bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons
Authors: Ichihara Kazuya , Matsumoto Akinobu , Nishida Hiroshi , Kito Yuki , Shimizu Hideyuki , Shichino Yuichi , Iwasaki Shintaro , Imami Koshi , Ishihama Yasushi , Nakayama Keiichi I 
Published: June 2021

Abstract
Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here, we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are most probably dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity
Authors: Bader Samuel B , Ma Tiffany S , Simpson Charlotte J , Liang Jiachen , Maezono Sakura Eri B , Olcina Monica M , Buffa Francesca M , Hammond Ester M 
Published: June 2021

Abstract
Tumor heterogeneity includes variable and fluctuating oxygen concentrations, which result in the accumulation of hypoxic regions in most solid tumors. Tumor hypoxia leads to increased therapy resistance and has been linked to genomic instability. Here, we tested the hypothesis that exposure to levels of hypoxia that cause replication stress could increase APOBEC activity and the accumulation of APOBEC-mediated mutations. APOBEC-dependent mutational signatures have been well-characterized, although the physiological conditions which underpin them have not been described. We demonstrate that fluctuating/cyclic hypoxic conditions which lead to replication catastrophe induce the expression and activity of APOBEC3B. In contrast, stable/chronic hypoxic conditions which induce replication stress in the absence of DNA damage are not sufficient to induce APOBEC3B. Most importantly, the number of APOBEC-mediated mutations in patient tumors correlated with a hypoxia signature. Together, our data support the conclusion that hypoxia-induced replication catastrophe drives genomic instability in tumors, specifically through increasing the activity of APOBEC3B.
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms
Authors: Figueiredo Rebeca Queiroz , Raschka Tamara , Kodamullil Alpha Tom , Hofmann-Apitius Martin , Mubeen Sarah , Domingo-Fernández Daniel 
Published: June 2021

Abstract
We attempt to address a key question in the joint analysis of transcriptomic data: can we correlate the patterns we observe in transcriptomic datasets to known interactions and pathway knowledge to broaden our understanding of disease pathophysiology? We present a systematic approach that sheds light on the patterns observed in hundreds of transcriptomic datasets from over sixty indications by using pathways and molecular interactions as a template. Our analysis employs transcriptomic datasets to construct dozens of disease specific co-expression networks, alongside a human protein-protein interactome network. Leveraging the interoperability between these two network templates, we explore patterns both common and particular to these diseases on three different levels. Firstly, at the node-level, we identify most and least common proteins across diseases and evaluate their consistency against the interactome as a proxy for their prevalence in the scientific literature. Secondly, we overlay both network templates to analyze common correlations and interactions across diseases at the edge-level. Thirdly, we explore the similarity between patterns observed at the disease-level and pathway knowledge to identify signatures associated with specific diseases and indication areas. Finally, we present a case scenario in schizophrenia, where we show how our approach can be used to investigate disease pathophysiology.
Organic molecules encapsulated in single-walled carbon nanotubes
Authors: Cadena Ana , Botka Bea , Kamarás Katalin 
Published: June 2021

Abstract
Hybrid materials based on carbon nanotubes continue to attract considerable interest due to the broad variety of both the cages outside and the encapsulated species inside. This review focuses on organic molecules as guests in single-walled carbon nanotube hosts. The majority of results presented here has been attained in recent years by various methods of optical spectroscopy, complemented by transmission electron microscopy. These spectroscopic methods yield information on electronic structure, as well as dynamic processes as structural transformations and chemical reactions.
Spaces of Peace
Authors: Björkdahl Annika , Kappler Stefanie 
Published: June 2021

Abstract
This chapter shows that war-making and peace-making “take place” and that sometimes the legacy of conflict obscures manifestations of peacebuilding. The analysis of a “bridge that divides” in the city of Mitrovica in northern Kosovo and a “wall that unites” in Belfast, Northern Ireland, casts light on the benefits that a spatial reading of peace can provide to understand the ways in which spatial infrastructures are lived by the people who use them. The process of space-making (the generation of meanings from a material location) will help explain the agency that emerges by the creators, users, and inhabitants of (post)conflict spaces.
Divine Revelation and Digital Religion
Authors: Sheldon Zachary , Campbell Heidi A. 
Published: June 2021

AbstractThis chapter considers the relationship between divine revelation and digital religion by exploring how revelation of divine or religious truth is presented and negotiated on the internet and within digital culture. Revelation is a fundamental component of religious practice and experience and has long been studied in its relation to mediation. Digital culture offers unique resources that allow individuals to receive, engage, and share in divine revelation in digital contexts. The multiplicity of digital contexts and their blended ties to offline practices in worship practices have become known as digital religion (Campbell 2013), which can be likened to a bridge which connects and extends religious practice online into offline religious spaces and contexts. This chapter will consider how revelation is understood and enacted in different spaces of digital religion by providing an overview of Digital Religion Studies and looking at Campbell and DeLashmutt’s (2014) research on multi-site churches to offer insights into how churches structure and negotiate their digital worship practices to assist people in engaging with divine revelation. In particular, we emphasize questions of presence and authority that churches ought to consider in regard to how their use of digital technology may impact views on divine revelation in digital contexts.
The Becoming of Change in 3D: Dialectics, Darwin, and Dewey
Authors: Farjoun Moshe 
Published: June 2021

Abstract
Dialectical development through a conflict process of affirmation, negation, and synthesis, provides a template, both for modelling organizational change, and for constructing new, synthetic conceptual models of change. This chapter highlights two other important means by which dialectics can stimulate new change models: as a relational process philosophy, and as an evolutionary theory. A selective review of the history of ideas about change, from Greek philosophy to Hegelian and Marxian dialectics, to Darwin, to pragmatism, underscores how relational process principles link several, not commonly connected, “becoming” literatures, and how these principles can stimulate key conceptual innovations. The contrast of dialectics with Darwin’s evolutionary theory uncovers several, non-obvious affinities: in underlying principles, change patterns, and mechanisms. The capacity of dialectics—as a philosophy and as an evolutionary theory—to inspire new ideas, is illustrated by a reading of Dewey’s work anew, and through other examples pertinent to contemporary phenomena.
Affirmation and Safety: An Intersectional Analysis of Trans and Nonbinary Youths in Quebec
Authors: Pullen Sansfaçon Annie , Gelly Morgane A , Ens Manning Kimberly 
Published: June 2021

Abstract
This article presents the results of a combined grounded theory and community-based participatory action research project with 54 trans and nonbinary youths (TNBY) residing in the province of Quebec, Canada. The project includes two important sensitizing concepts: intersectionality and recognition. In the research, intersectionality was defined as an approach that explores how people navigate manifold identities (class, race, disability, and so on) in the context of structural oppression. Authors applied an intersectional lens to the recruitment of research participants through an iterative, community-based process, and to the analysis of the oppressive structures that negatively influence the well-being of TNBY and the specific factors that enable TNBY to thrive. Drawing on Honneth’s concept of recognition, authors argue for a contextualized, dynamic, and relational understanding of how well-being is produced. Specifically, they show two presenting needs: one for affirmation and one for safety, access to which springs from resources of privilege that emerge in the environment in which young people are embedded and from which they self-advocate. Understanding the dynamic relationship between these two needs and how they shift according to context is an important component of applying an intersectional approach to supporting TNBY in social work settings.
Implementation of the MATRIX Staffing Grid Improves Nurse Satisfaction With Rehabilitation Unit Staffing
Authors: Riley Yahaddy , Stitt Jacqueline , Hill Cynthia M. , Stutzman Sonja E. , Venkatachalam Aardhra M. , Aguilera Veronica , Ifejika Nneka L. 
Published: June 2021

ABSTRACT

BACKGROUND: Information on nurse satisfaction and unit acuity is scarce in the literature. The purpose of this study is to evaluate the effect of the MATRIX Staffing Grid (MSG) on nurse assignment satisfaction in a 20-bed inpatient rehabilitation facility. METHODS: Prospective systematic implementation study of the MSG occurred in 5 phases: development, baseline, run-in, implementation, and sustainability. Pretest/posttest nursing satisfaction data were analyzed using Wilcoxon-Mann-Whitney tests. RESULTS: Analysis of 128 satisfaction surveys demonstrated that the median total satisfaction score increased by 35% after MSG implementation (P < .05), with no change in patient satisfaction or adverse event rates. CONCLUSION: A systematic approach to implementation of the MSG evidence-based practice significantly improved nursing satisfaction with patient assignment in a way that addressed specific needs. The MSG has now been adopted into practice at our institution. The MSG may be feasible for implementation in inpatient rehabilitation units to improve staffing satisfaction.
Oropharyngoesophageal Scintigraphy in a Case of Complex Swallowing Disorders After a Major Oral Surgery
Authors: Maccora Daria , Parrilla Claudio , Lanni Valerio , Galli Jacopo , Longobardi Ylenia , Valenza Venanzio 
Published: June 2021

Abstract
A 75-year-old woman had an occasional finding of a left tonsil mass for dysphagia, which resulted a high-grade squamous carcinoma. Therefore, the patient was sent to have a left pharyngectomy. After the pharyngectomy, the patient reported persistent swallowing disorders and nasal reflux. Consequently, she had an oropharyngoesophageal scintigraphy, demonstrating irregular oral and pharyngeal swallowing phases and confirming reflux episodes into the rhinopharynx and into the oropharynx. In line with these findings, the patient was send to rehabilitation; the abnormal functional mechanisms, previously identified by the scintigraphy, allowed to guide the speech therapy, with a progressive clinical improvement.
Early microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation
Authors: Elgarten Caitlin W. , Tanes Ceylan , Lee Jung-jin , Danziger-Isakov Lara A. , Grimley Michael S. , Green Michael , Michaels Marian G. , Barnum Jessie L. , Ardura Monica I. , Auletta Jeffery J. , Blumenstock Jesse , Seif Alix E. , Bittinger Kyle L. , Fisher Brian T. 
Published: June 2021

ABSTRACTBackgroundThe contribution of the gastrointestinal tract microbiome to outcomes after allogeneic hematopoietic cell transplantation (HCT) is increasingly recognized. Investigations of larger pediatric cohorts aimed at defining the microbiome state and associated metabolic patterns pre-transplant are needed.MethodsWe sought to describe the pre-transplant stool microbiome in pediatric allogenic HCT patients at four centers. We performed shotgun metagenomic sequencing and untargeted metabolic profiling on pre-transplant stool samples. Samples were compared with normal age-matched controls and by clinical characteristics. We then explored associations between stool microbiome measurements and metabolite concentrations.ResultsWe profiled stool samples from 88 pediatric allogeneic HCT patients, a median of 4 days before transplant. Pre-transplant stool samples differed from healthy controls based on indices of alpha diversity and in the proportional abundance of specific taxa and bacterial genes. Relative to stool from healthy patients, samples from HCT patients had decreased proportion of Bacteroides, Ruminococcaeae and genes involved in butyrate production, but were enriched for gammaproteobacterial species. No systematic differences in stool microbiome or metabolomic profiles by age, transplant indication or hospital were noted. Stool metabolites demonstrated strong correlations with microbiome composition.DiscussionStool samples from pediatric allogeneic HCT patients demonstrate substantial dysbiosis early in the transplant course. As microbiome disruptions associate with adverse transplant outcomes, pediatric-specific analyses examining longitudinal microbiome and metabolome change are imperative to identify causal associations and to inform rational design of interventions.
Adaptive doctors: preparing tomorrow’s doctors for practice in the Anthropocene Epoch
Authors: Slimings Claudia , Sisson Emily , Larson Connor , Bowles Devin , Hussain Rafat 
Published: June 2021

AbstractBackgroundThe future health workforce needs to be equipped with the knowledge, skills, and motivation to deliver sustainable healthcare and promote planetary health. The aim of this study was to design, implement and evaluate a new suite of planetary health learning activities piloted by medical students for a range of medical professionals.MethodsThe study consisted of three components: curriculum mapping, development of learning activities and evaluation. Curriculum mapping involved searching program learning outcomes using relevant search terms. Two learning activities were co-developed with medical students comprising of an e-learning component and an inquiry-based small group workshop presented to 99 2nd year students. Evaluation consisted of pre- and post-learning knowledge quizzes and a student feedback survey.ResultsA total of 30 learning outcomes were identified with the majority located in the first two years of the four-year program. The overall evaluation response rate was 49.5%, and 19% completed the feedback survey. The mean pre- and post-lesson scores, respectively, were 7.09 (SD=1.84) and 9.53 (SD=1.69) out of a possible score of 12, increasing by 2.37 points on average (95% confidence interval [CI] 1.66-3.09). Overall, the new activities were rated as excellent/good by 84.2% of respondents. The e-learning module rated more highly as a meaningful learning experience than the workshop (89% v. 63.2%). The most common criticism was the length of time it took to complete the e-learning.ConclusionStudents already had a good understanding of planetary health ‘facts’ and the e-learning lesson served to confirm, review and update their knowledge. Students embraced the opportunity to engage in interactive learning through the problem-solving group work activity. There is very little vertical alignment of environmental and climate issues across all four years of the medical program in our institution and a variety of learning approaches should be considered when revising the curriculum.
Lysosome Lipid Signaling from the Periphery to Neurons Regulates Longevity
Authors: Savini Marzia , Duffy Jonathon D. , Folick Andrew , Lee Yi-Tang , Hu Pei-Wen , Neve Isaiah A. , Jin Feng , Zhang Qinghao , Tillman Matthew , Ye Youqiong , Mair William B. , Wang Jin , Han Leng , Ortlund Eric A. , Wang Meng C. 
Published: June 2021

AbstractLysosomes are key cellular organelles that metabolize extra- and intracellular substrates. Alterations in lysosomal metabolism are implicated in aging-associated metabolic and neurodegenerative diseases. However, how lysosomal metabolism actively coordinates the metabolic and nervous systems to regulate aging remains unclear. Here, we report a fat-to-neuron lipid signaling pathway induced by lysosomal metabolism and its longevity promoting role in Caenorhabditis elegans. We discovered that lysosomal lipolysis in peripheral fat storage tissue up-regulates the neuropeptide signaling pathway in the nervous system to promote longevity. This cell-non-autonomous regulation requires the secretion from the fat storage tissue of a lipid chaperone protein LBP-3 and polyunsaturated fatty acids (PUFAs). LBP-3 binds to specific PUFAs, and acts through a nuclear hormone receptor NHR-49 and neuropeptide NLP-11 in neurons to extend lifespan. Together, these results reveal lysosomes as a signaling hub to coordinate metabolism and aging, and a lysosomal signaling mechanism that mediates intertissue communication to promote longevity.
High accuracy disturbance observer-based agile attitude stabilization with three-dimensional MSW
Authors: Tayebi Javad , Han Chao , Yu Yuanjin 
Published: June 2021

Purpose
The purpose of this paper is agile attitude control design with the novel three-dimensional (3D) magnetically suspended wheel (MSW) that is the preferred type for agile maneuvering compared to conventional control moment gyro due to frictionless, low vibration and long lifetime. This system does not require a separate steering law for pyramid arrangement to derive tilt angles. It is also conducting an agile maneuver with high accuracy despite the high-frequency disturbances.

Design/methodology/approach
In this paper, a disturbance observer-based attitude stabilization method is proposed for an agile satellite with a pyramid cluster of the novel 3D magnetically suspended wheel actuator. This strategy includes a disturbance observer and a linear quadratic regulator controller. The rotor shaft deflection of MSW is actively controlled to reduce vibration and producing gyro torque. The deflection angle of the pyramid cluster MSWs considered as control parameters. The closed-loop stability is proved by using the Lyapunov strategy. The efficiency and performance of the offered method verified by numerical simulation via MATLAB/SIMULINK software.

Findings
According to simulation results, the disturbance observer-based control controller stabilized the system with high accuracy and optimal tilt angles without any extra steering law equation. Hence, the system speed is increased, and the system error is minimized without separate steering law.

Practical implications
The magnetically suspended wheel is a new kind of inertia actuator for attitude control that has several benefits such as frictionless, high-speed rotor, clean environment and low vibration compared to the traditional wheel. It has complex nonlinear dynamics that cause have complicated controller design. The proposed strategy stabilizes the system and conducting an agile maneuver with high precision despite the high-frequency disturbances. It is applicable for some missions requiring high accuracies, like Earth observation and the solar observation mission that require a very accurate pointing control and a long lifetime.

Originality/value
This paper is the initial paper to design a pyramid array for magnetically suspended wheels. Compared to other research, this method doesn’t need a separate steering law of the MSWs cluster and presented optimal tilt angles with less computational. Also, it designs a disturbance observer-based controller for this system that proposed high accuracy and agile stabilization.
The transforming generation: increasing student awareness about the effects of economic decisions on sustainability
Authors: Sierra Javier , Suárez-Collado Ángela 
Published: June 2021

Purpose
There is a growing trend in higher education institutions to develop multi-disciplinary approaches to education for sustainable development and to implement student-centered and problem-based methodologies to increase student engagement and satisfaction. This paper aims to present an innovative methodology to increase student awareness about the effects of economic decisions on sustainability.

Design/methodology/approach
This method uses a videogame and two board games to simulate three spheres of economic interaction, namely, local, national and international. For every sphere, three key economic sectors and their relationships with fundamental sustainable development goals (SDGs) are addressed. This study uses pre- and post-simulation data to analyze the students’ perceptions regarding the usefulness of the simulations and their awareness about the effects of economic decisions on sustainability.

Findings
The implementation of this teaching and learning method demonstrated not only that active learning can effectively increase student awareness about the potential social and environmental consequences of economic decisions but also that students perceive games and simulations as useful teaching and learning tools.

Social implications
Students in these areas need to learn not only how to transform original ideas into successful projects but also to align financial results with social and environmental objectives. The methodology presented in this research allows to enhance learning from a multi-disciplinary perspective, helping the students to analyze different economic sectors and their connection with a number of SDGs through the lens of public economics.

Originality/value
The outbreak of the COVID-19 virus has shown the effects of a global pandemic at the economic, social and environmental levels. This paper presents an innovative active learning framework to increase sustainability awareness among students of economics, business and management.