Miracle-dz/UniFAR-FTUs huggingface dataset:
Satellite Remote Sensing Algorithm Development to Estimate Total Suspended Sediment Concentration for Highly Turbid Waters of Western Australia

ii Acknowledgements . iv Publications presented as part of this Thesis . v Reports written during Ph.D. Candidature . vi Statement of contribution of others . vii List of common symbols . viii List of Abbreviations . x Definition of key terms . xii List of Figures . xviii List of Tables . xxv . 1 1.1 Overview . 1 1.2 Background . 1 1.3 Research objectives and significance . 7 1.4 Thesis outline . 8 . 10 2.1 Overview . 10 2.2 Radiative Transfer Theory and optical properties of the water column . 10 2.2.1 Radiometric quantities in remote sensing . 10 2.2.2 IOP and AOP . 13
Design of RLS Adaptive Filter Equivalent for Human Body Communication Channel

Human body can be used as a communication channel for electrical signal transmission and thus offers a novel data communication means in biomedical monitoring systems. Human Body communication channel (on-body) may be proven as promising solution for Wireless Body Area networks (WBANs) in terms of simplicity, reliability, powerefficiency and security. This study proposes the design of an adaptive filter equivalent for human body communication channel. The simulations are based on Electronics and Telecommunication Research Institute (ETRI’s) measurement results obtained on human body within a frequency range of 5-50MHz. The measured frequency response is processed to obtain FIR filter matrix coefficients and further identified as RLS adaptive filter. The designing is done using system identification tool in MATLAB. Also a comparison is made between RLS and normalized LMS algorithm for adaptive filter design, which established the RLS adaptive filter as the promising solution for modeling Human Body Communication Channel. General Terms Biomedical Electronics
Galectin-3 Predicts Long-Term Cardiovascular Death in High-Risk Patients With Coronary Artery Disease

Objective— Galectin-3 (Gal-3) can affect atherogenesis by multiple mechanisms, but it remains scarcely known whether plasma Gal-3 levels predict cardiovascular events in patients with coronary artery disease. Therefore, we investigated if Gal-3 predicts cardiovascular death in patients with coronary artery disease of the Genetic and ENvironmental factors In Coronary Artery disease study. Approach and Results— In a prospective cohort study, we measured the plasma levels of Gal-3 in 1013 randomly selected patients who underwent coronary angiography and long-term follow-up to assess incident cardiovascular events. The primary end points were (1) cardiovascular death and (2) a composite of cardiovascular death, acute coronary syndrome, and stroke. Secondary end points entailed (1) acute myocardial infarction, (2) stroke, and (3) a composite fatal ischemic event including fatal myocardial infarction and stroke. The effect of Gal-3 on prognosis was assessed using Kaplan–Meier analysis and multivariate Cox’s regression. During long-term follow-up (median, 7.2 years), 115 cardiovascular deaths occurred (15.2%), more commonly in the high Gal-3 tertile (25.2%) than in the intermediate and the low tertiles (13.6% versus 7.5%, respectively; P<0.001). The adverse prognostic effect of high Gal-3 was confirmed in subgroup analysis of the patients with angiographically documented coronary artery disease and also of those with a normal left ventricular ejection fraction. At multivariate analysis, Gal-3 was a predictor of cardiovascular mortality (hazard ratio, 1.79; 95% confidence interval, 1.10–2.93; P=0.020) along with age, left ventricular ejection fraction, and coronary atherosclerotic burden. Conclusions— In high cardiovascular risk patients referred for coronary angiography Gal-3 is a strong independent predictor of cardiovascular death.
Optimization of fuzzy logic controllers with rule base size reduction using genetic algorithms

In this paper, we present the automatic design methods with rule base size reduction for fuzzy logic controllers (FLCs). The adaptive schema is divided into two phases: the first phase is concerned with the adaptive learning method for optimizing the MFs parameters based on the binary coded genetic algorithms. The second phase is about the learning and reducing: automatically generate the fuzzy rules and at the same time apply the genetic reduction technique to determine the minimum number of fuzzy rules required in building the fuzzy models. In the rule base, the redundant rules are removed by setting their all consequents weight factor to zero and merging the conflicting rules during the learning process. The real and binary coded coupled genetic algorithms are applied for generating the optimal controllers that reduce the rule base size and optimal selection of fuzzy sets. Optimizing the MFs of FLCs with learning and reducing the number of fuzzy control rules concurrently represents a way to improve the computational efficiency and interpretability of FLCs to minimize the errors. The control algorithm is successfully tested for intelligent control of two degrees of freedom inverted pendulum. Finally, the simulation studies exhibits competing results with high accuracy that demonstrate the effective use of the proposed algorithm.
The Naphthoquinone Diospyrin Is an Inhibitor of DNA Gyrase with a Novel Mechanism of Action*

Background: New antibacterial compounds are urgently needed; DNA gyrase is a well-validated target. Results: Diospyrin and other naphthoquinones inhibit DNA gyrase by binding to a novel site in the B subunit. Conclusion: Naphthoquinones are inhibitors of gyrase with a novel mechanism of action. Significance: Naphthoquinones have potential as antibacterial compounds against TB. Tuberculosis and other bacterial diseases represent a significant threat to human health. The DNA topoisomerases are excellent targets for chemotherapy, and DNA gyrase in particular is a well-validated target for antibacterial agents. Naphthoquinones (e.g. diospyrin and 7-methyljuglone) have been shown to have therapeutic potential, particularly against Mycobacterium tuberculosis. We have found that these compounds are inhibitors of the supercoiling reaction catalyzed by M. tuberculosis gyrase and other gyrases. Our evidence strongly suggests that the compounds bind to the N-terminal domain of GyrB, which contains the ATPase active site, but are not competitive inhibitors of the ATPase reaction. We propose that naphthoquinones bind to GyrB at a novel site close to the ATPase site. This novel mode of action could be exploited to develop new antibacterial agents.
Scalar quantization for large scale image search

Bag-of-Words (BoW) model based on SIFT has been widely used in large scale image retrieval applications. Feature quantization plays a crucial role in BoW model, which generates visual words from the high dimensional SIFT features, so as to adapt to the inverted file structure for indexing. Traditional feature quantization approaches suffer several problems: 1) high computational cost---visual words generation (codebook construction) is time consuming especially with large amount of features; 2) limited reliability---different collections of images may produce totally different codebooks and quantization error is hard to be controlled; 3) update inefficiency--once the codebook is constructed, it is not easy to be updated. In this paper, a novel feature quantization algorithm, scalar quantization, is proposed. With scalar quantization, a SIFT feature is quantized to a descriptive and discriminative bit-vector, of which the first tens of bits are taken out as code word. Our quantizer is independent of collections of images. In addition, the result of scalar quantization naturally lends itself to adapt to the classic inverted file structure for image indexing. Moreover, the quantization error can be flexibly reduced and controlled by efficiently enumerating nearest neighbors of code words. The performance of scalar quantization has been evaluated in partial-duplicate Web image search on a database of one million images. Experiments reveal that the proposed scalar quantization achieves a relatively 42% improvement in mean average precision over the baseline (hierarchical visual vocabulary tree approach), and also outperforms the state-of-the-art Hamming Embedding approach and soft assignment method.
Aorta of ApoE-Deficient Mice Responds to Atherogenic Stimuli by a Prelesional Increase and Subsequent Decrease in the Expression of Antioxidant Enzymes

Abstract— Oxidative stress has been implicated in the development of atherosclerotic lesions. We evaluated the relationship between extent of atherosclerotic lesion formation and vascular expression of pro- and antioxidant enzymes in apoE-deficient mice. On normal chow, these mice showed elevated serum cholesterol levels (7.5- to 9.5-fold), and age-dependent, spontaneous development of all stages of atherosclerotic lesions, starting at the age of 12 weeks. RNA was extracted from the aortic arch and descending aorta, and mRNA expression of pro- and antioxidant enzymes was measured with real-time PCR. Local infiltration of monocytes/macrophages, reflected by increased vascular expression of CD68 mRNA (>10-fold), indicated that the arch was more susceptible than the descending aorta. The expression of catalase-1 and various isoforms of superoxide dismutase, glutathione peroxidase, and glutathione S-transferase alpha was significantly increased in the aortic arch, but not in the descending aorta, in the period preceding lesion formation (age 6 to 12 weeks). These expression levels were 1.5 to 5 times higher than in age-matched wild-type animals. Remarkably, there was an inverse relationship between extent of lesion formation and the mRNA levels of antioxidant enzymes, most of which started to decline after 12 weeks, as lesions developed. In contrast, inducible nitric oxide synthase expression increased 4-fold in the aortic arch over the course of the disease. Our results suggest that the arterial wall responds to increased serum levels of atherogenic lipoproteins by stimulating expression of antioxidant enzymes. The observed co-ordinate decline in expression of many of these protective systems may greatly accelerate the development of atherosclerosis.
M-Convex VM Consolidation: Towards a Better VM Workload Consolidation

Consolidating virtual machine workload is a unique feature of cloud computing platforms that greatly reduces the operating cost of the cloud data center. Correctly consolidating VMs' workloads for a large scale cloud computing platform is nontrivial because a shortsighted scheme may save some cost in one aspect but becomes expensive in other aspects being neglected. In this paper, we present a framework that automates the VM consolidation process to improve the VMs and servers assignment whenever such improvement is possible. The proposed VM consolidation framework can achieve a balance among multiple administrative objectives (e.g., power cost, network cost) during the VM consolidation process. The solution method of solving the VM consolidation problem is designed based on the powerful and efficient semi quasi M-convex optimization framework. The proposed algorithm can also produce VM consolidation solutions that require minimal system reconfigurations (e.g., VM migrations, turning on/off servers). More importantly, the proposed algorithm can be implemented distributedly so that the scalability of the proposed framework is greatly improved. As a result, the proposed framework is efficient, scalable and highly practical.
Postnatal Innate Immune Development: From Birth to Adulthood

It is well established that adaptive immune responses are deficient in early life, contributing to increased mortality and morbidity. The developmental trajectories of different components of innate immunity are only recently being explored. Individual molecules, cells, or pathways of innate recognition and signaling, within different compartments/anatomical sites, demonstrate variable maturation patterns. Despite some discrepancies among published data, valuable information is emerging, showing that the developmental pattern of cytokine responses during early life is age and toll-like receptor specific, and may be modified by genetic and environmental factors. Interestingly, specific environmental exposures have been linked both to innate function modifications and the occurrence of chronic inflammatory disorders, such as respiratory allergies. As these conditions are on the rise, our knowledge on innate immune development and its modulating factors needs to be expanded. Improved understanding of the sequence of events associated with disease onset and persistence will lead toward meaningful interventions. This review describes the state-of-the-art on normal postnatal innate immune ontogeny and highlights research areas that are currently explored or should be further addressed.
Pros and cons of online cognitive–behavioural therapy

Summary Online cognitive–behavioural therapy (CBT) for depression has the potential to serve as an important addition to the care of people with mild to moderate depression. Although some studies show promising results, the need for proper diagnoses and human guidance must be considered when interpreting the modest effects found in studies with little or no guidance from a therapist.
Sexually Transmitted Infections: A Novel Screening Strategy for Improving Women’s Health in Vulnerable Populations

Background: Migrant women are one of the most vulnerable population to health problems and well-being. This study aimed at implementing a counseling and preventive strategy for sexually transmitted infections (STIs) in undocumented migrant women in Milan, Italy. Methods: Women (ages 18–65) were enrolled at the NAGA Centre (2012–2013) and asked for a urine sample in order to carry out molecular detection of Human papillomavirus (HPV), Chlamydia trachomatis (Ct), Trichomonas vaginalis (Tv), Neisseria gonorrhoeae (Ng)-DNA. Socio-demographic and sexual behavior information were collected. All HPV/Ct+ women were offered Pap tests and/or were prescribed antibiotic treatment. Results: 537/757 women participated in the study (acceptability rate: 70.9%). Most of the women were from Latin America (45.6%) and Eastern Europe (30.7%); >60% of them had stable partners, did not use contraception and had had at least one pregnancy. The prevalence rates of HPV, Ct, Tv and Ng infections were 24.2%, 7.8%, 4.8% and 0%, respectively. In all, 43.2% of the positive women agreed to undergo a gynecological examination and accepted suitable treatment. Conclusions: This study shows an overall high prevalence of STIs in undocumented migrant women in Milan. The screening strategy based on counseling and urine testing contributed to the successfully high acceptability rate. More appropriate health services that adequately address all aspects of women’s health are required.
Diuron: Postemergence Oxalis Control in Container-grown Plants

Abstract Three experiments were conducted to evaluate the effectiveness of postemergence applied diuron (Direx 4L) for oxalis control and crop safety in container nursery crops. The first experiment, treated on March 15, 2001, evaluated diuron at 0.14, 0.28, 0.56, and 1.12 kg ai/ha (0.125, 0.25, 0.5, and 1.0 lb ai/A) rates without a surfactant and provided a maximum of 74% oxalis control in liriope and 57% in camellia. Diuron caused slight to no injury on ‘Pink Icicle’ camellia, ‘Anthony Waterer’ spirea and ‘Big Blue’ liriope which dissipated completely by 60 DAT. Experiment two, treated on April 6, 2001, used higher rates and included a surfactant. Diuron provided excellent oxalis control at rates ≥ 0.56 kg ai/ha (0.5 lb ai/A) by 21 days after treatment (DAT) and reduced oxalis shoot fresh weight (SFW) and shoot dry weight (SDW) by ≥ 95%. Unlike the first experiment, no injury was observed on either liriope or camellia. Experiment three, treated on April 15, 2001, evaluated diuron rate and oxalis size on.
A connector of two-component regulatory systems promotes signal amplification and persistence of expression

Organisms rely on a variety of regulatory architectures to control gene transcription. Whereas the functional characteristics of particular architectures are well understood, the properties of newly discovered regulatory designs cannot be easily predicted. One emerging design depends on small proteins that connect two-component regulatory systems, which constitute the dominant form of bacterial signal transduction. These connectors enable one system to respond to the signal perceived by a different system. To understand the functional properties of such connector-mediated architectures, we investigated the pathway controlled by the PhoP-dependent connector protein PmrD of Salmonella enterica and contrasted it to the circuit in which genes are regulated directly by the transcription factor PhoP. The PmrD-mediated pathway displayed both signal amplification and persistence of expression when compared with the direct pathway. Mathematical modeling of the two pathways allowed us to identify critical factors responsible for signal amplification.
Associations between social support, psychological well‐being, decision making, empowerment, infant and young child feeding, and nutritional status in Ugandan children ages 0 to 24 months

Maternal capabilities-qualities of mothers that enable them to leverage skills and resources into child health-hold potential influence over mother's adoption of child caring practices, including infant and young child feeding. We developed a survey (n = 195) that assessed the associations of 4 dimensions of maternal capabilities (social support, psychological health, decision making, and empowerment) with mothers' infant and young child feeding practices and children's nutritional status in Uganda. Maternal responses were converted to categorical subscales and an overall index. Scale reliability coefficients were moderate to strong (α range = 0.49 to 0.80). Mothers with higher social support scores were more likely to feed children according to the minimum meal frequency (odds ratio [OR] [95% confidence interval (CI)] = 1.38 [1.10, 1.73]), dietary diversity (OR [95% CI] = 1.56 [1.15, 2.11]), iron rich foods, (OR [95% CI] = 1.47 [1.14, 1.89]), and minimally acceptable diet (OR [95% CI] = 1.55 [1.10, 2.21]) indicators. Empowerment was associated with a greater likelihood of feeding a minimally diverse and acceptable diet. The maternal capabilities index was significantly associated with feeding the minimum number of times per day (OR [95% CI] = 1.29 [1.03, 1.63]), dietary diversity (OR [95% CI] = 1.44 [1.06, 1.94]), and minimally acceptable diet (OR [95% CI] = 1.43 [1.01, 2.01]). Mothers with higher psychological satisfaction were more likely to have a stunted child (OR [95% CI] = 1.31 [1.06, 1.63]). No other associations between the capabilities scales and child growth were significant. Strengthening social support for mothers and expanding overall maternal capabilities hold potential for addressing important underlying determinants of child feeding in the Ugandan context.
A look at the bone marrow predicts the global outcome.

> There is no part of the millet that does not make a sound […] . > > —Zenos’s paradox of the Grain of Millet Just 15 years ago, the amount of hematopoietic stem cells (HSC) circulating in peripheral blood (PB) was considered ≈0. In a healthy subject, out of ≈6000 leukocytes per microliter, HSCs expressing the typical marker CD34 account for ≈3 cells/μL (≈0.05% of total). In hematology, increased PB CD34+ cells indicate the timing for HSC collection after mobilization, and helps in the diagnosis of leukemia. However, there was no interest in understanding the clinical meaning of half-of-zero—a reduction in circulating CD34+ cells below normal values—until a role for bone marrow (BM)–derived cells in vascular homeostasis was hypothesized. The discovery of endothelial progenitor cells (EPC) has fostered a new era in cardiovascular research, focused on regeneration versus damage. Although still awaiting definite clinical demonstration, a wealth of experimental data indicates that EPCs promote vascular repair and angiogenesis.1 Article, see p 289 CD34 is a sialomucin adhesion molecule with unknown function, which identifies HSC in the BM. Small amounts of CD34+ HSC also circulate in PB and through peripheral organs. Although sources other than BM have been hypothesized, >90% of circulating CD34+ cells originate from the BM.2 Experimental and proof-of-concept human studies suggest that BM-derived HSC can repopulate the vasculature and parenchymatous organs beyond hematopoietic tissues.3 In fact, the function and biological meaning of steady-state PB CD34+ HSC is largely unknown. Far from being the result of a passive shedding from the BM, HSCs (and EPCs) are continuously released from the BM to PB after a circadian rhythm regulated by the autonomous …
Generating effective test cases based on satisfiability modulo theory solvers for service‐oriented workflow applications

Web Service Business Process Execution Language (WS‐BPEL) is one of the most popular service‐oriented workflow applications. The unique features (e.g. dead path elimination semantics and correlation mechanism) of WS‐BPEL applications have raised enormous problems to its test case generation, especially in unit testing. Existing studies mainly assume that each path in the control flow graphs that correspond to WS‐BPEL applications is feasible, which always yields imprecise test cases or complicates testing results. The current study tackles this problem based on satisfiability modulo theory solvers. First, a new coverage criterion is proposed to measure the quality of test sets for testing WS‐BPEL applications. Second, decomposition algorithms are presented to obtain test paths that meet the proposed coverage criterion. Finally, this paper symbolically encodes each test path with several constraints by capturing the unique features of WS‐BPEL. These constraints are solved and the test cases (test paths and test data) are obtained with the help of satisfiability modulo theory solvers to test WS‐BPEL applications effectively. Experiments are conducted using our approach and other typical approaches (e.g. message‐sequence generation‐based approach and concurrent path analysis approach) with 10 WS‐BPEL applications. Experimental results demonstrate that the test cases generated by our approach can avoid instantiating idle instance and expose more faults. Copyright © 2015 John Wiley & Sons, Ltd.
T Cell Epitope Immunotherapy Induces a CD4+ T Cell Population with Regulatory Activity

Background Synthetic peptides, representing CD4+ T cell epitopes, derived from the primary sequence of allergen molecules have been used to down-regulate allergic inflammation in sensitised individuals. Treatment of allergic diseases with peptides may offer substantial advantages over treatment with native allergen molecules because of the reduced potential for cross-linking IgE bound to the surface of mast cells and basophils. Methods and Findings In this study we address the mechanism of action of peptide immunotherapy (PIT) in cat-allergic, asthmatic patients. Cell-division-tracking dyes, cell-mixing experiments, surface phenotyping, and cytokine measurements were used to investigate immunomodulation in peripheral blood mononuclear cells (PBMCs) after therapy. Proliferative responses of PBMCs to allergen extract were significantly reduced after PIT. This was associated with modified cytokine profiles generally characterised by an increase in interleukin-10 and a decrease in interleukin-5 production. CD4+ cells isolated after PIT were able to actively suppress allergen-specific proliferative responses of pretreatment CD4neg PBMCs in co-culture experiments. PIT was associated with a significant increase in surface expression of CD5 on both CD4+ and CD8+ PBMCs. Conclusion This study provides evidence for the induction of a population of CD4+ T cells with suppressor/regulatory activity following PIT. Furthermore, up-regulation of cell surface levels of CD5 may contribute to reduced reactivity to allergen.