Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of headache disorders on COVID-19 survival: a world population-based analysis

Importance: COVID-19 has not impacted people or countries uniformly. This disparity has prompted investigations to identify clinical and genetic predictors of COVID-19 mortality. Headache, a COVID-19 symptom, has been associated with positive disease prognosis. It is logical to consider whether primary headache disorders, among the most prevalent and disabling diseases globally, may also be associated with reduced viral mortality and thereby may have arisen as adaptive host defences. Objective: To study the relationship between COVID-19 mortality and primary headache disorders. Main outcome measure: Using a generalized additive model regression (GAM), we analysed data across 171 nations to identify variables which impact COVID-19 mortality rates (demographics, national wealth and government effectiveness, pandemic management indexes, latitude of the country's capital, prevalence of headache disorders and other diseases). We performed similar analyses of seasonal influenza mortality. Separately, we meta-analysed studies of COVID-19 inpatient survival reporting headache, using PRISMA guidelines. Results: In the global population-level analysis, we observed that a higher prevalence of headache disorders was associated with a higher COVID-19 mortality rate, and represented the main variable contributing to differences in COVID-19 mortality rates between countries (37.8%; F value=10.68). By contrast, we observed a negative trend between the prevalence of headache disorders and influenza death rates. Controversially, when considering headache as a symptom of COVID-19, in the 48 meta-analysed studies we observed a significantly higher risk ratio of survival (RR:2.178 [1.882-2.520], p<0.0001) among COVID-19 inpatients with headache. Conclusions and Relevance: Headache as a primary disorder is more prevalent in nations with higher COVID-19 mortality, whereas headache as a COVID-19 symptom is associated with enhanced survival. Further studies should clarify whether primary headache disorders represent a risk factor for mortality for COVID-19 or, rather, whether this association reflects evolutionary adaptive processes to enhance survival that, in the case of COVID-19, are insufficiently protective.
Photoluminescence study of novel phosphorus-doped ZnO nanotetrapods synthesized by chemical vapour deposition

Novel phosphorus-doped and undoped single crystal ZnO nanotetrapods were fabricated on sapphire by a simple chemical vapour deposition method, using phosphorus pentoxide (P2O5) as the dopant source. The optical properties of the samples were investigated by photoluminescence (PL) spectroscopy. Low-temperature PL measurements of phosphorus-doped and undoped samples were compared, and the results indicated a decrease in deep level defects due to the incorporation of a phosphorus acceptor dopant. The PL spectrum of the phosphorus-doped sample at 10 K exhibited several acceptor-bound exciton related emission peaks. The effect of phosphorus doping on the optical characteristics of the samples was investigated by excitation intensity and temperature dependent PL spectra. The acceptor-binding energies of the phosphorus dopant were estimated to be about 120 meV, in good agreement with the corresponding theoretical and experimental values in phosphorus-doped ZnO films and nanowires.
Methylome-wide association study of early life stressors and adult mental health

The environment and events that we are exposed to in utero, during birth and in early childhood influence our future physical and mental health. The underlying mechanisms that lead to these outcomes in adulthood are unclear, but long-term changes in epigenetic marks, such as DNA methylation, could act as a mediating factor or biomarker. DNA methylation data was assayed at 713,522 CpG sites from 9,537 participants of the Generation Scotland: Scottish Family Health Study, a family-based cohort with extensive data on genetic, medical, family history and lifestyle information. Methylome-wide association studies of eight early life environment phenotypes and two adult mental health phenotypes were conducted using DNA methylation data collected from adult whole blood samples. Two genes involved with different developmental pathways (PRICKLE2 and ABI1) were annotated to CpG sites associated with preterm birth (P < 1.27 x 10-9). A further two genes important to the development of sensory pathways (SOBP and RPGRIP1) were annotated to sites associated with low birth weight (P < 4.35 x 10-8). Genes and gene-sets annotated from associated CpGs sites and methylation profile scores were then used to quantify any overlap between the early life environment and mental health traits. However, there was no evidence of any overlap after applying a correction for multiple testing. Time of year of birth was found to be associated with a significant difference in estimated lymphocyte and neutrophil counts. Early life environments influence the risk of developing mental health disorders later in life; however, this study provides no evidence that this is mediated by stable changes to the methylome detectable in peripheral blood.
The Peptide Bond Quenches Indole Fluorescence

The effect of the peptide bond on protein fluorescence is an important unresolved question in tryptophan photophysics. Definitive evidence for the peptide group as a weak quencher of indole fluorescence was obtained from solute quenching studies with a series of model compounds. Two amides are required for detectable quenching of 3-methylindole fluorescence and the quenching rate depends on the distance between amides. The bimolecular rate constants kq of malonamide, N-acetylasparagine, N-acetylglycinamide, and N-acetylglutamine are 33 × 107, 8.8 × 107, 6.6 × 107, and 2.2 × 107 M-1 s-1, respectively. Transient absorption and temperature dependence of the fluorescence lifetime measured in the absence and presence of quencher gave strong circumstantial evidence for electron transfer as the quenching mechanism. Triplet yields were measured for five indole derivatives using transient absorption. Intersystem crossing rates were calculated from triplet yield and fluorescence lifetime data. The intersystem cross.
ROC plot and AUC with binary classifiers: pragmatic analysis of cognitive screening instruments

Receiver operating characteristic (ROC) plots are a performance graphing method showing the relative trade-off between test benefits (true positive rate) and costs (false positive rate) with the area under the curve (AUC) giving a scalar value of test performance. It has been suggested that ROC and AUC may be potentially misleading when examining binary predictors rather than continuous scales. The purpose of this study was to examine ROC plots and AUC values for two binary classifiers of cognitive status (applause sign, attended with sign), a cognitive screening instrument producing categorical data (Codex), and a continuous scale screening test (Mini-Addenbrooke's Cognitive Examination), the latter two also analysed with single fixed threshold tests. For each of these plots, AUC was calculated using different methods. The findings indicate that if categorical or continuous measures are dichotomised then the calculated AUC may be an underestimate, thus affecting screening or diagnostic test accuracy which in the context of clinical practice may prove to be misleading.
Analysis of accumulated SARS-CoV-2 seroconversion in North Carolina: The COVID-19 Community Research Partnership

Introduction The COVID-19 Community Research Partnership is a population-based longitudinal syndromic and sero-surveillance study. The study includes over 17,000 participants from six healthcare systems in North Carolina who submitted over 49,000 serology results. The purpose of this study is to use these serology data to estimate the cumulative proportion of the North Carolina population that has either been infected with SARS-CoV-2 or developed a measurable humoral response to vaccination. Methods Adult community residents were invited to participate in the study between April 2020 and February 2021. Demographic information was collected and daily symptom screen was completed using a secure, HIPPA-compliant, online portal. A portion of participants were mailed kits containing a lateral flow assay to be used in-home to test for presence of anti-SARS-CoV-2 IgM or IgG antibodies. The cumulative proportion of participants who tested positive at least once during the study was calculated. A standard Cox proportional hazards model was constructed to illustrate the probability of seroconversion over time up to December 20, 2020 (before vaccines available). A separate analysis was performed to describe the influence of vaccines during an extended period through February 15, 2021. Results 17,688 participants contributed at least one serology result. Approximately two-thirds of the population were female and almost three-quarters were between 30 and 64 years of age. The average number of serology test results submitted per participant was 3.0 ({+/-}1.9). At December 20, 2020, the overall probability of seropositivity in the CCRP population was 32.6%. At February 15, 2021 the probability among healthcare workers and non-healthcare workers was 49% and 83%, respectively. An inflection upward in the probability of seropositivity was demonstrated around the end of December, suggesting an influence of vaccinations, especially for healthcare workers. Among healthcare workers, those in the oldest age category (60+ years) were 38% less likely to have seroconverted by February 15, 2021. Conclusions Results of this study suggest more North Carolina residents may have been infected with SARS-CoV-2 than the number of documented cases as determined by positive RNA or antigen tests. The influence of vaccinations on seropositivity among North Carolina residents is also demonstrated. Additional research is needed to fully characterize the impact of seropositivity on immunity and the ultimate course of the pandemic.
Acceptability of contact management and care of simple cases of COVID-19 at home: a mixed-method study in Senegal

Introduction: In mid-2020, due to the health system challenges from increased COVID-19 cases, the Ministry of Health and Social Action in Senegal opted for contact management and care of simple cases at home. The objective of the study was to determine the acceptability of contact management, home care of simple cases of COVID-19, and its associated factors. Method: This was a sequential mixed-method study. We collected data from June 11, 2020, to July 10, 2020, for the quantitative survey (N=813) and from August 24 to September 16, 2020, for the qualitative survey (N=30). We carried out a sampling strategy using marginal quotas at the national level. We collected data using a structured questionnaire in a telephone interview for the quantitative survey and using an interview guide formulated from the initial results of the quantitative survey for the qualitative data. We assessed acceptability using binomial logistic regression combined with content analysis. Results: The care of simple cases of COVID-19 at home was well accepted (78.5%). This result was justified for some (saturation of the health system) but not for others (risk of contamination). The use of home contact management was less accepted (51.4%), with risk limitation as the main reason given. The acceptability of home-based care for simple cases was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.55 [95%CI: 1.04,2.28]), regular research into COVID-19 (ORaj: 2.12 [95%CI: 1.45,3.12]), belief in the existence of treatment (ORaj: 1.82 [95%CI: 1.19,2.83]), and confidence in institutional information (ORaj: 2.10 [95%CI: 1.43,3.10]). The acceptability of home-based contact management was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.77 [95%CI: 1.27,2.48]), regular research for information on COVID-19 (ORaj: 2.39 [95%CI: 1.76,3.26]), and confidence in the government in the fight against the epidemic (ORaj: 1.51 [95%CI: 1.10,2.08]). Conclusion: Regular information on the disease, knowledge of its mode of transmission and trust in institutions are factors in accepting COVID-19 management at the community level. Authorities should take these factors into account for better communication to improve the acceptability of home-based care. Keywords: COVID-19, Acceptability, Simple cases, Contacts, Mixed method, Senegal
Temporal Aspects of the Association between Exposure to the World Trade Center Disaster and Risk of Skin Melanoma

Rescue/recovery workers who responded to the World Trade Center (WTC) attacks on 9/11/2001 were exposed to known/suspected carcinogens. Studies have identified an increased risk of skin melanoma in this population, but the temporal aspects of the association have not been investigated. A total of 44,540 non-Hispanic White workers from the WTC Combined Rescue/Recovery Cohort were observed between 3/12/2002 and 12/31/2015. Cancer data were obtained via linkages with 13 state registries. Poisson regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI), using the New York State population as reference; change points in the HRs were estimated using profile likelihood. We observed 247 incident cases of skin melanoma. No increase in incidence was detected between 2002 and 2004. Beginning in 2005, the HR was 1.34 (95% CI 1.18-1.52). A dose-response relationship was observed according to time worked on the WTC effort. Risk of melanoma among non-Hispanic White WTC rescue/recovery workers was elevated, beginning in 2005. While WTC-related exposure to ultraviolet radiation or other agents might have contributed to this result, exposures other than the WTC effort and enhanced medical surveillance cannot be discounted. Our results support the continued surveillance of this population for melanoma.
A Data-driven Framework for Learning and Visualizing Characteristics of Thrombotic Event Phenotypes from Clinical Texts

Automatically identifying thrombotic phenotypes based on clinical data, particularly clinical texts, can be challenging. Although many investigators have developed targeted information extraction methods for identifying thrombotic phenotypes from radiology notes, these methods can be time consuming to train, require large amounts of training data, and may miss subtle textual clues predictive of a thrombotic phenotype from notes beyond the radiology note. We developed a generalizable, data-driven framework for learning, characterizing, and visualizing clinical concepts from both radiology and discharge summaries predictive of thrombotic phenotypes.
Unplanned hospital visits after ambulatory surgical care

Objectives: We sought to assess the rate of unplanned hospital visits among patients undergoing ambulatory surgery. Summary Background Data: The majority of surgeries performed in the United States now take place in outpatient settings. Post-discharge hospital visit rates have been shown to vary widely, suggesting variation in surgical or discharge care quality. Complicating efforts to address quality, most facilities and surgeons are unaware of their patients' hospital visits after surgery since patients may present to a different hospital. Methods: We used state-level, administrative data from the Agency for Healthcare Research and Quality's Healthcare Cost and Utilization Project from California to assess unplanned hospital visits after ambulatory surgery. To compare rates across centers, we determined the age, sex, and procedure-adjusted rates of hospital visits for each facility using 2-level, hierarchical, generalized linear models using methods similar to existing Centers for Medicare and Medicaid Services measures. Results: Among a total of 1,260,619 ambulatory same-day surgeries from 440 surgical facilities, the risk adjusted 30-day rate of unplanned hospital visits was 4.8%, with emergency department visits of 3.1% and hospital admissions of 1.7%. Several patient characteristics were associated with increased risk of unplanned hospitals visits, including increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure (p<0.001). Conclusions: The overall rate unplanned hospital visits within 30 days after same-day surgery is low but variable, suggesting a difference in the quality of care provided. Further, these rates are higher among specific patient populations and procedure types, suggesting areas for targeted improvement.
VXSlate: Combining Head Movement and Mobile Touch for Large Virtual Display Interaction

Virtual Reality (VR) headsets can open opportunities for users to accomplish complex tasks on large virtual displays, using compact setups. However, interacting with large virtual displays using existing interaction techniques might cause fatigue, especially for precise manipulations, due to the lack of physical surfaces. We designed VXSlate, an interaction technique that uses a large virtual display, as an expansion of a tablet. VXSlate combines a user’s head movements, as tracked by the VR headset, and touch interaction on the tablet. The user’s head movements position both a virtual representation of the tablet and of the user’s hand on the large virtual display. The user’s multi-touch interactions perform finely-tuned content manipulations.
Antibiotic residues in honey : a public health

Honey has numerous uses and composes formulations of many food, pharmaceutical, and cosmetic products due to its chemical, biological, and sensorial characteristics. In recent years, several reports and scientific articles claim the contamination of honey by antibiotics, a fact that is a public health problem since the ingestion of them can cause several side effects. In this sense, the purpose of this work was to carry out a literature review in international circulation databases about the contamination of honey by antibiotics in the last 10 years. It is observed in the literature that several quality control methods for evaluating this product have been developed, with the main objective of detecting trace concentrations of these compounds. In this context, the chromatographic techniques, rapid tests, immunoassays, and the use of emerging technologies that are considered sustainable for sample preparation stand out. When these methods are applied to honey samples, it is clear that the contamination of honeys by antibiotic residues has been growing every year, making it evident that programs for continuous monitoring of these residues in honeys are conducted. Also, not only has the amount of antibiotics increased, but also the diversity of assets being used. Regarding the residues present, the main antibiotics found in the evaluated samples belong to the class of tetracyclines, sulfonamides, aminoglycosides, macrolides, and amphenicols. However, few countries report maximum residue limits (MRL) allowed for these substances in honey, and in Brazil, as well as in the European Union, no MRL has been established for antibiotics in this product so far, which indicates that it is extremely important that MRL be adopted to ensure food safety for consumers.
A state space approach to fitting higher order moments of empirical financial series with GARCH model parameters

Here we have analysed a GARCH(1,1) model with the aim to fit higher order moments for different companies’ stock prices. When we assume a gaussian conditional distribution, we fail to capture any empirical data when fitting the first three even moments of financial time series. We show instead that a double gaussian conditional probability distribution better captures the higher order moments of the data. To demonstrate this point, we construct regions (phase diagrams) in the fourth and sixth order standardised moment space, where a GARCH(1,1) model can be used to fit these moments and compare them with ones obtained from empirical data for different sectors of the economy. We found that, the ability of the GARCH model with a double gaussian conditional distribution to fit higher order moments is dictated by the length of time window our data spans. It is seen for this model that we can only fit data collected within specific time window lengths and only with certain parameters of the conditional double gaussian distribution. This is indicated by the migration of the companies’ data out of the region of the phase diagram where GARCH is able to fit these moments. In order to overcome the non-stationarity of our modelling, we assume that the parameters of the GARCH model have time dependence.
Operation of a Vertical Thermosiphon Reboiler Experimental Facility at Reduced Pressures

Experimental data were obtained for the evaporation of water in a vertical thermosiphon reboiler having 50 tubes of 3 m length and 25.4 mm outer diameter. The effect of step changes in heat load was noted for operation over a pressure range from 0.2 to 1.0 bar. The reboiler behaviour exhibited three ‘operational modes’, and a definite transitional point that is independent of process pressure was observed between operational modes one and two. The influence of reduced pressures on the vertical thermosiphon reboiler sub-cooled heating length was significant. Overall heat transfer coefficients at 0.2 bar were about 60% of those at 1.0 bar and circulation rates were approximately halved. Two important considerations for the reboiler operation analysis were (a) the possible non-uniform behaviour of the reboiler tubes and (b) the change of phase and processes occurring on the reboiler shell as well as the tube side.
Hitting Minors on Bounded Treewidth Graphs. IV. An Optimal Algorithm

For a fixed finite collection of graphs F , the F-M-Deletion problem asks, given an n-vertex input graph G, for the minimum number of vertices that intersect all minor models in G of the graphs in F . by Courcelle’s Theorem, this problem can be solved in time fF (tw) · nO(1), where tw is the treewidth of G, for some function fF depending on F . In a recent series of articles, we have initiated the programme of optimizing asymptotically the function fF . Here we provide an algorithm showing that fF (tw) = 2O(tw · log tw) for every collection F . Prior to this work, the best known function fF was double-exponential in tw . In particular, our algorithm vastly extends the results of Jansen et al. [SODA 2014] for the particular case F = {K5, K3,3} and of Kociumaka and Pilipczuk [Algorithmica 2019] for graphs of bounded genus, and answers an open problem posed by Cygan et al. [Inf Comput 2017]. We combine several ingredients such as the machinery of boundaried graphs in dynamic programming via representatives, the Flat Wall Theorem, Bidimensionality, the irrelevant vertex technique, treewidth modulators, and protrusion replacement. Together with our previous results providing single-exponential algorithms for particular collections F [Theor Comput Sci 2020] and general lower bounds [J Comput Syst Sci 2020], our algorithm yields the following complexity dichotomy when F = {H} contains a single connected graph H, assuming the Exponential Time Hypothesis: fH(tw) = 2Θ(tw) if H is a contraction of the chair or the banner, and fH(tw) = 2Θ(tw · log tw) otherwise.