bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational redesign of TALE proteins for DNA-templated assembly of protein fibers
Authors: de Haas Robbert J. , Langowski Mark D. , Borst Andrew J. , Pillai Visakh V. S. , Hoffmann Gwendolyn E. , Bongers Martin , Cheng Suna , Treichel Catherine , Leaf Elizabeth M. , Wu Mengyu , Lynch Eric M. , Kollman Justin M. , Ruggeri Francesco S. , Walkey Carl , de Vries Renko , King Neil P. 
Published: October 2024

AbstractMany viral proteins self-assemble into capsid structures, often using their genetic material as a template for assembly. To date,de novodesigned capsid-like proteins do not require genetic material as a template for assembly, which can be both an advantage and a disadvantage depending on the use case. Templates are indispensable, for example, in the assembly of linear structures with well-defined lengths. As a first step towards fullyde novodesigned templated assembly, here we redesign proteins from the Transcription activator-like effector (TALE) family of transcriptional regulators to polymerize on double-stranded DNA (dsDNA) templates. Starting from natural TALE protein sequences, we created idealized repeat proteins with sequence-independent DNA binding properties that cooperatively self-assemble to form linear protein-DNA complexes with template-controlled lengths. We used high-resolution atomic force microscopy (AFM) and cryo electron microscopy (cryo-EM) to characterize the three-dimensional structures of the DNA-protein hybrid complexes. In these structures, a protein filament helically wraps around the dsDNA using a binding mode similar to that of natural TALE proteins. As an example application of these materials, we show the system can be used for repetitive peptide antigen display at precisely controlled repeat distances, and that such immunogens elicit robust antigen-specific antibodies in mice.
An all-in-one pipeline for thein vitrodiscovery andin vivotesting ofPlasmodium falciparummalaria transmission blocking drugs
Authors: Brancucci Nicolas M. B. , Gumpp Christin , van Gemert Geert-Jan , Yu Xiao , Passecker Armin , Nardella Flore , Thommen Basil T. , Chambon Marc , Turcatti Gerardo , Halby Ludovic , Blasco Benjamin , Duffey Maëlle , Arimondo Paola B. , Bousema Teun , Scherf Artur , Leroy Didier , Kooij Taco W. A. , Rottmann Matthias , Voss Till S. 
Published: October 2024

ABSTRACTElimination and eradication of malaria will depend on new drugs with potent activity againstPlasmodium falciparummature stage V gametocytes, the only stages able to infect the mosquito vector for onward parasite transmission. The identification of molecules active against these quiescent stages is difficult due to the specific biology of gametocyte maturation and challenges linked to their cultivationin vitro. Furthermore, the antimalarial drug development pipeline lacks a suitable animal model for evaluating the transmission-blocking potential of promising lead compounds and preclinical and clinical drug candidatesin vivo. Here, we established a transmission-blocking drug discovery and development platform based on transgenicP. falciparumparasites engineered to produce large numbers of pure stage V gametocytes expressing a red-shifted firefly luciferase as reporter for cellular viability. This NF54/iGP1_RE9Hulg8line facilitated the development of a highly efficient and robustin vitroscreening assay for the identification of stage V gametocytocidal compounds. Importantly, by infecting humanized NODscidIL2Rγnullmice with pure NF54/iGP1_RE9Hulg8stage V gametocytes, we also established a preclinicalP. falciparum in vivotransmission model. Using whole animal bioluminescence imaging and quantification of gametocyte densities over a period of 14 days, we assessed the gametocyte killing and clearance kineticsin vivoof antimalarial reference drugs as well as five clinical drug candidates and identified markedly different pharmacodynamic response profiles. Furthermore, we successfully integrated this mouse model with mosquito feeding assays and thus firmly established a valuable tool for the systematicin vivoevaluation of gametocytocidal and transmission-blocking drug efficacy.One sentence summaryWe applied robust new assays for gametocytocidal drug discovery andin vivoefficacy testing using a humanized mouse model for malaria transmission
DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria
Authors: Dalia Triana N. , Machouri Mérick , Lacrouts Céline , Fauconnet Yoann , Guerois Raphaël , Andreani Jessica , Radicella J. Pablo , Dalia Ankur B. 
Published: October 2024

ABSTRACTNatural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 years, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the post-synaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. UsingHelicobacter pyloriandVibrio choleraeas model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.SIGNIFICANCE STATEMENTBacteria can acquire novel traits like antibiotic resistance and virulence through horizontal gene transfer by natural transformation. During this process, cells take up free DNA from the environment and integrate it into their genome by homologous recombination. Many of the molecular details underlying this process, however, remain incompletely understood. In this study, we identify a new protein-protein interaction between ComM and DprA, two factors that promote homologous recombination during natural transformation in Gram-negative species. Through a combination of bioinformatics, structural modeling, cell biological assays, and complementary genetic approaches, we demonstrate that this interaction is required for DprA to recruit ComM to the site of homologous recombination.
High Throughput Viral Enumeration of Aquatic Ecosystems via Flow Cytometry
Authors: Bellanger Madeline , Visscher Pieter T , White Richard Allen 
Published: October 2024

AbstractFor the past 25 years, flow cytometry has been a gold standard for the direct measurement of viral-like particles (VLP) in aquatic ecosystems. Flow cytometry allows for higher throughput and costs less than alternative enumeration methods, leading to its broad usage in aquatic viral ecology. A major challenge associated with flow cytometry is the degradation of VLPs over time, making the use of high throughput plates not possible, thus lowering overall throughput. It has also been difficult to maintain a method with low contamination, high signal-to-noise ratios, and observations of real VLPs vs. fake particles. For these reasons, the use of flow cytometry has rapidly declined over the years due to the advent of massively parallel sequencing. Here, we describe a high throughput method in a 96 well plate format that provides a hands-free approach to viral enumeration. Our approach limits fake particles, noise levels, and cross-sample contamination. In a standard run, 60 samples can be measured for VLPs within 2.25 hours, which is ∼1 hour faster than the standard single tube approach and ∼1.5 hours faster than epifluorescence microscopy (EFM). Direct measurement of VLPs still provides a window into the viral-host interactions within aquatic ecosystems, which can be rapidly measured and resolved in a high throughput manner.
Opto2P-FCM: A MEMS based miniature two-photon microscope with two-photon patterned optogenetic stimulation
Authors: Futia Gregory L. , Zohrabi Mo , McCullough Connor , Teel Alec , Simoes de Souza Fabio , Oroke Ryan , Miscles Eduardo J. , Ozbay Baris N. , Kilborn Karl , Bright Victor M. , Restrepo Diego , Gopinath Juliet T. , Gibson Emily A. 
Published: October 2024

AbstractMultiphoton microscopy combined with optogenetic photostimulation is a powerful technique in neuroscience enabling precise control of cellular activity to determine the neural basis of behavior in a live animal. Two-photon patterned photostimulation has taken this further by allowing interrogation at the individual neuron level. However, it remains a challenge to implement imaging of neural activity with spatially patterned two-photon photostimulation in a freely moving animal. We developed a miniature microscope for high resolution two-photon fluorescence imaging with patterned two-photon optogenetic stimulation. The design incorporates a MEMS scanner for two-photon imaging and a second beam path for patterned two-photon excitation in a compact and lightweight design that can be head-attached to a freely moving animal. We demonstrate cell-specific optogenetics and high resolution MEMS based two-photon imaging in a freely moving mouse. The new capabilities of this miniature microscope design can enable cell-specific studies of behavior that can only be done in freely moving animals.
Transmission of SARS-CoV-2 on aircraft: A scoping review
Authors: Vardavas Constantine I. , Nikitara Katerina , Aslanoglou Katerina , Kamekis Apostolos , Ramesh Nithya , Symvoulakis Emmanouil , Phalkey Revati , Leonardi-Bee Jo , Mouchtouri Varvara , Hadjichristodoulou Christos , Baka Agoritsa , Lamb Favelle , Suk Jonathan E. , Robesyn Emmanuel 
Published: October 2024

ABSTRACTIntroductionThe assessment of empirical epidemiological data is needed to assess the transmissibility of SARS-CoV-2 in aircraft settings. This review summarises reported contact- tracing data and evaluates the secondary attack rates (SAR) and factors associated with SARS- CoV-2 transmission in aircraft, to provide insight for future decision making in the context of future respiratory pandemics.MethodsThis scoping literature review assessed studies published between December 2020 to November 2023 in Ovid Medline, Embase and Cochrane Library databases. The inclusion criteria were based on the PCC framework (P-Population, C-Concept, C-Context). The study population was restricted to passengers and crew (population) to assess transmission (concept) in an aircraft setting (context).ResultsThirty-one studies which assess SARS-CoV-2 transmission in 521 domestic and international flights were included in this systematic review. The SAR reported in the studies with an identified index case ranged from 0% to 16%. Significant variation in the reporting across studies was noted. Overall, the studies reported that using face masks or respirators by passengers and crew members during flight seemed to be a possible strategy for mitigating SARS-CoV-2 transmission while sitting within close proximity to index cases (≤2 seats in every direction) was associated with a higher SAR.ConclusionsOur results are consistent with sporadic clusters happening onboard aircraft. Close proximity to COVID-19 cases within the aircraft was associated with a higher SAR. Our findings further underscore the need for a systematic approach to examining and reporting SARS-CoV-2 transmission onboard aircraft. This evidence may assist policymakers and transportation authorities in the development of emergency preparedness measures and travel guidance during the post-pandemic COVID-19 era.
Ecological and social factors lead to variation in parental care between sexes in a burying beetle
Authors: Ma Donghui , Ma Long , Komdeur Jan 
Published: October 2024

AbstractSexual conflict over parental care represents a divergence in the evolutionary interests between males and females, consequently leading to distinct sex roles in parental care and reproductive strategies. However, whether and how various ecological and social environments influence such sex differences remains largely unclear. In the present study, using the burying beetlesNicrophorus vespilloides, we experimentally investigated the impacts of resource availability and inter- and intra-specific competition pressure on individual parental care and reproduction in males and females. We manipulated the resource availability for the breeding pairs by providing them with either large or small mouse carcasses, and constructed the presence of intra- and inter-specific competition, by introducing an additional, small pair of beetles and blowfly maggotsCalliphora, respectively. We expected that males would decrease their parental care, while females would increase theirs, in response to smaller carcass. We also expected that the presence of intra- and inter-specific competition differentially affected the cares of males and females. We found that, compared to males and females breeding on large carcasses, males did not change their care, whereas females increased their care, when breeding on small carcasses. In the presence of another pair of adults, both males and females increased their parental care, whereas in the presence of blowfly maggots they both decreased their parental care. Our results showed that males and females adjust their parental care based on resource availability and competition pressure, with sex-specific differences driven by ecological and social factors. Our study sheds light on the importance of sex-specific parental care in response to various external drivers which contributes to a better understanding of the evolution of sex conflict over parental care.
Control of spatiotemporal activation of organ-specific fibers in the vagus nerve by intermittent interferential current stimulation
Authors: Rossetti Nicolò , Song Weiguo , Schnepel Philipp , Jayaprakash Naveen , Koutsouras Dimitrios A. , Fichman Mark , Wong Jason , Levy Todd , Elgohary Mohamed , Qanud Khaled , Giannotti Alice , Barbe Mary F , Chen Frank Liu , Langereis Geert , Datta-Chaudhuri Timir , Mihajlović Vojkan , Zanos Stavros 
Published: October 2024

AbstractVagus nerve stimulation (VNS) is emerging as potential treatment for several chronic diseases, however, limited control of fiber activation to promote desired effects over side effects restricts clinical translation. Here we describe a new VNS method that relies on intermittent, interferential sinusoidal current stimulation (i2CS) through implanted, multi-contact epineural cuffs. In swine, i2CS elicits specific nerve potentials and end organ responses, distinct from equivalent non-interferential sinusoidal stimulation. Comparing experimental results with anatomical trajectories of nerve fascicles from end organs to the stimulation electrode indicates that i2CS activates organ-specific fascicles rather than the entire nerve. Experimental results and anatomically realistic, physiologically validated biophysical models of the vagus nerve demonstrate that i2CS reduces fiber activation at the focus of interference. Current steering and repetition frequency determine spatiotemporal pattern of vagal fiber activation, allowing tunable and precise control of neural and organ responses. In experiments in a cohort of anesthetized swine, i2CS has improved selectivity for a desired effect, mediated by smaller bronchopulmonary fibers, over a side effect, mediated by larger laryngeal fibers, compared to non-interferential sinusoidal or square pulse VNS.
A construction contract administration (CCA) framework for graduate architects’ professional development
Authors: Tiew Si Yee 
Published: October 2024

PurposeConstruction contract administration should be carried out by a person (normally engineer or architect depending on the type of contract) with expert technical knowledge of the construction process, strong leadership quality, highly developed interpersonal skills and an understanding of contractual, legislative and statutory underpinnings. However, due to a shortage of architects, graduate architects have been assigned to perform a partial role. Architectural firms are disappointed with the quality of the graduates and still note that they have to mentor them to be competent for their jobs. This paper aims to develop a construction contract administration (CCA) framework for graduate architects that aids the smooth running of a construction contract.Design/methodology/approachSeven housing projects in Malaysia have been selected as case studies. Documentation review and semi-structured interviews relevant to selected case studies were conducted to collect data to develop the CCA framework. The draft framework will then be validated through a focus group study.FindingsA total of 5 themes and 11 sub-themes with core tasks were developed in the CCA framework. The themes involved are claims and legal matters management, communication and relationship management, project management, design management and quality assessment and management. Sub-themes are authority matters, building certification, meetings, coordination checklist, letter writing, contract documentation, building material, design brief, building sustainability and workmanship quality standards, contractors’ submission and building details.Originality/valueThe contribution of this study can be utilized for developing further models in the future that would improve the work performance of graduate architects. The framework assists the university by moving forward to the professional practice stage. In addition, it indirectly enhances the potential of graduate architects to perform efficiently and intensifies the bonding between project stakeholders.
Silence in the workplace: what do we know from research?
Authors: Kim Hee Sun , Wang Jia 
Published: October 2024

Purpose
The purpose of this article is to examine the antecedents and consequences of organizational silence and employee silence to determine whether these two concepts should be distinguished rather than used interchangeably in research.

Design/methodology/approach
This study conducted a systematic literature review of 79 studies on organizational silence and 113 on employee silence, leading to three major findings.

Findings
First, this study shows that organizational silence is a collective phenomenon and employee silence occurs at the individual level; therefore, indicating they should be treated as two distinct concepts. Second, both types of silence are influenced by contextual factors (internal and external) and leadership. Third, organizational silence impacts both individual and organizational outcomes, whereas employee silence mainly affects an individual’s psychological health and performance.

Originality/value
This research clarifies the distinction between organizational silence and employee silence, offering guidance for researchers on how to approach these concepts. It also highlights the critical need to address workplace silence and the potential harm it may cause to both organizational and individual well-being if left unaddressed. Furthermore, this research supports organizational leaders and human resource developers in fostering a healthier work culture, improving performance and driving continuous improvement.
Who champions environmental sustainability? A stakeholder’s analysis of public assembly venues
Authors: Ross Walker J. , Murfree Jessica R. , Wang Zhelun 
Published: October 2024

PurposeDespite an abundance of literature regarding the motivations of sport and entertainment managers to adopt environmentally sustainable practices (ESPs) within their venue, there is little offered on which particular stakeholders motivate such action. This study examined the venues which host such events to identify the stakeholders who influence the adoption of ESPs, their specific roles and to highlight salient stakeholders who primarily motivate ESP adoption.Design/methodology/approachGuided by stakeholder theory as a framework for analysis, a qualitative study was employed which consisted of sixteen semi-structured interviews with venue personnel including presidents, general managers, operations directions and recycling coordinators. Participants were asked to discuss their venue’s management structure, stakeholder relations and ESPs.FindingsInternal stakeholders – particularly ownership and operations personnel – were salient stakeholders motivating ESP adoption, but the most unique stakeholder identified was that of a motivated “doer” from no particular role who simply possessed the power, legitimacy and urgency to act on ESPs. Thus, there was no single, identifiable stakeholder role to champion ESPs so much as there was a motivated, normatively legitimate stakeholder who wanted to be that champion.Originality/valueThis research contributes to the growing sport ecology literature and is the first to present the idea of a non-particular, doer stakeholder to champion ESPs within this industry rather than one with a more defined role within organizational structure.
Analysis of erosion and sealing characteristics of V-regulating ball valves for coal chemical industry
Authors: Zhang Weizheng , Huang Wenbin , Lin Hua , Liu Jingwei 
Published: October 2024

Purpose
This study aims to research the erosion wear characteristics and sealing performance of V-regulating ball valve in coal chemical process pipelines, which provides a theoretical reference for improving its antiwear and sealing performance.

Design/methodology/approach
Taking the V-regulating ball valve as the research object, based on the computational fluid dynamics and the theory of erosion wear, the authors studied its erosion characteristics under different medium parameters and analyzed the sealing performance under the heat-fluid–solid coupling working condition.

Findings
The erosion wear mechanism of the valve sealing surface is the simultaneous action of cutting and deformation. When the medium flow velocity, particle mass flow rate and particle size increase, the maximum erosion rate and average erosion rate in the V-regulating valve increase. The inner diameter Mises contact stress of the sealing surface is symmetrically distributed in a “wing shape,” and the contact stress of the outer diameter is distributed in a “butterfly shape.” Due to the superposition of thermal stress and pressure stress in the contact transition zone to produce a significant stress concentration.

Practical implications
The findings will provide a theoretical basis for improving the erosion resistance and sealing performance of V-regulating ball valve in coal chemical industry.

Social implications
V-type regulating ball valve is widely favored by coal chemical enterprises and petrochemical enterprises because of its wide adjustment ratio and good erosion resistance.

Originality/value
The V-regulating ball valve wear mechanism for cutting and deformation simultaneously, and its wear rate is positively correlated with the medium flow rate, particle mass flow rate and particle size. After the valve is opened, there is a significant stress concentration occurs in the contact transition zone due to the superposition of thermal stress and compressive stress. The findings will provide a theoretical basis for improving the erosion resistance and sealing performance of V-regulating ball valve in coal chemical industry.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-06-2024-0205/