bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling COVID-19 evolution in Italy with an augmented SIRD model using open data
Authors: Nardelli Vincenzo , Arbia Giuseppe , Palladino Andrea , Atzeni Luigi Giuseppe 
Published: April 2021

AbstractWe propose an augmented version of the traditional SIRD epidemic model and we estimate its parameters using the SaRs-Cov-2 Italian open-data. The model’s parameters are estimated partly using numerical optimization and partly with ABC. Our estimation procedure provides a good fit to real data.
FOCUSED REVIEW ON NUTRITIONAL STATUS OF PATIENTS WITH IMMUNOGLOBULIN LIGHT CHAIN AMYLOIDOSIS
Authors: Grigoletti Shana Souza , Zuchinali Priccila , Lemieux-Blanchard Émilie , Béchard Stéphanie , Lemieux Bernard , Bretanha Ribeiro Paula Aver , Tournoux François 
Published: April 2021

ABSTRACTBackgroundImmunoglobulin light chain (AL) amyloidosis is a complex disease marked by a poor clinical portrait and prognosis generally leading to organ dysfunction and shortened survival. We aimed to review the available evidence on whether AL amyloidosis can lead to malnutrition, thus having a negative impact on quality of life (QoL) and survival.MaterialsWe searched Pubmed with no restrictions to the year of publication or language. Retrospective or prospective, observational, and interventional studies that reported data regarding AL amyloidosis and nutritional status were included.ResultsFrom 62 articles retrieved, 23 were included. Malnutrition was prevalent in up to 65% of patients with AL Amyloidosis. Prevalence of weight loss of 10% or more ranged from 6 to 22% of patients, while a body mass index of < 22 kg/m2 was found in 22 to 42%. Weight loss, lower BMI and other indicators of poor nutritional status were negatively associated with quality of life and survival. Only one RCT focused on nutritional counseling was found and reported positive results on patients QoL and survival.ConclusionDespite inconsistencies across assessment criteria, the available data reveal that weight loss and malnutrition are common features in patients with AL amyloidosis. This review reinforces the premise that an impaired nutritional status can be negatively associated with QoL and survival in patients with AL amyloidosis, and therefore should be further investigated.
Ascorbic acid attenuates activation and cytokine production in sepsis-like monocytes
Authors: Schmidt Tobias , Kahn Robin , Kahn Fredrik 
Published: April 2021

AbstractSepsis manifests due to the host’s dysregulated immune response to an infection. High dose ascorbic acid (AA) has emerged as a potential treatment of sepsis, yet little is known regarding how ascorbic acid influences the immune system in sepsis, such as monocytes. The objective of this study is to investigate the effects of high dose AA on monocyte polarization and cytokine production in vitro.Monocytes were isolated from healthy donors (n=6) and polarized in vitro for 48hrs using lipopolysaccharide (LPS) and lipoteichoic acid (LTA). Polarization was confirmed by surface marker expression using flow cytometry. In parallel, monocytes from septic patients (n=3) were analyzed for polarization markers as a comparison to the in vitro polarization. The effect of AA on monocyte polarization was evaluated. Finally, monocytes were analyzed for cytokine production of TNF and IL-8 by intracellular staining.Both LPS and LTA induced polarization in healthy monocytes in vitro, with increased expression of both pro- (CD40 and PDL1, p<0.05) and anti-inflammatory (CD16 and CD163, p<0.05) polarization markers. This pattern resembled that of monocytes from septic patients. Treatment with AA significantly inhibited surface expression of CD16 and CD163 (p<0.05) in a dose dependent manner. Finally, AA attenuated LPS or LTA-induced cytokine production of IL-8 and TNF (both p<0.05) in a dose-dependent manner.Thus, AA attenuates cytokine production and upregulation of anti-, but not pro-inflammatory related markers in LPS or LTA polarized monocytes. This study provides important insight into the effects of high dose AA on monocytes, and potential implications in sepsis.Summary sentenceAscorbic acid inhibits production of IL-8, TNF, and upregulation of the polarization markers CD16 and CD163 in LPS or LTA polarized monocytes in vitro.
Knowledge and attitude of Iranian university students toward genital warts
Authors: Aryanian Zeinab , Mohammadi Maedeh , Babazadeh Arefeh , Etesami Ifa , Hatami Parvaneh , Barary Mohammad , Ebrahimpour Soheil , Sabbagh Parisa , Goodarzi Azadeh 
Published: April 2021

AbstractHuman papillomavirus (HPV) is one of the well-known causes of cervical cancer and one of the most prevalent sexually transmitted diseases (STDs). Since cervical cancer is one of the most common causes of morbidity and mortality in women, this study was performed to investigate students’ knowledge and attitudes in Babol University of Medical Sciences, Northern Iran, towards genital warts. This cross-sectional study assessed the perception and attitudes of 385 students at Babol University of Medical Sciences using a preconceived questionnaire. The data collection tool used in this study was a questionnaire that was confirmed to be valid and reliable. The participants’ mean age was 23.70 ± 3.27 years, with a range of 20-50 years. Evaluation of these students’ level of general information about HPV showed that 7 (1.8%) students had inadequate general information, 34 (8.8%) had moderate knowledge, and 344 (89.4%) had good general knowledge in this setting. There was also a significant association between students’ general knowledge of HPV and their field of study. Based on the present study results, the knowledge of the majority of Babol University of Medical Sciences students about genital warts was in a good range, and their knowledge about HPV routes of transmission was of moderate level. Moreover, the majority had an appropriate attitude to interact with people infected with HPV.
Incidences of poor-quality pharmaceutical products in Nepal
Authors: Neupane Astha , Bastakoti Maheshwor , Tamang Sabita , Giri Basant 
Published: April 2021

ABSTRACTPharmaceutical products are used to treat, prevent, and save lives of millions of people globally. However, pharmaceutical products known as substandard and falsified that do not meet regulatory standards and quality threaten the health of the population of today and future leading to socio-economic hardship, drug resistances and put life of patients in danger. We analyzed the recall notice from 2010 to 2020 issued by the department of drug administration (DDA), government of Nepal to understand the overview of substandard and falsified pharmaceutical products in Nepal. The number of recalled pharmaceutical products has significantly increased over the past decade in Nepal (p-value< 0.05). The most recalled drugs were antimicrobials followed by gastrointestinal medicines, vitamins and supplements, pain and palliative medicines among others. Number of recalled drugs manufactured by domestic pharmaceutical producers and imported ones were not significantly different. Majority of imported recalled drugs originated from India. Sixty-two percentage of recalled drugs were substandard, 11% were falsified and remaining 27% were not registered at the DDA. Similarly, sixty percentage of recalled drugs were modern and 35% were traditional ones. The hand sanitizers used to minimize the COVID-19 transmission contributed significantly to the list of recalled pharmaceutical products in 2020. Most of these sanitizers contained significant amount of methanol instead of ethyl alcohol or isopropyl alcohol. We also reviewed peer-reviewed research papers that reported data of substandard and falsified drugs. Only four such papers were found in literature. These papers reported issues with labeling, unregistered drugs and drugs failed in a number of laboratory testing. Since the recall data did not include number of samples tested and location of sample collected, a systematic study to understand the prevalence of substandard and falsified drugs in Nepal is recommended.Key questionsWhat is already known?Prevalence of substandard and falsified pharmaceutical products is a global threat to public health and socio-economy.What are the new findings?We analyzed drug recall data from department of drug administration in Nepal and report that the substandard and falsified pharmaceutical products are increasing significantly.Antimicrobial drugs were the most frequently recalled drugs. Drugs manufactured by domestic producers and imported ones were equally recalled. Allopathic drugs were recalled more than ayurvedic products.What do the new findings imply?This study suggested the problem of substandard and falsified pharmaceutical products is serious in Nepal. Integrated efforts from regulating agencies, manufacturers and pharmacies are recommended to minimize the circulation of such products in the country.
Aerosol and droplet generation in upper and lower gastrointestinal endoscopy: whole procedure and event-based analysis
Authors: Phillips Frank , Crowley Jane , Warburton Samantha , Gordon George S.D. , Parra-Blanco Adolfo 
Published: April 2021

ABSTRACTBackground and AimsAerosol generating procedures have become an important healthcare issue due to the COVID-19 pandemic, as the SARS-CoV-2 virus can be transmitted via aerosols. We aimed to characterise aerosol and droplet generation in gastrointestinal endoscopy, where there is little evidence.MethodsThis prospective observational study included patients undergoing routine per-oral gastroscopy (POG, n=36), trans-nasal endoscopy (TNE, n=11) and lower gastrointestinal (LGI) endoscopy (n=48). Particle counters took measurements near the appropriate orifice (two models used, diameter ranges 0.3μm-25μm and 20μm-3000μm). Quantitative analysis was performed by recording specific events and subtracting the background particles.ResultsPOG produced 1.96x the level of background particles (p<0.001) and TNE produced 2.00x (p<0.001) but a direct comparison shows POG produces 2.00x more particles than TNE. LGI procedures produce significant particle counts (p<0.001) with 2.4x greater production per procedure than POG but only 0.63x production per minute. Events significant relative to the room background particle count were: POG-throat spray (150.0x, p<0.001), oesophageal extubation (37.5x, p<0.001), coughing/gagging (25.8x, p<0.01); TNE-nasal spray (40.1x, p<0.001), nasal extubation (32.0x, p<0.01), coughing/gagging (20.0, p<0.01); LGI-rectal intubation (9.9x, p<0.05), rectal extubation (27.2x, p <0.01), application of abdominal pressure (9.6x, p <0.05), rectal insufflation/retroflexion (7.7x, p <0.01). These all produced particle counts larger than or comparable to volitional cough.ConclusionGastrointestinal endoscopy performed via the mouth, nose or rectum all generates significant quantities of aerosols and droplets. As the infectivity of procedures is not established, we therefore suggest adequate PPE is used for all GI endoscopy where there is a high population prevalence of COVID-19. Avoiding throat and nasal spray would significantly reduce particles generated from UGI procedures.
Coupling machine learning and high throughput multiplex digital PCR enables accurate detection of carbapenem-resistant genes in clinical isolates
Authors: Miglietta Luca , Moniri Ahmad , Pennisi Ivana , Malpartida-Cardenas Kenny , Abbas Hala , Hill-Cawthorne Kerri , Bolt Frances , Jauneikaite Elita , Davies Frances , Holmes Alison , Georgiou Pantelis , Rodriguez-Manzano Jesus 
Published: April 2021

AbstractRapid and accurate identification of patients colonised with carbapenemase-producing organisms (CPOs) is essential to adopt prompt prevention measures to reduce the risk of transmission. Recent studies have demonstrated the ability to combine machine learning (ML) algorithms with real-time digital PCR (dPCR) instruments to increase classification accuracy of multiplex PCR assays when using synthetic DNA templates. We sought to determine if this novel methodology could be applied to improve identification of the five major carbapenem-resistant genes in clinical CPO-isolates, which would represent a leap forward in the use of PCR-based data-driven diagnostics for clinical applications.We collected 253 clinical isolates (including 221 CPO-positive samples) and developed a novel 5-plex PCR assay for detection of blaIMP, blaKPC, blaNDM, blaOXA-48 and blaVIM. Combining the recently reported ML method ‘Amplification and Melting Curve Analysis’ (AMCA) with the abovementioned multiplex assay, we assessed the performance of the AMCA methodology in detecting these genes. The improved classification accuracy of AMCA relies on the usage of real-time data from a single-fluorescent channel and benefits from the kinetic/thermodynamic information encoded in the thousands of amplification events produced by high throughput real-time dPCR.The 5-plex showed a lower limit of detection of 10 DNA copies per reaction for each primer set and no cross-reactivity with other carbapenemase genes. The AMCA classifier demonstrated excellent predictive performance with 99.6% (CI 97.8-99.9%) accuracy (only one misclassified sample out of the 253, with a total of 160,041 positive amplification events), which represents a 7.9% increase (p-value < 0.05) compared to conventional melting curve analysis.This work demonstrates the use of the AMCA method to increase the throughput and performance of state-of-the-art molecular diagnostic platforms, without hardware modifications and additional costs, thus potentially providing substantial clinical utility on screening patients for CPO carriage.
A Tool for Translating Polygenic Scores onto the Absolute Scale Using Summary Statistics
Authors: Pain Oliver , Gillett Alexandra C. , Austin Jehannine C. , Folkersen Lasse , Lewis Cathryn M. 
Published: April 2021

AbstractBackgroundThere is growing interest in the clinical application of polygenic scores as their predictive utility increases for a range of health-related phenotypes. However, providing polygenic score predictions on the absolute scale is an important step for their safe interpretation. Currently, polygenic scores can only be converted to the absolute scale when a validation sample is available, presenting a major limitation in the interpretability and clinical utility of polygenic scores.MethodsWe have developed a method to convert polygenic scores to the absolute scale for binary and normally distributed phenotypes. This method uses summary statistics, requiring only the area-under-the-ROC curve (AUC) or variance explained (R2) by the polygenic score, and the prevalence of binary phenotypes, or mean and standard deviation of normally distributed phenotypes. Polygenic scores are converted using normal distribution theory. Given the AUC/R2of polygenic scores may be unknown, we also evaluate two methods (AVENGEME, lassosum) for estimating these values from genome-wide association study (GWAS) summary statistics alone. We validate the absolute risk conversion and AUC/R2estimation using data for eight binary and three continuous phenotypes in the UK Biobank sample.ResultsWhen the AUC/R2of the polygenic score is known, the observed and estimated absolute values were highly concordant. Across binary phenotypes, the mean absolute difference between the observed and estimated proportion of cases was 5%. For continuous phenotypes, the mean absolute difference between observed and estimated means was <0.3%. Estimates of AUC/R2from the lassosum pseudovalidation method were most similar to the observed AUC/R2values, though estimated values deviated substantially from the observed for autoimmune disorders.ConclusionThis study enables accurate interpretation of polygenic scores using only summary statistics, providing a useful tool for educational and clinical purposes. Furthermore, we have created interactive webtools implementing the conversion to the absolute scale for binary and normally distributed phenotypes (https://opain.github.io/GenoPred/PRS_to_Abs_tool.html). Several further barriers must be addressed before clinical implementation of polygenic scores, such as ensuring target individuals are well represented by the GWAS sample.
Exaggerated Right Ventricular Dysfunction in Females with Group 3 Pulmonary Hypertension
Authors: Prisco Sasha Z. , Kazmirczak Felipe , Prins Kurt W. , Thenappan Thenappan 
Published: April 2021

AbstractGroup 3 pulmonary hypertension (PH) patients have disproportionate right ventricular dysfunction (RVD) as compared to pulmonary arterial hypertension (PAH) patients, but the cause of the divergent RV phenotypes is unknown. One potential mechanism may be biological sex as females have better RV function than males. However, the combined effects of PH type and sex on RV function are unexplored. Therefore, we evaluated how sex and PH etiology modulated RVD in a single-center cohort study. Male sex was not associated with significant differences in RV function when comparing PH etiologies. However, female Group 3 patients had more pronounced RVD than female PAH patients. In particular, Group 3 females had marked reduction in RV function when pulmonary vascular resistance was matched. Group 3 females were older than PAH females, but the exaggerated RVD was still observed in postmenopausal (age≥55) Group 3 females. This suggests lung disease exacerbates RVD in Group 3 females.
CovidEnvelope: A Fast Automated Approach to Diagnose COVID-19 from Cough Signals
Authors: Hossain Md Zakir , Uddin Md. Bashir , Ahmed Khandaker Asif 
Published: April 2021

AbstractThe COVID-19 pandemic has a devastating impact on the health and well-being of global population. Cough audio signals classification showed potential as a screening approach for diagnosing people, infected with COVID-19. Recent approaches need costly deep learning algorithms or sophisticated methods to extract informative features from cough audio signals. In this paper, we propose a low-cost envelope approach, called CovidEnvelope, which can classify COVID-19 positive and negative cases from raw data by avoiding above disadvantages. This automated approach can pre-process cough audio signals by filter-out back-ground noises, generate an envelope around the audio signal, and finally provide outcomes by computing area enclosed by the envelope. It has been seen that reliable datasets are also important for achieving high performance. Our approach proves that human verbal confirmation is not a reliable source of information. Finally, the approach reaches highest sensitivity, specificity, accuracy, and AUC of 0.92, 0.87, 0.89, and 0.89 respectively. The automatic approach only takes 1.8 to 3.9 minutes to compute these performances. Overall, this approach is fast and sensitive to diagnose the people living with COVID-19, regardless of having COVID-19 related symptoms or not, and thus have vast applicability in human well-being by designing HCI devices incorporating this approach.
Estimating the effect of mobility on SARS-CoV-2 transmission during the first and second wave of the COVID-19 epidemic in Switzerland: a population-based study
Authors: Lison Adrian , Persson Joel , Banholzer Nicolas , Feuerriegel Stefan 
Published: April 2021

AbstractThe effect of mobility and its value for surveillance in different waves of the COVID-19 epidemic is still unclear. In this study, we compared the role of mobility during the first and second epidemic wave in Switzerland by analysing the link between daily travel distances and the effective reproduction number Rt of SARS-CoV-2. Here we used aggregated mobile phone data from a representative panel survey of the Swiss population to measure human mobility. We estimated the effects of reductions in daily travel distance on Rt via a regression model. We compared mobility effects between the first wave (March 2-April 7, 2020) and the second wave (October 1-December 10, 2020) across mode of transport, travel purpose, sociodemographic subgroup and movement radius. We found that human mobility was associated with the effective reproduction number of SARS-CoV-2 during both the first and second epidemic wave in Switzerland. The estimated relative effects of mobility were similar in both waves for all modes of transport, travel purposes, and sociodemographic subgroups but differed by movement radius. Moreover, smaller mobility reductions in the second wave translated into smaller overall reductions of Rt. Mobility data from mobile phones have a continued potential to support real-time surveillance of COVID-19 during epidemic waves.
COVID-19 Vaccine Prioritisation in Japan and South Korea
Authors: Chun June Young , Jeong Hwichang , Beutels Philippe , Ohmagari Norio , Kim Yongdai , Tsuzuki Shinya 
Published: April 2021

SummaryBackgroundDue to a limited initial supply of COVID-19 vaccines, the prioritisation of individuals for vaccination is of utmost importance for public health. Here, we provide the optimal allocation strategy for COVID-19 vaccines according to age in Japan and South Korea.MethodsCombining national case reports, age-specific contact matrices, and observed periods between each stages of infection (Susceptible-Exposed-Infectious-Quarantined), we constructed a compartmental model. We estimated the age-stratified probability of transmission given contact (qi) using Bayesian inference method and simulated different vaccination scenarios to reduce either case numbers or death toll. We also performed sensitivity analyses on the proportion of asymptomatic cases and vaccine efficacy.FindingsThe model inferred age-stratified probability of transmission given contact (qi) showed similar age-dependent increase in Japan and South Korea. Assuming the reported COVID-19 vaccine efficacy, our results indicate that Japan and South Korea need to prioritise individuals aged 20–35 years and individuals aged over 60 years, respectively, to minimise case numbers. To minimise the death toll, both countries need to prioritise individuals aged over 75 years. These trends were not changed by proportions of asymptomatic cases and varying vaccine efficacy on individuals under 20 years.InterpretationWe presented the optimal vaccination strategy for Japan and South Korea. Comparing the results of these countries demonstrates that not only the effective contact rates containing qi but also the age-demographics of current epidemic in Japan (dominance in 20s) and South Korea (dominant cases over 50s) affect vaccine allocation strategy.