gebhart/patrepeval huggingface dataset:
APOC3/A5 haplotypes, lipid levels, and risk of myocardial infarction in the Central Valley of Costa Rica (2005)

Genetic variation in the APOC3 and APOA5 genes has been associated with plasma triglyceride concentrations and may affect the risk of myocardial infarction (MI). To assess whether APOC3/A5 haplotypes are associated with risk of MI, we examined three single-nucleotide polymorphisms (SNPs) in APOC3 (3238C>G, -455T>C, and -482C>T) and six SNPs in the APOA5 gene (-1131T>C, c.-3A>G, c.56C>G, IVS3+476G>A, c.553G>T, and c.1259T>C) in incident cases (n = 1,703) of a first nonfatal MI matched for gender, age, and area of residence with population-based controls (n = 1,703). Conditional logistic regression models, adjusted for potential environmental confounders, were used for analysis. The common APOC3*222 haplotype was more frequent in cases than in controls (17.4% and 13.7%, respectively, P < 0.001) and was associated with increased risk of MI [odds ratio (OR) = 1.27; 95% confidence interval (95% CI), 1.09, 1.48] compared with APOC3*111 wild-type haplotype. This association was independent of the APOA5 SNPs. Although the APOC3 3238G, APOA5 -1131C, APOA5 c.-3G, and APOA5 c.1259C alleles were associated with higher triglyceride plasma concentrations, these effects could not explain the associations with MI in this population. In summary, this study supports the hypothesis that haplotypes in the APOC3 gene but not in the APOA5 gene increase susceptibility to MI.
Dynamic regulation of mitochondrial function by glucocorticoids (2009)

Glucocorticoids play an important biphasic role in modulating neural plasticity; low doses enhance neural plasticity and spatial memory behavior, whereas chronic, higher doses produce inhibition. We found that 3 independent measures of mitochondrial function-mitochondrial oxidation, membrane potential, and mitochondrial calcium holding capacity-were regulated by long-term corticosterone (CORT) treatment in an inverted "U"-shape. This regulation of mitochondrial function by CORT correlated with neuroprotection; that is, treatment with low doses of CORT had a neuroprotective effect, whereas treatment with high doses of CORT enhanced kainic acid (KA)-induced toxicity of cortical neurons. We then undertook experiments to elucidate the mechanisms underlying these biphasic effects and found that glucocorticoid receptors (GRs) formed a complex with the anti-apoptotic protein Bcl-2 in response to CORT treatment and translocated with Bcl-2 into mitochondria after acute treatment with low or high doses of CORT in primary cortical neurons. However, after 3 days of treatment, high, but not low, doses of CORT resulted in decreased GR and Bcl-2 levels in mitochondria. As with the in vitro studies, Bcl-2 levels in the mitochondria of the prefrontal cortex were significantly decreased, along with GR levels, after long-term treatment with high-dose CORT in vivo. These findings have the potential to contribute to a more complete understanding of the mechanisms by which glucocorticoids and chronic stress regulate cellular plasticity and resilience and to inform the future development of improved therapeutics.
Local feature view clustering for 3D object recognition (2005)

There have been important recent advances in object recognition through the matching of invariant local image features. However, the existing approaches are based on matching to individual training images. This paper presents a method for combining multiple images of a 3D object into a single model representation. This provides for recognition of 3D objects from any viewpoint, the generalization of models to non-rigid changes, and improved robustness through the combination of features acquired under a range of imaging conditions. The decision of whether to cluster a training image into an existing view representation or to treat it as a new view is based on the geometric accuracy of the match to previous model views. A new probabilistic model is developed to reduce the false positive matches that would otherwise arise due to loosened geometric constraints on matching 3D and non-rigid models. A system has been developed based on these approaches that is able to robustly recognize 3D objects in cluttered natural images in sub-second times.
Weighted PageRank algorithm (2004)

With the rapid growth of the Web, users easily get lost in the rich hyper structure. Providing the relevant information to users to cater to their needs is the primary goal of Website owners. Therefore, finding the content of the Web and retrieving the users' interests and needs from their behavior have become increasingly important. Web mining is used to categorize users and pages by analyzing user behavior, the content of the pages, and the order of the URLs that tend to be accessed. Web structure mining plays an important role in this approach. Two page ranking algorithms, HITS and PageRank, are commonly used in Web structure mining. Both algorithms treat all links equally when distributing rank scores. Several algorithms have been developed to improve the performance of these methods. The weighted PageRank algorithm (WPR), an extension to the standard PageRank algorithm, is introduced. WPR takes into account the importance of both the inlinks and the outlinks of the pages and distributes rank scores based on the popularity of the pages. The results of our simulation studies show that WPR performs better than the conventional PageRank algorithm in terms of returning a larger number of relevant pages to a given query.
Oxidant-mediated epithelial cell injury in idiopathic pulmonary fibrosis. (1987)

Lung inflammatory cells of patients with idiopathic pulmonary fibrosis (IPF) were evaluated for their ability to injure 5'Crlabeled AKD alveolar epithelial cells in the presence and absence of IPF alveolar epithelial lining fluid (ELF). The IPF cells were spontaneously releasing exaggerated amounts of superoxide (O2) and hydrogen peroxide (H202) compared with normal (P < 0.02). Cytotoxicity of the AKD cells was markedly increased when the IPF inflammatory cells were incubated with autologous ELF (P < 0.02). The majority of IPF patients had ELF myelo- peroxidase levels above normal (P < 0.002). Incubation of IPF ELF with AKD cells in the presence of H202 caused increased cellular injury (P < 0.01 compared with control), which was suppressed by methionine, a myeloperoxidase system scavenger. IPF patients with high concentrations of ELF myeloperoxidase deteriorated more rapidly than those with low ELF myeloper- oxidase (P < 0.05). Thus, IPF is characterized by an increased spontaneous production of oxidants by lung inflammatory cells, the presence of high concentrations of myeloperoxidase in the ELF of the lower respiratory tract, and a synergistic cytotoxic effect of alveolar inflammatory cells and ELF on lung epithelial cells, suggesting oxidants may play a role in causing the epithelial cell injury of this disorder.
Antiretroviral Drug Resistance in HIV‐2: Three Amino Acid Changes Are Sufficient for Classwide Nucleoside Analogue Resistance (2009)

Genotypic surveys suggest that human immunodeficiency virus type 1 (HIV-1) and HIV-2 evolve different sets of mutations in response to nucleoside reverse-transcriptase inhibitors (NRTIs). We used site-directed mutagenesis, culture-based phenotyping, and cell-free assays to determine the resistance profiles conferred by specific amino acid replacements in HIV-2 reverse transcriptase. Although thymidine analogue mutations had no effect on zidovudine sensitivity, the addition of Q151M together with K65R or M184V was sufficient for high-level resistance to both lamivudine and zidovudine in HIV-2, and the combination of K65R, Q151M, and M184V conferred classwide NRTI resistance. These data suggest that current NRTI-based regimens are suboptimal for treating HIV-2 infection.
Effect of an MMP-9/MMP-12 inhibitor on smoke-induced emphysema and airway remodelling in guinea pigs (2007)

An MMP-9/MMP-12 inhibitor can substantially ameliorate morphological emphysema, small airway remodelling and the functional consequences of these lesions in a non-murine species. These findings strengthen the idea that MMPs are important mediators of the anatomical changes behind COPD in humans, and suggest that MMP-9 and MMP-12 may be potential intervention targets.
Kernel-based machine learning protocol for predicting DNA-binding proteins (2005)

DNA-binding proteins (DNA-BPs) play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Attempts have been made to identify DNA-BPs based on their sequence and structural information with moderate accuracy. Here we develop a machine learning protocol for the prediction of DNA-BPs where the classifier is Support Vector Machines (SVMs). Information used for classification is derived from characteristics that include surface and overall composition, overall charge and positive potential patches on the protein surface. In total 121 DNA-BPs and 238 non-binding proteins are used to build and evaluate the protocol. In self-consistency, accuracy value of 100% has been achieved. For cross-validation (CV) optimization over entire dataset, we report an accuracy of 90%. Using leave 1-pair holdout evaluation, the accuracy of 86.3% has been achieved. When we restrict the dataset to less than 20% sequence identity amongst the proteins, the holdout accuracy is achieved at 85.8%. Furthermore, seven DNA-BPs with unbounded structures are all correctly predicted. The current performances are better than results published previously. The higher accuracy value achieved here originates from two factors: the ability of the SVM to handle features that demonstrate a wide range of discriminatory power and, a different definition of the positive patch. Since our protocol does not lean on sequence or structural homology, it can be used to identify or predict proteins with DNA-binding function(s) regardless of their homology to the known ones.
Gibberellins, brassinosteroids and light‐regulated development (1997)

ABSTRACT The regulation of plant development by light requires the action of several well‐studied plant hormones. However, the mechanism by which light and hormones affect identical developmental responses remains unclear. Recently, studies of mutants altered in light signal perception or transduction have suggested a role for gibberellins and brassinosteroids in light‐regulated development. For instance, mutants in the major light‐stable phytochrome from several plant species exhibit altered responsiveness to, or metabolism of, gibberellins. In contrast, mutants that develop as light‐grown plants in the absence of light have implicated a role for brassinosteroids in the control of cell elongation, the expression of photoregulated genes, and the promotion of apical dominance, leaf senescence and male fertility. Future studies should help elucidate whether light and hormones independently affect these developmental responses or whether hormones are involved in the sequence of events initiated by excitation of photoreceptors.
The role of Axin2 in calvarial morphogenesis and craniosynostosis (2005)

Axin1 and its homolog Axin2/conductin/Axil are negative regulators of the canonical Wnt pathway that suppress signal transduction by promoting degradation of beta-catenin. Mice with deletion of Axin1 exhibit defects in axis determination and brain patterning during early embryonic development. We show that Axin2 is expressed in the osteogenic fronts and periosteum of developing sutures during skull morphogenesis. Targeted disruption of Axin2 in mice induces malformations of skull structures, a phenotype resembling craniosynostosis in humans. In the mutants, premature fusion of cranial sutures occurs at early postnatal stages. To elucidate the mechanism of craniosynostosis, we studied intramembranous ossification in Axin2-null mice. The calvarial osteoblast development is significantly affected by the Axin2 mutation. The Axin2 mutant displays enhanced expansion of osteoprogenitors, accelerated ossification, stimulated expression of osteogenic markers and increases in mineralization. Inactivation of Axin2 promotes osteoblast proliferation and differentiation in vivo and in vitro. Furthermore, as the mammalian skull is formed from cranial skeletogenic mesenchyme, which is derived from mesoderm and neural crest, our data argue for a region-specific effect of Axin2 on neural crest dependent skeletogenesis. The craniofacial anomalies caused by the Axin2 mutation are mediated through activation of beta-catenin signaling, suggesting a novel role for the Wnt pathway in skull morphogenesis.
行動護理的另一種選擇－改良式e 化行動護理工作車 (2011)

為成功達成一年內全院病房導入護理資訊系統、落實床邊照護(Point of care)，即時完成資料輸入的目標，需要提供護理師適用之護理行動工作車。考量經費限制及使用習慣，遂改裝原使用之不鏽鋼護理工作車。改裝設計考量人因工程力學因素及感染管制原則，避免造成使用者身體之不適。本專案執行之結果：(1)達成一年內完成全院上線，並在e化護理行動工作車上使用護理資訊系統；(2)比較全面使用新購之塑鋼護理行動工作車，總經費節省約NT.9,600,000元；(3) 護理人員對改裝工作車的使用滿意；(4)應證電腦高度為140cm 時，最適合台灣平均身高為158公分之成年女性；工作車上電腦螢幕距離身體65公分，為最適操作電腦之距離。因此，本專案驗證，各醫院在經費有限下，改裝現有之不鏽鋼車，不失為可行之方案，深值大力推廣。
Chemical Control Over Protein-Protein Interactions: Beyond Inhibitors (2007)

Protein-protein interactions have become attractive drug targets and recent studies suggest that these interfaces may be amenable to inhibition by small molecules. However, blocking specific interactions may not be the only way of manipulating the extensive network of interacting proteins. Recently, several approaches have emerged for promoting these interactions rather than inhibiting them. Typically, these strategies employ a bifunctional ligand to simultaneously bind two targets, forcing their juxtaposition. Chemically "riveting" specific protein contacts can reveal important aspects of regulation, such as the consequences of stable dimerization or the effects of prolonged dwell time. Moreover, in some cases, entirely new functions arise when two proteins, which normally do not interact, are brought into close proximity with one another. Together with inhibitors, bifunctional molecules are part of a growing toolbox of chemical probes that can be used to reversibly and selectively control the interact-ome. Using these reagents, new insights into the dynamics of protein-protein interactions and their importance in biology are beginning to emerge. Future hurdles in this area lie in the development of robust synthetic platforms for rapidly generating compounds to meet the challenges of diverse protein-protein interfaces.
IL-6 Secreted from Senescent Mesenchymal Stem Cells Promotes Proliferation and Migration of Breast Cancer Cells (2014)

Human mesenchymal stem cells (hMSCs) are currently investigated for a variety of therapeutic applications. However, MSCs isolated from primary tissue cannot meet clinical grade needs and should be expanded in vitro for several passages. Although hMSCs show low possibility for undergoing oncogenic transformation, they do, similar to other somatic cells, undergo cellular senescence and their therapeutic potential is diminished when cultured in vitro. However, the role of senescent MSCs in tumor progression remains largely elusive. In the current study, by establishing senescent human umbilical cord mesenchymal stem cells (s-UCMSCs) through the replicative senescence model and genotoxic stress induced premature senescence model, we show that s-UCMSCs significantly stimulate proliferation and migration of breast cancer cells in vitro and tumor progression in a co-transplant xenograft mouse model compared with 'young' counterparts (defined as MSCs at passage 5, in contrast to senescent MSCs at passage 45). In addition, we identified IL-6, a known pleiotropic cytokine, as a principal mediator for the tumor-promoting activity of s-UCMSCs by induction of STAT3 phosphorylation. Depletion of IL-6 from s-UCMSCs conditioned medium partially abrogated the stimulatory effect of s-UCMSCs on the proliferation and migration of breast tumor cells.
Elevation of Exhaled Ethane Concentration in Asthma (2000)

Ethane is a product of lipid peroxidation as a result of oxidative stress and can be detected in the exhaled air. Oxidative stress plays a role in the pathogenesis of asthma. We measured exhaled ethane in 26 asthmatic subjects (mean age +/- SEM, 38 +/- 8 yr; 15 male, FEV(1) 60 +/- 4%) and compared it with exhaled nitric oxide (NO) measured by chemiluminescence, a noninvasive marker of oxidative stress and inflammation. Exhaled ethane was collected during a flow- and pressure-controlled exhalation into a reservoir discarding dead space air contaminated with ambient air. A sample of the expired air was analyzed by chromatography. Exhaled ethane levels were elevated in asthma patients not receiving steroid (n = 12, 2.06 +/- 0.30 ppb) compared with steroid-treated patients (n = 14, 0.79 +/- 0.10 ppb, p < 0.01) and to 14 nonsmoking control subjects (0.88 +/- 0.09 ppb, p < 0.05). In patients not receiving steroid treatment there was a positive correlation between exhaled ethane and NO (r = 0.55, p < 0.05) and air trapping assessed by the ratio of residual volume to total lung capacity (RV/ TLC) (r = 0.60, p < 0.05). In addition, untreated patients with FEV(1) < 60% predicted value had higher concentrations of ethane (2.86 +/- 0.37 ppb) compared with less obstructed patients (FEV(1) > 60%, 1.26 +/- 0.12 ppb, p < 0.05). NO concentrations were higher in patients not on steroid treatment (14.7 +/- 1.7 ppb) than in steroid-treated patients (8.6 +/- 0.5 ppb, p < 0.05). Exhaled ethane is elevated in asthma, reduced in steroid-treated patients, and correlates with NO and airway obstruction. It may be a useful noninvasive marker of oxidative stress.
Concanamycin A, a powerful tool for characterization and estimation of contribution of perforin- and Fas-based lytic pathways in cell-mediated cytotoxicity (1996)

Perforin- and Fas-based cytolytic pathways are two major mechanisms of cell-mediated cytotoxicity. Recently, we have shown that an inhibitor of vacuolar type H+-ATPase, concanamycin A (CMA), inhibits perforin-based cytotoxic activity, mostly due to accelerated degradation of perforin by an increase in the pH of lytic granules. Here we show that CMA failed to inhibit the cytolytic activity of CD4+ CTL clone and perforin-deficient CD8+ CTL clone, which exclusively mediate Fas-based cytotoxicity, although CMA inhibited acidification and induced drastic vacuolation of cytoplasmic granules in these clones. In a wide range of alloantigen-specific CTL, a significant amount of the lysis of Con A blasts from normal mice and of Fas-positive tumor cells remained unaffected even in excess concentrations of CMA. However, CMA almost completely inhibited the lysis of Con A blasts from lpr mice and of Fas low expressing or negative tumor cells. Cytolysis by alloantigen-specific CD8+ CTL derived from gld mice was completely prevented by CMA. Furthermore, CMA-insensitive cytolysis exerted by CD8+ CTL clone was completely inhibitable by soluble Fas molecules. Thus, these data clearly indicate not only that CMA-insensitive cytolysis mediated by alloantigen-specific CTL is Fas dependent, but also that CMA is a selective inhibitor to block only the perforin-based killing pathway. In contrast, brefeldin A blocked the Fas-based cytotoxicity, but only marginally reduced the perforin-based cytotoxicity. Moreover, CMA and brefeldin A in combination completely abrogated all cytolytic activity of alloantigen-specific CTL. Taken together, these results reveal that CTL mainly exert perforin-based cytotoxicity and complementary Fas-based cytotoxicity, and that CMA is a powerful tool to clarify the contributions of the two distinct cytolytic pathways.
Fluid velocity measurement using convective heat transfer coefficient measuring system (2007)

A system, built for measurement of convective heat transfer coefficient, h, was adapted and used to measure the h value and the fluid velocity simultaneously in various flow rates using tap water. The system is composed of a Wheatstone-bridge circuit which one arm is connected to a steerable catheter sensor whose tip is a thin film resistive temperature detector (RTD) sensor. The results presented a practical relationship between the local fluid velocity and the h value, which differs from what theory suggests. Further experiments using various flow rates of blood are needed in order to get the correlation between the h value and the local blood velocity for the estimation of the in vivo h value in any large blood vessel using the local blood velocity.
Polymerization of maleic acid and itaconic acid studied by FT‐Raman spectroscopy (2001)

Abstract In this research, we used a new redox free radical initiation system consisting of potassium persulfate (K 2 S 2 O 8 ) and sodium hypophosphite (NaH 2 PO 2 ). In the presence of NaH 2 PO 2 , the thermal decomposition of K 2 S 2 O 8 is accelerated, and the temperature required for the formation of free radical is reduced. We polymerized maleic acid (MA) using the K 2 S 2 O 8 /NaH 2 PO 2 initiation system in an aqueous solution, and monitored the polymerization process with FT‐Raman spectroscopy. The Raman spectroscopy data indicate the formation of a saturated carboxylic acid with the disappearance of the characteristic bands of MA as the thermal decomposition of K 2 S 2 O 8 progresses, thus indicating the formation of poly(maleic acid) (PMA). We also found that itaconic acid (IA) polymerizes in the presence of the new initiation system. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 81: 223–228, 2001
Capacitive-Piezoelectric Transducers for High-<inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math></inline-formula> Micromechanical AlN Resonators (2014)

A capacitive-piezoelectric (also known as, capacitive-piezo) transducer that combines the strengths of capacitive and piezoelectric mechanisms to achieve a combination of electromechanical coupling and Q higher than otherwise attainable by either mechanism separately, has allowed demonstration of a 1.2-GHz contour-mode aluminum nitride (AlN) ring resonator with Q > 3000 on par with the highest measured d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">31</sub> -transduced AlN-only piezoelectric resonators past 1 GHz, and a 50-MHz disk array with an even higher Q > 12 000. Here, the key innovation is to separate the piezoelectric resonator from its metal electrodes by tiny gaps to eliminate metal material and metal-to-piezoelectric interface losses thought to limit thin-film piezoelectric resonator Q, while also maintaining high electric field strength to preserve a strong piezoelectric effect. While Q increases, electromechanical coupling decreases, but the k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> · Q product can still increase overall. More importantly, use of the capacitive-piezo transducer allows a designer to trade electromechanical coupling for Q, providing a very useful method to tailor Q and coupling for narrowband radio frequency (RF) channel-selecting filters for which Q trumps coupling. This capacitive-piezo transducer concept does not require dc-bias voltages and allows for much thicker electrodes that reduce series resistance without mass loading the resonant structure. The latter is especially important as resonators and their supports continue to scale toward even higher frequencies. [2013-0395].