bluuebunny/crossref_metadata_2025 huggingface dataset:
Cellular resolution contributions to ictal population signals
Authors: Lau Lauren A. , Zhao Zhuoyang , Gomperts Stephen N. , Staley Kevin J. , Lillis Kyle P.
Published: May 2024

Objective

The increased amplitude of ictal activity is a common feature of epileptic seizures, but the determinants of this amplitude have not been identified. Clinically, ictal amplitudes are measured electrographically (using, e.g., electroencephalography, electrocorticography, and depth electrodes), but these methods do not enable the assessment of the activity of individual neurons. Population signal may increase from three potential sources: (1) increased synchrony (i.e., more coactive neurons); (2) altered active state, from bursts of action potentials and/or paroxysmal depolarizing shifts in membrane potential; and (3) altered subthreshold state, which includes all lower levels of activity. Here, we quantify the fraction of ictal signal from each source.

Methods

To identify the cellular determinants of the ictal signal, we measured single cell and population electrical activity and neuronal calcium levels via optical imaging of the genetically encoded calcium indicator (GECI) GCaMP. Spontaneous seizure activity was assessed with microendoscopy in an APP/PS1 mouse with focal cortical injury and via widefield imaging in the organotypic hippocampal slice cultures (OHSCs) model of posttraumatic epilepsy. Single cell calcium signals were linked to a range of electrical activities by performing simultaneous GECI‐based calcium imaging and whole‐cell patch‐clamp recordings in spontaneously seizing OHSCs. Neuronal resolution calcium imaging of spontaneous seizures was then used to quantify the cellular contributions to population‐level ictal signal.

Results

The seizure onset signal was primarily driven by increased subthreshold activity, consistent with either barrages of excitatory postsynaptic potentials or sustained membrane depolarization. Unsurprisingly, more neurons entered the active state as seizure activity progressed. However, the increasing fraction of active cells was primarily driven by synchronous reactivation and not from continued recruitment of new populations of neurons into the seizure.

Significance

This work provides a critical link between single neuron activity and population measures of seizure activity.
Dexmedetomidine preconditioning reduces ischaemia–reperfusion injury in equine model of large colon volvulus
Authors: Watkins Amanda , Engiles Julie , Long Alicia , Brandly Jerrianne , Hopster Klaus
Published: May 2024

Background

Large colon volvulus is a cause of colic in horses with high morbidity and mortality when not promptly treated. More treatment options are needed to improve the outcome of these cases by protecting against the damage caused by ischaemia and reperfusion injury.

Objectives

To determine the effect of preconditioning with dexmedetomidine prior to induction of ischaemia–reperfusion (IR) injury in a large colon volvulus model in the horse.

Study design

Randomised blinded in vivo experiments.

Methods

Horses received either a dexmedetomidine (DEX) or saline (CON) constant rate infusion (CRI) immediately following induction of anaesthesia. Venous, arterial, and transmural occlusion of a section of the large colon was performed for 3 h, after which the ligatures and clamps were removed to allow for reperfusion for 3 h. Biopsies of the large colon were taken at baseline, 1 and 3 h of ischaemia, and at 1 and 3 h of reperfusion.

Results

The severity of crypt epithelial loss (DEX = 2.1 [0.8–2.8], CON = 3.1 [2.5–4], p = 0.03) and mucosal haemorrhage was decreased (DEX = 2.1 [1.3–3], CON = 3.5 [2.5–4], p = 0.03) in group DEX compared to group CON when graded on a scale of 0–4. Crypt length remained longer (DEX = 369.5 ± 91.7 μm, CON = 238.5 ± 72.6 μm, p = 0.02) and interstitium to crypt (I:C) ratio remained lower (DEX = 1.4 (1–1.7), CON = 2.6 [1.8–5.9], p = 0.03) in group DEX compared to group CON during reperfusion.

Main limitations

Clinical applicability of pharmacologic preconditioning is limited.

Conclusion

Preconditioning with a dexmedetomidine CRI prior to IR injury demonstrated a protective effect histologically on the large colon in the horse. Further investigation into postconditioning with dexmedetomidine is warranted as a possible intervention in colic cases suspected of being large colon volvulus.
Global plant responses to intensified fire regimes
Authors: Grau‐Andrés Roger , Moreira Bruno , Pausas Juli G.
Published: May 2024

Aim

Global change factors, such as warming, heatwaves, droughts and land‐use changes, are intensifying fire regimes (defined here as increasing frequency or severity of fires) in many ecosystems worldwide. A large body of local‐scale research has shown that such intensified fire regimes can greatly impact on ecosystem structure and function through altering plant communities. Here, we aim to find general patterns of plant responses to intensified fire regimes across climates, habitats and fire regimes at the global scale.

Location

Worldwide.

Time period

Studies published 1962–2023.

Major taxa studied

Woody plants, herbs and bryophytes.

Methods

We carried out a global systematic review and meta‐analysis of the response of plant abundance, diversity and fitness to increased fire frequency or severity. To assess the context dependency of those responses, we tested the effect of the following variables: fire regime component (fire frequency or severity), time since the last fire, fire type (wildfire or prescribed fire), historical fire regime type (surface or crown fire), plant life form (woody plant, herb or bryophyte), habitat type and climate.

Results

Intensified fire regimes reduced overall plant abundance (Hedges' d = −0.24), diversity (d = −0.27), and fitness (d = −0.69). Generally, adverse effects of intensified fire regimes on plants were stronger due to increased severity than frequency, in wildfires compared to prescribed fires, and at shorter times since fire. Adverse effects were also stronger for woody plants than for herbs, and in conifer and mixed forests than in open ecosystems (e.g. grasslands and shrublands).

Main conclusions

Intensified fire regimes can substantially alter plant communities in many ecosystems worldwide. Plant responses are influenced by the specific fire regime component that is changing and by the biotic and abiotic conditions.
Health and social care managers' self‐assessed competence in knowledge management: A descriptive cross‐sectional study
Authors: Karsikas Eevi , Meriläinen Merja , Koivunen Kirsi , Kanste Outi
Published: May 2024

Aim

To describe health and social care managers' self‐assessed competence in knowledge management and the factors associated with management competence.

Background

It has been shown that the performance of an organization is as good as the competence of its managers, so health and social care managers' competence in knowledge management should be assessed to improve organizational performance.

Desgin

A descriptive cross‐sectional design.

Methods

A total of 116 managers participated from six Finnish public health and social care organizations. The data were collected in February and August 2022 using the managers' competence in knowledge management (MCKM) instrument and analysed using descriptive statistical methods.

Results

Health and social care managers rated their self‐reported total competence in knowledge management as good. Among the dimensions of knowledge management competence, managing a culture of competence received the highest rating, while planning competence development and cooperation was perceived as the weakest dimension. The results indicate that background factors such as the healthcare setting, the number of units managed and the number of direct staff had a statistically significant association with the health and social care managers' self‐assessed competence in planning competence development and cooperation.

Conclusion

Even though the health and social care managers' total self‐assessed competence level in knowledge management was rated as good, the results underscore the significance of continuous competence development among these managers in all dimensions of knowledge management.

Impact

By enhancing and clarifying managers' tasks and competence in knowledge management, managers can increase staff retention, attractiveness and work well‐being.

Implications

The results can be utilized to identify managers' strengths and weaknesses in knowledge management and, thus, effectively target their limited competence development resources.

Reporting Method

The STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) checklist.

Patient or Public Contribution

There is no patient or public contribution.
Editorial: No short‐cuts – translating neurobiological knowledge to clinical practice requires moving away from stand‐alone biomarkers to an integrative biopsychosocial approach
Authors: Jansen Lucres
Published: May 2024

Although decades of research have shown the importance of neurobiological factors in the development of mental health problems in children and adolescents, the translation of this knowledge to use in clinical practice has proven difficult. One of the pitfalls is the false assumption that biological factors are so fundamental that they overrule all other factors and can be used as stand‐alone biomarkers or tests for diagnostic purposes and treatment decisions. This assumption is false because all neurodevelopmental disorders result from complex interactions between biology and environment. Therefore, neurobiological assessments should never be used as a shortcut for diagnostic assessments that include the environment, including family, peers, and society at large. Instead, they should be integrated in the diagnostic process. This calls for empirically supported guidance on how to weigh information from neurobiological and psychosocial assessments in the diagnostic and treatment decision process.
Artificial fluorescent sensor reveals pre‐synaptic NMDA receptors switch cholecystokinin release and LTP in the hippocampus
Authors: Wong Yin‐Ting , Zheng Xuejiao , Lau Siu‐Hin , Sun Ka‐Hei Murphy , Chen Xi , Li Huangcan , Ng Siu‐Lung , Jiang HeHai , Lau Geoffrey Chun Yue , He Jufang
Published: May 2024

Cholecystokinin (CCK) has been confirmed to be essential in NMDA‐dependent long‐term potentiation (LTP) at mouse cortical synapses. This paper has proven that CCK is necessary for LTP induced by high‐frequency stimulation of mouse hippocampal synapses projected from the entorhinal cortex. We show that the subunit of the axonal NMDA receptor dominant modulates the activity‐induced LTP by triggering pre‐synaptic CCK release. A functional pre‐synaptic NMDA receptor is required to induce LTP mediated by the axonal Ca2+ elevation and CCK exocytosis at CCK‐specific neurons. Genetic depletion of the GluN1 subunit of NMDA receptors on CCK neurons, which projected from the entorhinal cortex largely abolished the axonal Ca2+ elevation and disturbed the secretion of CCK in hippocampus. These results demonstrate that activity‐induced LTP at the hippocampal synapse is CCK‐dependent, and CCK secretion from the axonal terminal is modulated by pre‐synaptic NMDA receptors.

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The impact of payday alternative loans on credit union performance and loan quality
Authors: Goenner Cullen F.
Published: May 2024

Federal regulators in 2010 amended lending rules to allow federal credit unions (FCU) to originate short‐term, small‐dollar amount loans, with an annual percentage rate of up to 1000 basis points above the otherwise imposed interest rate ceiling of 18 percent. The purpose of the change in policy was to allow FCUs the ability to provide their members with an alternative to payday loans. We find the decision to originate these higher‐interest loans is primarily influenced by the characteristics of a credit union's environment. Credit unions located in minority neighborhoods and in markets with fewer traditional financial services are more likely to participate in the payday alternative loan program. Participation in the program is shown to improve earnings performance without adversely affecting participants' loan quality. These results suggest credit unions can provide lower‐priced alternatives to payday loans that are beneficial to members and their credit unions.
Aesthetic management of lips and perioral region with Hylacross® and Vycross® hyaluronic‐acid based fillers: A document of recommendations
Authors: Díaz‐Aguayo Iratxe , Urdiales‐Gálvez Fernando , Benítez Paula A , Carvajal‐Larrate Antonio , Farollch‐Prats Lisandro , Hospido Ana , Mira Mar , Uva Luís , Zuluaga Luís
Published: May 2024

Background

Lip volumization and perioral rejuvenation with hyaluronic‐acid (HA) based dermal fillers are generating increasing interest and demand. However, this topic is still having many unmet needs nowadays. This document aimed to provide tips and recommendations that may help clinicians to achieve optimal and more predictable aesthetic outcomes.

Methods

A multidisciplinary group of aesthetic medicine doctors from Spain and Portugal reviewed the tools used for assessing the patient and aesthetic outcomes, as well as the different techniques and products used in lips/perioral rejuvenation.

Results

The consensus panel provided specific recommendations focusing on the basic information to collect before performing the aesthetic procedure; comprehensive approach to lips/perioral region rejuvenation; clinical and aesthetic assessment tools; product and technique selection; patient profile and needs; and safety issues (complications/adverse‐events).

Conclusions

The rapid evolution of techniques and tools for assessing the patient and aesthetic outcomes, as well as the development of new HA‐based fillers makes it necessary to update the clinical recommendations that guide the daily practice of clinicians, particularly those who have less experience with these procedures. This document addressed relevant subjects related to lip/perioral‐region rejuvenation to perform the correct procedure, with the appropriate HA‐based, on the right patient; to help specialists to obtain optimal and predictable aesthetic outcomes.
Rural comprehensive cancer care: Qualitative analysis of current challenges and opportunities
Authors: Evans Sydney , Seaman Aaron T. , Johnson Erin C. , Engelbart Jacklyn M. , Gao Xiang , Vikas Praveen , Phadke Sneha , Schroeder Mary C. , Lizarraga Ingrid M. , Charlton Mary E.
Published: May 2024

Purpose

While limited resources can make high‐quality, comprehensive, coordinated cancer care provision challenging in rural settings, rural cancer patients often rely on local hospitals for care. To develop resources and strategies to support high‐quality local cancer care, it is critical to understand the current experiences of rural cancer care physicians, including perceived strengths and challenges of providing cancer care in rural areas. 

Methods

Semi‐structured interviews were conducted with 13 cancer providers associated with all 12 non‐metropolitan/rural Iowa hospitals that diagnose or treat >100 cancer patients annually. Iterative thematic analysis was conducted to develop domains.

Findings

Participants identified geographic proximity and sense of community as strengths of local care. They described decision‐making processes and challenges related to referring patients to larger centers for complex procedures, including a lack of dedicated navigators to facilitate and track transfers between institutions and occasional lack of respect from academic physicians. Participants reported a desire for strengthening collaborations with larger urban/academic cancer centers, including access to educational opportunities, shared resources and strategies to collect and monitor data on quality, and clinical trials.

Conclusions

Rural cancer care providers are dedicated to providing high‐quality care close to home for their patients and would welcome opportunities to increase collaboration with larger centers to improve coordination and comprehensiveness of care, collect and monitor data on quality of care, and access continuing education opportunities. Further research is needed to develop implementation approaches that will extend resources, services, and expertise to rural providers to facilitate high‐quality cancer care for all cancer patients.
The need for critical and intersectional approaches to equity efforts in postgraduate medical education: A critical narrative review
Authors: Lam Justin T. H. , Coret Michal , Khalil Carlos , Butler Kat , Giroux Ryan J. , Martimianakis Maria Athina ( Tina)
Published: May 2024

Background

Racialised trainees in Canada and the USA continue to disproportionately experience discrimination and harassment in learning environments despite equity, diversity, and inclusion (EDI) reform efforts. Using critical approaches to understand what problems have been conceptualised and operationalised as EDI issues within postgraduate medical education (PGME) is important to inform ongoing learning environment reform in resident training.

Methods

We conducted a critical narrative review of EDI literature from 2009–2022 using critical race theory (CRT) and the concept of intersectionality to analyse how issues of discrimination in PGME have been studied. Our search yielded 2244 articles that were narrowed down to 349 articles for relevance to Canadian and American PGME contexts. We attended to reflexivity and our positionality in analysing the database and identifying themes related to EDI reform.

Results

Interest convergence was noted in how EDI reform was rationalised primarily by increased productivity. Problems of learner representation, gender inequities and curricular problems were conceptualised as EDI issues. The role that racism played in EDI‐related problems was largely invisible, as were explicit conceptualisations of race and gender as social constructs. Overall, there was a lack of critical or intersectional approaches in the literature reviewed. Misalignment was noted where studies would frame a problem through a critical lens, but then study the problem without attention to power.

Discussion

Interest convergence and epistemic injustice can account for the absence of critical approaches due to the alignment of existing EDI work with institutional interests and priorities. Interest convergence conceptually limits existing EDI reform efforts in PGME. CRT and intersectionality connect racialised learner experiences to systemic phenomena like racism and other forms of discrimination to challenge dominant assumptions. Because they attend to power, critical approaches are key to understanding why inequities have persisted to advance equity in learning environments for racialised and intersectionally marginalised learners.
Interspecific variation in Rubisco CO2/O2 specificity along the leaf economic spectrum across 23 woody angiosperm plants in the Pacific islands
Authors: Sakata Tsuyoshi , Matsuyama Shin , Kawai Kiyosada , Yasumoto Ko , Sekikawa Seikoh , Ishida Atsushi
Published: May 2024

The coordinated interspecific variation in leaf traits and leaf lifespan is known as the leaf economic spectrum (LES). The limitation of CO2 diffusion to chloroplasts within the lamina is significant in C3 photosynthesis, resulting in a shortage of CO2 for Rubisco. Although Rubisco CO2/O2 specificity (SC/O) should be adaptively adjusted in response to the interspecific variation in CO2 concentrations [CO2] associated with Rubisco, SC/O variations across species along the LES remain unknown.

We investigated the coordination among leaf traits, including SC/O, CO2 conductance, leaf protein content, and leaf mass area, across 23 woody C3 species coexisting on an oceanic island through phylogenetic correlation analyses.

A high SC/O indicates a high CO2 specificity of Rubisco. SC/O was negatively correlated with [CO2] at Rubisco and total CO2 conductance within lamina, while it was positively correlated with leaf protein across species, regardless of phylogenetic constraint. A simulation analysis shows that the optimal SC/O for maximizing photosynthesis depends on both [CO2] at Rubisco sites and leaf protein per unit leaf area.

SC/O is a key parameter along the LES axis and is crucial for maximizing photosynthesis across species and the adaptation of woody plants.
A big data scheme for heart disease classification in map reduce using jellyfish search flow regime optimization enabled Spinalnet
Authors: Jaya Mabel Rani Antony , Srivenkateswaran Chinnapillai , Vishnupriya Gurunathan , Subramanian Nalini , Ilango Poonguzhali , Jacintha Vijaya Kumar
Published: May 2024

Background

The disease related to the heart is serious and can lead to death. Precise heart disease prediction is imperative for the effective treatment of cardiac patients. This can be attained by machine learning (ML) techniques using healthcare data. Several models on the basis of ML predict and identify disease in the heart, but this model cannot manage a huge database because of the deficiency of the smart model. This paper provides an optimized SpinalNet with a MapReduce model to categorize heart disease.

Objective

The objective is to design a big data approach for heart disease classification using the proposed Jellyfish Search Flow Regime Optimization (JSFRO)‐based SpinalNet.

Method

The binary image conversion is applied on Electrocardiogram (ECG) images for converting the image to binary image. MapReduce model is adapted, in which the mappers execute feature extraction and the reducer performs heart disease classification. In the mapper phase, the features like statistical features, shape features and temporal features are extracted and in reducer, the SpinalNet with JSFRO is considered. Here, the training of SpinalNet is done with JSFRO, which is produced by the unification of Jellyfish Search Optimization (JSO) and Flow Regime Optimization (FRO).

Method

The JSFRO‐based SpinalNet offered effectual performance with the finest accuracy of 90.8%, sensitivity of 95.2% and specificity of 93.6%.
How useful is setting safety goals?
Authors: Sugawara Shin‐etsu
Published: May 2024

The study explores the multifaceted role of safety goals in fostering a risk‐informed culture, reflecting the global experience within the nuclear safety domain. Analysis of the phases of transition evoked by establishing and applying safety goals sheds light on the need for epistemic, reflexive, and practical transitions for better management of nuclear safety. This pivotal role of safety goals underscores the importance of recognizing them not as ready‐to‐use turnkey products but as catalysts for stakeholder dialog, reassessment of existing safety paradigms, and regulatory framework refinement. Finally, this study explores the challenges associated with standardizing safety goals globally and navigating the transition process within the framework of transition management.
Predictability and transparency of working conditions for food delivery platform workers across selected EU countries
Authors: Leschke Janine , Scheele Laura
Published: May 2024

While prior research has demonstrated the poor and unpredictable working conditions and ambiguous working arrangements characteristic of platform‐based food delivery, we lack research on the question of how well these workers are informed about essential aspects of their work, including protection of their rights, working time and schedules, and earnings. Comprehensive and transparent information on working conditions at an early stage is indispensable if workers are to be able to make informed decisions on taking up work and, where relevant, investing in equipment and exercising rights linked to a specific job. Drawing on the multi‐dimensional job quality literature, this article focuses on digital labour platforms in the food delivery sector across four countries: Denmark, Germany, the Netherlands and Spain. We exploit firm‐level variations, including with regard to the types of work arrangements used and the application—or not—of collective agreements. We draw on information provided to riders during the application process prior to the start of employment, including via websites and FAQs, as well as scrutiny of contracts, service agreements and collective bargaining agreements, where relevant. This information is complemented with interviews with trade union representatives. Our findings point to the relationship between a firm's choice of employment status and form of contract, on one hand, and the predictability and transparency of information provided to workers, on the other. Differences and similarities in such information seem to be more strongly bound to firm‐level decisions than to the welfare and industrial relations regimes in which the platform companies operate.
A Modular Nitinol Model With Lode Angle-Based Asymmetry and Improved Representation of the Superelastic Loops for Medical Device Applications
Authors: Mould John , Kelly Alex , Peterson Ash , Rebelo Nuno
Published: May 2024

We describe a phenomenological constitutive model for representing Nitinol in medical device applications. The intent is to capture some of the response features important to medical device applications that are neglected in prevalent state of the art models such as the Abaqus superelastic model, without losing any of the major capabilities that are already widely adopted. These features include better representation of the superelastic loops under compression which is needed to accurately assess bending—a primary response mode in slender medical devices. This model captures tension/compression asymmetry as a function of Lode angle rather than pressure as in some existing models. Test data show Lode angle functionality is superior. We will refer to this implementation as the Thornton Tomasetti (TT) model to distinguish it from other existing implementations that have evolved from the baseline underlying theory. We implement the model in a modular form suitable for use in commercial finite element software and describe initialization from laboratory test data. This model improves fidelity in representing the mechanical response of Nitinol, but as will be shown below, there is more to be done. Higher fidelity models lead to improved medical device simulations and hence better designs.
Habitual Nocturnal Sleep, Napping Behavior, and Recovery Following Training and Competition in Elite Water Polo: Sex-Related Effects
Authors: Koutouvakis Nickos G. , Geladas Nickos D. , Mouratidis Athanasios , Toubekis Argyris G. , Botonis Petros G.
Published: May 2024

Purpose: To examine nocturnal sleep patterns, napping behaviors, and subjective wellness responses of elite water polo players within an in-season week and to identify whether sleeping patterns differ between men and women. Methods: Sleep characteristics of 10 male and 17 female professional water polo players were objectively assessed during 1 week of the in-season period, including 5 training days, 1 match day, and 1 day of rest. Internal load (rating of perceived exertion × duration of training or match) was assessed 30 minutes posttraining or postmatch, and the total quality of recovery was recorded every morning. A series of multilevel models were used to analyze the data. Results: Time in bed and wake-up time were earlier on both training (P < .001) and rest days (P < .001) than on the day of the match. Internal workload did not predict any of the players’ sleeping patterns. Midday naps predicted less time in bed (P = .03) and likely less sleep time (P = .08). The total quality of recovery was predicted only by the total sleep time (P < .01). Women exhibited higher sleep efficiency (P < .001), less waking after sleep onset (P = .01), and a lower number of awakenings (P = .02) than men. Conclusions: The current results indicate that the nocturnal sleep patterns of elite water polo players are not associated with internal load and that women display better nocturnal sleep quality compared with men. As long naps interfere with nocturnal sleep, and total nocturnal sleep time predicts total quality of recovery, we suggest that athletes follow hygiene sleep strategies to facilitate adequate nocturnal sleep and next-day recovery.
Utilizing a Community of Practice for Teaching Personal and Social Responsibility: A Case Study
Authors: Shiver Victoria , Simonton Kelly L. , Simonton Angela , Alshuraymi Ali
Published: May 2024

The purpose was to understand two teachers’ experiences of implementing the teaching personal and social responsibility model over the span of one academic year due to their development and participation within a community of practice. A case study approach was utilized to gather and analyze qualitative data; three themes were developed. The teachers were marginalized by school personnel and received little recognition for their efforts. Student success was reported, but students were not ready to learn components of the model. Model implementation improved over time. Support from their community of practice allowed for reassurance, overcoming frustration, routine development, and value of the model. Without the community of practice, teachers indicated high potential for burnout of model use due to exhaustion associated with marginalization. The teaching personal and social responsibility model is well suited for a community of practice based on its call for continuous reflection and gradual empowerment.
Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates
Authors: Steichen Jon M. , Phung Ivy , Salcedo Eugenia , Ozorowski Gabriel , Willis Jordan R. , Baboo Sabyasachi , Liguori Alessia , Cottrell Christopher A. , Torres Jonathan L. , Madden Patrick J. , Ma Krystal M. , Sutton Henry J. , Lee Jeong Hyun , Kalyuzhniy Oleksandr , Allen Joel D. , Rodriguez Oscar L. , Adachi Yumiko , Mullen Tina-Marie , Georgeson Erik , Kubitz Michael , Burns Alison , Barman Shawn , Mopuri Rohini , Metz Amanda , Altheide Tasha K. , Diedrich Jolene K. , Saha Swati , Shields Kaitlyn , Schultze Steven E. , Smith Melissa L. , Schiffner Torben , Burton Dennis R. , Watson Corey T. , Bosinger Steven E. , Crispin Max , Yates John R. , Paulson James C. , Ward Andrew B. , Sok Devin , Crotty Shane , Schief William R.
Published: May 2024

Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo–electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.
Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments
Authors: Liu Hao , Matthies Michael , Russo John , Rovigatti Lorenzo , Narayanan Raghu Pradeep , Diep Thong , McKeen Daniel , Gang Oleg , Stephanopoulos Nicholas , Sciortino Francesco , Yan Hao , Romano Flavio , Šulc Petr
Published: May 2024

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
AlphaFold2 structures guide prospective ligand discovery
Authors: Lyu Jiankun , Kapolka Nicholas , Gumpper Ryan , Alon Assaf , Wang Liang , Jain Manish K. , Barros-Álvarez Ximena , Sakamoto Kensuke , Kim Yoojoong , DiBerto Jeffrey , Kim Kuglae , Glenn Isabella S. , Tummino Tia A. , Huang Sijie , Irwin John J. , Tarkhanova Olga O. , Moroz Yurii , Skiniotis Georgios , Kruse Andrew C. , Shoichet Brian K. , Roth Bryan L.
Published: May 2024

AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ
2
and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules and comparing results with those obtained from docking against the experimental structures. Hit rates were high and similar for the experimental and AF2 structures, as were affinities. Success in docking against the AF2 models was achieved despite differences between orthosteric residue conformations in the AF2 models and the experimental structures. Determination of the cryo–electron microscopy structure for one of the more potent 5-HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based drug design.
Enantioselective remote methylene C−H (hetero)arylation of cycloalkane carboxylic acids
Authors: Zhang Tao , Zhang Zi-Yu , Kang Guowei , Sheng Tao , Yan Jie-Lun , Yang Yuan-Bin , Ouyang Yuxin , Yu Jin-Quan
Published: May 2024

Stereoselective construction of γ- and δ-stereocenters in carbonyl compounds is a pivotal objective in asymmetric synthesis. Here, we report chiral bifunctional oxazoline-pyridone ligands that enable enantioselective palladium-catalyzed remote γ-C−H (hetero)arylations of free cycloalkane carboxylic acids, which are essential carbocyclic building blocks in organic synthesis. The reaction establishes γ-tertiary and α-quaternary stereocenters simultaneously in up to >99% enantiomeric excess, providing access to a wide range of cyclic chiral synthons and bioactive molecules. The sequential enantioselective editing of two methylene C–H bonds can be achieved by using chiral ligands with opposite configuration to construct carbocycles containing three chiral centers. Enantioselective remote δ-C−H (hetero)arylation is also realized to establish δ-stereocenters that are particularly challenging to access using classical methodologies.
In Science Journals
Authors: Vignieri Sacha , Yeston Jake S. , Szuromi Phil , Ray L. Bryan , Jiang Di , Grocholski Brent , Neuhofer Daniela , Scanlon Seth Thomas , Kelly Priscilla N. , Suleymanov Yury , Uzogara Ekeoma , Baek Amy E.
Published: May 2024

Highlights from the
Science
family of journals
mRNA-LNP prime boost evolves precursors toward VRC01-like broadly neutralizing antibodies in preclinical humanized mouse models
Authors: Wang Xuesong , Cottrell Christopher A. , Hu Xiaozhen , Ray Rashmi , Bottermann Maria , Villavicencio Paula Maldonado , Yan Yu , Xie Zhenfei , Warner John E. , Ellis-Pugh Jordan Renae , Kalyuzhniy Oleksandr , Liguori Alessia , Willis Jordan R. , Menis Sergey , Rämisch Sebastian , Eskandarzadeh Saman , Kubitz Michael , Tingle Ryan , Phelps Nicole , Groschel Bettina , Himansu Sunny , Carfi Andrea , Kirsch Kathrin H. , Weldon Stephanie R. , Nair Usha , Schief William R. , Batista Facundo D.
Published: May 2024

Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4-binding site of the HIV envelope (Env) have shown promise in clinical trials. Here, we preclinically validated a lipid nanoparticle–encapsulated nucleoside mRNA (mRNA-LNP) encoding eOD-GT8 60mer as a soluble self-assembling nanoparticle in mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation without exclusionary competition. Boosts drove precursor B cell participation in germinal centers; the accumulation of somatic hypermutations, including in key VRC01-class positions; and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles encoded by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversified along the bnAb pathway.
Enhancing probiotic impact: engineering
Saccharomyces boulardii
for optimal acetic acid production and gastric passage tolerance
Authors: de Carvalho Bruna Trindade , Subotić Ana , Vandecruys Paul , Deleu Sara , Vermeire Séverine , Thevelein Johan M.
Published: May 2024

Saccharomyces boulardii
has been a subject of growing interest due to its potential as a probiotic microorganism with applications in gastrointestinal health, but the molecular cause for its probiotic potency has remained elusive. The recent discovery that
S. boulardii
contains unique mutations causing high acetic acid accumulation and inhibition of bacterial growth provides a possible clue. The natural
S. boulardii
isolates Sb.P and Sb.A are homozygous for the recessive mutation
whi2
S270*
and accumulate unusually high amounts of acetic acid, which strongly inhibit bacterial growth. However, the homozygous
whi2
S270*
mutation also leads to acetic acid sensitivity and acid sensitivity in general. In the present study, we have constructed a new
S. boulardii
strain, derived from the widely therapeutically used CMCN I-745 strain (isolated from the pharmaceutical product Enterol), producing even higher levels of acetic acid while keeping the same tolerance toward low pH as the parent Enterol (ENT) strain. This newly engineered strain, named ENT3, has a homozygous deletion of
ACH1
and strong overexpression of
ALD4
. It is also able to accumulate much higher acetic acid concentrations when growing on low glucose levels, in contrast to the ENT wild-type and Sb.P strains. Moreover, we show the antimicrobial capacity of ENT3 against gut pathogens
in vitro
and observed that higher acetic acid production might correlate with better persistence in the gut in healthy mice. These findings underscore the possible role of the unique acetic acid production and its potential for improvement of the probiotic action of
S. boulardii
.

IMPORTANCE

Superior variants of the probiotic yeast
Saccharomyces boulardii
produce high levels of acetic acid, which inhibit the growth of bacterial pathogens. However, these strains also show increased acid sensitivity, which can compromise the viability of the cells during their passage through the stomach. In this work, we have developed by genetic engineering a variant of
Saccharomyces boulardii
that produces even higher levels of acetic acid and does not show enhanced acid sensitivity. We also show that the
S. boulardii
yeasts with higher acetic acid production persist longer in the gut, in agreement with a previous work indicating competition between probiotic yeast and bacteria for residence in the gut.
On the evolution of chromosomal regions with high gene strand bias in bacteria
Authors: Tomasch Jürgen , Kopejtka Karel , Shivaramu Sahana , Mujakić Izabela , Koblížek Michal
Published: May 2024

On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.

IMPORTANCE

On bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of “hybrid” chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at
ter
, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell’s information content.
Phage protein Gp11 blocks
Staphylococcus aureus
cell division by inhibiting peptidoglycan biosynthesis
Authors: Xu Qi , Tang Li , Liu Weilin , Xu Neng , Hu Yangbo , Zhang Yong , Chen Shiyun
Published: May 2024

Phages and bacteria have a long history of co-evolution. However, these dynamics of phage-host interactions are still largely unknown; identification of phage inhibitors that remodel host metabolism will provide valuable information for target development for antimicrobials. Here, we perform a comprehensive screen for early-gene products of ΦNM1 that inhibit cell growth in
Staphylococcus aureus
. A small membrane protein, Gp11, with inhibitory effects on
S. aureus
cell division was identified. A bacterial two-hybrid library containing 345 essential
S. aureus
genes was constructed to screen for targets of Gp11, and Gp11 was found to interact with MurG and DivIC. Defects in cell growth and division caused by Gp11 were dependent on MurG and DivIC, which was further confirmed using CRISPRi hypersensitivity assay. Gp11 interacts with MurG, the protein essential for cell wall formation, by inhibiting the production of lipid II to regulate peptidoglycan (PG) biosynthesis on the cell membrane. Gp11 also interacts with cell division protein DivIC, an essential part of the division machinery necessary for septal cell wall assembly, to disrupt the recruitment of division protein FtsW. Mutations in Gp11 result in loss of its ability to cause growth defects, whereas infection with phage in which the
gp11
gene has been deleted showed a significant increase in lipid II production in
S. aureus
. Together, our findings reveal that a phage early-gene product interacts with essential host proteins to disrupt PG biosynthesis and block
S. aureus
cell division, suggesting a potential pathway for the development of therapeutic approaches to treat pathogenic bacterial infections.

IMPORTANCE

Understanding the interplay between phages and their hosts is important for the development of novel therapies against pathogenic bacteria. Although phages have been used to control methicillin-resistant
Staphylococcus aureus
infections, our knowledge related to the processes in the early stages of phage infection is still limited. Owing to the fact that most of the phage early proteins have been classified as hypothetical proteins with uncertain functions, we screened phage early-gene products that inhibit cell growth in
S. aureus
, and one protein, Gp11, selectively targets essential host genes to block the synthesis of the peptidoglycan component lipid II, ultimately leading to cell growth arrest in
S. aureus
. Our study provides a novel insight into the strategy by which Gp11 blocks essential host cellular metabolism to influence phage-host interaction. Importantly, dissecting the interactions between phages and host cells will contribute to the development of new and effective therapies to treat bacterial infections.
Geochemical and petrological diversity of a transcrustal magmatic system driven by mushy magma mixing: Insights from the Triassic dike swarms in East Kunlun orogen, northern Tibetan Plateau
Authors: Xiong Fuhao , Yan Dongdong , Ma Changqian , Hou Mingcai , Wang Mingchi , Huang Hu , Wang Wei
Published: May 2024

Geochemical and petrological diversity within transcrustal magmatic systems usually reflects the magma properties and magmatic processes and thus is critical to understanding the origin of magmatic complexes and the evolution of continental crust. Herein, we present an integrated study on the petrology, mineralogy, geochronology, geochemistry, and Sr-Nd-Hf isotopes of Triassic mafic-felsic dikes in the East Kunlun orogenic belt, northern Tibetan Plateau, to elucidate the nature and evolution of the transcrustal magmatic system. The studied dikes intruding into the granodiorite pluton (ca. 235–233 Ma) comprise coeval ca. 220–218 Ma gabbroic diorite porphyry, diorite porphyry, granodiorite porphyry, and alkali-feldspar granite, resembling composite dike swarms. The macrocrysts in these dikes show various zoning patterns, indicating episodic magma recharge and crystal resorption. The compositional gap between the intermediate-mafic dikes (SiO2 = 52.9–67.8 wt%) and the granitic dikes (SiO2 > 75 wt%), as well as their homogeneous whole-rock Sr-Nd isotopes, with (87Sr/86Sr)i = 0.708387–0.710995 and εNd(t) = −5.83 to −4.34, but variable zircon Lu-Hf isotopes, i.e., εHf(t) = −7.67 to −0.36, demonstrates that magma mixing rather than cogenetic fractional crystallization accounts for their origin. In combination with thermobarometric insights, these results suggest that the mafic and felsic parental magmas originating from an enriched lithospheric mantle and ancient continental crust, respectively, were ultimately emplaced and stagnated at varying crustal depths (~22–30 km and 8–17 km). Subsequently, the felsic magma mush was replenished and rejuvenated by the underplated mafic magma, leading to varying degrees of crystal-melt and/or melt-melt mixing. This mush-facilitated crust-mantle magma mixing is an important mechanism accounting for the compositional diversity of the transcrustal magmatic system.
A sea of change: Tracing parasitic dynamics through the past millennia in the northern Adriatic, Italy
Authors: Fitzgerald Erin , Ryan Delaney , Scarponi Daniele , Huntley John Warren
Published: May 2024

Our study uses data from Holocene core samples and modern death assemblages to understand how human-induced environmental change in the northern Adriatic Sea (Italy) may have affected parasite-host dynamics in the economically important bivalve Chamelea gallina. Thirty-one radiocarbon dates confirm temporal distinctness between the periods before and after the onset of significant human influence and confirm that trematode prevalence has decreased by an order of magnitude over the past ~2 k.y. The median number of parasite-induced pits per bivalve host and parasite aggregation has also decreased significantly, signaling a substantial decrease in the effective population size of digenean trematodes. Gaussian finite mixture modeling of pit size does not support the hypothesis of parasite extinction. Combined, these results indicate the (potentially ongoing) collapse of parasite-host interactions in C. gallina in concert with human influence on the Adriatic and its transition to an “urban sea.”