bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between renin–angiotensin system inhibitors and COVID-19 complications
Authors: Liabeuf Sophie , Moragny Julien , Bennis Youssef , Batteux Benjamin , Brochot Etienne , Schmit Jean Luc , Lanoix Jean-Philippe , Andrejak Claire , Ganry Olivier , Slama Michel , Maizel Julien , Mahjoub Yazine , Masmoudi Kamel , Gras-Champel Valérie 
Published: May 2020

Abstract

Aims
To describe the characteristics of patients hospitalized with COVID-19 (including their long-term at-home medication use), and compare them with regard to the course of the disease. To assess the association between renin–angiotensin system inhibitors (RASIs) and disease progression and critical outcomes.

Methods and results
All consecutive hospitalized patients with laboratory-confirmed COVID-19 in a university hospital in Amiens (France) were included in this study. The primary composite endpoint was admission to an intensive care unit (ICU) or death before ICU admission. Univariable and multivariable logistic regression models were used to identify factors associated with the composite endpoint. Between 28 February 2020 and 30 March 2020, a total of 499 local patients tested positive for SARS-CoV-2. Of these, 231 were not hospitalized {males 33%; median [interquartile range (IQR)] age: 44 (32–54)}, and 268 were hospitalized [males 58%; median (IQR) age: 73 (61–84)]. A total of 116 patients met the primary endpoint: 47 died before ICU admission, and 69 were admitted to the ICU. Patients meeting the primary endpoint were more likely than patients not meeting the primary endpoint to have coronary heart disease and to have been taking RASIs; however, the two subsets of patients did not differ with regard to median age. After adjustment for other associated variables, the risk of meeting the composite endpoint was 1.73 times higher (odds ratio 1.73, 95% confidence interval 1.02–2.93) in patients treated at baseline with a RASI than in patients not treated with this drug class. This association was confirmed when the analysis was restricted to patients treated with antihypertensive agents.

Conclusions
We highlighted a potential safety signal for RASIs, the long-term use of which was independently associated with a higher risk of severe COVID-19 and a poor outcome. Due to the widespread use of this important drug class, formal proof based on clinical trials is needed to better understand the association between RASIs and complications of COVID-19.
Nursing Home Culture Change Practices and Survey Deficiencies: A National Longitudinal Panel Study
Authors: Lepore Michael J , Lima Julie C , Miller Susan C 
Published: May 2020

Abstract

Background and Objectives
Nursing home (NH) adoption of culture change practices has substantially increased in recent decades. We examined how increasing adoption of culture change practices affected the prevalence of health, severe health, and quality of life (QoL) deficiencies.

Research Design and Methods
Novel data on culture change practice adoption from a nationally representative NH panel (N = 1,585) surveyed in 2009/2010 and 2016/2017 were used to calculate change in practice adoption scores in 3 culture change domains (resident-centered care, staff empowerment, physical environment). These data were linked to data on health, severe health, and QoL deficiencies and facility-level covariates. Multinomial logistic regression models, with survey weights and inverse probability of treatment weighting, examined how increased culture change practice adoption related to change in deficiencies.

Results
We generally observed less increase in deficiencies when culture change practices increased. However, after weighting and controlling for baseline deficiencies and culture change scores, we found few statistically significant effects. Still, results show increased physical environment practices resulted in a higher likelihood of decreases or no change (vs increases) in QoL deficiencies; increased resident-centered care practices resulted in decreases or no change (vs increases) in health deficiencies; and increased staff empowerment practices resulted in a higher likelihood of no change (vs increases) in severe health deficiencies.

Discussion and Implications
This study provides some evidence that culture change practices can help reduce the risk of increasing some types of deficiencies, but the impact of increases in each culture change domain related differently to different types of deficiencies.
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
Authors: Krasheninnikova Ksenia , Diekhans Mark , Armstrong Joel , Dievskii Aleksei , Paten Benedict , O'Brien Stephen 
Published: May 2020

Abstract

Background
Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.

Findings
halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred–way, reference-free vertebrate alignments built with the Cactus system.

Conclusions
halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
Withering of tea leaves using heat pipe heat exchanger by utilizing low-temperature geothermal energy
Authors: Gunawan Yohanes , Putra Nandy , Hakim Imansyah Ibnu , Agustina Dinni , Mahlia Teuku Meurah Indra 
Published: May 2020

Abstract
The volume of Indonesian tea exports to the European Union (EU) decreased by 43% in 2014 because of the EU setting a maximum residue limit of anthraquinone (AQ) for tea as 0.02 mg/kg. The content of AQ in tea leaves increases when there is incomplete combustion in the combustion of firewood for the energy source of withering and drying of tea leaves. This study aims to develop and test a new concept for the direct use of low-temperature geothermal energy with a heat pipe heat exchanger (HPHE) for the withering of tea leaves as a solution for energy sources free from AQ. The geothermal fluid simulators use water, which is heated by heater and flowed by a pump. The HPHE used consists of 42 heat pipes and 181 fins. The heat pipe used has a length of 700 mm with an outer diameter of 10 mm. Each fin is made of aluminum with a thickness of 0.105 mm and a size of 76 × 345 mm2. The results show that the effectiveness of the HPHE varies from 66% to 79.59%. For 100 g of fresh tea leaves, the heating energy produced ranges from 15.21 W to 45.07 W, meaning it can wither tea leaves from 80% (w.b.) to 54% (w.b.) in a variety of 11 h 56 min to only 49.6 min. The Page mathematical model is the best model to represent the behavior of the tea leaves with this HPHE system.
Ceftriaxone treatment of spondylodiscitis and other serious infections with Cutibacterium acnes
Authors: Tiltnes Theo S , Kehrer Michala , Hughes Harriet , Morris Trefor E , Justesen Ulrik S 
Published: May 2020

Abstract

Objectives
To establish testing and treatment recommendations for a ceftriaxone once-daily dose regimen for systemic infections with Cutibacterium acnes.

Methods
A review of the literature and a retrospective evaluation of patients diagnosed with C. acnes spondylodiscitis and treated with ceftriaxone were performed. Ceftriaxone and penicillin MICs were determined for C. acnes isolates from blood and biopsies and the epidemiological cut-off (ECOFF) was determined with surveillance data from the UK Anaerobe Reference Laboratory in Cardiff.

Results
Limited clinical data exist from endocarditis and prosthetic joint infections using treatment with ceftriaxone 2 g once daily for C. acnes with ceftriaxone MICs ≤0.5 mg/L. In this case study, five patients were successfully treated with ceftriaxone as part of the treatment for spondylodiscitis with C. acnes. Ceftriaxone and penicillin MICs of the C. acnes isolates from the patients were 0.016–0.125 mg/L and 0.012–0.032 mg/L, respectively. The ceftriaxone ECOFF was 0.5 mg/L and the penicillin ECOFF was 0.25 mg/L based on available surveillance data.

Conclusions
From the data presented in this study it would be acceptable to consider treatment with a once-daily dose of ceftriaxone 2 g for systemic infections, including endocarditis, spondylodiscitis and prosthetic joint infections with C. acnes using a clinical breakpoint of ≤0.5 mg/L (the ECOFF). However, clinical data are still limited and the response of patients treated with ceftriaxone for serious infections with C. acnes should be monitored closely.
Pharmacokinetics of lopinavir/ritonavir oral solution to treat COVID-19 in mechanically ventilated ICU patients
Authors: Lê Minh Patrick , Jaquet Pierre , Patrier Juliette , Wicky Paul-Henri , Le Hingrat Quentin , Veyrier Marc , Kauv Juliette , Sonneville Romain , Visseaux Benoit , Laouénan Cédric , Bouadma Lila , Descamps Diane , de Montmollin Etienne , Peytavin Gilles , Timsit Jean-François 
Published: May 2020

Abstract

Background
The combination lopinavir/ritonavir is recommended to treat HIV-infected patients at the dose regimen of 400/100 mg q12h, oral route. The usual lopinavir trough plasma concentrations are 3000–8000 ng/mL. A trend towards a 28 day mortality reduction was observed in COVID-19-infected patients treated with lopinavir/ritonavir.

Objectives
To assess the plasma concentrations of lopinavir and ritonavir in patients with severe COVID-19 infection and receiving lopinavir/ritonavir.

Patients and methods
Mechanically ventilated patients with COVID-19 infection included in the French COVID-19 cohort and treated with lopinavir/ritonavir were included. Lopinavir/ritonavir combination was administered using the usual adult HIV dose regimen (400/100 mg q12h, oral solution through a nasogastric tube). A half-dose reduction to 400/100 mg q24h was proposed if lopinavir Ctrough was &gt;8000 ng/mL, the upper limit considered as toxic and reported in HIV-infected patients. Lopinavir and ritonavir pharmacokinetic parameters were determined after an intensive pharmacokinetic analysis. Biological markers of inflammation and liver/kidney function were monitored.

Results
Plasma concentrations of lopinavir and ritonavir were first assessed in eight patients treated with lopinavir/ritonavir. Median (IQR) lopinavir Ctrough reached 27 908 ng/mL (15 928–32 627). After the dose reduction to 400/100 mg q24h, lopinavir/ritonavir pharmacokinetic parameters were assessed in nine patients. Lopinavir Ctrough decreased to 22 974 ng/mL (21 394–32 735).

Conclusions
In mechanically ventilated patients with severe COVID-19 infections, the oral administration of lopinavir/ritonavir elicited plasma exposure of lopinavir more than 6-fold the upper usual expected range. However, it remains difficult to safely recommend its dose reduction without compromising the benefit of the antiviral strategy, and careful pharmacokinetic and toxicity monitoring are needed.
Evaluating patient attitudes to increased patient engagement with antimicrobial stewardship: a quantitative survey
Authors: Hughes Gerry , O’Toole Eilis , Talento Alida Fe , O’Leary Aisling , Bergin Colm 
Published: May 2020

Abstract

Background
Antimicrobial stewardship (AMS) describes interventions designed to optimize antimicrobial therapy, minimize adverse treatment consequences and reduce the spread of antimicrobial resistance (AMR). Previous research has investigated the patient’s role in healthcare infection prevention but the patient’s role in AMS has not been extensively explored.

Objectives
To investigate the willingness of hospital inpatients to question staff about prudent antimicrobial use in an Irish hospital and evaluate the impact of patient and public involvement in research (PPI) on this study.

Methods
A survey was co-designed with the hospital Patient Representative Group (PRG) to evaluate patient willingness to engage with prudent antimicrobial treatment. A random sample of 200 inpatients was selected to self-complete the survey using pen and paper. PRG members provided feedback on their involvement.

Results
Of the 200 inpatients randomly selected to participate, 120 did not fulfil the inclusion criteria. Of the remaining 80, 67 participated (response 84%). Median respondent age was 58 years, 30% were employed and 30% had a third-level education degree. Over 90% had not heard of AMS while just over 50% had not heard of AMR. Patients preferred asking factual questions rather than challenging ones but did not have a preference in asking questions of doctors compared with nurses. Older patients were less likely to ask questions. PRG members reported an overall positive experience as research collaborators.

Conclusions
Future patient-centred AMS interventions should empower patients to ask about antimicrobial treatment, in particular the older patient cohort. PPI is a valuable component of patient-centred research.
Predicting complications of diabetes mellitus using advanced machine learning algorithms
Authors: Ljubic Branimir , Hai Ameen Abdel , Stanojevic Marija , Diaz Wilson , Polimac Daniel , Pavlovski Martin , Obradovic Zoran 
Published: May 2020

AbstractObjectiveWe sought to predict if patients with type 2 diabetes mellitus (DM2) would develop 10 selected complications. Accurate prediction of complications could help with more targeted measures that would prevent or slow down their development.Materials and MethodsExperiments were conducted on the Healthcare Cost and Utilization Project State Inpatient Databases of California for the period of 2003 to 2011. Recurrent neural network (RNN) long short-term memory (LSTM) and RNN gated recurrent unit (GRU) deep learning methods were designed and compared with random forest and multilayer perceptron traditional models. Prediction accuracy of selected complications were compared on 3 settings corresponding to minimum number of hospitalizations between diabetes diagnosis and the diagnosis of complications.ResultsThe diagnosis domain was used for experiments. The best results were achieved with RNN GRU model, followed by RNN LSTM model. The prediction accuracy achieved with RNN GRU model was between 73% (myocardial infarction) and 83% (chronic ischemic heart disease), while accuracy of traditional models was between 66% – 76%.DiscussionThe number of hospitalizations was an important factor for the prediction accuracy. Experiments with 4 hospitalizations achieved significantly better accuracy than with 2 hospitalizations. To achieve improved accuracy deep learning models required training on at least 1000 patients and accuracy significantly dropped if training datasets contained 500 patients. The prediction accuracy of complications decreases over time period. Considering individual complications, the best accuracy was achieved on depressive disorder and chronic ischemic heart disease.ConclusionsThe RNN GRU model was the best choice for electronic medical record type of data, based on the achieved results.
Two Multivariate Calibration Models for Assay of Niacin in Complex Mixtures with Its Official Impurities: A Pharmaceutical Application
Authors: Naguib Ibrahim A , Abdallah Fatma F 
Published: May 2020

Abstract

Background
Niacin (NIA) is a water-soluble vitamin and the primary treatment of pellagra. No analytical method was found to assess NIA in complex mixtures with its official impurities.

Objective
Two validated, accurate, and selective chemometric models were developed to assay NIA in the presence of its four official impurities, including pyridine, a nephrotoxic and hepatotoxic substance. Additionally, the two selective chemometric models were compared by processing UV spectra in the range 220–305 nm and applying partial least squares regression (PLSR) and support vector regression (SVR) models.

Method
A five levels five factors experimental design was chosen to exhibit a training set of 25 mixtures that had numerous variable percentages of tested substances. A test set consisting of 10 mixtures was designed to confirm the predictive power of the suggested models.

Results
The presented results substantiate the strength of the developed multivariate calibration models to assay NIA specifically with high selectivity and accuracy (100.02 ± 1.312 and 100.04 ± 1.272 for PLSR and SVR models, respectively). The root mean square error of prediction for the validation set mixtures was applied as a main comparison tool and it was found to be 0.2016 and 0.1890 for PLSR and SVR models, respectively.

Conclusions
The results of the developed models and the reported HPLC method were statistically compared, where F-values and Student's t-tests did not show significant difference in regards to accuracy and precision. The SVR model proved to be more accurate than the PLSR model, producing a high generalization capacity, while PLSR was easy to implement and fast.

Highlights
Serena Partridge’s ‘Accessories’: Fabricating Uncertainty in the Brontë Parsonage Museum
Authors: Pouliot Amber 
Published: May 2020

Abstract
The 1861 sale of the Brontës’ personal effects sent relic hunters scrambling to collect the material remains of the famous family. In the second half of the nineteenth century, the collection, preservation, and veneration of relics, particularly those associated with a writer’s private, domestic life, were important aspects of literary celebrity culture and commemoration, and both the Brontë Society and the original Brontë Museum were established to collect material remains. Yet when Virginia Woolf visited the museum in 1904, she viewed Charlotte Brontë’s clothing, shoes, and accessories with considerable unease. Anticipating the concerns of the literary establishment, Woolf feared that access to Brontë’s material remains would encourage the domestic cult which had formed around her following the publication of Elizabeth Gaskell’s The Life of Charlotte Brontë (1857). She feared it would diminish the importance of Brontë’s writing by privileging a narrative of domestic rather than literary labour. This essay considers the creative-critical intervention of Serena Partridge’s ‘Accessories’ (2016), a collection of newly created pseudo-relics of Charlotte Brontë, framed by semi-fictional narratives that dramatize the construction, use, and significance of her personal possessions. I argue that ‘Accessories’ and biographical fiction are analogous modes of engaging with Brontë’s legacy. They respond to the anxieties articulated by Woolf through the fabrication – both literal and literary – of new pseudo-relics that (rather than emphasizing Brontë’s perceived conventional, domestic femininity) enable multiple interpretive possibilities while simultaneously acknowledging the contingent nature of our understanding of her experience.
WARPFIELD-EMP: The self-consistent prediction of emission lines from evolving H ii regions in dense molecular clouds
Authors: Pellegrini E W , Rahner D , Reissl S , Glover S C O , Klessen R S , Rousseau-Nepton L , Herrera-Camus R 
Published: May 2020

ABSTRACT
We present the warpfield emission predictor, warpfield-emp, which couples the 1D stellar feedback code warpfield with the cloudy H iiregion/PDR code and the polaris radiative transfer code, in order to make detailed predictions for the time-dependent line and continuum emission arising from the H ii region and PDR surrounding an evolving star cluster. warpfield-emp accounts for a wide range of physical processes (photoionization, stellar winds, supernovae, radiation pressure, gravity, thermal conduction, radiative cooling, dust extinction etc.) and yet runs quickly enough to allow us to explore broad ranges of different model parameters. We compare the results of an extensive set of models with SITELLE observations of a large sample of H ii regions in NGC 628 and find very good agreement, particularly for the highest signal-to-noise observations. We show that our approach of modelling individual clouds from first principles (instead of in terms of dimensionless quantities such as the ionization parameter) allows us to avoid long-standing degeneracies in the interpretation of H ii region diagnostics and enables us to relate these diagnostics to important physical parameters such as cloud mass or cluster age. Finally, we explore the implications of our models regarding the reliability of simple metallicity diagnostics, the properties of long-lived embedded clusters, and the role played by winds and supernovae in regulating H ii region and PDR line emission.
mCSM-membrane: predicting the effects of mutations on transmembrane proteins
Authors: Pires Douglas E V , Rodrigues Carlos H M , Ascher David B 
Published: May 2020

AbstractSignificant efforts have been invested into understanding and predicting the molecular consequences of mutations in protein coding regions, however nearly all approaches have been developed using globular, soluble proteins. These methods have been shown to poorly translate to studying the effects of mutations in membrane proteins. To fill this gap, here we report, mCSM-membrane, a user-friendly web server that can be used to analyse the impacts of mutations on membrane protein stability and the likelihood of them being disease associated. mCSM-membrane derives from our well-established mutation modelling approach that uses graph-based signatures to model protein geometry and physicochemical properties for supervised learning. Our stability predictor achieved correlations of up to 0.72 and 0.67 (on cross validation and blind tests, respectively), while our pathogenicity predictor achieved a Matthew's Correlation Coefficient (MCC) of up to 0.77 and 0.73, outperforming previously described methods in both predicting changes in stability and in identifying pathogenic variants. mCSM-membrane will be an invaluable and dedicated resource for investigating the effects of single-point mutations on membrane proteins through a freely available, user friendly web server at http://biosig.unimelb.edu.au/mcsm_membrane.