The Early Bird Catches The Term: Combining Twitter and News Data For Event Detection and Situational Awareness

Twitter updates now represent an enormous stream of information originating from a wide variety of formal and informal sources, much of which is relevant to real-world events. In this paper we adapt existing bio-surveillance algorithms to detect localised spikes in Twitter activity corresponding to real events with a high level of confidence. We then develop a methodology to automatically summarise these events, both by providing the tweets which fully describe the event and by linking to highly relevant news articles. We apply our methods to outbreaks of illness and events strongly affecting sentiment. In both case studies we are able to detect events verifiable by third party sources and produce high quality summaries

Why are feasibility studies accessing routinely collected health data? A systematic review

BACKGROUND: Feasibility trials are often undertaken to determine whether a larger randomised controlled trial (RCT) is achievable. In a recent review, 15 feasibility trials accessed routinely collected health data (RCHD) from UK national databases and registries. This paper looks at attributes of these trials and the reasons why they accessed RCHD. METHODS: We extracted data from all publicly available sources for the 15 feasibility studies found in a previous review of trials successfully accessing RCHD in the UK between 2013–2018 for the purpose of informing or supplementing participant data. We extracted trial characteristics, the registry accessed, and the way the RCHD was used. RESULTS: The 15 feasibility RCTs were conducted in a variety of disease areas, and were generally small (median sample size 100, range 41–4061) and individually randomised (60%, 9/15). The primary trial outcome was predominantly administrative (non-clinical) (80%, 12/15) such as feasibility of patient recruitment. They were more likely to recruit from secondary care (67%, 10/15) settings than primary (33%, 5/15). NHS Digital was the most commonly accessed registry (33% (5/15)) with SAIL databank (20% (3/15)), electronic Data Research and Innovation Service (eDRIS) and Paediatric Intensive Care Audit Network (PICANET) (each 13% 2/15) also being accessed. Where the information was clear, the trials used RCHD for data collection during the trial (47%, 7/15), follow-up after the trial (27%, 4/15) and recruitment (13%, 2/15). CONCLUSIONS: Between 2013 and 2018, 15 feasibility trials successfully accessed UK RCHD. Feasibility trials would benefit, as with other trials, from guidance on reporting the use of RCHD in protocols and publications

Outcomes following autologous hematopoietic stem cell transplant for patients with relapsed Wilms' tumor: a CIBMTR retrospective analysis.

Despite the marked improvement in the overall survival (OS) for patients diagnosed with Wilms' tumor (WT), the outcomes for those who experience relapse have remained disappointing. We describe the outcomes of 253 patients with relapsed WT who received high-dose chemotherapy (HDT) followed by autologous hematopoietic stem cell transplant (HCT) between 1990 and 2013, and were reported to the Center for International Blood and Marrow Transplantation Research. The 5-year estimates for event-free survival (EFS) and OS were 36% (95% confidence interval (CI); 29-43%) and 45% (95 CI; 38-51%), respectively. Relapse of primary disease was the cause of death in 81% of the population. EFS, OS, relapse and transplant-related mortality showed no significant differences when broken down by disease status at transplant, time from diagnosis to transplant, year of transplant or conditioning regimen. Our data suggest that HDT followed by autologous HCT for relapsed WT is well tolerated and outcomes are similar to those reported in the literature. As attempts to conduct a randomized trial comparing maintenance chemotherapy with consolidation versus HDT followed by stem cell transplant have failed, one should balance the potential benefits with the yet unknown long-term risks. As disease recurrence continues to be the most common cause of death, future research should focus on the development of consolidation therapies for those patients achieving complete response to therapy

The Genomic Signature of Crop-Wild Introgression in Maize

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies

Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology.

Trypanosoma cruzi, the flagellate protozoan agent of Chagas disease or American trypanosomiasis, is unable to synthesize sialic acids de novo. Mucins and trans-sialidase (TS) are substrate and enzyme, respectively, of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for T. cruzi life cycle. The acquisition of the sialyl residue allows the parasite to avoid lysis by serum factors and to interact with the host cell. A major drawback to studying the sialylation kinetics and turnover of the trypomastigote glycoconjugates is the difficulty to identify and follow the recently acquired sialyl residues. To tackle this issue, we followed an unnatural sugar approach as bioorthogonal chemical reporters, where the use of azidosialyl residues allowed identifying the acquired sugar. Advanced microscopy techniques, together with biochemical methods, were used to study the trypomastigote membrane from its glycobiological perspective. Main sialyl acceptors were identified as mucins by biochemical procedures and protein markers. Together with determining their shedding and turnover rates, we also report that several membrane proteins, including TS and its substrates, both glycosylphosphatidylinositol-anchored proteins, are separately distributed on parasite surface and contained in different and highly stable membrane microdomains. Notably, labeling for α(1,3)Galactosyl residues only partially colocalize with sialylated mucins, indicating that two species of glycosylated mucins do exist, which are segregated at the parasite surface. Moreover, sialylated mucins were included in lipid-raft-domains, whereas TS molecules are not. The location of the surface-anchored TS resulted too far off as to be capable to sialylate mucins, a role played by the shed TS instead. Phosphatidylinositol-phospholipase-C activity is actually not present in trypomastigotes. Therefore, shedding of TS occurs via microvesicles instead of as a fully soluble form

A simple method for estimating relative risk using logistic regression

<p>Abstract</p> <p>Background</p> <p>Odds ratios (OR) significantly overestimate associations between risk factors and common outcomes. The estimation of relative risks (RR) or prevalence ratios (PR) has represented a statistical challenge in multivariate analysis and, furthermore, some researchers do not have access to the available methods. Objective: To propose and evaluate a new method for estimating RR and PR by logistic regression.</p> <p>Methods</p> <p>A provisional database was designed in which events were duplicated but identified as non-events. After, a logistic regression was performed and effect measures were calculated, which were considered RR estimations. This method was compared with binomial regression, Cox regression with robust variance and ordinary logistic regression in analyses with three outcomes of different frequencies.</p> <p>Results</p> <p>ORs estimated by ordinary logistic regression progressively overestimated RRs as the outcome frequency increased. RRs estimated by Cox regression and the method proposed in this article were similar to those estimated by binomial regression for every outcome. However, confidence intervals were wider with the proposed method.</p> <p>Conclusion</p> <p>This simple tool could be useful for calculating the effect of risk factors and the impact of health interventions in developing countries when other statistical strategies are not available.</p

CD98hc facilitates B cell proliferation and adaptive humoral immunity.

The proliferation of antigen-specific lymphocytes and resulting clonal expansion are essential for adaptive immunity. We report here that B cell-specific deletion of the heavy chain of CD98 (CD98hc) resulted in lower antibody responses due to total suppression of B cell proliferation and subsequent plasma cell formation. Deletion of CD98hc did not impair early B cell activation but did inhibit later activation of the mitogen-activated protein kinase Erk1/2 and downregulation of the cell cycle inhibitor p27. Reconstitution of CD98hc-deficient B cells with CD98hc mutants showed that the integrin-binding domain of CD98hc was required for B cell proliferation but that the amino acid-transport function of CD98hc was dispensable for this. Thus, CD98hc supports integrin-dependent rapid proliferation of B cells. We propose that the advantage of adaptive immunity favored the appearance of CD98hc in vertebrates