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705 Aortic Graft Infection Managed with Bovine Patch, A Case Report and Literature Review. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Aim
to describe good outcomes in a case with Aortic graft infection (AGI) managed with Bovine patch and outline management of AGI.
Method
Literature review utilising keywords ‘’Aortic graft infection’’AND’’Bovine Patch’’ revealed initially 1350 articles, all studies in English were included, all duplicates were removed, screening was performed using the PRISMA flow. To correlate with the findings, we followed up a 72-year-old patient who presented with aortic graft infection followed by graft explantation and a fashioned Bovine graft insertion and followed up for 1 year for any re-infection in the clinics.
Results
Literature search resulted 73 articles discussing the role of Bovine Patch as a choice in prevention of Aortic graft re-infection. In our case, there was no clinical nor radiological evidence of Bovine patch re-infection for over a year. Literature review showed that AGI is a rare but serious complication with mortality up to 60%.The main management is IV antibiotics, followed by graft explantation and consideration of re-implantation of various types of grafts. The European society of vascular surgery (ESVS) guidelines recommend re-implantation with an aortic antibiotic soaked graft, yet re-infection rate is quoted at 20%. however, in our case Bovine graft was free from re-infection at 1 year follow up.
Conclusions
IV anitbioics and explantation remain the mainstay for treatment of aortic grafts infection, however, there is increasing evidence that Bovine grafts show excellent freedom from re-infection at follow up. Hence, this might be the conduit of choice when performing such surgeries; however, more evidence is needed.
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M284 EARLY PRESENTATION OF HYPOGAMMAGLOBULINEMIA IN A 6-MONTH-OLD WITH COMPOUND HETEROZYGOUS MUTATIONS IN TNFRSF13B. Ann Allergy Asthma Immunol 2020. [DOI: 10.1016/j.anai.2020.08.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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258P Goserelin for ovarian protection in premenopausal breast cancer patients receiving cyclophosphamide containing chemotherapy. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Abstract
Elimination of inadvertent binding is crucial for inhibitor design targeting conserved protein classes like kinases. Compounds in clinical trials provide a rich source for initiating drug design efforts by exploiting such secondary binding events. Considering both aspects, we shifted the selectivity of tozasertib, originally developed against AurA as cancer target, toward the pain target TrkA. First, selectivity-determining features in binding pockets were identified by fusing interaction grids of several key and off-target conformations. A focused library was subsequently created and prioritized using a multiobjective selection scheme that filters for selective and highly active compounds based on orthogonal methods grounded in computational chemistry and machine learning. Eighteen high-ranking compounds were synthesized and experimentally tested. The top-ranked compound has 10000-fold improved selectivity versus AurA, nanomolar cellular activity, and is highly selective in a kinase panel. This was achieved in a single round of automated in silico optimization, highlighting the power of recent advances in computer-aided drug design to automate design and selection processes.
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Yield and Some Water Relation of wheat (Triticum aestivum L.) Crop as Influenced by Irrigation Regime, Nitrogen Fertilization Rates and Dosses at North Nile Delta. JOURNAL OF SOIL SCIENCES AND AGRICULTURAL ENGINEERING 2018; 9:77-85. [DOI: 10.21608/jssae.2018.35537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinformatics 2017; 18:16. [PMID: 28056780 PMCID: PMC5217312 DOI: 10.1186/s12859-016-1433-7] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 12/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Annotations of the phylogenetic tree of the human kinome is an intuitive way to visualize compound profiling data, structural features of kinases or functional relationships within this important class of proteins. The increasing volume and complexity of kinase-related data underlines the need for a tool that enables complex queries pertaining to kinase disease involvement and potential therapeutic uses of kinase inhibitors. Results Here, we present KinMap, a user-friendly online tool that facilitates the interactive navigation through kinase knowledge by linking biochemical, structural, and disease association data to the human kinome tree. To this end, preprocessed data from freely-available sources, such as ChEMBL, the Protein Data Bank, and the Center for Therapeutic Target Validation platform are integrated into KinMap and can easily be complemented by proprietary data. The value of KinMap will be exemplarily demonstrated for uncovering new therapeutic indications of known kinase inhibitors and for prioritizing kinases for drug development efforts. Conclusion KinMap represents a new generation of kinome tree viewers which facilitates interactive exploration of the human kinome. KinMap enables generation of high-quality annotated images of the human kinome tree as well as exchange of kinome-related data in scientific communications. Furthermore, KinMap supports multiple input and output formats and recognizes alternative kinase names and links them to a unified naming scheme, which makes it a useful tool across different disciplines and applications. A web-service of KinMap is freely available at http://www.kinhub.org/kinmap/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1433-7) contains supplementary material, which is available to authorized users.
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Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding. IUCRJ 2017; 4:7-23. [PMID: 28250938 PMCID: PMC5331462 DOI: 10.1107/s2052252516016675] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
The most prevalent diseases manifested by Escherichia coli are acute and recurrent bladder infections and chronic inflammatory bowel diseases such as Crohn's disease. E. coli clinical isolates express the FimH adhesin, which consists of a mannose-specific lectin domain connected via a pilin domain to the tip of type 1 pili. Although the isolated FimH lectin domain has affinities in the nanomolar range for all high-mannosidic glycans, differentiation between these glycans is based on their capacity to form predominantly hydrophobic interactions within the tyrosine gate at the entrance to the binding pocket. In this study, novel crystal structures of tyrosine-gate mutants of FimH, ligand-free or in complex with heptyl α-d-O-mannopyranoside or 4-biphenyl α-d-O-mannopyranoside, are combined with quantum-mechanical calculations and molecular-dynamics simulations. In the Y48A FimH crystal structure, a large increase in the dynamics of the alkyl chain of heptyl α-d-O-mannopyranoside attempts to compensate for the absence of the aromatic ring; however, the highly energetic and stringent mannose-binding pocket of wild-type FimH is largely maintained. The Y137A mutation, on the other hand, is the most detrimental to FimH affinity and specificity: (i) in the absence of ligand the FimH C-terminal residue Thr158 intrudes into the mannose-binding pocket and (ii) ethylenediaminetetraacetic acid interacts strongly with Glu50, Thr53 and Asn136, in spite of multiple dialysis and purification steps. Upon mutation, pre-ligand-binding relaxation of the backbone dihedral angles at position 137 in the tyrosine gate and their coupling to Tyr48 via the interiorly located Ile52 form the basis of the loss of affinity of the FimH adhesin in the Y137A mutant.
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A Thiazole Analogue Exhibits an Anti-Proliferative Effect in Different Human Carcinoma Cell Lines and Its Mechanism Based on Molecular Modeling. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/abc.2017.71005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Abstract
Kinome-wide screening would have the advantage of providing structure-activity relationships against hundreds of targets simultaneously. Here, we report the generation of ligand-based activity prediction models for over 280 kinases by employing Machine Learning methods on an extensive data set of proprietary bioactivity data combined with open data. High quality (AUC > 0.7) was achieved for ∼200 kinases by (1) combining open with proprietary data, (2) choosing Random Forest over alternative tested Machine Learning methods, and (3) balancing the training data sets. Tests on left-out and external data indicate a high value for virtual screening projects. Importantly, the derived models are evenly distributed across the kinome tree, allowing reliable profiling prediction for all kinase branches. The prediction quality was further improved by employing experimental bioactivity fingerprints of a small kinase subset. Overall, the generated models can support various hit identification tasks, including virtual screening, compound repurposing, and the detection of potential off-targets.
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10
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AB1059 Clinical and Electrophysiological Evaluation of The Effectiveness of Local Insulin Injection in Management of Idiopathic Carpal Tunnel Syndrome (Prospective Study). Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.1035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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11
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11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. J Cheminform 2016; 8:18. [PMID: 29270804 PMCID: PMC4896257 DOI: 10.1186/s13321-016-0119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Abstract
The identification and design of selective compounds is important for the reduction of unwanted side effects as well as for the development of tool compounds for target validation studies. This is, in particular, true for therapeutically important protein families that possess conserved folds and have numerous members such as kinases. To support the design of selective kinase inhibitors, we developed a novel approach that allows identification of specificity determining subpockets between closely related kinases solely based on their three-dimensional structures. To account for the intrinsic flexibility of the proteins, multiple X-ray structures of the target protein of interest as well as of unwanted off-target(s) are taken into account. The binding pockets of these protein structures are calculated and fused to a combined target and off-target pocket, respectively. Subsequently, shape differences between these two combined pockets are identified via fusion rules. The approach provides a user-friendly visualization of target-specific areas in a binding pocket which should be explored when designing selective compounds. Furthermore, the approach can be easily combined with in silico alanine mutation studies to identify selectivity determining residues. The potential impact of the approach is demonstrated in four retrospective experiments on closely related kinases, i.e., p38α vs Erk2, PAK1 vs PAK4, ITK vs AurA, and BRAF vs VEGFR2. Overall, the presented approach does not require any profiling data for training purposes, provides an intuitive visualization of a large number of protein structures at once, and could also be applied to other target classes.
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13
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Design, synthesis, antimicrobial evaluation and molecular docking studies of some new 2,3-dihydrothiazoles and 4-thiazolidinones containing sulfisoxazole. J Enzyme Inhib Med Chem 2015; 31:236-46. [PMID: 25815670 DOI: 10.3109/14756366.2015.1016514] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microbial resistance to the available drugs poses a serious threat in modern medicine. We report the design, synthesis and in vitro antimicrobial evaluation of new functionalized 2,3-dihydrothiazoles and 4-thiazolidinones tagged with sulfisoxazole moiety. Compound 8d was most active against Bacillis subtilis (MIC, 0.007 µg/mL). Moreover, compounds 7c-d and 8c displayed significant activities against B. subtilis and Streptococcus pneumoniae (MIC, 0.03-0.06 µg/mL and 0.06-0.12 µg/mL versus ampicillin 0.24 µg/mL and 0.12 µg/mL; respectively). Compounds 7a and 7c-d were highly potent against Escherichia coli (MIC, 0.49-0.98 µg/mL versus gentamycin 1.95 µg/mL). On the other hand, compounds 7e and 9c were fourfolds more active than amphotericin B against Syncephalastrum racemosum. Molecular docking studies showed that the synthesized compounds could act as inhibitors for the dihydropteroate synthase enzyme (DHPS). This study is a platform for the future design of more potent antimicrobial agents.
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14
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15
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P-168 Definitive 3D concurrent chemoradiotherapy in locally advanced pancreatic cancer. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv233.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Haplosufficient genomic androgen receptor signaling is adequate to protect female mice from induction of polycystic ovary syndrome features by prenatal hyperandrogenization. Endocrinology 2015; 156:1441-52. [PMID: 25643156 DOI: 10.1210/en.2014-1887] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Polycystic ovary syndrome (PCOS) is associated with reproductive, endocrine, and metabolic abnormalities. Because hyperandrogenism is the most consistent PCOS feature, we used wild-type (WT) and androgen receptor (AR) knockout (ARKO) mice, together with a mouse model of PCOS, to investigate the contribution of genomic AR-mediated actions in the development of PCOS traits. PCOS features were induced by prenatal exposure to dihydrotestosterone (250 μg) or oil vehicle (control) on days 16-18 of gestation in WT, heterozygote, and homozygote ARKO mice. DHT treatment of WT mice induced ovarian cysts (100% vs 0%), disrupted estrous cycles (42% vs 100% cycling), and led to fewer corpora lutea (5.0±0.4 vs 9.8±1.8). However, diestrus serum LH and FSH, and estradiol-induced-negative feedback as well as hypothalamic expression of kisspeptin, neurokinin B, and dynorphin, were unaffected by DHT treatment in WT mice. DHT-treated WT mice exhibited a more than 48% increase in adipocyte area but without changes in body fat. In contrast, heterozygous and homozygous ARKO mice exposed to DHT maintained comparable ovarian (histo)morphology, estrous cycling, and corpora lutea numbers, without any increase in adipocyte size. These findings provide strong evidence that genomic AR signaling is an important mediator in the development of these PCOS traits with a dose dependency that allows even AR haplosufficiency to prevent induction by prenatal androgenization of PCOS features in adult life.
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Pocketome of human kinases: prioritizing the ATP binding sites of (yet) untapped protein kinases for drug discovery. J Chem Inf Model 2015; 55:538-49. [PMID: 25557645 DOI: 10.1021/ci500624s] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases are involved in a variety of diseases including cancer, inflammation, and autoimmune disorders. Although the development of new kinase inhibitors is a major focus in pharmaceutical research, a large number of kinases remained so far unexplored in drug discovery projects. The selection and assessment of targets is an essential but challenging area. Today, a few thousands of experimentally determined kinase structures are available, covering about half of the human kinome. This large structural source allows guiding the target selection via structure-based druggability prediction approaches such as DoGSiteScorer. Here, a thorough analysis of the ATP pockets of the entire human kinome in the DFG-in state is presented in order to prioritize novel kinase structures for drug discovery projects. For this, all human kinase X-ray structures available in the PDB were collected, and homology models were generated for the missing part of the kinome. DoGSiteScorer was used to calculate geometrical and physicochemical properties of the ATP pockets and to predict the potential of each kinase to be druggable. The results indicate that about 75% of the kinome are in principle druggable. Top ranking structures comprise kinases that are primary targets of known approved drugs but additionally point to so far less explored kinases. The presented analysis provides new insights into the druggability of ATP binding pockets of the entire kinome. We anticipate this comprehensive druggability assessment of protein kinases to be helpful for the community to prioritize so far untapped kinases for drug discovery efforts.
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Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology. J Comput Aided Mol Des 2014; 28:1191-204. [PMID: 25205292 DOI: 10.1007/s10822-014-9794-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/04/2014] [Indexed: 11/30/2022]
Abstract
Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r(2) of 0.71 and root-mean-squared-error of 1.25 kcal/mol (N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.
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Design, synthesis, antimicrobial evaluation and molecular docking studies of some new thiophene, pyrazole and pyridone derivatives bearing sulfisoxazole moiety. Eur J Med Chem 2014; 84:491-504. [DOI: 10.1016/j.ejmech.2014.07.052] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 01/14/2023]
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Application of solutions of Rhodamine B in dosimetry. Appl Radiat Isot 2014; 89:13-7. [PMID: 24561650 DOI: 10.1016/j.apradiso.2013.11.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 11/10/2013] [Accepted: 11/14/2013] [Indexed: 11/30/2022]
Abstract
Aqueous solutions of the organic dye Rhodamine B were found to be useful in measuring radiation doses in the range 0.1-2 kGy. Either spectrophotometric or spectrofluorometric measurements can be used. The dosimeter readout is unchanged for at least 60 days after irradiation if the solution is kept in the dark at room temperature. Effects of pH and the dye concentration on the dosimeter response were investigated. Radiation chemical yield and fluorescence quantum yield were also calculated.
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Expression of endogenous para-retroviral genes and molecular analysis of the integration events in its plant host Dahlia variabilis. Virus Genes 2013; 48:153-9. [PMID: 24258394 DOI: 10.1007/s11262-013-0998-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
The dahlia (Dahlia variabilis) genome contains an endogenous pararetrovirus sequence (EPRS) tentatively designated as DvEPRS. The DvEPRS shares genome structure and organization that is typical of members of the Caulimovirus genus. Studies were carried out to better understand the nature of this integration and to determine the gene expression of this DvEPRS. Genomic Southern hybridization showed multiple and random integration events of the DvEPRS in the dahlia genome. To investigate the presence of DvEPRS transcripts, RT-PCR was done on DNase-treated total RNA from DvEPRS-infected dahlia plants. Results showed the expression of open reading frames I, V, and VI. Direct PCR from sap extracts produced more intense DNA amplicons of Dahlia mosaic virus and Dahlia common mosaic virus which are believed to exist as typical episomal caulimoviruses, whereas significantly less intense amplicon was seen in case of DvEPRS in comparison with internal transcribed spacer region of dahlias amplicon. The DvEPRS in wild and cultivated species of Dahlia offer a model system to study the molecular events underlying the ecology, evolution and spread of DvEPRS within natural and managed ecosystems and the factors affecting integration of these EPRS in the plant genome.
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Molecular design and synthesis of HCV inhibitors based on thiazolone scaffold. Eur J Med Chem 2013; 68:19-32. [DOI: 10.1016/j.ejmech.2013.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 01/25/2023]
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Involvement of renal cytochromes P450 and arachidonic acid metabolites in diabetic nephropathy. J BIOL REG HOMEOS AG 2013; 27:693-703. [PMID: 24152838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Diabetic nephropathy (DN) is one of the most serious complications of type I and type II diabetes. DN is characterized by hyperfiltration, hypertrophy, extracellular matrix accumulation, and proteinuria. This advances into renal fibrosis and loss of renal function. Reactive oxygen species (ROS) and TGF-beta have been implicated in the pathogenesis of diabetic nephropathy. Early stages of diabetic nephropathy are also associated with alterations in renal sodium handling as well as hypertension; both are processes linked by involvement of the arachidonic acid (AA) metabolites, 20-hydroxyeicosatetraenoic acid (20-HETE, produced by cytochrome P450-4a, (CYP4A) and epoxyeicosatrienoic acids (EETs). Indeed, metabolism of AA is increased in a rat model of diabetes. In this study, we demonstrate that rats with streptozotocin-induced diabetes of 1 month duration develop renal hypertrophy and increased fibronectin and TGF-beta1 expression/cortical levels concomitant with an increase in CYP4A expression and 20 HETE production. These results were also paralleled by an increase in reactive oxygen species (ROS) production and NADPH oxidase activity. Treatment of diabetic rats with HET0016, selective inhibitor of CYP 4A, prevented all these changes. Our results suggest that diabetes-induced induction of CYP4A and 20-HETE production could be a major pathophysiological mechanism leading to activation of ROS through an NADPH dependent pathway and TGF-beta1 thus resulting in major renal pathology. Inhibitors of 20-HETE production could thus have an important therapeutic potential in the treatment of diabetic nephropathy.
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Analogs design, synthesis and biological evaluation of peptidomimetics with potential anti-HCV activity. Bioorg Med Chem 2013; 21:2742-55. [DOI: 10.1016/j.bmc.2013.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 02/23/2013] [Accepted: 03/03/2013] [Indexed: 02/01/2023]
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A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences. Int J Mol Sci 2013; 14:684-700. [PMID: 23344039 PMCID: PMC3565289 DOI: 10.3390/ijms14010684] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 12/21/2012] [Accepted: 12/26/2012] [Indexed: 11/16/2022] Open
Abstract
In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand–protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.
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Use of hyaluronan in the selection of sperm for intracytoplasmic sperm injection (ICSI): significant improvement in clinical outcomes--multicenter, double-blinded and randomized controlled trial. Hum Reprod 2012. [PMID: 23203216 PMCID: PMC3545641 DOI: 10.1093/humrep/des417] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
STUDY QUESTION Does the selection of sperm for ICSI based on their ability to bind to hyaluronan improve the clinical pregnancy rates (CPR) (primary end-point), implantation (IR) and pregnancy loss rates (PLR)? SUMMARY ANSWER In couples where ≤65% of sperm bound hyaluronan, the selection of hyaluronan-bound (HB) sperm for ICSI led to a statistically significant reduction in PLR. WHAT IS KNOWN AND WHAT THIS PAPER ADDS HB sperm demonstrate enhanced developmental parameters which have been associated with successful fertilization and embryogenesis. Sperm selected for ICSI using a liquid source of hyaluronan achieved an improvement in IR. A pilot study by the primary author demonstrated that the use of HB sperm in ICSI was associated with improved CPR. The current study represents the single largest prospective, multicenter, double-blinded and randomized controlled trial to evaluate the use of hyaluronan in the selection of sperm for ICSI. DESIGN Using the hyaluronan binding assay, an HB score was determined for the fresh or initial (I-HB) and processed or final semen specimen (F-HB). Patients were classified as >65% or ≤65% I-HB and stratified accordingly. Patients with I-HB scores ≤65% were randomized into control and HB selection (HYAL) groups whereas patients with I-HB >65% were randomized to non-participatory (NP), control or HYAL groups, in a ratio of 2:1:1. The NP group was included in the >65% study arm to balance the higher prevalence of patients with I-HB scores >65%. In the control group, oocytes received sperm selected via the conventional assessment of motility and morphology. In the HYAL group, HB sperm meeting the same visual criteria were selected for injection. Patient participants and clinical care providers were blinded to group assignment. PARTICIPANTS AND SETTING Eight hundred two couples treated with ICSI in 10 private and hospital-based IVF programs were enrolled in this study. Of the 484 patients stratified to the I-HB > 65% arm, 115 participants were randomized to the control group, 122 participants were randomized to the HYAL group and 247 participants were randomized to the NP group. Of the 318 patients stratified to the I-HB ≤ 65% arm, 164 participants were randomized to the control group and 154 participants were randomized to the HYAL group. MAIN RESULTS AND THE ROLE OF CHANCE HYAL patients with an F-HB score ≤65% demonstrated an IR of 37.4% compared with 30.7% for control [n = 63, 58, P > 0.05, (95% CI of the difference −7.7 to 21.3)]. In addition, the CPR associated with patients randomized to the HYAL group was 50.8% when compared with 37.9% for those randomized to the control group (n = 63, 58, P > 0.05). The 12.9% difference was associated with a risk ratio (RR) of 1.340 (RR 95% CI 0.89–2.0). HYAL patients with I-HB and F-HB scores ≤65% revealed a statistically significant reduction in their PLR (I-HB: 3.3 versus 15.1%, n = 73, 60, P = 0.021, RR of 0.22 (RR 95% CI 0.05–0.96) (F-HB: 0.0%, 18.5%, n = 27, 32, P = 0.016, RR not applicable due to 0.0% value) over control patients. The study was originally planned to have 200 participants per arm providing 86.1% power to detect an increase in CPR from 35 to 50% at α = 0.05 but was stopped early for financial reasons. As a pilot study had demonstrated that sperm preparation protocols may increase the HB score, the design of the current study incorporated a priori collection and analysis of the data by both the I-HB and the F-HB scores. Analysis by both the I-HB and F-HB score acknowledged the potential impact of sperm preparation protocols. BIAS, CONFOUNDING AND OTHER REASONS FOR CAUTION Selection bias was controlled by randomization. Geographic and seasonal bias was controlled by recruiting from 10 geographically unique sites and by sampling over a 2-year period. The potential for population effect was controlled by adjusting for higher prevalence rates of >65% I-HB that naturally occur by adding the NP arm and to concurrently recruit >65% and ≤65% I-HB subjects. Monitoring and site audits occurred regularly to ensure standardization of data collection, adherence to the study protocol and subject recruitment. Subgroup analysis based on the F-HB score was envisaged in the study design. GENERALIZABILITY TO OTHER POPULATIONS The study included clinics using different sperm preparation methods, located in different regions of the USA and proceeded in every month of the year. Therefore, the results are widely applicable. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Biocoat, Inc., Horsham, PA, USA. The statistical analysis plan and subsequent analyses were performed by Sherrine Eid, a biostatistician. The manuscript was prepared by Kathryn C. Worrilow, Ph.D. and the study team members. Biocoat, Inc. was permitted to review the manuscript and suggest changes, but the final decision on content was exclusively retained by the authors. K.C.W is a scientific advisor to Biocoat, Inc. S.E. is a consultant to Biocoat, Inc. D.W. has nothing to disclose. M.P., S.S., J.W., K.I., C.K. and T.E. have nothing to disclose. G.D.B. is a consultant to Cooper Surgical and Unisense. J.L. is on the scientific advisory board of Origio. TRIAL REGISTRATION NUMBER NCT00741494.
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Human Multipotent Adult Progenitor Cells Effectively Modulate Alloreactivity After Bone Marrow Transplantation Reducing GVHD While Preserving Graft-Versus-Leukemia Activity. Biol Blood Marrow Transplant 2012. [DOI: 10.1016/j.bbmt.2011.12.440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Increased clinical pregnancy rates (CPR) and statistically significant decrease in loss rates using hyaluronan in sperm selection: prospective, multi-center, double-blind, randomized clinical trial. Fertil Steril 2011. [DOI: 10.1016/j.fertnstert.2011.07.696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genomic characterization of pararetroviral sequences in wild Dahlia spp. in natural habitats. Arch Virol 2011; 156:2079-84. [DOI: 10.1007/s00705-011-1076-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 07/15/2011] [Indexed: 10/17/2022]
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P02-55 - Forensic psychiatric services in Kuwait and the need for mental heath legislation. Eur Psychiatry 2010. [DOI: 10.1016/s0924-9338(10)70669-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Differential Mechanisms for CD4+ and CD8+ Mediated Inflammation in the Development of Experimental Idiopathic Pneumonia Syndrome. Biol Blood Marrow Transplant 2009. [DOI: 10.1016/j.bbmt.2008.12.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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The hyaluronan binding assay HBA™: a novel and statistically significant predictor of clinical pregnancy (CP) in in vitro fertilization (IVF) and assisted reproductive technology (ART). Fertil Steril 2008. [DOI: 10.1016/j.fertnstert.2008.07.349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Use of Bromocresol Green Dyed Poly(Vinyl Butyral) Film for Dosimetric Applications. INT J POLYM MATER PO 2007. [DOI: 10.1080/00914030701220065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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A prospective randomized phase II trial of splenic irradiation (SI) versus supportive therapy (ST) for patients (Pts) with hypersplenism (HS) secondary (2ry) to splenic periportal fibrosis (SPPF). J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
16511 Background: HS 2ry to SPPF is a common problem in Egypt as a result of prevalence of bilharziasis. ST is the only option for the majority of pts who have poor performance status (PS) and cannot tolerate/refuse surgery. Methods: Aim of study was to evaluate the effect of SI versus ST on patients with HS 2ry to SPPF. Assessment of treatment was based on changes in Red Cell indices (RCI), Platelet indices (PI), splenic volume (SVol), and splenic vein diameter (SVD). In this study we had 19 evaluable Pts, 10 had SI and 9 had ST. Those who received SI had a twice weekly course of 1.5 Gy for a total of 3 weeks. RCI & PI were measured each visit, SVol & SVD (measured by duplex-Doppler US were measured initially, 3 & 6 months (mos) after treatment). Results: SVol & SVD increased significantly after 3 and 6 mos of ST, compared to insignificant decrease after 3 and 6 mos of SI. Platelet count (PC) significantly increased in all follow-ups (FU) after SI till 1.5 years compared to insignificant decreases in ST group after 3 and 6 mos. FU of mean platelet volume (MPV) and platelet distribution width (PDW) increased in ST group and decreased significantly in SI. Red blood cell (RBC) count and hemoglobin (Hb) levels increased significantly after SI till 6 and 9 mos respectively compared to insignificant decrease in RBC count and significant decrease in Hb level after 6 mos of ST. Changes in white blood cell counts were insignificant. After SI, changes in SVol showed significant positive correlations with changes in SVD and significant negative correlations with changes in PC. Changes in MPV showed significant positive correlation with changes in SVD. Side-effects (SE) seen with SI were moderate and transient. Conclusions: SI is a promising new modality of treatment with acceptable SE for pts with HS. Dose and schedule of SI should be modified according to pts PS. Changes in SVD are highly correlated with the degree of platelet and red cell turnover. Its predictive value for HS should be studied further. No significant financial relationships to disclose.
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Assessment of post-operative pain management at the American University of Beirut Medical Center. MIDDLE EAST JOURNAL OF ANAESTHESIOLOGY 2004; 17:1113-26. [PMID: 15651518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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Spectrophotometric readout for an alanine dosimeter for food irradiation applications. Radiat Phys Chem Oxf Engl 1993 2003. [DOI: 10.1016/s0969-806x(03)00107-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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[Lactating adenoma: radiologic aspects. A case report]. JOURNAL DE RADIOLOGIE 2001; 82:264-7. [PMID: 11287859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
We report the US and MRI appearance in a patient with a giant lactating adenoma detected during pregnancy and followed-up for 12 months postpartum. The different imaging features of lactating adenomas are discussed, especially at US and MRI. We discuss also the role of core biopsy in diagnosing pregnancy associated breast masses.
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The dietary habits of young people. NURSING TIMES 1997; 93:46-8. [PMID: 9455294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adolescence is a time when patterns of behaviour can be set for life. This research project sought to listen to young people and understand the things that influence their acceptance of and accessibility to a healthy diet.
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Assembly of the prothrombinase complex in the absence of prothrombin. J Biol Chem 1981; 256:9874-82. [PMID: 7275986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Intestinal mucosal changes in thalassaemia major. EGYPTIAN PEDIATRIC ASSOCIATION GAZETTE 1975; 23:261-5. [PMID: 1230351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ten infants and children suffering from Thalassaemia major, proven by clinical, hematological and biochemical criteria, were subjected to intestinal biopsy. Specimens were studied for histological and histochemical patterns. The histological picture showed shortening and fusion of villi with cellular infiltration. Reduced mucopolysaccharides and relatively normal alkaline phosphatase activity were demonstrated. The degree of histological and histochemical changes correlates with the degree of anemia. The effects of these changes on the iron absorption and the tissue hemosiderosis are aroused. The possibility of these changes, being non-specific and secondary to anemia and tissue hypoxia is also postulated.
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