bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep Learning-powered CT-less Multi-tracer Organ Segmentation from PET Images: A solution for unreliable CT segmentation in PET/CT Imaging
Authors: Salimi Yazdan , Mansouri Zahra , Shiri Isaac , Mainta Ismini , Zaidi Habib
Published: August 2024

Introduction

The common approach for organ segmentation in hybrid imaging relies on co-registered CT (CTAC) images. This method, however, presents several limitations in real clinical workflows where mismatch between PET and CT images are very common. Moreover, low-dose CTAC images have poor quality, thus challenging the segmentation task. Recent advances in CT-less PET imaging further highlight the necessity for an effective PET organ segmentation pipeline that does not rely on CT images. Therefore, the goal of this study was to develop a CT-less multi-tracer PET segmentation framework.

Methods

We collected 2062 PET/CT images from multiple scanners. The patients were injected with either18F-FDG (1487) or68Ga-PSMA (575). PET/CT images with any kind of mismatch between PET and CT images were detected through visual assessment and excluded from our study. Multiple organs were delineated on CT components using previously trained in-house developed nnU-Net models. The segmentation masks were resampled to co-registered PET images and used to train four different deep-learning models using different images as input, including non-corrected PET (PET-NC) and attenuation and scatter-corrected PET (PET-ASC) for18F-FDG (tasks #1 and #2, respectively using 22 organs) and PET-NC and PET-ASC for68Ga tracers (tasks #3 and #4, respectively, using 15 organs). The models’ performance was evaluated in terms of Dice coefficient, Jaccard index, and segment volume difference.

Results

The average Dice coefficient over all organs was 0.81±0.15, 0.82±0.14, 0.77±0.17, and 0.79±0.16 for tasks #1, #2, #3, and #4, respectively. PET-ASC models outperformed PET-NC models (P-value < 0.05). The highest Dice values were achieved for the brain (0.93 to 0.96 in all four tasks), whereas the lowest values were achieved for small organs, such as the adrenal glands. The trained models showed robust performance on dynamic noisy images as well.

Conclusion

Deep learning models allow high performance multi-organ segmentation for two popular PET tracers without the use of CT information. These models may tackle the limitations of using CT segmentation in PET/CT image quantification, kinetic modeling, radiomics analysis, dosimetry, or any other tasks that require organ segmentation masks.
Biological Insights from Schizophrenia-associated Loci in Ancestral Populations
Authors: Bigdeli Tim B. , Chatzinakos Chris , Bendl Jaroslav , Barr Peter B. , Venkatesh Sanan , Gorman Bryan R. , Clarence Tereza , Genovese Giulio , Iyegbe Conrad O. , Peterson Roseann E. , Kolokotronis Sergios-Orestis , Burstein David , Meyers Jacquelyn L. , Li Yuli , Rajeevan Nallakkandi , Sayward Frederick , Cheung Kei-Hoi ,   Project Among African-Americans to Explore Risks for Schizophrenia (PAARTNERS),   Consortium on the Genomics of Schizophrenia (COGS),   Genomic Psychiatry Cohort (GPC) Investigators, DeLisi Lynn E. , Kosten Thomas R. , Zhao Hongyu , Achtyes Eric , Buckley Peter , Malaspina Dolores , Lehrer Douglas , Rapaport Mark H. , Braff David L. , Pato Michele T. , Fanous Ayman H. , Pato Carlos N. , Consortium PsychAD ,   Cooperative Studies Program (CSP) #572,   Million Veteran Program (MVP), Huang Grant D. , Muralidhar Sumitra , Gaziano J. Michael , Pyarajan Saiju , Girdhar Kiran , Lee Donghoon , Hoffman Gabriel E. , Aslan Mihaela , Fullard John F. , Voloudakis Georgios , Harvey Philip D. , Roussos Panos
Published: August 2024

Large-scale genome-wide association studies of schizophrenia have uncovered hundreds of associated loci but with extremely limited representation of African diaspora populations. We surveyed electronic health records of 200,000 individuals of African ancestry in the Million Veteran and All of Us Research Programs, and, coupled with genotype-level data from four case-control studies, realized a combined sample size of 13,012 affected and 54,266 unaffected persons. Three genome-wide significant signals — nearPLXNA4,PMAIP1, andTRPA1— are the first to be independently identified in populations of predominantly African ancestry. Joint analyses of African, European, and East Asian ancestries across 86,981 cases and 303,771 controls, yielded 376 distinct autosomal loci, which were refined to 708 putatively causal variants via multi-ancestry fine-mapping. Utilizing single-cell functional genomic data from human brain tissue and two complementary approaches, transcriptome-wide association studies and enhancer-promoter contact mapping, we identified a consensus set of 94 genes across ancestries and pinpointed the specific cell types in which they act. We identified reproducible associations of schizophrenia polygenic risk scores with schizophrenia diagnoses and a range of other mental and physical health problems. Our study addresses a longstanding gap in the generalizability of research findings for schizophrenia across ancestral populations, underlining shared biological underpinnings of schizophrenia across global populations in the presence of broadly divergent risk allele frequencies.
Naloxone Administration and Survival in Overdoses Involving Opioids and Stimulants: An Analysis of Law Enforcement Data from 63 Pennsylvania Counties
Authors: Cano Manuel , Jones Abenaa , Silverstein Sydney M. , Daniulaityte Raminta , LoVecchio Frank
Published: August 2024

Background

In consideration of rising opioid-stimulant deaths in the United States, this study explored rates of naloxone administration and survival in suspected opioid overdoses with, versus without, stimulants co-involved.

Methods

The study analyzed 26,635 suspected opioid-involved overdoses recorded by law enforcement/first-responders in the Pennsylvania Overdose Information Network in 63 Pennsylvania counties, January 2018-July 2024. All measures, including suspected drug involvement, were based on first-responder assessment/report. Relative frequencies and chi-square tests were first used to compare suspected opioid overdoses with, versus without, stimulants (cocaine or methamphetamine) co-involved. Next, mediation analyses tested naloxone administration as a mediator in the association between stimulant co-involvement (in opioid overdoses) and survival.

Results

Naloxone was reportedly administered in 72.2% of the suspected opioid-no-cocaine overdoses, compared to 55.1% of the opioid-cocaine-involved overdoses, and 72.1% of the opioid-no-methamphetamine overdoses vs. 52.4% of the opioid-methamphetamine-involved overdoses. With respect to survival rates, 18.0% of the suspected opioid-no-cocaine overdoses ended in death, compared to 41.3% of the opioid-cocaine overdoses; 18.1% of the opioid-no-methamphetamine overdoses ended in death, versus 42.9% of the opioid-methamphetamine overdoses. In mediation analyses (adjusted for demographics, county, year, and other drug co-involvement), naloxone administration mediated 38.7% (95% Confidence Interval [CI], 31.3%-46.0%) of the association between suspected cocaine co-involvement and survival and 39.2% (95% CI, 31.3%-47.1%) of the association between suspected methamphetamine co-involvement and survival.

Conclusions

Among suspected opioid overdoses recorded in the Pennsylvania Overdose Information Network, stimulant co-involvement was associated with lower naloxone administration and higher fatality, with naloxone partially mediating the association between stimulant co-involvement and death.
Impact of Multiple Episodes of Cytomegalovirus Infection on Patient Outcomes in Allogeneic Hematopoietic Stem Cell Transplant Using a Pre-emptive Monitoring Strategy
Authors: Messina Julia A. , Saullo Jennifer L. , Wolf Steven , Li Yanhong , Tang Helen , Hill Lauren B. , Foster Gena G. , Grant Michael , Thomas Samantha M. , Miller Rachel A. , Alexander Barbara D. , Horwitz Mitchell , Sung Anthony D.
Published: August 2024

The impact of multiple episodes of clinically significant cytomegalovirus infection (csCMVi) on clinical outcomes during pre-emptive CMV monitoring in allogeneic hematopoietic stem cell transplant recipients (HCT) is not well understood.

We performed a retrospective cohort study of all consecutive patients undergoing their first allogeneic HCT at Duke between January 1, 2009 and December 31, 2013, during an era of pre-emptive CMV monitoring, prior to widespread use of letermovir prophylaxis. Consensus definitions were utilized for refractory and resistant CMV infection, bacteremia, invasive fungal disease, and renal dysfunction. The Kaplan-Meier method was used to estimate survival.

Three hundred eighty-eight adult patients underwent allogeneic HCT during the study time period with 91 patients (23%) having one episode of csCMVi and 79 patients (20%) having ≥ one episode of csCMVi. Risk factors for multiple episodes of csCMVi included having a transplant from a matched unrelated donor, cord blood as HCT source, and graft-versus-host disease prophylaxis with highly T-cell suppressive agents such as alemtuzumab. Patients with multiple episodes tended to develop csCMVi earlier post-transplant and were more likely to have CMV disease and to develop resistant CMV infection. There was no difference in rates of refractory CMV infection, bacteremia, invasive fungal disease, or survival. However, patients with multiple episodes of csCMV had reduced one-year relapse-related mortality compared to patients with one csCMVi episode.
The PIDDosome controls cardiomyocyte polyploidization during postnatal heart development
Authors: Leone M , Kinz N , Eichin F , Obwegs D , Sladky VC , Braun VZ , Rizzotto D , Englmaier L , Manzl C , Moos K , Mergner Julia , Giansanti P , Garcia MN , Marques MM , Jacotot ED , Savko C , Boerries M , Sussman MA , Villunger A
Published: August 2024

The adult mammalian heart is characterized by post-mitotic polyploid cardiomyocytes (CMs). Understanding how CMs regulate cell cycle exit and ploidy can help developing new heart regenerative therapies. Here, we uncover that the PIDDosome, a multi-protein complex activating the endopeptidase Caspase-2, helps to implement a CM-specific differentiation program that limits ploidy during postnatal heart development. DNA content analyses show that PIDDosome-loss causes a cell-autonomous increase in nuclear and cellular CM ploidy. Remarkably, increased ploidy does not affect cardiac structure nor function. PIDDosome-imposed ploidy restriction commences at postnatal day 7 (P7), reaching a plateau on P14. PIDDosome activation requires ANKRD26, targeting PIDD1 to mother centrioles. Opposite to prior observations in liver development, the PIDDosome limits CM polyploidization in a p53-independent manner but reliant onp21/Cdkn1a, a notion supported by nuclear RNA sequencing and genetic deletion experiments. Our results provide new insights how proliferation of polyploid CMs is restricted during postnatal heart development.
Modeling Decision-Making Under Uncertainty with Qualitative Outcomes
Authors: Korem Nachshon , Or Duek , Rounan Jia , Wertheimer Emily , Metviner Sierra , Grubb Michael , Levy Ifat
Published: August 2024

Modeling decision-making under uncertainty typically relies on quantitative outcomes. Many decisions, however, are qualitative in nature, posing problems for traditional models. Here, we aimed to model uncertainty attitudes in decisions with qualitative outcomes. Participants made choices between certain outcomes and the chance for more favorable outcomes in quantitative (monetary) and qualitative (medical) modalities. Using computational modeling, we estimated the values participants assigned to qualitative outcomes and compared uncertainty attitudes across domains. Our model provided a good fit for the data, including quantitative estimates for qualitative outcomes. The model outperformed a utility function in quantitative decisions. Additionally, we found an association between ambiguity attitudes across domains. Results were replicated in an independent sample. We demonstrate the ability to extract quantitative measures from qualitative outcomes, leading to better estimation of subjective values. This allows for the characterization of individual behavior traits under a wide range of conditions.

Author Summary

In the current study, we explored how people make decisions when the outcomes aren’t easily measured in numbers, such as in medical choices. Traditional mathematical models, which rely on numerical data, often fall short in these situations, leading to a gap in understanding how people evaluate these qualitative outcomes. Using hierarchical Bayesian modeling, we developed a model that bridges this gap by translating qualitative outcomes into individualized quantitative values, enabling us to better understand the underlying decision-making processes. Our model not only provides a better fit to real-world data than existing models with qualitative or quantitative outcomes but also allows for meaningful comparisons of how people handle uncertainty across different decision-making scenarios. This approach opens new doors for studying decision-making in areas where traditional methods struggle, offering a more nuanced view of human behavior in complex situations.
The VVBlue assay: a plate-readable, dye exclusion-based cell viability assay for the toxicological testing of chemicals
Authors: Vitipon Marianne , Akingbagbohun Esther , Rabilloud Thierry
Published: August 2024

A viability test for in vitro cultures, based on the intake of the textile dye Alphazurine A by dead cells and its exclusion by viable cells, is described. This test uses the affinity of Alphazurine A for proteins, so that the dye is retained in dead cells even after rinsing, while its anionic character prevents it from entering live cells. This feature makes this dye exclusion test amenable to a reading in a plate format. The Alphazurine viability test provides an indicator of the absolute number of dead cells present in the culture well. To reach a cell viability index, a “dead cells” control (e.g. cells killed with ethanol) must be added. We also describe a double viability test, which first uses the Alphazurine assay to provide the number of dead cells then a crystal violet assay to provide an index of the number of cells present in the plate. This double test provides a complete appraisal of the situation in the cell culture wells, and has been compared to other viability tests such as propidium iodide exclusion or tetrazolium reduction. Its performances to study the toxicity of substances such as pigments are also established, and allowed us to publish the first public toxicological data on the recently described Pigment Blue 86.
Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis
Authors: Wan Yinan , El Kholtei Jakob , Jenie Ignatius , Colomer-Rosell Mariona , Liu Jialin , Acedo Joaquin Navajas , Du Lucia Y. , Codina-Tobias Mireia , Wang Mengfan , Sawh Ahilya , Lin Edward , Chuang Tzy-Harn , Mango Susan E. , Yu Guoqiang , Bintu Bogdan , Schier Alexander F.
Published: August 2024

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high resolution has remained elusive. Here, we introduce awhole-embryo imaging platform usingmultiplexederror-robust fluorescent in-situhybridization (weMERFISH). We quantified the expression of 495 genes in whole-mount zebrafish embryos at subcellular resolution. Integration with single-cell multiomics data generated an atlas detailing the expression of 25,872 genes and the accessibility of 294,954 chromatin regions, explorable with an online interface MERFISHEYES (beta version). We found that temporal gene expression aligns with cellular maturation and morphogenetic movements, diverse expression patterns correspond to composites of tissue-specific accessible elements, and changes in gene expression generate sharp boundaries during gastrulation. These results establish a novel approach for whole-organism spatial transcriptomics, provide a comprehensive spatially resolved atlas of gene expression and chromatin accessibility, and reveal the diversity, precision and emergence of embryonic patterns.
Dissociating External and Internal Attentional Selection
Authors: Arora Kabir , Gayet Surya , Kenemans J. Leon , Van der Stigchel Stefan , Chota Samson
Published: August 2024

Visual Working Memory (VWM) stores visual information for upcoming actions. Just as attention can shift externally towards relevant objects in the visual environment, attention can shift internally towards (i.e., prioritize) VWM content that is relevant for upcoming tasks. Internal and external attentional selection share a number of key neural and functional characteristics, which include their spatial organization: recent work has shown that spatial attention is directed towards the previous location of a prioritized memory item, similar to how a perceived stimulus is prioritized. Attending stimuli that are physically present is useful, as it enhances processing of the relevant visual input. When prioritizing items in memory, however, attending the prior stimulus location cannot serve this purpose, as there is no visual input to enhance. Here, we address this apparent contradiction which highlights the gaps in our understanding of the mechanisms underlying external and internal visual attention. In two EEG experiments, we compare location-specific sensory enhancement during the attentional selection of external (perceived) as compared to internal (memorized) stimuli. During both internal and external selection we observed a lateralization of alpha oscillations and gaze position bias toward the previous locations of prioritized items, confirming earlier findings that suggested an inherent spatial organization within VWM. Critically, using Rapid Invisible Frequency Tagging (RIFT), we show that sensory enhancement at the attended location is only observed during external attentional selection of (perceived) stimuli. No such location-specific sensory enhancement was observed during attentional selection of items in VWM. Furthermore, we found no clear relationship across trials between alpha lateralization and sensory enhancement (measured through RIFT) during external attention, suggesting that these two metrics indeed reflect distinct cognitive mechanisms. In sum, using a novel combination of EEG and RIFT, we demonstrate a fundamental distinction between the neural mechanisms underlying the selection of perceived and memorized objects. Both types of selection operate within a spatial reference frame, but only external selection modulates early sensory processing. Our findings suggest that the visual system is not vestigially recruiting existing mechanisms of external attention for prioritization in VWM, but is instead using space as an organizational principle to store and select items in VWM.
A non-tethering role for the Drosophila Pol θ linker domain in promoting damage resolution
Authors: Blanch Justin R. , Krishnamurthy Manan , McVey Mitch
Published: August 2024

DNA polymerase theta (Pol θ) is an error-prone translesion polymerase that becomes crucial for DNA double-strand break repair when cells are deficient in homologous recombination or non-homologous end joining. In some organisms, Pol θ also promotes tolerance of DNA interstrand crosslinks. Due to its importance in DNA damage tolerance, Pol θ is an emerging target for treatment of cancer and disease. Prior work has characterized the functions of the Pol θ helicase-like and polymerase domains, but the roles of the linker domain are largely unknown. Here, we show that theDrosophila melanogasterPol θ linker domain promotes egg development and is required for tolerance of DNA double-strand breaks and interstrand crosslinks. While a linker domain with scrambled amino acid residues is sufficient for DNA repair, replacement of the linker with part of theHomo sapiensPol θ linker or a disordered region from the FUS RNA-binding protein does not restore function. These results demonstrate that the linker domain is not simply a random tether between the helicase-like and polymerase domains. Furthermore, they suggest that intrinsic amino acid residue properties, rather than protein interaction motifs, are more critical for Pol θ linker functions in DNA repair.
Behavioral screening defines three molecular Parkinsonism subgroups inDrosophila
Authors: Kaempf Natalie , Valadas Jorge S. , Robberechts Pieter , Schoovaerts Nils , Praschberger Roman , Ortega Antonio , Kilic Ayse , Chabot Dries , Pech Uli , Kuenen Sabine , Vilain Sven , Baz El-Sayed , Singh Jeevanjot , Davis Jesse , Liu Sha , Verstreken Patrik
Published: August 2024

Parkinsonism is defined by motor dysfunction, but the specific upstream molecular causes of these clinical symptoms can vary widely. We hypothesize that these causes converge onto a limited number of core cellular pathways. To investigate this, we created a new collection of 24 genetically very well-controlled animal models of familial forms of parkinsonism. Using unbiased behavioral screening and machine learning we identified three clusters of mutants that converge on (1) mitochondrial function; (2) retromer/vesicle trafficking; and (3) proteostasis/autophagy. Genes within each cluster have a similar genetic interaction profile and compounds that target specific molecular pathways ameliorate dopaminergic neuron dysfunction in a cluster-specific manner. This suggests that familial parkinsonism can be stratified into three broad functional groups and our findings pave the way for targeted biomarker discovery and drug development.
Analysing drivers of worldwide tidal wetland change
Authors: Perrodin Lucie , Navarro Alejandro , Toor Maren , Canto Robert , Becker Madison , Dong Yanzhu , Worthington Thomas , Murray Nicholas J.
Published: August 2024

Tidal wetlands are dynamic coastal ecosystems that can change in extent in response to a broad range of change drivers. We use high spatial resolution satellite imagery to estimate the relative influence of 18 classes of change drivers on observed tidal wetland gains and losses from 1999 to 2019, differentiating direct drivers as those observable at the site of ecosystem change, and indirect drivers as broader processes that influence changes without being directly visible. We developed a random sample of 2823 change detections from a global dataset of tidal wetland change and allocated each change event to driver classes using high-resolution time-series imagery. We identified that indirect drivers were the most widespread type of driver of tidal wetland change (70.9%), with flooding being the predominant driver for losses (47.5%) and unknown natural processes of change for gains (62.7%). Drivers often associated with climate change were evident in interpretations of wetland drivers, with increases in flooded area and reductions in vegetation cover suggesting the effects of relative sea level rise on tidal wetlands are observable in many areas. Our temporal analysis revealed that over 20 years, indirect drivers consistently contributed to larger proportions of gains and losses compared to direct drivers. Asia was the only continent where direct drivers of loss, such as agriculture (22.9%) and aquaculture (17.1%), outweighed indirect drivers, providing further evidence of the widespread transformation of Asia’s natural coastal ecosystems to anthropogenic shorelines. Globally, coastal land reclamations were mostly observed in mangrove ecosystems, where more than half of the observed losses were of anthropogenic origin. The most observed direct drivers of gains were altered land management and restoration, but none of them contributed to more than 5% of the total gains over 20 years. Our findings suggest a need for efficient conservation measures that allow the dynamic processes that characterise coastal ecosystems to persist, while simultaneously reducing the worldwide impact of direct human activities.
A non-canonical CDK, Pho85 regulates the restart of the cell-cycle following stress
Authors: Jin Natsuko , Jin Yui , Oikawa Yu , Nakano Akihiko , Ohsumi Yoshinori , Weisman Lois S.
Published: August 2024

Environmental stress induces an arrest of the cell cycle. Thus, release from this arrest is essential for cell survival. The cell-cycle-arrest occurs via the down regulation of the cyclins that drive the main cyclin dependent kinase, CDK1/Cdc28. However, it was not clear how cells escape this potentially fatal arrest. Here we show that prior to the restoration of CDK1/Cdc28 cyclins, a non-canonical CDK, Pho85, initiates a cascade to restart the cell cycle. We demonstrate that following stress, Pho85 phosphorylates the Sch9 kinase, which in turn directly phosphorylates the transcriptional inhibitor Whi5, the yeast analog of RB1/retinoblastoma, and a CDK1 target. This promotes Whi5 translocation from the nucleus, and the release of the stress-induced arrest at G1phase. In addition, we find that in parallel with Pho85, CDK1/Cdc28 also plays a role in the control of Whi5. Together, these findings provide insights into how cells re-enter the cell cycle during recovery from stress and reveal that a non-canonical CDK and cyclin takes on essential roles and acts via a pathway that functions in parallel with CDK1/Cdc28.
Computational modeling of left ventricular flow using PC-CMR-derived four-dimensional wall motion
Authors: Peighambari Seyed Babak , Mukherjee Tanmay , Mendiola Emilio A. , Darwish Amr , Timmins Lucas H. , Pettigrew Roderic I. , Shah Dipan J. , Avazmohammadi Reza
Published: August 2024

Intracardiac hemodynamics plays a crucial role in the onset and development of cardiac and valvular diseases. Simulations of blood flow in the left ventricle (LV) have provided valuable insight into assessing LV hemodynamics. While fully coupled fluid-solid modelings of the LV remain challenging due to the complex passive-active behavior of the LV wall myocardium, the integration of imaging-driven quantification of structural motion with computational fluid dynamics (CFD) modeling in the LV holds the promise of feasible and clinically translatable characterization of patient-specific LV hemodynamics. In this study, we propose to integrate two magnetic resonance imaging (MRI) modalities with the moving-boundary CFD method to characterize intracardiac LV hemodynamics. Our method uses the standard cine cardiac magnetic resonance (CMR) images to estimate four-dimensional myocardial motion, eliminating the need for involved myocardial material modeling to capture LV wall behavior. In conjunction with CMR, phase contrast-MRI (PC-MRI) was used to measure temporal blood inflow rates at the mitral orifice, serving as an additional boundary condition. Flow patterns, including velocity streamlines, vortex rings, and kinetic energy, were characterized and compared to the available data. Moreover, relationships between LV wall kinematic markers and flow characteristics were determined without myocardial material modeling and using a non-rigid image registration (NRIR) method. The fidelity of the simulation was quantitatively evaluated by validating the flow rate at the aortic outflow tract against respective PC-MRI measures. The proposed methodology offers a novel and feasible toolset that works with standard PC-CMR protocols to improve the clinical assessment of LV characteristics in prognostic studies and surgical planning.
Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining
Authors: Prillo Sebastian , An Kevin , Wu Wilson , Kristanto Ivan , Jones Matthew G. , Song Yun S. , Yosef Nir
Published: August 2024

CRISPR-Cas9 based lineage tracing technologies have enabled the reconstruction of single-cell phylo- genies from transcriptional readouts. However, developing tree-reconstruction algorithms with theoretical guarantees in this setting is challenging. In this work, we derive a reconstruction algorithm with theoret- ical guarantees using Neighbor-Joining (NJ) on distances that are moment-matched to estimate the true tree distances. We develop a series of tools to analyze this algorithm and prove its theoretical guarantees. When the parameters of the data generating process are known and there is no missing data, our results align with established results from common evolutionary models, such as Cavender-Farris-Neyman and Jukes-Cantor. However, to account for the realistic case where the parameters of the data generating process are not known and there is missing data, we develop new theory that shows for the first time that it is still possible to obtain reconstruction guarantees in the CRISPR-Cas9 case and in other models of evolution. Empirically, we show on both simulated lineage tracing data and on real data from a mouse model of lung cancer the improved performance of our method as compared to the traditional use of NJ.
Survival of hepatocytes from executioner caspase activation promotes liver regeneration by enhancing JAK/STAT3 activity
Authors: Cao Zhiyuan , Qin Lining , Liu Kaixuan , Yao Chen , Li Enhong , Hao Xiaoyu , Wang Molin , Jiang Baichun , Zou Yongxin , Hu Huili , Liu Qiao , Shao Changshun , Gong Yaoqin , Sun Gongping
Published: August 2024

Activation of executioner caspases, which is a key step in the apoptotic process, has been reported to promote tissue regeneration by sending pro-proliferation signals to the surrounding cells. However, whether executioner caspase activation (ECA) has cell-autonomous effect on tissue regeneration is not clear. Here, by generating transgenic mice carrying a lineage tracing system for cells that have experienced ECA, we demonstrate that transient ECA occurs in hepatocytes during liver regeneration after partial hepatectomy (PHx) or carbon tetrachloride (CCl4) treatment. Instead of committing apoptotic cell death, the majority of hepatocytes with ECA survive and proliferate to contribute to liver regeneration. Interestingly, inhibition of ECA in livers results in reduced hepatocyte proliferation and impaired regeneration, whereas increasing ECA to a level sufficient to kill hepatocytes also impedes regeneration, suggesting that ECA needs to be precisely controlled during liver regeneration. Mechanistic studies show that ECA promotes hepatocyte proliferation during regeneration through enhancing JAK/STAT3 activity. Our work reveals an essential role of survival of hepatocytes from ECA in liver regeneration.
Investigating the missing-wedge problem in small-angle X-ray scattering tensor tomography across real and reciprocal space
Authors: Nielsen Leonard C. , Tänzer Torne , Rodriguez-Fernandez Irene , Erhart Paul , Liebi Marianne
Published: August 2024

Small-angle-scattering tensor tomography is a technique for studying anisotropic nanostructures of millimetre-sized samples in a volume-resolved manner. It requires the acquisition of data through repeated tomographic rotations about an axis which is subjected to a series of tilts. The tilt that can be achieved with a typical setup is geometrically constrained, which leads to limits in the set of directions from which the different parts of the reciprocal space map can be probed. Here, we characterize the impact of this limitation on reconstructions in terms of the missing wedge problem of tomography, by treating the problem of tensor tomography as the reconstruction of a three-dimensional field of functions on the unit sphere, represented by a grid of Gaussian radial basis functions. We then devise an acquisition scheme to obtain complete data by remounting the sample, which we apply to a sample of human trabecular bone. Performing tensor tomographic reconstructions of limited data sets as well as the complete data set, we further investigate and validate the missing wedge problem by investigating reconstruction errors due to data incompleteness across both real and reciprocal space. Finally, we carry out an analysis of orientations and derived scalar quantities, to quantify the impact of this missing wedge problem on a typical tensor tomographic analysis. We conclude that the effects of data incompleteness are consistent with the predicted impact of the missing wedge problem, and that the impact on tensor tomographic analysis is appreciable but limited, especially if precautions are taken. In particular, there is only limited impact on the means and relative anisotropies of the reconstructed reciprocal space maps.
Young consumers' online experiential consumption behavior of foreign contemporary music: generational and gender differences in the refined stimulus-organism-response theory
Authors: Kim Wooyang , An Hyun Sang , Hantula Donald A. , Di Benedetto Anthony
Published: August 2024

Purpose

This study aims to examine the younger generations’ experiential consumption of foreign contemporary music online (i.e. digital music streaming services) by generation and gender in the US market.

Design/methodology/approach

The author proposes a sequential experiential consumption model by applying Jacoby’s refined stimulus-organism-response (S-O-R) theory to better understand the experiential sequences in foreign music consumption among young generations in the US market. The proposed model, using structural equation modeling (SEM), examines a cognitive permeable role and a hierarchical affective mediating role. Also, moderating roles of generation and gender are simultaneously tested in overall and specific causal relationships.

Findings

The refined S-O-R framework is superior to a linear one in better understanding young consumers’ online experiential foreign music consumption behavior. Moreover, hierarchical sequenced affective organismic behavior is crucial to enhance young consumers’ online music consumption experiences to regulate subsequent behavioral responses. Furthermore, gender differences but no generational differences exist in the experiential consumption process among young consumers. Nevertheless, the strength of S-O-R factors affecting experiential consumption seems idiosyncratic simultaneously in gender and generation.

Practical implications

The study suggests foreign music streaming services boost profitability by focusing on young consumers' psychological ownership and tailored experiences, encouraging a shift from freemium to premium subscriptions. Also, the findings recommend adopting phygital experiences using technologies like AR, VR and MR to enhance engagement and create unique, emotionally resonant experiences for young consumers, thus fostering a more profitable business model.

Originality/value

The authors address under-researched topics relevant to young generations by applying Jacoby’s refined S-O-R framework to foreign music consumption through online streaming. This approach delves into a lesser-explored consumer behavior framework, highlighting young generations’ musical trends. The model reveals cognitive and affective roles, offering advantages over traditional linear S-O-R models. It also uniquely incorporates the moderating effects of generation and gender in music consumption studies, addressing a gap in music-related studies.
Navigating negative events: the role of online destination brand experience in tourists' travel decisions
Authors: Shah Adnan Muhammad , Qayyum Abdul , Shah Mahmood , Jamil Raja Ahmed , Lee KangYoon
Published: August 2024

Purpose

This study addresses tourists' post-consumption perspectives on the impact of online destination experiences and animosity on travel decisions. Developing a framework based on the stimulus-organism-response (SOR) theory, we examine the previously unexplored relationship between post-negative events, online destination brand experience (ODBE), tourists' animosity and destination boycott intentions within the domestic tourism context.

Design/methodology/approach

Data from 355 actively engaged domestic travelers in Pakistan who follow destination social media pages (i.e. Instagram and Facebook) was analyzed using structural equation modeling.

Findings

The findings reveal that post-negative events ODBE significantly stimulate tourists' animosity, which in turn drives destination boycott intentions. The ODBE indirectly affects boycott intentions through animosity, acting as a partial mediator. The analysis highlights the significance of the users' prior experience levels (novice vs experienced). Multigroup analysis shows that novice visitors are more sensitive to negative online experiences, resulting in stronger animosity than experienced visitors. Animosity significantly drives boycott intentions, particularly among experienced visitors.

Originality/value

This study’s novelty lies in its comprehensive examination of post-negative events, focusing on how the ODBE influences tourists' negative emotions and boycott intentions. These findings offer valuable insights for tourism researchers and destination marketers, underscoring the importance of optimizing post-service failure ODBE strategies for brand repair, online reputation management, digital marketing innovation and customized service recovery to mitigate the impact of negative events.
The effects of quality perception and multisensory perception on purchase intention when consumers shop online
Authors: Han Bo , Li Pei , Tan Xiaoqin
Published: August 2024

Purpose

How to reduce uncertainty in clothing online purchasing has become a primary concern for consumers. This study aims to investigate the effects of quality perception and multisensory perception on consumer online clothing purchase intention and to explore the mediating effect of trust.

Design/methodology/approach

This study was conducted with consumers who have online clothing shopping experiences. A total of 539 valid samples were analyzed by bootstrap and structural equation model.

Findings

The result of this research revealed that perceived information quality, perceived service quality, perceived haptic imagery and perceived visual-audio cues have a significant influence on purchase intention. Additionally, consumers’ trust is positively correlated with purchase intention. Trust mediates the relationship between the perceptions (perceived information quality, perceived service quality, perceived haptic imagery and perceived visual-audio cues) and purchase intention, irrespectively.

Originality/value

To investigate the effects of multisensory perception on purchase intention, perceived haptic imagery is adopted as a variable in this study. This study investigates the mediating role of trust between multisensory perception and purchase intention. The findings of this study can enrich Stimulus-Organism-Response (S-O-R) framework and Information System (IS) success model in the field of clothing online shopping.
Investigating women’s work experience in hospitality with the job demands-resources theory
Authors: Zhong YunYing (Susan)
Published: August 2024

Purpose

This study aims to investigate the work experience of women in hospitality with the job demands-resources (JD-R) theory. By focusing on job resources, job demands (emotional and physical), work engagement, emotional exhaustion and turnover intention, this study examines (1) female workers’ perceptions of these variables; (2) how race, age and job positions affect perceptions and (3) structural relationships among these variables.

Design/methodology/approach

The study collected 412 responses from American female hospitality workers via an online survey. Descriptive statistics and independent T-tests were conducted using SPSS to analyze professional experiences and differences based on individual characteristics. Path analysis was conducted using Amos 28 to assess the structural relationships among variables.

Findings

Female hospitality workers generally feel engaged, experience low emotional exhaustion and have low turnover intention. Younger or front-line women reported higher emotional exhaustion, lower engagement and greater likelihood to quit. Unexpectedly, emotional resources do not significantly affect work engagement, but physical resources increase it.

Practical implications

The study provides directions to establish specific well-being and organizational support initiatives to retain female hospitality workers.

Originality/value

This study offers fresh insights into the JD-R theory by examining the experiences of American female hospitality employees using a non-comparative lens. Although existing literature highlights women’s unfavorable positions relative to male counterparts, this study reveals rather positive perspectives. Additionally, it presents a dual psychological process of how job resources and demands affect women’s work experience and the varying impacts of job demands on work engagement.
Over-the-top (OTT) platforms: a review, synthesis and research directions
Authors: Khanna Prateek , Sehgal Reetika , Gupta Ashish , Dubey Ashish Mohan , Srivastava Rajeev
Published: August 2024

Purpose

In this era of technological advancement, the capabilities of devices and telecommunications have changed the pattern of media consumption among consumers. This study examined the research landscape and advancements in OTT services.

Design/methodology/approach

This study adopted a hybrid review consisting of bibliometric and thematic analyses to present advancements in the OTT platforms. A hybrid review integrates both systematic and narrative approaches by emphasizing a literature search strategy and the study selection process.

Findings

This study focuses on previous literature to understand recent developments in the domain. The authors derive six major OTT themes: OTT infrastructure and technology advancement, OTT consumption behaviour, shifting trends towards OTT platforms, viewers’ engagement in digital media, OTT in the global market, OTT policies and regulatory mechanisms.

Practical implications

The findings of this study will be useful for marketers/stakeholders associated with the entertainment and media industries, such as sales promotion teams, media planners/advertisers, content management companies and policy regulators, to penetrate OTT viewers.

Originality/value

The literature related to OTT is progressively rising, but it remains highly fragmented because of inconsistencies in the methodologies and theories used in the domain of OTT. This study offers directions in terms of theory, methodology and future research on OTT services.
High risk of low birth weight in couples with advanced paternal age in in vitro fertilization treatment
Authors: Wan Yangyang , Wen Zhu , Liu Wenjing , Jiang Xiaohua , Wu Limin , Jiang Hui , Zhang Xiansheng , Shi Qinghua , Hua Juan
Published: August 2024

Background

With the development of socio‐economic conditions and a shift in attitudes towards fertility, there has been a gradual increase in delayed childbearing since the 2000s. Age plays a significant role in the decline of fertility. However, we know very little about the association of paternal age with reproductive outcomes.

Objectives

To investigate the correlation between advanced paternal age and semen quality, embryo quality, pregnancy, and neonatal outcomes in IVF cycles.

Materials and methods

In this study, after excluding female partners aged ≥35 years, we analyzed data from 761 infertile couples who underwent in vitro fertilization cycles at the First Affiliated Hospital of USTC between June 2020 and March 2023. Cases were classified into three groups according to the age of the male: <35 years (530 infertile couples), 35 years ≤ paternal age <40 years (125 infertile couples), and ≥40 years (106 infertile couples). Then, we compared the general clinical data arising from in vitro fertilization cycles between the three groups, including semen parameters, embryonic parameters, and pregnancy and neonatal birth outcomes.

Results

Data analysis showed that the duration of infertility and the incidence of secondary infertility were significantly higher in paternal age ≥35 years groups than those aged <35 years (all p < 0.05). We also observed a significant difference between ≥40 years and <35 years groups in terms of the normal fertilization rate, high‐quality embryo rate, clinical pregnancy rate, miscarriage rate, live birth rate, Apgar scores, and the low birth weight neonatal rate (all p < 0.05). The group with paternal age ≥40 years showed statistically significant differences in terms of clinical pregnancy rate, miscarriage rate, live birth rate, and low birth weight on multivariable logistic regression (all p < 0.05).

Conclusion

The results of our study indicate that advanced paternal age (≥40 years) has a significant impact on the embryo quality, pregnancy outcome, and neonatal outcome. Paternal age over 40 years is a risk for in vitro fertilization success rate.
Increased risk of bacterial pneumonia before and after respiratory syncytial virus infection in young children
Authors: Strandell Karin , Videholm Samuel , Tornevi Andreas , Björmsjö Maria , Silfverdal Sven Arne
Published: August 2024

Aim

The burden of respiratory disease is great among children. This study aimed to examine the temporal relationship between hospitalisation for respiratory syncytial virus (RSV) and bacterial pneumonia.

Methods

A Swedish population‐based cohort was created by combining data from the Swedish Medical Birth Register, the National Inpatient Register, the Cause of Death Register, the Total Population Register, and the Longitudinal Integration Database for Health Insurance and Labour Market Studies. Children born between 1998 and 2015 were included and followed for 2 years. We examined the temporal relationship between RSV hospitalisation and bacterial pneumonia using piecewise exponential models.

Results

The final cohort comprised 1 641 747 children, 48.5% were females. There were 23 632 RSV and 4722 bacterial pneumonia hospitalisations, with mean age of 137.8 and 424.2 days, respectively. RSV hospitalisation was associated with bacterial pneumonia with an adjusted incidence rate ratio (aIRR) of 3.18. The risk was highest in the first month after RSV hospitalisation, aIRR 11.19. The risk of bacterial pneumonia was elevated for 4 months after RSV hospitalisation and before RSV hospitalisation.

Conclusion

We found an increased risk for bacterial pneumonia hospitalisation in children hospitalised for RSV both before and after RSV hospitalisation, indicating a bidirectional relationship.
Epigenetic responses of trees to environmental stress in the context of climate change
Authors: Miryeganeh Matin , Armitage David W.
Published: August 2024

In long‐lived tree populations, when environmental change outpaces rates of evolutionary adaptation, plasticity in traits related to stress tolerance, dormancy, and dispersal may be vital for preventing extinction. While a population's genetic background partly determines its ability to adapt to a changing environment, so too do the many types of epigenetic modifications that occur within and among populations, which vary on timescales orders of magnitude faster than the emergence of new beneficial alleles. Consequently, phenotypic plasticity driven by epigenetic modification may be especially critical for sessile, long‐lived organisms such as trees that must rely on this plasticity to keep pace with rapid anthropogenic environmental change. While studies have reported large effects of DNA methylation, histone modification, and non‐coding RNAs on the expression of stress‐tolerance genes and resulting phenotypic responses, little is known about the role of these effects in non‐model plants and particularly in trees. Here, we review new findings in plant epigenetics with particular relevance to the ability of trees to adapt to or escape stressors associated with rapid climate change. Such findings include specific epigenetic influences over drought, heat, and salinity tolerance, as well as dormancy and dispersal traits. We also highlight promising findings concerning transgenerational inheritance of an epigenetic ‘stress memory’ in plants. As epigenetic information is becoming increasingly easy to obtain, we close by outlining ways in which ecologists can use epigenetic information better to inform population management and forecasting efforts. Understanding the molecular mechanisms behind phenotypic plasticity and stress memory in tree species offers a promising path towards a mechanistic understanding of trees' responses to climate change.