Miracle-dz/UniFAR-FTUs huggingface dataset:
No indications for overt innate immune suppression in critically ill COVID-19 patients

At the end of March 2020, there were in excess of 800.000 confirmed cases of coronavirus disease 2019 (COVID-19) worldwide. Several reports suggest that, in severe cases, COVID-19 may cause a hyperinflammatory 'cytokine storm'. However, unlike SARS-CoV infection, high levels of anti-inflammatory mediators have also been reported in COVID-19 patients. One study reported that 16% of COVID-19 patients who died developed secondary infection, which might indicate an immune-suppressed state. We explored kinetics of mHLA-DR expression, the most widely used marker of innate immune suppression in critically ill patients, in COVID-19 patients admitted to the ICU. Twenty-four confirmed COVID-19 patients were included, of which 75% was male and 79% had comorbidities. All patients were mechanically ventilated and exhibited large high levels of inflammatory parameters such as CRP and PCT. mHLA-DR expression levels were mostly within the normal range of 15000 - 45000 mAb/cell and showed no change over time. COVID-19 patients displayed notably higher mHLA-DR expression levels compared with bacterial septic shock patients. None of the COVID-19 patients developed a secondary infection. In conclusion, despite a pronounced inflammatory response, mHLA-DR expression kinetics indicate no overt innate immune suppression in COVID-19 patients. These data signify that innate immune suppression as a negative feedback mechanism following PAMP-induced inflammation appears not to be present in COVID-19.
ESTIMATION OF COVID-19 CASES IN FRANCE AND IN DIFFERENT COUNTRIES: HOMOGENEISATION BASED ON MORTALITY

Every day the authorities of different countries provide an estimate of the number of persons affected by Covid-19 and a count of fatality. We propose to use the fatality reported in each country to provide a better estimate (Ct0-estimated) of the number of cases at a given time t0. Ct0-estimated = (Ft0 / Fr-est) * (1+ [C(est-d) / C(est-3d)])6 With Ft0: number of actual fatalities reported in a country at time t0; Fr-est: estimated fatality rate; C(est-d): estimated fatalities 18 days before t0; C(est-3d): estimated fatalities 21 days before t0. Based on Ct0-estimated calculated using a fatality rate of 2%, we assessed the number of cases April 10th, 2020 in Belgium, China, France, Germany, Iran, Italy, South Korea, Netherlands, Spain, United Kingdom and USA. This number reached 2,872,097 in France and 924,892 persons in Germany. The proposed formulas also make it possible to evaluate the impact of policies to prevent the spread of epidemic on the appearance of new cases.
Spatial Correlation of Particulate Matter Pollution and Death Rate of COVID-19

The Coronavirus (COVID-19) epidemic, which was first reported in December 2019 in Wuhan, China, has caused 3,314 death as of March 31, 2020 in China. This study aimed to investigate the spatial associations of daily particulate matter (PM) concentrations with death rate of COVID-19 in China. We conducted a cross-sectional analysis to examine the spatial associations of daily PM2.5 and PM10 concentrations with death rate of COVID-19 in China through multiple linear regression method. We found that COVID-19 held higher death rates with increasing concentration of PM2.5 and PM10 levels in the spatial scale, which may affect the process of patients developed from mild to severe and finally influence the prognosis of COVID-19 patients.
Public perceptions and experiences of social distancing and social isolation during the COVID-19 pandemic: a UK-based focus group study

Objective This study explored UK public perceptions and experiences of social distancing and social isolation related to the COVID-19 pandemic. Design This qualitative study comprised five focus groups, carried out online during the early stages of the UK’s stay at home order (‘lockdown’), and analysed using a thematic approach. Setting Focus groups took place via online videoconferencing. Participants Participants (n=27) were all UK residents aged 18 years and older, representing a range of gender, ethnic, age and occupational backgrounds. Results Qualitative analysis revealed four main themes: (1) loss—participants’ loss of (in-person) social interaction, loss of income and loss of structure and routine led to psychological and emotional ‘losses’ such as loss of motivation, loss of meaning and loss of self-worth; (2) criticisms of government communication—participants reported a lack of trust in government and a lack of clarity in the guidelines around social distancing and isolation; (3) adherence—participants reported high self-adherence to social distancing guidelines but reported seeing or hearing of non-adherence in others; (4) uncertainty around social reintegration and the future—some participants felt they would have lingering concerns over social contact while others were eager to return to high levels of social activity. Most participants, and particularly those in low-paid or precarious employment, reported feeling that the social distancing and isolation associated with COVID-19 policy has had negative impacts on their mental health and well-being during the early stages of the UK’s ‘lockdown’. Conclusions A rapid response is necessary in terms of public health programming to mitigate the mental health impacts of COVID-19 social distancing and isolation. Social distancing and isolation ‘exit strategies’ must account for the fact that, although some individuals will voluntarily or habitually continue to socially distance, others will seek high levels of social engagement as soon as possible.
Towards reduction in bias in epidemic curves due to outcome misclassification through Bayesian analysis of time-series of laboratory test results: Case study of COVID-19 in Alberta, Canada and Philadelphia, USA

The aim of our work was to better understand misclassification errors in identification of true cases of COVID-19 and to study the impact of these errors in epidemic curves. We examined publically available time-series data of laboratory tests for SARS-CoV-2 viral infection, the causal agent for COVID-19, to try to explore, using a Bayesian approach, about the sensitivity and specificity of the PCR-based diagnostic test. Data originated from Alberta, Canada (available on 3/28/2020) and city of Philadelphia, USA (available on 3/31/2020). Our analysis revealed that the data were compatible with near-perfect specificity but it was challenging to gain information about sensitivity (prior and posterior largely overlapped). We applied these insights to uncertainty/bias analysis of epidemic curves into jurisdictions under the assumptions of both improving and degrading sensitivity. If the sensitivity improved from 60 to 95%, the observed and adjusted epidemic curves likely fall within the 95% confidence intervals of the observed counts. However, bias in the shape and peak of the epidemic curves can be pronounced, if sensitivity either degrades or remains poor in the 60-70% range. In the extreme scenario, hundreds of undiagnosed cases, even among tested, are possible, potentially leading to further unchecked contagion should these cases not self-isolate. The best way to better understand bias in the epidemic curves of COVID-19 due to errors in testing is to empirically evaluate misclassification of diagnosis in clinical settings and apply this knowledge to adjustment of epidemic curves, a task for which the Bayesian method we presented is well-suited.
Modeling Covid-19 dynamics for real-time estimates and projections: an application to Albanian data

The SARS-CoV-2 epidemic is one of the biggest challenges healthcare systems worldwide have ever had to face. To curb transmission many countries have adopted social distancing measures and travel restrictions. Estimating the effect of these measures in each context is challenging and requires mathematical models of the transmission dynamics. Projections for the future course of the epidemic strongly rely on model predictions and accurate representation of real-time data as they accumulate. Here I develop an SEIR modeling framework for Covid-19, to evaluate reported cases and fatalities, and to enable forecasting using evidence-based Bayesian parameter estimation. This Bayesian framework offers a tool to parametrize real-time dynamics of Covid-19 cases, and explore the effect of control as it unfolds in any setting. I apply the model to Covid-19 data from Albania, where drastic control measures were put in place already on the day of the first confirmed case. Evaluating the dynamics of reported cases 9-31 March 2020, I estimate parameters and make preliminary projections. Three weeks into the measures, Albanian data already indicate a strong signature of more than 40% transmission reduction, and lend support to a progressively increasing effect of control measures rather than a static one. In the Albanian setting, the model and data match well, projecting the peak of the outbreak may be around 5-15 April, and be contained within 300 active confirmed cases if control continues with the same trend. This framework can be used to understand the quantitative effects of different control measures in real-time, and inform adaptive intervention for success in other settings.
Favipiravir versus Arbidol for COVID-19: A Randomized Clinical Trial

Background No clinically proven effective antiviral strategy exists for the epidemic Coronavirus Disease 2019 (COVID-19). Methods We conducted a prospective, randomized, controlled, open-label multicenter trial involving adult patients with COVID-19. Patients were randomly assigned in a 1:1 ratio to receive conventional therapy plus Umifenovir (Arbidol) (200mg*3/day) or Favipiravir (1600mg*2/first day followed by 600mg*2/day) for 10 days. The primary outcome was clinical recovery rate of Day 7. Latency to relief for pyrexia and cough, the rate of auxiliary oxygen therapy (AOT) or noninvasive mechanical ventilation (NMV) were the secondary outcomes. Safety data were collected for 17 days. Results 240 enrolled COVID-19 patients underwent randomization; 120 patients were assigned to receive Favipiravir (116 assessed), and 120 to receive Arbidol (120 assessed). Clinical recovery rate of Day 7 does not significantly differ between Favipiravir group (71/116) and Arbidol group (62/120) (P=0.1396, difference of recovery rate: 0.0954; 95% CI: -0.0305 to 0.2213). Favipiravir led to shorter latencies to relief for both pyrexia (difference: 1.70 days, P<0.0001) and cough (difference: 1.75 days, P<0.0001). No difference was observed of AOT or NMV rate (both P>0.05). The most frequently observed Favipiravir-associated adverse event was raised serum uric acid (16/116, OR: 5.52, P=0.0014). Conclusions Among patients with COVID-19, Favipiravir, compared to Arbidol, did not significantly improve the clinically recovery rate at Day 7. Favipiravir significantly improved the latency to relief for pyrexia and cough. Adverse effects caused Favipiravir are mild and manageable. This trial is registered with Chictr.org. cn (ChiCTR2000030254).
The effectiveness of a web-based Dutch parenting program to prevent overweight in children 9–13 years of age: study protocol for a two-armed cluster randomized controlled trial

Background: Although parental support is an important component in overweight prevention programs for children, current programs pay remarkably little attention to the role of parenting. To close this gap, we developed a web-based parenting program for parents entitled “Making a healthy deal with your child”. This e-learning program can be incorporated into existing prevention programs, thereby improving these interventions by reinforcing the role of parenting and providing parents with practical tools for use in everyday situations in order to stimulate a healthy lifestyle. Here, we report the research design of a study to determine the effectiveness of our e-learning program. Methods/Design: The effectiveness of an e-learning program was studied in a two-armed cluster randomized controlled trial. Parents of children 9–13 years of age who live in the Nijmegen region, the Netherlands, and who participated in the existing school-based overweight prevention program “Scoring for Health” were invited to participate in this study. Our goal was to recruit 322 parent–child dyads. At the school grade level, parents were randomly assigned to either the intervention group (which received e-learning and a brochure) or the control group (which received only the brochure); the participants were stratified by ethnicity. Measurements were taken from both the parents and the children at baseline, and then 5 and 12 months after baseline. Primary outcomes included the child’s dietary and sedentary behavior, and level of physical activity. Secondary outcomes included general parenting style, specific parenting practices (e.g., set of rules, modeling, and monitoring), and parental self-efficacy. Discussion: We hypothesize that children of parents who follow the e-learning program will have a healthier diet, will be less sedentary, and will have a higher level of physical activity compared to the children in the control group. If the e-learning program is found to be effective, it can be incorporated into existing overweight prevention programs for children (e.g., “Scoring for Health”), as well as activities regarding Youth Health Care. Trial registration: Dutch Trial Register: NTR3938. Date of registration: April 7, 2013.
Factors Affecting Breastfeeding and Complementary Feeding Choices for Children Aged 24 to 48 Months

Objectives: The aim of this study was to evaluate factors that affected decisions regarding breastfeeding and complementary feeding practices in children aged 24 to 48 months. Methods: Children aged 24 to 48 months who were presented at the outpatient clinic of a single hospital over a 6-month period were included in the study. Children who were born prematurely, hospitalized in the neonatal intensive care unit, and those with a chronic disease were excluded. A questionnaire was administered to parents who provided consent. Data related to demographic characteristics, socioeconomic status, and infant nutrition practices were collected and analyzed. Results: A total of 100 cases were included. The distribution of the gender of the children was 49% female and 51% male, and the mean age was 36.2±7.8 months. The mean duration of exclusive breastfeeding was 4.83±1.23 months, the mean length of total breastfeeding was 17.65±8.44 months, and the mean initiation of complementary feeding was 5.71±1.23 months of age. The most frequent reason provided for the cessation of breastfeeding was the mother’s decision to wean. The duration of exclusive breastfeeding and the total length of breastfeeding feeding was significantly shorter among children who were born by cesarean section, and those who used a pacifier and or feeding bottle. Non-working mothers used formula for a longer period (p=0.043) and introduced solid foods and the use of utensils later than other mothers (p=0.001, p=0.03, respectively). Complementary food was provided to the infants of families whose monthly income level was less than TL 1000 earlier than in higher income level groups (p=0.04). The results of this study also showed that complementary food choices were most influenced by older members of the family and members of the mother’s immediate circle (42%) and healthcare professionals (36%). Mothers who received information about the addition of complementary food did not demonstrate a significantly different length of time devoted to exclusive breastfeeding; however, the duration of breastfeeding overall, alone and in combination with solid foods, increased (p=0.03). Conclusion: Before the birth, families should be informed and prepared regarding the necessity of exclusive breastfeeding for the first 6 months and the continuation of breastfeeding until 2 years of age, the potential impact of relevant factors related to the type of birth, and the potentially negative effects of the use of a pacifier or bottle. All members of the family, particularly mothers and close relatives, should be advised about proper complementary feeding techniques, including the need to increase the consistency of food gradually, introducing solid foods before the 10th month, and using natural, home-cooked items instead of prepared foods. The appropriate information and guidance should be provided to all families with consideration for their education level, social environment, and life conditions.
Enhanced Visual Search in Infancy Predicts Emerging Autism Symptoms

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Idarubicin and cytarabine in combination with gemtuzumab ozogamicin (IAGO) for untreated patients with high-risk MDS or AML evolved from MDS: a phase II study from the EORTC and GIMEMA Leukemia Groups (protocol 06013)

The primary objective of this trial was to assess the feasibility, toxicity profile, and antitumor activity of gemtuzumab ozogamicin (GO) combined with a chemotherapy remission-induction regimen in adults with untreated highrisk myelodysplastic syndrome (HR-MDS) or secondary acute myeloid leukemia (sAML). In this phase II trial, 30 patients with median age of 58 years received 1 day of GO as a 1-h infusion at the dose level of 5 mg/m on day 7 of the remission-induction course further consisting of a continuous infusion of cytarabine 100 mg/m/day for 10 days and idarubicin 12 mg/m/day on days 1, 3, and 5. A consolidation course, consisting of intermediate-dose cytarabine (A) and idarubicin (I) followed by hematopoietic stem cell transplantation (HSCT) was planned for patients in complete remission (CR). The primary endpoints were response rate (CR/CRi) and severe toxicity rate. The secondary endpoint(s) were survival and progression-free survival (PFS) from start of treatment. Thirteen patients (43 %) achieved CR (eight patients) or CR with incomplete hematopoietic recovery (CRi) (five patients). In patients who achieved CR or CRi, the median time to recovery of neutrophils to 0.5×10/l and of platelets to >50×10/l was 29 and 30 days, respectively. Grade 3 to 4 severe toxicities occurred in nine patients. The most prominent was liver toxicity, as shown by elevated bilirubin levels in 16 patients and one case of nonfatal veno-occlusive disease (VOD). All 13 patients with CR/CRi received consolidation therapy, which was followed by allogeneic HSCT in five patients and autologous HSCT in three patients. According to the statistical design of the study, the idarubicin and cytarabine in combination with gemtuzumab ozogamicin (IAGO) regimen did not show sufficient activity to warrant further exploration of this regimen in adult patients with HR-MDS or sAML.
The effect of the video game Mindlight on anxiety symptoms in children with an Autism Spectrum Disorder

Background: In the clinical setting, a large proportion of children with an autism spectrum disorder (ASD) experience anxiety symptoms. Because anxiety is an important cause of impairment for children with an ASD, it is necessary that effective anxiety interventions are implemented for these children. Recently, a serious game called Mindlight has been developed that is focused on decreasing anxiety in children. This approach is based on recent research suggesting that video games might be suitable as an intervention vehicle to enhance mental health in children. In the present study it will be investigated whether Mindlight is effective in decreasing (sub) clinical anxiety symptoms in children who are diagnosed with an ASD. Methods/Design: The present study involves a randomized controlled trial (RCT) with two conditions (experimental versus control), in which it is investigated whether Mindlight is effective in decreasing (sub) clinical anxiety symptoms in children with an ASD. For this study, children of 8–16 years old with a diagnosis of an ASD and (sub) clinical anxiety symptoms will be randomly assigned to the experimental (N = 60) or the control (N = 60) condition. Children in the experimental condition will play Mindlight for one hour per week, for six consecutive weeks. Children in the control condition will play the puzzle game Triple Town, also for one hour per week and for six consecutive weeks. All children will complete assessments at baseline, post-intervention and 3-months follow-up. Furthermore, parents and teachers will also complete assessments at the same time points. The primary outcome will be child report of anxiety symptoms. Secondary outcomes will be parent report of child anxiety, child/parent report of depressive symptoms, and parent/teacher report of social functioning and behavior problems. Discussion: This paper aims to describe a study that will examine the effect of the serious game Mindlight on (sub) clinical anxiety symptoms of children with an ASD in the age of 8–16 years old. It is expected that children in the experimental condition will show lower levels of anxiety symptoms at 3-months follow-up, compared to children in the control condition. If Mindlight turns out to be effective, it could be an important contribution to the already existing interventions for anxiety in children with an ASD. Mindlight could then be implemented as an evidence-based treatment for anxiety symptoms in children with an ASD in mental health institutes and special education schools. Trial registration: Dutch Trial Register NTR5069. Registered 20 April 2015.
Treatment and survival rates of stage IV pancreatic cancer at VA hospitals: a nation-wide study.

Background Metastatic pancreatic cancer (MPC) is associated with an extremely high mortality. Current NCCN guidelines recommend systemic therapy, as it is superior to best supportive care. Undertreatment of MPC continues to be an issue. Recent treatment and survival data of MPC in Veterans' Affairs' (VA) hospitals have not been published. The relationship between MPC treatment and survival and the American College of Surgeons' (ACS) Committee on Cancer (CoC) accreditation in VA hospitals has not been studied. Methods Nationwide data from the National Veterans Affairs Cancer Cube Registry was analyzed. In total, 6,775 patients were diagnosed with MPC between 2000 and 2014. CoC accreditation of each VA hospital was obtained using the ACS website. Results MPC constitutes 52.31% of all pancreatic cancer diagnosed (6,775/12,951 cases). The near totality was men (97.44%). The above 70 years age group and the 60-70 years age group were the most common ages at diagnosis with 39.39% and 38.02% respectively. The proportion of early-onset pancreatic cancer (EOPC) was 2.84%. When compared to all stages of pancreatic cancer, stage IV pancreatic cancer had a lower proportion of cancer originating from the head of the pancreas (39.33% versus 50.63%) and more originating from the tail (17.99% versus 13.39%). Tumors originating from head of the pancreas are more likely to cause biliary symptoms and thus are more likely to be caught at an earlier stage. Overall, treatment rate in the VA at the national level with first-line chemotherapy was 37.61%. The rate of treatment over the years has increased in a linear fashion from 33.01% in 2000 to 41.95% in 2014. This has corresponded with an increase of 1-5 years survival of 9.29% in 2000 to 22.99% in 2014 and 5-10 years survival from 0.96% in 2000 to 6.00% in 2012. Treatment rates in CoC-accredited and non-CoC accredited VA hospitals were similar (38.94% and 38.12%, respectively). Survival rates in CoC-accredited and non-COC accredited VAs were similar with a 1-5 years survival rate of 8.89% and 8.57%, respectively. Conclusions Treatment and survival of MPC have risen significantly in the past decade at VA hospitals. CoC accreditation is not associated with a change in treatment or survival rates.