Factorized Graph Representations for Semi-Supervised Learning from Sparse Data

Node classification is an important problem in graph data management. It is commonly solved by various label propagation methods that work iteratively starting from a few labeled seed nodes. For graphs with arbitrary compatibilities between classes, these methods crucially depend on knowing the compatibility matrix that must be provided by either domain experts or heuristics. Can we instead directly estimate the correct compatibilities from a sparsely labeled graph in a principled and scalable way? We answer this question affirmatively and suggest a method called distant compatibility estimation that works even on extremely sparsely labeled graphs (e.g., 1 in 10,000 nodes is labeled) in a fraction of the time it later takes to label the remaining nodes. Our approach first creates multiple factorized graph representations (with size independent of the graph) and then performs estimation on these smaller graph sketches. We define algebraic amplification as the more general idea of leveraging algebraic properties of an algorithm's update equations to amplify sparse signals. We show that our estimator is by orders of magnitude faster than an alternative approach and that the end-to-end classification accuracy is comparable to using gold standard compatibilities. This makes it a cheap preprocessing step for any existing label propagation method and removes the current dependence on heuristics.Comment: SIGMOD 2020 (Extended version

The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia.

The study of long noncoding RNAs (lncRNAs) is an emerging area of cancer research, in part due to their ability to serve as disease biomarkers. However, few studies have investigated lncRNAs in chronic lymphocytic leukemia (CLL). We have identified one particular lncRNA, treRNA, which is overexpressed in CLL B-cells. We measured transcript expression in 144 CLL patient samples and separated samples into high or low expression of treRNA relative to the overall median. We found that high expression of treRNA is significantly associated with shorter time to treatment. High treRNA also correlates with poor prognostic indicators such as unmutated IGHV and high ZAP70 protein expression. We validated these initial findings in samples collected in a clinical trial comparing the nucleoside analog fludarabine alone or in combination with the alkylating agent cyclophosphamide in untreated CLL samples collected prior to starting therapy (E2997). High expression of treRNA was independently prognostic for shorter progression free survival in patients receiving fludarabine plus cyclophosphamide. Given these results, in order to study the role of treRNA in DNA damage response we generated a model cell line system where treRNA was over-expressed in the human B-CLL cell line OSU-CLL. Relative to the vector control line, there was less cell death in OSU-CLL over-expressing treRNA after exposure to fludarabine and mafosfamide, due in part to a reduction in DNA damage. Therefore, we suggest that treRNA is a novel biomarker in CLL associated with aggressive disease and poor response to chemotherapy through enhanced protection against cytotoxic mediated DNA damage

The Spiderweb galaxy: a forming massive cluster galaxy at z~2

We present a deep image of the radio galaxy MRC 1138-262 taken with the Hubble Space Telescope (HST) at a redshift of z = 2.2. The galaxy is known to have properties of a cD galaxy progenitor and be surrounded by a 3 Mpc-sized structure, identified with a protocluster. The morphology shown on the new deep HST/ACS image is reminiscent of a spider's web. More than 10 individual clumpy features are observed, apparently star-forming satellite galaxies in the process of merging with the progenitor of a dominant cluster galaxy 11 Gyr ago. There is an extended emission component, implying that star formation was occurring over a 50 times 40 kpc region at a rate of more than 100 M_sun/yr. A striking feature of the newly named ``Spiderweb galaxy'' is the presence of several faint linear galaxies within the merging structure. The dense environments and fast galaxy motions at the centres of protoclusters may stimulate the formation of these structures, which dominate the faint resolved galaxy populations in the Hubble Ultra Deep Field. The new image provides a unique testbed for simulations of forming dominant cluster galaxies.Comment: 5 pages, 2 figures (reduced to grayscale); ApJ Letter

Adaptation of the Structured Clinical Interview for DSM-IV Disorders for assessing depression in women during pregnancy and post-partum across countries and cultures

BackgroundTo date, no study has used standardised diagnostic assessment procedures to determine whether rates of perinatal depression vary across cultures.AimsTo adapt the Structured Clinical Interview for DSM–IV Disorders (SCID) for assessing depression and other non-psychotic psychiatric illness perinatally and to pilot the instrument in different centres and cultures.MethodAssessments using the adapted SCID and the Edinburgh Postnatal Depression Scale were conducted during the third trimester of pregnancy and at 6 months postpartum with 296 women from ten sites in eight countries. Point prevalence rates during pregnancy and the postnatal period and adjusted 6-month period prevalence rates were computed for caseness, depression and major depression.ResultsThe third trimester and 6-month point prevalence rates for perinatal depression were 6.9% and 8.0%, respectively. Postnatal 6-month period prevalence rates for perinatal depression ranged from 2.1% to 31.6% across centres and there were significant differences in these rates between centres.ConclusionsStudy findings suggest that the SCID was successfully adapted for this context. Further research on determinants of differences inprevalence of depression across cultures isneeded

The Hubble Space Telescope Extragalactic Distance Scale Key Project. X. The Cepheid Distance to NGC 7331

The distance to NGC 7331 has been derived from Cepheid variables observed with HST/WFPC2, as part of the Extragalactic Distance Scale Key Project. Multi-epoch exposures in F555W (V) and F814W (I), with photometry derived independently from DoPHOT and DAOPHOT/ALLFRAME programs, were used to detect a total of 13 reliable Cepheids, with periods between 11 and 42 days. The relative distance moduli between NGC 7331 and the LMC, imply an extinction to NGC 7331 of A_V = 0.47+-0.15 mag, and an extinction-corrected distance modulus to NGC 7331 of 30.89+-0.14(random) mag, equivalent to a distance of 15.1 Mpc. There are additional systematic uncertainties in the distance modulus of +-0.12 mag due to the calibration of the Cepheid Period-Luminosity relation, and a systematic offset of +0.05+-0.04 mag if we applied the metallicity correction inferred from the M101 results of Kennicutt et al 1998.Comment: To be published in The Astrophysical Journal, 1998 July 1, v501 note: Figs 1 and 2 (JPEG files) and Fig 7 (multipage .eps file) need to be viewed/printed separatel

Microcystin aids in cold temperature acclimation: Differences between a toxic Microcystis wildtype and non-toxic mutant

For Microcystis aeruginosa PCC 7806, temperature decreases from 26 °C to 19 °C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin provided M. aeruginosa PCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, reactive oxygen species damage, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strain M. aeruginosa PCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19 °C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e., making microcystin) vs the shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents

Impressions of sexual unfaithfulness and their accuracy show a degree of universality

his research was supported by the Australian Research Council (ARC) Centre of Excellence in Cognition and its Disorders (CE110001021) and an ARC Discovery Outstanding Researcher Award to GR (DP130102300), an ARC Discovery project to GR and CS (DP170104602) and an ARC Professorial Fellowship to LS (DP110104594). The funders had no influence on the research.Peer reviewedPublisher PD

Comorbid health conditions and their impact on social isolation, loneliness, quality of life, and well-being in people with dementia: longitudinal findings from the IDEAL programme

BackgroundMost people with dementia have multiple health conditions. This study explores (1) number and type of health condition(s) in people with dementia overall and in relation to age, sex, dementia type, and cognition; (2) change in number of health conditions over two years; and (3) whether over time the number of health conditions at baseline is related to social isolation, loneliness, quality of life, and/or well-being.MethodsLongitudinal data from the IDEAL (Improving the experience of Dementia and Enhancing Active Life) cohort were used. Participants comprised people with dementia (n = 1490) living in the community (at baseline) in Great Britain. Health conditions using the Charlson Comorbidity Index, cognition, social isolation, loneliness, quality of life, and well-being were assessed over two years. Mixed effects modelling was used.ResultsOn average participants had 1.8 health conditions at baseline, excluding dementia; increasing to 2.5 conditions over two years. Those with vascular dementia or mixed (Alzheimer’s and vascular) dementia had more health conditions than those with Alzheimer’s disease. People aged ≥ 80 had more health conditions than those aged < 65 years. At baseline having more health conditions was associated with increased loneliness, poorer quality of life, and poorer well-being, but was either minimally or not associated with cognition, sex, and social isolation. Number of health conditions had either minimal or no influence on these variables over time.ConclusionsPeople with dementia in IDEAL generally had multiple health conditions and those with more health conditions were lonelier, had poorer quality of life, and poorer well-being