bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting tumor genomic test results to SEER registries via linkages
Authors: Petkov Valentina I , Byun Jung S , Ward Kevin C , Schussler Nicola C , Archer Natalie P , Bentler Suzanne , Doherty Jennifer A , Durbin Eric B , Gershman Susan T , Cheng Iona , Insaf Tabassum , Gonsalves Lou , Hernandez Brenda Y , Koch Lori , Liu Lihua , Monnereau Alain , Morawski Bozena M , Schwartz Stephen M , Stroup Antoinette , Wiggins Charles , Wu Xiao-Cheng , Bonds Sarah , Negoita Serban , Penberthy Lynne 
Published: August 2024

Abstract

Background
Precision medicine has become a mainstay of cancer care in recent years. The National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) Program has been an authoritative source of cancer statistics and data since 1973. However, tumor genomic information has not been adequately captured in the cancer surveillance data, which impedes population-based research on molecular subtypes. To address this, the SEER Program has developed and implemented a centralized process to link SEER registries’ tumor cases with genomic test results that are provided by molecular laboratories to the registries.

Methods
Data linkages were carried out following operating procedures for centralized linkages established by the SEER Program. The linkages used Match*Pro, a probabilistic linkage software, and were facilitated by the registries’ trusted third party (an honest broker). The SEER registries provide to NCI limited datasets that undergo preliminary evaluation prior to their release to the research community.

Results
Recently conducted genomic linkages included OncotypeDX Breast Recurrence Score, OncotypeDX Breast Ductal Carcinoma in Situ, OncotypeDX Genomic Prostate Score, Decipher Prostate Genomic Classifier, DecisionDX Uveal Melanoma, DecisionDX Preferentially Expressed Antigen in Melanoma, DecisionDX Melanoma, and germline tests results in Georgia and California SEER registries.

Conclusions
The linkages of cancer cases from SEER registries with genomic test results obtained from molecular laboratories offer an effective approach for data collection in cancer surveillance. By providing de-identified data to the research community, the NCI’s SEER Program enables scientists to investigate numerous research inquiries.
Toward real-time reporting of cancer incidence: methodology, pilot study, and SEER Program implementation
Authors: Chen Huann-Sheng , Negoita Serban , Schwartz Steve , Hsu Elizabeth , Hafterson Jennifer , Coyle Linda , Stevens Jennifer , Fernandez Anna , Potts Mary , Feuer Eric J 
Published: August 2024

Abstract

Background
A lag time between cancer case diagnosis and incidence reporting impedes the ability to monitor the impact of recent events on cancer incidence. Currently, the data submission standard is 22 months after a diagnosis year ends, and the reporting standard is 27.5 months after a diagnosis year ends. This paper presents the National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) Program’s efforts to minimize the lag and achieve “real-time” reporting, operationalized as submission within 2 months from the end of a diagnosis year.

Methods
Technology for rapidly creating a consolidated tumor case (CTC) from electronic pathology (e-path) reports is described. Statistical methods are extended to adjust for biases in incidence rates due to reporting delays for the most recent diagnosis years.

Results
A registry pilot study demonstrated that real-time submissions can approximate rates obtained from 22-month submissions after adjusting for reporting delays. A plan to be implemented across the SEER Program rapidly ascertains unstructured e-path reports and uses machine learning algorithms to translate the reports into the core data items that comprise a CTC for incidence reporting. Across the program, cases were submitted 2 months after the end of the calendar year. Registries with the most promising baseline values and a willingness to modify registry operations have joined a program to become certified as real-time reporting.

Conclusion
Advances in electronic reporting, natural language processing, registry operations, and statistical methodology, energized by the SEER Program’s mobilization and coordination of these efforts, will make real-time reporting an achievable goal.
The SEER Program’s longstanding commitment to making cancer resources available
Authors: Murphy Patricia K , Sellers Mark E , Bonds Sarah H , Scott Susan 
Published: August 2024

Abstract
The Surveillance, Epidemiology, and End Results (SEER) Program, an authoritative source of cancer statistics in the United States, has been funded by the National Cancer Institute (NCI) since 1973. The goals of SEER include measuring the cancer burden in the United States, making the results available, and supporting cancer research. These goals render products that serve as resources for different audiences, such as cancer registrars, researchers, and the public. Cancer registrars have access to a dedicated tab on the SEER website for questions, assistance with cancer coding, and training and technical resources such as SEER*Rx and SEER Data Management System (SEER*DMS). For researchers, SEER provides access to databases and software such as SEER*Stat and other linked databases such as SEER-Medicare that may offer answers to emerging issues in the field of cancer outcomes, cancer burden, health disparities, healthcare access, diagnosis, and prevention. The public can access cancer materials such as the SEER Cancer Stat Facts sheets, SEER*Explorer, and Did You Know? video series to learn more about cancer. SEER continues to update its resources with and ahead of legislation such as the Plain Writing Act and 21st Century Integrated Digital Experience Act (IDEA) to improve both clarity and user experience. Moving forward, SEER continues to promote awareness of SEER resources, remains accessible and understandable across all audiences, and standardizes how new resources are shared with these groups. The longstanding commitment to making cancer resources available is fundamental to the value of SEER, as evidenced by testimonials from members of various audience types.
Pre-implementation determinants for digital mental health integration in Chicago pediatric primary care
Authors: Stiles-Shields Colleen , Gustafson Erika L , Lim Paulina S , Bobadilla Gabriella , Thorpe Dillon , Summersett Williams Faith C , Donenberg Geri R , Julion Wrenetha A , Karnik Niranjan S 
Published: August 2024

Abstract

Objective
Pediatric primary care (PPC) is a common treatment site for pediatric mental health, but it is currently unable to meet the needs of all teen patients, particularly those with minoritized identities and/or marginalized experiences. Digital mental health (DMH) low-intensity treatments (LITs) can increase mental health screening and care capacity in PPC, but how this is done successfully without burdening providers, patients, or families is unclear. This paper presents a pre-implementation study aimed at understanding the implementation context (PPCs in Chicago, IL) for a specific DMH LIT.

Method
Using a mixed-methods design, quantitative data from an online survey of providers assessed current DMH practices in PPC, and qualitative interviews with Pediatricians and Pediatric Psychologists examined implementation determinants for a specific DMH LIT. Quantitative data were analyzed using descriptive statistics, and interviews were analyzed using rapid qualitative assessment.

Results
Survey reports (n = 105) and interviews (n = 6) indicated low current use of DMH. Providers in PPC clinics voiced multiple reasons for low usage and low perceived feasibility, including: Consolidated Framework for Implementation Research (CFIR) Inner Setting Domain (PPC clinic workflow, responsibility and ethical considerations, patient privacy and confidentiality), CFIR Outer Setting Domain (hospital and healthcare system factors), CFIR Innovation Domain (DMH design), and a cross-cutting theme of safety.

Conclusions
Provider-reported low feasibility for integrating DMH in PPC is a call to action to partner with interdisciplinary colleagues and identify how such settings can ethically and seamlessly deliver digital evidence-based and accessible screening and care prior to implementation.
Embrace the noise: it is ok to ignore measurement error in a covariate, sometimes
Authors: Dong Hao , Millimet Daniel L 
Published: August 2024

Abstract
In linear regression models, measurement error in a covariate causes ordinary least squares (OLS) to be biased and inconsistent. Instrumental variables (IV) is a common solution. While IV is also biased, it is consistent. Here, we undertake an asymptotic comparison of OLS and IV in the case where a covariate is mismeasured for ⌊Nδ⌋ of N observations with δ∈[0,1]. We show that OLS is consistent for δ&lt;1 and is asymptotically normal and more efficient than IV for δ&lt;0.5. Simulations and an application to the impact of body mass index on family income demonstrate the practical usefulness of this result.
Extended fiducial inference: toward an automated process of statistical inference
Authors: Liang Faming , Kim Sehwan , Sun Yan 
Published: August 2024

Abstract
While fiducial inference was widely considered a big blunder by R.A. Fisher, the goal he initially set—‘inferring the uncertainty of model parameters on the basis of observations’—has been continually pursued by many statisticians. To this end, we develop a new statistical inference method called extended Fiducial inference (EFI). The new method achieves the goal of fiducial inference by leveraging advanced statistical computing techniques while remaining scalable for big data. Extended Fiducial inference involves jointly imputing random errors realized in observations using stochastic gradient Markov chain Monte Carlo and estimating the inverse function using a sparse deep neural network (DNN). The consistency of the sparse DNN estimator ensures that the uncertainty embedded in observations is properly propagated to model parameters through the estimated inverse function, thereby validating downstream statistical inference. Compared to frequentist and Bayesian methods, EFI offers significant advantages in parameter estimation and hypothesis testing. Specifically, EFI provides higher fidelity in parameter estimation, especially when outliers are present in the observations; and eliminates the need for theoretical reference distributions in hypothesis testing, thereby automating the statistical inference process. Extended Fiducial inference also provides an innovative framework for semisupervised learning.
Politeness and Authority in 3 John: Epistolary Phraseology and Rhetoric Reconsidered
Authors: Kim Kyu Seop 
Published: August 2024

Abstract
This paper examines the phraseology of three epistolary formulae—namely, the formula valetudinis initialis (opening health wish formula), the formula of joy, and the καλῶς ποιήσεις formula, in Greco-Egyptian private letters written between the first century bce and third century ce. In particular, we observe that the letter writers make an opening health wish customarily when the letter recipients’ position/status is higher or at least equal to the writers—but rarely when the recipients’ position/status is lower than the writers. Furthermore, when the opening health wishes were made in expanded and reconfigured forms, they signal intensified courtesy to the recipients. The formula of joy also reinforced the favourable atmosphere when persuasion or request was intended. In this vein, the expanded and reconfigured formula valetudinis initialis used together with the formula of joy in 3 John 2–4 shows that the Elder does not intend to write his letter from the position of a higher authority. Furthermore, in requesting hospitality, he uses the καλῶς ποιήσεις formula, indicating his intention to persuade Gaius, whom he also includes in ‘us’ (3 John 12). Thus, the epistolary rhetoric of 3 John fits better with a correspondence between partners rather than an exhortation in an institutionalised hierarchy, unlike the case of the Ignatian letters.
Stellar flares are far-ultraviolet luminous
Authors: Berger Vera L , Hinkle Jason T , Tucker Michael A , Shappee Benjamin J , van Saders Jennifer L , Huber Daniel , Reep Jeffrey W , Sun Xudong , Yang Kai E 
Published: August 2024

ABSTRACT
We identify 182 flares on 158 stars within 100 pc of the Sun in both the near-ultraviolet (NUV; $1750\!-\!2750$ Å) and far-ultraviolet (FUV; $1350\!-\!1750$ Å) using high-cadence light curves from the Galaxy Evolution Explorer. Ultraviolet (UV) emission from stellar flares plays a crucial role in determining the habitability of exoplanetary systems. However, whether such UV emission promotes or threatens such life depends strongly on the energetics of these flares. Most studies assessing the effect of flares on planetary habitability assume a 9000 K blackbody spectral energy distribution that produces more NUV flux than FUV flux ($\mathcal {R} \equiv F_{\rm FUV} / F_{\rm NUV} \approx \frac{1}{6}$). Instead, we observe the opposite with the excess FUV reaching $\mathcal {R} \approx \frac{1}{2}\!-\!2$, roughly $3\!-\!12$ times the expectation of a 9000 K blackbody. The ratio of FUV to NUV time-integrated flare energies is 3.0 times higher on average than would be predicted by a constant 9000 K blackbody during the flare. Finally, we find that the FUV/NUV ratio at peak tentatively correlates (${\sim} 2 \sigma$ significance) both with total UV flare energy and with the G − RP colour of the host star. On average, we observe higher FUV/NUV ratios at peak in $E_{\text{UV}}\gt 10^{32}$ erg flares and in flares on fully convective stars.
The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae
Authors: Kang Jong-Soo , Yu Ji-Gao , Xiang Qiao-Ping , Zhang Xian-Chun 
Published: August 2024

Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian–Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes
Authors: Harding Emma F , Mercer Lewis K , Yan Grace J H , Waters Paul D , White Peter A 
Published: August 2024

Abstract
Retroviruses are an ancient viral family that have globally coevolved with vertebrates and impacted their evolution. In Australia, a continent that has been geographically isolated for millions of years, little is known about retroviruses in wildlife, despite the devastating impacts of a retrovirus on endangered koala populations. We therefore sought to identify and characterize Australian retroviruses through reconstruction of endogenous retroviruses from marsupial genomes, in particular the Tasmanian devil due to its high cancer incidence. We screened 19 marsupial genomes and identified over 80,000 endogenous retrovirus fragments which we classified into eight retrovirus clades. The retroviruses were similar to either Betaretrovirus (5/8) or Gammaretrovirus (3/8) retroviruses, but formed distinct phylogenetic clades compared to extant retroviruses. One of the clades (MEBrv 3) lost an envelope but retained retrotranspositional activity, subsequently amplifying throughout all Dasyuridae genomes. Overall, we provide insights into Australian retrovirus evolution and identify a highly active endogenous retrovirus within Dasyuridae genomes.
Varying Selection Pressure for a Na+ Sensing Site in Epithelial Na+ Channel Subunits Reflect Divergent Roles in Na+ Homeostasis
Authors: Wang Xue-Ping , Srinivasan Priyanka , El Hamdaoui Mustapha , Blobner Brandon M , Grytz Rafael , Kashlan Ossama B 
Published: August 2024

Abstract
The epithelial Na+ channel (ENaC) emerged early in vertebrates and has played a role in Na+ and fluid homeostasis throughout vertebrate evolution. We previously showed that proteolytic activation of the channel evolved at the water-to-land transition of vertebrates. Sensitivity to extracellular Na+, known as Na+ self-inhibition, reduces ENaC function when Na+ concentrations are high and is a distinctive feature of the channel. A fourth ENaC subunit, δ, emerged in jawed fishes from an α subunit gene duplication. Here, we analyzed 849 α and δ subunit sequences and found that a key Asp in a postulated Na+ binding site was nearly always present in the α subunit, but frequently lost in the δ subunit (e.g. human). Analysis of site evolution and codon substitution rates provide evidence that the ancestral α subunit had the site and that purifying selection for the site relaxed in the δ subunit after its divergence from the α subunit, coinciding with a loss of δ subunit expression in renal tissues. We also show that the proposed Na+ binding site in the α subunit is a bona fide site by conferring novel function to channels comprising human δ subunits. Together, our findings provide evidence that ENaC Na+ self-inhibition improves fitness through its role in Na+ homeostasis in vertebrates.
Variation in the Spectrum of New Mutations among Inbred Strains of Mice
Authors: López-Cortegano Eugenio , Chebib Jobran , Jonas Anika , Vock Anastasia , Künzel Sven , Tautz Diethard , Keightley Peter D 
Published: August 2024

Abstract
The mouse serves as a mammalian model for understanding the nature of variation from new mutations, a question that has both evolutionary and medical significance. Previous studies suggest that the rate of single-nucleotide mutations (SNMs) in mice is ∼50% of that in humans. However, information largely comes from studies involving the C57BL/6 strain, and there is little information from other mouse strains. Here, we study the mutations that accumulated in 59 mouse lines derived from four inbred strains that are commonly used in genetics and clinical research (BALB/cAnNRj, C57BL/6JRj, C3H/HeNRj, and FVB/NRj), maintained for eight to nine generations by brother–sister mating. By analyzing Illumina whole-genome sequencing data, we estimate that the average rate of new SNMs in mice is ∼μ = 6.7 × 10−9. However, there is substantial variation in the spectrum of SNMs among strains, so the burden from new mutations also varies among strains. For example, the FVB strain has a spectrum that is markedly skewed toward C→A transversions and is likely to experience a higher deleterious load than other strains, due to an increased frequency of nonsense mutations in glutamic acid codons. Finally, we observe substantial variation in the rate of new SNMs among DNA sequence contexts, CpG sites, and their adjacent nucleotides playing an important role.
Suppression of SMXL4 and SMXL5 confers enhanced thermotolerance through promoting HSFA2 transcription in Arabidopsis
Authors: Pan Yajie , Yu Bofan , Wei Xin , Qiu Yuping , Mao Xin , Liu Yuelin , Yan Wei , Linghu Qianyan , Li Wenyang , Guo Hongwei , Tang Zhonghua 
Published: August 2024

Abstract
Identifying the essential factors and underlying mechanisms regulating plant heat stress (HS) responses is crucial for mitigating the threat posed by HS on plant growth, development, distribution, and productivity. In this study, we found that the Arabidopsis (Arabidopsis thaliana) super-killer2 (ski2) dicer-like4 (dcl4) mutant, characterized by RNA processing defects and the accumulation of abundant 22-nt small interfering RNAs derived from protein-coding transcripts, displayed significantly increased expression levels of HS-responsive genes and enhanced thermotolerance. These traits primarily resulted from the suppression of SMAX1-LIKE4 (SMXL4) and SMXL5, which encode 2 putative transcriptional regulators that belong to the SMXL protein family. While smxl4 and smxl5 single mutants were similar to wild type, the smxl4 smxl5 double mutant displayed substantially heightened seedling thermotolerance. Further investigation demonstrated that SMXL4 and SMXL5 repressed the transcription of HEAT-SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), encoding a master regulator of thermotolerance, independently of ethylene-response factor–associated amphiphilic repression motifs. Moreover, SMXL4 and SMXL5 interacted with HSFA1d and HSFA1e, central regulators sensing and transducing HS stimuli, and antagonistically affected their transactivation activity. In addition, HSFA2 directly bound to the SMXL4 and SMXL5 promoters, inducing their expression during recovery from HS. Collectively, our findings elucidate the role of the SMXL4/SMXL5–HSFA2 regulatory module in orchestrating plant thermotolerance under HS.
Can digital technology drive the integration of sports and health industries? Evidence from global businesses
Authors: Li Jiannan 
Published: August 2024

Abstract
The integration in sports and health industries is attracting increasing research attention, however, there is less empirical evidence about role of digital technology adoption in affecting the industrial integration. This article extends relevant research from intra-state to including cross-board cases by combing data of merger and acquisition (M&A) in global sports and health industries as well as the country-level digital adoption index. It is shown that the integration in sports and health industries is positively associated with the digital technology adoption that the country in which the acquiror firm is located. Thus, it is beneficial for policymakers to promote the digital technology use when aiming to encourage the spontaneous industrial integration in sports and health industries.