Drug repositioning in SLE: crowd-sourcing, literature-mining and Big Data analysis.

Lupus patients are in need of modern drugs to treat specific manifestations of their disease effectively and safely. In the past half century, only one new treatment has been approved by the US Food and Drug Administration (FDA) for systemic lupus erythematosus (SLE). In 2014-2015, the FDA approved 71 new drugs, only one of which targeted a rheumatic disease and none of which was approved for use in SLE. Repositioning/repurposing drugs approved for other diseases using multiple approaches is one possible means to find new treatment options for lupus patients. "Big Data" analysis approaches this challenge from an unbiased standpoint whereas literature mining and crowd sourcing for candidates assessed by the CoLTs (Combined Lupus Treatment Scoring) system provide a hypothesis-based approach to rank potential therapeutic candidates for possible clinical application. Both approaches mitigate risk since the candidates assessed have largely been extensively tested in clinical trials for other indications. The usefulness of a multi-pronged approach to drug repositioning in lupus is highlighted by orthogonal confirmation of hypothesis-based drug repositioning predictions by "Big Data" analysis of differentially expressed genes from lupus patient samples. The goal is to identify novel therapies that have the potential to affect disease processes specifically. Involvement of SLE patients and the scientists that study this disease in thinking about new drugs that may be effective in lupus though crowd-sourcing sites such as LRxL-STAT (www.linkedin.com/in/lrxlstat) is important in stimulating the momentum needed to test these novel drug targets for efficacy in lupus rapidly in small, proof-of-concept trials conducted by LuCIN, the Lupus Clinical Investigators Network (www.linkedin.com/in/lucinstat).

Dehydration activates an NF-kappaB-driven, COX2-dependent survival mechanism in renal medullary interstitial cells.

Renal prostaglandin (PG) synthesis is mediated by cyclooxygenase-1 and -2 (COX1 and COX2). After dehydration, the maintenance of normal renal function becomes particularly dependent upon PG synthesis. The present studies were designed to examine the potential link between medullary COX1 and COX2 expression in hypertonic stress. In response to water deprivation, COX2, but not COX1, mRNA levels increase significantly in the renal medulla, specifically in renal medullary interstitial cells (RMICs). Water deprivation also increases renal NF-kappaB-driven reporter expression in transgenic mice. NF-kappaB activity and COX2 expression could be induced in cultured RMICs with hypertonic sodium chloride and mannitol, but not urea. RMIC COX2 expression was also induced by driving NF-kappaB activation with a constitutively active IkappaB kinase alpha (IKKalpha). Conversely, introduction of a dominant-negative IkappaB mutant reduced COX2 expression after hypertonicity or IKKalpha induction. RMICs failed to survive hypertonicity when COX2 was downregulated using a COX2-selective antisense or blocked with the selective nonsteroidal anti-inflammatory drug (NSAID) SC58236, reagents that did not affect cell survival in isotonic media. In rabbits treated with SC58236, water deprivation induced apoptosis of medullary interstitial cells in the renal papilla. These results demonstrate that water deprivation and hypertonicity activate NF-kappaB. The consequent increase in COX2 expression favors RMIC survival in hypertonic conditions. Inhibition of RMIC COX2 could contribute to NSAID-induced papillary injury.

Regulation of T cell proliferation by anti-CD49d and anti-CD29 monoclonal antibodies.

The beta 1 integrin VLA-4 (alpha 4 beta 1, CD49d/CD29), which is expressed on a large subpopulation of peripheral blood T lymphocytes, functions as a receptor for the endothelial adhesion protein VCAM-1 and the extracellular matrix protein fibronectin. Previous studies showed that immobilized fibronectin enhanced anti-CD3 monoclonal antibody (mAb)-induced T cell proliferation through binding to the integrins VLA-4 and VLA-5 (alpha 5 beta 1, CD49e/CD29). We studied the ability of the anti-CD49d mAb L25 to potentiate proliferation. T cell proliferation was induced by subthreshold concentrations of anti-CD3 mAb (mAb OKT3) coimmobilized with mAb L25 but not with coimmobilized anti-CD29 (beta 1) mAb. Soluble anti-CD29 mAb inhibited the proliferation induced by coimmobilized mAb OKT3 and L25 but not proliferation induced by mAb OKT3 with PMA or coimmobilized anti-CD26 mAb.

Human CD4+ T cell differentiation and effector function: implications for autoimmunity.

Human CD4+ memory T cells progress through stages of postthymic differentiation that have been characterized by distinct phenotypes. We have investigated the factors regulating cytokine production, and the correlation between phenotype and effector function in normal and autoimmune individuals. These studies suggest that antigen-induced proliferation in the periphery drives CD4+ T cells through successive stages of differentiation that culminate in optimal effector function and resistance to external modulatory influences. Moreover, these studies support the concept that in autoimmune individuals, the chronic accumulation of differentiated proinflammatory T cells perpetuate the inflammatory response resulting in aggressive disease.

Assessment of a positive selection technique using an avidin column to isolate human peripheral blood T cell subsets.

The current studies were designed to assess a new technique for positively selecting human T cells from whole peripheral blood mononuclear cells using the minimal amount of monoclonal antibody required to bind the T cell to an avidin column indirectly via a biotin-conjugated secondary antibody. Positive selection of T cells has previously been avoided because the saturating amounts of antibodies required for other isolation procedures can lead to aberrant results in assays of T cell activation and function. The avidin column technique for obtaining purified T cell subsets was compared to a multi-step procedure that included negative selection panning. The positive selection technique was easily performed within 4 h whereas the negative selection technique required a minimum of 12 h to complete. The avidin column technique proved to be a rapid and simple method for isolating T cell subsets of high purity and normal functional capabilities. Since minimal amounts of monoclonal antibodies were used for the purification protocol, no consistent inhibitory or stimulatory effect of the residual antibody was noted in assays of activation and proliferation of positively selected T cells compared to T cells isolated by negative selection panning.

Strategic allocation of ejaculates by male Adélie penguins.

Sperm competition theory suggests that males should strategically allocate sperm to those females that will bring them the best possible genetic returns. Although males of a number of species of insects and fishes have been shown to allocate sperm strategically, we provide, to our knowledge, the first evidence that an avian species is also capable of allocating ejaculates. Male Adélie penguins (Pygoscelis adeliae) are more likely to transfer sperm during extra-pair copulations (EPCs) than during pair copulations. We investigated the question of how males allocate ejaculates within the constraints of limited sperm availability and found (i) that males that engaged in EPC attempts ejaculated less often when copulating with their social partner than males that made no EPC attempts, and (ii) that there was no difference between males that were involved in failed EPC attempts and those that were involved in successful EPCs in the proportion of copulations that resulted in sperm transfer. These results indicate that males achieve strategic allocation of sperm within the constraints of limited sperm availability by withholding ejaculates from their social partners.

De novo dup (5p) in a patient with congenital hypoplasia of the adrenal gland.

We report on a black male child with congenital hypoplasia of the adrenal gland (CHA) with a de novo duplication of 5p [dir dup(5) (p13.3-->p15.1)], confirmed by fluorescence in situ hybridization (FISH). In addition to a characteristic clinical course, the patient has hyperpigmentation (melanoderma) since birth, normal external genitalia, marked elevation of ACTH, and absent response to an IV ACTH challenge. To the best of our knowledge, this is the first case of congenital hypoplasia of the adrenal gland associated with a chromosome abnormality. Reviews of dup (5p) and of our patient suggest that duplication of 5p13.3-pter has only minor phenotypic effect, while duplication of the relatively small critical segment p11-p13.2 apparently causes far more deleterious changes. The concurrence of CHA and dup(5p) in our patient may indicate the possible gene localization of an autosomal form of CHA to either at or near 5p13.3 or 5p15.1.

Regulation of the expression of adhesion molecules by human synoviocytes.

The capacity of synoviocytes to participate in inflammatory responses may be altered by the cytokine-enhanced expression of adhesion molecules such as intercellular adhesion molecule-1 (ICAM-1). To examine this possibility, the ability of selected cytokines to enhance ICAM-1 expression was examined. The data indicated that each of these cytokines (interleukin-1 beta greater than tumor necrosis factor-alpha, interferon-gamma much greater than interleukin-6) can up-regulate synoviocyte ICAM-1 expression. This can potentially increase the ability of these cells to interact with infiltrating inflammatory cells, thereby propagating immunologically mediated inflammation such as occurs in rheumatoid synovitis.

Ocular rosacea. Signs, symptoms, and tear studies before and after treatment with doxycycline.

OBJECTIVE: To examine ocular signs, symptoms, and results of tear analysis in patients with cutaneous rosacea before, during, and after doxycycline therapy. DESIGN: Before-after trial. SETTING: General community. PATIENTS OR OTHER PARTICIPANTS: Thirty-nine patients with cutaneous rosacea underwent dermatologic and ocular examinations, testing of tear break-up time, and Schirmer testing at baseline and 4, 8, and 12 weeks. Six patients did not complete the study. Baseline tear break-up time and results of Schirmer test were compared with those of 13 patients without rosacea who were matched for age and sex. INTERVENTION: Patients with rosacea were given doxycycline, 100 mg daily for 12 weeks. MAIN OUTCOME MEASURE: Statistically significant (P, .05) improvement in tear break-up time. RESULT: The most frequent ocular symptoms were dryness, itching, blurred vision, and photosensitivity, all of which improved significantly with treatment. All patients had signs of ocular disease, most commonly erythema and telangiectasia, meibomian gland dysfunction, and ciliary base injection. Significant improvement (P,.05) for scales, erythema and telangiectasia, ciliary base injection, bulbar injection, papillary hypertrophy, and punctate epithelial erosions was seen. Average tear break-up time for the patients with rosacea was 5.7 seconds, which improved to 10.8 seconds after 12 weeks of treatment (P = .007). Baseline tear break-up time was significantly lower than for the comparison group of normal subjects (P = .001). There was no correlation between severity of cutaneous disease and ocular disease. CONCLUSIONS: All patients with cutaneous rosacea had some degree of ocular involvement. Tear break-up time is abnormal in patients with rosacea. Ocular erythema and telangiectasia, meibomian gland dysfunction, and short tear break-up time in patients with cutaneous rosacea are indicators of ocular rosacea. Doxycycline, 100 mg daily, will improve ocular disease and increase the tear break-up time.

Shape matching using relaxation techniques.

The problem of finding approximate matches of pieces of shapes to parts of larger shapes is investigated. The shapes are represented by polygonal approximations. Initially, figures of merit are assigned to the matches between pairs of angles on the two shapes. Relaxation methods are then used to find acceptable combinations of these matches. This approach was tested on a data base consisting of digitized coastlines in various map projections. In nearly all cases, all matches except the correct one were eliminated by the relaxation processes.

Hierarchical constraint processes for shape analysis.

A major application of syntactic pattern recognition is the analysis of two-dimensional shape. This paper describes a new syntactic shape analysis technique which combines the constraint propagation techniques which have been so successful in computer vision with the syntactic representation techniques which have been successfully applied to a wide variety of shape analysis problems. Shapes are modeled by stratified shape grammars. These grammars are designed so that local constraints can be compiled from the grammar describing the appearance of pieces of shape at various levels of description. Applications to the analysis of airplane shapes are presented.

Efficient recovery of shape from texture.

Witkin proposed a maximum likelihood model for the recovery of surface orientation from image texture. We develop two efficient algorithms for solving this shape from texture problem and compare the results of these algorithms with the algorithm described in [1].

An empirical evaluation of generalized cooccurrence matrices.

A comparative study of generalized cooccurrence texture analysis tools is presented. A generalized cooccurrence matrix (GCM) reflects the shape, size, and spatial arrangement of texture features. The particular texture features considered in this paper are 1) pixel-intensity, for which generalized cooccurrence reduces to traditional cooccurrence; 2) edge-pixel; and 3) extended-edges. Three experiments are discussed-the first based on a nearest neighbor classifier, the second on a linear discriminant classifier, and the third on the Battacharyya distance figure of merit.

Local estimation of the uniform error threshold.

The theory behind selection of the ``uniform error'' threshold which equalizes the probability of misclassification in an image containing two classes is presented. It is shown how this threshold can be estimated using local operations. Some examples and possible extensions are considered.

Texture analysis using generalized co-occurrence matrices.

We present a new approach to texture analysis based on the spatial distribution of local features in unsegmented textures. The textures are described using features derived from generalized co-occurrence matrices (GCM). A GCM is determined by a spatial constraint predicate F and a set of local features P = {(Xi, Yi, di), i = 1,..., m} where (Xi, Yi) is the location of the ith feature, and di is a description of the ith feature. The GCM of P under F, GF, is defined by GF(i, j) = number of pairs, pk, pl such that F(pk, pl) is true and di and dj are the descriptions of pk and pl, respectively. We discuss features derived from GCM's and present an experimental study using natural textures.

Chlorinated hydrocarbons in the tissues of South Polar Skuas (Catharacta maccormicki) and Adélie Penguins (Pygoscelis adeliea) from Ross Sea, Antarctica.

High rates of egg infertility and embryo death in a colony of South Polar Skuas breeding in the Antarctic were similar to those in polluted North Atlantic populations of the Great Skua. Such loss could not be linked to factors such as organochlorine pollutants, as levels of DDE and PCBs in the contents of skua eggs from the population were only a small fraction of those in polluted skua populations from the Northern Hemisphere. Average eggshell thickness for skuas nesting on Ross Island has shown no significant change since the introduction of DDT. Concentrations of DDE and PCBs in South Polar Skuas were 13 and 22 times higher, respectively, than those in the eggs of sympatric Adélie Penguins, and this probably reflects the greater exposure of skuas to pollution when they migrate north of the Antarctic Convergence in winter. Residues in liver tissue showed a similar trend, and a higher rate of mixed function oxidase induction in skua liver compared to that of penguins is consistent with the trends seen in pollutant levels. The same PCB congener predominated in both skua and penguin samples. Comparisons with historical residue data suggest that global levels of DDT residues are declining.

In vitro hepatic metabolism of a CYP3A-mediated drug, quinine, in Adélie penguins.

Very little is known about Antarctic animals' ability to metabolise or detoxify xenobiotics. The activity of cytochromes P450 subfamily 3A (CYP3A) in Adélie penguin liver was studied by incubating penguin liver microsomes with a human CYP3A substrate, quinine, and results were compared with those from human liver microsomes. The mean maximum rate of metabolism (Vmax) for quinine in penguin livers was approximately five times less (160+/-72 versus 574+/-416 pmol/mg/min; P<0.01), and the mean Km (substrate affinity) for the formation of quinine's major metabolite (3-hydroxyquinine) was significantly greater than that observed in human livers (160+/-73 versus 83+/-19 microM; P<0.01). The mean intrinsic clearance (Vmax/Km) was 1.1+/-0.4 microl/min (penguin), i.e. sevenfold less than in human livers (7.4+/-5.9 microl/min, P<0.005), suggesting that penguins have much less ability than humans to eliminate xenobiotics having a similar metabolic nature to quinine (i.e. CYP3A substrates). 3-Hydroxyquinine formation in penguin liver was inhibited by specific CYP3A inhibitors, midazolam and troleandomycin, but not by other CYP inhibitors, indicating that quinine metabolism to 3-hydroxyquinine in Adélie penguin liver is likely to be catalysed by a CYP isoform resembling human CYP3A. Adélie penguin liver CYP isoforms could serve as biomarkers for the impact of environmental pollution.

An improved radial basis function network for visual autonomous road following.

We have developed a radial basis function network (RBFN) for visual autonomous road following. Preliminary testing of the RBFN was done using a driving simulator, and the RBFN was then installed on an actual vehicle at Carnegie Mellon University for testing in an outdoor road-following application. In our first attempts, the RBFN had some success, but it experienced some significant problems such as jittery control and driving failure. Several improvements have been made to the original RBFN architecture to overcome these problems in simulation and more importantly in actual road following, and the improvements are described in this paper.

Human expression recognition from motion using a radial basis function network architecture.

In this paper a radial basis function network architecture is developed that learns the correlation of facial feature motion patterns and human expressions. We describe a hierarchical approach which at the highest level identifies expressions, at the mid level determines motion of facial features, and at the low level recovers motion directions. Individual expression networks were trained to recognize the "smile" and "surprise" expressions. Each expression network was trained by viewing a set of sequences of one expression for many subjects. The trained neural network was then tested for retention, extrapolation, and rejection ability. Success rates were 88% for retention, 88% for extrapolation, and 83% for rejection.