A proof of concept reinforcement learning based tool for non parametric population pharmacokinetics workflow optimization.

The building of population pharmacokinetic models can be described as an iterative process in which given a model and a dataset, the pharmacometrician introduces some changes to the model specification, then perform an evaluation and based on the predictions obtained performs further optimization. This process (perform an action, witness a result, optimize your knowledge) is a perfect scenario for the implementation of Reinforcement Learning algorithms. In this paper we present the conceptual background and a implementation of one of those algorithms aiming to show pharmacometricians how to automate (to a certain point) the iterative model building process.We present the selected discretization for the action and the state space. SARSA (State-Action-Reward-State-Action) was selected as the RL algorithm to use, configured with a window of 1000 episodes with and a limit of 30 actions per episode. SARSA was configured to control an interface to the Non-Parametric Optimal Design algorithm, that was actually performing the parameter optimization.The Reinforcement Learning (RL) based agent managed to obtain the same likelihood and number of support points, with a distribution similar to the reported in the original paper. The total amount of time used by the train the agent was 5.5 h although we think this time can be further improved. It is possible to automatically find the structural model that maximizes the final likelihood for an specific pharmacokinetic dataset by using RL algorithm. The framework provided could allow the integration of even more actions i.e: add/remove covariates, non-linear compartments or the execution of secondary analysis. Many limitations were found while performing this study but we hope to address them all in future studies.

Developing New Drugs for Mycobacterium tuberculosis Therapy: What Information Do We Get from Preclinical Animal Models?

Preclinical animal models of infection are employed to develop new agents but also to screen among molecules to rank them. There are often major differences between human pharmacokinetic (PK) profiles and those developed by animal models of infection, and these may lead to substantial differences in efficacy relative to that seen in humans. Linezolid is a repurposed agent employed to great effect for therapy of Mycobacterium tuberculosis In this study, we used the hollow-fiber infection model (HFIM) to evaluate the impact of different pharmacokinetic profiles of mice and nonhuman primates (NHP) versus humans on bacterial cell kill as well as resistance suppression. We examined both plasma and epithelial lining fluid (ELF) profiles. We examined simulated exposures equivalent to 600 mg and 900 mg daily of linezolid in humans. For both plasma and ELF exposures, the murine PK profile provided estimates of effect that were biased low relative to human and NHP PK profiles. Mathematical modeling identified a linkage between minimum concentrations (Cmin) and bacterial kill and peak concentrations (Cpeak) and resistance suppression, with the latter being supported by a prospective validation study. Finding new agents with novel mechanisms of action against M. tuberculosis is difficult. It would be a tragedy to discard a new agent because of a biased estimate of effect in a preclinical animal system. The HFIM provides a system to benchmark evaluation of new compounds in preclinical animal model systems against human PK effects (species scale-up estimates of PK), to safeguard against unwarranted rejection of promising new agents.

The Combination of Fosfomycin plus Meropenem Is Synergistic for Pseudomonas aeruginosa PAO1 in a Hollow-Fiber Infection Model.

Treating high-density bacterial infections is a challenging clinical problem. We have a paucity of new agents that can address this problem. Pseudomonas aeruginosa is a particularly difficult pathogen to treat effectively because of the plethora of resistance mechanisms it carries. Fosfomycin is an agent discovered circa 40 years ago. Recently, it has been resurrected in the United States and studied for intravenous therapy. We hypothesized that, to maximize its utility, it would require combination chemotherapy when used in a clinical circumstance in high-bacterial-burden infections. We chose to examine the combination of meropenem plus fosfomycin. These agents were studied in the hollow-fiber infection model. We utilized a fully factorial study design, looking at 2 doses of meropenem alone (1 and 2 g 8-hourly) and two doses of fosfomycin alone (6 and 8 g 8-hourly), as well as all possible combinations plus a no-treatment control. We used a high-dimensional model of 5 inhomogeneous differential equations with 5 system outputs to analyze all data simultaneously. Combination therapy outperformed all monotherapy regimens, with all combinations driving >6 log10 CFU/ml of bacterial killing. Combination therapy was able to counterselect resistance emergence (meropenem mutants being killed by the combination, as well as fosfomycin mutants being killed by the combination) in all regimens studied. The analysis demonstrated that the combination was significantly synergistic for bacterial cell killing and resistance suppression. Meropenem plus fosfomycin is a promising combination for therapy of high-burden Pseudomonas aeruginosa infections and requires further study.

Secreted factor R-Spondin 2 is involved in refinement of patterning of the mammalian cochlea.

BACKGROUND: In the cochlea, patterning of the organ of Corti is tightly regulated to produce a single row of sound-detecting inner hair cells and three rows of outer hair cells, which amplify and refine the signal. The recently identified R-Spondin family of signaling molecules usually act as co-activators of Wnt signaling; it is thought that they regulate turnover of Wnt receptors at the membrane. We sought to test whether R-Spondins function in the developing cochlea. RESULTS: Expression analysis of all four members of the R-Spondin family showed that only R-Spondin2 (Rspo2) is expressed in the cochlea during development of the sensory epithelium. Examination of an Rspo2(-/-) mouse showed that loss of Rspo2 results in an additional single row of outer hair cells and disruption of peripheral innervation pattern. Addition of Rspo2 recombinant protein to organotypic cochlear cultures resulted in a small but significant decrease in the number of outer hair cells. CONCLUSIONS: Rspo2 is required to limit the number of outer hair cells to three rows and for optimal arrangement of peripheral nerve fibers. The Rspo2 gain- and loss-of-function studies show that in the ear, Rspo2 function is not consistent with its assigned role as a Wnt potentiator.

Role of Toll-like receptor 4 in hyperoxia-induced lung inflammation in mice.

OBJECTIVE: Prolonged exposure to hyperoxia causes lung inflammation, but the role of Toll-like receptor 4 (TLR4) in hyperoxia-induced signal transduction remains unclear. MATERIAL OR SUBJECTS: We evaluated neutrophil accumulation, signal transduction and cytokine production during hyperoxia, comparing TLR4 mutant (C3H/HeJ) and wild type (C3H/HeN) mice. METHODS: The mice were exposed to 80% oxygen in a hyperoxic chamber for 0 (control), 48, or 96 h. After the exposure, bronchoalveolar lavage (BAL) was performed for differential cell counting and cytokine measurement. In lung homogenate, activation of NF-kappaB and STAT1 was also examined. RESULTS: In C3H/HeJ mice, hyperoxia-induced neutrophil accumulation in BAL fluid was significantly decreased compared with C3H/HeN. Hyperoxia for 96 h caused NF-kappaB translocation in C3H/HeN mice, which was significantly attenuated in C3H/HeJ mice (p < 0.05). In contrast, STAT1 activation occurred as early as after 48 h of oxygen exposure, which did not differ between the two strains. The levels of TNF-alpha, IL-6, and KC in BAL fluid were increased after oxygen exposure, which was suppressed by the lack of TLR4 signaling. CONCLUSION: These results suggest that TLR4-dependent NF-kB activation may be an important process of the upregulation of proinflammatory mediators and subsequent neutrophil accumulation into the lung during hyperoxia.

The distribution of plantar pressures in American Indians with diabetes mellitus.

The primary purpose of this study was to determine the magnitude and duration of plantar pressures acting on the feet of American Indians with diabetes mellitus. A secondary purpose was to determine whether differences in the range of motion of the ankle and first metatarsophalangeal joints existed between American Indians with and without diabetes. Three groups of American Indian subjects were tested: a control group (n = 20); a group with diabetes but no peripheral neuropathy (n = 24); and a group with diabetes and peripheral neuropathy (n = 21). A floor-mounted pressure sensor platform was used to collect plantar pressure data while subjects walked barefoot. The results indicated that American Indians with diabetes have 1) a pattern of peak plantar pressure similar to patterns previously reported for non-American Indians with diabetes and 2) a reduction in ankle and first metatarsophalangeal joint range of motion in comparison with nondiabetic American Indians.

Structural basis of the interaction between IgG and Fcgamma receptors.

The binding of multivalent antigen-antibody complexes to receptors for the Fc portion of IgG (FcgammaR) induces the clustering of the FcgammaR and triggers cell activation leading to defence reactions against pathogens. The Fc portion of IgG consists of two identical polypeptide chains which are related to each other by a 2-fold axis and are folded in two structural domains, the C(H)2 domain, near the flexible hinge region of the IgG molecule, and the C(H)3 domain. We studied the interaction in solution between the Fc fragment of mouse IgG2b and the extracellular region of mouse FcgammaRII. We find that one Fc molecule binds one FcgammaRII molecule only. Using NMR spectroscopy, we show that FcgammaRII binds to a negatively charged area of the C(H)2 domain, corresponding to the lower hinge region, and that the binding of FcgammaRII onto one of the two symmetrically related sites on the Fc induces a conformational change in the other site. We therefore propose a model that explains why IgG molecules are unable to trigger FcgammaR-mediated cellular responses spontaneously in the absence of crosslinking by multivalent antigens.

Essential roles of noise in neural coding and in studies of neural coding.

We present examples of results from our studies of auditory primary afferent nerve fibers and populations of such fibers in the frog and gerbil. We take advantage of the natural dithering effect of internal noise, where it is sufficient, to construct highly predictive descriptive models (based on the Wiener series with kernels derived from white-noise analysis). Where the internal noise is insufficient, we enhance dithering by applying external acoustic noise together with our stimuli. Using acoustic noise as a background sound, orthogonal to the stimulus waveform, we show that under some circumstances such background sound can enhance the ability of individual fibers and populations of fibers to encode the stimulus waveform.

Predicting the temporal responses of non-phase-locking bullfrog auditory units to complex acoustic waveforms.

Axons from the basilar papilla of the American bullfrog (Rana catesbeiana) do not phase lock to stimuli within an octave of their best frequencies. Nevertheless, they show consistent temporal patterns of instantaneous spike rate (as reflected in peristimulus time histograms) in response to repeated stimuli in that frequency range. We show that the second-order Wiener kernels for these axons, derived from the cross-correlation of continuous (non-repeating), broad-band noise stimulus with the spike train produced in response to that stimulus, can predict with considerable precision the temporal pattern of instantaneous spike rate in response to a novel, complex acoustic waveform (a repeated, 100-ms segment of noise, band-limited to cover the single octaves above and below best frequency). Furthermore, we show that most of this predictive power is retained when the second-order Wiener kernel is reduced to the highest-ranking pair of singular vectors derived from singular-value decomposition, that the retained pair of vectors corresponds to a single auditory filter followed by an envelope-detection process, and that the auditory filter itself predicts the characteristic frequency (CF) of the axon and the shape of the frequency-threshold tuning curve in the vicinity of CF.

N-glycan structures of a recombinant mouse soluble Fcgamma receptor II.

N-glycans of a recombinant mouse soluble Fcgamma receptor II (sFcgammaRII) expressed in baby hamster kidney cells were released from glycopeptides by digestion with glycoamidase A (from sweet almond), and the reducing ends of the oligosaccharides were reductively aminated with 2-aminopyridine. The derivatized N-glycans were separated and structurally identified by a three-dimensional high-performance liquid chromatography (HPLC) mapping technique on three kinds of HPLC columns [Takahashi, et al. (1995) Anal. Biochem. 226:139-46]. Eighteen different major N-glycan structures were identified, of which six were neutral (45%), five mono-sialyl (49%), one di-sialyl (4.6%), five tri-sialyl (1.1%), and one tetra-sialyl (0.3%). All N-glycan structures determined were complex type with fucosylation at the N-acetylglucosamine residue of the reducing end, and N-acetylneuraminic acid, when present, was alpha-(2,3)-linked. The existence of a unique structure containing both N-acetylgalactosamine and alpha-(2,3)-N-acetylneuraminic acid residues at the reducing ends, as below, was confirmed by MALDI-TOF mass spectrometry. Carbohydrate sequence [see text]

Amodal completion as another perception of color-spreading stimuli.

We made a solid three-dimensional object of the Redies-Spillmann figure and found two kinds of completely different phenomena. First, transparent color-spreading was observed in the empty space around the object. Second, another perceptual organization occurred: observers perceived a cross as a cross-shaped slit through which to see, and then they perceived spreading color disappear entirely. They reported an apparent opaque occluding surface which was localized at the same depth as the slit but was in fact the background. They also reported a colored circle which was mostly occluded by the surface with a cross-shaped slit. We interpreted the circle as being amodally completed in the sense described by Kanizsa in 1955. Even when the figure was drawn on a piece of paper, we observed these two perceptions. We examined whether other stimuli causing neon color-spreading lead to reports of the perception for the Redies-Spillmann figure and found that all the stimuli we examined led to reports of the same kind of perception. Interestingly, the shape of color-spreading was the same as that of the amodal completion.

Time course of transmitter release calculated from simulations of a calcium diffusion model.

A three-dimensional presynaptic calcium diffusion model developed to account for characteristics of transmitter release was modified to provide for binding of calcium to a receptor and subsequent triggering of exocytosis. When low affinity (20 microM) and rapid kinetics were assumed for the calcium receptor triggering exocytosis, and stimulus parameters were selected to match those of experiments, the simulations predicted a virtual invariance of the time course of transmitter release to paired stimulation, stimulation with pulses of different amplitude, and stimulation in different calcium solutions. The large temperature sensitivity of experimental release time course was explained by a temperature sensitivity of the model's final rate limiting exocytotic process. Inclusion of calcium tail currents and a saturable buffer with finite binding kinetics resulted in high peak calcium transients near release sites, exceeding 100 microM. Models with a single class of calcium binding site to the secretory trigger molecule failed to produce sufficient synaptic facilitation under this condition. When at least one calcium ion binds to a different site having higher affinity and slow kinetics, facilitation again reaches levels similar to those seen experimentally. It is possible that the neurosecretory trigger molecule reacts with calcium at more than one class of binding site.

[The effect of lithium carbonate against leukopenia during systemic chemotherapy in patients with small cell carcinoma of the lung].

To investigate whether lithium carbonate ameliorates the leukopenia and infectious complication that accompany systemic chemotherapy, we studied 19 patients with small cell carcinoma of the lung receiving combination chemotherapy. Eight patients received systemic chemotherapy and lithium carbonate and 11 patients received systemic chemotherapy alone. The mean leukocyte count nadir during chemotherapy was significantly higher in the patients of the lithium group than in the patients of the control group (p less than 0.05). Percentage of infectious complication related to leukopenia was lower in the lithium group than in the control group, although there was no significant difference between these two groups. There was almost no significant side effect except for liver dysfunction in one patient. We therefore believe that lithium carbonate is an effective and safe drug against leukopenia during cytotoxic chemotherapy.