bluuebunny/crossref_metadata_2025 huggingface dataset:
Directed evolution-based discovery of ligands for in vivo restimulation of CAR-T cells
Authors: Grzywa Tomasz M. , Neeser Alexandra , Ramasubramanian Ranjani , Romanov Anna , Tannir Ryan , Mehta Naveen K. , Cossette Benjamin , Morgan Duncan M. , Goncalves Beatriz , Sukaj Ina , Bergaggio Elisa , Kadauke Stephan , Myers Regina M. , Paruzzo Luca , Ghilardi Guido , Cozzone Austin , Schuster Stephen J. , Frey Noelle , Zhang Libin , Yousefpour Parisa , Abraham Wuhbet , Suh Heikyung , Ruella Marco , Grupp Stephan A. , Chiarle Roberto , Wittrup K. Dane , Ma Leyuan , Irvine Darrell J.
Published: April 2024

Chimeric antigen receptor (CAR) T cell therapy targeting CD19 elicits remarkable clinical efficacy in B-cell malignancies, but many patients relapse due to failed expansion and/or progressive loss of CAR-T cells. We recently reported a strategy to potently restimulate CAR-T cellsin vivo, enhancing their functionality by administration of a vaccine-like stimulus comprised of surrogate peptide ligands for a CAR linked to a lymph node-targeting amphiphilic PEG-lipid (termed CAR-T-vax). Here, we demonstrate a general strategy to generate and optimize peptide mimotopes enabling CAR-T-vax generation for any CAR. Using the clinical CD19 CAR (FMC63) as a test case, we employed yeast surface display to identify peptide binders to soluble IgG versions of FMC63, which were subsequently affinity matured by directed evolution. CAR-T vaccines using these optimized mimotopes triggered marked expansion and memory development of CD19 CAR-T cells in both syngeneic and humanized mouse models of B-ALL/Lymphoma, and enhanced control of disease progression. This approach thus enables vaccine boosting to be applied to any clinically relevant CAR-T cell product.
Functional Assessment and Impact of Seizures on Cognitive Outcome in a Cohort of Individuals with KBG Syndrome
Authors: Sarino Kathleen P , Guo Lily , Yi Edward , Park Jiyeon , Kierzkowska Ola , Carter Drake , Marchi Elaine , Lyon Gholson J
Published: April 2024

OBJECTIVE

This study aimed to further examine the impact of epileptic seizures on neurocognitive outcomes in KBG syndrome, a rare genetic neurodevelopmental disorder characterized by pathogenic variants in the gene ANKRD11.

METHODS

A single clinician interviewed a cohort of individuals with genetically confirmed cases of KBG syndrome. Medical records and other relevant data were collected for each participant. To evaluate participants’ adaptive functioning, trained professionals conducted assessments using the Vineland–3 Adaptive Behavior Scales. The assessment compared individuals with epilepsy to those without seizures and covered the domains of communication, daily living skills, socialization, and maladaptive behaviors. Further comparisons were drawn based on insights from interviews and information extracted from participants’ medical records.

RESULTS

Thirty-nine individuals (22 males, 17 females) with KBG syndrome, confirmed through genetic analysis, were interviewed via videoconferencing by a single physician, followed by Vineland-3 assessment by trained raters. Individuals with KBG syndrome came from 36 unique families spanning 11 countries. While the KBG cohort displayed lower overall adaptive behavior composite scores compared to the average population, several members displayed standard scores at or higher than average, as well as higher scores compared to those with the neurodevelopmental disorder Ogden syndrome. Within the KBG cohort, males consistently scored lower than females across all domains, but none of these categories reached statistical significance. While the group with epilepsy exhibited overall lower scores than the non-seizure group in every category, statistical significance was only reached in the written communication subdomain. We predict this lack of significance is limited by low sample size, reducing study power.

CONCLUSIONS

Due to the rarity of KBG syndrome, our research provides valuable insights that can aid in epilepsy screening and inform assessment strategies for neurocognitive functioning in those with this condition. The cohort performed overall higher than expected with outliers existing in both directions. Although our results suggest that seizures might influence the trajectory of KBG syndrome, the approaching but overall absence of statistical significance between study groups underscores the necessity for a more extensive cohort to discern subtle variations in functioning. Conducting Vineland–3 assessments in the KBG syndrome population can enhance research insights regarding differences between those with and without epilepsy. Given the data collected, we recommend vigilant monitoring for seizures following a KBG diagnosis, with consideration for performing baseline EEG assessments.
Polycystins recruit cargo to distinct ciliary extracellular vesicle subtypes
Authors: Nikonorova Inna A. , desRanleau Elizabeth , Jacobs Katherine C. , Saul Joshua , Walsh Jonathon D. , Wang Juan , Barr Maureen M.
Published: April 2024

Therapeutic use of tiny extracellular vesicles (EVs) requires understanding cargo loading mechanisms. Here, we used a modular proximity label approach to identify EV cargo associated with the transient potential channel (TRP) polycystin PKD-2 ofC. elegans. Polycystins are conserved receptor-TRP channel proteins affecting cilium function; dysfunction causes polycystic kidney disease in humans and mating deficits inC. elegans. Polycystin-2 EV localization is conserved from algae to humans, hinting at an ancient and unknown function. We discovered that polycystins associate with and direct specific cargo to EVs: channel-like PACL-1, dorsal and ventral membrane C-type lectins PAMLs, and conserved tumor necrosis-associated factor (TRAF) signaling adaptors TRF-1 and TRF-2. Loading of these components relied on polycystin-1 LOV-1. Our modular EV-TurboID approach can be applied in both cell– and tissue-specific manners to define the composition of distinct EV subtypes, addressing a major challenge of the EV field.
Stress in utero: effects on gliovascular integrity in female infant offspring
Authors: Rodrigues Magda , Sousa Inês , Baptista Filipa , Coelho-Santos Vanessa
Published: April 2024

From early in life, experiences like prenatal stress profoundly affect long-term health and behavior. Maternal stress increases fetal exposure to glucocorticoids (GC), disrupting neurodevelopment and raising susceptibility to psychiatric disorders. Previous studies on synthetic GCs, such as dexamethasone (DEX), revealed impairments in neurogenesis and dendritic spine development. However, the influence of prenatal stress on the gliovascular interface remains unclear. This interface, involving the relationship between astrocytes and blood vessels, is essential for healthy brain development. Our study demonstrates that prenatal stress alters the expression and localization of astrocytic proteins crucial for maintaining vascular homeostasis, such as aquaporin-4, in female offspring exposed to DEX. While overall vascular density remains unaffected, it triggers morphological changes. Particularly, the hippocampus and prefrontal cortex exhibit heightened vulnerability to these effects. This study reveals prenatal stress as a potent disruptor of gliovascular development, urging deeper inquiry into its implications.
BatR: A novel regulator of antibiotic tolerance inPseudomonas aeruginosabiofilms
Authors: Piazza Ainelen , Dasanayaka Harshanie , Saalbach Gerhard , Martins Carlo , Trampari Eleftheria , Webber Mark A. , Harrison Freya , Malone Jacob G.
Published: April 2024

Pseudomonas aeruginosais a multidrug-resistant opportunistic human pathogen. Chronic infections are associated with biofilms, conferring resistance to antibiotics and complicating treatment strategies. This study focuses on understanding the role of the uncharacterized genePA3049, upregulated under biofilm conditions. In the context ofP. aeruginosabiofilms,PA3049plays a role in withstanding antimicrobial challenges bothin vitroand in clinically validated infection models. Under sub-inhibitory concentrations of antibiotic, the deletion ofPA3049resulted in reduced pyocyanin production and altered abundance of enzymes controlling denitrification, pyoverdine, and hydrogen cyanide biosynthesis. Notably, PA3049 directly interacts with two kinases implicated in stress response, inactivating their active sites. Renamed as theBiofilmantibiotic toleranceRegulator (BatR), PA3049 is a key player inP. aeruginosabiofilm maintenance and antimicrobial tolerance. These findings contribute to understanding the complex bacterial lifestyle in biofilms, shedding light on a previously uncharacterized gene with significant implications for combating multidrug-resistant infections.

IMPORTANCE

P. aeruginosais a multidrug-resistant ESKAPE pathogen that causes chronic biofilm-based infections and is a leading cause of mortality in cystic fibrosis (CF) patients. Understanding the molecular mechanisms underlyingP. aeruginosabiofilm resilience and antimicrobial resistance is crucial for developing effective therapeutic interventions. This study focuses on characterizing the genePA3049, now known as thebiofilmantibiotic toleranceRegulator(batR). BatR plays a central role withinP. aeruginosabiofilms, orchestrating adaptive responses to antimicrobial challenges. Our work sheds light on the contribution ofbatRto biofilm biology and its relevance in lung infections, where subinhibitory antibiotic concentrations make BatR pivotal for bacterial survival. By advancing our understanding ofP. aeruginosabiofilm regulation, this study holds significant promise for the development of innovative approaches against biofilm-associated infections to mitigate the growing threat of antimicrobial resistance.
Pyoverdine-antibiotic combination treatment: its efficacy and effects on resistance evolution inEscherichia coli
Authors: Vollenweider Vera , Roncoroni Flavie , Kümmerli Rolf
Published: April 2024

Antibiotic resistance is a growing concern for global health, demanding innovative and effective strategies to combat pathogenic bacteria. Pyoverdines, iron-chelating siderophores produced by environmentalPseudomonasspp., present a novel promising approach to induce growth arrest in pathogens through iron starvation. While we have previously demonstrated the efficacy of pyoverdines as antibacterials, our understanding of how these molecules interact with antibiotics and impact resistance evolution remains unknown. Here, we investigate the propensity of differentEscherichia colivariants to evolve resistance against pyoverdine, the cephalosporin antibiotic ceftazidime, and their combination. We found that strong resistance against ceftazidime and weak resistance against pyoverdine evolved in the wildtypeE. colistrain under single and combination treatment. Ceftazidime resistance was linked to mutations in outer membrane porin genes (envZandompF), whereas pyoverdine resistance was associated with mutations in the oligopeptide permease (opp) operon. In contrast, resistance phenotypes were attenuated under combination treatment, particularly in anE. colistrain carrying a costly multicopy plasmid. Altogether, our results show that pyoverdine as an antibacterial is particularly potent and evolutionarily robust against plasmid-carryingE. colistrains, presumably because iron starvation compromises both cellular metabolism and plasmid replication.
Using rapid invisible frequency tagging (RIFT) to probe the attentional distribution between speech planning and comprehension
Authors: Hustá Cecília , Meyer Antje , Drijvers Linda
Published: April 2024

Interlocutors often use the semantics of comprehended speech to inform the semantics of planned speech. Do representations of the comprehension and planning stimuli interact on a neural level? We used rapid invisible frequency tagging (RIFT) and EEG to probe the attentional distribution between spoken distractor words and target pictures in the picture-word interference (PWI) paradigm. We presented participants with auditory distractor nouns (auditory (f1); tagged at 54Hz) together with categorically related or unrelated pictures (visual (f2); tagged at 68Hz), which had to be named after a delay. RIFT elicits steady-state evoked potentials, which reflect attentional allocation to the tagged stimuli. When representations of the tagged stimuli interact, integrative effects have been observed at the intermodulation frequency resulting from an interaction of the base frequencies (f2±f1; Drijvers et al., 2021). Our results showed clear power increases at 54Hz and 68Hz during the tagging window, but no differences between related or unrelated conditions. More interestingly, we observed a larger power difference in the unrelated compared to the related condition at the intermodulation frequency (68Hz – 54Hz: 14Hz), indicating stronger interaction between the auditory and visual representations when they were unrelated. Our results go beyond standard PWI results (e.g., Bürki et al., 2020) by showing that participants do not have more difficulty visually attending to the related pictures or inhibiting the related auditory distractors. Instead, processing difficulties arise when the representations of the stimuli interact, meaning that participants might be trying to prevent integration between the auditory and visual representations in the related condition.

Significance statement

Studying speech planning during comprehension with EEG has been difficult due to a lack of appropriate methodology. This study demonstrates that rapid invisible frequency tagging (RIFT) can explore attentional allocation to speech planning and comprehension stimuli, as well as their interaction. Our results show that the content of the speech planning and comprehension representations affects their interaction in the neural signal, which should always be considered when these processes are studied jointly. In future work, RIFT could be used to investigate speech planning and comprehension in more conversational settings, as tagging can be added to videos or speech segments. This is the first study that demonstrates that RIFT can be used together with EEG to study cognitive phenomena.
Genomic diversity and evolution in the Hawaiian Islands endemic Kokia (Malvaceae)
Authors: Kayal Ehsan , Arick Mark A. , Hsu Chuan-yu , Thrash Adam , Yorkston Mitsuko , Morden Clifford W. , Wendel Jonathan F. , Peterson Daniel G. , Grover Corrinne E.
Published: April 2024

Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species.Kokiais an endangered flowering plant genus endemic to these islands, encompassing three extant and one extinct species. Recent studies provided evidence of unexpected genetic diversity withinKokia. Here, we provide high quality genome assemblies for all three extantKokiaspecies, including an improved genome forK. drynarioides. All threeKokiagenomes contain 12 chromosomes exhibiting high synteny within and betweenKokiaand the sister taxonGossypioides kirkii. Gene content analysis revealed a net loss of genes inK. cookeicompared to other species, whereas the gene complement inK. drynarioidesremains stable and that ofK. kauaiensisdisplays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the threeKokiaspecies at ∼1.2 million years ago (mya), with the sister taxa [K. cookei + K. drynarioides] diverging ∼0.8 mya.Kokiaappears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian Archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.
Mechanical Strategies Supporting Growth and Size Diversity in Filamentous Fungi
Authors: Chevalier Louis , Klingelschmitt Flora , Mousseron Ludovic , Minc Nicolas
Published: April 2024

The stereotypical tip growth of filamentous fungi supports their lifestyles and functions. It relies on the polarized remodeling and expansion of a protective elastic cell wall (CW) driven by large cytoplasmic turgor pressure. Remarkably, hyphal filament diameters, and cell elongation rates can vary extensively among different fungi. To date, however, how fungal cell mechanics may be adapted to support these morphological diversities while ensuring surface integrity remains unknown. Here, we combined super-resolution imaging and deflation assays, to measure local CW thickness, elasticity and turgor in a set of fungal species spread on the evolutionary tree that span a large range in cell size and growth speeds. While CW elasticity exhibited dispersed values presumably reflecting differences in CW composition, both thickness and turgor scaled in dose-dependence with cell diameter and growth speeds. Notably, larger cells exhibited thinner lateral CWs, and faster cells thinner apical CWs. Counterintuitively, turgor pressure was also inversely scaled with cell diameter and tip growth speed, challenging the idea that turgor is the primary factor dictating tip elongation rates. We propose that fast growing cells with rapid CW turnover have evolved strategies based on a less turgid cytoplasm and thin walls to safeguard wall integrity and survival.
Youth Psychotic Experiences: Diagnostic Associations and Evaluation of the CAPE-16
Authors: Birkenæs Viktoria , Parekh Pravesh , Hegemann Laura , Bakken Nora R. , Frei Evgeniia , Jaholkowski Piotr , Smeland Olav B. , Susser Ezra , Rodriguez Katrina M. , Tesfaye Markos , Andreassen Ole A. , Havdahl Alexandra , Sønderby Ida E.
Published: April 2024

Background

Adolescent self-reported psychotic experiences are associated with mental illness and could help guide prevention strategies. The Community Assessment of Psychic Experiences (CAPE) was developed over 20 years ago. In a rapidly changing society, where new generations of adolescents are growing up in an increasingly digital world, it is crucial to ensure high reliability and validity of the questionnaire.

Methods

In this observational validation study, we used unique transgenerational questionnaire and health registry data from the Norwegian Mother, Father, and Child Cohort, a population-based pregnancy cohort. Adolescents, aged ∼14 years, responded to the CAPE-16 (n= 18,835) and fathers to the CAPE-9 questionnaire (n= 28,793). We investigated the psychometric properties of CAPE-16 through factor analyses, measurement invariance testing across biological sex, response before/during the COVID-19 pandemic, and generations (comparison with fathers), and examined associations with later psychiatric diagnoses.

Outcomes

One third (33·4%) of adolescents reported lifetime psychotic experiences. We confirmed a three-factor structure (paranoia, bizarre thoughts, and hallucinations) of CAPE-16, and observed good scale reliability of the distress and frequency subscales (ω = ·86 and ·90). CAPE-16 measured psychotic experiences were invariant to biological sex and pandemic status. CAPE-9 was non-invariant across generations, with items related to understanding of the digital world (electrical influences) prone to bias. CAPE-16 sum scores were associated with a subsequent psychiatric diagnosis, particularly psychotic disorders (frequency:OR = 2·06; 97·5% CI = 1·70–2·46;distress:OR = 1·93; 97·5% CI = 1·63–2·26).

Interpretation

CAPE-16 showed robust psychometric properties across sex and pandemic status, and sum scores were associated with subsequent psychiatric diagnoses, particularly psychotic disorders. These findings suggest that with certain adjustments, CAPE-16 could have value as a screening tool for adolescents in the modern, digital world.

Funding

European Union’s Horizon 2020 Programme, Research Council of Norway, South-Eastern Norway Regional Health Authority, NIMH, and the KG Jebsen Stiftelsen.
Rhizobacteria inoculation of plants for reducing insect pests: A meta-analysis on insect behaviour and fitness
Authors: Zytynska Sharon E , Parker Megan , Sanchez-Mahecha Oriana
Published: April 2024

Rhizobacteria inoculation of plants has shown promising potential for enhancing resistance against insect pests by reducing herbivore fitness and altering herbivore-natural enemy interactions. Understanding interactions among specific rhizobacterial species and their plants in the rhizosphere is crucial for developing effective strategies to harness these benefits for pest management in agriculture. We present a meta-analysis examining the impact of rhizobacteria inoculation on herbivore interactions with plants. The findings indicate that rhizobacteria inoculation generally reduces herbivore fitness and host choice behaviours. Rhizobacteria inoculation may also enhance the recruitment of natural enemies of herbivores, thus increasing top-down predator control. The effects on herbivores varied significantly depending on the rhizobacterial species, withBacillusspp. showing stronger effects compared to other commonly studiedPseudomonasspp. Rhizobacteria notably reduced traits such as host choice, leaf consumption, survival, and reproduction of chewing herbivores, while primarily impacting sucking herbivores by reducing reproduction. Single-strain inoculants tended to perform better, especially for sucking herbivores, suggesting potential strain incompatibility issues with multi-strain inoculants. Furthermore, field trials showed less impact on insect fitness reduction compared to experiments under controlled conditions, possibly due to soil diversity and environmental factors affecting inoculant persistence. These results underscore the need for considering broader environmental interactions when developing effective rhizobacteria-based pest management strategies. Understanding specific and generalist rhizosphere interactions can aid in developing synthetic microbial communities with broad protective functions across various plants and environments.
Profiling the LAM family of contact site tethers provides insights into their regulation and function
Authors: Fenech Emma J. , Kupervaser Meital , Boshnakovska Angela , Ravid Shani , Castro Inês Gomes , Asraf Yeynit , Callegari Sylvie , Lens Christof , Rehling Peter , Schuldiner Maya
Published: April 2024

Membrane contact sites are molecular bridges between organelles that are sustained by tethering proteins and enable organelle communication. The endoplasmic reticulum (ER) membrane harbors many distinct families of tether proteins that enable the formation of contacts with all other organelles. One such example is the LAM (Lipid transfer proteinAtMembrane contact sites) family, composed of six members, each containing a lipid binding and transfer domain and an ER-embedded transmembrane segment. The family is divided into three homologous pairs each unique in their molecular architecture and localization to different ER subdomains. However, what determines the distinct localization of the different LAMs and which specific roles they carry out in each contact are still open questions. To address these, we utilized a labeling approach to profile the proximal protein landscape of the entire family. Focusing on unique interactors we could support that Lam5 resides at the ER-mitochondria contact site and demonstrate a role for it in sustaining mitochondrial activity. Capturing shared interactors of multiple LAMs, we show how the Lam1/3 and Lam2/4 paralogous pairs could be associated specifically with the plasma membrane. Overall, our work provides new insights into the regulation and function of the LAM family members. More globally it demonstrates how proximity labeling can help identify the shared or unique functions of paralogous proteins.
Electronic band structure of
Sb2Te3
Authors: Mohelsky I. , Wyzula J. , Le Mardelé F. , Abadizaman F. , Caha O. , Dubroka A. , Sun X. D. , Cho C. W. , Piot B. A. , Tanzim M. F. , Aguilera I. , Bauer G. , Springholz G. , Orlita M.
Published: April 2024

We report on Landau-level spectroscopy of an epitaxially grown thin film of the topological insulator Sb2Te3, complemented by ellipsometry and magnetotransport measurements. The observed response suggests that Sb2Te3 is a direct-gap semiconductor with the fundamental band gap located at the Γ point or along the trigonal axis, and its width reaches Eg=(190±10) meV at low temperatures. Our data also indicate the presence of other low-energy extrema with a higher multiplicity in both the conduction and valence bands. The conclusions based on our experimental data are confronted with and to a great extent corroborated by the electronic band structure calculated using the GW method.

Published by the American Physical Society
2024
First-order effect of electron-electron interactions on the anomalous Hall conductivity of massive Dirac fermions
Authors: Dumitriu-I. A. Daria , Deaconu Darius-A. , Kazantsev Alexander E. , Principi Alessandro
Published: April 2024

We investigate the first-order correction to the anomalous Hall conductivity of 2D massive Dirac fermions arising from electron-electron interactions. In a fully gapped system in the limit of zero temperature, we find that this correction vanishes, confirming the absence of perturbative corrections to the topological Hall conductivity. At finite temperature or chemical potential, we find that the total Hall response decays faster than in the noninteracting case, depending on the strength of electron-electron interactions. These features, which could potentially be observed experimentally, show the importance of two-body interactions for anomalous Hall transport.

Published by the American Physical Society
2024
Heavy-dense QCD, sign optimization, and Lefschetz thimbles
Authors: Başar Gökçe , Marincel Joseph
Published: April 2024

We study the heavy-dense limit of QCD on the lattice with heavy quarks at high density. The effective three-dimensional theory has a sign problem which is alleviated by sign optimization where the path integration domain is deformed in complex space in a way that minimizes the phase oscillations. We simulate the theory via a hybrid Monte Carlo approach, for different volumes, both to leading order and next-to-next-to leading order in the hopping expansion, and show that sign optimization successfully mitigates the sign problem at large enough volumes where usual reweighting methods fail. Finally we show that there is a significant overlap between the complex manifold generated by sign optimization and the Lefschetz thimbles associated with the theory.

Published by the American Physical Society
2024
Score-based diffusion models for generating liquid argon time projection chamber images
Authors: Imani Zeviel , Wongjirad Taritree , Aeron Shuchin
Published: April 2024

For the first time, we show high-fidelity generation of Liquid Argon Time Projection Chamber (LArTPC-like) data using a generative neural network. This demonstrates that methods developed for natural images do transfer to LArTPC-produced images, which, in contrast to natural images, are globally sparse but locally dense. We present the score-based diffusion method employed. We evaluate the fidelity of the generated images using several quality metrics, including modified measures used to evaluate natural images, comparisons between high-dimensional distributions, and comparisons relevant to LArTPC experiments.

Published by the American Physical Society
2024
Fast universal control of a flux qubit via exponentially tunable wave-function overlap
Authors: Krøjer Svend , Dahl Anders Enevold , Christensen Kasper Sangild , Kjaergaard Morten , Flensberg Karsten
Published: April 2024

Fast, high-fidelity control and readout of protected superconducting qubits are fundamentally challenging due to their inherent insensitivity. We propose a flux qubit variation which enjoys a tunable level of protection against relaxation to resolve this outstanding issue. Our qubit design, the double-shunted flux qubit (DSFQ), realizes a generic double-well potential through its three-junction ring geometry. One of the junctions is tunable, making it possible to control the barrier height and thus the level of protection. We analyze single- and two-qubit gate operations that rely on lowering the barrier. We show that this is a viable method that results in high-fidelity gates as the noncomputational states are not occupied during operations. Further, we show how the effective coupling to a readout resonator can be controlled by adjusting the externally applied flux while the DSFQ is protected from decaying into the readout resonator. Finally, we also study a double-loop gradiometric version of the DSFQ which is exponentially insensitive to variations in the global magnetic field, even when the loop areas are nonidentical.

Published by the American Physical Society
2024
Disentanglement of Evolutionary Constraints in Statistical Models of Proteins
Authors: Wang Haobo , Feng Shihao , Tsuboyama Kotaro , Liu Sirui , Rocklin Gabriel J. , Ovchinnikov Sergey
Published: April 2024

The exponential growth of protein sequences in the post-genomic era has revolutionized the application of generative sequence models for pivotal tasks such as contact prediction, protein design, alignment, and homology search. Despite remarkable progress in these areas, the interpretability of the modeled pairwise parameters remains limited due to complexities arising from coevolution, phylogeny, and entropy. While post-correction methods for contact prediction have been developed to eliminate entropy-related contributions from predicted contact maps, there is currently no direct approach to correct entropy in other applications reliant on raw parameters. In this paper, we investigate the sources of entropy signal and propose a novel spectral regularizer, LH (an abbreviation of Henri Lebesgue), to mitigate its impact during model fitting. By incorporating this regularizer into the GREMLIN framework (utilizing a Markov random field or Potts model), we enable the accurate inference of sparse contact maps while simultaneously improving interpretability and addressing overfitting concerns critical for sequence evaluation and design. To validate the efficacy of our approach, we design multiple protein sequences based on GREMLIN with both L2 and LH regularizers, and subsequently experimentally measure their using cDNA display proteolysis. Our findings demonstrate that proteins designed using the LH regularizer exhibit increased diversity and enhanced folding stability.

Published by the American Physical Society
2024
A Strontium Quantum-Gas Microscope
Authors: Buob Sandra , Höschele Jonatan , Makhalov Vasiliy , Rubio-Abadal Antonio , Tarruell Leticia
Published: April 2024

The development of quantum-gas microscopes has brought novel ways of probing quantum degenerate many-body systems at the single-atom level. Until now, most of these setups have focused on alkali atoms. Expanding quantum-gas microscopy to alkaline-earth elements will provide new tools, such as SU(N)-symmetric fermionic isotopes or ultranarrow optical transitions, to the field of quantum simulation. Here we demonstrate the site-resolved imaging of a 84Sr bosonic quantum gas in a Hubbard-regime optical lattice. The quantum gas is confined by a two-dimensional in-plane lattice and a light-sheet potential, which operate at the strontium clock-magic wavelength of 813.4 nm. We realize fluorescence imaging using the broad 461-nm transition, which provides high spatial resolution. Simultaneously, we perform attractive Sisyphus cooling with the narrow 689-nm intercombination line. We reconstruct the atomic occupation from the fluorescence images, obtaining imaging fidelities above 94%. Finally, we realize a 84Sr superfluid in the Bose-Hubbard regime. We observe its interference pattern upon expansion, a probe of phase coherence, with single-atom resolution. Our strontium quantum-gas microscope provides a new platform to study dissipative Hubbard models, quantum optics in atomic arrays, and SU(N) fermions at the microscopic level.

Published by the American Physical Society
2024
Bis[tris(diisobutyldithiocarbamato)-μ3-sulfido-tri-μ2-disulfido-trimolybdenum(IV)] sulfide tetrahydrofuran monosolvate
Authors: Fraker Addison , Donahue James P. , McSkimming Alex
Published: April 2024

The title compound, [Mo3(C9H18NS2)3(S2)3S]2S, crystallizes on a general position in the monoclinic space group P21/n (No. 14). The cationic [Mo3S7(S2CN
i
Bu2)3]+ fragments are joined by a monosulfide dianion that forms close S...S contacts to each of the disulfide ligands on the side of the Mo3 plane opposite the μ3
2− ligand. The two Mo3 planes are inclined at an angle of 40.637 (15)°, which gives the assembly an open clamshell-like appearance. One μ6-S2−...S2
2− contact, at 2.4849 (14) Å, is appreciably shorter than the remaining five, which are in the range 2.7252 (13)–2.8077 (14) Å.
Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-[(1Z,3E)-1-cyano-2,4-diphenylpenta-1,3-dien-1-yl]pyridine-3,5-dicarbonitrile monohydrate
Authors: Mamedov İbrahim G. , Khrustalev Victor N. , Akkurt Mehmet , Kerimli Fuad Sh. , Bhattarai Ajaya , Khalilov Ali N. , Naghiyev Farid N.
Published: April 2024

The asymmetric unit of the title compound, C25H18N6·H2O, comproses two molecules (I and II), together with a water molecule. The terminal phenyl groups attached to the methyl groups of the molecules I and II do not overlap completely, but are approximately perpendicular. In the crystal, the molecules are connected by N—H...N, C—H...N, O—H...N and N—H...O hydrogen bonds with each other directly and through water molecules, forming layers parallel to the (001) plane. C—H...π interactions between these layers ensure the cohesion of the crystal structure. A Hirshfeld surface analysis indicates that H...H (39.1% for molecule I; 40.0% for molecule II), C...H/H...C (26.6% for molecule I and 25.8% for molecule II) and N...H/H...N (24.3% for molecules I and II) interactions are the most important contributors to the crystal packing.
Synthesis, crystal structure and thermal properties of the dinuclear complex bis(μ-4-methylpyridine N-oxide-κ2
O:O)bis[(methanol-κO)(4-methylpyridine N-oxide-κO)bis(thiocyanato-κN)cobalt(II)]
Authors: Näther Christian , Jess Inke
Published: April 2024

Reaction of Co(NCS)2 with 4-methylpyridine N-oxide in methanol leads to the formation of crystals of the title compound, [Co2(NCS)4(C6H7NO)4(CH4O)2] or Co2(NCS)4(4-methylpyridine N-oxide)4(methanol)2. The asymmetric unit consist of one CoII cation, two thiocyanate anions, two 4-methylpyridine N-oxide coligands and one methanol molecule in general positions. The H atoms of one of the methyl groups are disordered and were refined using a split model. The CoII cations octahedrally coordinate two terminal N-bonded thiocyanate anions, three 4-methylpyridine N-oxide coligands and one methanol molecule. Each two CoII cations are linked by pairs of μ-1,1(O,O)-bridging 4-methylpyridine N-oxide coligands into dinuclear units that are located on centers of inversion. Powder X-ray diffraction (PXRD) investigations prove that the title compound is contaminated with a small amount of Co(NCS)2(4-methylpyridine N-oxide)3. Thermogravimetric investigations reveal that the methanol molecules are removed in the beginning, leading to a compound with the composition Co(NCS)2(4-methylpyridine N-oxide), which has been reported in the literature and which is of poor crystallinity.
Transnationalization of higher education in China and Asia: quality assurance and students’ learning experiences
Authors: Mok Ka Ho , Sawn Khai Tual
Published: April 2024

Purpose

This study aims to fill this research gap by providing a comprehensive exploration of the transnationalization of higher education in China and Asia, with a particular focus on how institutions maintain quality assurance and how student learning experiences are reported.

Design/methodology/approach

The transnationalization of higher education involves educational programs and services provided by institutions or universities in a country other than their home country where students from diverse countries are trained. The goal of transnational education is to offer higher education to students who face obstacles in physically entering the host country of a transnational program, encourage globalization, enhance cross-cultural communication and improve the quality of education by expanding students' learning opportunities, providing diverse educational experiences and elevating academic standards. The transnationalization of higher education has become a crucial endeavor in Asia, especially in countries such as China, Malaysia and Singapore, where rapid economic development and globalization have prompted the need to evolve into knowledge-driven economies to meet the increasing demand for higher education. The factors driving the expansion of transnational higher education in China and Asia include the desire for top-quality education, the allure of international students, the establishment of worldwide collaborations and aspirations to be recognized as centers of academic distinction. The rapid expansion and increasing importance of transnational higher education has underscored the vital role of quality assurance. To guarantee educational quality, maintain institutional reputation and improve overall student outcomes, several agencies and frameworks have been established to uphold international standards.

Findings

Based upon extensive literature reveiw and case analysis, our findings indicated the quality assurance assessment varies and is primarily influenced by host countries and provider polices. However, students in transnational higher education programs report satisfaction with their experienes and the quality of their programs, which tends to meet their expecations.

Originality/value

This study presents the first comprehsensive literatrue rewiew and case analysis of how transnational higher education in China, Sinapore, Malaysia and Vietnam uphold quality assurance and report students learning experiences. Additionally, the findings highlight why future researceh on this topic is crucial and why forestering colloboration among countries in Asian regions is imporant in term of growing geo-politics.
Competition and cooperation: a coopetition strategy for sustainable performance through serial mediation of knowledge sharing and open innovation
Authors: Abubakar Ahmed
Published: April 2024

Purpose

The purpose of this study is to examine the effect of the coopetition strategy (CS) (the simultaneous pursuit of collaboration and competition) on sustainable performance (SP) through the serial mediation of knowledge sharing (KS) and open innovation (OI).

Design/methodology/approach

A structured questionnaire was used to gather data from corporate business enterprises, and partial least squares structural equation modeling was used for analysis.

Findings

Empirical evidence supports the coopetition strategy's role in enhancing KS, which in turn fosters OI, leading to improved SP. It has also been concluded that KS and OI have a significant serial mediation effect on the relationship between CS and SP.

Practical implications

Through the integration of KS and inward-outward open innovation, the coopetition model enables coopetitors leverage each other’s resources and capacities for mutual sustainability. To fully benefit from it, small and medium-sized enterprises (SMEs) in the Gulf Cooperation Council (GCC) must change their perception of free competition and actively engage in coopetition activities, particularly in the realms of knowledge and OI.

Originality/value

The most novel contribution of this study to the growing body of knowledge on SP is the establishment of empirical evidence regarding the crucial role of a serial mediation of KS and OI in the relationship between CS and SP. Unlike earlier research, this study provides a structured perspective and understanding of how and why CS, KS and OI were leveraged to enhance the SP of SMEs.
The effect of job rotation on employee performance: the mediating role of HR strategy and training in the petrochemical industry
Authors: Alizadeh Majd Amirreza , Bell Robin , Ali Sa’ad , Davoodi Arefeh , Nasirifar Azadeh
Published: April 2024

Purpose

This study aims to investigate the impact of job rotation on employee performance and explores the mediating role of human resources (HR) strategy and training effectiveness on this relationship, within the petrochemical industry, which represents a highly specialist and hazardous industrial context.

Design/methodology/approach

Data was collected through a questionnaire which was distributed among the experts working in an Iranian petrochemical organization. Previously validated scales were used to measure job rotation, employee performance, HR strategy and training effectiveness, and partial least squares structural equation modeling was used for hypothesis testing.

Findings

The research findings indicated that job rotation had a negative effect on employee performance, while training effectiveness and HR strategy positively mediated the relationship between job rotation and employee performance. This highlights the importance of ensuring effective training and a HR strategy to support job rotation of skilled and specialist employees.

Practical implications

Managers of employees in specialist and hazardous industries, such as petrochemical workers, interested in job rotation to support employee career development, should be mindful of potential negative implications on employee performance. To support and improve employee performance, job rotation should be considered alongside HR strategy and training.

Originality/value

Previous research has largely focused on the value of job rotation to develop managers’ organizational understanding and to reduce injury within blue-collar work, which has led to a paucity of research into job rotation within highly skilled and specialist industrial roles. It is highlighted within the literature that it remains unclear what supports effective job rotation. This study addresses this lacuna by investigating how job rotation affects employee performance in a highly skilled and specialized industry and how strategy and training effectiveness mediate this effect.
How do wineries price their wine experiences?
Authors: Gergaud Olivier , Livat Florine
Published: April 2024

Purpose

This paper aims to model the price of cellar tours using a hedonic pricing approach. The authors analyze the complex relationship between the price of an add-on (here, cellar tours) and the price of the reference product (here, wine).

Design/methodology/approach

Thanks to a large database containing information on about 1,000 winery experiences, the authors regress the price of cellar tours on wine prices and on a broad set of objective characteristics that are (1) tour specific and (2) common to all tours offered by the winery. These exogenous controls include the type and style of experience offered, amenities and winemaking characteristics.

Findings

The authors show that the price of cellar tours follows the price of the most expensive wine sold by the winery, which is a proxy for reputation. The authors find that one of the main determinants of cellar tour prices is visit length: wineries charge more for longer experiences. The number of wines tasted during the visit also increases the price. Prices are higher in places where there is a high level of wine tourism activity, which might be a sign of authenticity.

Practical implications

Wine producers in different countries need to gain insights on how to price cellar tours, which are composite goods. The results can help practitioners price their winery experience according to common practices in different wine regions. The results may also be of interest to professionals in the tourism sector who are in charge of the pricing of by-products (e.g. tee-shirts, books, etc.), or for luxury fashion labels extending their brand in the catering industry with cafes and restaurants.

Originality/value

To the best of the authors’ knowledge, this paper is the first empirical analysis that examines the complex relationship between the price of an add-on and the price of the reference product in the context of wine tourism.
Can institutional investors influence media sentiment?
Authors: Wang Heng (Emily) , Zhu Xiaoyang
Published: April 2024

Purpose

The dissemination of misleading and false information through media can jeopardize a company’s reputation, thus posing a threat to its stock and performance. Institutional investors are known to influence capital markets. Therefore, this paper investigates whether institutional investors engage in shaping the media sentiment stock nexus, stabilize company stocks and enhance performance.

Design/methodology/approach

We first investigate the effect of media sentiment on market reactions by using panel regression models. To examine the role of institutional investors, we design a quasi-experiment by exploiting the Financial Crisis of 2008 and go further by examining the heterogeneity across levels of institutional ownership. Due to risk-averse, investors may respond asymmetrically to pessimistic and positive sentiment. Accordingly, we split the sample into two sub-types, good news and bad news, based on keywords representing positive or negative content.

Findings

We find supportive evidence that institutional investors have impacts on how the markets react to media news, and the impacts are heterogeneous in the face of bad and good news. We conjecture that institutional investors act as a stabilizer of stock prices through media sentiment management.

Originality/value

This paper confirms the distinctive effects of institutional investors on capital markets, and uncovers the behind-the-scenes intervention and possible causal link running from institutional investors to media sentiment management. It contributes to the broad field of institutional investors' behavior, media news involvement in capital markets and market efficiency.