Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibody profiling and prevalence in US patients during the SARS-CoV2 pandemic

Background Antibody diagnostics play an important role in disease detection and can potentially aid in monitoring of the immune responses to see if an individual has developed immunity. Developing high throughput diagnostics which does not involve handling of infectious material becomes imperative in the case of pandemics such as the recent outbreak of SARS-CoV2. Methods A protein microarray technology was used to detect the plurality of antibody response to four novel antigens namely S1 glycoprotein, Receptor binding domain (RBD), S2 glycoprotein and Nucleoprotein of the novel coronavirus named SARS-CoV2 using serum samples. A DBS card was additionally used to compare its performance with a venipuncture-based serum separator tube (SST) draw. Results The three main subclasses of antibodies IgM, IgA and IgG were analyzed to see the variations in immune responses in the affected population and compared to their microbial RT-PCR based NP swab results. The clinical sensitivity and specificity were determined to be 99.67% and 99.77%. In the matrix comparison study, which would enable patients to test without risk of transmitting the virus, DBS (Dried Blood Spot) matched with higher than 98% accuracy to a venipuncture-based SST collection. Conclusion Multiplex testing enables higher sensitivity and specificity which is essential while establishing exposure on a population scale. This flexible platform along with a discrete collection methodology would be crucial and broadly useful to scale up testing in current and future pandemics. Minimum sample volume that can be collected using DBS cards can be processed in this multiplex pillar plate format enabling the capacity to provide the reliability of high throughput analyzers while having the ease of collection similar to rapid tests.
Protein Folding Simulations in Kink Model

We develop a highly predictive energy function to describe the low temperature crystallographic structure of myoglobin with sub-\AA ngstr\"om precision. We use the energy function to investigate the way how myoglobin folds.For this we employ the Glauber protocol, with a variable ambient temperature. We first increase the temperature so that the structure unfolds into a random coil. We then lower thetemperature back to its original value, and monitor how the myoglobin folds towards its native state.We find that the folding proceeds by $\alpha$-helix nucleation, and that the ordering of helix formation parallels experimental observations. There is also a molten globule folding intermediate, with a radius of gyration that matches the experimentally measured value. We estimate the relative folding times between a random chain and molten globule, and between molten globule and the native state, and we find that the ratio is consistentwith the experimentally measured values. We also propose a number of novel experimental characteristics that could be measured in future experiments.
Seasonal Variation of Glucosinolate Hydrolysis Products in Commercial White and Red Cabbages (Brassica oleracea var. capitata)

Brassica vegetables contain glucosinolates, which are well-known for their potential to form health-promoting isothiocyanates. Among those crucifers, white and red cabbage are commonly consumed vegetables, exhibiting different glucosinolate and hydrolysis profiles thereof. Regarding the health beneficial effects from these vegetables, more information, especially concerning the seasonal variation of glucosinolate profiles and the formation of their bioactive hydrolysis products in commercial cabbages, is needed. In this study, glucosinolates and glucosinolate hydrolysis product profiles in red and white cabbages from three different food retailers were monitored over six different sampling dates across the selling season in autumn. For the first time, it was shown that, while glucosinolate profiles were similar in each cabbage variety, glucosinolate hydrolysis product profiles and hydrolysis behavior varied considerably over the season. The highest total isothiocyanate concentrations were observed in conventional red (1.66 μmol/g FW) and organic white (0.93 μmol/g FW) cabbages purchased at the first sampling date in September. Here, red cabbage was with up to 1.06 μmol/g FW of 4-(methylsulfinyl)butyl isothiocyanate (sulforaphane), an excellent source for this health-promoting isothiocyanate. Cabbages purchased 11 weeks later in autumn released lower levels of isothiocyanates, but mainly nitriles and epithionitriles. The results indicate that commercial cabbages purchased in early autumn could be healthier options than those purchased later in the year.
MicroRNA profiling as a novel diagnostic tool for identification of patients with inflammatory and/or virally induced cardiomyopathies

MicroRNAs (miRNAs) might be used as prospective biomarkers for the identification of unexplained heart failure caused by a viral and/or inflammatory process. The aim of this study was to identify and to evaluate prognostic miRNAs in serum of patients with inflammatory heart diseases diagnosed by endomyocardial biopsies.
The Perils and Pitfalls of Block Design for EEG Classification Experiments

A recent paper <xref ref-type="bibr" rid="ref1">[1]</xref> claims to classify brain processing evoked in subjects watching ImageNet stimuli as measured with EEG and to employ a representation derived from this processing to construct a novel object classifier. That paper, together with a series of subsequent papers <xref ref-type="bibr" rid="ref2">[2]</xref> , <xref ref-type="bibr" rid="ref3">[3]</xref> , <xref ref-type="bibr" rid="ref4">[4]</xref> , <xref ref-type="bibr" rid="ref5">[5]</xref> , <xref ref-type="bibr" rid="ref6">[6]</xref> , <xref ref-type="bibr" rid="ref7">[7]</xref> , <xref ref-type="bibr" rid="ref8">[8]</xref> , claims to achieve successful results on a wide variety of computer-vision tasks, including object classification, transfer learning, and generation of images depicting human perception and thought using brain-derived representations measured through EEG. Our novel experiments and analyses demonstrate that their results crucially depend on the block design that they employ, where all stimuli of a given class are presented together, and fail with a rapid-event design, where stimuli of different classes are randomly intermixed. The block design leads to classification of arbitrary brain states based on block-level temporal correlations that are known to exist in all EEG data, rather than stimulus-related activity. Because every trial in their test sets comes from the same block as many trials in the corresponding training sets, their block design thus leads to classifying arbitrary temporal artifacts of the data instead of stimulus-related activity. This invalidates all subsequent analyses performed on this data in multiple published papers and calls into question all of the reported results. We further show that a novel object classifier constructed with a random codebook performs as well as or better than a novel object classifier constructed with the representation extracted from EEG data, suggesting that the performance of their classifier constructed with a representation extracted from EEG data does not benefit from the brain-derived representation. Together, our results illustrate the far-reaching implications of the temporal autocorrelations that exist in all neuroimaging data for classification experiments. Further, our results calibrate the underlying difficulty of the tasks involved and caution against overly optimistic, but incorrect, claims to the contrary.
Solvent extraction in the process industries

Volume 1: 1. Contacting Equipment 1.1. Aromatics extraction with the Kuhni column, an application requiring an extreme design flexibility. 2. Processes. 2.1. Separation and recovery of nickel and cobalt in ammoniacal systems - process development. 3. Rare Earths. 3.1. Some progresses in solvent extraction of rare earth in China. 4. Hydrodynamics and Mass Transfer. 4.1. The effect of viscosity on drop transport and breakup in pulsed and stirred liquid-liquid extraction columns. 5. Metals (Reagents and Modifiers). 5.1. Liquid-liquid extraction and molecular modelling. Volume 2: 6. Supercritical Fluid Extraction. 6.1. Supercritical fluid extraction using amine-entrainers. 7. Inorganic Materials. 7.1. The development of liquid-liquid extraction processes for the inorganic chemical industry using steady-state simulation. 8. Liquid Membranes. 8.1. Metal separation by supported liquid membranes: effect of the membrane characteristics. 9. Biotechnology. 9.1. Interfacial mass transfer and partition studies during whole broth extraction. 10. Organic Chemicals. 10.1. Comparative studies with phenol, furfural and N-methyl-2-pyrrolidone as solvents for lube oils extraction. 11. Control and Modelling. 11.1. Control of liquid-liquid extraction columns. Volume 3: 12. Metals 2 (Metals Extraction). 12.1. The solvent extraction of As, Sb and Bi from copper refining electrolytes using organophosphorus reagents. 13. Nuclear 1. 13.1. Solvent extraction processes used for the recycling of irradiated nuclear fuel. 14. Environmental. 14.1. AmMAR: concept for metal waste recovery. 15. Fundamentals. 15.1. Interfacial phenomena in hydrometallurgical solvent extraction systems. 16. Nuclear 2. 16.1. Distribution coefficient measurements of Tc, Np[IV] and Np[Vi] between nitric acid solutions containing U and Pu and 30per cent TBP/n-dodecane. Part contents.
Formulation Technology: Emulsions, Suspensions, Solid Forms

Colloids, phases, interfaces Emulsions - properties and production Microemulsions, vesicles and liposomes Foams Production and properties of colloid suspensions and dispersions Solids Rheology Solubility parameters Solubility, crystallization Purification, detergency Cosmetics Pharmaceutical technology Food formulations Agroformulations Pigments and dyes.
New insights into signal transduction pathways in adrenal steroidogenesis: role of mitochondrial fusion, lipid mediators, and MAPK phosphatases

Hormone-receptor signal transduction has been extensively studied in adrenal gland. Zona glomerulosa and fasciculata cells are responsible for glucocorticoid and mineralocorticoid synthesis by adrenocorticotropin (ACTH) and angiotensin II (Ang II) stimulation, respectively. Since the rate-limiting step in steroidogenesis occurs in the mitochondria, these organelles are key players in the process. The maintenance of functional mitochondria depends on mitochondrial dynamics, which involves at least two opposite events, i.e., mitochondrial fusion and fission. This review presents state-of-the-art data on the role of mitochondrial fusion proteins, such as mitofusin 2 (Mfn2) and optic atrophy 1 (OPA1), in Ang II-stimulated steroidogenesis in adrenocortical cells. Both proteins are upregulated by Ang II, and Mfn2 is strictly necessary for adrenal steroid synthesis. The signaling cascades of steroidogenic hormones involve an increase in several lipidic metabolites such as arachidonic acid (AA). In turn, AA metabolization renders several eicosanoids released to the extracellular medium able to bind membrane receptors. This report discusses OXER1, an oxoeicosanoid receptor which has recently arisen as a novel participant in adrenocortical hormone-stimulated steroidogenesis through its activation by AA-derived 5-oxo-ETE. This work also intends to broaden knowledge of phospho/dephosphorylation relevance in adrenocortical cells, particularly MAP kinase phosphatases (MKPs) role in steroidogenesis. At least three MKPs participate in steroid production and processes such as the cellular cycle, either directly or by means of MAP kinase regulation. To sum up, this review discusses the emerging role of mitochondrial fusion proteins, OXER1 and MKPs in the regulation of steroid synthesis in adrenal cortex cells.
Intimate Partner Violence and Lower Relationship Quality Are Associated With Faster Biological Aging

The characteristics of people’s relationships have relevance to health—high quality romantic relationships are associated with improved health whereas intimate partner violence is associated with poorer health. Recently, increased attention has been focused on the biological processes underpinning these associations. A geroscience approach—examining whether close relationship characteristics are associated with biological aging—would complement previous research focused on individual disease pathways. This study used participants from the Dunedin Study (N = 974) to investigate relationship characteristics and biological aging across almost 20 years, from age 26 to 45. Being involved in romantic relationships was associated with slower biological aging, β = −0.12, p < . 001. This difference represented 2.9 years of aging over the two decades. Greater relationship quality was also associated with slower biological aging, β = −0.19, p < . 001, whereas higher levels of partner violence were associated with faster biological aging, β = 0.25, p < . 001. A 1 SD difference in these characteristics was associated with a difference of 1.0 and 1.3 years of aging over the two decades, respectively. Secondary analyses suggested that experiencing violence from a partner was more strongly associated with biological aging than perpetrating violence, and that the experience of physical violence was more strongly associated with aging than psychological violence. These findings suggest that the characteristics of romantic relationships have relevance for biological aging in midlife. Interventions designed to increase relationship quality and decrease partner violence could reduce future morbidity and early mortality by slowing people’s biological aging.
The impact of delayed heart rate recovery on prevalent hypertension

ABSTRACT Objectives: Delayed heart rate recovery (HRR) is considered an indicator of autonomic nervous dysfunction, which is a primary pathological mechanism of hypertension. The present study aimed to explore the independent association between delayed HRR and prevalent hypertension. Methods: In this cross-sectional study, 314 inpatients were recruited between January 2018 and December 2019. HRR was defined as the peak heart rate during exercise minus the 2nd-minute heart rate after exercise in the treadmill exercise test. Results: The mean HRR in the hypertension group was lower than that in the non-hypertension group (41 bpm vs. 46 bpm; P < 0.001). After full adjustment, each standard deviation increase in HRR was associated with a 35% decrease in the risk of prevalent hypertension (OR: 0.65, 95% CI: 0.48–0.87; P = 0.004). When the HRR was divided into quartiles, the risk in the top quartile was 26% of that in the bottom quartile (OR: 0.26, 95% CI: 0.12–0.56; P = 0.001). Furthermore, smooth curve fitting showed that the risk of prevalent hypertension decreased linearly with the increase in HRR. Conclusion: Delayed HRR was independently associated with prevalent hypertension. The association was linear and robust over the entire range of HRR. The present study suggested that delayed HRR could be used to optimize hypertension risk stratification.
Localized effect of treated wastewater effluent on the resistome of an urban watershed

Abstract Background Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a river’s complete set of antibiotic resistance genes (the “resistome") is affected by the release of treated effluent into surface waters. Results Here we used high-throughput, deep metagenomic sequencing to investigate the effect of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the river’s resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points was dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds. Conclusions Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect seems to be localized, with little measurable effect in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.
Luminescence imaging of leaf damage induced by lipid peroxidation products and its modulation by β-cyclocitral.

Lipid peroxidation is a primary event associated with oxidative stress in plants. This phenomenon secondarily generates bioactive and/or toxic compounds such as reactive carbonyl species (RCS), phytoprostanes and phytofurans, as confirmed here in Arabidopsis plants exposed to photo-oxidative stress conditions. We analyzed the effects of exogenous applications of secondary lipid oxidation products on Arabidopsis plants by luminescence techniques. Oxidative damage to attached leaves was measured by autoluminescence imaging, using a highly-sensitive CCD camera, and the activity of the detoxification pathway, dependent on the transcription regulator SCARECROW-LIKE 14 (SCL14), was monitored with a bioluminescent line expressing the firefly LUCIFERASE (LUC) gene under the control of the ALKENAL REDUCTASE (AER) gene promoter. We identified 4-hydroxynonenal (HNE), and to a lesser extent 4-hydroxyhexenal (HHE), as highly reactive compounds that are harmful to leaves and can trigger AER gene expression, contrary to other RCS (pentenal, hexenal) and to isoprostanoids. Although the levels of HNE and other RCS were enhanced in the SCL14-deficient mutant (scl14), exogenously applied HNE was similarly damaging to this mutant, its wild-type parent and a SCL14-overexpressing transgenic line (OE:SCL14). However, strongly boosting the SCL14 detoxification pathway and AER expression by a pre-treatment of OE:SCL14 with the signaling apocarotenoid β-cyclocitral cancelled the damaging effects of HNE. Conversely, in the scl14 mutant, the effects of β-cyclocitral and HNE were additive, leading to enhanced leaf damage. These results indicate that the cellular detoxification pathway induced by the low-toxicity β-cyclocitral targets highly toxic compounds produced during lipid peroxidation, reminiscent of a safener-type mode of action. This article is protected by copyright. All rights reserved.
Seven-Layer Model in Complex Networks Link Prediction: A Survey

Link prediction is the most basic and essential problem in complex networks. This study analyzes the observed topological, time, attributive, label, weight, directional, and symbolic features and auxiliary information to find the lack of connection and predict the future possible connection. For discussion and analysis of the evolution of the network, the network model is of great significance. In the past two decades, link prediction has attracted extensive attention from experts in various fields, who have published numerous high-level papers, but few combine interdisciplinary characteristics. This survey analyzes and discusses the existing link prediction methods. The idea of stratification is introduced into the classification system of link prediction for the first time and proposes the design idea of a seven-layer model, namely the network, metadata, feature classification, selection input, processing, selection, and output layers. Among them, the processing layer divides link prediction methods into similarity-based, probabilistic, likelihood, supervised learning, semi-supervised learning, unsupervised learning, and reinforcement learning methods. The input features, evaluation metrics, complex analysis, experimental comparisons, relative merits, common dataset and open-source implementations for each link prediction method are then discussed in detail. Through analysis and comparison, we found that the link prediction method based on graph structure features has better prediction performance. Finally, the future development direction of link prediction in complex networks is discussed.
Sociodemographic factors associated with patients hospitalised for coccidioidomycosis in California and Arizona, State Inpatient Database 2005–2011

Abstract Coccidioidomycosis is endemic in the Southwestern United States. Disseminated infection can be life-threatening and is responsible for hospitalisation and significant healthcare resource utilisation. There are limited data evaluating factors associated with hospitalisation for coccidioidomycosis. We conducted a cross-sectional study to assess incidence and factors associated with coccidioidomycosis-associated hospitalisation in California and Arizona. We analysed hospital discharge data obtained from the State Inpatient Dataset for California and Arizona between 2005 and 2011 and performed multivariable logistic regression examining factors associated with coccidioidomycosis-associated hospitalisation. During our time frame, we found 23 758 coccidioidomycosis-associated hospitalisations. Coccidioidomycosis incidence was over sixfold higher in Arizona compared to California (198.9 vs. 29.6/100 000 person-years). In our multivariable model, coccidioidomycosis-associated hospitalisation was associated with age group 40–49 years (referent group: age 18–29 years, adjusted odds ratio (aOR) = 1.50 (95% confidence interval (CI) 1.43–1.59)), African American race (referent group: Caucasian, aOR = 1.98 (95% CI 1.89–2.06)), residing in a large rural town (referent group: urban area, aOR = 2.28 (95% CI 2.19–2.39)), uncomplicated diabetes (aOR = 1.47 (95% CI 1.41–1.52)) chronic obstructive pulmonary disease (aOR = 1.59 (95% CI 1.54–1.65)) and higher number of comorbidities (aOR = 1.02 (95% CI 1.02–1.03) for each point in the Elixhauser score). Identifying persons at highest risk for hospitalisation with coccidioidomycosis may be helpful for future prevention efforts.