Miracle-dz/UniFAR-FTUs huggingface dataset:
Profiling antibody immune markers using nucleic acid systems

Author(s): Tsai, Cheng-ting | Advisor(s): Bertozzi, Carolyn R; Wemmer, David E | Abstract: Technology to profile nucleic acid materials has been greatly advanced over the past decade. Nowadays, tools such as real-time quantitative PCR (qPCR) and next generation sequencing (NGS) are standard workhorses for biomedical laboratory. However, in contrast to great advance in nucleic acid science, assays used to quantify proteins and antibodies immune markers remain much stagnant. Traditional assays immunoassays such as enzyme linked immunosorbent assays (ELISA) and western blots, invented almost half a century ago, are still widely used. These assays face limitations including low sensitivity, low specificity, limited multiplex power and requirement of large sample volume. To this end, I have thought to create a methodology that allows researchers to leverage advanced nucleic acid tools to profile protein and antibody immune markers. In this thesis, I will provide an overview on current landscapes of nucleic acid-based assays for protein and antibody immune markers, and discuss how the new nucleic acid-based assay that I developed differentiates and complements other nucleic acid tools. Then, I will describe in details about our new nucleic acid assays including the creation of protein-DNA conjugates and use of these reagents to transform protein/antibody identities into quantifiable nucleic acid signals. Furthermore, I will describe potential impact of such methods in research and clinical settings. Finally, I will discuss potential development that is required to make this assays widely deployable in research and clinical communities.
Three-Port Small Signal Admittance-Based Model of VSCs for Studies of Multi-Terminal HVDC Hybrid AC/DC Transmission Grids

Multi-terminal high voltage direct current (HVDC) systems, together with AC transmission systems and voltage source converters (VSCs), form hybrid AC/DC grids with complex dynamic and transient interactions. VSCs characterization taking into account DC- and AC-side dynamics in order to study these interactions is not yet well solved. This paper presents a three-port transfer admittance-based matrix model of VSCs that can be applied for such purpose. It is derived from dq-complex space vectors and characterizes both AC- and DC-side dynamics by relating AC- and DC-side current and voltages in a three-dimensional admittance transfer matrix which considers the VSC outer control loops. The paper also proposes a systematical procedure for studying multi-terminal HVDC hybrid AC/DC transmission grids by the Norton admittance method, where the proposed VSC model can be easily included in the Norton admittance matrix. This procedure allows the study of grid dynamics using impedance-based stability criteria. The proposed model and procedure are applied to a stability study in a multi-terminal HVDC hybrid AC/DC transmission grid. PSCAD/EMTDC simulations are used to validate the application.
What does the power outage on 9 August 2019 tell us about GB power system

The power outage on 9th August 2019 affected over 1 million customers in England and Wales and caused a major disruption to other critical infrastructures. While the power system responded exactly how it was designed to in response to an unsecured (N-2) event, it has uncovered important fault lines which may significantly affect reliability of the system in a near future. Over the last 10 years or so the GB power system has changed quite rapidly due to the decarbonisation drive and penetration of smart grids technologies. Hence it is increasingly difficult for the ESO to fully monitor, model and control the whole system and therefore the probability of hidden common modes of failures has increased. This would suggest that it might be prudent to strengthen the old (N-1) security standard by providing extra security margin. There were also other issues highlighted by the outage. Embedded generation reached such a high penetration level that it cannot be treated any longer as negative demand. Traditional under-frequency load shedding disconnects indiscriminately all customers on the disconnected feeders, including embedded generation and frequency response units, hence reducing its effectiveness. The ability of critical infrastructures and services to ride through the disturbances has to be closely monitored and tested. Finally, we have concluded that, in GB at least, power outages matter only if they affect critical infrastructures, especially transport, in London and the surrounding areas.
Study on The Antimicrobial Efficacy of Fabrics Finished With Nano Zinc Oxide Particles

In this paper, knitted fabrics were finished with Zinc Oxide nano particles of 30 nm & 90 nm size. To make knitted fabrics, 100% cotton and 67/33 Polyester / Cotton ring spun yarns made with varying twist factors were selected. Knitted fabrics were finished with nano ZnO particles by Exhaust – dry –cure method and the samples were evaluated for anti-microbial efficacy. Test results indicate that in general, anti-microbial efficacy of samples increases with increase in yarn twist and decrease in ZnO particle size. Polyester cotton blend samples show better anti-microbial efficacy than cotton samples.
Broadening the Impact of K–12 Science Education Collaborations in a Shifting Education Landscape

For more than 75 years, scientists and educators in New Mexico have provided programs that translate research on dryland ecosystems into broader scientific understanding for the public. Kindergarten through twelfth grade (K–12) students and teachers became a primary audience for these programs in the 1990s. Our team from the Jornada Long-Term Ecological Research Program, the US Department of Agriculture Agricultural Research Service Jornada Experimental Range, and the nonprofit Asombro Institute for Science Education navigated changes in K–12 science education to educate more than 200,000 students. The goal of this article is to describe our program’s responses to six education trends in order to provide experience-based guidance to others designing and delivering K–12 programs in a shifting science education landscape. We expect our experience will be relevant to others who are trying to scale their outreach programs to larger, more diverse communities while maintaining alignment with changing trends in education at local, state, and federal levels.
Endothelial Cell von Willebrand Factor Secretion in Health and Cardiovascular Disease

The main function of von Willebrand factor (vWF) is to initiate platelet adhesion upon vascular injury. The hallmark of acute and chronical inflammation is the widespread activation of endothelial cells which provokes excessive vWF secretion from the endothelial cell storage pool. The level of vWF in blood not only reflects the state of endothelial activation early on in the pathogenesis, but also predicts disease outcome. Elevation in the blood level of vWF occurs either by pathologic increase in the rate of basal vWF secretion or by increased evoked vWF release from dysfunctional/activated endothelial cells (ECs). The increase in plasma vWF is predictive of prothrombotic complications and multi-organ system failure associated with reduced survival in the context of severe inflammatory response syndrome, type II diabetes mellitus, stroke and other inflammatory cardiovascular disease states. This chapter focuses on the role of high circulating vWF levels in thrombotic and inflammatory disease while paying attention to the emerging vWFrelated drug development strategies.
WIM-based vehicle load models for urban highway bridge

With the rapid development of China's economy, many long-span bridges have been built and put into service. Vehicle load has been changing year by year in terms of the gross vehicle weight (GVW), the wheelbase and the traffic volume, especially the overload of heavy vehicles, which is a major challenge to the safety and durability of bridges. It is necessary to establish the vehicle load model through the measured traffic data for actual traffic conditions of the given bridge. In this study, the weigh-in-motion (WIM) data collected from an operational long-span urban highway bridge located in Wuhan, China, were used to analyze the statistical characteristics of vehicle loads. On the basis of the types of vehicles, (1) Considering the double or multimodal Gauss distribution characteristics of the GVW, the expectation maximization (EM) algorithm was used to estimate the statistical parameters of the Gauss distribution; (2) The generalized extreme value distribution (GEV) was used to develop the statistical model of the vehicle load extreme value; (3) The vehicle load extreme values in the design reference period of the urban highway bridge were estimated by the extreme value type I distribution; (4) According to the axle weight and the axle spacing, a statistical fatigue vehicle load model for the small and medium span urban highway bridges located in Wuhan, China was presented based on the Miner linear accumulated damage hypothesis and the effective fatigue damage principle.
Convective Drying Kinetics and Quality Parameters of European Cranberrybush

In this research, the effects of convective drying (60, 70, 80 and 90 °C) techniques on the drying kinetics, color, antioxidant capacity and total phenolic content of European cranberrybush were investigated in detail. To choose the best thin-layer drying models for the drying treatments, 10 mathematical models were compared for the experimental data. Depending on the evaluation by statistical tests, the Midilli et al model was determined to be the best suitable model to explain the drying behavior of European cranberrybush samples. All of the colorimetric parameters were influenced by drying temperatures. Antioxidant capacity and total phenolic content values of European cranberrybush samples displayed a significant reduction at low-temperature levels (60 and 70 °C) with regard to those at high-temperature levels (80 and 90 °C). In addition, the correlation analysis between antioxidant capacity and total phenolic content exhibited a high degree of correlation (R2= 0.8656).
Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of mutations spreading under relaxed selection. However, demonstrating the role of transition bias in adaptive evolution remains challenging. We addressed this challenge by analyzing adaptive antibiotic-resistance mutations in the major human pathogen Mycobacterium tuberculosis. We found strong evidence for transition bias in two independently curated datasets comprising 152 and 208 antibiotic resistance mutations. This was true at the level of mutational paths (distinct, adaptive DNA sequence changes) and events (individual instances of the adaptive DNA sequence changes), and across different genes and gene promoters conferring resistance to a diversity of antibiotics. It was also true for mutations that do not code for amino acid changes (in gene promoters and the ribosmal gene rrs), and for mutations that are synonymous to each other and are therefore likely to have similar fitness effects, suggesting that transition bias can be caused by a bias in mutation supply. These results point to a central role for transition bias in determining which mutations drive adaptive antibiotic resistance evolution in a key pathogen. Significance statement Whether and how transition bias influences adaptive evolution remain open questions. We studied 296 DNA mutations that confer antibiotic resistance to the human pathogen Mycobacterium tuberculosis. We uncovered strong transition bias among these mutations and also among the number of times each mutation has evolved in different strains or geographic locations, demonstrating that transition bias can influence adaptive evolution. For a subset of mutations, we were able to rule out an alternative selection-based hypothesis for this bias, indicating that transition bias can be caused by a biased mutation supply. By revealing this bias among M. Tuberculosis resistance mutations, our findings improve our ability to predict the mutational pathways by which pathogens overcome treatment.
Das Kluyveromyces lactis Killertoxin: Regulatoren des Zellimports und der intrazellulären Wirkung in Saccharomyces cerevisiae

In yeast, tRNA cleavage by the lethal zymocin toxin requires tRNA modification dependent on Elongator, a protein complex whose Elp1 subunit is phosphorylated. Elongator function depends on protein phosphatase Sit4 and consistently, zymocin resistant sit4∆ mutants cause hyperphosphorylation of Elp1. Here we show that casein kinase I (Hrr25) defects that cause zymocin resistance trigger hypophosphorylation of Elp1 and shifts to one or the other Elp1 form in hrr25 and sit4 mutants inactivate a tRNA suppressor that is Elongator-dependent. Since hyperand hypophosphorylated Elp1 forms are balanced in normal cells, changes that perturb this balance in the mutants therefore inactivate Elongator. In further support of Hrr25Sit4 antagonism, physical Hrr25•Sit4 interaction is dependent on the Sit4 effector Sap185 and Sit4 inactivation restores zymocin sensitivity and a normal ratio of the two Elp1 forms in hrr25 mutants. Moreover, Hrr25 binds to Elongator in a fashion dependent on Elongator partner Kti12 and Kti12 overexpression triggers Elp1 hyperphosphorylation similar to sit4 mutants. Intriguingly, hrr25 mutants block this Kti12 effect and show enhanced affinity of Elongator for Kti12. Collectively, our data suggest that rather than targeting Elp1, the Hrr25 kinase indirectly affects Elp1 phosphorylation states through Kti12 and control of Sit4dependent Elp1 dephosphorylation.
Antioxidant activity of citron peel (Citrus medica L.) essential oil and extract on stabilization of sunflower oil

Due to the unfavorable effects of synthetic antioxidants, the use of various sources of plant antioxidants to prevent foods oxidation, especially oil-based or fat-based varieties, has been recently got considerable attention. In this study, the antioxidant effect of essential oil and extract from the citron fruit (Citrus medica L.) was investigated on the thermal stability of sunflower oil. Aqueous, ethanolic, and methanolic extracts of citron peel (800 ppm), BHT synthetic antioxidant (200 ppm), and citron peel essential oil (800 ppm) were added to sunflower oil. The oil oxidation stability was evaluated during 5 days through analyzing the values of peroxide, anisidine, thiobarbituric acid, totox, and oxidative stability index (OSI). Results showed that the peroxide, anisidine, and totox value had an increasing trend over time. The effects of storage time, extract, and essential oil were statistically significant in reducing the oxidation rate of sunflower oil during storage. Ultrasonic-assisted ethanolic extract at 30 min showed the highest OSI. The results of this study demonstrated the positive effects of citron peel extract essential oil and on sunflower oil stability and its superiority over synthetic antioxidants.
Distinct Nanoscale Calcium Channel and Synaptic Vesicle Topographies Contribute to the Diversity of Synaptic Function

The nanoscale topographical arrangement of voltage-gated calcium channels (VGCC) and synaptic vesicles (SVs) determines synaptic strength and plasticity, but whether distinct spatial distributions underpin diversity of synaptic function is unknown. We performed single bouton Ca2+ imaging, Ca2+ chelator competition, immunogold electron microscopic (EM) localization of VGCCs and the active zone (AZ) protein Munc13-1, at two cerebellar synapses. Unexpectedly, we found that weak synapses exhibited 3-fold more VGCCs than strong synapses, while the coupling distance was 5-fold longer. Reaction-diffusion modelling could explain both functional and structural data with two strikingly different nanotopographical motifs: strong synapses are composed of SVs that are tightly coupled (∼10 nm) to VGCC clusters, whereas at weak synapses VGCCs were excluded from the vicinity (∼50 nm) of docked vesicles. The distinct VGCC-SV topographical motifs also confer differential sensitivity to neuromodulation. Thus VGCC-SV arrangements are not canonical across CNS synapses and their diversity could underlie functional heterogeneity.
Antimicrobial resistance surveillance in the South African private sector report for 2016

Aim: The relevance of surveillance for antimicrobial resistance is increasingly recognised in the light of a global action plan to combat resistance. This report presents antimicrobial susceptibility testing on ESKAPE pathogens from private sector laboratories in South Africa for 2016.Methods: Antimicrobial susceptibility testing (AST) performed on ESKAPE organisms (Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae and Escherichia coli) isolated from blood cultures at four private pathology laboratories in 2016 were analysed. Analysis and reporting of data were done via a uniform platform created by the NICD for national AST data.Results: AST were reported on 9 029 ESKAPE organisms including 58% Enterobacteriaceae, 28% Gram-positive bacteria and 14% Gram-negative bacteria and drug-bug combination was performed following the Global Antimicrobial Surveillance System (GLASS) guidelines by the World Health Organization.Conclusions: The most important resistance to address is a high level of ESBL in Enterobacteriaceae, which necessitates the use of carbapenems for treatment. Resistance to carbapenems is recorded in this report but not confirmation of genes by genotypic methods. During this period, no increase in vancomycin-resistant Enterococci was observed.
Universal Basic Income and Progressive Consumption Taxes

We provide a comprehensive quantitative evaluation of Universal Basic Income (UBI), evaluating different degrees of generosity and the fiscal alternatives to finance it. Replacing existing targeted transfers with a UBI of equal fiscal cost results in widespred welfare losses. In contrast, a combination of generous UBI (at least $15,000 per household) with a switch to progressive consumption taxation could be beneficial from the perspective of ex-ante expected welfare in the long run. However, the quantitative analysis of the transitional dynamics reveals non-trivial transitional costs for most current households.
Initial development of peach rootstock genotypes propagated by herbaceous cuttings

Abstract The peach tree is a temperate fruit tree propagated by grafting with the scion cultivar and the rootstock from seeds, generating low uniformity, a viable alternative is propagation by herbaceous cuttings. The objective of this study was to evaluate the performance of different genotypes of peach rootstock propagated by herbaceous cuttings. The experiment was carried out with standardized cuttings of 15 cm in length treated with 3,000 mg L-1 of IBA solution, then were transplanted into 3 L polyethylene bags. A completely randomized design with five replications was adopted, each plot consisting of three plants. Sixteen peach genotypes from UFV breeding program were tested: 713-3, 713-6, 713-7, 713-10, 813-2, 813-3, 813-5, 813-15, 913-3, 913-6, 913-11, 913-17, C6, C7 and C8. After 80 days the following parameters were evaluated: stem length (cm), stem diameter (mm) and internode length (cm). Data were subjected to analysis of variance by the F test and averages compared by the Scott-Knott test at a 5% probability level with the GENES statistical software. It can be concluded that the lower initial development was observed in genotype 1113-11 and the highest initial development was from genotypes 713-13 and 813-5.
Dynamic Event-Based Model Predictive Load Frequency Control for Power Systems Under Cyber Attacks

This article is concerned with the load frequency control (LFC) for the multi-area power system (MAPS) in the presence of cyber-attacks and disturbances. A resilient model predictive control (RMPC) strategy combined with the mixed <inline-formula> <tex-math notation="LaTeX">$H_{2} /H_{\infty } $ </tex-math></inline-formula> performance index and dynamic event-triggered mechanism (DETM) is developed by using the cone complementarity linearization algorithm and the linear matrix inequality technique. With the application of <inline-formula> <tex-math notation="LaTeX">$H_{2} /H_{\infty } $ </tex-math></inline-formula> performance index, the resilience of the controlled MAPS is achieved and the cyber-attacks launched on the MAPS can be dealt with effectively. The goal of the DETM is to enhance the communication efficiency by interrupting the communication of the MAPS, the triggering condition of which utilizes the internal dynamic variable. Moreover, rigorous derivations on the recursive feasibility of the RMPC are given. Finally, a MAPS is given to illustrate the validity of the presented control strategy.
Effect of paclitaxel and resveratrol on New Zealand rabbit semen

Objective: To examine the effects of paclitaxel and resveratrol on rabbit semen. Methods: This study consisted of four groups: control group (40 mL saline), paclitaxel group (5 mg/kg paclitaxel), resveratrol group (4 mg/kg resveratrol) and paclitaxel+resveratrol group (5 mg/kg paclitaxel+4 mg/kg resveratrol). Administrations were i.v. (in 40 mL saline) and continued 8 weeks. Sperm motility was evaluated using phase-contrast microscopy. Mitochondrial activity, membrane and acrosome integrity were performed by fluorescence staining. Lipid peroxidation, total glutathione and antioxidant potential levels were determined by spectrophotometry. Results: Paclitaxel decreased the sperm motility and fluorescence staining results compared to the control (P<0.05). The paclitaxel and resveratrol group showed better results of the same parameters compared to the paclitaxel group (P<0.05). No significant difference was observed in lipid peroxidation, total glutathione, antioxidant potential and fertility results (P>0.05). Results of this study showed that paclitaxel decreased semen parameters and resveratrol had a protective effect on these parameters. Conclusions: Paclitaxel has negative effects on spermatological indicators and biochemical assays, while resveratrol prevents these negative effects of paclitaxel.
Evaluation of Model-Based Tracking and its Application in a Robotic Production Line

The assessment of the accuracy and stability of model-based tracking approaches in the literature is a challenging task. Many of the presented methods lack a detailed evaluation or comparison to accurate ground truth data. Considering real world applications, it is hard to estimate the applicability of the respective method. In this paper we present methods to evaluate the accuracy and stability of model-based tracking approaches. Thereby, we focus on an industrial use and the robustness of the approach considering error sources like the influence of lighting over time, noise and the mechanical camera setup in general. The second part of this paper deals with the evaluation and application of model-based tracking in a robotic production line for gap measurements in the automotive industry. We present a method for synchronization with a conveyor setup and an operating robot. In this complex setup various error sources influence the output accuracy of the system. A further accuracy evaluation method is presented that uses the robot as a measurement device of the total error. The paper closes with the application of a model-based tracking system for robotic measurement tasks in a production line.