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Background: It has been hypothesised that injury risk after return to play following an injury absence is influenced by the amount of training completed before return to competition., Aim: To analyse if the number of completed training sessions between return to play and the first subsequent match appearance was associated with the odds of injury in men's professional football., Methods: From a cohort study, including 303 637 individual matches, 4805 first match appearances after return to play following moderate to severe injuries (≥8 days absence) were analysed. Rate ratios (RRs) were used to compare injury rates in the first match appearances with the average seasonal match injury rate. Odds ratios (ORs) were used to analyse associations between the number of completed training sessions and general (all injuries), muscle, and non-muscle injury odds., Results: Injury rate in the first match after return to play was increased by 87% compared with the average seasonal match injury rate (46.9 vs 25.0/1000 hours, RR=1.87; 95% CI 1.64 to 2.14). The odds of injury dropped 7% with each training session before the first match (OR 0.93; 95% CI 0.87 to 0.98). The same association was found for muscle injuries (OR 0.87; 95% CI 0.79 to 0.95) but not for non-muscle injuries (OR 0.99; 95% CI 0.91 to 1.07)., Conclusions: Injury rates in the first match after injury are higher than the average seasonal match injury rate, but the propensity for player injury is decreased when players complete more training sessions before their first match., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)

Aim: To determine the epidemiology of isolated syndesmotic injuries in professional football players., Methods: Data from 15 consecutive seasons of European professional football between 2001 and 2016 contributed to the dataset of this study. Match play and training data from a total of 3677 players from 61 teams across 17 countries have been included. Team medical staff recorded player exposure and time loss injuries. Injury incidence was defined as the number of injuries per 1000 player-hours. Injury burden was defined as number of days absence per 1000 player-hours. Seasonal trends for isolated syndesmotic injury incidence, isolated syndesmotic injury proportion of ankle ligament injuries and isolated syndesmotic injury burden were analysed via linear regression., Results: The isolated syndesmotic injury incidence was 0.05 injuries per 1000 hours of exposure (95% CI 0.04 to 0.06) or one injury per team every three seasons. The injury incidence during match play was 13 times higher compared with during training, 0.21 (95% CI 0.16 to 0.26) and 0.02 (95% CI 0.01 to 0.02), respectively. Out of the 1320 ankle ligament injuries registered during the 15 seasons, 94 (7%) were diagnosed as isolated syndesmotic injuries. An annual increase in injury incidence was observed (R 2 =0.495, b=0.003, 95% CI 0.001 to 0.004, P=0.003). However, no significant annual change of injury burden was observed (R 2 =0.033, b=0.032, 95% CI -0.073 to 0.138, P=0.520). Seventy-four per cent of the injuries were contact related, and the mean (±SD) absence following an isolated syndesmotic injury was 39 (±28) days., Conclusions: The incidence of isolated syndesmotic injuries in elite professional European football annually increased between 2001 and 2016., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2019. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Diabetes has become a major public health problem in the world. In this context, early assessment of glycemic control is essential in order to avoid life-threatening health complications. A panel of diabetes experts have recently proposed a list of recommendations when using Continuous Glucose Monitoring (CGM) for glycemic control assessment including a minimum of two weeks of CGM data. A recent study has further introduced a metric called Glucose Profile Indicator (GPI) for CGM based diabetes management including a subset of the recommended CGM metrics. In this pilot study, it was investigated if less than two weeks of CGM data would impact the performance of GPI compared to the proposed two weeks of CGM data. Furthermore, logistic regression (LR) was used to examine if an improvement could be achieved taking as input the CGM metrics used to quantify GPI. The population mean accuracy for accumulated day 1 to 13 varied between 72.8 ± 2.0% - 98.3 ± 0.4% with no clear sign of improvement using LR. Hence, this indicates a trade-off between the amount of available CGM data and the precision in which the GPI outcome using all 14 days can be achieved when considering features of the GPI alone. Future work is needed to investigate if this trade-off can be improved by the use of additional features of the CGM.

Objective: War-traumatized refugee children and adolescents have been overlooked in research on trauma-related dissociation, and whatever research has been conducted has relied almost exclusively on questionnaires. The present study was an exploration of dissociative experiences in multitraumatized war-refugee youth., Method: In this study, we used a mixed-method approach by grouping participants according to a Western-based dissociation measure (the Adolescent Dissociative Experiences Scale; Armstrong, Putnam, Carlson, Libero, & Smith, 1997), and conducting qualitative and quantitative analyses of their verbal descriptions of mental experiences related to dissociation in the aftermath of war and resettlement. The sample included 40 refugee youth, ages 13 to 21, 19 girls and 21 boys resettled in Sweden because of war and persecution., Results: Severe trauma-related dissociation was a problem for a considerable subgroup of the sample. Some dissociative experiences were present in all the sample; others were restricted to the most dissociative group. The correlates of severe dissociation included high frequency and severity of emotional dysregulation and intensity, negative self- and body-perception, depressive mood, and experiences of detachment., Conclusion: Clinicians are urged to be aware of and assess trauma-related dissociation in war-refugee youth, and consider not only dissociative phenomena, but also other important processes such as emotional dysregulation. (PsycINFO Database Record, ((c) 2018 APA, all rights reserved).)

Background: The association between match congestion and injury rates in professional football has yielded conflicting results., Aim: To analyse associations between match congestion on an individual player level and injury rates during professional football matches., Methods: Data from a prospective cohort study of professional football with 133 170 match observations were analysed with Poisson regressions. Associations between short-term match congestion, defined as number of days between two match exposures (≤3, 4, 5, 6 and 7-10 days) and injury rates were analysed. To analyse the influence of long-term match congestion, defined as individual match exposure hours in the 30 days preceding a match, observations were categorised into three groups (low, ≤4.5; medium, >4.5 to ≤7.5; and high, >7.5 hours)., Results: No differences in total match injury rates were found between the reference category (≤3 days) and the other categories of short-term congestion. Muscle injury rates were significantly lower in matches preceded by 6 (rate ratio (RR) 0.79; 95% CI 0.65 to 0.95) or 7-10 days (RR 0.81; 95% CI 0.71 to 0.93) compared with ≤3 days since the last match exposure. No differences in total and muscle injury rates between the three long-term match congestion groups were found., Conclusions: In this study of male professional football players, there were no match congestion-related differences in total match injury rates, but muscle injury rates during matches were lower when players were given at least 6 days between their match exposures., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Background: Tick-borne encephalitis (TBE) is one tick-transmitted disease where the human incidence has increased in some European regions during the last two decades. We aim to find the most important factors causing the increasing incidence of human TBE in Sweden. Based on a review of published data we presume that certain temperature-related variables and the population densities of transmission hosts, i.e. small mammals, and of primary tick maintenance hosts, i.e. cervids and lagomorphs, of the TBE virus vector Ixodes ricinus, are among the potentially most important factors affecting the TBE incidence. Therefore, we compare hunting data of the major tick maintenance hosts and two of their important predators, and four climatic variables with the annual numbers of human cases of neuroinvasive TBE. Data for six Swedish regions where human TBE incidence is high or has recently increased are examined by a time-series analysis. Results from the six regions are combined using a meta-analytical method., Results: With a one-year time lag, the roe deer (Capreolus capreolus), red deer (Cervus elaphus), mountain hare (Lepus timidus) and European hare (Lepus europaeus) showed positive covariance; the Eurasian elk (moose, Alces alces) and fallow deer (Dama dama) negative covariance; whereas the wild boar (Sus scrofa), lynx (Lynx lynx), red fox (Vulpes vulpes) and the four climate parameters showed no significant covariance with TBE incidence. All game species combined showed positive covariance., Conclusions: The epidemiology of TBE varies with time and geography and depends on numerous factors, i.a. climate, virus genotypes, and densities of vectors, tick maintenance hosts and transmission hosts. This study suggests that the increased availability of deer to I. ricinus over large areas of potential tick habitats in southern Sweden increased the density and range of I. ricinus and created new TBEV foci, which resulted in increased incidence of human TBE. New foci may be established by TBE virus-infected birds, or by birds or migrating mammals infested with TBEV-infected ticks. Generally, persistence of TBE virus foci appears to require presence of transmission-competent small mammals, especially mice (Apodemus spp.) or bank voles (Myodes glareolus).

With the fast growth of diabetes prevalence, the disease is now considered an epidemic. Diabetes is characterized by elevated glucose levels, that may be treated with insulin. Tight control of glucose is essential for prevention of complications and patients' well-being. In this paper we model the fasting glucose-insulin dynamics in type 2 diabetes, aiming at controlling the glucose level. Relevant clinical data are typically sparse and have a sampling period much greater than the fast dynamics in the glucose-insulin dynamics in humans. We adapt a physiological model such that important slow non-linear dynamics are identifiable and test the resulting model on deterministic simulated data and sparse, slow sampled clinical data.

Background: Rare multicentric lower-grade gliomas (LGGs) represent a unique opportunity to study the heterogeneity among distinct tumor foci in a single patient and to infer their origins and parallel patterns of evolution., Methods: In this study, we integrate clinical features, histology, and immunohistochemistry for 4 patients with multicentric LGG, arising both synchronously and metachronously. For 3 patients we analyze the phylogeny of the lesions using exome sequencing, including one case with a total of 8 samples from the 2 lesions., Results: One patient was diagnosed with multicentric isocitrate dehydrogenase 1 (IDH1) mutated diffuse astrocytomas harboring distinct IDH1 mutations, R132H and R132C; the latter mutation has been associated with Li-Fraumeni syndrome, which was subsequently confirmed in the patient's germline DNA and shown in additional cases with The Cancer Genome Atlas data. In another patient, phylogenetic analysis of synchronously arising grade II and grade III diffuse astrocytomas demonstrated a single shared mutation, IDH1 R132H, and revealed convergent evolution via non-overlapping mutations in ATRX and TP53. In 2 cases, there was divergent evolution of IDH1-mutated and 1p/19q-codeleted oligodendroglioma and IDH1-mutated and 1p/19q-intact diffuse astrocytoma, occurring synchronously in one case and metachronously in a second., Conclusions: Each tumor in multicentric LGG cases may arise independently or may diverge very early in their development, presenting as genetically and histologically distinct tumors. Comprehensive sampling of these lesions can therefore significantly alter diagnosis and management. Additionally, somatic IDH1 R132C mutation in either multicentric or solitary LGG identifies unsuspected germline TP53 mutation, validating the limited number of published cases.

Purpose: We aimed to validate GEMCaP (Genomic Evaluators of Metastatic Cancer of the Prostate) as a novel copy number signature predictive of prostate cancer recurrence., Materials and Methods: We randomly selected patients who underwent radical prostatectomy at Cleveland Clinic or University of Rochester from 2000 to 2005. DNA isolated from the cancer region was extracted and subjected to high resolution array comparative genomic hybridization. A high GEMCaP score was defined as 20% or greater of genomic loci showing copy number gain or loss in a given tumor. Cox regression was used to evaluate associations between the GEMCaP score and the risk of biochemical recurrence., Results: We report results in 140 patients. Overall 38% of patients experienced recurrence with a median time to recurrence of 45 months. Based on the CAPRA-S (Cancer of the Prostate Risk Assessment Post-Surgical) score 39% of the patients were at low risk, 42% were at intermediate risk and 19% were at high risk. The GEMCaP score was high (20% or greater) in 31% of the cohort. A high GEMCaP score was associated with a higher risk of biochemical recurrence (HR 2.69, 95% CI 1.51-4.77) and it remained associated after adjusting for CAPRA-S score and age (HR 1.94, 95% CI 1.06-3.56). The C-index of GEMCaP alone was 0.64, which improved when combined with the CAPRA-S score and patient age (C-index = 0.75)., Conclusions: A high GEMCaP score was associated with biochemical recurrence in 2 external cohorts. This remained true after adjusting for clinical and pathological factors. The GEMCaP biomarker could be an efficient and effective clinical risk assessment tool to identify patients with prostate cancer for early adjuvant therapy., (Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.)

Pancreatic β cells are highly specialized to regulate systemic glucose levels by secreting insulin. In adults, increase in β-cell mass is limited due to brakes on cell replication. In contrast, proliferation is robust in neonatal β cells that are functionally immature as defined by a lower set point for glucose-stimulated insulin secretion. Here we show that β-cell proliferation and immaturity are linked by tuning expression of physiologically relevant, non-oncogenic levels of c-Myc. Adult β cells induced to replicate adopt gene expression and metabolic profiles resembling those of immature neonatal β that proliferate readily. We directly demonstrate that priming insulin-producing cells to enter the cell cycle promotes a functionally immature phenotype. We suggest that there exists a balance between mature functionality and the ability to expand, as the phenotypic state of the β cell reverts to a less functional one in response to proliferative cues.

Personality is generally considered to be biologically founded in temperament, and temperamental qualities have proven to be relatively stable across childhood and into adulthood (Caspi, Roberts & Shiner, ). Temperament predicts important developmental outcomes such as academic performance (Muris, ), and social functioning (Eisenberg, Fabes, Guthrie & Reiser, ), and it has also been found to be strongly related to the etiology and maintenance of internalizing and externalizing psychopathology in children (Muris, Meesters & Blijlevens, ; Nigg, ). To allow for the possibility of making early interventions, identification of potential risk factors (such as temperamental dispositions) is of great importance (Rettew & McKee, ). As temperament is multidimensional and has many different manifestations, parents and teachers are valuable sources in providing information about children's temperament (Rothbart & Bates, ; Tackett, Slobodskaya, Mar et al., ), and caregiver questionnaires are frequently used in child personality research. However, such questionnaires are only useful if their reliability and validity have been established. The aim of the present study was to examine the psychometric properties of the Temperament in Middle Childhood Questionnaire (TMCQ; Simonds, Kieras, Rueda & Rothbart, ), which focuses specifically on the ages between 7 and 11 years. The TMCQ is the least validated of the Rothbart measures, and although reliability data have been presented, together with some validity data, for a computerized self-report version of the questionnaire (Simonds & Rothbart, ), information about the reliability and validity for the caregiver version is scant. In the present paper, we report such data for a Swedish sample., (© 2017 Scandinavian Psychological Associations and John Wiley & Sons Ltd.)

IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade. Successful cultures derived from IDH1 mutant, but not IDH1 wild type, gliomas systematically deleted IDH1 in vitro and in vivo, further suggestive of selection against the heterozygous mutant state as tumors progress. Tumors and cultures with IDH1 CNA had decreased 2HG, maintenance of G-CIMP, and DNA methylation reprogramming outside CGI. Thus, while IDH1 mutation initiates gliomagenesis, in some patients mutant IDH1 and 2HG are not required for later clonal expansions., Competing Interests: The authors declare no conflict of interest.

Diabetes has become one of the biggest health problems in the world. In this context, adherence to insulin treatment is essential in order to avoid life-threatening complications. In this pilot study, a novel adherence detection algorithm using Deep Learning (DL) approaches was developed for type 2 diabetes (T2D) patients, based on simulated Continuous Glucose Monitoring (CGM) signals. A large and diverse amount of CGM signals were simulated for T2D patients using a T2D adapted version of the Medtronic Virtual Patient (MVP) model for T1D. By using these signals, different classification algorithms were compared using a comprehensive grid search. We contrast a standard logistic regression baseline to Multi- Layer Perceptrons (MLPs) and Convolutional Neural Networks (CNNs). The best classification performance with an average accuracy of 77:5% was achieved with CNN. Hence, this indicates the potential of DL, when considering adherence detection systems for T2D patients.

Individuals with unresolved/disorganized representations of childhood trauma (U/d attachment) report more psychological distress than others, but little is known about their everyday mentation. In the present study adults with childhood trauma (N = 45) completed the Berkeley-Leiden Adult Attachment Questionnaire-Unresolved (BLAAQ-U) and the Adult Attachment Interview (AAI), and reported everyday mentation during 5 days of experience sampling. The BLAAQ-U and the AAI showed a medium association with each other, but only the former significantly predicted negative affect, dissociation, and low control/awareness of mentation. Contrary to our predictions, U/d attachment did not significantly predict mind wandering, but the BLAAQ-U predicted endorsements of a negative mind wandering style. U/d attachment, as assessed by both instruments, was associated with the Poor attentional control style and beliefs in anomalous mental phenomena. Experience sampling is a valuable way to investigate everyday experiences in individuals with U/d attachment.

Objective: To study adolescent traumatization and the impact of various types of trauma on dissociative experiences in a sample of 239 Swedish youngsters, 13 to 20 years of age, with diverse socioeconomic and migration backgrounds. We also evaluated whether the type of worst lifetime trauma was associated with higher rates of dissociation., Method: Quantitative and qualitative data on posttraumatic stress, dissociative experiences, and potentially traumatic events (PTEs), including participants' written descriptions of their worst lifetime trauma., Results: Most (92%) of the participants had been exposed to at least 1 PTE and 51% to 4 or more, during their life. Number of PTEs correlated with symptoms of posttraumatic stress and dissociation. There were higher rates of dissociation among economically vulnerable and second-generation war refugee participants. Emotional abuse by others (mostly peers) was the only significant predictor of dissociation when controlling for gender, age, total PTEs, posttraumatic stress, and poverty. Moderation analyses showed that lifetime worst traumas categorized as primarily emotional moderated and amplified the relation between total PTEs and dissociation, but only among girls., Conclusions: Our findings indicate that traumatization is very common among adolescents, with greater prevalence of dissociation among vulnerable groups, and that emotional traumas are linked to higher rates of dissociation, especially among girls. Researchers, clinicians, and school personnel need to focus more on immigrant status and low SES as vulnerability factors, and address the consequences of emotional abuse, including bullying, among adolescents. (PsycINFO Database Record, ((c) 2016 APA, all rights reserved).)

Background: There are limited data on the nature, type and incidence of illness in football. Previous studies indicate that gastrointestinal and respiratory tract illnesses are most common., Aim: To describe the incidence and burden of illness in male professional football., Methods: Over the 4-year study period, 2011-2014, 73 professional football teams in Europe participated, with a total of 1 261 367 player-days recorded. All time-loss illnesses were recorded by the medical staff of each club. A recordable illness episode was any physical or psychological symptom (not related to injury) that resulted in the player being unable to participate fully in training or match play., Results: A total of 1914 illness episodes were recorded. The illness incidence was 1.5 per 1000 player-days, meaning that, on average, a player experienced an illness episode every second season, with a median of 3 days absence per illness episode. Severe illness (absence >4 weeks) constituted 2% of all illnesses. Respiratory tract illness was the most common (58%), followed by gastrointestinal illness (38%). Respiratory tract illness, gastrointestinal illness and cardiovascular illness caused the highest illness burden., Conclusions: The illness incidence among male professional football players is low compared with the injury incidence. We found that the highest illness burden was caused by illness to the respiratory tract, gastrointestinal tract and cardiovascular system., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/)

This investigation set out to analyze the toxicity of surface sediments in a number of natural harbors and small boat harbors on the west coast of Sweden. This was done with the growth inhibition method with Ceramium tenuicorne. Also, concentrations of copper (Cu), lead (Pb), zinc (Zn), irgarol, organotin compounds, and polycyclic aromatic hydrocarbons (PAHs) in the sediments were analyzed. The small boat harbors were heavily polluted by Cu, Zn, butyltins, and PAHs, and to a lesser extent by Pb. The Cu, Pb, Zn, and butyltins probably originated from their past and/or present use in antifouling paints, whereas the PAHs probably had multiple sources, including boat motor exhausts. The measured toxicity of the sediment was generally related to their Cu, Zn, and butyltin content, although other toxic substances than those analyzed here probably contributed to the toxicity in some of the harbors. The natural harbor sediments contained less pollutants and were less toxic than the small boat harbor sediments. Nevertheless, our data indicate that the boating pressure today may be high enough to produce toxic effects even in natural harbors in pristine areas. The strongest relationship between toxicity and the major pollutants was obtained when the sediment toxicity was expressed as gram wet weight per liter compared with gram dry weight per liter and gram total organic carbon per liter. Hence, for pollutants that can be elutriated with natural sea water, sediment toxicity expressed as gram wet weight per liter appears preferable.

The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover 'functional 3D hotspots', regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 - known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Introduction and Methods: Pertussis has recently re-emerged in the United States. Timely surveillance is vital to estimate the burden of this disease accurately and to guide public health response. However, the surveillance of pertussis is limited by delays in reporting, consolidation and dissemination of data to relevant stakeholders. We fit and assessed a real-time predictive Google model for pertussis in California using weekly incidence data from 2009-2014., Results and Discussion: The linear model was moderately accurate (r = 0.88). Our findings cautiously offer a complementary, real-time signal to enhance pertussis surveillance in California and help to further define the limitations and potential of Google-based epidemic prediction in the rapidly evolving field of digital disease detection.

Glioblastoma (GBM) is the most common and aggressive human brain tumor. Human cytomegalovirus (HCMV) immediate-early (IE) proteins that are endogenously expressed in GBM cells are strong viral transactivators with oncogenic properties. Here, we show how HCMV IEs are preferentially expressed in glioma stem-like cells (GSC), where they colocalize with the other GBM stemness markers, CD133, Nestin, and Sox2. In patient-derived GSCs that are endogenously infected with HCMV, attenuating IE expression by an RNAi-based strategy was sufficient to inhibit tumorsphere formation, Sox2 expression, cell-cycle progression, and cell survival. Conversely, HCMV infection of HMCV-negative GSCs elicited robust self-renewal and proliferation of cells that could be partially reversed by IE attenuation. In HCMV-positive GSCs, IE attenuation induced a molecular program characterized by enhanced expression of mesenchymal markers and proinflammatory cytokines, resembling the therapeutically resistant GBM phenotype. Mechanistically, HCMV/IE regulation of Sox2 occurred via inhibition of miR-145, a negative regulator of Sox2 protein expression. In a spontaneous mouse model of glioma, ectopic expression of the IE1 gene (UL123) specifically increased Sox2 and Nestin levels in the IE1-positive tumors, upregulating stemness and proliferation markers in vivo. Similarly, human GSCs infected with the HCMV strain Towne but not the IE1-deficient strain CR208 showed enhanced growth as tumorspheres and intracranial tumor xenografts, compared with mock-infected human GSCs. Overall, our findings offer new mechanistic insights into how HCMV/IE control stemness properties in GBM cells., (©2015 American Association for Cancer Research.)

Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost., (© 2014 Scheinin et al.; Published by Cold Spring Harbor Laboratory Press.)

Brain trauma is known to activate inflammatory cells via various chemokine signals although their interactions remain to be characterized. Mice deficient in Ccl3, Ccr2 or Cxcl10 were compared with wildtype mice after controlled cortical impact injury. Expression of Ccl3 in wildtypes was rapidly upregulated in resident, regularly spaced reactive microglia. Ccl3-deficiency enhanced endothelial expression of platelet selectin and invasion of peripheral inflammatory cells. Appearance of Ccr2 transcripts, encoding the Ccl2 receptor, reflected invasion of lysozyme 2-expressing phagocytes and classical antigen-presenting dendritic cells expressing major histocompatibility complex class II. Ccr2 also directed clustered plasmacytoid dendritic cells positive for the T-cell attracting chemokine Cxcl10. A reduction in Ccr2 and dendritic cells was found in injured wildtype cortex after cyclophosphamide treatment resembling effects of Ccr2-deficiency. The findings demonstrate the feasibility to control inflammation in the injured brain by regulating chemokine-dependent pathways.

Purpose: When central nervous system axons are injured, regeneration is partly inhibited by myelin-associated inhibitors (MAIs). Following traumatic brain injury (TBI) in the rat, pharmacological neutralisation of the MAIs Nogo-A and myelin-associated glycoprotein (MAG) resulted in improved functional outcome. In contrast, genetic or pharmacological neutralization of the MAI receptors Nogo-66 receptor 1 (NgR1) or paired-immunoglobulin like receptor-B (PirB) showed an unaltered or impaired outcome following TBI in mice. The aim of the present study was thus to evaluate the MAI expression levels following TBI in mice., Methods: Quantitative reverse transcriptase PCR (qRT-PCR) was used to measure total RNA isolated from brains of young adult male C57BL/6 mice at one, three or seven days following controlled cortical impact TBI or sham injury. Hippocampal and neocortical tissue ipsi- and contralateral to the injury was analyzed for Nogo-A, oligodendrocyte-myelin glycoprotein (OMgp), MAG, and the MAI receptors PirB and NgR1, including its co-receptor Lingo1., Results: Compared to sham-injured controls, PirB neocortical expression was significantly upregulated at one day and NgR1 expression downregulated at seven days post-TBI. In the hippocampus, transcriptional upregulation was observed in Nogo-A (one day post-injury), MAG and PirB at seven days post-injury. In contrast, the hippocampal transcripts of NgR1 and Lingo1 were decreased at seven days post-injury. The expression of OMgp was unaltered at all time points post-injury., Conclusion: These results suggest that early dynamic changes in MAI gene expression occur following TBI in the mouse, particularly in the hippocampus, which may play an inhibitory role for post-injury regeneration and plasticity.

The IDAT file format is used to store BeadArray data from the myriad of genomewide profiling platforms on offer from Illumina Inc. This proprietary format is output directly from the scanner and stores summary intensities for each probe-type on an array in a compact manner. A lack of open source tools to process IDAT files has hampered their uptake by the research community beyond the standard step of using the vendor's software to extract the data they contain in a human readable text format. To fill this void, we have developed the illuminaio package that parses IDAT files from any BeadArray platform, including the decryption of files from Illumina's gene expression arrays. illuminaio provides the first open-source package for this task, and will promote wider uptake of the IDAT format as a standard for sharing Illumina BeadArray data in public databases, in the same way that the CEL file serves as the standard for the Affymetrix platform.

Background: The influence of fixture congestion on injury rates and team performance has only been scarcely investigated., Aim: To study associations between recovery time and match load and injury rates and team performance in professional football., Methods: Exposure and time loss injuries were registered prospectively from 27 teams over 11 seasons. Matches were grouped according to recovery days before each match (≤3 vs >3 days, and ≤4 vs ≥6 days). Injury rates and team performance were compared between groups. Match load in match sequences containing five consecutive matches was determined by the number of days separating the first match and the last training session during that match sequence. Linear regression was used to study associations between match load and injury rates and team performance., Results: Team performance showed no association with match load, or recovery days prior to matches, except for Europa League matches that indicated more matches lost with short recovery (≤3 days) (p=0.048). Total injury rates and muscle injury rates were increased in league matches with ≤4 days compared with ≥6 days' recovery (RR 1.09, 95% CI 1.00 to 1.18, and RR 1.32, 95% CI 1.15 to 1.51, respectively), specifically hamstring and quadriceps injuries. High match load was associated with increase in muscle injury rate in matches in the same match sequence (p=0.012), and increase in ligament injury rate in training in the subsequent match sequence (p=0.003)., Conclusions: Fixture congestion was associated with increased muscle injury rates but had no, or very limited, influence on team performance.

Background: The influence of injuries on team performance in football has only been scarcely investigated., Aim: To study the association between injury rates and team performance in the domestic league play, and in European cups, in male professional football., Methods: 24 football teams from nine European countries were followed prospectively for 11 seasons (2001-2012), including 155 team-seasons. Individual training and match exposure and time-loss injuries were registered. To analyse the effect of injury rates on performance, a Generalised Estimating Equation was used to fit a linear regression on team-level data. Each team's season injury rate and performance were evaluated using its own preceding season data for comparison in the analyses., Results: 7792 injuries were reported during 1 026 104 exposure hours. The total injury incidence was 7.7 injuries/1000 h, injury burden 130 injury days lost/1000 h and player match availability 86%. Lower injury burden (p=0.011) and higher match availability (p=0.031) were associated with higher final league ranking. Similarly, lower injury incidence (p=0.035), lower injury burden (p<0.001) and higher match availability (p<0.001) were associated with increased points per league match. Finally, lower injury burden (p=0.043) and higher match availability (p=0.048) were associated with an increase in the Union of European Football Association (UEFA) Season Club Coefficient, reflecting success in the UEFA Champions League or Europa League., Conclusions: Injuries had a significant influence on performance in the league play and in European cups in male professional football. The findings stress the importance of injury prevention to increase a team's chances of success.

Purpose: To investigate the epidemiology of upper extremity injuries in male elite football players and to describe their characteristics, incidence and lay-off times., Methods: Between 2001 and 2011, 57 male European elite football teams (2,914 players and 6,215 player seasons) were followed prospectively. Time-loss injuries and exposure to training and matches were recorded on individual basis., Results: In total, 11,750 injuries were recorded, 355 (3 %) of those affected the upper extremities giving an incidence of 0.23 injuries/1,000 h of football. The incidence in match play was almost 7 times higher than in training (0.83 vs. 0.12 injuries/1,000 h, rate ratio 6.7, 95 % confidence interval 5.5-8.3). As much as 32 % of traumatic match injuries occurred as a result of foul play situations. Goalkeepers had a significantly higher incidence of upper extremity injuries compared to outfield players (0.80 vs. 0.16 injuries/1,000 h, rate ratio 5.0, 95 % confidence interval 4.0-6.2). The average absence due to an upper extremity injury was 23 ± 34 days., Conclusions: Upper extremity injuries are uncommon among male elite football players. Goalkeepers, however, are prone to upper extremity injury, with a five times higher incidence compared to outfield players., Level of Evidence: II.

Background: Player activities in soccer matches are influenced by the match result and match venue. It is not known whether injury rates are influenced by these factors., Purpose: To investigate whether there are associations between injury rates and the match result, venue, and type of competition in male soccer., Study Design: Cohort study; Level of evidence, 3., Methods: Twenty-six professional clubs from 10 countries were followed prospectively during 9 seasons (2001-2002 to 2009-2010). All matches, and injuries occurring in these matches, were registered by the team's medical staff. An injury was registered if it resulted in player absence from training or matches. Information about match result, venue, and type of competition for all reported matches was gathered by the authors from online databases. Injury rates in matches with varying match characteristics were compared by use of generalized estimating equations. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated., Results: A total of 2738 injuries during 6010 matches were registered. There were no associations between odds of 1 injury occurrence and match result or type of competition, whereas the odds were decreased in matches played away compared with home matches (OR, 0.89; 95% CI, 0.80-0.99). The odds of 2 or more injury occurrences in a match were increased in matches resulting in a draw (OR, 1.39; 95% CI, 1.15-1.69) or loss (OR, 1.66; 95% CI, 1.38-1.98) compared with matches won and were decreased in other cup matches compared with league matches (OR, 0.57; 95% CI, 0.39-0.84) and in matches played away compared with home matches (OR, 0.70; 95% CI, 0.60-0.82). Finally, injuries with more than 1 week's absence occurred more frequently in Champions League matches compared with league matches both for matches with 1 injury (OR, 1.26; 95% CI, 1.09-1.45) and matches with 2 or more injuries (OR, 1.57; 95% CI, 1.13-2.20)., Conclusion: The odds of 2 or more injury occurrences in professional soccer were higher in matches resulting in a loss or a draw compared with a win, whereas the odds of injury occurrences were lower in matches played away compared with home matches. The rate of moderate and severe injuries increased with the importance of the match.

Background: Thinner and shorter needles for subcutaneous administration are continuously developed. Previous studies have shown that a thinner needle causes fewer occurrences of painful needle insertions and that a shorter needle decreases the occurrence of painful intramuscular injections. However, little is known about local drug delivery in relation to needle length and thickness. This study aimed to compare deposition depth and backflow from three hypodermic needles of 3 mm 34G (0.19 mm), 5 mm 32G (0.23 mm), and 8 mm 30G (0.30 mm) in length and thickness., Methods: Ex vivo experiments were carried out on pigs, in neck tissue comparable to human skin at typical injection sites. Six pigs were included and a total of 72 randomized injections were given, i.e. 24 subcutaneous injections given with each needle type. Accordingly, 400 μL was injected including 70% NovoRapid(®) (Novo Nordisk A/S, Bagsvμrd, Denmark) and 30% Xenetix(®) (Guerbet, Villepinte, France) contrast including 1 mg/mL Alcian blue. Surgical biopsies of injection sites were sampled and computer topographic (CT)-scanned in 3D to assess deposition and local distribution. Biopsies were prepared and stained to evaluate deposition in comparison to the CT-scanning findings. The backflow of each injection was collected with filter paper. The blue stains of filter paper were digitized and volume estimated by software calculation vs. control staining., Results: CT-scanning (n = 57) and histology (n = 10) showed that, regardless of injection depth, the bulk of the injection was in the subcutaneous tissue and did not propagate from subcutis into dermis. With the 8 mm 30G needle all injections apart from one intramuscular injection were located in the subcutaneous layer. The volume depositions peaked in 4-5 mm depth for the 3 mm 34G needle, in 5-6 mm depth for the 5 mm 32G needle, and in 9-10 mm depth for the 8 mm 30G needle. In general, injection depositions evaluated by histology and CT-scans compared well for the individual biopsies. The amount of backflow (n = 69) from the 3 mm 34G needle was smaller (P < 0.05) as compared to the 5 mm 32G and the 8 mm 30G needles. Analysis showed a correlation between backflow and the needle's outer dimension with the needle diameter being the pivotal parameter. Furthermore, CT-scanning and histology confirmed that local propagation of the injection and final distribution followed a route of less mechanical resistance as determined by connective tissue barriers preset in the site of injection., Conclusion: Needles as short as 3 mm efficiently delivered injections into the subcutaneous target. The amount of backflow was smaller with thinner needles. Local distribution was variable and determined by mechanical barriers preset in the tissue. CT-scans and histology were concordant., (© 2012 John Wiley & Sons A/S.)

Summary: CalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina., Availability: The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project.org/).

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

The advent of high-throughput biotechnologies, which can efficiently measure gene expression on a global basis, has led to the creation and population of correspondingly rich databases and compendia. Such repositories have the potential to add enormous scientific value beyond that provided by individual studies which, due largely to cost considerations, are typified by small sample sizes. Accordingly, substantial effort has been invested in devising analysis schemes for utilizing gene-expression repositories. Here, we focus on one such scheme, the Connectivity Map (cmap), that was developed with the express purpose of identifying drugs with putative efficacy against a given disease, where the disease in question is characterized by a (differential) gene-expression signature. Initial claims surrounding cmap intimated that such tools might lead to new, previously unanticipated applications of existing drugs. However, further application suggests that its primary utility is in connecting a disease condition whose biology is largely unknown to a drug whose mechanisms of action are well understood, making cmap a tool for enhancing biological knowledge.The success of the Connectivity Map is belied by its simplicity. The aforementioned signature serves as an unordered query which is applied to a customized database of (differential) gene-expression experiments designed to elicit response to a wide range of drugs, across of spectrum of concentrations, durations, and cell lines. Such application is effected by computing a per experiment score that measures "closeness" between the signature and the experiment. Top-scoring experiments, and the attendant drug(s), are then deemed relevant to the disease underlying the query. Inference supporting such elicitations is pursued via re-sampling. In this paper, we revisit two key aspects of the Connectivity Map implementation. Firstly, we develop new approaches to measuring closeness for the common scenario wherein the query constitutes an ordered list. These involve using metrics proposed for analyzing partially ranked data, these being of interest in their own right and not widely used. Secondly, we advance an alternate inferential approach based on generating empirical null distributions that exploit the scope, and capture dependencies, embodied by the database. Using these refinements we undertake a comprehensive re-evaluation of Connectivity Map findings that, in general terms, reveal that accommodating ordered queries is less critical than the mode of inference.

Purpose: Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis., Experimental Design: The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort., Results: The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70%-80% of lesions, termed 3q8pq20 subtype) from the remainder (20%-30% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts., Conclusions: Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,-8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC.

Motivation: High-throughput techniques facilitate the simultaneous measurement of DNA copy number at hundreds of thousands of sites on a genome. Older techniques allow measurement only of total copy number, the sum of the copy number contributions from the two parental chromosomes. Newer single nucleotide polymorphism (SNP) techniques can in addition enable quantifying parent-specific copy number (PSCN). The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods., Methods: We have adapted and enhanced the circular binary segmentation (CBS) algorithm for this purpose with focus on paired test and reference samples. The essence of paired parent-specific CBS (Paired PSCBS) is to utilize the original CBS algorithm to identify regions of equal total copy number and then to further segment these regions where there have been changes in PSCN. For the final set of regions, calls are made of equal parental copy number and loss of heterozygosity (LOH). PSCN estimates are computed both before and after calling., Results: The methodology is evaluated by simulation and on glioblastoma data. In the simulation, PSCBS compares favorably to established methods. On the glioblastoma data, PSCBS identifies interesting genomic regions, such as copy-neutral LOH., Availability: The Paired PSCBS method is implemented in an open-source R package named PSCBS, available on CRAN (http://cran.r-project.org/).

Differently homogenised and heat treated potato pulp, used as a dietary fibre additive in low-fat sausages, gave rise to an enhanced instrumentally and sensory measured firmness and compactness, respectively. This is believed to be due to the high content of insoluble fibre, which creates a fibrous network that enhances the texture of the sausage, while not interfering with the meat protein network. The process and frying losses of the sausages, using potato pulp as an additive, were not significantly different compared to the reference. Comparing the different potato pulp sausages using various kinds of heat treatment of the potato pulp significantly lowered the frying loss and increased the firmness. An explanation to these observations could be that the potato pulp exposed to shorter heat treatment compared with longer gave rise to a lower amount of amylase-leakage from the swelling starch granules caught in the potato pulp matrix., (Copyright © 2010 The American Meat Science Association. Published by Elsevier Ltd. All rights reserved.)

Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.

Sex in mammals is genetically determined and is defined at the cellular level by sex chromosome complement (XY males and XX females). The Y chromosome-linked gene sex-determining region Y (SRY) is believed to be the master initiator of male sex determination in almost all eutherian and metatherian mammals, functioning to upregulate expression of its direct target gene Sry-related HMG box-containing gene 9 (SOX9). Data suggest that SRY evolved from SOX3, although there is no direct functional evidence to support this hypothesis. Indeed, loss-of-function mutations in SOX3 do not affect sex determination in mice or humans. To further investigate Sox3 function in vivo, we generated transgenic mice overexpressing Sox3. Here, we report that in one of these transgenic lines, Sox3 was ectopically expressed in the bipotential gonad and that this led to frequent complete XX male sex reversal. Further analysis indicated that Sox3 induced testis differentiation in this particular line of mice by upregulating expression of Sox9 via a similar mechanism to Sry. Importantly, we also identified genomic rearrangements within the SOX3 regulatory region in three patients with XX male sex reversal. Together, these data suggest that SOX3 and SRY are functionally interchangeable in sex determination and support the notion that SRY evolved from SOX3 via a regulatory mutation that led to its de novo expression in the early gonad.

Motivation: Current algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs. In addition, most of the current CN methods are focused on total CNs, while it has been shown that allele-specific CNs are of paramount importance for some studies. Therefore, we have developed a summarization method that estimates high-quality allele-specific CNs., Results: The proposed method estimates the allele-specific DNA CNs for all Affymetrix SNP arrays dealing directly with the cross hybridization between probes within SNP probesets. This algorithm outperforms (or at least it performs as well as) other state-of-the-art algorithms for computing DNA CNs. It better discerns an aberration from a normal state and it also gives more precise allele-specific CNs., Availability: The method is available in the open-source R package ACNE, which also includes an add on to the aroma.affymetrix framework (http://www.aroma-project.org/).

We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG island methylator phenotype (G-CIMP). We validated G-CIMP in a set of non-TCGA glioblastomas and low-grade gliomas. G-CIMP tumors belong to the proneural subgroup, are more prevalent among lower-grade gliomas, display distinct copy-number alterations, and are tightly associated with IDH1 somatic mutations. Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds., ((c) 2010 Elsevier Inc. All rights reserved.)

Background: High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses., Results: We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances., Conclusions: TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH) in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific) CRMA v2 for Affymetrix or BeadStudio's (proprietary) XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package aroma.cn, which is part of the Aroma Project (http://www.aroma-project.org/).

Traumatic brain injury (TBI) in the mouse results in the rapid appearance of scattered clusters of cells expressing the chemokine Cxcl10 in cortical and subcortical areas. To extend the observation of this unique pattern, we used neuropathological mouse models using quantitative reverse transcriptase-polymerase chain reaction, gene array analysis, in-situ hybridization and flow cytometry. As for TBI, cell clusters of 150-200 mum expressing Cxcl10 characterize the cerebral cortex of mice carrying a transgene encoding the Swedish mutation of amyloid precursor protein, a model of amyloid Alzheimer pathology. The same pattern was found in experimental autoimmune encephalomyelitis in mice modelling multiple sclerosis. In contrast, mice carrying a SOD1(G93A) mutant mimicking amyotrophic lateral sclerosis pathology lacked such cell clusters in the cerebral cortex, whereas clusters appeared in the brainstem and spinal cord. Mice homozygous for a null mutation of the Cxcl10 gene did not show detectable levels of Cxcl10 transcript after TBI, confirming the quantitative reverse transcriptase-polymerase chain reaction and in-situ hybridization signals. Moreover, unbiased microarray expression analysis showed that Cxcl10 was among 112 transcripts in the neocortex upregulated at least threefold in both TBI and ageing TgSwe mice, many of them involved in inflammation. The identity of the Cxcl10(+) cells remains unclear but flow cytometry showed increased numbers of activated microglia/macrophages as well as myeloid dendritic cells in the TBI and experimental autoimmune encephalomyelitis models. It is concluded that the Cxcl10(+) cells appear in the inflamed central nervous system and may represent a novel population of cells that it may be possible to target pharmacologically in a broad range of neurodegenerative conditions.

We here present the first simulation of a complete molecularly imprinted polymer prepolymerization system. Molecular dynamics studies were performed for a system comprising a total of 1199 discrete molecules, replicating the components and concentrations employed in the corresponding polymer synthesis. The observed interactions correlate well with results obtained from (1)H NMR spectroscopic studies. Comparison with simulations performed in the absence of cross-linking agent (ethylene dimethacrylate) demonstrated its significance in the formation of ligand recognition sites. Moreover, the influence of events such as template-template (bupivacaine) and monomer-monomer (methacrylic acid) self-association, porogen-template interactions, and template conformational variability was revealed. The template recognition capacity of the modeled polymer system was verified by synthesis of imprinted and reference polymers and subsequent radioligand binding analysis. Collectively, through a series of statistical analyses of molecular trajectories in conjunction with spectroscopic data it was demonstrated that an ensemble of complex structures is present in the prepolymerization mixture and that this diversity is the basis for the binding site heterogeneity observed in molecularly imprinted polymers (MIPs) prepared using the noncovalent strategy.

Motivation: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also for identifying CN polymorphisms. In order for such studies to be successful and cost effective, the statistical methods have to be optimized. We propose a single-array preprocessing method for estimating full-resolution total CNs. It is applicable to all Affymetrix genotyping arrays, including the recent ones that also contain non-polymorphic probes. A reference signal is only needed at the last step when calculating relative CNs., Results: As with our method for earlier generations of arrays, this one controls for allelic crosstalk, probe affinities and PCR fragment-length effects. Additionally, it also corrects for probe sequence effects and co-hybridization of fragments digested by multiple enzymes that takes place on the latest chips. We compare our method with Affymetrix's CN5 method and the dChip method by assessing how well they differentiate between various CN states at the full resolution and various amounts of smoothing. Although CRMA v2 is a single-array method, we observe that it performs as well as or better than alternative methods that use data from all arrays for their preprocessing. This shows that it is possible to do online analysis in large-scale projects where additional arrays are introduced over time.

Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more than one platform for the same set of samples, and it is natural to want to combine the different estimates in order to meet this demand. Estimates from different platforms show different degrees of attenuation of the true CN changes. Similar differences can be observed in CNs from the same platform run in different labs, or in the same lab, with different analytical methods. This is the reason why it is not straightforward to combine CN estimates from different sources (platforms, labs and analysis methods)., Results: We propose a single-sample multi source normalization that brings full-resolution CN estimates to the same scale across sources. The normalized CNs are such that for any underlying CN level, their mean level is the same regardless of the source, which make them better suited for being combined across sources, e.g. existing segmentation methods may be used to identify aberrant regions. We use microarray-based CN estimates from 'The Cancer Genome Atlas' (TCGA) project to illustrate and validate the method. We show that the normalized and combined data better separate two CN states at a given resolution. We conclude that it is possible to combine CNs from multiple sources such that the resolution becomes effectively larger, and when multiple platforms are combined, they also enhance the genome coverage by complementing each other in different regions., Availability: A bounded-memory implementation is available in aroma.cn.

Background: Cruciate ligament ruptures and shoulder dislocations are often caused by trauma, but predisposing intrinsic factors might also influence the risk. These injuries are more common in those with a previously injured sibling, an observation that might indicate a genetic predisposition. It is well known that polymorphisms in the collagen I gene are associated not only with osteoporosis and osteoporotic fracture risk, but also with osteoarthritis., Hypothesis: Because collagen I is abundant in ligaments and tendons, the authors hypothesized that collagen I alpha1 Sp1 polymorphism also was related to the occurrence of cruciate ligament ruptures and shoulder dislocations., Study Design: Case-control study; Level of evidence, 3., Methods: A total of 358 patients and 325 randomly selected population-based female controls were included in the study. Of the cases, 233 had a cruciate ligament rupture and 126 had had a shoulder dislocation. Age-adjusted odds ratios (ORs) with 95% confidence intervals (CIs) estimated by unconditional logistic regression were used as measures of association., Results: Compared with the homozygous SS category, the heterozygous participants displayed a similar risk (OR, 1.06; 95% CI, 0.76-1.49), whereas the ss genotype was underrepresented in the injured population compared with the controls (OR, 0.15; 95% CI, 0.03-0.68). This latter estimate was similar for both cruciate ligament ruptures and shoulder dislocations, and was furthermore not modified by general joint laxity., Conclusion: The authors found a substantially decreased risk of these injuries associated with collagen type I alpha1 Sp1 polymorphism. The study might encourage other investigators to consider further research in the area of genes and soft tissue injuries.

Cerebral gene expressions change in response to traumatic brain injury (TBI), and future trauma treatment may improve with increased knowledge about these regulations. We subjected C57BL/6J mice to injury by controlled cortical impact (CCI). At various time points post-injury, mRNA from neocortex and hippocampus was isolated, and transcriptional alterations studied using quantitative real-time polymerase chain reaction (PCR) and gene array analysis. Spatial distribution of enhanced expression was characterized by in situ hybridization. Products of the upregulated transcripts serve functions in a range of cellular mechanisms, including stress, inflammation and immune responses, and tissue remodeling. We also identified increased transcript levels characterizing reactive astrocytes, oligodendrocytes, and microglia, and furthermore, we demonstrated a novel pattern of scattered cell clusters expressing the chemokine Cxcl10. Notably, a sustained increase in integrin alpha X (Itgax), characterizing antigen-presenting dendritic cells, was found with the transcript located to similar cell clusters. In contrast, T-cell receptor alpha transcript showed only a modest increase. The induced P-selectin (Selp) expression level in endothelial cells, and chemokines from microglia, may guide perivascular accumulation of extravasating inflammatory monocytes differentiating into dendritic cells. In conclusion, our study shows that following TBI, secondary injury chiefly involves inflammatory processes and chemokine signaling, which comprise putative targets for pharmaceutical neuroprotection.

Growth differentiation factor-1 (GDF1), a TGF-beta superfamily member, participates in early embryo patterning. Later functions are implied by the Gdf1 expression in the peripheral and central nervous system. Such roles of the gene have been difficult to study, because Gdf1 null mice die during late embryogenesis. Here, we report the production of a mouse carrying a conditional Gdf1 allele, with exon 2 flanked by loxP sites. Crossing these mice with CaMKIIalpha-Cre mice resulted in Gdf1 ablation in the forebrain postnatally. Such mice displayed no behavioral changes or altered expression levels in a set of hippocampal genes examined. However, excision of the floxed Gdf1 exon caused increased expression of the remaining part of the bicistronic Uog1-Gdf1 transcript in the hippocampus. This indicates that the transcript level is regulated by a negative feedback-loop, sensing presence of either the protein or the mRNA region encoded by Gdf1 exon 2.

Mothers (N= 35) and their adult children completed questionnaires and were interviewed in order to examine relationships between mothers' caregiving representations and their adult children's attachment representations, and relationships between attachment/caregiving representations and beliefs about mothering. Mothers' and their children's accounts of and present thinking about their past relationship were highly similar, indicating that the two parts develop concordant states of mind regarding their relationship. In contrast, there was no relationship between mothers' and their adult children's beliefs about mothering, suggesting that such beliefs are not simply passed on from generation to generation within families. Attachment/caregiving classification interacted with generation in influencing a belief that biological facts determine maternal behavior, young adults with preoccupied attachment being particularly prone to reject this idea. Attachment/caregiving classification also had a significant effect on participants' tendency to adhere to an idealized conception of mothering, this tendency being associated with a dismissive attachment/caregiving representation.

Motivation: Although copy-number aberrations are known to contribute to the diversity of the human DNA and cause various diseases, many aberrations and their phenotypes are still to be explored. The recent development of single-nucleotide polymorphism (SNP) arrays provides researchers with tools for calling genotypes and identifying chromosomal aberrations at an order-of-magnitude greater resolution than possible a few years ago. The fundamental problem in array-based copy-number (CN) analysis is to obtain CN estimates at a single-locus resolution with high accuracy and precision such that downstream segmentation methods are more likely to succeed., Results: We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays. Its core utilizes a multichip probe-level model analogous to that for high-density oligonucleotide expression arrays. We extend this model by adding an adjustment for sequence-specific allelic imbalances such as cross-hybridization between allele A and allele B probes. We focus on total CN estimates, which allows us to further constrain the probe-level model to increase the signal-to-noise ratio of CN estimates. Further improvement is obtained by controlling for PCR effects. Each part of the model is fitted robustly. The performance is assessed by quantifying how well raw CNs alone differentiate between one and two copies on Chromosome X (ChrX) at a single-locus resolution (27kb) up to a 200kb resolution. The evaluation is done with publicly available HapMap data., Availability: The proposed method is available as part of an open-source R package named aroma.affymetrix. Because it is a bounded-memory algorithm, any number of arrays can be analyzed.