bluuebunny/crossref_metadata_2025 huggingface dataset:
MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks
Authors: de Weerd Hendrik A , Badam Tejaswi V S , Martínez-Enguita David , Åkesson Julia , Muthas Daniel , Gustafsson Mika , Lubovac-Pilav Zelmina
Published: April 2020

Motivation

Complex diseases are due to the dense interactions of many disease-associated factors that dysregulate genes that in turn form the so-called disease modules, which have shown to be a powerful concept for understanding pathological mechanisms. There exist many disease module inference methods that rely on somewhat different assumptions, but there is still no gold standard or best-performing method. Hence, there is a need for combining these methods to generate robust disease modules.

Results

We developed MODule IdentiFIER (MODifieR), an ensemble R package of nine disease module inference methods from transcriptomics networks. MODifieR uses standardized input and output allowing the possibility to combine individual modules generated from these methods into more robust disease-specific modules, contributing to a better understanding of complex diseases.

Availability and implementation

MODifieR is available under the GNU GPL license and can be freely downloaded from https://gitlab.com/Gustafsson-lab/MODifieR and as a Docker image from https://hub.docker.com/r/ddeweerd/modifier.

Supplementary information

Supplementary data are available at Bioinformatics online.
New Measures for the Coronavirus Disease 2019 Response: A Lesson From the Wenzhou Experience
Authors: Ruan Linhui , Wen Min , Zeng Qingrun , Chen Chengshui , Huang Shengwei , Yang Su , Yang Jianjing , Wang Jingqiang , Hu Yuhuan , Ding Saidan , Zhang Ying , Zhang Hongxia , Feng Yuanjing , Jin Kunlin , Zhuge Qichuan
Published: April 2020

As the outbreak of coronavirus disease 2019 (COVID-19) has spread globally, determining how to prevent the spread is of paramount importance. We reported the effectiveness of different responses of 4 affected cities in preventing the COVID-19 spread. We expect the Wenzhou anti–COVID-19 measures may provide information for cities around the world that are experiencing this epidemic.
Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
Authors: Tangaro Marco Antonio , Donvito Giacinto , Antonacci Marica , Chiara Matteo , Mandreoli Pietro , Pesole Graziano , Zambelli Federico
Published: April 2020

Background

While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particular job types, tools development, and training activities. In such cases, a cloud-based Galaxy virtual instance represents an alternative that equips the user with complete control over the Galaxy instance itself without the burden of the hardware and software infrastructure involved in running and maintaining a Galaxy server.

Results

We present Laniakea, a complete software solution to set up a “Galaxy on-demand” platform as a service. Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, and then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM). Laniakea features deployment of single-server or cluster-backed Galaxy instances, sharing of reference data across multiple instances, data volume encryption, and support for VM image-based, Docker-based, and Ansible recipe-based Galaxy deployments. A Laniakea-based Galaxy on-demand service, named Laniakea@ReCaS, is currently hosted at the ELIXIR-IT ReCaS cloud facility.

Conclusions

Laniakea offers to scientific e-infrastructures a complete and easy-to-use software solution to provide a Galaxy on-demand service to their users. Laniakea-based cloud services will help in making Galaxy more accessible to a broader user base by removing most of the burdens involved in deploying and running a Galaxy service. In turn, this will facilitate the adoption of Galaxy in scenarios where classic public instances do not represent an optimal solution. Finally, the implementation of Laniakea can be easily adapted and expanded to support different services and platforms beyond Galaxy.
Variational full-waveform inversion
Authors: Zhang Xin , Curtis Andrew
Published: April 2020

Seismic full-waveform inversion (FWI) can produce high-resolution images of the Earth’s subsurface. Since full-waveform modelling is significantly nonlinear with respect to velocities, Monte Carlo methods have been used to assess image uncertainties. However, because of the high computational cost of Monte Carlo sampling methods, uncertainty assessment remains intractable for larger data sets and 3-D applications. In this study, we propose a new method called variational FWI, which uses Stein variational gradient descent to solve FWI problems. We apply the method to a 2-D synthetic example and demonstrate that the method produces accurate approximations to those obtained by Hamiltonian Monte Carlo. Since variational inference solves the problem using optimization, the method can be applied to larger data sets and 3-D applications by using stochastic optimization and distributed optimization.
Full wave sensitivity of SK(K)S phases to arbitrary anisotropy in the upper and lower mantle
Authors: Tesoniero Andrea , Leng Kuangdai , D. Long Maureen , Nissen-Meyer Tarje
Published: April 2020

Core-refracted phases such as SKS and SKKS are commonly used to probe seismic anisotropy in the upper and lowermost portions of the Earth’s mantle. Measurements of SK(K)S splitting are often interpreted in the context of ray theory, and their frequency dependent sensitivity to anisotropy remains imperfectly understood, particularly for anisotropy in the lowermost mantle. The goal of this work is to obtain constraints on the frequency dependent sensitivity of SK(K)S phases to mantle anisotropy, particularly at the base of the mantle, through global wavefield simulations. We present results from a new numerical approach to modelling the effects of seismic anisotropy of arbitrary geometry on seismic wave propagation in global 3-D earth models using the spectral element solver AxiSEM3D. While previous versions of AxiSEM3D were capable of handling radially anisotropic input models, here we take advantage of the ability of the solver to handle the full fourth-order elasticity tensor, with 21 independent coefficients. We take advantage of the computational efficiency of the method to compute wavefields at the relatively short periods (5 s) that are needed to simulate SK(K)S phases. We benchmark the code for simple, single-layer anisotropic models by measuring the splitting (via both the splitting intensity and the traditional splitting parameters ϕ and δt) of synthetic waveforms and comparing them to well-understood analytical solutions. We then carry out a series of numerical experiments for laterally homogeneous upper mantle anisotropic models with different symmetry classes, and compare the splitting of synthetic waveforms to predictions from ray theory. We next investigate the full wave sensitivity of SK(K)S phases to lowermost mantle anisotropy, using elasticity models based on crystallographic preferred orientation of bridgmanite and post-perovskite. We find that SK(K)S phases have significant sensitivity to anisotropy at the base of the mantle, and while ray theoretical approximations capture the first-order aspects of the splitting behaviour, full wavefield simulations will allow for more accurate modelling of SK(K)S splitting data, particularly in the presence of lateral heterogeneity. Lastly, we present a cross-verification test of AxiSEM3D against the SPECFEM3D_GLOBE spectral element solver for global seismic waves in an anisotropic earth model that includes both radial and azimuthal anisotropy. A nearly perfect agreement is achieved, with a significantly lower computational cost for AxiSEM3D. Our results highlight the capability of AxiSEM3D to handle arbitrary anisotropy geometries and its potential for future studies aimed at unraveling the details of anisotropy at the base of the mantle.
Risk of Severe Bacterial Infection in People Living Human Immunodeficiency Virus Infection in the Combined Antiretroviral Therapy Era
Authors: Melliez Hugues , Mary-Krause Murielle , Guiguet Marguerite , Carrieri Patrizia , Abgrall Sophie , Enel Patricia , Gallien Sébastien , Duval Xavier , Duvivier Claudine , Pavie Juliette , Siguier Martin , Freire-Maresca Anaenza , Tattevin Pierre , Costagliola Dominique
Published: April 2020

Background

Severe bacterial infections are the first cause of morbidity in people with human immunodeficiency virus (PWH). We aimed to assess their incidence and to analyze their determinants.

Methods

We studied human immunodeficiency virus (HIV)-1-infected individuals aged at least 15 years and prospectively followed between 2006 and 2015 in the French Hospital Database on HIV. The Andersen and Gill model was used to calculate the adjusted hazard ratios (HRs), focusing on heavy alcohol use and neutrophil function-altering comorbidities.

Results

Of 25 795 participants, 1414 developed 1883 severe bacterial infections. Between 2006 and 2009 and 2013 and 2015, the incidence fell from 13.2 (95% confidence interval [CI], 12.3–14.1) to 7.1 (95% CI, 6.3–7.8) per 1000 person-years. Heavy alcohol use was associated with an increased risk of severe bacterial infection (HR = 1.3, 95% CI = 1.1–1.7 for 40–80 g/day and HR = 1.6, 95% CI = 1.2–2.1 for >80 g/day), as were diabetes, chronic kidney disease, and end-stage liver disease (HR = 1.2, 95% CI = 1.0–1.4 when 1 comorbidity; HR = 2.3, 95% CI = 1.6–3.4 when more than 1 comorbidity), and nonacquired immune deficiency syndrome-defining malignancy (HR = 2.0; 95% CI, 1.6–2.4).

Conclusions

Heavy alcohol use was associated with an increased risk of severe bacterial infection, as were neutrophil function-altering comorbidities. Controlled-drinking approaches should be promoted and comorbidity management should be strengthened in PWH.
In vitro activity of ceftolozane/tazobactam alone and in combination with amikacin against MDR/XDR Pseudomonas aeruginosa isolates from Greece
Authors: Galani Irene , Papoutsaki Vassiliki , Karantani Irene , Karaiskos Ilias , Galani Lamprini , Adamou Panagiota , Deliolanis Ioannis , Kodonaki Antigoni , Papadogeorgaki Eleni , Markopoulou Margarita , Maraki Sofia , Damala Maria , Prifti Eleni , Vagiakou Eleni , Petinaki Efthimia , Fountoulis Kimon , Tsiplakou Sophia , Kirikou Helen , Souli Maria , Antoniadou Anastasia , Giamarellou Helen
Published: April 2020

Objectives

We evaluated the in vitro activity of ceftolozane/tazobactam and comparator agents against MDR non-MBL Pseudomonas aeruginosa isolates collected from nine Greek hospitals and we assessed the potential synergistic interaction between ceftolozane/tazobactam and amikacin.

Methods

A total of 160 non-MBL P. aeruginosa isolates collected in 2016 were tested for susceptibility to ceftolozane/tazobactam and seven comparator agents including ceftazidime/avibactam. Time–kill assays were performed for synergy testing using ceftolozane/tazobactam 60 or 7.5 mg/L, corresponding to the peak and trough concentrations of a 1.5 g q8h dose, respectively, in combination with 69 mg/L amikacin, corresponding to the free peak plasma concentration. Synergy was defined as a ≥2 log10 cfu/mL reduction compared with the most active agent.

Results

Overall, ceftolozane/tazobactam inhibited 64.4% of the P. aeruginosa strains at ≤4 mg/L. Colistin was the most active agent (MIC50/90, 0.5/2 mg/L; 96.3% susceptible) followed by ceftazidime/avibactam (MIC50/90, 4/16 mg/L; 80.6% susceptible). GES-type enzymes were predominantly responsible for ceftolozane/tazobactam resistance; 81.6% of the non-producers were susceptible. MICs for the P. aeruginosa isolates selected for synergy testing were 2–32 mg/L ceftolozane/tazobactam and 2–128 mg/L amikacin. The combination of ceftolozane/tazobactam with amikacin was synergistic against 85.0% of all the isolates tested and against 75.0% of the GES producers. No antagonistic interactions were observed.

Conclusions

Ceftolozane/tazobactam demonstrated good in vitro activity against MDR/XDR P. aeruginosa clinical isolates, including strains with co-resistance to other antipseudomonal drugs. In combination with amikacin, a synergistic interaction at 24 h was observed against 85.0% of P. aeruginosa strains tested, including isolates with ceftolozane/tazobactam MICs of 32 mg/L or GES producers.
Development and Validation of a Liquid Chromatography High-Resolution Mass Spectrometry (LC-HRMS) Bioanalytical Method for Quantifying Cannabinoids in Whole Blood: Application for Determining Recent Cannabis Use
Authors: DeGregorio Michael W , Audino Susan A , Montoya Edward , Phong Aron , Kao Chiao-Jung , Wurz Gregory T
Published: April 2020

Background

Cannabis legalization is expanding rapidly throughout the United States, but there is no reliable means of establishing recent use.

Objective

To develop and validate a bioanalytical method for determination of Δ9-tetrahydrocannabinol (Δ9-THC), cannabinol, 11-hydroxy-Δ9-THC, 11-nor-9-carboxy-Δ9-THC, and 8β,11-dihydroxy-Δ9-THC in whole blood microsamples by liquid chromatography high-resolution mass spectrometry (LC-HRMS).

Methods

Cannabinoid extraction from whole blood was performed using a mixture of n-hexane/ethyl acetate (90:10, v/v). Chromatographic separation was performed with a C18 column using a binary mobile phase gradient of water and acetonitrile, each with 0.1% formic acid. Detection was performed by positive ion mode heated electrospray ionization with full scan MS on an Orbitrap mass spectrometer. A clinical study was performed in 30 subjects to identify recent cannabis use based on analysis of cannabinoids in blood samples up to 200 min post-smoking.

Results

Acceptable linearity of all calibration curves was observed (r2>0.99) for all analytes over a 1–100 ng/mL concentration range, with acceptable accuracy. Limit of detection (LOD) was 0.5 ng/mL. Accuracy and precision met acceptance criteria for all analytes. Repeatability (CV) was <5% at low (3 ng/mL) and high (90 ng/mL) concentrations. In the clinical study, the ratios between 11-nor-9-carboxy-Δ9-THC and Δ9-THC fell immediately after smoking and returned to near baseline levels by 200 min post-smoking, which is consistent with recent use.

Conclusions and Highlights

The developed LC-HRMS bioanalytical method is suitable for quantification of five key cannabinoids in whole capillary blood microsamples and can be used in conjunction with a test for determining recent cannabis use.
The Cognitive Mechanisms in Music Listening Interventions for Pain: A Scoping Review
Authors: Howlin Claire , Rooney Brendan
Published: April 2020

Music interventions have been introduced in a range of pain management contexts, yet considerable inconsistencies have been identified across evaluation studies. These inconsistencies have been attributed to a lack of clarity around the prospective cognitive mechanisms of action underlying such interventions. The current systematic scoping review was conducted to examine the theoretical rationales provided in the literature for introducing music listening interventions (MLIs) in pain contexts. 3 search terms (music, listening, and pain) were used in four electronic databases, and 75 articles were included for analysis. Content analysis was used to identify that more intensive listening schedules were associated with chronic and cancer pain compared with procedural pain. The degree to which patients had a choice over the music selection could be categorized into 1 of 5 levels. Thematic synthesis was then applied to develop 5 themes that describe the cognitive mechanisms involved in MLIs for pain. These mechanisms were brought together to build the Cognitive Vitality Model, which emphasizes the role of individual agency in mediating the beneficial effects of music listening through the processes of Meaning-Making, Enjoyment, and Musical Integration. Finally, content analysis was used to demonstrate that only a small proportion of studies were explicitly designed to examine the cognitive mechanisms underlying MLIs and we have suggested ways to improve future practice and empirical research. We call on researchers to design and evaluate MLIs in line with the Cognitive Vitality Model of music listening interventions for pain.
Impact of high baseline Aspergillus-specific IgG levels on weight and quality-of-life outcomes of patients with chronic pulmonary aspergillosis
Authors: Bongomin Felix , Garcez Tomaz , Denning David W
Published: April 2020

This study aimed to evaluate the impact of quantitative baseline Aspergillus-specific immunoglobulin G (IgG) serum levels on weight changes of patients with chronic pulmonary aspergillosis (CPA) under antifungal treatment. We retrospectively reviewed data of patients diagnosed with CPA between April 2015 and March 2018 at the National Aspergillosis Centre (Manchester, UK). All patients were on continued antifungal treatment for 12 months. Data on Aspergillus-specific IgG levels, St George's quality of life (SGQoL) variables and weight at baseline, 6 months and 12 months were extracted. We defined a high serum Aspergillus-specific IgG as ≥ 200 mg/l (Group A) and low level < 200 mg/l (Group B). Forty-nine patients (37 male; 12 female), median age 65 years (range: 29–86) were studied. Overall, 33% (n = 16) of the patients were in Group A. The baseline characteristics between the two groups were similar. The median Charlson comorbidity index was 4 (range: 0–5) and 3 (range: 0–9) for Group A and Group B, respectively (P = .543). There was a sustained decline in median Aspergillus IgG levels from baseline, through 6 month to 12 months of continues therapy from 170 (range: 20–1110) to 121 (range: 20–1126), and finally 107 (15–937) mg/l, respectively (P < .001). Group A patients gained more weight at 6 months (9/15 [60%] vs. 7/33 [21%], P = .012) and at 12 months of treatment (9/15 [60%] vs. 7/33 [22%]), and more patients in Group B lost weight ((13/33 [41%] vs. 1/15 [7%]), P = .015). However, there was no difference in QoL outcomes across groups at 6 (P = .3) and 12 (P = .7) months. A very high Aspergillus IgG may confer a higher likelihood of weight gain as a key, objective marker of clinical response, if patients can tolerate 12 months of antifungal therapy.
Long-term statistics of pulsar glitches triggered by a Brownian stress accumulation process
Authors: Carlin J B , Melatos A
Published: April 2020

A microphysics-agnostic meta-model of rotational glitches in rotation-powered pulsars is developed, wherein the globally averaged internal stress accumulates as a Brownian process between glitches, and a glitch is triggered once a critical threshold is surmounted. Precise, falsifiable predictions are made regarding long-term event statistics in individual pulsars. For example, the Spearman cross-correlation coefficient between the size of a glitch and the waiting time until the next glitch should exceed 0.25 in all pulsars. Among the six pulsars with the most recorded glitches, PSR J0537−6910 and PSR J0835−4510 are consistent with the predictions of the meta-model, while PSR J1740−3015 and PSR J0631+1036 are not. PSR J0534+2200 and PSR J1341−6220 are only consistent with the meta-model, if there exists an undetected population of small glitches with small waiting times, which we do not resolve. The results are compared with a state-dependent Poisson process, another microphysics-agnostic meta-model in the literature. The results are also applied briefly to recent pulse-to-pulse observations of PSRJ0835−4510, which appear to reveal evidence for a negative fluctuation in rotation frequency just prior to the 2016 glitch.
Dark-ages reionization and galaxy formation simulation – XVIII. The high-redshift evolution of black holes and their host galaxies
Authors: Marshall Madeline A , Mutch Simon J , Qin Yuxiang , Poole Gregory B , Wyithe J Stuart B
Published: April 2020

Correlations between black holes and their host galaxies provide insight into what drives black hole–host co-evolution. We use the Meraxes semi-analytic model to investigate the growth of black holes and their host galaxies from high redshift to the present day. Our modelling finds no significant evolution in the black hole–bulge and black hole–total stellar mass relations out to a redshift of 8. The black hole–total stellar mass relation has similar but slightly larger scatter than the black hole–bulge relation, with the scatter in both decreasing with increasing redshift. In our modelling, the growth of galaxies, bulges, and black holes are all tightly related, even at the highest redshifts. We find that black hole growth is dominated by instability-driven or secular quasar-mode growth and not by merger-driven growth at all redshifts. Our model also predicts that disc-dominated galaxies lie on the black hole–total stellar mass relation, but lie offset from the black hole–bulge mass relation, in agreement with recent observations and hydrodynamical simulations.
Long-term mortality risk associated with citric acid- and acetic acid-based bicarbonate haemodialysis: a historical cohort propensity score-matched study in a large, multicentre, population-based study
Authors: Neri Luca , Bellocchio Francesco , Kircelli Fatih , Jirka Tomas , Levannier Martial , Guillaume Jean , Attaf David , Barbieri Carlo , Garbelli Mario , Stuard Stefano , Canaud Bernard , Chazot Charles
Published: April 2020

Background

Citric acid-based bicarbonate dialysate (CiD) is increasingly used in haemodialysis (HD) to improve haemodynamic tolerance and haemocompatibility associated with acetic acid-based bicarbonate dialysate. Safety concerns over CiD have been raised recently after a French ecological study reported higher mortality hazard in HD clinics with high CiD consumption. Therefore, we evaluated the mortality risk associated with various acidifiers (AcD, CiD) of bicarbonate dialysate.

Methods

In this multicentre, historical cohort study, we included adult incident HD patients (European, Middle-East and Africa Fresenius Medical Care network; 1 January 2014 to 31 October 2018). We recorded acidifiers of bicarbonate dialysis and dialysate composition for each dialysis session. In the primary intention-to-treat analysis, patients were assigned to the exposed group if they received CiD in >70% of sessions during the first 3 months (CiD70%), whereas the non-exposed group received no CiD at all. In the secondary analysis, exposure was assessed on a monthly basis for the whole duration of the follow-up.

Results

We enrolled 10 121 incident patients during the study period. Of them, 371 met the criteria for inclusion in CiD70%. After propensity score matching, mortality was 11.43 [95% confidence interval (CI) 8.86–14.75] and 12.04 (95% CI 9.44–15.35) deaths/100 person-years in the CiD0% and CiD70% groups, respectively (P = 0.80). A similar association trend was observed in the secondary analysis.

Conclusions

We did not observe evidence of increased mortality among patients exposed to CiD in a large European cohort of dialysis patients despite the fact that physicians were more inclined to prescribe CiD to subjects with worse medical conditions.
Expression of granulocyte macrophage-colony stimulating factor and its receptor in the synovium of osteoarthritis patients is negatively correlated with pain
Authors: van Helvoort Eefje M , Eijkelkamp Niels , Lafeber Floris P J G , Mastbergen Simon C
Published: April 2020

Objectives

The crosstalk between the immune and nervous system in the regulation of OA pain is increasingly becoming evident. GM-CSF signals in both systems and might be a new treatment target to control OA pain. Anti GM-CSF treatment has analgesic effects in OA without affecting synovitis scores, suggesting that treatment effects are not caused by local anti-inflammatory effects. We aimed to evaluate whether expression of GM-CSF and its receptor GM-CSFrα in synovial tissue is linked to synovial inflammation and/or knee pain in knee OA patients.

Methods

Cartilage and synovial tissue of knee OA patients (n = 20) was collected during total knee replacement. Cartilage damage was evaluated by histology and ex vivo matrix proteoglycan turnover. Synovial inflammation was evaluated by histology and ex vivo synovial production of TNF-α, (PGE2) and nitric oxide (NO). Numbers of synovial tissue cells expressing GM-CSF or GM-CSFrα were determined by immunohistochemistry. Pain was evaluated using WOMAC questionnaire and visual analogue scale (VAS) knee pain.

Results

Collected cartilage and synovial tissue had a typical OA phenotype with enhanced cartilage damage and synovial inflammation. GM-CSF and GM-CSFrα expressing cells in the synovial sublining correlated negatively with knee pain. Cartilage damage and synovial inflammation did not correlate with knee pain.

Conclusion

Unanticipated, the negative correlation between synovial tissue cells expressing GM-CSF(r) and OA knee pain suggests that local presence of these molecules does not promote pain, and that the role of GM-CSFr in OA pain is unrelated to local inflammation.

Trial registration

ToetsingOnline.nl NL18274.101.07.
Substance use disorder
Authors: Mackavey Carole , Kearney Kelly
Published: April 2020

Adolescence is a time for experimentation, often leading to impulsive decision-making and risky behavior that can cause harm. Many primary care clinicians lack training in managing positive substance use screens. Screening adolescent patients in primary care can help identify, prevent, and treat substance use disorder.
Safety, Feasibility, and Effectiveness of Weighted Blankets in the Care of Infants With Neonatal Abstinence Syndrome
Authors: Summe Virginia , Baker Rachel B. , Eichel Margaret M.
Published: April 2020

Background:

Nurses are caring for increasing numbers of infants diagnosed with neonatal abstinence syndrome (NAS). The recommended initial line of treatment to alleviate NAS symptoms includes nonpharmacologic interventions; however, there is little rigorous evidence on the effectiveness of nonpharmacologic interventions.

Purpose:

The purpose of this study was to assess the safety, feasibility, and effectiveness of weighted blankets in the care of NAS infants.

Methods:

This pilot study was a crossover randomized nonblinded controlled trial conducted at a level III neonatal intensive care unit. Infants' care included 30-minute sessions utilizing either a nonweighted or weighted blanket, with infants serving as their own controls.

Results:

A total of 16 patients were enrolled for a total of 67 weighted blanket sessions. To address safety, no adverse events were observed, the weighted blankets were never removed due to infant distress, and infants experienced no significant temperature change. To address feasibility, 94% of approached mothers were receptive to the use of weighted blankets and staff reported no obstacles to using the blanket. Finally, to assess effectiveness, there was a significant decrease in the infant's heart rate and Finnegan score when a weighted blanket was used. There was no significant change in respiratory rate with the use of a weighted blanket.

Implications for Practice:

Weighted blankets may be safe, feasible, and effective in decreasing NAS symptoms.

Implications for Research:

Larger studies are needed to thoroughly study the use of weighted blankets in this population and examine additional outcomes, such as need for pharmacologic intervention, length of hospital stay, and cost of hospital stay.
Initial ELSO Guidance Document: ECMO for COVID-19 Patients with Severe Cardiopulmonary Failure
Authors: Bartlett Robert H. , Ogino Mark T. , Brodie Daniel , McMullan David M. , Lorusso Roberto , MacLaren Graeme , Stead Christine M. , Rycus Peter , Fraser John F. , Belohlavek Jan , Salazar Leonardo , Mehta Yatin , Raman Lakshmi , Paden Matthew L.
Published: April 2020

Disclaimer: ECMO has, and will certainly continue, to play a role in the management of COVID-19 patients. It should be emphasized that this initial guidance is based on the current best evidence for ECMO use during this pandemic. Guidance documents addressing additional portions of ECMO care are currently being assembled for rapid publication and distribution to ECMO centers worldwide.
Comprehensive analysis of biomarkers for prostate cancer based on weighted gene co-expression network analysis
Authors: Chen Xuan , Wang Jingyao , Peng Xiqi , Liu Kaihao , Zhang Chunduo , Zeng Xingzhen , Lai Yongqing
Published: April 2020

Background:

Prostate cancer (PCa) is one of the leading causes of cancer-related death. In the present research, we adopted a comprehensive bioinformatics method to identify some biomarkers associated with the tumor progression and prognosis of PCa.

Methods:

Differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were applied for exploring gene modules correlative with tumor progression and prognosis of PCa. Clinically Significant Modules were distinguished, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to Annotation, Visualization and Integrated Discovery (DAVID). Protein–protein interaction (PPI) networks were used in selecting potential hub genes. RNA-Seq data and clinical materials of prostate cancer from The Cancer Genome Atlas (TCGA) database were used for the identification and validation of hub genes. The significance of these genes was confirmed via survival analysis and immunohistochemistry.

Results:

2688 DEGs were filtered. Weighted gene co-expression network was constructed, and DEGs were divided into 6 modules. Two modules were selected as hub modules which were highly associated with the tumor grades. Functional enrichment analysis was performed on genes in hub modules. Thirteen hub genes in these hub modules were identified through PPT networks. Based on TCGA data, 4 of them (CCNB1, TTK, CNN1, and ACTG2) were correlated with prognosis. The protein levels of CCNB1, TTK, and ACTG2 had a degree of differences between tumor tissues and normal tissues.

Conclusion:

Four hub genes were identified as candidate biomarkers and potential therapeutic targets for further studies of exploring molecular mechanisms and individual therapy on PCa.
Pioneering Orientation Using Multiple Teaching Methods and Low-Fidelity Simulation for Unlicensed Care Providers
Authors: Kiker Kelly , Eversman Shari , Kruggel Heather , Volkmann Charlotte
Published: April 2020

Patient care assistants (PCAs) are unlicensed personnel that perform direct patient care. Providing quality orientation is critical in supporting the transition of a PCA from new staff member to competent employee. PCAs have limited to no experience with simulation in prehire training. An 8-hour orientation day, using interactive teaching strategies and simulation, was successfully implemented at a large academic healthcare institution. This article explores the various teaching methods and outcomes of the class.
Exploring the Perceived Self-management Needs of Young Adults With Osteogenesis Imperfecta
Authors: Michalovic Alisha , Anderson Charlotte , Thorstad Kelly , Rauch Frank , Tsimicalis Argerie
Published: April 2020

Purpose

To explore the perceived self-management needs of young adults with osteogenesis imperfecta (OI) with the goal of optimizing the self-management and transitional care services.

Methods

A qualitative descriptive study was performed with young adults diagnosed with OI. Two semistructured interviews were conducted before and after their first appointment with a nurse practitioner in the adult healthcare settings (a new partnership initiated by the pediatric hospital). Data were transcribed and descriptively analyzed.

Results

Seven participants with OI types I, III, and IV were interviewed. Ages ranged from 23 to 34 years, and years since discharge from the pediatric hospital ranged from 3 to 10. Four themes emerged including (1) dropped in the jungle, with no one to call; (2) they do not know how to treat me; (3) I feel like I'm going to get back in the loop; and (4) self-managing what I know, how I know.

Conclusions

Similar to other childhood-onset conditions, adolescents and young adults with OI require education and mentorship, and clinicians in the adult healthcare system need to be prepared and supported to receive them. Collective efforts are needed to improve the self-management and transitional care needs for young adults with OI.
Colorectal Cancer Screening Practices Among Texas Nurse Practitioners and Physician Assistants
Authors: Laird Sandra A. , Raudonis Barbara M.
Published: April 2020

The purpose of this study was two-fold: (1) To describe and compare Texas Nurse Practitioners' and Physician Assistants' knowledge and use of current screening guidelines for individuals at varying risk for colorectal cancer and (2) to compare their recommendations for referral for genetic counseling for persons at increased risk for colorectal or endometrial cancer. The study used a descriptive correlational comparative design. A self-administered web-based survey was sent to the members of the Texas Nurse Practitioner Association and the Texas Academy of Physician Assistants. The questionnaire consisted of 44 items categorized in three domains: demographics, knowledge of national guidelines for risk-stratified colorectal cancer (CRC) screening, and referral for genetic counseling and CRC-screening practices. Data were collected from July through October 2014. More than 75% of the survey respondents reported confidence in their knowledge of the lifetime risk of colorectal cancer and the recommendations for screening in the average-risk adult. Fifty-one percent of both groups reported that they were familiar with Lynch syndrome; however, the nurse practitioners had a lower awareness of the lifetime risk of colorectal cancer associated with Lynch syndrome compared to the physician assistants. Only 34.1% of the nurse practitioners and 23.5% of the physician assistants were aware of the lifetime risk of developing endometrial cancer diagnosed before 60 years of age in women with Lynch syndrome, and only 39.6% of the physician assistants and 40% of the nurse practitioners reported performing a three-generation family history of cancer as a risk assessment. Less than 50% of the respondents would refer a patient with a personal or family history of colorectal or endometrial cancer diagnosed before the age of 60 years for genetic counseling. Nurse practitioners and physician assistants in primary care need more formal and continuing education in risk-stratified screening and referral for genetic counseling in adults at increased risk for colorectal cancer. The academic curricula of both disciplines need to include more content on genetic and genomic influences on the pathophysiology of colorectal cancer and the role of this information for screening and personalized treatment.
Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications
Authors: Wu Fan , Wang Aojie , Liu Mei , Wang Qimin , Chen Jun , Xia Shuai , Ling Yun , Zhang Yuling , Xun Jingna , Lu Lu , Jiang Shibo , Lu Hongzhou , Wen Yumei , Huang Jinghe
Published: April 2020

Background

The COVID-19 pandemic caused by SARS-CoV-2 coronavirus threatens global public health. Currently, neutralizing antibodies (NAbs) versus this virus are expected to correlate with recovery and protection of this disease. However, the characteristics of these antibodies have not been well studied in association with the clinical manifestations in patients.

Methods

Plasma collected from 175 COVID-19 recovered patients with mild symptoms were screened using a safe and sensitive pseudotyped-lentiviral-vector-based neutralization assay. Spike-binding antibody in plasma were determined by ELISA using RBD, S1, and S2 proteins of SARS-CoV-2. The levels and the time course of SARS-CoV-2-specific NAbs and the spike-binding antibodies were monitored at the same time.

Findings

SARS-CoV-2 NAbs were unable to cross-reactive with SARS-CoV virus. SARS-CoV-2-specific NAbs were detected in patients from day 10-15 after the onset of the disease and remained thereafter. The titers of NAb among these patients correlated with the spike-binding antibodies targeting S1, RBD, and S2 regions. The titers of NAbs were variable in different patients. Elderly and middle-age patients had significantly higher plasma NAb titers (P<0.0001) and spike-binding antibodies (P=0.0003) than young patients. Notably, among these patients, there were ten patients whose NAb titers were under the detectable level of our assay (ID50: < 40); while in contrast, two patients, showed very high titers of NAb, with ID50 :15989 and 21567 respectively. The NAb titers were positive correlated with plasma CRP levels but negative correlated with the lymphocyte counts of patients at the time of admission, indicating an association between humoral response and cellular immune response.

Interpretation

The variations of SARS-CoV-2 specific NAbs in recovered COVID-19 patients may raise the concern about the role of NAbs on disease progression. The correlation of NAb titers with age, lymphocyte counts, and blood CRP levels suggested that the interplay between virus and host immune response in coronavirus infections should be further explored for the development of effective vaccine against SARS-CoV-2 virus. Furthermore, titration of NAb is helpful prior to the use of convalescent plasma for prevention or treatment.

Funding

Ministry of Science and Technology of China, National Natural Science Foundation of China, Shanghai Municipal Health Commission, and Chinese Academy of Medical Sciences
Leveraging mRNAs sequences to express SARS-CoV-2 antigens in vivo
Authors: Zeng Chunxi , Hou Xucheng , Yan Jingyue , Zhang Chengxiang , Li Wenqing , Zhao Weiyu , Du Shi , Dong Yizhou
Published: April 2020

SARS-CoV-2 has rapidly become a pandemic worldwide; therefore, an effective vaccine is urgently needed. Recently, messenger RNAs (mRNAs) have emerged as a promising platform for vaccination. Here, we systematically investigated the untranslated regions (UTRs) of mRNAs in order to enhance protein production. Through a comprehensive analysis of endogenous gene expression and de novo design of UTRs, we identified the optimal combination of 5’ and 3’ UTR, termed as NASAR, which was five to ten-fold more efficient than the tested endogenous UTRs. More importantly, NASAR mRNAs delivered by lipid-derived nanoparticles showed dramatic expression of potential SARS-CoV-2 antigens both in vitro and in vivo. These NASAR mRNAs merit further development as alternative SARS-CoV-2 vaccines.
Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics
Authors: Waghmare Alpana , Krantz Elizabeth M. , Baral Subhasish , Vasquez Emma , Loeffelholz Tillie , Chung E. Lisa , Pandey Urvashi , Kuypers Jane , Duke Elizabeth R , Jerome Keith R. , Greninger Alexander L. , Reeves Daniel B. , Hladik Florian , Cardozo-Ojeda E. Fabian , Boeckh Michael , Schiffer Joshua T.
Published: April 2020

The SARS-CoV-2 pandemic demonstrates the need for accurate and convenient approaches to diagnose and therapeutically monitor respiratory viral infections. We demonstrated that self-sampling with foam swabs is well-tolerated and provides quantitative viral output concordant with flocked swabs. Using longitudinal home-based self-sampling, we demonstrate nasal cytokine levels correlate and cluster according to immune cell of origin. Periods of stable viral loads are followed by rapid elimination, which could be coupled with cytokine expansion and contraction using mathematical models. Nasal foam swab self-sampling at home provides a precise, mechanistic readout of respiratory virus shedding and local immune responses.
Design and performance analysis of novel multiphase induction motor with die-cast copper rotors using FEA for electric propulsion vehicles applications
Authors: Kaliyavarathan Sathishkumar , T.S. Sivakumaran
Published: April 2020

Purpose

The purpose of this paper is to study the development of novel multiphase induction motor (MPIM) with copper die cast rotor in the drive system of electric propulsion vehicles (EPV). It is estimated that the manufacturers are concerned about high torque,Efficiency, motor life, energy conservation and high thermal tolerance. To ensure maximum torque and efficiency with multiphase winding and copper die cast technology to increasing high thermal tolerance, life, energy conversations. On other hand, it is very important of EPV application.

Design/methodology/approach

The focus of the investigation is threefold: the modified method carried out on MPIM both stator and rotor can overcome the current scenario problem facing by electric vehicles manufacture and developed perfect suitable electric motor for EPV applications. The design and simulation carried out finite element method (FEM) that was more accurate calculations. Finally developed prototype model of MPIM with copper die cast are discussed with conventional three phase Die casting Induction motor.

Findings

The paper confirmed the multiphase copper die-cast rotor induction motor (MDCrIM) is providing better performance than conventional motor. Proposed motor can bring additional advantage like heat tolerances, long life and energy conversations.

Originality/value

The experiments confirmed the MDCIM suitable for EPV Applications. The modified MDCIM of both stator and rotor are giving better result and good performance compared to conventional method.
Checks and balances? Leadership configurations and governance practices of NGOs in Chile
Authors: Diaz Daniel A. , Rees Christopher J.
Published: April 2020

Purpose

The emergence of Governance practices in the non-governmental organisation (NGO) sector has become associated with increasingly high levels of organisational complexity. In the light of an expanding civil society sector in Chile and the emergence of formalised governance practices, this paper explores the construction of the Executive Director role in Chilean NGOs with reference to organisational functions, organisational dynamics, and external influences.

Design/methodology/approach

Grounded theory is used to explore qualitative data derived from a set of N = 39 interviews conducted in Chile These interviews involve NGO founders, funders, Executive Directors, scholars, consultants, and team members.

Findings

The findings reveal the pivotal role played by Executive Directors in conducting organisational activities which, in other types of organisations, are often distributed across various organisational functions. The data also highlight complex dynamics involving overt compliance with external regulatory requirements, uncertainties about financial sustainability, the recruitment of Executive Board members, the exercise of power by Executive Directors, and the influence of founders in leadership configurations.

Research limitations/implications

The implications of the study are discussed in relation to the governance and accountability of NGOs, the nature of the Executive Director role, the purpose of Executive Boards in the NGO sector, and the recruitment and training of Board members. It is noted that the study was conducted in the NGO sector in Chile; further research is necessary to establish the generalisability of the findings to other contexts.

Originality/value

This paper addresses the shortage of organisational research on NGOs. It contributes by offering analytical perspectives on organisational processes of Leadership and Governance. This paper highlights the relationship between, and interdependency of, those processes.
Opportunistic bacteria use quorum sensing to disturb coral symbiotic communities and mediate the occurrence of coral bleaching
Authors: Zhou Jin , Lin Zi‐Jun , Cai Zhong‐Hua , Zeng Yan‐Hua , Zhu Jian‐Ming , Du Xiao‐Peng
Published: April 2020

Coral associated microorganisms, especially some opportunistic pathogens can utilize quorum‐sensing (QS) signals to affect population structure and host health. However, direct evidence about the link between coral bleaching and dysbiotic microbiomes under QS regulation was lacking. Here, using 11 opportunistic bacteria and their QS products (AHLs, acyl‐homoserine‐lactones), we exposed Pocillopora damicornis to three different treatments: test groups (A and B: mixture of AHLs‐producing bacteria and cocktail of AHLs signals respectively); control groups (C and D: group A and B with furanone added respectively); and a blank control (group E: only seawater) for 21 days. The results showed that remarkable bleaching phenomenon was observed in groups A and B. The operational taxonomic units‐sequencing analysis shown that the bacterial network interactions and communities composition were significantly changed, becoming especially enhanced in the relative abundances of Vibrio, Edwardsiella, Enterobacter, Pseudomonas, and Aeromonas. Interestingly, the control groups (C and D) were found to have a limited influence upon host microbial composition and reduced bleaching susceptibility of P. damicornis. These results indicate bleaching's initiation and progression may be caused by opportunistic bacteria of resident microbes in a process under regulation by AHLs. These findings add a new dimension to our understanding of the complexity of bleaching mechanisms from a chemoecological perspective.
Shaping ability of XP‐endo Shaper and ProTaper Next in long oval‐shaped canals: a micro‐computed tomography study
Authors: Velozo C. , Silva S. , Almeida A. , Romeiro K. , Vieira B. , Dantas H. , Sousa F. , De Albuquerque D. S.
Published: April 2020

Aim

To evaluate the shaping ability of the single‐file XP‐endo Shaper system (XP‐S; FKG Dentaire, La Chaux‐de‐Fonds, Switzerland) employing a different working time and of the multiple‐file ProTaper Next system (Dentsply Sirona, Ballaigues, Switzerland) using micro‐computed tomography (micro‐CT) technology.

Methodology

Twenty long oval‐shaped canals in mandibular incisors were matched anatomically and scanned by micro‐CT (Skyscan 1172; Bruker micro‐CT, Kontich, Belgium). The canals were divided into two groups (n = 10) according to the canal preparation protocol: XP‐endo Shaper (XP‐S) with an extra 45 s of instrumentation and ProTaper Next (PTN X4). The images recorded before and after preparation were evaluated for morphometric measures of volume, surface area, structure model index and untouched walls. The data were compared statistically (Student's t‐test for homogenous variances and Mann–Whitney test) between the two groups (XP‐S and PTN X4) at α = 5%.

Results

Root canal preparation significantly increased all parameters (volume, surface area, structure model index and untouched walls) tested in each group (P < 0.05). There was no significant difference (P > 0.05) in the percentage increase of volume (107.50%–93.13%), surface area (27.74%–29.68%) or untouched canal wall (13.08%–11.74%) between XP‐S and PTN X4, respectively.

Conclusions

The XP‐endo Shaper system (single‐file) with an extra 45 s of instrumentation and the ProTaper Next system (multiple files) had a similar root canal shaping ability. Neither technique was able to fully prepare the long oval‐shaped canals of mandibular incisors.