Convolutional neural networks for segmentation and object detection of human semen

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 201

LEG OG PSYKOTERAPI – ELLER OMVENDT

Børns leg betragtes her i sig selv som potentielt terapeutisk. I legen transformeres tilsyneladende passivitet til aktivitet. Winnicotts »legende atmosfære« beskriver de lystfulde og de udforskende aspekter i børns – og voksnes – psykoterapeutiske arbejde. Børn og psykoterapeuters manglende kapacitet for at lege nævnes. Der gives en række eksempler på, hvordan det psykoterapeutiske opfattes som en udforskende og legende bevægelse fra én tilstand eller position hen mod en anden, som giver nye udsigtspunkter og handlemuligheder

U.B.K. UNIVERSITETETS BØRNEPSYKOLOGISKE KLINIK: – glimt af en udvikling over 50 år.

Baggrunden for oprettelsen i 1950 af Universitetets børnepsykologiske klinik ved Københavns Universitet med inspiration fra de amerikanske tværfaglige child guidance clinics beskrives og udviklingen op til etableringen af Institut for klinisk Psykologi i 1968, hvor der udover børneklinikken oprettes en voksenafdeling og en forskningsafdeling gennemgås, iblandet enkelte personlige erindringer fra et kandidatforløb over to år. Derefter gennemgås de efteruddannelses- og forskningsmæssige forhold ved UBK og betydningen for dansk klinisk børnepsykologi bliver omtalt.The backgrounds for establishing The Child Guidance Clinic of University of Copenhagen in 1950 inspired by the American Child Guidance movement are described. Developments in the clinic up to the establishment of Institute of Clinical Psychology in 1968 coloured by the author’s personal recollections from his two years post graduate clinical internship. The significance of the university-clinic for the establishment of Danish clinical child psychology is mentioned

DET NARRATIVE SOM KLINISK BEGREB: illustreret med exempler fra børnepsykoterapier

This article is inspired by Roy Schafer's Action Language and his introduction of the idea of narration into psychoanalytic psychotherapy. The transformation from a positivistic to a hermeneutic post modern position is touched upon. Children's narratives (stories and drawings) in a child psychotherapy context and a conflict between the child's narrative and that of the therapist are discussed. Based on a vignette from one of Winnicott's therapeutic consultations the development of an emancipating narrative commonly shared by child and therapist is discussed.Med udgangspunkt i Roy Schafers introduktion af narrationsbegrebet og dets relativistiske og postmoderne aspekter i psykoanalytisk terapi gennemgås en række exempler på børns konstruktioner af deres aktuelle subjektive selv- og omverdensopfattelser, som de udtrykkes i deres leg og tegninger i terapeutiske sammenhæng. Artiklen beskriver en konflikt mellem barnets og terapeutens beretninger, udviklingen af en fælles forståelse med et exempel fra en af Winnicotts terapeutiske konsultationer, samt en tegnings mulighed for at øge terapeutens indlevelse i barnets situation

Diagnostic markers for germ cell neoplasms: from placental-like alkaline phosphatase to micro-RNAs

This concise review summarises tissue and serum markers useful for differential diagnosis of germ cell tumours (GCT), with focus on the most common testicular GCT (TGCT). GCT are characterised by phenotypic heterogeneity due to largely retained embryonic pluripotency and aberrant somatic differentiation. TGCT that occur in young men are divided into two main types, seminoma and nonseminoma, both derived from a pre-invasive germ cell neoplasia in situ (GCNIS), which originates from transformed foetal gonocytes. In severely dysgenetic gonads, a GCNIS-resembling lesion is called gonadoblastoma. GCT occur rarely in young children (infantile GCT) in whom the pathogenesis is different (no GCNIS/gonadoblastoma stage) but the histopathological features are similar to the adult GCT. The rare spermatocytic tumour of older men is derived from post-pubertal spermatogonia that clonally expand due to gain-of function mutations in survival-promoting genes (e.g. FGFR3, HRAS), thus this tumour has a different expression profile than GCNIS-derived TGCT. Clinically most informative immunohistochemical markers for GCT, except teratoma, are genes expressed in primordial germ cells/gonocytes and embryonic pluripotency-related factors, such as placental-like alkaline phosphatase (PLAP), OCT4 (POU5F1), NANOG, AP-2γ (TFAP2C) and LIN28, which are not expressed in normal adult germ cells. Some of these markers can also be used for immunocytochemistry to detect GCNIS or incipient tumours in semen samples. Gene expression in GCT is regulated in part by DNA and histone modifications, and the epigenetic profile of these tumours is characterised by genome-wide demethylation, except nonseminomas. In addition, a recently discovered mechanism of post-genomic gene expression regulation involves small non-coding RNAs, predominantly micro-RNA (miR). Testicular GCT display micro-RNA profiles similar to embryonic stem cells. Targeted miRNA-based blood tests for miR-371-3 and miR-367 clusters are currently under development and hold a great promise for the future. In some patients miR-based tests may be even more sensitive than the classical serum tumour markers, β -chorio-gonadotrophin (β-hCG), α-fetoprotein (AFP) and lactate dehydrogenase (LDH), which are currently used in the clinic. In summary, research advances have provided clinicians with a panel of molecular markers, which allow specific diagnosis of various subtypes of GCT and are very useful for early detection at the precursor stage and for monitoring of patients during the follow-up

Gene expression profiles of mouse spermatogenesis during recovery from irradiation

<p>Abstract</p> <p>Background</p> <p>Irradiation or chemotherapy that suspend normal spermatogenesis is commonly used to treat various cancers. Fortunately, spermatogenesis in many cases can be restored after such treatments but knowledge is limited about the re-initiation process. Earlier studies have described the cellular changes that happen during recovery from irradiation by means of histology. We have earlier generated gene expression profiles during induction of spermatogenesis in mouse postnatal developing testes and found a correlation between profiles and the expressing cell types. The aim of the present work was to utilize the link between expression profile and cell types to follow the cellular changes that occur during post-irradiation recovery of spermatogenesis in order to describe recovery by means of gene expression.</p> <p>Methods</p> <p>Adult mouse testes were subjected to irradiation with 1 Gy or a fractionated radiation of two times 1 Gy. Testes were sampled every third or fourth day to follow the recovery of spermatogenesis and gene expression profiles generated by means of differential display RT-PCR. In situ hybridization was in addition performed to verify cell-type specific gene expression patterns.</p> <p>Results</p> <p>Irradiation of mice testis created a gap in spermatogenesis, which was initiated by loss of A1 to B-spermatogonia and lasted for approximately 10 days. Irradiation with 2 times 1 Gy showed a more pronounced effect on germ cell elimination than with 1 Gy, but spermatogenesis was in both cases completely reconstituted 42 days after irradiation. Comparison of expression profiles indicated that the cellular reconstitution appeared equivalent to what is observed during induction of normal spermatogenesis.</p> <p>Conclusion</p> <p>The data indicates that recovery of spermatogenesis can be monitored by means of gene expression, which could aid in designing radiation treatment regimes for cancer patients leading to better restoration of spermatogenesis.</p

TableButler – a Windows based tool for processing large data tables generated with high-throughput methods

<p>Abstract</p> <p>Background</p> <p>High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the study, dozens to hundreds of these data tables are generated. Before the actual statistical or cluster analysis, these data tables have to be combined and merged to expression matrices (e.g., in case of gene expression analysis). Gene annotations as well as information concerning the samples analyzed may be appended, renewed or extended. Often additional data values shall be computed or certain features must be filtered out.</p> <p>Results</p> <p>In order to perform these tasks, we have developed a Microsoft Windows based application, "<b><it>TableButler</it></b>", which allows biologists or clinicians without substantial bioinformatics background to perform a plethora of data processing tasks required to analyze the large-scale data.</p> <p>Conclusion</p> <p><b><it>TableButler </it></b>is a monolithic Windows application. It is implemented to handle, join and preprocess large tab delimited ASCII data files. The intuitive user interface enables scientists (e.g. biologists, clinicians or others) to setup workflows for their specific problems by simple drag-and drop like operations.</p> <p>For more details about <b><it>TableButler</it></b>, visit <url>http://www.OncoExpress.org/software/tablebutler</url>.</p

Transcriptome profiling of mice testes following low dose irradiation

BACKGROUND: Radiotherapy is used routinely to treat testicular cancer. Testicular cells vary in radio-sensitivity and the aim of this study was to investigate cellular and molecular changes caused by low dose irradiation of mice testis and to identify transcripts from different cell types in the adult testis. METHODS: Transcriptome profiling was performed on total RNA from testes sampled at various time points (n = 17) after 1 Gy of irradiation. Transcripts displaying large overall expression changes during the time series, but small expression changes between neighbouring time points were selected for further analysis. These transcripts were separated into clusters and their cellular origin was determined. Immunohistochemistry and in silico quantification was further used to study cellular changes post-irradiation (pi). RESULTS: We identified a subset of transcripts (n = 988) where changes in expression pi can be explained by changes in cellularity. We separated the transcripts into five unique clusters that we associated with spermatogonia, spermatocytes, early spermatids, late spermatids and somatic cells, respectively. Transcripts in the somatic cell cluster showed large changes in expression pi, mainly caused by changes in cellularity. Further investigations revealed that the low dose irradiation seemed to cause Leydig cell hyperplasia, which contributed to the detected expression changes in the somatic cell cluster. CONCLUSIONS: The five clusters represent gene expression in distinct cell types of the adult testis. We observed large expression changes in the somatic cell profile, which mainly could be attributed to changes in cellularity, but hyperplasia of Leydig cells may also play a role. We speculate that the possible hyperplasia may be caused by lower testosterone production and inadequate inhibin signalling due to missing germ cells