bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the gaps in transitional care to adulthood for patients in paediatric surgical specialties: a scoping review protocol
Authors: Lu Daisy , Wang Zhi , Clar Monique , Shen Jesse 
Published: July 2024

IntroductionTransitioning patients from their paediatric centres to adulthood is an important subject for many of these patients living with different chronic pathologies. There are few studies that assess its effectiveness in paediatric surgical pathologies. The overall objective of this scoping review is to assess the extent of the literature describing transitional programmes dedicated to young patients living with surgical conditions. The primary question will look to assess what transitional programmes are available for young patients living with surgical conditions either operated or not.Methods and analysisThe proposed scoping review will follow guidelines described by the Joanna Briggs Institute manual described by Peterset alin 2020. This protocol will employ the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols checklist. The concept that will be included in this review is the exposure of these patients to a transition of care pathway or care programmes. Patients between the ages of 16 and 30 with a surgical condition will be included. There will be no comparator. No specific outcomes will be assessed, however, the outcomes that will be found from the transition programmes will be reviewed. A knowledge synthesis librarian will search MEDLINE All (Ovid), Embase (Ovid), Web of Science Core Collection (Clarivate) and CINAHL Complete (EBSCOhost). The literature search will be limited to 2000 onwards publications. No language or age group limitation will be applied. The reference list of all included sources of evidence will be screened for additional studies. Screening of search results and data extraction from included studies will be completed in Covidence by two independent reviewers. We will also use the PAGER (Patterns, Advances, Gaps, Evidence for practice and Research recommendations) framework to report and summarise the results.Ethics and disseminationThis review does not require ethics approval. Our dissemination strategy includes peer review publication, conference presentation, co-constructed guidelines with stakeholders and policymakers.Trial registrationThis review is registered on OSF
Assessing the implications of sentinel lymph node removal in cervical cancer: an immunogenetic perspective – a SENTICOL ancillary study
Authors: Thareja Gaurav , Salvioni Anna , Lauzeral-Vizcaino Françoise , Halabi Najeeb , Mery-Lamarche Eliane , Thebault Noemie , Scarlata Clara-Maria , Michelas Marie , Navarro Anne-Sophie , Ferron Gwenaël , Lecuru Fabrice , Mathevet Patrice , Khalifa Jonathan , Ayyoub Maha , Rafii Arash , Martinez Alejandra 
Published: July 2024

BackgroundCervical cancer’s lymphatic spread primarily begins from the sentinel lymph nodes (SLNs), underlining their pivotal role in disease metastasis. However, these nodes’ immune gene expression profiles and immunoregulation mechanisms have yet to be explored.MethodsOur study aimed to elucidate the immune cell populations and their roles in the immune gene expression profile of negative SLNs compared with positive SLNs and non-SLNs using Nanostring RNA seq analysis. We performed a principal component analysis on the log2 normalized expression of 685 endogenous genes in the nCounter PanCancer Immune Profiling Panel, followed by an assessment of the differential expression of genes and immune cell type abundance.ResultsWe found significant variations in gene expression among the groups, with negative SLNs displaying overexpression of genes related to tumor-infiltrating immune cells, specifically innate cell populations. They also demonstrated the upregulation of genes involved in antigen presentation and T-cell priming. In contrast, positive SLNs were enriched in regulatory networks, suggesting their potential role in immune evasion. A comparison of negative SLNs and non-SLNs revealed increased innate and adaptive immune cell types, underscoring the ongoing T cell response to tumor antigens.ConclusionOur findings underscore a specific immunogenetic phenotype profile in negative SLNs, emphasizing their crucial role in the initial anticancer response, immunosurveillance, and the propagation of immune tolerance from the primary cervical tumor. These results highlight the potential of SLNs as a novel target for immunotherapy strategies and underscore the importance of new imaging methods for accurately identifying SLN status without removal. Future investigations are needed to understand further the immunological interplay within SLNs and their influence on cervical cancer progression.
Data from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L. 
Published: July 2024

<div>Abstract<p>Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. In this study, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to a loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell–intrinsic vulnerabilities.</p><p><b>Significance:</b> The ASPSCR1::TFE3 fusion propels the growth of alveolar soft part sarcoma by activating transcriptional programs that regulate proliferation, angiogenesis, mitochondrial biogenesis, and differentiation and can be therapeutically targeted to improve treatment.</p></div>
Earliest Metabolic Changes Associated with the Initiation of Pancreatic Cancer
Authors: Storz Peter 
Published: July 2024

Pancreatic cancer is usually detected at a late stage, when tumors have already metastasized; therefore, it has a poor prognosis with a 5-year survival rate of 11% to 12%. A key to targeting this high mortality is to develop methods for detecting the disease at a stage in which it is still local to the pancreas. However, this needs a better understanding of the events that govern pancreatic cancer oncogenesis. In this issue of Cancer Research, Neuß and colleagues report metabolic changes associated with acinar-to-ductal metaplasia (ADM), an initiating event that leads to the formation of precursor lesions for pancreatic ductal adenocarcinoma (PDAC). Their findings reveal a switch to aerobic glycolysis, increased c-MYC signaling, and increased serine metabolism as driving factors for the ADM process. These findings are important as they demonstrate that metabolic changes that drive the proliferation and metastasis of full-blown PDAC begin in the earliest lesions. The data not only provide insights into how PDAC develops but also a potential explanation for previously described findings, such as circulating lesion cells can be detected even when no carcinoma in situ is present. In summary, this article is highly relevant for furthering our understanding of how metabolic reprogramming drives the earliest events leading to PDAC development and could lay the groundwork for developing methods for early detection or intervention.See related article by Neuß et al., p. 2297
Is There a Mathematician on Board?
Authors: Fertig Elana J. 
Published: July 2024

Abstract
As convergence science is emerging as a theme in cancer research, scientists from diverse backgrounds, including mathematics, are increasingly entering our research community. The captain of a Southwest Airlines flight recently paged in jest for a mathematician to help support fuel calculations that would enable a flight to arrive safely at the American Association for Cancer Research (AACR) Annual Meeting, epitomizing the need for well-trained mathematicians to address pressing problems. Here, we summarize the roles mathematicians can play in cancer research and the support needed to facilitate their entry into the cancer research field. The inclusion of scientific diversity across quantitative and engineering disciplines is critical for advancing the understanding and treatment of cancer.
Novel Metabolites Associated With Blood Pressure After Dietary Interventions
Authors: Sun Yixi , Zhang Ruiyuan , Tian Ling , Pan Yang , Sun Xiao , Huang Zhijie , Fan Jia , Chen Jing , Zhang Kai , Li Shengxu , Chen Wei , Bazzano Lydia A. , Kelly Tanika N. , He Jiang , Bundy Joshua D. , Li Changwei 
Published: July 2024

BACKGROUND:
The blood pressure (BP) etiologic study is complex due to multifactorial influences, including genetic, environmental, lifestyle, and their intricate interplays. We used a metabolomics approach to capture internal pathways and external exposures and to study BP regulation mechanisms after well-controlled dietary interventions.

METHODS:
In the ProBP trail (Protein and Blood Pressure), a double-blinded crossover randomized controlled trial, participants underwent dietary interventions of carbohydrate, soy protein, and milk protein, receiving 40 g daily for 8 weeks, with 3-week washout periods. We measured plasma samples collected at baseline and at the end of each dietary intervention. Multivariate linear models were used to evaluate the association between metabolites and systolic/diastolic BP. Nominally significant metabolites were examined for enriching biological pathways. Significant ProBP findings were evaluated for replication among 1311 participants of the BHS (Bogalusa Heart Study), a population-based study conducted in the same area as ProBP.

RESULTS:

After Bonferroni correction for 77 independent metabolite clusters (α=6.49×10
−4
), 18 metabolites were significantly associated with BP at baseline or the end of a dietary intervention, of which 11 were replicated in BHS. Seven emerged as novel discoveries, which are as follows: 1-linoleoyl-GPE (18:2), 1-oleoyl-GPE (18:1), 1-stearoyl-2-linoleoyl-GPC (18:0/18:2), 1-palmitoyl-2-oleoyl-GPE (16:0/18:1), maltose, N-stearoyl-sphinganine (d18:0/18:0), and N6-carbamoylthreonyladenosine. Pathway enrichment analyses suggested dietary protein intervention might reduce BP through pathways related to G protein–coupled receptors, incretin function, selenium micronutrient network, and mitochondrial biogenesis.

CONCLUSIONS:
Seven novel metabolites were identified to be associated with BP at the end of different dietary interventions. The beneficial effects of protein interventions might be mediated through specific metabolic pathways.
A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth, and interactive QC with afni_proc.py and more
Authors: Taylor Paul A. , Glen Daniel R. , Chen Gang , Cox Robert W. , Hanayik Taylor , Rorden Chris , Nielson Dylan M. , Rajendra Justin K. , Reynolds Richard C. 
Published: July 2024

Abstract
Quality control (QC) assessment is a vital part of FMRI processing and analysis, and a typically underdiscussed aspect of reproducibility. This includes checking datasets at their very earliest stages (acquisition and conversion) through their processing steps (e.g., alignment and motion correction) to regression modeling (correct stimuli, no collinearity, valid fits, enough degrees of freedom, etc.) for each subject. There are a wide variety of features to verify throughout any single-subject processing pipeline, both quantitatively and qualitatively. We present several FMRI preprocessing QC features available in the AFNI toolbox, many of which are automatically generated by the pipeline-creation tool, afni_proc.py. These items include a modular HTML document that covers full single-subject processing from the raw data through statistical modeling, several review scripts in the results directory of processed data, and command line tools for identifying subjects with one or more quantitative properties across a group (such as triaging warnings, making exclusion criteria, or creating informational tables). The HTML itself contains several buttons that efficiently facilitate interactive investigations into the data, when deeper checks are needed beyond the systematic images. The pages are linkable, so that users can evaluate individual items across a group, for increased sensitivity to differences (e.g., in alignment or regression modeling images). Finally, the QC document contains rating buttons for each “QC block,” as well as comment fields for each, to facilitate both saving and sharing the evaluations. This increases the specificity of QC, as well as its shareability, as these files can be shared with others and potentially uploaded into repositories, promoting transparency and open science. We describe the features and applications of these QC tools for FMRI.
Agreement Switch in Verb-Echo Answers: Evidence for Distributed Ellipsis
Authors: Mendes Gesoel , Ruda Marta , Willer-Gold Jana , Ristić Bojana , Arsenijević Boban , Čordalija Nermina , Leko Nedžad , Malenica Frane , Marušič Franc Lanko , Masnikosa Irina , Milićev Tanja , Milićević Nataša , Mišmaš Petra , Mitić Ivana , Peti-Stantić Anita , Stanković Branimir , Tolić Matea , Tušek Jelena , Nevins Andrew 
Published: July 2024

Abstract
In this article, we claim that syntactic objects undergoing ellipsis can be targeted by both narrow syntactic and PF operations. We base this conclusion on experimental evidence from the interaction between single conjunct agreement and verb-echo answers in South Slavic, which we show to be derived via verb-stranding VP ellipsis. Adopting the view that Vocabulary Insertion replaces Q-variables on lexical heads (Halle 1991) and ellipsis is a syntactic operation which deletes Q-variables (Saab 2022), we demonstrate that constituents properly included in the ellipsis site can undergo Internal Merge in the narrow syntax, and can participate in PF processes from the derived position. The interaction between ellipsis, Internal Merge and Agree-Copy that accounts for these patterns of data follows naturally within the Distributed Ellipsis approach.
Beyond Ensemble Averages: Leveraging Climate Model Ensembles for Subseasonal Forecasting
Authors: Orlova Elena , Liu Haokun , Rossellini Raphael , Cash Benjamin A. , Willett Rebecca 
Published: July 2024

Abstract
Producing high-quality forecasts of key climate variables, such as temperature and precipitation, on subseasonal time scales has long been a gap in operational forecasting. This study explores an application of machine learning (ML) models as postprocessing tools for subseasonal forecasting. Lagged numerical ensemble forecasts (i.e., an ensemble where the members have different initialization dates) and observational data, including relative humidity, pressure at sea level, and geopotential height, are incorporated into various ML methods to predict monthly average precipitation and 2-m temperature 2 weeks in advance for the continental United States. For regression, quantile regression, and tercile classification tasks, we consider using linear models, random forests, convolutional neural networks, and stacked models (a multimodel approach based on the prediction of the individual ML models). Unlike previous ML approaches that often use ensemble mean alone, we leverage information embedded in the ensemble forecasts to enhance prediction accuracy. Additionally, we investigate extreme event predictions that are crucial for planning and mitigation efforts. Considering ensemble members as a collection of spatial forecasts, we explore different approaches to using spatial information. Trade-offs between different approaches may be mitigated with model stacking. Our proposed models outperform standard baselines such as climatological forecasts and ensemble means. In addition, we investigate feature importance, trade-offs between using the full ensemble or only the ensemble mean, and different modes of accounting for spatial variability.

Significance Statement
Accurately forecasting temperature and precipitation on subseasonal time scales—2 weeks–2 months in advance—is extremely challenging. These forecasts would have immense value in agriculture, insurance, and economics. Our paper describes an application of machine learning techniques to improve forecasts of monthly average precipitation and 2-m temperature using lagged physics-based predictions and observational data 2 weeks in advance for the entire continental United States. For lagged ensembles, the proposed models outperform standard benchmarks such as historical averages and averages of physics-based predictions. Our findings suggest that utilizing the full set of physics-based predictions instead of the average enhances the accuracy of the final forecast.
The 2023 Atlantic Hurricane Season: An Above-Normal Season despite Strong El Niño Conditions
Authors: Klotzbach Philip J. , Jones Jhordanne J. , Wood Kimberly M. , Bell Michael M. , Blake Eric S. , Bowen Steven G. , Caron Louis-Philippe , Chavas Daniel R. , Collins Jennifer M. , Gibney Ethan J. , Schreck Carl J. , Truchelut Ryan E. 
Published: July 2024

Abstract
The 2023 Atlantic hurricane season was above normal, producing 20 named storms, 7 hurricanes, 3 major hurricanes, and seasonal accumulated cyclone energy that exceeded the 1991–2020 average. Hurricane Idalia was the most damaging hurricane of the year, making landfall as a Category 3 hurricane in Florida, resulting in eight direct fatalities and 3.6 billion U.S. dollars in damage. The above-normal 2023 hurricane season occurred during a strong El Niño event. El Niño events tend to be associated with increased vertical wind shear across the Caribbean and tropical Atlantic, yet vertical wind shear during the peak hurricane season months of August–October was well below normal. The primary driver of the above-normal season was likely record warm tropical Atlantic sea surface temperatures (SSTs), which effectively counteracted some of the canonical impacts of El Niño. The extremely warm tropical Atlantic and Caribbean were associated with weaker-than-normal trade winds driven by an anomalously weak subtropical ridge, resulting in a positive wind–evaporation–SST feedback. We tested atmospheric circulation sensitivity to SSTs in both the tropical and subtropical Pacific and the Atlantic using the atmospheric component of the Community Earth System Model, version 2.3. We found that the extremely warm Atlantic was the primary driver of the reduced vertical wind shear relative to other moderate/strong El Niño events. The concentrated warmth in the eastern tropical Pacific in August–October may have contributed to increased levels of vertical wind shear than if the warming had been more evenly spread across the eastern and central tropical Pacific.
A Simple Model for Multiple Equilibria in Ice-Covered Oceans
Authors: Spall Michael A. 
Published: July 2024

Abstract
The existence of multiple equilibria (ice-covered and ice-free states) is explored using a set of coupled, nondimensional equations that describe the heat and salt balances in basins, such as the Arctic Ocean, that are subject to atmospheric forcing and two distinct water mass sources. Six nondimensional numbers describe the influences of atmospheric cooling, evaporation minus precipitation, solar radiation, atmospheric temperature, diapycnal mixing, and the temperature contrast between the two water masses. It is shown that multiple equilibria resulting from the dependence of albedo on ice cover exist over a wide range of parameter space, especially so in the weak mixing limit. Multiple equilibria can also occur if diapycnal mixing increases to O(10−4) m2 s−1 or larger under ice-free conditions due to enhanced upward mixing of warm, salty water from below. Sensitivities to various forcing parameters are discussed.

Significance Statement
The purpose of this study is to better understand under what circumstances high-latitude seas, such as the Arctic Ocean, can exist in either an ice-covered or an ice-free state. The temperature and salinity of the ocean, as well as the heat exchange with the atmosphere, are drastically different depending on which state the ocean is in. The theory presented here identifies how forcing from the atmosphere and ocean dynamics determines whether the ocean is ice covered, ice free, or possibly either one.
Unrelated donor transplantation with posttransplant cyclophosphamide vs ATG for myelodysplastic neoplasms
Authors: Chalandon Yves , Eikema Diderik-Jan , Moiseev Ivan , Ciceri Fabio , Koster Linda , Vydra Jan , Passweg Jakob , Rovira Montserrat , Ozcelik Tulay , Gedde-Dahl Tobias , Kröger Nicolaus , Potter Victoria , Yakoub-Agha Ibrahim , Rambaldi Alessandro , Itälä-Remes Maija , Tanase Alina , Onida Francesco , Gurnari Carmelo , Scheid Christof , Drozd-Sokolowska Joanna , Raj Kavita , McLornan Donal P. , Robin Marie 
Published: July 2024

Abstract
It has been reported in prospective randomized trials that antithymocyte globulin (ATG)–based graft-versus-host disease (GVHD) prophylaxis has benefits in the setting of allogeneic hematopoietic stem cell transplantation (allo-HSCT) with unrelated donors (UDs). However, the optimal GVHD prophylaxis strategy has been challenged recently by the increasing use of posttransplant cyclophosphamide (PTCY). We report from the European Society for Blood and Marrow Transplantation registry the outcomes of 960 patients with myelodysplastic neoplasms who underwent allo-HSCT from UD with PTCY or ATG as GVHD prophylaxis. The primary outcomes were overall survival (OS) and progression-free survival (PFS). The disease characteristics were similar in both groups. Day 28 neutrophil engraftment was significantly better with ATG (93% vs 85%). Over a median follow-up of 4.4 years, the 5-year OS was 58% with PTCY, and 49% in the ATG group. The 5-year PFS was higher for PTCY at 53% vs 44% for ATG. Grade 2 to 4 acute GVHD incidence was lower when PTCY was used (23%), whereas there was no difference in the incidence of chronic GVHD at 5 years. Multivariable analyses confirmed better OS and PFS with PTCY with a hazard ratio (HR) for ATG of 1.32 (1-1.74) and a better PFS for PTCY with a HR for ATG of 1.33. This study suggests that GVHD prophylaxis using PTCY instead of ATG in this setting remains a valid option. Further prospective randomized studies would be essential to confirm these results.