bluuebunny/crossref_metadata_2025_split huggingface dataset:
Change in Monarch Butterfly Winter Abundance Over the Past Decade: A Red List Perspective
Authors: Meehan Timothy D. , Crossley Michael S. 
Published: January 2023

Abstract1. Assessing invertebrate species for the IUCN Red List under Criterion A requires fitting an appropriate statistical model to available abundance data and calculating a ten-year change (TYC) estimate from predicted abundances. When the rate of change has not been constant across the entire time series, models that accommodate variable change rates are strongly recommended.2. The monarch butterfly (Danaus plexippus) was recently added to the IUCN Red List (A2ab Endangered) based on analysis of data on winter abundances in Mexico and the western USA between 1993 and 2020. TYC estimates in the monarch assessment came from models that assumed constant change rates. We conducted a Bayesian analysis of the same data using models that accommodated variable change rates and used those models to compute TYC estimates.3. Our results suggested that monarch population change rates have not been constant. The analysis yielded a model averaged TYC estimate of +5.23%, which was not statistically distinguishable from 0% and was considerably different from values of −46% and −72% in the assessment. The Bayesian posterior probability of a TYC value below −30% (A2ab Vulnerable) was 0.15 and that of a TYC value below −50% (A2ab Endangered) was 0.03.4. We suggest that a more thorough analysis of recent overwintering abundances will lead to an improved IUCN assessment for monarch butterflies. We recommend that other researchers evaluating monarch conservation status consider using models with variable change rates, as models with constant change rates may not accurately predict the trajectory of monarch abundances into the future.
Testing the accuracy of species distribution models based on community science data
Authors: Velde Mélusine , Cooper Jacob C. , Garrod Holly 
Published: January 2023

AbstractWhile traditional methods of tracking species, collecting specimens, and performing surveys are known to be accurate, additional opportunities to broaden the data pool are evolving. Community science data5has emerged as a new way of gathering large amounts of data, but little research has been done on its reliability for making models for novel locations. The goal of this project was to test the reliability of eBird data as the primary dataset for ecological niche modeling by determining the accuracy of models derived from the citizen-science based eBird dataset. I made species distribution models of 676 bird species in Costa Rica based on eBird observations to predict which species would be found in two localities in Costa Rica that were surveyed. I compared the predictions with these field surveys to determine the prediction success and Sorensen index of the models. Overall, I found that while spatio-temporal factors can affect the accuracy of ecological models, eBird data have great potential as data for species distribution modeling. The models more accurately predicted the community composition in the rural locality as opposed to the more urban locality, and the accuracy of the models increased when compared with data that covered two month as opposed to one month time periods. I tested to see how the number of observations per species influenced the predictive ability of the models and determined that an intermediate number of observations led to better models. These are important metrics to understand because modeling can be an informative and cost effective way to monitor inaccessible areas and can be used in conservation efforts.
Computational study ofPiper betleL. phytocompounds byinsilico and ADMETanalysis for prediction of potential xanthine oxidase inhibitory activity
Authors: Chakravarthi P. Vikrama , Karthikeyan M. , Lakshmanan L. , Murugesan S. , Arivuchelvan A. , Sukumar K. , Arulmozhi A. , Jagadeeswaran A. 
Published: January 2023

AbstractBackgroundXanthine oxidase (XO) enzyme is directly associated with pathogenesis of gout and indirectly with cancer, diabetes and metabolic syndromes. Allopurinol is a xanthine oxidase inhibitor which is useful in the treatment of gout but it causes side effects in humans and birds. Therefore, this study sought to identify the alternative compound from the natural resources with fewer side effects than the conventional ones.ObjectivesThe present study was designed to findout the xanthine oxidase inhibitory activity ofPiper betlephytocompounds in comparison with Allopurinol.MethodsThe detection of phytocompounds present in theP. betleL. extract was identified through Gas Chromatography Mass Spectrometry (GC-MS) analysis. Theinsilicoanalysis and ADMET properties were evaluated for the GC-MS derivedP.betlephytocompounds. Among the 32 phyto compounds ofP.betle, 18 were showed favourable affinity with xanthine oxidase and their different conformational structures were docked in schrodinger module with xanthine oxidase enzyme structure. The interpretation of results was carried out through GLIDE XP Scoring, GLIDE Energy, MM-GBSA energy and hydrogen bond and Pi-Pi interactions. Further the absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis were also carriedout using QIKPRO programme.ResultsThe results revealed that, the twelve phytocompounds ofP.betleshowed GLIDE XP docking score (−6.881 to - 4.766 Kcal/mol) higher than allopurinol (−4.535 Kcal/mol) and 11 phytocompounds showed higher GLIDE energy (−42.822 Kcal/mol to - 36.706 Kcal/mol) than allopurinol (−32.676 Kcal/mol). Chromonol and eugenol were the most potential compounds ofP.betlewhich showed both hydrogen bond and Pi-Pi interactions with the target xanthine oxidase as that of standard drug allopurinol. The selected phytocompounds satisfied the ADME descriptors and have no violation of Lipinski’s rule of five.ConclusionsTheinsilicoand ADMET profile study on the phytocompounds ofP.betlepredicted their promising potential xanthine oxidase inhibition activity and they could be developed as alternate molecules against synthetic agents byinvivoexperiments for the treatment of xanthine oxidase associated diseases like hyperuricimia and cardiovascular disorders.
Spinal cord injury in mice amplifies anxiety: a novel light-heat conflict test exposes increased salience of anxiety over heat
Authors: Lee Sydney E. , Greenough Emily K. , Fonken Laura K. , Gaudet Andrew D. 
Published: January 2023

AbstractSpinal cord injury (SCI) predisposes individuals to anxiety and chronic pain. Anxiety- and pain-like behavior after SCI can be tested in rodents, yet commonly used tests assess one variable and may not replicate effects of SCI or sex differences seen in humans. Thus, novel preclinical tests should be optimized to better evaluate behaviors relating to anxiety and pain. Here, we use our newly developed conflict test – the Thermal Increments Dark-Light (TIDAL) test – to explore how SCI affects anxiety- vs. pain-like behavior, and whether sex affects post-SCI behavior. The TIDAL conflict test consists of two plates connected by a walkway; one plate remains illuminated and at an isothermic temperature, whereas the other plate is dark but is heated incrementally to aversive temperatures. Control mice are tested with both plates illuminated (thermal place preference). Female and male mice received moderate T9 contusion SCI or remained uninjured. At 7 days post-operative (dpo), mice with SCI increased dark plate preference throughout the TIDAL conflict test compared to uninjured mice. SCI increased dark plate preference for both sexes, although female (vs. male) mice remained on the heated-dark plate to higher temperatures. Mice with SCI that repeated TIDAL at 7 and 21 dpo showed reduced preference for the dark-heated plate at 21 dpo. Overall, in female and male mice, SCI enhances the salience of anxiety (vs. heat sensitivity). The TIDAL conflict test meets a need for preclinical anxiety- and pain-related tests that recapitulate the human condition; thus, future rodent behavioral studies should incorporate TIDAL or other conflict tests to help understand and treat neurologic disorders.
The MTORC1-AHR pathway sustains translation and autophagy in tumours under tryptophan stress
Authors: Holfelder Pauline , Hensen Lucas , Prentzell Mirja Tamara , Navas Patricia Razquin , Solvay Marie , Sadik Ahmed , Sayeeram Deepak , Rehbein Ulrike , Bausbacher Tobias , Egger Anna-Sophia , Regin Leon , Heberle Alexander M. , Seifert Sophie , Leytens Alexandre , Kowar Alexander , Waltl Lorenz , Gollowitzer André , Kataura Tetsushi , Ouhadi Seema , Karabogdan Ivana , Hotze Madlen , Kipura Tobias , van Pijkeren Alienke , Zhang Yang , Peiris Maria Rodriguez , Barile Cecilia , Zhu Jingjing , Timpen Lea Emmy , Hatzmann Florian , Reintjes Anja , Berdel Bianca , Somarribas Patterson Luis F. , Reil Michèle , Peters Vera , Pittol Jose Ramos , van ˈt Land-Kuper Ineke , Eckhardt Lara E. , Sievers Philipp , Sahm Felix , Mohammed Shad A. , Börding Teresa , Harder Sönke , Loayza-Puch Fabricio , Korolchuk Viktor I. , Schlüter Hartmut , Dengjel Jörn , Koeberle Andreas , Hopf Carsten , Trump Saskia , Kwiatkowski Marcel , Sers Christine , Van den Eynde Benoit J. , Opitz Christiane A. , Thedieck Kathrin 
Published: January 2023

AbstractTumours face tryptophan (Trp) depletion, but the mechanisms sustaining protein biosynthesis under Trp stress remain unclear. We report that Trp stress increases the levels of the translation repressor EIF4EBP1. Yet, at the same time, EIF4EBP1 is selectively phosphorylated by the metabolic master regulator MTORC1 kinase, preventing EIF4EBP1 from inhibiting translation. MTORC1 activity under Trp stress is unexpected because the absence of amino acids is typically linked with MTORC1 inhibition. EIF4EBP1-sensitive translation in Trp starved cells is sustained by EGFR and RAS signalling to MTORC1. Via this mechanism, Trp stress enhances the synthesis and activity of the aryl hydrocarbon receptor (AHR). This is noteworthy as Trp catabolites are known to activate AHR, and therefore Trp stress was previously considered to inhibit AHR. Trp stress-induced AHR enhances the expression of key regulators of autophagy, which sustains intracellular Trp levels and Trp-charged tRNAs for translation. Hence, Trp stress switches MTORC1 from its established inhibitory function into an enhancer of autophagy, acting through AHR. The clinical potential of this fundamental mechanism is highlighted by the activity of the mTORC1-AHR pathway and an autophagy signature in 20% of glioblastoma patients, opening up new avenues for cancer therapy.
Ex vivotissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
Authors: Lang Niklas J. , Gote-Schniering Janine , Porras-Gonzalez Diana , Yang Lin , De Sadeleer Laurens J. , Jentzsch R. Christoph , Shitov Vladimir A. , Zhou Shuhong , Ansari Meshal , Agami Ahmed , Mayr Christoph H. , Kashani Baharak Hooshiar , Chen Yuexin , Heumos Lukas , Pestoni Jeanine C. , Geeraerts Emiel , Anquetil Vincent , Saniere Laurent , Wögrath Melanie , Gerckens Michael , Hatz Rudolf , Kneidinger Nikolaus , Behr Jürgen , Wuyts Wim A. , Stoleriu Mircea-Gabriel , Luecken Malte D. , Theis Fabian J. , Burgstaller Gerald , Schiller Herbert B. 
Published: January 2023

ABSTRACTPulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupledex vivocytokine and drug perturbations of human precision-cut lung slices (hPCLS) with scRNAseq and induced a multi-lineage circuit of fibrogenic cell states in hPCLS, which we show to be highly similar to thein vivocell circuit in a multi-cohort lung cell atlas from pulmonary fibrosis patients. Using micro-CT staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in theex vivohPCLS model provides evidence that the basaloid cell state was derived from alveolar type-2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in the hPCLS model and anti-fibrotic drug treatments showed highly cell type specific effects. Our work provides an experimental framework for perturbational single cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration and pathology. We further demonstrate that hPCLS offers novel avenues for scalable, high-resolution drug testing to accelerate anti-fibrotic drug development and translation.
Phosphorylation and Lamin B receptor modulate the accumulation of PERIOD protein foci
Authors: Li Mengna , Li Shujing , Zhang Luoying 
Published: January 2023

AbstractCircadian clock drives the 24h rhythm in our behavior and physiology. Previously, we have shown that inner nuclear membrane protein Lamin B receptor (LBR) regulates circadian rhythm in human cells andDrosophila, while the underlying mechanism is unclear (Lin et al., 2014). A very recent study reported that the circadian clock protein PERIOD is organized into discrete foci at the nuclear envelope in fly circadian neurons, which is believed to be important for controlling the subcellular localization of clock genes. Loss of LBR leads to disruption of these foci, but how they are regulated is yet unknown. Here we found that LBR likely facilitates PER foci accumulation by destabilizing the catalytic subunit of protein phosphatase 2A, MICROTUBULE STAR (MTS). MTS is known to dephosphorylate PER and hampers the accumulation of PER foci. On the other hand, the circadian kinase DOUBLETIME (DBT) which phosphorylates PER enhances the accumulation of the foci. These foci are likely phase-separated condensates, the formation of which mediated by intrinsically disordered region in PER. Taken together, here we demonstrate a key role for phosphorylation in promoting the accumulation of PER foci, while LBR modulates this process by impinging on the circadian phosphatase MTS.
Arp2/3 Complex Activity Enables Nuclear YAP for Naïve Pluripotency of Human Embryonic Stem Cells
Authors: Meyer Nathaniel P. , Singh Tania , Kutys Matthew L. , Nystul Todd , Barber Diane L. 
Published: January 2023

AbstractOur understanding of transitions of human embryonic stem cells between distinct stages of pluripotency relies predominantly on regulation by transcriptional and epigenetic programs with limited insight on the role of established morphological changes. We report remodeling of the actin cytoskeleton of human embryonic stem cells (hESCs) as they transition from primed to naïve pluripotency that includes assembly of a ring of contractile actin filaments encapsulating colonies of naïve hESCs. Activity of the Arp2/3 complex is required for the actin ring, uniform cell mechanics within naïve colonies, nuclear translocation of the Hippo pathway effectors YAP and TAZ, and effective transition to naïve pluripotency. RNA-sequencing analysis confirms that Arp2/3 complex activity regulates Hippo signaling in hESCs, and impaired naïve pluripotency with inhibited Arp2/3 complex activity is rescued by expressing a constitutively active, nuclear-localized YAP-S127A. These new findings on the cell biology of hESCs reveal a mechanism for cytoskeletal dynamics coordinating cell mechanics to regulate gene expression and facilitate transitions between pluripotency states.
Research on static fault tree analysis method for inerting system safety based on random number generation
Authors: Zhang Ruihua , Geng Leiming , Liu Weihua 
Published: January 2023

Purpose
To reduce the flammability exposure assessment time and meet the requirements of airworthiness regulations of transport aircraft, inerting system has become the standard configuration of modern civil aircraft. Therefore, airworthiness regulations put forward definite quantitative index requirements for the safety of inerting system, and to obtain the quantitative data of the safety of inerting system, it is necessary to solve the calculation method. As one of the quantitative/qualitative evaluation techniques for system safety, fault tree analysis is recognized by international airworthiness organizations and national airworthiness certification agencies. When fault tree analysis technology is applied to quantitative analysis of the safety of inerted system, there are still some problems, such as heavy margin of constructing fault tree, great difficulty, high requirement for analysts and poor accuracy of solving when there are too many minimum cut sets. However, based on tens of thousands of flight simulation tests, Monte Carlo random number generation method can solve this problem.

Design/methodology/approach
In this paper, the fault tree of airborne inerting system is established, and the top event is airborne inerting system losing air separation function. Monte Carlo method based on random number generation is used to carry out system security analysis. The reliability of this method is verified.

Findings
The static fault tree analysis method based on Monte Carlo random number generation can not only solve the problem of quantitative analysis of inerting system, but can also avoid the defects of complicated solution and inaccurate solution caused by the large number of minimum cut sets, and its calculation results have good reliability.

Practical implications
The research results of this paper can be used as supporting evidence for airworthiness compliance of airborne inerting system.

Originality/value
The research results of this paper can provide practical guidance for the current civil airworthiness certification work.
Investigating the experience of professional carers supporting individuals with intellectual disability who were at risk of admission – a qualitative study
Authors: Manandhar-Richardson Mizla , Woodrow Ceri , Cooper-Taylor Georgia 
Published: January 2023

Purpose
This study aims to understand the experiences of professional paid carers providing community support to people with intellectual disability “at risk of admission”. This study explores factors that were helpful or lacking in terms of the support the carers received from NHS health services during this time.

Design/methodology/approach
This study conducted semi-structured interview with eight participants. Thematic analysis was used to analyse the data.

Findings
Three main themes and ten subthemes were identified. The first main theme was “support systems” that were available or lacking for the client and their carers. The second main theme was “training and supervision” available to the carers and their team when the individual they supported needed additional support. The third theme was “change” clients encountered which included changes in the environment as well as changes because of COVID-19 pandemic.

Originality/value
To the best of the authors’ knowledge, this is the first study on experiences of carers during specifically high stress periods, such as when the clients they are supporting are at risk of hospital admission.
The assurance providers’ role in improving the independent assurance statement quality on sustainability reporting
Authors: Harindahyani Senny , Agustia Dian 
Published: January 2023

PurposeThis study aims to investigate the effect of assurance provider types on the independent assurance statement quality of Asian companies' sustainability report (SR) and examine environmental risk’s role as a moderating variable.Design/methodology/approachThis study analyzes large Asian companies' stand-alone SR using moderated regression analysis to test hypotheses. Textual analysis is conducted to identify environmental risk disclosures.FindingsThis study shows that accounting assurance providers affect independent assurance statement quality in terms of compliance with assurance statement elements, while nonaccounting assurance providers can better accommodate environmental risk information required by the intended users.Research limitations/implicationsThis study has several limitations. The research focuses on assurance statements and stand-alone SR of large companies in Asia; therefore, future research could examine similar analyses using integrated reports from Asia to investigate whether the results will differ. Additionally, this study does not divide assurance providers into Big-N and non-Big-N; thereby, it can be extended in future research.Practical implicationsAssurance providers need to consider environmental risk as a critical issue for the intended users to issue a high-quality independent assurance statement.Social implicationsAssurance statements issued by assurance providers increase public confidence in the reliability of the information contained in the SR. Therefore, regulators are expected to immediately set mandatory standards for sustainability assurance practices.Originality/valueThis study proves that accounting assurance providers can improve assurance statement quality. The variable environmental risk is also proven to be a pure moderator in negatively interacting the effect of assurance provider types on independent assurance statement quality.
Research and development reporting and stock performance: evidence from China
Authors: Bai Shuming , Koong Kai S. , Wang Yanni 
Published: January 2023

Purpose
China adopted its new Accounting Standards for Business Enterprises No. 6 in 2007, which substantially converges with the International Financial Reporting Standards. It stipulates that firms operating in China shall capitalize development costs provided specific criteria have been met. This paper aims to examine the effects of the new accounting policies of R&D on the value-relevance and stock performance of 36,299 Chinese firms-years from 2007 to 2020.

Design/methodology/approach
A comprehensive multi-stage analysis was conducted. Multiple linear regressions were performed on the pooled cross-sectional time-series total R&D, capitalized expenditures, expensed costs and other key financial factors to test for the effects of R&D on the stock prices, contemporaneous stock returns and subsequent stock returns for the full sample, capitalizer sample and expenser sample, respectively.

Findings
First, majority of Chinese firms (about 80% of those reported) elect to adopt expensing R&D approach, while about 20% deploys capitalization treatment. Second, key attributes such as size, profitability, leverage and R&D intensity are highly associated with capitalization propensity. Third, current capitalization affects the contemporaneous stock prices and stock returns (priced-in) with yearly volatility. Finally, intertemporal association exists between firms’ expensing costs and subsequent returns due to a delayed reaction.

Originality/value
As the world largest emerging economy, the results show that research and development information adds value, and capitalizers outperforms expensers in the area of stock performance. This strategy works irrespectively of economic development stage or capital market maturity. The findings call for more capitalization.