Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

Background: MicroRNA regulation is fundamentally responsible for fine-tuning the whole gene network in human and has been implicated in most physiological and pathological conditions. Studying regulatory impact of microRNA on various cellular and disease processes has resulted in numerous computational tools that investigate microRNA-mRNA interactions through the prediction of static binding site highly dependent on sequence pairing. However, what hindered the practical use of such target prediction is the interplay between competing and cooperative microRNA binding that complicates the whole regulatory process exceptionally. Results: We developed a new method for improved microRNA target prediction based on Dirichlet Process Gaussian Mixture Model (DPGMM) using a large collection of molecular features associated with microRNA, mRNA, and the interaction sites. Multiple validations based on microRNA-mRNA interactions reported in recent large-scale sequencing analyses and a screening test on the entire human transcriptome show that our model outperformed several state-of-the-art tools in terms of promising predictive power on binding sites specific to transcript isoforms with reduced false positive prediction. Last, we illustrated the use of predicted targets in constructing conditional microRNA-mediated gene regulation networks in human cancer. Conclusion: The probability-based binding site prediction provides not only a useful tool for differentiating microRNA targets according to the estimated binding potential but also a capability highly important for exploring dynamic regulation where binding competition is involved

Automatic Nonnutritive Suck Waveform Discrimination and Feature Extraction in Preterm Infants

Background and Objective: The emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. Thus, the goal was to develop and describe a crossplatform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. The NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (\u3c50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. The hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform

Automatic Nonnutritive Suck Waveform Discrimination and Feature Extraction in Preterm Infants

Background and Objective: +e emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. +us, the goal was to develop and describe a crossplatform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. +e NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (\u3c50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. +e hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform

Hysteresis of Electronic Transport in Graphene Transistors

Graphene field effect transistors commonly comprise graphene flakes lying on SiO2 surfaces. The gate-voltage dependent conductance shows hysteresis depending on the gate sweeping rate/range. It is shown here that the transistors exhibit two different kinds of hysteresis in their electrical characteristics. Charge transfer causes a positive shift in the gate voltage of the minimum conductance, while capacitive gating can cause the negative shift of conductance with respect to gate voltage. The positive hysteretic phenomena decay with an increase of the number of layers in graphene flakes. Self-heating in helium atmosphere significantly removes adsorbates and reduces positive hysteresis. We also observed negative hysteresis in graphene devices at low temperature. It is also found that an ice layer on/under graphene has much stronger dipole moment than a water layer does. Mobile ions in the electrolyte gate and a polarity switch in the ferroelectric gate could also cause negative hysteresis in graphene transistors. These findings improved our understanding of the electrical response of graphene to its surroundings. The unique sensitivity to environment and related phenomena in graphene deserve further studies on nonvolatile memory, electrostatic detection and chemically driven applications.Comment: 13 pages, 6 Figure

Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

Background: MicroRNA regulation is fundamentally responsible for fine-tuning the whole gene network in human and has been implicated in most physiological and pathological conditions. Studying regulatory impact of microRNA on various cellular and disease processes has resulted in numerous computational tools that investigate microRNA-mRNA interactions through the prediction of static binding site highly dependent on sequence pairing. However, what hindered the practical use of such target prediction is the interplay between competing and cooperative microRNA binding that complicates the whole regulatory process exceptionally. Results: We developed a new method for improved microRNA target prediction based on Dirichlet Process Gaussian Mixture Model (DPGMM) using a large collection of molecular features associated with microRNA, mRNA, and the interaction sites. Multiple validations based on microRNA-mRNA interactions reported in recent large-scale sequencing analyses and a screening test on the entire human transcriptome show that our model outperformed several state-of-the-art tools in terms of promising predictive power on binding sites specific to transcript isoforms with reduced false positive prediction. Last, we illustrated the use of predicted targets in constructing conditional microRNA-mediated gene regulation networks in human cancer. Conclusion: The probability-based binding site prediction provides not only a useful tool for differentiating microRNA targets according to the estimated binding potential but also a capability highly important for exploring dynamic regulation where binding competition is involved

Automatic Nonnutritive Suck Waveform Discrimination and Feature Extraction in Preterm Infants

Background and Objective: The emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. Thus, the goal was to develop and describe a crossplatform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. The NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (\u3c50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. The hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform

Automatic Nonnutritive Suck Waveform Discrimination and Feature Extraction in Preterm Infants

Background and Objective: +e emergence of the nonnutritive suck (NNS) pattern in preterm infants reflects the integrity of the brain and is used by clinicians in the neonatal intensive care unit (NICU) to assess feeding readiness and oromotor development. A critical need exists for an integrated software platform that provides NNS signal preprocessing, adaptive waveform discrimination, feature detection, and batch processing of big data sets across multiple NICU sites. +us, the goal was to develop and describe a crossplatform graphical user interface (GUI) and terminal application known as NeoNNS for single and batch file time series and frequency-domain analyses of NNS compression pressure waveforms using analysis parameters derived from previous research on NNS dynamics. Methods. NeoNNS was implemented with Python and the Tkinter GUI package. +e NNS signal-processing pipeline included a low-pass filter, asymmetric regression baseline correction, NNS peak detection, and NNS burst classification. Data visualizations and parametric analyses included time- and frequency-domain view, NNS spatiotemporal index view, and feature cluster analysis to model oral feeding readiness. Results. 568 suck assessment files sampled from 30 extremely preterm infants were processed in the batch mode (\u3c50 minutes) to generate time- and frequency-domain analyses of infant NNS pressure waveform data. NNS cycle discrimination and NNS burst classification yield quantification of NNS waveform features as a function of postmenstrual age. Hierarchical cluster analysis (based on the Tsfresh python package and NeoNNS) revealed the capability to label NNS records for feeding readiness. Conclusions. NeoNNS provides a versatile software platform to rapidly quantify the dynamics of NNS development in time and frequency domains at cribside over repeated sessions for an individual baby or among large numbers of preterm infants at multiple hospital sites to support big data analytics. +e hierarchical cluster feature analysis facilitates modeling of feeding readiness based on quantitative features of the NNS compression pressure waveform