Miracle-dz/UniFAR-FTUs huggingface dataset:
Automation of the BD GeneOhm Methicillin-Resistant Staphylococcus aureus Assay for High-Throughput Screening of Nasal Swab Specimens

ABSTRACT This study demonstrated that an automated version of the BD-GeneOhm methicillin-resistant Staphylococcus aureus (MRSA) assay (BD-MRSA), using achromopeptidase sample lysis and PCR setup performed on the Hamilton MICROLAB STARlet (Auto-MRSA), gave results comparable to those obtained with BD-MRSA. The positive- and negative-result concordance rates and overall concordance of BD-MRSA and Auto-MRSA were 98.2, 97.7, and 97.6%, respectively. Auto-MRSA required 60% less technical time than BD-MRSA, and the time required to obtain results was 50% of that required for BD-MRSA. Auto-MRSA provides a reliable, robust system for high-volume clinical use.
Differential regulation of the high‐affinity choline transporter by wild‐type and Swedish mutant amyloid precursor protein

The high‐affinity choline transporter (CHT) is responsible for choline uptake into cholinergic neurons, with this being the rate‐limiting step for acetylcholine production. Altering CHT protein disposition directly impacts choline uptake activity and cholinergic neurotransmission. Amyloid precursor protein (APP) interacts with CHT proteins and increases their endocytosis from the cell surface. The goal of this study was to examine regulation of CHT trafficking and activity by wild‐type APP (APPwt) and determine if this differs with Swedish mutant APP (APPSwe) in SH‐SY5Y human neuroblastoma cells. APPSwe differs from APPwt in its trafficking from the cell surface through endosomes. We report for the first time that CHT interacts significantly less with APPSwe than with APPwt. Surprisingly, however, CHT cell surface levels and choline uptake activity are decreased to the same extent and CHT co‐localization to early endosomes increased similarly in cells expressing either APPwt or APPSwe. A critical observation is that CHT co‐immunoprecipitates with βCTF from APPSwe‐expressing cells. We propose that decreased CHT function is mediated differently by APPwt and APPSwe; APPwt interaction with CHT facilitates its endocytosis from the cell surface, whereas the effect of APPSwe on CHT is mediated indirectly potentially by binding to the βCTF fragment or by Aβ released from cells.
Vortical electromagnetic waves with a stationary power flow

We show analytically that in source free medium vertical electromagnetic wave can be derived from electromagnetic field, described by electric and magnetic Hertz vectors. To characterize the wave's vorticity we examine moment values of the real Poynting vector versus various directions of Hertz vectors in respect of wave propagation. This enables us to distinguish pure circular polarized transverse waves, possessing constant modulus orbital angular momentum and time and space invariant Poynting vector, from those of vortical, consisting of two time invariant and two vortical time dependent components. Poynting vectors of vortical components depend on time and have opposite directions while the time unvarying components have the same direction towards the wave propagation. The result of interaction of two vortical components is time invariant orbital angular momentum and time independent power flux, which is directed perpendicular to the common power flux of unvarying components.
Noisy speech recognition using variance adapted likelihood measure

Because the norm of testing cepstral vector was shrinked in a noisy environment, the model parameters, i.e., mean vector and covariance matrix, should be adapted simultaneously. We propose a method called variance adapted likelihood measure (VALM) which adapts the mean vector using a projection-based scale factor and adapts the covariance matrix using a variance reduction function estimated from the training database. The variance reduction function can be obtained according to various phonetic units. In the hidden Markov model based experiments, the speech recognition performance is greatly improved by applying VALM. The most significant improvement is achieved when the variance reduction function is separately estimated for different state parameters.
Bidirectional pyramid-based PMVS with automatic sky masking

In this paper, we propose an improved method for generating a dense point cloud from aerial images captured by a UAV camera. The proposed method is based on a PMVS approach and generates a dense 3D points using a bidirectional pyramid images. This approach is suitable for the characteristics of the aerial image set when the distance between the camera and the subject is large. In addition, the proposed method uses an automatic sky masking technique to generate a clean reconstruction result free of noise components in the sky area. The proposed method is applied not only to open experimental images but also to UAV aerial images.
From user behaviours to collective semantics

The World Wide Web has developed into an important platform for social interactions with the rise of social networking applications of different kinds. Collaborative tagging systems, as prominent examples of these applications, allow users to share their resources and to interact with each other. By assigning tags to resources on the Web in a collaborative manner, users contribute to the emergence of complex networks now commonly known as folksonomies, in which users, documents and tags are interconnected with each other. To reveal the implicit semantics of entities involved in a folksonomy, one requires an understanding of the characteristics of the collective behaviours that create these interconnections. This thesis studies how user behaviours in collaborative tagging systems can be analysed to acquire a better understanding of the collective semantics of entities in folksonomies. We approach this problem from three different but closely related perspectives. Firstly, we study how tags are used by users and how their different intended meanings can be identified. Secondly, we develop a method for assessing the expertise of users and quality of documents in folksonomies by introducing the notion of implicit endorsement. Finally, we study the relations between documents induced from collaborative tagging and compare them with existing hyperlinks between Web documents. We show that, in each of these scenarios, it is crucial to consider the collective behaviours of the users and the social contexts in order to understand the characteristics of the entities. This project can be considered as a case study of the Social Web, the research outcomes of which can be easily generalised to many other social networking applications. It also fits into the larger framework for understanding the Web set out by the emerging interdisciplinary field of Web Science, as the work involves analyses of the interactions and behaviour of Web users in order to understand how we can improve existing systems and facilitate information sharing and retrieval on the Web.
Protection domain allocation for optical networks with partial wavelength conversion

In this paper, we propose an approach of optimal protection domain allocation, called OPDA (optimal protection domain allocation), for dynamically allocating spare capacity for a given working lightpath in WDM networks with partial wavelength conversion capability. The optimization process is formulated as a shortest path searching problem in a transferred graph of cycles and wavelength graph of paths. We conduct a series of experiments to verify the proposed approach on four networks with different topologies and traffic load. We conduct experiments to compare the blocking probability of using OPSA with four reported schemes. The results show that OPDA achieves the best performance.
Identificação e comparação entre controle preditivo com modelo não linear e PI sintonizados com PSO em sistema de separação gravitacional de águia-óleo

Os metodos de separacao de oleo e agua possuem, em sua maioria, aplicacoes reduzidas devido ao custo operacional, a baixa eficiencia de separacao e ao alto tempo de processamento da separacao. Porem, Esses metodos de tratamento sao importantes devido a necessidade de extracao dos contaminantes mais indesejados no processo de producao do petroleo, a agua, e ao mesmo tempo, a concentracao de oleo na agua deve ser minima (da ordem de 40 a 20ppm) para o descarte regular da fase aquosa ao mar. A partir dessa necessidade de tratamento primario objetiva-se, neste trabalho, estudar e implementar algoritmos de identificacao para modelos polinomiais NARX em malha fechada, detectando a estrutura dos modelos, e comparar estrategias de controle PI e preditivo utilizando os modelos NARX (Nonlinear Auto-Regressive with Exogenous Input) atualizados online em uma combinacao de separador trifasico em serie com tres baterias de hidrociclones. Os objetivos principais deste trabalho sao obter um processo otimizado de separacao trifasica que regule o sistema, mesmo na presenca de golfadas; mostrar que e possivel obter sintonias otimizadas para os controladores analisando a malha como um todo; e, avaliar e comparar as estrategias de controle PI e preditivo aplicadas ao processo. Para cumprir estes objetivos foi utilizado um simulador para representar o separador trifasico e os hidrociclones, alem de desenvolvidos algoritmos de identificacao de sistemas (NARX) utilizando MQR (Minimos Quadrados Recursivo), aliados a metodos de deteccao de estrutura de modelos. Tambem foram implementados algoritmos de controle preditivo com modelos NARX atualizados online, e algoritmos de otimizacao que utilizam PSO (Particle Swarm Optimization). O trabalho finaliza com a comparacao de resultados obtidos a partir da utilizacao dos controladores PI e preditivo no sistema simulado ambos com parâmetros otimizados atraves do algoritmo de nuvem de particulas, e concluindo que as otimizacoes realizadas tornam o regulatorio menos sensivel a perturbacoes externas (golfadas) e quando otimizados os dois controladores apresentam resultados similares, sendo os resultados do preditivo um pouco menos sensivel as perturbacoes
Multidimensional Data Exploration by Explicitly Controlled Animation

Understanding large multidimensional datasets is one of the most challenging problems in visual data exploration. One key challenge that increases the size of the exploration space is the number of views that one can generate from a single dataset, based on the use of multiple parameter values and exploration paths. Often, no such single view contains all needed insights. The question thus arises of how we can efficiently combine insights from multiple views of a dataset. We propose a set of techniques that considerably reduce the exploration effort for such situations, based on the explicit depiction of the view space, using a small multiple metaphor. We leverage this view space by offering interactive techniques that enable users to explicitly create, visualize, and follow their exploration path. This way, partial insights obtained from each view can be efficiently and effectively combined. We demonstrate our approach by applications using real-world datasets from air traffic control, software maintenance, and machine learning.
Palmar reconstruction of the triangular fibrocartilage complex for instability of the distal radioulnar joint: a biomechanical study

We developed a new triangular fibrocartilage complex reconstruction technique for distal radioulnar joint instability in which the palmar portion of the triangular fibrocartilage complex was predominantly reconstructed, and evaluated whether such reconstruction can restore stability of the distal radioulnar joint in seven fresh cadaver upper extremities. Distal radioulnar joint instability was induced by cutting all soft-tissue stabilizers around the distal ulna. Using a palmar approach, a palmaris longus tendon graft was sutured to the remnant of the palmar radioulnar and ulnocarpal ligaments. The graft was then passed through a bone tunnel created at the fovea and was sutured. Loads were applied to the radius, and dorsopalmar displacements of the radius relative to the ulna were measured using an electromagnetic tracking device in neutral rotation, 60° supination and 60° pronation. We compared the dorsopalmar displacements before sectioning, before reconstruction and after reconstruction. Dorsopalmar instability produced by sectioning significantly improved in all forearm positions after reconstruction.
Critical Yield Numbers of Rigid Particles Settling in Bingham Fluids and Cheeger Sets

We consider the fluid mechanical problem of identifying the critical yield number $Y_c$ of a dense solid inclusion (particle) settling under gravity within a bounded domain of Bingham fluid, i.e., the critical ratio of yield stress to buoyancy stress that is sufficient to prevent motion. We restrict ourselves to a two-dimensional planar configuration with a single antiplane component of velocity. Thus, both particle and fluid domains are infinite cylinders of fixed cross-section. We then show that such yield numbers arise from an eigenvalue problem for a constrained total variation. We construct particular solutions to this problem by consecutively solving two Cheeger-type set optimization problems. Finally, we present a number of example geometries in which these geometric solutions can be found explicitly and discuss general features of the solutions.
NMR metabolomics and lipid analyses in salmonid tissue

Salmonids are fatty fish and contain high amounts of omega-3 polyunsaturated fatty acids, beneficial in human nutrition. However, the aquaculture industry has expanded greatly in recent decades, increasing demand for fishmeal (FM) and fish oil (FO) for fish feed, while the supply of fish raw materials has remained static or declined. This has created a need for alternative sustainable raw materials for fish feeds. This thesis examined the effect of replacing FM or FO with alternative plant (vegetable oils (VO), sesamin), microbial (zygomycete-, yeast fungi) and marine (krill, mussel) raw materials on growth performance, lipid content, fatty acid composition, lipid classes and fish metabolism in Atlantic salmon (Salmo salar) and Arctic charr (Salvelinus alpinus). There was a significant negative effect on growth performance when sesamin, zygomycete fungi and extracted yeast were included in fish diets. Replacement of FM or FO with alternative materials affected the lipid profile in fish tissues, e.g. compared with the control, docosahexaenoic acid (DHA) level was higher in fish fed krill meal and mussel meal and lower in fish fed VO, but unaffected in fish fed extracted and non-extracted yeast and sesamin. Zygomycete fungi meal inclusion decreased fish lipid content, thereby increasing DHA by 54% of total lipid content. Metabolomics analyses revealed an effect on several metabolites depending on the diet. Inclusion of sesamin increased the levels of some metabolites associated with energy metabolism, suggesting metabolic disturbance in the fish. Replacement of FM with non-extracted yeast affected liver metabolites, while extracted yeast mainly increased muscle metabolite levels. These increases suggested that the test ingredients produced a significant response in fish muscle metabolism. The altered metabolic fingerprint in fish fed krill and mussel meal diets compared with FM suggested differences in ingredient composition and physiological response to the diets. These results provide new information on the effects of non-traditional ingredients on fish metabolism, e.g. lipid-, single-carbon metabolism and tricarboxylic acid cycle. More studies are needed to identify the biochemical mechanisms involved and commercialise alternative fish feed materials.
cDNA Array Analysis of Altered Gene Expression in Human Endothelial Cells in Response to Chlamydia pneumoniae Infection

ABSTRACT Strong epidemiological and pathological evidence supports a role for Chlamydia pneumoniae infection in atherosclerosis and human coronary heart disease. Animal models have shown that C. pneumoniae disseminates hematogenously in infected monocytes and macrophages, while in vitro data suggest that infected macrophages can transmit C. pneumoniae infection directly to endothelial cells. Endothelial cells may be key in vivo targets for C. pneumoniae infection; given that these cells are important in regulating the dynamics of the vessel wall, we used cDNA microarrays to study the transcriptional response of endothelial cells to infection with C. pneumoniae. cDNA arrays were used to characterize the mRNA expression profiles for 268 human genes following infection with C. pneumoniae, which were compared to mRNA profiles of uninfected cells. Selected genes of interest were further investigated by reverse transcription-PCR throughout a 24-h period of infection. C. pneumoniaeinfection upregulated mRNA expression for approximately 20 (8%) of the genes studied. Genes coding for cytokines (interleukin-1), chemokines (monocyte chemotactic protein 1 and interleukin-8), and cellular growth factors (heparin-binding epidermal-like growth factor, basic fibroblast growth factor, and platelet-derived growth factor B chain) were the most prominently upregulated. In addition to these families of genes, increases in mRNA levels for intracellular kinases and cell surface receptors with signal transduction activities were observed. Time course experiments showed that mRNA levels were upregulated within 2 h following infection. These results expand our knowledge of the response of endothelial cells to C. pneumoniae by further defining the repertoire of C. pneumoniae-inducible genes and provide new insight into potential mechanisms of atherogenesis. In addition, the use of cDNA microarrays may prove useful for the study of host cell responses to C. pneumoniae infection during latent and replicative stages of infection and related pathology.
Froecast the USA Stock Indices with GARCH-type Models

GARCH-type models have been highly developed since Engle [1982] presented ARCH process 30 years ago. Different kinds of GARCH-type models are applicable to different kinds of research purposes. As documented by many literatures that short-memory processes with level shifts will exhibit properties that make standard tools conclude long-memory is present. Therefore, in this paper, we want to forecast with GARCH-type models and consider structural breaks and the long-memory characteristic. We analyze structural breaks and use the FIGARCH [Baillie et al., 1996] model comparing with GARCH [Bollerslev, 1986] model and EGARCH [Nelson, 1991] model to forecast the conditional variance process of three USA stock indices: Dow Jones Industrials Average (DJIA) index, Standard & Poor 500 (S&P 500) index and NASDAQ Composite (NASDAQ) index by using different in-sample size, different error distributions and forecasting different steps. We find the FIGARCH model is sensitive to the changes of conditions, and forecast better than the other two GARCH-type models.
Improving participation by Aboriginal children in blood lead screening services in Broken Hill, NSW.

UNLABELLED Lead poses a health risk to young children with detrimental effects on their intellectual development. Attendance rates for Aboriginal children at routine blood lead screening and at follow-up appointments in Broken Hill, NSW, have declined in recent years. This study sought to identify strategies to improve the participation of Aboriginal children aged 1-4 years in blood lead screening services in Broken Hill. METHODS Attendance rates during the period 2000-2010 were determined using the Broken Hill Lead Management database. From June to August 2011, Aboriginal community members, service providers and public health staff were invited to interviews and focus groups to explore barriers, enablers and suggestions for improving participation. RESULTS In 2009, 27% of Aboriginal children aged 1-4 years attended blood lead screening and 29% of these children with blood lead levels over 15 µg/dL attended follow-up appointments. Barriers to participation in lead screening services included community perceptions, reduced service capacity, socio-economic and interorganisational factors. Enablers included using a culturally acceptable model, linking lead screening with routine health checks and using the finger-prick method of testing. CONCLUSIONS The final report for the study included recommendations to improve participation rates of Aboriginal children including using social marketing, formalising collaboration between health services, supporting disadvantaged families and employing an Aboriginal Health Worker.
Prognosis of Partial Epileptic Seizures in the Adolescent

Summary: Actuarial analysis was applied to the notes of 235 patients having a partial seizure for the first time between the ages of 12 and 18 years to establish the best predictive indicators of outcome. Among the factors considered to affect significantly the outcome were the seizure type (elementary or complex symptomatology), the initial EEG, the seizure frequency, the etiological factors, and an association with generalized seizures. Sex, age of onset, and topography of EEG paroxysmal abnormalities had no significance. An algorithm allows the prediction of the prognosis of these seizures at two different times immediately after a first seizure in some cases and after a 1‐year survey in others.
Peripheral T Cell Functions Correlate with the Severity of Chronic Obstructive Pulmonary Disease1

Adaptive immune processes have been implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). We hypothesized that peripheral T cell abnormalities may be present in afflicted patients. We tested this hypothesis by characterizing circulating T cells in COPD patients and correlated these findings with disease severity, smoking status, and use of inhaled glucocorticosteroids (ICS). Compared with normal controls, a lesser proportion of peripheral CD4 T cells from COPD subjects produced IL-10, whereas the CD8 T cells from these patients were more often activated and more frequently produced both IFN-γ and IL-4. COPD severity was significantly and inversely associated with the proportion of circulating CD4 T cells and directly correlated with CD4 production of IL-2, as well as frequency of CD8 T cell activation and CD8 IFN-γ production. Adjustments for current smoking status and ICS use by linear regression showed independent, and generally inhibitory, effects of these clinical variables on the abnormal T cell functions of these patients. We conclude that circulating T cells from COPD patients are abnormally activated and elaborate proinflammatory mediators with admixed features of Th1 and Th2 responses. Furthermore, many of these effector processes are significantly correlated with disease severity. These findings further implicate adaptive immune processes in COPD progression and indicate that facile assays of peripheral lymphocytes may provide useful insights into disease mechanisms. Current smoking and ICS use had independent effects on T cell functions among the COPD subjects, illustrating the importance of controlling for clinical parameters as covariates in immunological studies of patients afflicted with this disease.