bluuebunny/crossref_metadata_2025_split huggingface dataset:
Di-Gluebodies as covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures
Authors: Yi Gangshun , Mamalis Dimitrios , Ye Mingda , Carrique Loic , Fairhead Michael , Li Huanyu , Duerr Katharina L. , Zhang Peijun , Sauer David B. , von Delft Frank , Davis Benjamin G. , Gilbert Robert J. C. 
Published: June 2024

AbstractCryo-EM has become a routine structural biology method, yet elucidation of small proteins (<100 kDa) and increasing throughput remain challenging. Here, we describe covalently-dimerized engineered nanobodies, Di-Gluebodies, as novel and modular imaging scaffolds to address the challenges. They can simultaneously display two copies of the same protein or two distinct proteins, providing sufficient rigidity required by cryo-EM. We validate this method with multiple soluble and membrane targets, demonstrating that this provides a flexible and scalable platform for expanded protein structure determination.
Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation
Authors: Partipilo Gina , Bowman Emily K. , Palmer Emma J. , Gao Yang , Ridley Rodney S. , Alper Hal S. , Keitz Benjamin K. 
Published: June 2024

AbstractElectroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organismS. oneidensisand describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species,C. sakazakiiandV. fessusnot previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
The reduction of nuptial gifts in sclerosomatid Opiliones coincides with increased behavioural sexual conflict
Authors: Brown Tyler A. , Marinko Emily , Burns Mercedes 
Published: June 2024

AbstractNuptial gifts serve to increase donor fitness through a variety of pathways. Some nuptial gifts deliver benefits similar to those of antagonistic male behaviours: functioning to secure additional copulations, increase sperm transfer or storage, or increase paternity share. These commonalities may result in evolutionary transitions between solicitous and coercive strategies, wherein behavioural sexual conflict could function to secure mates in lieu of nuptial gifts. In temperate leiobunine harvesters (Arachnida: Opiliones), nuptial gifts have been repeatedly lost, resulting in two primary mating syndromes: an ancestral, sacculate state in which males endogenously produce high-investment nuptial gifts and females lack pregenital barriers, and a derived, nonsacculate state in which females have pregenital barriers and males produce significantly reduced, low-investment nuptial gifts. In this study, we investigated whether behavioural sexual conflict compensates for reduced nuptial gifts in nonsacculate harvesters by comparing the intensity of pre-, peri-, and postcopulatory mating behaviour between the nonsacculate speciesLeiobunum vittatumandL. euserratipalpeand the sacculate speciesL. aldrichiandL. bracchiolum. We additionally sought to establish an automated behavioural analysis pipeline by developing analogues for metrics traditionally scored manually. Our results revealed significantly different, potentially coercive, behaviour in nonsacculate species, indicating that the loss and reduction of pre- and pericopulatory nuptial gifts may contribute to increased behavioural antagonism. Mating behaviour also differed significantly betweenL. vittatumandL. euserratipalpe, indicating there are multiple suites of potentially antagonistic behaviours. Together, these results suggest that multiple behavioural strategies may be effective substitutes for nuptial gifts in leiobunine Opiliones, although the mechanisms through which male fitness is increased requires further research.HighlightsTemperate Opiliones have repeatedly evolved reduced nuptial gift investmentReduced-gift (nonsacculate) species possess morphology indicative of antagonismWe tested if mating behaviour differed between nonsacculate and sacculate speciesNonsacculates displayed significantly higher behavioural antagonism than sacculatesNonsacculate species differed in their suites of antagonistic behaviours
CRISPR adaptation inStreptococcus thermophiluscan be driven by phage environmental DNA
Authors: Croteau FR , Tran J , Hynes AP 
Published: June 2024

AbstractThe CRISPR-Cas system is a bacterial adaptative immune system which protects against infection by phages: viruses that infect bacteria. To develop immunity, bacteria integrate spacers — fragments of the invading nucleic acids — into their CRISPR array to serve as the basis for sequence-targeted DNA cleavage. However, upon infection, phages quickly take over the metabolism of the bacteria, leaving little time for the bacteria to acquire new spacers, transcribe them and use them to cut the invading DNA. To develop CRISPR immunity, bacteria must be safely exposed to phage DNA. Phage infection releases eDNA which could be involved in the development of CRISPR immunity. UsingS. thermophilusand phages 2972 and 858 as a model for CRISPR immunity, we show that eDNA is crucial to the development of optimal CRISPR immunity, as generation of phage-immune bacterial colonies decrease with eDNA digestion. Furthermore, it is phage eDNA specifically that impacts CRISPR immunity since its addition increases the generation of phage-immune colonies. We also show that the effect of eDNA is phage-specific, sequence specific and can even be traced to a region of the genome covering the early-expressed genes which differ between phages 2972 and 858. However, we also show that eDNA is not used as a source of genetic information for spacer acquisition. This suggests that the effect of eDNA involves a new mechanism of phage resistance. Moreover, the effect of eDNA is highly dependent on environmental conditions as variation in media suppliers are sufficient to interfere with this effect. These results link environmental conditions, specifically eDNA, to the CRISPR-Cas system, providing a better understanding of the context of the emergence of CRISPR immunity and could inform our understanding of the mechanisms through which bacteria detect the presence of phages before infection.
Human cytomegalovirus induces neuronal gene expression for viral maturation
Authors: Kelnhofer-Millevolte Laurel E , Smith Julian R , Nguyen Daniel H , Wilson Lea S , Lewis Hannah C , Arnold Edward A , Brinkley Mia R , Geballe Adam P , Ramachandran Srinivas , Avgousti Daphne C 
Published: June 2024

AbstractViral invasion of the host cell causes some of the most dramatic changes in biology. Human cytomegalovirus (HCMV) extensively remodels host cells, altering nuclear shape and generating a cytoplasmic viral-induced assembly compartment (vIAC). How these striking morphology changes take place in the context of host gene regulation is still emerging. Here, we discovered that histone variant macroH2A1 is essential for producing infectious progeny. Because virion maturation and cellular remodeling are closely linked processes, we investigated structural changes in the host cell upon HCMV infection. We discovered that macroH2A1 is necessary for HCMV-induced reorganization of the host nucleus, cytoskeleton, and endoplasmic reticulum. Furthermore, using RNA-seq we found that while all viral genes were highly expressed in the absence of macroH2A1, many HCMV-induced host genes were not. Remarkably, hundreds of these HCMV-induced macroH2A1-dependent host genes are associated with neuronal synapse formation and vesicle trafficking. Knock-down of these HCMV-induced neuronal genes during infection resulted in malformed vIACs and smaller plaques, establishing their importance to HCMV infection. Together, our findings demonstrate that HCMV manipulates host gene expression by hijacking a dormant neuronal secretory pathway for efficient virion maturation.
Binned top quark spin correlation and polarization observables for the LHC at 13.6 TeV
Authors: Bernreuther Werner , Chen Long , Si Zong-Guo 
Published: June 2024

We consider top-antitop quark (tt¯) production at the Large Hadron Collider (LHC) with subsequent decays into dileptonic final states. We use and investigate a set of leptonic angular correlations and distributions with which all the independent coefficient functions of the top-spin-dependent parts of the tt¯ production spin density matrices can be experimentally probed. We compute these observables for the LHC center-of-mass energy 13.6 TeV within the Standard Model at next-to-leading order in the QCD coupling including the mixed QCD weak corrections. We determine also the tt¯ charge asymmetry where we take in addition also the mixed QCD-QED corrections into account. In addition we analyze and compute possible new physics (NP) effects on these observables within effective field theory in terms of a gauge-invariant effective Lagrangian that contains the operators up to mass dimension six that are relevant for hadronic tt¯ production. First, we compute our observables inclusive in phase space. Then, in order to investigate which region in phase space has, for a specific observable, a high NP sensitivity, we determine our observables also in two-dimensional (Mtt¯,cosθt*) bins, where Mtt¯ denotes the tt¯-invariant mass and θt* is the top quark scattering angle in the tt¯ zero-momentum frame.

Published by the American Physical Society
2024
Closer scrutiny of cosmic ray proton energy losses
Authors: Esmaeili AmirFarzan , Esmaili Arman , Serpico Pasquale Dario 
Published: June 2024

The percent-level precision attained by modern cosmic ray (CR) observations motivates reaching a comparable or better control of theoretical uncertainties. Here we focus on energy-loss processes affecting low-energy CR protons (∼0.1–5  GeV), where the experimental errors are small and collisional effects play a comparatively larger role with respect to collisionless transport ones. We study three aspects of the problem: (i) We quantitatively assess the role of the nuclear elastic cross section, for the first time, providing analytical formulas for the stopping power and inelasticity; (ii) We discuss the error arising from treating both elastic and pion production inelastic interactions as continuous energy loss processes, as opposed to catastrophic ones. The former is the approximation used in virtually all modern numerical calculations; (iii) We consider subleading effects such as relativistic corrections, radiative and medium processes in ionization energy losses. Our analysis reveals that neglecting (i) leads to errors close to 1%, notably around and below 1 GeV, neglecting (ii) leads to errors reaching about 3% within the considered energy range, (iii) contributes to a minor effect, gauged at the level of 0.1%. Consequently, while (iii) can currently be neglected, (ii) warrants consideration, and we also recommend incorporating (i) into computations. We conclude with some perspectives on further steps to be taken towards a high-precision goal of theoretical CR predictions regarding the treatment of energy losses.

Published by the American Physical Society
2024
Phase-space entropy cascade and irreversibility of stochastic heating in nearly collisionless plasma turbulence
Authors: Nastac Michael L. , Ewart Robert J. , Sengupta Wrick , Schekochihin Alexander A. , Barnes Michael , Dorland William D. 
Published: June 2024

We consider a nearly collisionless plasma consisting of a species of “test particles” in one spatial and one velocity dimension, stirred by an externally imposed stochastic electric field—a kinetic analog of the Kraichnan model of passive advection. The mean effect on the particle distribution function is turbulent diffusion in velocity space—known as stochastic heating. Accompanying this heating is the generation of fine-scale structure in the distribution function, which we characterize with the collisionless (Casimir) invariant C2∝∫∫dxdv〈f2〉—a quantity that here plays the role of (negative) entropy of the distribution function. We find that C2 is transferred from large scales to small scales in both position and velocity space via a phase-space cascade enabled by both particle streaming and nonlinear interactions between particles and the stochastic electric field. We compute the steady-state fluxes and spectrum of C2 in Fourier space, with k and s denoting spatial and velocity wave numbers, respectively. In our model, the nonlinearity in the evolution equation for the spectrum turns into a fractional Laplacian operator in k space, leading to anomalous diffusion. Whereas even the linear phase mixing alone would lead to a constant flux of C2 to high s (towards the collisional dissipation range) at every k, the nonlinearity accelerates this cascade by intertwining velocity and position space so that the flux of C2 is to both high k and high s simultaneously. Integrating over velocity (spatial) wave numbers, the k-space (s-space) flux of C2 is constant down to a dissipation length (velocity) scale that tends to zero as the collision frequency does, even though the rate of collisional dissipation remains finite. The resulting spectrum in the inertial range is a self-similar function in the (k,s) plane, with power-law asymptotics at large k and s. Our model is fully analytically solvable, but the asymptotic scalings of the spectrum can also be found via a simple phenomenological theory whose key assumption is that the cascade is governed by a “critical balance” in phase space between the linear and nonlinear timescales. We argue that stochastic heating is made irreversible by this entropy cascade and that, while collisional dissipation accessed via phase mixing occurs only at small spatial scales rather than at every scale as it would in a linear system, the cascade makes phase mixing even more effective overall in the nonlinear regime than in the linear one.

Published by the American Physical Society
2024
Trauma or autism? – understanding how the effects of trauma and disrupted attachment can be mistaken for autism
Authors: Al-Attar Zainab , Worthington Rachel 
Published: June 2024

Purpose
Early bio-psycho-social experiences can dramatically impact all aspects of development. Both autism and traumagenic histories can lead to trans-diagnostic behavioural features that can be confused with one another during diagnostic assessment, unless an in-depth differential diagnostic evaluation is conducted that considers the developmental aetiology and underpinning experiences and triggers to trans-diagnostic behaviours.

Design/methodology/approach
This paper will explore the ways in which biological, cognitive, emotional and social sequelae of early trauma and attachment challenges, can look very similar to a range of neurodevelopmental disorders, including autism. Relevant literature and theory will be considered and synthesised with clinical knowledge of trauma and autism.

Findings
Recommendations are made for how the overlap between features of autism and trauma can be considered during assessments alongside consideration for interventions to enable people to access the most appropriate support for their needs.

Originality/value
Many features of the behaviours of individuals who have experienced early childhood trauma and disrupted or maladaptive attachments, may look similar to the behaviours associated with autism and hence diagnostic assessments of autism need to carefully differentiate traumagenic causes, to either dual diagnose (if both are present) or exclude autism, if it is not present. This has for long been recognised in child and adolescent autism specialist services but is less well developed in adult autism specialist services.
The effectiveness of family-based treatment and pharmacotherapy in an adolescent with anorexia nervosa and intellectual disability: a case report
Authors: Moradi Mehri , Salehian Razieh , Bozorg Bonnie , Bozorg Mina 
Published: June 2024

Purpose
This study aims to report the effectiveness of family based treatment and pharmacotherapy on an adolescent boy with anorexia nervosa and intellectual disability.

Design/methodology/approach
The authors reported the case of a 16-year-old boy with AN and ID and referred him to a family therapist and psychiatrist in Tehran.

Findings
The patient experienced fatigue, weakness, dissatisfaction, suicidal thoughts and self-harm signs over the past one year. He also had behaviors such as abstinence from eating and voluntary vomiting. He was diagnosed with AN and MDD.

Originality/value
The results suggest that these interventions can be effective but should be used with special consideration. Combining family therapy and pharmacotherapy might offer a chance to alleviate anorexia symptoms in people with ID.
Artificial intelligence: a catalyst to organizational learning and development in 21st century
Authors: Olusegun Suleiman , Hinson Robert Ebo , Zekeri Ochidi 
Published: June 2024

Purpose
The purpose of this study is to investigate how artificial intelligence is changing and promoting organizational learning and development in 21st century.

Design/methodology/approach
The paper adopted an exploratory study using the open-ended approach of quantum theory, including 55 depth interviews and one focus group discussion with employees representing top-level management, mid-level management and first-line management having mainly an artificial intelligence and organizational learning/strategies background.

Findings
The finding showed that when AI is strategically placed within an organization, there is opportunity for humans and AI to learn from one another to develop these new capabilities and core competencies that give an organizations added competitive advantage.

Research limitations/implications
Exploring artificial intelligence in a context at one sector (telecommunication sector), the research results may lack general acceptance because of disparities of AI adoption in other sectors. Therefore, researchers are encouraged to test the proposed propositions further in other sectors.

Practical implications
The paper includes implications for artificial intelligence sustainability as a tool for organizational learning and strategy. It is observed that AI has increased the demand for managerial skills such as creativity, innovation, troubleshooting, data mining, emotional intelligence, adaptability and problem-solving. The study showed that organizations will need to have an appropriate level of knowledge and skill in AI to be effective in leveraging it as an integral facet of their organizational strategy.

Originality/value
This study is novel on account of its applicability in AI’s ability to work harmoniously with human employees which can stimulate mutual learning between the two, resulting in a relationship similar to that of a relationship with a teammate or colleague in the workplace which will invariably results into competitive advantage.
“I love and dream of a future where we're all coaches” – an analysis of multiple perspectives on managerial coaching
Authors: Jones Jenni , Lundgren Henriette , Poell Rob 
Published: June 2024

Purpose
The purpose of this paper is to explore multiple perspectives on managerial coaching: why and how managers engage, employees and human resource development (HRD) professionals’ perspectives on the use and how HRD and managers can better support each other with it.

Design/methodology/approach
This study used secondary analysis of empirical data already collected through a transnational study from 20 different medium-size to large organisations in the Netherlands, the UK and the USA. For this study, 58 interviews referring to coaching were analysed from 18 of these organisations, from these 3 different countries and from 3 stakeholder groups: managers, employees and HRD professionals.

Findings
Findings show that managers perform a variety of “on the job” informal coaching roles and that HRD professionals lead the more formal aspects. Managers felt that HRD support was limited and hoped for more. A limited number of employees mentioned coaching, but those that did highlighted the different types of coaching they received in the workplace, referring to managers but with little recognition of HRD’s role. HRD professionals shared how they support managers through both informal and formal coaching approaches, but this was not fully acknowledged by neither managers nor employees.

Practical implications
The findings of this study contribute to the literature on devolved HRD practices, highlighting that managers are engaging more in managerial coaching with their teams, that potentially employees are not that aware of this and that managers and employees are not fully aware of HRD’s contribution to supporting coaching and feel they could do more. As a result, this study suggests that HRD professionals have a clear role to play in creating and leading the supportive organisational culture for coaching to thrive, not only in setting the “coaching scene” for managers to work within but also through offering support for long-term capacity building for all employees.

Originality/value
Through the diffusion of key HRD activities into managerial roles, and while internal coaching is gaining more momentum, managers now step up when coaching their teams. This study extends the limited prior research on managers’ and others’ (employees and HRD) beliefs about the coaching role in the workplace. This study highlights the changing role of the manager, the need for HRD to offer more support for the joint role that managers are taking (manager and coach) and the partnership potential for HRD professionals to include all stakeholders including employees.