Zgli: A Pipeline for Clustering by Compression with Application to Patient Stratification in Spondyloarthritis.

The normalized compression distance (NCD) is a similarity measure between a pair of finite objects based on compression. Clustering methods usually use distances (e.g., Euclidean distance, Manhattan distance) to measure the similarity between objects. The NCD is yet another distance with particular characteristics that can be used to build the starting distance matrix for methods such as hierarchical clustering or K-medoids. In this work, we propose Zgli, a novel Python module that enables the user to compute the NCD between files inside a given folder. Inspired by the CompLearn Linux command line tool, this module iterates on it by providing new text file compressors, a new compression-by-column option for tabular data, such as CSV files, and an encoder for small files made up of categorical data. Our results demonstrate that compression by column can yield better results than previous methods in the literature when clustering tabular data. Additionally, the categorical encoder shows that it can augment categorical data, allowing the use of the NCD for new data types. One of the advantages is that using this new feature does not require knowledge or context of the data. Furthermore, the fact that the new proposed module is written in Python, one of the most popular programming languages for machine learning, potentiates its use by developers to tackle problems with a new approach based on compression. This pipeline was tested in clinical data and proved a promising computational strategy by providing patient stratification via clusters aiding in precision medicine.

Persistence of IgG COVID-19 antibodies: A longitudinal analysis.

Background and aim: The kinetics of antibody production in response to coronavirus disease 2019 (COVID-19) infection is not well-defined yet. This study aimed to evaluate the antibody responses to SARS-CoV-2 and its dynamics during 9-months in a cohort of patients infected during the first phase of the pandemic. As a secondary aim, it was intended to evaluate the factors associated with different concentrations of IgG antibodies. Methods: A prospective cohort study was conducted from June 2020 to January 2021. This study recruited a convenience sample of adult individuals who where recently diagnosed with COVID-19 and were living in mainland Portugal. A total of 1,695 blood samples were collected from 585 recovered COVID-19 patients up to 9 months after SARS-CoV-2 acute infection. A blood sample was collected at baseline and three, 6 and 9 months after SARS-CoV-2 acute infection to assess the concentration of IgG antibody against SARS-CoV-2. Results: The positivity rate of IgG reached 77.7% in the first 3 months after symptom onset. The IgG persists at all subsequent follow-up time-points, which was 87.7 and 89.2% in the 6th and 9th months after symptom onset, respectively. Three distinct kinetics of antibody response were found within the 9 months after infection. Kinetic 1 (K1) was characterized by a constant low IgG antibody concentration kinetic (group size: 65.2%); kinetic 2 (K2), composed by constant moderate IgG kinetic (group size: 27.5%) and kinetic 3 (K3) characterized by higher IgG kinetic (group size: 7.3%). People with ≥56 years old (OR: 3.33; CI 95%: [1.64; 6.67]; p-value: 0.001) and symptomatic COVID-19 (OR: 2.08; CI 95%: [1.08; 4.00]; p-value: 0.031) had higher odds of a "Moderate IgG kinetic." No significant association were found regarding the "Higher IgG kinetic." Conclusion: Our results demonstrate a lasting anti-spike (anti-S) IgG antibody response at least 9 months after infection in the majority of patients with COVID-19. Younger participants with asymptomatic disease have lower IgG antibody positivity and possibly more susceptible to reinfection. This information contributes to expanding knowledge of SARS-CoV-2 immune response and has direct implications in the adoption of preventive strategies and public health policies.

Persistence of IgG COVID-19 antibodies: A longitudinal analysis

Background and aim The kinetics of antibody production in response to coronavirus disease 2019 (COVID-19) infection is not well-defined yet. This study aimed to evaluate the antibody responses to SARS-CoV-2 and its dynamics during 9-months in a cohort of patients infected during the first phase of the pandemic. As a secondary aim, it was intended to evaluate the factors associated with different concentrations of IgG antibodies. Methods A prospective cohort study was conducted from June 2020 to January 2021. This study recruited a convenience sample of adult individuals who where recently diagnosed with COVID-19 and were living in mainland Portugal. A total of 1,695 blood samples were collected from 585 recovered COVID-19 patients up to 9 months after SARS-CoV-2 acute infection. A blood sample was collected at baseline and three, 6 and 9 months after SARS-CoV-2 acute infection to assess the concentration of IgG antibody against SARS-CoV-2. Results The positivity rate of IgG reached 77.7% in the first 3 months after symptom onset. The IgG persists at all subsequent follow-up time-points, which was 87.7 and 89.2% in the 6th and 9th months after symptom onset, respectively. Three distinct kinetics of antibody response were found within the 9 months after infection. Kinetic 1 (K1) was characterized by a constant low IgG antibody concentration kinetic (group size: 65.2%);kinetic 2 (K2), composed by constant moderate IgG kinetic (group size: 27.5%) and kinetic 3 (K3) characterized by higher IgG kinetic (group size: 7.3%). People with ≥56 years old (OR: 3.33;CI 95%: [1.64;6.67];p-value: 0.001) and symptomatic COVID-19 (OR: 2.08;CI 95%: [1.08;4.00];p-value: 0.031) had higher odds of a "Moderate IgG kinetic.” No significant association were found regarding the "Higher IgG kinetic.” Conclusion Our results demonstrate a lasting anti-spike (anti-S) IgG antibody response at least 9 months after infection in the majority of patients with COVID-19. Younger participants with asymptomatic disease have lower IgG antibody positivity and possibly more susceptible to reinfection. This information contributes to expanding knowledge of SARS-CoV-2 immune response and has direct implications in the adoption of preventive strategies and public health policies.

SARS-CoV-2 Antibody Prevalence in the Portuguese Municipality of Vila Nova de Gaia after the First Wave of the Pandemic.

INTRODUCTION: Assessment of SARS-CoV-2 seroprevalence may detect the real spread of the virus because antibody data can provide a long-lasting measure of infection. Existing serological studies in Portugal have tested new serology methods, albeit with small sample sizes and a lack the focus on geographical regions with a high rate of infection cases. The aim of this study was to estimate the serological prevalence of SARS-CoV-2 in Vila Nova de Gaia, the most populous municipality in the north of Portugal and one of those most affected during the first pandemic wave. MATERIAL AND METHODS: A cross-sectional observational study was conducted between June 23rd and July 17th, 2020. Included in the cohort were 18- to 74-year-old men and women living in the municipality of Vila Nova de Gaia, who were sampled through a nonprobabilistic quota-based approach. Cases with a previous RT-PCR diagnosis of COVID-19 were excluded. Sociodemographic and clinical information was collected using a self-administered, written questionnaire. Blood samples were collected for serological laboratory analysis to detect and quantify SARS-CoV-2 anti-IgG antibodies. RESULTS: We tested 2754 participants. Our results show a SARS-CoV-2 seroprevalence of 3.03% (95% confidence interval: 2.37% - 3.87%). Being a smoker (odds ratio: 0.382, 95% confidence interval: 0.147 - 0.99) and having symptoms of COVID-19 (odds ratio: 2.480, 95% confidence interval: 1.360 - 4.522) were consistently associated with lower and higher odds of SARS-CoV-2 antibody presence, respectively, regardless of the analytic design. Moreover, without adjusting for any variables, having had contact with an infected person within the household was associated with increased odds of a positive test (odds ratio: 9.684, 95% confidence interval: 4.06 - 23.101); after adjusting, having self-reported chronic diseases (odds ratio: 0.448, 95% confidence interval: 0.213 - 0.941) was associated with decreased odds. CONCLUSION: This was the first study to estimate the serological prevalence of SARS-CoV-2 in one of the most populous municipalities in Portugal, representing the first step in the development of an epidemiological surveillance system in Portugal, which can help to improve the diagnosis of COVID-19.

COVID-19 mRNA vaccine and antibody response in lactating women: a prospective cohort study.

BACKGROUND: Immunological protection via breastfeeding is well known. The immunological profile of human milk changes during lactation. No clinical trials have been conducted in lactating women with the newest mRNA vaccines against SARS- CoV-2. A Few studies have shown the presence of antibodies in breastmilk after vaccination. The aim of this work is to study possible antibodies transfer via breastmilk and also the immunological characteristics of lactating women compared to non-lactating women, after using the BNT162b2 Pfizer vaccine. METHODS: This is a prospective cohort study with a convenience homogenous sample of 24 healthcare workers (14 lactating and 10 non-lactating women) enrolled at the time of COVID-19 vaccination. Clinical data was registered in a questionnaire. Titers of SARS-CoV-2 spike IgG, IgA and IgM were quantified in post vaccination blood and human milk. Antibody quantification was performed by an in-house ELISA to SARS-CoV-2 trimeric spike protein. RESULTS: All women showed immunity after vaccination with positive antibodies for IgM, IgA and IgG antibodies. The dominant serum antibody response was IgG. Modest levels of antibodies in breastmilk of lactating mothers were observed in this study, especially IgG in 42.9%. There was a moderate association between higher titers of IgG and a longer duration of breastfeeding (R= 0.55, p=0.041). CONCLUSIONS: Evidence of antibody transfer in human milk after COVID-19 vaccination is scarce. The presence of antibodies in human milk is reported, but immunization through breastfeeding is still to be established.

2022 EULAR points to consider for remote care in rheumatic and musculoskeletal diseases.

BACKGROUND: Remote care and telehealth have the potential to expand healthcare access, and the COVID-19 pandemic has called for alternative solutions to conventional face-to-face follow-up and monitoring. However, guidance is needed on the integration of telehealth into clinical care of people with rheumatic and musculoskeletal diseases (RMD). OBJECTIVE: To develop EULAR points to consider (PtC) for the development, prioritisation and implementation of telehealth for people with RMD. METHODS: A multidisciplinary EULAR task force (TF) of 30 members from 14 European countries was established, and the EULAR standardised operating procedures for development of PtC were followed. A systematic literature review was conducted to support the TF in formulating the PtC. The level of agreement among the TF was established by anonymous online voting. RESULTS: Four overarching principles and nine PtC were formulated. The use of telehealth should be tailored to patient's needs and preferences. The healthcare team should have adequate equipment and training and have telecommunication skills. Telehealth can be used in screening for RMD as preassessment in the referral process, for disease monitoring and regulation of medication dosages and in some non-pharmacological interventions. People with RMD should be offered training in using telehealth, and barriers should be resolved whenever possible.The level of agreement to each statement ranged from 8.5 to 9.8/10. CONCLUSION: The PtC have identified areas where telehealth could improve quality of care and increase healthcare access. Knowing about drivers and barriers of telehealth is a prerequisite to successfully establish remote care approaches in rheumatologic clinical practice.

One Year of COVID-19 in Pregnancy: A National Wide Collaborative Study.

INTRODUCTION: Even though the risk of COVID-19 in pregnancy may be increased, large-scale studies are needed to better understand the impact of the infection in this population. The aim of this study is to describe obstetric complications and the rate of vertical transmission in pregnant women with SARS-CoV-2 infection. MATERIAL AND METHODS: Detected cases of SARS-CoV-2 infection in pregnancy were registered in Portuguese hospitals by obstetricians. Epidemiological, pregnancy and childbirth data were collected. RESULTS: There were 630 positive cases in 23 Portuguese maternity hospitals, most at term (87.9%) and asymptomatic (62.9%). The most frequent maternal comorbidity was obesity. The rates of preterm birth and small-to-gestational-age were 12.1% and 9.9%, respectively. In the third trimester, 2.9% of pregnant women required respiratory support. There were eight cases (1.5%) of fetal death, including two cases of vertical transmission. There were five cases of postpartum respiratory degradation, but no maternal deaths were recorded. The caesarean section rate was higher in the first than in the second wave (68.5% vs 31.5%). RT-PCR SARS-CoV-2 positivity among newborns was 1.3%. CONCLUSION: SARS-Cov-2 infection in pregnancy may carry increased risks for both pregnant women and the fetuses. Individualized surveillance and the prophylaxis of this population with vaccination. is recommended in these cases.

Introdução: Apesar do risco da COVID-19 na gravidez poder ser acrescido, são necessários estudos em larga escala para o melhor conhecimento do impacto desta infeção nesta população. O objetivo deste estudo é descrever as complicações obstétricas e a taxa de transmissão vertical em grávidas com infeção a SARS-CoV-2. Material e Métodos: Os casos conhecidos de infeção por SARS-CoV-2 na gravidez foram registados nos hospitais portugueses por obstetras. Foram recolhidos dados epidemiológicos, da gravidez e do parto. Resultados: Registaram-se 630 casos positivos em 23 maternidades portuguesas, a maioria no termo (87,9%) e assintomática (62,9%). A comorbilidade materna mais frequente foi a obesidade. A taxa de parto pré-termo e de leves para a idade gestacional foi de 12,1% e 9,9%, respectivamente. No terceiro trimestre, 2,9% das grávidas necessitaram de suporte respiratório. Verificou-se uma taxa de 1,5% de morte fetal, incluindo dois casos de transmissão vertical. Houve cinco casos de degradação respiratória no pós-parto, mas sem mortes maternas registadas. A taxa de cesarianas foi mais elevada na primeira do que na segunda vaga (68,5% vs 31,5%). A positividade do RT-PCR SARS-CoV-2 entre os recém-nascidos foi de 1,3%. Conclusão: A infeção pelo SARS-Cov-2 na gravidez pode acarretar riscos aumentados para as grávidas e fetos. Recomenda-se uma vigilância individualizada nestes casos e a profilaxia desta população com a vacinação.

Evaluating SARS-CoV-2 Seroconversion Following Relieve of Confinement Measures.

Seroprevalence studies are crucial both for estimating the prevalence of SARS-CoV-2 exposure and to provide a measure for the efficiency of the confinement measures. Portuguese universities were closed on March 16th 2020, when Portugal only registered 62 SARS-CoV-2 infection cases per million. We have validated a SARS-CoV-2 ELISA assay to a stabilized full-length spike protein using 216 pre-pandemic and 19 molecularly diagnosed SARS-CoV-2 positive individual's samples. At NOVA University of Lisbon, presential work was partially resumed on May 25th with staggered schedules. From June 15th to 30th, 3-4 weeks after the easing of confinement measures, we screened 1,636 collaborators of NOVA university of Lisbon for the presence of SARS-CoV-2 spike specific IgA and IgG antibodies. We found that spike-specific IgG in 50 of 1,636 participants (3.0%), none of which had anti-spike IgA antibodies. As participants self-reported as asymptomatic or paucisymptomatic, our study also provides a measurement of the prevalence of asymptomatic/paucisymptomatic SARS-CoV-2 infections. Our study suggests that essential workers have a 2-fold increase in viral exposure, when compared to non-essential workers that observed confinement. Additional serological surveys in different population subgroups will paint a broader picture of the effect of the confinement measures in the broader community.

Staff SARS-CoV-2 Seroprevalence and Mental Health as Key Factors in University Response to COVID-19 Pandemic.

Background: In response to rapid global spread of the newly emerged coronavirus disease 2019 (COVID-19), universities transitioned to online learning and telework to decrease risks of inter-person contact. To help administrators respond to the COVID-19 pandemic and better understand its impacts, we surveyed SARS-CoV-2 seroprevalence among NOVA University employees and assessed community mental health. Methods: Data were collected from voluntary participants at six NOVA University locations, in the Lisbon metropolitan area, from June 15-30, 2020. All subjects provided written informed consent. Of 1,627 recruited participants (mean age 42.0 ± 12.3 years), 1,624 were tested. Prior to blood collection, participants completed a questionnaire that assessed: COVID-19 symptoms during the previous 14 days, chronic non-communicable diseases, chronic medication, anxiety, and depression symptoms. SARS-CoV-2 serology tests were then performed, and results communicated approximately 4 days after blood draw. Participants with positive serology tests were contacted to assess COVID-19 symptoms since February. Results: Estimated prevalence of SARS-CoV-2 IgG antibodies was 3.1% (n = 50), of which 43.5% reported symptoms in the previous 4 months. The Medical School had the highest seroprevalence (6.2%). Participants reported having at least one chronic disease (63.7%), depression-like symptoms (2.1%), and anxiety symptoms (8.1%). Rates of depression and anxiety symptoms were significantly higher in women, with sleep hours and occasional alcohol consumption negatively associated with depression. Male gender, older age, and sleep hours negatively associated with anxiety symptoms. School of employment and presence of comorbidities positively associated with anxiety. Conclusion: By measuring seroprevalence of SARS-CoV-2 antibodies among NOVA employees and assessing subjects' mental health, we aim to help administrators at European public universities in urban areas, such as Lisbon, Portugal, better understand the needs of their communities. This study resulted in implementation of a stricter contingency plan in the Medical School, while other schools continued to follow Government mitigation guidelines. These findings may also guide the development of tailored strategies to ensure physical and mental health of the academic community during this pandemic crisis. We conclude that, together with COVID-19 contingency plans, psychological support services and facilities to help people effectively face pandemic-associated challenges and minimise anxiety and depression should be implemented.

Sleep and Awakening Quality during COVID-19 Confinement: Complexity and Relevance for Health and Behavior.

OBJECTIVE: The aim of this study was to evaluate sleep and awakening quality (SQ and AQ) during COVID-19 in a large and diversified population in order to identify significant associations and risks in terms of demography, health and health-related behaviors, sleep variables, mental health, and attitudes. METHODS/RESULTS: Online surveys were used for data collection, received from 5479 individuals from the general population, sleep disorder patients, and COVID-involved (medical doctors (MDs) and nurses) and COVID-affected professionals (teachers, psychologists, and dentists). SQ and AQ were worse in adults, females, and high-education subjects. Feeling worse, having economic problems, depression, anxiety, irritability, and a high Calamity Experience Check List (CECL) score during COVID were significantly associated with poor SQ and AQ. Shorter sleep duration, increased latency, poor nutrition, low physical activity, increased mobile and social network use, more negative and less positive attitudes and behaviors were associated with poor AQ. CONCLUSIONS: The SQ logistic regression showed gender, morbidities, CECL, and awakenings as relevant, whereas, for AQ, relevant variables further included age and physical activity. Aiming to have a high stress compliance, each individual should sleep well, have important control of their mood, practice positive behaviors while dismissing negative behaviors and attitudes, practice exercise, have adequate nutrition, and beware of technologies and dependences.