Miracle-dz/UniFAR-FTUs huggingface dataset:
Modification of bare and functionalized Au(111) surfaces and ferromagnetism of Au and Pd nanoclusters

The purpose of this thesis is to provide a better understanding of the properties of surfaces covered by self-assembled monolayers (SAMs) as well as the magnetic properties of interacting nanoclusters of gold and palladium. Surfaces covered by SAMs were studied by investigating their possible metallization as well as the morphological changes in bare and SAM covered Au(111) surfaces induced by Ar irradiation. The ferromagnetism in bare Au and Pd nanoagglomerates produced by nanocluster deposition was also investigated. SAMs used for this thesis are dodecanethiols (DDT, CH3(CH2)11SH) for the study on Ar ion induced morphological effects, as well as 4-mercaptopyridine (4-MPy) and two different kinds of dithiocarbamates (DTCs, R2NCS2) for the metallization study. The Au and Pd clusters were generated using a gas aggregation source in the low energy-range. Surface morphologies were studied by the use of scanning tunnelling microscopy (STM), transmission electron microscopy (TEM) and atom force microscopy (AFM). X-ray photoelectron spectroscopy (XPS) was used to determine the chemical compositions of surfaces, whereas a superconducting interference device (SQUID) was utilized for magnetization measurements. Our results show that DDT covered surfaces are more susceptible for irradiation-induced surface morphology changes than the unmodified Au surfaces. Flame-annealing of a Au(111) surface prior to ion bombardment is also found to be more susceptible to irradiation-induced surface defects. Based on our results it also seems that SAMs of DDT, 4-MPy, DTC, and DTC2 are impenetrable for Pd clusters deposited at thermal energies. For assemblies of bare Au nanoclusters we present ferroand superparamagnetic behaviour dependent on the interactions between particles. The enhanced surface-to-volume atomic ratio is found to favour ferromagnetism in the case of bare Au nanoparticles. For palladium nanocluster thin films we show that the ferromagnetic behaviour is highly dependent on the growth mode and film thickness, as these cause variations in the Pd cluster structures and resulting film morphologies.
RNA Tertiary Structure

Ribonucleic acids are negatively charged polymers assembled from four different types of monomers. Each monomer is made of an invariant phosphorylated sugar to which is attached one of the four standard nucleic acid bases; the pyrimidines uracil and cytosine, and the purines guanine and adenine. The first level of organization is thus the sequence of bases attached to the sugar–phosphate backbone. In salty water, the RNA molecules fold back on themselves via Watson–Crick base pairing between the bases (A with U, G with C or U) leading to double-stranded helices interrupted by single-stranded regions in internal loops or hairpin loops. The enumeration of the base-paired regions or helices constitutes a description of the second level of organization, the secondary structure. The methods available to deduce the secondary structure of an RNA molecule are mainly of three types: the phylogenetic approach, the theoretical prediction, and chemical/enzymatic methods. The secondary structure of an RNA molecule is experimentally accessible and its content measurable. Under appropriate conditions, structured RNA molecules undergo a transition to a three-dimensional (3D) fold in which the helices and the unpaired regions are precisely organized in space. This folding process usually depends on the presence of divalent ions, such as magnesium ions, and on the temperature. The tertiary structure is the level of organization relevant for biological function of structured RNA molecules.
THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Development of Novel In Situ Microscopy Techniques for the Study of Water Interaction with Soft Materials

The transport of water in soft materials can occur in liquid or gas phase and is highly dependent on the material microstructure and the structure dynamics. Understanding these relationships is the basis for the development of predictive models that can aid the design of new and improved functional materials. The environmental scanning electron microscope (ESEM) enables the visualisation of the effects of hydration or dehydration on a specimen down to the nanometre scale, facilitating the understanding of the structure-property relationships. However, the full potential of the ESEM has not yet been explored, especially when it comes to the transport of water in materials. The aim of this work was to develop new ESEM-based methods that enable the in situ study of water interaction with soft materials in a controlled manner. We designed a sample stage that uses a manipulator to bring the specimen in contact with a water reservoir in the ESEM, rendering the point of contact between water and specimen available for visual studies. In addition, coupled with a piezoresistive atomic force microscopy (AFM) sensor, the setup enables the local measurement of displacements in the nanometre range with millisecond temporal resolution through force spectroscopy. Thus, it provides a sensitive probe for swelling, which is an important effect of the water interaction for many soft materials. The potential of the developed methods has been demonstrated on three different materials systems and geometries. The absorption and transport of liquid water in individual cellulose fibres were imaged for the first time. The volumes of absorbed droplets were typically in the range of 0.02 nL to 0.2 nL and the rate of absorption varied between different fibres. The method was also applied to phase-separated polymer films intended as controlled-release coatings in oral pharmaceutical formulations and enabled the first studies of the water interaction in the initial stage of wetting. Simultaneous probing of the microstructure and the local water transport properties of the films provided previously inaccessible information about the structure-transport relationships and the microstructural evolution caused by the water interaction. In addition, measurements of the time-dependent osmotic swelling of yeast cells in the ESEM were demonstrated with a high spatial and temporal resolution. This type of measurement is valuable for the understanding of the water transport properties of cell membranes. The versatility of the setup allows the technique to be applied to a wide range of different materials systems and geometries where the interaction with water is of interest.
Performance Comparison of Non-Data-Aided Symbol Timing-Error Detection for the Raised-Cosine and "Better Than" Raised-Cosine Pulses

The performance of non-data-aided feedback-loop symbol timing synchronization operating with the raised-cosine (RC) and the "better than" raised-cosine (BTRC) pulses is investigated. The individual effects of additive channel noise, self noise, and their product on the variance of the jitter are studied for the two pulses. The BTRC pulse is shown to have better synchronization performance than the conventional RC pulse, except when the signal-to-noise ratio is very large and the excess bandwidth is large. Furthermore, in the case where a prefilter removing self-noise is employed, the BTRC pulse always has a performance gain over the RC pulse. The gain is, for example, as much as 1.4 dB for excess bandwidth of 0.35 without a prefilter and is larger when the excess bandwidth is smaller or a prefilter is employed.
An explicit sharpness index related to global phase coherence

We propose a definition of a Sharpness Index that is closely related to the notion of Global Phase Coherence recently introduced for automatic image restoration and image quality assessment. Using Gaussian random fields instead of random phase images, we can estimate the probability that a random image has a given Total Variation, which leads us to an explicit formula and a fast algorithm. Theoretical arguments and numerical experiments are given to assess the similarity between the Sharpness Index and the Global Phase Coherence, and an application to non-parametric blind deconvolution is presented, that illustrates the possibilities offered by this new approach.
GROUPS OF TYPE E 7 OVER ARBITRARY FIELDS

Freudenthal triple systems come in two flavors, degenerate and nondegenerate. The best criterion for distinguishing between the two which is available in the literature is by descent. We provide an identity which is satisfied only by nondegenerate triple systems. We then use this to define algebraic structures whose automorphism groups produce all adjoint algebraic groups of type E 7 over an arbitrary field of characteristic ≠ 2, 3. The main advantage of these new structures is that they incorporate a previously unconsidered invariant (a symplectic involution) of these groups in a fundamental way. As an application, we give a construction of adjoint groups with Tits algebras of index 2 which provides a complete description of this involution and apply this to groups of type E 7 over a real-closed field.
Analysis of Sparse and Noisy Ocean Current Data Using Flow Decomposition. Part I: Theory

A new approach is developed to reconstruct a three-dimensional incompressible flow from noisy data in an open domain using a two-scalar (toroidal and poloidal) spectral representation. The results are presented in two parts: theory (first part) and application (second part). In Part I, this approach includes (a) a boundary extension method to determine normal and tangential velocities at an open boundary, (b) establishment of homogeneous open boundary conditions for the two potentials with a spatially varying coefficient k, (c) spectral expansion of k, (d) calculation of basis functions for each of the scalar potentials, and (e) determination of coefficients in the spectral decomposition of both velocity and k using linear or nonlinear regressions. The basis functions are the eigenfunctions of the Laplacian operator with homogeneous mixed boundary conditions and depend upon the spatially varying parameter k at the open boundary. A cost function used for poor data statistics is introduced to determine the optimal number of basis functions. An optimization scheme with iteration and regularization is proposed to obtain unique and stable solutions. In Part II, the capability of the method is demonstrated through reconstructing a 2D wind-driven circulation in a rotating channel, a baroclinic circulation in the eastern Black Sea, and a large-scale surface circulation in the Southern Ocean.
Improved power and efficiency for tapered lasers with optimized photonic crystal structures

High power and high beam quality laser sources are required in numerous applications such as nonlinear frequency conversion, optical pumping of solid-state and fiber lasers, material processing and others. Tapered lasers can provide a high output power while keeping a high beam quality. However, the conventional tapered lasers suffer from a large vertical beam divergence. We have demonstrated 2-mm long tapered lasers with photonic crystal structures. A high beam quality and a narrow vertical divergence are achieved. In this paper, we optimized the photonic crystal structure and fabricated a 4-mm long tapered laser to further increase the output power and the wall-plug efficiency. Compared with our precious wafer, the optimized structure has a lower doping level to reduce the internal loss. The period of the photonic crystal structure and the thickness of the upper cladding are also reduced. The device has a 1-mm long ridge-waveguide section and a 3-mm long tapered section. The taper angle is 4°. An output power of 7.3 W is achieved with a peak wall-plug efficiency of 46% in continuous-wave mode. The threshold current is around 500 mA and the slope efficiency is 0.93 W/A. In pulsed mode, the output power is 15.6 W and the maximum wall-plug efficiency is 48.1%. The far-field divergence with full width at half maximum is 6.3° for the lateral direction at 3 A. The vertical far-field beam divergence is around 11° at different injection levels. High beam qualities are demonstrated by beam quality factor M2 of 1.52 for the lateral direction and 1.54 for the vertical direction.
MLPNN Training via a Multiobjective Optimization of Training Error and Stochastic Sensitivity

The training of a multilayer perceptron neural network (MLPNN) concerns the selection of its architecture and the connection weights via the minimization of both the training error and a penalty term. Different penalty terms have been proposed to control the smoothness of the MLPNN for better generalization capability. However, controlling its smoothness using, for instance, the norm of weights or the Vapnik-Chervonenkis dimension cannot distinguish individual MLPNNs with the same number of free parameters or the same norm. In this paper, to enhance generalization capabilities, we propose a stochastic sensitivity measure (ST-SM) to realize a new penalty term for MLPNN training. The ST-SM determines the expectation of the squared output differences between the training samples and the unseen samples located within their Q -neighborhoods for a given MLPNN. It provides a direct measurement of the MLPNNs output fluctuations, i.e., smoothness. We adopt a two-phase Pareto-based multiobjective training algorithm for minimizing both the training error and the ST-SM as biobjective functions. Experiments on 20 UCI data sets show that the MLPNNs trained by the proposed algorithm yield better accuracies on testing data than several recent and classical MLPNN training methods.
A Probabilistic Patch-Based Label Fusion Model for Multi-Atlas Segmentation With Registration Refinement: Application to Cardiac MR Images

The evaluation of ventricular function is important for the diagnosis of cardiovascular diseases. It typically involves measurement of the left ventricular (LV) mass and LV cavity volume. Manual delineation of the myocardial contours is time-consuming and dependent on the subjective experience of the expert observer. In this paper, a multi-atlas method is proposed for cardiac magnetic resonance (MR) image segmentation. The proposed method is novel in two aspects. First, it formulates a patch-based label fusion model in a Bayesian framework. Second, it improves image registration accuracy by utilizing label information, which leads to improvement of segmentation accuracy. The proposed method was evaluated on a cardiac MR image set of 28 subjects. The average Dice overlap metric of our segmentation is 0.92 for the LV cavity, 0.89 for the right ventricular cavity and 0.82 for the myocardium. The results show that the proposed method is able to provide accurate information for clinical diagnosis.
Combined Transfer of Human VEGF165 and HGF Genes Renders Potent Angiogenic Effect in Ischemic Skeletal Muscle

Increased interest in development of combined gene therapy emerges from results of recent clinical trials that indicate good safety yet unexpected low efficacy of “single-gene” administration. Multiple studies showed that vascular endothelial growth factor 165 aminoacid form (VEGF165) and hepatocyte growth factor (HGF) can be used for induction of angiogenesis in ischemic myocardium and skeletal muscle. Gene transfer system composed of a novel cytomegalovirus-based (CMV) plasmid vector and codon-optimized human VEGF165 and HGF genes combined with intramuscular low-voltage electroporation was developed and tested in vitro and in vivo. Studies in HEK293T cell culture, murine skeletal muscle explants and ELISA of tissue homogenates showed efficacy of constructed plasmids. Functional activity of angiogenic proteins secreted by HEK293T after transfection by induction of tube formation in human umbilical vein endothelial cell (HUVEC) culture. HUVEC cells were used for in vitro experiments to assay the putative signaling pathways to be responsible for combined administration effect one of which could be the ERK1/2 pathway. In vivo tests of VEGF165 and HGF genes co-transfer were conceived in mouse model of hind limb ischemia. Intramuscular administration of plasmid encoding either VEGF165 or HGF gene resulted in increased perfusion compared to empty vector administration. Mice injected with a mixture of two plasmids (VEGF165+HGF) showed significant increase in perfusion compared to single plasmid injection. These findings were supported by increased CD31+ capillary and SMA+ vessel density in animals that received combined VEGF165 and HGF gene therapy compared to single gene therapy. Results of the study suggest that co-transfer of VEGF and HGF genes renders a robust angiogenic effect in ischemic skeletal muscle and may present interest as a potential therapeutic combination for treatment of ischemic disorders.
Predictors of warfarin non-adherence in younger adults after valve replacement surgery in the South Pacific

Objectives Globally, mechanical valves are predominant as replacements for adolescents and younger adults with rheumatic heart disease (RHD). Mechanical valve implantation necessitates lifelong antithrombotic management (warfarin) and associated lifestyle modification, with event-free survival largely dependent on international normalised therapeutic ratios (INRs) remaining within the target therapeutic range. There is limited information on factors that may influence warfarin adherence among younger people or those in resource-limited settings. This study sought to identify predictors of warfarin adherence after valve replacement surgery for RHD in Fiji (n=127). Methods A cross-sectional study design was used. Results The sample had a mean age of 31.23 years (SD 13.34) and a mean time-since-surgery of 3.72 years (SD 3.95). Just over half were women (n=71, 56%) and almost two-thirds were indigenous (I-taukei, n=78, 61%). Most had an isolated valve procedure (n=94, 74%) and at the time of survey, they were in New York Heart Association Class I (n=97, 76%). A quarter (n=33, 26%) reported poor adherence with anticoagulation therapy and 13.38% (n=17) reported complete warfarin cessation. While younger age was significantly associated with non-adherence to warfarin therapy (p=0.008), the independent predictors of people who discontinue warfarin completely were those not understanding why warfarin was needed (OR=9.97, p=0.006); a history of forgetting to take warfarin (OR=8.64, p=0.0013) and travel time to heart clinic >1 hour (OR=5.80, p=0.039). Conclusions While medication adherence is complex and multifactorial, the consequences of warfarin non-adherence are potentially catastrophic. These results provide an important first step towards the development of country-specific and disease-specific strategies to improve warfarin adherence.
Practices of Nigerian physiotherapists with respect to lifestyle risk factor assessment and intervention: A national cross-sectional survey

ABSTRACT Background: Resolutions of the World Health Organization and World Confederation for Physical Therapy declare health promotion a priority for health professionals including physiotherapists. Objective: To describe lifestyle-related risk factor assessment and intervention practices of Nigerian physiotherapists, their perceived barriers to such practices, and education needs. Methods: Physiotherapists (n = 650) were invited to complete a questionnaire with 23 questions about respondent demographics, lifestyle risk factor assessment, and management practices; barriers to such practices; and related education needs. Statistical analysis was descriptive. Results: Response rate was 69% (n = 451). Less than half of respondents indicated that they “always” advised smokers to quit or heavy drinkers to reduce alcohol consumption. Most respondents viewed diet and anthropometrics as risk factors that warrant being addressed, but few respondents did so. Physical inactivity and blood pressure were the commonest risk factors reportedly assessed. Perceived barriers to health promotion practices included time, knowledge, and access to other providers. Continuing education needs identified by respondents included methods for delivering advice regarding smoking cessation, diet, and alcohol consumption. Conclusions: Nigerian physiotherapists inconsistently assess lifestyle-related risks and intervene to address them. Continuing education is needed to address barriers to health promotion practices by meeting the perceived needs of Nigerian physiotherapists.
Effects of Single Neutron Interactions in Silicon Integrated Circuits

Measurements of the permanent effects of single fast neutron interactions in silicon depletion regions are reported for the first time. Increases in dark current density by as much as two orders of magnitude were observed for individual cells in an image sensor bombarded with 14-MeV neutrons. Single damage events and the distribution of a large number of events were measured. Experimental results are in good agreement with model calculations and statistical expectations. Long-term annealing data for single events are used in conjunction with previous macroscopic short-term annealing results to predict the early-time impact of individual damaged regions. Implications of the present results for VLSI/ULSI circuits are discussed, and examples of cases in which problems may occur are given. An approach is presented for assessing the susceptibility of any integrated circuit to the permanent effects of single neutron interactions.
Determination of residual contents of pesticides in rice (Oryza sativa L.) crop from different regions of Pakistan

The study was conducted to investigate the pesticide residues in unhusked and husked rice (Oryza sativa L.) on Basmati-385 and Irri-6 varieties in major rice growing areas of Punjab, Pakistan. The concentration of four pesticides was determined by gas chromatography with flame ionization detection (GC-FID). In all the 400 samples, four pesticides, i.e., Karate, Malathion, Novacran and Padan were found in concentrations ranging from 19 to 148 ppm. The mean levels of pesticides in all the samples were below or just crossed the threshold limiting values (TLV). So presently there is no serious health problem due to pesticide poisoning. The results present important information on the current contamination status of an important agricultural crop in Pakistan and highlight the need for immediate action to manage the use of some excessively applied and potentially persistent pesticides.
A Virtual Microscopy System to Scan, Evaluate and Archive Biomarker Enhanced Cervical Cytology Slides

Background: Although cytological screening for cervical precancers has led to a reduction of cervical cancer incidence worldwide it is a subjective and variable method with low single-test sensitivity. New biomarkers like p16 that specifically highlight abnormal cervical cells can improve cytology performance. Virtual microscopy offers an ideal platform for assisted evaluation and archiving of biomarker-stained slides. Methods: We first performed a quantitative analysis of p16-stained slides digitized with the Hamamatsu NDP slide scanner. From the results an automated algorithm was created to reliably detect cells, nuclei and p16-stained cells. The algorithm's performance was evaluated on two complete slides and tiles from 52 independent slides (11,628, 4094 and 25,619 cells/clusters, respectively). Results: We achieved excellent performance to discriminate unstained cells from nuclei and biomarker-stained cells. The automated algorithm showed a high overall and positive agreement (99.0–99.7% and 70.9–83.4%, respectively) with the gold standard and had a very high sensitivity (89.1–100.0%) and specificity (98.9–100.0%) to detect biomarker-stained cells. Conclusions: We implemented a virtual microscopy system allowing highly efficient automated prescreening and archiving of biomarker-stained slides. Based on the initial results, we will evaluate the performance of our system in large epidemiologic studies against disease endpoints.