Browsing by Subject "imaging"

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  • Viitanen, Arto Ilmari; Gullmets, Josef; Morikka, Jack George Anthony; Katajisto, Pekka; Mattila, Jaakko; Hietakangas, Ville (2021)
    The intestine is divided into functionally distinct regions along the anteroposterior (A/P) axis. How the regional identity influences the function of intestinal stem cells (ISCs) and their offspring remain largely unresolved. We introduce an imaging-based method, “Linear Analysis of Midgut” (LAM), which allows quantitative, regionally defined cellular phenotyping of the whole Drosophila midgut. LAM transforms image-derived cellular data from three-dimensional midguts into a linearized representation, binning it into segments along the A/P axis. Through automated multivariate determination of regional borders, LAM allows mapping and comparison of cellular features and frequencies with subregional resolution. Through the use of LAM, we quantify the distributions of ISCs, enteroblasts, and enteroendocrine cells in a steady-state midgut, and reveal unprecedented regional heterogeneity in the ISC response to a Drosophila model of colitis. Altogether, LAM is a powerful tool for organ-wide quantitative analysis of the regional heterogeneity of midgut cells.
  • Chandola, Chetan; Kalme, Sheetal; Casteleijn, Marco G.; Urtti, Arto; Neerathilingam, Muniasamy (2016)
    Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity and affinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety of applications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class of biomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. In this review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging. We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makes them a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potential drug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs, nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable for RNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior over protein-based binding molecules in terms of labelling and conjugation strategies.
  • Lehtonen, Sanna; Lewko, Barbara (2019)
  • Sahle, Ch J.; Mirone, A.; Vincent, T.; Kallonen, A.; Huotari, S. (2017)
    An algorithm to simultaneously increase the spatial and statistical accuracy of X-ray Raman scattering (XRS) based tomographic images is presented. Tomography that utilizes XRS spectroscopy signals as a contrast for the images is a new and promising tool for investigating local atomic structure and chemistry in heterogeneous samples. The algorithm enables the spatial resolution to be increased based on a deconvolution of the optical response function of the spectrometer and, most importantly, it allows for the combination of data collected from multiple analyzers and thus enhances the statistical accuracy of the measured images.
  • Mogollon, Isabel; Ahtiainen, Laura (2020)
    Embryonic development of ectodermal organs involves a very dynamic range of cellular events and, therefore, requires advanced techniques to visualize them. Ectodermal organogenesis proceeds in well-defined sequential stages mediated by tissue interactions. Different ectodermal organs feature shared morphological characteristics, which are regulated by conserved and reiterative signaling pathways. A wealth of genetic information on the expression patterns and interactions of specific signaling pathways has accumulated over the years. However, the conventional developmental biology methods have mainly relied on two-dimensional tissue histological analyses at fixed time points limiting the possibilities to follow the processes in real time on a single cell resolution. This has complicated the interpretation of cause and effect relationships and mechanisms of the successive events. Whole-mount tissue live imaging approaches are now revealing how reshaping of the epithelial sheet for the initial placodal thickening, budding morphogenesis and beyond, involve coordinated four dimensional changes in cell shapes, well-orchestrated cell movements and specific cell proliferation and apoptosis patterns. It is becoming evident that the interpretation of the reiterative morphogenic signals takes place dynamically at the cellular level. Depending on the context, location, and timing they drive different cell fate choices and cellular interactions regulating a pattern of behaviors that ultimately defines organ shapes and sizes. Here we review how new tissue models, advances in 3D and live tissue imaging techniques have brought new understanding on the cell level behaviors that contribute to the highly dynamic stages of morphogenesis in teeth, hair and related ectodermal organs during development, and in dysplasia contexts.
  • Figueras, Eduard; Martins, Ana; Borbely, Adina; Le Joncour, Vadim; Cordella, Paola; Perego, Raffaella; Modena, Daniela; Pagani, Paolo; Esposito, Simone; Auciello, Giulio; Frese, Marcel; Gallinari, Paola; Laakkonen, Pirjo; Steinkuhler, Christian; Sewald, Norbert (2019)
    Tumor targeting has emerged as an advantageous approach to improving the efficacy and safety of cytotoxic agents or radiolabeled ligands that do not preferentially accumulate in the tumor tissue. The somatostatin receptors (SSTRs) belong to the G-protein-coupled receptor superfamily and they are overexpressed in many neuroendocrine tumors (NETs). SSTRs can be efficiently targeted with octreotide, a cyclic octapeptide that is derived from native somatostatin. The conjugation of cargoes to octreotide represents an attractive approach for effective tumor targeting. In this study, we conjugated octreotide to cryptophycin, which is a highly cytotoxic depsipeptide, through the protease cleavable Val-Cit dipeptide linker using two different self-immolative moieties. The biological activity was investigated in vitro and the self-immolative part largely influenced the stability of the conjugates. Replacement of cryptophycin by the infrared cyanine dye Cy5.5 was exploited to elucidate the tumor targeting properties of the conjugates in vitro and in vivo. The compound efficiently and selectively internalized in cells overexpressing SSTR2 and accumulated in xenografts for a prolonged time. Our results on the in vivo properties indicate that octreotide may serve as an efficient delivery vehicle for tumor targeting.
  • Kauffold, Johannes; Peltoniemi, Olli; Wehrend, Axel; Althouse, Gary C. (2019)
    Simply Summary: Real-time ultrasonography (RTU) has become an essential diagnostic value when assessing female swine reproduction in either individual or groups of animals. Diagnostic application of RTU is applied throughout most stages of production, including gilt development, breeding, gestation and farrowing. Along with its most common use in on-farm assessment of pregnancy status, RTU is also used to troubleshoot disruptions in reproductive performance such as delayed puberty, prolonged wean-to-estrus interval, absence of post-weaning estrus, decreased conception and farrowing rates, vulval discharge, peripartum and puerperal disorders. This review aims to provide an overview on principles and clinical uses of RTU in female reproduction on commercial swine farms. Abstract: Within the past 30 years, through ongoing technology and portability developments, real-time (b-mode) ultrasonography (RTU) has increasingly become a valuable diagnostic tool in assessing the female reproductive tract in swine. Initially applied in swine production to visually determine pregnancy status, RTU use has expanded to include assessment of the peri-pubertal and mature non-pregnant females as well. Transabdominal and transrectal modalities to visualizing the reproductive tract in swine have been reported with the transabdominal approach more common due to the fact of its ease of accessibility, animal/personnel safety, and reduced time to perform. Adjustable frequency transducers are preferred as they allow optimization of image quality at various depths. If a single transducer frequency must be selected, a 5 MHz probe provides the best versatility for visualizing the reproductive tract in swine. Other basic requirements for ultrasound equipment which will be used on commercial swine farms include being light weight and easy to handle, readily cleanable and disinfectable, long battery-life, and good durability. When using RTU for pregnancy determination, diagnosis is based upon a combination of the animal's breeding records, the presence of embryonic fluid, and, depending upon gestational stage, fetal structures. If RTU is used as a diagnostic tool in assessing reproductive problems in an individual or a group of animals, sonographic evaluation of both the uterus and ovaries is performed. Tissues are delineated and assessed based upon their echogenicity, echotexture, and size. Uses of RTU in clinical practice may include assessment of delayed puberty, prolonged wean-to-estrus interval, absence of post-weaning estrus, herd disruptions in conception and farrowing rates, vulval discharge, peripartum and puerperal disorders. This review aims to provide an overview on principles and clinical uses of RTU with respect to application to address female reproductive performance issues in commercial swine operations.
  • Wasonga, Daniel; Kleemola, Jouko Heikki; Alakukku, Laura; Yaw, Afrane; Mäkelä, Pirjo (2021)
    Cassava has high energy value and rich nutritional content, yet its productivity in the tropics is seriously constrained by abiotic stresses such as water deficit and low potassium (K) nutrition. Systems that allow evaluation of genotypes in the field and greenhouse for nondestructive estimation of plant performance would be useful means for monitoring the health of plants for crop-management decisions. We investigated whether the red-green-blue (RGB) and multispectral images could be used to detect the previsual effects of water deficit and low K in cassava, and whether the crop quality changes due to low moisture and low K could be observed from the images. Pot experiments were conducted with cassava cuttings. The experimental design was a split-plot arranged in a completely randomized design. Treatments were three irrigation doses split into various K rates. Plant images were captured beginning 30 days after planting (DAP) and ended at 90 DAP when plants were harvested. Results show that biomass, chlorophyll, and net photosynthesis were estimated with the highest accuracy (R-2 = 0.90), followed by leaf area (R-2 = 0.76). Starch, energy, carotenoid, and cyanide were also estimated satisfactorily (R-2 > 0.80), although cyanide showed negative regression coefficients. All mineral elements showed lower estimation accuracy (R-2 = 0.14-0.48) and exhibited weak associations with the spectral indices. Use of the normalized difference vegetation index (NDVI), green area (GA), and simple ratio (SR) indices allowed better estimation of growth and key nutritional traits. Irrigation dose 30% of pot capacity enriched with 0.01 mM K reduced most index values but increased the crop senescence index (CSI). Increasing K to 16 mM over the irrigation doses resulted in high index values, but low CSI. The findings indicate that RGB and multispectral imaging can provide indirect measurements of growth and key nutritional traits in cassava. Hence, they can be used as a tool in various breeding programs to facilitate cultivar evaluation and support management decisions to avert stress, such as the decision to irrigate or apply fertilizers.
  • Aro, Katri; Tarkkanen, Jussi; Saat, Riste; Saarilahti, Kauko; Mäkitie, Antti; Atula, Timo (2018)
    BackgroundIn the absence of unified treatment protocol, we evaluated the management and outcomes of submandibular gland cancers in an unselected patient series. MethodsWe included all patients with resected submandibular gland cancer treated at the Helsinki University Hospital from 2000 to 2010 with a 5-year minimum follow-up. ResultsTwenty-five patients with cancer represented 30% of submandibular gland neoplasms, and most were adenoid cystic carcinomas (ACCs; 56%). At presentation, 3 patients showed clinical signs of probable malignancy. Of 22 neck dissection specimens, 5 patients (20%) had metastases with an occult metastasis rate of 4%. Cancer recurred in 11 patients (44%), of which 7 (28%) were only at a distant site. The 5-year disease-specific survival (DSS) and overall survival (OS) rates were 76%, and disease-free survival (DFS) was 68%. ConclusionMost tumors were ACCs differing from the histological pattern of parotid gland cancers. Occult metastases were rare. The rarity of submandibular gland cancer, its variable histological pattern, and varying biological behavior warrant centralized management.
  • Tenca, Andrea; Mustonen, Harri; Lind, Kati; Lantto, Eila; Kolho, Kaija-Leena; Boyd, Sonja; Arola, Johanna; Jokelainen, Kalle; Färkkilä, Martti (2018)
    Background & Aims Endoscopic retrograde cholangiography (ERCP) has been considered the gold standard for the diagnosis and follow-up of primary sclerosing cholangitis, but it has been replaced by less invasive magnetic resonance imaging and cholangiopancreatography (MRI-MRCP). However, the role of these two techniques in the evaluation of disease activity and severity needs to be elucidated. Methods Patients with primary sclerosing cholangitis (n: 48, male 31, median age: 35.7; 28.0-44.2) who underwent ERCP and MRI-MRCP within +/- 3 months for diagnosis or follow-up, were reviewed. ERCP and MRI-MRCP images were scored using the modified Amsterdam score. Serum and biliary cytology markers of disease activity and severity were related to the imaging findings. Agreement on the assessment of the ERCP/MRCP score was calculated by kappa-statistics. Spearman ' s rho was calculated when appropriate. Results The agreement between ERCP and MRCP in scoring bile duct changes for disease severity was only moderate (weighted kappa: 0.437; 95% CI: 0.211-0.644 for intra- and 0.512; 95% CI: 0.303-0.720 for extra-hepatic bile ducts). ERCP and MRCP intra-hepatic scores were associated to the surrogate marker alkaline phosphatase (P = .02 for both). A weak correlation between MRCP score for extra-hepatic bile ducts and liver transplantation/death was found (Spearman's rho = .362, 95% CI: 0.080-0.590, P = .022). A weak correlation between intra- (Spearman ' s rho = .322, 95% CI: 0.048-0.551, P = .022) and extra-hepatic (Spearman`s rho = .319, 95% CI: 0.045-0.549, P = .025) peribiliary enhancement on contrast-enhanced MRI and severity of biliary cytologic classification was found. Conclusions The overall agreement between ERCP and MRI-MRCP in assessing disease severity was moderate for intra- and extra-hepatic bile ducts. MRI-MRCP seems to have a minor role as surrogate marker of disease activity and progression in PSC.
  • Zaproudina, Nina; Rissanen, Antti-Pekka E.; Lipponen, Jukka A.; Vierola, Anu; Rissanen, Saara M.; Karjalainen, Pasi A.; Soinila, Seppo; Närhi, Matti (2018)
    Prevalence of masticatory parafunctions, such as tooth clenching and grinding, is higher among migraineurs than non-migraineurs, and masticatory dysfunctions may aggravate migraine. Migraine predisposes to cerebrovascular disturbances, possibly due to impaired autonomic vasoregulation, and sensitization of the trigeminovascular system. The relationships between clenching, migraine, and cerebral circulation are poorly understood. We used Near-Infrared Spectroscopy to investigate bilateral relative oxy- (%Δ[O2Hb]), deoxy- (%Δ[HHb]), and total (%Δ[tHb]) hemoglobin concentration changes in prefrontal cortex induced by maximal tooth clenching in twelve headache-free migraineurs and fourteen control subjects. From the start of the test, migraineurs showed a greater relative increase in right-side %Δ[HHb] than controls, who showed varying reactions, and right-side increase in %Δ[tHb] was also greater in migraineurs (p < 0.001 and p < 0.05, respectively, time-group interactions, Linear mixed models). With multivariate regression model, migraine predicted the magnitude of maximal blood pressure increases, associated in migraineurs with mood scores and an intensity of both headache and painful signs of temporomandibular disorders (pTMD). Although changes in circulatory parameters predicted maximal NIRS responses, the between-group differences in the right-side NIRS findings remained significant after adjusting them for systolic blood pressure and heart rate. A family history of migraine, reported by all migraineurs and four controls, also predicted maximal increases in both %Δ[HHb] and %Δ[tHb]. Presence of pTMD, revealed in clinical oral examination in eight migraineurs and eight controls, was related to maximal %Δ[HHb] increase only in controls. To conclude, the greater prefrontal right-side increases in cerebral %Δ[HHb] and %Δ[tHb] may reflect disturbance of the tooth clenching-related cerebral (de)oxygenation based on impaired reactivity and abnormal microcirculation processes in migraineurs. This finding may have an impact in migraine pathophysiology and help to explain the deleterious effect of masticatory dysfunctions in migraine patients. However, the role of tooth clenching as a migraine trigger calls for further studies.
  • Khan, Luqman; van Lanen, Rick; Hoogland, Govert; Schijns, Olaf; Rijkers, Kim; Kapsokalyvas, Dimitrios; van Zandvoort, Marc; Haeren, Roel (2021)
    Despite extensive research, the exact pathomechanisms associated with epileptic seizure formation and propagation have not been elucidated completely. Two-photon imaging (2PI) is a fluorescence-based microscopy technique that, over the years, has been used to evaluate pathomechanisms associated with epileptic seizures and epilepsy. Here, we review previous applications of 2PI in epilepsy. A systematic search was performed in multiple literature databases. We identified 38 publications that applied 2PI in epilepsy research. These studies described models of epileptic seizure propagation; anatomical changes and functional alterations of microglia, astrocytes, and neurites; and neurometabolic effects that accompany seizures. Moreover, various neurovascular alterations that accompany seizure onset and ictal events, such as blood vessel responses, have been visualized using 2PI. Lastly, imaging and quantitative analysis of oxidative stress and the aggregation of lipofuscin in the neurovasculature have been accomplished with 2PI. Cumulatively, these papers and their reported findings demonstrate that 2PI is an especially well-suited imaging technique in the domain of epilepsy research, and these studies have significantly improved our understanding of the disorder. The application of 2PI provides ample possibilities for future research, most interestingly on human brains, while also stretching beyond the field of epilepsy.
  • Uurasjärvi, Emilia; Sainio, Erika; Setälä, Outi; Lehtiniemi, Maiju; Koistinen, Arto (Elsevier, 2021)
    Environmental Pollution 288 (2021), 117780
    Despite the ubiquitousness of microplastics, knowledge on the exposure of freshwater fish to microplastics is still limited. Moreover, no standard methods are available for analyzing microplastics, and the quality of methods used for the quantification of ingested microplastics in fish should be improved. In this study, we studied microplastic ingestion of common wild freshwater fish species, perch (Perca fluviatilis) and vendace (Coregonus albula). Further, our aim was to develop and validate imaging Fourier-transform infrared spectroscopic method for the quantification of ingested microplastics. For this purpose, enzymatically digested samples were measured with focal plane array (FPA) based infrared microscope. Data was analyzed with siMPle software, which provides counts, mass estimations, sizes, and materials for the measured particles. Method validation was conducted with ten procedural blanks and recovery tests, resulting in 75% and 77% recovery rates for pretreatment and infrared imaging, respectively. Pretreatment caused contamination principally by small <100 μm microplastics. The results showed that 17% of perch and 25% of vendace had ingested plastic. Most of the fish contained little or no plastics, while some individuals contained high numbers of small particles or alternatively few large particles. Perch from one sampling site out of five had ingested microplastics, but vendace from all sampling sites had ingested microplastics. The microplastics found from fish were mostly small: 81% had particle size between 20 and 100 μm, and most of them were polyethylene, polypropylene, and polyethylene terephthalate. In conclusion, the implemented method revealed low numbers of ingested microplastics on average but needs further development for routine monitoring of small microplastics.