bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring differences in FFCO2 emissions in the United States: comparison of the Vulcan data product and the EPA national GHG inventory
Authors: Kato Anna , Gurney Kevin R , Roest Geoffrey S , Dass Pawlok 
Published: November 2023

Abstract
Quantitative assessment of greenhouse gas emissions is an essential step to plan, track, and verify emission reductions. Multiple approaches have been taken to quantify U.S. CO2 emissions from fossil fuel combustion (FFCO2), the primary driver of global climate change. A 2020 study analyzing atmospheric 14CO2 observations (a key check on bottom-up estimates) and multiple inventories found significant differences in the U.S. total FFCO2 emissions. The specific reasons for the differences were left for future work. Here, we take up this task and explore the differences between two widely used U.S. FFCO2 inventories, the Vulcan FFCO2 emissions data product and the Environmental Protection Agency (EPA) GHG inventory, developed using mostly independent data sources. Where possible, we isolate definitions and data sources to quantify/understand discrepancies. We find that the initial 2011 emissions difference (104 MtC yr−1; RD = 10.7%) can be reduced by aligning the two estimates to account for differing definitions of emission categories or system boundaries. Out of the remaining 90.6 MtC yr−1 gap (RD = 6.2%), we find that differences can be largely explained by data completeness, emission factors, and fuel heating values. The remaining difference, 45.4 MtC yr−1 (3.2%), is difficult to isolate due to limited EPA documentation and disaggregation of emissions by sector/fuel categories. Furthermore, the final net difference obscures countervailing gross differences (∼40 MtC yr−1) within individual sectors. Nevertheless, this comparison suggests the potential for a national estimation approach that can simultaneously satisfy reporting at the national/global scale and the local scale, maintaining internal consistency throughout and offering detailed decision support to a much wider array of stakeholders.
Increased Blood Pressure Variability Over a 16-Year Period Is Associated With Left Ventricular Diastolic Dysfunction in a Population-Based Cohort
Authors: Park Jae-Hyeong , Ahn Soon-Ki , Cho Goo-Yeong , Sung Ki-Chul , Lee Seung Ku , Kim Seong Hwan , Shin Chol 
Published: November 2023

Abstract

BACKGROUND
Left ventricular diastolic dysfunction (LVDD) is often associated with elevated blood pressure (BP). It is prevalent among hypertensive patients. Additionally, increased BP variability has been linked to LVDD. However, the precise connection between LVDD and BP variability within the general population remains unclear. Thus, this study aimed to evaluate this association in a general population.

METHODS
A total of 2,578 participants(1,311 females) with a mean age of 47.8 ± 6.7 years who had echocardiographic data from the Korean Genome and Epidemiology study with 16 years of follow-up were analyzed. LVDD was identified through the last echocardiography during the follow-up period. BP variability was assessed using mean, standard deviation (SD), and coefficient of variance (CV).

RESULTS
LVDD was detected in 249 individuals. The cohort was divided into an LVDD group and a normal LV diastolic function group. The LVDD group had a higher percentage of females, more advanced age, higher body mass index (BMI), higher BP and BUN levels, lower heart rate, lower hemoglobin, and lower serum creatinine than the normal LV diastolic function group. Remarkably, LVDD was associated with higher BP variability. In the multivariate analysis, LVDD was associated with increased age, female sex, increased BMI, hypertension, and increased BUN. Elevated mean systolic and diastolic BPs, SD of systolic BP, mean pulse pressure (PP), SD of PP, and CV of PP were significantly linked to LVDD even after adjusting for other significant variables in the multivariate analysis.

CONCLUSIONS
LVDD was identified in 249 (9.7%) participants. Increased long-term BP variability was significantly associated with LVDD in this population-based cohort.
A case series analysis of bicarbonate-based purge solution administration via Impella ventricular assist device
Authors: Sigala Mariah I , Harris Jesse E , Morton Celia , Donahue Kevin R , Kim Ju H 
Published: November 2023

Abstract

Purpose
The Impella device historically required a heparin-based purge solution to reduce the risk of biomaterial deposition to maintain pump function. In April 2022, the Food and Drug Administration approved utilization of bicarbonate-based purge solutions (BBPS) as an alternative to heparin for patients who are intolerant to heparin or in whom heparin is contraindicated. The purpose of this case series is to report patient outcomes of Impella support with BBPS use at our institution.

Summary
Eighteen patients who received BBPS via the Impella CP or Impella 5.5 device were included in our review. Patients were included if they had BBPS administration for greater than 24 hours. All patients were followed for 72 hours after cessation of BBPS. Indications for BBPS were coagulopathy (n = 5, 28%), suspected HIT (n = 2, 11%), confirmed HIT (n = 1, 6%), and major bleeding (n = 10, 56%). Three patients (17%) experienced an Impella complication while on BBPS. One patient required pump exchange, one required removal of the Impella device, and one received alteplase for suspected purge block. Of these, two patients experienced complications greater than 21 days into BBPS therapy.

Conclusion
This case series adds to the literature describing clinical outcomes for patients on Impella support with BBPS. While BBPS offers a viable option for the management of patients on Impella devices who are unable to tolerate heparin-based purge solutions, further data is needed to determine the longevity of the Impella device with BBPS to minimize risk of Impella complications.
FLED: a full-length eccDNA detector for long-reads sequencing data
Authors: Li Fuyu , Ming Wenlong , Lu Wenxiang , Wang Ying , Li Xiaohan , Dong Xianjun , Bai Yunfei 
Published: November 2023

AbstractReconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given the similarity of eccDNAs and their corresponding linear DNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length eccDNAs. Herein, a novel algorithm was developed, called Full-Length eccDNA Detection (FLED), to reconstruct the sequence of eccDNAs based on the strategy that combined rolling circle amplification and nanopore long-reads sequencing technology. Seven human epithelial and cancer cell line samples were analyzed by FLED and over 5000 full-length eccDNAs were identified per sample. The structures of identified eccDNAs were validated by both Polymerase Chain Reaction (PCR) and Sanger sequencing. Compared to other published nanopore-based eccDNA detectors, FLED exhibited higher sensitivity. In cancer cell lines, the genes overlapped with eccDNA regions were enriched in cancer-related pathways and cis-regulatory elements can be predicted in the upstream or downstream of intact genes on eccDNA molecules, and the expressions of these cancer-related genes were dysregulated in tumor cell lines, indicating the regulatory potency of eccDNAs in biological processes. The proposed method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics
Authors: Zhong Cheng , Tian Tian , Wei Zhi 
Published: November 2023

AbstractMotivationThe recent development of spatially resolved transcriptomics (SRT) technologies has facilitated research on gene expression in the spatial context. Annotating cell types is one crucial step for downstream analysis. However, many existing algorithms use an unsupervised strategy to assign cell types for SRT data. They first conduct clustering analysis and then aggregate cluster-level expression based on the clustering results. This workflow fails to leverage the marker gene information efficiently. On the other hand, other cell annotation methods designed for single-cell RNA-seq data utilize the cell-type marker genes information but fail to use spatial information in SRT data.ResultsWe introduce a statistical spatial transcriptomics cell assignment model, SPAN, to annotate clusters of cells or spots into known types in SRT data with prior knowledge of predefined marker genes and spatial information. The SPAN model annotates cells or spots from SRT data using predefined overexpressed marker genes and combines a mixture model with a hidden Markov random field to model the spatial dependency between neighboring spots. We demonstrate the effectiveness of SPAN against spatial and nonspatial clustering algorithms through extensive simulation and real data experiments.Availability and implementationhttps://github.com/ChengZ352/SPAN.
RNA interaction format: a general data format for RNA interactions
Authors: Schäfer Richard A , Rabsch Dominik , Scholz Guillaume E , Stadler Peter F , Hess Wolfgang R , Backofen Rolf , Fallmann Jörg , Voß Björn 
Published: November 2023

Abstract

Summary
RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardized data format that can capture the nature of all these different interactions in detail.

Availability and implementation
Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA–RNA and RNA–Protein interactions and provide reference implementations in C/C++, Python, and JavaScript. RIF is released under licence GNU General Public License version 3 (GNU GPLv3) and is available on https://github.com/RNABioInfo/rna-interaction-format.
PyPCN: protein contact networks in PyMOL
Authors: Rosignoli Serena , di Paola Luisa , Paiardini Alessandro 
Published: November 2023

Abstract

Motivation
Protein contact networks (PCNs) represent the 3D structure of a protein using network formalism. Inter-residue contacts are described as binary adjacency matrices, which are derived from the graph representation of residues (as α-carbons, β-carbons or centroids) and Euclidean distances according to defined thresholds. Functional characterization algorithms are computed on binary adjacency matrices to unveil allosteric, dynamic, and interaction mechanisms in proteins. Such strategies are usually applied in a combinatorial manner, although rarely in seamless and user-friendly implementations.

Results
PyPCN is a plugin for PyMOL wrapping more than twenty PCN algorithms and metrics in an easy-to-use graphical user interface, to support PCN analysis. The plugin accepts 3D structures from the Protein Data Bank, user-provided PDBs, or precomputed adjacency matrices. The results are directly mapped to 3D protein structures and organized into interactive diagrams for their visualization. A dedicated graphical user interface combined with PyMOL visual support makes analysis more intuitive and easier, extending the applicability of PCNs.

Availability and implementation
https://github.com/pcnproject/PyPCN.
The Relationships between Stress, Burnout, Mental Health and Well-Being in Social Workers
Authors: Maddock Alan 
Published: November 2023

Abstract
Stress and burnout can have several negative effects on the individual social worker’s work performance, along with their mental health and well-being. We are still unclear on how these negative effects play out, as no studies have examined what the relationships are between stress, burnout, anxiety, depression and well-being in social workers. This cross-sectional study attempted to identify the rates and correlates of stress, burnout, anxiety, depression and mental well-being of 121 social workers, using bivariate and multiple regression analyses. This study highlighted a significant proportion of social workers who reported mild to severe issues in anxiety, depression and mental well-being. This study highlighted that perceived stress is likely to be a universal risk factor for anxiety, depression, and mental well-being in social workers. Emotional exhaustion was also identified as a potential risk factor for anxiety, with personal accomplishment being a potential protective factor against depression and for positive mental well-being. This study provides promising preliminary evidence that if social workers who are experiencing issues with anxiety, depression and mental well-being are supported to reduce feelings of stress, emotional exhaustion, and increase feelings of personal accomplishment, they are likely to experience improvements in their mental health and job performance.
Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon
Authors: Sato Mitsuhiko P , Iwakami Satoshi , Fukunishi Kanade , Sugiura Kai , Yasuda Kentaro , Isobe Sachiko , Shirasawa Kenta 
Published: November 2023

Abstract
Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.
Impact of a clinician-to-clinician electronic consultation in heart failure patients with previous hospital admissions
Authors: Garcia-Vega David , Mazón-Ramos Pilar , Portela-Romero Manuel , Rodríguez-Mañero Moisés , Rey-Aldana Daniel , Sestayo-Fernández Manuela , Cinza-Sanjurjo Sergio , González-Juanatey José R 
Published: November 2023

Abstract

Aims
To evaluate the impact of an outpatient care management programme that includes a clinician-to-clinician e-consultation on delay time in care, hospital admissions, and mortality in a high-risk group of patients with heart failure (HF) and previous episodes of HF hospitalization (HFH).

Methods and results
We selected 6444 HF patients who visited the cardiology service at least once between 2010 and 2021. Of these, 4851 were attended in e-consult, and 2230 had previous HFH. Using an interrupted time series regression model, we analysed the impact of incorporating e-consult into the healthcare model in the group of patients with HFH and evaluated the elapsed time to cardiology care, HF, cardiovascular (CV), and all-cause hospital admissions and mortality, calculating the incidence relative risk (iRR). In the group of patients with HFH, the introduction of e-consult substantially decreased waiting times to cardiology care (8.6 [8.7] vs. 55.4 [79.9] days, P &lt; 0.001). In that group of patients, after e-consult implantation, hospital admissions for HF were reduced (iRR [95%CI]: 0.837 [0.840–0.833]), 0.900 [0.862–0.949] for CV and 0.699 [0.678–0.726] for all-cause hospitalizations. There was also lower mortality (iRR [95%CI]: 0.715 [0.657–0.798] due to HF, 0.737 [0.764–0.706] for CV and 0.687 [0.652–0.718] for all-cause). The improved outcomes after e-consultation implementation were significantly higher in the group of patients with previous HFH.

Conclusion
In patients with HFH, an outpatient care programme that includes an e-consult significantly reduced waiting times to cardiology care and was safe, with a lower rate of hospital admissions and mortality in the first year.
The case for assessing oracy in primary and secondary schools in England
Authors: Khan Sullivan Ameena , Thomas MacGregor Annabel 
Published: November 2023

Abstract
The recognition of the importance of supporting children to learn to, and through, talk (often referred to as ‘oracy’) increasingly has prominence in educational and political discourse. However in the past decade the assessment of spoken language has been removed from GCSE exams, and nothing has replaced this vital measure of communication at a fundamental point in young people's progression. This article argues that this has helped to ensure oracy - speaking and listening - remains on the periphery, when increasingly evidence indicates that it should be central to all children and young people's education.
The pace of mitochondrial molecular evolution varies with seasonal migration distance
Authors: Pegan Teresa M , Berv Jacob S , Gulson-Castillo Eric R , Kimmitt Abigail A , Winger Benjamin M 
Published: November 2023

Abstract
Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than “fast” species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.
Coordinated Regulation of Myonuclear DNA Methylation, mRNA, and miRNA Levels Associates With the Metabolic Response to Rapid Synergist Ablation-Induced Skeletal Muscle Hypertrophy in Female Mice
Authors: Ismaeel Ahmed , Thomas Nicholas T , McCashland Mariah , Vechetti Ivan J , Edman Sebastian , Lanner Johanna T , Figueiredo Vandré C , Fry Christopher S , McCarthy John J , Wen Yuan , Murach Kevin A , von Walden Ferdinand 
Published: November 2023

Abstract
The central dogma of molecular biology dictates the general flow of molecular information from DNA that leads to a functional cellular outcome. In skeletal muscle fibers, the extent to which global myonuclear transcriptional alterations, accounting for epigenetic and post-transcriptional influences, contribute to an adaptive stress response is not clearly defined. In this investigation, we leveraged an integrated analysis of the myonucleus-specific DNA methylome and transcriptome, as well as myonuclear small RNA profiling to molecularly define the early phase of skeletal muscle fiber hypertrophy. The analysis of myonucleus-specific mature microRNA and other small RNA species provides new directions for exploring muscle adaptation and complemented the methylation and transcriptional information. Our integrated multi-omics interrogation revealed a coordinated myonuclear molecular landscape during muscle loading that coincides with an acute and rapid reduction of oxidative metabolism. This response may favor a biosynthesis-oriented metabolic program that supports rapid hypertrophic growth.
Methadone prescribing by addiction specialists likely to leave communities without available methadone treatment
Authors: Joudrey Paul J , Halpern Dylan , Lin Qinyun , Paykin Susan , Mair Christina , Kolak Marynia 
Published: November 2023

Abstract
Methadone treatment for opioid use disorder is not available in most suburban and rural US communities. We examined 2 options to expand methadone availability: (1) addiction specialty physician or (2) all clinician prescribing. Using 2022 Health Resources and Services Administration data, we used mental health professional shortage areas to indicate the potential of addiction specialty physician prescribing and the location of federally qualified health centers (ie, federally certified primary care clinics) to indicate the potential of all clinician prescribing. We examined how many census tracts without an available opioid treatment program (ie, methadone clinic) are (1) located within a mental health professional shortage area and (2) are also without an available federally qualified health center. Methadone was available in 49% of tracts under current regulations, 63% of tracts in the case of specialist physician prescribing, and 86% of tracts in the case of all clinician prescribing. Specialist physician prescribing would expand availability to an additional 12% of urban, 18% of suburban, and 16% of rural tracts, while clinician prescribing would expand to an additional 30% of urban, 53% of suburban, and 58% of rural tracts relative to current availability. Results support enabling broader methadone prescribing privileges to ensure equitable treatment access, particularly for rural communities.
Eudaimonic entertainment overcoming resistance: an update and expansion of narrative persuasion models
Authors: Moyer-Gusé Emily , Wilson Julia 
Published: November 2023

Abstract
A growing body of research reveals that entertainment narratives are persuasive across a variety of topics. Models of narrative persuasion highlight key mechanisms, but one limitation of this theorizing is that it has not directly considered the full range of entertainment narratives that exist. Viewers select media content to fulfill various needs—hedonic needs for pleasure and enjoyment or more eudaimonic needs gratified by appreciation and mixed affective responses. Narrative persuasion theorizing would benefit from explicitly considering eudaimonic entertainment narratives and how they may uniquely lead to persuasion. Doing so will expand on existing narrative persuasion mechanisms and identify contingencies regarding when and for whom distinct types of entertainment narratives may persuade. This article builds on the entertainment overcoming resistance model by advancing a set of testable propositions regarding narrative persuasion by meaningful entertainment and offering an agenda for future research in this area.