Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation

<p>Abstract</p> <p>Background</p> <p>Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation.</p> <p>Results</p> <p>We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using <it>in vitro </it>time-course expression data for TFs and miRNAs. A set of TF→miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF→miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation.</p> <p>Conclusions</p> <p>The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process.</p

Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of Myasthenia Gravis

<p>Abstract</p> <p>Background</p> <p>About 5% of western populations are afflicted by autoimmune diseases many of which are affected by sex hormones. Autoimmune diseases are complex and involve many genes. Identifying these disease-associated genes contributes to development of more effective therapies. Also, association studies frequently imply genomic regions that contain disease-associated genes but fall short of pinpointing these genes. The identification of disease-associated genes has always been challenging and to date there is no universal and effective method developed.</p> <p>Results</p> <p>We have developed a method to prioritize disease-associated genes for diseases affected strongly by sex hormones. Our method uses various types of information available for the genes, but no information that directly links genes with the disease. It generates a score for each of the considered genes and ranks genes based on that score. We illustrate our method on early-onset myasthenia gravis (MG) using genes potentially controlled by estrogen and localized in a genomic segment (which contains the MHC and surrounding region) strongly associated with MG. Based on the considered genomic segment 283 genes are ranked for their relevance to MG and responsiveness to estrogen. The top three ranked genes, HLA-G, TAP2 and HLA-DRB1, are implicated in autoimmune diseases, while TAP2 is associated with SNPs characteristic for MG. Within the top 35 prioritized genes our method identifies 90% of the 10 already known MG-associated genes from the considered region without using any information that directly links genes to MG. Among the top eight genes we identified HLA-G and TUBB as new candidates. We show that our <it>ab-initio </it>approach outperforms the other methods for prioritizing disease-associated genes.</p> <p>Conclusion</p> <p>We have developed a method to prioritize disease-associated genes under the potential control of sex hormones. We demonstrate the success of this method by prioritizing the genes localized in the MHC and surrounding region and evaluating the role of these genes as potential candidates for estrogen control as well as MG. We show that our method outperforms the other methods. The method has a potential to be adapted to prioritize genes relevant to other diseases.</p

Social cognition in adults with autism spectrum disorders: Validation of the Edinburgh Social Cognition Test (ESCoT).

Objective: Many existing tests of social cognition are not appropriate for clinical use, due to their length, complexity or uncertainty in what they are assessing. The Edinburgh Social Cognition Test (ESCoT) is a new test of social cognition that assesses affective and cognitive Theory of Mind as well as inter- and intrapersonal understanding of social norms using animated interactions.Method: To support the development of the ESCoT as a clinical tool, we derived cut-off scores from a neurotypical population (n = 236) and sought to validate the ESCoT in a sample of Autism Spectrum Disorder (ASD; n = 19) adults and neurotypical controls (NC; n = 38) matched on age and education. The ESCoT was administered alongside established tests and questionnaire measures of ASD, empathy, systemizing traits and intelligence.Results: Performance on the subtests of the ESCoT and ESCoT total scores correlated with performance on traditional tests, demonstrating convergent validity. ASD adults performed poorer on all measures of social cognition. Unlike the ESCoT, performance on the established tests was predicted by verbal comprehension abilities. Using a ROC curve analysis, we showed that the ESCoT was more effective than existing tests at differentiating ASD adults from NC. Furthermore, a total of 42.11% of ASD adults were impaired on the ESCoT compared to 0% of NC adults.Conclusions: Overall these results demonstrate that the ESCoT is a useful test for clinical assessment and can aid in the detection of potential difficulties in ToM and social norm understanding

Injection of Radioactivities into the Forming Solar System

Meteorite studies have revealed the presence of short-lived radioactivities in the early solar system. The current data suggests that the origin of at least some of the radioactivities requires contribution from recent nucleosynthesis at a stellar site. This sets a strict time limit on the time available for the formation of the solar system and argues for the theory of the triggered origin of the solar system. According to this scenario, the formation of our planetary system was initiated by the impact of an interstellar shock wave on a molecular cloud core. The shock wave originated from a nearby explosive stellar event and carried with it radioactivities produced in the stellar source. In addition to triggering the collapse of the molecular cloud core, the shock wave also deposited some of the freshly synthesized radioactivities into the collapsing system. The radioactivities were then incorporated into the first solar system solids, in this manner leaving a record of the event in the meteoritic material. The viability of the scenario can be investigated through numerical simulations studying the processes involved in mixing shock wave material into the collapsing system. The high-resolution calculations presented here show that injection occurs through Rayleigh-Taylor instabilities, the injection efficiency is approximately 10%, and temporal and spatial heterogeneities in the abundances of the radioactivities existed at the time of their arrival in the forming solar system.Comment: 13 pages, including 3 figures. Better-quality figures available at http://www.public.asu.edu/~hvanhal/pubs

Acupuncture as analgesia for low back pain, ankle sprain and migraine in emergency departments: Study protocol for a randomized controlled trial

BACKGROUND: Pain is the most common reason that patients present to an emergency department (ED) and is often inadequately managed. Evidence suggests that acupuncture is effective for pain relief, yet it is rarely practiced in the ED. The current study aims to assess the efficacy of acupuncture for providing effective analgesia to patients presenting with acute low back pain, migraine and ankle sprain at the EDs of four hospitals in Melbourne, Australia. METHOD: The study is a multi-site, randomized, assessor-blinded, controlled trial of acupuncture analgesia in patients who present to an ED with low back pain, migraine or ankle sprain. Patients will be block randomized to receive either acupuncture alone, acupuncture as an adjunct to pharmacotherapy or pharmacotherapy alone. Acupuncture will be applied according to Standards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA). Pain after one hour, measured using a visual analogue scale (VAS), is the primary outcome. Secondary outcomes measures include the following instruments; the Oswestry low back pain disability questionnaire, 24-hour Migraine Quality of Life questionnaire and Patient's Global Assessment of Ankle Injury Scale. These measures will be recorded at baseline, 1 hour after intervention, each hour until discharge and 48±12 hours of ED discharge. Data will also be collected on the safety and acceptability of acupuncture and health resource utilization. DISCUSSION: The results of this study will determine if acupuncture, alone or as an adjunct to pharmacotherapy provides effective, safe and acceptable pain relief for patients presenting to EDs with acute back pain, migraine or ankle sprain. The results will also identify the impact that acupuncture treatment may have upon health resource utilisation in the ED setting. TRIAL REGISTRATION: Australia and New Zealand Clinical Trials Register (ANZCTR): ACTRN12609000989246

Can programme theory be used as a 'translational tool’ to optimise health service delivery in a national early years’ initiative in Scotland: a case study

Background Theory-based evaluation (TBE) approaches are heralded as supporting formative evaluation by facilitating increased use of evaluative findings to guide programme improvement. It is essential that learning from programme implementation is better used to improve delivery and to inform other initiatives, if interventions are to be as effective as they have the potential to be. Nonetheless, few studies describe formative feedback methods, or report direct instrumental use of findings resulting from TBE. This paper uses the case of Scotland’s, National Health Service, early years’, oral health improvement initiative (Childsmile) to describe the use of TBE as a framework for providing feedback on delivery to programme staff and to assess its impact on programmatic action.&lt;p&gt;&lt;/p&gt; Methods In-depth, semi-structured interviews and focus groups with key stakeholders explored perceived deviations between the Childsmile programme 'as delivered’ and its Programme Theory (PT). The data was thematically analysed using constant comparative methods. Findings were shared with key programme stakeholders and discussions around likely impact and necessary actions were facilitated by the authors. Documentary review and ongoing observations of programme meetings were undertaken to assess the extent to which learning was acted upon.&lt;p&gt;&lt;/p&gt; Results On the whole, the activities documented in Childsmile’s PT were implemented as intended. This paper purposefully focuses on those activities where variation in delivery was evident. Differences resulted from the stage of roll-out reached and the flexibility given to individual NHS boards to tailor local implementation. Some adaptations were thought to have diverged from the central features of Childsmile’s PT, to the extent that there was a risk to achieving outcomes. The methods employed prompted national service improvement action, and proposals for local action by individual NHS boards to address this.&lt;p&gt;&lt;/p&gt; Conclusions The TBE approach provided a platform, to direct attention to areas of risk within a national health initiative, and to agree which intervention components were 'core’ to its hypothesised success. The study demonstrates that PT can be used as a 'translational tool’ to facilitate instrumental use of evaluative findings to optimise implementation within a complex health improvement programme.&lt;p&gt;&lt;/p&gt

What are the living conditions and health status of those who don't report their migration status? a population-based study in Chile

BACKGROUND: Undocumented immigrants are likely to be missing from population databases, making it impossible to identify an accurate sampling frame in migration research. No population-based data has been collected in Chile regarding the living conditions and health status of undocumented immigrants. However, the CASEN survey (Caracterizacion Socio- Economica Nacional) asked about migration status in Chile for the first time in 2006 and provides an opportunity to set the base for future analysis of available migration data. We explored the living conditions and health of self-reported immigrants and respondents who preferred not to report their migration status in this survey. METHODS: Cross-sectional secondary analysis of CASEN survey in Chile in 2006. Outcomes: any disability, illness/accident, hospitalization/surgery, cancer/chronic condition (all binary variables); and the number of medical/emergency attentions received (count variables). Covariates: Demographics (age, sex, marital status, urban/rural, ethnicity), socioeconomic status (education level, employment status and household income), and material standard of living (overcrowding, sanitation, housing quality). Weighted regression models were estimated for each health outcome, crude and adjusted by sets of covariates, in STATA 10.0. RESULTS: About 1% of the total sample reported being immigrants and 0.7% preferred not to report their migration status (Migration Status - Missing Values; MS-MV). The MS-MV lived in more deprived conditions and reported a higher rate of health problems than immigrants. Some gender differences were observed by health status among immigrants and the MS-MV but they were not statistically significant. Regressions indicated that age, sex, SES and material factors consistently affected MS-MVs’ chance of presenting poor health and these patterns were different to those found among immigrants. Great heterogeneity in both the MS-MV and the immigrants, as indicated by wide confidence intervals, prevented the identification of other significantly associated covariates. CONCLUSION: This is the first study to look at the living conditions and health of those that preferred not to respond their migration status in Chile. Respondents that do not report their migration status are vulnerable to poor health and may represent undocumented immigrants. Surveys that fail to identify these people are likely to misrepresent the experiences of immigrants and further quantitative and qualitative research is urgently required

Short-lived Nuclei in the Early Solar System: Possible AGB Sources

(Abridged) We review abundances of short-lived nuclides in the early solar system (ESS) and the methods used to determine them. We compare them to the inventory for a uniform galactic production model. Within a factor of two, observed abundances of several isotopes are compatible with this model. I-129 is an exception, with an ESS inventory much lower than expected. The isotopes Pd-107, Fe-60, Ca-41, Cl-36, Al-26, and Be-10 require late addition to the solar nebula. Be-10 is the product of particle irradiation of the solar system as probably is Cl-36. Late injection by a supernova (SN) cannot be responsible for most short-lived nuclei without excessively producing Mn-53; it can be the source of Mn-53 and maybe Fe-60. If a late SN is responsible for these two nuclei, it still cannot make Pd-107 and other isotopes. We emphasize an AGB star as a source of nuclei, including Fe-60 and explore this possibility with new stellar models. A dilution factor of about 4e-3 gives reasonable amounts of many nuclei. We discuss the role of irradiation for Al-26, Cl-36 and Ca-41. Conflict between scenarios is emphasized as well as the absence of a global interpretation for the existing data. Abundances of actinides indicate a quiescent interval of about 1e8 years for actinide group production in order to explain the data on Pu-244 and new bounds on Cm-247. This interval is not compatible with Hf-182 data, so a separate type of r-process is needed for at least the actinides, distinct from the two types previously identified. The apparent coincidence of the I-129 and trans-actinide time scales suggests that the last actinide contribution was from an r-process that produced actinides without fission recycling so that the yields at Ba and below were governed by fission.Comment: 92 pages, 14 figure files, in press at Nuclear Physics

Comparing Breast Cancer Multiparameter Tests in the OPTIMA Prelim Trial: No Test Is More Equal Than the Others

Background: Previous reports identifying discordance between multiparameter tests at the individual patient level have been largely attributed to methodological shortcomings of multiple in silico studies. Comparisons between tests, when performed using actual diagnostic assays, have been predicted to demonstrate high degrees of concordance. OPTIMA prelim compared predicted risk stratification and subtype classification of different multiparameter tests performed directly on the same population. Methods: Three hundred thirteen women with early breast cancer were randomized to standard (chemotherapy and endocrine therapy) or test-directed (chemotherapy if Oncotype DX recurrence score &gt;25) treatment. Risk stratification was also determined with Prosigna (PAM50), MammaPrint, MammaTyper, NexCourse Breast (IHC4-AQUA), and conventional IHC4 (IHC4). Subtype classification was provided by Blueprint, MammaTyper, and Prosigna. Results: Oncotype DX predicted a higher proportion of tumors as low risk (82.1%, 95% confidence interval [CI] = 77.8% to 86.4%) than were predicted low/intermediate risk using Prosigna (65.5%, 95% CI = 60.1% to 70.9%), IHC4 (72.0%, 95% CI = 66.5% to 77.5%), MammaPrint (61.4%, 95% CI = 55.9% to 66.9%), or NexCourse Breast (61.6%, 95% CI = 55.8% to 67.4%). Strikingly, the five tests showed only modest agreement when dichotomizing results between high vs low/intermediate risk. Only 119 (39.4%) tumors were classified uniformly as either low/intermediate risk or high risk, and 183 (60.6%) were assigned to different risk categories by different tests, although 94 (31.1%) showed agreement between four of five tests. All three subtype tests assigned 59.5% to 62.4% of tumors to luminal A subtype, but only 121 (40.1%) were classified as luminal A by all three tests and only 58 (19.2%) were uniformly assigned as nonluminal A. Discordant subtyping was observed in 123 (40.7%) tumors. Conclusions: Existing evidence on the comparative prognostic information provided by different tests suggests that current multiparameter tests provide broadly equivalent risk information for the population of women with estrogen receptor (ER)–positive breast cancers. However, for the individual patient, tests may provide differing risk categorization and subtype information