bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hitomi HXT deconvolution imaging of the Crab Nebula dazzled by the Crab pulsar
Authors: Morii Mikio , Maeda Yoshitomo , Awaki Hisamitsu , Hagino Kouichi , Ishida Manabu , Mori Koji 
Published: February 2024

AbstractWe develop a new deconvolution method to recover the precise Crab Nebula image taken by the Hitomi HXT, suppressing the artifact due to the bright Crab pulsar. We extend the Richardson–Lucy method, introducing two components corresponding to the nebula and pulsar with regularization for smoothness and flux, respectively, and performing simultaneous deconvolution of multi-pulse-phase images. The structures, including the torus and jets, seen in the deconvolved nebula image at the lowest energy band of 3.6–15 keV appear consistent with those identified in the high-resolution Chandra X-ray image. Above 15 keV, we confirm NuSTAR’s findings that the nebula size decreases in higher energy bands. We find that the north-east side of the nebula is fainter in higher energy bands. Our deconvolution method is applicable for any telescope images of faint diffuse objects containing a bright point source.
Bridging the Gap in Garnet Diffusion Models at Low Temperatures: Recalibration Using Western Tianshan Eclogitic Breccia
Authors: Chen Junxing , Chu Xu 
Published: February 2024

Abstract
Models concerning the diffusion of divalent cations (Ca2+, Mg2+, Fe2+, and Mn2+) in garnet have been subject to extensive research and application over several decades, yet discrepancies among available models persist. Particularly the diffusion rate of Mn2+, which is the fastest in garnet, varies by more than two orders of magnitude for garnets in eclogite. In this study, we use an eclogitic breccia sample from the Western Tianshan (ultra-) high-pressure metamorphic belt for calibration. The thermobarometry indicates that the sample experienced exhumation from ~2.45 GPa, ~480°C to 1.85 GPa, ~515°C. Previous geochronological constraints estimate the exhumation duration to be a couple of million years to up to 15–20 Myr, with an average slab exhumation rate of ~3.5 mm/year. Although the estimates entail significant uncertainties, this range is still smaller than the discrepancy of Mn diffusion rate predicted among diffusion models. Thus, this natural sample provides valuable insights for calibrating the available diffusion models. Our analysis of garnet compositional profiles demonstrates that the diffusion rates (Di) at the pressure and temperature of interest are DCa:DFe:DMg:DMn = 0.2:0.4:1:2.4. By integrating garnet profiles, pressure–temperature–time information, and existing experimental data, we refine each diffusion model for Mn2+, thereby reducing the uncertainties associated with down-temperature extrapolation. Application of the newly calibrated models indicates that the oscillatory zoning of Mn2+ at the garnet rim is best described by a brief thermal excursion (~0.4 Myr, &gt;20°C) at ~1.9 GPa. This minor thermal pulse punctuating the general exhumation path could be indicative of shear heating between nappes or momentary involvement in the mantle wedge, suggesting stacking or partial reactivation of the thrusts during exhumation.
Photoacclimation in the kleptoplastidic ciliate Mesodinium rubrum and its cryptophyte prey Teleaulax amphioxeia: phenotypic variability and implications for red tide remote sensing
Authors: Pochic Victor , Gernez Pierre , Zoffoli Maria Laura , Séchet Véronique , Carpentier Liliane , Lacour Thomas 
Published: February 2024

Abstract
Mesodinium rubrum is a kleptoplastidic ciliate that sequesters the chloroplasts and nuclei of cryptophyte algae to perform photosynthesis. Blooms of M. rubrum can cause red tides in coastal oceans worldwide. Such red tides are detectable by remote sensing, and studying M. rubrum pigments and optical properties is a crucial step toward characterizing its blooms using satellite observation. Previous studies have shown that M. rubrum photoacclimates, modifying its pigment content depending on irradiance. Using cultures at different irradiance levels, we observed that photoacclimation in M. rubrum closely resembles that of its cryptophyte prey Teleaulax amphioxeia, leading to substantial phenotypic variability. In both species, phycoerythrin 545 cellular concentrations increased 3-fold between the highest and lowest irradiance, suggesting a major role in photoacclimation. Absorption cross-section decreased, and pigment-specific absorption coefficients increased with irradiance at the peak absorption wavelengths of chlorophyll a and phycoerythrin 545. After assessing the variability of absorption properties in M. rubrum, we combined field measurements and high-resolution Sentinel-2 satellite images to estimate chlorophyll a concentration of a coastal red tide and document small-scale spatio-temporal features. This work provides an overview of pigment photoacclimation in a peculiar phytoplankter and suggests guidelines for future studies of M. rubrum blooms.
Training an automated circulating tumor cell classifier when the true classification is uncertain
Authors: Nanou Afroditi , Stoecklein Nikolas H , Doerr Daniel , Driemel Christiane , Terstappen Leon W M M , Coumans Frank A W 
Published: February 2024

Abstract
Circulating tumor cell (CTC) and tumor-derived extracellular vesicle (tdEV) loads are prognostic factors of survival in patients with carcinoma. The current method of CTC enumeration relies on operator review and, unfortunately, has moderate interoperator agreement (Fleiss’ kappa 0.60) due to difficulties in classifying CTC-like events. We compared operator review, ACCEPT automated image processing, and refined the output of a deep-learning algorithm to identify CTC and tdEV for the prediction of survival in patients with metastatic and nonmetastatic cancers. Operator review is only defined for CTC. Refinement was performed using automatic contrast maximization CM-CTC of events detected in cancer and in benign samples (CM-CTC). We used 418 samples from benign diseases, 6,293 from nonmetastatic breast, 2,408 from metastatic breast, and 698 from metastatic prostate cancer to train, test, optimize, and evaluate CTC and tdEV enumeration. For CTC identification, the CM-CTC performed best on metastatic/nonmetastatic breast cancer, respectively, with a hazard ratio (HR) for overall survival of 2.6/2.1 vs. 2.4/1.4 for operator CTC and 1.2/0.8 for ACCEPT-CTC. For tdEV identification, CM-tdEV performed best with an HR of 1.6/2.9 vs. 1.5/1.0 with ACCEPT-tdEV. In conclusion, contrast maximization is effective even though it does not utilize domain knowledge.
Inferring networks from time series: A neural approach
Authors: Gaskin Thomas , Pavliotis Grigorios A , Girolami Mark 
Published: February 2024

Abstract
Network structures underlie the dynamics of many complex phenomena, from gene regulation and foodwebs to power grids and social media. Yet, as they often cannot be observed directly, their connectivities must be inferred from observations of the dynamics to which they give rise. In this work, we present a powerful computational method to infer large network adjacency matrices from time series data using a neural network, in order to provide uncertainty quantification on the prediction in a manner that reflects both the degree to which the inference problem is underdetermined as well as the noise on the data. This is a feature that other approaches have hitherto been lacking. We demonstrate our method’s capabilities by inferring line failure locations in the British power grid from its response to a power cut, providing probability densities on each edge and allowing the use of hypothesis testing to make meaningful probabilistic statements about the location of the cut. Our method is significantly more accurate than both Markov-chain Monte Carlo sampling and least squares regression on noisy data and when the problem is underdetermined, while naturally extending to the case of nonlinear dynamics, which we demonstrate by learning an entire cost matrix for a nonlinear model of economic activity in Greater London. Not having been specifically engineered for network inference, this method in fact represents a general parameter estimation scheme that is applicable to any high-dimensional parameter space.
Additional experiments required: A scoping review of recent evidence on key aspects of Open Peer Review
Authors: Ross-Hellauer Tony , Horbach Serge P J M 
Published: February 2024

Abstract
Diverse efforts are underway to reform the journal peer review system. Combined with growing interest in Open Science practices, Open Peer Review (OPR) has become of central concern to the scholarly community. However, what OPR is understood to encompass and how effective some of its elements are in meeting the expectations of diverse communities, are uncertain. This scoping review updates previous efforts to summarize research on OPR to May 2022. Following the PRISMA methodological framework, it addresses the question: “What evidence has been reported in the scientific literature from 2017 to May 2022 regarding uptake, attitudes, and efficacy of two key aspects of OPR (Open Identities and Open Reports)?” The review identifies, analyses and synthesizes 52 studies matching inclusion criteria, finding that OPR is growing, but still far from common practice. Our findings indicate positive attitudes towards Open Reports and more sceptical approaches to Open Identities. Changes in reviewer behaviour seem limited and no evidence for lower acceptance rates of review invitations or slower turnaround times is reported in those studies examining those issues. Concerns about power dynamics and potential backfiring on critical reviews are in need of further experimentation. We conclude with an overview of evidence gaps and suggestions for future research. Also, we discuss implications for policy and practice, both in the scholarly communications community and the research evaluation community more broadly.
Immune checkpoint inhibitor-mediated polymyalgia rheumatica versus primary polymyalgia rheumatica: comparison of disease characteristics and treatment requirement
Authors: Vermeulen Olof C B , Brouwer Elisabeth , Slart Riemer H J A , Sandovici Maria , Rutgers Abraham , Hilterman T Jeroen , Hiddinga Birgitta , Oosting Sjoukje F , Jalving Mathilde , de Heij Albert H , Knapen Daan G , Hospers Geke A P , van der Geest Kornelis S M 
Published: February 2024

Abstract

Objectives
To compare clinical characteristics, imaging findings and treatment requirements of patients with immune checkpoint inhibitor-mediated polymyalgia rheumatica (ICI-PMR) and primary PMR.

Methods
This single centre, retrospective cohort study compared ICI-PMR in patients with cancer (n = 15) to patients with primary PMR (n = 37). A comparison was made between clinical symptoms, laboratory markers, ultrasonography, 18F-FDG-PET/CT findings and treatment requirements related to PMR.

Results
Patients with ICI-PMR less frequently fulfilled the EULAR/ACR classification criteria for PMR (66.7%) than patients with primary PMR (97.3%). Morning stiffness, weight loss and elevation of the ESR were less frequently seen in patients with ICI-PMR. No differences were observed regarding the presence of inflammatory lesions on ultrasound of the shoulders and hips between the two groups. The Leuven and the Leuven/Groningen 18F-FDG-PET/CT scores were significantly lower in the ICI-PMR group. Finally, the ICI-PMR group could be managed with lower glucocorticoid doses than the primary PMR group, while this treatment could be discontinued more quickly.

Conclusion
Our findings indicate that ICI-PMR may have a milder course with less intense inflammation than primary PMR. ICI-PMR can be managed with a relatively low glucocorticoid dose. Our study underscores that ICI-PMR should be regarded as a PMR-like syndrome.
Differential role of fusiform gyrus coupling in depressive and anxiety symptoms during emotion perception
Authors: Edmiston Elliot Kale , Chase Henry W , Jones Neil , Nhan Tiffany J , Phillips Mary L , Fournier Jay C 
Published: February 2024

Abstract
Anxiety and depression co-occur; the neural substrates of shared and unique components of these symptoms are not understood. Given emotional alterations in internalizing disorders, we hypothesized that function of regions associated with emotion processing/regulation, including the anterior cingulate cortex (ACC), amygdala and fusiform gyrus (FG), would differentiate these symptoms. Forty-three adults with depression completed an emotional functional magnetic resonance imaging task and the Hamilton Depression and Anxiety Scales. We transformed these scales to examine two orthogonal components, one representing internalizing symptom severity and the other the type of internalizing symptoms (anxiety vs depression). We extracted blood oxygen level dependent signal from FG subregions, ACC, and amygdala and performed generalized psychophysiological interaction analyses to assess relationships between symptoms and brain function. Type of internalizing symptoms was associated with FG3-FG1 coupling (F = 8.14, P = 0.007). More coupling was associated with a higher concentration of depression, demonstrating that intra-fusiform coupling is differentially associated with internalizing symptom type (anxiety vs depression). We found an interaction between task condition and internalizing symptoms and dorsal (F = 4.51, P = 0.014) and rostral ACC activity (F = 4.27, P = 0.012). Post hoc comparisons revealed that less activity was associated with greater symptom severity during emotional regulation. Functional coupling differences during emotional processing are associated with depressive relative to anxiety symptoms and internalizing symptom severity. These findings could inform future treatments for depression.
Strategies to enhance treatment fidelity and music-based intervention reporting in dementia research
Authors: Reschke-Hernández Alaine E , Tranel Daniel 
Published: February 2024

Abstract
Creative solutions are needed to address the well-being of the growing number of individuals living with dementia. Music-based interventions (MBIs) are promising and can be cost-effective; however, empirical evidence for MBIs is limited and published findings have not been widely translated into practice. Here, we describe how we implemented strategies to enhance rigor in a randomized clinical trial of an MBI for persons with dementia. We examined the impact of a singing-based MBI on feelings, emotions, and social engagement, relative to a non-music treatment (verbal discussion), delivered in small group format (25 minutes, 3 times/week for 2 weeks). We implemented National Institutes of Health Behavior Change Consortium strategies regarding: (i) design, (ii) interventionist training, (iii) treatment delivery, (iv) treatment receipt, and (v) treatment skills enactment. We applied the MBI Reporting Criteria including: (i) theoretical framework, (ii) musical content, (iii) dosage, (iv) interventionist, (v) treatment fidelity, (vi) setting, and (vii) delivery unit. We analyzed data with a separate linear mixed model for each dependent variable. 32 older adults with dementia (65–97 years) participated. The MBI yielded significant positive effects on all measured outcomes (all p’s &lt; .05). Application of established guidelines enhanced methodological rigor and MBI reproducibility. To support translation of research into practice, clinicians should understand how to implement an MBI reported in research. Our study illustrates practical steps to address the need for improved MBI research in persons with dementia and can provide a model for others to enhance evidence-based practice with this population.
ASB3 promotes hepatocellular carcinoma progression by mediating DR5 ubiquitination in TRAIL resistance
Authors: Huang Linlin , Che Zhihui , Liu Fuchen , Ge Mengxiao , Wu Zhaohui , Wu Lijun , Chen Wenwen , Wang Zuoyun , Zhu Zhiling , Xu Wei , Dong Qiongzhu , Yang Dongqin 
Published: February 2024

AbstractAnkyrin‐repeat proteins with a suppressor of cytokine signaling box (ASB) proteins belong to the E3 ubiquitin ligase family. 18 ASB members have been identified whose biological functions are mostly unexplored. Here, we discovered that ASB3 was essential for hepatocellular carcinoma (HCC) development and high ASB3 expression predicted poor clinical outcomes. ASB3 silencing induced HCC cell growth arrest and apoptosis in vitro and in vivo. Liver‐specific deletion of Asb3 gene suppressed diethylnitrosamine (DEN)‐induced liver cancer development. Mechanistically, ASB3 interacted with death receptor 5 (DR5), which promoted ubiquitination and degradation of DR5. We further showed that ASB3 knockdown stabilized DR5 and increased the sensitivity of liver cancer cells to the treatment of tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL) in a DR5‐dependent manner in cellular and in animal models. In summary, we demonstrated that ASB3 promoted ubiquitination and degradation of DR5 in HCC, suggesting the potential of targeting ASB3 to HCC treatment and overcome TRAIL resistance.
Defining the Learning Health Care System: An International Health System Leadership Perspective
Authors: Maggio Lauren A. , Villalba Karina , German Deborah , Kanter Steven L. , Collard Harold R. 
Published: February 2024

Abstract

Purpose
Over the past 2 decades, many academic health centers (AHCs) have implemented learning health systems (LHSs). However, the LHS has been defined with limited input from AHC leaders. This has implications because these individuals play a critical role in LHS implementation and sustainability. This study aims to demonstrate how an international group of AHC leaders defines the LHS, and to identify key considerations they would pose to their leadership teams to implement and sustain the LHS.

Method
A semistructured survey was developed and administered in 2022 to members of the Association of Academic Health Centers President’s Council on the Learning Health System to explore how AHC leaders define the LHS in relation to their leadership roles. The authors then conducted a focus group, informed by the survey, with these leaders. The focus group was structured using the nominal group technique to facilitate consensus on an LHS definition and key considerations. The authors mapped the findings to an existing LHS framework, which includes 7 components: organizational, performance, ethics and security, scientific, information technology, data, and patient outcomes.

Results
Thirteen AHC leaders (100%) completed the survey and 10 participated in the focus group. The AHC leaders developed the following LHS definition: “A learning health system is a health care system in which clinical and care-related data are systematically integrated to catalyze discovery and implementation of new knowledge that benefits patients, the community, and the organization through improved outcomes.” The key considerations mapped to all LHS framework components, but participants also described as important the ability to communicate the LHS concept and be able to rapidly adjust to unforeseen circumstances.

Conclusions
The LHS definition and considerations developed in this study provide a shared foundation and road map for future discussions among leaders of AHCs interested in implementing and sustaining an LHS.
Altered Corneal Biomechanics According to the Biomechanical E-Staging in Pellucid Marginal Degeneration
Authors: Mergen Burak , Sideroudi Haris , Seitz Berthold , Flockerzi Elias 
Published: February 2024

Purpose:
The purpose of this study was to investigate corneal biomechanics in pellucid marginal degeneration (PMD) compared with healthy controls using Corvis ST (Oculus, Germany) by using the new biomechanical E-staging (based on the Corvis Biomechanical Factor, the linearized Corvis Biomechanical Index) together with tomographic parameters.

Methods:
Corneal biomechanical and topographic data of 75 eyes of 75 patients with PMD and 75 eyes of 75 age-matched and sex-matched healthy controls were investigated. Topographic parameters (K1, K2, Kmax, central corneal thickness (CCT), and Belin/Ambrósio Deviation Index (BAD-D) were evaluated in dependence of and correlated with the biomechanically defined E-stages. Biomechanical parameters were also recorded for the 2 groups.

Results:
Patients with PMD showed higher K2, Kmax, BAD-D, and Corvis Biomechanical Factor values and a lower CCT compared with healthy controls (P < 0.001). The E-stage was positively correlated with K1, K2, Kmax, BAD-D, and intraocular pressure difference and negatively correlated with CCT. Stage-dependent analysis revealed a significant increase in K1, K2, Kmax (P < 0.001), and BAD-D (P = 0.041) in stage E3 compared with E0 and a significant decrease in stage E2 in CCT (P = 0.009) compared with E0.

Conclusions:
This study showed that patients with PMD may have a reduced corneal stiffness compared with healthy controls which worsens with increasing E-stage. Significant changes in topographic parameters were observed at stage E2 for CCT and at stage E3 for K1, K2, Kmax, and BAD-D when compared with stage E0.
Machine-learning models are superior to severity scoring systems for the prediction of the mortality of critically ill patients in a tertiary medical center
Authors: Chou Ruey-Hsing , Hsu Benny Wei-Yun , Yu Chun-Lin , Chen Tai-Yuan , Ou Shuo-Ming , Lee Kuo-Hua , Tseng Vincent S. , Huang Po-Hsun , Tarng Der-Cherng 
Published: February 2024

Background:
Intensive care unit (ICU) mortality prediction helps to guide therapeutic decision making for critically ill patients. Several scoring systems based on statistical techniques have been developed for this purpose. In this study, we developed a machine-learning model to predict patient mortality in the very early stage of ICU admission.

Methods:
This study was performed with data from all patients admitted to the intensive care units of a tertiary medical center in Taiwan from 2009 to 2018. The patients’ comorbidities, co-medications, vital signs, and laboratory data on the day of ICU admission were obtained from electronic medical records. We constructed random forest and extreme gradient boosting (XGBoost) models to predict ICU mortality, and compared their performance with that of traditional scoring systems.

Results:
Data from 12,377 patients was allocated to training (n = 9901) and testing (n = 2476) datasets. The median patient age was 70.0 years; 9210 (74.41%) patients were under mechanical ventilation in the ICU. The areas under receiver operating characteristic curves for the random forest and XGBoost models (0.876 and 0.880, respectively) were larger than those for the Acute Physiology and Chronic Health Evaluation II score (0.738), Sequential Organ Failure Assessment score (0.747), and Simplified Acute Physiology Score II (0.743). The fraction of inspired oxygen on ICU admission was the most important predictive feature across all models.

Conclusion:
The XGBoost model most accurately predicted ICU mortality and was superior to traditional scoring systems. Our results highlight the utility of machine learning for ICU mortality prediction in the Asian population.