bluuebunny/crossref_metadata_2025 huggingface dataset:
Mpox virus (MPXV) vertical transmission and fetal demise in a pregnant rhesus macaque model
Authors: Krabbe Nicholas P. , Mitzey Ann M. , Bhattacharya Saswati , Razo Elaina R. , Zeng Xiankun , Bekiares Nell , Moy Amy , Kamholz Amy , Karl Julie A. , Daggett Gregory , VanSleet Grace , Morgan Terry , Capuano Saverio V. , Simmons Heather A. , Basu Puja , Weiler Andrea M. , O’Connor David H. , Friedrich Thomas C. , Golos Thaddeus G. , Mohr Emma L.
Published: May 2024

Infection with clade I Mpox virus (MPXV) results in adverse pregnancy outcomes, yet the potential for vertical transmission resulting in fetal harm with clade IIb MPXV, the clade that is currently circulating in the Western Hemisphere, remains unknown. We established a rhesus macaque model of vertical MPXV transmission with early gestation inoculation. Three pregnant rhesus macaques were inoculated intradermally with 1.5 × 10^5 plaque forming units (PFU) of clade IIb MPXV near gestational day (GD) 30 and animals were monitored for viremia and maternal and fetal well-being. Animals were euthanized to collect tissues at 5, 14, or 25 days post-inoculation (dpi). Tissues were evaluated for viral DNA (vDNA) loads, infectious virus titers, histopathology, MPXV mRNA and protein localization, as well as MPXV protein co-localization with placental cells including, Hofbauer cells, mesenchymal stromal cells, endothelial cells, and trophoblasts. vDNA was detected in maternal blood and skin lesions by 5 dpi. Lack of fetal heartbeat was observed at 14 or 25 dpi for two dams indicating fetal demise; the third dam developed significant vaginal bleeding at 5 dpi and was deemed an impending miscarriage. vDNA was detected in placental and fetal tissue in both fetal demise cases. MPXV localized to placental villi by ISH and IHC. Clade IIb MPXV infection in pregnant rhesus macaques results in vertical transmission to the fetus and adverse pregnancy outcomes, like clade I MPXV. Further studies are needed to determine whether antiviral therapy with tecovirimat will prevent vertical transmission and improve pregnancy outcomes.

One Sentence Summary

Clade IIb Mpox virus infection of pregnant rhesus macaques results in vertical transmission from mother to fetus and adverse pregnancy outcomes.
Single neuron contributions to the auditory brainstem EEG
Authors: Kuokkanen Paula T. , Kraemer Ira , Koeppl Christine , Carr Catherine E. , Kempter Richard
Published: May 2024

The auditory brainstem response (ABR) is an acoustically evoked EEG potential that is an important diagnostic tool for hearing loss, especially in newborns. The ABR originates from the response sequence of auditory nerve and brainstem nuclei, and a click-evoked ABR typically shows three positive peaks (‘waves’) within the first six milliseconds. However, an assignment of the waves of the ABR to specific sources is difficult, and a quantification of contributions to the ABR waves is not available. Here, we exploit the large size and physical separation of the barn owl first-order cochlear nucleus magnocellularis (NM) to estimate single-cell contributions to the ABR. We simultaneously recorded NM neurons’ spikes and the EEG, and found that ≥ 5, 000 spontaneous single-cell spikes are necessary to isolate a significant spike-triggered average response at the EEG electrode. An average single-neuron contribution to the ABR was predicted by convolving the spike-triggered average with the cell’s peri-stimulus time histogram. Amplitudes of predicted contributions of single NM cells typically reached 32.9 ± 1.1 nV (mean ± SE, range: 2.5 − 162.7 nV), or 0.07 ± 0.02% (median ± SE; range from 0.01% to 1%) of the ABR amplitude. The time of the predicted peak coincided best with the peak of the ABR wave II, independent of the click sound level. Our results suggest that individual neurons’ contributions to an EEG can vary widely, and that wave II of the ABR is shaped by NM units.

Significance statement

The auditory brainstem response (ABR) is a scalp potential used for the diagnosis of hearing loss, both clinically and in research. We investigated the contribution of single action potentials from auditory brainstem neurons to the ABR and provide direct evidence that action potentials recorded in a first order auditory nucleus, and their EEG contribution, coincide with wave II of the ABR. The study also shows that the contribution of single cells varies strongly across the population.
Excitation/Inhibition imbalance increases the proneness to experience the sound-induced flash illusion by impairing multisensory causal inference in the schizophrenia spectrum
Authors: Paredes Renato , Ferri Francesca , Romei Vincenzo , Seriès Peggy
Published: May 2024

Background and Hypothesis

The spectrum of schizophrenia is characterised by an altered sense of self with known impairments in tactile sensitivity, proprioception, body-self boundaries, and self-recognition. These are thought to be produced by failures in multisensory integration mechanisms, commonly observed as enlarged temporal binding windows during audiovisual illusion tasks. To our knowledge, there is an absence of computational explanations for multisensory integration deficits in patients with schizophrenia and individuals with high schizotypy, particularly at the neurobiological level.

Study Design

We implemented a multisensory causal inference network to reproduce the responses of individuals who scored low in schizotypy in a simulated double flash illusion task. Next, we explored the effects of Excitation/Inhibition imbalance, feedback weights, and synaptic density on the visual illusory responses of the network.

Study Results

Using quantitative fitting to empirical data, we found that an increase in recurrent excitation or cross-modal connectivity in the network enlarges the temporal binding window and increases the overall proneness to experience the illusion, matching the responses of individuals scoring high in schizotypy. Moreover, we found that an increase in the E/I balance by either neural mechanism increases the probability of inferring a common cause from the stimuli.

Conclusions

We propose an E/I imbalance account of reduced temporal discrimination in the SCZ spectrum and discuss possible links with Bayesian theories of schizophrenia. We highlight the importance of adopting a multisensory causal inference perspective to address body-related symptomatology of schizophrenia.
Feasibility and acceptability for LION, a fully remote, randomized clinical trial within the VA for light therapy to improve sleep in Veterans with and without TBI: An MTBI2sponsored protocol
Authors: Elliott Jonathan E. , Brewer Jessica S. , Keil Allison T. , Ligman Brittany R. , Bryant-Ekstrand Mohini D. , McBride Alisha A. , Powers Katherine , Sicard Savanah J. , Twamley Elizabeth W. , O’Neil Maya E. , Hildebrand Andrea D. , Nguyen Thuan , Morasco Benjamin J. , Gill Jessica M. , Dengler Bradley A. , Lim Miranda M.
Published: May 2024

Sleep-wake disturbances frequently present in Veterans with mild traumatic brain injury (mTBI). These TBI-related sleep impairments confer significant burden and commonly exacerbate other functional impairments. Therapies to improve sleep following mTBI are limited and studies in Veterans are even more scarce. In our previous pilot work, morning bright light therapy (MBLT) was found to be a feasible behavioral sleep intervention in Veterans with a history of mTBI; however, this was single-arm, open-label, and non-randomized, and therefore was not intended to establish efficacy. The present study, LION (light vs ion therapy) extends this preliminary work as a fully powered, sham-controlled, participant-masked randomized controlled trial (NCT03968874), implemented as fully remote within the VA (target n=120 complete). Randomization at 2:1 allocation ratio to: 1) active: MBLT (n=80), and 2) sham: deactivated negative ion generator (n=40); each with identical engagement parameters (60-min duration; within 2-hrs of waking; daily over 28-day duration). Participant masking via deception balanced expectancy assumptions across arms. Outcome measures were assessed following a 14-day baseline (pre-intervention), following 28-days of device engagement (post-intervention), and 28-days after the post-intervention assessment (follow-up). Primary outcomes were sleep measures, including continuous wrist-based actigraphy, self-report, and daily sleep dairy entries. Secondary/exploratory outcomes included cognition, mood, quality of life, circadian rhythm via dim light melatonin onset, and biofluid-based biomarkers. Participant drop out occurred in <10% of those enrolled, incomplete/missing data was present in <15% of key outcome variables, and overall fidelity adherence to the intervention was >85%, collectively establishing feasibility and acceptability for MBLT in Veterans with mTBI.
Prostad: The development and evaluation of a prostate cancer rapid diagnostic pathway, a protocol
Authors: Jones Katie , Rees Sarah , Farrington Steven , Chandran Arya , Moosa Sohail , MacKrell Janet , Shanbhag Savita , Ng Yeung , Sewell Berni , Jones Mari , Erdem Esra , Fitzsimmons Deborah , Rich Nick , Rance Jaynie , Gemine Rachel
Published: May 2024

Background

Delay to cancer diagnosis is associated with poorer outcomes. In response to delays to cancer diagnosis in the UK, a number of Rapid Diagnosis Centres (RDCs), Multi-Disciplinary Centres (MDCs) and other pathway reforms have been piloted and implemented in recent years. Prostate cancer is the most commonly diagnosed cancer for men or those assigned male at birth in the UK. In Wales, the recommended time to diagnosis is within 62 days from point of suspicion. For patients served by Hywel Dda University Health Board, current waiting times on the prostate cancer diagnostic pathway are prolonged, falling well outside the 28-day decision to treat and 62-day referral to treatment targets. A revised prostate cancer diagnostic pathway called Prostad (Wesh for “prostate”) has been developed and is currently being implemented with the aim of reducing time to diagnosis (or discharge) for patients referred for investigation. This protocol describes Prostad and the planned evaluation approach.

Methods

This is a mixed-method evaluation. It is shaped by patient and public involvement throughout and incorporates realist interviews with multiple stakeholders (including NHS staff and patients), process mapping, economic evaluation, and monitoring of the intervention against its aims using routinely collected data.

Discussion

To the authors’ knowledge, this is the first project of its kind to combine service aims evaluation, cost-effectiveness analysis and realist evaluation approaches, and as such promises findings applicable to organisations and individuals with regard to various aims and priorities. Continued patient and public involvement throughout the study constitutes one of its strengths.
An intra-family conserved high-order RNA structure within the M ORF is important for arterivirus subgenomic RNA accumulation and infectious virus production
Authors: Shang Pengcheng , Li Yanhua , Chen Chi , Brierley Ian , Firth Andrew E. , Fang Ying
Published: May 2024

Synthesis of subgenomic RNAs is a strategy commonly used by polycistronic positive sense single-stranded RNA viruses to express 3′-proximal genes. Members of the order ofNidovirales, including coronaviruses and arteriviruses, use a unique discontinuous transcription strategy to synthesize subgenomic RNAs. In this study,in silicosynonymous site conservation analysis and RNA structure folding predicted the existence of intra-family conserved high-order RNA structure within the M ORF of arteriviral genomes, which was further determined to be important for the transcription/accumulation of subgenomic RNAs and production of infectious viral particles. Mutations disrupting the stability of the RNA structures significantly decreased the accumulation of multiple subgenomic RNAs. In contrast, the impact of mutagenesis on full-length genomic RNA accumulation was limited. The degree to which wild-type levels of subgenomic RNA accumulation were maintained was found to correlate with the efficiency of infectious virus production. Moreover, the thermo-stability of stems within the high-order RNA structure is also well correlated with viral replication capacity and the maintenance of subgenomic RNA accumulation. This study is the first to report an intra-Arteriviridaeconserved high-order RNA structure that is located in a protein-coding region and functions as an importantcis-acting element to control the accumulation/transcription of arteriviral subgenomic RNAs. This work suggests a complex regulation mechanism between genome replication and discontinuous transcription in nidoviruses.

IMPORTANCE

Arteriviruses are a group of RNA viruses that infect different animal species. They can cause diseases associated with respiratory/reproductive syndromes, abortion, or haemorrhagic fever. Among arteriviruses, porcine reproductive and respiratory syndrome virus (PRRSV) and equine arteritis virus (EAV) are economically important veterinary pathogens. The challenge in control of arterivirus infection reflects our limited knowledge of viral biology. In this study, we conducted a comprehensive bioinformatical analysis of arteriviral genomes and discovered intra-family conserved regions in the M ORF with a high-order RNA structure. The thermo-stability of the RNA structure influences sgRNA transcription/accumulation and correlates with the level of infectious virus production. Our studies provide a new insight on arterivirus replication mechanism, which may have implications in developing disease control and prevention strategies.
Catalytically inactive subgroup VIII receptor-like cytoplasmic kinases regulate the immune-triggered oxidative burst inArabidopsis thaliana
Authors: Dias Márcia Gonçalves , Dharmasena Thakshila , Gonzalez-Ferrer Carmen , Maika Jan Eric , Gallo Maria Camila Rodriguez , Miguel Virginia Natali , Dou Ruoqi , Bredow Melissa , Siegel Kristen R , Uhrig Richard Glen , Simon Rüdiger , Monaghan Jacqueline
Published: May 2024

Protein kinases are key components of multiple cell signaling pathways. Several protein kinases of the receptor-like cytoplasmic kinase (RLCK) family have demonstrated roles in immune and developmental signaling across various plant species, making them a family of interest in the study of phosphorylation-based signal relay. Here, we present our investigation of a subfamily of RLCKs inArabidopsis thaliana. Specifically, we focus on subgroup VIII RLCKs: MAZ and its paralog CARK6, as well as CARK7 and its paralog CARK9. We found that both MAZ and CARK7 associate with the calcium-dependent protein kinase CPK28in planta,and furthermore that CPK28 phosphorylates both MAZ and CARK7 on multiple residues in areas that are known to be critical for protein kinase activation. Genetic analysis suggests redundant roles for MAZ and CARK6 as negative regulators of the immune-triggered oxidative burst. We find evidence that supports homo– and hetero-dimerization between CARK7 and MAZ, which may be a general feature of this protein family. Multiple biochemical experiments suggest that neither MAZ nor CARK7 demonstrate catalytic protein kinase activityin vitro.Interestingly, we find that a mutant variant of MAZ incapable of protein kinase activity is able to complementmaz-1mutants, suggesting noncatalytic roles of MAZin planta. Overall, our study identifies subgroup VIII RLCKs as new players in Arabidopsis immune signaling and highlights the importance of noncatalytic functions of protein kinases.
Cerebellar tonic inhibition orchestrates the maturation of information processing and motor coordination
Authors: Kwon Jea , Kim Sunpil , Woo Junsung , De Schutter Erik , Hong Sungho , Lee C. Justin
Published: May 2024

Tonic inhibition in cerebellar granule cells (GC) is crucial in information coding fidelity for motor coordination. It emerges in activity-dependent and -independent manners, and their interplay evolves with age. However, specific molecular and cellular mechanisms and how their change affects network-level computation and motor behavior remain unclear. Here we show that, while net tonic inhibitory current remains unchanged, the main source of tonic GABA switches from synaptic spillover (neuronal activity-dependent) to astrocytic Best1 (activity-independent) throughout adolescence (4-8 weeks) in mice. Computational modeling based on experimental data demonstrated that this switch down-regulates the internally generated network activity mediating mutual inhibition between GC clusters receiving different inputs, thereby enhancing their independence. Consistent with simulations, 3D-posture analysis revealed an age-dependent increase in independent limb movements during spontaneous motion, which was impaired in Best1 knockout mice. Our findings highlight the late-stage development of complex motor coordination driven by the emergence of astrocyte-mediated tonic inhibition.
Spatial selective auditory attention is preserved in older age but is degraded by peripheral hearing loss
Authors: Caso Andrea , Griffiths Timothy D , Holmes Emma
Published: May 2024

Interest in how ageing affects attention is long-standing, although interactions between sensory and attentional processing in older age have not been systematically studied. Here, we examined interactions between peripheral hearing and selective attention in a spatialised cocktail party listening paradigm, in which three talkers spoke different sentences simultaneously and participants were asked to report the sentence spoken by a talker at a particular location. By comparing a sample of older (N = 61; age = 55– 80 years) and younger (N = 58; age = 18–35 years) adults, we show that, as a group, older adults benefit as much as younger adults from preparatory spatial attention. Although, for older adults, this benefit significantly reduces with greater age-related hearing loss. These results demonstrate that older adults without hearing loss retain the ability to direct spatial selective attention, but this ability deteriorates with age-related hearing loss. Thus, reductions in spatial selective attention likely contribute to difficulties communicating in social settings for older adults with age-related hearing loss. Overall, these findings demonstrate a relationship between mild perceptual decline and attention in older age.
Distinct ventral tegmental area neuronal ensembles are indispensable for reward-driven approach and stress-driven avoidance behaviors
Authors: Koutlas Ioannis , Patrikiou Lefkothea , van der Starre Stef E. , Danko Diaz , Wolterink-Donselaar Inge G. , Luijendijk Mieneke C. M. , Adan Roger A.H. , Meye Frank J.
Published: May 2024

Assigning valence to stimuli for adaptive behavior is an essential function, involving the ventral tegmental area (VTA). VTA cell types are often defined through neurotransmitters (NT). However, valence function in VTA does not parse along NT-boundaries as, within each NT-class, certain neurons are excited by reward and others by stressors. Here we identify the co-activated mouse VTA neuronal ensembles for reward and stress, and determine their role in adaptive behaviors. We show that stimuli of opposite valence (opioid vs acute social stress) recruit two segregated intermingled small VTA neuronal ensembles. These two ensembles continue to be preferentially engaged by congruent valence stimuli. Stimulation of VTA stress- or reward ensembles is aversive/reinforcing, respectively. Strikingly, external valence stimuli fully require activity of these small discrete VTA ensembles for conferring approach/avoidance outcomes. Overall, our study identifies distinct small VTA ensembles for positive and negative valence coding and shows their indispensability for adaptive behavior.
Predicting Suicide Risk in Bipolar Disorder patients from Lymphoblastoid Cell Lines genetic signatures
Authors: Sharma Omveer , Nayak Ritu , Mizrahi Liron , Rike Wote Amelo , Choudhary Ashwani , Hussein Yara , Rosh Idan , Tripathi Utkarsh , Shemen Aviram , Squassina Alessio , Alda Martin , Stern Shani
Published: May 2024

This research investigates the genetic signatures associated with a high risk of suicide in Bipolar disorder (BD) patients through RNA sequencing analysis of lymphoblastoid cell lines (LCLs). By identifying differentially expressed genes (DEGs) and their enrichment in pathways and disease associations, we uncover insights into the molecular mechanisms underlying suicidal behavior. LCL gene expression analysis reveals significant enrichment in pathways related to primary immunodeficiency, ion channel, and cardiovascular defects. Notably, genes such asLCK,KCNN2, andGRIA1emerged as pivotal in these pathways, suggesting their potential roles as biomarkers. Machine learning models trained on a subset of the patients and then tested on other patients demonstrate high accuracy in distinguishing low and high-risk of suicide in BD patients. Moreover, the study explores the genetic overlap between suicide-related genes and several psychiatric disorders. This comprehensive approach enhances our understanding of the complex interplay between genetics and suicidal behavior, laying the groundwork for future prevention strategies.
Energy Deficit is a Key Driver of Sleep Homeostasis
Authors: Park Scarlet J. , Murphy Keith R. , Ja William W.
Published: May 2024

Sleep and feeding are vital homeostatic behaviors, and disruptions in either can result in substantial metabolic consequences. Distinct neuronal manipulations inDrosophilacan dissociate sleep loss from subsequent homeostatic rebound, offering an optimal platform to examine the precise interplay between these fundamental behaviors. Here, we investigate concomitant changes in sleep and food intake in individual animals, as well as respiratory metabolic expenditure, that accompany behavioral and genetic manipulations that induce sleep loss inDrosophila melanogaster. We find that sleep disruptions resulting in energy deficit through increased metabolic expenditure and manifested as increased food intake were consistently followed by rebound sleep. In contrast, “soft” sleep loss, which does not induce rebound sleep, is not accompanied by increased metabolism and food intake. Our results demonstrate that homeostatic sleep rebound is linked to energy deficit accrued during sleep loss. Collectively, these findings support the notion that sleep functions to conserve energy and highlight the need to examine the effects of metabolic therapeutics on sleep.
Three waves of ovarian follicles in juvenile mice
Authors: Yin Qi , Spradling Allan C.
Published: May 2024

We characterized 3 waves of ovarian follicles in juvenile mice using tissue clearing, lineage tracing and scRNAseq. Wave 1 follicles grow with little delay, and express steroidogenic cell inducers by 2 weeks, as thecal and interstitial gland cells arise. Beginning at 3 weeks, >80% of wave 1 follicles degrade their oocytes, turn over most granulosa cells, and cluster together in the medulla. Thecal cells increase further around holes left by oocytes, and during puberty (5 wk), highly express androgen biosynthetic genes. "Boundary follicles" at the medullar-cortical boundary, comprise the earliest-activated wave 2 follicles. They expressFoxl2as early as E14.5, and generate >70% of the first mature oocytes. Our results indicate the medulla’s broad importance in initial follicular development, and argue that gamete waves, a common animal strategy, serve specific purposes. Wave 1 follicle derivatives bring about high androgen expression during puberty that likely impacts sex-specific neurodevelopment, while boundary and wave 2 follicles support early and lifelong fertility. Consistent with their distinct roles, granulosa cells of antral wave 1 and wave 2 follicles differentially express multiple genes, includingWnt4andIgfbp5.

SIGNIFICANCE STATEMENT

We studied the ovaries of juvenile mice 2-6 weeks (wk) of age using transcriptomics and cell lineage to characterize the earliest developing groups of follicles. "Wave 1" follicles begin growing at birth in the ovarian medulla (central region), but most do not produce mature oocytes. Instead they remodel to generate cells synthesizing androgens at puberty, which likely affect sex-specific neurodevelopment. A newly recognized group, "boundary follicles" activate next at the medulla-cortex boundary; their oocytes mature and give rise to most early offspring. The remaining "wave 2" follicles constitute the quiescent ovarian reserve and activate in small groups throughout later life. Our results highlight the importance of specific spatially-localized follicle subgroups and show that they aid reproduction in distinct ways, some of which involve extensive cellular remodeling.
Ex Vivo Cortical Circuits Learn to Predict and Spontaneously Replay Temporal Patterns
Authors: Liu Benjamin , Buonomano Dean V.
Published: May 2024

It has been proposed that prediction and timing are computational primitives of neocortical microcircuits, specifically, that neural mechanisms are in place to allow neocortical circuits to autonomously learn the temporal structure of external stimuli and generate internal predictions. To test this hypothesis, we trained cortical organotypic slices on two specific temporal patterns using dual-optical stimulation. After 24-hours of training, whole-cell recordings revealed network dynamics consistent with training-specific timed prediction. Unexpectedly, there was replay of the learned temporal structure during spontaneous activity. Furthermore, some neurons exhibited timed prediction errors. Mechanistically our results indicate that learning relied in part on asymmetric connectivity between distinct neuronal ensembles with temporally-ordered activation. These findings further suggest that local cortical microcircuits are intrinsically capable of learning temporal information and generating predictions, and that the learning rules underlying temporal learning and spontaneous replay can be intrinsic to local cortical microcircuits and not necessarily dependent on top-down interactions.
Towards an unbiased characterization of genetic polymorphism: a comparison of 27A. thalianagenomes
Authors: Igolkina Anna A. , Vorbrugg Sebastian , Rabanal Fernando A. , Liu Hai-Jun , Ashkenazy Haim , Kornienko Aleksandra E. , Fitz Joffrey , Collenberg Max , Kubica Christian , Morales Almudena Mollá , Jaegle Benjamin , Wrightsman Travis , Voloshin Vitaly , Bezlepsky Alexander D. , Llaca Victor , Nizhynska Viktoria , Reichardt Ilka , Lanz Christa , Bemm Felix , Flood Pádraic J. , Nemomissa Sileshi , Hancock Angela , Guo Ya-Long , Kersey Paul , Weigel Detlef , Nordborg Magnus
Published: May 2024

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should solve the problem—except that characterizing and making sense of non-SNP variation is difficult even with perfect sequence data. Here we analyze 27 genomes ofArabidopsis thalianain an attempt to address these issues, and illustrate what can be learned by analyzing whole-genome polymorphism data in an unbiased manner. Estimated genome sizes range from 135 to 155 Mb, with differences almost entirely due to centromeric and rDNA repeats that are difficult to assemble. The completely assembled chromosome arms comprise roughly 120 Mb in all accessions, but are full of structural variants, largely due to transposable elements. Even with only 27 accessions, a pan-genome coordinate system that includes the resulting variation ends up being ∼ 70% larger than the size of any one genome. Our analysis reveals an incompletely annotated mobile-ome: we not only detect several novel TE families, but also find that existing TE annotation is a poor predictor of elements that have recently been active. In contrast to this, the genic portion, or “gene-ome”, is highly conserved. By annotating each genome using accession-specific transcriptome data, we find that 13% of all (non-TE) genes are segregating in our 27 accessions, but most of these are transcriptionally silenced. Finally, we show that with short-read data we previously massively underestimated genetic variation of all kinds, including SNPs—mostly in regions where short reads could not be mapped reliably, but also where reads were mapped incorrectly. We demonstrate that SNP-calling errors can be biased by the choice of reference genome, and that RNA-seq and BS-seq results can be strongly affected by mapping reads only to a reference genome rather than to the genome of the assayed individual. In conclusion, while whole-genome polymorphism data pose tremendous analytical challenges, they also have the potential to revolutionize our understanding of genome evolution.
How higher charmonia shape the puzzling data of the
e+e−→ηJ/ψ
cross section
Authors: Peng Tian-Cai , Bai Zi-Yue , Wang Jun-Zhang , Liu Xiang
Published: May 2024

Recently, the BESIII collaboration performed a precise measurement of the e+e−→ηJ/ψ cross section. It is puzzling that the resonance parameters of the reported Y(4230) show a substantial divergence from the previously measured results in both the open-charmed and hidden-charmed decay channels, and the line shape asymmetry of the data approaching 4.2 GeV also suggests that it might be difficult to characterize the details of the structure around 4.2 GeV by a single resonance. This has motivated our great curiosity about how the charmonium states are distributed in the measured energy range and how they shape the puzzling data of the e+e−→ηJ/ψ cross section. In this work, we use five theoretically constructed charmonia in the range of 4.0–4.5 GeV, i.e., ψ(4040), ψ(4160), ψ(4220), ψ(4380), and ψ(4415), to apply a combined fit to the data, in which their calculated decay ratios into ηJ/ψ via hadronic loop mechanism are taken as input. The fit results can reproduce the measured cross section data well, especially for the subtle line shape around 4.2 GeV, showing that the structure around 4.2 GeV is possible from the contribution of both ψ(4160) and ψ(4220).

Published by the American Physical Society
2024
Consequences of the
μ−τ
reflection symmetry for leptogenesis in a seesaw model with diagonal Dirac neutrino mass matrix
Authors: Zhao Zhen-hua , Shao Yan , Shi Hong-Yu
Published: May 2024

In this paper, we have studied the consequences of the μ−τ reflection symmetry for leptogenesis in the type-I seesaw model with diagonal Dirac neutrino mass matrix. We have first obtained the phenomenologically allowed values of the model parameters, which show that there may exist zero or equal entries in the Majorana mass matrix for the right-handed neutrinos, and then studied their predictions for three right-handed neutrino masses, which show that there may exist two nearly degenerate right-handed neutrinos. Then, we have studied the consequences of the model for leptogenesis. Due to the μ−τ reflection symmetry, leptogenesis can only work in the two-flavor regime. Furthermore, leptogenesis cannot work for the particular case of r=1. Accordingly, for some benchmark values of r≠1, we have given the constraints of leptogenesis for relevant parameters. Furthermore, we have investigated the possibilities of leptogenesis being induced by the renormalization group evolution effects for two particular scenarios. For the particular case of r=1, the renormalization group evolution effects will break the orthogonality relations among different columns of MD and consequently induce leptogenesis to work. For the low-scale resonant leptogenesis scenario which is realized for nearly degenerate right-handed neutrinos, the renormalization group evolution effects can break the μ−τ reflection symmetry and consequently induce leptogenesis to work.

Published by the American Physical Society
2024
Gravitational waves from domain wall collapses and dark matter in the SM with a complex scalar field
Authors: Pham Hieu The , Senaha Eibun
Published: May 2024

We study a domain wall induced by spontaneously broken Z2 symmetry and its gravitational wave signature in the standard model with a complex scalar in connection with dark matter physics. In a minimal setup, a linear term of the singlet field is added to the scalar potential as an explicit Z2 breaking term to make the domain wall unstable. We obtain its minimal size from cosmological constraints and show that the parameter space that can be probed by current and future pulsar time array experiments requires the vacuum expectation value of the singlet field to be greater than O(10–100)  TeV, along with a singletlike Higgs mass of O(1–100)  TeV. However, such a region is severely restricted by the dark matter relic density, which places an upper bound on the singlet vacuum expectation value at approximately 200 TeV, and limits the dark matter mass to about half of the singletlike Higgs boson mass.

Published by the American Physical Society
2024
Thermodynamic Bounds on Symmetry Breaking in Linear and Catalytic Biochemical Systems
Authors: Liang Shiling , De Los Rios Paolo , Busiello Daniel Maria
Published: May 2024

Living systems are maintained out of equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due to nonequilibrium conditions. Here, we use the matrix-tree theorem to derive upper and lower thermodynamic bounds on these symmetry-breaking features in linear and catalytic biochemical systems. Our bounds are independent of the kinetics and hold for both closed and open reaction networks. We also extend our results to master equations in the chemical space. Using our framework, we recover the thermodynamic constraints in kinetic proofreading. Finally, we show that the contrast of reaction-diffusion patterns can be bounded only by the nonequilibrium driving force. Our results provide a general framework for understanding the role of nonequilibrium conditions in shaping the steady-state properties of biochemical systems.

Published by the American Physical Society
2024
Additive manufacturing in the medical sector: from an empirical investigation of challenges and opportunities toward the design of an ecosystem model
Authors: Peron Mirco , Saporiti Nicolò , Shoeibi Majid , Holmström Jan , Salmi Mika
Published: May 2024

Purpose

This works provides a thorough understanding of the challenges and opportunities associated with Additive Manufacturing (AM) adoption in the medical sector. Through this analysis, we aim to better understand when to adopt AM, how to do so, and how such adoption might change in the future.

Design/methodology/approach

This research first conducted a systematic literature review (SLR) to identify AM challenges and opportunities in the medical sector, which were then validated through a Delphi study. The 18 Delphi study participants were also asked to suggest countermeasures for the challenges and help identify future AM adoption scenarios. Finally, these findings were analyzed according to the ecosystem pie model to design an ecosystem model for AM in the medical sector.

Findings

Among the 13 challenges and 13 opportunities identified, the lack of a skilled workforce and the responsiveness achievable via AM were by far the most relevant challenge and opportunity. Moreover, the participants identified countermeasures for 10 challenges, as well as three future AM adoption scenarios. Finally, leveraging these findings, an ecosystem model was developed.

Originality/value

This work contributes to the limited understanding of the AM challenges and opportunities in the medical sector. It helps medical practitioners to better understand the challenges and opportunities associated with AM and AM manufacturers to better identify where to focus their R&D efforts and how this would impact future AM adoption levels. Furthermore, this work extends current theory supporting the design of an ecosystem model for AM in the medical sector following the ecosystem pie model.
Theories of digital platforms for supply chain management: a systematic literature review
Authors: Culotta Carina , Blome Constantin , Henke Michael
Published: May 2024

Purpose

Digital platforms transform supply chains. However, no unified theoretical understanding of digital platforms exists. Thus, the underlying research aims at investigating platform theories for supply chain management tasks.

Design/methodology/approach

The authors conduct a systematic literature review to identify relevant theories in the context of digital platforms and synthesize the respective findings for supply chain management tasks.

Findings

In total, 43 papers and 41 different relevant theories are identified. The most prominent theories are the resource-based view, transaction cost economics, internalization theory and the dynamic capabilities approach. Digital platforms alter and change the boundary decisions of firms. Therefore, they have various implications for supply chain management tasks such as make-or-buy decisions or the orchestration of resources to sustain a competitive advantage.

Practical implications

The identified supply chain theories as well as platform theories and their overlap provide a meaningful starting point for discussing and developing new and platform-based supply chain management approaches in the B2B domain.

Originality/value

The conducted systematic literature review provides a first starting point for building a holistic theoretical approach to digital platforms in supply chains. Thus, the paper contributes a missing link for discussing digital platforms and their theoretical foundations for supply chain management tasks.
Drag story hour at public libraries: the reading child and the construction of fear and othering in Swedish cultural policy debate
Authors: Engström Lisa , Carlsson Hanna , Hanell Fredrik
Published: May 2024

Purpose

The purpose of the paper is to produce new knowledge about the positions that public libraries both take and are given in the conflicts over politics and identity that play out in contemporary cultural and library policy debates. Using conflicts over drag story hour at public libraries as case, the study seeks to contribute to an emerging body of research that delves into the challenges that public libraries as promoters of democracy are confronting in the conflictual political landscape of today.

Design/methodology/approach

The paper presents an analysis of debates reported in news articles concerning Drag story hour events held at Swedish public libraries. Utilizing the analytical lenses of discourse theory and plural agonistics, the analysis serves to make visible the lines of conflicts drawn in these debates – particularly focusing on the intersection of different meanings ascribed to the notion of the reading child, and how fear is constructed and used as an othering devise in these conflicts.

Findings

Different imaginings of the reading child and the construction and imagination of fear and safety shapes the Drag story hour debates. The controversies can be understood as a challenge to the previous hegemony regarding the direction and goals of Swedish cultural and library policy and the pluralistic democratic society these policies are meant to promote.

Originality/value

The paper offers new insights into the consequences of the revival of radical right politics, populism and societal polarization, and the different responses from public libraries.
Designing a collaborative product development process from a knowledge management perspective
Authors: Chaouni Benabdellah Abla , Zekhnini Kamar , Bag Surajit , Gupta Shivam , Lopes de Sousa Jabbour Ana Beatriz
Published: May 2024

Purpose

This study aims to propose a collaborative knowledge-based ontological research model for designing a collaborative product development process (PDP) while considering different design for X techniques.

Design/methodology/approach

This study follows a thematic literature analysis to identify the key design concepts needed to assess environmental, service, safety, manufacture and assembly, supply chain and quality concerns in developing a collaborative PDP.

Findings

The proposed model provides a guide for methodology, engineering and ontology evaluation metrics (verification, assessment and validation). The findings benefit both practitioners and managers because they address the key knowledge taxonomy needed to assist them in storing information, promoting teamwork and making decisions in a collaborative PDP while incorporating various design for X approaches and product life cycles.

Originality/value

This study introduces a novel knowledge-based collaborative ontological research model, which is specifically designed to tackle the challenges of developing collaborative products in the contemporary landscape. The model presents a significant and valuable contribution to the field by introducing an ontological approach for acquiring, representing and leveraging knowledge in a computer-interpretable format to support the design of collaborative products. In addition, it provides a comprehensive guide for evaluating the effectiveness and efficacy of the ontology developed.
A two-model integrated technology adoption framework for using blockchain in supply chain management: attitude towards blockchain as a mediator
Authors: Jum’a Luay , Mansour Marwan , Zimon Dominik , Madzík Peter
Published: May 2024

Purpose

This study aims to investigate the intention to use blockchain technology (BT) in the context of supply chain (SC) operations through an integrated technology adoption framework using two well-known models, the unified theory of acceptance and use of technology (UTAUT) and the technology acceptance model (TAM). Moreover, the study looked at the direct effect of TAM and UTAUT elements on attitude toward BT, as well as the role of attitude toward BT as a mediator between TAM and UTAUT elements and intention to use BT.

Design/methodology/approach

The study used a quantitative research method, and a structured questionnaire was used to gather primary data. The final sample, drawn using a convenience sampling that consisted of 273 managers from the Jordanian manufacturing sector. Structural equation modeling statistical method was conducted using the Smart PLS program to test hypotheses in the proposed study framework.

Findings

The study has provided intriguing results. It found that two UTAUT elements, namely performance expectancy and social influence and one TAM element, namely perceived usefulness, have a significant impact on the attitude toward BT. Besides that, the study found that attitude toward BT significantly mediated the relationship between UTAUT-TAM elements and intention to use BT. The findings revealed that three elements namely performance expectancy, social influence and perceived usefulness have statistical significance on intention to use BT through the mediation of attitude. Finally, there is a direct significant positive relationship between the attitude toward BT and intention to use it.

Research limitations/implications

The study helps decision-makers, South Carolina practitioners and academics recognize the fundamental factors that increase manufacturing firms’ intentions to use blockchain in their SCs. This gives decision-makers a better understanding of why users accept or reject BT, as well as how to improve user acceptability through technological design. Future studies should seek for a bigger sample size and use random sampling techniques. Furthermore, the study should be replicated in other industries or developing countries to validate the findings.

Originality/value

There is a scarcity of studies identifying the factors that increase blockchain adoption intention in SCM and developing countries. This study differs in that it examines BT intention to use in the context of SC using an integrated technology adoption framework that uses two well-known models, UTAUT and TAM, whereas other studies typically use only one model/theory. Moreover, given the importance of attitude in behavior, this study also investigated the effect of TAM-UTAUT elements on attitude toward BT, as well as the role of attitude toward BT as a mediator between TAM and UTAUT elements and intention to use BT.
Method as democratizing; through researcher positionality and empirical inclusivity
Authors: Babri Maira
Published: May 2024

Purpose

The purpose of this paper is to present how my positionality as a researcher aligned with the works of Latour in terms of methodological inspirations and allowed me to develop a critical vantage point and simultaneously adopt a heterogeneously rather than hierarchically informed approach to ordering the world, which I argue serves as a basis for a more inclusive study of management systems.

Design/methodology/approach

I reflect on my own positionality as a researcher and share how my interpretation of Latour's ontology through some of his ideas and concepts, particularly symmetry, power, translation and agency, allowed me to incorporate and organize heterogeneous actors depicted in different empirical materials into space-time contexts and subsequently theorize organizing and management practices as agential, multiple and becoming.

Findings

A base in Latour’s ontology has equipped me with openness towards empirical settings, which I argue retains a democratic approach to theorization, i.e. theorization, which remains mindful of inadvertent assumptions about power, hierarchy or the taken for granted. This approach has also given me a form of personal resilience as a researcher.

Originality/value

The originality of this paper lies in presenting and developing the concept of method as democratizing. I argue that Latour’s approach to the empirical allows for at least two forms of active democratizing, one relating to the researcher as self and the other in how it incorporates the empirical actors into research, making possible the inclusivity of heterogeneity in analyses of organizations and organizing.
Isolating the effect of rater experience as a time‐variant predictor of performance ratings
Authors: Borba Diogo , Spence Jeffrey R.
Published: May 2024

A defining but sometimes overlooked characteristic of performance appraisals is that they are cyclical. The cyclical nature of performance appraisals makes it important to consider time‐variant definitions and operationalizations of constructs such as rater experience. In the current study, we work to clarify the association between rater experience and performance ratings by operationalizing rater experience as the number of appraisal cycles raters participated in. We did so while controlling for other similar but distinct operationalizations of experience such as span of control (number of ratees per rater) and familiarity with ratees. Furthermore, we employed a multilevel longitudinal design and analysis that allowed us to model rater experience as a time‐variant predictor of performance ratings and isolate its effects from both between‐rater and organizational context effects. The data were real appraisal data from a large South American company that contained 9233 ratees, across five appraisal cycles from 893 raters in 29 different business units, resulting in 24,608 observations. Our results revealed that rater experience had a small but statistically significant positive association with performance ratings. We also found that familiarity and span of control, were positively and negatively associated with performance ratings, respectively. Implications for practice and research are discussed.