GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration

This paper shows how to significantly accelerate cone-beam CT reconstruction and 3D deformable image registration using the stream-processing model. We describe data-parallel designs for the Feldkamp, Davis and Kress (FDK) reconstruction algorithm, and the demons deformable registration algorithm, suitable for use on a commodity graphics processing unit. The streaming versions of these algorithms are implemented using the Brook programming environment and executed on an NVidia 8800 GPU. Performance results using CT data of a preserved swine lung indicate that the GPU-based implementations of the FDK and demons algorithms achieve a substantial speedup--up to 80 times for FDK and 70 times for demons when compared to an optimized reference implementation on a 2.8 GHz Intel processor. In addition, the accuracy of the GPU-based implementations was found to be excellent. Compared with CPU-based implementations, the RMS differences were less than 0.1 Hounsfield unit for reconstruction and less than 0.1 mm for deformable registration.     

Role of retrograde dilatation in the management of pharyngo-esophageal corrosive strictures

Pharyngo-esophageal corrosive stricture is a complex clinical scenario. If an esophageal opening cannot be found orally through endoscopy, a retrograde approach with a mini-laparotomy and gastrostomy should be attempted. This study primarily aimed at defining the role of preoperative retrograde dilatation of pharyngo-esophageal corrosive strictures. A retrospective analysis of 51 cases of pharyngo-esophageal corrosive strictures identified between 1997-2005 was performed. The demographic details were analyzed. The details of the injury to the pharynx either in isolation or in combination were noted and the management details were recorded. In 21 patients preoperative retrograde dilatation was considered and the technique was successful in 14 (Group I). In seven the technique failed (Group II) and these patients underwent transhiatal resection and gastric pull-through and/or retrosternal pharyngocoloplasty. In Group I patients the postoperative stay was significantly less than in Group II (12 +/- 2.03 days vs. 18 +/- 4.32 days; p = 0.001) Recurrent aspiration, respiratory tract infections, choking sensation and the need for tracheostomy were less frequent in Group I. The overall functional assessment was good in Group I. For treatment of pharyngo-esophageal obstruction, if antegrade dilatation is not possible due to technical reasons, retrograde dilatation is a viable option before opting for organ replacement/bypass procedures. There is no best replacement of the native organ to maintain quality of life.     

Synthetic di-sulfated iduronic acid attenuates asthmatic response by blocking T-cell recruitment to inflammatory sites

Identification of carbohydrate sequences that determine affinity to specific chemokines is a critical step for strategies to interfere with chemokine-mediated leukocyte trafficking. Here, we first characterized the development of allergic asthma in Tie2-dependent and inducible Ext1-knockout (Tie2-Ext1^iKO) mice. We showed that heparan sulfate is essential for leukocyte recruitment in the peribronchial region and bronchoalveolar lavage fluid (BALF), and is crucial for induction of airway hyperresponsiveness. Our glycan microarray showed a unique affinity profile of chemokine CCL20 to substructures of heparin and heparin-like oligo/di/monosaccharides. Among them, we identified a synthetic and not naturally occurring monosaccharide, 2,4-O-di-sulfated iduronic acid (Di-S-IdoA), as a potential inhibitor for CCL20–heparan sulfate interaction. Mice injected with Di-S-IdoA via tail vain or nasal inhalation showed attenuated leukocyte recruitment into inflammatory sites and BALF. These results demonstrate a critical role of chemokine–heparan sulfate interaction in the asthma development and Di-S-IdoA as a potential drug for asthma treatment.Asthma is a common allergic disease characterized by chronic airway inflammation, mucus hypersecretion, and airway hyperreactivity to inhaled allergens (1). Despite the importance of T lymphocytes in adaptive immunity and host defense, their accumulation in airway in allergic asthma causes Th2-mediated pulmonary inflammation. The asthmatic inflammatory response is orchestrated by T-cell trafficking network among lung, blood circulation, secondary lymphoid organ, and peripheral tissue (2). Of note, the significant increase of T cells in the airway in asthma is mostly due to T-cell recruitment from regional lymph nodes rather than their proliferation at the inflamed site (3). Therefore, a therapeutic approach that shuts off the trafficking pathway of pathogenic T cells should significantly inhibit the Th2-mediated inflammation in allergic asthma.It is well known that the destination of T-cell trafficking pathway is tightly restricted by the profile of chemokines, lipid chemoattractants, and T-cell chemokine receptors. As a part of immune surveillance, naïve T cells and central memory T cells constantly access secondary lymphoid organs from blood circulation via specialized high endothelial venules (HEVs). The interaction between T cells and HEV cells includes in a stepwise manner (4, 5), L-selectin–dependent tethering and rolling, activation, firm arrest, and transendothelial migration. Besides 6-sulfo sialyl Lewis X as a L-selectin ligand, HEVs constitutively express chemokine CCL21 and CCL19 and attract T cells that express its cognate receptor CCR7 (5). In contrast to this homeostatic homing, circulating T cells interact with inflamed blood vessels in lung after asthmatic exposure to an inhaled allergen. Among numerous combinations of chemokines and their receptors, there is considerable evidence that CCL20 and its cognate receptor CCR6 may contribute to the pathogenesis of asthma (6). CCL20-CCR6 plays a key role in the recruitment of Th17 (7) cells and Th2 cells (8). Indeed, CCL20 is highly enriched on inflammatory epithelium (9) and CCR6 is expressed on memory T cells infiltrated in the lung during allergic inflammation (7). In addition, CCR6-deficient mice have decreased airway responsiveness, and reduced recruitment of eosinophils into lung (10, 11). These findings suggest that CCL20-CCR6 axis is a putative target for the treatment of asthma.Cumulative evidence in vivo and in vitro indicates that chemokines cannot be functionally active in HEVs and inflamed sites without their interaction with heparan sulfate (12). Heparan sulfate protects chemokines from proteolysis, immobilizes them on the endothelium surface and produces chemokine gradients in the vasculature. Heparan sulfate is composed of repeating disaccharide units of uronic acid [glucuronic acid (GlcA) or iduronic acid (IdoA)] and N-acetylglucosamine (GlcNAc) carbohydrates. Some of GlcA (or IdoA) carbohydrates are subsequently O-sulfated, and GlcNAc carbohydrates are partially modified with N-deacetylation and N-sulfation (13). Previous reports have indicated that the sulfation patterns in heparan sulfate are more restricted than expected (14), and the sulfation is associated with respiratory distress (15) and asthma (16). It is believed that there are specific interactions between heparan sulfate and chemokines (17). Nevertheless, the nontemplate nature of long carbohydrate chains (<25,000 disaccharide units) and conformational plasticity still make it difficult to identify the common sequences of heparan sulfate that display affinity to specific chemokines. In this regard, our previously established glycan microarray system (18, 19) is a powerful tool to define the selectivity in heparan sulfate–chemokine interactions.Recently, we established the exostoses-1 (Ext1) gene conditional knockout Tie2-Ext1^iKO mouse model, in which GlcA/IdoA-GlcNAc repeat of heparan sulfate can be abrogated in endothelial cells in a tetracycline-inducible manner (20). In this study, Tie2-Ext1^iKO mouse showed significant reduction of both leukocyte recruitment to lung tissues and of airway hyperresponsiveness in ovalbumin (OVA) asthma model. Moreover, glycan microarray analysis surprisingly identified that an unnatural and synthetic monosaccharide, 2,4-O-di-sulfated iduronic acid (Di-S-IdoA) has a high affinity to recombinant CCL20. Intravenous and inhalation challenges of Di-S-IdoA significantly inhibited the leukocyte infiltration in bronchoalveolar lavage fluid (BALF). Our finding that even a monosaccharide can attenuate airway inflammation suggests its potential use as an antiasthma therapy that can be administered by inhalation.     

mGluR5 and GABAA receptor‐specific parametric PET atlas construction—PET/MR data processing pipeline,validation, and application

The glutamate and γ‐aminobutyric acid neuroreceptor subtypes mGluR₅ and GABA_A are hypothesized to be involved in the development of a variety of psychiatric diseases. However, detailed information relating to their in vivo distribution is generally unavailable. Maps of such distributions could potentially aid clinical studies by providing a reference for the normal distribution of neuroreceptors and may also be useful as covariates in advanced functional magnetic resonance imaging (MR) studies. In this study, we propose a comprehensive processing pipeline for the construction of standard space, in vivo distributions of non‐displaceable binding potential (BP _ND), and total distribution volume (V _T) based on simultaneously acquired bolus‐infusion positron emission tomography (PET) and MR data. The pipeline was applied to [¹¹C]ABP688‐PET/MR (13 healthy male non‐smokers, 26.6 ± 7.0 years) and [¹¹C]Flumazenil‐PET/MR (10 healthy males, 25.8 ± 3.0 years) data. Activity concentration templates, as well as V _T and BP _ND atlases of mGluR₅ and GABA_A, were generated from these data. The maps were validated by assessing the percent error δ from warped space to native space in a selection of brain regions. We verified that the average δ_ABP = 3.0 ± 1.0% and δ_FMZ = 3.8 ± 1.4% were lower than the expected variabilities σ of the tracers (σ_ABP = 4.0%–16.0%, σ_FMZ = 3.9%–9.5%). An evaluation of PET‐to‐PET registrations based on the new maps showed higher registration accuracy compared to registrations based on the commonly used [¹⁵O]H₂O‐template distributed with SPM12. Thus, we conclude that the resulting maps can be used for further research and the proposed pipeline is a viable tool for the construction of standardized PET data distributions.     

PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach

The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools are available for this purpose. Hence, we have developed a tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates. This tool consists of an ensemble of machine-learning-based predictors for determining the presence of temperate markers (integrase, Cro/CI repressor, immunity repressor, DNA partitioning protein A, and antirepressor) along with the integration of the ABRicate tool to determine the presence of antibiotic resistance genes and virulence genes. Using the biological features of the temperate markers, we were able to predict the presence of the temperate markers with high MCC scores (>0.70), corresponding to the lifestyle of the phages with an accuracy of 96.5%. Additionally, the screening of 183 lytic phage genomes revealed that six phages were found to contain AMR or virulence genes, showing that not all lytic phages are suitable to be used for therapy. The suite of predictors, PhageLeads, along with the integrated ABRicate tool, can be accessed online for in silico selection of suitable therapeutic phage candidates from single genome or metagenomic contigs.     

Specific detection of fungal pathogens by 18S rRNA gene PCR in microbial keratitis

Background  

The sensitivity and specificity of 18S rRNA polymerase chain reaction (PCR) in the detection of fungal aetiology of microbial keratitis was determined in thirty patients with clinical diagnosis of microbial keratitis.