bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton pump inhibitors and risk of gastric cancer: population-based cohort study
Authors: Abrahami Devin , McDonald Emily Gibson , Schnitzer Mireille E , Barkun Alan N , Suissa Samy , Azoulay Laurent 
Published: July 2021

ObjectiveTo determine whether new users of proton pump inhibitors (PPIs) are at an increased risk of gastric cancer compared with new users of histamine-2 receptor antagonists (H2RAs).DesignUsing the UK Clinical Practice Research Datalink, we conducted a population-based cohort study using a new-user active comparator design. From 1 January 1990 to 30 April 2018, we identified 973 281 new users of PPIs and 193 306 new users of H2RAs. Cox proportional hazards models were fit to estimate HRs and 95% CIs of gastric cancer, and the number needed to harm was estimated using the Kaplan-Meier method. The models were weighted using standardised mortality ratio weights using calendar time-specific propensity scores. Secondary analyses assessed duration and dose–response associations.ResultsAfter a median follow-up of 5.0 years, the use of PPIs was associated with a 45% increased risk of gastric cancer compared with the use of H2RAs (HR 1.45, 95% CI 1.06 to 1.98). The number needed to harm was 2121 and 1191 for five and 10 years after treatment initiation, respectively. The HRs increased with cumulative duration, cumulative omeprazole equivalents and time since treatment initiation. The results were consistent across several sensitivity analyses.ConclusionThe findings of this large population-based cohort study indicate that the use of PPIs is associated with an increased risk of gastric cancer compared with the use of H2RAs, although the absolute risk remains low.
Clinical phenotypes and outcomes of SARS-CoV-2, influenza, RSV and seven other respiratory viruses: a retrospective study using complete hospital data
Authors: Hedberg Pontus , Karlsson Valik John , van der Werff Suzanne , Tanushi Hideyuki , Requena Mendez Ana , Granath Fredrik , Bell Max , Mårtensson Johan , Dyrdak Robert , Hertting Olof , Färnert Anna , Ternhag Anders , Naucler Pontus 
Published: July 2021

BackgroundAn understanding of differences in clinical phenotypes and outcomes COVID-19 compared with other respiratory viral infections is important to optimise the management of patients and plan healthcare. Herein we sought to investigate such differences in patients positive for SARS-CoV-2 compared with influenza, respiratory syncytial virus (RSV) and other respiratory viruses.MethodsWe performed a retrospective cohort study of hospitalised adults and children (≤15 years) who tested positive for SARS-CoV-2, influenza virus A/B, RSV, rhinovirus, enterovirus, parainfluenza viruses, metapneumovirus, seasonal coronaviruses, adenovirus or bocavirus in a respiratory sample at admission between 2011 and 2020.ResultsA total of 6321 adult (1721 SARS-CoV-2) and 6379 paediatric (101 SARS-CoV-2) healthcare episodes were included in the study. In adults, SARS-CoV-2 positivity was independently associated with younger age, male sex, overweight/obesity, diabetes and hypertension, tachypnoea as well as better haemodynamic measurements, white cell count, platelet count and creatinine values. Furthermore, SARS-CoV-2 was associated with higher 30-day mortality as compared with influenza (adjusted HR (aHR) 4.43, 95% CI 3.51 to 5.59), RSV (aHR 3.81, 95% CI 2.72 to 5.34) and other respiratory viruses (aHR 3.46, 95% CI 2.61 to 4.60), as well as higher 90-day mortality, ICU admission, ICU mortality and pulmonary embolism in adults. In children, patients with SARS-CoV-2 were older and had lower prevalence of chronic cardiac and respiratory diseases compared with other viruses.ConclusionsSARS-CoV-2 is associated with more severe outcomes compared with other respiratory viruses, and although associated with specific patient and clinical characteristics at admission, a substantial overlap precludes discrimination based on these characteristics.
Awareness, perceptions of and compliance with tobacco control policies among naswar vendors in Khyber Pakhtunkhwa Pakistan
Authors: Ahmad Fayaz , Khan Zohaib , Siddiqi Kamran , Khan Muhammad Naseem , Kibria Zeeshan , Forberger Sarah , Bauld Linda , Kanaan Mona , Zeeb Hajo 
Published: July 2021

IntroductionRegulatory compliance in the retail environment is integral to the success of tobacco control. We assessed compliance among naswar (smokeless tobacco product widely used in South Asia) vendors with tobacco control laws. We also assessed their awareness of tobacco-related harms and policies and perceived effect of policies on their sales.MethodsWe surveyed 286 naswar vendors in three districts of the Khyber Pakhtunkhwa province of Pakistan. We recruited general and specialty vendors from urban and rural areas through multistage cluster sampling. Compliance was measured for promotion, sale to/by minors and tax paid on naswar. We used logistic regression analyses for assessing the association between the outcome variables (awareness of tobacco harms and laws, perceptions about the effect of policies on business and compliance with laws) and their predictors.ResultsMost vendors (70%) were aware of tobacco-related harms of naswar. Although educated vendors were more aware of tobacco control policies, the greatest awareness was for a ban on sales to/by minors (21% overall). The majority of vendors (76%) violated this policy (measured by self-report), and violations were more common among rural than urban vendors (OR 2.27, 95% CI 1.05 to 4.96). Most vendors (71%) violated a ban on promotion of naswar. Vendors perceived tax increases and sales ban to/by minors as most detrimental for business.ConclusionsThere was poor awareness and compliance among naswar vendors in Pakistan with tobacco control laws. This study finds potential areas for policy interventions that can reduce urban/rural disparities in implementation of and compliance with tobacco control laws.
Exploring the gateway hypothesis of e-cigarettes and tobacco: a prospective replication study among adolescents in the Netherlands and Flanders
Authors: Martinelli Thomas , Candel Math J J M , de Vries Hein , Talhout Reinskje , Knapen Vera , van Schayck Constant P , Nagelhout Gera E 
Published: July 2021

BackgroundStudies demonstrated that adolescent e-cigarette use is associated with subsequent tobacco smoking, commonly referred to as thegateway effect. However, most studies only investigated gateways from e-cigarettes to tobacco smoking. This study replicates a cornerstone study revealing a positive association between both adolescent e-cigarette use and subsequent tobacco use; and tobacco and subsequent e-cigarette use in the Netherlands and Flanders.DesignThe longitudinal design included baseline (n=2839) and 6-month (n=1276) and 12-month (n=1025) follow-up surveys among a school-based cohort (mean age: 13.62). Ten high schools were recruited as a convenience sample. The analyses involved (1) associations of baseline e-cigarette use and subsequent tobacco smoking among never smokers; (2) associations of e-cigarette use frequency at baseline and tobacco smoking frequency at follow-up; and (3) the association of baseline tobacco smoking and subsequent e-cigarette use among non-users of e-cigarettes.FindingsConsistent with prior findings, baseline e-cigarette use was associated with higher odds of tobacco smoking at 6-month (OR=1.89; 95% CI 1.05 to 3.37) and 12-month (OR=5.63; 95% CI 3.04 to 10.42) follow-ups. More frequent use of e-cigarettes at baseline was associated with more frequent smoking at follow-ups. Baseline tobacco smoking was associated with subsequent e-cigarette use (OR=3.10; 95% CI 1.58 to 6.06 at both follow-ups).ConclusionOur study replicated the positive relation between e-cigarette use and tobacco smoking in both directions for adolescents. This may mean that the gateway works in two directions, that e-cigarette and tobacco use share common risk factors, or that both mechanisms apply.
On the existence of the global conformal gauge in string theory
Authors: Katanaev M. O. 
Published: July 2021

AbstractThe global conformal gauge is playing the crucial role in string theory providing the basis for quantization. Its existence for two-dimensional Lorentzian metric is known locally for a long time. We prove that if a Lorentzian metric is given on a plain then the conformal gauge exists globally on the whole $${{\mathbb {R}}}^2$$

R

2

. Moreover, we prove the existence of the conformal gauge globally on the whole worldsheets represented by infinite strips with straight boundaries for open and closed bosonic strings. The global existence of the conformal gauge on the whole plane is also proved for the positive definite Riemannian metric.
Robustness of a dynamical systems model with a plastic self-organising vector field to noisy input signals
Authors: Janson N. B. , Kloeden P. E. 
Published: July 2021

AbstractWe investigate the robustness with respect to random stimuli of a dynamical system with a plastic self-organising vector field, previously proposed as a conceptual model of a cognitive system and inspired by the self-organised plasticity of the brain. This model of a novel type consists of an ordinary differential equation subjected to the time-dependent “sensory” input, whose time-evolving solution is the vector field of another ordinary differential equation governing the observed behaviour of the system, which in the brain would be neural firings. It is shown that the individual solutions of both these differential equations depend continuously over finite time intervals on the input signals. In addition, under suitable uniformity assumptions, it is shown that the non-autonomous pullback attractor and forward omega limit set of the given two-tier system depend upper semi-continuously on the input signal. The analysis holds for both deterministic and noisy input signals, in the latter case in a pathwise sense.
A simple model predicting in-hospital death in patients with type A acute aortic dissection
Authors: Wang Min , Luo Liyan , Xia Xiaohong , Jiang Jiahong , Zhang Litao , Ge Gaoxia , Dong Ning 
Published: July 2021

Background: Type A acute aortic dissection (TAAAD) is a destructive cardiovascular disease, with high morbidity and mortality rates. Identifying the high-risk TAAAD patients at an early stage is urgently necessary. Methods: A retrospective study of 160 patients was carried out. The admission data were retrospectively gathered. Logistic regression analysis and receiver operator characteristic curve (AUC) was utilized. Results: Compared with the survivor group, the nonsurvivor group was older, had higher D-dimer levels, red blood cell distribution width (RDW) levels and platelet distribution width (PDW) levels, and lower fibrinogen levels, platelet levels and plateletcrit levels. Multivariate analysis displayed that four independent factors, age (hazard ratio (HR): 7.877, 95% confidence interval (CI) 2.740–22.641, p < 0.001), D-dimer (HR: 3.791, 95% CI 1.520–9.452, p = 0.004), RDW (HR: 3.300, 95% CI 1.109–9.825, p = 0.032), PDW (HR: 3.755, 95% CI 1.436–9.815, p = 0.007) were incorporated into the model. The predict accuracy of the model (AUC 0.861, 95% CI 0.798–0.911, p < 0.001) was best. Conclusions: Age, D-dimer, RDW and PDW are independent markers of in-hospital death in TAAAD patients and the newly established model has better performance in predicting high-risk patients. This model can be used as a quick screening tool to assess the prognosis of patients in individualizing.
The real-world outcomes of vedolizumab in patients with ulcerative colitis in Korea: a multicenter retrospective study
Authors: Ye Byong Duk , Cheon Jae Hee , Song Ki Hwan , Kim Joo Sung , Kim Young-Ho , Yoon Hyuk , Lee Kang-Moon , Kang Sang-Bum , Jang Byung Ik , Park Jae Jun , Kim Tae Oh , Lee Dae-Wook , Foo Chee Yoong , Shin Jeong Eun , Park Dong Il 
Published: July 2021

Aim: This study examined the real-world effectiveness and safety outcomes of vedolizumab in ulcerative colitis (UC) patients who had failed anti-tumor necrosis factor (anti-TNF) therapy in Korea. Methods: A retrospective chart review study was conducted in adults with moderate to severely active UC who had failed anti-TNF agents and subsequently received vedolizumab. Clinical response and clinical remission at week 6 and 14 after vedolizumab initiation was evaluated. Safety outcomes were also reported. Outcome rates were compared with a matched sub-cohort derived from the open-label sub-cohort of the GEMINI 1 trial using the optimal matching method. Results: A total of 105 patients (mean age, 45.3 years; 63.8% male) were included. At week 6, 55.8% ( n = 43/77) achieved a clinical response and 18.2% ( n = 14/77) achieved clinical remission. At week 14, 73.2% ( n = 52/71) achieved a clinical response and 39.4% ( n = 28/71) achieved clinical remission. When non-response imputation was used, the clinical response rate at week 6 and week 14 were 40.1% ( n = 43/105) and 49.5% ( n = 52/105) respectively. Of the 105 patients, 16 (15.2%) experienced at least one adverse event. The matched analysis showed that the clinical response rate at week 6 was higher in the matched sub-cohort of this study (24/47, 51.1%) versus the matched sub-cohort from the GEMINI 1 open-label cohort (12/47, 34.3%, p = 0.019). The clinical remission rates at week 6 were similar (7/47, 14.9% versus 9/47, 19.1%, p = 0.785). Conclusions: In the real-world setting, vedolizumab is effective and well tolerated within the first 14 weeks of use in Korea. The proportion of patients experiencing clinical response and clinical remission at 6 and 14 weeks appeared to be largely consistent with that observed in real-world studies from other regions and populations.
Surface Integrity of Ultrasonically-Assisted Milled Ti6Al4V Alloy Manufactured by Selective Laser Melting
Authors: Guo Sai , Du Wei , Jiang Qinghong , Dong Zhigang , Zhang Bi 
Published: July 2021

AbstractThe Ti6Al4V parts produced by the existing selective laser melting (SLM) are mainly confronted with poor surface finish and inevitable interior defects, which substantially deteriorates the mechanical properties and performances of the parts. In this regard, ultrasonically-assisted machining (UAM) technique is commonly introduced to improve the machining quality due to its merits in increasing tool life and reducing cutting force. However, most of the previous studies focus on the performance of UAM with ultrasonic vibrations applied in the tangential and feed directions, whereas few of them on the impact of ultrasonic vibration along the vertical direction. In this study, the effects of feed rate on surface integrity in ultrasonically-assisted vertical milling (UAVM) of the Ti6Al4V alloy manufactured by SLM were systemically investigated compared with the conventional machining (CM) method. The results revealed that the milling forces in UAVM showed a lower amplitude than that in CM due to the intermittent cutting style. The surface roughness values of the parts produced by UAVM were generally greater than that by CM owing to the extra sinusoidal vibration textures induced by the milling cutter. Moreover, the extra vertical ultrasonic vibration in UAVM was beneficial to suppressing machining chatter. As feed rate increased, surface microhardness and thickness of the plastic deformation zone in CM raised due to more intensive plastic deformation, while these two material properties in UAVM were reduced owing to the mitigated impact effect by the high-frequency vibration of the milling cutter. Therefore, the improved surface microhardness and reduced thickness of the subsurface deformation layer in UAVM were ascribed to the vertical high-frequency impact of the milling cutter in UAVM. In general, the results of this study provided an in-depth understanding in UAVM of Ti6Al4V parts manufactured by SLM.
HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Authors: Ferravante Carlo , Memoli Domenico , Palumbo Domenico , Ciaramella Paolo , Di Loria Antonio , D’Agostino Ylenia , Nassa Giovanni , Rizzo Francesca , Tarallo Roberta , Weisz Alessandro , Giurato Giorgio 
Published: July 2021

Abstract
Background
Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks.

Results
We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets.

Conclusions
HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that lead to a comprehensive taxonomy profile of each sample by querying different source databases, and it is customizable according to specific users’ needs.
Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites
Authors: Müller-Schüssele Stefanie J. , Bohle Finja , Rossi Jacopo , Trost Paolo , Meyer Andreas J. , Zaffagnini Mirko 
Published: July 2021

Abstract
Background
Flexibility of plant metabolism is supported by redox regulation of enzymes via posttranslational modification of cysteine residues, especially in plastids. Here, the redox states of cysteine residues are partly coupled to the thioredoxin system and partly to the glutathione pool for reduction. Moreover, several plastid enzymes involved in reactive oxygen species (ROS) scavenging and damage repair draw electrons from glutathione. In addition, cysteine residues can be post-translationally modified by forming a mixed disulfide with glutathione (S-glutathionylation), which protects thiol groups from further oxidation and can influence protein activity. However, the evolution of the plastid glutathione-dependent redox network in land plants and the conservation of cysteine residues undergoing S-glutathionylation is largely unclear.

Results
We analysed the genomes of nine representative model species from streptophyte algae to angiosperms and found that the antioxidant enzymes and redox proteins belonging to the plastid glutathione-dependent redox network are largely conserved, except for lambda- and the closely related iota-glutathione S-transferases. Focussing on glutathione-dependent redox modifications, we screened the literature for target thiols of S-glutathionylation, and found that 151 plastid proteins have been identified as glutathionylation targets, while the exact cysteine residue is only known for 17% (26 proteins), with one or multiple sites per protein, resulting in 37 known S-glutathionylation sites for plastids. However, 38% (14) of the known sites were completely conserved in model species from green algae to flowering plants, with 22% (8) on non-catalytic cysteines. Variable conservation of the remaining sites indicates independent gains and losses of cysteines at the same position during land plant evolution.

Conclusions
We conclude that the glutathione-dependent redox network in plastids is highly conserved in streptophytes with some variability in scavenging and damage repair enzymes. Our analysis of cysteine conservation suggests that S-glutathionylation in plastids plays an important and yet under-investigated role in redox regulation and stress response.
An illuminated respiratory activity monitoring system identifies priming-active compounds in plant seedlings
Authors: Loogen Judith , Müller André , Balzer Arne , Weber Sophie , Schmitz Kathrin , Krug Roxanne , Schaffrath Ulrich , Pietruszk Jörg , Conrath Uwe , Büchs Jochen 
Published: July 2021

Abstract
Background
Growing large crop monocultures and heavily using pesticides enhances the evolution of pesticide-insensitive pests and pathogens. To reduce pesticide use in crop cultivation, the application of priming-active compounds (PrimACs) is a welcome alternative. PrimACs strengthen the plant immune system and could thus help to protect plants with lower amounts of pesticides. PrimACs can be identified, for example, by their capacity to enhance the respiratory activity of parsley cells in culture as determined by the oxygen transfer rate (OTR) using the respiration activity monitoring system (RAMOS) or its miniaturized version, µRAMOS. The latter was designed for with suspensions of bacteria and yeast cells in microtiter plates (MTPs). So far, RAMOS or µRAMOS have not been applied to adult plants or seedlings, which would overcome the limitation of (µ)RAMOS to plant suspension cell cultures.

Results
In this work, we introduce a modified µRAMOS for analysis of plant seedlings. The novel device allows illuminating the seedlings and records the respiratory activity in each well of a 48-well MTP. To validate the suitability of the setup for identifying novel PrimAC in Arabidopsis thaliana, seedlings were grown in MTP for seven days and treated with the known PrimAC salicylic acid (SA; positive control) and the PrimAC candidate methyl 1-(3,4-dihydroxyphenyl)-2-oxocyclopentane-1-carboxylate (Tyr020). Twenty-eight h after treatment, the seedlings were elicited with flg22, a 22-amino acid peptide of bacterial flagellin. Upon elicitation, the respiratory activity was monitored. The evaluation of the OTR course reveals Tyr020 as a likely PrimAC. The priming-inducing activity of Tyr020 was confirmed using molecular biological analyses in A. thaliana seedlings.

Conclusion
We disclose the suitability of µRAMOS for identifying PrimACs in plant seedlings. The difference in OTR during a night period between primed and unprimed plants was distinguishable after elicitation with flg22. Thus, it has been shown that the µRAMOS device can be used for a reliable screening for PrimACs in plant seedlings.
The burden of hand, foot, and mouth disease among children under different vaccination scenarios in China: a dynamic modelling study
Authors: Liu Zhixi , Tian Jie , Wang Yue , Li Yixuan , Liu-Helmersson Jing , Mishra Sharmistha , Wagner Abram L. , Lu Yihan , Wang Weibing 
Published: July 2021

Abstract
Background
Hand, foot, and mouth disease (HFMD) is a common illness in young children. A monovalent vaccine has been developed in China protecting against enterovirus-71, bivalent vaccines preventing HFMD caused by two viruses are under development.

Objective
To predict and compare the incidence of HFMD under different vaccination scenarios in China.

Methods
We developed a compartmental model to capture enterovirus transmission and the natural history of HFMD in children aged 0–5, and calibrated to reported cases in the same age-group from 2015 to 2018. We compared the following vaccination scenarios: different combinations of monovalent and bivalent vaccine; a program of constant vaccination to that of pulse vaccination prior to seasonal outbreaks.

Results
We estimate 1,982,819, 2,258,846, 1,948,522 and 2,398,566 cases from 2015 to 2018. Increased coverage of monovalent vaccine from 0 to 80% is predicted to decrease the cases by 797,262 (49.1%). Use of bivalent vaccine at an 80% coverage level would decrease the cases by 828,560. Use of a 2.0× pulse vaccination for the bivalent vaccine in addition to 80% coverage would reduce cases by over one million. The estimated R0 for HFMD in 2015–2018 was 1.08, 1.10, 1.35 and 1.17.

Conclusions
Our results point to the benefit of bivalent vaccine and using a pulse vaccination in specific months over routine vaccination. Other ways to control HFMD include isolation of patients in the early stage of dissemination, more frequent hand-washing and ventilation, and better treatment options for patients.