bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Mode Decomposition for Transient Cavitation Bubbles Imaging in Pulsed High Intensity Focused Ultrasound Therapy
Authors: Song Minho , Sapozhnikov Oleg A. , Khokhlova Vera A. , Khokhlova Tatiana D. 
Published: March 2024

AbstractPulsed high-intensity focused ultrasound (pHIFU) can induce sparsede novoinertial cavitation without the introduction of exogenous contrast agents, promoting mild mechanical disruption in targeted tissue. Because the bubbles are small and rapidly dissolve after each HIFU pulse, mapping transient bubbles and obtaining real-time quantitative metrics correlated to tissue damage are challenging. Prior work introduced Bubble Doppler, an ultrafast power Doppler imaging method as a sensitive means to map cavitation bubbles. The main limitation of that method was its reliance on conventional wall filters used in Doppler imaging and optimized for imaging blood flow rather than transient scatterers. This study explores Bubble Doppler enhancement using dynamic mode decomposition (DMD) of a matrix created from a Doppler ensemble for mapping and extracting the characteristics of transient cavitation bubbles. DMD was first testedin silicowith a numerical dataset mimicking the spatiotemporal characteristics of backscattered signal from tissue and bubbles. The performance of DMD filter was compared to other widely used Doppler wall filters - singular value decomposition (SVD) and infinite impulse response (IIR) highpass filter. DMD was then applied to anex vivotissue dataset where each HIFU pulse was immediately followed by a plane wave Doppler ensemble.In silicoDMD outperformed SVD and IIR high pass filter andex vivoprovided physically interpretable images of the modes associated with bubbles and their corresponding temporal decay rates. These DMD modes can be trackable over the duration of pHIFU treatment using k-means clustering method, resulting in quantitative indicators of treatment progression.Abstract Figure
Awareness is determined by emotion and gender
Authors: Jugović Ema , Poyo Solanas Marta , de Gelder Beatrice 
Published: March 2024

SummaryTraditionally, consciousness studies focus on domain general cognitive processes rather than on specific information reaching subjective awareness. The present study (N= 45) used visual masking and whole-body images to investigate whether the specific emotional expression as well as gender of the stimuli and of the participants impact awareness. Our results show that participants’ awareness responses reflect differences in the specific emotion of the stimuli, that these differences are a function of the gender of the stimuli as well as the gender of the participants and that minimal awareness may be associated with emotion specific features of the body images. Overall, we observed that threatening expressions are more easily detected than fearful ones, especially by males presented with male stimuli. Our findings underscore the importance of affective factors for theories of consciousness and underscore the significance of gender differences in emotional processing, often overlooked in past face and body emotion recognition studies.
Dock-and-lock binding of SxIP ligands is required for stable and selective EB1 interactions
Authors: Almeida Teresa , Hargreaves Eleanor , Zech Tobias , Barsukov Igor 
Published: March 2024

SUMMARYEnd Binding protein 1 (EB1) is a key component of the signalling networks located at the plus ends of microtubules. It incorporates an N-terminal microtubule binding CH domain and the C-terminal EBH domain that interacts with the SxIP-containing sequences of other microtubule plus end tracking proteins (+TIPs). By using a series of SxIP containing peptides derived from the microtubule-actin cross-linking factor, MACF, we show that the SxIP motif itself binds to EBH with low affinity, and the full interaction requires contribution of the post-SxIP residues. Based on the solution structure and dynamics of the EBH/MACF complex we proposed a two-step ‘dock-and-lock’ model for the EBH interaction with targets, where the SxIP motif initially binds to a partially-formed EBH pocket, which subsequently induces folding of the unstructured C-terminus and transition to the stable complex. We dissect contributions from different interactions into the binding and design MACF mutations of the post-SxIP region that enhance the affinity by two orders of magnitude, leading to a nanomolar interaction. We verify the enhanced recruitment of the mutated peptide to the dynamic plus ends of MTs in a live cell experiment. Our model explains EB1’s interaction with the SxIP-containing ligands and can be used to design of small molecule inhibitors that can block SxIP interaction with EB1.
Quantification of NAD+T1and T2relaxation times using downfield1H MRS at 7 T in human brain in vivo
Authors: Swago Sophia , Wilson Neil E. , Elliott Mark A. , Reddy Nanga Ravi Prakash , Reddy Ravinder , Witschey Walter R. 
Published: March 2024

AbstractIntroductionThe purpose of this study was to use a single-slice spectrally-selective sequence to measure T1and T2relaxation times of NAD+proton resonances in the downfield1H MRS spectrum in human brain at 7 T in vivo and assess the propagation of relaxation time uncertainty in NAD+quantification.MethodsDownfield spectra from 7 healthy volunteers were acquired at multiple echo times in all subjects to measure T2relaxation, and saturation recovery data were to measure T1relaxation. The downfield acquisition used a spectrally-selective 90° sinc pulse for excitation centered at 9.1 ppm with a bandwidth of 2 ppm, followed by a 180° spatially-selective Shinnar-Le Roux refocusing pulse for localization. For the multiple echo experiment, spectra were collected with echo times ranging from 13 to 33 ms. For the saturation recovery experiment, saturation was performed prior to excitation using the same spectrally-selective sinc pulse as was used for excitation. Saturation delay times (TS) ranged from 100 to 600 ms. Uncertainty propagation analysis was performed analytically and with Monte Carlo simulation.ResultsThe mean ± standard deviation of T1relaxation times of the H2, H6, and H4 protons were 152.7 ± 16.6, 163.6 ± 22.3, and 169.9 ± 11.2 ms, respectively. The mean ± standard deviation of T2relaxation times of the H2, H6, and H4 protons were 32.5 ± 7.0, 27.4 ± 5.2, and 38.1 ± 11.7 ms, respectively. The mean R2of the H2 and H6 T1fits were 0.98. The mean R2of the H4 proton T1fit was 0.96. The mean R2of the T2fits of the H2 and H4 proton resonances were 0.98, while the mean R2of the T2fits of the H4 proton was 0.93. The relative uncertainty in NAD+concentration due to relaxation time uncertainty was 8.5%-11%.ConclusionUsing downfield spectrally-selective spectroscopy with single-slice localization, we found NAD+T1and T2relaxation times to be approximately 162 ms and 32 ms respectively in the human brain in vivo at 7 T.
Spatiotemporal dynamics of cyanobacteriumDolichospermum lemmermanniipopulations in a bloom-prone region of Lake Superior
Authors: Wood Andrew W. , Callaghan Jake D. , Loiselle Reane , McManus Robert M. , Brovold Sandra S. , Wellard Kelly Holly A. , Alexson Elizabeth E. , Sterner Robert W. , Hudson Matthew J. , Sheik Cody S. 
Published: March 2024

AbstractCyanobacterial Harmful Algal Blooms (cHABs) are increasingly common in marine and freshwater environments, including the Laurentian Great Lakes (LGL). Lake Superior has seen two large-scale cyanobacterial blooms (2012 and 2018) along the Wisconsin shoreline west of the Apostle Islands, caused by the cyanobacteriumDolichospermum lemmermannii.The drivers of bloom formation in Lake Superior are not yet certain, with many factors known to trigger blooms elsewhere in the LGL being absent in Lake Superior. Furthermore, little is known aboutD. lemmermannii’s spatial structure or phenology. Thus, we sought to track the seasonal population dynamics ofD. lemmermanniito shed light on its growth, physiology, and abundance. In 2021, we used 16S rRNA amplicon and shotgun metagenomic sequencing to characterize spatiotemporal patterns ofD. lemmermanniiabundance and diversity along the bloom-prone Wisconsin shore of Lake Superior. In 2022, we performed net tows and direct colony counts in another localized area. No large-scale bloom event was observed during either year, though several smaller blooms were observed.D. lemmermanniiabundances were low at nearly all sites and sampling times. Spikes in abundance occurred in July and September, particularly near Siskiwit Bay, a hotspot of bloom formation. We also observed a seasonal shift in heterocyte and akinete abundance indicative of late-season nutrient limitation. Most striking was the seasonal turnover ofD. lemmermanniistrains, suggesting strain adaptation to specific environmental conditions. These results offer valuable and actionable insights for managers and provide a foundation for additional work to clarify drivers of bloom formation in Lake Superior.
ORF48 is required for optimal lytic replication of Kaposi’s Sarcoma-Associated Herpesvirus
Authors: Veronese Beatriz H S , Nguyen Amy , Patel Khushil , Paulsen Kimberly , Ma Zhe 
Published: March 2024

AbstractKaposi’s sarcoma-associated herpesvirus (KSHV) establishes persistent infection in the host by encoding a vast network of proteins that aid immune evasion. One of these targeted innate immunity pathways is the cGAS-STING pathway, which inhibits the reactivation of KSHV from latency. Previously, we identified multiple cGAS/STING inhibitors encoded by KSHV, suggesting that the counteractions of this pathway by viral proteins are critical for maintaining a successful KSHV life cycle. However, the detailed mechanisms of how these viral proteins block innate immunity and facilitate KSHV lytic replication remain largely unknown. In this study, we report that ORF48, a previously identified negative regulator of the cGAS/STING pathway, is required for optimal KSHV lytic replication. We used both siRNA and deletion-based systems to evaluate the importance of intact ORF48 in the KSHV lytic cycle. In both systems, loss of ORF48 resulted in defects in lytic gene transcription, lytic protein expression, viral genome replication and infectious virion production. ORF48 genome deletion caused more robust and global repression of the KSHV transcriptome, possibly due to the disruption of RTA promoter activity. Mechanistically, overexpressed ORF48 was found to interact with endogenous STING in HEK293 cells. Compared with the control cell line, HUVEC cells stably expressing ORF48 exhibited repressed STING-dependent innate immune signaling upon ISD or diABZI treatment. However, the loss of ORF48 in our iSLK-based lytic system failed to induce IFNβ production, suggesting a redundant role of ORF48 on STING signaling during the KSHV lytic phase. Thus, ORF48 is required for optimal KSHV lytic replication through additional mechanisms that need to be further explored.Author SummaryKaposi sarcoma-associated herpesvirus (KSHV) causes persistent infection in a host that leads to two deadly cancers, Kaposi Sarcoma and Primary Effusion Lymphoma, especially in immunocompromised people. Unfortunately, there is no vaccine or viral-specific treatment for KSHV-related diseases, due to our limited knowledge of detailed immune evasion strategies by KSHV. KSHV blocks multiple immune pathways to maintain its lifelong infection, one of which is the DNA-sensing cGAS-STING pathway. Here, we reported that ORF48, a KSHV-encoded STING inhibitor is required for optimal KSHV lytic reactivation and viral production. A successful KSHV infection requires both intact ORF48 DNA and mRNA at different stages of its lytic life cycle. Further study reveals that ORF48 binds to STING and blocks STING-dependent innate immunity, and additional mechanisms may contribute to its role in lytic replication. Our findings provide insight into viral immune evasion strategies, which would contribute to a better understanding of all viral diseases.
E. coliprepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients
Authors: Gervais Théo , Kscheschinski Bjoern , Mell Michael , Goepfert Nevil , van Nimwegen Erik , Julou Thomas 
Published: March 2024

AbstractIt is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their phenotype during starvation and what controls the concentration of different gene products inside the cells. Here we used microfluidics with quantitative fluorescence microscopy to quantitatively monitor growth and gene expression in many independent single-cellE. colilineages as cells were switched from exponential growth to carbon starvation.In contrast to the hypothesis that stationary phase at the population level may reflect a balance between continuing growth and death in different sub-populations, we found that all cells immediately enter growth arrest, that cells further in their cell cycle subsequently undergo reductive division, and no cell death occurs for more than two days. Second, we observed dramatic time-dependent changes in protein production that are highly homogeneous across single cells. Some promoters shut off protein production immediately, some show a slow exponential decay of production on a 10 h time scale, while others exhibit a transient burst of increased production before decaying exponentially at different rates. Notably, the reduction in protein production 30-60 h into starvation relative to production in exponential phase varies by more than two orders of magnitude across promoters and is highly correlated with production in the first 10 h of starvation.Control experiments show that protein degradation itself also decays expo-nentially and using mathematical modeling we show how the fold-change in a gene’s protein concentration between exponential phase and late starvation depends on the size of the expression burst at the onset of starvation, the rate of subsequent production decay, and the rate of degradation decay. For many genes, the expression in late starvation is driven by production during the first 10 h. Finally, we establish that this expression program at the onset of starvation is critical for cell viability. In particular, by inhibiting gene expression during different periods of starvation, we show that tolerance to stress later in starvation is determined by gene expression occurring during the first 10 h.Our study provides a foundation for quantitative studies of bacterial starvation by uncovering a gene expression program that fundamentally remodels the proteome during the first 10 h of starvation, is highly homogeneous across single cells, sets the proteome later in starvation, and is crucial for stress tolerance.
Neurophysiological measures of covert semantic processing in neurotypical adolescents actively ignoring spoken sentence inputs: A high-density event-related potential (ERP) study
Authors: Toffolo Kathryn K. , Freedman Edward G. , Foxe John J. 
Published: March 2024

AbstractLanguage comprehension requires semantic processing of individual words and their context within a sentence. Well-characterized event-related potential (ERP) components (the N400 and late positivity component (LPC/P600)) provide neuromarkers of semantic processing, and are robustly evoked when semantic errors are introduced into sentences. These measures are useful for evaluating semantic processing in clinical populations, but it is not known whether they can be evoked in more severe neurodevelopmental disorders where explicit attention to the sentence inputs cannot be objectively assessed (i.e., when sentences are passively listened to). We evaluated whether N400 and LPC/P600 could be detected in adolescents who were explicitly ignoring sentence inputs. Specifically, it was asked whether explicit attention to spoken inputs was required for semantic processing, or if a degree of automatic processing occurs when the focus of attention is directed elsewhere? High-density ERPs were acquired from twenty-two adolescents (7-12 years), under two experimental conditions: 1) individuals actively determined whether the final word in a sentence was congruent or incongruent with sentence context, or 2) passively listened to background sentences while watching a video. When sentences were ignored, N400 and LPC/P600 were robustly evoked to semantic errors, albeit with reduced amplitudes and protracted/delayed latencies. Statistically distinct topographic distributions during passive versus active paradigms pointed to distinct generator configurations for semantic processing as a function of attention. Covert semantic processing continues in neurotypical adolescents when explicit attention is withdrawn from sentence inputs. As such, this approach could be used to objectively investigate semantic processing in populations with communication deficits.
Mriyaviruses: Small Relatives of Giant Viruses
Authors: Yutin Natalya , Mutz Pascal , Krupovic Mart , Koonin Eugene V. 
Published: March 2024

AbstractThe phylumNucleocytoviricotaconsists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to theNucleocytoviricota.In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCP) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of theNucleocytoviricotaand accordingly would comprise a class which we propose to name “Mriyaviricetes” (after Ukrainian Mriya, dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of theNucleocytoviricota. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the familyYaraviridaeand proposed new family “Gamadviridae”. The previously characterized members of these families, Yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of theNucleocytoviricota,and RNA polymerase subunits encoded by all cytoplasmic viruses among theNucleocytoviricota, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.ImportanceThe origin of giant viruses of eukaryotes that belong to the phylumNucleocytoviricotais not thoroughly understood and remains a matter of major interest and debate. Here we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35-45 kilobases that appears to comprise a distinct class within the phylumNucleocytoviricotathat we provisionally named“Mriyaviricetes”.Mriyaviruses appear to be the closest identified relatives of the ancestors of theNucleocytoviricota.Analysis of proteins encoded in mriyavirus genomes suggest that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members ofNucleocytoviricota.
Spectroscopy of helium-tagged
C60
anions
Authors: Kappe Miriam , Martini Paul , Schiller Arne , Gruber Elisabeth , Zappa Fabio , Krasnokutski Serge A. , Scheier Paul , Gatchell Michael 
Published: March 2024

We present measurements of the electronic absorption spectrum of He-tagged buckminsterfullerene anions, C60−. Using a technique that allows for the efficient tagging of complex molecular anions with He, we achieve atomically resolved action spectra that provide an accurate determination of the gas-phase absorption spectrum in the near-infrared regime. In total we identify 27 absorption bands between 895 and 1057 nm.

Published by the American Physical Society
2024
The dark side of mentoring: A Viewpoint
Authors: Oyewunmi Adebukola E. , Hinson Robert Ebo 
Published: March 2024

Purpose
This paper examines the dark side of mentoring, its far-reaching effects and organizational interventions for navigating it.

Design/methodology/approach
Literature review and narrative analysis are adopted to achieve the objective of the paper.

Findings
Review of extant literature highlights the multiple consequences of the dark side of mentoring. Recommendations include specialized training interventions, period appraisals of formal mentoring arrangements, zero-tolerance ethical frameworks and employee assistance programmers.

Originality/value
A substantive portion of literature on mentoring has lauded its benefits for career progression and competitive advantage. This viewpoint explores its limitations and liabilities in an organization.
Building brand equity as a dynamic capability during Gautrain public–private partnership patronage guarantee controversy
Authors: Mthombeni Morris , Ruiters Michele , Scheepers Caren Brenda , Pearson Hayley 
Published: March 2024

Learning outcomes
After completion of the case study, the students will be able to gain knowledge on public–private partnerships (PPPs) in emerging markets; understand how to apply the sensing element of the dynamic capabilities framework in analysing context, especially in emerging market context; and understand how to apply the dynamic capabilities framework to the process of developing brand equity.

Case overview/synopsis
On 20 March 2020, in Johannesburg South Africa, Dr Barbara Jensen Vorster, the head of corporate communications and marketing at the Gautrain Management Agency, was considering her dilemma of how to manage stakeholders at a time when the patronage guarantee was under question. The nature of the Gautrain PPP transport contract entailed a revenue guarantee that was called a patronage guarantee. How did they build their Gautrain brand equity during the Gautrain PPP patronage guarantee controversy? This case study highlights the perspectives of multiple stakeholders which places the Gautrain brand equity under strain. The Gautrain brand identity was created to project an integrated, overarching brand position for the construction project and later the operating company. The logo illustrated Africanisation, and the slogan “For People on the Move” represented a modern collaborative approach. Upholding the status of the brand is an important quest for the corporate communications and marketing team, and therefore the issue around the patronage guarantee must be addressed. This case study illustrates contrasting views about the Gautrain being elitist versus the rapid rail train enabling economic prosperity. The pro-prosperity versus pro-economic development values were at the heart of the different opinions around the patronage guarantee. Students are therefore confronted with their own values while the case study aims to drive an awareness or consciousness around these issues in an emerging market.

Complexity academic level
This case study is appropriate for advanced undergraduate and Master of Business Administration courses focused on marketing, communications and/or stakeholder management, such as in business and society courses. At both levels, the case study will be valuable in generating discussion on communications models and how to manage stakeholders ranging from government to community representatives. In courses where dynamic capabilities theory is taught, this case study will offer a specific application of this model in the context of brand communications and building brand equity in times of controversy.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship.