bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contralateral delay activity and alpha lateralization reflect retinotopic and screen-centered reference frames in visual memory
Authors: Mössing Wanja A. , Schroeder Svea C. Y. , Biel Anna Lena , Busch Niko A. 
Published: June 2023

AbstractThe visual system represents objects in a lateralized manner, with contralateral cortical hemispheres responsible for left and right visual hemifields. This organization extends to visual short-term memory (VSTM), as evidenced by electrophysiological indices of VSTM maintenance: contralateral delay activity (CDA) and alpha-band lateralization. However, it remains unclear if VSTM represents object locations in gaze-centered (retinotopic) or screen-centered (spatiotopic) coordinates, especially after eye movements. In two experiments, participants encoded the colors of target objects and made a lateral saccade during the maintenance interval, thereby shifting the object’s location on the retina. A non-lateralized probe stimulus was then presented at the new fixation for a change detection task. The CDA maintained lateralization towards the target’s original retinotopic location, unaffected by subsequent saccades, and did not invert polarity even when a saccade brought that location into the opposite hemifield. We also found conventional alpha lateralization towards the target’s location before a saccade. After a saccade, however, alpha was lateralized towards the screen center regardless of the target’s original location, even in a control condition without any memory requirements. This suggest that post-saccadic alpha-band lateralization reflects attentional processes unrelated to memory, while pre- and post-saccade CDA reflect VSTM maintenance in a retinotopic reference frame.
Development and Optimisation of in vitro Sonodynamic Therapy for Glioblastoma
Authors: Keenlyside Andrew , Marples Theodore , Gao Zifan , Hu Hong , Nicely Lynden Guy , Nogales Joaquina , Li Han , Landgraf Lisa , Solth Anna , Melzer Andreas , Hossain-Ibrahim Kismet , Huang Zhihong , Banerjee Sourav , Joseph James 
Published: June 2023

AbstractBackgroundSonodynamic therapy (SDT) is currently on critical path for glioblastoma therapeutics. However, the molecular mechanisms underlying the therapeutic functions of SDT remain enigmatic due to the lack of intricately optimised instrumentation capable of modulating SDT delivery in vitro. We established and validated an automated in vitro SDT system and assessed its SDT efficacy.MethodsAn automated in vitro SDT system was established and validated to allow the application and mapping of focused ultrasound fields under varied acoustic exposure conditions and setup configurations. Ultrasound field simulations were performed to assess the acoustic energy exposure. Systematic in vitro investigations were performed to optimise ultrasound frequency, intensity, plate base material, thermal effect, and the integration of live cells.ResultsIn the presence of 5-ALA, focused ultrasound induces apoptotic cell death in primary patient-derived glioma cells with concurrent upregulation of intracellular reactive oxygen species. Intriguingly, primary glioma stem neurospheres also exhibit remarkably reduced 3D growth upon SDT exposure. Further, ultrasound field simulations performed established acoustic field distribution and the impact of acoustic standing waves within the well-plates.ConclusionsThe optimised in vitro SDT system and associated ultrasound field simulations establish the basis for further understanding of SDT and its therapeutic potentials in cancer.
Measuring stimulus-related redundant and synergistic functional connectivity with single cell resolution in auditory cortex
Authors: Koçillari Loren , Celotto Marco , Francis Nikolas A. , Mukherjee Shoutik , Babadi Behtash , Kanold Patrick O. , Panzeri Stefano 
Published: June 2023

AbstractMeasures of functional connectivity have played a central role in advancing our understanding of how information is communicated within the brain. Traditionally, these studies have focused on identifying redundant functional connectivity, which involves determining when activity is similar across different sites. However, recent research has highlighted the potential importance of also identifying synergistic connectivity—that is, connectivity that gives rise to information not contained in either site alone. Here, we measured redundant and synergistic functional connectivity with individual-neuron resolution in the primary auditory cortex of the mouse during a perceptual task. Specifically, we identified pairs of neurons that exhibited directed functional connectivity between them, as measured using Granger Causality. We then used Partial Information Decomposition to quantify the amount of redundant and synergystic information carried by these neurons about auditory stimuli. Our findings revealed that functionally connected pairs carry proportionally more redundancy and less synergy than unconnected pairs, suggesting that their functional connectivity is primarily redundant in nature. Furthermore, we observe that the proportion of redundancy is higher for correct than for incorrect behavioral choices, supporting the notion that redundant connectivity is beneficial for behavior.
Systematic Characterization of LSD metabolites inC. elegansby ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry
Authors: Silveira Christiane Martins de Vasconcellos , dos Santos Vanessa Farelo , Ornelas Isis Moraes , Carrilho Beatriz de Sá , Ventura Matheus Antônio Vieira de Castro , Pereira Henrique Marcelo Gualberto , Rehen Stevens Kastrup , Junqueira Magno 
Published: June 2023

AbstractPsychedelic compounds have gained renewed interest for their potential therapeutic applications, but their metabolism and effects on complex biological systems remain poorly understood. Here, we present a systematic characterization of LSD metabolites in the model organismCaenorhabditis elegansusing state-of-the-art analytical techniques. By employing ultra-high performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS), we identified and quantified a range of LSD metabolites, shedding light on their metabolic pathways and offering insights into their pharmacokinetics. Our study demonstrates the suitability ofC. elegansas a valuable model system for investigating the metabolism of psychedelic compounds and provides a foundation for further research on the therapeutic potential of LSD. These findings contribute to the growing body of knowledge in the field and highlight the importance of advanced analytical methodologies in elucidating the effects of psychedelic substances on biological systems.
State-dependent dynamics of cuttlefish mantle activity
Authors: Cohen-Bodénès Sophie , Neri Peter 
Published: June 2023

ABSTRACTCuttlefish skin is a powerful rendering device, capable of producing extraordinary changes in visual appearance over a broad range of temporal scales. This unique ability is typically associated with camouflage, however cuttlefish often produce skin patterns that do not appear connected with the surrounding environment, such as fast large-scale fluctuations with wave-like characteristics. Little is known about the functional significance of these dynamic patterns. In this study, we develop novel tools for analyzing pattern dynamics, and we demonstrate their utility for detecting changes in feeding state that occur without concomitant changes in sensory stimulation. Under these conditions, we find that the dynamic properties of specific pattern components differ for different feeding states, despite no measurable change in the overall expression of those components. These dynamic changes are therefore not detectable by conventional analyses focusing on pattern expression, requiring analytical tools specifically targeted to pattern dynamics.
A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types
Authors: Tibi Muhammad , Biton Stav , Hochgerner Hannah , Lin Zhige , Givon Shachar , Ophir Osnat , Shay Tal , Mueller Thomas , Segev Ronen , Zeisel Amit 
Published: June 2023

AbstractTeleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon; the seat of plastic behavior, learning and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting inde novomolecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly and spatially conserved goldfish homologues. We further suggest different elements of a hippocampalformation across the goldfish pallium. Together, our atlas provides new insights to organization and evolution of vertebrate forebrains and may serve as a resource for the functional study underlying cognition in teleost fish.TeaserDetailed mapping of goldfish forebrain cells unwraps how 450 million years of evolution may have impacted brain function
Comparative 3D genome analysis between neural retina and RPE reveals differentialcis-regulatory interactions at retinal disease loci
Authors: D’haene Eva , Soriano Victor López , Martínez-García Pedro Manuel , Kalayanamontri Soraya , Dueñas Rey Alfredo , Sousa-Ortega Ana , Naranjo Silvia , Van de Sompele Stijn , Vantomme Lies , Mahieu Quinten , Vergult Sarah , Neto Ana Bastos , Gómez-Skarmeta José Luis , Martínez-Morales Juan R. , Bauwens Miriam , Tena Juan J. , De Baere Elfride 
Published: June 2023

ABSTRACTVision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment ofcis-regulatory elements (CREs) in 3D nuclear space.To understand the role of differential chromatin architecture in establishing tissue-specific expression patterns at IRD loci in the human neural retina and the RPE, we mapped genome-wide chromatin interactions by applyingin situHi-C and H3K4me3 HiChIP to human adult post-mortem donor retinas. A comparative 3D genome analysis between neural retina and RPE/choroid revealed that almost 60% of 290 known IRD genes were marked by differential 3D genome structure and/orcis-regulatory interactions. One of these genes wasABCA4, which is implicated in the most common autosomal recessive IRD. We zoomed in on tissue-specific chromatin interactions at theABCA4locus using high-resolution UMI-4C assays. Upon integration with bulk and single-cell epigenomic datasets andin vivoenhancer assays in zebrafish, we revealed tissue-specific CREs interacting withABCA4.In summary, through extensive comparative 3D genome mapping, based on genome-wide (Hi-C), promoter-centric (HiChIP) and locus-specific (UMI-4C) assays of human neural retina and RPE, we have shown that gene regulation at key IRD loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes of IRD genes, but also delineate the search space for non-coding genomic variation underlying unsolved IRD.Abstract Figure
Compensatory mutations are associated with increasedin vitrogrowth in resistant clinical samples ofMycobacterium tuberculosis
Authors: Brunner Viktoria , Fowler Philip W 
Published: June 2023

AbstractMutations inMycobacterium tuberculosisassociated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness ofM. tuberculosispopulations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase ofM. tuberculosis, using over 70,000M. tuberculosisgenomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests to investigate the association of putative CMs with resistance-conferring mutations much more power. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higherin vitrogrowth densities, and hence presumably with higher fitness, in resistant samples in the more virulentM. tuberculosisLineages 2 and 3. In Lineage 2, our results even suggest the association of CM presence with significantly higherin vitrogrowth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasise the integral role of CMs and lineage affiliation in resistance spread and increases the urgency for antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics forM. tuberculosisinfections to not only improve patient outcomes but also to prevent the spread of resistant strains.
Pangenome genotyped structural variation improves molecular phenotype mapping in cattle
Authors: Leonard Alexander S. , Mapel Xena M. , Pausch Hubert 
Published: June 2023

AbstractExpression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so the genomic variation is often called from short read alignments which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved assemblies to identify small and structural variation and genotype them with PanGenie in 307 short read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation, and confidently genotype close to 21M small and 43k structural variants in the larger population. We validate 85% of these structural variants (with MAF>0.1) directly with a subset of 25 short read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTLs forSTN1andMYH7and SV-sQTLs forCEP89andASAH2. Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.
Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation
Authors: Jensen Axel , Swift Frances , de Vries Dorien , Beck Robin , Kuderna Lukas F.K. , Knauf Sascha , Chuma Idrissa S. , Keyyu Julius D. , Kitchener Andrew C. , Farh Kyle , Rogers Jeffrey , Marques-Bonet Tomas , Detwiler Kate M. , Roos Christian , Guschanski Katerina 
Published: June 2023

AbstractUnderstanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as a potential facilitator of adaptive radiations. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world’s largest primate radiations, we show that rampant gene flow characterizes their evolutionary history, and identify ancient hybridization across deeply divergent lineages differing in ecology, morphology and karyotypes. Lineages experiencing gene flow tend to be more species-rich than non-admixed lineages. Mitochondrial transfers between distant lineages were likely facilitated by co-introgression of co-adapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. This study provides important insights into the prevalence, role and outcomes of ancestral hybridization in a large mammalian radiation.
Converting Organic Municipal Solid Waste into Volatile Fatty Acids and Biogas: Experimental Pilot and Batch Studies with Statistical Analysis
Authors: Borhany Hojjat 
Published: June 2023

AbstractBackgroundItaly can augment its profit from biorefinery products by altering the operation of digesters or different designs to obtain more precious bio-products like volatile fatty acids (VFAs) than biogas from organic municipal solid waste. In this context, recognizing the process stability and outputs through operational interventions and its technical and economic feasibility is a critical issue. Hence, the present study is an anaerobic digester in Treviso in northern Italy.ObjectivesThis research compares the novel line, consisting of pretreatment, acidogenic fermentation, and anaerobic digestion, with single-step anaerobic digestion regarding financial profit and surplus energy. Therefore, a mass flow model was created and refined based on the outputs from the experimental and numerical studies. These studies examine the influence of hydraulic retention time (HRT), pretreatment, biochar addition, and fine-tuned feedstock/inoculum (FS/IN) ratio on bio-products and operational parameters.MethodsVFA concentration, VFA weight ratio distribution (VWRD), and biogas yield were quantified by gas chromatography. Then, attest was conducted to analyze the significance of dissimilar HRTs in changing the VFA content. Further, a feasible biochar dosage was identified for an assumed FS/IN ratio with an adequate long HRT using the First-Order (FO) rate model. Accordingly, the parameters for a mass flow model were adopted for 70,000 population equivalents to determine the payback period and surplus energy for two scenarios. We also explored the effectiveness of amendments in improving the process kinetics.ResultsBoth HRTs were identical concerning the VFA/SCOD (0.88 kg/kg) and VWRD: mainly acetic acid (40%), butyric acid (24%), and caproic acid (17%). However, a significantly higher mean VFA content was confirmed for HRT 4.5d than the quantity for HRT 3d (30.77 vs 27.66, g-SCOD/L) using attest (t =- 2.68, df=8,P=.03, CI=95%). In this research, 83% of the fermented volatile solids were converted into biogas to obtain a specific methane production of 0.133 (/kg−VS). While biochar addition improved only the maximum methane content by 20% (86% v/v), the feedstock/inoculum ratio of 0.3 (volatile solid basis) with thermal plus fermentative pretreatment improved the hydrolysis rate substantially (0.57 vs 0.07, 1/d). Furthermore, the biochar dosage of 0.12 (g-biochar/g-VS) with HRT 20d was identified as a feasible solution. Principally, our novel line payback period would be almost 2 years with surplus energy of +2251 (MJ/d) compared to 45 years and +21567 (MJ/d) for single-step anaerobic digestion.ConclusionsThis research elaborated on the advantage of the refined novel line over the single-step anaerobic digestion and confirmed its financial and technical feasibility. Further, changing HRT and other amendments significantly raised the VFA concentration and the process kinetics and stability.
Organizing construction logistics outsourcing: a logistics strategy perspective
Authors: Haglund Petter , Janné Mats 
Published: June 2023

Purpose
The construction industry shows an increased interest in how to manage logistics within construction projects. Often construction logistics is outsourced to a logistics service provider (LSP). However, construction logistics is normally approached either as a strategic decision or as an operational issue and rarely as a tactical concern. The purpose of this study is to explore how to organize the logistics outsourcing decision at strategic, tactical and operational levels.

Design/methodology/approach
This study is performed as a single-case study within a construction corporation, containing (amongst others) a building contractor (BC) and a construction equipment rental company (CERC) offering logistics services.

Findings
The study shows that to procure construction logistics service successfully, BCs need logistics capabilities at strategic and tactical levels to maintain an alignment between the use of logistics services and operational characteristics. Simultaneously, CERC’s need to design their service offerings to correspond to the needs of the BC.

Research limitations/implications
This study builds on a single-case study of a Swedish construction corporation. Further research is needed to better understand current logistics outsourcing and development practices and how these can be improved to foster better logistics management at the project level.

Practical implications
BCs find suggestions of different logistics organization structures and suitable outsourcing arrangements. CERCs and LSPs can use the findings to understand their customers’ needs and adapt service offerings.

Originality/value
To the best of the authors’ knowledge, this study is one of the first studies of how two companies within a corporation can work together to develop construction logistics service offerings.
Girls’ and young women’s leader identity development: a scoping review
Authors: Dixon Sakina , Niewoehner-Green Jera Elizondo , Smulowitz Stacy , Smith Deborah N. , Rutstein-Riley Amy , Thomas Trenae M. 
Published: June 2023

Purpose
This scoping review aims to examine peer-reviewed literature related to girls’ (age 0–18) and young women’s (age 19–30) leader identity development.

Design/methodology/approach
This study uses a scoping review. A research librarian was consulted at the start of the project. Two sets of search terms (one for each age group) were identified and then used to find publications via our selected databases. The search results were uploaded to Covidence and evaluated using the determined inclusion and exclusion criteria. The final sample of articles for the review was analyzed using exploratory coding methods.

Findings
From the analysis, four domains were identified that influence girls’ and young women’s leader identity development: relationships, personal characteristics, meaningful engagement and social identities.

Originality/value
To the best of the authors’ knowledge, this is the first study to solely explore girls’ and young women’s leader identity development. The factors and domains identified provide useful guidance for future research and practice. The findings reveal considerations about leader identity that can inform the creation of effective leadership development initiatives for girls early in their lifespan. These interventions could provide girls with a strong leadership foundation that could drastically alter their leadership trajectories in adulthood. Previous research has conveyed the advantages of having more women participate in leadership. Thus, this potential not only benefits girls and women but organizations and society at large.