Deep learning for screening of interstitial lung disease patterns in high-resolution CT images.

AIM: To develop a screening tool for the detection of interstitial lung disease (ILD) patterns using a deep-learning method. MATERIALS AND METHODS: A fully convolutional network was used for semantic segmentation of several ILD patterns. Improved segmentation of ILD patterns was achieved using multi-scale feature extraction. Dilated convolution was used to maintain the resolution of feature maps and to enlarge the receptive field. The proposed method was evaluated on a publicly available ILD database (MedGIFT) and a private clinical research database. Several metrics, such as success rate, sensitivity, and false positives per section were used for quantitative evaluation of the proposed method. RESULTS: Sections with fibrosis and emphysema were detected with a similar success rate and sensitivity for both databases but the performance of detection was lower for consolidation compared to fibrosis and emphysema. CONCLUSION: Automatic identification of ILD patterns in a high-resolution computed tomography (CT) image was implemented using a deep-learning framework. Creation of a pre-trained model with natural images and subsequent transfer learning using a particular database gives acceptable results.

First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes.

BACKGROUND: P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38α), recent studies indicate that family members such as MAPK13 (p38δ) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases. METHODS: To facilitate the design of potent and specific inhibitors, we present here the structural, biophysical, and functional characterization of two new MAPK13-inhibitor complexes, as well as the first comprehensive structural, biophysical, and functional analysis of MAPK13 complexes with four different inhibitor compounds of greatly varying potency. RESULTS: These inhibitors display IC50 values either in the nanomolar range or micromolar range (>800-fold range). The nanomolar inhibitors exhibit much longer ligand-enzyme complex half-lives compared to the micromolar inhibitors as measured by biolayer interferometry. Crystal structures of the MAPK13 inhibitor complexes reveal that the nanomolar inhibitors engage MAPK13 in the DFG-out binding mode, while the micromolar inhibitors are in the DFG-in mode. Detailed structural and computational docking analyses suggest that this difference in binding mode engagement is driven by conformational restraints imposed by the chemical structure of the inhibitors, and may be fortified by an additional hydrogen bond to MAPK13 in the nanomolar inhibitors. CONCLUSIONS: These studies provide a structural basis for understanding the differences in potency exhibited by these inhibitors. GENERAL SIGNIFICANCE: They also provide the groundwork for future studies to improve specificity, potency, pharmacodynamics, and pharmacokinetic properties.

Effectiveness of knowledge of result and knowledge of performance in the learning of a skilled motor activity by healthy young adults.

[Purpose] The acquisition of motor skills are fundamental to human life. There is a lack of research on whether knowledge of performance or knowledge of result as augmented feedback is more effective. The objective of this study was to compare the effectiveness of knowledge of result and knowledge of performance in the learning of a skilled motor activity by healthy young adults. [Subjects and Methods] A total of thirty healthy young adult males and females without any neurological or musculoskeletal impairment, between the age of 18-30 years were the subjects of the study. They were randomly allocated to 2 groups: group 1 was given knowledge of result as feedback, and knowledge of performance was given as feedback to group 2. Both the groups practiced the task of throwing a soft spongy ball for 6 days per week for 4 weeks, with 40 trials each day. The outcome measure used was the distance of the throw. [Results] The results were analyzed using the t-test. The mean distances thrown by both the groups showed highly significant improvements and throwing distance of group 2 showed better improvement than that of group 1. [Conclusion] Both types of augmented feedback were effective at improving skilled motor activity, but the knowledge of performance group showed better improvement than the knowledge of result group.

PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection.

Enhancing the response to interferon could offer an immunological advantage to the host. In support of this concept, we used a modified form of the transcription factor STAT1 to achieve hyper-responsiveness to interferon without toxicity and markedly improve antiviral function in transgenic mice and transduced human cells. We found that the improvement depended on expression of a PARP9-DTX3L complex with distinct domains for interaction with STAT1 and for activity as an E3 ubiquitin ligase that acted on host histone H2BJ to promote interferon-stimulated gene expression and on viral 3C proteases to degrade these proteases via the immunoproteasome. Thus, PARP9-DTX3L acted on host and pathogen to achieve a double layer of immunity within a safe reserve in the interferon signaling pathway.

Interferon response and respiratory virus control are preserved in bronchial epithelial cells in asthma.

BACKGROUND: Some investigators find a deficiency in IFN production from airway epithelial cells infected with human rhinovirus in asthma, but whether this abnormality occurs with other respiratory viruses is uncertain. OBJECTIVE: To assess the effect of influenza A virus (IAV) and respiratory syncytial virus (RSV) infection on IFN production and viral level in human bronchial epithelial cells (hBECs) from subjects with and without asthma. METHODS: Primary-culture hBECs from subjects with mild to severe asthma (n = 11) and controls without asthma (hBECs; n = 7) were infected with live or ultraviolet-inactivated IAV (WS/33 strain), RSV (Long strain), or RSV (A/2001/2-20 strain) with multiplicity of infection 0.01 to 1. Levels of virus along with IFN-ß and IFN-λ and IFN-stimulated gene expression (tracked by 2'-5'-oligoadenylate synthetase 1 and myxovirus (influenza virus) resistance 1 mRNA) were determined up to 72 hours postinoculation. RESULTS: After IAV infection, viral levels were increased 2-fold in hBECs from asthmatic subjects compared with nonasthmatic control subjects (P < .05) and this increase occurred in concert with increased IFN-λ1 levels and no significant difference in IFNB1, 2'-5'-oligoadenylate synthetase 1, or myxovirus (influenza virus) resistance 1mRNA levels. After RSV infections, viral levels were not significantly increased in hBECs from asthmatic versus nonasthmatic subjects and the only significant difference between groups was a decrease in IFN-λ levels (P < .05) that correlated with a decrease in viral titer. All these differences were found only at isolated time points and were not sustained throughout the 72-hour infection period. CONCLUSIONS: The results indicate that IAV and RSV control and IFN response to these viruses in airway epithelial cells is remarkably similar between subjects with and without asthma.

High-throughput screening normalized to biological response: application to antiviral drug discovery.

The process of conducting cell-based phenotypic screens can result in data sets from small libraries or portions of large libraries, making accurate hit picking from multiple data sets important for efficient drug discovery. Here, we describe a screen design and data analysis approach that allow for normalization not only between quadrants and plates but also between screens or batches in a robust, quantitative fashion, enabling hit selection from multiple data sets. We independently screened the MicroSource Spectrum and NCI Diversity Set II libraries using a cell-based phenotypic high-throughput screening (HTS) assay that uses an interferon-stimulated response element (ISRE)-driven luciferase-reporter assay to identify interferon (IFN) signal enhancers. Inclusion of a per-plate, per-quadrant IFN dose-response standard curve enabled conversion of ISRE activity to effective IFN concentrations. We identified 45 hits based on a combined z score ≥2.5 from the two libraries, and 25 of 35 available hits were validated in a compound concentration-response assay when tested using fresh compound. The results provide a basis for further analysis of chemical structure in relation to biological function. Together, the results establish an HTS method that can be extended to screening for any class of compounds that influence a quantifiable biological response for which a standard is available.

Preparación y caracterización de complejos de rufinamida con HP-beta-ciclodextrina por el método de amasado para mejorar la solubilidad / Preparation and characterization of rufinamide HP-beta-cyclodextrin complexes prepared by the kneading method for solubility enhancement

Objetivos: La presente investigación se refiere a la preparación y caracterización de complejos de rufinamida HP-β-ciclodextrina preparados por el método de amasado. Material y métodos: La rufinamida fue donada por la empresa Torrent Pharmaceuticals limitado. HP-β-ciclodextrina (HP-β-CD) se adquirió de Himedia, India. Metanol y ácido clorhídrico se obtuvieron de SD Fine Chem. SA. Ltd., India. Se utilizó el método de amasado para preparar complejos de inclusión de rufinamida. El estudio de la fase de solubilidad se realizó para comprobar la formación de complejos de inclusión. Los complejos preparados se caracterizaron por diferentes métodos como DSC, FTIR, X-RPD y ensayo de disolución in vitro. Resultados: Se encontró que se producían formación de complejos en la relación 1:1. La constante de estabilidad encontrada fue de 221,27 M-1. Los estudios de DSC, FTIR confirmaron la formación del complejo de inclusión. Mediante X-RPD se confirmó la naturaleza amorfa del complejo. Conclusiones: El estudio de disolución in vitro mostró que la proporción 1:1.5 liberaba alrededor de50% de fármaco en 30 min y a los 60 minutos se consiguió una liberación del 70% (AU)

Aims: The present investigation concerns the preparation and characterization of Rufinamide HP-β-cyclodextrin complexes prepared by the kneading method. Material & methods: Rufinamide was procured as a gift sample from Torrent Pharmaceuticals limited. HP-β-cyclodextrin (HP-β-CD) was purchased from Himedia, India. Methanol and Hydrochloric Acid were purchased from S. D. Fine Chem. Pvt. Ltd., India. kneading method was selected to prepare inclusion complexation of Rufinamide. Phase solubility study was performed to check formation of inclusion complex. Prepared complex were characterize by different methods like DSC study, FTIR study, X-RPD study & in-vitro dissolution study. Results: It was found that there is a formation of 1:1 inclusion complex between HP-β-CD as stability constant was found to be 221.27 M-1. DSC study, FTIR study had given supporting data for formation of inclusion complex. Amorphous nature of the complex was confirmed from the X-RPD study. Conclusions: From in-vitro dissolution study it was found that 1:1.5 complex showed around 50%drug released in 30 min & more than 70% of Drug release in 60 mins (AU)

IL-13-induced airway mucus production is attenuated by MAPK13 inhibition.

Increased mucus production is a common cause of morbidity and mortality in inflammatory airway diseases, including asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. However, the precise molecular mechanisms for pathogenic mucus production are largely undetermined. Accordingly, there are no specific and effective anti-mucus therapeutics. Here, we define a signaling pathway from chloride channel calcium-activated 1 (CLCA1) to MAPK13 that is responsible for IL-13-driven mucus production in human airway epithelial cells. The same pathway was also highly activated in the lungs of humans with excess mucus production due to COPD. We further validated the pathway by using structure-based drug design to develop a series of novel MAPK13 inhibitors with nanomolar potency that effectively reduced mucus production in human airway epithelial cells. These results uncover and validate a new pathway for regulating mucus production as well as a corresponding therapeutic approach to mucus overproduction in inflammatory airway diseases.

A Longitudinal Study of the Relation Between Depressive Symptomatology and Parenting Practices.

This longitudinal study examined whether mothers' depressive symptomatology predicted parenting practices in a sample of 199 mothers of 3-year-old children with behavior problems who were assessed yearly until age 6. Higher maternal depressive symptoms were associated with higher overreactivity and laxness and lower warmth when children were 6 years old. Higher maternal depressive symptoms were also related to increases in overreactivity across the preschool years. Moreover, depression and parenting practices (overreactivity and laxness) covaried over time within mothers. These results provide evidence of a strong link between maternal depression and parenting during the preschool years.

High throughput screening for small molecule enhancers of the interferon signaling pathway to drive next-generation antiviral drug discovery.

Most of current strategies for antiviral therapeutics target the virus specifically and directly, but an alternative approach to drug discovery might be to enhance the immune response to a broad range of viruses. Based on clinical observation in humans and successful genetic strategies in experimental models, we reasoned that an improved interferon (IFN) signaling system might better protect against viral infection. Here we aimed to identify small molecular weight compounds that might mimic this beneficial effect and improve antiviral defense. Accordingly, we developed a cell-based high-throughput screening (HTS) assay to identify small molecules that enhance the IFN signaling pathway components. The assay is based on a phenotypic screen for increased IFN-stimulated response element (ISRE) activity in a fully automated and robust format (Z'>0.7). Application of this assay system to a library of 2240 compounds (including 2160 already approved or approvable drugs) led to the identification of 64 compounds with significant ISRE activity. From these, we chose the anthracycline antibiotic, idarubicin, for further validation and mechanism based on activity in the sub-µM range. We found that idarubicin action to increase ISRE activity was manifest by other members of this drug class and was independent of cytotoxic or topoisomerase inhibitory effects as well as endogenous IFN signaling or production. We also observed that this compound conferred a consequent increase in IFN-stimulated gene (ISG) expression and a significant antiviral effect using a similar dose-range in a cell-culture system inoculated with encephalomyocarditis virus (EMCV). The antiviral effect was also found at compound concentrations below the ones observed for cytotoxicity. Taken together, our results provide proof of concept for using activators of components of the IFN signaling pathway to improve IFN efficacy and antiviral immune defense as well as a validated HTS approach to identify small molecules that might achieve this therapeutic benefit.

Host epithelial-viral interactions as cause and cure for asthma.

Research on the pathogenesis of asthma has concentrated on initial stimuli, genetic susceptibilities, adaptive immune responses, and end-organ alterations (particularly in airway mucous cells and smooth muscle) as critical steps leading to disease. Recent evidence indicates that the innate immune cell response to respiratory viruses also contributes to the development of inflammatory airway disease. We further develop this concept by raising the issue that the interaction between host airway epithelial cells and respiratory viruses is another aspect of innate immunity that is also a critical determinant of asthma. We also introduce a rationale for how antiviral performance at the epithelial cell level might be improved to prevent acute infectious illness and chronic inflammatory disease caused by respiratory viruses.

Novel CHST6 gene mutations in 2 unrelated cases of macular corneal dystrophy.

PURPOSE: To investigate the possible mutations in the carbohydrate sulfotransferase 6 (CHST6) gene of 2 unrelated cases of macular corneal dystrophy (MCD) and to report atypical stromal deposits in one of them. METHODS: Corneal tissues were stained with antisulfated keratan sulfate (KS), antitransforming growth factor beta 1-induced protein (TGFBIp), thioflavin-T, alcian blue, and Masson trichrome. Sequencing was performed to identify potential mutations in the CHST6 gene and the fourth and twelfth exons of the TGFBI gene. RESULTS: Alcian blue staining revealed the presence of multiple subepithelial and intrastromal mucopolysaccharide deposits, confirming the diagnosis of MCD in both cases. Immunofluorescence staining in case 1 revealed the presence of sulfated KS only in the keratocytes and select endothelial cells, consistent with MCD type IA. Preferential expression of sulfated KS was observed in keratocytes and extracellular stromal matrix in case 2, consistent with MCD type II. Atypical subepithelial and superficial stromal deposits were observed in case 1, which stained positively with alcian blue, eosin, Masson trichrome, and thioflavin-T indicating the presence of hyaline and amyloid materials. CHST6 gene sequencing revealed 2 heterozygous mutations in case 1 (a p.Arg211Gln and a novel mutation of p.Arg177Gly) and a novel homozygous mutation of p.Pro186Arg in case 2. No mutations were found in exons 4 or 12 of the TGFBI gene in case 1. CONCLUSIONS: Secondary hyalinosis and amyloidosis occur in a case of MCD type IA with a novel p.Arg177Gly mutation in CHST6. A novel p.Pro186Arg mutation in CHST6 is associated with MCD type II in an African American.

Granular and lattice deposits in corneal dystrophy caused by R124C mutation of TGFBIp.

PURPOSE: Both granular and lattice deposits are present in Avellino corneal dystrophy (ACD), primarily associated with the R124H mutation of transforming growth factor-ß-induced (TGFBIp). We investigated the presence of these deposits in other TGFBI mutations and the use of Thioflavin-T (ThT), a fluorescent amyloid stain for characterizing corneal amyloid deposits. METHODS: Surgical corneal specimens of 3 unrelated patients clinically diagnosed with ACD were studied. Corneal sections from normal individuals and patients with prior lattice corneal dystrophy (LCD) were used as controls. Histochemical studies were performed with Congo red and Masson trichrome stains, and fluorescent imaging with scanning laser confocal microscopy was performed for ThT and anti-TGFBIp antibody staining. RESULTS: Clinical and histopathological findings supported the diagnoses of ACD in these 3 cases in whom granular deposits stained with Masson trichrome and lattice deposits stained with ThT and Congo red showed birefringence and dichroism as expected. However, genotyping revealed a heterozygous R124C mutation in each case. In addition to classical stromal deposits, unique subepithelial TGFBIp aggregates, which stain with neither ThT nor trichrome, were observed. In control LCD sections, stromal deposits were stained with ThT but not with trichrome, confirming lack of granular deposits. CONCLUSIONS: Our results demonstrate that both granular and lattice corneal deposits can be associated with R124C mutation in addition to the more common R124H mutation. An additional feature of nonhyaline, nonamyloid, TGFBIp subepithelial deposits might substantiate the categorization of such cases as a variant form of ACD. This study further validates ThT staining for detection of amyloid TGFBIp deposits.

Predicting attention-deficit/hyperactivity disorder and oppositional defiant disorder from preschool diagnostic assessments.

The present study examined the power of measures of early preschool behavior to predict later diagnoses of attention-deficit/hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD)/conduct disorder (CD). Participants were 168 children with behavior problems at age 3 who underwent a multimethod assessment of ADHD and ODD symptoms and were followed annually for 3 years. Fifty-eight percent of 3-year-old children with behavior problems met criteria for ADHD and/or ODD/CD 3 years later. Using a diagnostic interview and rating scales at age 3, the authors could accurately predict later diagnostic status for 3/4 of children for ADHD and for 2/3 of children for ODD/CD. Predictive power of the best models did not increase significantly at age 4 and age 5 compared with age 3. Results provide support for the validity of early diagnoses of ADHD, although caution is needed in making diagnoses because a significant minority of children with early hyperactivity and inattention do outgrow their problems.

Exploring the mechanism of beta-amyloid toxicity attenuation by multivalent sialic acid polymers through the use of mathematical models.

beta-Amyloid peptide (A beta), the primary protein component in senile plaques associated with Alzheimer's disease (AD), has been implicated in neurotoxicity associated with AD. Previous studies have shown that the A beta-neuronal membrane interaction plays a role in the mechanism of A beta toxicity. More specifically, it is thought that A beta interacts with ganglioside rich and sialic acid rich regions of cell surfaces. In light of such evidence, we have used a number of different sialic acid compounds of different valency or number of sialic acid moieties per molecule to attenuate A beta toxicity in a cell culture model. In this work, we proposed various mathematical models of A beta interaction with both the cell membrane and with the multivalent sialic acid compounds, designed to act as membrane mimics. These models allow us to explore the mechanism of action of this class of sialic acid membrane mimics in attenuating the toxicity of A beta. The mathematical models, when compared with experimental data, facilitate the discrimination between different modes of action of these materials. Understanding the mechanism of action of A beta toxicity inhibitors should provide insight into the design of the next generation of molecules that could be used to prevent A beta toxicity associated with AD.

Molecular characterization of toll-like receptor 2 of ruminants and comparative expression in nilgai (Boselaphus tragocamelus) vs. buffalo (Bubalus bubalis).

Toll-like receptors play role in the innate immune responses and orchestrate the adaptive immunity by induction of proinflammatory cytokines and up-regulation of costimulatory molecules. The present study has characterized TLR2 cDNA in nilgai, buffalo, sheep and goat that recognizes the peptidoglycan of Gram-positive bacteria. TLR2 coding sequences were amplified from monocytes cDNA and cloned in pGEMT-easy vector for nucleotide sequencing. Sequence analysis revealed 2355-bp-long TLR2 open reading frame encoding 784 amino acids in all the species studied. Nilgai TLR2 has 97.8% to 95.1% identity at nucleotide level and 96.2% to 92.7% identity at amino acid level with other ruminant species studied. Nonsynonymous substitutions exceeding synonymous substitutions indicated evolution of this receptor through positive selection among ruminants. Furthermore, basal TLR2 messenger RNA expression in different immune cells and tissues quantified by real-time polymerase chain reaction revealed highest level in in vitro derived dendritic cells followed by peripheral blood mononuclear cells. Skin and testes also expressed significant level in both nilgai and buffalo. Comparatively, nilgai immune cells and tissues expressed more TLR2 transcript than buffalo, thus elucidating stronger armamentarium of antibacterial immunity in nilgai as compared to buffalo.

Attenuation of beta-amyloid-induced toxicity by sialic-acid-conjugated dendrimers: role of sialic acid attachment.

beta-Amyloid (Abeta) is the primary protein component of senile plaques in Alzheimer's disease and is believed to be associated with neurotoxicity in the disease. We and others have shown that Abeta binds with relatively high affinity to clustered sialic acid residues on cell surfaces and that removal of cell surface sialic acids attenuates Abeta toxicity. We have also shown that sialic acid functionalized dendrimeric polymers can act as mimics of cell surface sialic acid clusters and attenuate Abeta-induced neurotoxicity. In the current study, we prepared sialic-acid-conjugated dendrimers using a physiologically relevant attachment of the sialic acid to the dendrimeric termini, and evaluated the Abeta toxicity attenuation properties of the dendrimers. We compared performance of sialic-acid-conjugated dendrimeric polymers in which the sialic acid moieties were attached to dendrimeric termini via the anomeric hydroxyl group of the sialic acid, a physiological attachment, to polymers in which the attachment was made via the carboxylic acid group on the sialic acid, a non-physiological attachment. This work enhances our understanding of Abeta-cell surface binding and is a step towards the development of new classes of sequestering agents as therapeutics for the prevention of Abeta toxicity in AD.

Characterisation of peacock (Pavo cristatus) mitochondrial 12S rRNA sequence and its use in differentiation from closely related poultry species.

1. Poaching of peacocks, the national bird of India, is illegal. People kill this beautiful pheasant bird for tail feathers and mix the meat with chicken or turkey. Differentiation of the meat of these species is essential in order to address the ambiguity about the origin of the sample. 2. The present study was carried out to investigate the use of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of mitochondrial 12S rRNA gene for identification of these species. 3. Peacock mitochondrial 12S rRNA partial gene was amplified using universal primers, cloned and characterised. It was found to be 446 nucleotides long. 4. Sequence analysis revealed 86.8 and 84.1% similarity with reported turkey and chicken sequences, respectively. Sequence and phylogenetic analysis showed that the peacock is much closer to the turkey than the chicken. 5. PCR-RFLP of 446 bp amplicon using commonly available restriction enzymes AluI and Sau3AI produced a differential pattern for identifying these poultry species unambiguously.

Psychopharmacological studies on Tragia involucrata root extract.

The methanol fraction of the root extract of Tragia involucrata was investigated for psychopharmacological activity in rodents. It produced an alteration of behavioural pattern and a reduction in spontaneous motility. A significant potentiation of pentobarbitone-induced sleep, a decrease of body temperature, suppression of the aggressive behaviour pattern and of the conditioned avoidance response (CAR) were observed with the fraction. These suggest that the methanol fraction of the T. involucrata root extract possesses significant central nervous system depressant action.

Antioxidant activity of the methanol fraction of Pluchea indica root extract.

Studies were carried out to evaluate the influence of the methanol fraction of Pluchea indica Less root extract (PIRE), the dual inhibitors (BW 755C and phenidone) and vitamin on both in vivo and in vitro free radical-scavenging activities, CCl(4)-induced lipid peroxidation and the metabolism of arachidonic acid by lipoxygenase. PIRE produced significant antiinflammatory activity against glucose oxidase-induced paw oedema (in vivo), inhibited hydroxyl radical and superoxide generation, lysis of erythrocytes induced by hydrogen peroxide, CCl(4)-induced lipid peroxidation and also dioxygenase activity of lipoxygenase (both in the presence and absence of hydrogen peroxide). Significantly higher free radical-scavenging activity was observed with BW 755C and phenidone compared with PIRE. However, both BW 755C and phenidone stimulated hydroxyl radical generation compared with the observed inhibitory effects of PIRE and vitamin E.