Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional studies of accessory factors associated with base excision repair

BRIAN PACHKOWSKI: Functional Studies of Accessory Factors Associated with Base Excision Repair (Under the direction of James A. Swenberg, D.V.M., Ph.D.) Exposure to environmental and cellular mutagens is ubiquitous and, as a consequence, DNA is constantly faced with the possibility of becoming damaged. Base excision repair (BER) removes some of this damage to limit the impact of these exposures on cell physiology and ultimately human health. The function of core BER enzymes may be enhanced by other protein accessory factors, namely poly(ADP-ribose) polymerase-1 (PARP-1) and x-ray repair cross complementing gene 1 (XRCC1). The main hypothesis of this research was that genetic approaches using cellular knockout and complementation models can evaluate whether the accessory proteins PARP-1 and XRCC1 are determinants of BER efficiency. While numerous biochemical studies have implicated PARP-1 in BER, the role of this protein in BER is somewhat uncertain. The first aim of this research was to evaluate the role of PARP-1 in BER in vertebrate cells. Chicken cells lacking PARP-1 were treated with an alkylating agent under different scenarios with subsequent endpoint measurements. PARP-1 was necessary as a survival factor during chronic exposure but did not appear relevant in acute exposures until the late stages of BER. In the absence of exposure, the DNA lesions measured were equal between PARP-1 proficient and deficient cells. XRCC1 acts as a scaffold for numerous protein interactions necessary for proficient BER. However, the presence of polymorphic forms of XRCC1 in the human population may
Performance Assessment Comparison of Variable Fin Density Microchannels With Offset Configurations

Current technologies for the cooling of integrated circuits (IC) chips employ single-phase liquid flow through microchannel heat sinks. The surface temperature in these devices increases along the flow direction, leading to low heat transfer coefficients toward the channel exit. Enhancement of the heat transfer coefficient while mitigating the temperature nonuniformity has been possible with the utilization of variable fin density microchannels. A microchannel cooling layer suitable for three-dimensional (3D) stacking of IC chips is studied in this paper. The effect of the variation of geometrical parameters and operating conditions on the overall performance of the cooling layer is reported. The overall performance of eight different configurations presenting offset strip fins with variable fin density has been evaluated and compared to two cases with smooth rectangular microchannels, one case for each channel height. The cooling layer, with a length of 8 mm and a width of 7.92 mm, dissipates a total thermal power of 200 W by means of pumping coolant through 12 flow channels. Results from this investigation demonstrate the capability of the proposed configurations to decrease the surface temperature nonuniformities and to maintain the surface temperature below the allowable limits for IC chips while achieving low pressure drops. A parameter for the overall performance assessment, named the overall performance index, has been proposed; by computing and properly comparing the values for this parameter, the best performing configuration is identified.
Influence of modifications (from AoB2015 to v0.5) in the Vegetation Optimality Model

Abstract. The Vegetation Optimality Model (VOM, Schymanski et al., 2009, 2015) is an optimality-based, coupled water–vegetation model that predicts vegetation properties and behaviour based on optimality theory rather than calibrating vegetation properties or prescribing them based on observations, as most conventional models do. Several updates to previous applications of the VOM have been made for the study in the accompanying paper of Nijzink et al. (2022), where we assess whether optimality theory can alleviate common shortcomings of conventional models, as identified in a previous model inter-comparison study along the North Australian Tropical Transect (NATT, Whitley et al., 2016). Therefore, we assess in this technical paper how the updates to the model and input data would have affected the original results of Schymanski et al. (2015), and we implemented these changes one at a time. The model updates included extended input data, the use of variable atmospheric CO2 levels, modified soil properties, implementation of free drainage conditions, and the addition of grass rooting depths to the optimized vegetation properties. A systematic assessment of these changes was carried out by adding each individual modification to the original version of the VOM at the flux tower site of Howard Springs, Australia. The analysis revealed that the implemented changes affected the simulation of mean annual evapotranspiration (ET) and gross primary productivity (GPP) by no more than 20 %, with the largest effects caused by the newly imposed free drainage conditions and modified soil texture. Free drainage conditions led to an underestimation of ET and GPP in comparison with the results of Schymanski et al. (2015), whereas more fine-grained soil textures increased the water storage in the soil and resulted in increased GPP. Although part of the effect of free drainage was compensated for by the updated soil texture, when combining all changes, the resulting effect on the simulated fluxes was still dominated by the effect of implementing free drainage conditions. Eventually, the relative error for the mean annual ET, in comparison with flux tower observations, changed from an 8.4 % overestimation to an 10.2 % underestimation, whereas the relative errors for the mean annual GPP remained similar, with an overestimation that slightly reduced from 17.8 % to 14.7 %. The sensitivity to free drainage conditions suggests that a realistic representation of groundwater dynamics is very important for predicting ET and GPP at a tropical open-forest savanna site as investigated here. The modest changes in model outputs highlighted the robustness of the optimization approach that is central to the VOM architecture.
Sustainable Treatment and Reuse of Municipal Wastewater: For Decision Makers and Practicing Engineers

In many countries, especially in developing countries, many people are lacking access to water and sanitation services and this inadequate service is the main cause of diseases in these countries. Application of appropriate wastewater treatment technologies, which are effective, low cost (in investment and especially in operation and maintenance), simple to operate, proven technologies, is a key component in any strategy aimed at increasing the coverage of wastewater treatment. Sustainable Treatment and Reuse of Municipal Wastewater presents the concepts of appropriate technology for wastewater treatment and the issues of strategy and policy for increasing wastewater treatment coverage. The book focuses on the resolution of wastewater treatment and disposal problems in developing countries, however the concepts presented are valid and applicable anywhere and plants based on combined unit processes of appropriate technology can also be used in developed countries and provide to them the benefits described. Sustainable Treatment and Reuse of Municipal Wastewater presents the basic engineering design procedures to obtain high quality effluents by treatment plants based on simple, low cost and easy to operate processes. The main message of the book is the idea of the ability to combine unit processes to create a treatment plant based on a series of appropriate technology processes which jointly can generate any required effluent quality. A plant based on a combination of appropriate technology unit processes is still easy to operate and is usually of lower costs than conventional processes in terms of investment and certainly in operation and maintenance. ISBN: 9781780400167 (Print) ISBN: 9781780400631 (eBook)
Managerial compensation and fixed intangible assets investment: the role of managerial ownership and firm characteristics

PurposeThis study examines how cash and stock bonus compensations influence top executives to allocate a firm's resources to fixed intangible assets investment and the extent to which this relationship is conditional on executives' ownership, firm growth, internal cash flow and leverage.Design/methodology/approachUsing data from 213 non-financial and non-utility UK FTSE 350 firms for the period 2007–2015, generating a total of 1,748 firm-year observations, panel econometric methods are employed to test the authors’ model.FindingsThe authors observe that executives' cash bonus compensation positively impacts fixed intangible assets investment. However, executives' stock bonus compensation has a negative and significant influence on fixed intangible assets. The authors further observe that executives either cash bonus or stock bonus crucially invest more in fixed intangible assets when the firm has a growth potential. Also, both cash bonus and stock bonus executives in firms with lower internal cash flow spend less on fixed intangible assets. Similar results are also observed for those stock bonus-motivated executives with an increase in fixed intangible assets for low leverage firms but a decrease for high leverage ones.Research limitations/implicationsA key limitation of this study is its concentration on a single country (United Kingdom). Thus, future studies can expand the focus of this study by looking at it from the perspective of multiple countries.Practical implicationsThe practical relevance of the study results is that firms with high growth opportunity in fixed intangible assets activity can use more cash bonus compensation (risk-avoiding incentive) to induce corporate executives to invest more in such activity. This finding is particularly important given the increasing appetite of firms in this knowledge-based economy to create expansion through fixed intangible assets investment. That is, for firms to increase fixed intangible assets investment, this study suggests that executive cash bonus compensation cannot be ignored.Originality/valueWhile this paper builds on the classic Q theory of investment literature, it is the first – to the best of the authors’ knowledge – to explore how cash and stock bonus compensations influence top executives to allocate a firm's resources to fixed intangible assets investment and the extent to which this relationship is conditional on executives' ownership, firm growth, internal cash flow and leverage.
Critical Success Factors for Managing Technology-Intensive Teams in the Global Enterprise

Abstract: The challenges of managing culturally diverse and globally dispersed project teams are examined in a field study of technology-intensive product developments. The article aims to improve the understanding of team performance in multinational project environments with implications for leadership assessment and organizational development. The results suggest that multinational team performance involves a complex set of variables related to the organizational ambience, business process, managerial tools, and most importantly, to the people in the organization. Team leaders must effectively manage relations across the entire work process, including support functions, suppliers, sponsors, and partners. Emphasis on common values and goals helps in bridging cultural and organizational differences, and in unifying the multinational team. Personal interest, pride and satisfaction with the work, professional work challenge, accomplishments, recognition, and the skill sets of the team members were identified as the strongest drivers toward unifying culturally diverse project teams and their work processes, and building a true partnership among all the contributing organizations.
Pregnant Women and Endocrine Disruptors: Role of P2X7 Receptor and Mitochondrial Alterations in Placental Cell Disorders

In pregnant women, the lungs, skin and placenta are exposed daily to endocrine-disrupting chemicals (EDCs). EDCs induce multiple adverse effects, not only on endocrine organs, but also on non-endocrine organs, with the P2X7 cell death receptor being potentially the common key element. Our objective was first to investigate mechanisms of EDCs toxicity in both endocrine and non-endocrine cells through P2X7 receptor activation, and second, to compare the level of activation in lung, skin and placental cells. In addition, apoptosis in placental cells was studied because the placenta is the most exposed organ to EDCs and has essential endocrine functions. A total of nine EDCs were evaluated on three human cell models. We observed that the P2X7 receptor was not activated by EDCs in lung non-endocrine cells but was activated in skin and placenta cells, with the highest activation in placenta cells. P2X7 receptor activation and apoptosis are pathways shared by all tested EDCs in endocrine placental cells. P2X7 receptor activation along with apoptosis induction could be key elements in understanding endocrine placental and skin disorders induced by EDCs.
Prodromal Cognitive Deficits and the Risk of Subsequent Parkinson’s Disease

Background: There is growing interest in identifying individuals who are in the prodromal phase of Parkinson’s disease (PD), as these individuals are potentially suitable for inclusion in intervention trials to prevent clinically manifest PD. However, it is less clear whether—and to what extent—cognitive deficits are present in prodromal PD. Methods: A systematic query was conducted through PubMed and Embase for prospective observational cohort studies that (a) assessed cognitive performance in individuals free of manifest PD at baseline and (b) subsequently followed up participants for incident PD. We grouped the results by cognitive domain, and for domains that had been reported in at least three separate studies, we performed random-effects, inverse variance meta-analyses based on summary statistics. Results: We identified nine articles suitable for inclusion, with a total of 215 patients with phenoconversion and 13,524 individuals remaining disease-free at follow-up. The studies were highly heterogeneous in study design, study population, and cognitive test batteries. Studies that included only cognitive screening measures such as MMSE or MoCA reported no association between worse cognitive performance and onset of manifest PD (combined odds ratio 1.08; 95% confidence interval 0.66–1.77). By contrast, studies that used extensive cognitive testing batteries found that global cognitive deficits were associated with an increased risk of manifest PD. In domain-specific analyses, there was evidence for an association between worse executive functioning (OR 1.45; 95% CI 1.10–1.92), but not memory (OR 1.20; 95% CI 0.85–1.70) or attention (OR 0.98; 95% CI 0.23–4.26), and clinically manifest PD. Conclusion: Although some caution due to high heterogeneity among published studies is warranted, the available evidence suggests that global and executive cognitive deficits are prodromal features of PD. Collaborative prospective studies with extensive cognitive test batteries are required to shed light on domain-specific deficits, temporal relations, and subgroup differences in prodromal cognitive deficits in PD.
Design of an Intelligent Hydroponics System to Identify Macronutrient Deficiencies in Chili

Nutrient contents are important for plants. Lack of macronutrients causes plant damage. Several macronutrient deficiencies exhibit similar visual characteristics that are difficult for ordinary farmers to identify. Collaboration between Computer Vision technology and IoT has become a nondestructive method for nutrient monitoring and control, included in the hydroponic system. Computer vision plays a role in processing plant image data based on specific characteristics. However, the analysis of one characteristic cannot represent plant health. In addition, knowing the percentage of macronutrient deficiencies is also needed to support precision agriculture systems. Therefore, we propose a Multi Layer Perceptron architecture that can perform multi-tasks, namely, identification and estimation. In addition, the optimal architecture will also be sought based on the characteristics of the combination of three features in the form of texture, color, and leaf shape. Based on analysis and design, our proposed model has a high potential for identifying and estimating macronutrient deficiency at the same time as well and can be applied to support precision agriculture in Indonesia. Keywords—Multi Layer perceptron; internet of things; feature combination; leaf image; nutrient deficiency
Unsteady Aerodynamics Simulation of a Heavy-Duty Truck in Wind Gusts Coupled With Vehicle Motion Analysis in Six Degrees of Freedom

A one-way coupled analysis was used to investigate both the unsteady aerodynamic forces on a simplified heavy-duty truck in strong wind gusts and their effects on its motion. The vehicle model for the dynamics simulation was extended to six degrees of freedom (6DoF). First, a transitional aerodynamics simulation was conducted for the simplified truck with a fixed vehicle attitude but subject to a sudden crosswind. Based on the visualized results of this aerodynamics simulation, flow phenomena generating transitional aerodynamic forces and moments are discussed, especially those acting in the vertical direction. While the truck was running into the crosswind region, the growth and breakdown of a large-scale vortex above the container generated a transitional behavior of aerodynamic lift and pitching moment. Next, time series of the six components of the aerodynamic forces and moments were input into the vehicle dynamics simulation. By comparing the results with those of a quasi-steady aerodynamics simulation, the effect of transitional aerodynamics on vertical motions was clarified, with the largest difference found in a rolling motion. Moreover, the effect of considering 6DoF was investigated by also conducting the vehicle dynamics simulation with 3DoF. The consideration of dynamics in the vertical direction changed the estimation of tire forces, which were related to a vertical load on the tire. Finally, the effects of considering 6DoF were also identified for horizontal motions.Copyright © 2011 by JSME
A General Solution to the Aircraft Trim Problem

Trim defines conditions for both design and analysis based on aircraft models. In fact, we often define these analysis points more broadly than the conditions normally associated with trim conditions to facilitate that analysis or design. In simulations, these analysis points establish initial conditions comparable to flight conditions. Based on aerodynamic and propulsion systems models of an aircraft, trim analysis can be used to provide the data needed to define the operating envelope or the performance characteristics. Linear models are typically derived at trim points. Control systems are designed and evaluated at points defined by trim conditions. And these trim conditions provide us a starting point for comparing one model against another, one implementation of a model against another implementation of the same model, and the model to flight-derived data. In this paper we define what we mean by trim, examine a variety of trim conditions that have proved useful and derive the equations defining those trim conditions. Finally we present a general approach to trim through constrained minimization of a cost function based on the nonlinear, six-degree-of freedom state equations coupled with the aerodynamic and propulsion system models. We provide an example of how a trim algorithm is used with a simulation by showing an example from JSBSim.
Association of Interleukin Genes IL10 and IL10RB with Parameters of Overweight in Military Students

Background: To date, nearly 300 single-nucleotide polymorphisms (SNPs) associated with BMI, waist-to-hip ratio, and other adiposity traits have been identified by GWAS. With regards to IL10, at least 49 IL10-associated polymorphisms have been reported. However, little is known regarding the relationship between SNPs of the IL10 gene and the risk of obesity in young men. The aim of the present study was to investigate the relationship between SNPs of the IL10 and IL10RB genes and the risk of obesity in young men. Methods: A cohort of 139 male students were enrolled and the following IL10 and IL10RB SNPs were analyzed: IL10 (rs1518110), IL10 (rs3024491), IL10RB (rs2834167). The subjects were divided into groups depending on obesity parameters: body mass index (BMI), fat mass index (FMI) and fat percentage (Fat%). Statistical analysis was conducted for a single locus and haplotypes, an association between SNPs and body composition parameters was tested with four genetic models: dominant, recessive, codominant and overdominant mode of inheritance (MOI). Results: Significant association was found for interaction IL10 (rs1518110) × IL10RB (rs2834167) with Fat% value exceeding 20 in codominant (p-value = 0.03, OR = 0.34, 95% CI 0.08 1.44) and dominant model (p-value = 0.03, OR = 0.34, 95% CI 0.08 1.44) Conclusion: Our study shows for the first time that there is a correlation between the occurrence of specific polymorphisms of IL10 gene (rs1518110, rs3024491 and rs2834167) and the possibility of obesity.
Design of adaptive H ∞ filter for implementing on state-of-charge estimation based on battery state-of-charge-varying modelling

This study suggests a new method for modelling lithium-ion battery types and state-of-charge (SOC) estimation using adaptive H∞ filter (AHF). First, a universal linear model with some free parameters is considered for dynamical behaviour of the battery. The battery voltage and SOC are used as states of the model. Then for every period in the charge/discharge process the free parameters of the model are identified. Each period of process is associated with a specific SOC value, hence the parameters can be regarded as functions of SOC in the entire process. The functions are determined based on polynomial approximation and least squares method. The proposed SOC-varying model is incorporated in AHF for SOC estimation. Moreover, a new method for adjusting the tuning parameters of the filter is suggested. The proposed method is verified by experimental tests on a lithium-ion battery and is compared with adaptive extended Kalman filter and square-root unscented Kalman filter
Transfer Learning based Performance Comparison of the Pre-Trained Deep Neural Networks

Deep learning has grown tremendously in recent years, having a substantial impact on practically every discipline. Transfer learning allows us to transfer the knowledge of a model that has been formerly trained for a particular task to a new model that is attempting to solve a related but not identical problem. Specific layers of a pre-trained model must be retrained while the others must remain unmodified to adapt it to a new task effectively. There are typical issues in selecting the layers to be enabled for training and layers to be frozen, setting hyperparameter values, and all these concerns have a substantial effect on training capabilities as well as classification performance. The principal aim of this study is to compare the network performance of the selected pre-trained models based on transfer learning to help the selection of a suitable model for image classification. To accomplish the goal, we examined the performance of five pre-trained networks, such as SqueezeNet, GoogleNet, ShuffleNet, Darknet-53, and Inception-V3 with different Epochs, Learning Rates, and Mini-Batch Sizes to compare and evaluate the network’s performance using confusion matrix. Based on the experimental findings, Inception-V3 has achieved the highest accuracy of 96.98%, as well as other evaluation metrics, including precision, sensitivity, specificity, and f1-score of 92.63%, 92.46%, 98.12%, and 92.49%, respectively. Keywords—Transfer learning; deep neural networks; image classification; Convolutional Neural Network (CNN) models