bluuebunny/crossref_metadata_2025_split huggingface dataset:
The plot must thicken: a call for increased attention to social surprises in scenarios of climate futures
Authors: Keys Patrick W 
Published: July 2023

Abstract
Climate change scenarios are typically based on trajectories of greenhouse gas emissions out into the future. These emissions are then incorporated into climate and earth system models to simulate pathways of global climate change. These pathways are often communicated as the average of numerous model simulations. Though essential for calculating the role of greenhouse gas emissions on the climate system, this approach inadvertently masks the fact that our future will conform to something akin to a single model simulation, or storyline—rather than the average of many simulations. Human responses to and interactions with these climate storylines will not necessarily be expected or rational. As such, potential social surprises could lead to multiple plotlines emerging from a single earth system storyline. Such social surprises are explored in three examples: net zero emissions achievement, low climate sensitivity, and solar climate intervention. Climate change scenarios are fundamentally dependent on policy pathways that in practice will be influenced by public perception and expectation. Thus, it is essential for climate change scenarios to recognize and incorporate the potential for heterogeneous social surprises to unexpected climate changes.
An Intestinal Th17 Subset is Associated with Inflammation in Crohn’s Disease and Activated by Adherent-invasive Escherichia coli
Authors: Paroni Moira , Leccese Gabriella , Ranzani Valeria , Moschetti Giorgia , Chiara Matteo , Perillo Federica , Ferri Sara , Clemente Francesca , Noviello Daniele , Conforti Francesco Simone , Ferrero Stefano , Karnani Bhavna , Bosotti Roberto , Vasco Chiara , Curti Serena , Crosti Maria Cristina , Gruarin Paola , Rossetti Grazisa , Conte Maria Pia , Vecchi Maurizio , Pagani Massimiliano , Landini Paolo , Facciotti Federica , Abrignani Sergio , Caprioli Flavio , Geginat Jens 
Published: July 2023

Abstract
IFNγ-producing ex-Th17 cells [‘Th1/17’] were shown to play a key pathogenic role in experimental colitis and are abundant in the intestine. Here, we identified and characterised a novel, potentially colitogenic subset of Th17 cells in the intestine of patients with Crohn’s disease [CD]. Human Th17 cells expressing CCR5 [‘pTh17’] co-expressed T-bet and RORC/γt and produced very high levels of IL-17, together with IFN-γ. They had a gene signature of Th17 effector cells and were distinct from established Th1/17 cells. pTh17 cells, but not Th1/17 cells, were associated with intestinal inflammation in CD, and decreased upon successful anti-TNF therapy with infliximab. Conventional CCR5[-]Th17 cells differentiated to pTh17 cells with IL-23 in vitro. Moreover, anti-IL-23 therapy with risankizumab strongly reduced pTh17 cells in the intestine. Importantly, intestinal pTh17 cells were selectively activated by adherent-invasive Escherichia coli [AIEC], but not by a commensal/probiotic E. coli strain. AIEC induced high levels of IL-23 and RANTES from dendritic cells [DC]. Intestinal CCR5+Th1/17 cells responded instead to cytomegalovirus and were reduced in ulcerative colitis [UC], suggesting an unexpected protective role. In conclusion, we identified an IL-23–inducible subset of human intestinal Th17 cells. pTh17 cells produced high levels of pro-inflammatory cytokines, were selectively associated with intestinal inflammation in CD, and responded to CD-associated AIEC, suggesting a key colitogenic role.
Predictors of pituitary tumour behaviour: an analysis from long-term follow-up in 2 tertiary centres
Authors: Lenders Nèle F , Earls Peter E , Wilkinson Adam C , Costin Monique , Hofer Monika , Shein Tint T , Harvey Richard J , Krishnan Gayathri , Picallo Maria , Pal Aparna , Wass John , McCormack Ann I 
Published: July 2023

Abstract

Objectives
To determine the clinical utility of assessment of tumour invasion, markers of proliferation, and the French clinicopathological classification in pituitary tumour prognostication.

Methods
This is a retrospective evaluation of adult patients undergoing pituitary surgery at Oxford University and St Vincent's Hospitals, between 1989 and 2016, with at least 12 months of clinical data. Invasion was assessed radiologically, proliferative markers (Ki67, mitotic count, p53) by immunohistochemistry. Tumours were graded according to the clinicopathological classification. Intra- and interlaboratory variability of histopathology reporting was evaluated.

Outcomes
(1) Tumour recurrence (radiological or reintervention ≥12 months postoperatively) and/or (2) “aggressive behaviour” (≥4 interventions and/or invasive tumour with recurrence/reintervention between 12 and 24 months postoperatively).

Results
A total of 386 patients were included, age at surgery was 56 (interquartile range [IQR] 41-67) years, 54% were male, and median follow-up was 90 months (range 44-126). Tumours were predominantly clinically nonfunctioning (252, 65%), with overall 53% invasive, and 10% that demonstrated ≥2 proliferative marker positivity. Recurrence was predicted by invasiveness (hazards ratio [HR] 1.6 [1.10-2.37], P .02), elevated mitotic count (HR 2.17 [1.21-3.89], P .01), grade (2b vs 1a HR 2.32 [1.06-5.03], P .03), and absence of gross total resection (HR 3.70 [1.72-8.00], P .01). Clinically defined aggressiveness was associated with elevated Ki67, mitotic count, and invasiveness. Ki67 reporting methodologies showed moderate correlation across laboratories (Phi 0.620), whereas p53 reporting reproducibility was poor (Phi 0.146).

Conclusions
Proliferative markers, including Ki67 and mitotic count, but not p53, are important in predicting the development of aggressive pituitary tumour behaviour.
Chromosome-level genome assembly of Hydractinia symbiolongicarpus
Authors: Kon-Nanjo Koto , Kon Tetsuo , Horkan Helen R , Febrimarsa  , Steele Robert E , Cartwright Paulyn , Frank Uri , Simakov Oleg 
Published: July 2023

Abstract
Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism.
Parameter Estimation and Species Tree Rooting Using ALE and GeneRax
Authors: Williams Tom A , Davín Adrián A , Morel Benoit , Szánthó Lénárd L , Spang Anja , Stamatakis Alexandros , Hugenholtz Philip , Szöllősi Gergely J 
Published: July 2023

Abstract
ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria—where there is less certainty about the root position—ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
Science, Religion, and Morality
Authors: Stone Alison 
Published: July 2023

Abstract
The relations among science, morality, and religion were intensely debated by Victorian intellectuals, but generally, women’s contributions to these debates have been ignored. This chapter restores them to the record. It looks, first, at Frances Power Cobbe (1822–1904) and her account of how morality necessarily depends on religion, specifically Christianity. Second, the chapter considers the different engagements with Darwinism of Cobbe and Frances Julia Wedgwood (1833–1913). Third, the chapter introduces a pair of debates, one between Cobbe and Vernon Lee (1856–1935), the other between Cobbe and Annie Besant (1847–1933). Both Lee and Besant defended versions of secularism while Cobbe counterargued that no secularist morality was possible.
Augusta Ada Lovelace (1815–1852)
Authors: Krämer Sybille 
Published: July 2023

Abstract
In recent literature Ada Lovelace is considered the first programmer and a pioneer of information technology. But what justifies our interpreting her as an original philosopher as well? This chapter distinguishes three philosophical aspects of her thought: (1) The idea that the universality of the machine is not founded in the calculation of numbers, but in the computation of general symbols. (2) The idea of a “science of operations,” the core of which is to manipulate and combine not quantities, but patterns. This idea stands in the intellectual tradition of an ars combinatoria, a characteristica universalis, and a mathesis universalis. (3) A reflection on the relationship between human being and machine, not as a substitution and surpassing of humans by the machine, but from the perspective that human and machine can provide mutual assistance. Lovelace’s contribution to philosophy can be summarized as “ontology and ethics of operativity.”
Arendt, Poetry and Music
Authors: Sjöholm Cecilia 
Published: July 2023

Abstract
This chapter focuses on Hannah Arendt’s concept of sounding. It explores Arendt’s focus on music and poetry producing the phenomena of aesthetics and politics. Arendt’s assertion of an intrinsic relationship between music and poetry offers a way of interpreting musical and poetic works as inherently political. Mood, tone, and sounding belong to the world of appearances that hold inherent political capacity by displaying an explosive ability to give voice to the dispossessed. The chapter then considers Arendt’s basic assumption that music and poetry, as artworks, uphold an ontological status of permanence, while also referencing an immersion in emotions and radical subjectivity.
Expanding Phenomenological Methods
Authors: Høffding Simon 
Published: July 2023

Abstract
This chapter argues that musicking and musical absorption constitute a ripe field for phenomenological investigations because such musical activity engages a number of intertwined bodily, affective, and cognitive capacities, such as different forms of memory, attention, reflection and meta-cognition, imagination, mind wandering, and empathy. These capacities, in turn, connect back to core discussions in orthodox phenomenological philosophy. From here, the chapter ventures into a presentation of using qualitative, “phenomenological interviews” for enlightening the phenomenology of musical absorption while critically engaging with core insights in debates on expertise and the psychology of music. Finally, the chapter expands to include insights from physiological and psychological experimental science proposing how one could structure “research concerts” that integrate phenomenological, qualitative, and quantitative traditions into live citizen science events.
The osmotic stress–activated receptor-like kinase DPY1 mediates SnRK2 kinase activation and drought tolerance in Setaria
Authors: Zhao Meicheng , Zhang Qi , Liu Hong , Tang Sha , Shang Chunyue , Zhang Wei , Sui Yi , Zhang Yuxue , Zheng Chunyan , Zhang Hui , Liu Cuimei , Chu Jinfang , Jia Guanqing , Wang Haigang , Liu Xigang , An Diaoguo , Zhu Feng , Zhi Hui , Wu Chuanyin , Diao Xianmin 
Published: July 2023

Abstract
Plant genomes encode many receptor-like kinases (RLKs) that localize to the cell surface and perceive a wide variety of environmental cues to initiate downstream signaling cascades. Whether these RLKs participate in dehydration stress signaling in plants is largely unknown. DROOPY LEAF1 (DPY1), a leucine-rich repeat (LRR)-RLK, was recently shown to regulate plant architecture by orchestrating early brassinosteroid signaling in foxtail millet (Setaria italica). Here, we show that DPY1 is essential for the acclimation of foxtail millet to drought stress. DPY1 can be phosphorylated and activated in response to osmotic stress and is required for more than half of osmotic stress–induced global phosphorylation events, including the phosphorylation of sucrose nonfermenting kinase 2s (SnRK2s), the central kinases involved in osmotic stress. DPY1 acts upstream of STRESS-ACTIVATED PROTEIN KINASE 6 (SAPK6, a subclass I SnRK2) and is required for full SAPK6 activation, thereby allowing regulation of downstream genes to mount a response against drought stress. These signaling events are largely independent of DPY1-mediated brassinosteroid signaling. The DPY1-SAPK6 module is specific to seed plants and is absent in ancestral nonseed plants. Our findings reveal a dehydration stress–activated RLK that plays an indispensable role in osmotic stress signaling and mediates SnRK2 activation at the cell surface.
CardioMotion: identification of functional and structural cardiotoxic liabilities in small molecules through brightfield kinetic imaging
Authors: Stebbeds William , Raniga Kavita , Standing David , Wallace Iona , Bayliss James , Brown Andrew , Kasprowicz Richard , Dalmas Wilk Deidre , Deakyne Julianna , Clements Peter , Chaudhary Khuram W , Rossman Eric I , Bahinski Anthony , Francis Jo 
Published: July 2023

Abstract
Cardiovascular toxicity is an important cause of drug failures in the later stages of drug development, early clinical safety assessment, and even postmarket withdrawals. Early-stage in vitro assessment of potential cardiovascular liabilities in the pharmaceutical industry involves assessment of interactions with cardiac ion channels, as well as induced pluripotent stem cell-derived cardiomyocyte-based functional assays, such as calcium flux and multielectrode-array assays. These methods are appropriate for the identification of acute functional cardiotoxicity but structural cardiotoxicity, which manifests effects after chronic exposure, is often only captured in vivo. CardioMotion is a novel, label-free, high throughput, in vitro assay and analysis pipeline which records and assesses the spontaneous beating of cardiomyocytes and identifies compounds which impact beating. This is achieved through the acquisition of brightfield images at a high framerate, combined with an optical flow-based python analysis pipeline which transforms the images into waveform data which are then parameterized. Validation of this assay with a large dataset showed that cardioactive compounds with diverse known direct functional and structural mechanisms-of-action on cardiomyocytes are identified (sensitivity = 72.9%), importantly, known structural cardiotoxins also disrupt cardiomyocyte beating (sensitivity = 86%) in this method. Furthermore, the CardioMotion method presents a high specificity of 82.5%.
The Experiences of Nursing Students for Whom English Is an Additional Language in Preparing for and Taking Examinations
Authors: Cooper-Lara Peter 
Published: July 2023

Abstract

AIM
This study explored the experiences of prelicensure nursing students for whom English is an additional language when preparing for and taking course examinations.

BACKGROUND
English-as-an-additional-language students face challenges related to language comprehension on nursing examinations. Recognizing their unique obstacles may assist in designing equitable assessments and processes that improve outcomes.

METHOD
Responding to 14 semistructured, guided questions, 16 students discussed their experiences preparing for and taking nursing examinations.

RESULTS
Three primary themes related to student academic success emerged: psychological factors, perseverance, and factors affecting outcomes. Data revealed language as a factor that affected outcomes. Positive factors of note included self-confidence and diligence to succeed.

CONCLUSION
The results outline challenges faced by nursing students for whom English is an additional language and include strategies for promoting equity and academic success.
CONTOUR Australia: Condition of Submental Fullness and Treatment Outcomes with Belkyra Registry
Authors: Boxley Sarah G. , Lin Frank , Lee See Neville , St. Rose Suzanne , Battucci Simona , Simonyi Susan 
Published: July 2023

Background:
Submental fat (SMF) contributes to an aged or overweight appearance that may negatively impact an individual’s psychological well-being. Deoxycholic acid (ATX-101) is an injectable formulation of deoxycholic acid approved to treat SMF. The Condition of Submental Fullness and Treatment Outcomes Registry (CONTOUR) Australia study was designed to understand treatment patterns and outcomes with ATX-101 in Australia.

Methods:
CONTOUR Australia was a phase 4, prospective, observational, multicenter registry that enrolled adults considering treatment for SMF reduction.

Results:
The registry enrolled 86 patients from six sites. Significant changes from baseline through the end of treatment indicated improvement in mild to moderate fullness associated with SMF on the Clinician-Reported SMF Rating Scale and the Patient-Reported SMF Rating Scale, improvement in SMF-associated psychological impact after treatment on the Patient-Reported SMF Impact Scale, no overall worsening in skin laxity based on Submental Skin Laxity Grade, and increased patient satisfaction with the face/chin on the Subject Self-Rating Scale after receiving treatment. Adverse events were all mild and mostly related to the injection site (ie, bruising and swelling).

Conclusion:
CONTOUR Australia observed clinically meaningful and significant outcomes and further supports ATX-101 as a well-tolerated and effective treatment for SMF reduction.
ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin
Authors: Cacho-Navas Cristina , López-Pujante Carmen , Reglero-Real Natalia , Colás-Algora Natalia , Cuervo Ana , Conesa José Javier , Barroso Susana , Rivas Gema de , Ciordia Sergio , Paradela Alberto , D’Agostino Gianluca , Manzo Carlo , Feito Jorge , Andrés Germán , Molina-Jiménez Francisca , Majano Pedro , Correas Isabel , Carazo Jose María , Nourshargh Sussan , Huch Meritxell , Millán Jaime 
Published: July 2023

ABSTRACTEpithelial Intercellular Adhesion Molecule (ICAM)-1 is apically polarized, interacts with and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures (BCs). We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.
An application on forecasting for stock market prices: hybrid of some metaheuristic algorithms with multivariate adaptive regression splines
Authors: Sabancı Dilek , Kılıçarslan Serhat , Adem Kemal 
Published: July 2023

PurposeBorsa Istanbul 100 Index, known as BIST100, is the main indicator to measure the performance of the 100 highest stocks publicly traded in Borsa Istanbul concerning market and trading volume. BIST 100 index prediction is a popular research domain for its complex data structure caused by stock price, commodity, interest rate and exchange rate effects. The study proposed hybrid models using both Genetic, Particle Swarm Optimization, Harmony Search and Greedy algorithms from metaheuristic algorithms approach for dimension reduction, and MARS for prediction.Design/methodology/approachThis paper aims to model in the simplest way through metaheuristic algorithms hybridized with the MARS model the effects of stock, commodity, interest and exchange rate variables on BIST 100 during the Covid-19 pandemic period (in the process of closing) between January 2020 and June 2021.FindingsThe most suitable hybrid model was chosen as PSO & MARS by calculating the RMSE, MSE, GCV, MAE, MAD, MAPE and R2 measurements of training, test and overall dataset to check every model's efficiency. Empirical results demonstrated that the proposed PSO & MARS hybrid modeling procedure gave results both as good as the MARS model and a simpler and non-complex model structure.Originality/valueUsing metaheuristic algorithms as a supporting tool for variable selection can help to identify important independent variables and contribute to the establishment of more non-complex models.ing, test and overall dataset to check every model's efficiency.