Visual analysis of social networks in space and time using smartphone logs

We designed and applied novel interactive visualisation to investigate how social networks - derived from smartphone logs - are embedded in time and space. Social networks were identified through direct calls between participants and calls to mutual contacts of participants. Direct contact between participants was sparse and deriving networks through mutual contacts helped enrich the social networks. Our resulting interactive visualisation tool offers four linked and co-ordinated views of spatial, temporal, individual and social network aspects of the data. Brushing and altering techniques help us investigate how these aspects relate. We also simultaneously display some demographic and attitudinal variables to help add context to the behaviours we observe. Using these techniques, we were able to characterise spatial and temporal aspects of participants' social networks and suggest explanations for some of them. We reflect on the extent to which such analysis helps us understand social communication behaviour

Exploring gendered cycling behaviours within a large-scale behavioural data-set

Analysing over 10 million journeys made by members of London’s Cycle Hire Scheme, we find that female customers’ usage characteristics are demonstrably different from those of male customers. Usage at weekends and within London’s parks characterises women’s journeys, whereas for men, a commuting function is more clearly identified. Some of this variation is explained by geodemographic differences and by an atypical period of usage during the first 3 months after the scheme’s launch. Controlling for each of these variables brings some convergence between men and women. However, many differences are preserved. Studying the spatio-temporal context under which journeys are made, we find that women’s journeys are highly spatially structured. Even when making utilitarian cycle trips, routes that involve large, multi-lane roads are comparatively rare, and instead female cyclists preferentially select areas of the city associated with slower traffic streets and with cycle routes slightly offset from major roads

Studying commuting behaviours using collaborative visual analytics

Mining a large origin–destination dataset of journeys made through London’s Cycle Hire Scheme (LCHS), we develop a technique for automatically classifying commuting behaviour that involves a spatial analysis of cyclists’ journeys. We identify a subset of potential commuting cyclists, and for each individual define a plausible geographic area representing their workplace. All peak-time journeys terminating within the vicinity of this derived workplace in the morning, and originating from this derived workplace in the evening, we label commutes. Three techniques for creating these workplace areas are compared using visual analytics: a weighted mean-centres calculation, spatial k-means clustering and a kernel density-estimation method. Evaluating these techniques at the individual cyclist level, we find that commuters’ peak-time journeys are more spatially diverse than might be expected, and that for a significant portion of commuters there appears to be more than one plausible spatial workplace area. Evaluating the three techniques visually, we select the density-estimation as our preferred method. Two distinct types of commuting activity are identified: those taken by LCHS customers living outside of London, who make highly regular commuting journeys at London’s major rail hubs; and more varied commuting behaviours by those living very close to a bike-share docking station. We find evidence of many interpeak journeys around London’s universities apparently being taken as part of cyclists’ working day. Imbalances in the number of morning commutes to, and evening commutes from, derived workplaces are also found, which might relate to local availability of bikes. Significant decisions around our workplace analysis, and particularly these broader insights into commuting behaviours, are discovered through exploring this analysis visually. The visual analysis approach described in the paper is effective in enabling a research team with varying levels of analysis experience to participate in this research. We suggest that such an approach is of relevance to many applied research contexts

Locally-varying explanations behind the United Kingdom\u27s vote to leave the European Union

Explanations behind area-based (Local Authority-level) voting preference in the 2016 referendum on membership of the European Union are explored using aggregate-level data. Developing local models, special attention is paid to whether variables explain the vote equally well across the country. Variables describing the post-industrial and economic successfulness of Local Authorities most strongly discriminate variation in the vote. To a lesser extent this is the case for variables linked to metropolitan and big city contexts, which assist the Remain vote, those that distinguish more traditional and nativist values, assisting Leave, and those loosely describing material outcomes, again reinforcing Leave. Whilst variables describing economic competitiveness co-vary with voting preference equally well across the country, the importance of secondary variables - those distinguishing metropolitan settings, values and outcomes - does vary by region. For certain variables and in certain areas, the direction of effect on voting preference reverses. For example, whilst levels of European Union migration mostly assist the Remain vote, in parts of the country the opposite effect is observed

Locally-varying explanations behind the United Kingdom\u27s vote to leave the European Union

Explanations behind area-based (Local Authority-level) voting preference in the 2016 referendum on membership of the European Union are explored using aggregate-level data. Developing local models, special attention is paid to whether variables explain the vote equally well across the country. Variables describing the post-industrial and economic successfulness of Local Authorities most strongly discriminate variation in the vote. To a lesser extent this is the case for variables linked to metropolitan and big city contexts, which assist the Remain vote, those that distinguish more traditional and nativist values, assisting Leave, and those loosely describing material outcomes, again reinforcing Leave. Whilst variables describing economic competitiveness co-vary with voting preference equally well across the country, the importance of secondary variables - those distinguishing metropolitan settings, values and outcomes - does vary by region. For certain variables and in certain areas, the direction of effect on voting preference reverses. For example, whilst levels of European Union migration mostly assist the Remain vote, in parts of the country the opposite effect is observed

LIPIcs, Volume 277, GIScience 2023, Complete Volume

LIPIcs, Volume 277, GIScience 2023, Complete Volum

Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR, and SPINK1 variants were associated with pancreatitis risk. We now report two significant genome-wide associations identified and replicated at PRSS1-PRSS2 (1×10-12) and x-linked CLDN2 (p < 1×10-21) through a two-stage genome-wide study (Stage 1, 676 cases and 4507 controls; Stage 2, 910 cases and 4170 controls). The PRSS1 variant affects susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous (or hemizygous male) CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men – male hemizygous frequency is 0.26, female homozygote is 0.07

ABCA7 frameshift deletion associated with Alzheimer disease in African Americans

Objective: To identify a causative variant(s) that may contribute to Alzheimer disease (AD) in African Americans (AA) in the ATP-binding cassette, subfamily A (ABC1), member 7 (ABCA7) gene, a known risk factor for late-onset AD. Methods: Custom capture sequencing was performed on ∼150 kb encompassing ABCA7 in 40 AA cases and 37 AA controls carrying the AA risk allele (rs115550680). Association testing was performed for an ABCA7 deletion identified in large AA data sets (discovery n = 1,068; replication n = 1,749) and whole exome sequencing of Caribbean Hispanic (CH) AD families. Results: A 44-base pair deletion (rs142076058) was identified in all 77 risk genotype carriers, which shows that the deletion is in high linkage disequilibrium with the risk allele. The deletion was assessed in a large data set (531 cases and 527 controls) and, after adjustments for age, sex, and APOE status, was significantly associated with disease (p = 0.0002, odds ratio [OR] = 2.13 [95% confidence interval (CI): 1.42–3.20]). An independent data set replicated the association (447 cases and 880 controls, p = 0.0117, OR = 1.65 [95% CI: 1.12–2.44]), and joint analysis increased the significance (p = 1.414 × 10−5, OR = 1.81 [95% CI: 1.38–2.37]). The deletion is common in AA cases (15.2%) and AA controls (9.74%), but in only 0.12% of our non-Hispanic white cohort. Whole exome sequencing of multiplex, CH families identified the deletion cosegregating with disease in a large sibship. The deleted allele produces a stable, detectable RNA strand and is predicted to result in a frameshift mutation (p.Arg578Alafs) that could interfere with protein function. Conclusions: This common ABCA7 deletion could represent an ethnic-specific pathogenic alteration in AD

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

A novel Alzheimer disease locus located near the gene encoding tau protein

APOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer’s Project (IGAP) Consortium in APOE ε4+ (10,352 cases and 9,207 controls) and APOE ε4- (7,184 cases and 26,968 controls) subgroups as well as in the total sample testing for interaction between a SNP and APOE ε4 status. Suggestive associations (P<1x10-4) in stage 1 were evaluated in an independent sample (stage 2) containing 4,203 subjects (APOE ε4+: 1,250 cases and 536 controls; APOE ε4-: 718 cases and 1,699 controls). Among APOE ε4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 datasets (best SNP, rs2732703, P=5·8x10-9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100 kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4- subjects (MS4A6A/MS4A4A/ MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significansignificantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6x10-7) is noteworthy because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P<1.3x10-8), frontal cortex (P<1.3x10-9), and temporal cortex (P<1.2x10-11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2x10-6) and temporal cortex (P=2.6x10-6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared to persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted