu Tong 
Published: May 2024

PurposeSocial network group decision-making (SNGDM) has rapidly developed because of the impact of social relationships on decision-making behavior. However, not only do social relationships affect decision-making behavior, but decision-making behavior also affects social relationships. Such complicated interactions are rarely considered in current research. To bridge this gap, this study proposes an SNGDM model that considers the interaction between social trust relationships and opinion evolution.Design/methodology/approachFirst, the trust propagation and aggregation operators are improved to obtain a complete social trust relationship among decision-makers (DMs). Second, the evolution of preference information under the influence of trust relationships is measured, and the development of trust relationships during consensus interactions is predicted. Finally, the iteration of consensus interactions is simulated using an opinion dynamics model. A case study is used to verify the feasibility of the proposed model.FindingsThe proposed model can predict consensus achievement based on a group’s initial trust relationship and preference information and effectively captures the dynamic characteristics of opinion evolution in social networks.Originality/valueThis study proposes an SNGDM model that considers the interaction of trust and opinion. The proposed model improves trust propagation and aggregation operators, determines improved preference information based on the existing trust relationships and predicts the evolution of trust relationships in the consensus process. The dynamic interaction between the two accelerates DMs to reach a consensus.
Complex environmental control of growth in a dominant Mediterranean‐alpine shrub species
Authors: Albrecht Eike Corina , Dobbert Svenja , Pape Roland , Löffler Jörg 
Published: May 2024

Abstract

Mediterranean‐alpine plants are exposed to harsh conditions, forcing them to perform with well‐adapted physiological strategies to withstand the dual stressors that arise from winter cold and summer drought. Such growth strategies are not yet fully understood, although they gain importance with regard to the resilience of species in the face of ongoing climate variability.

Here, we aimed at understanding shrub growth in a widespread Mediterranean‐alpine species, Cytisus galianoi Talavera & Gibbs. Using long‐term time series of stem diameter change obtained from dendrometer measurements across the species´ range, we were able to characterise its spatiotemporal growth plasticity. Furthermore, separating water‐related fluctuations in stem diameter from irreversible stem increment allowed us to disentangle the species´ seasonal growth patterns. Using fine‐scale measurements of on‐site environmental conditions, we were then able to identify micro‐ecological drivers controlling the species´ growth processes by applying correlation analysis and partial least squares regressions.

We show the species´ adaptation to the spatial heterogeneity across its range for the first time. Our findings highlight that the combination of bimodality and overall high growth plasticity likely allows the species to cover a wide geographical range across alpine areas and over a wide range of weather conditions. We show the environmental control of bimodal growth in C. galianoi, and the importance of pre‐growth environmental control, leading to pronounced carry‐over effects. These lead to a major advantage in resisting adverse growth conditions and adapting to changing conditions.

Synthesis: Overall, our findings improve the understanding of the species´ ecological niche and show that preceding photosynthetic activity helps C. galianoi to perform even under unfavourable conditions in winter and during the active growth phase, challenging the general assumption on the coupling of growth to specific seasons and suggesting that the species is capable of adapting to future climate variability.