bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomarkers of Exposure and Biomarkers of Potential Harm in Adult Smokers Who Switch to e-Vapor Products Relative to Cigarette Smoking in a 24-week, Randomized, Clinical Trial
Authors: Edmiston Jeffery S , Webb Katy M , Wang Jingzhu , Oliveri Douglas , Liang Qiwei , Sarkar Mohamadi 
Published: February 2022

Abstract

Introduction
Long-term health effects of e-vapor products (EVPs) are not well-established. We compared biomarkers of exposure (BoE) to select harmful and potentially harmful constituents and biomarkers of potential harm (BoPH) in adult smokers who switched to EVPs versus continued smoking for 24 weeks.

Methods
Adult smokers (n = 450, &gt;10 cigarettes per day for ≥10 years) were randomly assigned to continue smoking (control) or switch to one of two cartridge-based EVPs (test 1: classic; test 2: menthol, 4% nicotine). BoE and BoPH were measured at baseline and 12 weeks. The results presented here are from a subset of 150 control and EVP subjects (switchers with exhaled carbon monoxide &lt;8 ppm and &lt;10% baseline cigarettes per day) followed for 24 total weeks.

Results
Total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol and carboxyhemoglobin were significantly reduced (p &lt; .0001) in tests 1 and 2 at 24 weeks. Urinary nicotine equivalents were not statistically significantly different between the control and EVP groups. At week 24, statistically significant reductions (p &lt; .05) were observed for white blood cell counts, 11-dehydrothromboxane β2, and sICAM in both test groups, and there were several significant changes in measures of pulmonary function. High-density lipoprotein cholesterol and 8-epi-prostaglandin-F2α were directionally favorable in both EVP groups versus control.

Conclusions
We demonstrate that significant reductions of selected harmful and potentially harmful constituents in EVP aerosol results in significant reductions in BoEs and favorable changes in BoPHs after switching to EVPs for 24 weeks. These changes approached those reported for smoking cessation, suggesting that switching to exclusive use of the EVPs may be less harmful than continuing smoking.

Implications
Cigarette smoking causes serious diseases. Switching from cigarettes to a noncombustible product is a potential harm reduction pathway for adult smokers unable or unwilling to quit. Long-term health effects of e-vapor products (EVPs) compared with continued smoking have not been extensively studied. We present biomarker of exposure evidence on select harmful and potentially harmful constituents and biomarkers of potential harm related to inflammation and oxidative stress in adult smokers switching to two EVPs. This study demonstrates significant reductions in biomarkers of exposure (except for nicotine) accompanied with favorable changes in various biomarkers of potential harm, including pulmonary function. The totality of evidence suggests that exclusive EVP use may present lower health risks compared with smoking cigarettes.
Small Towns, Big Cities: Rural and Urban Disparities Among Hospitalized Patients With COVID-19 in the Central Savannah River Area
Authors: Hamilton Caroline A , Ayyala Deepak , Walsh David , Bramwell Christian , Walker Christopher , Wilson Dib Rita , Gosse Jessica , Ladak Amber , Morissette Patricia , Rao Arni , Chao Andrew , Vazquez Jose 
Published: February 2022

Abstract

Background
There is a lack of data surrounding the impact of coronavirus disease 2019 (COVID-19) among rural and urban communities. This study aims to determine whether there are differences in epidemiologic characteristics and clinical outcomes among individuals with COVID-19 among these communities.

Methods
This was a retrospective analysis of 155 patients admitted to a single-center tertiary academic hospital located in Augusta, Georgia, with a large proportion of hospitalized patients transferred from or residing in rural and urban counties. Hospitalized adult patients were included in the study if they were admitted to AUMC between March 13, 2020, and June 25, 2020, and had a positive polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 regardless of the presence or absence of symptomatology. Demographics, admission data, and 30-day outcomes were examined overall and by geographical variation.

Results
Urban patients were more likely to be admitted to the general medical floor (P = .01), while rural patients were more likely to require an escalation in the level of care within 24 hours of admission (P = .02). In contrast, of the patients who were discharged or expired at day 30, there were no statistically significant differences in either total hospital length of stay or intensive care unit length of stay between the populations.

Conclusions
There may be many social determinants of health that limit a rural patient’s ability to seek prompt medical care and contribute to decompensation within the first 24 hours of admission. This study provides insight into the differences in clinical course among patients admitted from different community settings and when accounting for comorbid conditions.
Identification of New ATG8s-binding Proteins with Canonical LC3-interacting Region in Autophagosomes of Barley Callus
Authors: Buerte B , Zeng Zhanghui , Zhou Chun , Lian Guiwei , Guo Fu , Wang Junhui , Han Ning , Zhu Muyuan , Bian Hongwu 
Published: February 2022

Abstract
Autophagy is essential to maintain cellular homeostasis for normal cell growth and development. In selective autophagy, ATG8 plays a crucial role in cargo target recognition by binding to various adaptors and receptors with the ATG8-interacting motif, also known as the LC3-interacting region (LIR). However, the process of autophagy in the callus, as a proliferating cell type, is largely unknown. In this study, we overexpressed green fluorescent protein (GFP)-ATG8a and GFP-ATG8b transgenic barley callus and checked their autophagic activities. We identified five new ATG8 candidate interactors containing the canonical LIR motif by using immunoprecipitation coupled with mass spectrometry: RPP3, COPE, NCLN, RAE1 and CTSL. The binding activities between these candidate interactors and ATG8 were further demonstrated in the punctate structure. Notably, RPP3 was colocalized in ATG8-labeled autophagosomes under tunicamycin-induced endoplasmic reticulum stress. Glutathione S-transferase pull-down assays showed that the interaction between RPP3 and ATG8 could be prevented by mutating the LIR of RPP3 or the LIR docking site (LDS) of ATG8, suggesting that RPP3 directly interacted with ATG8 in an LIR-dependent manner via the LDS. Our findings would provide the basis for further investigations on novel receptors and functions of autophagy in plants, especially in the physiological state of cell de-differentiation.
Loss of a pyridoxal-phosphate phosphatase rescues Arabidopsis lacking an endoplasmic reticulum ATP carrier
Authors: Altensell Jacqueline , Wartenberg Ruth , Haferkamp Ilka , Hassler Sebastian , Scherer Vanessa , Steensma Priscille , Fitzpatrick Teresa B , Sharma Anurag , Sandoval-Ibañez Omar , Pribil Mathias , Lehmann Martin , Leister Dario , Kleine Tatjana , Neuhaus H Ekkehard 
Published: February 2022

Abstract
The endoplasmic reticulum (ER)-located ATP/ADP-antiporter (ER-ANT1) occurs specifically in vascular plants. Structurally different transporters mediate energy provision to the ER, but the cellular function of ER-ANT1 is still unknown. Arabidopsis (Arabidopsis thaliana) mutants lacking ER-ANT1 (er-ant1 plants) exhibit a photorespiratory phenotype accompanied by high glycine levels and stunted growth, pointing to an inhibition of glycine decarboxylase (GDC). To reveal whether it is possible to suppress this marked phenotype, we exploited the power of a forward genetic screen. Absence of a so far uncharacterized member of the HaloAcid Dehalogenase (HAD)-like hydrolase family strongly suppressed the dwarf phenotype of er-ant1 plants. Localization studies suggested that the corresponding protein locates to chloroplasts, and activity assays showed that the enzyme dephosphorylates, with high substrate affinity, the B6 vitamer pyridoxal 5′-phosphate (PLP). Additional physiological experiments identified imbalances in vitamin B6 homeostasis in er-ant1 mutants. Our data suggest that impaired chloroplast metabolism, but not decreased GDC activity, causes the er-ant1 mutant dwarf phenotype. We present a hypothesis, setting transport of PLP by ER-ANT1 and chloroplastic PLP dephosphorylation in the cellular context. With the identification of this HAD-type PLP phosphatase, we also provide insight into B6 vitamer homeostasis.
Legitimacy of Algorithmic Decision-Making: Six Threats and the Need for a Calibrated Institutional Response
Authors: Grimmelikhuijsen Stephan , Meijer Albert 
Published: February 2022

Abstract
Algorithmic decision-making in government has emerged rapidly in recent years, leading to a surge in attention for this topic by scholars from various fields, including public administration. Recent studies provide crucial yet fragmented insights on how the use of algorithms to support or fully automate decisions is transforming government. This article ties together these insights by applying the theoretical lenses of government legitimacy and institutional design. We identify how algorithmic decision-making challenges three types of legitimacy—input, throughput, and output—and identify institutional arrangements that can mitigate these threats. We argue that there is no silver bullet to maintain legitimacy of algorithmic government and that a multiplicity of different institutional mechanisms is required, ranging from legal structures and civic participation to closer monitoring of algorithmic systems. We conclude with a framework to guide future research to better understand the implications of institutional design for the legitimacy of algorithmic government.
Effect of Probiotics on the Frequency of CD4+ T-Cells in HIV-Infected Children and Adolescents: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Sachdeva Meenakshi , Sra Harnoor K , Agarwal Amit , Chauhan Anil , Pradhan Pranita , Singh Manvi , Singh Meenu 
Published: February 2022

ABSTRACT

Background
Depletion of CD4+ T-cells in the gut-associated lymphoid tissue is the hallmark of HIV infection, with only partial restoration by potent antiretroviral therapy (ART). Gut dysbiosis, together with disruption of mucosal integrity contributes to chronic immune activation that further exacerbates the disease. Data from randomized controlled trials in pediatric HIV patients have indicated potential of probiotics in complementing routine ART in managing HIV-associated gastrointestinal complications. We have systematically extracted data from these trials and performed meta-analysis to quantify the effect of probiotics on CD4+ T-cell counts and any adverse events associated with their supplementation.

Methods
A systematic search through multiple databases yielded three studies that were pooled using fixed-effect model. Risk of bias assessment was done by the Cochrane risk of bias tool and publication bias was assessed by Egger’s test.

Results
Included studies had moderate risk of bias and Egger’s statistics revealed no publication bias (p &gt; 0.05). Pooled analysis showed significant improvement in CD4+ T-cell counts, with mean difference, 123.92 (95% CI: 104.36–143.48), p &lt; 0.0001, no heterogeneity (I2=0) among the included trials. Subgroup analysis also depicted improvement in CD4+ T-cell counts irrespective of treatment duration, in both ART naïve and treated patients. No adverse effects with probiotic consumption were reported.

Conclusions
Probiotics supplementation led to an improvement in CD4+ T-cell counts among HIV-infected children with no observed adverse effects. Despite the inherent limitations of included studies, our systematic review would justify more well-designed, large-scale trials in children, which may guide pediatricians on whether to incorporate probiotics as an adjunct therapy to routine ART.
Structural Reforms and Labor Productivity Growth in Developing Countries: Intra or Inter-Reallocation Channel?
Authors: Konte Maty , Kouamé Wilfried A , Mensah Emmanuel B 
Published: February 2022

Abstract
This paper employs sectoral data to draw conclusions on how structural reforms—implemented during the period 1975–2005—affected differences in cross-country aggregate labor productivity growth in developing countries. Most important, it explores how the effects of reforms on productivity growth are distributed between the intrasectoral and intersectoral components of labor productivity growth. The findings indicate that most of the trade, product market, and financial sector reforms have increased productivity growth. Looking at the subcomponents of labor productivity growth, the results show that structural reforms work mainly through the intra-allocative efficiency channel but not through the interallocative efficiency channel. The intrasectoral component is the main driver of the impacts of reforms on productivity growth, with a contribution that ranges from 76 percent to 96 percent depending on the reform measure considered. The paper also examines the role of labor market regulations and finds that labor market rigidity/flexibility matters for how specific reforms induce reallocation of resources within and across sectors.
Endophthalmitis after corneal suture removal
Authors: Staropoli Patrick C. , Yannuzzi Nicolas A. , Jacobs David , Flynn Harry W. 
Published: February 2022

Introduction:
To report 2 patients with acute-onset endophthalmitis after intraocular lens exchange and delayed corneal suture removal.

Patient and Clinical Findings:
An 83-year-old woman and a 64-year-old man developed pain, decreased vision, corneal infiltrate, marked intraocular inflammation, and vitreous membranes after corneal suture removal. Topical povidone–iodine was not used before suture removal, and the wounds showed negative results for Seidel test at presentation.

Diagnosis, Intervention, Outcomes:
Both patients were diagnosed with acute-onset endophthalmitis. One received vitreous tap and injection (T&I) and the other received both T&I and pars plana vitrectomy. Intravitreal vancomycin and ceftazidime were administered in both patients. Cultures demonstrated streptococcal species. Outcomes were poor: 1 eye was enucleated and the other showed light perception.

Conclusions:
Endophthalmitis in the setting of corneal suture removal can be associated with severe vision loss. Topical povidone–iodine antisepsis and topical antibiotics should be considered for endophthalmitis prophylaxis in this procedure.
Antitobacco advertising and lung cancer stigma: a qualitative study of the experiences of people with a lung cancer diagnosis
Authors: Rose Shiho , Boyes Allison W. , Kelly Brian , Bridge Paula , Carlson Melissa , Coutts Emily , Paul Chris 
Published: February 2022

Abstract
Stigma is often experienced by people affected by lung cancer due to the known links between lung cancer and smoking. Antitobacco campaigns, although attempting to “de-normalise” smoking, may contribute to stigmatising people affected by cancer. The study examined how people diagnosed with lung cancer recall and respond to antitobacco advertisements postdiagnosis. Sixteen qualitative semi-structured interviews were conducted with people with a lung cancer diagnosis who were recruited from an Australian clinical cancer registry. Interviews were analysed using thematic analysis. Participants mostly recalled narrative style antitobacco advertisements. A wide array of emotional responses to the advertisements were reported, including relief, shame, worry, discomfort, and resignation. Some participants avoided the advertisements altogether. Although some participants found the advertisements to be promoting stigma, others did not. Participants were not opposed to the broadcasting of antitobacco advertisements. Rather, the advertisements were perceived as appropriate and necessary. In conclusion, although people diagnosed with lung cancer reported experiencing some negative emotional responses to antitobacco advertising, they were supportive of its continuance.
Deep learning-based approach for detecting signs of atrial septal defect on chest radiographs: a proof of concept study
Authors: Matsuoka Ryo , Akazawa Hiroshi , Kodera Satoshi , Soma Katsura , Yagi Hiroki , Umei Masahiko , Kadowaki Hiroshi , Ishida Junichi , Shinohara Hiroki , Katsushika Susumu , Ieki Hirotaka , Yamaguchi Toshihiro , Higashikuni Yasutomi , Fujiu Katsuhito , Ito Kaoru , Yao Atsushi , Komuro Issei 
Published: February 2022

AbstractMany patients with atrial septal defects (ASD) are asymptomatic and undiagnosed during the first few decades of life, but have overt heart failure, arrhythmias, cerebral infarction, and increased mortality in adults with advancing age. To provide a non-invasive, easy-to-use, and effective method for detecting ASD, we aimed to develop and validate a deep learning-based algorithm to diagnose ASD on chest radiographs. The ASD dataset was created from 173 chest radiographs of 74 patients with ASD and 170 chest radiographs of 100 patients without ASD. Convolutional neural network models (VGG16, ResNet50, DenseNet121, and Xception) for diagnosing ASD were pretrained using two different datasets, the large-scale real-world ImageNet dataset and the ChestX-ray14 dataset released by National Institutes of Health, followed by a round of training using the training set of the ASD dataset. Model performance was evaluated by five-fold stratified cross-validation. The best performance in ImageNet pretraining was achieved by ResNet50 model, and the cross-validation area under the curve (AUC) was 0.95, with sensitivity of 0.86, specificity of 0.87, and overall accuracy of 0.87. The best performance in ChestX-ray pretraining was achieved by Xception, and the cross-validation AUC was 0.93, with sensitivity of 0.85, specificity of 0.85, and overall accuracy of 0.85. The diagnostic performances of these models were comparable to those of cardiologists. Gradient-weighted Class Activation Mapping showed that the ImageNet-pretrained model focused on bilateral hilar regions, while the ChestX-ray14-pretrained model focused on areas around cardiac silhouette and lower lung fields. Our deep learning-based algorithms made a diagnosis of ASD on the input chest radiographs with high accuracy, and had potential to help clinicians make accurate diagnosis of ASD from routine chest radiography, leading to improvement of prognosis and quality of life in patients with ASD.
VeChat: Correcting errors in long reads using variation graphs
Authors: Luo Xiao , Kang Xiongbin , Schönhuth Alexander 
Published: February 2022

AbstractError correction is the canonical first step in long-read sequencing data analysis. The current standard is to make use of a consensus sequence as a template. However, in mixed samples, such as metagenomes or organisms of higher ploidy, consensus induced biases can mask true variants affecting haplotypes of lower frequencies, because they are mistaken as errors.The novelty presented here is to use graph based, instead of sequence based consensus as a template for identifying errors. The advantage is that graph based reference systems also capture variants of lower frequencies, so do not mistakenly mask them as errors. We present VeChat, as a novel approach to implement this idea: VeChat distinguishes errors from haplotype-specific true variants based on variation graphs, which reflect a popular type of data structure for pangenome reference systems. Upon initial construction of an ad-hoc variation graph from the raw input reads, nodes and edges that are due to errors are pruned from that graph by way of an iterative procedure that is based on principles from frequent itemset mining. Upon termination, the graph exclusively contains nodes and edges reflecting true sequential phenomena. Final re-alignments of the raw reads indicate where and how reads need to be corrected.Extensive benchmarking experiments demonstrate that PacBio and ONT reads corrected by VeChat contain 4 to 15, or, respectively, 2 to 10 times less errors than when corrected state of the art approaches. VeChat is implemented in an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat.
Gene Expression Meta-Analysis of Colon Rectal Cancer Tumour Cells Reveals Genes in Association With Tumorogenesis
Authors: Vaja Rutvi 
Published: February 2022

AbstractBackgroundEvery year, more than 12 million people are diagnosed with colorectal cancer(CRC), and more than 600,000 people die from it, making it second most deadly form of cancer.This work analyzes differential gene expression across CRC and other glandular tumour samples to identify expression changes potentially contributing to the development of CRC tumorogenesis.MethodsThis work defines 13 gene signatures representing four CRC tumour and 10 other glandular tumours that are colonic by origin.Gene Set Enrichment Analysis (GSEA) is used to define positive and negative CRC gene panels from GSEA-identified leading-edge genes using two CRC signatures. GSEA then is used to verify enrichment and leading-edge gene membership of CRC panels in two independent CRC gene signatures. Analysis is then extended to four individual and 10 glandular tumour signatures. Genes most associated with CRC tumorogenesis are predicted by intersecting membership of GSEA-identified leading-edges across signatures.ResultsSignificant enrichment is observed between CRC gene identification signatures, from which the positive (55 genes) and negative (77 genes) CRC panels are defined. Non-random significant enrichment is observed between CRC gene panels and verification signatures, from which 54 over- and 72 under-expressed genes are shared across leading-edges. Considering other glandular tumour samples individually and in combination with CRC, significant non-random enrichment is observed across these signatures. Eight solute carrier family genes such as (SLC25A32, SLC22A3, SLC25A20, SLC36A1, SLC26A3,SLC9A2, SLC4A4 and SLC26A2) from the CRC panel were shared commonly across all the gene signatures leading-edges, regardless of the colonic tumour type.ConclusionThis meta-analysis identifies gene expression changes associated with the process of CRC tumorogenesis. These changes may contribute to developing therapeutic treatments available for CRC patients.