In natural conversation, the minimal gaps and overlaps of the turns at talk indicate an accurate regulation of the timings of the turn-taking system. Here we studied how the turn-taking affects the gaze of a non-involved viewer of a two-person conversation. The subjects were presented with a video of a conversation while their eye gaze was tracked with an infrared camera. As a control, the video was presented without sound and the sound with still image of the speakers. Turns at talk directed the gaze behaviour of the viewers; the gaze followed, rather than predicted, the speakership change around the turn transition. Both visual and auditory cues presented alone also induced gaze shifts towards the speaking person, although significantly less and later than when the cues of both modalities were available. These results show that the organization of turn-taking has a strong influence on the gaze patterns of even non-involved viewers of the conversation, and that visual and auditory cues are in part redundant in guiding the viewers’ gaze.
Sleep is essential for normal and healthy living. Lack of good quality sleep affects physical, mental and emotional functions. Currently, the treatments of obesity-related sleep disorders focus more on suppressing sleep-related symptoms pharmaceutically and are often accompanied by side effects. Thus, there is urgent need for alternative ways to combat chronic sleep disorders. This study will investigate underlying mechanisms of the effects of exercise and diet intervention on obesity-related sleep disorders, the role of gut microbiota in relation to poor quality of sleep and day-time sleepiness, as well as the levels of hormones responsible for sleep-wake cycle regulation.
Participants consist of 330 (target sample) Finnish men aged 30 to 65 years. Among them, we attempt to randomize 180 (target sample) with sleep disorders into exercise and diet intervention. After screening and physician examination, 101 men with sleep disorders are included and are randomly assigned into three groups: exercise (n = 33), diet (n = 35), and control (n = 33). In addition, we attempt to recruit a target number of 150 healthy men without sleep disorders as the reference group. The exercise group undergoes a six-month individualized progressive aerobic exercise program based on initial fitness level. The diet group follows a six month specific individualized diet program. The control group and reference group are asked to maintain their normal activity and diet during intervention. Measurements are taken before and after the intervention. Primary outcomes include objective sleep measurements by polysomnography and a home-based non-contact sleep monitoring system, and subjective sleep evaluation by questionnaires. Secondary outcome measures include anthropometry, body composition, fitness, sleep disorder-related lifestyle risk factors, composition of gut microbiota and adipose tissue metabolism, as well as specific hormone and neurotranmitter levels and inflammatory biomarkers from venous blood samples.
It is expected that the improvement of sleep quality after exercise and diet intervention will be evident both in subjective and objective measures of quality of sleep. Additionally, the change of sleep quality induced by exercise and diet intervention is expected to be related to the changes in specific hormones and inflammatory biomarkers, and in the composition of gut microbiota.
Current Controlled Trials ISRCTN77172005
Lifestyle intervention; Sleep disorders; Quality of sleep; Obstructive sleep apnea; Insomnia; Sleep measurement; Obesity; Gut microbiota; Neurotransmitters
Birth weight within the normal range is associated with a variety of adult-onset diseases, but the mechanisms behind these associations are poorly understood1. Previous genome-wide association studies identified a variant in the ADCY5 gene associated both with birth weight and type 2 diabetes, and a second variant, near CCNL1, with no obvious link to adult traits2. In an expanded genome-wide association meta-analysis and follow-up study (up to 69,308 individuals of European descent from 43 studies), we have now extended the number of genome-wide significant loci to seven, accounting for a similar proportion of variance to maternal smoking. Five of the loci are known to be associated with other phenotypes: ADCY5 and CDKAL1 with type 2 diabetes; ADRB1 with adult blood pressure; and HMGA2 and LCORL with adult height. Our findings highlight genetic links between fetal growth and postnatal growth and metabolism.
Hospital isolation rooms are vital for the containment (when under negative pressure) of patients with, or the protection (when under positive pressure) of patients, from airborne infectious agents. Such facilities were essential for the management of highly contagious patients during the 2003 severe acute respiratory syndrome (SARS) outbreaks and the more recent 2009 A/H1N1 influenza pandemic. Many different types of door designs are used in the construction of such isolation rooms, which may be related to the space available and affordability. Using colored food dye as a tracer, the qualitative effects of door-opening motions on the dissemination of potentially contaminated air into and out of a single isolation room were visualized and filmed using Reynolds-number-equivalent, small-scale, water-tank models fitted with programmable door-opening and moving human figure motions. Careful scaling considerations involved in the design and construction of these water-tank models enabled these results to be accurately extrapolated to the full-scale situation. Four simple types of door design were tested: variable speed single and double, sliding and hinged doors, in combination with the moving human figure. The resulting video footage was edited, synchronized and presented in a series of split-screen formats. From these experiments, it is clear that double-hinged doors pose the greatest risk of leakage into or out of the room, followed by (in order of decreasing risk) single-hinged, double-sliding and single-sliding doors. The relative effect of the moving human figure on spreading any potential contamination was greatest with the sliding doors, as the bulk airflows induced were large relative to those resulting from these door-opening motions. However, with the hinged doors, the airflows induced by these door-opening motions were significantly greater. Further experiments involving a simulated ventilated environment are required, but from these findings alone, it appears that sliding-doors are far more effective for hospital isolation room containment.
Many cancer predisposition syndromes are rare or have incomplete penetrance, and traditional epidemiological tools are not well suited for their detection. Here we have used an approach that employs the entire population based data in the Finnish Cancer Registry (FCR) for analyzing familial aggregation of all types of cancer, in order to find evidence for previously unrecognized cancer susceptibility conditions. We performed a systematic clustering of 878,593 patients in FCR based on family name at birth, municipality of birth, and tumor type, diagnosed between years 1952 and 2011. We also estimated the familial occurrence of the tumor types using cluster score that reflects the proportion of patients belonging to the most significant clusters compared to all patients in Finland. The clustering effort identified 25,910 birth name-municipality based clusters representing 183 different tumor types characterized by topography and morphology. We produced information about familial occurrence of hundreds of tumor types, and many of the tumor types with high cluster score represented known cancer syndromes. Unexpectedly, Kaposi sarcoma (KS) also produced a very high score (cluster score 1.91, p-value <0.0001). We verified from population records that many of the KS patients forming the clusters were indeed close relatives, and identified one family with five affected individuals in two generations and several families with two first degree relatives. Our approach is unique in enabling systematic examination of a national epidemiological database to derive evidence of aberrant familial aggregation of all tumor types, both common and rare. It allowed effortless identification of families displaying features of both known as well as potentially novel cancer predisposition conditions, including striking familial aggregation of KS. Further work with high-throughput methods should elucidate the molecular basis of the potentially novel predisposition conditions found in this study.
The aim of the study was to evaluate the long-term outcome of patients successfully resuscitated from pre-hospital cardiac arrest with initial pulseless electrical activity (PEA), because the long-term outcome of these patients is unknown. Survival, neurological status one year after cardiac arrest and self-perceived quality of life after five years were assessed.
This retrospective study included adult patients resuscitated from PEA between August 2001 and March 2003 in three urban areas in southern Finland. A validated questionnaire was sent to patients while neurological status according to the Cerebral Performance Category (CPC) -classification was assessed based on medical database notes recorded during follow-up evaluations.
Out of 99 included patients in whom resuscitation was attempted, 41 (41%) were successfully resuscitated and admitted to hospital. Ten (10%) patients were discharged from hospital. Seven were alive after one year and six after five years following cardiac arrest. Five of the seven patients alive one year after resuscitation presented with the same functional level as prior to cardiac arrest.
Patients with initial PEA have been considered to have poor prognosis, but in our material, half of those who survived to hospital discharge were still alive after 5 years. Their self-assessed quality of life seems to be good with only mild to moderate impairments in activities of daily life.
There are no nationwide, comprehensive public health programmes on allergic disorders with set goals and systematic follow-up. The Finnish initiative is based on the idea that the so called allergy epidemic in modern, urban societies is caused by inadequately developed or broken tolerance. The immune system is not trained to make the difference between danger and non-danger (allergy) or the difference between self and non-self (autoimmune diseases). The immune dysfunction leads to inappropriate inflammatory responses and clinical symptoms. The 10-year implementation programme is aimed to reduce burden of allergies both at the individual and societal levels. This is done by increasing both immunological and psychological tolerance and changing attitudes to support health instead of medicalising common and mild allergy symptoms. Severe forms of allergy are in special focus, e.g. asthma attacks are prevented proactively by improving disease control with the help of guided self-management. Networking of allergy experts with primary care doctors and nurses as well with pharmacists is the key for effective implementation. Non-governmental organizations have started a campaign to increase allergy awareness and knowledge among patients and general public. It is time to act, when allergic individuals are becoming a majority of Western populations and their numbers are in rapid increase worldwide. The first results of the Finnish Programme indicate that allergy burden can be reduced with relatively simple means.
Allergy programme; Asthma attack; Immune tolerance; Public health programme; Self-management
Gastrointestinal (GI) adverse effects such as erosion and increased permeability are common during the use of nonsteroidal anti-inflammatory drugs (NSAIDs). Our objective was to assess whether Bifidobacterium animalis ssp. lactis 420 protects against NSAID-induced GI side effects in a rat model. A total of 120 male Wistar rats were allocated into groups designated as control, NSAID, and probiotic. The NSAID and probiotic groups were challenged with indomethacin (10 mg/kg−1; single dose). The probiotic group was also supplemented daily with 1010 CFU of B. lactis 420 for seven days prior to the indomethacin administration. The control group rats received no indomethacin or probiotic. The permeability of the rat intestine was analysed using carbohydrate probes and the visual damage of the rat stomach mucosa was graded according to severity. B. lactis 420 significantly reduced the indomethacin-induced increase in stomach permeability. However, the protective effect on the visual mucosal damage was not significant. The incidence of severe NSAID-induced lesions was, nevertheless, reduced from 50% to 33% with the probiotic treatment. To conclude, the B. lactis 420 supplementation protected the rats from an NSAID-induced increase in stomach permeability and may reduce the formation of more serious GI mucosal damage and/or enhance the recovery rate of the stomach mucosa.
Atherosclerosis is a complex disease with hundreds of genes influencing its progression. In addition, the phenotype of the disease varies significantly depending on the arterial bed.
We characterized the genes generally involved in human advanced atherosclerotic (AHA type V–VI) plaques in carotid and femoral arteries as well as aortas from 24 subjects of Tampere Vascular study and compared the results to non-atherosclerotic internal thoracic arteries (n=6) using genome-wide expression array and QRT-PCR. In addition we determined genes that were typical for each arterial plaque studied. To gain a comprehensive insight into the pathologic processes in the plaques we also analyzed pathways and gene sets dysregulated in this disease using gene set enrichment analysis (GSEA). According to the selection criteria used (>3.0 fold change and p-value <0.05), 235 genes were up-regulated and 68 genes down-regulated in the carotid plaques, 242 genes up-regulated and 116 down-regulated in the femoral plaques and 256 genes up-regulated and 49 genes down-regulated in the aortic plaques. Nine genes were found to be specifically induced predominantly in aortic plaques, e.g., lactoferrin, and three genes in femoral plaques, e.g., chondroadherin, whereas no gene was found to be specific for carotid plaques. In pathway analysis, a total of 28 pathways or gene sets were found to be significantly dysregulated in atherosclerotic plaques (false discovery rate [FDR] <0.25).
This study describes comprehensively the gene expression changes that generally prevail in human atherosclerotic plaques. In addition, site specific genes induced only in femoral or aortic plaques were found, reflecting that atherosclerotic process has unique features in different vascular beds.
There is a need for methods that are able to identify rare variants that cause low or moderate penetrance disease susceptibility. To answer this need, we introduce a rule-based haplotype comparison method, Haplous, which identifies haplotypes within multiple samples from phased genotype data and compares them within and between sample groups. We demonstrate that Haplous is able to accurately identify haplotypes that are identical by descent, exclude common haplotypes in the studied population and select rare haplotypes from the data. Our analysis of three families with multiple individuals affected by lymphoma identified several interesting haplotypes shared by distantly related patients.
Dynamics and balance of allergen specific IgE, IgG4 and IgA binding may contribute to the development of tolerance in cow's milk allergy. Profiling of antibody binding to cow's milk protein epitopes may help in predicting natural history of allergy.
To investigate differences in IgE, IgG4 and IgA binding to cow's milk epitopes over time between patients with early recovery or with persisting cow's milk allergy.
We studied serum samples at the time of diagnosis (mean age 7 months), one year later and at follow-up (mean age 8.6 years) from 11 patients with persisting IgE-mediated cow's milk allergy at age 8-9 years, and 12 patients who recovered by age 3 years. We measured the binding of IgE, IgG4 and IgA antibodies to sequential epitopes derived from five major cow's milk proteins with a peptide microarray-based immunoassay. We analyzed the data with a novel image processing method together with machine learning prediction.
IgE epitope binding patterns were stable over time in patients with persisting cow's milk allergy, whereas binding decreased in patients who recovered early. Binding patterns of IgE and IgG4 overlapped. Among patients who recovered early, the signal of IgG4 binding increased while that of IgE decreased over time. IgE and IgG4 binding to a panel of αs1-, αs2-, β-and κ-casein regions predicted outcome with significant accuracy.
Attaining tolerance to cow's milk is associated with decreased epitope binding by IgE and a concurrent increase in corresponding epitope binding by IgG4.
cow's milk allergy; tolerance; epitope; IgE; IgG4; IgA
Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4 and BMP7, in particular, have been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We explored the effects of BMP4 and BMP7 treatment on global gene transcription in seven breast cancer cell lines during a 6-point time series, using a whole-genome oligo microarray. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data.
Both ligands had a strong effect on gene expression, although the response to BMP4 treatment was more pronounced. The cellular functions most strongly affected by BMP signaling were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMPs, but also highlighted a synexpression group of genes for both ligands. Interestingly, the majority of the genes within these synexpression groups were shared by the two ligands, probably representing the core molecular responses common to BMP4 and BMP7 signaling pathways.
All in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target genes relevant in breast cancer.
bone morphogenetic protein; breast cancer; BMP4; BMP7; expression microarray
The incidence of breast cancer is increasing in the Western world and there is an urgent need for studies of the mechanisms of sex steroids in order to develop novel preventive strategies. Diet modifications may be among the means for breast cancer prevention. Angiogenesis, key in tumor progression, is regulated by the balance between pro- and anti-angiogenic factors, which are controlled in the extracellular space. Sampling of these molecules at their bioactive compartment is therefore needed. The aims of this study were to explore if tamoxifen, one of the most used anti-estrogen treatments for breast cancer affected some of the most important endogenous angiogenesis regulators, vascular endothelial growth factor (VEGF), angiogenin, and endostatin in normal breast tissue in vivo and if a diet supplementation with flaxseed had similar effects as tamoxifen in the breast. Microdialysis was used for in situ sampling of extracellular proteins in normal breast tissue of women before and after six weeks of tamoxifen treatment or before and after addition of 25 g/day of ground flaxseed to the diet or in control women. We show significant correlations between estradiol and levels of VEGF, angiogenin, and endostatin in vivo, which was verified in ex vivo breast tissue culture. Moreover, tamoxifen decreased the levels of VEGF and angiogenin in the breast whereas endostatin increased significantly. Flaxseed did not alter VEGF or angiogenin levels but similar to tamoxifen the levels of endostatin increased significantly. We conclude that one of the mechanisms of tamoxifen in normal breast tissue include tipping of the angiogenic balance into an anti-angiogenic state and that flaxseed has limited effects on the pro-angiogenic factors whereas the anti-angiogenic endostatin may be modified by diet. Further studies of diet modifications for breast cancer prevention are warranted.
Peak bone mass, attained by early adulthood, is influenced by genetic and life-style factors. Early infant feeding and duration of breastfeeding in particular, associate with several health-related parameters in childhood. The aim of this study was to examine whether the effects of early infant feeding extend to peak bone mass and other bone health characteristics at adult age.
Methods and Findings
A cohort of 158 adults (76 males) born in Helsinki, Finland, 1975, prospectively followed up from birth, underwent physical examination and bone densitometry to study bone area, bone mineral content (BMC), and bone mineral density (BMD) at 32 years of age. Life-style factors relevant for bone health were recorded. For data analysis the cohort was divided into three equal-size groups according to the total duration of breastfeeding (BF): Short (≤3 months), Intermediate and Prolonged (≥7 months) BF groups. In males short BF is associated with higher bone area, BMC, and BMD compared to longer BF. Males in the Short BF group had on average 4.7% higher whole body BMD than males in the Prolonged BF group. In multivariate analysis, after controlling for multiple confounding factors, the influence of BF duration on adult bone characteristics persisted in males. Differences between the three feeding groups were observed in lumbar spine bone area and BMC, and whole body BMD (MANCOVA; p = 0.025, p = 0.013, and p = 0.048, respectively), favoring the Short BF group. In women no differences were observed.
In men, early infant milk feeding may have a significant impact on adult bone health. A potential explanation is that the calcium and phosphate contents were strikingly higher in formula milk and commercial cow milk/cow milk dilutions as opposed to human milk. Our novel finding merits further studies to determine means to ensure optimal bone mass development in infants with prolonged breastfeeding.
Patients presenting with ST-segment elevation myocardial infarction (STEMI) frequently use warfarin. Fibrinolytic agents and warfarin both increase bleeding risk, but only a few studies have been published concerning the bleeding risk of warfarin-prescribed patients receiving fibrinolysis. The objective of this study was to define the prevalence for intracranial haemorrhage (ICH) or major bleeding in patients on warfarin treatment receiving pre-hospital fibrinolysis.
This was an observational cohort study. Data for this retrospective case series were collected in Helsinki Emergency Medical Service catchment area from 1.1.1997 to 30.6.2010. All warfarin patients with suspected ST-segment elevation myocardial infarction (STEMI), who received pre-hospital fibrinolysis, were included. Bleeding complications were detected from Medical Records and classified as ICH, major or minor bleeding.
Thirty-six warfarin patients received fibrinolysis during the study period. Fourteen patients had bleeding complications. One (3%, 95% CI 0-15%) patient had ICH, six (17%, 95% CI 7-32%) had major and seven (19%, 95% CI 9-35%) had minor bleeding. The only fatal bleeding occurred in a patient with ICH. Patients' age, fibrinolytic agent used or aspirin use did not predispose to bleeding complications. High International Normalized Ratio (INR) seemed to predispose to bleedings with values over 3, but no statistically significant difference was found.
Bleedings occur frequently in warfarin patients treated with fibrinolysis in the real world setting, but they are rarely fatal.
Background and Purpose
Advances in the management of acute ischemic stroke and medical imaging are creating pressure to replace the rigid one-third middle cerebral artery (MCA) and non-contrast-enhanced CT (NCCT) Alberta Stroke Program Early CT Score (ASPECTS) thresholds used for the selection of patients eligible for intravenous thrombolytic therapy. The identification of potentially salvageable ischemic brain tissue lies at the core of this issue. In this study, the role of CT perfusion ASPECTS in the detection of reversible ischemia was analyzed.
Materials and Methods
We retrospectively reviewed the clinical and imaging data of 92 consecutive patients who received intravenous thrombolytic therapy for acute (duration <3 h) ischemic stroke. Most of the patients underwent admission multimodal CT, and all patients had follow-up NCCT at 24 h. ASPECTS was assigned to all modalities and correlated with clinical and imaging parameters. Receiver-operating characteristic curve analysis was performed to determine optimal thresholds for different parameters to predict clinical outcome.
A perfusion defect could be detected in 50% of the patients. ASPECTS correlated inversely with the clinical outcome in the following order: follow-up NCCT > cerebral blood volume (CBV) > mean transit time (MTT) > admission NCCT. The follow-up NCCT and the CBV displayed a statistically significant difference from the admission NCCT, while the MTT did not reach statistical significance. The threshold that best differentiated between good and bad clinical outcome on admission was CBV ASPECTS ≥7. In patients with CT perfusion ASPECTS mismatch, MTT and CBV ASPECTS essentially provided the lower and upper limits for the follow-up NCCT ASPECTS, thus defining the spectrum of possible outcomes. Furthermore, CT perfusion ASPECTS mismatch strongly correlated (r = 0.83) with the mismatch between the tissue at risk and the final infarct, i.e. the amount of salvaged tissue. This finding suggests that the CT perfusion ASPECTS mismatch adequately identifies the amount of potentially salvageable ischemic brain tissue.
Parameters derived from the use of CT perfusion ASPECTS can detect reversible ischemia and are correlated with clinical outcome.
ASPECTS; Computed tomography; Perfusion; Stroke; Thrombolytic therapy
IFN-γR1 deficiency is a genetic etiology of Mendelian susceptibility to mycobacterial diseases, and includes two forms of complete recessive deficiency, with or without cell surface expression, and two forms of partial deficiency, dominant or recessive. We report here a novel form of partial and recessive Interferon γ receptor 1 (IFN-γR1) deficiency, which is almost as severe as complete deficiency. The patient is homozygous for a mutation of the initiation codon (M1K). No detectable expression and function of IFN-γR1 were found in the patient's fibroblasts. However, IFN-γR1 expression was found to be impaired, but not abolished, on the EBV-transformed B cells, which could respond weakly to IFN-γ. The mechanism underlying this weak expression involves leaky translation initiation at both non-AUG codons and the third AUG codon at position 19. It results in the residual expression of IFN-γR1 protein of normal molecular weight and function. The residual IFN-γ signaling documented in this novel form of partial IFN-γR1 deficiency was not ubiquitous and was milder than that seen in other forms of partial IFN-γR1 deficiency, accounting for the more severe clinical phenotype of the patient, which was almost as severe as that of patients with complete deficiency.
How does expertise influence the perception of representational and abstract paintings? We asked 20 experts on art history and 20 laypersons to explore and evaluate a series of paintings ranging in style from representational to abstract in five categories. We compared subjective esthetic judgments and emotional evaluations, gaze patterns, and electrodermal reactivity between the two groups of participants. The level of abstraction affected esthetic judgments and emotional valence ratings of the laypersons but had no effect on the opinions of the experts: the laypersons’ esthetic and emotional ratings were highest for representational paintings and lowest for abstract paintings, whereas the opinions of the experts were independent of the abstraction level. The gaze patterns of both groups changed as the level of abstraction increased: the number of fixations and the length of the scanpaths increased while the duration of the fixations decreased. The viewing strategies – reflected in the target, location, and path of the fixations – however indicated that experts and laypersons paid attention to different aspects of the paintings. The electrodermal reactivity did not vary according to the level of abstraction in either group but expertise was reflected in weaker responses, compared with laypersons, to information received about the paintings.
art perception; esthetic judgment; eye-movement; electrodermal activity
Mother's diet during pregnancy is important, since plant lignans and their metabolites, converted by the intestinal microflora to enterolignans, are proposed to possess multiple health benefits. Aim of our study was to investigate whether a dietary intervention affects lignan concentrations in the serum of pregnant women.
A controlled dietary intervention trial including 105 first-time pregnant women was conducted in three intervention and three control maternity health clinics. The intervention included individual counseling on diet and on physical activity, while the controls received conventional care. Blood samples were collected on gestation weeks 8-9 (baseline) and 36-37 (end of intervention). The serum levels of the plant lignans 7-hydroxymatairesinol, secoisolariciresinol, matairesinol, lariciresinol, cyclolariciresinol, and pinoresinol, and of the enterolignans 7-hydroxyenterolactone, enterodiol, and enterolactone, were measured using a validated method.
The baseline levels of enterolactone, enterodiol and the sum of lignans were higher in the control group, whereas at the end of the trial their levels were higher in the intervention group. The adjusted mean differences between the baseline and end of the intervention for enterolactone and the total lignan intake were 1.6 ng/ml (p = 0.018, 95% CI 1.1-2.3) and 1.4 ng/mg (p = 0.08, 95% CI 1.0-1.9) higher in the intervention group than in the controls. Further adjustment for dietary components did not change these associations.
The dietary intervention was successful in increasing the intake of lignan-rich food products, the fiber consumption and consequently the plasma levels of lignans in pregnant women.
Coordinated efforts to collect large-scale data sets provide a basis for systems level understanding of complex diseases. In order to translate these fragmented and heterogeneous data sets into knowledge and medical benefits, advanced computational methods for data analysis, integration and visualization are needed.
We introduce a novel data integration framework, Anduril, for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.
We have integrated multidimensional molecular and clinical data from 338 subjects having glioblastoma multiforme, one of the deadliest and most poorly understood cancers, using Anduril. The central objective of our approach is to identify genetic loci and genes that have significant survival effect. Our results suggest several novel genetic alterations linked to glioblastoma multiforme progression and, more specifically, reveal Moesin as a novel glioblastoma multiforme-associated gene that has a strong survival effect and whose depletion in vitro significantly inhibited cell proliferation. All analysis results are available as a comprehensive website.
Our results demonstrate that integrated analysis and visualization of multidimensional and heterogeneous data by Anduril enables drawing conclusions on functional consequences of large-scale molecular data. Many of the identified genetic loci and genes having significant survival effect have not been reported earlier in the context of glioblastoma multiforme. Thus, in addition to generally applicable novel methodology, our results provide several glioblastoma multiforme candidate genes for further studies.
Anduril is available at http://csbi.ltdk.helsinki.fi/anduril/
The glioblastoma multiforme analysis results are available at http://csbi.ltdk.helsinki.fi/anduril/tcga-gbm/
Enterolactone (EL) is an enterolignan found in human subjects. In this pilot study, the enantiomeric ratios of serum EL were determined in serum from healthy adults during consumption of habitual diet, and after an 8-day supplementation with flaxseed (25 g/day). (−)EL dominated in all serum samples collected during habitual diet consumption. However, the ratio of (−)EL and (+)EL enantiomers differed markedly between individuals. Flaxseed ingestion increased significantly the proportion of (+)EL in all subjects. Moreover, a small but significant increase in serum (−)EL concentration was measured. After flaxseed ingestion, (−)EL concentrations correlated with those of (+)EL suggesting that the stereochemistry of the parent plant lignan in flaxseed is not a major determinant of EL formation in human subjects. Comparison of EL concentrations obtained with the validated chromatographic methods (HPLC-MS/MS, HPLC-CEAD, and GC-MS) and the time-resolved fluoroimmunoassay (TR-FIA) revealed that the immunoassay method underestimates human serum EL concentrations after the flaxseed ingestion.
Aleutian disease (AD), a common infectious disease in farmed minks worldwide, is caused by Aleutian mink disease virus (AMDV). Serodiagnosis of AD in minks has been based on detection of AMDV antibodies by counterimmunoelectrophoresis (CIE) since the 1980s. The aim of this study was to develop and evaluate an enzyme-linked immunosorbent assay (ELISA) based on recombinant virus-like particles (VLPs) for identifying AMDV antibodies from mink sera. AMDV capsid protein (VP2) of a Finnish wild-type strain was expressed by the baculovirus system in Spodoptera frugiperda 9 insect cells and was shown to self-assemble to VLPs (with an ultrastructure similar to that of the actual virion). A direct immunoglobulin G ELISA was established using purified recombinant AMDV VP2 VLPs as an antigen. Sera from farmed minks were collected to evaluate the AMDV VP2 ELISA (n = 316) and CIE (n = 209) based on AMDV VP2 recombinant antigen in parallel with CIE performed using a commercially available traditional antigen. CIE performed with the recombinant antigen had a sensitivity and specificity of 100% and ELISA a sensitivity of 99% and a specificity of 97%, with reference to CIE performed with the commercial antigen. The results show that the recombinant AMDV VP2 VLPs are antigenic and that AMDV VP2 ELISA is sensitive and specific and encourage further development of the method for high-throughput diagnostics, involving hundreds of thousands of samples in Finland annually.
Lignans and their in vivo metabolites, especially enterolactone (ENL), have attracted substantial interest as potential chemopreventive agents for prostate cancer. Preclinical and clinical interventions performed with lignan-rich flaxseed that use surrogate biomarkers as endpoints suggest that lignans may attenuate prostate carcinogenesis in individuals with increased risk or with diagnosed cancer. No unequivocal prostate cancer risk reduction has been found for lignans in epidemiological studies, suggesting that lignan concentrations found in populations consuming a regular non-supplemented diet are not chemopreventive in prostate cancer. Presumably, the main obstacles in assessing the efficacy of food lignans is limited knowledge of the serum and tissue lignan concentrations required for the putative prevention. Further clinical studies performed with the purified compounds are required to substantiate a health claim.
lignan; phytoestrogen; diet; prostate cancer; health claim; surrogate biomarker
To take a step towards real-life-like experimental setups, we simultaneously recorded magnetoencephalographic (MEG) signals and subject's gaze direction during audiovisual speech perception. The stimuli were utterances of /apa/ dubbed onto two side-by-side female faces articulating /apa/ (congruent) and /aka/ (incongruent) in synchrony, repeated once every 3 s. Subjects (N = 10) were free to decide which face they viewed, and responses were averaged to two categories according to the gaze direction. The right-hemisphere 100-ms response to the onset of the second vowel (N100m’) was a fifth smaller to incongruent than congruent stimuli. The results demonstrate the feasibility of realistic viewing conditions with gaze-based averaging of MEG signals.
auditory cortex; eye tracking; human; magnetoencephalography; McGurk illusion
The effective population size (Ne) is a critical evolutionary and conservation parameter that can indicate the adaptive potential of populations. Robust estimates of Ne of endangered taxa have been previously hampered by estimators that are sensitive to sample size. We estimated Ne on two remaining populations of the endangered Miami blue butterfly, a formerly widespread taxon in Florida. Our goal was to determine the consistency of various temporal and point estimators on inferring Ne and to determine the utility of this information for understanding the role of genetic stochasticity. We found that recently developed ‘unbiased estimators’ generally performed better than some older methods in that the former had more realistic Ne estimates and were more consistent with what is known about adult population size. Overall, Ne/N ratios based on census point counts were high. We suggest that this pattern may reflect genetic compensation caused by reduced reproductive variance due to breeding population size not being limited by resources. Assuming Ne and N are not heavily biased, it appears that the lack of gene flow between distant populations may be a greater genetic threat in the short term than the loss of heterozygosity due to inbreeding.
conservation genetics; Cyclargus thomasi bethunebakeri; Lepidoptera; microsatellites; Ne