ABSTRACT
Since their proposal in 2016, the FAIR principles have been largely discussed by different communities and initiatives involved in the development of infrastructures to enhance support for data findability, accessibility, interoperability, and reuse. One of the challenges in implementing these principles lies in defining a well-delimited process with organized and detailed actions. This paper presents a workflow of actions that is being adopted in the VODAN BR pilot for generating FAIR (meta)data for COVID-19 research. It provides the understanding of each step of the process, establishing their contribution. In this work, we also evaluate potential tools to (semi)automatize (meta)data treatment whenever possible. Although defined for a particular use case, it is expected that this workflow can be applied for other epidemical research and in other domains, benefiting the entire scientific community.
ABSTRACT
Introduction: The SARS-CoV-2 (COVID-19) pandemic continues in the United States, and patients actively receiving chemotherapy are known to be at enhanced risk for developing symptomatic disease. Our study evaluated the prevalence of COVID-19 among patients and providers of our community-facing county health system during the B1.1.529 ("Omicron") COVID-19 variant wave. Method(s): We retrospectively analyzed patients that received care and clinical providers whom worked at the Jackson Memorial Hospital Hematology/Oncology clinic in Miami, Florida from December 1st, 2021 through April 30th, 2022. After categorizing basic demographic factors for individuals whom tested positive for COVID-19 during the study timeframe, we analyzed additional risk factors leading to COVID-19 positivity including, but not limited to, vaccination status, previous COVID-19 positivity, and active receipt of chemotherapeutics. We then analyzed outcomes related to COVID-19, including treatment with advanced COVID-19 therapies such as oral or intravenous antivirals, monoclonal antibodies, convalescent plasma, steroids, or interleukin-6 inhibitors;interactions with inpatient services including emergency department (ED)/urgent care visits, inpatient and/or ICU admissions, and deaths from COVID-19. We finally assessed quality outcomes such as delay in cancer-directed therapy. This study was approved by the University of Miami IRB and Jackson Health System Clinical Trials Office. Result(s): 498 patients and 18 providers were retrospectively analyzed during the study timeframe. 49 patients tested positive for COVID-19 (9.84%), while 6 providers tested positive (33.3%) (p = 0.015). Patients whom tested positive were 51.0% female (n = 25), 26.5% Black (n = 13), 73.5% Hispanic/Latinx (n = 36), and 2.05% Asian (n = 1). Only 6.12% patients had tested positive for COVID-19 previously (n = 3), and 42.9% were considered unvaccinated (n = 21) while 14.3% were boosted (n = 7). 73.5% (n = 36) presented with symptomatic disease, 46.9% (n = 23) sought care at an ED/urgent care, 32.6% (n = 13) were admitted to the hospital, 6.12% were admitted to the ICU (n = 3), and 16.3% (n = 8) received advanced therapeutics. There were 2 (8.0%) COVID-19-related deaths (and another outside our study timeframe) among 23 non-COVID-19 related deaths in the patient population (p = 0.75). More than half of the patients whom tested positive experienced a cancer treatment delay (n = 27/49;55.1%). Conclusion(s): The prevalence of COVID-19 positivity in our patient cohort during the initial Omicron wave mirrored local, state, and national trends, however a statistically significant greater proportion of our providers tested positive. COVID-19 positivity conferred appreciable disparities in the presentation of disease as well as receipt of cancer treatment. COVID-19 positivity was more likely to result in symptomatic disease and ED/urgent care visit in cancer patients without previous COVID infection and unvaccinated status. COVID-19 accounted for 8.0% of our clinic's total mortality.
ABSTRACT
The COVID-19 pandemic and the global actions to address it have highlighted the importance of clinical care data for more detailed studies of the virus and its effects. Extracting and processing such data, in terms of confidentiality issues, is a challenge. In addition, the mechanisms necessary for their publication are aimed at reuse in research to better understand the effects of this pandemic or other viral outbreaks. This paper describes a modular, scalable, distributed, and flexible platform, based on a generic architecture, to promote the publication of FAIR clinical research data. This platform collects heterogeneous data from Electronic Health Records, transforms these data into interconnected and interoperable (meta)data that are processable by software agents, and publishes them through technological solutions such as repositories and FAIR Data Point. Copyright © 2022 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved.
ABSTRACT
Background: In the thick of the ongoing global crises of the COVID-19 pandemic, uprisings against anti-Black racism and police brutality, and anti-Asian racism and violence, Black, indigenous, and people of color (BIPOC) adolescent and young adult (AYA) cancer patients may be particularly vulnerable and exploited. Whilst embroiled in sociopolitical complexity, BIPOC AYAs are increasingly called upon to contribute as patient advocates in AYA oncology research and advocacy. Researchers, clinicians, and advocates in AYA oncology must dismantle long-standing racism and create meaningful structural change. The purpose of this study is to derive vital best practices for implementing antiracist patient engagement in AYA oncology research and advocacy that are co-developed by BIPOC AYA cancer patients and oncology professionals. Methods: We utilized a modified Delphi technique with a panel of BIPOC AYA cancer patients (n = 32) to build consensus opinions on professional recommendations from a prior study (Cheung et al., 2021), and to generate antiracist best practices in patient engagement. The Delphi study was comprised of three consecutive and iterative survey rounds over the course of 8 months in 2021;participants were BIPOC AYAs diagnosed with cancer between ages 15-36 years. Results: Results detail best practices for the implementation of antiracist patient engagement across all research activities within the Patient-Centered Outcomes Research Institute's (PCORI) Framework for Patient Engagement. For example, BIPOC AYAs agreed with oncology professionals' high priority recommendation for including BIPOC AYAs at the highest levels of decision making in research topic selection. As such, a best practice is for researchers to ensure that such representatives not only hold BIPOC AYA identity, but also hold direct experience with the particular oncology diagnosis, issue, or other outcome of interest. Additionally, BIPOC AYAs concurred with oncology professionals' high priority for “transparency, honesty, and trust” as a core principle for best practices in patient engagement. They further explained that trustworthy relationships are especially important when collaborating with teens and young adults, who are developmentally just coming into their own. When describing successful experiences of inclusion, participants ranked “build collaborative relationships with BIPOC AYA communities and listen to patients not usually heard” and “recruit a diverse range of BIPOC patients and let them give actual input into the study” as the highest priority best practices. Conclusions: Findings from this study are instructional for AYA oncology researchers, clinicians, and advocates to prevent harmful tokenism and implement genuine antiracist inclusion to advance health equity. Future research should investigate best practices within unique clinical settings.
ABSTRACT
Since their proposal in 2016, the FAIR principles have been largely discussed by different communities and initiatives involved in the development of infrastructures to enhance support for data findability, accessibility, interoperability, and reuse. One of the challenges in implementing these principles lies in defining a well-delimited process with organized and detailed actions. This paper presents a workflow of actions that is being adopted in the VODAN BR pilot for generating FAIR (meta)data for COVID-19 research. It provides the understanding of each step of the process, establishing their contribution. In this work, we also evaluate potential tools to (semi)automatize (meta)data treatment whenever possible. Although defined for a particular use case, it is expected that this workflow can be applied for other epidemical research and in other domains, benefiting the entire scientific community. © 2022, Springer Nature Switzerland AG.
ABSTRACT
Consumer countries and blocs, including the UK and the EU, are defining legal measures to tackle deforestation linked to commodity imports, potentially requiring imported goods to comply with the relevant producer countries' land-use laws. Nonetheless, this measure is insufficient to address global deforestation. Using Brazil's example of a key exporter of forest-risk commodities, here we show that it has similar to 3.25 Mha of natural habitat (storing similar to 152.8 million tons of potential CO2 emissions) at a high risk of legal deforestation until 2025. Additionally, the country's legal framework is going through modifications to legalize agricultural production in illegally deforested areas. What was illegal may become legal shortly. Hence, a legality criterion adopted by consumer countries is insufficient to protect forests and other ecosystems and may worsen deforestation and conversion risks by incentivizing the weakening of social-environmental protection by producer countries.
ABSTRACT
Background: SARS-CoV-2 is associated with diverse clinical presentations ranging from asymptomatic infection to lethal complications. Small studies have suggested inferior outcomes in patients (pts) on active cancer treatment. This finding was not independently validated in our prior report on 928 pts, which included treatments administered within 4 weeks of COVID-19 diagnosis. Here, we examine outcomes related to systemic cancer treatment within one year of lab-confirmed SARS-CoV-2 infection in an expanded cohort. Method(s): The COVID-19 and Cancer Consortium (CCC19) registry (NCT04354701) was queried for pts ever receiving systemic treatment. Treatment type, cancer type, stage, and COVID-19 outcomes were examined. Pts were stratified by time from last treatment administration: <2 wk, 2-4 wk, 1-3 mo, or 3-12 mo. Standardized incidence ratios (SIR) of mortality by treatment type and timing were calculated. Result(s): As of 31 July 2020, we analyzed 3920 pts;42% received systemic anti-cancer treatment within 12 mo (Table). 159 distinct medications were administered. The highest rate of COVID-19-associated complications were observed in pts treated within 1-3 months prior to COVID-19;all-cause mortality in this group was 26%. 30-day mortality by most recent treatment type was 20% for chemotherapy, 18% for immunotherapy, 17% for chemoradiotherapy, 29% for chemoimmunotherapy, 20% for targeted therapy, and 11% for endocrine therapy. SIR of mortality was highest for chemoimmunotherapy or chemotherapy <2 wks, and lowest for endocrine treatments. A high SIR was also found for targeted agents within 3-12 mo. Pts untreated in the year prior to COVID-19 diagnosis had a mortality of 14%. [Formula presented] Conclusion(s): 30-day mortality was highest amongst cancer pts treated 1-3 months prior to COVID-19 diagnosis and those treated with chemoimmunotherapy. Except for endocrine therapy, mortality for subgroups was numerically higher than in pts untreated within a year prior to COVID-19 diagnosis. Clinical trial identification: NCT04354701. Legal entity responsible for the study: The COVID-19 and Cancer Consortium (CCC19). Funding(s): National Cancer Institute (P30 CA068485). Disclosure: T.M. Wise-Draper: Research grant/Funding (self), Travel/Accommodation/Expenses: AstraZeneca;Research grant/Funding (self): BMS;Research grant/Funding (self): Tesaro/GSK;Advisory/Consultancy: Shattuck Labs;Leadership role, Travel/Accommodation/Expenses, HNC POA Lead: Caris Life Sciences;Research grant/Funding (self), Travel/Accommodation/Expenses: Merck;Travel/Accommodation/Expenses: Eli Lilly;Travel/Accommodation/Expenses: Bexion. A. Elkrief: Research grant/Funding (self): AstraZeneca. B.I. Rini: Advisory/Consultancy, Research grant/Funding (self), Travel/Accommodation/Expenses: Merck;Advisory/Consultancy, Research grant/Funding (self): Roche;Advisory/Consultancy, Research grant/Funding (self), Travel/Accommodation/Expenses: Pfizer;Advisory/Consultancy, Research grant/Funding (self): AVEO;Advisory/Consultancy, Research grant/Funding (self), Travel/Accommodation/Expenses: BMS;Advisory/Consultancy: arravive;Advisory/Consultancy: 3D medicines;Advisory/Consultancy: Synthorx;Advisory/Consultancy: Surface Oncology;Shareholder/Stockholder/Stock options: PTC Therapeutics;Research grant/Funding (self): AstraZeneca. D.B. Johnson: Advisory/Consultancy: Array Biopharma;Advisory/Consultancy, Research grant/Funding (self): BMS;Advisory/Consultancy: Janssen;Advisory/Consultancy: Merck;Advisory/Consultancy: Novartis;Research grant/Funding (self): Incyte;Leadership role: ASCO melanoma scientific committee chair;Leadership role: NCCN Melanoma committee. G. Lopes: Honoraria (self), Travel/Accommodation/Expenses: Boehringer Ingelheim;Advisory/Consultancy, Research grant/Funding (institution), Travel/Accommodation/Expenses: Pfizer;Advisory/Consultancy, Research grant/Funding (self), Research grant/Funding (institution): AstraZeneca;Research grant/Funding (institution): Merck;Research grant/Funding (institution): EMD Serono;Research gr
ABSTRACT
The global population is ageing at an unprecedented rate. With changes in life expectancy across the world, three major issues arise: an increasing proportion of senior citizens;cognitive and physical problems progressively affecting the elderly;and a growing number of single-person households. The available data proves the ever-increasing necessity for efficient elderly care solutions such as healthcare service and assistive robots. Additionally, such robotic solutions provide safe healthcare assistance in public health emergencies such as the SARS-CoV-2 virus (COVID-19). CHARMIE is an anthropomorphic collaborative healthcare and domestic assistant robot capable of performing generic service tasks in non-standardised healthcare and domestic environment settings. The combination of its hardware and software solutions demonstrates map building and self-localisation, safe navigation through dynamic obstacle detection and avoidance, different human-robot interaction systems, speech and hearing, pose/gesture estimation and household object manipulation. Moreover, CHARMIE performs end-to-end chores in nursing homes, domestic houses, and healthcare facilities. Some examples of these chores are to help users transport items, fall detection, tidying up rooms, user following, and set up a table. The robot can perform a wide range of chores, either independently or collaboratively. CHARMIE provides a generic robotic solution such that older people can live longer, more independent, and healthier lives. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
ABSTRACT
Background: Patients with coronavirus disease 2019 (COVID-19) and cancer have worse clinical outcomes compared to those without cancer. Primary studies have examined this population, but most had small sample sizes and conflicting results. Prior meta-analyses exclude most US and European data or only examine mortality. The present meta-analysis evaluates the prevalence of several clinical outcomes in cancer patients with COVID-19, including new emerging data from Europe and the US. Methods: A systematic search of PubMED, medRxiv, JMIR and Embase by two independent investigators included peer-reviewed papers and preprints up to July 8, 2020. The primary outcome was mortality. Other outcomes were ICU and non-ICU admission, mild, moderate and severe complications, ARDS, invasive ventilation, stable, and clinically improved rates. Study quality was assessed through the Newcastle-Ottawa scale. Random effects model was used to derive prevalence rates, their 95% confidence intervals (CI) and 95% prediction intervals (PI). Results: Thirty-four studies (N = 4,371) were included in the analysis. The mortality prevalence rate was 25.2% (95% CI: 21.1-29.7;95% PI: 9.8-51.1;I2= 85.4), with 11.9% ICU admissions (95% CI: 9.2-15.4;95% PI: 4.3- 28.9;I2= 77.8) and 25.2% clinically stable (95% CI: 21.1-29.7;95% PI: 9.8-51.1;I2= 85.4). Furthermore, 42.5% developed severe complications (95% CI: 30.4-55.7;95% PI: 8.2- 85.9;I2= 94.3), with 22.7% developing ARDS (95% CI: 15.4-32.2;95% PI: 5.8-58.6;I2= 82.4), and 11.3% needing invasive ventilation (95% CI: 6.7-18.4;95% PI: 2.3-41.1;I2= 79.8). Post-follow up, 49% clinically improved (95% CI: 35.6-62.6;95% PI: 9.8-89.4;I2= 92.5). All outcomes had large I2 , suggesting high levels of heterogeneity among studies, and wide PIs indicating high variability within outcomes. Despite this variability, the mortality rate in cancer patients with COVID-19, even at the lower end of the PI (9.8%), is higher than the 2% mortality rate of the non-cancer with COVID-19 population, but not as high as what other meta-analyses conclude, which is around 25%. Conclusions: Patients with cancer who develop COVID-19 have a higher probability of mortality compared to the general population with COVID-19, but possibly not as high as previous studies have shown. A large proportion of them developed severe complications, but a larger proportion recovered. Prevalence of mortality and other outcomes published in prior meta-analyses did not report prediction intervals, which compromises the clinical utilization of such results.
ABSTRACT
Background: Cancer has been described as a risk factor for worse prognosis in people with Covid-19. However, there are few studies informing on the characteristics of cancer patients that have asymptomatic SARS-cov2 infection. The ACHOCC-19 study included asymptomatic patients. Methods: Analytical cohort study of patients with cancer and SARScov2 infection in Colombia. From April 1 to October 31, 2020, we collected data on demographic and clinical variables related to cancer and COVID-19 infection. We describe the characteristics and outcomes of patients who had no symptoms of COVID19. Association between outcomes and prognostic variables was analyzed using logistic regression models. Results: We included 742 patients, of which 205 (27.6%) were asymptomatic. Of these 62.2% were older than 61 years, 66% were women, 1.42% were smokers. The most frequent malignancy was breast cancer (25%), followed by colon-rectum (14.6%), sarcoma/soft tissues (5.66%) and lung cancer (5.19%). Patients were more likely to be asymptomatic if they had fewer comorbidities (0-1 comorbidities: 84% asymptomatic, 2 comorbidities: 10.85%, more than 2 comorbidities: 5.15%). 90.5% lived in urban areas and 53.37% had low income. 35.4% of patients had metastatic disease, 8.7% had progressive cancer, 40% had stable disease or partial response. No patient had an ECOG PS of 4 or more, and only 1.91% had ECOG 3. In logistic regression analysis statistically significant associations for having symptomatic disease included: man, presence of 1, 2 or > 2 comorbidities, ECOG 1,2 or 3 and cancer in progression. On the other hand, the statistically significant ORs for having asymptomatic disease were age between 18 and 30 years old, cancer in remission and receiving non-cytotoxic treatment. Table sumarizes ORs and their respective 95% CIs of the variables adjusted in the logistic regression model. Conclusions: In our stumdy, cancer patients had a higher probability of asymptomatic COVID-19 infection if they were women, between the ages of 18 and 30 years, had cancer in remission , ECOG 0 and no comorbidities. This is the first cohort of patients with cancer and asymptomatic covid 19 with a significant sample size in Latin America.
ABSTRACT
Background: Oncology patients experience more severe disease outcomes from COVID-19 infection than the general population. BCG is a live bovine tuberculosis bacillus with immunotherapeutic effects in urothelial cancers;it is also used as vaccination against Mycobacterium tuberculosis in parts of the world. As BCG vaccination has been associated with broad protection against viral pathogens, BCG exposure through vaccination or intravesical therapy may modulate host immunity and reduce the severity of COVID-19 infection. We report the effect of BCG exposure on COVID-19 severity in oncology patients from the CCC19 registry. Methods: The CCC19 registry (NCT04354701) was used to identify patients with prior BCG exposure. Cohort A received intravesical treatment for bladder carcinoma, and cohort B received prior BCG vaccination. Each cohort was matched 3:1 to non-BCG-exposed controls by age, sex, race, primary cancer type, cancer status, ECOG performance status (PS) and calendar time of COVID-19 infection. The primary endpoint was COVID-19 severity reported on an ordinal scale (uncomplicated, hospitalized, admitted to ICU +/- ventilated, died within 30 days) of patients exposed to prior BCG compared to matched non-exposed controls. 2-sided Wilcoxon ranksum tests were used. Results: As of 6-Feb-2021 we included 124 patients with BCG exposure, 68 patients with bladder carcinoma who had received intravesical BCG (Cohort A), and 64 cancer patients with prior BCG vaccination (Cohort B). Median age was 76 years, IQR 69-83 (Cohort A) and 67 years, IQR 62-74 (Cohort B). Bladder cancer pts were predominately male (78%) vs 55% for Cohort B. Patients with PS 2+ were uncommon, 18% in Cohort A and 16% in Cohort B. COVID-19 illness severity was no different in patients exposed to prior intravesicular BCG (p=0.87). COVID-19 illness severity was no different in patients exposed to prior intradermal BCG vaccination (p=0.60). Conclusions: Despite this being the largest such cohort reported to date, we failed to demonstrate an association of prior BCG exposure with modulation of severity of COVID19 illness. Prospective trials evaluating the protective effect of BCG vaccination are ongoing and will add further insight into the effect of BCG on COVID-19 illness.
ABSTRACT
From state-based developmentalism to community-based initiatives to market-based conservation, the Brazilian Amazon has been a laboratory of development interventions for over 50 years. The region is now confronting a devastating COVID-19 pandemic amid renewed environmental pressures and increasing social inequities. While these forces are shaping the present and future of the region, the Amazon has also become an incubator of local innovations and efforts confronting these pressures. Often overlooked, place-based initiatives involving individual and collective-action have growing roles in promoting regional sustainability. We review the history of development interventions influencing the emergence of place-based initiatives and their potential to promoting changes in productive systems, value-aggregation and market-access, and governance arrangements improving living-standards and environmental sustainability. We provide examples of initiatives documented by the AGENTS project, contextualizing them within the literature. We reflect on challenges and opportunities affecting their trajectories at this critical juncture for the future of the region. © 2021 The Authors
ABSTRACT
Background: There are limited data on COVID-19 in patients with cancer. We characterize the outcomes of patients with cancer and COVID-19 and identify potential prognostic factors. Methods: The COVID- 19 and Cancer Consortium (CCC19) cohort study includes patients with active or prior hematologic or invasive solid malignancies reported across academic and community sites. Results: We included 1,018 cases accrued March-April 2020. Median age was 66 years (range, 18-90). Breast (20%) and prostate (16%) cancers were most prevalent;43% of patients were on active anti-cancer treatment. At time of data analysis, 106 patients (10.4%) have died and 26% met the composite outcome of death, severe illness requiring hospitalization, and/or mechanical ventilation. In multivariable logistic regression analysis, independent factors associated with increased 30- day mortality were age, male sex, former smoking, ECOG performance status (2 versus 0/1: partially adjusted odds ratio (pAOR) 2.74, 95% CI 1.31-5.7;3/4 versus 0/1: pAOR 5.34, 95% CI 2.44-11.69), active malignancy (stable/responding, pAOR 1.93, 95% CI 1.06-3.5;progressing, pAOR 3.79, 95% CI 1.78-8.08), and receipt of azithromycin and hydroxychloroquine. Tumor type, race/ethnicity, obesity, number of comorbidities, recent surgery, and type of active cancer therapy were not significant factors for mortality. Conclusions: All-cause 30-day mortality and severe illness in this cohort were significantly higher than previously reported for the general population and were associated with general risk factors as well as those unique to patients with cancer. Cancer type and treatment were not independently associated with increased 30-day mortality. Longer follow-up is needed to better understand the impact of COVID-19 on outcomes in patients with cancer, including the ability to continue specific cancer treatments.
ABSTRACT
The COVID-19 pandemic caused a change in our society and put health systems in crisis worldwide. Different risk factors and comorbidities have been found that increase the risk of mortality when acquiring this infection. The use of alternative devices to the cigarette like the electronic cigarettes, the vapers have been studied widely and generators of great controversy since it has been discovered that they also produce different pulmonary affections. When developing the SARS-CoV2 infection, different theories have been generated about the greater predisposition to a worse prognosis of people who use electronic cigarettes; however, the information on this continues in discovery. A group of experts made up of oncologists, infectologists, pulmonologists, and epidemiologists met to review the literature and then generate theories about the impact of electronic cigarettes on SARS-CoV2 infection.