bluuebunny/crossref_metadata_2025_split huggingface dataset:
mapquik: Efficient low-divergence mapping of long reads in minimizer space
Authors: Ekim Barış , Sahlin Kristoffer , Medvedev Paul , Berger Bonnie , Chikhi Rayan 
Published: December 2022

AbstractDNA sequencing data continues to progress towards longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (PacBio HiFi) to a reference genome, which poses challenges in terms of accuracy and computational resources when using cutting-edge read mapping approaches that are designed for all types of alignments. A natural idea would be to optimize efficiency with longer seeds to reduce the probability of extraneous matches; however, contiguous exact seeds quickly reach a sensitivity limit. We introducemapquik, a novel strategy that creates accurate longer seeds by anchoring alignments through matches ofkconsecutively-sampled minimizers (k-min-mers) and only indexingk-min-mers that occur once in the reference genome, thereby unlocking ultra-fast mapping while retaining high sensitivity. We demonstrate thatmapquiksignificantly accelerates the seeding and chaining steps — fundamental bottlenecks to read mapping — for both the human and maize genomes with>96% sensitivity and near-perfect specificity. On the human genome,mapquikachieves a 30× speed-up over the state-of-the-art toolminimap2, and on the maize genome, a 350× speed-up overminimap2, makingmapquikthe fastest mapper to date. These accelerations are enabled not only by minimizer-space seeding but also a novel heuristic 𝒪(n) pseudo-chaining algorithm, which improves over the long-standing 𝒪(nlogn) bound. Minimizer-space computation builds the foundation for achieving real-time analysis of long-read sequencing data.
Peptide collision cross sections of 22 post-translational modifications
Authors: Will Andreas , Oliinyk Denys , Meier Florian 
Published: December 2022

AbstractRecent advances have rekindled the interest in ion mobility spectrometry as an additional dimension of separation in mass spectrometry (MS)-based proteomics. It separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ∼4700 pairs of matching modified and unmodified peptide ions by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.3%. On a global level, we observed a redistribution in them/zvs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between – 1.1% (lysine formylation) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM depending on the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
RanGTP regulates the augmin complex
Authors: Kraus Jodi , Travis Sophie M , King Matthew R , Petry Sabine 
Published: December 2022

SUMMARYSpindles are composed of microtubules that must nucleate at the right place and time during mitosis. Spindle microtubule nucleation is regulated by the GTPase Ran, which, through importin-αβ, releases a gradient of spindle assembly factors (SAFs) centered at chromosomes. Branching MT nucleation generates most spindle MTs and requires the augmin complex. InXenopus laevis, Ran can control branching through the SAF TPX2, TPX2 is non-essential in other organisms. Thus, how Ran regulates branching MT nucleation in the absence of TPX2 is unknown. Here, we use in vitro pulldowns and TIRF microscopy to show that augmin is itself a SAF. Augmin directly interacts with both importins through two nuclear localization sequences on the Haus8 subunit, which overlap the MT binding site. Moreover, Ran controls localization of augmin to MTs in bothXenopusegg extract and in vitro. By uncovering that RanGTP directly regulates augmin, we demonstrate how Ran controls branching MT nucleation and, thereby, spindle assembly and cell division.
Integrating human iPSC-derived macrophage progenitors into retinal organoids to generate a mature retinal microglial niche
Authors: Usui-Ouchi Ayumi , Giles Sarah , Ouchi Yasuo , Mills Elizabeth A , Friedlander Martin , Eade Kevin T 
Published: December 2022

AbstractIn the retina, microglia are resident immune cells that are essential for retinal development and function. Retinal microglia play a central role in mediating pathological degeneration in diseases such as glaucoma, retinitis pigmentosa, age-related neurodegeneration, ischemic retinopathy and diabetic retinopathy. Current models of mature human retinal organoids (ROs) derived from iPS cell (hiPSC) do not contain resident microglia integrated into retinal layers. Increasing cellular diversity in ROs by including resident microglia would more accurately represent the native retina and better model diseases in which microglia play a key role. In this study, we develop a new 3Din vitrotissue model of microglia-containing retinal organoids by co-culturing ROs and hiPSC-derived macrophage precursor cells (MPCs). We optimized the parameters for successful integration of MPCs into retinal organoids. We then reproducibly integrate MPCs into ROs where they develop into mature microglia (iMG) as seen by 1) migration to the appropriate anatomical locations; 2) development of a mature resting morphology; and 3) expression of mature microglial markers. We show that while in the ROs, MPCs migrate to the equivalent of the outer plexiform layer where retinal microglia cells reside in healthy retinal tissue. While there, they develop a mature morphology characterized by small cell bodies and long branching processes which is only observedin vivo. During this maturation process these microglia cycle through an activated phase followed by a stable mature phase characterized by cell-type specific microglia markers Tmem119 and P2ry12. This co-culture system may be useful for understanding the pathogenesis of retinal diseases involving retinal microglia and for drug discovery.
Translating Membrane Geometry into Protein Function: Multifaceted Membrane Interactions of Human Atg3 Promote LC3-Phosphatidylethanolamine Conjugation during Autophagy
Authors: Ye Yansheng , Tyndall Erin R. , Bui Van , Bewley Maria C. , Wang Guifang , Hong Xupeng , Shen Yang , Flanagan John M. , Wang Hong-Gang , Tian Fang 
Published: December 2022

AbstractAutophagosome formation is the hallmark of macroautophagy (herein referred to as autophagy) and requires the covalent conjugation of LC3 proteins (or Atg8 in yeast) to the amino headgroup of PE (phosphatidylethanolamine) lipids. Atg3 is an enzyme that catalyzes the final step of this reaction by transferring LC3 from an LC3-Atg3 intermediate to PEs in targeted membranes. Here, we determine the solution structure of human Atg3 (hAtg3) and demonstrate that the catalytically important regions of hAtg3 are conformationally dynamic. Furthermore, we reveal that these regions and hAtg3’s N-terminal membrane curvature-sensing amphipathic helix concurrently interact with the membrane. These structural studies indicate that hAtg3 exploits a multifaceted membrane-association mechanism to position its catalytic center at the membrane surface and to bring the reaction substrates of LC3 and PE lipids to proximity for effective LC3-PE conjugation. In addition, our studies demonstrate that the interaction of the His266 residue with the membrane is primarily responsible for hAtg3’s pH-dependent activity. Our investigations advance an emerging concept that the interactions of Atg3 with the highly curved membrane rims of the phagophore spatially regulate autophagosome biogenesis.
Reversibility of resistance in a fluctuation test experiment modifies the tail of the Luria-Delbrück distribution
Authors: Bokes Pavol , Hlubinová Anna , Singh Abhyudai 
Published: December 2022

AbstractWe consider a fluctuation test experiment in which cell colonies are grown from a single cell until they reach a given population size, and then they are exposed to treatment. While they grow, the cells may, with a low probability, acquire resistance to treatment and pass it on to their offspring. Unlike the classical Luria–Delbrück fluctuation test and motivated by recent work on drug-resistance acquisition in cancer/microbial cells, we allow for the resistant cell state to switch back to a drug-sensitive state. This modification does not affect the central part of the (Luria–Delbrück) distribution of the number of resistant survivors: the previously developed approximation by the Landau probability density function applies. However, the right tail of the modified distribution deviates from the power law decay of the Landau distribution. We demonstrate that the correction factor is equal to the Landau cumulative distribution function.
Identifying the cavitation erosion stages of AA5083 by electrochemical noise analyses
Authors: Zhu Yesen , Liu Zhe , Qin Zhenbo , Hou Mengyang , Hu Taoyong , Yuan Quan 
Published: December 2022

Purpose
The purpose of this paper is to study the cavitation erosion stages of AA5083 by electrochemical noise (EN).

Design/methodology/approach
EN technology including noise resistance and fast Fourier transform were used to characterize the electrochemical process during the cavitation erosion process.

Findings
AA5083 suffers from uniform corrosion during the cavitation erosion process. The whole cavitation erosion process can be divided into three stages: incubation stage, acceleration stage and steady-state stage. EN signals showed obvious differences in different stages of cavitation erosion.

Originality/value
EN technique is a suitable method that can be used to study cavitation erosion mechanism and identify cavitation erosion stages.
An empirical model for assessing consumer behaviour towards hotel sustainable practices: a study from emerging economy
Authors: Sharma Shikha , Mahajan Anupama , Virmani Naveen , Kukreja Gagan , Mehta Kamakshi 
Published: December 2022

Purpose
Adopting sustainable practices is highly required in hotels. This study aims to assess consumer behaviour towards adopting sustainable practices in hotels. In addition, mediating role of consumer attitude (CAtt) is assessed between consumer awareness (CA) and willingness to pay.

Design/methodology/approach
An empirical study was carried out to analyse the integrative research model of CA, CAtt and willingness to pay premium price (WTPPP) for sustainable practices adoption in five-star hotels in emerging economies. Responses from 447 respondents were collected and analysed. Structural equation modelling was performed using SPSS 21.0.

Findings
The research outcomes indicate the partial mediation of CAtt between CA and WTPPP. Furthermore, consumer satisfaction has been found to have a moderating effect on the relationship between CAtt and willingness to pay a premium price.

Originality/value
The research results add to the literature by analysing prominent factors affecting willingness to pay premium for adopting sustainable practices in five-star hotels.
A dynamic capabilities approach of Industry 4.0: the experiences of managers operating in two emerging economies
Authors: Vu Oanh Thi Kim , Duarte Alonso Abel , Buitrago Solis M. Alejandra , Goyzueta Samuel , Nguyen Trung , McClelland Robert , Tran Thanh Duc , Nguyen Ngan , Huynh Hoa Thi Ngoc , Atay Erhan 
Published: December 2022

Purpose
The purpose of this study is to examine the implementation of Industry 4.0 (I4.0) through the lens of the dynamic capabilities framework. Contrary to most existing research, this study chooses a cross-national viewpoint, exploring companies operating in two emerging economies.

Design/methodology/approach
Semi-structured interviews were conducted with 80 company managers operating in eight industries in Vietnam and Bolivia. The chosen inductive analysis was supported by qualitative content analysis and data structure.

Findings
The analysis reveals 13 conceptual dimensions. For instance, sensing opportunities underlines tangible and intangible “direct prospects”, such as enhanced accuracy, speed and cost effectiveness, whereas “operational management pressures” (sensing threats) identify the dilemma of changing individuals’ mindset, recruitment and addressing financial needs. While there is an overall agreement in key dimensions, differences between managers from both countries also arise, including staff’s adaptation and constant upskilling.

Originality/value
Empirically, this study responds to calls for cross-national studies investigating I4.0 initiatives. In doing so, the data gathered from company managers engaged in business in emerging economies afford new perspectives, with practitioner value. Theoretically, the numerous dimensions emerging from the data analysis provide useful conceptual insights to understand managerial aspects in considering and adapting to I4.0 expectations and requirements. These insights are reinforced by the development of a conceptual model that illuminates the initiatives, efforts and challenges of embracing this phenomenon.
Examining the mediating role of team growth mindset on the relationship of individual mindsets and shared leadership
Authors: Han Soo Jeoung , Xie Lei , Beyerlein Michael , Boehm Rodney 
Published: December 2022

Purpose
As a cornerstone of team performance, learning depends on each member’s mindset. Drawing on implicit theories of intelligence, the purpose of this study is to investigate the relationships among individual members’ mindsets and shared leadership (SL) behaviors in design teams and the mediation role of team growth mindset (TGM) on that relationship.

Design/methodology/approach
The authors analyzed survey results based on individuals who participated in an international design competition. To test the hypothesized model, the data was analyzed by using SEM using Mplus 7.

Findings
The results indicated that an individual growth mindset (IGM; but not an individual-fixed mindset) has significant and positive direct effects on a team growth mindset and SL behaviors. In addition, a TGM mediates the relationship between an IGM and SL.

Originality/value
The research discusses several theoretical and practical implications for human resource development professionals and scholars to improve understanding of a TGM and its influence on individual mindsets and SL behaviors.
Governance in Moroccan public hospitals: critical analysis and perspectives for action
Authors: Mourajid Yassmine , Ghafili Asmaa , Chahboune Mohamed , Hilali Abderraouf , Fihri Fassi Chaima 
Published: December 2022

PurposeThe purpose of this paper is to analyse the framework of hospital governance in order to understanding the persistence of dysfunctions that have caused the deterioration of the image and quality of Moroccan public hospital services.Design/methodology/approachThe analysis of the hospital governance model has used a conceptual framework examining four dimensions: institutional, financial, accountability and decision-making dimensions. This framework operationalization was highlighted through a documentary review of the main regulatory and legal texts as well as multiple case studies, using semi-structured interviews with the key stakeholders, considering their expertise and implication in the governance process.FindingsThe study was able to highlight that the governance structure of Moroccan public hospitals has been subject to numerous legislative provisions and modern management instruments. However, the limited autonomy, the resources shortage, dilapidated equipment, the chronic budget deficit, staff demotivation, the lack of accountability mechanisms have led to the deterioration of the quality of care and, hence, to patient's dissatisfaction.Practical implicationsThe analysis formed the basis for a series of recommendations. These were mainly aimed at rethinking the current governance model by setting up an institutional policy to improve the current governance structures and monitoring mechanisms of hospitals, as well as revising the instruments for planning and evaluating the provision of care and services according to the real needs of the population, taking into account the financial limits.Social implicationsThe hospital governance framework is proving to be a powerful tool for identifying the problems contributing to sub-optimal hospital performance, and calls for policy interventions to improve the organisation organization and delivery of hospital services with greater patient involvement.Originality/valueThis study was the first to analyse the Moroccan hospital governance model, using a comprehensive and structured evaluation methodology designed for public hospitals and supported by extensive data collection which made it possible to offer a broad and in-depth view of the actual functioning of these institutions.
Young people's identities in digital worlds
Authors: Hällgren Camilla , Björk Åsa 
Published: December 2022

PurposeThis conceptual paper takes identity, digital technology, young people and education as a combined starting point and suggests how to research young people’s identity practices in and out of school. Today’s young people form their identities in a world that is increasingly imbued by digital technologies. What is evident too is that these technologies and the use of them are not restricted to one single context. Rather, digital technologies mediate multiple contexts simultaneously – to an extent where they collapse. This means that school and leisure time, public and private, digital and analog, virtual and material, time and place, social contexts and audiences, through digital technology, merge in various ways in young people’s identity practices and everyday life.Design/methodology/approachLittle is known about what identity practices in collapsing contexts means to young people in their lives and how educators and others can support them. Most studies to date investigate digital technology use as a discrete phenomenon and few studies concern young people’s identity practices in contexts, as they occur. In an increasingly digital world, where dependency on digital technologies continues this forms an urgent knowledge gap to bridge. In particular to guide educators, and others, who support young people as they live and learn through interconnected spaces in and out of school. The conceptual approach of this paper is of importance to better understand how to bridge this gap.FindingsThis paper suggests a research approach that extends previous research at the intersection of identity, young people, digital technology by outlining extended ways for thinking about identity in a digital world that can be useful for investigating identity as an existential practice, extending beyond identity representations, in conditions mediated by contemporary digital technologies and in collapsing contexts. What is also included are methodological considerations about researching young people, identity and technology as dynamic research objects, rendering a holistic approach.Research limitations/implicationsIt is a conceptual paper that addresses identity, digital technology, young people and education as a combined starting point to outline further research.Originality/valueThe Guided Tour Technique and Social Media Research is suggested as possible methodologies for holistic and ethically sensitive, empirical research on identity, digital technology, young people and education.
Methods of classifying Tunisian investors into homogeneous groups
Authors: Chenini Hajer , Jarboui Anis 
Published: December 2022

PurposeFinancial theory is based on the assumption of rationality of individuals. Defenders of behavioral finance recommend that the rationality hypothesis of efficiency theory is too narrow and irrelevant (Barberis and Thaler, 2002). The irrationality of the investor is reflected in his choice and his behaviour. However, his choice depends on the way the problem is formulated and described. The irrational investor does not think in terms of final wealth but rather in terms of gains and losses.Design/methodology/approachThis research is interested in the methods of classification of the investors in homogeneous groups. In the study, the classification method used to group individual in the sample is the dynamic aggregation method. However, to identify the number of groups to use in this method, the authors also used the hierarchical method on a sub-sample. Thus, to this end the authors present a topological analysis to test the hypothesis of the heterogeneity of Tunisian investor groups in terms of belief.FindingsThe results suggest that the majority of investors are quite irrational. Therefore, the Tunisian investor considers itself irrational because of the presence of several anomalies in its behavior.Originality/valueThis research proposes to help identify the variables that are truly determining in the process of interpreting information. The authors wish to formulate recommendations for the use of information, in order to help professionals and investors in the orientation of the investment strategy. In particular, the authors attempt to indicate the variables to which attention should be paid. In addition, behavioral financial analysis is useful for investors. Thus, taking into account certain irrational phenomena is important to make a decision. In addition, it allows to better identify the investor's own shortcomings and to detect certain negative trends.
The impact of Industry 4.0 technologies and the soft side of TQM on organisational performance: a multiple case study analysis on manufacturing organisations
Authors: Margherita Emanuele Gabriel , Braccini Alessio Maria 
Published: December 2022

PurposeThe purpose of this study is to explore how Industry 4.0 (I40) technologies support workers' engagement in soft total quality management (TQM) practices for organisational performance.Design/methodology/approachThe authors conducted a multiple case study of six Italian manufacturing organisations that operate with I40 production and implement TQM practices. The authors concentrated on the relationship between I40 technologies and soft TQM aspects.FindingsI40 technologies provide two forms of engagement with workers. Workers can act as machine supervisors and expert assembly operators. Organisations use five soft TQM practices to involve and develop workers for TQM that vary according to automation levels. The five soft TQM practices are top management design around workers, incremental trials with I40 technologies, worker empowerment, I40 sociotechnical collaboration and individual feedback systems.Originality/valueIn the literature that focusses primarily on how I40 technologies support the hard side of TQM by creating a data-driven and automated quality management system, the authors illustrate how the workforce can be engaged in I40 with five soft TQM practices to improve organisational performance. Thus, the authors complement the theory of hard and soft TQM aspects for I40 production systems.