The Evolution of Bias - Generalized

Fry (1996) showed that galaxy bias has the tendency to evolve towards unity, i.e. in the long run, the galaxy distribution tends to trace that of matter. Generalizing slightly Fry's reasoning, we show that his conclusion remains valid in theories of modified gravity (or equivalently, complex clustered dark energy). This is not surprising: as long as both galaxies and matter are subject to the same force, dynamics would drive them towards tracing each other. This holds, for instance, in theories where both galaxies and matter move on geodesics. This relaxation of bias towards unity is tempered by cosmic acceleration, however: the bias tends towards unity but does not quite make it, unless the formation bias were close to unity. Our argument is extended in a straightforward manner to the case of a stochastic or nonlinear bias. An important corollary is that dynamical evolution could imprint a scale dependence on the large scale galaxy bias. This is especially pronounced if non-standard gravity introduces new scales to the problem: the bias at different scales relaxes at different rates, the larger scales generally more slowly and retaining a longer memory of the initial bias. A consistency test of the current (general relativity + uniform dark energy) paradigm is therefore to look for departure from a scale independent bias on large scales. A simple way is to measure the relative bias of different populations of galaxies which are at different stages of bias relaxation. Lastly, we comment on the possibility of directly testing the Poisson equation on cosmological scales, as opposed to indirectly through the growth factor.Comment: 8 pages, 2 figures. References added. Accepted for publication in Physical Review

Development of a Consensus Statement for the Definition, Diagnosis, and Treatment of Acute Exacerbations of Idiopathic Pulmonary Fibrosis Using the Delphi Technique.

© 2015, The Author(s).Introduction: There is a lack of agreed and established guidelines for the treatment of acute exacerbations of idiopathic pulmonary fibrosis (AE-IPF). This reflects, in part, the limited evidence-base underpinning the management of AE-IPF. In the absence of high-quality evidence, the aim of this research was to develop a clinician-led consensus statement for the definition, diagnosis and treatment of AE-IPF. Methods: A literature review was conducted to obtain published material on the definition and treatment of AE-IPF. The results of this review were circulated to an online panel of clinicians for review. Statements were then shared with ten expert respiratory clinicians who regularly treat patients with IPF. A Delphi technique was then used to develop a consensus statement for the definition, diagnosis and treatment of AE-IPF. During the first round of review, clinicians rated the clarity of each statement, the extent to which the statement should be included and provided comments. In two subsequent rounds of review, clinicians were provided with the group median inclusion rating for each statement, and any revised wording of statements to aid clarity. Clinicians were asked to repeat the clarity and inclusion ratings for the revised statements. Results: The literature review, online panel discussion, and face-to-face meeting generated 65 statements covering the definition, diagnosis, and management of AE-IPF. Following three rounds of blind review, 90% of clinicians agreed 39 final statements. These final statements included a definition of AE-IPF, approach to diagnosis, and treatment options, specifically: supportive measures, use of anti-microbials, immunosuppressants, anti-coagulants, anti-fibrotic therapy, escalation, transplant management, and long-term management including discharge planning. Conclusion: This clinician-led consensus statement establishes the ‘best practice’ for the management and treatment of AE-IPF based on current knowledge, evidence, and available treatments. Funding: Boehringer Ingelheim Ltd., Bracknell, West Berkshire, UK

The Origin of Solar Activity in the Tachocline

Solar active regions, produced by the emergence of tubes of strong magnetic field in the photosphere, are restricted to within 35 degrees of the solar equator. The nature of the dynamo processes that create and renew these fields, and are therefore responsible for solar magnetic phenomena, are not well understood. We analyze the magneto-rotational stability of the solar tachocline for general field geometry. This thin region of strong radial and latitudinal differential rotation, between the radiative and convective zones, is unstable at latitudes above 37 degrees, yet is stable closer to the equator. We propose that small-scale magneto-rotational turbulence prevents coherent magnetic dynamo action in the tachocline except in the vicinity of the equator, thus explaining the latitudinal restriction of active regions. Tying the magnetic dynamo to the tachocline elucidates the physical conditions and processes relevant to solar magnetism.Comment: 10 pages, 1 figure, accepted for publication in ApJ

Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin.

Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease

What do we really know about the appropriateness of radiation emitting imaging for low back pain in primary and emergency care? A systematic review and meta-analysis of medical record reviews

Background Since 2000, guidelines have been consistent in recommending when diagnostic imaging for low back pain should be obtained to ensure patient safety and reduce unnecessary tests. This systematic review and meta-analysis was conducted to determine the pooled proportion of CT and x-ray imaging of the lumbar spine that were considered appropriate in primary and emergency care. Methods Pubmed, CINAHL, The Cochrane Database of Systematic Reviews and Embase were searched for synonyms of “low back pain”, “guidelines”, and “adherence” that were published after 2000. Titles, abstracts, and full texts were reviewed for inclusion with forward and backward tracking on included studies. Included studies had data extracted and synthesized. Risk of bias was performed on all studies, and GRADE was performed on included studies that provided data on CT and x-ray separately. A random effect, single proportion meta-analysis model was used. Results Six studies were included in the descriptive synthesis, and 5 studies included in the meta-analysis. Five of the 6 studies assessed appropriateness of x-rays; two of the six studies assessed appropriateness of CTs. The pooled estimate for appropriateness of x-rays was 43% (95% CI: 30%, 56%) and the pooled estimate for appropriateness of CTs was 54% (95% CI: 51%, 58%). Studies did not report adequate information to fulfill the RECORD checklist (reporting guidelines for research using observational data). Risk of bias was high in 4 studies, moderate in one, and low in one. GRADE for x-ray appropriateness was low-quality and for CT appropriateness was very-low-quality. Conclusion While this study determined a pooled proportion of appropriateness for both x-ray and CT imaging for low back pain, there is limited confidence in these numbers due to the downgrading of the evidence using GRADE. Further research on this topic is needed to inform our understanding of x-ray and CT appropriateness in order to improve healthcare systems and decrease patient harms

Current helicity of active regions as a tracer of large-scale solar magnetic helicity

We demonstrate that the current helicity observed in solar active regions traces the magnetic helicity of the large-scale dynamo generated field. We use an advanced 2D mean-field dynamo model with dynamo saturation based on the evolution of the magnetic helicity and algebraic quenching. For comparison, we also studied a more basic 2D mean-field dynamo model with simple algebraic alpha quenching only. Using these numerical models we obtained butterfly diagrams both for the small-scale current helicity and also for the large-scale magnetic helicity, and compared them with the butterfly diagram for the current helicity in active regions obtained from observations. This comparison shows that the current helicity of active regions, as estimated by $-{\bf A \cdot B}$ evaluated at the depth from which the active region arises, resembles the observational data much better than the small-scale current helicity calculated directly from the helicity evolution equation. Here ${\bf B}$ and ${\bf A}$ are respectively the dynamo generated mean magnetic field and its vector potential. A theoretical interpretation of these results is given.Comment: 11 pages, 5 figures, revised versio

Penetrance of HNPCC-related cancers in a retrolective cohort of 12 large Newfoundland families carrying a MSH2 founder mutation: an evaluation using modified segregation models

<p>Abstract</p> <p>Background</p> <p>Accurate risk (penetrance) estimates for associated phenotypes in carriers of a major disease gene are important for genetic counselling of at-risk individuals. Population-specific estimates of penetrance are often needed as well. Families ascertained from high-risk disease clinics provide substantial data to estimate penetrance of a disease gene, but these estimates must be adjusted for possible specific sources of bias.</p> <p>Methods</p> <p>A cohort of 12 independently ascertained HNPCC families harbouring a founder MSH2 mutation was identified from a cancer genetics clinic in St. John's, Newfoundland, Canada. Carrier status was known for 247 family members but phenotype information on up to 85 additional relatives with unknown carrier status was available; using modified segregation models these additional individuals could be included in the analyses. Three HNPCC-related phenotypes were evaluated as age at diagnosis of: any HNPCC cancer (first cancer), colorectal cancer (CRC), and endometrial cancer (EC) for females.</p> <p>Results</p> <p>Lifetime (age 70) risk estimates for male and female carriers were similar for developing any HNPCC cancer (Males = 98.2%, 95% Confidence Interval (CI) = (93.8%, 99.9%); Females = 92.8%, 95% CI = (82.4%, 99.1%)) but female carriers experienced substantially reduced lifetime risk for developing CRC compared to male carriers (Females = 38.9%, 95% CI = (24.2%, 62.1%); Males = 84.5%, 95% CI = (67.3%, 91.3%)). Female non-carriers had very low lifetime risk for these two outcomes while male non-carriers had lifetime risks intermediate to the female carriers and non-carriers. Female carriers had a lifetime risk of developing EC of 82.4%. Relative risks for developing any HNPCC cancer (carriers relative to non-carriers) were substantially greater for females compared to their male counterparts (Females = 54.8, 95%CI = (4.4, 379.8); Males = 9.7, 95% CI = (0.3, 23.8)). Relative risks for developing CRC at age 70 were substantially greater for females compared to their male counterparts (Females = 23.7, 95%CI = (5.6, 137.9); Males = 6.8%, 95% CI = (2.3, 66.2)). However, the risk of developing CRC decreased with age among both genders.</p> <p>Conclusion</p> <p>The proposed modified segregation-based models used to estimate age-specific risks for HNPCC phenotypes can reduce bias due to ascertainment and missing genotype information as well as provide estimates of absolute and relative risks.</p

Examining the Polymorphisms in the Hypoxia Pathway Genes in Relation to Outcome in Colorectal Cancer

Introduction Colorectal cancer is a common malignancy. Identification of genetic prognostic markers may help prognostic estimations in colorectal cancer. Genes that regulate response to hypoxia and other genes that are regulated under the hypoxic conditions have been shown to play roles in cancer progression. In this study, we hypothesized that genetic variations in the hypoxia pathway genes were associated with the risk of outcome in colorectal cancer patients. Methods This study was performed in two phases. In the first phase, 49 SNPs from six hypoxia pathway genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12) in 272 colorectal cancer patients were analyzed. In the second phase, 77 SNPs from seven hypoxia pathway genes (HIF1A, HIF1B, HIF2A, HIF2B, HIF3A, LOX and CXCL12) were analyzed in an additional cohort of 535 patients. Kaplan Meier, Cox univariate and multivariable regression analyses were performed to analyze the relationship between the SNPs and overall survival (OS), disease free survival (DFS) or disease specific survival (DSS). Since this was a hypothesis-generating study, no correction for multiple testing was applied. Results In phase I, one SNP (HIF2A rs11125070) was found to be associated with DFS in multivariable analysis; yet association of a proxy polymorphism (HIF2A rs4953342) was not detected in the phase II patient cohort. In phase II, associations of two SNPs (HIF2A rs4953352 and HIF2B rs12593988) were significant in both OS and DFS multivariable analyses. However, association of HIF2A rs4953352 was not replicated in the phase I cohort using a proxy SNP (HIF2A rs6706003). Conclusion Overall, our study did not find a convincing evidence of association of the investigated polymorphisms with the disease outcomes in colorectal cance

Classifying the unclassifiable – A Delphi study to reach consensus on the fibrotic nature of diseases

Background Traditionally, clinical research has focused on individual fibrotic diseases or fibrosis in a particular organ. However, it is possible for people to have multiple fibrotic diseases. While multi-organ fibrosis may suggest shared pathogenic mechanisms, yet there is no consensus on what constitutes a fibrotic disease and therefore fibrotic multimorbidity. Aim A Delphi study was performed to reach consensus on which diseases may be described as fibrotic. Methods Participants were asked to rate a list of diseases, sub-grouped according to eight body regions, as ‘fibrotic manifestation always present’, ‘can develop fibrotic manifestations’, ‘associated with fibrotic manifestations’ or ‘not fibrotic nor associated’. Classifications of ‘fibrotic manifestation always present’ and ‘can develop fibrotic manifestations’ were merged and termed ‘fibrotic’. Clinical consensus was defined according to the interquartile range, having met a minimum number of responses. Clinical agreement was used for classification where diseases did not meet the minimum number of responses (required for consensus measure), were only classified if there was 100% consensus on disease classification. Results After consulting experts, searching the literature and coding dictionaries, a total of 323 non-overlapping diseases which might be considered fibrotic were identified; 92 clinical specialists responded to the first round of the survey. Over three survey rounds, 240 diseases were categorized as fibrotic via clinical consensus and 25 additional diseases through clinical agreement. Conclusion Using a robust methodology, an extensive list of diseases was classified. The findings lay the foundations for studies estimating the burden of fibrotic multimorbidity, as well as investigating shared mechanisms and therapies