bluuebunny/crossref_metadata_2025_split huggingface dataset:
A packaging signal-binding protein regulates the assembly checkpoint of integrative filamentous phages
Authors: Yeh Ting-Yu , Feehley Michael C. , Feehley Patrick J. , Ooi Vivian Y. , Hung Yi-Yung , Wang Shao-Cheng , Contreras Gregory P. 
Published: March 2024

ABSTRACTMany integrative filamentous phages not only lack Ff coliphage homologues essential for assembly but also have distinct packaging signals (PS). Their encapsidation remains completely uncharacterized to date. Here we report the first evidence of a PS-dependent checkpoint for integrative filamentous phage assembly. Suppressor screening of PS-deficient phages identified an unknown protein, PSB15 (PS-binding15kDa), crucial for encapsidation. The WAGFXF motif of the PSB15 N-terminus directly binds to PS DNA with conformational change, while suppressor mutations relieve DNA binding specificity constraints to rescue assembly arrest. PSB15 interacts with phospholipid cardiolipin via its basic helix and C-terminus, and recruits PS DNA to the inner membrane (IM). The PSB15-PS complex is released from the IM by interaction between its hydrophobic linker and thioredoxin (Trx), a host protein that is required for Ff assembly but whose mechanisms are still unclear. Live cell imaging shows that thioredoxin and DNA binding regulate the dwelling time of PSB15 at cell poles, suggesting that they both facilitate the dissociation of PSB15 from the IM. Loss of PSB15 or its PS-binding and IM-targeting/dissociation activity compromised virus egress, indicating that the PS/PSB15/Trx complex establishes a regulatory phage assembly checkpoint critical for integrative phage infection and life cycles.
Energy landscapes of peptide-MHC binding
Authors: Collesano Laura , Łuksza Marta , Lässig Michael 
Published: March 2024

AbstractMolecules of the Major Histocompatibility Complex (MHC) present short protein fragments peptides on the cell surface, an important step in T cell immune recognition. MHC-I molecules process peptides from intracellular proteins; MHC-II molecules act in antigen-presenting cells and present peptides derived from extracellular proteins. Here we show that the sequence-dependent energy landscapes of MHC-peptide binding encode class-specific nonlinearities (epistasis). MHC-I has a smooth landscape with global epistasis; the binding energy is a simple deformation of an underlying linear trait. This form of epistasis enhances the discrimination between strong-binding peptides. In contrast, MHC-II has a rugged landscape with idiosyncratic epistasis: binding depends on detailed amino acid combinations at multiple positions of the peptide sequence. The form of epistasis affects the learning of energy landscapes from training data. For MHC-I, a low-complexity problem, we derive a simple matrix model of binding energies that outperforms current models trained by machine learning. For MHC-II, higher complexity prevents learning by simple regression methods. Epistasis also affects the energy and fitness effects of mutations in antigen-derived peptides (epitopes). In MHC-I, large-effect mutations occur predominantly in anchor positions of strong-binding epitopes. In MHC-II, large effects depend on the background epitope sequence but are broadly distributed over the epitope, generating a bigger target for escape mutations from T cell immunity than for MHC-I.Author SummaryT cell immunity involves the binding of short peptides to the intracellular MHC recognition machinery. Understanding how the binding energy depends on the peptide sequence is key to computationally predict immune recognition and immune escape evolution, for example, of pathogens and cancer cells. We find nonlinear energy landscapes that depend on the recognition pathway: smooth and easy to learn for MHC class I, rugged and difficult to learn for class II. Together, this work establishes links between biophysical origin, nonlinear structure, learnability from data, and biological implications for protein interaction landscapes.
Adaptation ofPseudomonas aeruginosato repeated invasion into a commensal competitor
Authors: Wheatley Rachel M. , Shaw Liam P. , Shah Sarah , Lindon Selina , MacLean R. Craig 
Published: March 2024

AbstractThe host-associated microbiome is an important barrier to bacterial pathogen colonization and can mediate protection through a variety of mechanisms. We wanted to investigate the potential consequences of selection imposed by commensal bacterial competitors on an invading bacterial pathogen. To do this, we tested the ability of the opportunistic pathogenPseudomonas aeruginosato invade pre-established communities of an abundant commensal bacterium in the human microbiome,Staphylococcus epidermidis. We passaged ten independent lines ofP. aeruginosathrough daily invasion into a pre-establishedS. epidermidispopulation (coculture evolved lines), alongside daily passage through monoculture conditions (monoculture evolved lines). The monoculture evolved lines showed strong parallel evolution in the Wsp (Wrinkly spreader phenotype) signal transducing system involved in biofilm formation, and significantly elevated biofilm formation. On the other hand, adaptation toS. epidermidisoccurred via mutations in a diverse set of genes, and the coculture evolved lines showed much weaker evidence for parallel evolution, suggesting that the selective pressure imposed by competition withS. epidermidisis more complex than the pressure imposed by culture conditions. Interestingly, the elevated biofilm formation phenotype seen in the monoculture evolved lines was not observed in the lines evolved in the presence ofS. epidermidis, raising the question of whether enhanced biofilm formation did not evolve withS. epidermidispresent because it was not beneficial, or becauseS. epidermidismay be able to restrict this evolutionary path by inhibiting biofilm formation.
Concepts and methods for predicting viral evolution
Authors: Meijers Matthijs , Ruchnewitz Denis , Eberhardt Jan , Karmakar Malancha , Łuksza Marta , Lässig Michael 
Published: March 2024

SummaryThe seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the websiteprevir.app.
Adipose tissue microvascular endothelial cells form a tight vascular barrier that selectively transcytoses fatty acid tracers
Authors: Schipper Ruby , Ioannidou Anna , Maestri Alice , Baganha Fabiana , Werngren Olivera , Olofsson Peder S. , Malin Stephen G. , Fisher Rachel M. , Hagberg Carolina E. 
Published: March 2024

AbstractIn organs with continuous, non-leaky capillaries like white adipose tissue and the heart, microvascular endothelial cells (ECs) serve as a vital barrier, facilitating nutrient delivery to underlying tissues. While capillary heterogeneity between organs is well established, how these vascular layers have adapted their key functions – such as fatty acid transport – to their respective organs remains unclear, largely due to the lack of organotypic endothelial model systems. Here we demonstrate that the vascular barrier in white adipose tissue, a crucial organ for whole-body fatty acid handling, exhibits comparable impermeability to that of heart and muscle. To investigate if the adipose endothelium possesses tissue-specific functions for facilitating fatty acid transport, we developed anin vitrodual tracing-system that allows simultaneous monitoring of barrier integrity and fatty acid transport dynamics by modifying the classic transwell culture. Using this system, we can show human adipose-derived primary ECs selectively transport fluorescent fatty acid tracers while excluding other tracers like dextrans, a phenomenon not observed in other cultured human ECs. Additionally, our findings reveal EC-type specific responses to various transcytosis inhibitors. Our results underscore the unique characteristics of the adipose endothelium and enhances our understanding of how microvascular permeability and transport dynamics have adapted to their specific organ physiology.
A comparative analysis of COVID-19 pandemic effects on students’ academic performance in higher education sector
Authors: Magatef Sima , Abuhussein Tala , Ashour Laila , Rehman Shafique Ur , Al-Okaily Manaf 
Published: March 2024

Purpose
This study aims to focus on exploring the impact of the COVID-19 pandemic on the students’ academic performance in Jordanian higher education during the outbreak of the pandemic, evaluating the e-learning education and evaluating online education in practical lessons during the pandemic according to the university type, educational level, academic year and different specializations or faculty.

Design/methodology/approach
This study provides quantitative and qualitative analysis on the students’ e-learning performance during the pandemic. It presents the analysis of online learning preference of 424 questionnaires and 85 structured interviews with the university’s students and examines whether there is significant impact of the COVID-19 pandemic on their academic performance.

Findings
The findings of this study present evidence of students’ improvement in their academic performance and lend credence to the notion that organizational characteristics may play a role in the adaptation of emergency remote teaching. This was evident that more scientific-based faculties (engineering, pharmaceutical and medicine) faced more challenges during the pandemic, and it negatively influenced students’ performance. This was justifiable to the need for a more practical one-to-one interaction and integration.

Originality/value
The findings of this research present evidence of students’ improvement in their academic performance and lend credence to the notion that organizational characteristics may play a role in the adaptation of emergency remote teaching. This was evident that more scientific-based faculties (engineering, pharmaceutical and medicine) faced more challenges during the pandemic and it negatively influenced students’ performance. This was justifiable to the need for a more practical one-to-one interaction and integration.
Investigating links between teacher leadership, collective efficacy and teacher commitment in Egyptian schools: a mediated-effects analysis
Authors: Hammad Waheed , Polatcan Mahmut , Morad Hosam 
Published: March 2024

PurposeResearch investigating the impact of school leadership on teachers’ emotions and practices has mostly focused on the leadership behaviors of school principals, thus ignoring the potential leadership qualities of other school members, especially teachers. The current study aimed to bridge this gap by providing further insight into the link between teacher leadership and teacher outcomes in Egyptian schools. Specifically, the study examined the mediating role of collective teacher efficacy in the relationship between teacher leadership and teacher commitment.Design/methodology/approachThe study employed structural equation modeling and bootstrapping to analyze survey data collected from 497 teachers in primary and middle schools in Damietta city, Egypt.FindingsThe results supported our proposition that teachers’ leadership practices have more indirect than direct effects on teacher commitment through collective teacher efficacy. That is, teacher leadership practices positively affect teachers’ efficacy beliefs, which, in turn, increase their sense of commitment to school.Originality/valueThe study adds a new aspect to the literature by investigating the potential role of teacher leadership in promoting positive teacher attitudes that can have a positive impact on student learning. This is significant given the growing emphasis that educational systems place on enhancing school effectiveness. Specifically, understanding the factors that contribute to teacher commitment can inform strategies for retaining effective teachers and improving the overall quality of the teaching workforce. Additionally, since most of the empirical research on teacher leadership has been produced in Western contexts, it is important to enrich the field with studies conducted in other societies, especially in the Arab region.
Development and validation of teachers’ e-readiness scale: a study on higher education institutions in India
Authors: Kohli Jasneet Kaur , Raj Rahul , Rawat Navneet , Gupta Ashulekha 
Published: March 2024

PurposeDue to the growing complexity involved in leveraging the endless possibilities of ICT on all levels, the technical competence of faculties of higher education institutions (HEI) and effective methods for fostering e-readiness has become questionable.Design/methodology/approachThis research has developed and validated an empirically supported e-readiness scale, which can be used by HEIs to assess faculty members’ preparedness toward online teaching. The measurement model and the structural model were developed as the results of exploratory factor analysis and confirmatory factor analysis (n = 245). The previously identified components and their indicators were validated using the structural models and the final scale was developed with five dimensions (“online technological readiness, pedagogical readiness, institutional readiness, learning and delivery readiness and content readiness”).FindingsThe faculties’ e-readiness assessment tool, as a useful tool, could aid institutions in identifying problems that affect the implementation of e-learning or digitalization in the institutions and developing strategies in response.Research limitations/implicationsLike any research this research also has some limitations and can be considered as future research probability like the responses for this research were collected from HEI in India; however, a cross-cultural study can be conducted to understand the parameters across the globe. Although the psychometric qualities of the e-readiness scale are acceptable, additional research in various higher educational environments, both nationally and internationally, is required to further establish the scale’s relevance, validation and generalizability.Originality/valueAlthough many scales have been developed to assess the readiness level in the education sector, a scale, that holistically measures, the readiness level of faculties from an overall perspective was required. This scale can be used to recognize the e-readiness level of teachers in HEIs. This scale can also help the institutions assess the readiness level of their faculty members and address any improvements required in their teaching and learning pedagogy, further acknowledging training needs.
Spillover effects of microcredit on the GDP of surrounding cantons in Ecuador
Authors: Ordóñez Vizcaíno Carlos Fernando , Téllez Valle Cecilia , Giráldez Puig Pilar 
Published: March 2024

PurposeThe aim of this paper is to analyse the spillover effects of microcredit on the economy of Ecuador, with a particular focus on its potential as a poverty alleviation mechanism.Design/methodology/approachTo address our research questions, we take into account the distance between cantons (Ecuador’s own administrative distribution) by adopting a spatial autoregressive (SAR) model. To this end, a database will be constructed with macroeconomic information about the country, broken down by canton (administrative division of Ecuador), and in a 2019 cross section, with a total of 1,331 microcredit operations in all 221 of Ecuador’s cantons.FindingsWe find a positive effect of microcredit on these neighbouring regions in terms of wealth generation.Research limitations/implicationsWe acknowledge that this study is limited to Ecuadorian cantons. Nonetheless, it is crucial to emphasize that focussing on an under-represented developing country like Ecuador adds significant value to the research.Practical implicationsFacilitating access to microcredit is one of the main solutions to address the goals proposed in the sustainable development goals (SDGs).Social implicationsMicrocredit activity contributes to the creation of value and wealth in Ecuador, exerting a spillover effect in neighbouring areas that can generate positive multiplier effects and alleviate poverty. For all of the above reasons, our proposal for the country is to support and promote microcredit as one of the main solutions to address the goals proposed in the SDGs.Originality/valueThe novelty of this study lies in the use of spatial econometrics to observe the indirect effects of microcredit on the regions bordering the canton in which it was issued, thus examining the spatial effects of microcredit on wealth distribution.
A proposed digital transformation model for implementation by digital leaders
Authors: Razmak Jamil , Farhan Wejdan 
Published: March 2024

PurposeThe purpose of this study was threefold: to trace the extent to which digital transformation strategies are being implemented in organizations; to statistically measure, validate, predict and examine how digital leaders perceive a synthesized digital transformation model (DTM); and to explore whether leaders with different demographic characteristics perceive the DTM similarly.Design/methodology/approachThe study authors surveyed 778 leaders/managers from the United Arab Emirates (UAE) to assess the synthetized DTM consisting of four dimensions and nine perception constructs that represent how leaders manage employees in a digital environment. The survey questions were adapted from the 2014 Westerman leading digital book published in Harvard business press.FindingsThe general findings revealed that UAE organizations that were already in the digital transformation stage before COVID-19 reacted and responded extremely quickly to speed up the implementation of their respective digital transformation strategies. We concluded that our proposed and synthetized DTM is valid and predictable, and can be adapted to trace the stages of digital transformation by leaders. A positive relationship was found between the DTM’s four dimensions and their related constructs as perceived by the leaders, regardless of differences in their demographic characteristics.Originality/valueThe synthesized digital transformation model is unique in that the authors believe there is no other research that purports to synthesize, validate and correlate using the digital transformation campus dimensions and its related constructs, reflecting leaders' perceptions toward adopting this campus. As well, this is the first UAE study to explore and compare the perspectives of leaders on their digital practices after COVID-19 in a country that has an established IT infrastructure.
Occupations and occupational therapy practice with Chinese older adults living with life‐limiting illnesses in Singapore: A focus group study
Authors: Lim Geck Hoon , Yong Celine , Breen Lauren J. , Keesing Sharon , Buchanan Angus 
Published: March 2024

AbstractIntroductionWhile Singapore is rapidly ageing and the need for palliative care services is projected to rise, there has been limited exploration of the occupations of Chinese older adults with life‐limiting conditions. This study is the third in a series of three studies aimed to address this issue. This study also sought to discuss future directions for occupational therapy practice with Chinese older adults living with life‐limiting illnesses in Singapore.MethodThe study adopted a qualitative exploratory design using focus groups. Participants were recruited using convenience and snowball sampling. Inclusion criteria were occupational therapists who had attained full registration status with the Allied Health Professionals Council in Singapore, had two or more years of practice as an occupational therapist, and had a current or recent palliative care caseload.FindingsThree focus groups with 16 participants were conducted, and three themes were constructed from the data through reflexive thematic analysis. Reflections on culture and occupations is about the impact of a collectivist culture on occupations, such as tensions new caregivers experience between keeping clients safe and respecting clients' choices. It also highlights that there will always be individual differences within any cultural group. Challenges of occupational therapy practice in palliative care describe the need for therapists to be comfortable with rest and ethical tensions participants faced with billing for sessions that mainly involved time spent conversing with clients and when clients and caregivers' goals differed. Finally, Moving forward is about the importance of having mentors and the learning needs of occupational therapists in palliative care.ConclusionOccupational therapists experienced in providing services to palliative care clients in Singapore emphasised the collectivist nature of Singaporean Chinese families and contributed more information to its possible impact on occupations and occupational therapy practice and made suggestions for future practice.
Expanding the special education professional toolbox: A case study of a digitalised special education practice in Sweden
Authors: Holmgren Martin 
Published: March 2024

AbstractTwo educational trends that have had major impacts on school policies of the last few decades are inclusive education and digitalisation. To that end, the purpose of this study is to examine how inclusive education and the digitalisation of education are related, understood, and represented in one case of Swedish special education practice. Using activity theory as a theoretical framework, the results of this study suggest that the meaning of inclusive education has shifted, and that digitalisation has entailed both congruencies and contradictions in special education activities aiming for inclusive education. Although digitalisation was described as providing alternatives for inclusive school practices, new expectations and work assignments sometimes exceeded the special educators' professional knowledge.