Data mining of the GAW14 simulated data using rough set theory and tree-based methods

Rough set theory and decision trees are data mining methods used for dealing with vagueness and uncertainty. They have been utilized to unearth hidden patterns in complicated datasets collected for industrial processes. The Genetic Analysis Workshop 14 simulated data were generated using a system that implemented multiple correlations among four consequential layers of genetic data (disease-related loci, endophenotypes, phenotypes, and one disease trait). When information of one layer was blocked and uncertainty was created in the correlations among these layers, the correlation between the first and last layers (susceptibility genes and the disease trait in this case), was not easily directly detected. In this study, we proposed a two-stage process that applied rough set theory and decision trees to identify genes susceptible to the disease trait. During the first stage, based on phenotypes of subjects and their parents, decision trees were built to predict trait values. Phenotypes retained in the decision trees were then advanced to the second stage, where rough set theory was applied to discover the minimal subsets of genes associated with the disease trait. For comparison, decision trees were also constructed to map susceptible genes during the second stage. Our results showed that the decision trees of the first stage had accuracy rates of about 99% in predicting the disease trait. The decision trees and rough set theory failed to identify the true disease-related loci

Quantum Anomalous Hall Effect in Hg1−y_{1-y}Mny_{y}Te Quantum Wells

The quantum Hall effect is usually observed when the two-dimensional electron gas is subjected to an external magnetic field, so that their quantum states form Landau levels. In this work we predict that a new phenomenon, the quantum anomalous Hall effect, can be realized in Hg$_{1-y}$Mn$_{y}$Te quantum wells, without the external magnetic field and the associated Landau levels. This effect arises purely from the spin polarization of the $Mn$ atoms, and the quantized Hall conductance is predicted for a range of quantum well thickness and the concentration of the $Mn$ atoms. This effect enables dissipationless charge current in spintronics devices.Comment: 5 pages, 3 figures. For high resolution figures see final published version when availabl

Mining association language patterns using a distributional semantic model for negative life event classification

AbstractPurposeNegative life events, such as the death of a family member, an argument with a spouse or the loss of a job, play an important role in triggering depressive episodes. Therefore, it is worthwhile to develop psychiatric services that can automatically identify such events. This study describes the use of association language patterns, i.e., meaningful combinations of words (e.g., <loss, job>), as features to classify sentences with negative life events into predefined categories (e.g., Family, Love, Work).MethodsThis study proposes a framework that combines a supervised data mining algorithm and an unsupervised distributional semantic model to discover association language patterns. The data mining algorithm, called association rule mining, was used to generate a set of seed patterns by incrementally associating frequently co-occurring words from a small corpus of sentences labeled with negative life events. The distributional semantic model was then used to discover more patterns similar to the seed patterns from a large, unlabeled web corpus.ResultsThe experimental results showed that association language patterns were significant features for negative life event classification. Additionally, the unsupervised distributional semantic model was not only able to improve the level of performance but also to reduce the reliance of the classification process on the availability of a large, labeled corpus

Epidemiology of extended-spectrum β-lactamases in Enterobacterales in Taiwan for over two decades

The emergence of antimicrobial resistance among microorganisms is a serious public health concern, and extended-spectrum β-lactamases (ESBL)-producing Enterobacterales is one of the major concerns among antibiotic-resistant bacteria. Although the prevalence of ESBL in Enterobacterales has been increasing with time, the prevalence of ESBL could differ according to the species, hospital allocation, sources of infections, nosocomial or community acquisitions, and geographic regions. Therefore, we conducted a comprehensive review of the epidemiology of ESBL-producing Enterobacterales in Taiwan. Overall, the rates of ESBL producers are higher in northern regions than in other parts of Taiwan. In addition, the genotypes of ESBL vary according to different Enterobacterales. SHV-type ESBLs (SHV-5 and SHV-12) were the major types of Enterobacter cloacae complex, but Serratia marcescens, Proteus mirabilis, Escherichia coli, and Klebsiella pneumoniae were more likely to possess CTX-M-type ESBLs (CTX-M-3 and CTX-M-14). Moreover, a clonal sequence type of O25b-ST131 has been emerging among urinary or bloodstream E. coli isolates in the community in Taiwan, and this clone was potentially associated with virulence, ESBL (CTX-M-15) production, ciprofloxacin resistance, and mortality. Finally, the evolution of the genetic traits of the ESBL-producing Enterobacterales isolates helps us confirm the interhospital and intrahospital clonal dissemination in several regions of Taiwan. In conclusion, continuous surveillance in the investigation of ESBL production among Enterobacterales is needed to establish its long-term epidemiology

Extracting Expert Knowledge and Building Strategic Decision in International Logistics and Kaohsiung Area

Evaluating the development and investment direction of complex transportation system for Kaohsiung international logistics is very important to Taiwan. According to the effect of internal and external variables factors, it is necessary to inspect the Kaohsiung metropolitan area epistemic development plan and trend of domestic industry develop international logistics. In order to achieve the benefits of developing logistics integration; we set the Kaohsiung harbour and airport as the core of this study. Exploring that how to strengthen the international logistics function and develop the strategy to improve the economic environment of Kaohsiung area. Consequently, this study is to extract critical expert knowledge and to build strategic decision to improve the economic environment of Kaohsiung area and international logistics

A rare, highly aggressive primitive neuroectodermal tumor of the kidney: Case report and literature review

AbstractWe report a case of a 14-year-old boy who initially suffered from a sudden onset of abdominal pain for 2 weeks with a protrusive soft mass over the left upper abdomen. No obvious symptomatic symptoms or body weight loss were observed. However, early lung metastasis was detected after an initial computed tomographic examination. Even after we performed salvage en bloc resection of the huge retroperitoneal tumor after primary neoadjuvant chemotherapy, the final outcome was still poor. A diagnosis according to radiologic findings was uncharacteristic. Finally, a pathologic diagnosis based on histologic and immunohistochemical results revealed a rare renal peripheral primitive neuroectodermal tumor

Neuronal degeneration in autonomic nervous system of Dystonia musculorum mice

<p>Abstract</p> <p>Background</p> <p><it>Dystonia musculorum </it>(<it>dt</it>) is an autosomal recessive hereditary neuropathy with a characteristic uncoordinated movement and is caused by a defect in the <it>bullous pemphigoid antigen 1 </it>(<it>BPAG1</it>) gene. The neural isoform of <it>BPAG1 </it>is expressed in various neurons, including those in the central and peripheral nerve systems of mice. However, most previous studies on neuronal degeneration in <it>BPAG1</it>-deficient mice focused on peripheral sensory neurons and only limited investigation of the autonomic system has been conducted.</p> <p>Methods</p> <p>In this study, patterns of nerve innervation in cutaneous and iridial tissues were examined using general neuronal marker protein gene product 9.5 via immunohistochemistry. To perform quantitative analysis of the autonomic neuronal number, neurons within the lumbar sympathetic and parasympathetic ciliary ganglia were calculated. In addition, autonomic neurons were cultured from embryonic <it>dt/dt </it>mutants to elucidate degenerative patterns <it>in vitro</it>. Distribution patterns of neuronal intermediate filaments in cultured autonomic neurons were thoroughly studied under immunocytochemistry and conventional electron microscopy.</p> <p>Results</p> <p>Our immunohistochemistry results indicate that peripheral sensory nerves and autonomic innervation of sweat glands and irises dominated degeneration in <it>dt/dt </it>mice. Quantitative results confirmed that the number of neurons was significantly decreased in the lumbar sympathetic ganglia as well as in the parasympathetic ciliary ganglia of <it>dt/dt </it>mice compared with those of wild-type mice. We also observed that the neuronal intermediate filaments were aggregated abnormally in cultured autonomic neurons from <it>dt/dt </it>embryos.</p> <p>Conclusions</p> <p>These results suggest that a deficiency in the cytoskeletal linker BPAG1 is responsible for dominant sensory nerve degeneration and severe autonomic degeneration in <it>dt/dt </it>mice. Additionally, abnormally aggregated neuronal intermediate filaments may participate in neuronal death of cultured autonomic neurons from <it>dt/dt </it>mutants.</p

TGF-β inhibits IL-1β-activated PAR-2 expression through multiple pathways in human primary synovial cells

To investigate the mechanism how Transforming growth factor-β(TGF-β) represses Interleukin-1β (IL-1β)-induced Proteinase-Activated Receptor-2 (PAR-2) expression in human primary synovial cells (hPSCs). Human chondrocytes and hPSCs isolated from cartilages and synovium of Osteoarthritis (OA) patients were cultured with 10% fetal bovine serum media or serum free media before treatment with IL-1β, TGF-β1, or Connective tissue growth factor (CTGF). The expression of PAR-2 was detected using reverse transcriptase-polymerase chain reaction (RT-PCR) and western blotting. Collagen zymography was performed to assess the activity of Matrix metalloproteinases-13 (MMP-13). It was demonstrated that IL-1β induces PAR-2 expression via p38 pathway in hPSCs. This induction can be repressed by TGF-β and was observed to persist for at least 48 hrs, suggesting that TGF-β inhibits PAR-2 expression through multiple pathways. First of all, TGF-β was able to inhibit PAR-2 activity by inhibiting IL-1β-induced p38 signal transduction and secondly the inhibition was also indirectly due to MMP-13 inactivation. Finally, TGF-β was able to induce CTGF, and in turn CTGF represses PAR-2 expression by inhibiting IL-1β-induced phospho-p38 level. TGF-β could prevent OA from progression with the anabolic ability to induce CTGF production to maintain extracellular matrix (ECM) integrity and to down regulate PAR-2 expression, and the anti-catabolic ability to induce Tissue inhibitors of metalloproteinase-3 (TIMP-3) production to inhibit MMPs leading to avoid PAR-2 over-expression. Because IL-1β-induced PAR-2 expressed in hPSCs might play a significantly important role in early phase of OA, PAR-2 repression by exogenous TGF-β or other agents might be an ideal therapeutic target to prevent OA from progression

Conserved charged amino acid residues in the extracellular region of sodium/iodide symporter are critical for iodide transport activity

<p>Abstract</p> <p>Background</p> <p>Sodium/iodide symporter (NIS) mediates the active transport and accumulation of iodide from the blood into the thyroid gland. His-226 located in the extracellular region of NIS has been demonstrated to be critical for iodide transport in our previous study. The conserved charged amino acid residues in the extracellular region of NIS were therefore characterized in this study.</p> <p>Methods</p> <p>Fourteen charged residues (Arg-9, Glu-79, Arg-82, Lys-86, Asp-163, His-226, Arg-228, Asp-233, Asp-237, Arg-239, Arg-241, Asp-311, Asp-322, and Asp-331) were replaced by alanine. Iodide uptake abilities of mutants were evaluated by steady-state and kinetic analysis. The three-dimensional comparative protein structure of NIS was further modeled using sodium/glucose transporter as the reference protein.</p> <p>Results</p> <p>All the NIS mutants were expressed normally in the cells and targeted correctly to the plasma membrane. However, these mutants, except R9A, displayed severe defects on the iodide uptake. Further kinetic analysis revealed that mutations at conserved positively charged amino acid residues in the extracellular region of NIS led to decrease NIS-mediated iodide uptake activity by reducing the maximal rate of iodide transport, while mutations at conserved negatively charged residues led to decrease iodide transport by increasing dissociation between NIS mutants and iodide.</p> <p>Conclusions</p> <p>This is the first report characterizing thoroughly the functional significance of conserved charged amino acid residues in the extracellular region of NIS. Our data suggested that conserved charged amino acid residues, except Arg-9, in the extracellular region of NIS were critical for iodide transport.</p