Modeling and decoding motor cortical activity using a switching Kalman filter

We present a switching Kalman filter model for the real-time inference of hand kinematics from a population of motor cortical neurons. Firing rates are modeled as a Gaussian mixture where the mean of each Gaussian component is a linear function of hand kinematics. A "hidden state" models the probability of each mixture component and evolves over time in a Markov chain. The model generalizes previous encoding and decoding methods, addresses the non-Gaussian nature of firing rates, and can cope with crudely sorted neural data common in on-line prosthetic applications.     

Absolute configuration of monodentate phosphine ligand enantiomers on Cu(111)

Scanning tunneling microscopy (STM) has been employed to investigate the chirality of monophosphine compounds that are highly efficient chiral ligands in transition-metal-catalyzed organic transformations. The absolute configuration of 1-(2-diphenyphosphino-1-naphthyl)isoquinoline enantiomers with axial chirality was discriminated directly by the "marker" group, PPh(2) substitutes. Although the two enantiomer molecules adsorb on a Cu(111) surface and form well-defined (4 x 4) structures, the positions of PPh(2) substitutes in the molecular adlayers are different. The mirror symmetry between two adlayers is demonstrated. On the basis of STM results, structural models are proposed to interpret the chiral adsorption. The results presented here supply a straightforward method for axial chirality analysis in adsorbed adlayers by STM.     

A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry

Recent advances in phosphopeptide enrichment prior to mass spectrometric analysis show genuine promise for characterization of phosphoproteomes. Tandem mass spectrometry of phosphopeptide ions, using collision-activated dissociation (CAD), often produces product ions dominated by the neutral loss of phosphoric acid. Here we describe a novel method, termed Pseudo MS(n), for phosphopeptide ion dissociation in quadrupole ion trap mass spectrometers. The method induces collisional activation of product ions, those resulting from neutral loss(es) of phosphoric acid, following activation of the precursor ion. Thus, the principal neutral loss product ions are converted into a variety of structurally informative species. Since product ions from both the original precursor activation and all subsequent neutral loss product activations are simultaneously stored, the method generates a "composite" spectrum containing fragments derived from multiple precursors. In comparison to analysis by conventional MS/MS (CAD), Pseudo MS(n) shows improved phosphopeptide ion dissociation for 7 out of 10 synthetic phosphopeptides, as judged by an automated search algorithm (TurboSEQUEST). A similar overall improvement was observed upon application of Pseudo MS(n) to peptides generated by enzymatic digestion of a single phosphoprotein. Finally, when applied to a complex phosphopeptide mixture, several phosphopeptides mis-assigned by TurboSEQUEST under the conventional CAD approach were successfully identified after analysis by Pseudo MS(n).     

The emergence of temporal hyperacuity from widely tuned cell populations

Typically, individual neural cells operate on a millisecond time scale yet behaviorally animals reveal sub-microsecond acuity. Our model resolves this huge discrepancy by using populations of many widely tuned cells to attain sub-microsecond resolution in a temporal discrimination task. An echolocating bat uses its auditory system to locate objects and it demonstrates remarkable temporal precision in psychophysical tasks. Auditory cells were simulated using realistic parameters and connected in three ascending layers with descending projections from auditory cortex. Coincidence detection of firing collicular cells at thalamus and subsequent integration of multiple inputs at cortex, produce an estimate of time represented as the mean of the active cortical population. Multiple estimates allow the model bat to use memory to recognize predictable change in stimuli values. The best performance is produced using cortical feedback and a computation of target time based on combining the current and previous estimates. Temporal hyperacuity is attained through population coding of physiologically realistic cells but depends on the inherent properties of the psychophysical task.     

Role of soil freezing events in interannual patterns of stream chemistry at the Hubbard Brook Experimental Forest,New Hampshire

Soil freezing is a disturbance of the below ground environment, potentially resulting in increased losses of NO3- and surface water acidification. Here, we report the effects of soil freezing on interannual variation in stream chemistry at the Hubbard Brook Experimental Forest, New Hampshire. Data from 1970 to 1997 of soil frost depth, snow cover, precipitation, air temperature, and stream discharge and chemistry were used in a stepwise linear regression model to select the variables that best predicted deviations of annual stream concentrations from 4-year running averages. Variables quantifying soil freezing severity were selected as significant predictors of short-term fluctuations in stream K+, NO3-, Ca2+, and Mg2+ concentrations from 1970 to 1989, explaining 59 and 47% of the short-term variability in K+ and NO3-, respectively. Fine-root mortality and disturbance of root-soil-microbe interactions, with subsequent effects on decomposition and nutrient uptake, likely contributed to the mobilization of K+ and NO3- to streamwater following severe soil freezing events. The relationship between soil freezing and stream chemistry, however, weakened during the period 1990-1997. Because soil freezing has had inconsistent effects on stream chemistry during the period 1970-1997, it is unclear whether future changes in the frequency, duration, and depth of soil freezing events as the result of changes in the snow cover regime under a warmer climate will have significant impacts on the losses of NO3- and nutrient-base cations from temperate northern ecosystems.     

Changes in wine yeast storage carbohydrate levels during preadaptation,rehydration and low temperature fermentations

The metabolism of glycogen and trehalose was analysed in a wine yeast strain fermenting at 25 and 13 degrees C. Trehalose and glycogen degradation were completed during the lag phase of fermentation. Ammonia was taken up rapidly and once it had been reduced to negligible amounts, the synthesis of trehalose started. Glycogen followed a similar pattern. If trehalose synthesis was taken as a stress indicator, the fermentation at 13 degrees C could not be considered stressful because the maximum concentrations are similar at both temperatures. In industrial fermentations, and after a preadaptation in grape must for several hours at 18 degrees C, the lag phase was reduced significantly, and this may be why trehalose and glycogen were completely depleted at the beginning of the low temperature fermentation. Various preadaptation conditions were tested so that their influence on trehalose and glycogen degradation could be determined. The presence of fermentable carbon sources, such as glucose or fructose, triggered the mobilisation and use of trehalose. However, just increasing the osmotic pressure did not reduce the trehalose content. No such differences were observed in glycogen metabolism.     

Synthesis and utilisation of folate by yoghurt starter cultures and probiotic bacteria

Thirty-two bacterial isolates from species commonly used in yoghurts and fermented milks were examined for their ability to synthesise or utilise folate during fermentation of skim milk. The organisms examined included the traditional yoghurt starter cultures, Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus, and probiotic lactobacilli, bifidobacteria, and Enterococcus faecium. Folate was synthesised by S. thermophilus, bifidobacteria, and E. faecium. S. thermophilus was the dominant producer, elevating folate levels in skim milk from 11.5 ng g⁻¹ to between 40 and 50 ng g⁻¹. Generally, lactobacilli depleted the available folate in the skim milk. Fermentations with mixed cultures showed that folate production and utilisation by the cultures was additive. Fermentations using a combination of Bifidobacterium animalis and S. thermophilus resulted in a six-fold increase in folate concentration. Although increased folate levels in yoghurts and fermented milks are possible through judicious selection of inoculum species, the folate levels remain relatively low in terms of recommended daily allowance.     

Assembly interdependence among the S. cerevisiae bud neck ring proteins Elm1p,Hsl1p and Cdc12p

In Saccharomyces cerevisiae, a complex comprising more than 20 different polypeptides assembles in a ring at the neck between the mother cell and the bud. This complex functions to coordinate cell morphology with cell division. Relatively little is known about this control system, including the physical relationships between the components of the neck ring. This study addressed the assembly interactions of three components of the ring, specifically the protein kinases Elm1p and Hsl1p and the septin Cdc12p. Specific amino acid substitutions in each of these three proteins were identified that either cause or suppress a characteristic phenotype of abnormally elongated cells and delay in the G(2)-M transition. Each protein was fused to green fluorescent protein, and its ability to localize at the neck was monitored in vivo in cells of various genotypes. Localization of Hsl1p to the neck requires Elm1p function. Elm1p localized normally in the absence of Hsl1p, although a specific point mutation in Hsl1p clearly affected Elm1p localization. The cdc12-122 mutation prevented assembly of Elm1p or Hsl1p into the neck ring. Normal assembly of Cdc12p at the neck was dependent upon Elm1p and also, to a smaller extent, on Hsl1p. Ectopic localization of Cdc12p at the bud tip was observed frequently in elm1 mutants and also, to a lesser extent, in hsl1 mutants. Thus, Elm1p is a key factor in the assembly and/or maintenance of Hsl1p, as well as at least one septin, into the bud neck ring.     

Calibration and evaluation of a transportable in vivo monitoring system for accident monitoring of internal contamination

A transportable in vivo monitoring system has been constructed and calibrated. The system uses two hyper pure germanium detectors--one for measuring whole body activities, by measuring activity in the torso, and the second for determining activities of radioiodine in the thyroid. The optimum counting geometries have been determined and the system has been calibrated for subjects of different ages and builds. The complete system is transported in two trailers which are pulled by ordinary motor vehicles. The minimum detectable activity (MDA) for 137Cs in whole body for a 10 min counting interval at the 95% confidence level is 200 Bq. The MDA for a count of 131I in thyroid is 20 Bq. The system is capable of detecting activities that are equivalent to a dose of 1 mSv for a wide range of radionuclides.