bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do we measure organisational wellness? Development of a comprehensive patient-centred and employee-centred visual analytical solution
Authors: Watkins Scott Christopher , Hammerschmidt Christine , Gray Geoffrey M , Green Angela , Varughese Anna , Ahumada Luis 
Published: December 2022

BackgroundDashboards are visual information systems frequently employed by healthcare organisations to track key quality improvement and patient safety performance metrics. The typical healthcare dashboard focuses on specific metrics, disease processes or units within a larger healthcare organisation. Here, we describe the development of a visual analytical solution (keystone dashboard) for monitoring an entire healthcare organisation.MethodsThe improvement team reviewed and assessed various data sources across the organisation and selected a group of patient and employee related metrics that afforded a broad overview of the organisation’s well-being. Metrics spanned the organisation and included data from patient safety, quality improvement, human resources, risk management and medical staff affairs. Each metric was assigned a numeric weight that correlated with its impact. A visual model incorporating the various data fields was then constructed.ResultsThe keystone dashboard incorporates a data heatmap and density visualisation to emphasis areas of higher density and/or weighted values. The heatmap is used to indicate the weight/magnitude of each metric within a data range in two dimensions: location and time. The visualisation ‘heats up’ depending on the combination of counts events and their assigned impact for the reporting month. Most data sources update in near real time.SummaryThe keystone dashboard serves as a comprehensive and collaborative integration of data from patient safety, quality improvement, human resources, risk management and medical staff affairs. This visual analytical solution incorporates and analyses metrics into a single view with the intent of providing valuable insight into the health of an entire organisation. This dashboard is unique as it provides a broad overview of a healthcare organisation by incorporating key metrics that span the organisation.
Characterising the axial phenotype of psoriatic arthritis: a study comparing axial psoriatic arthritis and ankylosing spondylitis with psoriasis from the REGISPONSER registry
Authors: Michelena Xabier , López-Medina Clementina , Erra Alba , Juanola Xavier , Font-Ugalde Pilar , Collantes Eduardo , Marzo-Ortega Helena 
Published: December 2022

AimsTo explore the clinical and radiographical characteristics of axial psoriatic arthritis (PsA) and to compare it with ankylosing spondylitis (AS) with psoriasis.MethodsCross-sectional study from the national multicentre registry REGISPONSER where participants fulfilled the European Spondyloarthropathy Study Group spondyloarthritis criteria at entry. Clinical, laboratory and radiographical characteristics between patients classified as axial PsA and AS with psoriasis by their rheumatologist are compared according to HLA-B27 status.ResultsOf 2367 patients on REGISPONSER, n=405 had PsA, of whom 27% (n=109) had axial involvement as per the treating rheumatologist. 30% (n=26/86) of axial PsA were HLA-B27 positive. In the AS group, 9% (127/1422) had a history of psoriasis and were more frequently male, with longer diagnostic delay and more anterior uveitis than those with axial PsA who had more peripheral involvement and nail disease. Patients with HLA-B27-negative axial PsA reported less inflammatory pain and structural damage compared with AS with psoriasis. By contrast, HLA-B27-positive axial PsA shared clinical characteristics similar to AS and psoriasis although with a lower BASRI score. In the multivariable analysis, patients with AS and psoriasis were independently associated with HLA-B27 positivity (OR 3.34, 95% CI 1.42 to 7.85) and lumbar structural damage scored by BASRI (OR 2.14, 95% CI 1.4 to 3.19).ConclusionThe more prevalent axial PsA phenotype is predominantly HLA-B27 negative and presents different clinical and radiological manifestations when compared with AS with psoriasis. There is great heterogeneity in what rheumatologists consider axial PsA from a clinical and imaging perspective, highlighting the need for research into possible genetic drivers and a consensus definition.
Chapter 13. Biozonation of the Jurassic–lowermost Cretaceous of the North Sea region
Authors: Copestake Philip , Partington Mark A. 
Published: December 2022

Abstract
An updated, integrated biozonation scheme for the Jurassic (Hettangian)–lowermost Cretaceous (Upper Berriasian) of the North Sea Basin incorporates 49 palynology biozones plus subzones (based on dinocysts, spores and pollen) and 27 microfaunal zones plus subzones (based on foraminifera, radiolaria and ostracods) to provide the essential chronostratigraphic calibration of the defined sequences. The biozonation scheme is tied to standard ammonite zonal chronostratigraphy wherever possible. Parts of the biozonation scheme are also applicable to onshore UK (boreholes and outcrops), onshore Denmark (boreholes) and offshore Netherlands.
Estimation of Neutral Mutation Rates and Quantification of Somatic Variant Selection Using cancereffectsizeR
Authors: Mandell Jeffrey D. , Cannataro Vincent L. , Townsend Jeffrey P. 
Published: December 2022

AbstractSomatic nucleotide mutations can contribute to cancer cell survival, proliferation, and pathogenesis. Although research has focused on identifying which mutations are “drivers” versus “passengers," quantifying the proliferative effects of specific variants within clinically relevant contexts could reveal novel aspects of cancer biology. To enable researchers to estimate these cancer effects, we developed cancereffectsizeR, an R package that organizes somatic variant data, facilitates mutational signature analysis, calculates site-specific mutation rates, and tests models of selection. Built-in models support effect estimation from single nucleotides to genes. Users can also estimate epistatic effects between paired sets of variants, or design and test custom models. The utility of cancer effect was validated by showing in a pan-cancer dataset that somatic variants classified as likely pathogenic or pathogenic in ClinVar exhibit substantially higher effects than most other variants. Indeed, cancer effect was a better predictor of pathogenic status than variant prevalence or functional impact scores. In addition, the application of this approach toward pairwise epistasis in lung adenocarcinoma showed that driver mutations in BRAF, EGFR, or KRAS typically reduce selection for alterations in the other two genes. Companion reference data packages support analyses using the hg19 or hg38 human genome builds, and a reference data builder enables use with any species or custom genome build with available genomic and transcriptomic data. A reference manual, tutorial, and public source code repository are available at https://townsend-lab-yale.github.io/cancereffectsizeR. Comprehensive estimation of cancer effects of somatic mutations can provide insights into oncogenic trajectories, with implications for cancer prognosis and treatment.Significance:An R package provides streamlined, customizable estimation of underlying nucleotide mutation rates and of the oncogenic and epistatic effects of mutations in cancer cohorts.
Novel Paired Normal Prostate and Prostate Cancer Model Cell Systems Derived from African American Patients
Authors: Jung Mira , Kowalczyk Keith , Hankins Ryan , Bandi Gaurav , Kallakury Bhaskar , Carrasquilla Michael A. , Banerjee Partha P. , Grindrod Scott , Dritschilo Anatoly 
Published: December 2022

Prostate cancer is the most frequently diagnosed solid malignancy in men. African American (AA) men are at greater risk for developing prostate cancer, and experience higher mortality rates, as compared with Caucasian American men. However, mechanistic studies to understand this health disparity have been limited by the lack of relevant in vitro and in vivo models. There is an urgent need for preclinical cellular models to investigate molecular mechanisms underlying prostate cancer in AA men. We collected clinical specimens from radical prostatectomies of AA patients and established 10 paired tumor-derived and normal epithelial cell cultures from the same donors, which were further cultivated to extend the growth under “conditional reprogramming.” Clinical and cellular annotations characterized these model cells as intermediate risk and predominantly diploid. Immunocytochemical analyses demonstrated variable expression levels of luminal (CK8) and basal (CK5, p63) markers in both normal and tumor cells. However, expression levels of TOPK, c-MYC, and N-MYC were markedly increased only in tumor cells. To determine cell utility for drug testing, we examined viability of cells following exposure to the antiandrogen (bicalutamide) and two PARP inhibitors (olaparib and niraparib) and observed decreased viability of tumor-derived cells as compared with viability of normal prostate-derived cells.Significance:Cells derived from prostatectomies of AA patients conferred a bimodal cellular phenotype, recapitulating clinical prostate cellular complexity in this model cell system. Comparisons of viability responses of tumor derived to normal epithelial cells offer the potential for screening therapeutic drugs. Therefore, these paired prostate epithelial cell cultures provide an in vitro model system suitable for studies of molecular mechanisms in health disparities.
The Splicing Factor PTBP1 RepressesTP63 γIsoform Production in Squamous Cell Carcinoma
Authors: Taylor William , Deschamps Stéphane , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann 
Published: December 2022

The TP63 gene encodes the p63 transcription factor. It is frequently amplified or overexpressed in squamous cell carcinomas. Owing to alternative splicing, p63 has multiple isoforms called α, β, γ, and δ. The regulatory functions of p63 are isoform specific. The α isoform inhibits the epithelial-to-mesenchymal transition (EMT) and controls apoptosis, while the γ isoform promotes EMT. Using The Cancer Genome Atlas data, we observed that a higher proportion of the TP63γ isoform is a detrimental factor for the survival of patients with head and neck squamous cell carcinoma (HNSCC) and is accompanied by the downregulation of desmosomal genes. By a correlation-based approach, we investigated the regulation of the production of the TP63γ isoform. According to our analysis of GTEx data, the expression of the RNA-binding protein PTBP1 (polypyrimidine tract binding protein 1) is negatively correlated with the abundance of TP63γ in several tissues. Accordingly, we demonstrated that PTBP1 depletion in HNSCC cell lines, keratinocyte or Xenopus embryos leads to an increase in TP63γ isoform abundance. By RNA immunoprecipitation and in vitro interaction assays, we showed that PTBP1 directly binds to TP63 pre-mRNA in close proximity to the TP63γ-specific exon. Intronic regions around the TP63γ-specific exon were sufficient to elicit a PTBP1-dependent regulation of alternative splicing in a splice reporter minigene assay.Together, these results identify TP63γ as an unfavorable prognostic marker in HNSCC, and identify PTBP1 as the first direct splicing regulator of TP63γ production and a potential route toward TP63 isoform control.Significance:Quantifying TP63γ isoforms in patients’ tumors could allow for the early detection of patients with HNSCC with an early loss in desmosomal gene expression and poor prognostic. The identification of PTBP1 as a transacting factor controlling TP63γ production may allow to control TP63γ expression.
Scientific Attitude Inventory of Junior High School Students During Pandemic
Authors: Capiral Christine Ivy S. 
Published: December 2022

The study sought to analyze the scientific attitude inventory of junior high school students during pandemic. The scientific attitudes are the most important outcomes of science teaching. It is the combination of many qualities and virtues that is reflected in a person's behavior and actions. The aim of the present study is to check scientific attitude inventory among junior high school students. This study covers 350 students from the different grade levels. Subjects were selected using a stratified random sampling method. Scientific Attitude Scale (SAS) of Bajwa and Mahajan (2012) was administered to collect the data. The statistical treatments that were used in this study are Independent T-test and One way Analysis of Variance (ANOVA) to determine the significant difference assessment of respondents about scientific attitude inventory when grouped according to their profile characteristics. On the other hand, the data statistical treatments that were used to determine the significant relationship of scientific attitude and academic performance is Spearman’s Rho Correlation Coefficient. The findings of the study revealed that there is no significant difference between scientific attitude and profile characteristics of the respondents. It also revealed that there is no significant relationship between scientific attitude and academic performance of the respondents. It may therefore be concluded that the scientific attitude of students during pandemic have less in comparison to the normal.
Sensitivity of the Southern Hemisphere Wintertime Teleconnection to the Location of ENSO Heating
Authors: Gillett Z. E. , Hendon H. H. , Arblaster J. M. , Lin H. 
Published: December 2022

Abstract
The Southern Hemisphere extratropical atmospheric circulation response to anomalous convection in the tropical western and eastern Pacific Ocean is distinctly different. The response to westward-located heating has a meridional dipole in the South Pacific with large zonal scale and appears unable to be interpreted simply as a stationary Rossby wave train that disperses poleward and eastward from a tropical source like the meridionally arched response to eastward-located heating. This study investigates the cause of this asymmetry by examining the daily evolution of the response to suddenly switching on steady diabatic heating over a western and central/eastern equatorial Pacific location using large-ensemble integrations from the Community Atmosphere Model version 5. We focus on the austral winter months when the subtropical jet supports the development of an effective Rossby wave source in the subtropical westerlies and acts as a waveguide. We show that the subtropical jet strongly influences the height response to the western tropical Pacific heating, promoting prominent zonal circumglobal propagation. Development of a transient eddy feedback in the extratropical storm track after approximately 10 days appears to play a primary role in establishing the time-mean response, which we test through comparison with similar experiments conducted using a simplified linear model. Conversely, the height anomalies for eastern tropical Pacific heating, farther away from the subtropical jet core, have larger meridional propagation, dispersing in a typical Hoskins–Karoly manner into the Southern Hemisphere extratropics, while the transient eddy feedback plays a secondary role for the establishment of the steady response.
Achieving Realistic Runoff in the Western United States with a Land Surface Model Forced by Dynamically Downscaled Meteorology
Authors: Bass Benjamin , Rahimi Stefan , Goldenson Naomi , Hall Alex , Norris Jesse , Lebow Zachary J. 
Published: December 2022

Abstract
In this study, we calibrate a regional climate model’s (RCM) underlying land surface model (LSM). In addition to providing a realistic representation of runoff across the hydroclimatically diverse western United States, this is done to take advantage of the RCM’s ability to physically resolve meteorological forcing data in ungauged regions, and to prepare the calibrated hydrologic model for tight coupling, or the ability to represent land surface–atmosphere interactions, with the RCM. Specifically, we use a 9-km resolution meteorological forcing dataset across the western United States, from the fifth generation ECMWF Reanalysis (ERA5) downscaled by the Weather Research Forecasting (WRF) regional climate model, as an offline forcing for Noah-Multiparameterization (Noah-MP). We detail the steps involved in producing an LSM capable of accurately representing runoff, including physical parameterization selection, parameter calibration, and regionalization to ungauged basins. Based on our model evaluation from 1954 to 2021 for 586 basins with daily natural streamflow, the streamflow bias is reduced from 24.2% to 4.4%, and the median daily Nash–Sutcliffe efficiency (NSE) is improved from 0.12 to 0.36. When validating against basins with monthly natural streamflow data, we obtain a similar reduction in bias and a median monthly NSE improvement from 0.18 to 0.56. In this study, we also discover the optimal setup when using a donor-basin method to regionalize parameters to ungauged basins, which can vary by 0.06 NSE for unique designs of this regionalization method.

Significance Statement
This study provides useful guidance for improving a land surface model to accurately represent runoff across a spatially extensive and hydroclimatically diverse region (the western United States). The land surface model is updated to represent runoff more accurately at gauged basins, and then additionally updated for basins without observational data using a mathematical approach called the donor-basin method. We make use of a regional climate model’s reanalysis-derived meteorological data and its underlying land surface model to achieve realistic runoff. The calibrated land surface model can thus be tightly coupled in subsequent studies in a manner that should more accurately reflect runoff conditions. Findings from this study will serve as a useful reference for the atmospheric (and hydrologic) modeling communities and their ability to represent large-scale hydrology accurately.
A Theory for Why Even Simple Covariance Localization Is So Useful in Ensemble Data Assimilation
Authors: Morzfeld Matthias , Hodyss Daniel 
Published: December 2022

Abstract
Covariance localization has been the key to the success of ensemble data assimilation in high dimensional problems, especially in global numerical weather prediction. We review and synthesize optimal and adaptive localization methods that are rooted in sampling error theory and that are defined by optimality criteria, e.g., minimizing errors in forecast covariances or in the Kalman gain. As an immediate result, we note that all optimal localization methods follow a universal law and are indeed quite similar. We confirm the similarity of the various schemes in idealized numerical experiments, where we observe that all localization schemes we test—optimal and nonadaptive schemes—perform quite similarly in a wide array of problems. We explain this perhaps surprising finding with mathematical rigor on an idealized class of problems, first put forward by Bickel and others to study the collapse of particle filters. In combination, the numerical experiments and the theory show that the most important attribute of a localization scheme is the well-known property that one should dampen spurious long-range correlations. The details of the correlation structure, and whether or not these details are used to construct the localization, have a much smaller effect on posterior state errors.

Significance Statement
Covariance localization has been the key to the success of ensemble data assimilation (DA) in global numerical weather prediction. In this paper, we synthesize a large body of literature on optimal localization and then report and explain a number of surprising observations.
Minimally Invasive Lower Anterior Resections – Better than Open But Not All the Same
Authors: Lim Joseph S , Brant Nicholson , Downs John M. , Apple William , Stadler Ronney , Jeyarajah Dhiresh Rohan 
Published: December 2022

Background/Objective: Optimal approach for lower anterior resection has been closely debated. The relatively new addition of the robotic approach adds a layer of complexity to this topic. The majority of the literature has compared the possible approaches between two techniques; however, only a few studies have comprehensively compared all 3 approaches at the same time, especially in a non-academic center. Study Design: This is a retrospective cohort study of a prospectively maintained database of data from a large group of private-practice colorectal surgeons in a large metropolitan area. Specifically, rectal resections using open, laparoscopic, and robotic approaches were queried. A total of 130 patients underwent open, laparoscopic, or robotic oncological lower anterior resection from 2016 to January 2020. Results: Statistical significance of length of stay was noted between the three approaches with the mean length of stay for open being 8.08 days, laparoscopic being 7.04 days, and robotic being 4.96 days (P < .005). No statistical significance was noted for estimated blood loss, operating time, or postoperative complications including anastomotic leak, ileus, pneumonia, pulmonary embolism, surgical site infection, and urinary tract infection. When directly comparing any minimally invasive surgery approach to open, estimated blood loss was decreased in addition to the shortened length of stay (P < .05). Conclusions: This study demonstrates that MIS LAR has significant benefit over the open approach. However, finding that robotic surgery had was superior to laparoscopic LAR which was surprising and important. This experience in the private world raises the question as to whether robotic LAR should be considered the standard of care.
To what extent do post-traumatic mental health and other problems reflect pre-existing problems? Findings from the prospective comparative population-based VICTIMS-study
Authors: van der Velden Peter G. , Contino Carlo , Das Marcel , Wittmann Lutz 
Published: December 2022

Background: Findings from prospective studies question the assumption that mental health problems observed in traumatized adults mainly reflect the effects of potentially traumatic events. Aims: Aim of the present comparative prospective study is to clarify the extent to which victims of potentially traumatic events with mental health, social, financial, and/or legal problems, already suffered from such problems before these events. Method: Data was extracted from three surveys of the prospective VICTIMS-study (T1 = 2018, T2 = 2019, T3 = 2020), conducted with the population-based longitudinal LISS-panel. Differences between victims ( n = 340, victimized by violence, accidents, and serious threats in the 12 months before T3) and nonvictims ( n = 3,872, not victimized by such events in this period), were examined using multivariate logistic regression analyses. Results: The large majority of victims with current (at T3) anxiety and depression symptomatology (74%), general mental health problems (71%), partner/family (67%), financial (76%), and legal problems (58%), and lack of support (79%), already had these problems (at T1 and/or at T2). A similar pattern was observed among nonvictims. Of the victims with current probable PTSD (at T3), 87% already had any mental health problem. At T3, among both groups, the incidence of problems was substantially lower than their prevalence. The large majority of victims with post-event mental health, social, financial, and legal problems already suffered from these problems in the past. Conclusions: When victims seek help for their problems, professional care providers should be aware that in most cases, as among nonvictims, these problems are chronic/re-current rather than new problems.