Segmentation of nerve bundles and ganglia in spine MRI using particle filters

14th International Conference, Toronto, Canada, September 18-22, 2011, Proceedings, Part IIIAutomatic segmentation of spinal nerve bundles that originate within the dural sac and exit the spinal canal is important for diagnosis and surgical planning. The variability in intensity, contrast, shape and direction of nerves seen in high resolution myelographic MR images makes segmentation a challenging task. In this paper, we present an automatic tracking method for nerve segmentation based on particle filters. We develop a novel approach to particle representation and dynamics, based on Bézier splines. Moreover, we introduce a robust image likelihood model that enables delineation of nerve bundles and ganglia from the surrounding anatomical structures. We demonstrate accurate and fast nerve tracking and compare it to expert manual segmentation.National Institutes of Health (U.S.) (NAMIC award U54-EB005149)National Science Foundation (U.S.) (CAREER grant 0642971

Accuracy of an Artificial Intelligence Deep Learning Algorithm Implementing a Recurrent Neural Network With Long Short-term Memory for the Automated Detection of Calcified Plaques From Coronary Computed Tomography Angiography

Purpose: The purpose of this study was to evaluate the accuracy of a novel fully automated deep learning (DL) algorithm implementing a recurrent neural network (RNN) with long short-term memory (LSTM) for the detection of coronary artery calcium (CAC) from coronary computed tomography angiography (CCTA) data. Materials and Methods: Under an IRB waiver and in HIPAA compliance, a total of 194 patients who had undergone CCTA were retrospectively included. Two observers independently evaluated the image quality and recorded the presence of CAC in the right (RCA), the combination of left main and left anterior descending (LM-LAD), and left circumflex (LCx) coronary arteries. Noncontrast CACS scans were allowed to be used in cases of uncertainty. Heart and coronary artery centerline detection and labeling were automatically performed. Presence of CAC was assessed by a RNN-LSTM. The algorithm's overall and per-vessel sensitivity, specificity, and diagnostic accuracy were calculated. Results: CAC was absent in 84 and present in 110 patients. As regards CCTA, the median subjective image quality, signal-to-noise ratio, and contrast-to-noise ratio were 3.0, 13.0, and 11.4. A total of 565 vessels were evaluated. On a per-vessel basis, the algorithm achieved a sensitivity, specificity, and diagnostic accuracy of 93.1% (confidence interval [CI], 84.3%-96.7%), 82.76% (CI, 74.6%-89.4%), and 86.7% (CI, 76.8%-87.9%), respectively, for the RCA, 93.1% (CI, 86.4%-97.7%), 95.5% (CI, 88.77%-98.75%), and 94.2% (CI. 90.2%-94.6%), respectively, for the LM-LAD, and 89.9% (CI, 80.2%-95.8%), 90.0% (CI, 83.2%-94.7%), and 89.9% (CI, 85.0%-94.1%), respectively, for the LCx. The overall sensitivity, specificity, and diagnostic accuracy were 92.1% (CI, 92.1%-95.2%), 88.9% (CI. 84.9%-92.1%), and 90.3% (CI, 88.0%-90.0%), respectively. When accounting for image quality, the algorithm achieved a sensitivity, specificity, and diagnostic accuracy of 76.2%, 87.5%, and 82.2%, respectively, for poor-quality data sets and 93.3%, 89.2% and 90.9%, respectively, when data sets rated adequate or higher were combined. Conclusion: The proposed RNN-LSTM demonstrated high diagnostic accuracy for the detection of CAC from CCTA

Microcalcifications in breast cancer: novel insights into the molecular mechanism and functional consequence of mammary mineralisation.

BACKGROUND: Mammographic microcalcifications represent one of the most reliable features of nonpalpable breast cancer yet remain largely unexplored and poorly understood. METHODS: We report a novel model to investigate the in vitro mineralisation potential of a panel of mammary cell lines. Primary mammary tumours were produced by implanting tumourigenic cells into the mammary fat pads of female BALB/c mice. RESULTS: Hydroxyapatite (HA) was deposited only by the tumourigenic cell lines, indicating mineralisation potential may be associated with cell phenotype in this in vitro model. We propose a mechanism for mammary mineralisation, which suggests that the balance between enhancers and inhibitors of physiological mineralisation are disrupted. Inhibition of alkaline phosphatase and phosphate transport prevented mineralisation, demonstrating that mineralisation is an active cell-mediated process. Hydroxyapatite was found to enhance in vitro tumour cell migration, while calcium oxalate had no effect, highlighting potential consequences of calcium deposition. In addition, HA was also deposited in primary mammary tumours produced by implanting the tumourigenic cells into the mammary fat pads of female BALB/c mice. CONCLUSION: This work indicates that formation of mammary HA is a cell-specific regulated process, which creates an osteomimetic niche potentially enhancing breast tumour progression. Our findings point to the cells mineralisation potential and the microenvironment regulating it, as a significant feature of breast tumour development

Reactivity of limestones from different sources in Turkey

This paper presents a study on the reactivity of natural limestones from five deposits in Turkey. The conversion rates of carbonates in size fractions of the samples were measured in a stirred suspension of 2.5 1 at 20 degreesC and a constant-pH value of 5 obtained with the addition of HCl solutions by a pH control pump. Particle size and the dolomite content of the limestones were found to be the most influential parameters in the reactivity measurements

Effect of the genotype, explant source and culture medium in somatic embryogenesis and organogenesis in Vaccaria hispanica (Mill.) Rauschert

[EN] Vaccaria hispanica is an interesting species with attractive agronomic properties and a wealth of valuable bioactive compounds, potentially useful for many different purposes. Surprisingly, the number of studies focused on the development of in vitro tools for a rapid production of clonal populations is extremely limited. In the present study, two wild Turkish genotypes, previously characterized as high starch and saponin producers, are used to explore the possibilities of regenerating clonal plants through somatic embryogenesis and organogenesis. This work investigates the independent effects of genotype, type of explant and composition of the culture medium, and the interactions among them, in the growth and proliferation of calli from the explants, and the induction of somatic embryogenesis and organogenesis fron the callus surface. Some of the interactions were found significant to promote these processes. V. hispanica proved to be especially responsive for callus induction from all the explants tested. Particular explant types and combinations of plant growth regulators have been identified as especially suitable to induce the different morphogenic processes. V. hispanica is remarkably prone to produce thin adventitious roots, which may be a problem when trying to induce somatic embryogenesis or shoot organogenesis. However, this can be exploited to develop a convenient system for in vitro secondary metabolite production.The study was funded by the TUBITAK (The Scientific and Technological Research Council of Turkey) (TOVAG 1001 Project No: 112O136) and Scientific Research Projects Coordination Unit of Akdeniz University (Project No: FYL-2016-1719).Bedir, H.; Ari, E.; Elif Vural, G.; Seguí-Simarro, JM. (2022). Effect of the genotype, explant source and culture medium in somatic embryogenesis and organogenesis in Vaccaria hispanica (Mill.) Rauschert. Plant Cell Tissue and Organ Culture (PCTOC). 150(2):329-343. https://doi.org/10.1007/s11240-022-02275-83293431502Alonso-Herrada J, Rico-Resendiz F, Campos-Guillen J, Guevara-Gonzalez RG, Torres-Pacheco I, Cruz-Hernandez A (2016) Establishment of in vitro regeneration system for Acaciella angustissima (Timbe) a shrubby plant endemic of México for the production of phenolic compounds. Ind Crops Prod 86:49–57Anzidei M, Bennici A, Schiff S, Tani C, Mori B (2000) Organogenesis and somatic embryogenesis in Foeniculum vulgare: histological observations of developing embryogenic callus. Plant Cell Tissue Organ Cult 61(1):69–79Ari E, Bedir H, Deniz IG, Genc I, Seguí-Simarro JM (2022) Evaluation of the androgenic competence of 66 wild Turkish Vaccaria hispanica (Mill.) Rauschert genotypes through microspore culture. Plant Cell Tissue Organ Cult 148:209–214. https://doi.org/10.1007/s11240-021-02169-1Ari E, Buyukalaca S (2006) In vitro regeneration of vaccaria pyramidata. In: 22nd International Eucarpia Symposium - Section Ornamentals- Breeding for Beauty, Sanremo, Italy (11–15 September 2006)Asthana P, Jaiswal VS, Jaiswal U (2011) Micropropagation of Sapindus trifoliatus L. and assessment of genetic fidelity of micropropagated plants using RAPD analysis. Acta Physiol Plant 33(5):1821–1829Asthana P, Rai MK, Jaiswal U (2017) Somatic embryogenesis from sepal explants in Sapindus trifoliatus, a plant valuable in herbal soap industry. Ind Crops Prod 100:228–235Balsevich JJ (2008) Prarie carnation (Saponaria vaccaria)—a potential new industrial/medicinal crop for the Prairies. In Fuelling the farm, SSCA annual conference, Regina, Saskatchewan, Canada (12–14 February 2008). pp 46–50Bao J, Zhang H, Xu D, Yang S (2016) Establishment of culture system of Vaccaria segetalis hairy roots and determination of vaccarin. Chin Tradit Herb Drugs 47(1):138–142. https://doi.org/10.7501/j.issn.0253-2670.2016.01.021Bhansali RR (1990) Somatic embryogenesis and regeneration of in plantles in pomegranate. Ann Bot—London 66(3):249–253Cakilcioglu U, Khatun S, Turkoglu I, Hayta S (2011) Ethnopharmacological survey of medicinal plants in Maden (Elazig-Turkey). J Ethnopharmacol 137(1):469–486Cam IB, Balci-Torun F, Topuz A, Ari E, Deniz IG, Genc I (2018) Physical and chemical properties of cow cockle seeds (Vaccaria hispanica (Mill.) Rauschert) genetic resources of Turkey. Ind Crops Prod 126:190–200Casas JL, Olmos E, Piqueras A (2010) In vitro propagation of carnation (Dianthus caryophyllus L.). Protocols for in vitro propagation of ornamental plants. Humana Press, Totowa, pp 109–116Chen X, Qu Y, Sheng L, Liu J, Huang H, Xu L (2014) A simple method suitable to study de novo root organogenesis. Front Plant Sci 5:208Chen H, Guo T, Wang D, Qin R (2018) Vaccaria hypaphorine impairs RANKL-induced osteoclastogenesis by inhibition of ERK, p38, JNK and NF-κB pathway and prevents inflammatory bone loss in mice. Biomed Pharmacother 97:1155–1163Christianson M, Warnick DA (1983) Competence and determination in the process of in vitro shoot organogenesis. Dev Biol 95(2):288–293Condie JA, Nowak G, Reed DW, Balsevich JJ, Reaney MJ, Arnison PG, Covello PS (2011) The biosynthesis of Caryophyllaceae-like cyclic peptides in Saponaria vaccaria L. from DNA-encoded precursors. Plant J 67(4):682–690Da Costa CT, De Almeida MR, Ruedell CM, Schwambach J, Maraschin FDS, Fett-Neto AG (2013) When stress and development go hand in hand: main hormonal controls of adventitious rooting in cuttings. Front Plant Sci 4:133Deepak KV, Narayanan GS, Prakash M, Murugan S, Anandan R (2019) Efficient plant regeneration and histological evaluations of regenerants through organogenesis and somatic embryogenesis in Spermacoce hispida L.—an underutilized medicinally important plant. Ind Crops Prod 134:292–302Duddu HS, Johnson EN, Blackshaw RE, Shirtliffe SJ (2015) Evaluation of seed persistence in cow cockle. Crop Sci 55(2):899–909Faisal M, Alatar AA, El-Sheikh MA, Abdel-Salam EM, Qahtan AA (2018) Thidiazuron induced in vitro morphogenesis for sustainable supply of genetically true quality plantlets of Brahmi. Ind Crops Prod 118:173–179Feher A (2005) Why somatic plant cells start to form embryos? Somatic embryogenesis. Springer, Berlin, Heidelberg, pp 85–101Feher A (2015) Somatic embryogenesis—stress-induced remodeling of plant cell fate. Biochim Biophys Acta Gene Regul Mech 1849(4):385–402Frey L, Saranga Y, Janick J (1992) Somatic embryogenesis in carnation. HortScience 27(1):63–65Gehlot P, Bohra N, Harwani D (2015) Endophytic microorganism and their functions. Microbes: in Action (editors: Singh, J. and Gehlot, p.) Agrobios (india) 412:167–187Ghazi TD, Cheema HV, Nabors MW (1986) Somatic embryogenesis and plant regeneration from embryogenic callus of soybean Glycine max L. Plant Cell Rep 5(6):452–456Grand View Research (2020) Nutraceutical market size worth $722.49 Billion By 2027. Available at https://www.grandviewresearch.com/press-release/global-nutraceuticals-market. Accessed 10 Sept 2021Güçlü-Üstündağ Ö, Mazza G (2007) Saponins: properties, applications and processing. Crit Rev Food Sci Nutr 47(3):231–258Hutchison MJ, Murch SJ, Saxena PK (1996) Morphoregulatory role of TDZ: evidence of the involvement of endogenous auxin in TDZ-induced somatic embryogenesis of geranium (Pelargonium horturum Bailey). J Plant Physiol 149:573–579Ishtiaq M, Maqbool M, Ajaib M, Ahmed M, Hussain I, Khanam H et al (2021) Ethnomedicinal and folklore inventory of wild plants used by rural communities of valley Samahni, District Bhimber Azad Jammu and Kashmir, Pakistan. PLoS ONE 16(1):e0243151Jimenez VM (2005) Involvement of plant hormones and plant growth regulators on in vitro somatic embryogenesis. Plant Growth Regul 47(2):91–110Karnovsky MJ (1965) A formaldehyde-glutaraldehyde fixative of high osmolality for use in electron microscopy. J Cell Biol 27(2):137A-138AKlimaszewska K, Keller WA (1985) High frequency plant regeneration from thin cell layer explants of Brassica napus. Plant Cell Tissue Organ Cult 4(3):183–197Koga M, Hirashima K, Nakahara T (2000) Genetic transformation in Vaccaria pyramidata using Agrobacterium rhizogenes. Plant Biotechnol 17(2):163–166Lima AO, Quecine MC, Fungaro MH, Andreote FD, Maccheroni W, Araujo WL et al (2005) Molecular characterization of a β-1, 4-endoglucanase from an endophytic Bacillus pumilus strain. Appl Microbiol Biotechnol 68(1):57–65Lin YH, Chang C, Chang WC (2000) Plant regeneration from callus culture of a Paphiopedilum hybrid. Plant Cell Tissue Organ Cult 62(1):21–25Liu CM, Xu ZH, Chua NH (1993) Auxin polar transport is essential for the establishment of bilateral symmetry during early plant embryogenesis. Plant Cell 5(6):621–630Mazza G, Biliaderis CG, Przybylski R, Oomah BD (1992) Compositional and morphological characteristics of cow cockle (Saponaria vaccaria) seed, a potential alternative crop. J Agric Food Chem 40(9):1520–1523Meesapyodsuk D, Balsevich J, Reed DW, Covello PS (2007) Saponin biosynthesis in Saponaria vaccaria. cDNAs encoding β-amyrin synthase and a triterpene carboxylic acid glucosyltransferase. Plant Physiol 143(2):959–969Michalczuk L, Cooke TJ, Cohen JD (1992) Auxin levels at different stages of carrot embryogenesis. Phytochemistry 31:1097–1103Minocha SC, Minocha R (1995) Role of polyamines in somatic embryogenesis. In: Bajaj YPS (ed) Somatic embryogenesis and synthetic seed I. Biotechnology in agriculture and forestry, vol 30. Springer, Berlin, pp 53–70Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497Murthy BNS, Murch SJ, Saxena PK (1998) Thidiazuron: a potent regulator of in vitro plant morphogenesis. In Vitro Cell Dev Biol Plant 34(4):267Nitsch J, Nitsch C (1969) Haploid plants from pollen grains. Science 163:85–87O’Brien TP, McCully ME (1981) The study of plant structure. Principles and selected methods. Termacarphi Pty Ltd, VictoriaOrhan IE, Senol FS, Haznedaroglu MZ, Koyu H, Erdem SA, Yilmaz G, Cicek M, Yaprak AE, Ari E, Kucukboyaci N, Toker G (2017) Neurobiological evaluation of thirty-one medicinal plant extracts using microtiter enzyme assays. Clin Phytoscience 2(1):1–12Radojevic L (1988) Plant regeneration of Aesculus hippocastanum L. (horse chestnut) through somatic embryogenesis. J Plant Physiol 132(3):322–326Sang S, Lao A, Chen Z, Uzawa J, Fujimoto Y (2003) Chemistry and bioactivity of the seeds of Vaccaria segetalis. Oriental foods and herbs: chemistry and health effects. American Chemical Society, Washington, pp 279–291Schmidt JF, Moore MD, Pelcher LE, Covello PS (2007) High efficiency Agrobacterium rhizogenes-mediated transformation of Saponaria vaccaria L. (Caryophyllaceae) using fluorescence selection. Plant Cell Rep 26(9):1547–1554Slesak H, Popielarska M, Goralski G (2005) Morphological and histological aspects of 2, 4-D effects on rape explants (Brassica napus L. cv. Kana) cultured in vitro. Acta Biol Crac Ser Bot 47(1):219–226Tang W (2000) High-frequency plant regeneration via somatic embryogenesis and organogenesis and in vitro flowering of regenerated plantlets in Panax ginseng. Plant Cell Rep 19(7):727–732Thomas C, Meyer D, Himber C, Steinmetz A (2004) Spatial expression of a sunflower SERK gene during induction of somatic embryogenesis and shoot organogenesis. Plant Physiol Biochem 42(1):35–42Verdeil JL, Alemanno L, Niemenak N, Tranbarger TJ (2007) Pluripotent versus totipotent plant stem cells: dependence versus autonomy? Trends Plant Sci 12(6):245–252Verma SK, Yucesan BB, Gurel S, Gurel E (2011) Indirect somatic embryogenesis and shoot organogenesis from cotyledonary leaf segments of Digitalis lamarckii Ivan., an endemic medicinal species. Turk J Biol 35(6):743–750Verma SK, Das AK, Cingoz GS, Uslu E, Gurel E (2016) Influence of nutrient media on callus induction, somatic embryogenesis and plant regeneration in selected Turkish crocus species. Biotechnol Rep 10:66–74Von Arnold S, Sabala I, Bozhkov P, Dyachok J, Filonova L (2002) Developmental pathways of somatic embryogenesis. Plant Cell, Tissue Organ Cult 69(3):233–249Wang J, Zhang Y, Li Y, Wang X, Liu Z, Nan W, Zhao C, Wang F, Ma J, Bi Y (2016) Involvement of polar auxin transport in the inhibition of Arabidopsis seedling growth induced by Stenotrophomonas maltophilia. Biol Plant 60(2):299–310Willenborg CJ, Johnson EN (2013) Influence of seeding date and seeding rate on cow cockle, a new medicinal and industrial crop. Ind Crops Prod 49:554–560Wong KH, Tan WL, Kini SG, Xiao T, Serra A, Sze SK, Tam JP (2017) Vaccatides: antifungal glutamine-rich Hevein-like peptides from Vaccaria hispanica. Front Plant Sci 8:1100Xu L (2018) De novo root regeneration from leaf explants: wounding, auxin, and cell fate transition. Curr Opin Plant Biol 41:39–45Yao L, Wang J, He J, Huang L, Gao W (2021) Endophytes, biotransforming microorganisms, and engineering microbial factories for triterpenoid saponins production. Crit Rev Biotechnol. https://doi.org/10.1080/07388551.2020.1869691Zheng MY, Konzak CF (1999) Effect of 2, 4-dichlorophenoxyacetic acid on callus induction and plant regeneration in anther culture of wheat (Triticum aestivum L.). Plant Cell Rep 19(1):69–73Zhou J, Ma H, Guo F, Luo X (1994) Effect of thidiazuron on somatic embryogenesis of Cayratia japonica. Plant Cell Tissue Organ Cult 36(1):73–79Zhou G, Tang L, Wang T, Zhou X, Kou Z, Wu J, Wang Z (2016) Phytochemistry and pharmacological activities of Vaccaria hispanica (Miller) Rauschert: a review. Phytochem Rev 15(5):813–82

CONCENTRATION-DEPENDENCE OF NMR T1 IN AGAR SOLUTIONS

In this study, in order to explain solvent proton relaxation mechanism, the spin-lattice relaxation time (T1) of agar solutions was measured as a function of agar concentration. Relaxation measurements were carried out by a FT-NMR spectrometer operating at 60 MHz and inversion recovery pulse squence was used. Relaxation rate(1/T1a) was linearly proportional to concentration of agar solution (C), and the T1 mechanism of solvent water protons in agar solutions should be caused by the chemical exchange of water protons between free and bound water

classification

The aims of this study were to investigate the anatomy of the minor fissure and its variations on high-resolution CT (HRCT) sections and to propose a detailed classification. The prospective study included 67 patients who were referred to CT for various indications. High-resolution CT examinations (1.5-mm collimation) were obtained through the region of the minor fissure. The CT scans were assessed for the presence, completeness, and configuration of the minor fissure. Various configurations of the minor fissure were classified into four major types, based on whether the highest portion of the middle lobe upper surface was medial (type I), lateral (type II), posterior (type III), or central (type TV). Minor fissure was identified in 65 (97%) of 67 patients, and absent in 2 (3%) cases. The fissure was incomplete in 35 (54%) of 65 patients. Type-I minor fissure is seen in 28 (43%) patients, type II in 22 (34%), type III in 5 (8%), and type IV in 2 (3%) patients. Because the majority of the fissure was absent in 8 (12%) of 35 patients with incomplete fissure, they were considered indeterminate. Comprehensive knowledge of the various configurations of the minor fissure is helpful in correct localization of a lesion and its extension. In equivocal cases, limited thin-section CT scans through the fissure delineate the anatomy more clearly and provide greater degree of precision in localizing pulmonary lesions

high-resolution computed tomography

The purpose of the study was to evaluate the radiological anatomy of oblique fissures (OFs) on high-resolution computed tomography (HRCT) scans. We retrospectively reviewed HRCT scans of 144 patients with normal lung parenchyma. The uppermost level of OFs with respect to the ribs, configuration (concave, straight, convex and others), orientation (medial or lateral facing), rotation and completeness of OFs were recorded. The most cranial level of the left OF was seen between the third and sixth ribs, and all but one were seen above or at the same level as the right OF. The uppermost extent of the OF was between the third and fourth intercostal space and seventh rib on the right lung. Only 2.2% of the right and 1.6% of the left OFs followed a parallel course to the ribs. The configuration of the OFs was generally concave in the upper zones (85.8% on the right and 72.1% on the left) and convex in the middle and lower lung zones (79.3% on the right and 73.9% on the left); 62.5% of the right and 59.7% of the left OFs were incomplete. Suprahilar portions of both OFs (98.9% on the right and 96.7% on the left) and the infrahilar portion of the right OF (54.2%) were generally facing laterally, whereas the infrahilar portion of the left OF was facing medially (80.9%). Angles of the MFs differed at the upper and lower levels. We detected reversal of 21 OFs in their craniocaudal course. In conclusion, the radiological anatomy of the right OF differs from the left OF. The uppermost extent of the left OF is almost always higher than the right. Thus, higher position of the right OF compared with the left almost always indicates a pathological process. Assessment of the angles of the OFs or comparison of the two sides cannot be used for the diagnosis of parenchymal disease like atelectasis. Occasionally, the classical propeller-like configuration is disrupted by the reverse course of the caudal part of the OF.C1 Hacettepe Univ, Fac Med, Dept Radiol, TR-06100 Ankara, Turkey.Pamukkale Univ, Fac Med, Dept Radiol, Denizli, Turkey

pulmonary nodules

The purpose of this study was to investigate the diagnostic accuracy of low-dose helical computed tomography by comparing the number of nodules detected at low- and standard-dose CT. The prospective study included 25 patients who were referred to CT scan for the assessment of pulmonary metastases. All patients underwent CT examinations at both standard- (200 mA, 120 kV, collimation 5 mm, table feed 10 mm per rotation) and low-dose (50 mA, 120 kV, collimation 5 mm, table feed 10 mm per rotation), The number of nodules detected at each protocol was recorded. The size of the nodules was measured electronically and categorized as 0.05). Four hundred ninety-one (87.7%) nodules were detected at both standard- or low-dose CT, 42 (7.5%) nodules were observed only at standard-dose CT, and 27 (4.8%) nodules were seen only at low-dose CT. The sensitivity of low-dose CT was 92.5% for all nodules, 88.1% for nodules <5 mm, and 97.4% for nodules 2:5 mm. No significant image artifact interfering with nodule detection was observed at low-dose CT. The low-dose CT protocol used in this study provided images of adequate quality; thus, it can be used reliably in the detection or exclusion of pulmonary nodules