Miracle-dz/UniFAR-FTUs huggingface dataset:
A new command governor architecture for transient response shaping

In this paper, we develop a control framework for stabilization and command following of nonlinear uncertain dynamical systems. The proposed methodology consists of a new command governor architecture and an adaptive controller. The command governor is a dynamical system that adjusts the trajectory of a given command to follow an ideal reference system capturing a desired closed‐loop dynamical system behavior in transient time. Specifically, we show that the controlled nonlinear uncertain dynamical system can approach the ideal reference system by choosing the design parameter of the command governor. In addition, an adaptive element is used to asymptotically assure that the error between the controlled nonlinear uncertain dynamical system and the ideal reference system is reduced in long term. Therefore, the proposed methodology not only has closed‐loop transient and steady‐state performance guarantees but can also shape the transient response by adjusting the trajectory of the given command with the command governor. We highlight that there exists a trade‐off between the adaptive controller's learning rate and the command governor's design parameter. This key feature of our framework allows rapid suppression of system uncertainties without resorting to a high learning rate in the adaptive controller. Furthermore, we discuss the robustness properties of the proposed approach with respect to high‐frequency dynamical system content such as measurement noise and ∕ or unmodeled dynamics. A numerical example is provided to demonstrate the efficacy of the proposed architecture. Copyright © 2012 John Wiley & Sons, Ltd.
Downlink Power Allocation with Pricing in CDMA

In this paper, we present an approach for power allocation to maximize the effective system throughput with pricing on the downlink in a CDMA system. We present a pricing policy and obtain the optimum powers for the users to maximize the effective system throughput incorporating this pricing policy. We also study the asymptotic behavior of the system (i.e., when the number of users and the available bandwidth are large). We show that in such a system, all users obtain equal SIR at the optimum point irrespective of their locations and processing gains. We also derive an expression for the maximum asymptotic spectral efficiency
TDP-43 post-translational modifications in health and disease

ABSTRACT Introduction: Nuclear factor TDP-43 is a ubiquitously expressed RNA binding protein that plays a key causative role in several neurodegenerative diseases, especially in the ALS/FTD spectrum. In addition, its aberrant aggregation and expression has been recently observed in other type of diseases, such as myopathies and Niemann-Pick C, a lysosomal storage disease. Areas covered: This review aims to specifically cover the post-translational modifications (PTMs) that can affect TDP-43 function and cellular status both in health and disease. To this date, these include phosphorylation, formation of C-terminal fragments, disulfide bridge formation, ubiquitination, acetylation, and sumoylation. Recently published articles on these subjects have been reviewed in this manuscript. Expert opinion: Targeting aberrant TDP-43 expression in neurodegenerative diseases is a very challenging task due to the fact that both its overexpression and downregulation are considerably toxic to cells. This characteristic makes it difficult to therapeutically target this protein in a generalized manner. An alternative approach could be the identification of specific aberrant PTMs that promote its aggregation or toxicity, and developing novel therapeutic approaches toward their selective modification.
Motor parameter auto-identification based on sensorless startup procedure for PMSM drives

In order to automatically identify the electrical parameters of PMSMs, rather than measure the parameters using instruments such as RLC meters, this paper proposes an approach in which the testing voltage is injected into the motor from the drive. Based on the analysis of equivalent circuits of the PMSMs as well as the phase voltage and phase current information recorded from standstill to sensorless control operation, the RLS method is employed to estimate the values of electrical parameters of the PMSMs. Moreover, the automatic motor parameter identification algorithm developed in this paper is also integrated into the open loop startup procedure of the sensorless control drive. Consequently, the proposed automatic motor parameter identification method has attractive features such as fast identification and being highly convenient. In addition, both the proposed automatic motor parameter identification method and the sensorless control drive developed in this paper are implemented using a low-cost 16-bit microcontroller. Two commercial surface-type and interior-type PMSMs are used in the experiments to assess the performance of the proposed approach. Experimental results verify the effectiveness of the proposed automatic motor parameter identification method.
A Study of the Optical Clearing by OCT

Optical clearing can effectively control the optical properties of in tissue using the optical immersing technique by hyperosmotic agents and be paid more and more attention in the biomedical and optical field.This mothed could reduce the number of the multiple scattered photons,increase the depth of the optical imaging,and get a better contrast grade of images.We measured the change of the optical properties of the tissue of the different depth during the optical clearing process using optical coherence tomography(OCT). We applied the gradient of the OCT signal algorithm to analyze the temporal and spatial distribution of the scattering coefficient during the clearing process.It was demonstrated experimentally that optical clearing could effectively improve the OCT imaging depth.During the process of the optical clearing,the scattering coefficient,the range and the time and the trend of the change of the scattering coefficient changed with the different depth,which was related to the tissue microstructure,the clearing effect due to the microstructure and the diffuse process of the agent.The results could be used to understand the process and the mechanism of the optical clearing.
A multi‐dimensional functional principal components analysis of EEG data

The electroencephalography (EEG) data created in event‐related potential (ERP) experiments have a complex high‐dimensional structure. Each stimulus presentation, or trial, generates an ERP waveform which is an instance of functional data. The experiments are made up of sequences of multiple trials, resulting in longitudinal functional data and moreover, responses are recorded at multiple electrodes on the scalp, adding an electrode dimension. Traditional EEG analyses involve multiple simplifications of this structure to increase the signal‐to‐noise ratio, effectively collapsing the functional and longitudinal components by identifying key features of the ERPs and averaging them across trials. Motivated by an implicit learning paradigm used in autism research in which the functional, longitudinal, and electrode components all have critical interpretations, we propose a multidimensional functional principal components analysis (MD‐FPCA) technique which does not collapse any of the dimensions of the ERP data. The proposed decomposition is based on separation of the total variation into subject and subunit level variation which are further decomposed in a two‐stage functional principal components analysis. The proposed methodology is shown to be useful for modeling longitudinal trends in the ERP functions, leading to novel insights into the learning patterns of children with Autism Spectrum Disorder (ASD) and their typically developing peers as well as comparisons between the two groups. Finite sample properties of MD‐FPCA are further studied via extensive simulations.
Towards the low cost manufacture of dye-sensitized solar cells using inkjet technology

This work presents a novel means of producing dye-sensitized solar cells (DSSCs), using an inkjet printing technique. To manufacture a completely inkjet-printed DSSC, all layers must be considered and a thorough analysis of the suitability of the printing process has previously been unreported. For DSSCs to become commercially viable they must have long term operational stability, be efficient, have a low environmental impact and low manufacturing cost. Inkjet printing is an additive manufacturing process, meaning that material is only deposited where needed, minimising the material wastage. Several nanoparticle materials were investigated including titanium dioxide (TiO2), carbon black as a low cost replacement for platinum and PEDOT:PSS as a low cost replacement to the widely used spiro-MeOTAD 92,2' ,7,7'-tetrkis(N,N-di-p-methoxyphenylamine)-9,9-spirobifluorene) solid-state hole transport material. A highly porous network of metal-oxide nanocrystals is a fundamental building block to produce DSSCs. The morphology of this layer can greatly influence the efficiency of the cell and therefore a significant amount of this project was spent on developing suitable ink and printing this layer. Titanium dioxide (TiO2) is widely used within the development of photoanodes due to its low cost, stability and low impact on the environment. However, it can be difficult to create a stable dispersion within water due to the natural tendency for the material to agglomerate. An aqueous TiO2 nanoparticle dispersion was developed and several additive materials were explored in an effort to optimize the ink. The initial ink was printed to produce a layer 2.6 μm thick which, once incorporated into a DSSC, resulted in a promising efficiency of 3.50%. Inkjet printed carbon black counter electrodes with thicknesses of 10.24 μm, lead to efficiencies of 2.59%, whilst inkjet printed PEDOT:PSS solid state hole transport material resulted in a very low efficiency of 0.08%. Whilst the PEDOT:PSS and carbon did not produce suitable results for this application, it is suggested that further materials are still investigated due to the benefits of the manufacturing technique. Therefore, it can be concluded that this work shows the capability of inkjet printing for low-cost solar cells, with exciting potential application to other printed electronic applications.
Reasoning about High-Level Constructs in Hardware/Software Formal Verification

Author(s): Long, Jiang | Advisor(s): Brayton, Robert K | Abstract: The ever shrinking feature size of modern electronic chips leads tomore designs being done as well as more complex chips beingdesigned. These in turn lead to greater use of high-levelspecifications and to more sophisticated optimizations applied at theword -level. These steps make it more difficult to verify that thefinal design is faithful to the initial specification. We tackle twosteps in this process and their formal equivalence checking to helpverify the correctness of the steps.First, we present LEC, a combinational equivalence checking tool that is learning driven. It focuses on data-path equivalencechecking with the goal of transforming the two logics under comparison to be moresimilar in order to reduce the complexity of a final Boolean (bit-level)solving. LEC does equivalence checking of combinational logic between two RTL (word-level) designs, one the original and one an optimized RTL version. LEC features an open architecture such that users and developers canlearn with the system as new designs and optimizations are met, and then it can be modularly extended with new proof procedures as they are discovered. To address the use of higher level specifications, we build a simple trusted C to Verilog translation procedure based on theLLVM compiler infrastructure. The translator was designed to implement an almost vertatimtranslation of the C language operators and control structures intothe Verilog \emph{always\_ff} and \emph{always\_comb} blocks through traversing LLVMBytecode programs. The procedure reliably bridges the language barrierbetween software and hardware and allows hardware synthesisand verification techniques to be applied readily.In combination, these two procedures allow for equivalence checkingbetween a software-like specification and an optimized word-level RTLimplementation.
[Dosimetric analysis of volumetric modulated arc therapy and intensity modulated radiotherapy for patients undergone breast-conserving operation].

OBJECTIVE To compare the dosimetric differences between volumetric modulated arc therapy and intensity modulated radiotherapy for breast cancer patients after breast-conserving surgery. METHODS Ten patients who received radiotherapy after breast-conserving surgery were selected. Eclipse planning system was used to design volumetric rotating intensity-modulated (2F-RapidArc) and two field intensity-modulated radiation therapy (2F-IMRT) planning for each patient. 2F-RapidArc plans were made using two partial arcs with gantry rotation from 287°-293° to 152°-162°, and 0° to 90 ° was avoidance sector. The gantry angle of 2F-IMRT were 301°-311° and 125°-135°. The prescription dose was 46 Gy/23 fractions. All plans required 95% of the target volume receiving the prescription dose. The dose distribution of the target, organs at risk, machine unit (MU) and treatment time were compared. RESULTS 2F-RapidArc and 2F-IMRT plans' uniformity index was 1.12±0.02 and 1.11±0.03 (P=0.282), respectively; conformal index was 0.80±0.03 and 0.65±0.04 (P<0.001), respectively. V110 of plan target volume was 20.98%±14.47% and 10.43%±10.49% (P=0.030), respectively. Compared with the 2F-IMRT, 2F-RapidArc plans had a higher dosimetric parameters for left lung: V5 (48.06%±17.32% vs. 24.23%±6.56%,P=0.001), V10 (28.89±9.28 vs.17.07±4.78%,P=0.004), Dmean [(9.70±2.14) Gy vs. (6.86±1.77) Gy, P=0.002], increased the double lung: V5 (22.85%±7.55% vs. 11.01%± 2.95%,P=0.001), V10 (13.16%±4.33% vs. 7.76%± 2.16%, P=0.006), Dmean [(4.66±0.95) Gy vs. (3.17±0.82) Gy, P=0.001], reduced the left lung: V40 (3.58%±1.46% vs. 6.19%±3.04%, P=0.006), reduced the double lung: V40 (1.61%±0.64% vs. 2.81%± 1.39%,P=0.005), increased cardiac: V5 (39.3%±17.19% vs. 8.79%±4.24%, P<0.001), V10 (21.31%±13.8% vs. 5.73%±3.42%, P=0.002), V20 (7.80%±6.08% vs. 4.05%±2.85%,P=0.018), Dmean [(0.64±0.25) Gy vs. (0.29±1.39) Gy,P<0.001],reduced the heart: V40(0.50%±0.40% vs. 1.86%±1.94%,P=0.037),increased the contralateral breast Dmean [(1.63±1.26) Gy vs. (0.09±0.05) Gy, P=0.004]. Compared with 2F-IMRTplan, 2F-RapidArc increased the treatment time [(132.9±7.2) s vs. (140.3±11.6) s, P=0.030]. Both the machine units were almost the same [(467.0±30.4) MU vs. (494.7±44.9) MU, P=0.094]. CONCLUSION Both 2F-RapidArc and 2F-IMRT plans could reach the clinical requirements. 2F-RapidArc had a better conformal index, reduced the high dose area, but increased the low dose regions of the lung, heart, body area, and increased the average dose of the contralateral breast. The treatment time of 2F-RapidArc was longer than that of 2F-IMRT, and the MU of 2F-RapidArc and 2F-IMRT plans were almost the same.
Stereoselective Inhibition of Renal Basolateral Human Organic Anion Transporter 3 by Lansoprazole Enantiomers

Lansoprazole, a proton pump inhibitor, potently inhibits human organic anion transporter, hOAT3 (SLC22A8). Lansoprazole has an asymmetric atom in its structure and is clinically administered as a racemic mixture of (R)-and (S)-enantiomers. However, little is known about the stereoselective inhibitory potencies of lansoprazole against hOAT3 and its homolog, hOAT1. In the present study, the stereoselective inhibitory effect of lansoprazole was evaluated using hOAT1-and hOAT3-expressing cultured cells. hOAT1 and hOAT3 transported [14C]p-aminohippurate and [3H]estrone-3-sulfate (ES) with Michaelis-Menten constants of 29.8 ± 4.0 and 30.1 ± 9.0 µmol/L respectively. Lansoprazole enantiomers inhibited hOAT1- and hOAT3-mediated transport of each substrate in a concentration-dependent manner. The IC50 value of (S)-lansoprazole against hOAT3-mediated transport of [3H]ES (0.61 ± 0.08 µmol/L) was significantly lower than that of (R)-lansoprazole (1.75 ± 0.31 µmol/L). In contrast, stereoselectivity was not demonstrated for the inhibition of hOAT1. Furthermore, (S)-lansoprazole inhibited hOAT3-mediated transport of pemetrexed and methotrexate (hOAT3 substrates) more strongly than the corresponding (R)-lansoprazole. This study is the first to demonstrate that the stereoselective inhibitory potency of (S)-lansoprazole against hOAT3 is greater than that of (R)-lansoprazole. The present findings provide novel information about the drug interactions associated with lansoprazole.
Radiation-Induced Attenuation of Perfluorinated Polymer Optical Fibers for Radiation Monitoring

Due to some of their unique properties, optical fiber dosimeters are attractive and extensively researched devices in several radiation-related areas. This work evaluates the performance and potential of commercial perfluorinated polymer optical fibers (PF-POFs) for radiation monitoring applications. Gamma radiation-induced attenuation (RIA) of two commercial PF-POFs is evaluated in the VIS spectral region. Influence of a dose rate and temperature on RIA measurement is investigated, along with defect stability and measurement repeatability. Co-extruded PF-POFs are identified as more suitable for radiation monitoring applications due to lower dose-rate dependence. With co-extruded PF-POF, RIA measurement holds potential for highly-sensitive radiation monitoring with good reproducibility. The results show that operation in the blue part of the spectrum provides most favorable performance in terms of the largest nominal radiation sensitivity, lower temperature, and dose-rate dependence as well as higher defect stability. We demonstrate for the first time to our knowledge, that PF-POFs can be used for distributed detection of radiation with doses down to tens of Grays. The off-the-shelf, user-friendly PF-POF could be of interest as a cheap, disposable sensor for various applications, especially of a more qualitative nature.
pmx Webserver: A User Friendly Interface for Alchemistry

With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the usability of alchemical methods for amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserver allows amino acid mutation selection in five contemporary molecular mechanics force fields. In addition, a complete mutation scan with a user defined amino acid is supported. The output generated by the webserver is directly compatible with the Gromacs molecular dynamics engine and can be used with any of the alchemical free energy calculation setup. Furthermore, we present a database of input files and precalculated free energy differences for tripeptides approximating a disordered state of a protein, of particular use for protein stability studies. Finally, the usage of the webserver and its output is exemplified by performing an alanine scan and investigating thermodynamic stability of the Trp cage mini protein. The webserver is accessible at http://pmx.mpibpc. mpg.de.
5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription.
Gait recovery following spinal cord injury in mice: Limited effect of treadmill training

Background: Several studies in rodents with complete spinal cord transections have demonstrated that treadmill training improves stepping movements. However, results from studies in incomplete spinal cord injured animals have been conflicting and questions regarding the training dosage after injury remain unresolved. Objectives: To assess the effects of treadmill-training regimen (20 minutes daily, 5 days a week) for 3, 6 or 9 weeks on the recovery of locomotion in hemisected SCI mice. Methods: A randomized and blinded controlled experimental trial used a mouse model of incomplete spinal cord injury (SCI). After a left hemisection at T10, adult male mice were randomized to trained or untrained groups. The trained group commenced treadmill training one week after surgery and continued for 3, 6 or 9 weeks. Quantitative kinematic gait analysis was used to assess the spatiotemporal characteristics of the left hindlimb prior to injury and at 1, 4, 7 and 10 weeks post-injury. Results: One week after injury there was no movement of the left hindlimb and some animals dragged their foot. Treadmill training led to significant improvements in step duration, but had limited effect on the hindlimb movement pattern. Locomotor improvements in trained animals were most evident at the hip and knee joints whereas recovery of ankle movement was limited, even after 9 weeks of treadmill training. Conclusion: These results demonstrate that treadmill training may lead to only modest improvement in recovery of hindlimb movement after incomplete spinal cord injury in mice.