Browsing by Subject "TRACT"

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  • Strobbe, Floortje; Benard, Melanie; Rossen, Noortje G.; de Vos, Willem M.; Kumar, Nitin; Lawley, Trevor D.; Zoetendal, Erwin G.; Hugenholtz, Floor; Ponsioen, Cyriel Y. (2021)
    We evaluated a novel 'protected' biopsy method to reliably ascertain the spatial distribution of the mucosa-adherent colonic microbiota. Apart from minor differences at genus level, overall similarities along the colon were high between the various areas, irrespective of protected or unprotected sampling.
  • Rooijers, Koos; Kolmeder, Carolin; Juste, Catherine; Dore, Joel; de Been, Mark; Boeren, Sjef; Galan, Pilar; Beauvallet, Christian; de Vos, Willem M.; Schaap, Peter J. (2011)
  • Vlas, Tatjana; Brkic, Biljana Georgievski; Stevic, Zorica; Vukic, Marjana; Durovic, Olivera; Kostic, Dejan; Stanisavljevic, Natasa; Marinkovic, Ivan; Kapor, Slobodan; Marinkovic, Slobodan (2022)
    Objectives: There are scarce data regarding pontine arteries anatomy, which is the basis for ischemic lesions following their occlusion. The aim of this study was to examine pontine vasculature and its relationships with the radiologic and neuro-logic features of pontine infarctions. Materials and methods: Branches of eight basilar arteries and their twigs, including the larger intrapontine branches, were microdis-sected following an injection of a 10% mixture of India ink and gelatin. Two addi-tional brain stems were prepared for microscopic examination after being stained with luxol fast blue and cresyl violet. Finally, 30 patients with pontine infarctions underwent magnetic resonance imaging (MRI) in order to determine the position and size of the infarctions. Results: The perforating arteries, which averaged 5.8 in number and 0.39 mm in diameter, gave rise to paramedian and anteromedial branches, and also to anterolateral twigs (62.5%). The longer leptomeningeal and cere-bellar arteries occasionally gave off perforating and anterolateral twigs, and either the lateral or posterior branches. Occlusion of some of these vessels resulted in the para-median (30%), anterolateral (26.7%), lateral (20%), and combined infarctions (23.3%), which were most often isolated and unilateral, and rarely bilateral (10%). They were located in the lower pons (23.3%), middle (10%) or rostral (26.7%), or in two or three portions (40%). Each type of infarction usually produced characteristic neurologic signs. The clinical significance of the anatomic findings was discussed. Conclusions: There was a good correlation between the intrapontine vascular territories, the position, size and shape of the infarctions, and the type of neurologic manifestations. (c) 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (
  • Ali, Abir Salwa; Gronberg, Malin; Federspiel, Birgitte; Scoazec, Jean-Yves; Hjortland, Geir Olav; Gronbaek, Henning; Ladekarl, Morten; Langer, Seppo W.; Welin, Staffan; Vestermark, Lene Weber; Arola, Johanna; Osterlund, Pia; Knigge, Ulrich; Sorbye, Halfdan; Grimelius, Lars; Janson, Eva Tiensuu (2017)
    Background Gastroenteropancreatic neuroendocrine carcinomas (GEP-NECs) are aggressive, rapidly proliferating tumors. Therapeutic response to current chemotherapy regimens is usually short lasting. The aim of this study was to examine the expression and potential clinical importance of immunoreactive p53 protein in GEP-NEC. Materials and methods Tumor tissues from 124 GEP-NEC patients with locally advanced or metastatic disease treated with platinum-based chemotherapy were collected from Nordic centers and clinical data were obtained from the Nordic NEC register. Tumor proliferation rate and differentiation were re-evaluated. All specimens were immunostained for p53 protein using a commercially available monoclonal antibody. Kaplan-Meier curves and cox regression analyses were used to assess progression-free survival (PFS) and overall survival (OS). Results All tumor tissues were immunoreactive for either one or both neuroendocrine biomarkers (chromogranin A and synaptophysin) and Ki67 index was >20% in all cases. p53 immunoreactivity was only shown in 39% of the cases and was not found to be a prognostic marker for the whole cohort. However, p53 immunoreactivity was correlated with shorter PFS in patients with colorectal tumors (HR = 2.1, p = 0.03) in a univariate analysis as well as to poorer PFS (HR = 2.6, p = 0.03) and OS (HR = 3.4, p = 0.02) in patients with colorectal tumors with distant metastases, a correlation which remained significant in the multivariate analyses. Conclusion In this cohort of GEP-NEC patients, p53 expression could not be correlated with clinical outcome. However, in patients with colorectal NECs, p53 expression was correlated with shorter PFS and OS. Further studies are needed to establish the role of immunoreactive p53 as a prognostic marker for GEP-NEC patients.
  • Kolmeder, Carolin A.; Salojarvi, Jarkko; Ritari, Jarmo; de Been, Mark; Raes, Jeroen; Falony, Gwen; Vieira-Silva, Sara; Kekkonen, Riina A.; Corthals, Garry L.; Palva, Airi; Salonen, Anne; de Vos, Willem M. (2016)
    Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (10(10) cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
  • Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri; Tonkin-Hill, Gerry; Pesonen, Maiju; Xu, Yingying; Sipola, Aleksi; Sanchez-Buso, Leonor; Lees, John A.; Chewapreechi, Claire; Bentley, Stephen D.; Harris, Simon R.; Parkhill, Julian; Croucher, Nicholas J.; Corander, Jukka (2019)
    Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which adjusts for the phylogenetic signal in the data without requiring an explicit phylogenetic tree. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Simulations demonstrate the usefulness of our method and give some insight to when this type of analysis is most likely to be successful. Application of the method to large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
  • Hyvärinen, I.; Hukkinen, M.; Kivisaari, R.; Parviainen, H.; Nordin, A.; Pakarinen, M. P. (2019)
    Aim: The incidence of pancreaticobiliary maljunction is thought to approximate 1:100,000 within Western populations. We aimed to study the significance of pancreaticobiliary maljunction in biliary tract malignancies. Methods: Medical records and magnetic resonance cholangiopancreatography images of 252 consecutive patients treated for biliary malignancies during 2005-2016 were reviewed. Patients with other known risk factors for biliary cancers (n = 27) were excluded. A common pancreaticobiliary channel measuring > 10 mm outside the duodenal wall was defined as pancreaticobiliary maljunction. Main Results: Of the 225 patients, a reliably interpretable preoperative magnetic resonance cholangiopancreatography was available for 73 (32%). Sex (47% vs 57% females) and age at diagnosis (67 vs 66 years) were similar among patients with or without an magnetic resonance cholangiopancreatography (p = ns for both). In magnetic resonance cholangiopancreatography, a pancreaticobiliary maljunction with a median length of 20 mm (range 10-23 mm) was identified in four patients (5.5%, 95% confidence interval 1.6-14), while none had evident accompanying biliary tree dilatation. Pancreaticobiliary maljunction patients were significantly more often females (100% vs 43%, p = 0.043), less likely to have intrahepatic bile duct cancer (0% vs 65%, p = 0.019) while more likely to have gallbladder cancer (75% vs 22%, p = 0.044) compared to the others. Age at diagnosis (66 vs 67 years, p = 0.898), extrahepatic bile duct cancer incidence (25% vs 13%, p = 0.453), and survival status at last follow-up (50% vs 42% alive, p = 1.000) were comparable between the subgroups. Conclusion: The prevalence of pancreaticobiliary maljunction is substantially higher in adults with biliary malignancies than one would expect based on its incidence, reinforcing the etiologic role of pancreaticobiliary maljunction especially in females with gallbladder cancer.
  • Murtola, Tiina; Alku, Paavo; Malinen, Jarmo; Geneid, Ahmed (2018)
    High-speed videoendoscopy, glottal inverse filtering, and physical modeling can be used to obtain complementary information about speech production. In this study, the three methodologies are combined to pursue a better understanding of the relationship between the glottal air flow and glottal area. Simultaneously acquired high-speed video and glottal inverse filtering data from three male and three female speakers were used. Significant correlations were found between the quasi-open and quasi-speed quotients of the glottal area (extracted from the high-speed videos) and glottal flow (estimated using glottal inverse filtering), but only the quasi-open quotient relationship could be represented as a linear model. A simple physical glottal flow model with three different glottal geometries was optimized to match the data. The results indicate that glottal flow skewing can be modeled using an inertial vocal/subglottal tract load and that estimated inertia within the glottis is sensitive to the quality of the data. Parameter optimisation also appears to favour combining the simplest glottal geometry with viscous losses and the more complex glottal geometries with entrance/exit effects in the glottis.
  • Xu, Man; Perdomo , Maria; Mattola, Salla; Pyöriä, Lari; Toppinen, Mari; Qiu, Jianming; Vihinen-Ranta, Maija; Hedman, Klaus; Nokso-Koivisto, Johanna; Aaltonen, Leena-Maija; Söderlund-Venermo, Maria (2021)
    Human bocavirus 1 (HBoV1), a nonenveloped single-stranded DNA parvovirus, causes mild to life-threatening respiratory tract infections, acute otitis media, and encephalitis in young children. HBoV1 often persists in nasopharyngeal secretions for months, hampering diagnosis. It has also been shown to persist in pediatric palatine and adenoid tonsils, which suggests that lymphoid organs are reservoirs for virus spread; however, the tissue site and host cells remain unknown. Our aim was to determine, in healthy nonviremic children with preexisting HBoV1 immunity, the adenotonsillar persistence site(s), host cell types, and virus activity. We discovered that HBoV1 DNA persists in lymphoid germinal centers (GCs), but not in the corresponding tonsillar epithelium, and that the cell types harboring the virus are mainly naive, activated, and memory B cells and monocytes. Both viral DNA strands and both sides of the genome were detected, as well as infrequent mRNA. Moreover, we showed, in B-cell and monocyte cultures and ex vivo tonsillar B cells, that the cellular uptake of HBoV1 occurs via the Fc receptor (FcγRII) through antibody-dependent enhancement (ADE). This resulted in viral mRNA transcription, known to occur exclusively from double-stranded DNA in the nucleus, however, with no detectable productive replication. Confocal imaging with fluorescent virus-like particles moreover disclosed endocytosis. To which extent the active HBoV1 GC persistence has a role in chronic inflammation or B-cell maturation disturbances, and whether the virus can be reactivated, will be interesting topics for forthcoming studies. IMPORTANCE Human bocavirus 1 (HBoV1), a common pediatric respiratory pathogen, can persist in airway secretions for months hampering diagnosis. It also persists in tonsils, providing potential reservoirs for airway shedding, with the exact location, host cell types, and virus activity unknown. Our study provides new insights into tonsillar HBoV1 persistence. We observed HBoV1 persistence exclusively in germinal centers where immune maturation occurs, and the main host cells were B cells and monocytes. In cultured cell lines and primary tonsillar B cells, we showed the virus uptake to be significantly enhanced by HBoV1-specific antibodies, mediated by the cellular IgG receptor, leading to viral mRNA synthesis, but without detectable productive replication. Possible implications of such active viral persistence could be tonsillar inflammation, disturbances in immune maturation, reactivation, or cell death with release of virus DNA, explaining the long-lasting HBoV1 airway shedding.
  • Mäkitaipale, Johanna; Airas, Niina; Engblom, Sanna; Linden, Jere (2022)
    Background: Earlier studies indicate that the risk for uterine tumours in rabbits may be as high as 60-80%. This high occurrence and the need for routine neutering of non-breeding pet rabbits have recently been in the spotlight. Methods: This study aimed to describe and compare macroscopic and histopathological alterations in uteri collected from domestic rabbits of various ages neutered, deceased, or euthanized without a suspected uterine disorder (NoUD; n = 94) and from rabbits with a suspected uterine disorder (UD; n = 22). Results: In the NoUD group, uteri of 41 rabbits (44%) displayed histopathological findings and 12 rabbits (13%) had neoplasms. Samples from thirteen rabbits (14%) evinced histopathological findings with no macroscopic alterations. The most frequent diagnoses were cystic endometrial hyperplasia (26% of the 41 uteri), adenocarcinoma (9%), and polyps (5%). In the UD group, uteri from 21 (95%) out of 22 rabbits exhibited pathological alterations; in 2 (10%) of these, the changes (cystic endometrial hyperplasias) were seen only in histology. The most frequent diagnoses in the uteri of the UD group were cystic endometrial hyperplasia (77%) and adenocarcinoma (54%). Uterine malignant neoplasia affected 40% of all rabbits aged over 3 years, and the odds of a malignant uterine tumour in these rabbits were approximately 19-fold higher than in rabbits aged under 3 years. Conclusions and clinical relevance: Uterine disorders are common in domestic rabbits, even without a suspected uterine disease, and the risk of uterine neoplasia markedly increases after 3 years of age. A macroscopically normal uterus may have pathological changes and ovariohysterectomy should be therefore preferred over ovariectomy at least in older rabbits.
  • van Passel, Mark W. J.; Kant, Ravi; Zoetendal, Erwin G.; Plugge, Caroline M.; Derrien, Muriel; Malfatti, Stephanie A.; Chain, Patrick S. G.; Woyke, Tanja; Palva, Airi; de Vos, Willem M.; Smidt, Hauke (2011)
  • Buntin, Nirunya; de Vos, Willem M.; Hongpattarakere, Tipparat (2017)
    The adhesion ability to mucin varied greatly among 18 Lactobacillus plantarum isolates depending on their isolation habitats. Such ability remained at high level even though they were sequentially exposed to the gastrointestinal (GI) stresses. The majority of L. plantarum isolated from shrimp intestine and about half of food isolates exhibited adhesion ability (51.06-55.04%) about the same as the well-known adhesive L. plantarum 299v. Interestingly, five infant isolates of CIF17A2, CIF17A4, CIF17A5, CIF17AN2, and CIF17AN8 exhibited extremely high adhesion ranging from 62.69 to 72.06%. Such highly adhesive property correlating to distinctively high cell surface hydrophobicity was significantly weaken after pretreatment with LiCl and guanidine-HCl confirming the entailment of protein moiety. Regarding the draft genome information, all molecular structures of major cell wall-anchored proteins involved in the adhesion based on L. plantarum WCSF1, including lp_0964, lp_1643, lp_3114, lp_2486, lp_3127, and lp_3059 orthologues were detected in all isolates. Exceptionally, the gene-trait matching between yeast agglutination assay and the relevant mannose-specific adhesin (lp_1229) encoding gene confirmed the Msa absence in five infant isolates expressed distinctively high adhesion. Interestingly, the predicted flagellin encoding genes (fliC) firstly revealed in lp_1643, lp_2486, and lp_3114 orthologues may potentially contribute to such highly adhesive property of these isolates.