bluuebunny/crossref_metadata_2025 huggingface dataset:
Modified early warning score-based clinical decision support: cost impact and clinical outcomes in sepsis
Authors: Horton Devin J , Graves Kencee K , Kukhareva Polina V , Johnson Stacy A , Cedillo Maribel , Sanford Matthew , Dunson William A , White Michael , Roach Dave , Arego John J , Kawamoto Kensaku
Published: May 2020

Objective

The objective of this study was to assess the clinical and financial impact of a quality improvement project that utilized a modified Early Warning Score (mEWS)-based clinical decision support intervention targeting early recognition of sepsis decompensation.

Materials and Methods

We conducted a retrospective, interrupted time series study on all adult patients who received a diagnosis of sepsis and were exposed to an acute care floor with the intervention. Primary outcomes (total direct cost, length of stay [LOS], and mortality) were aggregated for each study month for the post-intervention period (March 1, 2016–February 28, 2017, n = 2118 visits) and compared to the pre-intervention period (November 1, 2014–October 31, 2015, n = 1546 visits).

Results

The intervention was associated with a decrease in median total direct cost and hospital LOS by 23% (P = .047) and .63 days (P = .059), respectively. There was no significant change in mortality.

Discussion

The implementation of an mEWS-based clinical decision support system in eight acute care floors at an academic medical center was associated with reduced total direct cost and LOS for patients hospitalized with sepsis. This was seen without an associated increase in intensive care unit utilization or broad-spectrum antibiotic use.

Conclusion

An automated sepsis decompensation detection system has the potential to improve clinical and financial outcomes such as LOS and total direct cost. Further evaluation is needed to validate generalizability and to understand the relative importance of individual elements of the intervention.
Facts, Evidence and the Burden of Proof in the World Bank Group Sanctions System
Authors: Åhman Joachim
Published: May 2020

The large and growing number of international judicial and quasi-judicial bodies has made international procedural law an important part of public international law. This article examines how procedural rules of a certain type—provisions related to facts, evidence, and the burden of proof—have been designed in the World Bank Group Sanctions System. The main conclusion is that such rules play a central role, and that considerable efforts have been made during the last two decades to develop a well-functioning body of procedural provisions. However, the article also argues that certain parts of the system could be developed further, in order to make it as clear as possible what is expected from the different actors in the proceedings.
Organ Culture and Grafting of Choroid Plexus into the Ventricular CSF of Normal and Hydrocephalic HTx Rats
Authors: Johanson Conrad E , Vío Karin , Guerra Monserrat , Salazar Paula , Jara María Clara , Rodríguez Sara , Ortega Eduardo , Castañeyra-Ruiz Leandro , McAllister J Patrick , Rodríguez Esteban M
Published: May 2020

Choroid plexus (CP) may aid brain development and repair by secreting growth factors and neurotrophins for CSF streaming to ventricular and subventricular zones. Disrupted ventricular/subventricular zone progenitors and stem cells lead to CNS maldevelopment. Exploring models, we organ cultured the CP and transplanted fresh CP into a lateral ventricle of postnatal hydrocephalic (hyHTx) and nonhydrocephalic (nHTx) rats. After 60 days in vitro, the cultured choroid ependyma formed spherical rings with beating cilia. Cultured CP expressed endocytotic caveolin 1 and apical aquaporin 1 and absorbed horseradish peroxidase from medium. Transthyretin secretory protein was secreted by organ-cultured CP into medium throughout 60 days in vitro. Fresh CP, surviving at 1 week after lateral ventricle implantation of nHTx or hyHTx did not block CSF flow. Avascular 1-week transplants in vivo expressed caveolin 1, aquaporin 1, and transthyretin, indicating that grafted CP may secrete trophic proteins but not CSF. Our findings encourage further exploration on CP organ culture and grafting for translational strategies. Because transplanted CP, though not producing CSF, may secrete beneficial molecules for developing brain injured by hydrocephalus, we propose that upon CP removal in hydrocephalus surgery, the fractionated tissue could be transplanted back (ventricular autograft).
Aggressive Medulloblastoma-Derived Exosomal miRNAs Promote In Vitro Invasion and Migration of Tumor Cells Via Ras/MAPK Pathway
Authors: Zhu Liang-Yi , Wu Xiao-Yu , Liu Xiao-Dan , Zheng Dan-Feng , Li Hai-Shuang , Yang Bao , Zhang Jing , Chang Qing
Published: May 2020

Medulloblastomas (MBs) are currently divided into 4 molecular subgroups: WNT, SHH, Group 3, and Group 4. Among them, Group 3 MB has the worst prognosis, and 40%–50% of Group 3 cases are already metastatic at the time of diagnosis. Emerging evidence indicates that exosomes drive tumor invasion, but very little is known about exosomes in MBs. In this study, we initially discovered that exosomes isolated from Group 3 MB cell lines altered in vitro behaviors of a less invasive SHH MB cell line and yielded a much more aggressive phenotype. RNA-sequencing analysis revealed 7 exosomal miRNAs with markedly different expression levels between the SHH and Group 3 MB cell lines. They were all predicted to be related to the Ras/MAPK pathway according to the Kyoto Encyclopedia of Genes and Genomes data analysis. Increased expression of miR-181a-5p, miR-125b-5p, and let-7b-5p was further confirmed in Group 3 MB cells with real-time PCR and was shown to increase in vitro invasion and migratory abilities of tumor cells through the activation of ERK in Ras/MAPK pathway. Collectively, our findings suggest that exosomal miRNAs have a critical role in MB progression in vitro and might serve as diagnostic biomarkers and therapeutic targets.
Toward an Infrastructural Sublime: Narrating Interdependency in Karen Tei Yamashita’s Los Angeles
Authors: Kim Jina B
Published: May 2020

This article examines the vibrant city infrastructures of Karen Tei Yamashita's 1997 novel Tropic of Orange in order to highlight interdependency as political and aesthetic value. The novel's emphasis on urban support systems—the oft-unnoticed roads, pipes, wires, and labor networks that allow the city to function—positions infrastructure as itself a critical lens, one that can reassess the relationship of ethnic American literature and subjectivity to the values of self-ownership, protest, and independence. By amplifying the overlooked support networks that underpin fictions of self-sufficiency, Yamashita's Tropic of Orange diverges from the narrative of self-ownership as liberatory endpoint. Instead, it recuperates the much-maligned category of dependency, positioning dependency as a vital site of aesthetic and political possibility within anti-racist and anti-capitalist struggle. This recuperation proves particularly significant in light of pernicious and persistent dependency mythologies, such as the “illegal immigrant,” that frame racialized subjects as drains on the public. Infrastructure, as an often unseen entity nonetheless central to the operation of cities and the global distribution of resources, represents a key vehicle in Tropic of Orange for thinking about contemporary ecologies of assistance, power, and provision, and for mapping the global imbalances of power that render certain dependencies hypervisible while erasing others.
Color around the Globe: Langston Hughes and Black Internationalism in China
Authors: Lai-Henderson Selina
Published: May 2020

Langston Hughes was the first African American writer to set foot on Chinese soil. Having visited Mexico, Europe, and West Africa before he turned twenty-two, Hughes eventually also made his way to the Soviet Union, Japan, and China in 1933. At the age of thirty-one, he accomplished what none of his contemporaries or predecessors had been able to achieve—to rewrite the public image of African Americans in the Chinese cultural and intellectual imagination. Crucially, his visit to China pushed beyond the limits of black internationalism as he responded to American and European global hegemony through using China as an experimental ground. At a time when the Soviet Union held center stage in communist revolutionary thought, Hughes's Chinese encounters challenged the assumption within the American and African American communities that China was largely irrelevant in the discourse of proletarianism. The internationalist perspectives that he obtained from the sojourn offered him a powerful tool to communicate the struggles of black citizenship at home in a global context. It stimulated a racial consciousness that defied national, geographical, and political boundaries of the US color line.
“Voice Might Discover Him”: Representations and Failures of Voice in Frank J. Webb’s The Garies and Their Friends
Authors: Millan Diego
Published: May 2020

This article takes up the representation of voice in Frank J. Webb's 1857 novel The Garies and Their Friends to examine the relationship between Blackness, aurality, and text. Doing so requires an approach tuned to the novel's aural-linguistic dimensions that acknowledges that a character's speaking produces a diegetic sound and that the way characters interact with one another relies, in part, on how each perceives another's voice. It also means looking for how a text conveys a sense of sound both through techniques such as italics and capitalization and through instances of overt narration. Specifically, moments of mistaken identity pivot on the disruption of one character's accumulated presumptions concerning the sound of another character's voice and highlight how sound and listening reinforce processes of racialization, a dynamic Jennifer Lynn Stoever identifies through her work on the sonic color line. Instances of vocalization—moments when characters are depicted speaking and when the text itself performs vocality—defamiliarize social formations along the sonic color line long enough for the novel to scrutinize their underlying premises. Scenes in which characters' voices escape their assumed meaning trouble constructions of racial identity, particularly whiteness and its assumed control over speech. The Garies and Their Friends thus generates an alternative mode through which to critique the safeguarding of whiteness. Ultimately, the novel brings together overlapping meanings of voice, such as physiologically produced acoustic sounds and distinctive literary or authorial decisions, as a meditation on the interplay between voice and writing.
A Hero and His Newspaper: Unsettling Myths of Italian America
Authors: Salter Sarah H
Published: May 2020

Italian American ethnic identity has long been constituted by struggles and inequalities endured by Italians in post-unification rural Italy and their subsequent racialized oppression in urban centers of the US North in the era of mass migration. Until now, the presumed stability of mass migration identity has created the general terms for understanding Italian America. In this essay, a New Orleans microhistory illuminated through the 1849 newspaper Il Monitore del Sud, the first Italian-language newspaper published in the United States, reshapes foundational understandings of Italian American identity. The newspaper's antebellum account of New Orleans Italian America includes nationalist aesthetic expressions and political affiliations that American political discourse has not yet found an adequate language to describe and that Italian American studies has not yet confronted. In bringing this prehistory to light, my work with antebellum Italian Americans complicates understandings of multi-ethnic collectivity by examining how intercultural myth-making underwrites communal historiography. Together, the ethnic perceptions memorialized in Il Monitore del Sud and the power operations revealed in concurrent civic records expose how collective conditions of white supremacy come to be naturalized and forgotten, becoming history's flotsam. The creation of Italian America's communal historiography, I argue, shows us something larger about the operations of US white supremacy: how its emotional logic depends simultaneously on the exploitation of vulnerable others and the enactment of vulnerability from within the exploiting group.
全谷物定义与健康声称全球概况
Authors: Mathews Rebecca , Chu YiFang
Published: May 2020

增加全谷物摄入量的建议是世界各国膳食指南的一部分，为了帮 助消费者满足这个建议，一些国家及健康促进机构制定了用于食品标 签或健康声称的全谷物食品合格标准，其他国家尚未制定类似的指南。 本文综述了现有的全谷物定义及健康声称。虽然对全谷物定义的共识 似乎日益增强，但在产品不是100% 全谷物时定义全谷物食品存在明 显的差异。此外，虽然一些国家已经批准可以使用全谷物健康声称，但 其他国家认为此类声称尚未得到足够的证据证实。
评估膳食纤维、全谷物和健康关系证据图
Authors: McKeown Nicola M , Livingston Kara A , Sawicki Caleigh M , Miller Kevin B
Published: May 2020

证据图是一种非常实用的证据总结方法，通过证据图可以全面检 索所关注问题的相关研究，准确展示该领域科学文章存在的问题。利 用证据图，可实现文献的系统检索，提取研究关键信息，形成信息数 据库。塔夫茨大学和国际生命科学学会(ILSI)北美分会创建了膳食 纤维和人类健康证据数据库，并公开，每年都会定期更新。该数据库 汇编了膳食纤维干预研究，包括10 种预先设定的生理健康结局指标， 包括体重/肥胖、血压、肠道微生物群和骨骼健康。根据美国食品和药 品监督管理局(FDA)颁布的新版食品标签要求，只有在有足够证据 支持膳食纤维与某种生理健康益处相关时，才能在标签上标识“膳食 纤维”。因此，该数据库和证据图的应用潜力就显得特别重要。基于膳 食纤维数据库的成功案例，塔夫茨大学和通用磨坊贝尔健康与营养研 究所又合作开发了一个全谷物数据库和证据图。该项工作强调了所报

告的全谷物数据一致性的重要性，包括全谷物的消费量和类型以及干 预的依从性。
Ushering in Antifungal Stewardship: Perspectives of the Hematology Multidisciplinary Team Navigating Competing Demands, Constraints, and Uncertainty
Authors: Ananda-Rajah Michelle R , Fitchett Samuel , Ayton Darshini , Peleg Anton Y , Fleming Shaun , Watson Eliza , Cairns Kelly , Peel Trisha
Published: May 2020

Background

The social, contextual, and behavioral determinants that influence care in patients at risk for invasive fungal diseases (IFD) are poorly understood. This knowledge gap is a barrier to the implementation of emerging antifungal stewardship (AFS) programs. We aimed to understand the barriers and enablers to AFS, opportunities for improvement, and perspectives of AFS for hematology patients at a major medical center in Australia.

Methods

Semistructured, face-to-face interviews were conducted with 35 clinicians from 6 specialties (hematology, infectious diseases, pharmacy, nursing, radiology, respiratory), followed by thematic analysis mapped to a behavioral change framework.

Results

Access to fungal diagnostics including bronchoscopy was identified as the key barrier to rational prescribing. Collective decision making was the norm, aided by an embedded stewardship model with on-demand access to infectious diseases expertise. Poor self-efficacy/knowledge among prescribers was actually an enabler of AFS, because clinicians willingly deferred to infectious diseases for advice. A growing outpatient population characterized by frequent care transitions was seen as an opportunity for AFS but neglected by an inpatient focused model, as was keeping pace with emerging fungal risks. Ad hoc surveillance, audit, and feedback practices frustrated population-level quality improvement for all actors. Antifungal stewardship was perceived as a specialized area that should be integrated within antimicrobial stewardship but aligned with the cultural expectations of hematologists.

Conclusions

Antifungal stewardship is multifaceted, with fungal diagnostics a critical gap and outpatients a neglected area. Formal surveillance, audit, and feedback mechanisms are essential for population-level quality improvement. Resourcing is the next challenge because complex immunocompromised patients require personalized attention and audit of clinical outcomes including IFD is difficult.
Variations in Seasonal Influenza Vaccine Effectiveness due to Study Characteristics: A Systematic Review and Meta-analysis of Test-Negative Design Studies
Authors: Okoli George N , Racovitan Florentin , Righolt Christiaan H , Mahmud Salaheddin M
Published: May 2020

Background

Study characteristics influence vaccine effectiveness (VE) estimation. We examined the influence of some of these on seasonal influenza VE estimates from test-negative design (TND) studies.

Methods

We systematically searched bibliographic databases and websites for full-text publications of TND studies on VE against laboratory-confirmed seasonal influenza in outpatients after the 2009 pandemic influenza. We followed the Cochrane Handbook for Systematic Reviews of Interventions guidelines. We examined influence of source of vaccination information, respiratory specimen swab time, and covariate adjustment on VE. We calculated pooled adjusted VE against H1N1 and H3N2 influenza subtypes, influenza B, and all influenza using an inverse-variance random-effects model.

Results

We included 70 full-text articles. Pooled VE against H1N1 and H3N2 influenza subtypes, influenza B, and all influenza was higher for studies that used self-reported vaccination than for those that used medical records. Pooled VE was higher with respiratory specimen collection within ≤7 days vs ≤4 days of symptom onset, but the opposite was observed for H1N1. Pooled VE was higher for studies that adjusted for age but not for medical conditions compared with those that adjusted for both. There was, however, a lack of statistical significance in almost all differences in pooled VE between compared groups.

Conclusions

The available evidence is not strong enough to conclude that influenza VE from TND studies varies by source of vaccination information, respiratory specimen swab time, or adjustment for age/medical conditions. The evidence is, however, indicative that these factors ought to be considered while designing or evaluating TND studies of influenza VE.
Mapping the Afterlife
Authors: Gee Emma
Published: May 2020

This book is a tour of afterlife landscapes from Homer to Dante. It argues that the topography of the afterlife in Greek and Roman tradition, and in Dante, reflects the state of “scientific” knowledge at the time of the various contexts in which we find it, and the landscape of the Other World is a way of exploring and assimilating the shape of this world. This book posits that there is a dominant spatial idiom in afterlife landscapes, which the author calls the “journey-vision paradigm.” By this she means the presence of two kinds of space in afterlife representations—the horizontal journey of the soul across the afterlife landscape, and a synoptic vision of the universe. This has, in studies of individual texts, often been characterized as an inconsistency or anomaly: many scholars have argued that the vision of the universe is out of place in the underworld landscape. However, when one looks across the entire tradition, one finds that afterlife landscapes, almost without exception, contain these two kinds of space in one form or another. The function of this double vision of space—the journey-vision paradigm—is an attempt to harmonize the underworld, as the landscape of the soul, with the “scientific” universe, and to understand humanity in terms of the cosmos, and vice versa.
Collective Victimhood as a Form of Adaptation
Authors: Bilewicz Michał , Liu James
Published: May 2020

This chapter posits that responses to collective victimization that are maladaptive at the intergroup level may be adaptive at the intragroup level. Specifically, the endorsement of conspiracy theories could be seen as an adaptive response in societies that were historically frequently victimized and at the receiving end of actual conspiracies. In such contexts, hypervigilance and mistrust may prevent future victimization. To test this role of history and macro influences more generally on collective victimhood and endorsement of conspiracy theories, the authors use data from nationally representative samples in countries that are at the center or periphery of the global world order (United Kingdom and Spain, Ukraine and Poland, respectively). In peripheral countries with a history of collective victimization, perceived collective victimhood was associated with endorsement of conspiracy theories and mistrust of the government. These relationships were not significant in central countries with a history of imperialism and domination.
Collective Victimhood Resulting From Structural Violence
Authors: Mari Silvia , Bentrovato Denise , Durante Federica , Wassermann Johan
Published: May 2020

This chapter discusses collective victimization resulting from structural violence, and how the effects of inequality can have similar deleterious consequences for peoples’ ability to meet basic needs. Social class and structural violence have been underexamined so far in the literature on collective victimhood. However, considering collective victim beliefs due to structural violence—which are related to, but distinct from relative deprivation—enriches our understanding of relevant experiences and extends the collective victim beliefs that should be assessed. The authors show with empirical examples from Italy and South Africa that collective victim beliefs about structural violence are distinct from collective victim beliefs about direct violence. They also reveal that collective victim beliefs about structural violence may predict different outcomes, such as the preference for different forms of acknowledgment or the need for empowerment and acceptance.
Design and Application of Employee Engagement Surveys
Authors: Meyer John P.
Published: May 2020

This chapter provides an evidence-based guide to the design and application of employee engagement surveys. It begins with a discussion of the meaning of engagement and the importance of distinguishing it from related concepts such as job satisfaction and affective organizational commitment. Next, it addresses the question of “engagement with what?” Employees can be engaged (or disengaged) in specific tasks, the job itself, team projects, the organization’s mission, as well as other work and nonwork activities or entities. The behavioral implications of engagement in these various targets can be quite different, so it is important to consider carefully the intended target and the desired objectives of engagement when designing surveys. Finally, the chapter addresses the selection and measurement of key drivers of engagement. This information is useful in designing strategies for maintaining or building engagement. While the popular press is replete with “best practices” for fostering engagement, it is argued here that what works in one context will not necessarily work in another. However, research has identified a set of “best principles” that can be used to guide context-specific interventions. The chapter concludes with a set of recommendations for the design and administration of engagement surveys, interpretation and feedback of the results, and development of intervention strategies.
Truth vs. Progress Realism about Spin
Authors: Saatsi Juha
Published: May 2020

Scientific realism about spin is easily motivated. But what does it amount to? To answer this question, Chapter 3 contrasts in general terms two epistemological conceptions of realism—truth-content vs. progress realism—before problematizing truth-content realism in the context of quantum physics. After articulating the challenge faced by truth-content realism, the chapter argues that progress realism avoids it, offering a stable middle ground between anti-realism and traditional truth-content realism.
Pragmatist Quantum Realism
Authors: Healey Richard
Published: May 2020

Realism comes in many varieties, in science and elsewhere. Van Fraassen’s influential formulation took scientific realism to include the view that science aims to give us, in its theories, a literally true story of what the world is like. So understood, a quantum realist takes quantum theory to aim at correctly representing the world: many would add that its success justifies believing this representation is more or less correct. But quantum realism has been understood both more narrowly and more broadly. A pragmatist considers use prior to representation and this has prompted some to dub pragmatist views anti-realist, including the view of quantum theory that the author has been developing recently. But whether a pragmatist view of quantum theory should be labeled anti-realist depends not only on its ingredients but also on how that label should be applied. Pragmatism offers a healthy diet of quantum realism.
Perturbing Realism
Authors: Ruetsche Laura
Published: May 2020

Effective Realism marshals ideologies and technologies of our best current physics— the interacting quantum field theories making up the Standard Model—to articulate a selective realism resistant to skeptical affronts such as the Pessimistic Metainduction. Chapter 15 attempts an empiricist re-appropriation of the putatively realist commitments Effective Realists stake out. It also argues that resisting empiricist reappropriation entangles selective realists in something alarmingly similar to the very project of ‘Standard Interpretation’ they regard as misguided.
Judicial Review of the European Central Bank’s Actions
Authors: Markakis Menelaos
Published: May 2020

This chapter focuses on judicial review of the European Central Bank’s actions by the EU courts. It does not purport to examine all issues related to the legal accountability of the ECB across its main domains of action. Instead, it focuses on the role of the Court of Justice of the European Union (CJEU) in reviewing general reforms, in the light of cases such as Pringle, Gauweiler, and Weiss, and asks: what should be the scope, test (or standard) and intensity of review of the ECB’s actions? When should the CJEU defer to the ECB’s assessment? Though the emphasis in this chapter is on monetary policy measures, the final section of the chapter also looks briefly at the role of the CJEU in reviewing the ECB’s actions in its ‘new fields of competence’, namely banking supervision and in the context of financial assistance programmes, where the ECB is a member of the ‘Troika’ (or ‘Quadriga’).
Can Real Social Epistemic Networks Deliver the Wisdom of Crowds?
Authors: Sullivan Emily , Sondag Max , Rutter Ignaz , Meulemans Wouter , Cunningham Scott , Speckmann Bettina , Alfano Mark
Published: May 2020

Most experimental philosophy employs small-N studies with randomization. Additional light may be shed on philosophical questions by large-scale observational studies that employ Big Data methodologies. This chapter explains and showcases the promising methodology of testimonial network analysis and visualization for experimental epistemology, arguing that it can be used to gain insights and answer philosophical questions in social epistemology. The use case is the epistemic community that discusses vaccine safety primarily in English on Twitter. In two studies, the authors show, using both statistical analysis and exploratory data visualization, that there is almost no neutral or ambivalent discussion of vaccine safety on Twitter. Roughly half the accounts engaging with this topic are pro-vaccine, while the other half is con-vaccine. The results also indicate that these two camps rarely engage with one another, and that the con-vaccine camp has greater epistemic reach and receptivity than the pro-vaccine camp. In light of these findings, the authors question whether testimonial networks as they are currently constituted on popular forums such as Twitter are living up to their promise of delivering the wisdom of crowds.
‘He is to freonde god’: Wealth and Avarice in Cynewulf’s Juliana
Authors: Michelet Fabienne L
Published: May 2020

This article explores the motif of wealth and avarice in the Old English Juliana. It examines the changes that Cynewulf brings to his Latin source, specifically to the portrayal of Juliana’s pagan antagonists. They are depicted as rich and greedy men, indicated by Heliseus’s hoarded wealth and by Affricanus’s mention of the financial obligations that a marriage between his daughter and Heliseus would create. Various relevant historical and theological contexts that the poem mobilizes are discussed, as they shed light on issues of wealth and its proper uses. This article argues that the pagans’ avarice is central to the poem’s design and it offers new readings of Juliana as a poem that speaks to the duties of those in power, to the contingent nature of earthly rule, and to the perils of wealth.
Deep learning enables sleep staging from photoplethysmogram for patients with suspected sleep apnea
Authors: Korkalainen Henri , Aakko Juhani , Duce Brett , Kainulainen Samu , Leino Akseli , Nikkonen Sami , Afara Isaac O , Myllymaa Sami , Töyräs Juha , Leppänen Timo
Published: May 2020

Study Objectives

Accurate identification of sleep stages is essential in the diagnosis of sleep disorders (e.g. obstructive sleep apnea [OSA]) but relies on labor-intensive electroencephalogram (EEG)-based manual scoring. Furthermore, long-term assessment of sleep relies on actigraphy differentiating only between wake and sleep periods without identifying specific sleep stages and having low reliability in identifying wake periods after sleep onset. To address these issues, we aimed to develop an automatic method for identifying the sleep stages from the photoplethysmogram (PPG) signal obtained with a simple finger pulse oximeter.

Methods

PPG signals from the diagnostic polysomnographies of susptected OSA patients (n = 894) were utilized to develop a combined convolutional and recurrent neural network. The deep learning model was trained individually for three-stage (wake/NREM/REM), four-stage (wake/N1+N2/N3/REM), and five-stage (wake/N1/N2/N3/REM) classification of sleep.

Results

The three-stage model achieved an epoch-by-epoch accuracy of 80.1% with Cohen’s κ of 0.65. The four- and five-stage models achieved 68.5% (κ = 0.54), and 64.1% (κ = 0.51) accuracies, respectively. With the five-stage model, the total sleep time was underestimated with a mean bias error (SD) of of 7.5 (55.2) minutes.

Conclusion

The PPG-based deep learning model enabled accurate estimation of sleep time and differentiation between sleep stages with a moderate agreement to manual EEG-based scoring. As PPG is already included in ambulatory polygraphic recordings, applying the PPG-based sleep staging could improve their diagnostic value by enabling simple, low-cost, and reliable monitoring of sleep and help assess otherwise overlooked conditions such as REM-related OSA.
Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile
Authors: Okada Yuta , Okugawa Shu , Ikeda Mahoko , Kobayashi Tatsuya , Saito Ryoichi , Higurashi Yoshimi , Moriya Kyoji
Published: May 2020

Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining

Clostridioides difficile

show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and

C. difficile

isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133

C

.

difficile

isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in

C. difficile

. These findings provide a foundation for further functional and clinical research of the agr loci.
Sphingomonas montanisoli sp. nov., isolated from mountain soil
Authors: Xu Zixiao , Zhang Yuxiao , Muhammad Yasir , Wang Gejiao
Published: May 2020

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of

Sphingomonas crocodyli

CCP-7T (97.0%),

Sphingomonas jatrophae

S5-249T (96.6%) and

Sphingomonas starnbergensis

382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with

S. crocodyli

CCP-7T,

S. jatrophae

S5-249T and

S. starnbergensis

382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains (

S. crocodyli

BCRC 81096T and

S. jatrophae

DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with

S. crocodyli

BCRC 81096T and

S

.

jatrophae

DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1
 ω7c and/or C18 : 1
 ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).
Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov
Authors: Ikeyama Nao , Toyoda Atsushi , Morohoshi Sho , Kunihiro Tadao , Murakami Takumi , Mori Hiroshi , Iino Takao , Ohkuma Moriya , Sakamoto Mitsuo
Published: May 2020

Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the familyErysipelotrichaceaeand formed a monophyletic cluster with ‘Absiella argi’ strain N6H1-5 (99.4% sequence similarity) andEubacteriumsp. Marseille-P5640 (99.3 %).Eubacterium dolichumJCM 10413T(94.2 %) andEubacterium tortuosumATCC 25548T(93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, ‘A. argi’ JCM 30884 andEubacteriumsp. Marseille-P5640 shared 98.7–99.1% average nucleotide identity (ANI) with each other. Moreover, thein silicoDNA–DNA hybridization (DDH) values among three strains were 88.4–90.6%, indicating that these strains represent the same species. Strain 9CBEGH2Tshowed 21.5–24.1 %in silicoDDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2Tand other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for ‘A. argi’ strains identified because the name ‘A. argi’ has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2Trepresents a novel species of a novel genus, for which the nameAmedibacterium intestinalegen. nov., sp. nov. is proposed. The type strain ofA. intestinaleis 9CBEGH2T(=JCM 33778T=DSM 110575T).
Teunia siamensis f.a., sp. nov., a novel tremellaceous yeast species isolated from soil in a secondary peat swamp forest area
Authors: Khunnamwong Pannida , Lertwattanasakul Noppon , Limtong Savitree
Published: May 2020

The strain DMKU-XD44, representing an anamorphic novel yeast species, was isolated from soil collected in a peat swamp forest (PSF) area in Rayong Botanical Garden in eastern Thailand. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Teunia cuniculi CBS 10309T was the most closely related species. The novel species differed from the T. cuniculi type by 2.5 % (14 nucleotide substitutions) in the D1/D2 region of the LSU rRNA gene and by 8.0 % (40 nucleotide substitutions) in the ITS region. The results of a phylogenetic analysis, based on the combined sequences of the ITS region and the D1/D2 region, indicated that DMKU-XD44 represents a member of the Teunia clade in the Cryptococcaceae (Tremellales, Tremellomycetes, Agaricomycotina and Basidiomycota) and is phylogenetically distinct from other species of the genus Teunia in the clade. Therefore, DMKU-XD44 represents a novel species of the genus Teunia. The name Teunia siamensis f.a., sp. nov. is proposed. The holotype is DMKU-XD44, while the MycoBank number is MB 832816.
Maribacter algarum sp. nov., a new member of the family Flavobacteriaceae isolated from the red alga Gelidium amansii
Authors: Zhang Jin-Yu , Xia Yu , Feng Xi , Mu Da-Shuai , Du Zong-Jun
Published: May 2020

A Gram-stain-negative, rod-shaped (0.2–0.3×1.0-2.4 µm), catalase-positive, oxidase-negative and non-motile bacterium, designated strain RZ26T, was isolated from the marine red algae collected from the coast of Weihai, PR China. Growth of strain RZ26T occurred at 15–33 °C (optimum, 25–28 °C), pH 6.0–9.5 (optimum, pH 7.0–7.5) and 0.5–5.0 % (w/v) NaCl (optimum, 2.0–3.0 %). Resuls of phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ26T was most closely related to

Maribacter spongiicola

DSM 25233T (96.2 % sequence similarity), followed by

Maribacter forsetii

DSM 18668T (96.1 %) and

Maribacter vaceletii

DSM 25230T (95.4 %). The average nucleotide identity and the average amino acid identity values between strain RZ26T and

M. sedimenticola

KCTC 12966T,

M. spongiicola

DSM 25233T,

M. vaceletii

DSM 25230T and

M. forsetii

DSM 18668T were 75.6, 76.2, 76.0, 76.7, 64.3, 63.9, 68.6 and 68.0 %, respectively. The digital DNA–DNAhybridization values based on the draft genomes between strain RZ26T and

M. sedimenticola

KCTC 12966T,

M. spongiicola

DSM 25233T and

M. vaceletii

DSM 25230T were 38.0, 35.1 and 37.1 %, respectively. The major fatty acids in strain RZ26T were iso-C17 : 0 3-OH, iso-C15 : 0 and C16 : 1
 ω7c/C16 : 1
 ω6c. The major respiratory quinone was MK-6. The dominant polar lipid was phosphatidylethanolamine. The DNA G+C content was 38.0 mol%. Phylogenetic analysis shows strain RZ26T fell within a clade comprising species of the genus

Maribacter

. Polyphasic taxonomy indicates that the isolate represents a novel species of the genus

Maribacter

, for which the name Maribacter algarum sp. nov. is proposed, with type strain RZ26T (=KCTC 62992T=MCCC 1H00362T).
Gracilibacillus salitolerans sp. nov., a moderate halophile isolated from saline soil in Northwest China
Authors: Gan Longzhan , Li Xiaoguang , Chen Jia , Zhang Shihao , Zhang Ruoshi , Peng Biyu , Tian Yongqiang
Published: May 2020

A moderately halophilic strain, designated SCU50T, was recovered from a saline soil sample and characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain SCU50T belonged to the genus

Gracilibacillus

and was most closely related to

Gracilibacillus thailandensis

TP2-8T (98.1 % similarity) and

Gracilibacillus orientalis

XH-63T (97.7 %). Genomic average nucleotide identity and digital DNA–DNA hybridization analyses confirmed the separate species status of the new isolate relative to other recognized

Gracilibacillus

species. The genome size was about 5.09 Mbp and the DNA G+C content was 36.7 mol%. The strain grew optimally at 10–15 % (w/v) NaCl, pH 6.5–7.5 and 25–30 °C. It contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the dominant fatty acids and menaquinone-7 as the major respiratory quinone. The polar lipid profile was examined and found to comprise diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The cell-wall peptidoglycan type was A1γ based on meso-diaminopimelic acid. Combining the data from phenotypic, chemotaxonomic, genomic and phylogenetic characterization, it was concluded that strain SCU50T should be assigned as representing a novel species within the genus

Gracilibacillus

. Thus, a novel taxon named Gracilibacillus salitolerans sp. nov. was first established, with SCU50T (=CGMCC 1.17336T=KCTC 43107T) as the type strain.
ICTV Virus Taxonomy Profile: Hepadnaviridae
Authors: Magnius Lars , Mason William S. , Taylor John , Kann Michael , Glebe Dieter , Dény Paul , Sureau Camille , Norder Heléne ,   ICTV Report Consortium
Published: May 2020

The family Hepadnaviridae comprises small enveloped viruses with a partially double-stranded DNA genome of 3.0–3.4 kb. All family members express three sets of proteins (preC/C, polymerase and preS/S) and replication involves reverse transcription within nucleocapsids in the cytoplasm of hepatocytes. Hepadnaviruses are hepatotropic and infections may be transient or persistent. There are five genera: Parahepadnavirus, Metahepadnavirus, Herpetohepadnavirus, Avihepadnavirus and Orthohepadnavirus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Hepadnaviridae, which is available at ictv.global/report/hepadnaviridae.
Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species
Authors: Xu Zhixiao , Li Na , Guo Yaqiong , Feng Yaoyu , Xiao Lihua
Published: May 2020

The three common intestinal Cryptosporidium species in cattle differ significantly in host range, pathogenicity and public health significance. While Cryptosporidium parvum is pathogenic in pre-weaned calves and has a broad host range, C. bovis and C. ryanae are largely non-pathogenic and bovine-specific species in post-weaned calves. Thus far, only the genome of C. parvum has been sequenced. To improve our understanding of the genetic determinants of biological differences among Cryptosporidium spcies, we sequenced the genomes of C. bovis and C. ryanae and conducted a comparative genomics analysis. The genome of C. bovis has a gene content and organization more similar to C. ryanae than to other Cryptosporidium species sequenced to date; the level of similarity in amino acid and nucleotide sequences between the two species is 75.2 and 69.4 %, respectively. A total of 3723 and 3711 putative protein-encoding genes were identified in the genomes of C. bovis and C. ryanae, respectively, which are fewer than the 3981 in C. parvum. Metabolism is similar among the three species, although energy production pathways are further reduced in C. bovis and C. ryanae. Compared with C. parvum, C. bovis and C. ryanae have lost 14 genes encoding mucin-type glycoproteins and three for insulinase-like proteases. Other gene gains and losses in the two bovine-specific and non-pathogenic species also involve the secretory pathogenesis determinants (SPDs); they have lost all genes encoding MEDLE, FLGN and SKSR proteins, and two of the three genes for NFDQ proteins, but have more genes encoding secreted WYLE proteins, secreted leucine-rich proteins and GPI-anchored adhesin PGA18. The only major difference between C. bovis and C. ryanae is in nucleotide metabolism. In addition, half of the highly divergent genes between C. bovis and C. ryanae encode secreted or membrane-bound proteins. Therefore, C. bovis and C. ryanae have gene organization and metabolic pathways similar to C. parvum, but have lost some invasion-associated mucin glycoproteins, insulinase-like proteases, MEDLE secretory proteins and other SPDs. The multiple gene families under positive selection, such as helicase-associated domains, AMP-binding domains, protein kinases, mucins, insulinases and TRAPs could contribute to differences in host specificity and pathogenicity between C. parvum and C. bovis. Biological studies should be conducted to assess the contribution of these copy number variations to the narrow host range and reduced pathogenicity of C. bovis and C. ryanae.
Induction of clpP expression by cell-wall targeting antibiotics in Streptococcus mutans
Authors: Khara Pratick , Biswas Saswati , Biswas Indranil
Published: May 2020

Streptococcus mutansis one of the major bacteria of the human oral cavity that is associated with dental caries. The pathogenicity of this bacterium is attributed to its ability to rapidly respond and adapt to the ever-changing conditions of the oral cavity. The major player in this adaptive response is ClpP, an intracellular protease involved in degradation of misfolded proteins during stress responses.S. mutansencodes a singleclpPgene with an upstream region uniquely containing multiple tandem repeat sequences (RSs). Here, we explored expression ofclpPwith respect to various stresses and report some new findings. First, we found that at sub-inhibitory concentration, certain cell-wall damaging antibiotics were able to induceclpPexpression. Specifically, third- and fourth-generation cephalosporins that target penicillin-binding protein 3 (PBP3) strongly enhanced theclpPexpression. However, induction ofclpPwas weak when the first-generation cephalosporins with lower affinity to PBP3 were used. Surprisingly, carbapenems, which primarily target PBP2, induced expression ofclpPthe least. Second, we found that a single RS element was capable of inducingclpPexpression as efficiently as with the wild-type seven RS elements. Third, we found that the RS-element-mediated modulation ofclpPexpression was strain dependent, suggesting that specific host factors might be involved in the transcription. And finally, we observed that ClpP regulates its own expression, as the expression ofclpP-gusAwas higher in aclpP-deficient mutant. This suggests that ClpP is involved in the degradation of activator(s) involved in its own transcription.
Theoretical investigation of pre-symptomatic SARS-CoV-2 person-to-person transmission in households
Authors: Arav Yehuda , Klausner Ziv , Fattal Eyal
Published: May 2020

Since its emergence, the phenomenon of SARS-CoV-2 transmission by seemingly healthy individuals has become a major challenge in the effort to achieve control of the pandemic. Identifying the modes of transmission that drive this phenomenon is a perquisite in devising effective control measures, but to date it is still under debate. To address this problem, we have formulated a detailed mathematical model of discrete human actions (such as coughs, sneezes, and touching) and the decay of the virus in the environment. To take into account both discrete and continuous events we have extended the common modelling approach and employed a hybrid stochastic mathematical framework. This allows us to calculate higher order statistics which are crucial for the reconstruction of the observed distributions. We focused on transmission within a household, the venue with the highest risk of infection and validated the model results against the observed secondary attack rate and the serial interval distribution. Detailed analysis of the model results identified the dominant driver of pre-symptomatic transmission as the contact route via hand-face transfer and showed that wearing masks and avoiding physical contact are an effective prevention strategy. These results provide a sound scientific basis to the present recommendations of the WHO and the CDC.