bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redefining rock doves,Columba livia, using historical whole genome sequences
Authors: Hernández-Alonso Germán , Ramos-Madrigal Jazmín , Pacheco George , van Grouw Hein , Cavill Emily Louisa , Ciucani Marta Maria , Sinding Mikkel-Holger S. , Gopalakrishnan Shyam , Gilbert M. Thomas P. 
Published: April 2023

SummaryThe domestic pigeon’s exceptional phenotypic diversity was key in developing Darwin’s Theory of Evolution and establishing the concept of artificial selection in domestic species. However, unlike its domestic counterpart, its wild progenitor, the rock doveColumba livia, has received considerably less attention. Therefore, questions regarding their domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock dove samples representing all currently recognised subspecies and spanning the species’ original geographic distribution. Our dataset includes three specimens from Darwin’s collection and the type specimens of five different taxa. We characterised rock doves’ population structure, genomic diversity and gene-flow patterns. We show the West African subspeciesC. l. gymnocyclusis basal to rock doves and domestic pigeons. Our results show gene-flow signals between the rock dove’s sister speciesC. rupestrisand all rock doves except the West African populations. Our results led us to propose an evolutionary model for the rock dove considering the Pleistocene refugia theory. We propose that today’s rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least one domestication event in the Levant region that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
Proteasome gene expression is controlled by the coordinated functions of multiple transcription factors
Authors: Gilda Jennifer E. , Nahar Asrafun , Kasiviswanathan Dharanibalan , Tropp Nadav , Gilinski Tamar , Lahav Tamar , Mandel-Gutfreund Yael , Park Soyeon , Cohen Shenhav 
Published: April 2023

SUMMARYProteasome activity is crucial for cellular integrity, but how tissues adjust proteasome content in response to catabolic stimuli is uncertain. Here, we demonstrate that transcriptional coordination by multiple transcription factors is required to increase proteasome content and activate proteolysis in catabolic states. Using denervated mouse muscle as a model system for accelerated proteolysisin vivo, we reveal that a two-phase transcriptional program activates genes encoding proteasome subunits and assembly chaperones to boost an increase in proteasome content. Initially, gene induction is necessary to maintain basal proteasome levels, and in a more delayed phase (7-10 d after denervation) it stimulates proteasome assembly to meet cellular demand for excessive proteolysis. Intriguingly, the transcription factors PAX4 and α-PALNRF-1control the expression of proteasome among other genes in a combinatorial manner, driving cellular adaptation to muscle denervation. Consequently, PAX4 and α-PALNRF-1represent new therapeutic targets to inhibit proteolysis in catabolic diseases (e.g. type-2 diabetes, cancer).
Associated socio-demographic and psychological factors of childhood overprotection/overcontrol experiences among Chinese university students: a nationwide survey
Authors: Zhang Jiamei , Wu Zhipeng , Tao Haojuan , Chen Min , Yu Miaoyu , Zhou Liang , Sun Meng , Lv Dongsheng , Cui Guangcheng , Yi Qizhong , Tang Hong , An Cuixia , Liu Zhening , Huang Xiaojun , Long Yicheng 
Published: April 2023

AbstractThe childhood experiences of being overprotected and overcontrolled by family members have been suggested to be potentially traumatic. However, the possible associated factors of these experiences among young people are still not well studied. This study aimed to investigate the possible associated factors of childhood overprotection/overcontrol (OP/OC) experiences in young populations in a relatively large, nationwide sample of Chinese university students. A total of 5,823 university students across nine different provinces in China were recruited and included in the data analyses. All participants completed the OP/OC subscale in a recently developed 33-item Childhood Trauma Questionnaire (CTQ-33) to assess their OP/OC experiences. Data were also collected on socio-demographic information and multiple psychological characteristics of all participants. Binary logistic regression was conducted to investigate the associated factors of OP/OC. The prevalence of childhood OP/OC was estimated as 15.63% (910/5,823) based on a cutoff of OP/OC subscale score ≥ 13. Binary logistic regression suggested that being male, being a single child, having depression, having psychotic-like experiences, lower family functioning, and lower psychological resilience were independently associated with childhood OP/OC experiences (all corrected-p<0.05). The OP/OC was also positively associated with all the other trauma subtypes (abuses and neglects) in the CTQ-33. Post-hoc analyses suggested that OP/OC experiences were associated with depression in only females, and associated with anxiety in only males. Our results may provide initial evidence that childhood OP/OC experiences would have negative effects on young people’s mental health which merits further investigations, especially in clinical populations.
Optimization of Cas12a for multiplexed genome-scale transcriptional activation
Authors: Griffith Audrey L , Zheng Fengyi , McGee Abby V , Miller Nathan , Szegletes Zsofia M , Reint Ganna , Gademann Fabian , Nwolah Ifunanya , Hegde Mudra , Liu Yanjing V , Goodale Amy , Doench John G 
Published: April 2023

ABSTRACTCas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition and we compare these results to those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
SEL1L-HRD1 interaction is prerequisite for the formation of a functional HRD1 ERAD complex
Authors: Lin Liangguang Leo , Wei Xiaoqiong , Wang Huilun Helen , Pederson Brent , Torres Mauricio , Lu You , Li Zexin Jason , Liu Xiaodan , Mao Hancheng , Wang Hui , Zhao Zhen , Sun Shengyi , Qi Ling 
Published: April 2023

SUMMARYThe SEL1L-HRD1 protein complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD); however, definitive evidence for the importance of SEL1L in HRD1 ERAD is lacking. Here we report that attenuation of the interaction between SEL1L and HRD1 impairs HRD1 ERAD function and has pathological consequences in mice. Our data show thatSEL1Lvariantp.Ser658Pro(SEL1LS658P) previously identified in Finnish Hound suffering cerebellar ataxia is a recessive hypomorphic mutation, causing partial embryonic lethality, developmental delay, and early-onset cerebellar ataxia in homozygous mice carrying the bi-allelic variant. Mechanistically,SEL1LS658Pvariant attenuates the SEL1L-HRD1 interaction and causes HRD1 dysfunction by generating electrostatic repulsion between SEL1L F668 and HRD1 Y30 residues. Proteomic screens of SEL1L and HRD1 interactomes revealed that the SEL1L-HRD1 interaction is prerequisite for the formation of a functional HRD1 ERAD complex, as SEL1L recruits not only the lectins OS9 and ERLEC1, but the E2 UBE2J1 and retrotranslocon DERLIN, to HRD1. These data underscore the pathophysiological importance and disease relevance of the SEL1L-HRD1 complex, and identify a key step in organizing the HRD1 ERAD complex.
Building functional circuits in multispecies brains
Authors: Throesch Benjamin T. , Khadeesh bin Imtiaz Muhammad , Muñoz-Castañeda Rodrigo , Sakurai Masahiro , Hartzell Andrea L. , James Kiely N. , Rodriguez Alberto R. , Martin Greg , Lippi Giordano , Kupriyanov Sergey , Wu Zhuhao , Osten Pavel , Izpisua Belmonte Juan Carlos , Wu Jun , Baldwin Kristin K. 
Published: April 2023

AbstractThe genome is the ultimate architect of the brain. Its evolutionary variations build the neural circuits that endow each species with its innate senses and behaviors. A central question for neuroscience and translational medicine is whether neural circuits from two species can be made to function in an intact brain. Here, we establish genetic tools and use blastocyst complementation to selectively build and test interspecies neural circuits in rat-mouse brains. Despite ∼10-20 million years of evolution and prominent differences in brain size and cellular composition, rat pluripotent stem cells injected into mouse blastocysts widely populate and persist in the mouse brain. Unexpectedly, the mouse niche reprograms the birthdates of cortical and hippocampal rat neurons, where they also form synaptically active rat-mouse circuits. By genetically disabling host olfactory circuitry, we show that rat neurons restore synaptic information flow from the nose to the cortex. Rat neurons can also rescue a primal olfactory behavior (food-seeking), though less than mouse controls. By enabling a mouse to sense the world with rat neurons, we highlight the power of interspecies neural blastocyst complementation to uncover mechanisms of neural circuit development and evolution, and to inform efforts to rescue neural circuits affected by injury or disease.
High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin
Authors: Braun Dotan , Rosenberg Ayelet , Haruvi Ravid , Malamud Dorel , Barbara Rani , Kawashima Takashi 
Published: April 2023

AbstractSerotonergic psychedelics are emerging therapeutics for psychiatric disorders, yet their underlying mechanisms of action in the brain remain largely elusive. Zebrafish have evolutionarily conserved serotonergic circuits and subcortical targets such as the brainstem regions and the cerebellum, providing a promising model for studying the subcortical effects of serotonergic drugs. Here, we developed a wide-field behavioral tracking system for larval zebrafish and investigated the effects of psilocybin, a psychedelic serotonin receptor agonist. Machine learning analyses of precise body kinematics identified latent behavioral states reflecting spontaneous exploration, visually-driven rapid swimming, and irregular swim patterns following stress exposure. Using this method, we identified two main behavioral effects of acute psilocybin treatment: [i] increased rapid swimming in the absence of visual stimuli and [ii] prevention of irregular swim patterns following stress exposure. Together, these effects indicate that psilocybin induces a brain state that is both stimulatory and anxiolytic. These findings pave the way for using larval zebrafish to elucidate subcortical mechanisms underlying the behavioral effects of serotonergic psychedelics.
Risk assessment method for controlled flight into terrain of airlines based on QAR data
Authors: Guo Chaochao , Sun Youchao , Su Siyu , Peng Chong 
Published: April 2023

Purpose
The purpose of this paper is to assess the risk of controlled flight into terrain (CFIT) for airlines and to develop a practical method for evaluating and predicting CFIT risk to ensure safe and efficient airline operations.

Design/methodology/approach
In accordance with the monitoring project specification issued by the Flight Standards Department of the Civil Aviation Administration of China (CAAC), a preliminary draft of evaluation indicators for CFIT risk was developed based on the literature review and semi-structured interviews. Fifteen aviation experts were then selected and invited to participate in a Delphi method to revise the draft. Analytic hierarchy process (AHP) and entropy weight method were used to determine the combined weight of the indicators. The variable fuzzy set model and quick access recorder (QAR) data were applied to evaluate the CFIT risk of an airline from 2007 to 2018, and the classification results were compared with actual operational data.

Findings
The research findings reveal that the six most significant monitoring items affecting CFIT risk are incorrect configuration settings during landing, loss of altitude during climbing, ground proximity warning, G/S deviation, flap extension delay during landing and incorrect takeoff configuration. The CFIT risk of airlines has shown an increasing trend since 2015. The values in 2010, 2017 and 2018 were greater than 2 and less than 2.5, indicating that the CFIT risk is at Level 2, close to Level 3, and the risk is low but approaching medium.

Practical implications
Using the combination weight determined by AHP and entropy weight method to rank the weight of 15 monitoring items, airlines can take necessary measures (simulator training, knowledge training) to reduce the occurrence of monitoring items with high weight to reduce CFIT risk. This risk assessment method can quantitatively evaluate the CFIT risk of airlines and provide theoretical guidance and technical support for airlines to formulate safety management measures and flight training programs, enabling the interconnection between QAR data and flight quality.

Originality/value
The proposed method in this study differs from traditional approaches by offering a quantitative assessment of CFIT risk for airlines and enabling the interconnection between QAR data and flight quality.
Examining the impact of resilience strategies in mitigating medicine shortages in the United Kingdom's (UK) pharmaceutical supply chain (PSC)
Authors: Vann Yaroson Emilia , Breen Liz , Hou Jiachen , Sowter Julie 
Published: April 2023

PurposeMedicine shortages have a detrimental impact on stakeholders in the pharmaceutical supply chain (PSC). Existing studies suggest that building resilience strategies can mitigate the effects of these shortages. As such, this research aims to examine whether resilience strategies can reduce the impact of medicine shortages in the United Kingdom's (UK) PSC.Design/methodology/approachA sequential mixed-methods approach that involved qualitative and quantitative research enquiry was employed in this study. The data were collected using semi-structured interviews with 23 key UK PSC actors at the qualitative stage. During the quantitative phase, 106 respondents completed the survey questionnaires. The data were analysed using partial least square-structural equation modelling (PLS-SEM).FindingsThe results revealed that reactive and proactive elements of resilience strategies helped tackle medicine shortages. Reactive strategies increased relational issues such as behavioural uncertainty, whilst proactive strategies mitigated them.Practical implicationsThe findings suggest that PSC managers and decision-makers can benefit from adopting structural flexibility and proactive strategies, which are cost-effective measures to tackle medicine shortages. Also engaging in strategic alliances as a proactive strategy mitigates relational issues that may arise in a complex supply chain (SC).Originality/valueThis study is the first to provide empirical evidence of the impact of resilience strategies in mitigating medicine shortages in the UK's PSC.
The social construction of systemic risk: towards an actionable framework for risk governance
Authors: Maskrey Andrew , Jain Garima , Lavell Allan 
Published: April 2023

PurposeThis paper explores the building blocks of risk governance systems that are equipped to manage systemic risk in the 21st century. Whilst approaches to risk governance have been evolving for more than a decade, recent disasters have shown that conventional risk management solutions need to be complemented with a multidimensional risk approach to govern complex risks and prevent major, often simultaneous, crises with cascading and knock-on effects on multiple, interrelated systems at scale. The paper explores which risk governance innovations will be essential to provide the enabling environment for sustainable development that is resilient to interrelated shocks and risks.Design/methodology/approachThis interdisciplinary literature review-based thought piece highlights how systemic risk is socially constructed and identifies guiding principles for systemic risk governance that could be actionable by and provide entry points for local and national governments, civil society and the private sector. particularly in low- and middle-income countries (LMIC), in a way that is relevant to the achievement of the 2030 Agenda for Sustainable Development. This considers preparedness, response and resilience, but more importantly prospective and corrective risk control and reduction strategies and mechanisms. Only when systemic risk is framed in a way that is relevant to the political agendas of countries will it be possible to begin a dialogue for its governance.FindingsThe paper identifies opportunities at the global, national and local levels, which together draw up a viable framework for systemic risk governance that (1) embraces the governance of sustainability and resilience through a strengthened holistic governance framework for social, economic, territorial and environmental development; (2) improves managing conventional risk to ultimately manage systemic risks; (3) fosters the understanding of vulnerability and exposure to gain insight into systemic risk; (4) places a greater focus on prospective risk management; (5) manages systemic risk in local infrastructure systems, supply chains and ecosystems; (6) shifts the focus from protecting privatized gains to managing socialized risk.Originality/valueThe choices and actions that societies take on the path of their development are contributing intentionally or unintentionally to the construction of systemic risks, which result in knock-on effects among interconnected social, environmental, political and economic systems. These risks are manifesting in major crises with cascading effects and a real potential to undermine the achievement of the SDGs, as COVID-19 is a stark reminder of. This paper offers the contours of a new risk governance paradigm that is able to navigate the new normal in a post-COVID world and is equipped to manage systemic risk.
Predicting psychologists’ approach to academic reciprocity and data sharing with a theory of collective action
Authors: Lee Tae Hee , Jung Mina , Kim Youngseek 
Published: April 2023

PurposeThis study aims to investigate the factors influencing the data sharing habits of psychologists with respect to academic reciprocity.Design/methodology/approachA research model was developed based on Ostrom’s (2003) theory of collective action to map psychologists’ underlying motivations for data sharing. The model was validated by data from a survey of 427 psychologists, primarily from the psychological sciences and related disciplines.FindingsThis study found that data sharing among psychologists is driven primarily by their perceptions of community benefits, academic reciprocity and the norms of data sharing. This study also found that academic reciprocity is significantly influenced by psychologists’ perceptions of community benefits, academic reputation and the norms of data sharing. Both academic reputation and academic reciprocity are affected by psychologists’ prior experiences with data reuse. Additionally, psychologists’ perceptions of community benefits and the norms of data sharing are significantly affected by the perception of their academic reputation.Research limitations/implicationsThis study suggests that Ostrom’s (2003) theory of collective action can provide a new theoretical lens in understanding psychologists’ data sharing behaviours.Practical implicationsThis study suggests several practical implications for the design and promotion of data sharing in the research community of psychology.Originality/valueTo the best of the authors’ knowledge, this is one of the initial studies that applied the theory of collective action to the mechanisms of reputation, community benefits, norms and reciprocity in psychologists’ data sharing behaviour. This research demonstrates that perceived community benefits, academic reputation and the norms of data sharing can all encourage academic reciprocity, and psychologists’ perceptions of community benefits, academic reciprocity and data sharing norms all facilitate their data sharing intentions.
Information seeking, sharing behaviour, and copyright violations among students in India in the digital age
Authors: A. Subaveerapandiyan , Sinha Priyanka , Kumari Madhuri , Amees Mohammad 
Published: April 2023

Purpose
The present study investigates information-sharing behaviour and awareness of students towards the infringement of copyright and associated rights while information sharing. The purpose of this study is to seek answers to the issue of whether or not students infringe on the rights of others and, if they do, whether they do so deliberately or unwittingly. Even though the Copyright Act and copyrighted works are often disregarded, students, teachers and peers are long-term trading and adapting new e-resources for their use.

Design/methodology/approach
The study collected data from students in India through a survey using Google Forms from January 2022 to May 2022. It analysed it using SPSS software to identify behaviour patterns, trends and factors influencing actions and awareness regarding potential copyright issues during data sharing.

Findings
The study finds that many students in India engage in copyright infringement, either deliberately or unwittingly. Many students are unaware of copyright laws and regulations and do not understand the consequences of their actions.

Research limitations/implications
The study’s findings are limited to students in Tamil Nadu, India, and may not represent students in other countries or regions. The findings can inform policies and educational programmes that promote ethical and legal behaviour among students and help reduce the incidence of copyright infringement.

Originality/value
This study’s originality and value stem from its unique approach of merging information sharing, seeking and copyright concepts.