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Suitable reference genes for relative quantification of miRNA expression in prostate cancer

Annika Schaefer, Monika Jung, Kurt Miller, Michael Lein, Glen Kristiansen, Andreas Erbersdobler, Klaus Jung
2010 Experimental and Molecular Medicine  
K (2010) . Suitable reference genes for relative quantification of miRNA expression in prostate cancer. Experimental and Molecular Medicine, 42(11):749-758. Abstract Real time quantitative PCR (qPCR) is the method of choice for miRNA expression studies. For relative quantification of miRNAs, normalization to proper reference genes is mandatory. Currently, no validated reference genes for miRNA qPCR in prostate cancer are available. In this study, the expression of four putative reference genes
more » ... hsa-miR-16, hsa-miR-130b, RNU6-2, SNORD7) was examined with regard to their use as normalizer. After SNORD7 was already shown an inappropriate reference gene in preliminary experiments using total RNA pools, we studied the expression of the putative reference genes in tissue and normal adjacent tissue sample pairs from 76 men with untreated prostate carcinoma collected after radical prostatectomy. hsa-miR-130b and RNU6-2 showed no significantly different expression between the matched malignant and non-malignant tissue samples, whereas hsa-miR-16 was significantly underexpressed in malignant tissue. Softwares geNorm and Normfinder predicted hsa-miR-130b and the geometric mean of hsa-miR-130b and RNU6-2 as the most stable reference genes. Normalization of the four miRNAs hsa-miR-96, hsa-miR-125b, hsa-miR-205, and hsa-miR-375, which were previously shown to be regulated, shows that normalization to hsa-mir-16 can lead to biased results. We recommend using hsa-miR-130b or the geometric mean of hsa-miR-130b and small RNA RNU6-2 for normalization in miRNA expression studies of prostate cancer. Abstract Real time quantitative PCR (qPCR) is the method of choice for miRNA expression studies. For relative quantification of miRNAs, normalization to proper reference genes is mandatory. Currently, no validated ref- erence genes for miRNA qPCR in prostate cancer are available. In this study, the expression of four putative reference genes (hsa-miR-16, hsa-miR-130b, RNU6-2, SNORD7) was examined with regard to their use as normalizer. After SNORD7 was already shown an inappropriate reference gene in preliminary experiments using total RNA pools, we studied the expression of the putative reference genes in tissue and normal adjacent tissue sample pairs from 76 men with untreated prostate carcinoma collected after radical prostatectomy. hsa-miR-130b and RNU6-2 showed no significantly different expression between the matched malignant and non-malignant tissue samples, whereas hsa-miR-16 was significantly underexpressed in malignant tissue. Softwares geNorm and Normfinder predicted hsa-miR-130b and the geometric mean of hsa-miR-130b and RNU6-2 as the most stable reference genes. Normalization of the four miRNAs hsa-miR-96, hsa-miR-125b, hsa-miR-205, and hsa-miR-375, which were previously shown to be regulated, shows that normalization to hsa-mir-16 can lead to biased results. We recommend using hsa-miR-130b or the geometric mean of hsa-miR-130b and small RNA RNU6-2 for normalization in miRNA expression studies of prostate cancer.
doi:10.3858/emm.2010.42.11.076 pmid:20890088 pmcid:PMC2992854 fatcat:4gj2eytx5zdctcmlsavxhal6ni

Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations

Mari Gabrielsen, Aina Westrheim Ravna, Kurt Kristiansen, Ingebrigt Sylte
2011 Journal of Molecular Modeling  
The serotonin (5-HT) transporter (SERT) plays an important role in the termination of 5-HT-mediated neurotransmission by transporting 5-HT away from the synaptic cleft and into the presynaptic neuron. In addition, SERT is the main target for antidepressant drugs, including the selective serotonin reuptake inhibitors (SSRIs). The three-dimensional (3D) structure of SERT has not yet been determined, and little is known about the molecular mechanisms of substrate binding and transport, though such
more » ... information is very important for the development of new antidepressant drugs. In this study, a homology model of SERT was constructed based on the 3D structure of a prokaryotic homologous leucine transporter (LeuT) (PDB id: 2A65). Eleven tryptamine derivates (including 5-HT) and the SSRI (S)-citalopram were docked into the putative substrate binding site, and two possible binding modes of the ligands were found. To study the conformational effect that ligand binding may have on SERT, two SERT-5-HT and two SERT-(S)-citalopram complexes, as well as the SERT apo structure, were embedded in POPC lipid bilayers and comparative molecular dynamics (MD) simulations were performed. Our results show that 5-HT in the SERT-5-HT B complex induced larger conformational changes in the cytoplasmic parts of the transmembrane helices of SERT than any of the other ligands. Based on these results, we suggest that the formation and breakage of ionic interactions with amino acids in transmembrane helices 6 and 8 and intracellular loop 1 may be of importance for substrate translocation.
doi:10.1007/s00894-011-1133-1 pmid:21670993 pmcid:PMC3283764 fatcat:hvxukqzah5ftxfeomjagytzr5u

Brain-type and liver-type fatty acid-binding proteins: new tumor markers for renal cancer?

Angelika Tölle, Monika Jung, Michael Lein, Manfred Johannsen, Kurt Miller, Holger Moch, Klaus Jung, Glen Kristiansen
2009 BMC Cancer  
Renal cell carcinoma (RCC) is the most common renal neoplasm. Cancer tissue is often characterized by altered energy regulation. Fatty acid-binding proteins (FABP) are involved in the intracellular transport of fatty acids (FA). We examined the level of brain-type (B) and livertype (L) FABP mRNA and the protein expression profiles of both FABPs in renal cell carcinoma. Methods: Paired tissue samples of cancerous and noncancerous kidney parts were investigated. Quantitative RT-PCR,
more » ... mistry and western blotting were used to determine B-and L-FABP in tumor and normal tissues. The tissue microarray (TMA) contained 272 clinicopathologically characterized renal cell carcinomas of the clear cell, papillary and chromophobe subtype. SPSS 17.0 was used to apply crosstables (χ 2 -test), correlations and survival analyses. Results: B-FABP mRNA was significantly up-regulated in renal cell carcinoma. In normal tissue B-FABP mRNA was very low or often not detectable. RCC with a high tumor grading (G3 + G4) showed significantly lower B-FABP mRNA compared with those with a low grading (G1 + G2). Western blotting analysis detected B-FABP in 78% of the cases with a very strong band but in the corresponding normal tissue it was weak or not detectable. L-FABP showed an inverse relationship for mRNA quantification and western blotting. A strong B-FABP staining was present in 52% of the tumor tissues contained in the TMA. In normal renal tissue, L-FABP showed a moderate to strong immunoreactivity in proximal tubuli. L-FABP was expressed at lower rates compared with the normal tissues in 30.5% of all tumors. There was no correlation between patient survival times and the staining intensity of both FABPs. Conclusion: While B-FABP is over expressed in renal cell carcinoma in comparison to normal renal tissues L-FABP appears to be reduced in tumor tissue. Although the expression behavior was not related to the survival outcome of the RCC patients, it can be assumed that these changes indicate fundamental alterations in the fatty metabolism in the RCC carcinogenesis. Further studies should identify the role of both FABPs in carcinogenesis, progression and with regard to a potential target in RCC.
doi:10.1186/1471-2407-9-248 pmid:19622156 pmcid:PMC2732640 fatcat:fohjgeybqrb2re6hxnotfe26tq

Interaction Codes within the Family of Mammalian Phox and Bem1p Domain-containing Proteins

Trond Lamark, Maria Perander, Heidi Outzen, Kurt Kristiansen, Aud Øvervatn, Espen Michaelsen, Geir Bjørkøy, Terje Johansen
2003 Journal of Biological Chemistry  
Kristiansen, G. Bjørkøy, and T. Johansen, unpublished data. T. Lamark, M. Perander, H. Outzen, K. Kristiansen, Aud Øvervatn, E. Michaelsen, G. Bjørkøy, and T. Johansen, unpublished data.  ... 
doi:10.1074/jbc.m303221200 pmid:12813044 fatcat:vqmteoh4hnd7ridwrbbkp6gexi

Differences in PAR-2 activating potential by king crab (Paralithodes camtschaticus), salmon (Salmo salar), and bovine (Bos taurus) trypsin

Anett K Larsen, Kurt Kristiansen, Ingebrigt Sylte, Ole-Morten Seternes, Berit E Bang
2013 BMC Research Notes  
Salmon trypsin is shown to increase secretion of the pro-inflammatory cytokine interleukin (IL)-8 from human airway epithelial cells through activation of PAR-2. Secretion of IL-8 induced by king crab trypsin is observed in a different concentration range compared to salmon trypsin, and seems to be only partially related to PAR-2 activation. This report aim to identify differences in the molecular structure of king crab trypsin (Paralithodes camtschaticus) compared to salmon (Salmo salar) and
more » ... vine trypsin (Bos taurus) that might influence the ability to activate protease-activated receptor-2 (PAR-2). Results: During purification king crab trypsin displayed stronger binding capacity to the anionic column used in fast protein liquid chromatography compared to fish trypsins, and was identified as a slightly bigger molecule. Measurements of enzymatic activity yielded no obvious differences between the trypsins tested. Molecular modelling showed that king crab trypsin has a large area with strong negative electrostatic potential compared to the smaller negative areas in bovine and salmon trypsins. Bovine and salmon trypsins also displayed areas with strong positive electrostatic potential, a feature lacking in the king crab trypsin. Furthermore we have identified 3 divergent positions (Asp 196 , Arg 244 , and Tyr 247 ) located near the substrate binding pocket of king crab trypsin that might affect the binding and cleavage of PAR-2. Conclusion: These preliminary results indicate that electrostatic interactions could be of importance in binding, cleavage and subsequent activation of PAR-2.
doi:10.1186/1756-0500-6-281 pmid:23870109 pmcid:PMC3733831 fatcat:w2zdib3qrrgmxco746fqhthwt4

Identification of Novel Serotonin Transporter Compounds by Virtual Screening

Mari Gabrielsen, Rafał Kurczab, Agata Siwek, Małgorzata Wolak, Aina W. Ravna, Kurt Kristiansen, Irina Kufareva, Ruben Abagyan, Gabriel Nowak, Zdzisław Chilmonczyk, Ingebrigt Sylte, Andrzej J. Bojarski
2014 Journal of Chemical Information and Modeling  
The serotonin (5-hydroxytryptamine, 5-HT) transporter (SERT) plays an essential role in the termination of serotonergic neurotransmission by removing 5-HT from the synaptic cleft into the presynaptic neuron. It is also of pharmacological importance being targeted by antidepressants and psychostimulant drugs. Here, five commercial databases containing approximately 3.24 million drug-like compounds have been screened using a combination of two-dimensional (2D) fingerprint-based and
more » ... al (3D) pharmacophore-based screening and flexible docking into multiple conformations of the binding pocket detected in an outward-open SERT homology model. Following virtual screening (VS), selected compounds were evaluated using in vitro screening and full binding assays and an in silico hit-to-lead (H2L) screening was performed to obtain analogues of the identified compounds. Using this multistep VS/H2L approach, 74 active compounds, 46 of which had K(i) values of ≤1000 nM, belonging to 16 structural classes, have been identified, and multiple compounds share no structural resemblance with known SERT binders.
doi:10.1021/ci400742s pmid:24521202 pmcid:PMC3982395 fatcat:pbxb47lzsfbnzbgdhvlsticfzy

KLK15 is a prognostic marker for progression-free survival in patients with radical prostatectomy

Anja Rabien, Florian R. Fritzsche, Monika Jung, Angelika Tölle, Eleftherios P. Diamandis, Kurt Miller, Klaus Jung, Glen Kristiansen, Carsten Stephan
2010 International Journal of Cancer  
In search of biomarkers for prostate cancer, we evaluated the expression of the human kallikrein-related peptidase KLK15 in samples of prostatic adenocarcinomas from radical prostatectomies. Twenty-five pairs of cancerous and adjacent normal prostatic tissue were selected by laser capture microdissection. The tissue was used for quantification of KLK15 mRNA by reverse-transcriptase polymerase chain reaction. Immunohistochemical expression of the KLK15 protein in 193 samples of prostatic
more » ... cinoma was analysed in relation to clinicopathological parameters of the patients and disease progression. Expression of KLK15 correlated with the pathological tumour stage and Gleason score of the cases, both at mRNA and at protein level. While mRNA expression in the tumour was elevated, the protein level of KLK15 was reduced compared with adjacent normal tissue and to prostatic intraepithelial neoplasia. Univariate Kaplan-Meier analysis showed a significant association of dichotomised KLK15 levels with disease progression defined by prostate-specific antigen relapse (p 5 0.001). Multivariate analysis according to the Cox proportional hazards regression model identified dichotomised KLK15 expression, corrected for the patient parameters age, preoperative prostate-specific antigen level, pathological tumour stage, Gleason score and surgical margin status, as an independent prognostic factor for poor outcome (inclusion model, hazard ratio 1.802, 95% confidence interval 1.037-3.132, p 5 0.037). We suggest KLK15 as a new independent tumour marker for patients at risk for disease progression after radical prostatectomy.
doi:10.1002/ijc.25435 pmid:20473923 fatcat:pboaco3d5nhothykb4utfg4th4

Sarcosine in Urine after Digital Rectal Examination Fails as a Marker in Prostate Cancer Detection and Identification of Aggressive Tumours

Florian Jentzmik, Carsten Stephan, Kurt Miller, Mark Schrader, Andreas Erbersdobler, Glen Kristiansen, Michael Lein, Klaus Jung
2010 European Urology  
1) Service d'urologie, hôpital Tenon, groupe hospitalo-universitaire EST (AP-HP), université Paris-VI, Paris (2) Secteur vétérinaire de Paris, école militaire, Paris Résumé La problématique de la détection du cancer repose sur l'efficacité des tests diagnostics, et plus particulièrement sur la sensibilité et la spécificité des biomarqueurs. Dans le domaine urologique, les marqueurs urinaires sont particulièrement intéressants du fait de leur contact avec la tumeur. La corrélation entre l'odeur
more » ... es urines et la présence d'un cancer a été récemment évoquée, grâce à l'utilisation de chiens dressés (dotés d'un odorat puissant), et confirmée dans notre propre expérience. Ces résultats évoquent une signature moléculaire du cancer, dont la caractérisation physicochimique fait appel à des démarches de recherches nouvelles. Cet article fait le point sur les avancées actuelles dans ce domaine ainsi que sur les possibles applications dans le futur.
doi:10.1016/j.eururo.2010.01.035 pmid:20117878 fatcat:7uurwuvkjzelnjg7qrb2rfrb2a

In silico site-directed mutagenesis of the Daphnia magna ecdysone receptor identifies critical amino acids for species-specific and inter-species differences in agonist binding

Linn M. Evenseth, Kurt Kristiansen, You Song, Knut Erik Tollefsen, Ingebrigt Sylte
2019 Computational Toxicology  
Molting is an essential process in the life cycle of arthropods and is regulated by complex neuroendocrine pathways where activation of the ecdysone receptor (EcR) plays a major role. The EcR forms a non-covalent heterodimer with the ultraspiracle protein (USP) when activated by endogenous ecdysteroids, but can also be activated by several insecticides and other environmental chemicals. Environmental release of exogenous chemicals may thus represent a risk to non-target species due to
more » ... ic conservation of the EcR in arthropods. In the present study, structural analysis and homology models of the EcR from the freshwater crustacean Daphnia magna were used to characterise the agonist binding pocket and identify amino acids responsible for differences in agonist binding between arthropod species. The analysis showed that the binding pockets of steroidal and non-steroidal agonists are partly overlapping, and the phylogenetically conserved Thr59 is a key residue for binding both types of agonists. In silico site-directed mutagenesis and MM-GBSA dG calculations revealed that Cys100 (D. magna numbering) is a structural determinant for cross species affinities. Other determinants are Val129 for both types of agonists, Thr132 for steroidal agonists and Asp134 for non-steroidal agonists. The present results can be used to predict cross species sensitivity for EcR agonists, and shows that homology modelling and affinity predictions may contribute to identifying susceptible species for EcR-mediated endocrine disruption.
doi:10.1016/j.comtox.2019.100091 fatcat:jtuw37moovfn5naykhqnnbapku

In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility Derived From the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Tool

Jon A Doering, Sehan Lee, Kurt Kristiansen, Linn Evenseth, Mace G Barron, Ingebrigt Sylte, Carlie A LaLone
2018 Toxicological Sciences  
doi:10.1093/toxsci/kfy186 pmid:30060110 fatcat:pvxvls4e6jdrfh4ahu47lthdue

Renal cell neoplasias: reversion-inducing cysteine-rich protein with Kazal motifs discriminates tumor subtypes, while extracellular matrix metalloproteinase inducer indicates prognosis

Anja Rabien, Carsten Stephan, Ergin Kilic, Wilko Weichert, Glen Kristiansen, Kurt Miller, Klaus Jung, Andreas Erbersdobler
2013 Journal of Translational Medicine  
Matrix metalloproteinases can promote invasion and metastasis, which are very frequent in renal cell carcinoma even at the time of diagnosis. Knowing the reversion-inducing cysteine-rich protein with Kazal motifs (RECK) as an inhibitor of matrix metalloproteinases and the extracellular matrix metalloproteinase inducer (EMMPRIN) protein as inducer, we aimed to determine their expression, localization and possible antagonistic action in the pathogenesis and progression of renal cell tumors in a
more » ... trospective study. Methods: Tumor and adjacent normal tissues of 395 nephrectomized patients were immunostained for RECK and EMMPRIN on a tissue microarray. Results: RECK strongly decreased in renal cell carcinoma compared to normal counterparts (Wilcoxon signed rank test, P < 0.001), and it discriminated tumor entities showing the highest expression in oncocytomas. EMMPRIN, however, could be significantly correlated to pT stage and Fuhrman grading (Spearman's correlation coefficient r s = 0.289 and r s = 0.382, respectively). Higher expression of EMMPRIN was associated with decreased overall survival in Kaplan-Meier analysis (P < 0.001), and the EMMPRIN level could independently predict survival for cases without metastasis and involvement of lymph nodes. Decreased RECK expression was confirmed by Western blotting in tissue of eight normal/tumor matches of patients after radical nephrectomy, whereas the EMMPRIN pattern appeared to be heterogeneous. Conclusions: We propose RECK down regulation in renal cell carcinoma to be an early event that facilitates tumor formation and progression. EMMPRIN, however, as a prognostic tumor marker, increases only when aggressiveness is proceeding and could add an additional step to invasive properties of renal cell carcinoma.
doi:10.1186/1479-5876-11-258 pmid:24131772 pmcid:PMC3853196 fatcat:nnxhyb2pebghpalow43mvbepki

Down-regulation of the pro-apoptotic XIAP associated factor-1 (XAF1) during progression of clear-cell renal cancer

Carsten Kempkensteffen, Florian Rudolf Fritzsche, Manfred Johannsen, Steffen Weikert, Stefan Hinz, Manfred Dietel, Marc-Oliver Riener, Holger Moch, Klaus Jung, Hans Krause, Kurt Miller, Glen Kristiansen
2009 BMC Cancer  
BACKGROUND: Decreased expression of the interferon-stimulated, putative tumour suppressor gene XAF1 has been shown to play a role during the onset, progression and treatment failure in various malignancies. However, little is yet known about its potential implication in the tumour biology of clear-cell renal cell cancer (ccRCC). METHODS: This study assessed the expression of XAF1 protein in tumour tissue obtained from 291 ccRCC patients and 68 normal renal tissue samples, utilizing
more » ... emistry on a tissue-micro-array. XAF1 expression was correlated to clinico-pathological tumour features and prognosis. RESULTS: Nuclear XAF1 expression was commonly detected in normal renal-(94.1%) and ccRCC (91.8%) samples, without significant differences of expression levels. Low XAF1 expression in ccRCC tissue, however, was associated with progression of tumour stage (p = 0.040) and grade (p < 0.001). Low XAF1 tumour levels were also prognostic of significantly shortened overall survival times in univariate analysis (p = 0.018), but did not provide independent prognostic information. CONCLUSION: These data suggest down-regulation of XAF1 expression to be implicated in ccRCC progression and implies that its re-induction may provide a therapeutic approach. Although the prognostic value of XAF1 in ccRCC appears to be limited, its predictive value remains to be determined, especially in patients with metastatic disease undergoing novel combination therapies of targeted agents with Interferon-alpha. Abstract Background: Decreased expression of the interferon-stimulated, putative tumour suppressor gene XAF1 has been shown to play a role during the onset, progression and treatment failure in various malignancies. However, little is yet known about its potential implication in the tumour biology of clear-cell renal cell cancer (ccRCC). Methods: This study assessed the expression of XAF1 protein in tumour tissue obtained from 291 ccRCC patients and 68 normal renal tissue samples, utilizing immunohistochemistry on a tissuemicro-array. XAF1 expression was correlated to clinico-pathological tumour features and prognosis. Results: Nuclear XAF1 expression was commonly detected in normal renal-(94.1%) and ccRCC (91.8%) samples, without significant differences of expression levels. Low XAF1 expression in ccRCC tissue, however, was associated with progression of tumour stage (p = 0.040) and grade (p < 0.001). Low XAF1 tumour levels were also prognostic of significantly shortened overall survival times in univariate analysis (p = 0.018), but did not provide independent prognostic information. Conclusion: These data suggest down-regulation of XAF1 expression to be implicated in ccRCC progression and implies that its re-induction may provide a therapeutic approach. Although the prognostic value of XAF1 in ccRCC appears to be limited, its predictive value remains to be determined, especially in patients with metastatic disease undergoing novel combination therapies of targeted agents with Interferon-alpha.
doi:10.1186/1471-2407-9-276 pmid:19664236 pmcid:PMC3087333 fatcat:tjpcshzci5anbli2p6uf4xa4zq

Ibuprofen-in-cyclodextrin-in-W/O/W emulsion – Improving the initial and long-term encapsulation efficiency of a model active ingredient

Magnus N. Hattrem, Kåre A. Kristiansen, Finn L. Aachmann, Morten J. Dille, Kurt I. Draget
2015 International Journal of Pharmaceutics  
A challenge with formulating water-in-oil-in-water (W/O/W) emulsions is the uncontrolled release of encapsulated compound prior to application. Pharmaceuticals and nutraceuticals usually have amphipathic nature, which may contribute to leakage of the active ingredient. In the present study, cyclodextrins (CyDs) were used to impart a change in the relative polarity and size of a model compound (ibuprofen) by the formation of inclusion complexes. Various inclusion complexes (2hydroxypropyl
more » ... CyD-, α-CyD-and -CyD-ibuprofen) were prepared and presented within W/O/W emulsions and the initial and long-term encapsulation efficiency was investigated. HP-β-CyD-ibuprofen provided the highest retention of ibuprofen in comparison to a W/O/W emulsion with unassociated ibuprofen confined within the inner water phase, with a 4 fold increase in the encapsulation efficiency. An improved, although lower encapsulation efficiency was obtained for the inclusion complex -CyD-ibuprofen in comparison to HP-β-CyD-ibuprofen, while α-CyDibuprofen had similar encapsulation efficiency as unassociated ibuprofen. The lower encapsulation efficiency of ibuprofen in combination with α-CyD and γ-CyD was attributed to a lower association constant for the γ-CyD-ibuprofen inclusion complex and the ability of α-CyD to form inclusion complexes with fatty acids. For the W/O/W emulsion prepared with HP--CyD-ibuprofen, the highest retention of ibuprofen was obtained at hyper-and iso-osmotic conditions and by using an excess molar ratio of CyD in comparison to ibuprofen. In the last part of the study it was suggested that the chemical modification of the HP--CyD molecule did not influence the encapsulation of ibuprofen, as similar encapsulation efficiency was obtained for an inclusion complex prepared with mono-1-glucose--CyD.
doi:10.1016/j.ijpharm.2015.03.059 pmid:25839416 fatcat:6jvsjipppzdgzaotk72xfbigy4

A Linear Combination of Pharmacophore Hypotheses as a New Tool in Search of New Active Compounds – An Application for 5-HT1A Receptor Ligands

Dawid Warszycki, Stefan Mordalski, Kurt Kristiansen, Rafał Kafel, Ingebrigt Sylte, Zdzisław Chilmonczyk, Andrzej J. Bojarski, Andrea Cavalli
2013 PLoS ONE  
This study explores a new approach to pharmacophore screening involving the use of an optimized linear combination of models instead of a single hypothesis. The implementation and evaluation of the developed methodology are performed for a complete known chemical space of 5-HT 1A R ligands (3616 active compounds with K i < 100 nM) acquired from the ChEMBL database. Clusters generated from three different methods were the basis for the individual pharmacophore hypotheses, which were assembled
more » ... o optimal combinations to maximize the different coefficients, namely, MCC, accuracy and recall, to measure the screening performance. Various factors that influence filtering efficiency, including clustering methods, the composition of test sets (random, the most diverse and cluster population-dependent) and hit mode (the compound must fit at least one or two models from a final combination) were investigated. This method outmatched both single hypothesis and random linear combination approaches.
doi:10.1371/journal.pone.0084510 pmid:24367669 pmcid:PMC3867515 fatcat:jncg46hgi5bcdohjnrdosdg2ay

Capturing quantitative zooplankton information in the sea: Performance test of laser optical plankton counter and video plankton recorder in a Calanus finmarchicus dominated summer situation

Sünnje L. Basedow, Kurt S. Tande, M. Fredrika Norrbin, Stian A. Kristiansen
2013 Progress in Oceanography  
We compared two optical plankton counters, the Laser Optical Plankton Counter (LOPC) 1 and the Video Plankton Recorder (VPR) for their abundance estimates of Calanus fin-2 marchicus during an early summer situation (June 2008) in two North Norwegian fjords. 3 The LOPC was mounted on the VPR frame in order to sample the same body of water. 4 The combined system of LOPC and VPR was operated by vertical profiling from the sur-5 face to 100 m of depth in several locations of the fjords representing
more » ... different blooming 6 conditions and zooplankton community structures. Data from the two instruments, as 7 well as from CTD-F, were logged concurrently and retrieved on deck after about 15 depth 8 profiles. Primary data were analysed according to standard routines, and choices made 9 during sampling and analyses (sampling volume, selection of size range, transparency of 10 particles, statistics) are discussed. Data were averaged for every 5, 10 and 15 m depth 11 bins. The vertical profiles of C. finmarchicus CIV-CVI abundance that were obtained 12 by LOPC and VPR, respectively, showed a striking similarity. No significant differences 13 between profiles sampled by these two instruments were observed when data were binned 14 into 15 m bins. At low abundances (< 100 Calanus sp. L −1 ) profiles were significantly 15 different when data were binned into 5-or 10-m bins. This is attributed to the small sam-16 pling volumes of the LOPC and the VPR, and to very patchy distributions of copepods, 17 resulting in a high standard deviation between consecutive profiles. Based on the results 18 we conclude that the time is mature for a more extensive use of optical instruments to 19 estimate zooplankton abundances and distributions in the sea. 20 2
doi:10.1016/j.pocean.2012.10.005 fatcat:wpb5dzvd65hotl53dksejntb6q
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