bluuebunny/crossref_metadata_2025_split huggingface dataset:
The compartmentalised nature of neuronal mitophagy: molecular insights and implications
Authors: Borbolis Fivos , Palikaras Konstantinos 
Published: September 2022

AbstractThe maintenance of a healthy mitochondrial network and the ability to adjust organelle population in response to internal or external stimuli are essential for the function and the survival of eukaryotic cells. Over the last two decades several studies have demonstrated the paramount importance of mitophagy, a selective form of autophagy that removes damaged and/or superfluous organelles, in organismal physiology. Post-mitotic neuronal cells are particularly vulnerable to mitochondrial damage, and mitophagy impairment has emerged as a causative factor in multiple neurodegenerative pathologies, including Alzheimer's disease and Parkinson's disease among others. Although mitochondrial turnover is a multifaceted process, neurons have to tackle additional complications, arising from their pronounced bioenergetic demands and their unique architecture and cellular polarisation that render the degradation of distal organelles challenging. Mounting evidence indicates that despite the functional conservation of mitophagy pathways, the unique features of neuronal physiology have led to the adaptation of compartmentalised solutions, which serve to ensure seamless mitochondrial removal in every part of the cell. In this review, we summarise the current knowledge concerning the molecular mechanisms that mediate mitophagy compartmentalisation and discuss their implications in various human pathologies.
Is the desire for life rational?
Authors: de Ray Christophe 
Published: September 2022

AbstractThe question of the meaning of life has long been thought to be closely intertwined with that of the existence of God. I offer a new theistic, anti-naturalist argument from the meaning of life. It is argued that the desire for life is irrational on naturalism, since there would be no good reason to believe that life is worthwhile on the whole if naturalism were true. As I show, the same cannot be argued of theism. Since it is clear that the desire for life is not irrational, it is concluded that we have strong reason to prefer theism over naturalism.
A SENSE OF THE IRREVERSIBLE: AN INTRODUCTION TO THE MUSIC OF ANN CLEARE
Authors: Carey Christian 
Published: September 2022

AbstractThis article examines the music of composer Ann Cleare, focusing on representative works that display her use of microtonality, unconventional scoring, multimedia and extended techniques. It also discusses Cleare's connection to Irish language and poetry, environmentalism and visual art. Several chamber pieces are analysed. The article concludes with discussion of large-scale compositions, including the eyam cycle about the 1665 plague village in Derbyshire, England, and the forthcoming Brexit opera The Little Lives.
FORMS OF MAKING: RICHARD EMSLEY'S FOR PIANO AND STILL/S
Authors: Rutherford-Johnson Tim 
Published: September 2022

AbstractThis article considers the recent music of the British composer Richard Emsley. It takes as a framework Tim Ingold's reflections on the creation of knowledge, not as the study of fixed objects but as a study with them, expressed in his 2013 book Making. The article examines the forces of resistance and opportunity that have shaped Emsley's creation of an algorithmic compositional method, and its use and adaptation in two groups of works: the series for piano (1997–) and the cycle Still/s (2002–19). The origins of for piano lie in a creative block that Emsley suffered between 1987 and 1996, during which time he began experimenting with using simple computer programs to create algorithmic compositions. Still/s extends this practice into a cycle of 24 pieces for instrumental quintet, originally inspired by a collaboration with the painter Joan Key. What emerges from both collections of pieces is not a form-based way of making but a practice, out of which forms might be discovered, and which requires skills of attentiveness, or what Ingold calls ‘correspondence’. The origins and subsequent elaborations of both for piano and Still/s show how the music itself has altered Emsley and his ways of working.
REFLECTIONS ON TEACHING COMPOSITION FOR CONFIDENCE, EQUITY AND COMMUNITY
Authors: Power Ian 
Published: September 2022

AbstractThe increasing precarity of arts academic jobs, combined with a much needed focus on equity and decolonisation, are de-privileging and destabilising the experimental music tradition and contemporary composer identity. As a result, composition departments are pursuing a paradox: scrambling to focus on specific marketable skills while also broadening the genres taught. After teaching in a composition department, a generalised arts department and a prison college programme, I describe methods to provide skills training for students interested in different genres, even if those genres are not the specialty of a department's faculty. These include: (1) discrete ‘levels’ of creative thought, from high-level questions of art's purpose to ground-level skills training; (2) creative process assignments, in which students plan and document their way through a prompt, developing a practical discipline into which desired skills can be incorporated; and (3) formal spaces for students to learn from each other, one-on-one, getting deeper into the similarities and differences they have. The goal is to empower students not simply via marketability, but by developing a sense of vocation without tethering creativity to employment, so that students may more realistically and more potently design their own lives in music.
The empire strikes back: Some responses to Bruineberg and colleagues
Authors: Ramstead Maxwell J. D. 
Published: September 2022

Abstract
In their target paper, Bruineberg and colleagues provide us with a timely opportunity to discuss the formal constructs and philosophical implications of the free energy principle. I critically discuss their proposed distinction between Pearl and Friston blankets. I then critically assess the distinction between inference with a model and inference within a model in light of instrumentalist approaches to science.
Good theoretical debate, but insufficient proof of concept
Authors: Spiegel Rainer 
Published: September 2022

Abstract
Bruineberg and colleagues argue that the patellar reflex cannot be modeled sufficiently with a Friston blanket due to counterintuitive sensorimotor boundaries. Although I agree with their theoretical discussion, their model of the patellar reflex is insufficiently based on clinical knowledge. Consequently, this example should not be applied to challenge Friston blankets. I will provide an alternative example.
Who tailors the blanket?
Authors: Suzuki Keisuke , Miyahara Katsunori , Miyazono Kengo 
Published: September 2022

Abstract
The gap between the Markov blanket and ontological boundaries arises from the former's inability to capture the dynamic process through which biological and cognitive agents actively generate their own boundaries with the environment. Active inference in the free-energy principle (FEP) framework presupposes the existence of a Markov blanket, but it is not a process that actively generates the latter.
Recurrent, nonequilibrium systems and the Markov blanket assumption
Authors: Aguilera Miguel , Buckley Christopher L. 
Published: September 2022

Abstract
Markov blankets – statistical independences between system and environment – have become popular to describe the boundaries of living systems under Bayesian views of cognition. The intuition behind Markov blankets originates from considering acyclic, atemporal networks. In contrast, living systems display recurrent, nonequilibrium interactions that generate pervasive couplings between system and environment, making Markov blankets highly unusual and restricted to particular cases.
Embracing sensorimotor history: Time-synchronous and time-unrolled Markov blankets in the free-energy principle
Authors: Virgo Nathaniel , Rosas Fernando E. , Biehl Martin 
Published: September 2022

Abstract
The free-energy principle (FEP) builds on an assumption that sensor–motor loops exhibit Markov blankets in stationary state. We argue that there is rarely reason to assume a system's internal and external states are conditionally independent given the sensorimotor states, and often reason to assume otherwise. However, under mild assumptions internal and external states are conditionally independent given the sensorimotor history.
Navigators’ views of a collision avoidance decision support system for maritime navigation
Authors: Aylward Katie , Weber Reto , Lundh Monica , MacKinnon Scott N. , Dahlman Joakim 
Published: September 2022

AbstractMaritime navigation is a complex task involving the acquisition, analysis, and interpretation of information using seamanship, professional knowledge, and technology. As the maritime industry transitions towards maritime autonomous surface ships (MASS), there is an increasing gap between the operator and the technology. This paper explores a collision avoidance decision support system for navigation from the navigator's perspective. The system, developed by Wärtsilä, is called Advanced Intelligent Manoeuvring (AIM) and can generate suggestions for course or speed alterations based on data from surrounding traffic. Nineteen Swedish navigators completed three ship traffic scenarios with and without decision support. Qualitative data were collected using interviews and analysed with thematic analysis. The results show that the participants perceive the decision support system as an advisory tool to visualise how traffic situations could unfold, a task currently difficult for most navigators. This paper discusses the present and near future of maritime navigation, highlighting the benefits of automation, while remaining vigilant about the potential dangers.
Differences in Satellite‐Based Latent Heating Profiles Between the 2015/2016 Disruption and Westerly Phase of the Quasi‐Biennial Oscillation
Authors: Kim Donghyeck , Shin Dong‐Bin , Kim Jiseob , Kang Min‐Jee , Lee Hyun‐Kyu , Chun Hye‐Young 
Published: September 2022

AbstractLatent heating (LH) profiles from the Tropical Rainfall Measuring Mission (TRMM) and the Global Precipitation Measurement mission (GPM) were employed to examine the LH distribution during the quasi‐biennial oscillation (QBO) disruption in the 2015/2016 Northern Hemispheric (NH) winter. We used the LH anomalies from the observation era climatology to compensate for the discontinuity between the TRMM and GPM LH. The difference in the LH anomalies (LHd) between the 2015/2016 winter and the typical winter coinciding with the westerly QBO phase revealed that deeper convective systems in the 2015/2016 winter shifted to the equator, releasing more latent heat relative to the convective systems in the winters coinciding with the westerly QBO phase. Comparison of the LHds calculated for each winter of 1998–2019 shows that the changes in the convective systems in the 2015/2016 winter were statistically exceptional among the changes in other winters. Inside the convective systems, stronger latent heat release and more frequent occurrences of deep convective and deep‐stratiform rain cells made up the total LHd during the 2015/2016 winter. Specifically, convective rain cells mainly derived the LHd of the convective systems in the 2015/2016 winter, except in February 2016. The results suggest that the LH increase from the typical winter with the westerly QBO phase may be considered an unusual equatorial wave source during the 2015/2016 QBO disruption. The signatures of the LHd profiles in the 10°S–10°N zonal band are sourced from the abnormal convective systems that were shifted from the western Pacific to the central‐to‐eastern Pacific.
Radio Refractive Index of Wet Atmosphere Estimated From Site Test Interferometer Data
Authors: Morabito David D. , Wu Longtao , Heckman David 
Published: September 2022

AbstractThe atmosphere plays a significant role in degrading Ka‐band (32 GHz) radio and optical communications for single antenna communications as well as degrading interferometric measurements such as used for radio astronomy and multi‐antenna arrays. Higher frequencies such as deep space Ka‐band (32 GHz) and near‐Earth K‐band (26 GHz) are more susceptible to this atmospheric degradation than at the lower frequency bands of S‐band (2.3 GHz) and X‐band (8.4 GHz). The various sources of atmospheric degradation include rain attenuation, cloud attenuation, gaseous attenuation, atmospheric noise temperature increase, and scintillation. For this study, we have focused on the strength of the turbulence caused principally by the wet atmosphere represented by the refractive index structure parameter Cn2, which is a measure of the variance of the refractive index over small incremental distances along the signal path, and thus is a strong function of water vapor variations at microwave frequencies. Here we provide a comprehensive study of this parameter derived from years of Site Test Interferometer measurements acquired from a variety of climates. We found that the strongest diurnal variation and correlation of Cn2 measurements with its model occurred for Goldstone, California representing a high‐desert climate, while weaker correlations were found for Kennedy Space Center representing a sub‐tropical climate, and Canberra, Australia and Madrid, Spain representing temperate climates. We quantified periods where the strongest correlation was observed such as Goldstone summers (as high as 0.7 for ∼3‐day periods) where the days are typically hot and humid while nights tend to be colder and drier.
Scaling Land‐Atmosphere Interactions: Special or Fundamental?
Authors: Desai Ankur R. , Paleri Sreenath , Mineau James , Kadum Hawwa , Wanner Luise , Mauder Matthias , Butterworth Brian J. , Durden David J. , Metzger Stefan 
Published: September 2022

AbstractThe highly interactive and variable nature of scales of space and time featured in components of the Earth system imparts enormous complexity to land‐atmosphere interactions. Here, we introduce an open special collection on Advances in Scaling and Modeling of Land‐Atmosphere Interactions that features articles in JGR: Biogeosciences, JGR: Atmospheres, Journal of Advances in the Modeling of Earth Systems, and Earth & Space Science. Collectively, these articles identify interactions across multiple processes, in field experiments, long‐term observations, and numerical simulations, which are then used to advance theories of scale interaction to improve predictive models.
Comment on “On the Estimation of Potential Evaporation Under Wet and Dry Conditions” by Z. Tu and Y. Yang
Authors: Szilagyi Jozsef 
Published: September 2022

AbstractIt is argued here that the wet‐surface temperature (Tws) estimation method employed by Tu and Yang for their potential evaporation estimates yields physically unreachable low values not only during dry, but frequently under wet environmental conditions as well. For these reasons it is claimed that the wet‐surface temperature estimation method of Szilagyi and Jozsa (2008, https://doi.org/10.1016/j.jhydrol.2008.03.008) may produce more realistic Tws values than the one by Yang and Roderick (2019, https://doi.org/10.1002/qj.3481) as employed by Tu and Yang (2022, https://doi.org/10.1029/2021WR031486).
MLKL post-translational modifications: road signs to infection, inflammation and unknown destinations
Authors: Liccardi Gianmaria , Annibaldi Alessandro 
Published: September 2022

AbstractNecroptosis is a caspase-independent modality of cell death that requires the activation of the executioner MLKL. In the last ten years the field gained a substantial amount of evidence regarding its involvement in host response to pathogens, TNF-induced inflammatory diseases as well as pathogen recognition receptors (PRR)-induced inflammation. However, there are still a lot of questions that remain unanswered. While it is clear that there are specific events needed to drive MLKL activation, substantial differences between human and mouse MLKL not only highlight different evolutionary pressure, but also provide potential insights on alternative modalities of activation. While in TNF-induced necroptosis it is clear the involvement of the RIPK3 mediated phosphorylation, it still remains to be understood how certain inflammatory in vivo phenotypes are not equally rescued by either RIPK3 or MLKL loss. Moreover, the plethora of different reported phosphorylation events on MLKL, even in cells that do not express RIPK3, suggest indeed that there is more to MLKL than RIPK3-mediated activation, not only in the execution of necroptosis but perhaps in other inflammatory conditions that include IFN response. The recent discovery of MLKL ubiquitination has highlighted a new checkpoint in the regulation of MLKL activation and the somewhat conflicting evidence reported certainly require some untangling. In this review we will highlight the recent findings on MLKL activation and involvement to pathogen response with a specific focus on MLKL post-translational modifications, in particular ubiquitination. This review will highlight the outstanding main questions that have risen from the last ten years of research, trying at the same time to propose potential avenues of research.
Retinoic acid and RARγ maintain satellite cell quiescence through regulation of translation initiation
Authors: Luo Wenzhe , Xu Yueyuan , Liu Ruige , Liao Yinlong , Wang Sheng , Zhang Haoyuan , Li Xinyun , Wang Heng 
Published: September 2022

AbstractIn adult skeletal muscle, satellite cells are in a quiescent state, which is essential for the future activation of muscle homeostasis and regeneration. Multiple studies have investigated satellite cell proliferation and differentiation, but the molecular mechanisms that safeguard the quiescence of satellite cells remain largely unknown. In this study, we purposely activated dormant satellite cells by using various stimuli and captured the in vivo-preserved features from quiescence to activation transitions. We found that retinoic acid signaling was required for quiescence maintenance. Mechanistically, retinoic acid receptor gamma (RARγ) binds to and stimulates genes responsible for Akt dephosphorylation and subsequently inhibits overall protein translation initiation in satellite cells. Furthermore, the alleviation of retinoic acid signaling released the satellite cells from quiescence, but this restraint was lost in aged cells. Retinoic acid also preserves the quiescent state during satellite cell isolation, overcoming the cellular stress caused by the isolation process. We conclude that active retinoic acid signaling contributes to the maintenance of the quiescent state of satellite cells through regulation of the protein translation initiation process.
Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells
Authors: Tessier Sarah , Ferhi Omar , Geoffroy Marie-Claude , González-Prieto Román , Canat Antoine , Quentin Samuel , Pla Marika , Niwa-Kawakita Michiko , Bercier Pierre , Rérolle Domitille , Tirard Marilyn , Therizols Pierre , Fabre Emmanuelle , Vertegaal Alfred C. O. , de Thé Hugues , Lallemand-Breitenbach Valérie 
Published: September 2022

AbstractMembrane-less organelles are condensates formed by phase separation whose functions often remain enigmatic. Upon oxidative stress, PML scaffolds Nuclear Bodies (NBs) to regulate senescence or metabolic adaptation. PML NBs recruit many partner proteins, but the actual biochemical mechanism underlying their pleiotropic functions remains elusive. Similarly, PML role in embryonic stem cell (ESC) and retro-element biology is unsettled. Here we demonstrate that PML is essential for oxidative stress-driven partner SUMO2/3 conjugation in mouse ESCs (mESCs) or leukemia, a process often followed by their poly-ubiquitination and degradation. Functionally, PML is required for stress responses in mESCs. Differential proteomics unravel the KAP1 complex as a PML NB-dependent SUMO2-target in arsenic-treated APL mice or mESCs. PML-driven KAP1 sumoylation enables activation of this key epigenetic repressor implicated in retro-element silencing. Accordingly, Pml−/− mESCs re-express transposable elements and display 2-Cell-Like features, the latter enforced by PML-controlled SUMO2-conjugation of DPPA2. Thus, PML orchestrates mESC state by coordinating SUMO2-conjugation of different transcriptional regulators, raising new hypotheses about PML roles in cancer.
Alternative ANKHD1 transcript promotes proliferation and inhibits migration in uterine corpus endometrial carcinoma
Authors: Sun Wenhuizi , Huang Runzhi , Li Zhenyu , Zhu Yaru , Bai Yan , Wu Siyu , Wang Jingshuai , Xiao Yan , Xian Shuyuan , Tong Xiaowen , Zhang Jie , Guo Yi , Ouyang Yiqin 
Published: September 2022

AbstractAlternative splicing (AS) is common in gene expression, and abnormal splicing often results in several cancers. Overall survival-associated splicing events (OS-SEs) have been used to predict prognosis in cancer. The aim of this study was to investigate the presence and function of OS-SEs in uterine corpus endometrial carcinoma (UCEC). Based on TCGA and TCGASpliceSeq databases, gene expression and the AS data of UCEC samples were retrieved. An alternate terminator of ANKHD1 transcripts named ANKHD1-BP3 was found to be significantly related to metastasis and OS in UCEC and significantly associated with HSPB1. The upregulated expression of HSPB1 induced downregulation of ANKHD1-BP3 and promoted tumor metastasis. These findings indicate that HSPB1, a splicing factor, regulates the expression of ANKHD1-BP3 to promote metastasis in UCEC.
Stress responses to repeated captures in a wild ungulate
Authors: Trondrud L. Monica , Ugland Cassandra , Ropstad Erik , Loe Leif Egil , Albon Steve , Stien Audun , Evans Alina L. , Thorsby Per Medbøe , Veiberg Vebjørn , Irvine R. Justin , Pigeon Gabriel 
Published: September 2022

AbstractWhile capture-mark-recapture studies provide essential individual-level data in ecology, repeated captures and handling may impact animal welfare and cause scientific bias. Evaluating the consequences of invasive methodologies should be an integral part of any study involving capture of live animals. We investigated short- and long-term stress responses to repeated captures within a winter on the physiology, behaviour, and reproductive success of female Svalbard reindeer (Rangifer tarandus platyrhynchus). Short-term responses were evaluated using serum concentrations of glucocorticoids and catecholamines during handling, and post-release recovery times in heart rate and activity levels. Repeated captures were associated with an increase in measured catecholamines and glucocorticoids, except cortisone, and delayed recovery in heart rate but not activity. Four months later, in summer, individuals captured repeatedly in winter exhibited a small increase in behavioural response to human disturbance and had a lower probability of being observed with a calf, compared to animals not captured, or captured only once. Our findings imply that single annual capture events have no significant negative consequences for Svalbard reindeer, but repeated captures within a season may impact offspring survival in the same year. Such unanticipated side effects highlight the importance of addressing multiple indicators of animal responses to repeated captures.