bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socially (Un)constructed Subjectivity
Authors: Zahavi Dan 
Published: January 2025

Abstract
The chapter discusses and criticizes a variety of social constructivist approaches to first-person experience. It first considers evidence from developmental psychology and then turns to ideas found in the anthropological and sociological literature. It argues that strong constructivist positions like the ones found in Markus and Kitayama, Geertz and Collins often conflate different explanatory agendas and frequently move from the claim that our experiential life is shaped by social interaction and culture to the claim that it is enabled by social interaction and culture. This chapter argues that careful distinctions between various cultural, conceptual, and experiential perspectives on the different dimensions of self are needed.
The Living and the Dead
Authors: King Laura 
Published: January 2025

Abstract
This chapter outlines the book’s approach, methodology, and its parameters in terms of period and place. It summarizes the book’s focus on the relationship between living and dead within families, arguing that there are politics at work in who gets to be remembered and what counts as history at both a societal and family level. It outlines the methodology of ‘collaborative critical family history’, involving in-depth collaboration with family historians, as well as interviews and access to their personal archives. It explores the effect of bringing the author’s own family into the research. It puts forward the book’s key arguments, that death and the dead are very present in family life, that family histories are a key way in which families make themselves, and that this methodology allows us to examine those processes of history-making as well as what families did in the past.
Stories
Authors: King Laura 
Published: January 2025

Abstract
This final main chapter examines perhaps the most slippery and the most meaningful part of how families connect with their dead and their histories—storytelling. It considers how stories are told within families, and why. It examines how stories change in their telling, and mean different things to different people. It considers the wide range of emotions stories can bring about, and how families navigate both the positive tales of success with the secrets and difficult moments in a family’s past. In doing so, it navigates how stories are a key material from which families’ identities and shared sense of themselves are made.
Comparative evaluation of PD-L1 expression and tumor immune microenvironment in molecular subtypes of muscle-invasive bladder cancer and its correlation with survival outcomes
Authors: Khandakar Hena , Kaushal Seema , Seth Amlesh , Sahoo Ranjit K , Narwal Anubhav , Jangir Hemlata , Nayak Brusabhanu , Dinda Amit K 
Published: January 2025

Abstract

Objectives
Immune checkpoint inhibitors have revolutionized treatment of platinum-refractory advanced bladder cancer, offering hope where options are limited. Response varies, however, influenced by factors such as the tumor’s immune microenvironment and prior therapy. Muscle-invasive bladder cancer (MIBC) is stratified into molecular subtypes, with distinct clinicopathologic features affecting prognosis and treatment. This study assessed the expression of programmed cell death 1 ligand 1 (PD-L1) and other immune markers in MIBC, categorized by molecular phenotype.

Methods
Using GATA3 and CK5/6 immunohistochemistry, 90 neoadjuvant chemotherapy–naive MIBC cases were classified into luminal and non-luminal subtypes. The immune microenvironment was characterized through immunostaining for PD-L1, CD4, and CD8. We applied PD-L1 positivity thresholds of 1% or greater for tumor cells and 5% or greater for immune cells. Tumors were examined for PD-L1 expression, histologic subtypes, and immune cell infiltration.

Results
Varied expression of PD-L1 and T-cell subtype densities were observed among MIBC subtypes. The double-negative subtype displayed the highest PD-L1 immune cell expression and stromal CD4 and CD8 T-cell densities, indicating an active immune profile. The basal subtype exhibited the highest PD-L1 positivity in tumor cells. In contrast, the luminal type showed the lowest PD-L1 tumor and immune cell expression, with high intratumoral CD4 T-cell density. Although PD-L1 expression in tumor or immune cells did not independently affect survival, patients with basal and double-negative tumors had poorer overall survival.

Conclusions
This study highlighted the immune diversity of MIBC in the context of molecular subtypes. Distinct molecular and immune profiles could guide the development of predictive signatures for enhanced immunotherapy response in advanced bladder cancer.
Laboratory-developed tests and in vitro diagnostics: A regulatory overview for anatomic pathology
Authors: Genzen Jonathan R , Miller Lauren J , Rets Anton V , Affolter Kajsa E 
Published: January 2025

Abstract

Objectives
The US Food and Drug Administration’s Final Rule on laboratory-developed tests was published on May 6, 2024. The objective of this article is to explain the Final Rule and existing in vitro diagnostic regulations in the context of anatomic pathology.

Methods
The Final Rule, US in vitro diagnostic regulations, guidance documents, government publications, websites, news articles, and publications were reviewed, with sources including the Federal Register, the Code of Federal Regulations, the US Code, statutory text, PubMed, and Internet resources. Regulations applicable to device classifications and product codes relevant to anatomic pathology were highlighted.

Results
The Final Rule outlines requirements and enforcement discretion policies applicable to anatomic pathology, including the Food and Drug Administration’s targeted enforcement discretion for “1976-type” laboratory-developed tests and partial enforcement discretion with laboratory-developed tests for unmet needs. Existing regulations, including the classification and requirements applicable to Class I, II, and III medical devices, are reviewed, including those for immunohistochemistry kits and reagents, analyte specific reagents, and research use only reagents and equipment.

Conclusions
Pathologists, laboratory directors, managers, and supervisors responsible for anatomic pathology testing should be familiar with existing regulations and the Final Rule to ensure compliance with federal laws and regulations.
HER2 fluorescence in situ hybridization groups 2-4 breast cancers classified as positive after targeted recounts following equivocal (2+) immunohistochemistry
Authors: Wilcock Diane , Sirohi Deepika , Coleman Joshua F , Adelhardt Parisa , Kim Jong Taek , Albertson Daniel , Affolter Kajsa , Beech Cameron , Jedrzkiewicz Jolanta , Ruano Ana L , Cleary Allison S , Mahlow Jonathan , Balatico Michael , Gulbahce H Evin 
Published: January 2025

Abstract

Objectives
To investigate the correlation between the extent of (percentage of tumor cells) immunohistochemistry (IHC) staining and final human epidermal growth factor receptor 2 (HER2)–positive result in fluorescence in situ hybridization (FISH) groups 2 to 4 with equivocal (2+) IHC requiring second, blinded FISH evaluation.

Methods
Breast cancer cases submitted for HER2 FISH testing with group 2 to 4 results were included.

Results
Of the 2548 cases with HER2 FISH groups 2 to 4 that had HER2 IHC performed, 1104 (43.3%) (76/182 [41.8%] of group 2, 94/161 [58.4%] of group 3, 934/2205 [42.4%] of group 4) had equivocal (2+) IHC. After second blinded, IHC-guided recounts, 217 of 1104 (19.7%) (17/76 [22.4%], 75/94 [79.8%], 125/934 [13.4%] of FISH groups 2, 3, 4 with IHC 2+, respectively) had final HER2-positive status. Only 13 of 217 (6%) of the cases with HER2-positive status had more than 50% circumferential staining of the tumor targeted for rescoring.

Conclusions
In over 90% of HER2 FISH group 2 to 4 breast cancers with equivocal (2+) IHC followed by targeted, blinded second FISH evaluation and final HER2-positive result, the amplified population of tumor cells was limited (&lt;50%). Current guidelines recommend cancers having 10% to 50% of the subpopulation with amplified cells classified as having genetic heterogeneity (GH), which have a poor response to targeted therapies. Identifying these tumors as having GH and/or repeat testing may be recommended.
EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events
Authors: Wang Yubo , Zhu Haoran , Wang Yansong , Yang Yuning , Huang Yujian , Zhang Jian , Wong Ka-chun , Li Xiangtao 
Published: January 2025

Abstract

Motivation
Predicting RNA-binding proteins (RBPs) is central to understanding post-transcriptional regulatory mechanisms. Here, we introduce EnrichRBP, an automated and interpretable computational platform specifically designed for the comprehensive analysis of RBP interactions with RNA.

Results
EnrichRBP is a web service that enables researchers to develop original deep learning and machine learning architectures to explore the complex dynamics of RBPs. The platform supports 70 deep learning algorithms, covering feature representation, selection, model training, comparison, optimization, and evaluation, all integrated within an automated pipeline. EnrichRBP is adept at providing comprehensive visualizations, enhancing model interpretability, and facilitating the discovery of functionally significant sequence regions crucial for RBP interactions. In addition, EnrichRBP supports base-level functional annotation tasks, offering explanations and graphical visualizations that confirm the reliability of the predicted RNA-binding sites. Leveraging high-performance computing, EnrichRBP provides ultra-fast predictions ranging from seconds to hours, applicable to both pre-trained and custom model scenarios, thus proving its utility in real-world applications. Case studies highlight that EnrichRBP provides robust and interpretable predictions, demonstrating the power of deep learning in the functional analysis of RBP interactions. Finally, EnrichRBP aims to enhance the reproducibility of computational method analyses for RBP sequences, as well as reduce the programming and hardware requirements for biologists, thereby offering meaningful functional insights.

Availability and implementation
EnrichRBP is available at https://airbp.aibio-lab.com/. The source code is available at https://github.com/wangyb97/EnrichRBP, and detailed online documentation can be found at https://enrichrbp.readthedocs.io/en/latest/.
Bipartite interference and air pollution transport: estimating health effects of power plant interventions
Authors: Zigler Corwin , Liu Vera , Mealli Fabrizia , Forastiere Laura 
Published: January 2025

Abstract
Evaluating air quality interventions is confronted with the challenge of interference since interventions at a particular pollution source likely impact air quality and health at distant locations, and air quality and health at any given location are likely impacted by interventions at many sources. The structure of interference in this context is dictated by complex atmospheric processes governing how pollution emitted from a particular source is transformed and transported across space and can be cast with a bipartite structure reflecting the two distinct types of units: (i) interventional units on which treatments are applied or withheld to change pollution emissions; and (ii) outcome units on which outcomes of primary interest are measured. We propose new estimands for bipartite causal inference with interference that construe two components of treatment: a “key-associated” (or “individual”) treatment and an “upwind” (or “neighborhood”) treatment. Estimation is carried out using a covariate adjustment approach based on a joint propensity score. A reduced-complexity atmospheric model characterizes the structure of the interference network by modeling the movement of air parcels through time and space. The new methods are deployed to evaluate the effectiveness of installing flue-gas desulfurization scrubbers on 472 coal-burning power plants (the interventional units) in reducing Medicare hospitalizations among 21,577,552 Medicare beneficiaries residing across 25,553 ZIP codes in the United States (the outcome units).
Validation of non-invasive methods for the measurement of gonadal and inter-renal steroid hormones in a desert-adapted amphibian (Scaphiopus couchii)
Authors: Baugh Alexander T , Cho Callie , Onyango-Opiyo Alice , Rodner Sophie A , Mieth Senna , Oakes Daniel , Halstead Liam 
Published: January 2025

Abstract
For aquatic and semi-aquatic vertebrates like amphibians, it is possible to estimate excreted hormone levels using non-invasive methods such as waterborne and salivary sampling. These techniques allow monitoring of endocrine activity over varying, repeated and simultaneous integration periods while minimizing handling-related stress that can ‘contaminate’ hormone estimates, including estimates of baseline glucocorticoids. Here we have validated the extraction and quantification of three steroid hormones (corticosterone, CORT; 17-b estradiol, E2; testosterone, TST) in Couch’s spadefoots (Scaphiopus couchii)—a desert-adapted anuran of special interest for physiology, evolution and conservation—using non-invasive waterborne and minimally invasive salivary hormone methods. We combined extraction and enzyme immunoassay methods to conduct conventional technical validations of parallelism, recovery and time-course. Next, we carried out biological validations by testing the correlation between excreted and circulating concentrations and conducting pharmacological challenges. We found that all three hormones can be precisely estimated from 60-min water baths, exhibit robust parallelism, and have high recoveries. Further, we demonstrated that secretory responses to pharmacological challenges can be detected in waterborne CORT in male and female frogs; in TST and E2 in male frogs, but not consistently for TST or E2 in female frogs. Lastly, plasma hormone concentrations were consistently correlated with their waterborne complements for CORT (both sexes), as well as TST and E2 in males (but not females). Plasma CORT was also positively correlated with salivary CORT. Together, our findings suggest that sampling waterborne and salivary hormones offers a minimally invasive method that field endocrinologists and conservation physiologists can use to obtain biologically informative endocrine estimates from desert-adapted amphibians.
Pacific Northwest native plants and native cultivars, part I: pollinator visitation
Authors: Hayes Jen J-M , Bell Nicole C , Best Lincoln R , Bruslind Svea R , Johnson Devon O , Mead Mallory E , Spofford Tyler S , Langellotto Gail A 
Published: January 2025

Abstract
Planting native flora is a popular conservation strategy for pollinators. When searching for native plants, consumers may encounter cultivars of native plants, which can have different phenotypic traits than plants found in wild populations (“wild-type native plants”). Previous research evaluating pollinator visitation to wild-type native plants and native cultivars has yielded mixed results, in terms of whether their visitation rates are similar or distinct. We established a garden experiment in Corvallis, Oregon, to examine pollinator visitation and utilization of Pacific Northwest native plant species and cultivars. Over 3 years, we collected and observed bees (Hymenoptera: Apoidea), butterflies (Lepidoptera: Papilionoidea), and syrphid flies (Diptera: Syrphidae) to understand (i) if plant pairs had different visitation rates, (ii) whether any pollinators were associated with differential visitation, and (iii) if specialist taxa preferred wild types over cultivars. Pollinator visitation rates varied by plant and pollinator groupings, but in comparisons between native plant and cultivar pairs, native plants were preferred 37.2% of the time (n = 29 comparisons), cultivars 7.7% of the time (n = 6), and there was no difference in 55.1% of comparisons (n = 43). Our pollinator community data found native plants had greater observed total pollinator richness (except for 1 tie) and bee richness than cultivars, though predicted richness varied. Specialist bees were collected more often from wild types. Cultivars with high visitation rates were minimally developed selections, as opposed to interspecific hybrids. Our results join a growing body of literature in suggesting wild-type native and minimally developed plants should be emphasized for supporting pollinator fauna.
Preventing common mental health problems by increasing neighbourhood socioeconomic status: a mental health impact assessment in Rotterdam, the Netherlands
Authors: Kosīte Daina , van Lenthe Frank J , Nieuwenhuijsen Mark J , Beenackers Mariëlle A 
Published: January 2025

Abstract
Neighbourhood socioeconomic status (NSES) has been identified as a determinant of mental health. In this study, we aimed to quantify how many cases of common mental health problems could be prevented by increasing NSES in the most socioeconomically deprived neighbourhoods in Rotterdam, the Netherlands, and how the increases in NSES would affect mental health inequalities. We used publicly available data for conducting a quantitative Health Impact Assessment (HIA) of two counterfactual policy scenarios. In Scenario 1, we set the NSES to the Rotterdam median score for all neighbourhoods which were below the Rotterdam median. In Scenario 2, we set the NSES score to the Dutch national average socioeconomic status score for the neighbourhoods that were below the national average. We estimated that Scenario 1 could prevent 5847 (95% CI, 2700–7999) or 10.7% of annual cases of common mental health problems, and Scenario 2 could prevent 10 713 (95% CI, 4875–14 799) or 19.6% of annual cases in Rotterdam while also reducing mental health inequalities between neighbourhoods in both scenarios. Given the substantial improvements in population mental health that enhanced neighbourhood socioeconomic conditions would bring, policy implementation is urgently needed.
Advancing personalized medicine: key priorities for clinical studies and funding systems based on a Europe–China collaborative Delphi survey
Authors: Osti Tommaso , Savoia Cosimo , Farina Sara , Beccia Flavia , Causio Francesco Andrea , Wang Lily , Wang Wenya , Fotino Carmen , Cadeddu Chiara , Ricciardi Walter , Boccia Stefania 
Published: January 2025

Abstract
Personalized medicine (PM) has the potential to revolutionize healthcare by delivering treatments tailored to individual patients based on their unique characteristics. However, ensuring its effective implementation presents complex challenges, particularly in terms of long-term sustainability. To address these challenges, the IC2PerMed project fosters collaboration between the European Union and China. This study, building on insights from the project, aims to identify key priorities for advancing PM, focusing on Clinical Studies and Funding Systems, with special attention to optimizing resource management, distribution, and protection to support sustainable development. A two-round Delphi survey was conducted to achieve consensus on common priorities among China and Europe related to Clinical Studies and Funding Systems. Consensus was measured using the Content Validity Index, requiring an agreement level of 80% or higher for item inclusion. The survey identified 20 key priorities in PM research, split evenly between research initiatives and funding mechanisms. Notable priorities include developing technology for deep phenotyping, standardizing methodological approaches, and fostering public–private collaborations. In funding, the emphasis was placed on involving patient voices in research design and establishing synergies among funders to support larger projects. The findings underscore the importance of structured collaboration between Europe and China in advancing personalised medicine. By addressing identified priorities in research and funding, this initiative can significantly enhance the efficacy of PM, ultimately improving healthcare outcomes globally. The study sets a precedent for future international partnerships aimed at fostering innovation in health sciences.
Cell integrity limits ploidy in budding yeast
Authors: Barker Juliet , Murray Andrew , Bell Stephen P 
Published: January 2025

Abstract
Evidence suggests that increases in ploidy have occurred frequently in the evolutionary history of organisms and can serve adaptive functions to specialized somatic cells in multicellular organisms. However, the sudden multiplication of all chromosome content may present physiological challenges to the cells in which it occurs. Experimental studies have associated increases in ploidy with reduced cell survival and proliferation. To understand the physiological challenges that suddenly increased chromosome content imposes on cells, we used S. cerevisiae to ask how much chromosomal DNA cells may contain and what determines this limit. We generated polyploid cells using 2 distinct methods causing cells to undergo endoreplication and identified the maximum ploidy of these cells, 32–64C. We found that physical determinants that alleviate or exacerbate cell surface stress increase and decrease the limit to ploidy, respectively. We also used these cells to investigate gene expression changes associated with increased ploidy and identified the repression of genes involved in ergosterol biosynthesis. We propose that ploidy is inherently limited by the impacts of growth in size, which accompany whole-genome duplication, to cell surface integrity.
Data reuse in agricultural genomics research: challenges and recommendations
Authors: Hafner Alenka , DeLeo Victoria , Deng Cecilia H , Elsik Christine G , S Fleming Damarius , Harrison Peter W , Kalbfleisch Theodore S , Petry Bruna , Pucker Boas , Quezada-Rodríguez Elsa H , Tuggle Christopher K , Koltes James E 
Published: January 2025

Abstract
The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Here, we identify the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research. We propose possible solutions stakeholders could implement to mitigate and overcome these challenges and provide an optimistic perspective on the future of genomics and transcriptomics data reuse.
Divisional Applications and Patent Portfolios in Europe: Will Patenting Strategies Change after the Introduction of the Unitary Patent and the UPC?
Authors: Arezzo Emanuela 
Published: January 2025

Abstract
For many years now, at least in some central sectors in modern economies, we have witnessed the collapse of the classical idea that the invention would be protected by a single title of protection. More and more often, companies protect their innovations through patent portfolios, also because of the strategic advantages that the cluster grants to the owner. This paper aims to analyse the discipline of divisional patents as a tool for building a patent portfolio or cluster. The article will then focus on how (and if) the patenting strategies of companies that typically hold portfolios of exclusive rights will change following the recent entry into force of the new unitary patent and the Unified Patent Court.