bluuebunny/crossref_metadata_2025_split huggingface dataset:
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
Authors: Zheng Hongyu , Sarkar Hirak , Raphael Benjamin J. 
Published: February 2025

AbstractSpatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active development with each technology having varying spatial resolution (subcellular, single-cell, or multicellular regions), gene coverage (targeted vs. whole-transcriptome), and sequencing depth per location. For example, the widely used 10x Genomics Visium platform measures whole transcriptomes from multiple-cell-sized spots, while the 10x Genomics Xenium platform measures a few hundred genes at subcellular resolution. A number of studies apply multiple SRT technologies to slices that originate from the same biological tissue. Integration of data from different SRT technologies can overcome limitations of the individual technologies enabling the imputation of expression from unmeasured genes in targeted technologies and/or the deconvolution of ad-mixed expression from technologies with lower spatial resolution. We introduce Spatial Integration for Imputation and Deconvolution (SIID), an algorithm to reconstruct a latent spatial gene expression matrix from a pair of observations from different SRT technologies. SIID leverages a spatial alignment and uses a joint non-negative factorization model to accurately impute missing gene expression and infer gene expression signatures of cell types from ad-mixed SRT data. In simulations involving paired SRT datasets from different technologies (e.g., Xenium and Visium), SIID shows superior performance in reconstructing spot-to-cell-type assignments, recovering cell-type-specific gene expression, and imputing missing data compared to contemporary tools. When applied to real-world 10x Xenium-Visium pairs from human breast and colon cancer tissues, SIID achieves highest performance in imputing holdout gene expression. A PyTorch implementation of SIID is available athttps://github.com/raphael-group/siid.
Transcriptome-proteome profiling inBurkholderia thailandensisduring the transition from exponential to stationary phase
Authors: Al-Tohamy Ahmed , Donnarumma Fabrizio , Grove Anne 
Published: February 2025

AbstractBacterial cells commonly exist in stationary phase, for instance within a host cell.Burkholderia thailandensisis closely related to, and a surrogate for highly pathogenicBurkholderiaspecies. Understanding the molecular mechanisms that characterize the transition ofB. thailandensisfrom exponential to stationary phases is critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of gene and protein expression changes during entry into stationary phase. We identified 928 differentially expressed genes and 832 differentially expressed proteins. Genes encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were among the most highly upregulated in stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated along with proteins involved in synthesis of secondary metabolites. Markedly downregulated proteins included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during early stationary phase; RpoS is typically abundant during stationary phase and critical for expression of stress-response genes. Our data therefore point to distinct adaptive mechanisms inB. thailandensis, including post-translational regulation.
Perceptual Decision-Making During Whisker-Guided Navigation Causally Depends on a Single Cortical Barrel Column
Authors: Armstrong Alex G. , Vlasov Yurii A. 
Published: February 2025

AbstractPerceptually driven behavioral choices ae thought to develop gradually from sensation to perception in somatosensory cortex to guide decision-making in higher order cortical areas. Primary somatosensory cortex wS1 of rodents related to their mystacial whiskers has been a model system to study this information flow. However, the role of wS1 in this process is often debated based on controversial results of loss-of-function behavioral experiments that often require prolonged training and movement restraints. Here, to elucidate the role of wS1 in decision-making, we develop an ethological whisker-guided virtual reality (VR) paradigm that closely mimics natural navigation in underground burrows. Untrained mice are navigating at high speed the left and right turns by sensing VR walls with just a pair of their C2 whiskers. We inactivate less than 200 neurons in layer 4 of C2 barrel that results in loss of ability to produce turns contralateral to the lesion. Using probabilistic model of collision avoidance in the presence of noise and uncertainties we hypothesize that wS1 is involved in a feedback control loop that requires continuous updates and predictions to infer the optimal path for collision avoidance.
A curated great ape genome diversity panel
Authors: Han Sojung , Riyahi Sepand , Huang Xin , Kuhlwilm Martin 
Published: February 2025

AbstractStudying the genetic diversity of non-human great apes is important for research questions in evolution as well as human diversity and disease. Genomic data of the three great ape clades (Pan, Gorilla, Pongo) has been published across multiple studies over more than one decade. However, unlike in humans, no comprehensive dataset on great ape diversity is available, due to different scopes of the original studies. Here, we present a curated dataset of 203 high coverage (≥12-fold) whole genomes, including 77 chimpanzee, 14 bonobo, 77 gorilla and 35 orangutan individuals sequenced on the Illumina platform. By integrating data from captive individuals, we contextualize them with data from wild individuals. We discuss issues with previously published data leading to removal of individuals due to low sequencing depth, missing data, or occurrence of duplicate individuals. This resource of files in CRAM and gVCF format, as well as segregating sites per clade, will allow researchers to address questions related to human and great ape evolution and diversity in a comparative manner.
Toxoplasma in a natural population of chimpanzees
Authors: Chabry Mathieu , Hobaiter Catherine , Zuberbühler Klaus , Koella Jacob C. 
Published: February 2025

AbstractToxoplasma gondiiis a unicellular parasite that can infect most warm-blooded animals. In humans, it is linked to schizophrenia and other neurological disorders. It is also responsible for congenital toxoplasmosis, which can be lethal or cause severe neurological damage in the developing foetus. More subtle behavioural effects have been observed in various species, including humans, in particular increased risk-taking, which is thought to increase the parasite’s transmission to feline predators, the definitive hosts. We investigated the prevalence ofToxoplasma gondiiin wild eastern chimpanzees (Pan troglodytes schweinfurthii) in the Budongo Forest, Uganda. We tested 45 individuals of two communities, one of which (Sonso) has a home range overlapping with human settlements. In this community, the prevalence was 22.7% (N=5 of 22), whereas in the neighbouring, but more isolated, Waibira community none of the 23 individuals tested were infected. The majority of infected Sonso individuals were adult males and/or high-ranking group members, attributes associated with increased risk-taking behaviour in chimpanzees and other animals. While further work is necessary to reveal the causal relation between infection and behaviour, our findings open new avenues of research for the neural impact of parasites on primate social behaviour.
Second-order nonlinear piezo-optic properties of single crystal lithium niobate thin films
Authors: Pionteck Mike N. , Roeper Matthias , Koppitz Boris , Seddon Samuel D. , Rüsing Michael , Padberg Laura , Eigner Christof , Silberhorn Christine , Sanna Simone , Eng Lukas M. 
Published: February 2025

Stress plays a crucial role in thin films and layered systems, and thus significantly influences the material's electrical, mechanical and (nonlinear) optical responses. Despite lithium niobate's wide applicability as a nonlinear optical material, the impact of mechanical stress on its nonlinear optical properties is not well characterized. In this work, we systematically study both experimentally and theoretically, the nonlinear optical responses of thin film lithium niobate (TFLN) single crystals. Compressive and tensile stress is applied in our experiment using a piezodriven strain cell. We then record the second-harmonic-generated (SHG) response in back-reflection geometry, and compare these results to theoretical modeling using density functional theory (DFT). Both methods consistently reveal that uniaxial stress induces changes of the nonlinear optical susceptibility of certain tensor elements on the order of up to 1 pm/(V GPa). The exact value depends on the tensor element that is addressed in our SHG analysis, on the crystal orientation, and also whether using compressive or tensile stresses. Furthermore, a lowering of the crystal symmetry when applying stress along the x or y crystallographic axes is observed by the appearance of new nonlinear optical tensor elements within the strained crystals.

Published by the American Physical Society
2025
Robust spin-orbit coupling in semimetallic
SrIrO3
under hydrostatic pressure
Authors: Fuchs D. , Jaiswal A. K. , Wilhelm F. , Wang D. , Rogalev A. , Le Tacon M. 
Published: February 2025

The semimetallic behavior of the perovskite iridate SrIrO3 shifts the end member of the strongly spin-orbit (SO) coupled Ruddlesden-Popper series Srn+1IrnO3n+1 away from the Mott insulating regime and the half-filled pseudospin Jeff=12 ground state well established in the layered iridates (n=1 and 2). To investigate the robustness of the SO coupled ground state of SrIrO3, x-ray absorption spectroscopy was carried out at the Ir L2,3 edges under hydrostatic pressure up to 50 GPa at room temperature. The effective SO coupling was deduced from the branching ratio (BR) of the Ir L2 and L3 white lines. With increasing pressure, the BR decreases, and the Ir L2,3 peak positions shift to higher energies. The number of 5d holes remains constant, indicating that the spectral weight redistribution and peak shifts arise from orbital mixing between t2g and eg related states. The expectation value of the angular part of the SO operator 〈LS〉 decreases by ∼15% at 50 GPa. This reduction, which is very similar to that observed in the layered iridates, is well explained by an increase of the octahedral crystal field due to the shortening of the Ir-O bond length under compression. Consistent with theoretical predictions, the orbital mixing and 〈LS〉 decrease as the crystal field increases. However, the effective SO coupling remains robust against pressure and does not indicate a covalency-driven breakdown within the investigated pressure range.

Published by the American Physical Society
2025
SLAM-IMU coupling-based construction personnel positioning in invalid scenario of satellite and aerial triangulation
Authors: Gao Yiling , Wang Chen , Huang Liping , Wang Defa , Chen Zhibin 
Published: February 2025

PurposeTo help supervisors understand the positions of workers in real-time, provide safety guidance for workers and reduce the occurrence of accidents. This study proposes a real-time positioning algorithm based on multi-source information coupling, aiming to solve the problem of workers’ autonomous positioning in signal-blind areas.Design/methodology/approachThe proposed algorithm utilizes the visual SLAM and IMU sensors to perceive the environment, construct three-dimensional images, improve the accuracy of corner point matching, pre-integrate the raw IMU data, and adopt the tightly coupled method to couple the visual and inertial navigation data, thereby establishing a binocular visual SLAM and IMU coupling real-time positioning model.FindingsThe real-time positioning technology based on the coupling of visual SLAM and IMU shows good positioning effect and calculation speed in indoor sites, has good adaptability and accuracy in different building construction scenarios, and the positioning error can be controlled within 3%.Originality/valueThe successful construction of the real-time positioning method effectively alleviates the problem of inaccurate positioning caused by signal blind areas in the existing positioning management system, helps protect the lives and safety of construction site workers and improves the management efficiency of construction site supervisors.
Appraising hyperinflation threat to achieving Sustainable Development Goals 1 and 2: Nigerian public sector construction artisans' perspective
Authors: Ebekozien Andrew , Thwala Wellington Didibhuku 
Published: February 2025

PurposeIn less than a decade, hyperinflation rate increases in many developing countries have raised pertinent concerns about fundamental issues facing fixed salaries of low-income earners. This may hinder achieving Sustainable Development Goals 1 (no poverty) and 2 (zero hunger). There is a paucity of research regarding the impact of the hyperinflation rate on public sector construction artisans. This study investigated the impact of hyperinflation and its outcome on the Nigerian public sector construction artisans and recommended ways to reduce these impacts and, by extension, improve the achievement of Goals 1 and 2.Design/methodology/approachThe researchers adopted a qualitative approach to collect data. This study engaged 30 interviewees across three of Nigeria’s cities using semi-structured interviews. This research adopted a thematic approach and attained saturation at the 26th participant.FindingsThis study shows that the impact of hyperinflation on Nigeria’s public sector construction artisans, if not curbed, might hinder achieving Goals 1 and 2. Findings identified the major impacts and suggested ways to mitigate them and, by extension, improve the achievement of Goals 1 and 2. This includes overhauling the Central Bank of Nigeria (CBN) to create people and investment/production policies, addressing foreign exchange rate volatility through financial stabilisation instruments, overhauling Nigerian National Petroleum Corporation, reinstating fuel subsides and addressing the issue of internal insecurity.Originality/valueAs a part of the research’s implications, this study suggested measures to mitigate hyperinflation on public sector construction artisans. Findings also will stir government policymakers to review existing economic policies (fuel subsidy removal, floating of foreign exchange and high interest rates) to be pro-masses friendly and promote productivity.
Intergenerational justice as a framework for social media archiving
Authors: Shiozaki Ryo 
Published: February 2025

PurposeThis conceptual study aims to explore the rationale of preservation institutions in archiving new types of documents, such as social media, rather than focusing on traditionally valued materials or established cultural heritage.Design/methodology/approachRecognising the need to include the perspectives of both current and future generations, this study reviews and organises various theories of intergenerational justice to determine whether they can provide a solid justification.FindingsNo single theory of intergenerational justice fully endorses the long-term preservation of user-generated content. However, utilitarianism can offer a compelling justification for large-scale archiving, whereas other views, including communitarianism, support selective approaches.Originality/valueThis study is the first to extensively apply intergenerational justice theories to the field of digital preservation, providing a foundational framework for justifying the preservation of emerging forms of digital documents, albeit to a limited extent.
The maverick factor: the role of positively deviant change agents in radical organizational change
Authors: Jordan Ree , Fitzsimmons Terrance W. , Callan Victor J. 
Published: February 2025

PurposeThis paper explores the phenomenon of organizational maverickism, proposing that mavericks, alongside innovators and entrepreneurs, play a crucial role in driving transformational change. While the actions of innovators and entrepreneurs as change agents are well understood, this paper focuses predominantly on how the practices of mavericks also provide significant contributions to achieving game-changing organizational outcomes.Design/methodology/approachA literature review and conceptual paper highlighting the beneficial nature of maverickism to organizational change efforts, positioning maverickism as a valid change agent role alongside entrepreneurship and innovation.FindingsThe positively deviant nature of mavericks has high potential for creating radical organizational change strategies. Organizational change is more likely to be successful when the entrepreneurial, innovator and maverick mindsets are used to their optimum advantage.Research limitations/implicationsFrom this conceptual paper and its arguments, new research directions to guide theory building and organizational practice are identified.Practical implicationsWhen organizational managers and leaders more fully understand the beneficial practices of mavericks, they are more likely to actively employ them in more meaningful roles as organizational change agents, together with innovators and entrepreneurs.Originality/valueThis paper closes the knowledge gap in understanding maverickism that is an under-researched and under-theorized phenomenon. The arguments in this paper identify a number of areas for future research.
Blockchain and smart contracts: transforming digital entrepreneurial finance and venture funding
Authors: Robusti César da Silva , Avelar Aline Bento Ambrósio , Farina Milton Carlos , Gananca Claudio Alexandre 
Published: February 2025

PurposeThis study conducts a systematic review to analyze the impact of blockchain technology and smart contracts on digital entrepreneurial finance and venture funding. It aims to investigate how these technologies can transform business operations, offering enhanced transparency, security and efficiency in various financial contexts.Design/methodology/approachA systematic literature review was conducted following PRISMA guidelines to assess the effectiveness of blockchain and smart contracts in generating business value. The study used the Scopus database to identify relevant articles published between 2015 and 2023. Quantitative and qualitative analyses were performed on the data using IRAMUTEQ software and Bibliometrix tool, both based in the “R” programming language.FindingsThe study reveals significant potential for blockchain and smart contracts to disrupt traditional venture funding models by automating contract execution and reducing administrative costs. Blockchain’s secure, decentralized ledger offers advantages in peer-to-peer transactions and risk mitigation, particularly in supply chain management and international trade. However, challenges related to scalability, energy consumption and regulatory compliance were also identified.Research limitations/implicationsDespite the contributions, systematic review of the literature has limitations. Only articles in English, published in journals, were considered for this research, omitting, for example, conference articles and research in other languages, which may also contain relevant information.Originality/valueThe study contributes to the existing literature by synthesizing recent advancements in blockchain and smart contract applications within entrepreneurial finance. It highlights the transformative potential of these technologies while addressing their limitations and offering insights into future research directions. The findings provide valuable implications for academics, practitioners and policymakers interested in leveraging blockchain for financial innovation.
Transformative service in healthcare: understanding secondary vulnerability and coping mechanisms in end-of-life care
Authors: Carlini Joan , Riedel Aimee , Lehman Kim , Ranse Kristen 
Published: February 2025

PurposeThis study aims to investigate the notion of secondary vulnerability among transformative service providers, particularly frontline healthcare professionals (HCP), during the provision of end-of-life care. It seeks to understand how stressors and coping mechanisms influence vulnerability and subsequently impact service outcomes for patients and frontline employees.Design/methodology/approachThe research framework, based on the Transactional Model of Stress and Coping, was used to explore secondary vulnerability among frontline healthcare providers. A qualitative, interpretive approach was employed involving semi-structured interviews for data collection. The interview transcripts were analysed using a two-stage process, starting with inductive analysis and followed by deductive analysis.FindingsSecondary vulnerability is conceptualized along with its implications, shedding light on the role of stress and coping mechanisms in responding to vulnerable situations. It identifies the interplay between situational and personal factors that influence service outcomes for both HCPs and patients.Practical implicationsBy recognizing stressors and coping strategies, organizations can implement support programs to enhance HCP well-being and improve care quality for patients experiencing vulnerability. Training programs can equip HCPs with effective coping mechanisms to mitigate the impact of secondary vulnerability on service outcomes.Originality/valueThis research contributes to the literature by addressing a gap in understanding regarding secondary vulnerability among transformative service providers. By integrating theories from various fields, including consumer vulnerability, transformative service mediation, healthcare services, and stress and coping mechanisms, it offers a novel perspective on the dynamics of vulnerability in end-of-life care in a healthcare setting.
Impact of family facilitation and work facilitation on work-life balance of female library professionals in Bangladesh
Authors: Tabassum Mashiat , Ahmed S.M. Zabed 
Published: February 2025

PurposeThe aim of this paper is to examine the impact of family facilitation (FF) and work facilitation (WF) on work-life balance (WLB) of female library professionals in Bangladesh.Design/methodology/approachA survey questionnaire was distributed to female librarians identified through various professional networks. The questionnaire included demographic questions and scale items measuring satisfaction levels regarding FF, WF and WLB. Ordinal regressions were utilized to analyze the effect of demographic and job-related factors on WLB. Moreover, structural equation modeling was applied to assess the proposed relationships among FF, WF and WLB.FindingsA total of 158 female librarians participated in this study. Participants expressed satisfaction with family support and colleague relationships but had moderate to low satisfaction with work flexibility and compensation for extra work. Their WLB satisfaction was also found to be moderate. The results of ordinal regressions revealed significant associations between several demographic and work-related factors and different levels of WLB. The results of the structural equation model showed a significant impact of family and work facilitations on WLB. It also revealed the significant indirect effect of FF on WLB through the mediation of WF.Originality/valueThis is the first study to assess the influence of FF and WF on WLB among female library and information science professionals in Bangladesh. The study findings emphasize the need for implementing policies and practices to improve their WLB.