bluuebunny/crossref_metadata_2025 huggingface dataset:
LEVERAGING THE POWER OF 3D BRAIN-WIDE IMAGING AND MAPPING TOOLS FOR BRAIN INJURY RESEARCH IN MURINE MODELS
Authors: Anwer Mehwish , LeDue Jeffrey , Wang Zefang , Wang Sarah , Cheng Wai Hang , Burdyniuk Mariia , Cheung Honor , Fan Jianjia , Barron Carlos , Cripton Peter A , Cembrowski Mark S , Rossi Fabio , Murphy Timothy H , Wellington Cheryl L
Published: April 2023

Despite the fundamental importance of understanding impaired brain activity exhibited in post-traumatic epilepsy and other neurological impairments associated with traumatic brain injury (TBI), knowledge of how brain injury affects neuronal activity remains remarkably incomplete. We describe a whole-brain imaging and analysis approach to identify alterations in neuronal activity after TBI as a complementary method to conventional two-dimensional (2D) histological approaches. Here we report an easy-to-follow experimental pipeline to quantify changes in the whole mouse brain using tissue clearing, light sheet microscopy (LSM) and an optimised open-access atlas registration workflow. We validated the outcome of the pipeline using high throughput image analysis software and a secondary atlas registration method. Using the CHIMERA (Closed-Head Impact Model of Engineered Rotational Acceleration) TBI model, TRAP2 mice were subjected to repeated mild TBI or sham treatment followed by tamoxifen injection to lock c-Fos activity after TBI. Brains were SHIELD fixed and passively cleared for imaging of c-Fos+ cells throughout the rostro-caudal axis of the brain using a light sheet microscope equipped with a specialized whole-brain imaging chamber. Volumetric images were stitched and 3D rendered using Arivis Vision4D image analysis software. For quantitative analysis, 2D image stacks were exported to segment c-Fos+ cells and register them to the Allen Mouse Brain Atlas using the BrainQuant3D python package. As a result, c-Fos+ cell counts were estimated throughout the brain and heatmaps were generated. We identified a brain-wide reduction in c-Fos cell density in the TBI group compared to sham controls, indicative of TBI-induced changes in whole brain neuronal activity. Further studies using multi-dimensional imaging coupled with analysis tools will deepen our understanding of post-TBI brain-wide dynamics.
Geographical Survey of the Mycobiome and Microbiome of Southern California Glassy-winged Sharpshooters
Authors: Ettinger Cassandra L. , Wu-Woods Jessica , Kurbessoian Tania L. , Brown Dylan J. , de Souza Pacheco Inaiara , Vindiola Beatriz G. , Walling Linda L. , Atkinson Peter W. , Byrne Frank J. , Redak Richard , Stajich Jason E.
Published: April 2023

The glassy-winged sharpshooter,Homalodisca vitripennisGermar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen,Xylella fastidiosa. While studies have focused onX. fastidiosaor known symbionts ofH. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here we characterize the mycobiome and the microbiome ofH. vitripennisacross Southern California and explore correlations with captivity and host insecticide-resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS1) region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while theH. vitripennismycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wildH. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide-resistance status in wildH. vitripennis. This study serves as a foundational look at theH. vitripennismycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide-resistance status and investigate whether microbial communities should be considered inH. vitripennismanagement practices.
Ancient methicillin-resistantStaphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection
Authors: Benvenga Vanni , Cuénod Aline , Purushothaman inithi , Dasen Gottfried , Weisser Maja , Bassetti Stefano , Roloff Tim , Siegemund Martin , Heininger Ulrich , Bielicki Julia , Wehrli Marianne , Friderich Paul , Frei Reno , Widmer Andreas , Herzog Kathrin , Fankhauser Hans , Nolte Oliver , Bodmer Thomas , Risch Martin , Dubuis Olivier , Pranghofer Sigrid , Calligaris-Maibach Romana , Graf Susanne , Tschudin-Sutter Sarah , Perreten Vincent , Seth-Smith Helena M.B , Egli Adrian
Published: April 2023

Few methicillin-resistantStaphylococcus aureus(MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes.

We accessed 451 ancient (1965-1987) Swiss MRSA isolates, stored in the Culture Collection of Switzerland. We determined phenotypic antimicrobial resistance (AMR) and performed Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international genomes from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmeccassette types, AMR, and virulence genes.

Among the 451 ancient Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-IIII. Early MRSA were predominantly from clonal complex (CC) 8. From 1980 to the end of the 20thcentury we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally.

The combined analysis of 1761 ancient and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss and international MRSA across time.
The Crystal Structure of the Hsp90-LA1011 Complex and the Mechanism by which LA1011 may Improve the Prognosis of Alzheimer’s Disease
Authors: Roe S. Mark , Török Zsolt , McGown Andrew , Horváth Ibolya , Spencer John , Pázmány Tamás , Vigh László , Prodromou Chrisostomos
Published: April 2023

Chaperone systems play a major role in the decline of cognition and contribute to neurological pathologies such as Alzheimer’s disease (AD). While such a decline may occur naturally with age or with stress or trauma, the mechanisms involved have remained elusive. The current models suggest that amyloid-β (Aβ) plaque formation leads to the hyperphosphorylation of tau by a Hsp90 dependent process that triggers tau neurofibrillary tangle formation and neurotoxicity. Several co-chaperones of Hsp90 can influence the phosphorylation of tau, including FKBP51, FKBP52 and PP5. In particular elevated levels of FKBP51 occur with age and stress and are further elevated in AD. Recently, the dihydropyridine, LA1011 was shown to reduce tau pathology and amyloid plaque formation in transgenic AD mice, probably through its interaction with Hsp90 although the precise mode of action is currently unknown. Here, we present a co-crystal structure of LA1011 in complex with a fragment of Hsp90. We show that LA1011 can disrupt binding of FKBP51, which might help to rebalance the Hsp90-FKBP51 chaperone machinery and provide a favourable prognosis towards AD. Clinically, this is highly significant, as AD is generally a disease affecting older patients, where slowing of disease progression could result in AD no longer being life limiting.
Harmonizing and aligning M/EEG datasets with covariance-based techniques to enhance predictive regression modeling
Authors: Mellot Apolline , Collas Antoine , Rodrigues Pedro L. C. , Engemann Denis , Gramfort Alexandre
Published: April 2023

Neuroscience studies face challenges in gathering large datasets, which limits the use of machine learning (ML) approaches. One possible solution is to incorporate additional data from large public datasets; however, data collected in different contexts often exhibit systematic differences called dataset shifts. Various factors,e.g., site, device type, experimental protocol, or social characteristics, can lead to substantial divergence of brain signals that can hinder the success of ML across datasets. In this work, we focus on dataset shifts in recordings of brain activity using MEG and EEG. State-of-the-art predictive approaches on M/EEG signals classically represent the data by covariance matrices. Model-based dataset alignment methods can leverage the geometry of covariance matrices, leading to three steps: recentering, re-scaling, and rotation correction. This work explains theoretically how differences in brain activity, anatomy, or device configuration lead to certain shifts in data covariances. Using controlled simulations, the different alignment methods are evaluated. Their practical relevance is evaluated for brain age prediction on one MEG dataset (Cam-CAN,n=646) and two EEG datasets (TUAB,n=1385; LEMON,n=213). When the target sample included recordings from the same subjects with a different task among the same dataset, paired rotation correction was essential ((rest-passive) or +0.17 (rest-smt)). When the target dataset included new subjects and a new task, re-centering led to improved performance (for rest-passive,for rest-smt). For generalization to an independent dataset sampled from a different population and recorded with a different device, re-centering was necessary to achieve brain age prediction performance close to within domain prediction performance. This study demonstrates that the generalization of M/EEG-based regression models across datasets can be substantially enhanced by applying domain adaptation procedures that can statistically harmonize diverse datasets.
Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes
Authors: Haberman Nejc , Digby Holly , Faraway Rupert , Cheung Rebecca , Jobbins Andrew M , Parr Callum , Yasuzawa Kayoko , Kasukawa Takeya , Yip Chi Wai , Kato Masaki , Takahashi Hazuki , Carninci Piero , Vernia Santiago , Ule Jernej , Sibley Christopher R , Martinez-Sanchez Aida , Lenhard Boris
Published: April 2023

The 3’ untranslated region (3’UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis gene expression (CAGE), a method for the detection of capped 5’ ends of mRNAs, additionally reveals a large number of apparently 5’ capped RNAs derived from 3’UTRs. Here we provide the first direct evidence that these 3’UTR-derived RNAs are indeed capped and often more abundant than the corresponding full-length mRNAs. By using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP) and CAGE following siRNA knockdowns, we find that these 3’UTR-derived RNAs likely originate from AGO2-mediated cleavage, and most often occur at locations with potential to form RNA-G-quadruplexes and are enriched by RNA-binding protein UPF1. High-resolution imaging and long-read sequencing analysis validates several 3’UTR-derived RNAs, demonstrates their abundance and shows that they tend not to co-localise with the parental mRNAs. We also find that production of 3’UTR-derived RNA could explain the previously reported role of a 3’UTR G-quadruplex in regulating the production of APP protein. Taken together, we provide new insights into the origin and abundance of 3’UTR-derived RNAs, show the utility of CAGE-seq for their quantitative detection, and provide a rich dataset for exploring new biology of a poorly understood new class of RNAs.
Exploration-exploitation mechanisms in recurrent neural networks and human learners in restless bandit problems
Authors: Tuzsus D. , Brands A. , Pappas I. , Peters J.
Published: April 2023

A key feature of animal and human decision-making is to balance the exploration of unknown options for information gain (directed exploration) versus selecting known options for immediate reward (exploitation), which is often examined using restless bandit tasks. Recurrent neural network models (RNNs) have recently gained traction in both human and systems neuroscience work on reinforcement learning, due to their ability to show meta-learning of task domains. Here we comprehensively compared the performance of a range of RNN architectures as well as human learners on restless four-armed bandit problems. The best-performing architecture (LSTM network with computation noise) exhibited human-level performance. Computational modeling of behavior first revealed that both human and RNN behavioral data contain signatures of higher-order perseveration, i.e., perseveration beyond the last trial, but this effect was more pronounced in RNNs. In contrast, human learners, but not RNNs, exhibited a positive effect of uncertainty on choice probability (directed exploration). RNN hidden unit dynamics revealed that exploratory choices were associated with a disruption of choice predictive signals during states of low state value, resembling a win-stay-loose-shift strategy, and resonating with previous single unit recording findings in monkey prefrontal cortex. Our results highlight both similarities and differences between exploration behavior as it emerges in meta-learning RNNs, and computational mechanisms identified in cognitive and systems neuroscience work.
Evaluating the interplay between estrous cyclicity and induced seizure susceptibility inScn2aK1422Emice
Authors: Echevarria-Cooper Dennis M. , Kearney Jennifer A.
Published: April 2023

Pathogenic variants inSCN2Aare associated with a range of neurodevelopmental disorders (NDD).SCN2A-related NDD show wide phenotypic heterogeneity, suggesting that modifying factors must be considered in order to properly elucidate the mechanisms of pathogenic variants. Recently, we characterized neurological phenotypes in a mouse model of the variantSCN2A-p.K1422E. We demonstrated that heterozygousScn2aK1422Efemale mice showed a distinct, reproducible distribution of flurothyl-induced seizure thresholds. Women with epilepsy often show a cyclical pattern of altered seizure susceptibility during specific phases of the menstrual cycle which can be attributed to fluctuations in hormones and corresponding changes in neurosteroid levels. Rodent models have been used extensively to examine the relationship between the estrous (menstrual) cycle, steroid hormones, and seizure susceptibility. However, the effects of the estrous cycle on seizure susceptibility have not been evaluated in the context of an epilepsy-associated genetic variant. To determine whether the estrous cycle affects susceptibility to flurothyl-induced seizures inScn2aK1422Efemale mice, estrous cycle monitoring was performed in mice that had undergone ovariectomy (OVX), sham surgery, or no treatment prior to seizure induction. Removing the influence of circulating sex hormones via OVX did not affect the non-unimodal distribution of flurothyl seizure thresholds observed inScn2aK1422Efemales. Additionally, flurothyl seizure thresholds were not associated with estrous cycle stage in mice that underwent sham surgery or were untreated. These data suggest that variation inScn2aK1422Eflurothyl seizure threshold is not significantly influenced by the estrous cycle and, by extension, fluctuations in ovarian hormones. Interestingly, untreatedScn2aK1422Efemales showed evidence of disrupted estrous cyclicity, an effect not previously described in a genetic epilepsy model. This unexpected result highlights the importance of considering sex specific effects and the estrous cycle in support of more inclusive biomedical research.
A Bacterial Living Therapeutics with Engineered Protein Secretion Circuits To Eliminate Breast Cancer Cells
Authors: Shahid Gozeel Binte , Ahan Recep Erdem , Ostaku Julian , Seker Urartu Ozgur Safak
Published: April 2023

Cancer therapy can be limited by potential side effects, and bacteria-based living cancer therapeutics have gained scientific interest in recent years. However, the full potential of bacteria as therapeutics has yet to be explored due to engineering challenges. n this study, we present a bacterial device designed to specifically target and eliminate breast cancer cells. We have engineeredEscherichia coli(E. coli) to secrete a Shiga toxin, HlyE, which is a pore-forming protein that binds to HER2 receptors on breast cancer cells. This binding is facilitated by a nanobody expressed on the bacteria’s surface via the Ag43 autotransporter protein system. Our findings demonstrate that the nanobody efficiently binds to HER2+ cells in vitro, and we have utilized the YebF secretion system to secrete HlyE and kill the target cancer cells. Overall, our results highlight the potential of our engineered bacteria as an innovative strategy for breast cancer treatment.
Ventral hippocampal CCK interneurons gate context-reward memory
Authors: Nguyen Robin , Sivakumaran Sanghavy , Lambe Evelyn K. , Kim Jun chul
Published: April 2023

Associating contexts with rewards depends on hippocampal circuits, with local inhibitory interneurons positioned to play an important role in shaping activity. Here, we hypothesize that the encoding of context-reward memory requires a ventral hippocampus (vHPC) to nucleus accumbens (NAc) circuit that is gated by CCK interneurons. In a sucrose conditioned place preference (CPP) task, optogenetically inhibiting vHPC-NAc terminals impaired the acquisition of place preference. Transsynaptic rabies tracing revealed vHPC-NAc neurons were monosynaptically innervated by CCK interneurons. Using intersectional genetic targeting of CCK interneurons,ex vivooptogenetic activation of CCK interneurons increased GABAergic transmission onto vHPC-NAc neurons, whilein vivooptogenetic inhibition of CCK interneurons increased cFos in these neurons. Notably, CCK interneuron inhibition during sucrose CPP learning increased time spent in the sucrose-associated location, suggesting enhanced place-reward memory. Our findings reveal a previously unknown hippocampal microcircuit crucial for modulating the strength of contextual reward learning.
Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining
Authors: Cullati Sierra N. , Zhang Eric , Shan Yufan , Guillen Rodrigo X. , Chen Jun-Song , Navarrete-Perea Jose , Elmore Zachary C. , Ren Liping , Gygi Steven P. , Gould Kathleen L.
Published: April 2023

The CK1 family are conserved serine/threonine kinases with numerous substrates and cellular functions. The fission yeast CK1 orthologues Hhp1 and Hhp2 were first characterized as regulators of DNA repair, but the mechanism(s) by which CK1 activity promotes DNA repair had not been investigated. Here, we found that deleting Hhp1 and Hhp2 or inhibiting CK1 catalytic activities in yeast or in human cells activated the DNA damage checkpoint due to persistent double-strand breaks (DSBs). The primary pathways to repair DSBs, homologous recombination and non-homologous end joining, were both less efficient in cells lacking Hhp1 and Hhp2 activity. In order to understand how Hhp1 and Hhp2 promote DSB repair, we identified new substrates using quantitative phosphoproteomics. We confirmed that Arp8, a component of the INO80 chromatin remodeling complex, is a bona fide substrate of Hhp1 and Hhp2 that is important for DSB repair. Our data suggest that Hhp1 and Hhp2 facilitate DSB repair by phosphorylating multiple substrates, including Arp8.
Phase variation in LPS O-antigen biosynthetic gene cluster of the rice pathogenXanthomonas oryzaepv.oryzae
Authors: Madhavan Vishnu Narayanan , Bansal Kanika , Kumar Sanjeet , Midha Samriti , Patil Prabhu B. , Patel Hitendra Kumar , Sonti Ramesh V.
Published: April 2023

Bacteria respond to environmental cues in different ways. Phase variation is one such adaptation where heritable and reversible changes in DNA aid bacteria to alter the expression of specific genes. The bacterial plant pathogenXanthomonas oryzaepv.oryzae(Xoo) causes the serious bacterial blight disease of rice. The mucoid phenotype of Xoo colonies is attributed to the secreted exopolysaccharide (EPS), xanthan gum. Spontaneous non-mucoid variants of Xoo which are deficient in EPS production and virulence were observed to accumulate in long-term stationary phase cultures. This phenomenon was termed stationary phase variation and variant colonies as stationary phase variants (SPV). Several but not all of these SPVs have been earlier described to carry spontaneous insertions of endogenous insertion sequence elements in thegumoperon which encodes genes involved in EPS biosynthesis. In this study, we show that a number of SPVs harbour variations in the lipopolysaccharide (LPS) outer antigen (O-antigen) biosynthetic gene cluster. The data revealed that the vast majority of variations are due to either insertion of endogenous insertion sequence (IS) elements or slipped strand mispairing (SSM). Also, it was observed that many of these SPVs exhibited reversion to wild type mucoid phenotype via restoration of the wild type genotype. The results indicate that the phenomenon of phase variation is occurring in the LPS O-antigen biosynthetic gene cluster of Xoo.
Evaluating possible maternal effect lethality and genetic background effects inNaa10knockout mice
Authors: Lyon Gholson J. , Longo Joseph , Garcia Andrew , Inusa Fatima , Marchi Elaine , Shi Daniel , Dörfel Max , Arnesen Thomas , Aldabe Rafael , Lyons Scott , Nashat Melissa A. , Bolton David
Published: April 2023

Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene,NAA10,encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants inNAA10. In mice,Naa10is not an essential gene, as there exists a paralogous gene,Naa12, that substantially rescuesNaa10knockout mice from embryonic lethality, whereas double knockouts (Naa10−/YNaa12−/−)are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of “maternal effect lethality” for heterozygousNaa10−/Xfemale mice, but we do observe a small amount of embryonic lethality in theNaa10−/ymale mice on the inbred genetic background in this different animal facility.
MetPlast: an R package to evaluate Metabolic Plasticity using Information Theory statistical framework
Authors: D’Andrea Lucio , Perez de Souza Leonardo , Fernie Alisdair R. , Bombarely Aureliano
Published: April 2023

MetPlast, is an R package that provides the functionalities necessary to analyze biological samples’ metabolic plasticity. This package takes advantage of the statistical framework provided by the Information Theory to quantify and defined metabolic plasticity parameters. Using previous implemented formula based on Shannon entropy we automatize the calculation and visualization of a set of metabolic plasticity indexes including metabolic diversity, metabolome specialization, and metabolite specialization. We use a publicly available metabolic data set on tomato domestication to demonstrate the power of the present tool to evaluate changes in metabolic plasticity parameters. Thus, MetPlast represents a new and invaluable member of the computational metabolomics toolbox, that will certainly help scientists to unveil hidden information in cell metabolomic landscape.

Availability and implementation

Freely available athttps://github.com/danlucio86/MetPlast
Methods Optimization for the Expression and Purification of Human Calcium Calmodulin-Dependent Protein Kinase II Alpha
Authors: Bolton Scott C. , Thompson David H. , Kinzer-Ursem Tamara L.
Published: April 2023

Calcium/calmodulin-dependent protein kinase II (CaMKII) is a complex multifunctional kinase that is highly expressed in central nervous tissues and plays a key regulatory role in the calcium signaling pathway. Despite over 30 years of recombinant expression and characterization studies, CaMKII continues to be investigated for its impact on signaling cooperativity and its ability to bind multiple substrates through its multimeric hub domain. Here we compare and optimize protocols for the generation of full-length wild-type human calcium/calmodulin-dependent protein kinase II alpha (CaMKIIα). Side-by-side comparison of expression and purification in both insect and bacterial systems shows that the insect expression method provides superior yields of the desired autoinhibited CaMKIIα holoenzymes. Utilizing baculovirus insect expression system tools, our results demonstrate a high yield method to produce homogenous, monodisperse CaMKII in its autoinhibited state suitable for biophysical analysis. Advantages and disadvantages of these two expression systems (baculovirus insect cell versusEscherichia coliexpression) are discussed, as well as purification optimizations to maximize the enrichment of full-length CaMKII.
VISTA: Visualizing the Spatial Transcriptome of theC. elegansNervous System
Authors: Liska David , Wolfe Zachery , Norris Adam
Published: April 2023

Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode wormC. elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm’s invariant cell lineage and a series of recently-generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a “spatial heatmap” in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated fromin vivoreporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation, and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future.

Availability and Implementation

VISTA is freely available at the following URL:https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA
Harmonic radiation contribution and X-ray transmission at the Small Quantum Systems instrument of European XFEL
Authors: Baumann Thomas M. , Boll Rebecca , De Fanis Alberto , Grychtol Patrik , Ilchen Markus , Jastrow Ulf Fini , Kato Masahiro , Lechner Christoph , Maltezopoulos Theophilos , Mazza Tommaso , Montaño Jacobo , Music Valerija , Ovcharenko Yevheniy , Rennhack Nils , Rivas Daniel E. , Saito Norio , Schmidt Philipp , Serkez Svitozar , Sorokin Andrey , Usenko Sergey , Yan Jiawei , Geloni Gianluca , Tanaka Takahiro , Tiedtke Kai , Meyer Michael
Published: April 2023

Transmission measurements of the soft X-ray beamline to the Small Quantum Systems (SQS) scientific instrument at the SASE3 undulator of European XFEL are presented. Measurements are reported for a wide range of photon energies (650 eV to 2400 eV), using X-ray gas monitors as well as a bolometric radiometer. The results are in good agreement with simulations for the beam transport and show a transmission of up to 80% over the whole photon energy range. The contribution of second- and third-harmonic radiation of the soft X-ray undulator is determined at selected photon energies by performing transmission measurements using a gas absorber to provide variable attenuation of the incoming photon flux. A comparison of the results with semi-analytic calculations for the generation of free-electron laser pulses in the SASE3 undulator reveals an influence of apertures along the beam transport on the exact harmonic content to be accounted for at the experiment. The second-harmonic content is measured to be in the range of 0.1% to 0.3%, while the third-harmonic contributed a few percent to the SASE3 emission. For experiments at the SQS instrument, these numbers can be reduced through specific selections of the mirror reflection angles.
Customers' purchase intention of renewable energy in Jordan: the case of solar panel systems using an extended theory of planned behavior (TPB)
Authors: Almrafee Mohammad , Akaileh Mustafa
Published: April 2023

Purpose

This study aims to examine the influence of various factors on the customers’ purchase intention of renewable energy in Jordan. The hypotheses and model of the study were adopted from previous studies.

Design/methodology/approach

The present study was undertaken based on an online survey of 428 Jordanians who are nonusers of renewable energy. The sample was selected using a stratified random sampling method using a structured questionnaire method. Data were analyzed using SPSS version 25.

Findings

The results indicated that attitudes, subjective norms (social influence), perceived price, knowledge and perceived behavioral control significantly affect the purchase intention of Jordanian customers to adopt renewable energy. Moreover, the study confirms that there are statistically significant differences between demographic variables such as age, income and education about renewable energy purchasing intentions, whereas gender was not significant.

Research limitations/implications

Some limitations have been identified. First, the generalizability of the findings is one of the common limitations of scientific research, and this study is not an exception. In this regard, the current study has been carried out in the south of Jordan. Therefore, to expand the validity of the findings, future studies need to be attempted in other places in Jordan. Second, the existing study focused on solar panel systems as a form of renewable energy. Future studies could focus on other kinds of renewable energy, such as wind energy. Third, although the sample size of this study was appropriate and sufficient, future studies could use larger samples to enhance the robustness of the results.

Practical implications

The findings of the current study could help practitioners in the renewable energy industry by identifying the key factors that motivate Jordanian customers to purchase and use such technology. They may use the findings of this study in the formulation of marketing policies and the development of marketing strategies to attract more customers to purchase and use renewable energy appliances like solar panels.

Originality/value

This is one of the few studies in the energy industry of Jordan devoted to developing and testing a model of determinants of purchasing intentions for solar panel systems that focuses on renewable energy purchasing behavior. Further, this study used demographic variables as control variables, which makes the study different from other studies by investigating the role of demographic characteristics in the context of the purchase intention for solar panel systems.
The usefulness of sensor fusion for unmanned aerial vehicle indoor positioning
Authors: Guo Hang , Chen Xin , Yu Min , Uradziński Marcin , Cheng Liang
Published: April 2023

Purpose

In this study, an indoor sensor information fusion positioning system of the quadrotor unmanned aerial vehicle (UAV) was investigated to solve the problem of unstable indoor flight positioning.

Design/methodology/approach

The presented system was built on Light Detection and Ranging (LiDAR), Inertial Measurement Unit (IMU) and LiDAR-Lite devices. Based on this, one can obtain the aircraft's current attitude and the position vector relative to the target and control the attitudes and positions of the UAV to reach the specified target positions. While building a UAV positioning model relative to the target for indoor positioning scenarios under limited Global Navigation Satellite Systems (GNSS), the system detects the environment through the NVIDIA Jetson TX2 (Transmit Data) peripheral sensor, obtains the current attitude and the position vector of the UAV, packs the data in the format and delivers it to the flight controller. Then the flight controller controls the UAV by calculating the posture to reach the specified target position.

Findings

The authors used two systems in the experiment. The first is the proposed UAV, and the other is the Vicon system, our reference system for comparison purposes. Vicon positioning error can be considered lower than 2 mm from low to high-speed experiments. After comparison, experimental results demonstrated that the system could fully meet the requirements (less than 50 mm) in real-time positioning of the indoor quadrotor UAV flight. It verifies the accuracy and robustness of the proposed method compared with that of Vicon and achieves the aim of a stable indoor flight preliminarily.

Originality/value

Vicon positioning error can be considered lower than 2 mm from low to high-speed experiments. After comparison, experimental results demonstrated that the system could fully meet the requirements (less than 50 mm) in real-time positioning of the indoor quadrotor UAV flight. It verifies the accuracy and robustness of the proposed method compared with that of Vicon and achieves the aim of a stable indoor flight preliminarily.
Implementation strategies to screen, refer and link women involved in the carceral system to PrEP for HIV prevention
Authors: Dauria Emily , Rodriguez Christopher , Bauerle Bass Sarah , Tolou-Shams Marina , Christopoulos Katerina
Published: April 2023

Purpose

Women involved in the carceral system (CS) experience several conditions that increase their risk for HIV (e.g. high rates of substance use, psychiatric disorders, histories of victimization). The purpose of this study is to explore perspectives on potential strategies to connect women in the CS to pre-exposure prophylaxis (PrEP) services.

Design/methodology/approach

This study conducted in-depth interviews with 27 women involved in the CS eligible for PrEP. Using vignettes, interviews explored attitudes, barriers and facilitators toward PrEP screening, referral and linkage facilitated via a CS stakeholder, an mHealth application or providing PrEP service referrals during detention via a navigator.

Findings

Most women were, on average, 41.3 years, from racial and ethnic minority groups (56% black/African American; 19% Latinx). Inductive thematic analysis revealed CS involved women expressed mostly positive attitudes toward CS-based PrEP implementation. Younger women were more accepting of and interested in mHealth interventions. Implementation facilitators included leveraging relationships with trusted allies (e.g. “peers”) and existing systems collaborations. Recommended implementation strategies included providing HIV and PrEP-specific education and training for system stakeholders and addressing issues related to privacy, system mistrust and stigma.

Originality/value

Results provide a critical foundation for the implementation of interventions to improve PrEP access for women involved in the CS and have important implications for implementation strategies for all adults involved in the CS. Improving access to PrEP among this population may also support progress toward addressing national disparities in PrEP uptake, where women, black and Latinx populations have substantial unmet need.
Microfinance institutions and female entrepreneurship in Sub-Saharan Africa: avoidable female unemployment thresholds
Authors: Asongu Simplice , Odhiambo Nicholas M.
Published: April 2023

Purpose

This study aims to contribute to the extant literature by assessing how microfinance institutions (MFIs) affect female entrepreneurship, contingent on female unemployment levels.

Design/methodology/approach

The study focuses on 44 countries in sub-Saharan Africa for the period 2004–2018. The empirical evidence is based on interactive quantile regressions, which put emphasis on nations with high, low and intermediate levels of business constraints. The analysis is tailored to provide avoidable female unemployment levels in the implementation of policies designed for MFIs to promote female business ownership.

Findings

The hypotheses that MFIs are favorable for female business owners and some critical rates of female unemployment should be avoided in order for the favorable incidence to be maintained is exclusively valid in the 10th quantiles of the cost of business by females and time to start-up a business by females. Policy implications are discussed.

Originality/value

This study has complemented the extant literature by providing actionable female unemployment critical masses that governments can act upon in tailoring the relevance of MFIs in the doing of business by females.
Birds of a feather flock together? Leader–member trait mindfulness congruence effects on work outcomes
Authors: Zhang Linlin , Jiang Haoran , Hu Tongwen , Zhang Zhenduo
Published: April 2023

Purpose

Drawing upon person–supervisor fit theory, a model is developed to illustrate how leader–member trait mindfulness (in)congruence may impact leader–member exchange (LMX) and how such trait mindfulness (in)congruence can indirectly influence taking charge.

Design/methodology/approach

Polynomial regression and response surface methodology are used to analyze 237 valid matched leader–member dyads.

Findings

LMX increases as leaders' and members' trait mindfulness become more aligned; LMX is higher when leader–member dyads are congruent at high levels (vs low levels). In the case of incongruence, LMX is higher when the member's trait mindfulness exceeds that of the leader. Furthermore, the relationship between leader–member trait mindfulness (in)congruence and taking charge is mediated by LMX.

Practical implications

The joint and interactive role of high trait mindfulness in leader–member dyads can help them to generate high-quality interpersonal exchange, as well as to cope with challenges posed by present and future changes.

Originality/value

The linear, nonlinear, simultaneous and interactive effects of dyadic trait mindfulness expand previous research, clarifying that the evaluation of leader–member congruence and incongruence at various degrees, and for various patterns of trait mindfulness, is more informative than examining the direct effect alone.
Beyond lean manufacturing and sustainable performance: are the circular economy practices worth pursuing?
Authors: Maldonado-Guzmán Gonzalo , Garza-Reyes Jose Arturo
Published: April 2023

Purpose

The need to improve sustainability in manufacturing firms, which would allow them to reduce the emission of pollutants and the generation of industrial waste, has stimulated the adoption of circular economy (CE) alongside lean manufacturing (LM) practices to significantly improve the sustainable performance of organizations. However, empirical evidence provided in previous studies and that has related the practices of LM, CE and sustainable performance do not allow establishing an interconnection between these three concepts. Therefore, this paper fills this gap in the literature by exploring the relationship between these three concepts.

Design/methodology/approach

A quantitative study in which data were collected from 460 managers working in the automotive industry in Mexico was conducted. The data allowed the testing and validation of four hypotheses through the use of partial least squares structural equation modeling (PLS SEM).

Findings

The results obtained suggest that LM practices have a significant positive influence both on sustainable performance and CE. In turn, the results also demonstrate the existence of a significant positive relationship between CE and the sustainable performance of manufacturing firms in the automotive industry as well as that CE has a positive role in mediating the interconnection between LM practices and sustainable performance.

Practical implications

The results obtained from the present study will allow entrepreneurs in the automotive industry and industry professionals as well as government authorities to formulate more effective policies and strategies to support the improvement of environmental sustainability performance in the manufacturing sector.

Originality/value

This is one of the first studies that have investigated the relationship between LM, CE and sustainable performance, particularly, in the automotive sector.
The infinity vaccine war: linguistic regularities and audience engagement of vaccine debate on Twitter
Authors: Peng Rachel X. , Wang Ryan Yang
Published: April 2023

Purpose

As public health professionals strive to promote vaccines for inoculation efforts, fervent anti-vaccination movements are marshaling against it. This study is motived by a need to better understand the online discussion around vaccination. The authors identified the sentiments, emotions and topics of pro- and anti-vaxxers’ tweets, investigated their change since the pandemic started and further examined the associations between these content features and audiences’ engagement.

Design/methodology/approach

Utilizing a snowball sampling method, data were collected from the Twitter accounts of 100 pro-vaxxers (266,680 tweets) and 100 anti-vaxxers (248,425 tweets). The authors are adopting a zero-shot machine learning algorithm with a pre-trained transformer-based model for sentiment analysis and structural topic modeling to extract the topics. And the authors use the hurdle negative binomial model to test the relationships among sentiment/emotion, topics and engagement.

Findings

In general, pro-vaxxers used more positive tones and more emotions of joy in their tweets, while anti-vaxxers utilized more negative terms. The cues of sadness predominantly encourage retweets across the pro- and anti-vaccine corpus, while tweets amplifying the emotion of surprise are more attention-grabbing and getting more likes. Topic modeling of tweets yields the top 15 topics for pro- and anti-vaxxers separately. Among the pro-vaxxers’ tweets, the topics of “Child protection” and “COVID-19 situation” are positively predicting audiences’ engagement. For anti-vaxxers, the topics of “Supporting Trump,” “Injured children,” “COVID-19 situation,” “Media propaganda” and “Community building” are more appealing to audiences.

Originality/value

This study utilizes social media data and a state-of-art machine learning algorithm to generate insights into the development of emotionally appealing content and effective vaccine promotion strategies while combating coronavirus disease 2019 and moving toward a global recovery.

Peer review

The peer review history for this article is available athttps://publons.com/publon/10.1108/OIR-03-2022-0186
Improving the functionality of biodegradable food packaging materials via porous nanomaterials
Authors: Jafarzadeh Shima , Forough Mehrdad , Kouzegaran Vahid Javan , Zargar Masoumeh , Garavand Farhad , Azizi‐Lalabadi Maryam , Abdollahi Mehdi , Jafari Seid Mahdi
Published: April 2023

Non‐biodegradability and disposal problems are the major challenges associated with synthetic plastic packaging. This review article discusses a new generation of biodegradable active and smart packaging based on porous nanomaterials (PNMs), which maintains the quality and freshness of food products while meeting biodegradability requirements. PNMs have recently gained significant attention in the field of food packaging due to their large surface area, peculiar structures, functional flexibility, and thermal stability. We present for the first time the recently published literature on the incorporation of various PNMs into renewable materials to develop advanced, environmentally friendly, and high‐quality packaging technology. Various emerging packaging technologies are discussed in this review, along with their advantages and disadvantages. Moreover, it provides general information about PNMs, their characterization, and fabrication methods. It also briefly describes the effects of different PNMs on the functionality of biopolymeric films. Furthermore, we examined how smart packaging loaded with PNMs can improve food shelf life and reduce food waste. The results indicate that PNMs play a critical role in improving the antimicrobial, thermal, physicochemical, and mechanical properties of natural packaging materials. These tailor‐made materials can simultaneously extend the shelf life of food while reducing plastic usage and food waste.
Propofol mediates non‐small cell lung cancer growth in part by regulating circ_0003028‐related mechanisms
Authors: Zhang Xiuli , Liu Dongzhi , Wang Ping , Liu Naihe
Published: April 2023

Background

Circular RNAs (circRNAs) are associated with propofol‐mediated inhibitory effect on non‐small cell lung cancer (NSCLC) progression. Circular hsa_circ_0003028 (circ_0003028) exerts a tumor‐promoting role in NSCLC. However, it is unclear whether propofol can mediate NSCLC progression via regulating circ_0003028 expression.

Methods

A total of 36 NSCLC patients were recruited in the study. Cell viability, proliferation, apoptosis, migration, and invasion were determined by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT), colony formation, flow cytometry, and transwell assays. Relative expression of circ_0003028 in NSCLC samples and cells was detected by quantitative real‐time polymerase chain reaction (RT‐qPCR). Analysis of the latent binding of circ_0003028 to miR‐1305 was done by bioinformatic analysis and confirmed by luciferase reporter and RNA immunoprecipitation (RIP) assays. Xenografting in mice was done to verify the relationship between propofol and circ_0003028.

Results

Significant upregulation of circ_0003028 was detected in NSCLC samples and cells. Functionally, propofol treatment reduced circ_0003028 expression in NSCLC cells, and circ_0003028 overexpression impaired propofol‐mediated inhibitory effect on NSCLC cell proliferation, migration, and invasion. Interestingly, circ_0003028 could compete with miR‐1305 as a competing endogenous RNA and upregulate CORO1C expression in NSCLC cells.

Conclusion

Propofol‐mediated inhibiting effect on NSCLC growth partly depended on the circ_0003028/miR‐1305/CORO1C axis.