bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental taxes in the European Union and their use as a means of environmental restoration
Authors: Tsiantikoudis S , Galatsidas S , Paschalidou A , Zafeiriou E , Arabatzis G 
Published: December 2022

Abstract
Environmental degradation caused by intense human activities has allured scientific and social concerns. Environmental taxes are a part of a wider policy context integrating various tools, including pricing instruments, subsidies, and investment in public infrastructure. Environmental taxes are the only fiscal policy tool the revenue which can be used for environmental protection purposes. They are used in modern societies, as means of optimizing consumers’ and producers’ behavior. These taxes generate revenues that can be used by governments to invest in environmental protection projects or in the effective management of natural resources. Eastern European countries’ environmental taxation regime, is a successful example since appropriate policies and actions were used for environmental degradation resilience along with the formerly degraded land restoration and funding environmental information dissemination programs for local communities. The present work aims to unveil successful practices adopted related to the implementation of environmental taxation in European countries and the use of their revenues in projects and actions to protect the environment and limit the anthropogenic impacts. In addition, a comparative analysis of individual EU countries efficiency in the use of taxation for mitigation of natural environment degradation is conducted with significant findings for policymakers.
Effectiveness of interventions in older adults with cognitive frailty: a systematic review and meta-analysis of randomised controlled trials
Authors: Zheng Lufang , Wang Cong , Qiu Yiming , Li Xin , Zhang Xueyan , Zhang Meishuang , Ma Tianjiao , Li Guichen , Chen Li 
Published: December 2022

Abstract

Background
interventions targeting older adults with cognitive frailty have grown rapidly in recent years with inconsistent findings. However, there is no meta-analysis that has synthesised pooled estimates.

Objective
to synthesise the pooled effect of current targeted interventions in older people with cognitive frailty.

Methods
we conducted a systematic search in PubMed, Embase, Web of Science, the Cochrane Library, the JBI database and three Chinese databases (CNKI, Wan-Fang and VIP) for literature from the inception of the database until 8 March 2022. The mean difference or standardised mean difference with 95% CIs was calculated. The methodological quality was assessed by the Cochrane RoB 2.0. The certainty of evidence was assessed using the GRADE criteria.

Results
thirteen randomised controlled trials with a total of 1,089 participants were included. The results of the meta-analysis showed that older adults with cognitive frailty in the intervention groups had significant improvement in frailty score [MD = −1.67, 95% CI (−2.39, −0.95), P &lt; 0.00001, I2 = 97%], global cognitive function [MD = 3.38, 95% CI (1.90, 4.85), P &lt; 0.00001, I2 = 93%], mobility [MD = −0.96, 95% CI (−1.27, −1.66), P &lt; 0.00001, I2 = 0%], muscle strength [SMD = 0.75, 95% CI (0.09, 1.41), P = 0.03, I2 = 85%] and nutritional status [MNA:MD = 5.64, 95% CI (3.99, 7.29), P &lt; 0.00001, I2 = 89%; ALB: MD = 3.23, 95% CI (0.76, 5.71), P = 0.01, I2 = 93%; PALB: MD = 54.52, 95% CI (25.26, 83.77), P = 0.0003, I2 = 96%; TRF: MD = 0.64, 95% CI (0.22, 1.06), P = 0.003, I2 = 97%]. The overall certainty of the evidence ranged from low to moderate.

Conclusions
interventions targeting older adults with cognitive frailty are effective in improving physical frailty, global cognitive function, physical function and nutritional status with low to moderate certainty. More research is still needed in the future to further enrich the evidence in these fields.

PROSPERO number
CRD42022318758.
Changes in anticoagulant and antiplatelet drug supply at US hospitals before and during the COVID-19 pandemic (2018-2021)
Authors: Wong Paul J , Mosley Scott A , Ng Tien M H , Shooshtari Andrew , Alexander G Caleb , Qato Dima M 
Published: December 2022

Abstract

Purpose
Antithrombotic agents have a role in coronavirus disease 2019 (COVID-19) treatment, but the pandemic disrupted medication supply. This study examined changes in the volume of oral and parenteral anticoagulant and antiplatelet medications at US hospitals during the pandemic.

Methods
IQVIA National Sales Perspective (NSP) data was used to determine the monthly volume of anticoagulants and antiplatelets purchased at US hospitals between January 2018 and February 2021. Mean monthly medication volumes, reported as extended units (EUs), and year-over-year changes in medication volume were determined. A single-group interrupted time series analysis was used to evaluate changes in the rate of growth of monthly medication volumes before (January 2019-February 2020) and during (March 2020-February 2021) the COVID-19 pandemic.

Results
Overall, there was a 43.4% decline in the total volume of anticoagulants and antiplatelets at US hospitals in March 2020, driven by a decrease in heparin volume. Mean monthly volumes decreased significantly (P &lt; 0.05) for parenteral anticoagulants (–106,691,340 EU [95% CI, –200,033,910 to –13,348,780]), oral anticoagulants (–354,800 EU [95% CI, –612,180 to –97,420]), and parenteral antiplatelets (–391,880 EU [95% CI, –535,420 to –248,330]). During the pandemic, the monthly volume of oral anticoagulants, parenteral anticoagulants, and parenteral antiplatelets grew significantly more than in the prepandemic period. This growth was primarily seen in volumes of apixaban, argatroban, enoxaparin, heparin, eptifibatide, and tirofiban. Apixaban and heparin volumes continued a prepandemic uptrend, while argatroban and eptifibatide volumes reversed trend.

Conclusion
Rapid changes in anticoagulant and antiplatelet volume at US hospitals during the COVID-19 pandemic highlight the need for institutional protocols to manage fluctuating medication volume demands.
VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2
Authors: Zhou Zhi-Jian , Yang Chen-Hui , Ye Sheng-Bao , Yu Xiao-Wei , Qiu Ye , Ge Xing-Yi 
Published: December 2022

Abstract
Genomic recombination is an important driving force for viral evolution, and recombination events have been reported for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the Coronavirus Disease 2019 pandemic, which significantly alter viral infectivity and transmissibility. However, it is difficult to identify viral recombination, especially for low-divergence viruses such as SARS-CoV-2, since it is hard to distinguish recombination from in situ mutation. Herein, we applied information theory to viral recombination analysis and developed VirusRecom, a program for efficiently screening recombination events on viral genome. In principle, we considered a recombination event as a transmission process of ``information'' and introduced weighted information content (WIC) to quantify the contribution of recombination to a certain region on viral genome; then, we identified the recombination regions by comparing WICs of different regions. In the benchmark using simulated data, VirusRecom showed a good balance between precision and recall compared to two competing tools, RDP5 and 3SEQ. In the detection of SARS-CoV-2 XE, XD and XF recombinants, VirusRecom providing more accurate positions of recombination regions than RDP5 and 3SEQ. In addition, we encapsulated the VirusRecom program into a command-line-interface software for convenient operation by users. In summary, we developed a novel approach based on information theory to identify viral recombination within highly similar sequences, providing a useful tool for monitoring viral evolution and epidemic control.
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data
Authors: Chen Siqi , Yan Xuhua , Zheng Ruiqing , Li Min 
Published: December 2022

AbstractSingle-cell RNA-sequencing technology (scRNA-seq) brings research to single-cell resolution. However, a major drawback of scRNA-seq is large sparsity, i.e. expressed genes with no reads due to technical noise or limited sequence depth during the scRNA-seq protocol. This phenomenon is also called ‘dropout’ events, which likely affect downstream analyses such as differential expression analysis, the clustering and visualization of cell subpopulations, cellular trajectory inference, etc. Therefore, there is a need to develop a method to identify and impute these dropout events. We propose Bubble, which first identifies dropout events from all zeros based on expression rate and coefficient of variation of genes within cell subpopulation, and then leverages an autoencoder constrained by bulk RNA-seq data to only impute those values. Unlike other deep learning-based imputation methods, Bubble fuses the matched bulk RNA-seq data as a constraint to reduce the introduction of false positive signals. Using simulated and several real scRNA-seq datasets, we demonstrate that Bubble enhances the recovery of missing values, gene-to-gene and cell-to-cell correlations, and reduces the introduction of false positive signals. Regarding some crucial downstream analyses of scRNA-seq data, Bubble facilitates the identification of differentially expressed genes, improves the performance of clustering and visualization, and aids the construction of cellular trajectory. More importantly, Bubble provides fast and scalable imputation with minimal memory usage.
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data
Authors: Yu Runzhou , Cai Dehan , Sun Yanni 
Published: December 2022

AbstractMotivationRNA viruses tend to mutate constantly. While many of the variants are neutral, some can lead to higher transmissibility or virulence. Accurate assembly of complete viral genomes enables the identification of underlying variants, which are essential for studying virus evolution and elucidating the relationship between genotypes and virus properties. Recently, third-generation sequencing platforms such as Nanopore sequencers have been used for real-time virus sequencing for Ebola, Zika, coronavirus disease 2019, etc. However, their high per-base error rate prevents the accurate reconstruction of the viral genome.ResultsIn this work, we introduce a new tool, AccuVIR, for viral genome assembly and polishing using error-prone long reads. It can better distinguish sequencing errors from true variants based on the key observation that sequencing errors can disrupt the gene structures of viruses, which usually have a high density of coding regions. Our experimental results on both simulated and real third-generation sequencing data demonstrated its superior performance on generating more accurate viral genomes than generic assembly or polish tools.Availability and implementationThe source code and the documentation of AccuVIR are available at https://github.com/rainyrubyzhou/AccuVIR.Supplementary informationSupplementary data are available at Bioinformatics online.
Multiple pathways of lipid dysregulation in amyotrophic lateral sclerosis
Authors: Phan Katherine , He Ying , Bhatia Surabhi , Pickford Russell , McDonald Gordon , Mazumder Srestha , Timmins Hannah C , Hodges John R , Piguet Olivier , Dzamko Nicolas , Halliday Glenda M , Kiernan Matthew C , Kim Woojin Scott 
Published: December 2022

AbstractAmyotrophic lateral sclerosis is a rapidly progressing neurodegenerative disease characterized by the degeneration of motor neurons and loss of various muscular functions. Dyslipidaemia is prevalent in amyotrophic lateral sclerosis with aberrant changes mainly in cholesterol ester and triglyceride. Despite this, little is known about global lipid changes in amyotrophic lateral sclerosis or in relation to disease progression. The present study incorporated a longitudinal lipidomic analysis of amyotrophic lateral sclerosis serum with a comparison with healthy controls using advanced liquid chromatography-mass spectrometry. The results established that diglyceride, the precursor of triglyceride, was enriched the most, while ceramide was depleted the most in amyotrophic lateral sclerosis compared with controls, with the diglyceride species (18:1/18:1) correlating significantly to neurofilament light levels. The prenol lipid CoQ8 was also decreased in amyotrophic lateral sclerosis and correlated to neurofilament light levels. Most interestingly, the phospholipid phosphatidylethanolamine and its three derivatives decreased with disease progression, in contrast to changes with normal ageing. Unsaturated lipids that are prone to lipid peroxidation were elevated with disease progression with increases in the formation of toxic lipid products. Furthermore, in vitro studies revealed that phosphatidylethanolamine synthesis modulated TARDBP expression in SH-SY5Y neuronal cells. Finally, diglyceride, cholesterol ester and ceramide were identified as potential lipid biomarkers for amyotrophic lateral sclerosis diagnosis and monitoring disease progression. In summary, this study represents a longitudinal lipidomics analysis of amyotrophic lateral sclerosis serum and has provided new insights into multiple pathways of lipid dysregulation in amyotrophic lateral sclerosis.
Aberrant allometric scaling of cortical folding in preterm-born adults
Authors: Schmitz-Koep Benita , Menegaux Aurore , Zimmermann Juliana , Thalhammer Melissa , Neubauer Antonia , Wendt Jil , Schinz David , Wachinger Christian , Daamen Marcel , Boecker Henning , Zimmer Claus , Priller Josef , Wolke Dieter , Bartmann Peter , Sorg Christian , Hedderich Dennis M 
Published: December 2022

AbstractA universal allometric scaling law has been proposed to describe cortical folding of the mammalian brain as a function of the product of cortical surface area and the square root of cortical thickness across different mammalian species, including humans. Since these cortical properties are vulnerable to developmental disturbances caused by preterm birth in humans and since these alterations are related to cognitive impairments, we tested (i) whether cortical folding in preterm-born adults follows this cortical scaling law and (ii) the functional relevance of potential scaling aberrances. We analysed the cortical scaling relationship in a large and prospectively collected cohort of 91 very premature-born adults (&lt;32 weeks of gestation and/or birthweight &lt;1500 g, very preterm and/or very low birth weight) and 105 full-term controls at 26 years of age based on the total surface area, exposed surface area and average cortical thickness measured with structural magnetic resonance imaging and surface-based morphometry. We found that the slope of the log-transformed cortical scaling relationship was significantly altered in adults (very preterm and/or very low birth weight: 1.24, full-term: 1.14, P = 0.018). More specifically, the slope was significantly altered in male adults (very preterm and/or very low birth weight: 1.24, full-term: 1.00, P = 0.031), while there was no significant difference in the slope of female adults (very preterm and/or very low birth weight: 1.27, full-term: 1.12, P = 0.225). Furthermore, offset was significantly lower compared with full-term controls in both male (very preterm and/or very low birth weight: −0.546, full-term: −0.538, P = 0.001) and female adults (very preterm and/or very low birth weight: −0.545, full-term: −0.538, P = 0.023), indicating a systematic shift of the regression line after preterm birth. Gestational age had a significant effect on the slope in very preterm and/or very low birth weight adults and more specifically in male very preterm and/or very low birth weight adults, indicating that the difference in slope is specifically related to preterm birth. The shape or tension term of the scaling law had no significant effect on cognitive performance, while the size of the cortex did. Results demonstrate altered scaling of cortical surface and cortical thickness in very premature-born adults. Data suggest altered mechanical forces acting on the cortex after preterm birth.
Treg specialization and functions beyond immune suppression
Authors: Astarita Jillian L , Dominguez Claudia X , Tan Corey , Guillen Jovanny , Pauli Mariela L , Labastida Rosario , Valle Jose , Kleinschek Melanie , Lyons Jesse , Zarrin Ali A 
Published: December 2022

SummaryThe actions of the immune system are finely tuned, involving complex communication and coordination between diverse immune and non-immune cells across the tissues of the body. A healthy immune system requires a precise balance between immunity and tolerance. Regulatory T cells (Tregs) have long been appreciated as one of the master regulators of this balance; their importance is underscored by the autoimmunity that develops in mice and humans when Tregs are missing or dysfunctional. In addition to the immunoregulatory roles of Tregs in suppressing autoimmunity and inflammation via control of adaptive and innate immune responses, several non-immune modulatory functions of Tregs have been identified in recent years. In this review, we have highlighted the growing literature on the action of Tregs in metabolism, stem cell maintenance, tissue repair, and angiogenesis. Alongside Tregs’ immune suppressive role, these non-suppressive activities comprise a key function of Tregs in regulating health and disease. As Tregs receive increasing attention as therapeutic targets, understanding their non-canonical functions may become an important feature of Treg-directed interventions.
Combination therapy of a TRPV2 agonist with a TNF inhibitor achieves sustained suppression of disease severity and reduced joint damage
Authors: Laragione Teresina , Harris Carolyn , Gulko Percio S 
Published: December 2022

AbstractWe aimed to compare a transient receptor potential vanilloid 2 (TRPV2) agonist with a TNF inhibitor, and to test the potential of their combination in collagen-induced arthritis (CIA) as a potential future strategy for rheumatoid arthritis (RA). Following the onset of CIA DBA1/j mice were started on treatment with either vehicle, etanercept (8 mg/kg three times a week), the TRPV2 agonist O1821 (20–30 mg/kg/day), or a combination of both. Mice were scored over a 61-day period. Synovial tissues were obtained for RNA sequencing. Mice on monotherapy with either O1821 or etanercept developed milder clinical disease. The O1821 protection was observed at an earlier time-point than in the etanercept group. The combination therapy group achieved a more robust and sustained reduction in disease severity than either monotherapy group. All treatment groups had reduced scores for synovial inflammation, synovial hyperplasia, and erosive changes, compared with controls, with the combination group achieving the most significant protection. RNA sequencing and pathway analyses of synovial tissues identified pathways and processes regulated by the TRPV2 agonist, such as chemotaxis and cytokine receptor signaling, including IL6R. The combination therapy affected additional pathways not seen in the monotherapy groups. In conclusion, the TRPV2 agonist achieved an overall similar reduction in arthritis severity and histology scores as etanercept, but the combination therapy achieved a more sustained disease control and more pronounced reduction in joint damage, suggesting a potential future option for improving disease control in RA. RNA sequencing analyses identified new pathways regulated by TRPV2, and also by the combination treatment.
Determination of 23 Amino Acids and Amines in Plasma and Cortex of C57BL/6 Mice with HPLC–FLD
Authors: Zhang Jing , Yang Junqing , Luo Ying , Li Jiansha , Gong Tao , Huang Suqiong , Xiong Yan , Jiang Xinhui 
Published: December 2022

Abstract
Using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate as a pre-column derivatization reagent, optimized derivatization and chromatography parameters, a simple high-performance liquid chromatography fluorescence detector (HPLC–FLD) method was developed and validated to determine 23 related amines in plasma and cortex of C57BL/6 mice with cerebral ischemia–reperfusion injury. The prepared samples were separated on a ZORBAX SB-C18 column (4.6 mm × 250 mm, 5 μm) with 60% acetonitrile (ACN) and 20 mM sodium acetate solution (pH adjusted to 5.0 by phosphoric acid). All analytes achieved good separation within 1.2 h at a flow rate of 1 mL/min. The limits of detection and limits of detection quantitation of the method were ranged from (0.1–9.2) to (0.3–30.6) ng/mL, respectively. The analytical method was apt for simultaneously determining 23 amino acids in plasma and cortex. Our results revealed that the relevant amino acids were significantly altered (P &lt; 0.05) in C57BL/6 mice.
Assessment of the clinical and allergy profiles of PPI responsive and non-responsive eosinophilic esophagitis
Authors: Goldin Alison H , Muftah Mayssan , Mangla Shikha , Hornick Jason L , Hsu Blatman Karen , Hamilton Matthew J , Lo Wai-Kit , Chan Walter W 
Published: December 2022

Summary
A subset of patients with eosinophilic esophagitis (EoE) respond to proton-pump inhibitor (PPI) therapy, however they cannot be distinguished prior to PPI trial and the mechanism of PPI response remains unclear. Improved understanding of the distinct patient phenotypes in PPI-responsive EoE (PPI-r-EoE), PPI-non-responsive EoE (PPI-nr-EoE) and erosive esophagitis (EE) may help guide management. The aim of this paper is to compare the clinical and allergy profiles of PPI-r-EoE versus PPI-nr-EoE and EE. This was a retrospective case-control study of EoE patients (&gt;15 eos/hpf on esophageal biopsies) at a tertiary center. EE controls were identified from the pathology database. EoE patients were classified as PPI-r-EoE or PPI-nr-EoE based on histologic response to twice-daily PPI for ≥8 weeks. Patient demographics, comorbidities, symptoms, allergy history and endoscopic findings were recorded. Univariate analyses were performed using the Fisher-exact test or t-test. Multivariable analyses were performed using logistic regression. In all, 104 EoE (57 PPI-r-EoE/47 PPI-nr-EoE) and 80 EE subjects were included. On multivariable analyses, allergic conditions (aOR 20.1, P &lt; 0.0001) and rings (aOR 108.3, P = 0.001) were independent predictors for PPI-r-EoE versus EE, whereas allergic conditions (aOR 4.8, P = 0.03), rings (aOR 27.5, P = 0.002) and furrows (aOR 17.1, P = 0.04) were independent predictors for PPI-nr-EoE versus EE. Esophageal rings was the only significant predictor found in PPI-nr-EoE versus PPI-r-EoE (OR 2.5, P = 0.03). Allergic conditions and esophageal rings are significantly more prevalent in PPI-r-EoE and PPI-nr-EoE compared with EE. PPI-r-EoE appears clinically similar to PPI-nr-EoE and significantly different from EE. Further studies are needed to delineate the underlying pathophysiology of PPI-r-EoE versus PPI-nr-EoE.