Miracle-dz/UniFAR-FTUs huggingface dataset:
Preserving subject variability in group fMRI analysis: performance evaluation of GICA vs. IVA

Independent component analysis (ICA) is a widely applied technique to derive functionally connected brain networks from fMRI data. Group ICA (GICA) and Independent Vector Analysis (IVA) are extensions of ICA that enable users to perform group fMRI analyses; however a full comparison of the performance limits of GICA and IVA has not been investigated. Recent interest in resting state fMRI data with potentially higher degree of subject variability makes the evaluation of the above techniques important. In this paper we compare component estimation accuracies of GICA and an improved version of IVA using simulated fMRI datasets. We systematically change the degree of inter-subject spatial variability of components and evaluate estimation accuracy over all spatial maps (SMs) and time courses (TCs) of the decomposition. Our results indicate the following: (1) at low levels of SM variability or when just one SM is varied, both GICA and IVA perform well, (2) at higher levels of SM variability or when more than one SMs are varied, IVA continues to perform well but GICA yields SM estimates that are composites of other SMs with errors in TCs, (3) both GICA and IVA remove spatial correlations of overlapping SMs and introduce artificial correlations in their TCs, (4) if number of SMs is over estimated, IVA continues to perform well but GICA introduces artifacts in the varying and extra SMs with artificial correlations in the TCs of extra components, and (5) in the absence or presence of SMs unique to one subject, GICA produces errors in TCs and IVA estimates are accurate. In summary, our simulation experiments (both simplistic and realistic) and our holistic analyses approach indicate that IVA produces results that are closer to ground truth and thereby better preserves subject variability. The improved version of IVA is now packaged into the GIFT toolbox (http://mialab.mrn.org/software/gift).
Agile Usability Engineering

In recent years, agile methods for software and web engineering have reached widespread acceptance in the community. In contrary to classic, heavy-weight software engineering processes like the V-model, agile methods (Ambler 2002) begin coding very early while having a shorter requirements engineering up-front as well as less documentation. Following the paradigm of Extreme Programming (Beck 1999), implementation of code takes place in small increments and iterations, and small releases are delivered to the customer after each development cycle. During a short claims analysis, called the exploration phase, the development team writes user stories trying to describe user needs and roles; the interviewed people need not necessarily be the real users of the later software product. Seen from a human-computer engineering perspective, Extreme Programming (XP) thus often fails to collect real user data and starts coding with just assumptions about user needs. The development in small increments may work properly as long as the software has no focus on the user interface (UI). Changes to software architecture most often have no impact on what the user sees and interacts with.
Automated Front Wall Feature Extraction and Material Assessment Using Fused LIDAR and Through-Wall Radar Imagery

Military forces operating in urban environments are facing numerous challenges. One of them consists in being able to identify buildings material to support missions involving tactical breach or blast damage prediction. This paper reports on a method that combines both LIDAR and through-wall radar imagery to provide detailed information about a building front wall features and its construction material. The LIDAR and 3-D through-wall synthetic aperture radar (TWSAR) are mounted on a vehicle which is driven in front of a building/wall of interest. The acquired LIDAR point cloud is post-processed to automatically extract information on the front wall of buildings using a plane search strategy and cluster extraction to generate a front wall occupancy grid. This occupancy grid is used by the through-wall radar processing algorithms to restrict imagery to the areas of the wall that are exempt of doors, windows, or any other external feature. Based on typical features found in the through-wall radar images of the front wall, the type of wall is categorized as vinyl/gypsum/wood studs, cinder block, brick and cinder block, poured concrete, or others. The combination of LIDAR and through-wall radar offers the unique opportunity to automate the front wall feature extraction and material assessment and to provide timely information to a potential user.
The cytoskeletal system of nucleated erythrocytes. I. Composition and function of major elements

We have studied the dogfish erythrocyte cytoskeletal system, which consists of a marginal band of microtubules (MB) and trans-marginal band material (TBM). The TBM appeared in whole mounts as a rough irregular network and in thin sections as a surface-delimiting layer completely enclosing nucleus and MB. In cells incubated at 0 degrees C for 30 min or more, the MB disappeared but the TBM remained. MB reassembly occurred with rewarming, and was inhibited by colchicine. Flattened elliptical erythrocyte morphology was retained even when MBs were absent. Total solubilization of MB and TBM at low pH, or dissolution of whole anucleate cytoskeletons, yielded components comigrating with actin, spectrin, and tubulin standards during gel electrophoresis. Mass-isolated MBs, exhibiting ribbonlike construction apparently maintained by cross-bridges, contained four polypeptides in the tubulin region of the gel. Only these four bands were noticeably increased in the soluble phase obtained from cells with 0 degrees C- disassembled MBs. The best isolated MB preparations contained tubulin but no components comigrating with high molecular weight microtubule- associated proteins, spectrin, or actin. Actin and spectrin therefore appear to be major TBM constituents, with tubulin localized in the MB. The results are interpreted in terms of an actin- and spectrin- containing subsurface cytoskeletal layer (TBM), related to that of mammalian erythrocytes, which maintains cell shape in the absence of MBs. Observations on abnormal pointed erythrocytes containing similarly pointed MBs indicate further that the MB can deform the TBM from within so as to alter cell shape. MBs may function in this manner during normal cellular morphogenesis and during blood flow in vivo.
Contemporary cost‐effectiveness analysis comparing sequential bacillus Calmette‐Guerin and electromotive mitomycin versus bacillus Calmette‐Guerin alone for patients with high‐risk non–muscle‐invasive bladder cancer

Sequential bacillus Calmette‐Guerin (BCG) and electromotive mitomycin (sequential therapy) have been shown in a randomized prospective trial to be superior to therapy with BCG alone in patients with high‐risk non–muscle‐invasive bladder cancer. The objective of the current study was to compare the costs and benefits of these 2 treatment strategies by performing a 5‐year and 10‐year cost‐effectiveness study.
A Budgerigar Melopsittacus undulatus from the Pliocene of Riversleigh, North-western Queensland

Three carpometacarpi and a tarsometatarsus of a small parrot, recovered from the Early Pliocene-aged deposits at Rackham’s Roost Site, Riversleigh, north-western Queensland, are indistinguishable from those of the living Budgerigar Melopsittacus undulatus, and are referred to this species. The presence of this species suggests that the palaeoenvironment at Riversleigh during the Pliocene was open woodland, similar to the habitat occurring there today.
Crucial Role of Tumor Necrosis Factor Receptor 1 Expression on Nonhematopoietic Cells for B Cell Localization within the Splenic White Pulp

During immune responses the initial activation of B cells takes place in T cell zones of periarteriolar lymphoid sheaths (PALS) of the splenic white pulp. After initial activation, B cells migrate into the primary follicles and, in association with follicular dendritic cells (FDCs), undergo clonal expansion and differentiation giving rise to germinal centers (GCs). Peanut agglutinin binding (PNA+) cells of the GC differentiate further into memory or plasma cells. Here we report that in tumor necrosis factor receptor 1–deficient mice (TNFR1−/−), the location of B cells was altered and that plasma cells were abnormally distributed in the splenic PALS. In contrast to lymphotoxin α–deficient mice (LTα−/−), bone marrow or fetal liver transplantation did not correct the abnormal organization of the spleen, location of B cells, the lack of an FDC network, nor the antibody response in TNFR1−/− mice. These results argue for a crucial role of TNFR1 expression on nonhematopoietic cells for the maintenance of the splenic architecture and proper B cell location. In addition, the lack in development of an FDC network after adoptive transfer suggests that either FDCs are not of bone marrow origin or that they depend on signals from nonhematopoietic cells for maturation.
The C-Terminal Segment of the Cysteine-Rich Interdomain of Plasmodium falciparum Erythrocyte Membrane Protein 1 Determines CD36 Binding and Elicits Antibodies That Inhibit Adhesion of Parasite-Infected Erythrocytes

ABSTRACT Attachment of erythrocytes infected by Plasmodium falciparum to receptors of the microvasculature is a major contributor to the pathology and morbidity associated with malaria. Adhesion is mediated by the P. falciparum erythrocyte membrane protein 1 (PfEMP-1), which is expressed at the surface of infected erythrocytes and is linked to both antigenic variation and cytoadherence. PfEMP-1 contains multiple adhesive modules, including the Duffy binding-like domain and the cysteine-rich interdomain region (CIDR). The interaction between CIDRα and CD36 promotes stable adherence of parasitized erythrocytes to endothelial cells. Here we show that a segment within the C-terminal region of CIDRα determines CD36 binding specificity. Antibodies raised against this segment can specifically block the adhesion to CD36 of erythrocytes infected with various parasite strains. Thus, small regions of PfEMP-1 that determine binding specificity could form suitable components of an antisequestration malaria vaccine effective against different parasite strains.
Power analysis attack of QCA circuits: A case study of the Serpent cipher

Quantum-dot cellular automata (QCA) technology is an attractive alternative to CMOS for future digital designs. A powerful attack based on power analysis has become a significant threat to the security of CMOS cryptographic circuits. As there is no current flow in QCA, the power consumption of a QCA circuit is extremely low compared to its CMOS counterpart. Therefore, in this paper an investigation is carried out to ascertain if QCA circuits could be immune to power analysis attacks based on a case study of the Serpent cipher. In comparison to a previous design, the proposed QCA implementation of a sub-module of the Serpent cipher is more efficient in terms of complexity, area and latency. By using an upper bound power model, the first power analysis attack of a QCA cryptographic circuit is presented. Simulation results show that even though the power consumption is low, it can still be correlated with the correct key guess, and all possible subkeys applied to the Serpent sub-module can be revealed in a best case scenario for attackers. The security of practical QCA devices is also discussed and could be greatly improved by applying a smoother clock.
Superelastic shape memory alloy composite bars for reinforcing concrete structures

Superelastic shape memory alloys (SMAs) are a class of metallic alloys that have the unique property of being able to undergo large amounts of plastic strain while remaining elastic and dissipating energy. This thesis explored a strategy for adding ductility and energy dissipation to FRP reinforcing bars through the use of SMA-fiber reinforced polymer (SMA-FRP) composites, an innovative type of composite that consists of a polymer matrix reinforced with small diameter superelastic SMA wires with and without additional conventional fiber reinforcement. In this study an analytical model for the behavior of SMA-FRPs was developed based on experimental results. This model was then used in a parametric study to determine the effect of the composition of the composite on its performance. After which, the SMA-FRP bars were explored as reinforcement for concrete structures with analyses at the section, substructure, and structural levels. From this study it was found that SMA-FRP reinforcing bars behave in a ductile manner and are capable of dissipating energy. Furthermore, it was found that SMA-FRP bars have more potential to improve the ductility and energy dissipation capability of concrete structures compared to conventional FRP bars. iii ACKNOWLEDGEMENTS
Passive attitude estimation using gyroscopes and all-accelerometer IMU

In this paper, a novel approach to estimate a vehicle attitude using gyroscopes and an array of linear tri-axial accelerometers arranged in a certain configuration is presented. This configuration provides direct angular acceleration measurements that will be of great value once the quaternion dynamical equation is solved using Unscented Kalman filter. Various new states and measurements models based on the rotational quaternion are presented. Using this approach, estimating the attitude of a vehicle using linear accelerometers along with gyroscopes enables a completely passive attitude estimation under the simultaneous actions of vehicle varying center of gravity position, unknown varying gravitational field, and an accelerating vehicle without any singularity being involved in the states or measurements models which were not reported in the related literature to the best of authors' knowledge.
Performance analysis of joint switched diversity and adaptive modulation

In this paper, a simple and practical system based on a switched diversity scheme with adaptive modulation is presented. This system provides a reduced number of channel estimation while offering the optimum spectral efficiency given by a selection diversity system. In addition, the switching threshold is easily manipulated so as to make an efficient use of the tradeoff between spectral efficiency and channel estimation overhead. An extension of switched diversity into a multiuser scheduling is later also considered. This switch-based multiuser access scheme results in a lower average feedback load than that for the optimal selection-based multiuser scheme. Numerical results show that we can obtain a trade-off between spectral efficiency and the feedback load by choosing the switching threshold appropriately.
Performance of Hybrid Positioning System Combining GPS and Television Signals

In spite of the global coverage and the penetration into a daily life of GPS (global positioning system), GPS receivers have not been able to overcome the critical weakness of a GPS signal in indoor and urban areas due to its low signal power level after a long journey from satellites. One of the best solutions to this problem is the adoption of powerful terrestrial signals such as television, WiFi, and cellular communication signals. Among these signals, because TV transmitters have the highest level of signal powers, fixed geometries, and frequency diversities, TV signals are considered to be the strongest candidate as alternative ranging sources in urban and indoor areas. The combination of space-based signals such as GPS and land-based signals such as TV is ideal for a seamless universal positioning service, providing coverage to users in open spaces as well as restricted or closed space such as office buildings. To assess the benefits of a hybrid positioning system combining GPS and television signals, a prototype of TV signal based posi- tioning systems and a GPS receiver are used for the positioning field tests in the San Francisco Bay area, where measurements sites are selected from indoor and outdoor areas in urban, suburban, residential, and rural regions. The performance of the hybrid system is presented across the categorized areas, showing the promising aspects of the combination of space signals and terrestrial signals.
Multifunctionalized carbon nanotubes as advanced multimodal nanomaterials for biomedical applications

Abstract The increasing importance of nanotechnology in the field of biomedical applications has encouraged the development of new nanomaterials endowed with multiple functions. Novel nanoscale drug delivery systems with diagnostic, imaging and therapeutic properties hold many promises for the treatment of different types of diseases, including cancer, infection and neurodegenerative syndromes. Functionalized carbon nanotubes (CNTs) are one of the most recent type of nanomaterial developed in biomedicine as they can be designed and imparted with multimodal capabilities. Indeed, the possibility of inserting different functionalities on CNTs is opening the possibility to exploit them on new strategies that combine diagnosis with improved therapeutic efficacies. In this review, we describe the different approaches that have been recently developed to generate multifunctionalized CNTs for biomedical applications. In particular, covalent and non-covalent double and triple functionalization methods are discussed, putting in evidence their use in vitro and in vivo and highlighting the advantages and the drawbacks of these new systems. Preclinical studies have demonstrated that multifunctional CNTs are highly promising when combining diagnostic, imaging and therapeutic modalities.
Trace-driven optimization of networks-on-chip configurations

Networks-on-chip (NoCs) are becoming increasingly important in general-purpose and application-specific multi-core designs. Although uniform router configurations are appropriate for general-purpose NoCs, router configurations for application-specific NoCs can be non-uniformly optimized to application-specific traffic characteristics. In this paper, we specifically consider the problem of virtual channel (VC) allocation in application-specific NoCs. Prior solutions to this problem have been average-rate driven. However, average-rate models are poor representations of real application traffic, and can lead to designs that are poorly matched to the application. We propose an alternate trace-driven paradigm in which configuration of NoCs is driven by application traces. We propose two simple greedy trace-driven VC allocation schemes. Compared to uniform allocation, we observe up to 51% reduction in the number of VCs under a given average packet latency constraint, or up to 74% reduction in average packet latency with same number of VCs. Our results suggest that average-rate driven methods cannot effectively select appropriate links for VC allocation because they fail to consider the impact of traffic bursts. As a case study, we compare our proposed approach with an existing average-rate driven method and observe up to 35% reduction in the number of VCs for a given target latency.
ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour

A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate and modify models using SBML solver output as an initial parameter set, allowing interventions to be applied once a steady state has been reached. Additionally, multiple SBML models can be generated where a subset of parameter values are perturbed using local and global sensitivity analysis techniques, revealing the model’s sensitivity to the intervention. To illustrate the capabilities of ASPASIA, we demonstrate how this tool has generated novel hypotheses regarding the mechanisms by which Th17-cell plasticity may be controlled in vivo. By using ASPASIA in conjunction with an SBML model of Th17-cell polarisation, we predict that promotion of the Th1-associated transcription factor T-bet, rather than inhibition of the Th17-associated transcription factor RORγt, is sufficient to drive switching of Th17 cells towards an IFN-γ-producing phenotype. Our approach can be applied to all SBML-encoded models to predict the effect that intervention strategies have on system behaviour. ASPASIA, released under the Artistic License (2.0), can be downloaded from http://www.york. ac.uk/ycil/software.
Analysis of common deafness gene mutations in deaf people from unique ethnic groups in Gansu Province, China

Abstract Conclusions: The GJB2 gene mutation characteristic of Dongxiang was the interaction result of ethnic background and geographical environment, and Yugur exhibited the typical founder effect. The SLC26A4 gene mutation characteristic of Dongxiang was related to caucasian backgrounds and selection of purpose exons, i.e. ethnic background and the penetrance of ethnic specificity caused the low mtDNA1555A>G mutation frequency in Dongxiang. Objectives: To determine the prevalence of GJB2 and SLC26A4 genes and mtDNA1555A>G mutations and analyze the ethnic specificity in the non-syndromic sensorineural hearing loss (NSHL) of unique ethnic groups in Gansu Province. Methods: Peripheral blood samples were obtained from Dongxiang, Yugur, Bonan, and ethnic Han groups with moderately severe to profound NSHL in Gansu Province. Bidirectional sequencing (or enzyme digestion) was applied to identify the sequence variations. Results: The pathogenic allele frequency of the three gene mutations was different. The frequency of the GJB2 gene among the Dongxiang, Yugur, Bonan, and ethnic Han groups was 9.03%, 12.5%, 5.88%, and 12.17%, respectively. No difference was found between the ethnic groups. The frequencies of the SLC26A4 genes were 3.23%, 8.33%, 0%, and 9.81%, respectively. The mutation frequency of mtDNA1555A>G was 0%, 0%, 0%, and 6.03%, respectively. No difference was found between the ethnic groups, except for the Dongxiang and ethnic Han groups, both in SLC26A4 gene and mtDNA1555A>G.
Predictive Current Controller for Inverter Fed Medium Voltage Drives with LC Filter

The switching frequency of power semiconductor devices in high power medium voltage drives is limited because of high switching losses. These drives often comprise an LC output filter. The filter introduce a resonant circuit that may be excited for instance by fast control transients. One option to avoid such oscillations is applying damping control methods, which on the other hand usually require switching frequencies well above the filter resonance. This paper presents a new predictive stator current controller that avoids the excitation of the filter resonance, realizes active damping and enables fast current control while maintaining low switching frequency. Feasibility and good dynamic performance of the proposed control method is demonstrated by simulation results of a 2.4 kV induction motor drive and by experimental results obtained from a 55 kW prototype a.c. drive.