Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal Serological Analysis and Neutralizing Antibody Levels in Coronavirus Disease 2019 Convalescent Patients

Abstract Background Understanding the longitudinal trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is crucial for diagnosis of prior infection and predicting future immunity. Methods We conducted a longitudinal analysis of coronavirus disease 2019 convalescent patients, with neutralizing antibody assays and SARS-CoV-2 serological assay platforms using SARS-CoV-2 spike (S) or nucleocapsid (N) antigens. Results Sensitivities of serological assays in diagnosing prior SARS-CoV-2 infection changed with time. One widely used commercial platform that had an initial sensitivity of >95% declined to 71% at 81–100 days after diagnosis. The trajectories of median binding antibody titers measured over approximately 3–4 months were not dependent on the use of SARS-CoV-2 N or S proteins as antigen. The median neutralization titer decreased by approximately 45% per month. Each serological assay gave quantitative antibody titers that were correlated with SARS-CoV-2 neutralization titers, but S-based serological assay measurements better predicted neutralization potency. Correlation between S-binding and neutralization titers deteriorated with time, and decreases in neutralization titers were not predicted by changes in S-binding antibody titers. Conclusions Different SARS-CoV-2 serological assays are more or less well suited for surveillance versus prediction of serum neutralization potency. Extended follow-up should facilitate the establishment of appropriate serological correlates of protection against SARS-CoV-2 reinfection.
Weakly Supervised Deep Learning-Based Optical Coherence Tomography Angiography

Optical coherence tomography angiography (OCTA) is a promising imaging modality for microvasculature studies. Deep learning networks have been widely applied in the field of OCTA reconstruction, benefiting from its powerful mapping capability among images. However, these existing deep learning-based methods depend on high-quality labels, which are hard to acquire considering imaging hardware limitations and practical data acquisition conditions. In this article, we proposed an unprecedented weakly supervised deep learning-based pipeline for OCTA reconstruction task, in the absence of high-quality training labels. The proposed pipeline was investigated on an in vivo animal dataset and a human eye dataset by a cross-validation strategy. Compared with supervised learning approaches, the proposed approach demonstrated similar or even better performance in the OCTA reconstruction task. These investigations indicate that the proposed weakly supervised learning strategy is well capable of performing OCTA reconstruction, and has a certain potential towards clinical applications.
Reliability and Validity of the Function-Focused Care Checklist for Caregivers.

PURPOSE The purpose of this study was to test the reliability and validity of the Function-Focused Care Checklist for Caregivers using Rasch analysis. DESIGN This was a descriptive study using data from the study "Testing the Dissemination and Implementation of Function-Focused Care for Assisted Living Using the Evidence Integration Triangle. " The study was approved by a university institutional review board. METHODS A Rasch analysis was completed, which included 691 staff-resident observations from 85 assisted living facilities. FINDINGS There was evidence of internal consistency (alpha coefficient of .93), construct validity except for a high OUTFIT statistic for wheelchair mobility, and hypothesis testing based on an increase in performance of function-focused care by caregivers over 12 months. CONCLUSIONS The findings provided psychometric support for the measure and guidance for revisions. CLINICAL RELEVANCE This measure can be used clinically to teach caregivers to provide function-focused care to residents in assisted living.
Influence of cancellous bone material and dead zone on stress-strain, bone stimulus and bone remodelling around the tibia for total ankle replacement

Extreme bone resorption due to bone remodelling is one of the reasons for ankle component loosening. Finite element (FE) analysis has been effectively used nowadays for pre-clinical analysis of orthopaedic implants. For FE modelling, the selection of bone material and dead zone play a vital role to understand the bone remodelling. This study deals with the effects of different cancellous elastic modulus-density relationships and dead zone on bone remodelling around the tibia owing to total ankle replacement (TAR), using finite element analysis with physiological loading conditions. This study also investigated the bone stimulus distribution in the tibia to identify the initial indication of bone density changes due to bone remodelling. Additionally, the Hoffman failure criterion was used to investigate the chances of implant-bone interface failure due to different cancellous bone material modelling and bone remodelling. The present bone remodelling study consists of three different dead or lazy zones (±0.75, ±0.60 and ±0.35) to examine the influence of the dead zone on bone remodelling. Differences in stress/strain distribution were observed in the tibia bone due to different cancellous bone material modelling. Despite little variations, bone density changes due to bone remodelling were found to be almost similar for two FE models having different cancellous bone material. Similar to these results, the effect of different dead zone on bone density changes due to bone remodelling was found to be minimal. Bone stimulus distribution in the cancellous bone was found to be almost similar for FE models having different cancellous bone material modelling and different dead zones. To understand the stress/strain and interface related failure of the tibial component, cancellous bone material modelling plays a crucial role. However, cancellous bone material modelling and dead zone have minimal influence on bone remodelling around the tibia cancellous bone due to TAR.
Prompting Pedagogical Change through Promoting Active Lifestyles Paradoxes

This study explored approaches to promoting active lifestyles (PAL) in schools which aimed to inform and develop physical education (PE) trainees and teachers’ health-related philosophies and pedagogies. Thirty-two secondary school PE trainees and teachers involved in a University-based Initial Teacher Education partnership in England participated in this study during the period 2015–2019. The participants were involved in professional development which included an introduction to research-informed PAL ‘paradoxes’ associated with promoting active lifestyles. Participants were asked to review their own health-related philosophies and practices in light of these paradoxes and were encouraged to use them to influence their own pedagogies as well as those of colleagues/peers. Participants found the PAL paradoxes interesting, surprising and perplexing; expressed a keen desire to address and solve them; and experienced the joys and challenges of influencing colleagues’/peers’ health-related philosophies and pedagogies. The findings suggest that this innovative low-cost, flexible and accessible approach to pedagogical change has the potential to engage PE teachers, increase their effectiveness as promoters of physical activity, and to greatly enhance the subject’s contribution to public health. This is significant, given calls for new pedagogical approaches and teachers’ previously reported lack of engagement in professional development in this area.
Phylogenetic analysis of maximal oxygen consumption during exercise (V̇O2,max) and ecological correlates among lizard species

ABSTRACT The maximum amount of oxygen consumed during forced exercise (V̇O2,max) sets the upper limit to the effort that can be sustained over relatively long periods and can limit activity levels in nature. Among ectotherms, V̇O2,max is primarily affected by body size and body temperature, but it should also co-adapt with behavior, ecology and life history aspects. We compiled published data from 11 different families of lizards, including 58 species and 7 populations (total of 65 data points) and tested whether V̇O2,max was related to diet (herbivore, insectivore, insectivore/carnivore, carnivore and omnivore), climate (tropical, temperate and arid), nocturnality, viviparity or family. We fitted models that included body mass and measurement temperature as covariates, and all possible combinations of other independent variables using ordinary least squares (OLS) and phylogenetic regressions assuming an Ornstein–Uhlenbeck model of residual trait evolution (RegOU). The sum of Akaike weights for each independent variable revealed viviparity (Σwi=0.996) and the combined set of dummy variables coding for helodermatids, varanids and skinks (Σwi=0.996) as the most important predictors. These three families had relatively high V̇O2,max and are composed mainly of active foragers that probably benefit from higher V̇O2,max. Viviparity had a negative effect on V̇O2,max. Ecological or behavioral factors associated with viviparity (e.g. activity levels), but not included here, may explain this effect. The average allometric slope of V̇O2,max from the top eight models (which accounted for 99% of the cumulative evidence) was 0.803, which is similar to that reported previously for lizards and for mammals in general. Summary: Among species of lizards, helodermatids, varanids and skinks (which are mainly active foragers) have relatively high maximal aerobic capacity during forced exercise (V̇O2,maxV̇O2,max), whereas viviparous species have relatively low V̇O2,maxV̇O2,max.
The Nutritional Impact of Milk Beverages in Reducing Nutrient Inadequacy among Children Aged One to Five Years in the Philippines: A Dietary Modelling Study

Around half of Filipino children are not consuming any dairy products on a given day, which has shown to be associated with increased risk of inadequate nutrient intakes. The current study applies dietary modelling to assess the nutritional impact of meeting dairy recommendations in reducing nutrient inadequacy in children aged one to five years in the Philippines. Dietary intake data of Filipino children aged one to five years (n = 3864) were analyzed from the 8th National Nutrition Survey 2013. Children who did not meet national dairy recommendations were identified. Two scenarios were applied, based on two types of commonly consumed milk products by the survey participants. In scenario one, one serving of powdered milk was added to the diet of these children. In scenario two, one serving of a young children milk (YCM) or preschool children milk (PCM) was added to the diet of children aged one to two years and three to five years, respectively. Mean nutrient intakes and percentages of children with inadequate intakes were estimated before and after applying modelling scenarios. Scenario one demonstrated improvement in calcium, phosphorus, sodium, vitamin A and riboflavin intakes, while in scenario two, further improvement of intakes of a wider range of nutrients including iron, selenium, zinc, magnesium, potassium, vitamins C, D, E, thiamin, niacin, vitamins B6, and B12 was observed. In both scenarios, if all children would meet their dairy recommendations, theoretical reductions in population nutrient inadequacy would be observed for all micronutrients, for example, only 20% of children aged one to two years would be inadequate in vitamin A instead of the current 60%, iron inadequacy would see a 5% reduction, and approximately 10% reduction for calcium and 20% reduction for folate. The present study is the first to apply dietary modelling to assess the theoretical impact of meeting dairy recommendations on nutrient inadequacy in children in the Philippines. Dairy consumption should be encouraged as part of the strategy to reduce nutrient inadequacies. Calcium, iron, vitamins D, E, and folate are of concern in the Philippines as the level of inadequacies are extremely high in early years, YCM and PCM can help increase the intake of these nutrients.
Environmental Issues and Neurological Manifestations Associated with COVID-19 Pandemic: New Aspects of the Disease?

Coronavirus (SARS-CoV-2) emerged in China in December 2019 and rapidly caused a global health pandemic. Current evidence seems to suggest a possible link with ecosystem disequilibrium and even air pollution. The primary manifestations affect respiratory and circulatory systems, but neurological features are also being reported through case reports and case series. We summarize neurological symptoms and complications associated with COVID-19. We have searched for original articles published in PubMed/Medline, PubMed Central and Google Scholar using the following keywords: “COVID-19”, “Coronavirus”, “pandemic”, “SARS-COV-2”, “neurology”, “neurological”, “complications” and “manifestations”. We found around 1000 publications addressing the issue of neurological conditions associated with COVID-19 infection. Amongst those, headache and dizziness are the most common reported symptoms followed by encephalopathy and delirium, while the most frequent complications are cerebrovascular accidents, Guillain–Barré syndrome, acute transverse myelitis, and acute encephalitis. Specific symptoms affecting the peripheral nervous system such as hyposmia and dysgeusia are the most common manifestations recorded in the selected studies. Interestingly, it was noted that these kinds of neurological symptoms might precede the typical features, such as fever and cough, in COVID patients. Neurological symptoms and complications associated with COVID-19 should be considered as a part of the clinical features of this novel global pandemic.
Morphology, Morphogenesis and Phylogenetic Position of the Soil Hypotrichous Ciliate, Parabistichella dieckmanni (Foissner, 1998) Foissner, 2016 (Ciliophora, Hypotrichia), with Notes on the Phylogeny of Parabistichella

The morphology, morphogenesis and molecular phylogeny of Parabistichella dieckmanni (Foissner, 1998) Foissner, 2016, isolated from north China, were investigated. The Chinese population was characterized as having five to seven frontal cirri in corona, four to seven buccal cirri arranged in a row, two to four short frontal rows and two long frontoventral rows, three to seven transverse cirri, four macronuclear nodules, three dorsal kineties following a Gonostomum‐pattern, and caudal cirri absent. Morphogenetic research reveals that the main characteristics during binary fission are as follows: (1) the long left frontoventral row is formed by two or three anlagen; (2) the posterior part of the parental adoral zone of membranelles is renewed, and the oral primordium of the opisthe is formed intrakinetally; (3) FVT‐anlagen I to VI (or V, VII) produce each a frontal cirrus to form the frontal corona; (4) development of dorsal kineties follows the Gonostomum‐pattern. Phylogenetic analyses showed that P. dieckmanni does not group with other Parabistichella species. Therefore, the genus Parabistichella is polyphyletic. Additionally, Parabistichella variabilis n. comb. (basionym: Bistichella variabilis He & Xu, 2011) and Parabistichella cheni n. nom. (basionym: Parabistichella variabilis Jiang et al., 2013) were suggested.
Mechanical and Biocompatibility Properties of Calcium Phosphate Bioceramics Derived from Salmon Fish Bone Wastes

Natural calcium phosphates derived from fish wastes are a promising material for biomedical application. However, their sintered ceramics are not fully characterized in terms of mechanical and biological properties. In this study, natural calcium phosphate was synthesized through a thermal calcination process from salmon fish bone wastes. The salmon-derived calcium phosphates (sCaP) were sintered at different temperatures to obtain natural calcium phosphate bioceramics and then were investigated in terms of their microstructure, mechanical properties and biocompatibility. In particular, this work is concerned with the effects of grain size on the relative density and microhardness of the sCaP bioceramics. Ca/P ratio of the sintered sCaP ranged from 1.73 to 1.52 when the sintering temperature was raised from 1000 to 1300 °C. The crystal phase of all the sCaP bioceramics obtained was biphasic and composed of hydroxyapatite (HA) and tricalcium phosphate (TCP). The density and microhardness of the sCaP bioceramics increased in the temperature interval 1000–1100 °C, while at temperatures higher than 1100 °C, these properties were not significantly altered. The highest compressive strength of 116 MPa was recorded for the samples sintered at 1100 °C. In vitro biocompatibility was also examined in the behavior of osteosarcoma (Saos-2) cells, indicating that the sCaP bioceramics had no cytotoxicity effect. Salmon-derived biphasic calcium phosphates (BCP) have the potential to contribute to the development of bone substituted materials.
Modification of Grey Water Treatment Using Combination of Cascade Aeration and Biofiltration

A combination of cascade aeration and biofiltration systems is one of the available ecological treatments to reduce the concentration of pollutants in grey water and resolve the problem of acute water crisis supply in Iraq. An experimental constructed grey water treatment system has been installed at Al-Mustansiriya University, College of Engineering during the period from January to December 2012. The performance of the treatment schemes has been evaluated by monitoring the quality of the raw grey water and effluent on these samples which are: pH, COD (chemical oxygen demand), TSS (total suspended solids), TDS (total dissolved solids), PO4 3- (phosphates), NO3 2- (nitrates), NO - (nitrites), oils & grease, NH3-N (ammonia-nitrogen) and some anions and cations. The average removal rate of COD was more than 60% that of NH3-N, NO3-N, NO2-N, TDS and TSS that were 55%-89%, 59%-74%, 79%-98%, 17%-52% and 51%-87%, respectively. Also the results indicate that the removal efficiency of ions concentrations such as Ca 2+ , Mg 2+ , Na + , K + were 78%-96%, 73%-97%, 14%-47% and 44%-64%, respectively, while for cations such as SO4 2- , Cl - and PO4 3- , the removal efficiencies were 33%-79%, 27%-61% and 81%-99%, respectively. Finally oils & grease was 79%-88%.
Prognostic value of TNF-α-308 and IFN-γ-874 single nucleotide polymorphisms and their plasma levels in patients with aplastic anemia

Background Aplastic anemia (AA), an unusual hematological disease, is characterized by hypoplasia of the bone marrow and failure to form blood cells of all three lineages resulting in pancytopenia. This study aimed to investigate TNF-α-308 and IFN-γ-874 gene polymorphisms and their respective plasma protein levels in patients with AA and healthy controls. Methods Two hundred and forty individuals were included in this study; the case group comprised 120 AA patients, while 120 healthy individuals served as controls. Genotyping was performed using the PCR-restriction length fragment polymorphism method and TNF-α-308 and IFN-γ-874 plasma levels were evaluated using an ELISA kit. Results There was a significantly higher prevalence of the IFN-γ-874 genotype in patients with AA than in healthy controls, while the TNF-α-308 genotype was associated with lower risk of developing AA. Furthermore, the levels of both TNF-α-308 and IFN-γ-874 were higher in the plasma of AA patients. Conclusion Our findings suggest that the IFN-γ-874 genotype may be a greater risk factor in the causation of AA, whereas the TNF-α-308 genotype has a protective role in the North Indian population.
Stochastic time-dependent enzyme kinetics: closed-form solution and transient bimodality

We derive an approximate closed-form solution to the chemical master equation describing the Michaelis-Menten reaction mechanism of enzyme action. In particular, assuming that the probability of a complex dissociating into enzyme and substrate is significantly larger than the probability of a product formation event, we obtain expressions for the time-dependent marginal probability distributions of the number of substrate and enzyme molecules. For delta function initial conditions, we show that the substrate distribution is either unimodal at all times or else becomes bimodal at intermediate times. This transient bimodality, which has no deterministic counterpart, manifests when the initial number of substrate molecules is much larger than the total number of enzyme molecules and if the frequency of enzyme-substrate binding events is large enough. Furthermore, we show that our closed-form solution is different from the solution of the chemical master equation reduced by means of the widely used discrete stochastic Michaelis-Menten approximation, where the propensity for substrate decay has a hyperbolic dependence on the number of substrate molecules. The differences arise because the latter does not take into account enzyme number fluctuations while our approach includes them. We confirm by means of stochastic simulation of all the elementary reaction steps in the Michaelis-Menten mechanism that our closed-form solution is accurate over a larger region of parameter space than that obtained using the discrete stochastic Michaelis-Menten approximation.
Association between Acute Pancreatitis and COVID-19: Could Pancreatitis Be the Missing Piece of the Puzzle about Increased Mortality Rates?

Abstract Background The COVID-19 pandemic caused by SARS-CoV-2 commenced in Wuhan China in 2019 and soon spread worldwide. SARS-CoV-2 enters the cell by binding to the ACE II receptor and begins viral replication. The effects and clinical findings of SARS-CoV-2 on the liver, kidney, heart, gastrointestinal (GI) system and especially lungs have been widely discussed. However, the effects on the pancreas—another organ that also expresses ACE II—have not been studied. Methods This work prospectively evaluated data from 316 patients who were admitted with a diagnosis of COVID-19 pneumonia. The patients were categorized into three according to the severity of pneumonia (mild, severe, critical). Demographic data, rate of pancreatitis, biochemical parameters, and radiological images from each group were analyzed. The patients were divided into two groups and outcomes were compared: COVID-19 patients with acute pancreatitis (Group P) and without acute pancreatitis (Group C). Results The median age was 54 (18–87), and the median age for patients with acute pancreatitis was 55 (26–84). As an expected finding, we found a positive correlation between advanced age and mortality (p = 0.0003). 12.6% of the patients had acute pancreatitis. While pancreatitis was not seen in patients on mild status, the rate of pancreatitis was 32.5% in critical patients. Hospitalization and mortality rates were higher in patients with COVID-19 accompanied by acute pancreatitis (p = 0.0038 and p < 0.0001, respectively). C-Reactive Protein (CRP) and ferritin were significantly higher in those who had pancreatitis (p < 0.0001). D-Dimer and procalcitonin levels had only a small difference (p = 0.1127 and p = 0.3403, respectively) Conclusion Acute pancreatitis alone is a clinical condition that can lead to mortality and may be one of the reasons for the exaggerated immune response developing in the progression of COVID-19. Our results point out that the presence of pancreatic damage triggered by SARS-CoV-2 can deteriorate the clinical condition of patients and the mortality rate may increase in these patients.