bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial selective ER-phagy remodels the ER during neurogenesis
Authors: Hoyer Melissa J. , Capitanio Cristina , Smith Ian R. , Paoli Julia C. , Bieber Anna , Jiang Yizhi , Paulo Joao A. , Gonzalez-Lozano Miguel A. , Baumeister Wolfgang , Wilfling Florian , Schulman Brenda A. , Harper J. Wade 
Published: June 2023

SUMMARYThe endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis: a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodeling, as autophagy-deficient neuronsin vivodisplay axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of ER and the role of individual ER-phagy receptors is limited. Here, we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodeling duringin vitrodifferentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
Two Classes of DNA Gyrase Inhibitors Elicit Distinct Evolutionary Trajectories Toward Resistance in Gram-Negative Pathogens
Authors: Leyn Semen A. , Kent James E. , Zlamal Jaime E. , Elane Marinela L. , Vercruysse Maarten , Osterman Andrei L. 
Published: June 2023

AbstractComprehensive knowledge of mechanisms driving the acquisition of antimicrobial resistance is essential for the development of new drugs with minimized resistibility. To gain this knowledge, we combine experimental evolution in a continuous culturing device, the morbidostat, with whole genome sequencing of evolving cultures followed by characterization of drug-resistant isolates. Here, this approach was used to assess evolutionary dynamics of resistance acquisition against DNA gyrase/topoisomerase TriBE inhibitor GP6 inEscherichia coliandAcinetobacter baumannii. The evolution of GP6 resistance in both species was driven by a combination of two classes of mutational events: (i) amino acid substitutions near the ATP-binding site of the GyrB subunit of the DNA gyrase target; and (ii) various mutations and genomic rearrangements leading to upregulation of efflux pumps, species-specific (AcrAB/TolC inE. coliand AdeIJK inA. baumannii) and shared by both species (MdtK). A comparison with the experimental evolution of resistance to ciprofloxacin (CIP), previously performed using the same workflow and strains, revealed fundamental differences between these two distinct classes of compounds. Most notable were non-overlapping spectra of target mutations and distinct evolutionary trajectories that, in the case of GP6, were dominated by upregulation of efflux machinery prior to (or even in lieu) of target modification. Most of efflux-driven GP6-resistant isolates of both species displayed a robust cross-resistance to CIP, while CIP-resistant clones showed no appreciable increase in GP6-resistance.ImportanceThe significance of this work is in assessing the mutational landscape and evolutionary dynamics of resistance acquisition against a novel antibiotic, GP6. This approach showed that, in contrast to ciprofloxacin (CIP), a previously studied a canonical DNA gyrase/topoisomerase-targeting clinical antibiotic, evolution of GP6-resistance is driven largely by early and most prominent mutational events leading to upregulation of efflux machinery. An identified asymmetry in cross-resistance of evolved GP6- vs CIP-resistant clones provides important guidelines for rational selection of potential treatment regimens. This study illustrates the utility of the established morbidostat-based comparative resistomics workflow for the assessment of new drug candidates and clinical antibiotics.
SpatialSPM: Statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets
Authors: Ohn Jungyoon , Seo Mi-Kyoung , Park Jeongbin , Lee Daeseung , Choi Hongyoon 
Published: June 2023

AbstractSpatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its location for each sample, it is challenging to compare spatial gene expression patterns across tissue samples with different shapes and coordinates. Here, we propose a method that reconstructs ST data into multi-dimensional image matrices to ensure comparability across different samples through spatial registration process. We demonstrated the applicability of this method by using two mouse brain ST datasets to investigate and directly compare gene expression in a specific anatomical region of interest, pixel by pixel, across various biological statuses. It can produce statistical parametric maps to find specific regions with differentially expressed genes across tissue samples. Our approach provides an efficient way to analyze ST datasets and may offer detailed insights into various biological conditions.
Bats possess the anatomical substrate for a laryngeal motor cortex
Authors: Nevue Alexander A. , Mello Claudio V. , Portfors Christine V. 
Published: June 2023

SummaryCortical neurons that make direct connections to motor neurons in the brainstem and spinal cord are specialized for fine motor control and learning [1, 2]. Imitative vocal learning, the basis for human speech, requires the precise control of the larynx muscles [3]. While much knowledge on vocal learning systems has been gained from studying songbirds [4], an accessible laboratory model for mammalian vocal learning is highly desirable. Evidence indicative of complex vocal repertoires and dialects suggests that bats are vocal learners [5, 6], however the circuitry that underlies vocal control and learning in bats is largely unknown. A key feature of vocal learning animals is a direct cortical projection to the brainstem motor neurons that innervate the vocal organ [7]. A recent study [8] described a direct connection from the primary motor cortex to medullary nucleus ambiguus in the Egyptian fruit bat (Rousettus aegyptiacus). Here we show that a distantly related bat, Seba’s short-tailed bat (Carollia perspicillata) also possesses a direct projection from the primary motor cortex to nucleus ambiguus. Our results, in combination with Wirthlin et al. [8], suggest that multiple bat lineages possess the anatomical substrate for cortical control of vocal output. We propose that bats would be an informative mammalian model for vocal learning studies to better understand the genetics and circuitry involved in human vocal communication.
A super-pangenome of the North American wild grape species
Authors: Cochetel Noé , Minio Andrea , Guarracino Andrea , Garcia Jadran F. , Figueroa-Balderas Rosa , Massonnet Mélanie , Kasuga Takao , Londo Jason , Garrison Erik , Gaut Brandon , Cantu Dario 
Published: June 2023

AbstractCapturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
The role of embryonic origins and suture proximity in repair of cranial bone
Authors: Doro Daniel , Liu Annie , Lau Jia Shang , Rajendran Arun Kumar , Healy Christopher , Grigoriadis Agamemnon E. , Iseki Sachiko , Liu Karen J. 
Published: June 2023

AbstractThe cranial sutures are proposed to be a stem cell niche, harbouring skeletal stem cells (SSCs) that are directly involved in development, homeostasis, and healing. Like the craniofacial bones, the sutures are formed from both mesoderm and neural crest. During cranial repair, neural crest cells have been proposed to be key players; however, neural crest contributions to the sutures are not well defined, and the relative importance of suture proximity is unclear. Here, we combine calvarial wounding experiments with genetically labelled mouse models to demonstrate that suture proximity predicts the efficiency of cranial repair. Furthermore, we define the neural crest-mesoderm boundary within the sutures and demonstrate thatGli1+ andAxin2+ SSCs are present in all calvarial sutures examined. We propose that the position of the defect determines the availability of neural crest-derived progenitors, which appear to be a key element in the repair of calvarial defects.Summary statementThis study provides a new examination of the embryonic origins of cranial sutures in mouse. Using genetic lineage labelling, we identify specific contributions of neural crest cells and associated skeletal stem cells during repair of calvarial wounds. This is extremely relevant considering recent findings regarding the role of suture-residing stem cells.
Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade inKEAP1mutant lung cancer
Authors: Pillai Ray , LeBoeuf Sarah E. , Hao Yuan , New Connie , Blum Jenna L. E. , Rashidfarrokhi Ali , Huang Shih Ming , Bahamon Christian , Wu Warren L. , Karadal-Ferrena Burcu , Herrera Alberto , Ivanova Ellie , Cross Michael , Bossowski Jozef P. , Ding Hongyu , Hayashi Makiko , Rajalingam Sahith , Karakousi Triantafyllia , Sayin Volkan I. , Khanna Kamal M. , Wong Kwok-Kin , Wild Robert , Tsirigos Aristotelis , Poirier John T. , Rudin Charles M. , Davidson Shawn M. , Koralov Sergei B. , Papagiannakopoulos Thales 
Published: June 2023

AbstractLoss-of-function mutations inKEAP1frequently occur in lung cancer and are associated with resistance to standard of care treatment, highlighting the need for the development of targeted therapies. We have previously shown thatKEAP1mutant tumors have increased glutamine consumption to support the metabolic rewiring associated with NRF2 activation. Here, using patient-derived xenograft models and antigenic orthotopic lung cancer models, we show that the novel glutamine antagonist DRP-104 impairs the growth ofKEAP1mutant tumors. We find that DRP-104 suppressesKEAP1mutant tumor growth by inhibiting glutamine-dependent nucleotide synthesis and promoting anti-tumor CD4 and CD8 T cell responses. Using multimodal single-cell sequencing andex vivofunctional assays, we discover that DRP-104 reverses T cell exhaustion and enhances the function of CD4 and CD8 T cells culminating in an improved response to anti-PD1 therapy. Our pre-clinical findings provide compelling evidence that DRP-104, currently in phase 1 clinical trials, offers a promising therapeutic approach for treating patients withKEAP1mutant lung cancer. Furthermore, we demonstrate that by combining DRP-104 with checkpoint inhibition, we can achieve suppression of tumor intrinsic metabolism and augmentation of anti-tumor T cell responses.
Stability analysis for scheduled air traffic flow
Authors: Han Yun-Xiang 
Published: June 2023

Purpose
Modeling and system performance analysis play an important role in the planning of air traffic system. In particular, this paper aims to concentrate on the modeling and the performance evaluation of air transportation system.

Design/methodology/approach
It has shown that system matrices inherent in the airspace network can be acquired based on the service times of flights. This paper deals with a logical modeling which can avoid temporal synchronization conflict of resources. As a result, a class of queuing system is investigated to obtain a representation of the airspace network dynamics using dioid model.

Findings
The analysis of the air traffic system is conducted by solving the system state model. This indicates that it is feasible to use eigenvalues of system model for acquiring characteristics of the considered air transport systems.

Practical implications
The departure scheduling prototype presented in this paper can offer air traffic controller a decision support tool to build optimal departure sequences for aircraft.

Originality/value
The properties of max-plus algebra described allow us to apply linear algebra concepts like eigenvalue and eigenvectors to obtain a solution to the air traffic system being modeled. By solving and analyzing the dioid model, this paper evaluated some performance measures of airspace network.
Impact of Covid-19 pandemic on quality of work life of nurses – a major human rights component
Authors: T.S. Nanjundeswaraswamy , Bharath Sindu , Nagesh P. , K.M. Vignesh 
Published: June 2023

Purpose
This study aims to evaluate and compare the quality of work life (QWL) of nurses, in pre- and post-COVID-19 pandemic situations.

Design/methodology/approach
The study adopts a descriptive research design. Data were collected during the pre- and post-pandemic periods. The target sampling unit of the study comprises nurses working in Bangalore city, Karnataka, India. The minimum sample size was determined (Bartlett et al., 2001) as 385. The scale validation is carried out. The factors for the present study were explored using exploratory factor analysis and confirmed by confirmatory factor analysis. Model fitness (proposed measurement model) is ensured by using fit indices. The linear regression method was used to measure the level of QWL of nurses.

Findings
The present study noted that key factors that affects the QWL of nursing staff are work condition; work environment; work-life balance; compensation and reward; career development; job satisfaction and security; organization culture; relationship among co-workers and stress. Further, it is noticed that QWL of nurses pre-COVID-19 pandemic is 87.2%, while post-COVID-19 pandemic, it is 67%.

Research limitations/implications
Present study can be extended to address the same research question by considering sampling unit such as therapist, technicians and sanitarians who have equally undergone tremendous pressure during pandemic.

Practical implications
The study outcome provides references for organizations engaged in health services to understand the extreme job conditions posed by pandemic. The constructive inspiration (physio-social and organizational support) reinforces the nurses to continue in their professions by decreasing negative impact.

Originality/value
The research paper extends the contributions of Hwang (2002), Nikeghbal et al. (2021), Howie–Esquivel et al. (2022) and Rania et al. (2023) and add to the existing body of the QWL literature. The outcome of the research records the prevailing conditions of pandemic and its effect on changes in work environment with specific reference to health-care sector.
The impact of a coach training intervention on undergraduate students
Authors: McFarlane Julie 
Published: June 2023

PurposeThis paper explores the impact of a coach training programme in a UK higher education institution (UKHEI). This paper evaluates the use of coach training to equip undergraduate students with the skills needed to set goals and navigate stressors in personal and professional life.Design/methodology/approachAn interpretivist research design was chosen to gather detailed information about the participants. Data were collected via a multi-method approach comprising participant observations, individual reflections and surveys amongst 18 students. Each method allowed the researcher to interpret the participants' perspectives of social reality.FindingsThe inductive analysis revealed three key themes related to the impact of coach training: a greater awareness of self, enhanced relationships with others and a renewed focus on the future. The findings also showed that coach training provided students with a goal-focussed, judgement-free strategy to address issues related to university stressors such as burnout.Research limitations/implicationsThe conclusions drawn from the study are placed in the context of the wider coaching debate yet are not generalisable. They illustrate a strong link between coach training and the positive impact on the students increased sense of self, their renewed view of the world and how they want to engage with the training.Practical implicationsThe results of this study highlight the need for further research into the impact of coaching and coach training initiatives on UKHEI students. The study also proposes that coaching strategies should be embedded into the curriculum to better prepare graduates to navigate the transition from university life to professional life.Originality/valueThis paper provides empirical evidence of the positive impacts of coach training on UKHEI students. This paper contributes to an understanding of coach training's potential impact on students' engagement in, and enjoyment of, the higher education learning journey. This paper also provides a foundation for future empirical research in this area.
Revisiting Zakat with a distribution of weighted Shapley value
Authors: Tlemsani Issam , Matthews Robin , Mohamed Hashim Mohamed Ashmel 
Published: June 2023

Purpose
This paper aims to extend the Shapley value (SV) into a discussion of Zakat, a Pillar of Islam. Lloyd Shapley was awarded the Nobel Prize in Economics in 2012. This study shows that their relationship is significant for all nations, that of levelling up. An important but neglected paper by Datta (1939) showed insights provided by the Power Law, or as it is sometimes called, the Pareto distribution, into the role of Zakat in raising the income of all above the subsistence level. The Pareto distribution describes the prevailing tendency. The SV illustrates the interdependence perspective of Zakat with the Pareto distribution, wealth, income and poverty. Payoffs apply equally to both givers and receivers. For this study’s purposes, payoffs are considered as transferable utilities. They are formed by individuals who willingly cooperate in society rather than atomistic individuals who act independently. Zakat represents the recognition that society needs to be cooperative rather than individualistic; people cooperate in groups or societies to create value. SV implications and axioms are evaluated with an illustration.

Design/methodology/approach
This study extends Datta’s approach by introducing distribution weights into the SV. The authors set out the concept of weighted Shapley values that retain the elements of randomness and marginal contribution to a coalition contained in pure/true SVs and weights that follow a ley-Pareto distribution. This paper is a viewpoint work that relies primarily on the author’s qualitative interpretation.

Findings
The findings indicate that individual members of a coalition make multiple contributions that are often unrewarded. The contribution of one member of a coalition is dependent upon the contribution of others. The measure of contributions is payoffs, which have both monetary and non-monetary aspects; transferable payoffs or utilities are usually assumed. Furthermore, the significant agents in society or an organisation are stakeholders rather than the usual categories: managers, staff, shareholders, etc.

Practical implications
Contextualising these concepts within the Islamic values and principles that guide Zakat administration is crucial to ensure that the distribution of Zakat funds is fair, equitable and meets the needs of all eligible recipients. By applying these concepts appropriately, Zakat administrators can ensure that the Zakat system functions effectively and fulfils its religious obligation.

Originality/value
The novelty of this paper is that it blends the SV and the idea behind Zakat by introducing the idea of alternatives of Shapley weights. The link between the institution of Zakat and SV in terms of equality, poverty elimination and wealth distribution should be at the top of the research agenda.
Making an M&A work: equal strategic partnerships smooth the path
Authors: Ström Viktor , Braunerhjelm Pontus , Esmaeilzadeh Saeid 
Published: June 2023

Purpose
By providing equal weight to buyers and sellers, the purpose of this paper is to enhance our understanding of the determinants underlying successful mergers and acquisitions (M&As) involving a specific segment of firms involved in such undertakings, i.e., knowledge-intensive innovative and entrepreneurial (KIE) firms.

Design/methodology/approach
A multiple case study, based on eight semi-structured interviews with CEOs representing acquirers and the acquired firms, investigates the focal phenomenon this study addresses.

Findings
The results suggest that knowledge-intensive, innovative and entrepreneurial firms promote entrepreneurial intentions and allow value creation of M&As through four overarching measures. These are buyer–seller fit, aligned incentives, long-term thinking and perpetual alliance.

Research limitations/implications
The outcomes of this research may have limited generalizable due to the chosen research methodology. Therefore, this study recommends future studies testing the validity of these findings.

Practical implications
The authors have clarified the drawbacks of integration when being involved in M&As with KIE firms. These drawbacks primarily revolved around not eliminating the entrepreneurs’ autonomy and their routines, but it is also partly related to letting them keep their identity (i.e. their brand) as well as retaining employees’ trust in the new owner.

Originality/value
Contrary to most papers, this study has taken an approach giving equal weight to both buyers and sellers. In doing so, this study clarified the drawbacks of integration when it involves M&As with KIE firms.