bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Utility of In-house Metagenomic Next-generation Sequencing for the Diagnosis of Lower Respiratory Tract Infections and Analysis of the Host Immune Response
Authors: Chen Hongbin , Yin Yuyao , Gao Hua , Guo Yifan , Dong Zhao , Wang Xiaojuan , Zhang Yawei , Yang Shuo , Peng Qiusheng , Liu Yudong , Wang Hui 
Published: October 2020

Abstract

Background
Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem.

Methods
This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People’s Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups.

Results
Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI–, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9.

Conclusions
Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.
Utility of a Simple Scoring System in Differentiating Bacterial Infections in Cases of Fever of Unknown Origin
Authors: Xu Teng , Wang Li , Wu Shi , Zhou Fenfen , Huang Haihui 
Published: October 2020

AbstractBackgroundInfectious disease is the leading cause of fever of unknown origin (FUO). Serum inflammatory markers historically used to diagnose bacterial infection have sufficient diagnostic sensitivity but low specificity. This study aimed to develop a simple scoring system for differentiating bacterial infections from other causes of early-stage FUO.MethodsThis study included a retrospective cohort of patients presenting with FUO at the Huashan Hospital (January 2014 to June 2017). The diagnostic utility of serum inflammatory markers for bacterial infection was evaluated using the receiver operating characteristic (ROC) curve analysis. Relevant markers were subsequently measured prospectively in a separate cohort of FUO patients (December 2017 to May 2019). A scoring system was based on inflammatory markers and other test results.ResultsBacterial infection was identified in 34% of patients in the retrospective cohort. The area under the ROC curve (AUC) was 0.644 (95% confidence interval [CI], .595–.693) for C-reactive protein, 0.624 (95% CI, .573–.675) for procalcitonin, and 0.646 (95% CI, .595–.697) for serum ferritin (SF) in diagnosing bacterial infection. Bacterial infection was found in 29% of cases in the prospective cohort. A model based on serum amyloid A (SAA) and SF levels and neutrophil percentage yielded an AUC of 0.775 (95% CI, .695–.854). Validation analysis indicated lower probability (&lt;15%) of bacterial infection for patients with a score &lt;16.5 points.ConclusionsA scoring system based on SAA and SF levels and neutrophil percentage can help distinguish bacterial infection from other causes of FUO, potentially reducing antibiotic use.
Mediatization and the Absence of the Environment
Authors: Kannengießer Sigrid , McCurdy Patrick 
Published: October 2020

AbstractMediatization remains a key concept for theorizing how our ever-evolving and intensifying media and communications environment underwrites and (re)constructs our social world, yet the socio-ecological effects of mediatization processes remain relatively unacknowledged within this research field. However, mediatization must be conceptualized as a cogent process whose impact extends beyond the confines of the “media environment” to the natural environment. We make this argument by reviewing how three dominant traditions of mediatization scholarship: (a) institutionalist, (b) cultural/social constructivist, and (c) materialist conceptualize “the environment.” We argue that scholars rarely acknowledge the materialist dimension of mediatization despite it being a fundamental aspect of mediatization processes. Consequently, we bring discourse surrounding the materiality of mediatization to the fore by drawing on theories of materiality from media and communication studies in general and highlighting three material dimensions of mediatization processes in particular: (a) resources, (b) energy, and (c) waste. In doing so, we make explicit the implicit material dimensions of mediatization processes that have been largely overlooked but are directly linked to how we understand, theorize and react to the societal, cultural, economic, environmental transformations brought about by media.
SPEG: a key regulator of cardiac calcium homeostasis
Authors: Campbell Hannah , Aguilar-Sanchez Yuriana , Quick Ann P , Dobrev Dobromir , Wehrens Xander H T 
Published: October 2020

Abstract
Proper cardiac Ca2+ homeostasis is essential for normal excitation–contraction coupling. Perturbations in cardiac Ca2+ handling through altered kinase activity has been implicated in altered cardiac contractility and arrhythmogenesis. Thus, a better understanding of cardiac Ca2+ handling regulation is vital for a better understanding of various human disease processes. ‘Striated muscle preferentially expressed protein kinase’ (SPEG) is a member of the myosin light chain kinase family that is key for normal cardiac function. Work within the last 5 years has revealed that SPEG has a crucial role in maintaining normal cardiac Ca2+ handling through maintenance of transverse tubule formation and phosphorylation of junctional membrane complex proteins. Additionally, SPEG has been causally impacted in human genetic diseases such as centronuclear myopathy and dilated cardiomyopathy as well as in common acquired cardiovascular disease such as heart failure and atrial fibrillation. Given the rapidly emerging role of SPEG as a key cardiac Ca2+ regulator, we here present this review in order to summarize recent findings regarding the mechanisms of SPEG regulation of cardiac excitation–contraction coupling in both physiology and human disease. A better understanding of the roles of SPEG will be important for a more complete comprehension of cardiac Ca2+ regulation in physiology and disease.
COVID-19 resulting in bilateral pulmonary emboli and a right ventricular thrombus: association or causation? A case report
Authors: Kaplan Jason G , Kanwal Arjun , Malek Ryan , Dickey John Q , Keirn Richard , Zweig Bryan , Minter David 
Published: October 2020

Abstract

Background
SARS-CoV-2 is a novel viral illness originating out of Wuhan China in late 2019. This global pandemic has infected nearly 3 million people and accounted for 200 000 deaths worldwide, with those numbers still climbing.

Case summary
We present a 54-year-old patient who developed respiratory failure requiring endotracheal intubation from her infection with SARS-CoV-2. This patient was subsequently found to have a right ventricular thrombus and bilateral pulmonary emboli, likely contributing to her respiratory status. On the 14th day of hospitalization, the patient was successfully extubated, and 5 days later was discharged to the rehabilitation unit.

Discussion
SARS-CoV-2 presents primarily with pulmonary symptoms; however, many patients, particularly those who are severely ill, exhibit adverse events related to hypercoagulability. The exact mechanism explaining this hypercoagulable state has yet to be elucidated, but these thrombotic events have been linked to the increased inflammation caused by SARS-CoV-2. This novel viral illness is still largely misunderstood, but the hypercoagulable state, seen in severely ill patients, appears to play a major role in disease progression and prognosis.
Tramps’ Tales: Discovering the Life-Stories of Late Victorian and Edwardian Vagrants
Authors: Crowson N J 
Published: October 2020

Abstract
This article addresses a question that challenged British policy-makers at the turn of the twentieth century: who were the tramps? Using genealogical methods, the article shows the extent, and detail, with which it is now possible to reconstruct a vagrant’s life. Understanding these life-stories, of people trapped in a system of state control and surveillance, opens up the potential to unravel the strategies and inner logics that they were applying in order to survive. For the most part, these individuals were punished and criminalised by the New Poor Law and 1824 Vagrancy Act on the basis of their personal condition, state of being and socio-economic status. The article will illustrate how it is now possible to pinpoint a tramp’s movements around the country, and understand the individuality of these routes. And finally, in addressing the debates about why people found themselves in this predicament, the article argues that individual fragilities contributed significantly to the circumstances they experienced.
Do Economic Hardship and Pressure Really Influence Parenting?
Authors: Schmiedeberg Claudia , Bozoyan Christiane 
Published: October 2020

AbstractPoverty and its effect on parenting in the context of the family stress model have a long tradition in research, but results are rather mixed. Following this theoretical approach, we analyse whether poverty and financial pressure are associated with disrupted parenting. We draw on data from the German Family Panel pairfam and implement both between and within approaches to test whether parenting behaviours are associated with economic hardship and pressure. While basic between-group regressions confirm the link between economic hardship and parenting as predicted by the family stress model, we do not find a significant association of poverty and parenting when including additional confounders or using fixed-effects models. We conclude that rather than the financial situation itself unobserved heterogeneity causes differences in parenting behaviours between better and worse off families, at least in Germany.
UtilisingGalleria mellonella larvae for studying in vivo activity of conventional and novel antimicrobial agents
Authors: Piatek Magdalena , Sheehan Gerard , Kavanagh Kevin 
Published: October 2020

ABSTRACTThe immune response of insects displays many structural and functional similarities to the innate immune response of mammals. As a result of these conserved features, insects may be used for evaluating microbial virulence or for testing the in vivo efficacy and toxicity of antimicrobial compounds and results show strong similarities to those from mammals. Galleria mellonella larvae are widely used in this capacity and have the advantage of being easy to use, inexpensive to purchase and house, and being free from the ethical and legal restrictions that relate to the use of mammals in these tests. Galleria mellonella larvae may be used to assess the in vivo toxicity and efficacy of novel antimicrobial compounds. A wide range of antibacterial and antifungal therapies have been evaluated in G. mellonella larvae and results have informed subsequent experiments in mammals. While insect larvae are a convenient and reproducible model to use, care must be taken in their use to ensure accuracy of results. The objective of this review is to provide a comprehensive account of the use of G. mellonella larvae for assessing the in vivo toxicity and efficacy of a wide range of antibacterial and antifungal agents.
The AHK-Wales Report Card 2018: Policy Measures - is it possible to ‘score’ qualitative data?
Authors: Ward Malcolm R , Tyler Richard , Edwards Lowri C , Miller Maggie C , Williams Simon , Stratton Gareth 
Published: October 2020

Summary
Comprehensive and meaningful policy analysis in the field of physical activity is difficult, not least because of the variable influence of other policy domains. However, in 2011 a Policy Assessment Tool (PAT) was developed by members of the WHO European Network for the Promotion of Health-Enhancing Physical Activity (HEPA Europe) and tested in several different countries. In 2014, Wales joined a global initiative, active healthy kids (AHK) Global Alliance, that supported the development of country level ‘Report Cards’ scoring a range of indicators that influence physical activity amongst children and young people, one of which was labelled ‘Government Strategies and Investments’. For the first two Report Cards this indicator and its associated ‘score’ was informed subjectively by expert consensus. In 2018, it was decided to utilize the Policy Audit Tool Version 2 (PAT v2) developed by HEPA Europe to aid analysis and to develop and test a scoring rubric aligned to the tool. The subsequent process indicated that the tool could be applied and translated into a ‘grade’ that could be used in conjunction with the other indicators of the AHK Report Card to generate overall Report Card grades. The use of both the HEPA PAT v2 and the scoring rubric offers an opportunity to provide greater consistency and potential for developing both comparative and trend data when assessing policy impact on physical activity in children and young people. These tools should be utilized by the AHK Global Alliance in future Report Cards.
Filtrations in Module Categories, Derived Categories, and Prime Spectra
Authors: Matsui Hiroki , Takahashi Ryo 
Published: October 2020

AbstractLet $R$ be a commutative noetherian ring. The notion of $n$-wide subcategories of ${\operatorname{\mathsf{Mod}}}\ R$ is introduced and studied in Matsui–Nam–Takahashi–Tri–Yen in relation to the cohomological dimension of a specialization-closed subset of ${\operatorname{Spec}}\ R$. In this paper, we introduce the notions of $n$-coherent subsets of ${\operatorname{Spec}}\ R$ and $n$-uniform subcategories of $\mathsf{D}({\operatorname{\mathsf{Mod}}}\ R)$ and explore their interactions with $n$-wide subcategories of ${\operatorname{\mathsf{Mod}}}\ R$. We obtain a commutative diagram that yields filtrations of subcategories of ${\operatorname{\mathsf{Mod}}}\ R$, $\mathsf{D}({\operatorname{\mathsf{Mod}}}\ R)$ and subsets of ${\operatorname{Spec}}\ R$ and complements classification theorems of subcategories due to Gabriel, Krause, Neeman, Takahashi, and Angeleri Hügel–Marks–Šťovíček–Takahashi–Vitória.
International Trade and Public Protest: Evidence from Russian Regions
Authors: Palmtag Tabea , Rommel Tobias , Walter Stefanie 
Published: October 2020

Abstract
How does economic globalization influence domestic political stability? Building on innovations in trade theory, we argue that international trade amplifies political discontent and protest in contexts in which trade losers concentrate, but has a pacifying effect in contexts dominated by beneficiaries of free trade. We examine this argument focusing on variation in Russian regions. Using negative binomial regression models on data from 2007 to 2012, we show that regional education levels condition the effect of trade intensity on protest frequency. High exposure to trade leads to more protests in regions with low average education levels, but fewer protests in regions in which residents are well-educated. Probing the underlying mechanism, we find that the effect of trade on regional economic welfare is conditioned by education levels, that poorly educated Russians face more economic difficulties when they live in regions exposed to trade, and that economically aggrieved individuals participate more in protests.
White Paper: Bridging the gap between surveillance data and antimicrobial stewardship in the outpatient sector—practical guidance from the JPIAMR ARCH and COMBACTE-MAGNET EPI-Net networks
Authors: Arieti Fabiana , Göpel Siri , Sibani Marcella , Carrara Elena , Pezzani Maria Diletta , Murri Rita , Mutters Nico T , Lòpez-Cerero Lorena , Voss Andreas , Cauda Roberto , Tacconelli Evelina ,   the ARCH working group, Adegnika Ayola Akim , Arieti Fabiana , Rajendran Nithya Babu , Bielicki Julia , Borrmann Steffen , Carrara Elena , Cauda Roberto , Compri Monica , De Angelis Giulia , Duro Raquel , Galia Liliana , Gastmeier Petra , Giske Christian , Göpel Siri , Goossens Herman , Kahlmeter Gunnar , Kanj Souha S , Kostyanev Tomislav , Leibovici Leonard , Lucet Jean-Christophe , López-Cerero Lorena , Mader Rodolphe , Mazzaferri Fulvia , Mazzolini Elena , Mendelson Marc , Murri Rita , Mutters Nico T , Paul Mical , Pezzani Maria Diletta , Presterl Elisabeth , enk Hanna R , Sandulescu Oana , Song Le Huu , Schrijver Remco , Scudeller Luigia , Sharland Mike , Sibani Marcella , Tacconelli Evelina , Torumkuney Didem , Velavan Thirumalaisamy P , Voss Andreas 
Published: October 2020

Abstract

Background
The outpatient setting is a key scenario for the implementation of antimicrobial stewardship (AMS) activities, considering that overconsumption of antibiotics occurs mainly outside hospitals. This publication is the result of a joint initiative by the JPIAMR ARCH and COMBACTE-MAGNET EPI-Net networks, which is aimed at formulating a set of target actions for linking surveillance data with AMS activities in the outpatient setting.

Methods
A scoping review of the literature was carried out in three research areas: AMS leadership and accountability; antimicrobial usage and AMS; antimicrobial resistance and AMS. Consensus on the actions was reached through a RAND-modified Delphi process involving over 40 experts in infectious diseases, clinical microbiology, AMS, veterinary medicine or public health, from 18 low-, middle- and high-income countries.

Results
Evidence was retrieved from 38 documents, and an initial 25 target actions were proposed, differentiating between essential or desirable targets according to clinical relevance, feasibility and applicability to settings and resources. In the first consultation round, preliminary agreement was reached for all targets. Further to a second review, 6 statements were re-considered and 3 were deleted, leading to a final list of 22 target actions in the form of a practical checklist.

Conclusions
This White Paper is a pragmatic and flexible tool to guide the development of calibrated surveillance-based AMS interventions specific to the outpatient setting, which is characterized by substantial inter- and intra-country variability in the organization of healthcare structures, maintaining a global perspective and taking into account the feasibility of the target actions in low-resource settings.
Blood Phosphatidylethanol Concentrations Following Regular Exposure to an Alcohol-Based Mouthwash
Authors: Reisfield Gary M , Teitelbaum Scott A , Jones Joseph T , Mason Dana , Bleiweis Max , Lewis Ben 
Published: October 2020

Abstract
Direct biomarkers of ethanol are used to monitor individuals who are required to abstain from ethanol consumption. In recent years, blood phosphatidylethanol (PEth) has gained acceptance in clinical and forensic contexts as an abstinence marker. Its elimination half-life of several days provides a window of detection of days to weeks. However, there is no research addressing the extent of PEth formation related to extraneous ethanol exposures. To assess the degree of ethanol absorption and subsequent formation of blood PEth related a common extraneous exposure, regular use of an ethanol-containing mouthwash, we recruited 16 participants to gargle with an alcohol-based mouthwash (21.6% ethanol) 4 times daily, for 12 consecutive days. Blood was analyzed for PEth 16:0/18:1 by liquid chromatography–tandem mass spectrometry. Our hypothesis that blood PEth concentrations would not equal or exceed 20 ng/mL was confirmed. Although the data suggest that regular use of mouthwash is unlikely to result in suprathreshold PEth concentrations, this work highlights the importance of considering extraneous ethanol exposures in clinical decision-making and in future research.
Violent Crime and the Overmilitarization of US Policing
Authors: Masera Federico 
Published: October 2020

Abstract
Using new data at the police department level, I propose an identification strategy for estimating the causal effect that police militarization has on reducing violent crime. I show that previous estimates are likely to be contaminated by unobserved factors that simultaneously determine militarization and violent crime. Upon addressing this issue, I find a point estimate that is 20 times larger than those estimated previously. I then find that one-fourth of the effect of militarization is due to the displacement of violent crime to neighboring areas. Police departments overmilitarize because they do not consider this externality. These new findings have significant implications for the policy debate concerning the costs and benefits of police militarization (JEL H56, H76, K42).
Explicit analyses of proof/refutation interaction for constructible falsity and Heyting–Brouwer logic
Authors: Ferguson Thomas Macaulay 
Published: October 2020

Abstract
Nelson’s logic of constructible falsity $\textsf{N}$ and Rauszer’s Heyting–Brouwer logic $\textsf{HB}$ are well-known cases of extensions of intuitionistic logic $\textsf{Int}$ enriched with novel connectives. Wansing has suggested that Gödel’s provability interpretation of $\textsf{Int}$ can be extended to these systems by pairing the category of formal proofs with a distinct category of formal refutations. In this paper, we extend the framework of Artemov’s justification logic to provide explicit analyses of $\textsf{N}$ and $\textsf{HB}$ (and the dual-intuitionistic logic $\textsf{DualInt}$) that respect a distinction between proofs and refutations. The application distinguishes the categories by reinterpreting the agents of multiple-agent justification logic as devices that operate exclusively on one or the other category. The analyses reveal that differences between $\textsf{N}$ and $\textsf{HB}$ can be reduced to competing interaction principles characterizing the coordination between proofs and refutations. We conclude by reappraising some of the unusual features of $\textsf{HB}$ in light of the explicit analysis of $\textsf{HB}$.