Clinical Applications of Resting State Functional Connectivity

During resting conditions the brain remains functionally and metabolically active. One manifestation of this activity that has become an important research tool is spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal of functional magnetic resonance imaging (fMRI). The identification of correlation patterns in these spontaneous fluctuations has been termed resting state functional connectivity (fcMRI) and has the potential to greatly increase the translation of fMRI into clinical care. In this article we review the advantages of the resting state signal for clinical applications including detailed discussion of signal to noise considerations. We include guidelines for performing resting state research on clinical populations, outline the different areas for clinical application, and identify important barriers to be addressed to facilitate the translation of resting state fcMRI into the clinical realm

Towards a consensus regarding global signal regression for resting state functional connectivity MRI

The number of resting state functional connectivity MRI studies continues to expand at a rapid rate along with the options for data processing. Of the processing options, few have generated as much controversy as global signal regression and the subsequent observation of negative correlations (anti-correlations). This debate has motivated new processing strategies and advancement in the field, but has also generated significant confusion and contradictory guidelines. In this article, we work towards a consensus regarding global signal regression. We highlight several points of agreement including the fact that there is not a single “right” way to process resting state data that reveals the “true” nature of the brain. Although further work is needed, different processing approaches likely reveal complementary insights about the brain's functional organisation

The Case Against Intensive Farming of Food Animals

The well-being of American agriculture is indeed a complex subject, fraught with interrelationships, predictions, recriminations, and at times, high emotionalism. In this paper, we will be concentrating on several aspects of the entire picture that we feel are fundamental to the issue of animal welfare in modern agriculture. First, we will take a brief look at two farm animal species maintained in very restrictive systems, that is, battery-caged laying hens and tethered and/or crated brood sows. Next, the human costs in terms of occupational diseases and consumer health hazards will be considered. Finally, some humane alternatives to the factory systems for these species will be presented

Characterizing energy flow in kelp forest food webs: a geochemical review and call for additional research

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Elliott Smith, E. A., & Fox, M. D. Characterizing energy flow in kelp forest food webs: a geochemical review and call for additional research. Ecography. 2021,https://doi.org/10.1111/ecog.05566.Kelp forests are highly productive coastal habitats that serve as biodiversity hotspots and provide valuable ecosystem services. Despite being one the largest marine biomes, kelp forests have been drastically understudied relative to other marine systems. Notably, while the role of kelp as habitat-forming, or ‘foundation species', is well-documented, a comprehensive understanding of kelp forest food web structure is lacking, particularly regarding the importance of kelp-derived energy/nutrients to consumers. Here, we provide a biogeographic perspective on the energetic underpinning of kelp forests based on published literature. We targeted studies which used geochemical proxies – stable isotope analysis – to examine the transfer of carbon from kelp to local consumers. These studies (n = 94) were geographically skewed, with > 40% from Northern European Seas and Temperate Northeast Pacific. Quantitative estimates for the percentage of kelp energy (or kelp + macroalgae if sources were pooled) incorporated by local consumers came from 43 publications, which studied 141 species and 35 broader taxonomic groups. We examined these data for trends among functional groups and across upwelling regimes. No patterns are evident at present, perhaps due to the paucity or variability of available data. However, energetic subsides from kelps clearly support a wide range of diverse taxa around the globe. We also characterized biogeographic patterns in δ13C values of kelps and particulate organic matter (POM, a phytoplankton proxy), to evaluate potential limitations of stable isotope analysis in disentangling the relative contributions of pelagic versus benthic resources to coastal food webs. Globally, kelps and POM differed by > 4.5‰, but there was substantial variation among regions and kelp species. Accordingly, we discuss advances in stable isotope techniques which are facilitating more precise analysis of these complex energetic pathways. We end by proposing four main avenues of critical future research that will shed light on the resilience of these communities to global change.This material is based upon work supported by the National Science Foundation under Grant no. (NSF 1907163) issued to EES. MF was supported by a Woods Hole Oceanographic Institution Postdoctoral Scholarship

Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, M. D., Fox, M. D., Kelly, E. L. A., Zgliczynski, B. J., Sandin, S. A., & Smith, J. E. Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific. Plos One, 15(2), (2020): e0228448, doi:10.1371/journal.pone.0228448.Upwelling is an important source of inorganic nutrients in marine systems, yet little is known about how gradients in upwelling affect primary producers on coral reefs. The Southern Line Islands span a natural gradient of inorganic nutrient concentrations across the equatorial upwelling region in the central Pacific. We used this gradient to test the hypothesis that benthic autotroph ecophysiology is enhanced on nutrient-enriched reefs. We measured metabolism and photophysiology of common benthic taxa, including the algae Porolithon, Avrainvillea, and Halimeda, and the corals Pocillopora and Montipora. We found that temperature (27.2–28.7°C) was inversely related to dissolved inorganic nitrogen (0.46–4.63 μM) and surface chlorophyll a concentrations (0.108–0.147 mg m-3), which increased near the equator. Contrary to our prediction, ecophysiology did not consistently track these patterns in all taxa. Though metabolic rates were generally variable, Porolithon and Avrainvillea photosynthesis was highest at the most productive and equatorial island (northernmost). Porolithon photosynthetic rates also generally increased with proximity to the equator. Photophysiology (maximum quantum yield) increased near the equator and was highest at northern islands in all taxa. Photosynthetic pigments also were variable, but chlorophyll a and carotenoids in Avrainvillea and Montipora were highest at the northern islands. Phycobilin pigments of Porolithon responded most consistently across the upwelling gradient, with higher phycoerythrin concentrations closer to the equator. Our findings demonstrate that the effects of in situ nutrient enrichment on benthic autotrophs may be more complex than laboratory experiments indicate. While upwelling is an important feature in some reef ecosystems, ancillary factors may regulate the associated consequences of nutrient enrichment on benthic reef organisms.This work was supported by funding from the Moore Family Foundation, the Gordon and Betty Moore Foundation, the Scripps family, and anonymous donors. The funders had no role in study design, data collection and analysis, or preparation of the manuscript

Disentangling the Origin and Heating Mechanism of Supernova Dust: Late-Time Spitzer Spectroscopy of the Type IIn SN 2005ip

This paper presents late-time near-infrared and {\it Spitzer} mid-infrared photometric and spectroscopic observations of warm dust in the Type IIn SN 2005ip in NGC 2906. The spectra show evidence for two dust components with different temperatures. Spanning the peak of the thermal emission, these observations provide strong constraints on the dust mass, temperature, and luminosity, which serve as critical diagnostics for disentangling the origin and heating mechanism of each component. The results suggest the warmer dust has a mass of $\sim 5 \times 10^{-4}~$\msolar, originates from newly formed dust in the ejecta, or possibly the cool, dense shell, and is continuously heated by the circumstellar interaction. By contrast, the cooler component likely originates from a circumstellar shock echo that forms from the heating of a large, pre-existing dust shell $\sim 0.01 - 0.05$~\msolar~by the late-time circumstellar interaction. The progenitor wind velocity derived from the blue edge of the He 1 1.083 \micron~P Cygni profile indicates a progenitor eruption likely formed this dust shell $\sim$100 years prior to the supernova explosion, which is consistent with a Luminous Blue Variable (LBV) progenitor star.Comment: 12 pages, 10 figures, Accepted to Ap

Minkowski functionals: An MRI texture analysis tool for determination of the aggressiveness of breast cancer

Purpose: This work aims to see whether Minkowski Functionals can be used to distinguish between cancer types before chemotherapy treatment has begun, and whether a response to treatment can be predicted by an initial scan alone. Methods: Fat-nulled T1w 3T DCE-MRI scans were taken of 100 cases of biopsy confirmed breast cancer and a series of binary images created on lesion containing slices. Minkowski Functionals were calculated for each binary image and the change in these values as the binary threshold was raised was described using 6th order polynomials. These polynomials were used to compare between patient sub-groups, for triple negative breast cancer (TNBC) status, chemotherapy response, biopsy grade, nodal status, and lymphovascular invasion status. Results: When using Minkowski Functionals statistically significant (p<0.05) differences were found between TNBC status, biopsy grade, and lymphovascular invasion status sub-groups for all methodologies. The analysis performance did not appear to be affected by the number of threshold steps used. Most notably, very strong differences (p≤0.01) were found between TNBC and other intrinsic subtype patients. When analysed with a binary logistic regression model, an AUC value of 0.917 (0.846 – 0.987, 95% CI) for TNBC classification was found. Conclusion: The method of texture analysis presented here provides a novel way to characterise tumours, and demonstrates clear differences between cancer groups which are detectable before treatment begins, and can help with treatment planning as a valuable prognosis tool

Late-Time Circumstellar Interaction in a Spitzer Selected Sample of Type IIn Supernovae

Type IIn supernovae (SNe IIn) are a rare (< 10%) subclass of core-collapse SNe that exhibit relatively narrow emission lines from a dense, pre-existing circumstellar medium (CSM). In 2009, a warm Spitzer survey observed 30 SNe IIn discovered in 2003 - 2008 and detected 10 SNe at distances out to 175 Mpc with unreported late-time infrared emission, in some cases more than 5 years post-discovery. For this single epoch of data, the warm-dust parameters suggest the presence of a radiative heating source consisting of optical/X-ray emission continuously generated by ongoing CSM interaction. Here we present multi-wavelength follow-up observations of this sample of 10 SNe IIn and the well-studied Type IIn SN 2010jl. A recent epoch of Spitzer observations reveals ongoing mid-infrared emission from nine of the SNe in this sample. We also detect three of the SNe in archival WISE data, in addition to SNe 1987A, 2004dj, and 2008iy. For at least five of the SNe in the sample, optical and/or X-ray emission confirms the presence of radiative emission from ongoing CSM interaction. The two Spitzer nondetections are consistent with the forward shock overrunning and destroying the dust shell, a result that places upper limits on the dust-shell size. The optical and infrared observations confirm the radiative heating model and constrain a number of model parameters, including progenitor mass-loss characteristics. All of the SNe in this sample experienced an outburst on the order of tens to hundreds of years prior to the SN explosion followed by periods of less intense mass loss. Although all evidence points to massive progenitors, the variation in the data highlights the diversity in SN IIn progenitor evolution. While these observations do not identify a particular progenitor system, they demonstrate that future, coordinated, multi-wavelength campaigns can constrain theoretical mass-loss models.Comment: 10 pages, 6 figures, accepted to AJ (with comments

Raised erythrocyte creatine in patients with pulmonary arterial hypertension – Evidence for subclinical hemolysis

SummaryBackgroundPulmonary arterial hypertension (PAH) has been associated with hemolytic conditions such as sickle cell disease but the possible role of hemolysis in the pathogenesis or pathophysiology of other forms of PAH has not been studied. Erythrocyte lifespan is the gold-standard test of hemolysis and may be measured by assaying erythrocyte creatine (EC) levels. EC decreases as the erythrocyte ages, so patients with hemolysis have high EC levels.MethodsWe measured EC and other parameters of hemolysis in patients with idiopathic and connective tissue associated PAH and normal controls.ResultsIn patients with PAH (n = 40), EC levels were higher than in controls n = 30 (patients EC 1.72 mcmol/g HgB 95%CI[1.51, 1.96], controls EC 1.05 mcmol/g HgB [0.93, 1.19], p < 0.0001). High levels of EC correlated with worse 6 min walk (r = −0.42, p < 0.0001) and worse functional class (p = 0.002). Other indirect indices of hemolysis (total lactate dehydrogenase, red cell distribution width) were also increased in patients with PAH relative to controls.ConclusionsThere is evidence of subclinical hemolysis in patients with PAH, and higher levels of hemolysis are associated with poorer exercise capacity