Analyzing Stability of Equilibrium Points in Neural Networks: A General Approach

Networks of coupled neural systems represent an important class of models in computational neuroscience. In some applications it is required that equilibrium points in these networks remain stable under parameter variations. Here we present a general methodology to yield explicit constraints on the coupling strengths to ensure the stability of the equilibrium point. Two models of coupled excitatory-inhibitory oscillators are used to illustrate the approach.Comment: 20 pages, 4 figure

Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.

The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 - 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 - 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes

A Novel Adaptive Spectrum Noise Cancellation Approach for Enhancing Heartbeat Rate Monitoring in a Wearable Device

This paper presents a novel approach, Adaptive Spectrum Noise Cancellation (ASNC), for motion artifacts removal in Photoplethysmography (PPG) signals measured by an optical biosensor to obtain clean PPG waveforms for heartbeat rate calculation. One challenge faced by this optical sensing method is the inevitable noise induced by movement when the user is in motion, especially when the motion frequency is very close to the target heartbeat rate. The proposed ASNC utilizes the onboard accelerometer and gyroscope sensors to detect and remove the artifacts adaptively, thus obtaining accurate heartbeat rate measurement while in motion. The ASNC algorithm makes use of a commonly accepted spectrum analysis approaches in medical digital signal processing, discrete cosine transform, to carry out frequency domain analysis. Results obtained by the proposed ASNC have been compared to the classic algorithms, the adaptive threshold peak detection and adaptive noise cancellation. The mean (standard deviation) absolute error and mean relative error of heartbeat rate calculated by ASNC is 0.33 (0.57) beats·min-1 and 0.65%, by adaptive threshold peak detection algorithm is 2.29 (2.21) beats·min-1 and 8.38%, by adaptive noise cancellation algorithm is 1.70 (1.50) beats·min-1 and 2.02%. While all algorithms performed well with both simulated PPG data and clean PPG data collected from our Verity device in situations free of motion artifacts, ASNC provided better accuracy when motion artifacts increase, especially when motion frequency is very close to the heartbeat rate

Evaluation of MERRA Land Surface Estimates in Preparation for the Soil Moisture Active Passive Mission

The authors evaluated several land surface variables from the Modern-Era Retrospective Analysis for Research and Applications (MERRA) product that are important for global ecological and hydrological studies, including daily maximum (Tmax) and minimum (Tmin) surface air temperatures, atmosphere vapor pressure deficit (VPD), incident solar radiation (SWrad), and surface soil moisture. The MERRA results were evaluated against in situ measurements, similar global products derived from satellite microwave [the Advanced Microwave Scanning Radiometer for Earth Observing System (EOS) (AMSR-E)] remote sensing and earlier generation atmospheric analysis [Goddard Earth Observing System version 4 (GEOS-4)] products. Relative to GEOS-4, MERRA is generally warmer (~0.5°C for Tmin and Tmax) and drier (~50 Pa for VPD) for low- and middle-latitude regions (\u3c50°N) associated with reduced cloudiness and increased SWrad. MERRA and AMSR-E temperatures show relatively large differences (\u3e3°C) in mountainous areas, tropical forest, and desert regions. Surface soil moisture estimates from MERRA (0–2-cm depth) and two AMSR-E products (~0–1-cm depth) are moderately correlated (R ~ 0.4) for middle-latitude regions with low to moderate vegetation biomass. The MERRA derived surface soil moisture also corresponds favorably with in situ observations (R = 0.53 ± 0.01, p \u3c 0.001) in the midlatitudes, where its accuracy is directly proportional to the quality of MERRA precipitation. In the high latitudes, MERRA shows inconsistent soil moisture seasonal dynamics relative to in situ observations. The study’s results suggest that satellite microwave remote sensing may contribute to improved reanalysis accuracy where surface meteorological observations are sparse and in cold land regions subject to seasonal freeze–thaw transitions. The upcoming NASA Soil Moisture Active Passive (SMAP) mission is expected to improve MERRA-type reanalysis accuracy by providing accurate global mapping of freeze–thaw state and surface soil moisture with 2–3-day temporal fidelity and enhanced (≤9 km) spatial resolution

Recent climate and fire disturbance impacts on boreal and arctic ecosystem productivity estimated using a satellite-based terrestrial carbon flux model

Warming and changing fire regimes in the northern (≥45°N) latitudes have consequences for land-atmosphere carbon feedbacks to climate change. A terrestrial carbon flux model integrating satellite Normalized Difference Vegetation Index and burned area records with global meteorology data was used to quantify daily vegetation gross primary productivity (GPP) and net ecosystem CO2 exchange (NEE) over a pan-boreal/Arctic domain and their sensitivity to climate variability, drought, and fire from 2000 to 2010. Model validation against regional tower carbon flux measurements showed overall good agreement for GPP (47 sites: R = 0.83, root mean square difference (RMSD) = 1.93 g C m−2 d−1) and consistency for NEE (22 sites: R = 0.56, RMSD = 1.46 g C m−2 d−1). The model simulations also tracked post-fire NEE recovery indicated from three boreal tower fire chronosequence networks but with larger model uncertainty during early succession. Annual GPP was significantly (p \u3c 0.005) larger in warmer years than in colder years, except for Eurasian boreal forest, which showed greater drought sensitivity due to characteristic warmer, drier growing seasons relative to other areas. The NEE response to climate variability and fire was mitigated by compensating changes in GPP and respiration, though NEE carbon losses were generally observed in areas with severe drought or burning. Drought and temperature variations also had larger regional impacts on GPP and NEE than fire during the study period, though fire disturbances were heterogeneous, with larger impacts on carbon fluxes for some areas and years. These results are being used to inform development of similar operational carbon products for the NASA Soil Moisture Active Passive (SMAP) mission

Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds

Background: The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60), secondary myogenesis (d 135), as well as beginning (d 195) and final stages (birth) of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24) were from Hereford dams and crossed with either Wagyu (high intramuscular fat) or Piedmontese (GDF8 mutant) sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. Results: We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5) RNA at birth. The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth. We also document evidence for timing differences in differentiation events between the two breeds. Conclusion: Taken together, these findings provide a detailed description of molecular events accompanying skeletal muscle differentiation in the bovine, as well as gene expression differences that may underpin the phenotype differences between the two breeds. In addition, this study has highlighted a non-coding RNA, which is abundantly expressed and developmentally regulated in bovine fetal muscle

Optimal input potential functions in the interacting particle system method

The assessment of the probability of a rare event with a naive Monte-Carlo method is computationally intensive, so faster estimation methods, such as variance reduction methods, are needed. We focus on one of these methods which is the interacting particle (IPS) system method. The method requires to specify a set of potential functions. The choice of these functions is crucial, because it determines the magnitude of the variance reduction. So far, little information was available on how to choose the potential functions. To remedy this, we provide the expression of the optimal potential functions minimizing the asymptotic variance of the estimator of the IPS method

Fate and Transport of Steroid Hormones and Veterinary Antibiotics Derived from Cattle Farms

Concentrated animal feeding operations (CAFOs) have been identified as one of the most important sources for the release of animal hormones and veterinary antibiotics into the aquatic environment. Funded by a USDA research grant, Dr. Wei Zheng set out to identify and quantify the environmental fate and transport of several commonly-occurring steroid hormones, veterinary antibiotics, and their metabolites. Findings were published in the following papers: Xiaolin Li, Wei Zheng, Michael L. Machesky, Scott R. Yates, and Michael Katterhenry (2011). Journal of Agricultural and Food Chemistry 2011 59 (18), 10176-10181 DOI: 10.1021/jf202325c Wei Zheng, Xiaolin Li, Scott R. Yates, and Scott A. Bradford (2012). Environmental Science & Technology 46 (10), 5471-5478. DOI: 10.1021/es301551h Xiaolin Li, Wei Zheng, Walton R. Kelly (2013). Science of the Total Environment 445-446, 22-28. DOI: 10.1016/j.scitotenv.2012.12.035 Wei Zheng, Yonghong Zou, Xiaolin Li, Michael L. Machesky (2013). Journal of Hazardous Materials 258-259, 109-115. DOI: 10.1016/j.jhazmat.2013.04.038 Yonghong Zou and Wei Zheng Environmental Science & Technology 2013 47 (10), 5185-5192 DOI: 10.1021/es400624w.U.S. Department of AgricultureOpe

Comparative Analysis of Upper Ocean Heat Content Variability from Ensemble Operational Ocean Analyses

Upper ocean heat content (HC) is one of the key indicators of climate variability on many time-scales extending from seasonal to interannual to long-term climate trends. For example, HC in the tropical Pacific provides information on thermocline anomalies that is critical for the longlead forecast skill of ENSO. Since HC variability is also associated with SST variability, a better understanding and monitoring of HC variability can help us understand and forecast SST variability associated with ENSO and other modes such as Indian Ocean Dipole (IOD), Pacific Decadal Oscillation (PDO), Tropical Atlantic Variability (TAV) and Atlantic Multidecadal Oscillation (AMO). An accurate ocean initialization of HC anomalies in coupled climate models could also contribute to skill in decadal climate prediction. Errors, and/or uncertainties, in the estimation of HC variability can be affected by many factors including uncertainties in surface forcings, ocean model biases, and deficiencies in data assimilation schemes. Changes in observing systems can also leave an imprint on the estimated variability. The availability of multiple operational ocean analyses (ORA) that are routinely produced by operational and research centers around the world provides an opportunity to assess uncertainties in HC analyses, to help identify gaps in observing systems as they impact the quality of ORAs and therefore climate model forecasts. A comparison of ORAs also gives an opportunity to identify deficiencies in data assimilation schemes, and can be used as a basis for development of real-time multi-model ensemble HC monitoring products. The OceanObs09 Conference called for an intercomparison of ORAs and use of ORAs for global ocean monitoring. As a follow up, we intercompared HC variations from ten ORAs -- two objective analyses based on in-situ data only and eight model analyses based on ocean data assimilation systems. The mean, annual cycle, interannual variability and longterm trend of HC have been analyze