Template independent component analysis with spatial priors for accurate subject-level brain network estimation and inference.

Independent component analysis is commonly applied to functional magnetic resonance imaging (fMRI) data to extract independent components (ICs) representing functional brain networks. While ICA produces reliable group-level estimates, single-subject ICA often produces noisy results. Template ICA is a hierarchical ICA model using empirical population priors to produce more reliable subject-level estimates. However, this and other hierarchical ICA models assume unrealistically that subject effects are spatially independent. Here, we propose spatial template ICA (stICA), which incorporates spatial priors into the template ICA framework for greater estimation efficiency. Additionally, the joint posterior distribution can be used to identify brain regions engaged in each network using an excursions set approach. By leveraging spatial dependencies and avoiding massive multiple comparisons, stICA has high power to detect true effects. We derive an efficient expectation-maximization algorithm to obtain maximum likelihood estimates of the model parameters and posterior moments of the latent fields. Based on analysis of simulated data and fMRI data from the Human Connectome Project, we find that stICA produces estimates that are more accurate and reliable than benchmark approaches, and identifies larger and more reliable areas of engagement. The algorithm is computationally tractable, achieving convergence within 12 hours for whole-cortex fMRI analysis.

Spatial Bayesian GLM on the cortical surface produces reliable task activations in individuals and groups.

The general linear model (GLM) is a widely popular and convenient tool for estimating the functional brain response and identifying areas of significant activation during a task or stimulus. However, the classical GLM is based on a massive univariate approach that does not explicitly leverage the similarity of activation patterns among neighboring brain locations. As a result, it tends to produce noisy estimates and be underpowered to detect significant activations, particularly in individual subjects and small groups. A recently proposed alternative, a cortical surface-based spatial Bayesian GLM, leverages spatial dependencies among neighboring cortical vertices to produce more accurate estimates and areas of functional activation. The spatial Bayesian GLM can be applied to individual and group-level analysis. In this study, we assess the reliability and power of individual and group-average measures of task activation produced via the surface-based spatial Bayesian GLM. We analyze motor task data from 45 subjects in the Human Connectome Project (HCP) and HCP Retest datasets. We also extend the model to multi-run analysis and employ subject-specific cortical surfaces rather than surfaces inflated to a sphere for more accurate distance-based modeling. Results show that the surface-based spatial Bayesian GLM produces highly reliable activations in individual subjects and is powerful enough to detect trait-like functional topologies. Additionally, spatial Bayesian modeling enhances reliability of group-level analysis even in moderately sized samples (n=45). Notably, the power of the spatial Bayesian GLM to detect activations above a scientifically meaningful effect size is nearly invariant to sample size, exhibiting high power even in small samples (n=10). The spatial Bayesian GLM is computationally efficient in individuals and groups and is convenient to implement with the open-source BayesfMRI R package.

New Characterization Measures of Pore Shape and Connectivity Applied to Coatings used for Controlled Drug Release.

Pore geometry characterization-methods are important tools for understanding how pore structure influences properties such as transport through a porous material. Bottlenecks can have a large influence on transport and related properties. However, existing methods only catch certain types of bottleneck effects caused by variations in pore size. We here introduce a new measure, geodesic channel strength, which captures a different type of bottleneck effect caused by many paths coinciding in the same pore. We further develop new variants of pore size measures and propose a new way of visualizing 3-D characterization results using layered images. The new measures together with existing measures were used to characterize and visualize properties of 3-D FIB-SEM images of three leached ethyl-cellulose/hydroxypropyl-cellulose films. All films were shown to be anisotropic, and the strongest anisotropy was found in the film with lowest porosity. This film had very tortuous paths and strong geodesic channel-bottlenecks, while the paths through the other two films were relatively straight with well-connected pore networks. The geodesic channel strength was shown to give important new visual and quantitative insights about connectivity, and the new pore size measures provided useful information about anisotropies and inhomogeneities in the pore structures. The methods have been implemented in the freely available software MIST.

A Bayesian General Linear Modeling Approach to Cortical Surface fMRI Data Analysis.

Cortical surface fMRI (cs-fMRI) has recently grown in popularity versus traditional volumetric fMRI. In addition to offering better whole-brain visualization, dimension reduction, removal of extraneous tissue types, and improved alignment of cortical areas across subjects, it is also more compatible with common assumptions of Bayesian spatial models. However, as no spatial Bayesian model has been proposed for cs-fMRI data, most analyses continue to employ the classical general linear model (GLM), a "massive univariate" approach. Here, we propose a spatial Bayesian GLM for cs-fMRI, which employs a class of sophisticated spatial processes to model latent activation fields. We make several advances compared with existing spatial Bayesian models for volumetric fMRI. First, we use integrated nested Laplacian approximations (INLA), a highly accurate and efficient Bayesian computation technique, rather than variational Bayes (VB). To identify regions of activation, we utilize an excursions set method based on the joint posterior distribution of the latent fields, rather than the marginal distribution at each location. Finally, we propose the first multi-subject spatial Bayesian modeling approach, which addresses a major gap in the existing literature. The methods are very computationally advantageous and are validated through simulation studies and two task fMRI studies from the Human Connectome Project.

Inhibition of IRF5 cellular activity with cell-penetrating peptides that target homodimerization.

The transcription factor interferon regulatory factor 5 (IRF5) plays essential roles in pathogen-induced immunity downstream of Toll-, nucleotide-binding oligomerization domain-, and retinoic acid-inducible gene I-like receptors and is an autoimmune susceptibility gene. Normally, inactive in the cytoplasm, upon stimulation, IRF5 undergoes posttranslational modification(s), homodimerization, and nuclear translocation, where dimers mediate proinflammatory gene transcription. Here, we report the rational design of cell-penetrating peptides (CPPs) that disrupt IRF5 homodimerization. Biochemical and imaging analysis shows that IRF5-CPPs are cell permeable, noncytotoxic, and directly bind to endogenous IRF5. IRF5-CPPs were selective and afforded cell type- and species-specific inhibition. In plasmacytoid dendritic cells, inhibition of IRF5-mediated interferon-α production corresponded to a dose-dependent reduction in nuclear phosphorylated IRF5 [p(Ser462)IRF5], with no effect on pIRF5 levels. These data support that IRF5-CPPs function downstream of phosphorylation. Together, data support the utility of IRF5-CPPs as novel tools to probe IRF5 activation and function in disease.

Ulcerative, granulomatous glossitis and enteritis caused by Rhodococcus equi in a heifer.

Rhodococcus equi infection in horses is common and is characterized by pyogranulomatous pneumonia and ulcerative enterocolitis. R. equi clinical disease in cattle, however, is rare and typically manifests as granulomatous lymphadenitis discovered in the abattoir. A 19-mo-old female Santa Gertrudis had a history of intermittent inappetence and weight loss for a 3-mo period before euthanasia. Gross and histologic examination revealed severe, chronic, ulcerative, and granulomatous inflammation in the tongue, pharynx, and small intestine. Also, the heifer had severe, granulomatous pharyngeal and mesenteric lymphadenitis. Bacterial cultures from the ileum, tongue, and liver yielded numerous-to-moderate numbers of R. equi. PCR analysis of the isolate detected the linear virulence plasmid vapN, which is often identified in bovine isolates (traA- and vapN-positive). The bacteria also lack the circular plasmids vapA and vapB that are associated with virulence in horses and swine, respectively. We report herein an atypical and unusual clinical presentation of R. equi infection in cattle, which has zoonotic potential.

Fast Bayesian whole-brain fMRI analysis with spatial 3D priors.

Spatial whole-brain Bayesian modeling of task-related functional magnetic resonance imaging (fMRI) is a great computational challenge. Most of the currently proposed methods therefore do inference in subregions of the brain separately or do approximate inference without comparison to the true posterior distribution. A popular such method, which is now the standard method for Bayesian single subject analysis in the SPM software, is introduced in Penny et al. (2005b). The method processes the data slice-by-slice and uses an approximate variational Bayes (VB) estimation algorithm that enforces posterior independence between activity coefficients in different voxels. We introduce a fast and practical Markov chain Monte Carlo (MCMC) scheme for exact inference in the same model, both slice-wise and for the whole brain using a 3D prior on activity coefficients. The algorithm exploits sparsity and uses modern techniques for efficient sampling from high-dimensional Gaussian distributions, leading to speed-ups without which MCMC would not be a practical option. Using MCMC, we are for the first time able to evaluate the approximate VB posterior against the exact MCMC posterior, and show that VB can lead to spurious activation. In addition, we develop an improved VB method that drops the assumption of independent voxels a posteriori. This algorithm is shown to be much faster than both MCMC and the original VB for large datasets, with negligible error compared to the MCMC posterior.

Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors.

Tankyrase activity has been linked to the regulation of intracellular axin levels, which have been shown to be crucial for the Wnt pathway. Deregulated Wnt signaling is important for the genesis of many diseases including cancer. We describe herein the discovery and development of a new series of tankyrase inhibitors. These pyranopyridones are highly active in various cell-based assays. A fragment/structure based optimization strategy led to a compound with good pharmacokinetic properties that is suitable for in vivo studies and further development.

Design and synthesis of 2-N-substituted indazolone derivatives as non-carboxylic acid glycogen synthase activators.

Glycogen synthase (GS) catalyzes the transfer of glucose residues from UDP-glucose to a glycogen polymer chain, a critical step for glucose storage. Patients with type 2 diabetes normally exhibit low glycogen levels and decreased muscle glucose uptake is the major defect in whole body glucose disposal. Therefore, activating GS may provide a potential approach for the treatment of type 2 diabetes. In order to identify non-carboxylic acids GS activators, we designed and synthesized a series of 2-N-alkyl- and 2-N-aryl-indazolone derivatives and studied their activity in activating human GS.

Discovery and optimization of 2-phenyloxazole derivatives as diacylglycerol acyltransferase-1 inhibitors.

In a discovery effort to find safe and effective DGAT-1 inhibitors, we have identified 2-phenyloxazole 4-carboxamide 1 as a conformationally constrained analog of a hydrazide hit, which was previously identified from high-throughput screening. Further optimization of this series has led to chemically more stable 2-phenyloxazole-based DGAT-1 inhibitor 25 with improved solubility, cell-based activity, and pharmacokinetic properties. Compound 25 also demonstrated in vivo efficacy in a diet-induced obesity (DIO) rat model.

Discovery of 1-arylcarbonyl-6,7-dimethoxyisoquinoline derivatives as glutamine fructose-6-phosphate amidotransferase (GFAT) inhibitors.

Through high throughput screening and subsequent hit identification and optimization, we synthesized a series of 1-arylcarbonyl-6,7-dimethoxyisoquinoline derivatives as the first reported potent and reversible GFAT inhibitors. SAR studies of this class of compounds indicated significant impact on GFAT inhibition potency by substitutions on the A-ring and C-ring. The ketone group was found to be necessary for high potency. Compound 28 (RO0509347) demonstrated potent GFAT inhibition (IC(50)=1µM) with a desirable pharmacokinetic profile in rats, and showed significant efficacy in reducing the glucose excursion in an OGTT test in ob/ob mice.

Discovery of orally active carboxylic acid derivatives of 2-phenyl-5-trifluoromethyloxazole-4-carboxamide as potent diacylglycerol acyltransferase-1 inhibitors for the potential treatment of obesity and diabetes.

Diacylglycerol acyltransferase-1 (DGAT-1) is the enzyme that catalyzes the final and committed step of triglyceride formation, namely, the acylation of diacylglycerol with acyl coenzyme A. DGAT-1 deficient mice demonstrate resistance to weight gain on high fat diet, improved insulin sensitivity, and reduced liver triglyceride content. Inhibition of DGAT-1 thus represents a potential novel approach for the treatment of obesity, dyslipidemia, and metabolic syndrome. In this communication, we report the identification of the lead structure 6 and our lead optimization efforts culminating in the discovery of potent, selective, and orally efficacious carboxylic acid derivatives of 2-phenyl-5-trifluoromethyloxazole-4-carboxamides. In particular, compound 29 (DGAT-1 enzyme assay, IC(50) = 57 nM; CHO-K1 cell triglyceride formation assay, EC(50) = 0.5 µM) demonstrated dose dependent inhibition of weight gain in diet induced obese (DIO) rats (0.3, 1, and 3 mg/kg, p.o., qd) during a 21-day efficacy study. Furthermore, compound 29 demonstrated improved glucose tolerance determined by an oral glucose tolerance test (OGTT).

Accidental intra-auricular artery injection of ceftiofur in two beef steers.

Two beef steers accidentally injected into a branch of the auricular artery with an oil-based formulation of ceftiofur died within 5 minutes of injection. Notable pathologic findings included distention and obstruction of cerebral and cerebellar arteries by a whitish tan material and hemorrhages within meningeal spaces, the choroid plexus, cerebrum, and cerebellum. Lipid material was identified within cerebral blood vessels in frozen sections stained with oil red O. This report describes an unusual case of brain ischemia in beef cattle.

Classification of Actinobacillus spp isolates from horses involved in mare reproductive loss syndrome.

OBJECTIVE: To identify Actinobacillus spp isolates recovered from fetuses and pericardial fluid from horses affected with mare reproductive loss syndrome (MRLS) and determine whether these bacterial species are the same as those isolated from clinically normal horses. SAMPLE POPULATION: Isolates of actinobacilli recovered from 18 horses with pericarditis and 109 fetuses aborted by mares affected by MRLS. Procedures-Actinobacillus spp isolates were identified to the level of species or subspecies by use of conventional phenotypic tests and biochemical and enzyme test kits. The 16S rRNA gene from selected isolates was amplified, purified, and sequenced. Sequence data were compared with sequence data for actinobacilli in GenBank. RESULTS: Of the 109 isolates obtained from fetuses, 14 were Actinobacillus equuli subsp equuli, 65 were A equuli subsp haemolyticus, 28 were Bisgaard taxon 10-like bacterium, and 2 were Actinobacillus genomospecies 1. Of the 18 isolates from horses with pericarditis, 4 were A equuli subsp equuli, 13 were A equuli subsp haemolyticus, and 1 was Bisgaard taxon 10-like bacterium. Comparisons with published data and GenBank data revealed that the isolates recovered from horses with MRLS were the same as those isolated from the oral cavity or alimentary tract of healthy horses. CONCLUSIONS AND CLINICAL RELEVANCE: Actinobacillus spp isolates recovered from fetuses and pericardial fluid samples of horses affected by MRLS in 2001 to 2003 were identical to Actinobacillus spp found in the oral cavity and alimentary tracts of healthy horses.

Microbiologic and pathologic findings in an epidemic of equine pericarditis.

During the spring and summer of 2001 and in association with the mare reproductive loss syndrome, 22 terminal and 12 clinical cases of equine pericarditis were diagnosed in central Kentucky. Actinobacillus species were the principal isolates from 8 of 10 nontreated, terminally affected and 3 of 10 clinically affected horses. Enterococcus faecalis and Streptococcus zooepidemicus were cultured from the remaining 2 nontreated terminal cases. No viruses were isolated in tissue culture. Nucleic acid of equine herpesvirus-2 was detected in pericardial and tracheal wash fluids of 3 and 1 individuals, respectively. Microscopic alterations in sections of heart and parietal pericardium were consistent with chronic fibrinous bacterial pericarditis. This report confirms a significant role of Actinobacillus species in equine pericarditis and describes an epidemic of this infrequently observed syndrome in the horse.

Equine abortion and premature birth associated with Cellulosimicrobium cellulans infection.

During the 2002 and 2003 foaling seasons, Cellulosimicrobium (Cellumonas) cellulans (formerly Oerskovia xanthineolytica) was the principal microorganism isolated from fetal tissues or placentas from cases of equine abortion, premature birth, and term pregnancies. Significant pathologic findings included chronic placentitis and pyogranulomatous pneumonia. In addition, microscopic and macroscopic alterations in the allantochorion from 4 of 7 cases of placentitis were similar to those caused by Crossiella equi and other nocardioform bacteria. This report confirms a causative role of C. cellulans infection in equine abortion.

Meningeal worm in a reintroduced elk population in Kentucky.

Meningeal worm (Parelaphostrongylus tenuis) has been implicated in the failure of several elk (Cervus elaphus) restoration attempts in the eastern United States. However, limited post-release monitoring and a paucity of published literature prevents a clear understanding of this parasite's role in past failures. During winters of 1997-2001, the Kentucky Department of Fish and Wildlife Resources translocated 1,044 elk from western states to eastern Kentucky (USA) in an effort to restore a free-ranging population. We monitored 521 radio-collared elk over 4 yr to determine the impact meningeal worm had on population establishment. Thirty (23%) of 129 non-capture related mortalities were attributed to meningeal worm. Twenty-two (73%) of these meningeal worm-caused mortalities were animals < 3 yr old. If younger elk born in Kentucky suffer higher mortality rates than older translocated elk, the population growth observed during the initial years of restoration may be temporary. Additional research is necessary to determine the influence meningeal worm will have on elk population growth in Kentucky.

Oxazole- and imidazole-based Ser-Leu dipeptide mimetics in potent inhibitors of antigen presentation by MHC class II DR molecules.

Imidazole and oxazole derivatives 1 to 4 were designed and prepared as dipeptide mimetics to replace the Ser-Leu dipeptide sequence of Ro-25-9980 (Ac-(Cha)-RAMA-S-L-NH2), a peptidic inhibitor of antigen binding to major histocompatibility complex (MHC) class II DR molecules linked to rheumatoid arthritis (RA). The most potent analog in binding assays (IC50 = 30 nM in DRB1*0401 binding; 1.6 times as potent as Ro 25-9980) was 16, Ac-(Cha)RAMA-(S)S-psi(oxazole)-L-NH2. The SAR of peptide hybrids 10 to 24, prepared by incorporating the dipeptide mimetics 1 to 4 is discussed. Of these hybrids, 23 and 24, analogs that incorporated the imidazole and oxazole mimetics as well as optimized variants at positions 3 to 5, were found to have 70 to 80 nM binding affinity comparable to the parent peptide in DRB 1*0401 binding and were also active in DRB1*0101 binding, while being resistant to proteolysis by cathepsin B. Both of these compounds showed inhibitory activity in an antigen-stimulated T-cell proliferation assay, indicating their potential to suppress autoimmune responses and as leads for therapeutic agents to treat RA.

trans,anti,trans-Tetra(spirotetrahydrofuranyl)cyclohexane-1,2-dione. Stereocontrolled Synthesis and Definition of Its Susceptibility to Photoisomerization.

The title alpha-diketone (18) has been synthesized in stereocontrolled fashion. The ability to introduce the four contiguous spirocyclic ether oxygens in extended trans fashion rests on the ability of the Normant reagent (ClMgCH(2)CH(2)CH(2)OMgCl) to engage in chelation control during 1,2-addition to an alpha-oxy substituted cyclohexanone. The successful pathway is dependent on the ability of osmium tetraoxide to add (slowly) across the double bond of the cyclohexene precursor. The highly substituted 1,2-cyclohexanedione is quite sensitive to light and rearranges by means of an interesting photoisomerization process to a laterally fused pyran system. A likely mechanistic pathway for this intramolecular isomerization is presented.