bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian Nonparametric Analysis of the 2003 Outbreak of Highly Pathogenic Avian Influenza in the Netherlands
Authors: Seymour Rowland G. , Kypraios Theodore , O’Neill Philip D. , Hagenaars Thomas J. 
Published: August 2021

Abstract
Infectious diseases on farms pose both public and animal health risks, so understanding how they spread between farms is crucial for developing disease control strategies to prevent future outbreaks. We develop novel Bayesian nonparametric methodology to fit spatial stochastic transmission models in which the infection rate between any two farms is a function that depends on the distance between them, but without assuming a specified parametric form. Making nonparametric inference in this context is challenging since the likelihood function of the observed data is intractable because the underlying transmission process is unobserved. We adopt a fully Bayesian approach by assigning a transformed Gaussian process prior distribution to the infection rate function, and then develop an efficient data augmentation Markov Chain Monte Carlo algorithm to perform Bayesian inference. We use the posterior predictive distribution to simulate the effect of different disease control methods and their economic impact. We analyse a large outbreak of avian influenza in the Netherlands and infer the between-farm infection rate, as well as the unknown infection status of farms which were pre-emptively culled. We use our results to analyse ring-culling strategies, and conclude that although effective, ring-culling has limited impact in high-density areas.
Bringing abolition in: Addressing carceral logics in social science research
Authors: Davies Elizabeth Jordie , Jackson Jenn M. , Streeter Shea 
Published: August 2021

AbstractObjectiveIn this essay, we review and offer theoretical groundings and empirical approaches to the study of abolition.MethodsWe begin by demonstrating the ways police and prisons have been used to exploit and dominate marginalized people and argue that abolition offers a path to finding solutions to public safety and racial justice. We draw from black feminist and abolitionist political thought to show how abolition makes space to upend systems of power and domination and develop systems that address the root causes of violence.ResultsWe assert that abolitionist research will not only focus on activists’ calls for dismantling the police but will also recognize and engage with activists’ proposals for reimagining public safety. We suggest that social scientists who study abolition, American uprisings, and policing must understand the differences between transformative changes based in abolitionist frameworks versus those that center mass incarceration as a societal given and, ultimately, further reproduce the status quo.ConclusionWe conclude by suggesting that social scientists must question how researcher practices and universities uphold carceral logics and entrenched hierarchies, determining that abolitionist study will meaningfully engage with the distribution of power.
Complete Genomes of Clade G6
Saccharibacteria
Suggest a Divergent Ecological Niche and Lifestyle
Authors: Baker Jonathon L. 
Published: August 2021

ABSTRACT

Saccharibacteria
(formerly TM7) have reduced genomes and a small cell size and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of
Saccharibacteria
inhabiting the human oral cavity, complete genomes of oral
Saccharibacteria
were previously limited to the G1 clade. In this study, nanopore sequencing was used to obtain three complete genome sequences from clade G6. Phylogenetic analysis suggested the presence of at least 3 to 5 distinct species within G6, with two discrete taxa represented by the 3 complete genomes. G6
Saccharibacteria
were highly divergent from the more-well-studied clade G1 and had the smallest genomes and lowest GC content of all
Saccharibacteria
. Pangenome analysis showed that although 97% of shared pan-
Saccharibacteria
core genes and 89% of G1-specific core genes had putative functions, only 50% of the 244 G6-specific core genes had putative functions, highlighting the novelty of this group. Compared to G1, G6 harbored divergent metabolic pathways. G6 genomes lacked an F
1
F
o
ATPase, the pentose phosphate pathway, and several genes involved in nucleotide metabolism, which were all core genes for G1. G6 genomes were also unique compared to that of G1 in that they encoded
d
-lactate dehydrogenase, adenylate cyclase, limited glycerolipid metabolism, a homolog to a lipoarabinomannan biosynthesis enzyme, and the means to degrade starch. These differences at key metabolic steps suggest a distinct lifestyle and ecological niche for clade G6, possibly with alternative hosts and/or host dependencies, which would have significant ecological, evolutionary, and likely pathogenic implications.

IMPORTANCE
Saccharibacteria
are ultrasmall parasitic bacteria that are common members of the oral microbiota and have been increasingly linked to disease and inflammation. However, the lifestyle and impact on human health of
Saccharibacteria
remain poorly understood, especially for the clades with no complete genomes (G2 to G6) or cultured isolates (G2 and G4 to G6). Obtaining complete genomes is of particular importance for
Saccharibacteria
, because they lack many of the “essential” core genes used for determining draft genome completeness, and few references exist outside clade G1. In this study, complete genomes of 3 G6 strains, representing two candidate species, were obtained and analyzed. The G6 genomes were highly divergent from that of G1 and enigmatic, with 50% of the G6 core genes having no putative functions. The significant difference in encoded functional pathways is suggestive of a distinct lifestyle and ecological niche, probably with alternative hosts and/or host dependencies, which would have major implications in ecology, evolution, and pathogenesis.
Effects of local handwashing agents on microbial contamination of hands in the rural settings of northwest Ethiopia: protocol for a two-arm, clustered-randomised controlled trial
Authors: Gizaw Zemichael , Yalew Alemayehu Worku , Bitew Bikes Destaw , Lee Jiyoung , Bisesi Michael 
Published: August 2021

IntroductionHands play a part in the transmission of infections. Handwashing with soap sufficiently reduces the level of hand contamination and the spread of infections. As soap is not usually available due to cost, ash is often used as a zero-cost alternative to soap in the rural settings of developing countries. However, there is limited evidence on the effectiveness of ash to reduce microbial contamination of hands. This study is, therefore, designed to assess the effect of ash on microbial contamination of hands in the rural settings of northwest Ethiopia.Methods and analysisA two-arm clustered-randomised controlled trial will be employed. A total of 11 clusters per arm will be selected using simple random sampling technique. A total of 220 mothers or caregivers of under-5 children will be included in each arm. After providing health education on effective handwashing process, we will ask study subjects to do the usual activities. We will then take swab samples from the dominant hand before washing. After swabbing, participants will be asked to wash their hands with water only and with ash by following effective handwashing procedures. We will again take swab samples from the dominant hand after washing and drying. Finally, we will compare each intervention arm against the control. A generalised estimating equation (GEE) with robust SE estimation will be used to account the cluster nature of data.Ethics and disseminationResults will be published in peer-reviewed journal and presented at international conferences. The protocol is approved by the Institutional Review Board of the University of Gondar, Ethiopia.Trial registration numberPan African Clinical Trial Registry; PACTR202011855730652.
Comparing the reporting and conduct quality of exercise and pharmacological randomised controlled trials: a systematic review
Authors: Adams Scott C , McMillan Julia , Salline Kirsten , Lavery Jessica , Moskowitz Chaya S , Matsoukas Konstantina , Chen Maggie M Z , Santa Mina Daniel , Scott Jessica M , Jones Lee W 
Published: August 2021

ObjectiveEvaluate the quality of exercise randomised controlled trial (RCT) reporting and conduct in clinical populations (ie, adults with or at risk of chronic conditions) and compare with matched pharmacological RCTs.DesignSystematic review.Data sourcesEmbase (Elsevier), PubMed (NLM) and CINAHL (EBSCO).Study selectionRCTs of exercise in clinical populations with matching pharmacological RCTs published in leading clinical, medical and specialist journals with impact factors ≥15.Review methodsOverall RCT quality was evaluated by two independent reviewers using three research reporting guidelines (ie, Consolidated Standards of Reporting Trials (CONSORT; pharmacological RCTs)/CONSORT for non-pharmacological treatments; exercise RCTs), CONSORT-Harms, Template for Intervention Description and Replication) and two risk of bias assessment (research conduct) tools (ie, Cochrane Risk of Bias, Jadad Scale). We compared research reporting and conduct quality within exercise RCTs with matched pharmacological RCTs, and examined factors associated with quality in exercise and pharmacological RCTs, separately.FindingsForty-eight exercise RCTs (11 658 patients; median sample n=138) and 48 matched pharmacological RCTs were evaluated (18 501 patients; median sample n=160). RCTs were conducted primarily in cardiovascular medicine (43%) or oncology (31%). Overall quality score (composite of all research reporting and conduct quality scores; primary endpoint) for exercise RCTs was 58% (median score 46 of 80; IQR: 39–51) compared with 77% (53 of 68; IQR: 47–58) in the matched pharmacological RCTs (p≤0.001). Individual quality scores for trial reporting and conduct were lower in exercise RCTs compared with matched pharmacological RCTs (p≤0.03). Factors associated with higher overall quality scores for exercise RCTs were journal impact factor (≥25), sample size (≥152) and publication year (≥2013).Conclusions and relevanceResearch reporting and conduct quality within exercise RCTs is inferior to matched pharmacological RCTs. Suboptimal RCT reporting and conduct impact the fidelity, interpretation, and reproducibility of exercise trials and, ultimately, implementation of exercise in clinical populations.PROSPERO registration numberCRD42018095033.
Psychosocial impact of COVID-19 pandemic on Malaysian families: a cross-sectional study
Authors: Zainudeen Zarina Thasneem , Abd Hamid Intan Juliana , Azizuddin Muhd Nur Akmal , Abu Bakar Firdaus Farhani , Sany Salina , Zolkepli Izzal Asnira , Mangantig Ernest 
Published: August 2021

ObjectiveTo investigate the psychosocial impact of COVID-19 on Malaysian families.DesignA cross-sectional study performed using an anonymous online questionnaire distributed through social media, email and the Department of Social Welfare.SettingMalaysian families were invited to answer the questionnaires. The sampling was performed between 12 May 2020 and 9 June 2020.InterventionThe psychological impact was assessed using the Impact of Event Scale-Revised (IES-R) and Children’s Revised Impact of Event Scale (CRIES). The mental health status was assessed using the Depression, Anxiety and Stress Scale (DASS) 21.Main outcome measure(1) Psychological impact on Malaysian families. (2) Prevalence of mental health status of Malaysian families during COVID-19 pandemic.ResultA total of 409 Malaysian families have responded (409 parents and 348 children), 154 respondents (38%) reported high psychological impact (score 14) for psychological construct and 189 respondents (46%) reported high psychological impact (score 6) for behavioural construct. A significantly higher proportion of respondents with not permanent employment status of the family lead reported high psychological impact. The prevalence of anxiety reported from family respondents was 23%. Forty-five children answered the DASS-21 questionnaire; 28.5% reported anxiety, 31.4% reported depression and 13.3% reported stress. The job security status of the family lead was found to be the predictive factor for the mean total IES-R score (psychological construct) and ethnicity for mean total CRIES-8 and CRIES-13.ConclusionRates of depression and anxiety during the COVID-19 pandemic were high. Findings suggest that urgent measures to ensure job security among Malaysian families are important to reduce the impact of the COVID-19 pandemic on psychosocial and mental health outcomes.
Perturbative correction terms to electromagnetic self-force due to metric perturbation: astrophysical and cosmological implications
Authors: Sarkar Arnab , Ali Amna , Nasri Salah 
Published: August 2021

AbstractWe consider the equation of motion of a charged particle or a charged compact object in curved space-time, under the reaction of electromagnetic radiation and also consider a physical situation such that the charged particle or compact object emits gravitational radiation, thereby gravitational radiation reaction also acts on it. We investigate the effect of this metric perturbation i.e. the gravitational radiation on the electromagnetic self-force. We show that, besides the interaction terms derived by Zimmerman and Poisson (Phys Rev D 90:084030, 2014), additional perturbative terms are generated, which are linear in metric perturbation and are generated due to perturbation of the electromagnetic self-force by the metric perturbation. We discuss the conditions of significance of these perturbative terms and also the interaction terms with respect to the gravitational self-force in various astrophysical and cosmological cases; such as the motion of charged particles around black holes, some extreme mass-ratio inspirals (EMRIs) involving sufficiently accelerated motion of charged stars (specially neutron stars) or charged stellar mass black holes around supermassive black holes, and motion of charged particles around charged primordial black holes formed in the early Universe etc. We find that in some astrophysical and cosmological cases these perturbative terms can have significant effect in comparison with the gravitational radiation-reaction term.
Denial and Pragmatism: Islam and the Danish State
Authors: Netterstrøm Kasper Ly 
Published: August 2021

Abstract
From halal food to the veil, this article analyses the relationship between Islam and the Danish state. It finds a coexistence of two modes of dealing with Islam: an official approach dominated by denial of the existence of Islam within Danish society and an unwillingness to recognise Muslim religious practices; and a pragmatic approach, mostly found at the local level, that focuses on finding practical solutions. This article argues that the official resistance to recognising Islam makes it comparatively harder for the Danish state to influence the country’s Muslim religious sphere.
Communication as Transmission and as Ritual: Dewey’s Account of Communication and Carey’s Cultural Approach
Authors: Midtgarden Torjus 
Published: August 2021

Abstract
James W. Carey saw a tension between two views of communication in John Dewey’s work: a transmission view which takes communication as transmission of messages for the control of distance and people, and a ritual view which conceives communication as constructing and maintaining a cultural world. This article shows how Dewey may be seen to apply both views in analysing two complementary aspects of communication. It points out how Dewey’s naturalistic perspectives on culture and meaning provide a basis for his analysis and have affinities with Carey’s cultural approach to communication. The article further considers Dewey’s analysis through Carey’s critical reminder that models of communication serve both as representations and as guidance for action. Finally, Dewey’s and Carey’s approaches are contrasted by focusing on their epistemological and ontological underpinnings.
Biclausal vs. monoclausal focus constructions in Tilapa Otomi
Authors: Palancar Enrique L. 
Published: August 2021

Abstract
This paper tackles issues that involve distinguishing clefts from other monoclausal focus constructions when describing the syntax of lesser-known languages. I concentrate on Tilapa Otomi, which is, morphologically speaking, the most conservative language of the Otomi family from Mexico (Oto-Pamean; Oto-Manguean). I propose that Tilapa Otomi has (at least) two specialized focus constructions: one that is a biclausal, and which I analyze as a cleft construction, and another that is monoclausal, and it is thus not a cleft but which could be superficially mistaken to be a cleft with a zero copula. I use various syntactic tests to distinguish both constructions, which mainly involve word order and negation.
Expanding the Application of Soil Moisture Monitoring Systems through Regression-Based Transformation
Authors: Crow Wade T. , Reichle Rolf H. , Dong Jianzhi 
Published: August 2021

AbstractRelative to other geophysical variables, soil moisture (SM) estimates derived from land surface models (LSMs) and land data assimilation systems (LDAS) are difficult to transfer between platforms and applications. This difficulty stems from the highly model-dependent nature of LSM SM estimates and differences in the vertical support of discretized SM values. As a result, operational SM estimates generated by one LSM (or LDAS) cannot generally be directly applied to a hydrologic monitoring or forecast system designed around a second LSM. This lack of transferability is particularly problematic for LDAS applications, where the time, expertise, and computational resources required to generate an operational LDAS analysis cannot be practically duplicated for every LSM-specific application. Here, we develop a set of simple regression tools for translating SM estimates between LSMs and multiple LDAS analyses. Results demonstrate that simple multivariate linear regression—utilizing independent variables based on multilayer and temporally lagged SM estimates—can significantly improve upon baseline transformation approaches using direct percentile matching. The proposed regression approaches are effective for both the LSM-to-LSM and LDAS-to-LDAS transformation of multilayer SM percentiles. Application of this approach will expand the utility of existing, high-quality (but LSM-specific) operational sources of SM information like the NASA Soil Moisture Active Passive Level-4 Soil Moisture product.
Evaluation of Current Pressure Ulcer Staging
Authors: Stefanopoulos Stavros , Qiu Qiong , Alshaibani Khalid , Bauer Karen , Ahmed Ayman , Nazzal Munier , Osman Mohamed F. 
Published: August 2021

Background We sought to assess health professionals’ satisfaction with the National Pressure Injury Advisory Panel staging system (NPUAP). Methods A paper survey assessing the satisfaction with the NPUAP was distributed to participants of a national wound care meeting. A total of 88 surveys were completed. Results were tabulated using SPSS. Results The survey response rate was 50%. Nearly all respondents (95.0%) used NPAUP for documentation. 75.3% indicated that a better staging system was needed. When participants were asked to evaluate their current staging system, 63.5% stated that the system does not adequately reflect patient’s clinical condition, 61.6% felt that the current staging system was not easily reproducible, 58.0% believed that the current staging system was generally easy-to-use, and 43.9% indicated that it is unable to suggest management recommendations. When asked about an ideal classification system, the respondents proposed incorporating tissue necrosis (97.6%), depth of tissue involvement (96.3%), discharge documentation (92.5%), presence of osteomyelitis (90%), local infection (88.8%), and systemic infection (80.0%). Overall, 67.0% of the participants wanted to use a classification system that would reflect the progress of injury healing and could be used to indicate the need for intervention. Discussion Health care workers caring for pressure injury patients indicated dissatisfaction with the NPAUP.
Response of Laryngopharyngeal Symptoms to Transoral Incisionless Fundoplication in Patients with Refractory Proven Gastroesophageal Reflux
Authors: Snow Grace E. , Dbouk Mohamad , Akst Lee M. , Ihde Glenn , Zarnegar Rasa , Janu Peter , Murray Michael , Eskarous Hany , Sohagia Amit , Dhar Shumon I. , Irene Canto Marcia 
Published: August 2021

Objective: Patients with laryngopharyngeal reflux (LPR) symptoms may not respond to proton pump inhibitors (PPI) if they have an alternative laryngeal diagnosis or high-volume reflux. Transoral incisionless fundoplication (TIF) or TIF with concomitant hiatal hernia repair (cTIF) are effective in decreasing symptoms of gastroesophageal reflux disease (GERD) but are not well studied in patients with LPR symptoms. This prospective multicenter study assessed the patient-reported and clinical outcomes after TIF/cTIF in patients with LPR symptoms and proven GERD. Methods: Patients with refractory LPR symptoms (reflux symptom index [RSI] > 13) and with erosive esophagitis, Barrett’s esophagus, and/or pathologic acid reflux by distal esophageal pH testing were evaluated before and after a minimum of 6 months after TIF/cTIF. The primary outcome was normalization of RSI. Secondary outcomes were >50% improvement in GERD-Health-Related Quality of Life (GERD-HRQL), normalization of esophageal acid exposure time, discontinuation of PPI, and patient satisfaction. Results: Forty-nine patients had TIF (n = 26) or cTIF (n = 23) with at least 6 months follow-up. Mean pre- and post TIF/cTIF RSI were 23.6 and 5.9 (mean difference: 17.7, P < .001). Post TIF/cTIF, 90% of patients had improved GERD-HQRL score, 85% normalized RSI, 75% normalized esophageal acid exposure time, and 80% discontinued PPI. No serious procedure-related adverse events occurred. Patient satisfaction was 4% prior to TIF/cTIF and 73% after TIF/cTIF ( P < .001). Conclusion: In patients with objective evidence of GERD, TIF, or cTIF are safe and effective in controlling LPR symptoms as measured by normalization of RSI and improvement in patient satisfaction after TIF/cTIF. Level of Evidence Level 4