The structural components of the Azotobacter vinelandii iron-only nitrogenase, AnfDKG, form a protein complex within the plant mitochondrial matrix.

A long-held goal of synthetic biology has been the transfer of a bacterial nitrogen-fixation pathway into plants to reduce the use of chemical fertiliser on crops such as rice, wheat and maize. There are three classes of bacterial nitrogenase, named after their metal requirements, containing either a MoFe-, VFe- or FeFe-cofactor, that converts N2 gas to ammonia. Relative to the Mo-nitrogenase the Fe-nitrogenase is not as efficient for catalysis but has less complex genetic and metallocluster requirements, features that may be preferable for engineering into crops. Here we report the successful targeting of bacterial Fe-nitrogenase proteins, AnfD, AnfK, AnfG and AnfH, to plant mitochondria. When expressed as a single protein AnfD was mostly insoluble in plant mitochondria, but coexpression of AnfD with AnfK improved its solubility. Using affinity-based purification of mitochondrially expressed AnfK or AnfG we were able to demonstrate a strong interaction of AnfD with AnfK and a weaker interaction of AnfG with AnfDK. This work establishes that the structural components of the Fe-nitrogenase can be engineered into plant mitochondria and form a complex, which will be a requirement for function. This report outlines the first use of Fe-nitrogenase proteins within a plant as a preliminary step towards engineering an alternative nitrogenase into crops.

The computational stance in biology.

The goal of this article is to call attention to, and to express caution about, the extensive use of computation as an explanatory concept in contemporary biology. Inspired by Dennett's 'intentional stance' in the philosophy of mind, I suggest that a 'computational stance' can be a productive approach to evaluating the value of computational concepts in biology. Such an approach allows the value of computational ideas to be assessed without being diverted by arguments about whether a particular biological system is 'actually computing' or not. Because there is sufficient difference of agreement among computer scientists about the essential elements that constitute computation, any doctrinaire position about the application of computational ideas seems misguided. Closely related to the concept of computation is the concept of information processing. Indeed, some influential computer scientists contend that there is no fundamental difference between the two concepts. I will argue that despite the lack of widely accepted, general definitions of information processing and computation: (1) information processing and computation are not fully equivalent and there is value in maintaining a distinction between them and (2) that such value is particularly evident in applications of information processing and computation to biology. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Extravasation reactions associated with the administration of pamidronate: 11 cases (2008-2013).

Pamidronate is a bisphosphonate drug widely utilized in veterinary oncologic practice for the palliation of malignant osteolysis. Pamidronate has not been previously reported to cause tissue injury upon extravasation in dogs. The medical records of 11 client-owned dogs undergoing palliative treatment for primary bone tumors with known or suspected pamidronate extravasation reactions were reviewed. The majority of adverse events were low grade in nature, however in some cases, the reactions were severe and led to euthanasia in one instance. Time to complete resolution of lesions ranged from within several days to greater than one and a half months. Aside from the dog that was euthanized, no long-term sequelae of extravasation were identified. Treatments employed to address the reactions varied widely. Pamidronate extravasation reaction appears to be an uncommon, but potentially serious complication of intravenous administration.

Efficiency of Ipratropium Bromide and Albuterol Deposition in the Lung Delivered via a Soft Mist Inhaler or Chlorofluorocarbon Metered-Dose Inhaler.

The propellant-free Combivent Respimat Soft Mist Inhaler (CVT-R) was developed to replace the chlorofluorocarbon-propelled Combivent metered-dose inhaler (CVT-MDI). This steady-state pharmacokinetic (PK) substudy evaluated drug lung-delivery efficiency, using data from two phase III safety and efficacy trials. PK parameters were obtained from well-controlled population PK analyses. Area under the plasma concentration-time curve (AUC), maximum observed plasma concentration (C(max)), and minimum observed plasma concentration (C(min)) showed systemic exposure to ipratropium bromide and albuterol delivered via the CVT-R was proportional to ex-mouthpiece delivered dose. Although the labeled dose of ipratropium bromide in the CVT-R was half that in the CVT-MDI, the systemic exposure was comparable. No PK interaction for the ipratropium bromide and albuterol Respimat drug components was demonstrated. Ipratropium bromide alone resulted in similar exposure to the combination of ipratropium bromide and albuterol. These results show that CVT-R delivers drug more efficiently to the lung than CVT-MDI.

Controlling the action of chlorine radical: from lab to environment.

The strength of Bz-Cl˙ complexation has been explored using density functional theory (DFT) calculations, including dispersion-corrected (DFT-D) calculations. Of the methods tested, the ωB97X-D method seems the best performing, along with the previously tested MPW1K method. The effect of substituent (X = NO(2), F, Cl, Br, H, CH(3), OCH(3), OH, NH(2) and N(CH(3))(2)) on the stabilities of the Ar-Cl˙π-like intermediates show a good correlation with the linear free energy relationships used experimentally, but this is not the case for Ar-Cl˙σ-complexes, suggesting the transition state of abstraction as being π-like in nature. The role of PAH and lignin derivatives in mediating chlorination reactions in nature is explored. Stable π-complexes were identified for lignin derivatives, indicating humic substances may mediate chlorine atom reactivity at the marine boundary layer, in addition to forming chlorolignins.

Efficacy and safety of ipratropium bromide/albuterol delivered via Respimat inhaler versus MDI.

We compared the efficacy and safety of ipratropium bromide/albuterol delivered via Respimat inhaler, a novel propellant-free inhaler, versus chlorofluorocarbon (CFC)-metered dose inhaler (MDI) and ipratropium Respimat inhaler in patients with COPD. This was a multinational, randomized, double-blind, double-dummy, 12-week, parallel-group, active-controlled study. Patients with moderate to severe COPD were randomized to ipratropium bromide/albuterol (20/100mcg) Respimat inhaler, ipratropium bromide/albuterol MDI [36mcg/206mcg (Combivent Inhalation Aerosol MDI)], or ipratropium bromide (20mcg) Respimat inhaler. Each medication was administered four times daily. Serial spirometry was performed over 6h (0.15min, then hourly) on 4 test days. The primary efficacy variable was forced expiratory volume in 1s (FEV(1)) change from test day baseline at 12 weeks. A total of 1209 of 1480 randomized, treated patients completed the study; the majority were male (65%) with a mean age of 64 yrs and a mean screening pre-bronchodilator FEV(1) (percent predicted) of 41%. Ipratropium bromide/albuterol Respimat inhaler had comparable efficacy to ipratropium bromide/albuterol MDI for FEV(1) area under the curve at 0-6h (AUC(0-6)), superior efficacy to ipratropium Respimat inhaler for FEV(1) AUC(0-4) and comparable efficacy to ipratropium Respimat inhaler for FEV(1) AUC(4-6). All active treatments were well tolerated. This study demonstrates that ipratropium bromide/albuterol 20/100mcg inhaler administered four times daily for 12 weeks had equivalent bronchodilator efficacy and comparable safety to ipratropium bromide/albuterol 36mcg/206mcg MDI, and significantly improved lung function compared with the mono-component ipratropium bromide 20 mcg Respimat inhaler. [Clinical Trial Identifier Number: NCT00400153].

Modeling spatiotemporal covariance for magnetoencephalography or electroencephalography source analysis.

We propose a new model to approximate spatiotemporal noise covariance for use in neural electromagnetic source analysis, which better captures temporal variability in background activity. As with other existing formalisms, our model employs a Kronecker product of matrices representing temporal and spatial covariance. In our model, spatial components are allowed to have differing temporal covariances. Variability is represented as a series of Kronecker products of spatial component covariances and corresponding temporal covariances. Unlike previous attempts to model covariance through a sum of Kronecker products, our model is designed to have a computationally manageable inverse. Despite increased descriptive power, inversion of the model is fast, making it useful in source analysis. We have explored two versions of the model. One is estimated based on the assumption that spatial components of background noise have uncorrelated time courses. Another version, which gives closer approximation, is based on the assumption that time courses are statistically independent. The accuracy of the structural approximation is compared to an existing model, based on a single Kronecker product, using both Frobenius norm of the difference between spatiotemporal sample covariance and a model, and scatter plots. Performance of ours and previous models is compared in source analysis of a large number of single dipole problems with simulated time courses and with background from authentic magnetoencephalography data.

Improving source detection and separation in a spatiotemporal Bayesian inference dipole analysis.

Most existing spatiotemporal multi-dipole approaches for MEG/EEG source localization assume that the dipoles are active for the full time range being analysed. If the actual time range of activity of sources is significantly shorter than the time range being analysed, the detectability, localization and time-course determination of such sources may be adversely affected, especially for weak sources. In order to improve detectability and reconstruction of such sources, it is natural to add active time range information (starting time point and ending time point of source activation) for each candidate source as unknown parameters in the analysis. However, this adds additional nonlinear free parameters that could burden the analysis and could be unfeasible for some methods. Recently, we described a spatiotemporal Bayesian inference multi-dipole analysis for the MEG/EEG inverse problem. This approach treated the number of dipoles as a free parameter, produced realistic uncertainty estimates using a Markov chain Monte Carlo numerical sampling of the posterior distribution and included a method to reduce the unwanted effects of local minima. In this paper, our spatiotemporal Bayesian inference multi-dipole analysis is extended to incorporate active time range parameters of starting and stopping time points. The properties of this analysis in comparison to the previous one without active time range parameters are demonstrated through extensive studies using both simulated and empirical MEG data.

Spatiotemporal Bayesian inference dipole analysis for MEG neuroimaging data.

Recently, we described a Bayesian inference approach to the MEG/EEG inverse problem that used numerical techniques to estimate the full posterior probability distributions of likely solutions upon which all inferences were based [Schmidt, D.M., George, J.S., Wood, C.C., 1999. Bayesian inference applied to the electromagnetic inverse problem. Human Brain Mapping 7, 195; Schmidt, D.M., George, J.S., Ranken, D.M., Wood, C.C., 2001. Spatial-temporal bayesian inference for MEG/EEG. In: Nenonen, J., Ilmoniemi, R. J., Katila, T. (Eds.), Biomag 2000: 12th International Conference on Biomagnetism. Espoo, Norway, p. 671]. Schmidt et al. (1999) focused on the analysis of data at a single point in time employing an extended region source model. They subsequently extended their work to a spatiotemporal Bayesian inference analysis of the full spatiotemporal MEG/EEG data set. Here, we formulate spatiotemporal Bayesian inference analysis using a multi-dipole model of neural activity. This approach is faster than the extended region model, does not require use of the subject's anatomical information, does not require prior determination of the number of dipoles, and yields quantitative probabilistic inferences. In addition, we have incorporated the ability to handle much more complex and realistic estimates of the background noise, which may be represented as a sum of Kronecker products of temporal and spatial noise covariance components. This reduces the effects of undermodeling noise. In order to reduce the rigidity of the multi-dipole formulation which commonly causes problems due to multiple local minima, we treat the given covariance of the background as uncertain and marginalize over it in the analysis. Markov Chain Monte Carlo (MCMC) was used to sample the many possible likely solutions. The spatiotemporal Bayesian dipole analysis is demonstrated using simulated and empirical whole-head MEG data.

Glacial biogeography of North American coho salmon (Oncorhynchus kisutch).

To study the glacial biogeography of coho we examined 20 microsatellite loci and mitochondrial DNA D-loop sequence in samples from Alaska to California. Microsatellite data divided our samples among five biogeographic regions: (1) Alaska and northern coastal British Columbia; (2) the Queen Charlotte Islands; (3) the mainland coast of British Columbia and northern Washington State; (4) the Thompson River; and (5) Oregon and California. The D-loop sequence data suggested three geographical regions: (1) Oregon and California; (2) the Thompson River; and (3) all the other sites north of the southern ice margin. Microsatellite data revealed no difference in the number of alleles in different regions, but mitochondrial DNA data revealed a cline of decreasing diversity from south to north. We suggest that the two signals presented by these different marker types illuminate two time frames in the history of this species. Endemic microsatellite diversity in Alaska and on the Queen Charlotte Islands provides evidence in favour of Fraser Glaciation refugia in these regions. The loss of mitochondrial variation from south to north suggests that one of the earlier, more extensive, Pleistocene glaciations eliminated coho from its northern range.

Comparison of ipratropium bromide 0.03% with beclomethasone dipropionate in the treatment of perennial rhinitis in children.

OBJECTIVE: To compare the safety and efficacy of ipratropium bromide 0.03% (IB) with beclomethasone dipropionate 0.042% (BDP) in the treatment of perennial rhinitis in children. METHODS: Thirty-three children with nonallergic perennial rhinitis (NAPR) and 113 with allergic perennial rhinitis (APR) were randomly assigned to either IB or BDP for 6 months in a single-blind, multicenter protocol in which the physician was blinded to treatment. At each visit, patients and physicians rated symptom control of rhinorrhea, nasal congestion, and sneezing. Patients also completed quality of life questionnaires at baseline and after 6 months of therapy. RESULTS: Both treatments showed a significant improvement in control of rhinorrhea, congestion, and sneezing compared with baseline over the 6 months of treatment (P < .05). Only for the control of sneezing was BDP consistently better than IB (P < .05). Among the patients given IB, 61% to 73% assessed the control of rhinorrhea as good or excellent on different study visit days, 43% to 60% similarly rated the control of nasal congestion, and 39% to 43% the control of sneezing. The results for BDP were 68% to 78% for the control of rhinorrhea, 55% to 72% for the control of nasal congestion, and 54% to 68% for the control of sneezing. Quality of life assessment documented that both drugs significantly reduced interference with daily activities and disturbance of mood due to rhinorrhea compared with baseline (P < .05). Both treatments were well tolerated with IB causing less nasal bleeding and irritation than BDP. CONCLUSIONS: Ipratropium bromide was safe and effective in controlling rhinorrhea and diminishing the interference by rhinorrhea in school attendance, concentration on school work, and sleep. Ipratropium bromide was as effective as BDP in the control of rhinorrhea and showed a relatively good effect on congestion. Patient and physician assessment favored BDP in the control of sneezing.

Single vs. paired visual stimulation: superposition of early neuromagnetic responses and retinotopy in extrastriate cortex in humans.

Neuromagnetic techniques were used in conjunction with magnetic resonance imaging (MRI) techniques to: (1) localize and characterize cortical sources evoked by visual stimuli presented at different locations in the lower right visual field; (2) examine the superposition of cortical responses by comparing the summation of responses to the presentation of single stimuli with responses to paired stimuli; and (3) examine the spatial resolution of magnetoencephalographic (MEG) techniques by comparing the identified source locations evoked by the presentation of single vs. paired stimuli. Using multi-dipole, non-linear minimization analyses, three sources were localized for each stimulus condition during the initial 80-170 ms poststimulus interval for all subjects. In addition to an occipital source, two extrastriate sources were identified: occipital-parietal and occipital-temporal. Each source evidenced a systematic shift in location associated with changes in stimulus placement parallel to the vertical meridian. To our knowledge, this is the first demonstration of retinotopic organization of extrastriate areas, using non-invasive neuromagnetic techniques. The paired presentation of stimuli reflected superposition of the responses evoked by single stimuli but only for early activity up to 150 ms poststimulus. Undersummation was evident after 150 ms. All sources identified for single stimuli were also identified in the paired-stimulus responses; but at the expense of larger errors for some of the estimated parameters.

Bayesian inference applied to the electromagnetic inverse problem.

We present a new approach to the electromagnetic inverse problem that explicitly addresses the ambiguity associated with its ill-posed character. Rather than calculating a single "best" solution according to some criterion, our approach produces a large number of likely solutions that both fit the data and any prior information that is used. Whereas the range of the different likely results is representative of the ambiguity in the inverse problem even with prior information present, features that are common across a large number of the different solutions can be identified and are associated with a high degree of probability. This approach is implemented and quantified within the formalism of Bayesian inference, which combines prior information with that of measurement in a common framework using a single measure. To demonstrate this approach, a general neural activation model is constructed that includes a variable number of extended regions of activation and can incorporate a great deal of prior information on neural current such as information on location, orientation, strength, and spatial smoothness. Taken together, this activation model and the Bayesian inferential approach yield estimates of the probability distributions for the number, location, and extent of active regions. Both simulated MEG data and data from a visual evoked response experiment are used to demonstrate the capabilities of this approach.

The anticholinergic agent, ipratropium bromide, is useful in the treatment of rhinorrhea associated with perennial allergic rhinitis.

The effects of the new ipratropium bromide nasal spray on rhinorrhea associated with perennial allergic rhinitis were studied in 219 patients over eight weeks in a multicenter, randomized, double-blind trial. The purpose of the study was to determine whether the new spray reduces nasal hypersecretion in allergic patients without causing excessive dryness or other potential cholinergic side effects. The investigators compared two doses of the spray (42 or 84 mcg/nostril t.i.d.) to placebo. Two hundred and nineteen patients were admitted to the study; 176 completed it. Study design included one week of screening to confirm a diagnosis of perennial allergic rhinitis with clinically significant rhinorrhea, one week of single-blind treatment with a placebo consisting of the saline vehicle of the spray, an eight-week double-blind treatment-comparison period, and one week of follow-up without treatment. Both doses of ipratropium bromide nasal spray significantly reduced the hypersecretion associated with PAR, compared with placebo. The two doses of active drug were equally effective. Treatment differences were noticeable during the first week and remained relatively stable during the eight-week treatment period. There was no evidence of nasal rebound after discontinuation of treatment. The incidence of side effects was comparable to placebo. The spray was well-tolerated, and was not associated with any significant adverse events.

Ipratropium bromide nasal spray 0.03% provides additional relief from rhinorrhea when combined with terfenadine in perennial rhinitis patients; a randomized, double-blind, active-controlled trial.

Medical treatment of perennial rhinitis is aimed at providing symptomatic relief of individual symptoms. Multiple agents are administered when no single agent provides complete relief. Studies assessing the benefit/risk of combined therapy are important, especially for newly available agents such as ipratropium bromide nasal spray, a topical anticholinergic agent approved for the treatment of rhinorrhea in allergic and nonallergic perennial rhinitis. The objective was to determine whether the combined use of ipratropium bromide nasal spray 0.03% (42 mcg per nostril) administered three times daily with a nonsedating antihistamine (terfenadine, 60 mg administered twice daily) is safe and provides greater clinical benefit than use of the placebo nasal spray plus terfenadine. Our method was a multicenter, 6-week, double-blind, randomized, active-controlled, crossover trial of 205 patients with perennial rhinitis (114 allergic and 91 nonallergic), 18 to 75 years of age, who had clinically significant rhinorrhea. After a 1-week run-in period, patients were treated for 2 weeks with one of the two treatment regimens, followed by a 1-week washout period, and then were treated for another 2 weeks with the other treatment regimen. Daily diary symptoms scores of rhinorrhea, congestion, and sneezing were obtained, as well as biweekly patient and physician global assessments of treatment effectiveness of each of the nasal symptoms. Ipratropium bromide nasal spray plus terfenadine was more effective than vehicle plus terfenadine in reducing the average severity (38% versus 28%) and duration (46% versus 30%) of rhinorrhea during the 2 weeks of treatment from baseline (p < 0.05). The advantage of ipratropium bromide nasal spray plus terfenadine was evident by the second day of treatment and continued throughout the 2-week treatment period. Of patients who responded more to one treatment than another, 69% responded to ipratropium bromide nasal spray plus terfenadine, compared to 31% to vehicle plus terfenadine (p < 0.05). Both physicians and patients rated control of rhinorrhea and sneezing by ipratropium bromide nasal spray plus terfenadine as superior to vehicle plus terfenadine (p < 0.05). The symptom of congestion was controlled equally well by both treatments. Combined active therapy was well tolerated with no increase in adverse events over that seen previously with ipratropium bromide nasal spray alone. The combination of ipratropium bromide nasal spray with terfenadine is more effective than vehicle plus terfenadine for the treatment of rhinorrhea, and does not result in a potentiation of adverse drug reactions.

Ipratropium nasal spray in children with perennial rhinitis.

OBJECTIVE: To compare the efficacy and safety of ipratropium nasal spray and placebo administered twice each day for 4 weeks in pediatric patients with perennial rhinitis who had rhinorrhea as a major complaint. METHODS: This was a multicenter, double-blind, parallel group study. Patients aged 6 to 18 years with symptoms of perennial nonallergic (PNAR) or perennial allergic rhinitis (PAR) were randomized to receive ipratropium (42 micrograms per nostril) or placebo nasal spray, double-blind, twice each day for 4 weeks. Efficacy was evaluated by nasal symptoms, especially anterior rhinorrhea, and quality of life. Previous caregivers for rhinitis and medications used in the past were also evaluated. RESULTS: A total of 202 patients were empanelled, 162 with PAR, 40 with PNAR; of these 151 with mild-severe rhinorrhea were evaluated for efficacy. Treatment with ipratropium reduced symptoms of rhinorrhea primarily in patients with PNAR. In patients with PAR this response was less pronounced, and was seen as a modest decrease in the severity of rhinorrhea noted in the first 2 weeks of treatment. Quality of life assessments confirmed that rhinorrhea was bothersome to these pediatric patients, and suggested that treatment with ipratropium nasal spray was associated with an improvement, especially in the patients with PNAR. There were few adverse events; these were similar in the two treatment groups. CONCLUSIONS: Ipratropium nasal spray 0.03% administered at a dose of 42 micrograms/nostril bid is a safe and effective new therapy for control of anterior rhinorrhea in pediatric patients with PNAR. Twice daily administration is adequate for patients with PNAR, but patients with PAR might benefit from more frequent administration (e.g., tid).

Nonlinear analysis of biological systems using short M-sequences and sparse-stimulation techniques.

The m-sequence pseudorandom signal has been shown to be a more effective probing signal than traditional Gaussian white noise for studying nonlinear biological systems using cross-correlation techniques. The effectiveness is evidenced by the high signal-to-noise (S/N) ratio and speed of data acquisition. However, the "anomalies" that occur in the estimations of the cross-correlations represent an obstacle that prevents m-sequences from being more widely used for studying nonlinear systems. The sparse-stimulation method for measuring system kernels can help alleviate estimation errors caused by anomalies. In this paper, a "padded sparse-stimulation" method is evaluated, a modification of the "inserted sparse-stimulation" technique introduced by Sutter, along with a short m-sequence as a probing signal. Computer simulations show that both the "padded" and "inserted" methods can effectively eliminate the anomalies in the calculation of the second-order kernel, even when short m-sequences were used (length of 1023 for a binary m-sequence, and 728 for a ternary m-sequence). Preliminary experimental data from neuromagnetic studies of the human visual system are also presented, demonstrating that the system kernels can be measured with high signal-to-noise (S/N) ratios using short m-sequences.

Retinotopic organization of human visual cortex: departures from the classical model.

Retinotopic mapping strategies similar to those used for invasive electrophysiological studies to identify multiple visual areas in monkeys have been adapted for noninvasive studies in humans, using magnetic recordings of brain activity in conjunction with anatomical magnetic resonance imaging. The retinotopic organization of the primary visual area (V1) in the left hemisphere of human subjects was examined by presenting a small patterned stimuli near the vertical and horizontal meridians in the lower right visual field. In contrast with the classical model of V1 retinotopy, our results suggest that the representation of the horizontal meridian does not necessarily correspond in a one-to-one manner with the base of the calcarine fissure and that some lower field stimuli can activate regions in the lower bank of the fissure. The results also indicate significant individual variability in the details of how V1 maps around the calcarine fissure.