Probing the local structure of electroluminescing rutile TiO2 with neutron diffuse scattering and atomistic modelling

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Using association rules mining to explore pattern of Chinese medicinal formulae (prescription) in treating and preventing breast cancer recurrence and metastasis.

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SWATH-MS Quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling

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Human Platelet-Rich Plasma- and Extracellular Matrix-Derived Peptides Promote Impaired Cutaneous Wound Healing In Vivo

Previous work in our laboratory has described several pro-angiogenic short peptides derived from endothelial extracellular matrices degraded by bacterial collagenase. Here we tested whether these peptides could stimulate wound healing in vivo. Our experiments demonstrated that a peptide created as combination of fragments of tenascin X and fibrillin 1 (comb1) applied into cranial dermal wounds created in mice treated with cyclophosphamide to impair wound healing, can improve the rate of wound closure. Furthermore, we identify and characterize a novel peptide (UN3) created and modified from two naturally-occurring peptides, which are present in human platelet-rich plasma. In vitro testing of UN3 demonstrates that it causes a 50% increase in endothelial proliferation, 250% increase in angiogenic response and a tripling of epithelial cell migration in response to injury. Results of in vivo experiments where comb1 and UN3 peptides were added together to cranial wounds in cyclophosphamide-treated mice leads to improvement of wound vascularization as shown by an increase of the number of blood vessels present in the wound beds. Application of the peptides markedly promotes cellular responses to injury and essentially restores wound healing dynamics to those of normal, acute wounds in the absence of cyclophosphamide impairment. Our current work is aimed at understanding the mechanisms underlying the stimulatory effects of these peptides as well as identification of the cellular receptors mediating these effects.National Institutes of Health (U.S.) (Grant EY15125)National Institutes of Health (U.S.) (Grant EY19533)Wound Care Partners, LL

Movement Protein Pns6 of Rice dwarf phytoreovirus Has Both ATPase and RNA Binding Activities

Cell-to-cell movement is essential for plant viruses to systemically infect host plants. Plant viruses encode movement proteins (MP) to facilitate such movement. Unlike the well-characterized MPs of DNA viruses and single-stranded RNA (ssRNA) viruses, knowledge of the functional mechanisms of MPs encoded by double-stranded RNA (dsRNA) viruses is very limited. In particular, many studied MPs of DNA and ssRNA viruses bind non-specifically ssRNAs, leading to models in which ribonucleoprotein complexes (RNPs) move from cell to cell. Thus, it will be of special interest to determine whether MPs of dsRNA viruses interact with genomic dsRNAs or their derivative sRNAs. To this end, we studied the biochemical functions of MP Pns6 of Rice dwarf phytoreovirus (RDV), a member of Phytoreovirus that contains a 12-segmented dsRNA genome. We report here that Pns6 binds both dsRNAs and ssRNAs. Intriguingly, Pns6 exhibits non-sequence specificity for dsRNA but shows preference for ssRNA sequences derived from the conserved genomic 5′- and 3′- terminal consensus sequences of RDV. Furthermore, Pns6 exhibits magnesium-dependent ATPase activities. Mutagenesis identified the RNA binding and ATPase activity sites of Pns6 at the N- and C-termini, respectively. Our results uncovered the novel property of a viral MP in differentially recognizing dsRNA and ssRNA and establish a biochemical basis to enable further studies on the mechanisms of dsRNA viral MP functions

Situação epidemiológica e a relação com variáveis meteorológicas da HFMD em Guangzhou, sul da China, 2008-2012

A doença de mão-pé-e-boca (HFMD) está se tornando doença extremamente comum transmitida pelo ar e contato em Guangzhou, sul da China, levando preocupação às autoridades de saúde pública acerca da sua incidência aumentada. Neste estudo foi usada parte ecológica e regressão binomial negativa para identificar o status epidêmico da HFMD e sua relação com variáveis meteorológicas. Durante 2008-2012 um total de 173.524 casos confirmados de HFMD foram apresentados, 12 com morte, elevando o índice de fatalidade a 0,69 por 10.000. As incidências anuais de 2008 a 2010 foram 60,56, 132,44, 311,40, 402,76 e 468,59 por 100.000, respectivamente, mostrando tendência de rápido aumento. Cada 1 °C de aumento da temperatura correspondeu a aumento de 9,47% (95% CI 9,36% a 9,58%) no número semanal de casos de HFMD, enquanto a 1 hPa de aumento da pressão atmosférica correspondeu a decréscimo no número de casos de 7,53% (95% CI - 7,60% a - 7,45%). De maneira semelhante cada aumento de 1% na humidade relativa correspondeu a aumento de 1,48% ou 3,3% e a um aumento de 1 metro por hora na velocidade do vento correspondeu a um aumento de 2,18% ou 4,57%, no número de casos semanais de HFMD, dependendo das variáveis consideradas no modelo. Estes achados revelaram que o status epidêmico do HFMD em Guangzhou é caracterizado por alta morbidade, mas baixa fatalidade. Fatores referentes ao tempo tiveram influência significante na incidência do HFMD.Hand-foot-and-mouth disease (HFMD) is becoming one of the extremely common airborne and contact transmission diseases in Guangzhou, southern China, leading public health authorities to be concerned about its increased incidence. In this study, it was used an ecological study plus the negative binomial regression to identify the epidemic status of HFMD and its relationship with meteorological variables. During 2008-2012, a total of 173,524 HFMD confirmed cases were reported, 12 cases of death, yielding a fatality rate of 0.69 per 10,000. The annual incidence rates from 2008 to 2012 were 60.56, 132.44, 311.40, 402.76, and 468.59 (per 100,000), respectively, showing a rapid increasing trend. Each 1 °C rise in temperature corresponded to an increase of 9.47% (95% CI 9.36% to 9.58%) in the weekly number of HFMD cases, while a one hPa rise in atmospheric pressure corresponded to a decrease in the number of cases by 7.53% (95% CI -7.60% to -7.45%). Similarly, each one percent rise in relative humidity corresponded to an increase of 1.48% or 3.3%, and a one meter per hour rise in wind speed corresponded to an increase of 2.18% or 4.57%, in the weekly number of HFMD cases, depending on the variables considered in the model. These findings revealed that epidemic status of HFMD in Guangzhou is characterized by high morbidity but low fatality. Weather factors had a significant influence on the incidence of HFMD

Feasibility and analysis of bipolar concentric recording of Electrohysterogram with flexible active electrode

The conduction velocity and propagation patterns of Electrohysterogram (EHG) provide fundamental information about uterine electrophysiological condition. The accuracy of these measurements can be impaired by both the poor spatial selectivity and sensitivity to the relative direction of the contraction propagation associated with conventional disc electrodes. Concentric ring electrodes could overcome these limitations the aim of this study was to examine the feasibility of picking up surface EHG signals using a new flexible tripolar concentric ring electrode (TCRE), and to compare it with conventional bipolar recordings. Simultaneous recording of conventional bipolar signals and bipolar concentric EHG (BC-EHG) were carried out on 22 pregnant women. Signal bursts were characterized and compared. No significant differences among channels in either duration or dominant frequency in the Fast Wave High frequency range were found. Nonetheless, the high pass filtering effect of the BC-EHG records resulted in lower frequency content within the range 0.1 to 0.2 Hz than the bipolar ones. Although the BC-EHG signal amplitude was about 5-7 times smaller than that of bipolar recordings, similar signal-to-noise ratio was obtained. These results suggest that the flexible TCRE is able to pick up uterine electrical activity and could provide additional information for deducing uterine electrophysiological condition.The authors are grateful to the Obstetrics Unit of the Hospital Universitario La Fe de Valencia (Valencia, Spain), where the recording sessions were carried out. The work was supported in part by the Ministerio de Ciencia y Tecnologia de Espana (TEC2010-16945), by the Universitat Politecnica de Valencia (PAID SP20120490) and Generalitat Valenciana (GV/2014/029) and by General Electric Healthcare.Ye Lin, Y.; Alberola Rubio, J.; Prats Boluda, G.; Perales Marin, AJ.; Desantes, D.; Garcia Casado, FJ. (2015). Feasibility and analysis of bipolar concentric recording of Electrohysterogram with flexible active electrode. Annals of Biomedical Engineering. 43(4):968-976. https://doi.org/10.1007/s10439-014-1130-5S968976434Alberola-Rubio, J., G. Prats-Boluda, Y. Ye-Lin, J. Valero, A. Perales, and J. Garcia-Casado. Comparison of non-invasive electrohysterographic recording techniques for monitoring uterine dynamics. Med. Eng. Phys. 35(12):1736–1743, 2013.Besio, W. G., K. Koka, R. Aakula, and W. Dai. Tri-polar concentric ring electrode development for laplacian electroencephalography. IEEE Trans. Biomed. Eng. 53(5):926–933, 2006.Devasahayam, S. R. Signals and Systems in Biomedical Engineering. Berlin: Springer, 2013.Devedeux, D., C. Marque, S. Mansour, G. Germain, and J. Duchene. Uterine electromyography: a critical review. Am. J. Obstet. Gynecol. 169(6):1636–1653, 1993.Estrada, L., A. Torres, J. Garcia-Casado, G. Prats-Boluda, and R. Jane. Characterization of laplacian surface electromyographic signals during isometric contraction in biceps brachii. Conf. Proc. IEEE Eng Med. Biol. Soc. 2013:535–538, 2013.Euliano, T. Y., D. Marossero, M. T. Nguyen, N. R. Euliano, J. Principe, and R. K. Edwards. Spatiotemporal electrohysterography patterns in normal and arrested labor. Am. J. Obstet. Gynecol. 200(1):54–57, 2009.Farina, D., and C. Cescon. Concentric-ring electrode systems for noninvasive detection of single motor unit activity. IEEE Trans. Biomed. Eng. 48(11):1326–1334, 2001.Fele-Zorz, G., G. Kavsek, Z. Novak-Antolic, and F. Jager. A comparison of various linear and non-linear signal processing techniques to separate uterine EMG records of term and pre-term delivery groups. Med. Biol. Eng Comput. 46(9):911–922, 2008.Garfield, R. E., and W. L. Maner. Physiology and electrical activity of uterine contractions. Semin. Cell Dev. Biol. 18(3):289–295, 2007.Garfield, R. E., W. L. Maner, L. B. Mackay, D. Schlembach, and G. R. Saade. Comparing uterine electromyography activity of antepartum patients vs. term labor patients. Am. J. Obstet. Gynecol. 193(1):23–29, 2005.Garfield, R. E., H. Maul, L. Shi, W. Maner, C. Fittkow, G. Olsen, and G. R. Saade. Methods and devices for the management of term and preterm labor. Ann. N. Y. Acad. Sci. 943(1):203–224, 2001.Hassan, M., J. Terrien, C. Muszynski, A. Alexandersson, C. Marque, and B. Karlsson. Better pregnancy monitoring using nonlinear correlation analysis of external uterine electromyography. IEEE Trans. Biomed. Eng. 60(4):1160–1166, 2013.Kaufer, M., L. Rasquinha, and P. Tarjan. Optimization of multi-ring sensing electrode set, Conference proceedings of IEEE Engineering in Medicine and Biology Society, 1990, pp. 612–613.Koka, K., and W. G. Besio. Improvement of spatial selectivity and decrease of mutual information of tri-polar concentric ring electrodes. J. Neurosci. Methods 165(2):216–222, 2007.Lu, C.-C., and P. P. Tarjan. Pasteless, active, concentric ring sensors for directly obtained laplacian cardiac electrograms. J. Med. Biol. Eng. 22(4):199–203, 2002.Lucovnik, M., W. L. Maner, L. R. Chambliss, R. Blumrick, J. Balducci, Z. Novak-Antolic, and R. E. Garfield. Noninvasive uterine electromyography for prediction of preterm delivery. Am. J. Obstet. Gynecol. 204(3):228.e1–228.e10, 2011.Maner, W. L., and R. E. Garfield. Identification of human term and preterm labor using artificial neural networks on uterine electromyography data. Ann. Biomed. Eng. 35(3):465–473, 2007.Maner, W. L., R. E. Garfield, H. Maul, G. Olson, and G. Saade. Predicting term and preterm delivery with transabdominal uterine electromyography. Obstet. Gynecol. 101(6):1254–1260, 2003.Marque, C., J. M. Duchene, S. Leclercq, G. S. Panczer, and J. Chaumont. Uterine EHG processing for obstetrical monitoring. IEEE Trans. Biomed. Eng. 33(12):1182–1187, 1986.Marque, C. K., J. Terrien, S. Rihana, and G. Germain. Preterm labour detection by use of a biophysical marker: the uterine electrical activity. BMC. Pregnancy Childbirth. 7(Suppl1):S5, 2007.Maul, H., W. L. Maner, G. Olson, G. R. Saade, and R. E. Garfield. Non-invasive transabdominal uterine electromyography correlates with the strength of intrauterine pressure and is predictive of labor and delivery. J. Matern. Fetal Neonatal Med. 15(5):297–301, 2004.Miles, A. M., M. Monga, and K. S. Richeson. Correlation of external and internal monitoring of uterine activity in a cohort of term patients. Am. J. Perinatol. 18(3):137–140, 2001.Prats-Boluda, G., J. Garcia-Casado, J. L. Martinez-de-Juan, and Y. Ye-Lin. Active concentric ring electrode for non-invasive detection of intestinal myoelectric signals. Med. Eng. Phys. 33(4):446–455, 2010.Prats-Boluda, G., Y. Ye-Lin, E. Garcia-Breijo, J. Ibañez, and J. Garcia-Casado. Active flexible concentric ring electrode for non-invasive surface bioelectrical recordings. Meas. Sci. Technol. 23(12):1–10, 2012.Rabotti, C., M. Mischi, S. G. Oei, and J. W. Bergmans. Noninvasive estimation of the electrohysterographic action-potential conduction velocity. IEEE Trans. Biomed. Eng. 57(9):2178–2187, 2010.Rabotti, C., S. G. Oei, H. J. van ‘t, and M. Mischi. Electrohysterographic propagation velocity for preterm delivery prediction. Am. J. Obstet. Gynecol. 205(6):e9–e10, 2011.Rooijakkers, M. J., S. Song, C. Rabotti, S. G. Oei, J. W. Bergmans, E. Cantatore, and M. Mischi. Influence of electrode placement on signal quality for ambulatory pregnancy monitoring. Comput. Math. Methods Med. 2014(1):960980, 2014.Schlembach, D., W. L. Maner, R. E. Garfield, and H. Maul. Monitoring the progress of pregnancy and labor using electromyography. Eur. J. Obstet. Gynecol. Reprod. Biol. 144(Suppl1):S33–S39, 2009.Sikora, J., A. Matonia, R. Czabanski, K. Horoba, J. Jezewski, and T. Kupka. Recognition of premature threatening labour symptoms from bioelectrical uterine activity signals. Arch. Perinatal Med. 17(2):97–103, 2011.Terrien, J., C. Marque, and B. Karlsson. Spectral characterization of human EHG frequency components based on the extraction and reconstruction of the ridges in the scalogram, Conference proceedings of IEEE Engineering in Medicine and Biology Society, 2007, pp. 1872–1875.Terrien, J., C. Marque, T. Steingrimsdottir, and B. Karlsson. Evaluation of adaptive filtering methods on a 16 electrode electrohysterogram recorded externally in labor, 11th Mediterranean Conference on Medical and Biomedical Engineering and Computing, 2007, Vol. 16, pp. 135–138.U.S. Preventive Services Task Force. Guide to clinical preventive services: an assessment of the effectiveness of 169 interventions. Baltimore: Willams & Wilkins, 1989

High prevalence of plasmid-mediated 16S rRNA methylase gene rmtB among Escherichia coli clinical isolates from a Chinese teaching hospital

<p>Abstract</p> <p>Background</p> <p>Recently, production of 16S rRNA methylases by Gram-negative bacilli has emerged as a novel mechanism for high-level resistance to aminoglycosides by these organisms in a variety of geographic locations. Therefore, the spread of high-level aminoglycoside resistance determinants has become a great concern.</p> <p>Methods</p> <p>Between January 2006 and July 2008, 680 distinct <it>Escherichia coli </it>clinical isolates were collected from a teaching hospital in Wenzhou, China. PCR and DNA sequencing were used to identify 16S rRNA methylase and extended-spectrum β-lactamase (ESBL) genes, including <it>armA </it>and <it>rmtB</it>, and in situ hybridization was performed to determine the location of 16S rRNA methylase genes. Conjugation experiments were subsequently performed to determine whether aminoglycoside resistance was transferable from the <it>E. coli </it>isolates via 16S rRNA methylase-bearing plasmids. Homology of the isolates harboring 16S rRNA methylase genes was determined using pulse-field gel electrophoresis (PFGE).</p> <p>Results</p> <p>Among the 680 <it>E. coli </it>isolates, 357 (52.5%), 346 (50.9%) and 44 (6.5%) isolates were resistant to gentamicin, tobramycin and amikacin, respectively. Thirty-seven of 44 amikacin-resistant isolates harbored 16S rRNA methylase genes, with 36 of 37 harboring the <it>rmtB </it>gene and only one harboring <it>armA</it>. The positive rates of 16S rRNA methylase genes among all isolates and amikacin-resistant isolates were 5.4% (37/680) and 84.1% (37/44), respectively. Thirty-one isolates harboring 16S rRNA methylase genes also produced ESBLs. In addition, high-level aminoglycoside resistance could be transferred by conjugation from four <it>rmtB</it>-positive donors. The plasmids of incompatibility groups IncF, IncK and IncN were detected in 34, 3 and 3 isolates, respectively. Upstream regions of the <it>armA </it>gene contained <it>IS</it>CR1 and <it>tnpU</it>, the latter a putative transposase gene,. Another putative transposase gene, <it>tnpD</it>, was located within a region downstream of <it>armA</it>. Moreover, a transposon, Tn<it>3</it>, was located upstream of the <it>rmtB</it>. Nineteen clonal patterns were obtained by PFGE, with type H representing the prevailing pattern.</p> <p>Conclusion</p> <p>A high prevalence of plasmid-mediated <it>rmtB </it>gene was found among clinical <it>E. coli </it>isolates from a Chinese teaching hospital. Both horizontal gene transfer and clonal spread were responsible for the dissemination of the <it>rmtB </it>gene.</p

COMMD1-Mediated Ubiquitination Regulates CFTR Trafficking

The CFTR (cystic fibrosis transmembrane conductance regulator) protein is a large polytopic protein whose biogenesis is inefficient. To better understand the regulation of CFTR processing and trafficking, we conducted a genetic screen that identified COMMD1 as a new CFTR partner. COMMD1 is a protein associated with multiple cellular pathways, including the regulation of hepatic copper excretion, sodium uptake through interaction with ENaC (epithelial sodium channel) and NF-kappaB signaling. In this study, we show that COMMD1 interacts with CFTR in cells expressing both proteins endogenously. This interaction promotes CFTR cell surface expression as assessed by biotinylation experiments in heterologously expressing cells through regulation of CFTR ubiquitination. In summary, our data demonstrate that CFTR is protected from ubiquitination by COMMD1, which sustains CFTR expression at the plasma membrane. Thus, increasing COMMD1 expression may provide an approach to simultaneously inhibit ENaC absorption and enhance CFTR trafficking, two major issues in cystic fibrosis

An integrated ChIP-seq analysis platform with customizable workflows

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), enables unbiased and genome-wide mapping of protein-DNA interactions and epigenetic marks. The first step in ChIP-seq data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence reads). The next step consists of interpreting the biological meaning of the peaks through their association with known genes, pathways, regulatory elements, and integration with other experiments. Although several programs have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually not well suited for thorough, integrative analysis of the detected peaks.</p> <p>Results</p> <p>To address the peak interpretation challenge, we have developed ChIPseeqer, an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. The novelty of our approach is the capability to combine several computational tools in order to create easily customized workflows that can be adapted to the user's needs and objectives. In this paper, we describe the main components of the ChIPseeqer framework, and also demonstrate the utility and diversity of the analyses offered, by analyzing a published ChIP-seq dataset.</p> <p>Conclusions</p> <p>ChIPseeqer facilitates ChIP-seq data analysis by offering a flexible and powerful set of computational tools that can be used in combination with one another. The framework is freely available as a user-friendly GUI application, but all programs are also executable from the command line, thus providing flexibility and automatability for advanced users.</p