bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagynella pangooli sp. nov. from decaying baobab tree from Senegal with the notes on genus Metagynella Berlese, 1919 (Acari: Mesostigmata: Metagynuridae)
Authors: Kontschán Jeno
Published: July 2021

A new species of Metagynella, M. pangooli sp. nov. is described based on female and male specimens collected from decaying baobab trees (Adansonia digitata) in Senegal. The new species differs from congeners by the sculptural pattern of the dorsal shield and the shape of the sternal shield. A list and a new key to the known Metagynella species are also presented.
Reverse engineering of a recording mix with differentiable digital signal processing
Authors: Colonel Joseph T. , Reiss Joshua
Published: July 2021

A method to retrieve the parameters used to create a multitrack mix using only raw tracks and the stereo mixdown is presented. This method is able to model linear time-invariant effects such as gain, pan, equalisation, delay, and reverb. Nonlinear effects, such as distortion and compression, are not considered in this work. The optimization procedure used is the stochastic gradient descent with the aid of differentiable digital signal processing modules. This method allows for a fully interpretable representation of the mixing signal chain by explicitly modelling the audio effects rather than using differentiable blackbox modules. Two reverb module architectures are proposed, a “stereo reverb” model and an “individual reverb” model, and each is discussed. Objective feature measures are taken of the outputs of the two architectures when tasked with estimating a target mix and compared against a stereo gain mix baseline. A listening study is performed to measure how closely the two architectures can perceptually match a reference mix when compared to a stereo gain mix. Results show that the stereo reverb model performs best on objective measures and there is no statistically significant difference between the participants' perception of the stereo reverb model and reference mixes.
Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme
Authors: Liu Chang , Shi Wei , Becker Scott T. , Schatz David G. , Liu Bin , Yang Yang
Published: July 2021

A proofreader in SARS-CoV-2

Although vaccines provide protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there remains a need for antivirals to treat COVID-19. Nucleotide analog drugs such as remdesivir, which target the viral RNA polymerase, have potential but are compromised by exoribonuclease (ExoN) activity that removes incorrect nucleotides from newly synthesized RNA. Liu
et al
. determined the structure of the complex that harbors the ExoN activity (nsp10–nsp-14) bound to a mimic of RNA that has incorporated an incorrect nucleotide. The structure shows how the RNA is recognized and suggests how ExoN specifically removes mismatched nucleotides. It also provides clues for designing nucleotide analogs that may evade excision. —VV
Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus
Authors: Tarasova Elvira , Dhindwal Sonali , Popp Matthew , Hussain Sakeenah , Khayat Reza
Published: July 2021

CRESS-DNA viruses encompass a significant portion of the biosphere’s virome. However, little is known about the structure of Rep responsible for initiating the RCR of CRESS-DNA viruses.
Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria
Authors: Keffer Jessica L. , McAllister Sean M. , Garber Arkadiy I. , Hallahan Beverly J. , Sutherland Molly C. , Rozovsky Sharon , Chan Clara S.
Published: July 2021

Iron is practically ubiquitous across Earth’s environments, central to both life and geochemical processes, which depend heavily on the redox state of iron. Although iron oxidation, or “rusting,” can occur abiotically at near-neutral pH, we find neutrophilic iron-oxidizing bacteria (FeOB) are widespread, including in aquifers, sediments, hydrothermal vents, pipes, and water treatment systems.
Interplay between Nucleoid-Associated Proteins and Transcription Factors in Controlling Specialized Metabolism in
Streptomyces
Authors: Zhang Xiafei , Andres Sara N. , Elliot Marie A.
Published: July 2021

Specialized metabolic clusters in
Streptomyces
are the source of many clinically prescribed antibiotics. However, many clusters are not expressed in the laboratory due to repression by the nucleoid-associated protein Lsr2.
Turnover of Variant Surface Glycoprotein in Trypanosoma brucei Is a Bimodal Process
Authors: Garrison Paige , Khan Umaer , Cipriano Michael , Bush Peter J. , McDonald Jacquelyn , Sur Aakash , Myler Peter J. , Smith Terry K. , Hajduk Stephen L. , Bangs James D.
Published: July 2021

African trypanosomes, the protozoan agent of human African trypanosomaisis, avoid the host immune system by switching expression of the variant surface glycoprotein (VSG). VSG is a long-lived protein that has long been thought to be turned over by hydrolysis of its glycolipid membrane anchor.
From obduction to collision: A transect across Ordovician to Devonian sedimentary basins of the Québec Appalachians, Canada
Authors: Perrot Morgann G. , De Souza Stéphane , Tremblay Alain
Published: July 2021

This three-day field trip focuses on the stratigraphy and the structural characteristics of the late- and post-Taconian sedimentary basins of the southern Québec Appalachians, with a particular emphasis on N-to-S and W-to-E structural and lithological variations. In order to discuss various aspects of the regional structural evolution of these basins, we will visit a series of key outcrops following three sections, the Beauce/Thetford-Mines sections, the Sherbrooke section, and the Coaticook section.
Occurrence and mining of coal and sand deposits in the Middle Eocene Domengine Formation of the Mount Diablo Coalfield, California
Authors: Sullivan Raymond , Sullivan Morgan D. , Dedmon Patrick , Edwards Stephen
Published: July 2021

Mount Diablo Coalfield was the largest producer of coal in California from the 1860s to 1906. The now-depleted coalfield is located on the northeast limb of the Mount Diablo anticline. The mineable coal seams occur in the Middle Eocene Domengine Formation, which is predominantly composed of quartz-rich sandstone with several thin coal seams. As many as 26 mine operations were established to mine the coal, and it has been estimated that the total production exceeded 4 million tons. The coal fueled the industrial growth of the major cities of northern California. The mines closed at the turn of the nineteenth century as competition from better coals from Washington Territory and overseas entered the market. After coal mining was abandoned, sand operations were established in the early and mid-twentieth century to mine the silica-rich sandstone. The extraction methods used for sand were underground room-and-pillar mining and surface open-pit mining. The high-quality sand was used widely in the production of pottery and glass, and in foundries. Previous studies have interpreted the environment of deposition of these quartz-rich sandstone and coal deposits as barrier island with tidal channels or delta, tidal shelf, and marsh complexes along a north-south–trending shoreline. However, the excellent exposures in the sand mines display abundant evidence for their deposition in a fluvial/estuarine system. Their regional distribution indicates that they were deposited in a northeast-southwest–trending incised-valley system formed by fluvial incision during a lowstand. The incised valley was filled with fluvial and estuarine deposits made up of quartz-rich sand brought in by streams that flowed westward from the Sierra Nevada.
COVID-19-related vasculopathy of the brain
Authors: Liang Hui Wen , Mung Sai Man , Douglass Chris , Jude Edward B
Published: July 2021

The COVID-19 pandemic is revealing growing reports of atypical presentation of the disease beyond the respiratory system. SARS-CoV-2 infection has been linked to multisystem vasculopathy including cardiopulmonary, cerebral and renal vasculature, potentially brought on by a dysregulated host immune response in a probable setting of a cytokine storm. Here, we describe a case of a previously healthy and active 74-year-old man presenting with acute cognitive decline with preceding non-specific influenza-like symptoms. He was then diagnosed with cerebral amyloid angiopathy (CAA)-associated intracerebral haemorrhage and was found to be COVID-19 positive. COVID-19-induced immune response may have further compromised the cerebral vessels already weakened by CAA, triggering multiple microhaemorrhages leading to clinical presentation. The limited evidence about the heterogeneity of COVID-19 manifestations suggests that clinicians should be aware and screen for concurrent COVID-19 in patients presenting with neurological features during the peak of this pandemic, as this offers the best chance for better clinical outcome.
Physeal injury in a skeletally immature male athlete
Authors: Richey Bradley , Foley Davelaar Cassidy M
Published: July 2021

A 12-year-old skeletally immature male athlete presented for evaluation with acute bilateral knee pain. Initial radiographs revealed subtle lucency of the medial proximal tibial physis and MRI was recommended. On MRI, broad-based intravasation of the physis into the proximal femoral and tibial physes was observed. This represented physeal widening, a phenomenon that has been observed in skeletally immature athletes presenting for acute knee pain. While such changes to the physis may be quite prominent on MRI, conventional radiographic findings may be much more subtle. As many causes of chronic knee pain in this population are managed with active rehabilitation, a high index of suspicion for this diagnosis in the presence of physeal abnormalities may warrant evaluation with MRI. The literature suggests this pathology will resolve with rest, but, if weight-bearing activities are continued, there is a risk for significant growth abnormalities.
Entrectinib-related myocarditis in a young female patient with metastatic non-small cell lung cancer
Authors: Fonseca Marta , Chen Daniel H , Walker John Malcolm , Ghosh Arjun K
Published: July 2021

A 51-year-old woman presented with a 2-week history of off balance, left lower limb weakness and neglect and neck pain radiating down the right arm. Investigations revealed a metastatic, ROS1 fusion-positive, non-small cell lung cancer, and treatment with entrectinib, a recently approved multikinase inhibitor, was started. Two weeks after, she was admitted to the emergency department with new-onset pressure-like chest pain and dyspnoea. Laboratory evaluation showed elevated troponin and mild left ventricular systolic dysfunction with reduced global longitudinal strain on transthoracic echocardiogram. Cardiac magnetic resonance revealed mild oedema and non-ischaemic fibrosis. A diagnosis of drug-induced myocarditis was made. Cardioprotective medication with an angiotensin-converting enzyme inhibitor and a beta-blocker was started. Entrectinib was temporarily discontinued and restarted at a reduced dose after a multidisciplinary team meeting involving both the oncology and cardio-oncology teams. This is the second described case of entrectinib-induced myocarditis and the first one without eosinophilia.
Central retinal artery occlusion in a patient who contracted COVID-19 and review of similar cases
Authors: Ucar Fikret , Cetinkaya Servet
Published: July 2021

A 54-year-old male patient applied to our clinic with a sudden and painless loss of vision in his right eye. He was suffering from COVID-19. His best-corrected visual acuity of the right eye was finger counting from 30 cm. The fundus examination revealed the presence of a ‘cherry-red spot’ appearance in the right eye. In optical coherence tomography imaging, hyper-reflectivity was observed in the inner retinal layers as well as increased retinal thickness in the right eye. In fundus fluorescein angiography, delayed arterial filling and prolonged arteriovenous transit time were observed in the right eye. The patient was diagnosed with central retinal artery occlusion after the COVID-19 infection. In this study, we report this case and its management.
Corneal confocal microscopy identifies corneal nerve fibre loss and increased dendritic cells in patients with long COVID
Authors: Bitirgen Gulfidan , Korkmaz Celalettin , Zamani Adil , Ozkagnici Ahmet , Zengin Nazmi , Ponirakis Georgios , Malik Rayaz A
Published: July 2021

Background/Aims

Long COVID is characterised by a range of potentially debilitating symptoms which develop in at least 10% of people who have recovered from acute SARS-CoV-2 infection. This study has quantified corneal sub-basal nerve plexus morphology and dendritic cell (DC) density in patients with and without long COVID.

Methods

Forty subjects who had recovered from COVID-19 and 30 control participants were included in this cross-sectional comparative study undertaken at a university hospital. All patients underwent assessment with the National Institute for Health and Care Excellence (NICE) long COVID, Douleur Neuropathique 4 (DN4) and Fibromyalgia questionnaires, and corneal confocal microscopy (CCM) to quantify corneal nerve fibre density (CNFD), corneal nerve branch density (CNBD), corneal nerve fibre length (CNFL), and total, mature and immature DC density.

Results

The mean time after the diagnosis of COVID-19 was 3.7±1.5 months. Patients with neurological symptoms 4 weeks after acute COVID-19 had a lower CNFD (p=0.032), CNBD (p=0.020), and CNFL (p=0.012), and increased DC density (p=0.046) compared with controls, while patients without neurological symptoms had comparable corneal nerve parameters, but increased DC density (p=0.003). There were significant correlations between the total score on the NICE long COVID questionnaire at 4 and 12 weeks with CNFD (ρ=−0.436; p=0.005, ρ=−0.387; p=0.038, respectively) and CNFL (ρ=−0.404; p=0.010, ρ=−0.412; p=0.026, respectively).

Conclusion

Corneal confocal microscopy identifies corneal small nerve fibre loss and increased DCs in patients with long COVID, especially those with neurological symptoms. CCM could be used to objectively identify patients with long COVID.
Dimensions of safety culture: a systematic review of quantitative, qualitative and mixed methods for assessing safety culture in hospitals
Authors: Churruca Kate , Ellis Louise A , Pomare Chiara , Hogden Anne , Bierbaum Mia , Long Janet C , Olekalns Aleksandra , Braithwaite Jeffrey
Published: July 2021

Background

The study of safety culture and its relationship to patient care have been challenged by variation in definition, dimensionality and methods of assessment. This systematic review aimed to map methods to assess safety culture in hospitals, analyse the prevalence of these methods in the published research literature and examine the dimensions of safety culture captured through these processes.

Methods

We included studies reporting on quantitative, qualitative and mixed methods to assess safety culture in hospitals. The review was conducted using four academic databases (PubMed, CINAHL, Scopus and Web of Science) with studies from January 2008 to May 2020. A formal quality appraisal was not conducted. Study purpose, type of method and safety culture dimensions were extracted from all studies, coded thematically, and summarised narratively and using descriptive statistics where appropriate.

Results

A total of 694 studies were included. A third (n=244, 35.2%) had a descriptive or exploratory purpose, 225 (32.4%) tested relationships among variables, 129 (18.6%) evaluated an intervention, while 13.8% (n=96) had a methodological focus. Most studies exclusively used surveys (n=663; 95.5%), with 88 different surveys identified. Only 31 studies (4.5%) used qualitative or mixed methods. Thematic analysis identified 11 themes related to safety culture dimensions across the methods, with ‘Leadership’ being the most common. Qualitative and mixed methods approaches were more likely to identify additional dimensions of safety culture not covered by the 11 themes, including improvisation and contextual pressures.

Discussion

We assessed the extent to which safety culture dimensions mapped to specific quantitative and qualitative tools and methods of assessing safety culture. No single method or tool appeared to measure all 11 themes of safety culture. Risk of publication bias was high in this review. Future attempts to assess safety culture in hospitals should consider incorporating qualitative methods into survey studies to evaluate this multi-faceted construct.
‘Function First’: how to promote physical activity and physical function in people with long-term conditions managed in primary care? A study combining realist and co-design methods
Authors: Law Rebecca-Jane , Langley Joseph , Hall Beth , Burton Christopher , Hiscock Julia , Williams Lynne , Morrison Val , Lemmey Andrew , Lovell-Smith Candida , Gallanders John , Cooney Jennifer Kate , Williams Nefyn
Published: July 2021

Objectives

To develop a taxonomy of interventions and a programme theory explaining how interventions improve physical activity and function in people with long-term conditions managed in primary care. To co-design a prototype intervention informed by the programme theory.

Design

Realist synthesis combining evidence from a wide range of rich and relevant literature with stakeholder views. Resulting context, mechanism and outcome statements informed co-design and knowledge mobilisation workshops with stakeholders to develop a primary care service innovation.

Results

A taxonomy was produced, including 13 categories of physical activity interventions for people with long-term conditions.

Abridged realist programme theory

Routinely addressing physical activity within consultations is dependent on a reinforcing practice culture, and targeted resources, with better coordination, will generate more opportunities to address low physical activity. The adaptation of physical activity promotion to individual needs and preferences of people with long-term conditions helps affect positive patient behaviour change. Training can improve knowledge, confidence and capability of practice staff to better promote physical activity. Engagement in any physical activity promotion programme will depend on the degree to which it makes sense to patients and professions, and is seen as trustworthy.

Co-design

The programme theory informed the co-design of a prototype intervention to: improve physical literacy among practice staff; describe/develop the role of a physical activity advisor who can encourage the use of local opportunities to be more active; and provide materials to support behaviour change.

Conclusions

Previous physical activity interventions in primary care have had limited effect. This may be because they have only partially addressed factors emerging in our programme theory. The co-designed prototype intervention aims to address all elements of this emergent theory, but needs further development and consideration alongside current schemes and contexts (including implications relevant to COVID-19), and testing in a future study. The integration of realist and co-design methods strengthened this study.
Adapting the Community-based Health Planning and Services (CHPS) to engage poor urban communities in Ghana: protocol for a participatory action research study
Authors: Abboah-Offei Mary , Gyasi Darkwa Akosua , Ayim Andrews , Ansah-Ofei Adelaide Maria , Dovlo Delanyo , Awoonor‐Williams John K , Agongo Erasmus Emmanuel Akurugu , Agyepong Irene Akua , Elsey Helen
Published: July 2021

Introduction

With rapid urbanisation in low-income and middle-income countries, health systems are struggling to meet the needs of their growing populations. Community-based Health Planning and Services (CHPS) in Ghana have been effective in improving maternal and child health in rural areas; however, implementation in urban areas has proven challenging. This study aims to engage key stakeholders in urban communities to understand how the CHPS model can be adapted to reach poor urban communities.

Methods and analysis

A Participatory Action Research (PAR) will be used to develop an urban CHPS model with stakeholders in three selected CHPS zones: (a) Old Fadama (Yam and Onion Market community), (b) Adedenkpo and (c) Adotrom 2, representing three categories of poor urban neighbourhoods in Accra, Ghana. Two phases will be implemented: phase 1 (‘reconnaissance phase) will engage and establish PAR research groups in the selected zones, conduct focus groups and individual interviews with urban residents, households vulnerable to ill-health and CHPS staff and key stakeholders. A desk review of preceding efforts to implement CHPS will be conducted to understand what worked (or not), how and why. Findings from phase 1 will be used to inform and co-create an urban CHPS model in phase 2, where PAR groups will be involved in multiple recurrent stages (cycles) of community-based planning, observation, action and reflection to develop and refine the urban CHPS model. Data will be managed using NVivo software and coded using the domains of community engagement as a framework to understand community assets and potential for engagement.

Ethics and dissemination

This study has been approved by the University of York’s Health Sciences Research Governance Committee and the Ghana Health Service Ethics Review Committee. The results of this study will guide the scale-up of CHPS across urban areas in Ghana, which will be disseminated through journal publications, community and government stakeholder workshops, policy briefs and social media content. This study is also funded by the Medical Research Council, UK.
Early respiratory diagnosis: benefits of enhanced lung function assessment
Authors: Sylvester Karl P , Youngs Luke , Rutter M A , Beech Ross , Mahadeva Ravi
Published: July 2021

Introduction

The National Health Service for England Long Term Plan identifies respiratory disease as one of its priority workstreams. To assist with earlier and more accurate diagnosis of lung disease they recommend improvement in delivery of quality-assured spirometry. However, there is a likelihood that patients will present with abnormal gas exchange when spirometry results are normal and therefore there will be a proportion of patients whose time to diagnosis is still protracted. We wished to determine the incidence rate of this occurring within our Trust.

Methods

A retrospective review of all patients attending the lung function laboratory for their first pulmonary function assessment from June 2006 to December 2020 was undertaken. Forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) >−1.64 standardised residual (SR) was used to confirm no obstructive lung function abnormality and FVC >−1.64 SR to confirm no suggestion of a restrictive lung function abnormality. Lung gas transfer for carbon monoxide (TLCO) and transfer coefficient of the lung for carbon monoxide (KCO) <−1.64 SR confirmed the presence of a gas exchange abnormality. Spirometry and gas transfer reference values generated by the Global Lung Initiative were used to determine normality.

Results

Of 12 835 eligible first visits with normal FEV1/FVC and FVC, 4856 (37.8%) were identified as having an abnormally low TLCO and 3302 (25.7%) presenting with an abnormally low KCO. Of 3494 with FEV1/FVC SR <−1.64, 3316 also had a ratio of <0.70, meaning 178 (5%) of patients in this cohort would have been misclassified as having obstructive lung disease using the 0.70 cut-off recommended by the Global Initiative for Chronic Obstructive Lung Disease for diagnosing obstructive lung disease.

Discussion

In conclusion, to assist with ensuring more accurate and timely diagnosis of lung disease and enhance patients’ diagnostic pathway, we recommend the performance of lung gas transfer measurements alongside spirometry in all healthcare settings. To assess and monitor gas transfer at the earliest opportunity we recommend this is implemented into new models being developed within community hubs. This will increase the identification of lung function abnormalities and provide patients with a definitive diagnosis earlier.
Primary-level palliative care national capacity: Pallium Canada
Authors: Pereira Jose , Chary Srini , Faulkner Jonathan , Tompkins Bonnie , Moat Jeffrey B
Published: July 2021

The need to improve access to palliative care across many settings of care for patients with cancer and non-cancer illnesses is recognised. This requires primary-level palliative care capacity, but many healthcare professionals lack core competencies in this area. Pallium Canada, a non-profit organisation, has been building primary-level palliative care at a national level since 2000, largely through its Learning Essential Approaches to Palliative Care (LEAP) education programme and its compassionate communities efforts. From 2015 to 2019, 1603 LEAP course sessions were delivered across Canada, reaching 28 123 learners from different professions, including nurses, physicians, social workers and pharmacists. This paper describes the factors that have accelerated and impeded spread and scale-up of these programmes. The need for partnerships with local, provincial and federal governments and organisations is highlighted. A social enterprise model, that involves diversifying sources of revenue to augment government funding, enhances long-term sustainability. Barriers have included Canada’s geopolitical realities, including large geographical area and thirteen different healthcare systems. Some of the lessons learned and strategies that have evolved are potentially transferrable to other jurisdictions.
Performance of the Hull Salford Cambridge Decision Rule (HSC DR) for early discharge of patients with findings on CT scan of the brain: a CENTER-TBI validation study
Authors: Marincowitz Carl , Gravesteijn Benjamin , Sheldon Trevor , Steyerberg Ewout , Lecky Fiona
Published: July 2021

Background

There is international variation in hospital admission practices for patients with mild traumatic brain injury (TBI) and injuries on CT scan. Only a small proportion of patients require neurosurgical intervention, while many guidelines recommend routine admission of all patients. We aim to validate the Hull Salford Cambridge Decision Rule (HSC DR) and the Brain Injury Guidelines (BIG) criteria to select low-risk patients for discharge from the emergency department.

Method

A cohort from 18 countries of Glasgow Coma Scale 13–15 patients with injuries on CT imaging was identified from the multicentre Collaborative European NeuroTrauma Effectiveness Research in TBI (CENTER-TBI) Study (conducted from 2014 to 2017) for secondary analysis. A composite outcome measure encompassing need for ongoing hospital admission was used, including seizure activity, death, intubation, neurosurgical intervention and neurological deterioration. We assessed the performance of our previously derived prognostic model, the HSC DR and the BIG criteria at predicting deterioration in this validation cohort.

Results

Among 1047 patients meeting the inclusion criteria, 267 (26%) deteriorated. Our prognostic model achieved a C-statistic of 0.81 (95% CI: 0.78 to 0.84). The HSC DR achieved a sensitivity of 100% (95% CI: 97% to 100%) and specificity of only 4.7% (95% CI: 3.3% to 6.5%) for deterioration. Using the BIG criteria for discharge from the ED achieved a higher specificity (13.3%, 95% CI: 10.9% to 16.1%) and lower sensitivity (94.6%, 95% CI: 90.5% to 97%), with 12/105 patients recommended for discharge subsequently deteriorating, compared with 0/34 with the HSC DR.

Conclusion

Our decision rule would have allowed 3.5% of patients to be discharged, none of whom would have deteriorated. Use of the BIG criteria may select patients for discharge who have too high a risk of subsequent deterioration to be used clinically. Further validation and implementation studies are required to support use in clinical practice.
Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals
Authors: Tarallo Sonia , Ferrero Giulio , De Filippis Francesca , Francavilla Antonio , Pasolli Edoardo , Panero Valentina , Cordero Francesca , Segata Nicola , Grioni Sara , Pensa Ruggero Gaetano , Pardini Barbara , Ercolini Danilo , Naccarati Alessio
Published: July 2021

Objectives

MicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored.

Design

We performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age.

Results

We found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p <0.05) and confirmed trends of expression levels of such miRNAs in vegans and vegetarians compared with an independent cohort of 45 omnivores. Two miRNAs related to lipid metabolism, miR-636 and miR-4739, were inversely correlated to the non-omnivorous diet duration, independently of subject age. Seventeen miRNAs correlated (|rho|>0.22, adj. p <0.05) with the estimated intake of nutrients, particularly animal proteins, phosphorus and, interestingly, lipids. In omnivores, higherPrevotellaandRoseburiaand lowerBacteroidesabundances than in vegans and vegetarians were observed. Lipid metabolism-related miR-425-3p and miR-638 expression levels were associated with increased abundances of microbial species, such asRoseburiasp. CAG 182 andAkkermansia muciniphila,specific of different diets. An integrated analysis identified 25 miRNAs, 25 taxa and 7 dietary nutrients that clearly discriminated (area under the receiver operating characteristic curve=0.89) the three diets.

Conclusion

Stool miRNA profiles are associated with specific diets and support the role of lipids as a driver of epigenetic changes and host-microbial molecular interactions in the gut.
Carotid webs produce greater hemodynamic disturbances than atherosclerotic disease: a DSA time–density curve study
Authors: Park Charlie C , El Sayed Retta , Risk Benjamin B , Haussen Diogo C , Nogueira Raul G , Oshinski John N , Allen Jason W
Published: July 2021

Background

Carotid webs (CaWs) are associated with ischemic strokes in younger patients without degrees of stenosis that are traditionally considered clinically significant.

Objective

To compare the hemodynamic parameters in the internal carotid artery (ICA) bulbar segment in patients with CaW with those in patients with atherosclerotic lesions using time–density curve (TDC) analysis of digital subtraction angiography (DSA) images.

Methods

We retrospectively assessed DSA images of 47 carotid arteries in 41 adult patients who underwent ICA catheter angiography for evaluation after ischemic stroke. Hemodynamic parameters, including full width at half maximum (FWHM) and area under the time–density curve (AUC) as proxies for increased flow stasis, were calculated using TDC analyses of a region of interest (ROI) in the ICA bulb immediately rostral to the web/atherosclerotic plaque, relative to a standardized ROI in the ipsilateral distal common carotid artery (eg, relative FWHM (rFWHM)). Hemodynamic parameters were compared using non-parametric Kruskal-Wallis tests. Logistic regression was used to predict CaW versus mild/moderate atherosclerosis for each hemodynamic parameter, adjusting for degree of stenosis.

Results

Mean age of patients was 56.0±13 years, with 22 (53.7%) women. 17 CaWs, 22 atherosclerotic plaques (15 mild/moderate and 7 severe), and eight normal carotid arteries were assessed. Significant between-group differences were present in the relative total AUC (p<0.001), relative AUC at wash out (p=0.031), and relative FWHM (p=0.001). Logistic regression to predict CaW versus mild/moderate atherosclerosis showed that rAUC total had the highest predictive value (pAUC=0.96, 95% CI 0.90 to 1.00), followed by rFWHM (0.87, 95% CI 0.74 to 1.00), and rAUC WO (0.74, 95% CI (0.57 to 0.91).

Conclusion

CaW results in larger local hemodynamic disruption, characterized by flow stasis, than mild/moderate carotid atherosclerotic lesions, suggesting that CaWs may produce larger regions of thrombogenic flow stasis.
Who is providing HIV diagnostic testing? Comparing HIV testing by general practitioners and sexual health centres in five regions in the Netherlands, 2011−2018
Authors: Bogers Saskia J , Twisk Denise E , Beckers Loes M , Götz Hannelore M , Meima Bram , Kroone Michelle , Hoornenborg Elske , Ott Alewijn , Luning-Koster Marleen N , Dukers-Muijrers Nicole H T M , Hoebe Christian J P A , Kampman Carolina J G , Bosma Froukje , Schim van der Loeff Maarten , Geerlings Suzanne , van Bergen Jan
Published: July 2021

Objectives

General practitioners (GPs) and sexual health centres (SHCs) are the main providers of HIV testing and diagnose two-thirds of HIV infections in the Netherlands. We compared regional HIV testing and positivity by GPs versus SHCs to gain insight into strategies to improve HIV testing, to enable timely detection of HIV infections.

Methods

Laboratory data (2011–2018) on HIV testing by GPs and SHCs in five Dutch regions with varying levels of urbanisation were evaluated. Regional HIV testing rates per 10 000 residents ≥15 years (mean over period and annual) were compared between providers using negative binomial generalised additive models and additionally stratified by sex and age (15–29 years, 30–44 years, 45–59 years, ≥60 years). χ2 tests were used to compare positivity percentage between the two groups of providers.

Results

In the study period, 505 167 HIV tests (GP 36%, SHC 64%) were performed. The highest HIV testing rates were observed in highly urbanised regions, with large regional variations. The HIV testing rates ranged from 28 to 178 per 10 000 residents by GPs and from 30 to 378 per 10 000 by SHCs. Testing rates by GPs were lower than by SHCs in three regions and comparable in two. In all regions, men were tested less by GPs than by SHCs; for women, this varied by region. Among those aged 15–29 years old, GPs’ testing rates were lower than SHCs’, while this was reversed in older age categories in four out of five regions. The overall mean HIV positivity was 0.4%. In contrast to other regions, positivity in Amsterdam was significantly higher among individuals tested by GPs than by SHCs.

Conclusions

This retrospective observational study shows that besides SHCs, who perform opt-out testing for key groups, GPs play a prominent role in HIV testing, especially in non-key populations, such as women and older individuals. Large regional variation exists, requiring region-specific interventions to improve GPs’ HIV testing practices.
MadFlow: automating Monte Carlo simulation on GPU for particle physics processes
Authors: Carrazza Stefano , Cruz-Martinez Juan , Rossi Marco , Zaro Marco
Published: July 2021

We present , a first general multi-purpose framework for Monte Carlo (MC) event simulation of particle physics processes designed to take full advantage of hardware accelerators, in particular, graphics processing units (GPUs). The automation process of generating all the required components for MC simulation of a generic physics process and its deployment on hardware accelerator is still a big challenge nowadays. In order to solve this challenge, we design a workflow and code library which provides to the user the possibility to simulate custom processes through the MadGraph5_aMC@NLO framework and a plugin for the generation and exporting of specialized code in a GPU-like format. The exported code includes analytic expressions for matrix elements and phase space. The simulation is performed using the VegasFlow and PDFFlow libraries which deploy automatically the full simulation on systems with different hardware acceleration capabilities, such as multi-threading CPU, single-GPU and multi-GPU setups. The package also provides an asynchronous unweighted events procedure to store simulation results. Crucially, although only Leading Order is automatized, the library provides all ingredients necessary to build full complex Monte Carlo simulators in a modern, extensible and maintainable way. We show simulation results at leading-order for multiple processes on different hardware configurations.
INSURANCE CONSUMPTION AND ECONOMIC POLICY UNCERTAINTY IN INDIA: AN ANALYSIS OF ASYMMETRIC EFFECTS
Authors: KUMAR SIDDHARTH , SAHU NARESH CHANDRA , KUMAR PUSHP
Published: July 2021

This study examines the asymmetric effect of economic policy uncertainty (EPU) on life and non-life insurance consumption in India using monthly data from April 2004–October 2020. The paper has employed a nonlinear autoregressive distributed lag (NARDL) model with a structural break. The results reveal that there exists an asymmetric effect of EPU on life insurance as well as non-life life insurance consumption. A negative relationship is found between EPU and insurance consumption in both life and non-life insurance. Based on the findings, the study suggests the policymakers to consider the asymmetric effects of EPU while formulating insurance-related policies in India.
Breaking the Symmetry in Queues with Delayed Information
Authors: Doldo Philip , Pender Jamol , Rand Richard
Published: July 2021

Giving customers queue length information about a service system has the potential to influence the decision of a customer to join a queue. Thus, it is imperative for managers of queueing systems to understand how the information that they provide will affect the performance of the system. To this end, we construct and analyze a two-dimensional deterministic fluid model that incorporates customer choice behavior based on delayed queue length information. Reports in the existing literature always assume that all queues have identical parameters and the underlying dynamical system is symmetric. However, in this paper, we relax this symmetry assumption by allowing the arrival rates, service rates, and the choice model parameters to be different for each queue. Our methodology exploits the method of multiple scales and asymptotic analysis to understand how to break the symmetry. We find that the asymmetry can have a large impact on the underlying dynamics of the queueing system.
Complex Behavior of a Hyperchaotic TNC Oscillator: Coexisting Bursting, Space Magnetization, Control of Multistability and Application in Image Encryption Based on DNA Coding
Authors: Tagne Mogue R. L. , Folifack Signing V. R. , Kengne J. , Kountchou M. , Njitacke Z. T.
Published: July 2021

In this work, several new aspects of the dynamics of the well-known TNC hyperchaotic oscillator are investigated. Numerous novelties appear in this work, namely particular structures of space magnetization, the coexistence of bursting patterns, the coexistence of up to four asymmetric different attractors, offset-boosting, and antimonotonicity. In addition to this interesting and particular combination of features in the TNC oscillator, the control of multistability phenomenon is carried out using linear augmentation control scheme. Finally, knowing that the protection of digital images is of particularly great interest, the complexity of pseudo-random hyperchaotic sequences of the TNC oscillator is combined with the similarity that the DNA coding shares with the binary code to build a new image encryption algorithm with strong robustness and high speed. This algorithm is successfully evaluated using cropping attack, noise attack and differential attack. The results obtained demonstrate that the proposed algorithm is efficient and of good quality.
Spatiotemporal Dynamics and Pattern Formations of an Activator-Substrate Model with Double Saturation Terms
Authors: Zhong Shihong , Wang Jinliang , Xia Juandi , Li You
Published: July 2021

By using center manifold theory, Poincaré–Bendixson theorem, spatiotemporal spectrum and dispersion relation of linear operators, the spatiotemporal dynamics of an activator-substrate model with double saturation terms under the homogeneous Neumann boundary condition are considered in the present paper. It is surprising to find that the system can induce new dynamics, such as subcritical Hopf bifurcation and the coexistence of two limit cycles. Moreover, Turing instability in equilibrium mainly generates stripe patterns, while homogeneous periodic solutions mainly generate spot patterns or spot-stripe patterns, where the pattern formations are enormously consistent with the theoretical results. Interestingly, Turing instability can create equilibrium and periodic solution simultaneously in the subcritical Hopf bifurcation, which is the new finding of the diffusion-driven instability. In fact, those theoretical methods are also valid for finding the patterns of other models in one-dimensional space.
Model predictive control with random batch methods for a guiding problem
Authors: Ko Dongnam , Zuazua Enrique
Published: July 2021

We model, simulate and control the guiding problem for a herd of evaders under the action of repulsive drivers. The problem is formulated in an optimal control framework, where the drivers (controls) aim to guide the evaders (states) to a desired region of the Euclidean space. The numerical simulation of such models quickly becomes unfeasible for a large number of interacting agents, as the number of interactions grows [Formula: see text] for [Formula: see text] agents. For reducing the computational cost to [Formula: see text], we use the Random Batch Method (RBM), which provides a computationally feasible approximation of the dynamics. First, the considered time interval is divided into a number of subintervals. In each subinterval, the RBM randomly divides the set of particles into small subsets (batches), considering only the interactions inside each batch. Due to the averaging effect, the RBM approximation converges to the exact dynamics in the [Formula: see text]-expectation norm as the length of subintervals goes to zero. For this approximated dynamics, the corresponding optimal control can be computed efficiently using a classical gradient descent. The resulting control is not optimal for the original system, but for a reduced RBM model. We therefore adopt a Model Predictive Control (MPC) strategy to handle the error in the dynamics. This leads to a semi-feedback control strategy, where the control is applied only for a short time interval to the original system, and then compute the optimal control for the next time interval with the state of the (controlled) original dynamics. Through numerical experiments we show that the combination of RBM and MPC leads to a significant reduction of the computational cost, preserving the capacity of controlling the overall dynamics.
A Family of Software Reliability Models with Bathtub-Shaped Fault Detection Rate
Authors: Nafreen Maskura , Fiondella Lance
Published: July 2021

Researchers have proposed several software reliability growth models, many of which possess complex parametric forms. In practice, software reliability growth models should exhibit a balance between predictive accuracy and other statistical measures of goodness of fit, yet past studies have not always performed such balanced assessment. This paper proposes a framework for software reliability growth models possessing a bathtub-shaped fault detection rate and derives stable and efficient expectation conditional maximization algorithms to enable the fitting of these models. The stages of the bathtub are interpreted in the context of the software testing process. The illustrations compare multiple bathtub-shaped and reduced model forms, including classical models with respect to predictive and information theoretic measures. The results indicate that software reliability growth models possessing a bathtub-shaped fault detection rate outperformed classical models on both types of measures. The proposed framework and models may therefore be a practical compromise between model complexity and predictive accuracy.
Sparse sufficient dimension reduction with heteroscedasticity
Authors: Cheng Haoyang , Cui Wenquan
Published: July 2021

Heteroscedasticity often appears in the high-dimensional data analysis. In order to achieve a sparse dimension reduction direction for high-dimensional data with heteroscedasticity, we propose a new sparse sufficient dimension reduction method, called Lasso-PQR. From the candidate matrix derived from the principal quantile regression (PQR) method, we construct a new artificial response variable which is made up from top eigenvectors of the candidate matrix. Then we apply a Lasso regression to obtain sparse dimension reduction directions. While for the “large [Formula: see text] small [Formula: see text]” case that [Formula: see text], we use principal projection to solve the dimension reduction problem in a lower-dimensional subspace and projection back to the original dimension reduction problem. Theoretical properties of the methodology are established. Compared with several existing methods in the simulations and real data analysis, we demonstrate the advantages of our method in the high dimension data with heteroscedasticity.
A Property Satisfying Reducedness over Centers
Authors: Jin Hailan , Kwak Tai Keun , Lee Yang , Piao Zhelin
Published: July 2021

This article concerns a ring property called pseudo-reduced-over-center that is satisfied by free algebras over commutative reduced rings. The properties of radicals of pseudo-reduced-over-center rings are investigated, especially related to polynomial rings. It is proved that for pseudo-reduced-over-center rings of nonzero characteristic, the centers and the pseudo-reduced-over-center property are preserved through factor rings modulo nil ideals. For a locally finite ring [Formula: see text], it is proved that if [Formula: see text] is pseudo-reduced-over-center, then [Formula: see text] is commutative and [Formula: see text] is a commutative regular ring with [Formula: see text] nil, where [Formula: see text] is the Jacobson radical of [Formula: see text].
The Even Part of Finite-Dimensional Modular Lie Superalgebra Γ
Authors: Fan Yusi , Xu Xiaoning , Chen Liangyun
Published: July 2021

Let [Formula: see text] be the underlying base field of characteristic [Formula: see text] and denote by [Formula: see text] the even part of the finite-dimensional Lie superalgebra [Formula: see text]. We give the generator sets of the Lie algebra [Formula: see text]. Using certain properties of the canonical tori of [Formula: see text], we describe explicitly the derivation algebra of [Formula: see text].
Experimental Study on the Effect of Conductive Carbon Black Super-P on the Properties of Composite Mortar
Authors: He Wei , Wang Yawei , Xu Jihang
Published: July 2021

Conductive carbon black Super-P (CSP) is a kind of nanomaterial, which is often used as conductive agent. It has excellent conductivity and low production cost. In this paper, CSP was used as the admixture to prepare composite mortar (with the specific gravity of cementitious material). The consistency, mechanical properties, electrical conductivity and temperature sensitivity of composite mortar were studied. The mechanism of CSP was analyzed by scanning electron microscope (SEM) and X-ray diffraction (XRD). The results show that the consistency of composite mortar decreases with the addition of CSP. The mechanical properties of composite mortar first increase and then decrease with the increase of CSP content. The addition of CSP greatly improves the conductivity of mortar. When the CSP content is 0.5–2%, the resistivity decreases rapidly and the seepage threshold appears. When the content of the mixture is large, the influence of different curing conditions on resistivity is small. SEM and XRD analysis show that CSP can fill micro pores and conduct electricity through tunnels, and does not change the composition of hydration products of composite mortar, and the formation of calcium hydroxide can be inhibited when the content is small. This paper explores the properties of CSP composite mortar, which provides theoretical and experimental basis for the preparation and application of conductive mortar.