Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a thermal sensor for probing small volumes

This thesis presents the design, fabrication and characterisation of a thermal micro-sensor capable of operating on small scale samples. It was initially characterised by measuring the thermal conductivity of 100 μl liquid droplets and thin materials (sheets of paper) before being applied to the measurement of the water content of plant leaves. The device consists of a micro-heater and two thin-film thermocouples formed on a flexible polyimide substrate and used microfabrication techniques to precisely pattern the sensing elements. The heater was used to induce a temperature gradient within a sample in contact with the device, which was recorded as a difference in temperature (ΔT) between the two thermocouples. Various experiments have demonstrated that ∆T was dependent on the total thermal resistance (consisting of the bulk thermal conductivity and thermal contact resistance) of the sample under inspection. The device’s sensitivity to bulk thermal conductivity was shown by recording the variation in ∆T for 100 μl droplets of glycerine/water mixtures. Different compositions of the mixture served as thermal conductivity standards. The measurement of mixtures of propanol/water further demonstrated that the device could be used to indirectly monitor the composition of small volume binary solutions by measurement of the thermal conductivity. By monitoring the thermal conductivity of wetted paper, it was shown that the device was sensitive to the increase in the total thermal resistance as the paper dried out. Furthermore, theoretical and experimental drying times were in agreement and exhibited a similar dependence on the air temperature. This provided clear evidence of the device’s ability to monitor thermal conductivity of small samples. The final element of this work was the real-time monitoring of the water content of plant leaves. The device was clamped to an abscised leaf which was allowed to dry over a period of 6 hours. A comparison between the weight of the leaf and ∆T measurements showed a linear dependence. It was found that the changes in thermal properties were dominated by the water content of the leaf. The device was subsequently shown to be sensitive to changes in the water content of the leaves of plants subjected to water stress conditions, demonstrating its ability to monitor the real-time water content in-situ.
Cord Blood 25-Hydroxyvitamin D3 and Allergic Disease During Infancy

OBJECTIVE: There has been growing interest in vitamin D insufficiency as a predisposing factor for allergy development based on immunoregulatory properties and epidemiological studies. The aim of this study was to investigate the association between vitamin D exposure in utero and allergic outcomes in the first year of life. METHODS: Cord blood (CB) vitamin D was measured in 231 high-risk infants from an Australian prospective birth cohort. CB 25-hydroxyvitamin D3 (25[OH]D3) concentration was analyzed in relation to maternal vitamin D intake and the development of infant eczema, allergen sensitization, and immunoglobulin E-mediated food allergy. RESULTS: Maternal intake of supplemental vitamin D was significantly correlated with CB 25(OH)D3 concentration (ρ = 0.244, P = .003), whereas dietary vitamin D did not influence CB levels. There was significant seasonal variation in CB 25(OH)D3 concentration suggesting that sunlight exposure was an important determinant. Lower CB vitamin D status was observed in infants that developed eczema (P = .018), and eczema was significantly more likely in those with concentrations <50 nmol/L in comparison with those with concentrations ≥75 nmol/L (odds ratio 2.66; 95% confidence interval 1.24–5.72; P = .012). This association remained significant after adjustment for multiple confounding factors. The associations between CB 25(OH)D3 concentration and allergen sensitization, immunoglobulin E-mediated food allergy, and eczema severity (SCORing Atopic Dermatitis) were not significant. CONCLUSIONS: Reduced vitamin D status in pregnancy may be a risk factor for the development of eczema in the first year of life, reinforcing the need to explore the role of vitamin D exposure during development for disease prevention.
Caudate Nucleus Volume Mediates the Link between Cardiorespiratory Fitness and Cognitive Flexibility in Older Adults

The basal ganglia play a central role in regulating the response selection abilities that are critical for mental flexibility. In neocortical areas, higher cardiorespiratory fitness levels are associated with increased gray matter volume, and these volumetric differences mediate enhanced cognitive performance in a variety of tasks. Here we examine whether cardiorespiratory fitness correlates with the volume of the subcortical nuclei that make up the basal ganglia and whether this relationship predicts cognitive flexibility in older adults. Structural MRI was used to determine the volume of the basal ganglia nuclei in a group of older, neurologically healthy individuals (mean age 66 years, N = 179). Measures of cardiorespiratory fitness (VO2max), cognitive flexibility (task switching), and attentional control (flanker task) were also collected. Higher fitness levels were correlated with higher accuracy rates in the Task Switching paradigm. In addition, the volume of the caudate nucleus, putamen, and globus pallidus positively correlated with Task Switching accuracy. Nested regression modeling revealed that caudate nucleus volume was a significant mediator of the relationship between cardiorespiratory fitness, and task switching performance. These findings indicate that higher cardiorespiratory fitness predicts better cognitive flexibility in older adults through greater grey matter volume in the dorsal striatum.
Strength-based Signal Detection in PAM OOK Concentration-Encoded Molecular Communication

In this paper, the expressions of achievable strength-based suboptimum detection probabilities of concentration-encoded molecular communication (CEMC) system have been derived based on pulse-amplitude modulated (PAM) on-off keying (OOK) modulation scheme. Results show that the detection performance of a PAM OOK CEMC system significantly depends on the statistical parameters of diffusion noise and intersymbol interference (ISI). Analytical performances of ISI-free and ISI-affected scenarios have been explained and compared based on receiver operating characteristics (ROC) curves for impulse (i.e. spike)-modulated (IM) and PAM schemes. It is shown that the effects of diffusion noise and ISI on ROC can be explained separately based on their communication range-dependent statistics.
Real-time logics: complexity and expressiveness

A unifying framework for the study of real-time logics is developed. In analogy to the untimed case, the underlying classical theory of timed state sequences is identified, it is shown to be nonelementarily decidable, and its complexity and expressiveness are used as a point of reference. Two orthogonal extensions of PTL (timed propositional temporal logic and metric temporal logic) that inherit its appeal are defined: they capture elementary, yet expressively complete, fragments of the theory of timed state sequences, and thus are excellent candidates for practical real-time specification languages. <<ETX>>
Study of 80W-10Ta-7Ni-3Fe high density alloys

Ferromagnetic Ni-Mn-Fe-Ga single crystal of a pseudoquaternary Heusler alloy has been invested as a new magnetic field control actuator material. A single crystal of Ni52Mn16.4Fe8Ga23. 6 was grown in [001] direction of the cubic parent phase by the Czochralski method. The field-controlled shape memory effect and the temperature dependent of the magnetic-field-induced strain (MFIS) in Ni52Mn16.4Fe8Ga23. 6 single crystal were investigated by measuring the field enhanced transformation strain and the MFIS with a magnetic field applied in different directions. The results show that such material combined with the martensitic transformation can produce the large field-enhanced transformation strain and the large MFIS. It is found that the MFIS is almost temperature independent, the maximum decreasing magnitude of the saturated MFIS is less than 10% from 265 K to 100 K. In addition, the direction in which the MFIS has the largest value is always the [001], namely the growth direction of the crystals. The results are discussed with reference to the shape memory characteristics of the alloys and the mechanism of the preferentially orientation of martensitic variants.
Denoising Strategy for Convolutionally-Coded Bidirectional Relaying

In this paper, we present a forwarding strategy for two-stage bidirectional relaying in which trellis-coded modulation (TCM) is employed. We reveal that adaptive network coding cannot resolve distance shortening occurred at specific channel conditions when a certain TCM is used. To overcome this issue, we introduce an improved amplify-and-forward (AF) scheme termed pseudo AF (PAF). The proposed strategy adaptively switches network coding and PAF according to the channel information. Computer simulations demonstrate that the proposed approach can improve throughput performance.
Fitting Multilevel Models When Predictors and Group Effects Correlate

Random effects models (that is, regressions with varying intercepts that are modeled with error) are avoided by some social scientists because of potential issues with bias and uncertainty estimates. Particularly, when one or more predictors correlate with the group or unit effects, a key Gauss-Markov assumption is violated and estimates are compromised. However, this problem can easily be solved by including the average of each individual-level predictors in the group-level regression. We explain the solution, demonstrate its effectiveness using simulations, show how it can be applied in some commonly-used statistical software, and discuss its potential for substantive modeling.
Use of Raman Spectroscopy to Decrease Time for Identifying the Species of Candida Growth in Cultures

Background The objective of this study is to establish Raman signatures from pure cultures of different Candida species using Raman Spectroscopy (RS) and use these signatures for rapid identification of unknown Candida species. Methods Pure cultures of five Candida species were evaluated using RS to build a limited signature library. ‘Raman Processing’ (RP) software was used for Principal Component Analysis (PCA) and Differential Functional Analysis (DFA). Results Eleven principal components described at least 95% variance in the spectra. Raman signatures from these known Candida species were able to identify the species of unknown Candida cultures with 100% accuracy. Conclusion Raman spectroscopy can improve early identification of Candida species and may facilitate early optimal antifungal therapy.
The improvement of dyeability of flax fibre by microwave treatment

Purpose – To develop a method based on urea/microwave treatment for improving the dyeability of the flax fibre.Design/methodology/approach – The treatment was carried out under a variety of conditions in terms of the power of the microwave, the time of microwave treatment and the use of urea in the treatment solution. The physical chemical properties of the treated flax fibres were characterised using a variety of techniques including scanning electron microscopy (SEM), X‐ray diffractometry, spectrophotometric measurement and tensile measurement.Findings – It was found that the treated flax fibres had significantly improved dyeability. The causes to the improvement of the dyeability of the flax fibre were found to be the increased absorption of dye on the fibre and the increased reaction probability between the dye and the fibre. The procedure for optimum modification appeared to be soaking the flax fabrics in 10 per cent urea solution; treating the fabrics with microwave at 350 W for 2.5 minutes; and tre.
A Study on Corporate Social Responsibility Practices amongst Business Organisations in Malaysia

Corporate social responsibility (CSR) has emerged as a form of sustainability governance with advantages to the economic, environment and social progress. According to a study by ACCA Malaysia in 2004, there was only 43% of companies had reported to some extent in the social performance while 26% were pending to do so in future and most CSR commitment was expressed in terms of charity (Mallenbaker.net 2006). This shows that current awareness on CSR has increased among organisations in Malaysia. Therefore, this research aims to analyse the extent of CSR practices among different types of organisation and industries in Malaysia.
Peptides from the Variable Region of Specific Antibodies Are Shared among Lung Cancer Patients

Late diagnosis of lung cancer is still the main reason for high mortality rates in lung cancer. Lung cancer is a heterogeneous disease which induces an immune response to different tumor antigens. Several methods for searching autoantibodies have been described that are based on known purified antigen panels. The aim of our study is to find evidence that parts of the antigen-binding-domain of antibodies are shared among lung cancer patients. This was investigated by a novel approach based on sequencing antigen-binding-fragments (Fab) of immunoglobulins using proteomic techniques without the need of previously known antigen panels. From serum of 93 participants of the NELSON trial IgG was isolated and subsequently digested into Fab and Fc. Fab was purified from the digested mixture by SDS-PAGE. The Fab containing gel-bands were excised, tryptic digested and measured on a nano-LC-Orbitrap-Mass-spectrometry system. Multivariate analysis of the mass spectrometry data by linear canonical discriminant analysis combined with stepwise logistic regression resulted in a 12-antibody-peptide model which was able to distinguish lung cancer patients from controls in a high risk population with a sensitivity of 84% and specificity of 90%. With our Fab-purification combined Orbitrap-mass-spectrometry approach, we found peptides from the variable-parts of antibodies which are shared among lung cancer patients.
Senescent Cardiac Fibroblast Is Critical for Cardiac Fibrosis after Myocardial Infarction

Senescence is a recognized mechanism of cardiovascular diseases; however, its contribution to myocardial fibrosis and rupture after infarction and the underlying mechanisms remain unclear. Here we showed that senescent cardiac fibroblasts markedly accumulated in heart after myocardial infarction. The expression of key senescence regulators, especially p53, was significantly up-regulated in the infarcted heart or hypoxia-treated fibroblasts. Furthermore, knockdown of endogenous p53 by siRNA in fibroblasts markedly reduced hypoxia-induced cell senescence, cytokine expression but increased collagen expression, whereas increased expression of p53 protein by adenovirus infection had opposite effects. Consistent with in vitro results in cardiac fibroblasts, p53 deficiency in vivo significantly decreased the accumulation of senescent fibroblasts, the infiltration of macrophages and matrix metalloproteinases, but enhanced collagen deposition after myocardial infarction. In conclusion, these results suggest that the p53-mediated fibroblast senescence limits cardiac collagen production, and inhibition of p53 activity could represent a novel therapeutic target to increase reparative fibrosis and to prevent heart rupture after myocardial infarction.
Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
Constraining global air‐sea gas exchange for CO2 with recent bomb 14C measurements

The 14CO2 released into the stratosphere during bomb testing in the early 1960s provides a global constraint on air‐sea gas exchange of soluble atmospheric gases like CO2. Using the most complete database of dissolved inorganic radiocarbon, DI14C, available to date and a suite of ocean general circulation models in an inverse mode we recalculate the ocean inventory of bomb‐produced DI14C in the global ocean and confirm that there is a 25% decrease from previous estimates using older DI14C data sets. Additionally, we find a 33% lower globally averaged gas transfer velocity for CO2 compared to previous estimates (Wanninkhof, 1992) using the NCEP/NCAR Reanalysis 1 1954–2000 where the global mean winds are 6.9 m s−1. Unlike some earlier ocean radiocarbon studies, the implied gas transfer velocity finally closes the gap between small‐scale deliberate tracer studies and global‐scale estimates. Additionally, the total inventory of bomb‐produced radiocarbon in the ocean is now in agreement with global budgets based on radiocarbon measurements made in the stratosphere and troposphere. Using the implied relationship between wind speed and gas transfer velocity ks = 0.27〈u102〉(Sc/660)−0.5 and standard partial pressure difference climatology of CO2 we obtain an net air‐sea flux estimate of 1.3 ± 0.5 PgCyr−1 for 1995. After accounting for the carbon transferred from rivers to the deep ocean, our estimate of oceanic uptake (1.8 ± 0.5 PgCyr−1) compares well with estimates based on ocean inventories, ocean transport inversions using ocean concentration data, and model simulations.
Resting state connectivity and cognitive performance in adults with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy

Cognitive impairment is an inevitable feature of cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), affecting executive function, attention and processing speed from an early stage. Impairment is associated with structural markers such as lacunes, but associations with functional connectivity have not yet been reported. Twenty-two adults with genetically-confirmed CADASIL (11 male; aged 49.8 ± 11.2 years) underwent functional magnetic resonance imaging at rest. Intrinsic attentional/executive networks were identified using group independent components analysis. A linear regression model tested voxel-wise associations between cognitive measures and component spatial maps, and Pearson correlations were performed with mean intra-component connectivity z-scores. Two frontoparietal components were associated with cognitive performance. Voxel-wise analyses showed an association between one component cluster and processing speed (left middle temporal gyrus; peak −48, −18, −14; Z E = 5.65, p FWE corr = 0.001). Mean connectivity in both components correlated with processing speed (r = 0.45, p = 0.043; r = 0.56, p = 0.008). Mean connectivity in one component correlated with faster Trailmaking B minus A time (r = −0.77, p < 0.001) and better executive performance (r = 0.56, p = 0.011). This preliminary study provides evidence for associations between cognitive performance and attentional network connectivity in CADASIL. Functional connectivity may be a useful biomarker of cognitive performance in this population.
Primal-Dual Plug-and-Play Image Restoration

We propose a new plug-and-play image restoration method based on primal-dual splitting. Existing plug-and-play image restoration methods interpret any off-the-shelf Gaussian denoiser as one step of the so-called alternating direction method of multipliers (ADMM). This makes it possible to exploit the power of such a highly-customized Gaussian denoising method for general image restoration tasks in a plug-and-play fashion. However, the ADMM-based plug-and-play approach (ADMMPnP) has several limitations: 1) it often requires a problem-specific iterative method in solving a subproblem, which results in a computationally expensive inner loop; and 2) it is specialized to handle the formulation of a regularization (plug-and-play) term plus a data-fidelity term, so that it does not allow to impose hard constraints useful for image restoration. Our approach resolves these issues by leveraging the nature of primal-dual splitting, yielding a very flexible plug-and-play image restoration method. Experimental results demonstrate that the proposed method is much more efficient than ADMMPnP with an inner loop, whereas it keeps the same efficiency as ADMMPnP in the case where the subproblem of ADMMPnP can be solved efficiently.
Germ Cell Expression of an Isolated Human Endogenous Retroviral Long Terminal Repeat of the HERV-K/HTDV Family in Transgenic Mice

ABSTRACT In contrast to most other human endogenous retroviral families, various HERV-K members have open reading frames that code for functional viral proteins which can form noninfectious particles in some germ cell tumors. The HERV-K viral genes are highly transcribed in germ cell tumors but are transcribed to lower or undetectable levels in most other tissue and tumor types. To further analyze the expression patterns of these proviruses, long terminal repeats (LTRs) were isolated from the human genome and used in reporter gene assays. Expression of some HERV-K LTRs was found to be high in human and murine germ cell tumors (testicular teratocarcinomas) and low in non-germ-cell tumors. Furthermore, upon differentiation of a teratocarcinoma cell line, the expression of an active LTR dropped dramatically, suggesting developmental regulation of these proviral LTRs. Transgenic mice harboring an active LTR driving lacZ expression were generated and analyzed. Adult mouse testes showed the highest levels of expression, and the transgene staining appeared to be restricted primarily to the more undifferentiated spermatocytes. Most other tissues analyzed revealed very low or undetectable levels of expression both by reverse transcription-PCR and by Northern blot analysis. Whether the restricted expression of HERV-K in germ cells and in germ cell-derived tumors is of significant importance during development or tumorigenesis remains to be elucidated. Germ line expression of these viruses would allow for their expansion and movement, while somatic repression would ensure limited insertional mutagenesis and misexpression in an individual.