bluuebunny/crossref_metadata_2025 huggingface dataset:
Putting computational models of immunity to the test - an invited challenge to predictB. pertussisvaccination outcomes
Authors: Shinde Pramod , Willemsen Lisa , Anderson Michael , Aoki Minori , Basu Saonli , Burel Julie G , Cheng Peng , Dastidar Souradipto Ghosh , Dunleavy Aidan , Einav Tal , Forschmiedt Jamie , Fourati Slim , Garcia Javier , Gibson William , Greenbaum Jason A , Guan Leying , Guan Weikang , Gygi Jeremy P , Ha Brendan , Hou Joe , Hsiao Jason , Huang Yunda , Jansen Rick , Kakoty Bhargob , Kang Zhiyu , Kobie James J , Kojima Mari , Konstorum Anna , Lee Jiyeun , Lewis Sloan A , Li Aixin , Lock Eric F , Mahita Jarjapu , Mendes Marcus , Meng Hailong , Neher Aidan , Nili Somayeh , Olsen Lars Rønn , Orfield Shelby , Overton James A. , Pai Nidhi , Parker Cokie , Qian Brian , Rasmussen Mikkel , Reyna Joaquin , Richardson Eve , Safo Sandra , Sorenson Josey , Srinivasan Aparna , Thrupp Nicky , Tippalagama Rashmi , Trevizani Raphael , Ventz Steffen , Wang Jiuzhou , Wu Cheng-Chang , Ay Ferhat , Grant Barry , Kleinstein Steven H , Peters Bjoern
Published: September 2024

Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predictingB. pertussisbooster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features
Authors: Chen Yichao , Zhang Yuhan , He Yongqun
Published: September 2024

Many vaccine design programs have been developed, including our own machine learning approaches Vaxign-ML and Vaxign-DL. Using deep learning techniques, Vaxign-DL predicts bacterial protective antigens by calculating 509 biological and biomedical features from protein sequences. In this study, we first used the protein folding ESM program to calculate a set of 1,280 features from individual protein sequences, and then utilized the new set of features separately or in combination with the traditional set of 509 features to predict protective antigens. Our result showed that the usage of ESM-derived features alone was able to accurately predict vaccine antigens with a performance similar to the orginal Vaxign-DL prediction method, and the usage of the combined ESM-derived and orginal Vaxign-DL features significantly improved the prediction performance according to a set of seven scores including specificity, sensitivity, and AUROC. To further evaluate the updated methods, we conducted a Leave-One-Pathogen-Out Validation (LOPOV) study, and found that the usage of ESM-derived features significantly improved the the prediction of vaccine antigens from 10 bacterial pathogens. This research is the first reported study demonstrating the added value of protein folding features for vaccine antigen prediction.
Genetic diversity and demographic history of the largest remaining migratory population of blue wildebeest (Connochaetes taurinus taurinus) in southern Africa
Authors: Szarmach Stephanie J. , Teeter Katherine C. , M’soka Jassiel , Dröge Egil , Ndakala Hellen , Chifunte Clive , Becker Matthew S. , Lindsay Alec R.
Published: September 2024

The blue wildebeest (Connochaetes taurinus taurinus) is a keystone species in the savannahs of southern Africa, where it maintains shortgrass plains and serves as an important prey source for large carnivores. Despite being the second largest migratory wildebeest population, the wildebeest of the Greater Liuwa Ecosystem (GLE) of western Zambia have remained largely unstudied, until recently. While studies have increased understanding of recent demography, migration, and population limiting factors, the level of genetic diversity, patterns of gene flow, and long-term demographic history of blue wildebeest in the GLE remains unknown. Most genetic studies of wildebeest have focused on small, heavily-managed populations, rather than large, migratory populations of high conservation significance. We used restriction-site associated DNA sequencing (RAD-seq) to assess genetic diversity, population structure, and demographic history of blue wildebeest in the GLE. Using SNPs from 1,730 loci genotyped across 75 individuals, we found moderate levels of genetic diversity in GLE blue wildebeest (He = 0.210), no evidence of inbreeding (FIS = 0.033), and an effective population size of about one tenth the estimated population size. No genetic population structure was evident within the GLE. Analyses of the site frequency spectrum found signatures of expansion during the Middle Pleistocene followed by population decline in the Late Pleistocene and early Holocene, a pattern previously observed in other African ungulates. These results will supplement field studies in developing effective conservation plans for wildebeest as they face continued and increasing threats of habitat loss, poaching, and other human impacts across their remaining range.
Neural Circuit Underlying Individual differences in Visual Escape Habituation
Authors: Liu Xuemei , Lai Juan , Han Chuanliang , Huang Kang , Yang Qin , Liu Yuanming , Zhu Xutao , Wei Pengfei , Tan Liming , Xu Fuqiang , Wang Liping
Published: September 2024

Emotions, like fear, are internal states enabling organisms to effectively confront environmental threats. When repeatedly exposed to predators, individuals show divergent adaptive responses. However, the neural circuit mechanisms underlying individual differences in to repeated threats remain largely unknown. Here, we identify two distinct types of visual escape,consistent escape (T1) and rapid habituation (T2),with unambiguous arousal states to repetitive threat stimuli. We systematically investigate distinct pathways originating from the superior colliculus (SC) and insula that project to the basolateral amygdala (BLA), with relay stations in the mediodorsal thalamus (MD) and ventral tegmental area (VTA), mediating T1 and T2 behavioral types. Additionally, we identify the MD as a critical hub integrating SC and insula inputs, projecting to the BLA and contributing to reduced arousal and attenuated defensive behaviors against looming stimuli. Our findings offer significant insights into the mechanisms of internal states, arousal modulation, and behavioral adaptability.
Stopping Speed as State, Not Trait: Exploring Within-Animal Varying Stopping Speeds in a Multi-Session Stop-Signal Task
Authors: ter Horst Jordi , Cohen Michael X , Englitz Bernhard
Published: September 2024

Being able to reactively stop ongoing movements is important for safe navigation through the environment. Reactive stopping is typically studied using the stop-signal task, where participants are occasionally instructed to stop initiated movements. The speed of stopping, also referred to as the stop-signal reaction time (SSRT), is not observable because successful stopping lacks a response, but can be estimated. Researchers most often acquire one session of data per participant to estimate the speed of stopping, but sometimes more sessions of data are acquired to maximize the signal-to-noise ratio, for example when the task is combined with neural recordings such as electrophysiology. However, it is unknown whether the estimated stopping speed is a fixed trait or a state that can vary under identical experimental conditions. In this study, we investigate whether a separately estimated SSRT for each acquired session is statistically meaningful compared to estimating an across-session SSRT, by collecting many sessions in which male rats performed a stop-signal task. Results revealed that within-animal stopping speeds meaningfully changed from session to session and were not following a trend over time (e.g., due to task learning). Single-session SSRT estimates with lower reliabilities were associated with higher go trial response time variabilities, lower skewness levels of the go trial response time distribution, and lower stop accuracies. We also explored which factors explained changing SSRTs, and showed that motivation, shared motor dynamics, and attention could play a role. In conclusion, we encourage researchers to treat SSRTs as state-like variables when collecting multi-session stop-signal task data, as our results have convincingly shown that stopping speeds are far from trait-like under identical experimental conditions. This session-by-session approach will help future research in which neural signatures of reactive stopping need to be extracted in a time-precise manner, because time-locking stop-related neural activity to session-specific SSRTs is expected to capture the signature more precisely as opposed to an across-session SSRT.
A 15-Gene prognostic signature with TFAP2B functioning in Platinum Resistance of Ovarian Carcinoma
Authors: Hu Yang , Wang Ping , Xiang Jian , Han Lu , Zhang Biyun , Liu Xiaohua , Nie Hua , Chen Guobing , Qin Weibing
Published: September 2024

Resistance to platinum is the main challenge in the chemotherapy of ovarian cancer (OV). Therefore, developing a response signature to platinum is essential for the precision therapy of OV. Existing quantitative signatures of platinum are susceptible to batch effects and sequencing platform variations. To address this, we developed a transcriptome-based platinum signature, named PRSM, consisting of 15 genes, based on within-sample prognostic and relative expression ordering of genes, to predict individual responses to platinum in OV. The PRSM model demonstrated superior classification accuracy compared to previous quantitative signatures. Resistant samples classified by PRSM exhibited poorer overall survival, lower SNV neoantigen load, tumor mutational burden, and distinct methylation patterns compared to sensitive samples. Pathway analysis revealed the activation of MYC targets V2 and oxidative phosphorylation in resistant tumors. Single-cell analysis highlighted the roles of NK and epithelial cells in resistance. Among the 15 core genes, five (TFAP2B, KRT81, PAGE1, CRNN, UGT2B17) were linked to poor prognosis, with TFAP2B having the highest contribution to PRSM. Overexpression of TFAP2B in A2780 cells enhanced cisplatin sensitivity, while in A2780cis cells, it inhibited growth. In brief, our findings provide a multi-dimensional view of platinum resistance in ovarian cancer, introducing a robust predictive model and identifying potential therapeutic targets.
Deep mutational scanning of the human insulin receptor ectodomain to inform precision therapy for insulin resistance
Authors: Aslanzadeh Vahid , Brierley Gemma V. , Kumar Rupa , Çubuk Hasan , Vigouroux Corinne , Matreyek Kenneth A. , Kudla Grzegorz , Semple Robert K.
Published: September 2024

The insulin receptor (INSR) entrains tissue growth and metabolism to nutritional conditions. Complete loss of function in humans leads to extreme insulin resistance and infantile mortality, while loss of 80-90% function permits longevity of decades. Even low-level activation of severely compromised receptors, for example by anti-receptor monoclonal antibodies, thus offers the potential for decisive clinical benefit. A barrier to genetic diagnosis and translational research is the increasing identification ofINSRvariants of uncertain significance. We employed saturation mutagenesis coupled to multidimensional flow-based assays to stratify approximately 14,000 INSR extracellular domain missense variants by cell surface expression, insulin binding, and insulin- or monoclonal antibody-stimulated signaling. The resulting function scores correlate strongly with clinical syndromes, offer insights into dynamics of insulin binding, and reveal novel potential gain-of-function variants. This INSR sequence-function map has high biochemical, diagnostic and translational utility, aiding rapid identification of variants amenable to activation by non-canonical INSR agonists.
Adapting COVID-19 research infrastructure to capture influenza and RSV alongside SARS-CoV-2 in UK healthcare workers winter 2022/23: Evaluation of the SIREN Winter Pressures pilot study
Authors: Russell Sophie , Munro Katie , Foulkes Sarah , Broad Jonathan , Sparkes Dominic , Atti Ana , Islam Jasmin , Hopkins Susan , Hall Victoria ,   SIREN study group
Published: September 2024

Background

In 2022, with high early winter respiratory virus circulation, SIREN, a prospective healthcare worker cohort study monitoring SARS-CoV-2, ran a pilot study introducing multiplex PCR testing for SARS-CoV-2, influenza A/B, and RSV to investigate winter pressures. Three pathways were trialled: (A) on-site swabbing with local laboratory testing, (B) on-site swabbing with UKHSA-commissioned laboratory testing, and (C) postal swabbing with UKHSA-commissioned laboratory testing. Here, we compare pathways in relation to recruitment, testing coverage, participant acceptability, and UKHSA SIREN research team feedback.

Methods

We conducted a mixed methods evaluation using metrics of quality assurance and study fidelity (participant recruitment and retention; multiplex PCR testing timing and coverage), an adapted NIHR ‘participant in research’ feedback questionnaire, and thematic analysis of a UKHSA SIREN research team workshop.

Results

With 7,774 participants recruited, target recruitment (N=7,500) was achieved. Thirty-nine sites took part in the sub-study (4,289 participants). Thirty-three used pathway A, and six used pathway B. 3,485 participants enrolled to pathway C (27.8% of invitees). The median number of tests per participant was similar across pathways (6; 4; 5). However, sites using local laboratories showed a wide variation in the date they switched to multiplex testing (28thNovember 2022 to 16thMarch 2023). Consequently, influenza and RSV testing coverage was higher for pathways using UKHSA-commissioned laboratories (100.0% vs 45.6% at local laboratories). 1,204/7,774 (15.5%) participants completed the feedback survey. All pathways were acceptable to participants; 98.9% of postal and 97.5% of site-based participants ‘would consider taking part again’.

Conclusion

Transitioning SARS-CoV-2 PCR testing to include influenza and RSV was challenging to achieve rapidly across multiple sites. The postal testing pathway proved more agile, and UKHSA-commissioned laboratory testing provided more comprehensive data collection than local laboratory testing. This sub-study indicates that postal protocols are effective, adaptable at pace, and acceptable to participants.
Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants
Authors: Hernández Víctor Sánchez de Medina , García Marintia Mayola Nava , Clavel Marion , Papareddy Ranjith K. , Andreev Veselin I. , Mathur Varsha , Mohseni Azadeh , García-León Marta , Gao Peng , de la Concepción Juan Carlos , Picchianti Lorenzo , Grujic Nenad , Kobylinska Roksolana , Abdrakhmanov Alibek , Duvergé Héloïse , Anand Gaurav , Leibrock Nils , Bianchi Anita , Raffeiner Margot , Crawford Timothy Scott , Argirò Luca , Matuszkiewicz Mateusz , Wun Cheuk-Ling , Kanne Jakob Valdbjørn , Meinhart Anton , Roitinger Elisabeth , Bäurle Isabel , Kang Byung Ho , Petersen Morten , Üstün Suayib , Kulathu Yogesh , Clausen Tim , Ramundo Silvia , Dagdas Yasin
Published: September 2024

Selective autophagy is a fundamental protein quality control pathway that safeguards proteostasis by degrading damaged or surplus cellular components, particularly under stress. This process is orchestrated by selective autophagy receptors (SARs) that direct specific cargo for degradation. While significant strides have been made in understanding the molecular framework of selective autophagy, the diversity of SAR repertoires across species remain largely unexplored. Through a comparative interactome analysis across five model organisms, we identified a suite of conserved and lineage-specific SAR candidates. Among these, we validated CESAR as a conserved SAR critical for proteostasis under heat stress. CESAR specifically facilitates the degradation of hydrophobic, ubiquitinated protein aggregates and is indispensable for heat stress tolerance. Our study offers a rich resource for SAR discovery and positions CESAR as a pivotal regulator of proteostasis, with broad implications for improving stress resilience in plants.
Bioactivity Analysis of Secondary Metabolites from Actinomycetes’ Isolated from Coastal Sediments
Authors: Shubhro Kumar , Rimi Arifa Afrose , Islam Md. Emdadul , Islam Kazi Didarul , Billah Md. Morsaline , Mia Mijan , Rahman SM Mahbubur
Published: September 2024

The rising threat of antibiotic resistance underscores the need for new antibiotics. Marine actinomycetes have emerged as promising sources of bioactive compounds. In this study, 22 isolates from marine sediments were morphologically identified, with nine confirmed as actinomycetes through 16S rRNA gene sequencing. Five strains-Streptomyces olivoverticillatus(T-2),Streptomyces cyaneus(T-4),Nocardiopsis synnemataformans(T-7),Streptomyces albogriseolus(T-8), andStreptomyces atrovirens(T-9)- exhibited significant antibacterial activity. Cultured in Starch Casein Broth, their metabolites were tested for antibacterial, antioxidant, anticoagulation, and anti-inflammatory activities. T-4 and T-8 demonstrated notable antimicrobial action, T-8 showing potent DPPH radical scavenging (372.09 ± 11.05 µg/mL). T-9 inhibited trypsin (IC50435.12 ± 15.88 µg/mL) and had a prothrombin time of 12.08 ± 1.46 minutes. T-8 enhanced RBC membrane stabilization (IC50140.08 ± 2.30 µg/mL). These findings suggest that marine sediment-derived actinomycetes hold significant therapeutic potential and warrant further study.
CSF pressure in fetal micein utero: External factors pressurize the intraventricular space
Authors: Tsujikawa Koichiro , Muramatsu Reina , Miyata Takaki
Published: September 2024

Previous experiments inducing leakage of embryonic cerebrospinal fluid (CSF) suggest the necessity of intraventricular CSF pressure (PCSF) for brain morphogenesis. Nevertheless, how embryonic PCSFoccurs is unclear, especiallyin utero. Using a Landis water manometer, we measured PCSFin fetal mice isolated from the amniotic cavity (PCSF-ISO). At embryonic day (E) 13, PCSF-ISOwas 82.7 Pa. Intraventricular injections of ≥2 μl of saline elevated PCSF-ISOby ∼30%. Intraventricularly injecting inhibitors of CSF secretion decreased PCSF-ISOby ∼30%. Shh-mediated cerebral-wall expansion and the resulting ventricular narrowing did not significantly increase PCSF-ISO. Removal of the brain-surrounding contractile tissues decreased PCSF-ISOby 80-90%. The intraamniotic pressure measuredin utero(PAF-IU) was 1030.7 Pa. Our direct measurement revealed that the PCSFin utero(PCSF-IU) was 1076.4 Pa, confirming the susceptibility of PCSFto external factors. Subsequent PCSFmeasurements under hydrostatic pressure loading suggested that PCSF-IU= PCSF-ISO+ PAF-IU, a relationship further used to estimate PCSF-IUat other ages when direct measurement was not possible. The estimated PCSF-IUdecreased almost constantly from E10 to E16 (2000 ➔ 500 Pa).
Bidirectional Upregulation of Klotho by Triiodothyronine and Baicalein: Mitigating Chronic Kidney Disease and Associated Complications in Aged BALB/c Mice
Authors: Mohanty Saswat Kumar , Sahu Vikas Kumar , Singh Bhanu Pratap , Suchiang Kitlangki
Published: September 2024

Chronic kidney disease (CKD) is a global health challenge marked by progressive renal decline and increased mortality. The interplay between CKD and hypothyroidism, particularly nonthyroidal low-triiodothyronine (T3) syndrome, exacerbates disease progression, driven by HPT axis dysfunction and reduced Klotho levels due to Wnt–β-catenin pathway activation. This study explored Klotho as a link between CKD and hypothyroidism using an adenine-induced CKD aged mouse model. Exogenous T3 and baicalein (BAI), targeting the Wnt pathway, were used to upregulate Klotho expression. Combined T3 and BAI treatment significantly increased Klotho levels, surpassing individual effects, and suppressed key signaling molecules (TGF, NFκB, GSK3), mitigating renal fibrosis and CKD complications, including cardiovascular disorders and dyslipidemia. This bidirectional approach, enhancing Klotho via T3 and sustained Wnt pathway inhibition, offers a novel and effective strategy for CKD management, particularly in elderly patients with hypothyroidism.
The antimicrobial potential of traditional remedies of Indigenous Peoples from Canada against MRSA planktonic and biofilm bacteria in wound-infection mimetic conditions
Authors: Rieger Colin D. , Soliman Ahmed M. , Kaplia Kateryna , Ghosh Nilrup , Lopez Alexa Cervantes , Venkatesan Surya Arcot , Flores Abraham Gildaro Guevara , Belin Matheus Antônio Filiol , Allen Florence , Reynolds Margaret , McKenna Betty , Lavallee Harold , Weenie Archie , Favel Thomas , Gendron Fidji , Ziffle Vincent E. , El-Halfawy Omar M.
Published: September 2024

Methicillin-resistantStaphylococcus aureus(MRSA) is the leading cause of wound infections, often progressing into serious invasive bloodstream infections. MRSA disproportionately affects Indigenous peoples in Canada with higher rates of skin and wound infections, an example of persistent gaps in health outcomes between Indigenous and non-Indigenous peoples precipitated by the legacy of colonialism. Conversely, Indigenous peoples have long used natural remedies for infections and other diseases; however, their knowledge was rarely considered for modern medicine. The stagnant antibiotic discovery pipeline and alarming rise of resistance to current antibiotics prompted us to turn to Indigenous medicine as an untapped source of antimicrobials. As such, we collected and prepared 85 extracts of medicinal plants of value to Indigenous Peoples spanning the Canadian Prairies. We explored the antimicrobial potential of these extracts against MRSA under wound infection-mimetic conditions compared to culture media typically used to study bacterial antibiotic responses and biofilms but not adequately representative of infection sites. We identified extracts with MRSA growth inhibitory [e.g., bergamot, dock, gaillardia, and dandelion extracts] and biofilm prevention and eradication [e.g., gumweed extracts] activities. Extracts, including those of chokecherry, hoary puccoon, and Northern bedstraw, were only active under wound infection-mimetic conditions, highlighting the relevance of antibiotic discovery under host-relevant conditions. Testing growth inhibitory extracts against anS. aureuscross-resistance platform suggested that they act through mechanisms likely distinct from known antibiotic classes. Together, through an interdisciplinary partnership leveraging Western approaches and traditional Indigenous knowledge, we identified plant extracts with promising antimicrobial potential for drug-resistant MRSA wound infections.
Dimerization-dependent gel-like condensation with dsDNA underpins the activation of human cGAS
Authors: Lueck Jacob , Strom Alexander , Wu Shuai , Wendorff Hannah , Sohn Jungsan
Published: September 2024

Cyclic G/AMP Synthase (cGAS) initiates inflammatory responses against pathogenic double-stranded (ds)DNA. Although it is well established that cGAS forms phase-separated condensates with dsDNA, their function remains poorly defined. We report here that the dimerization of cGAS on dsDNA creates a mesh-like network, leading to gel-like condensate formation. Although cGAS binds to and forms condensates with various nucleic acids, only dsDNA permits the dimerization necessary for activation and gelation. cGAS co-condenses dsDNA and other nucleic acids but retains a distinct dsDNA-mediated gel-like substate, which single-stranded RNA can dissolve and deactivate the enzyme. Moreover, gel-like, but not liquid-like, condensation not only protects bound dsDNA from exonucleases, but also limits the mobility of NTPs and the dinucleotide intermediate for efficient cGAMP synthesis. Together, our results show that enzymes can finetune surrounding microenvironments to regulate their signaling activities.
Stress response of membrane-based cell organelles in budding yeast
Authors: Peng Sheng , Li-zhe Bai , Hong Cao , Dan Li
Published: September 2024

The organelles of yeast demonstrate diverse morphological traits in response to different stress stimuli. However, there is a lack of systematic reports on the structural changes induced by stress stimuli in all membrane-based organelles. Here, we utilized a set of fluorescent protein-based organelle markers to highlight the distinct characteristics of yeast under various stress triggers, including high temperature, hydrogen peroxide, acetic acid, and ethyl alcohol. We found that all of these organelles undergo alterations in structure or function in response to the four stress triggers we tested. Specifically, filamentous mitochondria rupture into smaller segments when exposed to the above four stress conditions. The structure of the endoplasmic reticulum (ER) remains relatively unchanged, but its function is affected. Additionally, high temperature and hydrogen peroxide can induce the Ire1p-mediated ER unfolded protein response (UPR). The translocation of most nuclear-localized proteins to the cytosol is dependent on the specific stress conditions employed. Under the above stress conditions, the vacuole undergoes fusion, resulting in the formation of a larger vacuole from multiple smaller ones. Meanwhile, acetic acid-induced stress leads to the translocation of vacuole-localized proteins Prc1p and Pep4p to unknown puncta, while Ybh3p relocates from the inner vacuole to the vacuole membrane. Proteins localized in the early Golgi, late Golgi, and late endosomes exhibit distinct traits, such as fading away or mis-localization. The structure and function of peroxisomes, lipid droplets, and autophagosomes also undergo modifications. Furthermore, upon exposure to high temperature and ethanol, apoptosis-related proteins Yca1, Aif1, and Mmi1 aggregate instead of remaining dispersed.
Identification of Transposon Insertion Sites in MaizeMu-Tagged Mutants Using Mu-Seq
Authors: Marcon Caroline , Brox Alexa , Win Yan Naing , Stöcker Tyll , Du Xuelian , Schoof Heiko , Hochholdinger Frank
Published: September 2024

Mutator(Mu) transposons facilitate untargeted insertional mutagenesis in maize by moving within the genome and disrupting genes. Such an approach has been used to generate collections such as theBonnMuresource, aMu-tagged maize population for functional genomics studies. Mutant-Seq (Mu-Seq) is a sequencing-based method for the high-throughput identification and mapping ofMuinsertion sites. The approach involves the construction of multiplexed sequencing libraries (known as Mu-Seq libraries) fromMu-tagged populations, followed by high-throughput sequencing and data processing using the Mu-Seq Workflow Utility (MuWU) tool, to determine the location ofMuinsertions. Here, we provide a detailed protocol for Mu-Seq, from the generation of the maizeMu-tagged mutant population to data analysis. Researchers can use this approach to develop mutant collections customized to specific genetic backgrounds of interest, which can aid in characterizing genotype-specific mutations and identifying candidate genes linked to visible mutant phenotypes.
Nature of electrically detected magnetic resonance in highly nitrogen-doped
6H
-SiC single crystals
Authors: Holiatkina M. , Solodovnyk A. , Laguta O. , Neugebauer P. , Kalabukhova E. , Savchenko D.
Published: September 2024

This work focuses on unraveling electron paramagnetic resonance (EPR) and electrically detected magnetic resonance (EDMR) properties of n-type 6H silicon carbide (SiC) single crystals with high concentrations of uncompensated nitrogen (N) donors, which is essential for fundamental understanding of spin-related phenomena, developing spin-based devices, optimizing materials and devices, and advancing research in quantum information and spintronics. Utilizing low-temperature multifrequency EPR spectroscopy (9.4–395.12 GHz), we identified two intense signals labeled as S line and S1 line in the 6H-SiC crystals with ND–NA≈8×1018 and 4×1019cm−3. In addition, in 6H-SiC crystals with ND–NA≈8×1018cm−3, a low-intensity triplet from N donors substituting the quasicubic “k2” nonequivalent position (Nk2) was observed. The S line [g⊥=2.0029(2),g∥=2.0038(2)] was assigned to the exchange interaction of conduction electrons and Nk2, while the S1 line [g⊥=2.0030(2),g∥=2.0040(2)] is caused by the exchange spin coupling of localized N donors at the “k1” and “k2” positions. The S1 line was observed in high-frequency EDMR spectra of 6H-SiC with ND–NA≈8×1018cm−3, and its emergence was explained by an enhancement of the hopping conductivity due to the EPR-induced temperature increase mechanism. No EDMR spectra were found to occur in the 6H-SiC crystals with ND–NA≈4×1019cm−3, which is close to the critical donor concentration value for a semiconductor-metal transition. Thus it can be concluded that this N donor concentration is too high for the appearance of spin-dependent scattering and too low for the emergence of EPR-induced hopping mechanisms in 6H-SiC.

Published by the American Physical Society
2024
Tcc+
and
χc1(3872)
with the complex scaling method and
DD(D¯)π
three-body effect
Authors: Lin Zi-Yang , Cheng Jian-Bo , Zhu Shi-Lin
Published: September 2024

We use the leading-order contact interactions and one-pion-exchange potentials to investigate the newly observed double-charm state Tcc+. We employ the complex scaling method to search for the poles on the first Riemann sheet with respect to the DD* threshold and the second Riemann sheet with respect to the DDπ threshold. The DDπ three-body effect is important in this system since the intermediate states can go on shell. We involve the three-body effect through an energy-dependent one-pion-exchange potential, which results in a unitary cut at the DDπ three-body threshold. We find a pole corresponding to the Tcc+ on the physical Riemann sheet. Its width is around 80 keV and nearly independent of the choice of the cutoff. Assuming the DD¯π and DD¯* channels as the main decay channels, we apply the similar calculations to the χc1(3872), and find its width is even smaller. The isospin breaking effect is so significant for the χc1(3872) that it is mainly a molecular state of D0D¯*0. Furthermore, we introduce a revised Schrödinger equation for unstable particles to include the contribution of the D* width, which is also revised by the three-body effect.

Published by the American Physical Society
2024
QCD-gravity double-copy in the Regge regime: Shock wave propagators
Authors: Raj Himanshu , Venugopalan Raju
Published: September 2024

In a previous paper [H. Raj and R. Venugopalan, ], we demonstrated a double-copy relation between inclusive gluon radiation in shock wave collisions of ultrarelativistic nuclei and inclusive graviton radiation in trans-Planckian gravitational shock wave collisions. We compute here the corresponding gravitational shock wave propagators in general relativity and demonstrate that they too obey a double-copy relation to gluon shock wave propagators computed previously. These results provide key input in a renormalization group approach toward computing the high frequency radiation spectrum in close black hole encounters.

Published by the American Physical Society
2024
Production of dileptonic bound states in the Higgs boson decay
Authors: Martynenko F. A. , Martynenko A. P. , Eskin A. V.
Published: September 2024

The production of single and paired lepton bound states in the decay of the Higgs boson has been studied. We explore different decay mechanisms that contribute significantly to the decay width. The decay widths are calculated taking into account relativistic corrections in the decay amplitude and in the wave function of the bound state of leptons.

Published by the American Physical Society
2024
Entanglement membrane in exactly solvable lattice models
Authors: Rampp Michael A. , Rather Suhail A. , Claeys Pieter W.
Published: September 2024

Entanglement membrane theory is an effective coarse-grained description of entanglement dynamics and operator growth in chaotic quantum many-body systems. The fundamental quantity characterizing the membrane is the entanglement line tension. However, determining the entanglement line tension for microscopic models is in general exponentially difficult. We compute the entanglement line tension in a recently introduced class of exactly solvable yet chaotic unitary circuits, so-called generalized dual-unitary circuits, obtaining a nontrivial form that gives rise to a hierarchy of velocity scales with vE<vB. For the lowest level of the hierarchy, L¯2 circuits, the entanglement line tension can be computed entirely, while for the higher levels the solvability is reduced to certain regions in spacetime. This partial solvability enables us to place bounds on the entanglement velocity. We find that L¯2 circuits saturate certain bounds on entanglement growth that are also saturated in holographic models. Furthermore, we relate the entanglement line tension to temporal entanglement and correlation functions. We also develop methods of constructing generalized dual-unitary gates, including constructions based on complex Hadamard matrices that exhibit additional solvability properties and constructions that display behavior unique to local dimension greater than or equal to three. Our results shed light on entanglement membrane theory in microscopic Floquet lattice models and enable us to perform nontrivial checks on the validity of its predictions by comparison to exact and numerical calculations. Moreover, they demonstrate that generalized dual-unitary circuits display a more generic form of information dynamics than dual-unitary circuits.

Published by the American Physical Society
2024
Exploring the impact of team engagement on patient satisfaction: insights from social support and transactive memory system
Authors: Wang Siqi , Zhang Xiaofei
Published: September 2024

Purpose

Research on the impact of the engagement of online medical teams (OMTs) on patient evaluation, for example, satisfaction, remains insufficient. This study attempts to recognize the underlying mechanism of how OMTs’ engagement influences patient satisfaction by adopting social support as the mediator. This study also scrutinizes the moderating effects of the transactive memory system (TMS) on the link between OMTs’ engagement and social support.

Design/methodology/approach

We utilized a linear model that had fixed effects controlled at the team level for analysis. A bootstrapping approach using 5,000 samples was employed to test the mediation effect.

Findings

Our results reveal that OMTs’ engagement improves informational and emotional support, thereby promoting patient satisfaction. Specialization and credibility strengthen the impact of OMTs’ engagement on informational and emotional support. Simultaneously, coordination has an insignificant influence on the link between OMTs’ engagement and social support.

Originality/value

This study contributes to the literature on OMTs, social support, and TMS, providing insights into patients’ perceptions of OMTs’ engagement during online team consultation. This study also generates several implications for the practice of online health communities and OMTs.
What kind of education research was funded by the government in China? A decade-long investigation (2010–2020)
Authors: Pan Pengfei , Yin Yue Melody
Published: September 2024

Purpose

The key purpose of this study is to systematically examine the landscape of education research funded by the National Plan of Educational Research Funding (NPERF) in China. The study aims to: (1) identify the thematic focus areas that reflect the national education agenda, (2) analyze the general funding patterns of education research projects and (3) gain insights into the distinctive nature of the research agenda in China. The study employs a rigorous data-driven approach to offer valuable insights into the dynamic discourses within the field of education research in China, which has received relatively little attention despite its potential significance.

Design/methodology/approach

In this study, we utilized word co-occurrence analysis and corpus-based frequency analysis to analyze the research projects funded by the National Plan of Educational Research Funding (NPERF) from 2011 to 2020.

Findings

The key characteristics of these projects highlight the focus on higher education research, addressing the interests of specific cohorts of students, teachers and disadvantaged populations. Furthermore, these projects demonstrate a remarkable responsiveness to the policy needs of the country and a robust inclination toward an international comparative framework.

Research limitations/implications

The findings offer valuable insights into the landscape and features of funded education research in China, revealing a strong emphasis on addressing practical needs and enhancing the capacity of the education system in the country.

Originality/value

This paper presents a systematic examination of the topics covered in funded research under the National Plan of Educational Research Funding (NPERF) scheme from 2011 to 2020. It contributes to the advancement of understanding regarding knowledge traditions and practices in the Chinese context. Methodologically, this paper is the first in the literature to be prototyped with a word co-occurrence analysis approach to systematically investigate the funded education research in China. Additionally, it includes the development of a comprehensive corpus list to uncover the key characteristics of the funded projects. The analysis provides unique insights into the priorities and directions of education research supported by the Chinese government, which are of potential interest to international readers.
Hall of mirrors to enhance a network professional learning community for ECEC centre leaders
Authors: Bøe Marit , Kristiansen Elsa
Published: September 2024

Purpose

In view of the expanding global interest in leadership learning and development programmes for centre leaders, this study aims to investigate how an early childhood education leadership programme can enhance Norwegian centre leaders’ learning and development as a network professional learning community (PLC) by way of Schön’s reflective model, the hall of mirrors.

Design/methodology/approach

In this qualitative case study, we interviewed four centre leaders, the owner of the centres and a facilitator and/or coach from the local work and competence centre for inclusive work who was leading the leadership programme.

Findings

The findings demonstrate three aspects of the hall of mirrors that enhanced the centre leaders as a network PLC: engaging in collective inquiry towards shared visions and values, enhancing professionalism through distributed leadership and cultivating a trusting learning climate.

Research limitations/implications

Data were collected in a single smaller municipality in Norway and therefore may not be generalisable to other areas.

Practical and social implications

The findings can be used to further discuss how early childhood education and care (ECEC) leadership development programmes can be employed to establish and sustain professional leadership teams and professional learning communities.

Originality/value

As there are parallels between the leadership programme and the workplace and the programme promoted a network PLC, this study contributes to existing knowledge by offering a transformative reflective model for leadership learning and change through the reconceptualisation of the hall of mirrors.
Fuzzy synthetic evaluation of the critical drivers of UAVs’ deployment for construction in Nigeria
Authors: Aliu John , Aghimien Douglas Omoregie , Olumide David Ogungbayi , Oke Ayodeji Emmanuel
Published: September 2024

Purpose

The slow adoption of unmanned aerial vehicles (UAVs) in the construction industry, particularly in developing countries like Nigeria, underscores the need for a deeper understanding of the critical factors influencing their adoption. This study aims to identify these factors using the Technology-Organization-Environment (TOE) framework and address uncertainties in their prioritization through Fuzzy Synthetic Evaluation (FSE). The utility of this approach lies in its ability to provide construction organizations with actionable insights to enhance operational efficiency and competitiveness through effective UAV adoption.

Design/methodology/approach

A post-positivist philosophical stance was adopted, wherein quantitative data were gathered from construction professionals in Nigeria via a questionnaire survey. The collected data were analyzed using the Cronbach alpha test as a measure of internal consistency and the FSE test to synthesize critical drivers for the adoption of UAVs.

Findings

The study found that drivers related to technology and organization are the most critical drivers. This implies that variables related to technology and organization warrant a higher level of focus if UAVs are to continue gaining popularity within the construction industry. Additionally, this study identified that logistic management, construction monitoring and site surveying represent the most critical areas of UAV application within the construction industry.

Practical implications

The emphasis on technology and organizational drivers as critical factors suggests that construction companies should prioritize investments in technology infrastructure and cultivate an organizational culture that embraces innovation. This may involve providing training to construction professionals to enhance their technological skills and fostering a leadership culture that champions technology adoption.

Originality/value

This study introduces novelty by applying the TOE framework, which has received limited attention in UAV adoption studies within construction. Additionally, the use of FSE addresses uncertainties in prioritizing critical drivers, particularly relevant in developing countries facing unique technological challenges. By assigning priority to these factors, this research lays the groundwork for a more informed and strategic approach to UAV adoption.
Online grocery services evolution and trends: a bibliometric approach
Authors: Khalek Sk Abu , Samanta Tamal , Behera Chandan Kumar
Published: September 2024

Purpose

Online grocery service (OGS) has significantly grown in recent years, particularly during the Covid-19 pandemic. This surge has attracted significant scholarly attention and resulted in many scientific articles in the last five years. Adopting a bibliometric review approach, this study attempts to comprehensively and systematically analyse the academic literature on OGS.

Design/methodology/approach

A Scopus search using pertinent keywords followed by PRISMA screening identified 384 relevant articles. Articles were analysed using VOSviewer and Biblioshiny, which employed citation and thematic analysis.

Findings

The study identifies the significantly impactful authors, articles, and journals. While the analysis reveals the evolution across four time-frames, it also highlights the clusters representing the literature strands. Six major themes are identified in the literature, and potential future research enquiries are suggested.

Originality/value

As the first study to include over 350 articles, it comprehensively represents the current state of the OGS literature, utilising performance and thematic analysis techniques. The article contributes significantly to the academic discourse surrounding OGS by synthesising and presenting diverse themes. Further, the future research questions provide a foundation for advancing the literature and guiding future scholarly work in the OGS domain.
Impacts of blockchain cooperation project announcements on corporate stock market values: a loose coupling theory perspective
Authors: Liu Weihua , Long Shangsong , Wang Jingkun
Published: September 2024

Purpose

As a disruptive technology, blockchain technology brings new opportunities and challenges to operations management. We aim to examine the influences of blockchain cooperation project announcements (BCPAs) on firms’ stock market reactions in an emerging market. From 2016 to 2021, a total of 113 BCPAs of listed firms from the Chinese A-share market are selected as samples.

Design/methodology/approach

This study is based on the loose coupling theory and uses the event study method and probit regression analysis.

Findings

We find BCPAs positively affect the firm’s stock price on the day they are released. Compared with vertical BCPAs in a supply chain, horizontal BCPAs exert a more positive market reaction. Moreover, a BCPA with a partner within a shorter geographical distance exerts a more positive influence on market reaction. Contrary to the intuition of the decentralized blockchain feature that one-to-many cooperation leads to better benefits, one-to-one BCPAs exert a more positive effect on market reaction than one-to-many BCPAs. We further find that (1) industry type has a certain impact on cooperation mode selection, and (2) manufacturing firms are more inclined to choose one-to-one cooperation than those in service industry.

Originality/value

We focus on the impact of blockchain cooperative announcements and additionally use the probit regression models to analyze the influencing factors of cooperation mode selection and find the critical role of the industry type, which complements the existing empirical research on blockchain announcements and is conducive to provide decision-making reference for managers.
Decades of research on international performance of SMEs; where are we and what are the priorities for the next decade?
Authors: Safargholi Alireza , Yousefzadeh Faezeh , Rezvani Mehran , Farokhmanesh Taraneh , Mobaraki Mohammad Hassan , Yadollahi Farsi Jahangir
Published: September 2024

Purpose

Small and medium-sized enterprises (SMEs) are highly concerned about every aspect of their international performance (IP) due to their limited resources. However, the literature has not given equal attention to every necessary aspect and has left some fields unexplored. Moreover, different approaches to assessing SME IP have made the literature even more fragmented. This research aims to identify the gaps in the research context and assessment methods of this concept.

Design/methodology/approach

A systematic literature review and a thematic analysis method are employed to review 272 journal papers published in high-quality journals.

Findings

By extracting six contexts in which the concept of international performance of SMEs has been analyzed, this study integrates the research themes with geographical domains and highlights which contexts require more attention. Moreover, this study provides a comprehensive review of the current state of this concept’s operationalization methods, illustrating the level of fragmentation and differences in the literature. Following the presentation of an enriched future research agenda, this study guides scholars on the current gaps and needs for research in specific contexts and domains while providing suggestions for a more cohesive assessment of the concept.

Originality/value

This study is the first to systematically review the research concerning the foreign performance of firms with less than 500 employees, extract their research context, illustrate uninvestigated fields and provide helpful suggestions about the concept’s operationalization method based on a comprehensive review of the extant assessment methods.