Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies.

OBJECTIVE: Predictive disease modeling using electronic health record data is a growing field. Although clinical data in their raw form can be used directly for predictive modeling, it is a common practice to map data to standard terminologies to facilitate data aggregation and reuse. There is, however, a lack of systematic investigation of how different representations could affect the performance of predictive models, especially in the context of machine learning and deep learning. MATERIALS AND METHODS: We projected the input diagnoses data in the Cerner HealthFacts database to Unified Medical Language System (UMLS) and 5 other terminologies, including CCS, CCSR, ICD-9, ICD-10, and PheWAS, and evaluated the prediction performances of these terminologies on 2 different tasks: the risk prediction of heart failure in diabetes patients and the risk prediction of pancreatic cancer. Two popular models were evaluated: logistic regression and a recurrent neural network. RESULTS: For logistic regression, using UMLS delivered the optimal area under the receiver operating characteristics (AUROC) results in both dengue hemorrhagic fever (81.15%) and pancreatic cancer (80.53%) tasks. For recurrent neural network, UMLS worked best for pancreatic cancer prediction (AUROC 82.24%), second only (AUROC 85.55%) to PheWAS (AUROC 85.87%) for dengue hemorrhagic fever prediction. DISCUSSION/CONCLUSION: In our experiments, terminologies with larger vocabularies and finer-grained representations were associated with better prediction performances. In particular, UMLS is consistently 1 of the best-performing ones. We believe that our work may help to inform better designs of predictive models, although further investigation is warranted

Underwater Communication Acoustic Transducers: A Technology Review

This paper provides a comprehensive review on transducer technologies for underwater communications. The popularly used communication transducers, such as piezoelectric acoustic transducers, electromagnetic acoustic transducers, and acousto-optic devices are reviewed in detail. The reasons that common air communication technologies are invalid die to the differences between the media of air and water are addresses. Because of the abilities to overcome challenges the complexity of marine environments, piezoelectric acoustic transducers are playing the major underwater communication roles for science, surveillance, and Naval missions. The configuration and material properties of piezoelectric transducers effects on signal output power, beamwidth, amplitude, and other properties are discussed. The methods of code and decode communication information signals into acoustic waves are also presented. Finally, several newly developed piezoelectric transducers are recommended for future studies

Observations and Modeling of the Mars Low‐Altitude Ionospheric Response to the 10 September 2017 X‐Class Solar Flare

Solar extreme ultraviolet and X‐ray photons are the main sources of ionization in the Martian ionosphere and can be enhanced significantly during a solar flare. On 10 September 2017, the Mars Atmosphere and Volatile EvolutioN orbiter observed an X8.2 solar flare, the largest it has encountered to date. Here we investigate the ionospheric response before, during, and after this event with the SuperThermal Electron Transport model. We find good agreement between modeled and measured photoelectron spectra. In addition, the high photoelectron fluxes during the flare provide adequate statistics to allow us to clearly and repeatedly identify the carbon Auger peak in the ionospheric photoelectron energy spectra at Mars for the first time. By applying photochemical equilibrium, O2+ and CO2+ densities are obtained and compared with Mars Atmosphere and Volatile EvolutioN observations. The variations in ion densities during this event due to the solar irradiance enhancement and the neutral atmosphere expansion are discussed.Plain Language SummarySolar extreme ultraviolet and X‐ray photons are the main source of ionization in the Martian ionosphere, photoionizing the neutral particles and producing photoelectrons and ions. These short‐wavelength photon fluxes can be enhanced by a factor of a few to orders of magnitudes during a solar flare (the result of the rapid conversion of magnetic energy to kinetic energy in the solar corona). On 10 September 2017, the Mars Atmosphere and Volatile EvolutioN mission encountered the largest solar flare (X8.2) to date. The comprehensive measurements from Mars Atmosphere and Volatile EvolutioN provide us with an opportunity to evaluate the ionospheric response to this flare event in detail with models. In particular, we investigate the photoelectron flux and ion density response to the flare with an electron transport model. The modeled and measured photoelectron fluxes are in a good agreement. Ion density enhancement at a fixed altitude is from tens of percent to 1500% due to a combination of intensified solar photon fluxes and the heated and then expanded neutral atmosphere during this flare event.Key PointsThe modeled and measured photoelectron spectra are in good agreement during an X8.2 solar flare eventThe carbon Auger peak is clearly and repeatedly identified in electron energy spectra of the Martian ionosphere for the first timeThe ion density enhancement due to the flare at a fixed altitude is from tens to 1,500%Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/145576/1/grl57692.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145576/2/grl57692_am.pd

Quantum Holographic Encoding in a Two-dimensional Electron Gas

The advent of bottom-up atomic manipulation heralded a new horizon for attainable information density, as it allowed a bit of information to be represented by a single atom. The discrete spacing between atoms in condensed matter has thus set a rigid limit on the maximum possible information density. While modern technologies are still far from this scale, all theoretical downscaling of devices terminates at this spatial limit. Here, however, we break this barrier with electronic quantum encoding scaled to subatomic densities. We use atomic manipulation to first construct open nanostructures--"molecular holograms"--which in turn concentrate information into a medium free of lattice constraints: the quantum states of a two-dimensional degenerate Fermi gas of electrons. The information embedded in the holograms is transcoded at even smaller length scales into an atomically uniform area of a copper surface, where it is densely projected into both two spatial degrees of freedom and a third holographic dimension mapped to energy. In analogy to optical volume holography, this requires precise amplitude and phase engineering of electron wavefunctions to assemble pages of information volumetrically. This data is read out by mapping the energy-resolved electron density of states with a scanning tunnelling microscope. As the projection and readout are both extremely near-field, and because we use native quantum states rather than an external beam, we are not limited by lensing or collimation and can create electronically projected objects with features as small as ~0.3 nm. These techniques reach unprecedented densities exceeding 20 bits/nm2 and place tens of bits into a single fermionic state.Comment: Published online 25 January 2009 in Nature Nanotechnology; 12 page manuscript (including 4 figures) + 2 page supplement (including 1 figure); supplementary movie available at http://mota.stanford.ed

A global method for coupling transport with chemistry in heterogeneous porous media

Modeling reactive transport in porous media, using a local chemical equilibrium assumption, leads to a system of advection-diffusion PDE's coupled with algebraic equations. When solving this coupled system, the algebraic equations have to be solved at each grid point for each chemical species and at each time step. This leads to a coupled non-linear system. In this paper a global solution approach that enables to keep the software codes for transport and chemistry distinct is proposed. The method applies the Newton-Krylov framework to the formulation for reactive transport used in operator splitting. The method is formulated in terms of total mobile and total fixed concentrations and uses the chemical solver as a black box, as it only requires that on be able to solve chemical equilibrium problems (and compute derivatives), without having to know the solution method. An additional advantage of the Newton-Krylov method is that the Jacobian is only needed as an operator in a Jacobian matrix times vector product. The proposed method is tested on the MoMaS reactive transport benchmark.Comment: Computational Geosciences (2009) http://www.springerlink.com/content/933p55085742m203/?p=db14bb8c399b49979ba8389a3cae1b0f&pi=1

Long COVID in Children and Youth After Infection or Reinfection with the Omicron Variant: A Prospective Observational Study

To describe the prevalence of long COVID in children infected for the first time (n=332) or reinfected (n=243) with Omicron variant SARS-CoV-2, compared with test-negative children (n=311). 12-16% infected with Omicron met the research definition of long COVID at 3 and 6 months after infection, with no evidence of difference between cases of first-positive and reinfection (pchi-square=0.17)

Symptom Profiles of Children and Young People 12 Months after SARS-CoV-2 Testing: A National Matched Cohort Study (The CLoCk Study)

Background: Although 99% of children and young people have been exposed to SARS-CoV-2, the long-term prevalence of post-COVID-19 symptoms in young people is unclear. The aim of this study is to describe symptom profiles 12 months after SARS-CoV-2 testing. Method: A matched cohort study of a national sample of 20,202 children and young people who took a SARS-CoV-2 PCR test between September 2020 and March 2021. Results: 12 months post-index-test, there was a difference in the number of symptoms reported by initial negatives who never tested positive (NN) compared to the other three groups who had at least one positive test (p < 0.001). Similarly, 10.2% of the NN group described five-plus symptoms at 12 months compared to 15.9–24.0% in the other three groups who had at least one positive test. The most common symptoms were tiredness, sleeping difficulties, shortness of breath, and headaches for all four groups. For all these symptoms, the initial test positives with subsequent reports of re-infection had higher prevalences than other positive groups (p < 0.001). Symptom profiles, mental health, well-being, fatigue, and quality of life did not vary by vaccination status. Conclusions: Following the pandemic, many young people, particularly those that have had multiple SARS-CoV-2 positive tests, experience a range of symptoms that warrant consideration and potential investigation and intervention

Puntos de inflexión en los gradientes de composición de las comunidades de plantas acuáticas de diferentes continentes

Unravelling patterns and mechanisms of biogeographical transitions is crucial if we are to understand compositional gradients at large spatial extents, but no studies have thus far examined breakpoints in community composition of freshwater plants across continents. Using a dataset of almost 500 observations of lake plant community composition from six continents, we examined, for the first time, if such breakpoints in geographical space exist for freshwater plants and how well a suite of ecological factors (including climatic and local environmental variables) can explain transitions in community composition from the subtropics to the poles. Our combination of multivariate regression tree (MRT) analysis and k-means partitioning suggests that the most abrupt breakpoint exists between temperate to boreal regions on the one hand and freshwater plant communities harbouring mainly subtropical or Mediterranean assemblages on the other. The spatially structured variation in current climatic conditions is the most likely candidate for controlling these latitudinal patterns, although one cannot rule out joint effects of eco-evolutionary constraints in the harsher high-latitude environments and post-glacial migration lags after Pleistocene Ice Ages. Overall, our study supports the foundations of global regionalisation for freshwater plants and anticipates further biogeographical research on freshwater plant communities once datasets have been harmonised for conducting large-scale spatial analyses.publishedVersio

Puntos de inflexión en los gradientes de composición de las comunidades de plantas acuáticas de diferentes continentes

Sección: SIBECOL-AIL Meeting in Aveiro-2022[EN] Unravelling patterns and mechanisms of biogeographical transitions is crucial if we are to understand compositional gradients at large spatial extents, but no studies have thus far examined breakpoints in community composition of freshwater plants across continents. Using a dataset of almost 500 observations of lake plant community composition from six continents, we examined, for the first time, if such breakpoints in geographical space exist for freshwater plants and how well a suite of ecological factors (including climatic and local environmental variables) can explain transitions in community composition from the subtropics to the poles. Our combination of multivariate regression tree (MRT) analysis and k-means partitioning suggests that the most abrupt breakpoint exists between temperate to boreal regions on the one hand and freshwater plant communities harbouring mainly subtropical or Mediterranean assemblages on the other. The spatially structured variation in current climatic conditions is the most likely candidate for controlling these latitudinal patterns, although one cannot rule out joint effects of eco-evolutionary constraints in the harsher high-latitude environments and post-glacial migration lags after Pleistocene Ice Ages. Overall, our study supports the foundations of global regionalisation for freshwater plants and anticipates further biogeographical research on freshwater plant communities once datasets have been harmonised for conducting large-scale spatial analyses[ES] Desentrañar los patrones y mecanismos que subyacen a las transiciones biogeográficas es un requisito fundamental a la hora de comprender los gradientes de composición de las comunidades ecológicas a grandes extensiones espaciales, si bien ningún estudio ha examinado explícitamente estos puntos de inflexión para comunidades de plantas acuáticas de diferentes continentes. Utilizando una completa base de datos que condensa un total de casi 500 observaciones individuales sobre las comunidades florísticas lacustres de seis continentes, este trabajo pretende delinear las transiciones biogeográficas en plantas acuáticas a escala global, así como valorar el papel que desempeñan diversos mecanismos ecológicos (a saber, las condiciones climáticas y las características locales del hábitat) sobre estos puntos de inflexión en el espacio geográfico comprendido entre las latitudes subtropicales y los polos. Nuestros resultados obtenidos mediante la ejecución simultánea de árboles de regresión multivariante (MRT) y algoritmos de agrupación por k-medias demuestran la existencia de un punto de inflexión entre las regiones templadas y boreales y los lagos localizados en las bandas subtropicales y en las inmediaciones del Mediterráneo. La estructura espacial que subyace a la distribución de los condicionantes climáticos en nuestro planeta parece ser el principal mecanismo de control de dichas transiciones biogeográficas, si bien estos patrones latitudinales también podrían explicarse en base a constricciones eco-evolutivas en las regiones más septentrionales y a la colonización diferencial de los territorios norteños antaño cubiertos por el hielo durante el Último Máximo Glacial. En síntesis, nuestro estudio proporciona una base teórica preliminar para futuras investigaciones encaminadas a delimitar las unidades geográficas de los principales componentes de la flora acuática contemporánea y también anticipa un creciente interés por los estudios de carácter fitogeográfico en las aguas continentales, si bien los análisis venideros deberán prestar especial atención a la armonización de datos biológicos potencialmente heterogéneos en naturaleza y con orígenes disparesSIJGG was funded by the European Union Next Generation EU/PRTR (grant no. AG325). Academy of Finland supported JH, JGG (grant no. 331957), and JA (grant no. 322652). CFL appreciates financial support from the Spanish Ministry of Science and Technology (grant no. CL2017- 84176R). BAL was supported by National Research, Development, and Innovation Office (grant no. NKFIH, OTKA FK127939) and by the Bolyai János Research Scholarship of the Hungarian Academy of Sciences. SK was supportedby NWO Vidi (grant no. 203098). LR was funded by MESRSI (Ministry of Higher Education, Scientific Research and Innovation of Morocco) as part of the BiodivRestore Program (RESPOND Project) and by the Tour du Valat Foundation. Sampling of the Brazilian coastal lakes was financed by NWO (grant no. W84-549), the National Geographic Society (grant no. 7864-5), and CNPq (grants no. 480122, 490409, 311427