Tampere University of Applied Sciences

We propose a novel image denoising strategy based on an enhanced sparse representation in transform domain. The enhancement of the sparsity is achieved by grouping similar 2-D image fragments (e.g., blocks) into 3-D data arrays which we call "groups." Collaborative filtering is a special procedure developed to deal with these 3-D groups. We realize it using the three successive steps: 3-D transformation of a group, shrinkage of the transform spectrum, and inverse 3-D transformation. The result is a 3-D estimate that consists of the jointly filtered grouped image blocks. By attenuating the noise, the collaborative filtering reveals even the finest details shared by grouped blocks and, at the same time, it preserves the essential unique features of each individual block. The filtered blocks are then returned to their original positions. Because these blocks are overlapping, for each pixel, we obtain many different estimates which need to be combined. Aggregation is a particular averaging procedure which is exploited to take advantage of this redundancy. A significant improvement is obtained by a specially developed collaborative Wiener filtering. An algorithm based on this novel denoising strategy and its efficient implementation are presented in full detail; an extension to color-image denoising is also developed. The experimental results demonstrate that this computationally scalable algorithm achieves state-of-the-art denoising performance in terms of both peak signal-to-noise ratio and subjective visual quality.

Magnetoencephalography (MEG) is a noninvasive technique for investigating neuronal activity in the living human brain. The time resolution of the method is better than 1 ms and the spatial discrimination is, under favorable circumstances, 2-3 mm for sources in the cerebral cortex. In MEG studies, the weak 10 fT-1 pT magnetic fields produced by electric currents flowing in neurons are measured with multichannel SQUID (superconducting quantum interference device) gradiometers. The sites in the cerebral cortex that are activated by a stimulus can be found from the detected magnetic-field distribution, provided that appropriate assumptions about the source render the solution of the inverse problem unique. Many interesting properties of the working human brain can be studied, including spontaneous activity and signal processing following external stimuli. For clinical purposes, determination of the locations of epileptic foci is of interest. The authors begin with a general introduction and a short discussion of the neural basis of MEG. The mathematical theory of the method is then explained in detail, followed by a thorough description of MEG instrumentation, data analysis, and practical construction of multi-SQUID devices. Finally, several MEG experiments performed in the authors' laboratory are described, covering studies of evoked responses and of spontaneous activity in both healthy and diseased brains. Many MEG studies by other groups are discussed briefly as well.

Abstract Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored 1,2 . FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10 –11 ) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.

Members of the recently recognized SRC-1 family of transcriptional coactivators interact with steroid hormone receptors to enhance ligand-dependent transcription. AIB1, a member of the SRC-1 family, was cloned during a search on the long arm of chromosome 20 for genes whose expression and copy number were elevated in human breast cancers. AIB1 amplification and overexpression were observed in four of five estrogen receptor-positive breast and ovarian cancer cell lines. Subsequent evaluation of 105 unselected specimens of primary breast cancer found AIB1 amplification in approximately 10 percent and high expression in 64 percent of the primary tumors analyzed. AIB1 protein interacted with estrogen receptors in a ligand-dependent fashion, and transfection of AIB1 resulted in enhancement of estrogen-dependent transcription. These observations identify AIB1 as a nuclear receptor coactivator whose altered expression may contribute to development of steroid-dependent cancers.

Recent theoretical work has suggested that brain oscillations in the theta band are involved in active maintenance and recall of working memory representations. To test this theoretical framework we recorded neuromagnetic responses from 10 subjects performing the Sternberg task. Subjects were required to retain a list of 1, 3, 5 or 7 visually presented digits during a 3-s retention period. During the retention period we observed ongoing frontal theta activity in the 7-8.5-Hz band recorded by sensors over frontal brain areas. The activity in the theta band increased parametrically with the number of items retained in working memory. A time-frequency analysis revealed that the task-dependent theta was present during the retention period and during memory scanning. Following the memory task the theta activity was reduced. These results suggest that theta oscillations generated in frontal brain regions play an active role in memory maintenance.

Recent epidemiological and laboratory-based studies suggest that the anti-diabetic drug metformin prevents cancer progression. How metformin diminishes tumor growth is not fully understood. In this study, we report that in human cancer cells, metformin inhibits mitochondrial complex I (NADH dehydrogenase) activity and cellular respiration. Metformin inhibited cellular proliferation in the presence of glucose, but induced cell death upon glucose deprivation, indicating that cancer cells rely exclusively on glycolysis for survival in the presence of metformin. Metformin also reduced hypoxic activation of hypoxia-inducible factor 1 (HIF-1). All of these effects of metformin were reversed when the metformin-resistant Saccharomyces cerevisiae NADH dehydrogenase NDI1 was overexpressed. In vivo, the administration of metformin to mice inhibited the growth of control human cancer cells but not those expressing NDI1. Thus, we have demonstrated that metformin's inhibitory effects on cancer progression are cancer cell autonomous and depend on its ability to inhibit mitochondrial complex I.DOI: http://dx.doi.org/10.7554/eLife.02242.001.

Muscle injuries are one of the most common traumas occurring in sports. Despite their clinical importance, few clinical studies exist on the treatment of these traumas. Thus, the current treatment principles of muscle injuries have either been derived from experimental studies or been tested only empirically. Although nonoperative treatment results in good functional outcomes in the majority of athletes with muscle injuries, the consequences of failed treatment can be very dramatic, possibly postponing an athlete's return to sports for weeks or even months. Moreover, the recognition of some basic principles of skeletal muscle regeneration and healing processes can considerably help in both avoiding the imminent dangers and accelerating the return to competition. Accordingly, in this review, the authors have summarized the prevailing understanding on the biology of muscle regeneration. Furthermore, they have reviewed the existing data on the different treatment modalities (such as medication, therapeutic ultrasound, physical therapy) thought to influence the healing of injured skeletal muscle. In the end, they extend these findings to clinical practice in an attempt to propose an evidence-based approach for the diagnosis and optimal treatment of skeletal muscle injuries.

In this paper, the computational and practical aspects of a realistically-shaped multilayer model for the conductivity geometry of the human head are discussed. A novel way to handle the numerical difficulties caused by the presence of the poorly conducting skull is presented. Using our method, both the potential on the surface of the head and the magnetic field outside the head can be computed accurately. The procedure was tested with the multilayer sphere model, for which analytical expressions are available. The method is then applied to a realistically-shaped head model, and it is numerically shown that for the computation of B, produced by cerebral current sources, it is sufficient to consider a brain-shaped homogeneous conductor only since the secondary currents on the outer interfaces give only a negligible contribution to the magnetic field outside the head. Comparisons with the sphere model are also included to pinpoint areas where the homogeneous conductor model provides essential improvements in the calculation of the magnetic field outside the head.

We present an extension of the BM3D filter to volumetric data. The proposed algorithm, BM4D, implements the grouping and collaborative filtering paradigm, where mutually similar d-dimensional patches are stacked together in a (d+1)-dimensional array and jointly filtered in transform domain. While in BM3D the basic data patches are blocks of pixels, in BM4D we utilize cubes of voxels, which are stacked into a 4-D "group." The 4-D transform applied on the group simultaneously exploits the local correlation present among voxels in each cube and the nonlocal correlation between the corresponding voxels of different cubes. Thus, the spectrum of the group is highly sparse, leading to very effective separation of signal and noise through coefficient shrinkage. After inverse transformation, we obtain estimates of each grouped cube, which are then adaptively aggregated at their original locations. We evaluate the algorithm on denoising of volumetric data corrupted by Gaussian and Rician noise, as well as on reconstruction of volumetric phantom data with non-zero phase from noisy and incomplete Fourier-domain (k-space) measurements. Experimental results demonstrate the state-of-the-art denoising performance of BM4D, and its effectiveness when exploited as a regularizer in volumetric data reconstruction.

The identification of the Drosophila melanogaster Toll pathway cascade and the subsequent characterization of TLRs have reshaped our understanding of the immune system. Ever since, Drosophila NF-κB signaling has been actively studied. In flies, the Toll receptors are essential for embryonic development and immunity. In total, nine Toll receptors are encoded in the Drosophila genome, including the Toll pathway receptor Toll. The induction of the Toll pathway by gram-positive bacteria or fungi leads to the activation of cellular immunity as well as the systemic production of certain antimicrobial peptides. The Toll receptor is activated when the proteolytically cleaved ligand Spatzle binds to the receptor, eventually leading to the activation of the NF-κB factors Dorsal-related immunity factor or Dorsal. In this study, we review the current literature on the Toll pathway and compare the Drosophila and mammalian NF-κB pathways.

We present a simple and usable noise model for the raw-data of digital imaging sensors. This signal-dependent noise model, which gives the pointwise standard-deviation of the noise as a function of the expectation of the pixel raw-data output, is composed of a Poissonian part, modeling the photon sensing, and Gaussian part, for the remaining stationary disturbances in the output data. We further explicitly take into account the clipping of the data (over- and under-exposure), faithfully reproducing the nonlinear response of the sensor. We propose an algorithm for the fully automatic estimation of the model parameters given a single noisy image. Experiments with synthetic images and with real raw-data from various sensors prove the practical applicability of the method and the accuracy of the proposed model.

The heterogeneity of common variable immunodeficiency (CVID) calls for a classification addressing pathogenic mechanisms as well as clinical relevance. This European multicenter trial was initiated to develop a consensus of 2 existing classification schemes based on flowcytometric B-cell phenotyping and the clinical course. The clinical evaluation of 303 patients with the established diagnosis of CVID demonstrated a significant coincidence of granulomatous disease, autoimmune cytopenia, and splenomegaly. Phenotyping of B-cell subpopulations confirmed a severe reduction of switched memory B cells in most of the patients that was associated with a higher risk for splenomegaly and granulomatous disease. An expansion of CD21(low) B cells marked patients with splenomegaly. Lymphadenopathy was significantly linked with transitional B-cell expansion. Based on these findings and pathogenic consideration of B-cell differentiation, we suggest an improved classification for CVID (EUROclass), separating patients with nearly absent B cells (less than 1%), severely reduced switched memory B cells (less than 2%), and expansion of transitional (more than 9%) or CD21(low) B cells (more than 10%). Whereas the first group contains all patients with severe defects of early B-cell differentiation, severely reduced switched memory B cells indicate a defective germinal center development as found in inducible constimulator (ICOS) or CD40L deficiency. The underlying defects of expanded transitional or CD21(low) B cells remain to be elucidated. This trial is re-gistered at http://www.uniklinik-freiburg.de/zks/live/uklregister/Oeffentlich.html as UKF000308.

Mitogen-activated protein kinase (MAPK) pathways constitute a large modular network that regulates a variety of physiological processes, such as cell growth, differentiation, and apoptotic cell death. The function of the ERK pathway has been depicted as survival-promoting, in essence by opposing the proapoptotic activity of the stress-activated c-Jun NH(2)-terminal kinase (JNK)/p38 MAPK pathways. However, recently published work suggests that extracellular regulated kinase (ERK) pathway activity is suppressed by JNK/p38 kinases during apoptosis induction. In this review, we will summarize the current knowledge about JNK/p38-mediated mechanisms that negatively regulate the ERK pathway. In particular, we will focus on phosphatases (PP2A, MKPs) as inhibitors of ERK pathway activity in regulating apoptosis. A model proposed in this review places the negative regulation of the ERK pathway in a central position for the cellular decision-making process that determines whether cells will live or die in response to apoptosis-promoting signals. In addition, we will discuss the potential functional relevance of negative regulation of ERK pathway activity, for physiological and pathological conditions (e.g., cellular transformation).

In Finland, coronary heart disease (CHD) incidence was very high in the 1960s and 1970s. In line with this high incidence, the Seven Countries Study showed that the level of serum cholesterol in Finns was also the highest among the investigated countries in the 1960s. Because several studies indicated that the atherosclerotic process starts early in life, and in accord with the World Health Organization Recommendation of 1978 which stated that studies assessing atherosclerosis precursors in children should be initiated, a program was launched in Finland in the late 1970s to study cardiovascular risk in the youth. The Cardiovascular Risk in Young Finns Study was designed as a collaborative effort between five university departments of medical schools (i.e. in Helsinki, Kuopio, Oulu, Tampere and Turku) and several other institutions in Finland. The aim was to study the levels of CHD risk factors and their determinants in children and adolescents of various ages in different parts of the country. Two pilot studies were carried out in 1978 (N1⁄4 264, age 8 years) and in 1979 (N1⁄4 634, aged 3, 12 and 17 years). The first main cross-sectional (baseline) study was performed in 1980. The baseline study included 3596 children and adolescents aged 3, 6, 9, 12, 15 and 18 years. Between 1980 and 1992, these cohorts were followed up at 3-year intervals. The latest examination of the Cardiovascular Risk in Young Finns Study was performed in 2001, when the participants were young adults, aged 24–39 years. At the time of writing, the 27-year (i.e. 27 years since the start of the study when the participants are aged 30–45 years) follow-up field studies are being conducted, and will be completed in the beginning of 2008.

We present a novel approach to still image denoising based on effective filtering in 3D transform domain by combining sliding-window transform processing with block-matching. We process blocks within the image in a sliding manner and utilize the block-matching concept by searching for blocks which are similar to the currently processed one. The matched blocks are stacked together to form a 3D array and due to the similarity between them, the data in the array exhibit high level of correlation. We exploit this correlation by applying a 3D decorrelating unitary transform and effectively attenuate the noise by shrinkage of the transform coefficients. The subsequent inverse 3D transform yields estimates of all matched blocks. After repeating this procedure for all image blocks in sliding manner, the final estimate is computed as weighed average of all overlapping blockestimates. A fast and efficient algorithm implementing the proposed approach is developed. The experimental results show that the proposed method delivers state-of-art denoising performance, both in terms of objective criteria and visual quality.

Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation.

The shape-adaptive discrete cosine transform ISA-DCT) transform can be computed on a support of arbitrary shape, but retains a computational complexity comparable to that of the usual separable block-DCT (B-DCT). Despite the near-optimal decorrelation and energy compaction properties, application of the SA-DCT has been rather limited, targeted nearly exclusively to video compression. In this paper, we present a novel approach to image filtering based on the SA-DCT. We use the SA-DCT in conjunction with the Anisotropic Local Polynomial Approximation-Intersection of Confidence Intervals technique, which defines the shape of the transform's support in a pointwise adaptive manner. The thresholded or attenuated SA-DCT coefficients are used to reconstruct a local estimate of the signal within the adaptive-shape support. Since supports corresponding to different points are in general overlapping, the local estimates are averaged together using adaptive weights that depend on the region's statistics. This approach can be used for various image-processing tasks. In this paper, we consider, in particular, image denoising and image deblocking and deringing from block-DCT compression. A special structural constraint in luminance-chrominance space is also proposed to enable an accurate filtering of color images. Simulation experiments show a state-of-the-art quality of the final estimate, both in terms of objective criteria and visual appearance. Thanks to the adaptive support, reconstructed edges are clean, and no unpleasant ringing artifacts are introduced by the fitted transform.

Qualinet White Paper on Definitions of Quality of Experience Output from the fifth Qualinet meeting, Novi Sad, March 12, 2013

It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We discovered that the transmembrane domain of tyrosine kinase receptor 2 (TRKB), the brain-derived neurotrophic factor (BDNF) receptor that promotes neuronal plasticity and antidepressant responses, has a cholesterol-sensing function that mediates synaptic effects of cholesterol. We then found that both typical and fast-acting antidepressants directly bind to TRKB, thereby facilitating synaptic localization of TRKB and its activation by BDNF. Extensive computational approaches including atomistic molecular dynamics simulations revealed a binding site at the transmembrane region of TRKB dimers. Mutation of the TRKB antidepressant-binding motif impaired cellular, behavioral, and plasticity-promoting responses to antidepressants in vitro and in vivo. We suggest that binding to TRKB and allosteric facilitation of BDNF signaling is the common mechanism for antidepressant action, which may explain why typical antidepressants act slowly and how molecular effects of antidepressants are translated into clinical mood recovery.

The Janus kinase (Jak) family is one of ten recognized families of non-receptor tyrosine kinases. Mammals have four members of this family, Jak1, Jak2, Jak3 and Tyrosine kinase 2 (Tyk2). Birds, fish and insects also have Jaks. Each protein has a kinase domain and a catalytically inactive pseudo-kinase domain, and they each bind cytokine receptors through amino-terminal FERM (Band-4.1, ezrin, radixin, moesin) domains. Upon binding of cytokines to their receptors, Jaks are activated and phosphorylate the receptors, creating docking sites for signaling molecules, especially members of the signal transducer and activator of transcription (Stat) family. Mutations of the Drosophila Jak (Hopscotch) have revealed developmental defects, and constitutive activation of Jaks in flies and humans is associated with leukemia-like syndromes. Through the generation of Jak-deficient cell lines and gene-targeted mice, the essential, nonredundant functions of Jaks in cytokine signaling have been established. Importantly, deficiency of Jak3 is the basis of human autosomal recessive severe combined immunodeficiency (SCID); accordingly, a selective Jak3 inhibitor has been developed, forming a new class of immunosuppressive drugs.