bluuebunny/crossref_metadata_2025_split huggingface dataset:
ActivePPI: quantifying protein–protein interaction network activity with Markov random fields
Authors: Wang Chuanyuan , Xu Shiyu , Sun Duanchen , Liu Zhi-Ping 
Published: September 2023

AbstractMotivationProtein–protein interactions (PPI) are crucial components of the biomolecular networks that enable cells to function. Biological experiments have identified a large number of PPI, and these interactions are stored in knowledge bases. However, these interactions are often restricted to specific cellular environments and conditions. Network activity can be characterized as the extent of agreement between a PPI network (PPIN) and a distinct cellular environment measured by protein mass spectrometry, and it can also be quantified as a statistical significance score. Without knowing the activity of these PPI in the cellular environments or specific phenotypes, it is impossible to reveal how these PPI perform and affect cellular functioning.ResultsTo calculate the activity of PPIN in different cellular conditions, we proposed a PPIN activity evaluation framework named ActivePPI to measure the consistency between network architecture and protein measurement data. ActivePPI estimates the probability density of protein mass spectrometry abundance and models PPIN using a Markov-random-field-based method. Furthermore, empirical P-value is derived based on a nonparametric permutation test to quantify the likelihood significance of the match between PPIN structure and protein abundance data. Extensive numerical experiments demonstrate the superior performance of ActivePPI and result in network activity evaluation, pathway activity assessment, and optimal network architecture tuning tasks. To summarize it succinctly, ActivePPI is a versatile tool for evaluating PPI network that can uncover the functional significance of protein interactions in crucial cellular biological processes and offer further insights into physiological phenomena.Availability and implementationAll source code and data are freely available at https://github.com/zpliulab/ActivePPI.
Teaching modern pancreatic surgery: close relationship between centralization, innovation, and dissemination of care
Authors: Perri Giampaolo , van Hilst Jony , Li Shen , Besselink Marc G , Hogg Melissa E , Marchegiani Giovanni 
Published: September 2023

Abstract

Background
Pancreatic surgery is increasingly moving towards centralization in high-volume centres, supported by evidence on the volume–outcome relationship. At the same time, minimally invasive pancreatic surgery is becoming more and more established worldwide, and interest in new techniques, such as robotic pancreatoduodenectomy, is growing. Such recent innovations are reshaping modern pancreatic surgery, but they also represent new challenges for surgical training in its current form.

Methods
This narrative review presents a chosen selection of literature, giving a picture of the current state of training in pancreatic surgery, together with the authors’ own views, and in the context of centralization and innovation towards minimally invasive techniques.

Results
Centralization of pancreatic surgery at high-volume centres, volume–outcome relationships, innovation through minimally invasive technologies, learning curves in both traditional and minimally invasive surgery, and standardized training paths are the different, but deeply interconnected, topics of this article. Proper training is essential to ensure quality of care, but innovation and centralization may represent challenges to overcome with new training models.

Conclusion
Innovations in pancreatic surgery are introduced with the aim of increasing the quality of care. However, their successful implementation is deeply dependent on dissemination and standardization of surgical training, adapted to fit in the changing landscape of modern pancreatic surgery.
Extracellular vesicles long RNA profiling identifies abundant mRNA, circRNA and lncRNA in human bile as potential biomarkers for cancer diagnosis
Authors: Zong Huajie , Yu Wenqian , Lai Hongyan , Chen Bing , Zhang Hena , Zhao Jingjing , Huang Shenglin , Li Yan 
Published: September 2023

Abstract
Extracellular vesicles (EVs) are bilayered membrane vesicles produced by living cells and secreted into the extracellular matrix. Bile is a special body fluid that is secreted by the liver cells, and extracellular vesicles long RNAs (exLRs) have not been explored in bile. In this study, exLR sequencing (exLR-seq) was performed on 19 bile samples from patients with malignant cancer or patients with biliary stones. A total of 8649 mRNAs, 13 823 circRNAs and 1105 lncRNAs were detected. The KEGG pathway analysis revealed that differentially expressed exLRs were enriched in mTOR and AMPK signaling pathway. We identified five mRNAs (EID2, LLPH, ATP6V0A2, RRP9 and MTRNR2L10), three lncRNAs (AC015922.2, AL135905.1 and LINC00921) and six circRNAs (circASH1L, circATP9A, circCLIP1, circRNF138, circTIMMDC1 and circANKRD12) were enriched in bile EV samples with cancer, and these exLRs may be potential markers used to distinguish malignant cancers from benign biliary diseases. Moreover, the tissue/cellular source components of EVs were analyzed using the EV-origin algorithm. The absolute abundance of CD4_naive and Th1 cell source in bile EVs from cancer patients were significantly increased. In summary, our study presented abundant exLRs in human bile EVs and provides some basis for the selection of tumor diagnostic markers.
A national clinician survey on the British Society for Dermatological Surgery guidelines on antithrombotic agent use in skin surgery
Authors: Butt Eman , Hunt William , Defty Clare , Hussain Walayat , Bray Adam , Wernham Aaron 
Published: September 2023

Abstract
Antithrombotic medication is taken by 14–22% patients undergoing skin surgery, with more patients now taking direct oral anticoagulants (DOACs). The latest evidence suggests that the risk of stopping DOACs perioperatively is low in skin surgery, particularly for primary closures, but remains unclear for more complex procedures. The 2016 British Society for Dermatological Surgery (BSDS) guidelines suggest that clinicians could consider stopping DOACs in patients for 24–48 h, based on individual bleeding risk. We surveyed BSDS members to better understand clinical practice and guideline adherence with a view to updating the guidance. The results demonstrated that there is consistency among clinicians in the management of patients on more established antithrombotic agents, such as aspirin, clopidogrel and warfarin. However, there is a higher perceived risk of significant haematomas following higher-risk procedures such as larger flaps or grafts with DOACs vs. other antithrombotics postoperatively. Stopping DOACs perioperatively for 24–48 h for higher-risk procedures can be cautiously considered following an individual risk assessment and informed discussion with the patient.
Mendelian randomization analysis implicates bidirectional associations between brain imaging-derived phenotypes and ischemic stroke
Authors: Jia Yiming , Sun Hongyan , Sun Lulu , Wang Yinan , Xu Qingyun , Liu Yi , Chang Xinyue , He Yu , Guo Daoxia , Shi Mengyao , Chen Guo-Chong , Zheng Jin , Zhang Yonghong , Zhu Zhengbao 
Published: September 2023

Abstract
Brian imaging-derived phenotypes (IDPs) have been suggested to be associated with ischemic stroke, but the causality between them remains unclear. In this bidirectional two-sample Mendelian randomization (MR) study, we explored the potential causal relationship between 461 imaging-derived phenotypes (n = 33,224, UK Biobank) and ischemic stroke (n = 34,217 cases/406,111 controls, Multiancestry Genome-Wide Association Study of Stroke). Forward MR analyses identified five IDPs associated with ischemic stroke, including mean diffusivity (MD) in the right superior fronto-occipital fasciculus (1.22 [95% CI, 1.11–1.34]), MD in the left superior fronto-occipital fasciculus (1.30 [1.17–1.44]), MD in the anterior limb of the right internal capsule (1.36 [1.22–1.51]), MD in the right anterior thalamic radiation (1.17 [1.09–1.26]), and MD in the right superior thalamic radiation (1.23 [1.11–1.35]). In the reverse MR analyses, ischemic stroke was identified to be associated with three IDPs, including high isotropic or free water volume fraction in the body of corpus callosum (beta, 0.189 [95% confidence interval, 0.107–0.271]), orientation dispersion index in the pontine crossing tract (0.175 [0.093–0.257]), and volume of the third ventricle (0.219 [0.138–0.301]). This bidirectional two-sample MR study suggested five predictors and three diagnostic markers for ischemic stroke at the brain-imaging level. Further studies are warranted to replicate our findings and clarify underlying mechanisms.
A novel deep-learning image condition for locating earthquake
Authors: Kuang Wenhuan , Zhang Jie , Zhang Wei 
Published: September 2023

SUMMARY
Migration-based earthquake location methods may encounter the polarity reversal issue due to the non-explosive components of seismic sources, leading to an unfocused migration image. Such a problem usually makes it difficult to accurately retrieve the optimal location from the migrated source image. In this study, by taking advantage of the general pattern recognition ability of the convolutional neural network, we propose a novel deep-learning image condition (DLIC) to address this issue. The proposed DLIC measures the goodness of waveform alignments for both P and S waves, and it follows the geophysical principle of seismic imaging that the best-aligned waveforms represent fully a best-imaged source location. A synthetic test shows that the DLIC can effectively overcome the polarity reversal issues. Real data applications to southern California show that the DLIC can enhance the focusing of the migrated source image over the classic source scanning algorithm. Further tests show that the DLIC applies to continuous seismic data, to regions with few previously recorded earthquakes, and has the potential to locate small earthquakes. The proposed DLIC shall benefit the migration-based source location methods.
The crisis of physician well-being in Nepal: a multifaceted dilemma demanding urgent intervention
Authors: Singh Bivek 
Published: September 2023

Abstract
The healthcare system in Nepal faces challenges despite the establishment of numerous medical colleges and an increasing number of doctors. The distribution of medical colleges is disproportionately concentrated in urban areas, leaving rural populations without quality health care. The mental well-being of physicians is a growing concern, with studies indicating high levels of burnout, stress, and depression among healthcare workers, worsened by the Coronavirus Disease 2019 (COVID-19) pandemic. Rising suicide rates among medical professionals highlight the severity of burnout and depression in the healthcare sector. Factors contributing to this crisis include inadequate recruitment in government hospitals, a shortage of healthcare professionals, and inefficiencies in resource distribution. Attacks on physicians have become alarmingly frequent, necessitating comprehensive studies to understand the challenges faced by different specialties and the impact of rural versus urban settings. To address these issues, prompt filling of vacant positions in government hospitals and prioritizing physicians’ mental health is crucial. The government should offer competitive salaries, effective management, and supportive working environments to combat the brain drain. Initiatives inspiring professionals to stay in Nepal, along with maintaining the National Health Insurance Program and controlling healthcare privatization, are necessary. Resilience training, professional programs, and improved infrastructure in government medical colleges are vital. This crisis demands global attention and a national study to evaluate burnout, depression, and suicide among healthcare professionals. By addressing these challenges and supporting the well-being of healthcare workers, Nepal can work toward a sustainable healthcare system that provides quality care for all.
Nine Explananda in Search of an Explanans
Authors: Davies David 
Published: September 2023

AbstractIntuitively speaking, a multiple artwork is one that admits of multiple ‘instances’ which are capable of playing a particular role in the appreciation of the work. The ‘explananda’ in the title of this article are things that have been proposed as requiring explanation by any adequate ontology of multiple artworks so conceived. This assumes that the ontology of art is in the business of explaining certain things, an assumption I defend. At least nine purported explananda have been proposed in the relevant literature. I begin by offering a preliminary sketch of these explananda, identifying how they are grounded in our ordinary artistic practice and discourse, and how they have structured recent debates in the ontology of art. I next argue that the notion of ‘instance’ must be understood in a particular way if instance multiplicity is to capture the standard distinction between singular and multiple art forms. I then assess the relative significance and implications of the nine explananda for an adjudication of the debates in the ontology of art. I identify problems for the historically dominant ‘type’ theory of multiples, and propose an alternative account that speaks to all nine explananda. I conclude by reflecting on where this leaves us and how we should proceed.
SAI-CH-6: Development of a Short Form of the State Anxiety Inventory for Children At-Risk for Type 1 Diabetes
Authors: Driscoll Kimberly A , Melin Jessica , Lynch Kristian F , Smith Laura B , Johnson Suzanne Bennett 
Published: September 2023

Abstract

Objective
To develop a reliable and valid short form of the State Anxiety Subscale of the State-Trait Anxiety Inventory for Children (STAI-CH) in the Environmental Determinants of Diabetes in the Young (TEDDY) study.

Methods
A Development Sample of 842 10-year-old TEDDY children completed the STAI-CH State Subscale about their type 1 diabetes (T1D) risk. The best 6 items (three anxiety-present and three anxiety-absent) for use in a short form (SAI-CH-6) were identified via item-total correlations. SAI-CH-6 reliability was examined in a Validation Sample (n = 257) of children who completed the full 20-item STAI-CH State Subscale and then again in an Application Sample (n = 2,710) who completed only the SAI-CH-6. Expected associations between the children’s SAI-CH-6 scores and country of residence, sex, T1D family history, accuracy of T1D risk perception, worry about getting T1D, and their parents’ anxiety scores were examined.

Results
The SAI-CH-6 was reliable (α = 0.81–0.87) and highly correlated with the full 20-item STAI-CH State Subscale (Development Sample: r = 0.94; Validation Sample: r = 0.92). SAI-CH-6 scores detected significant differences in state anxiety symptoms associated with T1D risk by country, T1D family history, accuracy of T1D risk perception, and worry about getting T1D and were correlated with the child’s parent’s anxiety.

Conclusion
The SAI-CH-6 appears useful for assessing children’s state anxiety symptoms when burden and time limitations prohibit the use of the STAI-CH. The utility of the SAI-CH-6 in older children with and without chronic conditions needs to be assessed.
The effect of the adiabatic assumption on asteroseismic scaling relations for luminous red giants
Authors: Zinn Joel C , Pinsonneault Marc H , Bildsten Lars , Stello Dennis 
Published: September 2023

ABSTRACT
Although stellar radii from asteroseismic scaling relations agree at the per cent level with independent estimates for main sequence and most first-ascent red giant branch (RGB) stars, the scaling relations over-predict radii at the tens of per cent level for the most luminous stars ($R \gtrsim 30 \, \mathrm{R}_{\odot }$). These evolved stars have significantly superadiabatic envelopes, and the extent of these regions increase with increasing radius. However, adiabaticity is assumed in the theoretical derivation of the scaling relations as well as in corrections to the large frequency separation. Here, we show that a part of the scaling relation radius inflation may arise from this assumption of adiabaticity. With a new reduction of Kepler asteroseismic data, we find that scaling relation radii and Gaia radii agree to within at least 2 per cent for stars with $R \lesssim 30\, \mathrm{R}_{\odot }$, when treated under the adiabatic assumption. The accuracy of scaling relation radii for stars with $50\, \mathrm{R}_{\odot }\lesssim R \lesssim 100\, \mathrm{R}_{\odot }$, however, is not better than $10~{{\ \rm per \, cent}}-15~{{\ \rm per \, cent}}$ using adiabatic large frequency separation corrections. We find that up to one third of this disagreement for stars with $R \approx 100\, \mathrm{R}_{\odot }$ could be caused by the adiabatic assumption, and that this adiabatic error increases with radius to reach 10 per cent at the tip of the RGB. We demonstrate that, unlike the solar case, the superadiabatic gradient remains large very deep in luminous stars. A large fraction of the acoustic cavity is also in the optically thin atmosphere. The observed discrepancies may therefore reflect the simplified treatment of convection and atmospheres.
Determination method of co-orbital objects in the solar system
Authors: Ding Ying , Qi Yi , Qiao Dong 
Published: September 2023

ABSTRACT
In this paper, based on two-dimensional maps from the semi-analytical Hamiltonian approach, we proposed an improved determination method to classify co-orbital objects in the solar system without numerical integration. Taking advantage of a simple pattern analysis, we present two certainty conditions to recognize co-orbital objects with uncertain orbital parameters. Then, our determination method is applied to classify potential co-orbital objects (PCOs) of Mars, Jupiter, Saturn, Uranus, and Neptune, and then their results are verified through numerical integration in the multiplanet model, respectively. Through our method, we identify 11 new co-orbital objects for the first time, including four Mars trojans i.e. tadpole (TP) objects, one short-term Mars quasi-satellite (QS), one Mars horseshoe (HS), one Jupiter QS, one short-term Uranus trojan, one Uranus PCO, and one Neptune PCO with short-term transitions between QS and HS, and one Neptune PCO with short-term transition between QS and TP. Numerical computation shows that except Saturn PCOs significantly perturbed by Jupiter, our determination method for co-orbital objects in the solar system is effective, but it cannot deal with the classification of PCOs near the boundary of different co-orbital regions. Since our method does not rely on time-consuming numerical integration, it is efficient and suitable for a large amount of screening for numerous co-orbital objects in the solar system.
De-noising of galaxy optical spectra with autoencoders
Authors: Scourfield M , Saintonge A , de Mijolla D , Viti S 
Published: September 2023

ABSTRACT
Optical spectra contain a wealth of information about the physical properties and formation histories of galaxies. Often though, spectra are too noisy for this information to be accurately retrieved. In this study, we explore how machine learning methods can be used to de-noise spectra and increase the amount of information we can gain without having to turn to sample averaging methods such as spectral stacking. Using machine learning methods trained on noise-added spectra – Sloan Digital Sky Survey (SDSS) spectra with Gaussian noise added – we investigate methods of maximizing the information we can gain from these spectra, in particular from emission lines, such that more detailed analysis can be performed. We produce a variational autoencoder (VAE) model, and apply it on a sample of noise-added spectra. Compared to the flux measured in the original SDSS spectra, the model values are accurate within 0.3–0.5 dex, depending on the specific spectral line and signal-to-noise ratio. Overall, the VAE performs better than a principal component analysis method, in terms of reconstruction loss and accuracy of the recovered line fluxes. To demonstrate the applicability and usefulness of the method in the context of large optical spectroscopy surveys, we simulate a population of spectra with noise similar to that in galaxies at z = 0.1 observed by the Dark Energy Spectroscopic Instrument (DESI). We show that we can recover the shape and scatter of the mass–metallicity relation in this ‘DESI-like’ sample, in a way that is not possible without the VAE-assisted de-noising.
Chemical enrichment of ICM within the Centaurus cluster – I. Radial profiles
Authors: Gatuzz Efrain , Sanders J S , Dennerl K , Liu A , Fabian A C , Pinto C , Eckert D , Walker S A , ZuHone J 
Published: September 2023

ABSTRACT
We examine deep XMM–Newton European Photon Imaging Camera pn observations of the Centaurus cluster to study the hot intracluster medium (ICM) and radial metal distributions within such an environment. We found that the best-fitting spectral model corresponds to a lognormal temperature distribution, with discontinuities around ∼10, ∼50, and ∼100 kpc, also observed in the abundance distributions. We measured the radial profiles of O, Si, S, Ar, Ca, and Fe. These profiles reveal prominent negative gradients for distances &lt;90 kpc, which then transition to flatter profiles. We modelled X/Fe ratio profiles with a linear combination of core-collapse supernova and Type Ia supernova (SNIa) models. The best-fitting model suggests a uniform SNIa percentage contribution to the total cluster enrichment, thus supporting an early enrichment of the ICM, with most of the metals present being produced before clustering.
The cosmological simulation code OpenGadget3 – implementation of meshless finite mass
Authors: Groth Frederick , Steinwandel Ulrich P , Valentini Milena , Dolag Klaus 
Published: September 2023

ABSTRACT
Subsonic turbulence plays a major role in determining properties of the intracluster medium (ICM). We introduce a new meshless finite mass (MFM) implementation in OpenGadget3 and apply it to this specific problem. To this end, we present a set of test cases to validate our implementation of the MFM framework in our code. These include but are not limited to: the soundwave and Kepler disc as smooth situations to probe the stability, a Rayleigh–Taylor and Kelvin–Helmholtz instability as popular mixing instabilities, a blob test as more complex example including both mixing and shocks, shock tubes with various Mach numbers, a Sedov blast wave, different tests including self-gravity such as gravitational freefall, a hydrostatic sphere, the Zeldovich-pancake, and a 1015 M⊙ galaxy cluster as cosmological application. Advantages over smoothed particle hydrodynamics (SPH) include increased mixing and a better convergence behaviour. We demonstrate that the MFM-solver is robust, also in a cosmological context. We show evidence that the solver preforms extraordinarily well when applied to decaying subsonic turbulence, a problem very difficult to handle for many methods. MFM captures the expected velocity power spectrum with high accuracy and shows a good convergence behaviour. Using MFM or SPH within OpenGadget3 leads to a comparable decay in turbulent energy due to numerical dissipation. When studying the energy decay for different initial turbulent energy fractions, we find that MFM performs well down to Mach numbers $\mathcal {M}\approx 0.01$. Finally, we show how important the slope limiter and the energy-entropy switch are to control the behaviour and the evolution of the fluids.