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"Mclaughlin, Ian"
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Deriving the Spiritual from the Material: A Speculatively Realist Perspective
2025
The existence of the spiritual can be deduced from knowledge of the material. There is an inherent affinity between speculation and spirituality: an embrace of gaps in knowledge. Speculative Realisms’ rejection of both existential anthropocentrism and correlationism in favor of more empathetic, a-, pan-, or metacentric perspectives, allows for a flat ontology where all objects equally exist and allow us to describe how the spiritual exists outside of thought. This perspective allows us to derive the existence of the spiritual via the examination of interactions between material objects. By showing how all objects, whether material or abstract, have a spiritual aspect, this paper advocates for a holistic understanding of reality that recognizes the interconnectedness of all objects.
Journal Article
Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
2019
Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and a new target-enrichment sequence analysis tool developed by Pacific Biosciences to interrogate the sequence structure of expanded repeats. The sequencing was successful in identifying a previously described interruption within an unexpanded allele and provided sequence data on expanded alleles greater than 2000 bases in length. The data revealed considerable heterogeneity in the size distribution of expanded repeats within each patient. Detailed analysis of the long sequence reads did not reveal any instances of interruptions to the expanded CAG repeats, but did reveal novel variants within the AGG repeats that flank the CAG repeats in two of the five samples from clinically unaffected patients with expansions. This first examination of the sequence structure of CAG repeats in CTG18.1 suggests that factors other than interruptions to the repeat structure account for the absence of disease in some elderly patients with repeat expansions in the TCF4 gene.
Journal Article
Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease
2018
Background
Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the
C9orf72
‘GGGGCC’ (G
4
C
2
) repeat that causes approximately 5–7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences’ (PacBio) and Oxford Nanopore Technologies’ (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing G
4
C
2
repeat expansion. We also report the first long-read sequencing data characterizing the
C9orf72
G
4
C
2
repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9.
Results
Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human
C9orf72
repeat expansion using 15 flow cells. We obtained 8× coverage across the
C9orf72
locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained > 800× coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual’s repeat region was > 99% G
4
C
2
content, though we cannot rule out small interruptions.
Conclusions
Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in
C9orf72
expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-G
4
C
2
content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.
Journal Article
The utility of split function testing in determining recovery of glomerular filtration rate after living kidney donation: a cohort study
by
McManus, Siobhan K.
,
Glen, Julie A.
,
Crowe, Kirsty J.
in
Adult
,
Analysis
,
Blood & organ donations
2025
Background
A number of UK transplantation centres use isotope studies to estimate the relative contribution from each kidney in living kidney donor assessment. The evidence that the estimation of pre-donation split function of the non-donated kidney influences post-donation renal recovery is limited. The aim of this study was to analyse whether, in the context of other donor factors, the split function of the non-donated kidney predicts the percentage recovery of glomerular filtration rate (GFR) at one-year post-donation.
Methodology
A retrospective cohort analysis was undertaken on 291 living kidney donors in the Glasgow Renal and Transplant Unit between 1
st
January 2011 and 1
st
June 2022. Univariable and multivariable linear regression analysis was used to analyse the impact of donor factors on recovery of renal function at one year relative to baseline isotope GFR (iGFR) or to estimated GFR (eGFR by Chronic Kidney Disease Epidemiology Collaboration [CKD-EPI] formula). Sub-analyses of donor outcome (% recovery of iGFR and eGFR at one year) were undertaken using single-measures ANOVA and grouping of donors by pre-donation isotope uptake of the non-donated kidney.
Results
Median recovery of pre-donation GFR at 1 year was 70.0% (IQR 64.8-75.5). On linear regression analysis there was no significant association found between split function of the non-donated kidney and the percentage recovery of iGFR, although a small significant association was found for eGFR. There was no significant difference between mean iGFR or eGFR recovery on sub-analysis of donor outcomes.
Conclusions
This study demonstrated no clinically important predictive relationship between percentage recovery of renal function at 1 year after living kidney donation and pre-donation split function within the range accepted for donation in our centre.
Journal Article
Application of a small molecule calcium influx inducer as a vaccine adjuvant: enhancing Th2-biased immune responses
by
Chan, Michael
,
Carson, Dennis A.
,
Hayashi, Tomoko
in
adjuvant
,
Adjuvants
,
Adjuvants, Immunologic - pharmacology
2026
Vaccines are highly effective in preventing the spread of communicable diseases and are critical to overall public health. As immune stimulants vaccine adjuvants augment the level and longevity of these protective responses. Seeking novel adjuvants using parallel high throughput screens and subsequent systematic structure-activity relationship studies we identified an analogue of a hit compound,
, that in screening assays retained
induction of calcium (Ca
) influx, tetraspanin CD63 EV reporter activity and cell viability. Here, we further our analyses of the biological activity of
related its potential use as a vaccine adjuvant.
was tested for activation of murine bone marrow-derived dendritic cells (mBMDC) by flow cytometry for Ca
entry, levels of CD80 and CD86 expression, and
stimulation of antigen-specific T cell proliferation. Cytokines and IgG responses from BALB/c mice injected with
as a single agent or as an adjuvant with ovalbumen were measured by ELISA.
triggered store-operated Ca
entry in mBMDC as well as increases in CD80 and CD86 surface expression. In co-culture experiments, this compound amplified the stimulation of cognate T cell proliferation. Intramuscular injection of
elicited minimal systemic cytokine and chemokine release. When used as an adjuvant with ovalbumen,
generated a significant antigen-specific IgG1 response with a higher splenocyte T helper 2 (Th2) cytokine response.
activated mBMDCs associated with EV release and a store-operated calcium entry response. Enhanced cognate T cell proliferation was mediated either through direct engagement with compound-stimulated mBMDCs or indirectly via immunostimulatory extracellular vesicles released by
-activated mBMDCs.
elicited minimal systemic cytokine and chemokine release, demonstrating a promising safety profile. When used as an adjuvant in a murine vaccination model,
enhanced the IgG1 response with an associated T helper 2 cytokine profile. Hence this compound shows promise as an adjuvant if a Th2 response is beneficial or in combination with other agents to provide a balanced immune response in vaccines.
Journal Article
Tobacco industry responsibility for butts: a Model Tobacco Waste Act
by
Novotny, Thomas E
,
Curtis, Clifton
,
Freiberg, Mike
in
Cellulose acetate
,
Cigarettes
,
Climate change
2017
Cigarette butts and other postconsumer products from tobacco use are the most common waste elements picked up worldwide each year during environmental cleanups. Under the environmental principle of Extended Producer Responsibility, tobacco product manufacturers may be held responsible for collection, transport, processing and safe disposal of tobacco product waste (TPW). Legislation has been applied to other toxic and hazardous postconsumer waste products such as paints, pesticide containers and unused pharmaceuticals, to reduce, prevent and mitigate their environmental impacts. Additional product stewardship (PS) requirements may be necessary for other stakeholders and beneficiaries of tobacco product sales and use, especially suppliers, retailers and consumers, in order to ensure effective TPW reduction. This report describes how a Model Tobacco Waste Act may be adopted by national and subnational jurisdictions to address the environmental impacts of TPW. Such a law will also reduce tobacco use and its health consequences by raising attention to the environmental hazards of TPW, increasing the price of tobacco products, and reducing the number of tobacco product retailers.
Journal Article
Reducing Tobacco Use and Access Through Strengthened Minimum Price Laws
by
Ribisl, Kurt
,
McLaughlin, Ian
,
Laird-Metke, Elisa
in
Cigarettes
,
City ordinances
,
Commerce - economics
2014
Higher prices reduce consumption and initiation of tobacco products. A minimum price law that establishes a high statutory minimum price and prohibits the industry’s discounting tactics for tobacco products is a promising pricing strategy as an alternative to excise tax increases. Although some states have adopted minimum price laws on the basis of statutorily defined price “markups” over the invoice price, existing state laws have been largely ineffective at increasing the retail price. We analyzed 3 new variations of minimum price laws that hold great potential for raising tobacco prices and reducing consumption: (1) a flat rate minimum price law similar to a recent enactment in New York City, (2) an enhanced markup law, and (3) a law that incorporates both elements.
Journal Article
A novel calcium influx inducer and a TLR7 agonist are synergistic co-adjuvants that enhance cross-reactive immunity against influenza in young and aged mice
by
Chan, Michael
,
Carson, Dennis A.
,
Pu, Minya
in
Adjuvants
,
Adjuvants, Immunologic - administration & dosage
,
Adjuvants, Immunologic - pharmacology
2026
Vaccine adjuvants play a crucial role in the efficacy of vaccines, particularly in immunocompromised populations. Newer agents and combination strategies are needed for adequate defense against emerging pathogens and their evolving variants. Here we report the benefit of a synergistic combination of two adjuvants: a Toll-like receptor 7 agonist, 1V270, and a calcium influx inducer, 2G272, that elicit Th1 and Th2 biased immune responses, respectively. In vitro,2G272 significantly enhanced cytokine production induced by 1V270 in human and mouse primary cells, compared to a low activity analog, 2E281, identified from structure-activity relationship studies. Using A/California/07/2009 (H1N1) inactivated influenza A virus (IIAV) as the antigen, the combination adjuvant (2G272 + 1V270) magnified IgG1 and IgG2a responses against hemagglutinin (HA) accompanied by greater hemagglutinin inhibition titers and increased germinal center formation in the draining lymph nodes of immunized BALB/c mice at comparable levels to FDA-approved comparators, MF59 and AS01B. The combination adjuvant also enhanced H1 HA-specific T cell responses, augmenting antigen-specific IFNγ secretion. Importantly, the 2G272 + 1V270 combined adjuvant promoted cross-reactive antibody and cellular immune responses against other HAs in phylogenic Group 1: H5, H11, and in Group 2: H3. C57BL/6 aged mice immunized with H1N1 IIAV and 2G272 + 1V270 generated significant anti-H1 IgG1 responses and IFNγ splenic T cell responses to H1 which were cross-reactive with H5 and H3. Collectively, our findings suggest that 2G272 + 1V270 may be a versatile vaccine co-adjuvant system for promoting a larger breadth of cross reactive Th1/Th2 immune responses and robust GC B cell formation, including in the elderly population.
Journal Article