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410 results on '"Almstrup, Kristian"'

1. Iron Oxide Nanoparticles as a Contrast Agent for Synchrotron Imaging of Sperm

Author

Lindhøj, Mette Bjerg, Cooper, Susan Rudd, Anker, Andy S., Bonnin, Anne, Kristensen, Mie, Qvortrup, Klaus, Almstrup, Kristian, Jensen, Kirsten M. Ø., Dyrby, Tim B., and Sporring, Jon

Subjects
Physics - Medical Physics, Physics - Biological Physics
Abstract

Fast phase-contrast imaging offered by modern synchrotron facilities opens the possibility of imaging dynamic processes of biological material such as cells. Cells are mainly composed of carbon and hydrogen, which have low X-ray attenuation, making cell studies with X-ray tomography challenging. At specific low energies, cells provide contrast, but cryo-conditions are required to protect the sample from radiation damage. Thus, non-toxic labelling methods are needed to prepare living cells for X-ray tomography at higher energies. We propose using iron oxide nanoparticles due to their proven compatibility in other biomedical applications. We show how to synthesize and attach iron oxide nanoparticles and demonstrate that cell-penetrating peptides facilitate iron oxide nanoparticle uptake into sperm cells. We show results from the TOMCAT Nanoscope (Swiss Light Source), showing that iron oxide nanoparticles allow the heads and midpiece of fixed sperm samples to be reconstructed from X-ray projections taken at 10 keV., Comment: 21 pages, 6 figures

Published
2023

5. The molecular evolution of spermatogenesis across mammals

Author

Murat, Florent, Mbengue, Noe, Winge, Sofia Boeg, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Belles, Meritxell Riera, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marques-Bonet, Tomas, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, and Kaessmann, Henrik

Published
2023
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8. The piRNA-pathway factor FKBP6 is essential for spermatogenesis but dispensable for control of meiotic LINE-1 expression in humans

Author

Wyrwoll, Margot J., Gaasbeek, Channah M., Golubickaite, Ieva, Stakaitis, Rytis, Oud, Manon S., Nagirnaja, Liina, Dion, Camille, Sindi, Emad B., Leitch, Harry G., Jayasena, Channa N., Sironen, Anu, Dicke, Ann-Kristin, Rotte, Nadja, Stallmeyer, Birgit, Kliesch, Sabine, Grangeiro, Carlos H.P., Araujo, Thaís F., Lasko, Paul, D’Hauwers, Kathleen, Smits, Roos M., Ramos, Liliana, Xavier, Miguel J., Conrad, Don F., Almstrup, Kristian, Veltman, Joris A., Tüttelmann, Frank, and van der Heijden, Godfried W.

Published
2022
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9. Environmental factors in declining human fertility

Author

Skakkebæk, Niels E., Lindahl-Jacobsen, Rune, Levine, Hagai, Andersson, Anna-Maria, Jørgensen, Niels, Main, Katharina M., Lidegaard, Øjvind, Priskorn, Lærke, Holmboe, Stine A., Bräuner, Elvira V., Almstrup, Kristian, Franca, Luiz R., Znaor, Ariana, Kortenkamp, Andreas, Hart, Roger J., and Juul, Anders

Published
2022
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10. Diverse monogenic subforms of human spermatogenic failure

Author

Nagirnaja, Liina, Lopes, Alexandra M., Charng, Wu-Lin, Miller, Brian, Stakaitis, Rytis, Golubickaite, Ieva, Stendahl, Alexandra, Luan, Tianpengcheng, Friedrich, Corinna, Mahyari, Eisa, Fadial, Eloise, Kasak, Laura, Vigh-Conrad, Katinka, Oud, Manon S., Xavier, Miguel J., Cheers, Samuel R., James, Emma R., Guo, Jingtao, Jenkins, Timothy G., Riera-Escamilla, Antoni, Barros, Alberto, Carvalho, Filipa, Fernandes, Susana, Gonçalves, João, Gurnett, Christina A., Jørgensen, Niels, Jezek, Davor, Jungheim, Emily S., Kliesch, Sabine, McLachlan, Robert I., Omurtag, Kenan R., Pilatz, Adrian, Sandlow, Jay I., Smith, James, Eisenberg, Michael L., Hotaling, James M., Jarvi, Keith A., Punab, Margus, Rajpert-De Meyts, Ewa, Carrell, Douglas T., Krausz, Csilla, Laan, Maris, O’Bryan, Moira K., Schlegel, Peter N., Tüttelmann, Frank, Veltman, Joris A., Almstrup, Kristian, Aston, Kenneth I., and Conrad, Donald F.

Published
2022
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11. Convolutional neural networks for segmentation and object detection of human semen

Author

Nissen, Malte Stær, Krause, Oswin, Almstrup, Kristian, Kjærulff, Søren, Nielsen, Torben Trindkær, and Nielsen, Mads

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We compare a set of convolutional neural network (CNN) architectures for the task of segmenting and detecting human sperm cells in an image taken from a semen sample. In contrast to previous work, samples are not stained or washed to allow for full sperm quality analysis, making analysis harder due to clutter. Our results indicate that training on full images is superior to training on patches when class-skew is properly handled. Full image training including up-sampling during training proves to be beneficial in deep CNNs for pixel wise accuracy and detection performance. Predicted sperm cells are found by using connected components on the CNN predictions. We investigate optimization of a threshold parameter on the size of detected components. Our best network achieves 93.87% precision and 91.89% recall on our test dataset after thresholding outperforming a classical mage analysis approach., Comment: Submitted for Scandinavian Conference on Image Analysis 2017

Published
2017

12. Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies

Author

Portnoi, Marie-France, Dumargne, Marie-Charlotte, Rojo, Sandra, Witchel, Selma F, Duncan, Andrew J, Eozenou, Caroline, Bignon-Topalovic, Joelle, Yatsenko, Svetlana A, Rajkovic, Aleksandar, Reyes-Mugica, Miguel, Almstrup, Kristian, Fusee, Leila, Srivastava, Yogesh, Chantot-Bastaraud, Sandra, Hyon, Capucine, Louis-Sylvestre, Christine, Validire, Pierre, de Malleray Pichard, Caroline, Ravel, Celia, Christin-Maitre, Sophie, Brauner, Raja, Rossetti, Raffaella, Persani, Luca, Charreau, Eduardo H, Dain, Liliana, Chiauzzi, Violeta A, Mazen, Inas, Rouba, Hassan, Schluth-Bolard, Caroline, MacGowan, Stuart, McLean, WH Irwin, Patin, Etienne, Meyts, Ewa Rajpert-De, Jauch, Ralf, Achermann, John C, Siffroi, Jean-Pierre, McElreavey, Ken, and Bashamboo, Anu

Subjects
Rare Diseases, Contraception/Reproduction, Infertility, Clinical Research, Genetics, Aetiology, 2.1 Biological and endogenous factors, Reproductive health and childbirth, 46, XX Disorders of Sex Development, Adolescent, Child, Disorder of Sex Development, 46, XY, Female, Humans, Male, Mutation, Missense, Oligospermia, Primary Ovarian Insufficiency, SOXE Transcription Factors, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

SOX8 is an HMG-box transcription factor closely related to SRY and SOX9. Deletion of the gene encoding Sox8 in mice causes reproductive dysfunction but the role of SOX8 in humans is unknown. Here, we show that SOX8 is expressed in the somatic cells of the early developing gonad in the human and influences human sex determination. We identified two individuals with 46, XY disorders/differences in sex development (DSD) and chromosomal rearrangements encompassing the SOX8 locus and a third individual with 46, XY DSD and a missense mutation in the HMG-box of SOX8. In vitro functional assays indicate that this mutation alters the biological activity of the protein. As an emerging body of evidence suggests that DSDs and infertility can have common etiologies, we also analysed SOX8 in a cohort of infertile men (n = 274) and two independent cohorts of women with primary ovarian insufficiency (POI; n = 153 and n = 104). SOX8 mutations were found at increased frequency in oligozoospermic men (3.5%; P

Published
2018

13. Cohort profile: The Copenhagen Analgesic Study—The COPANA cohort

Author

Fischer, Margit Bistrup, primary, Mola, Gylli, additional, Scheel, Lone, additional, Wraae, Katrine Bak, additional, Rom, Ane Lilleøre, additional, Frederiksen, Hanne, additional, Johannsen, Trine Holm, additional, Almstrup, Kristian, additional, Sundberg, Karin, additional, Hegaard, Hanne Kristine, additional, Juul, Anders, additional, and Hagen, Casper P., additional

Published
2024
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17. New analysis of atypical spermatocytic tumours reveals extensive heterogeneity and plasticity of germ cell tumours†.

Author

Rajpert‐De Meyts, Ewa, Goriely, Anne, and Almstrup, Kristian

Subjects
GERM cells, CYTOLOGY, TUMORS, PHENOTYPIC plasticity, PROTEIN kinases
Abstract

Testicular germ cell tumours (TGCTs) derived from immature (type I) and pluripotent germ cell neoplasia in situ (GCNIS, type II) are characterised by remarkable phenotypic heterogeneity and plasticity. In contrast, the rare spermatocytic tumour (SpT, type III), derived from mature spermatogonia, is considered a homogenous and benign tumour but may occasionally present as an anaplastic or an aggressive sarcomatoid tumour. While various oncogenic processes had been proposed, the precise mechanism driving malignant progression remained elusive until the molecular characterisation of a series of atypical SpTs described in a recent issue of The Journal of Pathology. The emerging picture suggests the presence of two distinct trajectories for SpTs, involving either RAS/mitogen‐activated protein kinase pathway mutations or a ploidy shift with secondary TP53 mutations and/or gain of chromosome 12p, the latter known as pathognomonic for type II GCNIS‐derived TGCTs. Here, we discuss the implications of these findings, seen from the perspective of germ cell biology and the unique features of different TGCTs. The evolving phenotype of SpTs, induced by genomic and epigenetic changes, illustrates that the concept of plasticity applies to all germ cell tumours, making them inherently heterogenous and capable of significant transformation during progression. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Identification of 22 susceptibility loci associated with testicular germ cell tumors

Author

Pluta, John, Pyle, Louise C., Nead, Kevin T., Wilf, Rona, Li, Mingyao, Mitra, Nandita, Weathers, Benita, D’Andrea, Kurt, Almstrup, Kristian, Anson-Cartwright, Lynn, Benitez, Javier, Brown, Christopher D., Chanock, Stephen, Chen, Chu, Cortessis, Victoria K., Ferlin, Alberto, Foresta, Carlo, Gamulin, Marija, Gietema, Jourik A., Grasso, Chiara, Greene, Mark H., Grotmol, Tom, Hamilton, Robert J., Haugen, Trine B., Hauser, Russ, Hildebrandt, Michelle A. T., Johnson, Matthew E., Karlsson, Robert, Kiemeney, Lambertus A., Lessel, Davor, Lothe, Ragnhild A., Loud, Jennifer T., Loveday, Chey, Martin-Gimeno, Paloma, Meijer, Coby, Nsengimana, Jérémie, Quinn, David I., Rafnar, Thorunn, Ramdas, Shweta, Richiardi, Lorenzo, Skotheim, Rolf I., Stefansson, Kari, Turnbull, Clare, Vaughn, David J., Wiklund, Fredrik, Wu, Xifeng, Yang, Daphne, Zheng, Tongzhang, Wells, Andrew D., Grant, Struan F. A., Rajpert-De Meyts, Ewa, Schwartz, Stephen M., Bishop, D. Timothy, McGlynn, Katherine A., Kanetsky, Peter A., and Nathanson, Katherine L.

Published
2021
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20. Convolutional Neural Networks for Segmentation and Object Detection of Human Semen

Author

Nissen, Malte S., Krause, Oswin, Almstrup, Kristian, Kjærulff, Søren, Nielsen, Torben T., Nielsen, Mads, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Sharma, Puneet, editor, and Bianchi, Filippo Maria, editor

Published
2017
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24. Supplementary Table 4 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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26. Supplementary Figure 3 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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27. Supplementary Figure 2 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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28. Supplementary Table 1 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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29. Supplementary Table 3 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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30. Supplementary Table 2 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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32. Supplementary Figure 1 from Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte

Author

Sonne, Si Brask, primary, Almstrup, Kristian, primary, Dalgaard, Marlene, primary, Juncker, Agnieszka Sierakowska, primary, Edsgard, Daniel, primary, Ruban, Ludmila, primary, Harrison, Neil J., primary, Schwager, Christian, primary, Abdollahi, Amir, primary, Huber, Peter E., primary, Brunak, Søren, primary, Gjerdrum, Lise Mette, primary, Moore, Harry D., primary, Andrews, Peter W., primary, Skakkebaek, Niels E., primary, Meyts, Ewa Rajpert-De, primary, and Leffers, Henrik, primary

Published
2023
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36. The molecular evolution of spermatogenesis across mammals

Author

Murat, Florent, primary, Mbengue, Noe, additional, Winge, Sofia Boeg, additional, Trefzer, Timo, additional, Leushkin, Evgeny, additional, Sepp, Mari, additional, Cardoso-Moreira, Margarida, additional, Schmidt, Julia, additional, Schneider, Celine, additional, Mößinger, Katharina, additional, Brüning, Thoomke, additional, Lamanna, Francesco, additional, Belles, Meritxell Riera, additional, Conrad, Christian, additional, Kondova, Ivanela, additional, Bontrop, Ronald, additional, Behr, Rüdiger, additional, Khaitovich, Philipp, additional, Pääbo, Svante, additional, Marques-Bonet, Tomas, additional, Grützner, Frank, additional, Almstrup, Kristian, additional, Schierup, Mikkel Heide, additional, and Kaessmann, Henrik, additional

Published
2022
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41. Involvement of epigenetic modifiers in the pathogenesis of testicular dysgenesis and germ cell cancer

Author

Lawaetz Andreas C. and Almstrup Kristian

Subjects
epigenetic modifiers, germ cell cancer, jumonji c-domain containing, testicular dysgenesis, Biology (General), QH301-705.5
Abstract

Testicular germ cell cancer manifests mainly in young adults as a seminoma or non-seminoma. The solid tumors are preceded by the presence of a non-invasive precursor cell, the carcinoma in situ cell (CIS), which shows great similarity to fetal germ cells. It is therefore hypothesized that the CIS cell is a fetal germ cell that has been arrested during development due to testicular dysgenesis. CIS cells retain a fetal and open chromatin structure, and recently several epigenetic modifiers have been suggested to be involved in testicular dysgenesis in mice. We here review the possible involvement of epigenetic modifiers with a focus on jumonji C enzymes in the development of testicular dysgenesis and germ cell cancer in men.

Published
2015
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42. Diverse Monogenic Subforms of Human Spermatogenic Failure

Author

Nagirnaja, Liina, primary, Lopes, Alexandra M., additional, Charng, Wu-Lin, additional, Miller, Brian, additional, Stakaitis, Rytis, additional, Golubickaite, Ieva, additional, Stendahl, Alexandra, additional, Luan, Tianpengcheng, additional, Friedrich, Corinna, additional, Mahyari, Eisa, additional, Fadial, Eloise, additional, Kasak, Laura, additional, Vigh-Conrad, Katinka, additional, Oud, Manon S., additional, Xavier, Miguel J., additional, Cheers, Samuel R., additional, James, Emma R., additional, Guo, Jingtao, additional, Jenkins, Timothy G, additional, Riera-Escamilla, Antoni, additional, Barros, Alberto, additional, Carvalho, Filipa, additional, Fernandes, Susana, additional, Gonçalves, João, additional, Gurnett, Christina A., additional, Jørgensen, Niels, additional, Jezek, Davor, additional, Jungheim, Emily S, additional, Kliesch, Sabine, additional, McLachlan, Robert I., additional, Omurtag, Kenan R, additional, Pilatz, Adrian, additional, Sandlow, Jay, additional, Smith, James, additional, Eisenberg, Michael L., additional, Hotaling, James M, additional, Jarvi, Keith A., additional, Punab, Margus, additional, Rajpert-De Meyts, Ewa, additional, Carrell, Douglas T., additional, Krausz, Csilla, additional, Laan, Maris, additional, O’Bryan, Moira K., additional, Schlegel, Peter N., additional, Tüttelmann, Frank, additional, Veltman, Joris A., additional, Almstrup, Kristian, additional, Aston, Kenneth I., additional, and Conrad, Donald F., additional

Published
2022
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48. The seminal plasma microbiome of men with testicular germ cell tumours described by small RNA sequencing.

Author

Mørup, Nina, Main, Ailsa Maria, Jørgensen, Niels, Daugaard, Gedske, Juul, Anders, and Almstrup, Kristian

Subjects
NON-coding RNA, RNA sequencing, GERM cells, HUMAN gene mapping, VIRAL genomes, GERM cell tumors, RETROVIRUSES
Abstract

Background: It has been estimated that microorganisms are involved in the pathogenesis of approximately 20% of all cancers. Testicular germ cell tumours (TGCTs) are the most common type of malignancy in young men and arise from the precursor cell, germ cell neoplasia in situ (GCNIS). The microbiome of seminal plasma and testicular tissue has not been thoroughly investigated in regard to TGCTs. Objectives: To investigate the differences in the seminal plasma microbiome between men with TGCT or GCNIS‐only compared with controls. Materials and methods: The study population consisted of patients with GCNIS‐only (n = 5), TGCT (n = 18), and controls (n = 25) with different levels of sperm counts in the ejaculate. RNA was isolated from the seminal plasma and sequenced. Reads not mapping to the human genome were aligned against a set of 2784 bacterial/archaeal and 4336 viral genomes using the Kraken pipeline. Results: We identified reads from 2172 species and most counts were from Alteromonas mediterranea, Falconid herpesvirus 1, and Stigmatella aurantiaca. Six species (Acaryochloris marina, Halovirus HGTV‐1, Thermaerobacter marianensis, Thioalkalivibrio sp. K90mix, Burkholderia sp. YI23, and Desulfurivibrio alkaliphilus) were found in significantly (q‐value < 0.05) higher levels in the seminal plasma of TGCT and GCNIS‐only patients compared with controls. In contrast, Streptomyces phage VWB was found at significantly higher levels among controls compared with TGCT and GCNIS‐only patients combined. Discussion: Often the microbiome is analysed by shotgun or 16S ribosomal sequencing whereas our present data build on small RNA sequencing. This allowed us to identify more viruses and phages compared with previous studies but also makes the results difficult to directly compare. Conclusion: Our study is the first to report identification of the microbiome species in seminal plasma of men with TGCT and GCNIS‐only, which potentially could be involved in the pathogenesis of TGCTs. Further studies are, however, needed to confirm our findings. [ABSTRACT FROM AUTHOR]

Published
2023
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