ConStance: Modeling Annotation Contexts to Improve Stance Classification

Manual annotations are a prerequisite for many applications of machine learning. However, weaknesses in the annotation process itself are easy to overlook. In particular, scholars often choose what information to give to annotators without examining these decisions empirically. For subjective tasks such as sentiment analysis, sarcasm, and stance detection, such choices can impact results. Here, for the task of political stance detection on Twitter, we show that providing too little context can result in noisy and uncertain annotations, whereas providing too strong a context may cause it to outweigh other signals. To characterize and reduce these biases, we develop ConStance, a general model for reasoning about annotations across information conditions. Given conflicting labels produced by multiple annotators seeing the same instances with different contexts, ConStance simultaneously estimates gold standard labels and also learns a classifier for new instances. We show that the classifier learned by ConStance outperforms a variety of baselines at predicting political stance, while the model's interpretable parameters shed light on the effects of each context.Comment: To appear at EMNLP 201

Detecting Anomalously Similar Entities in Unlabeled Data

In this work, the goal is to detect closely-linked entities within a data set. The entities of interest have a tie causing them to be similar, such as a shared origin or a channel of influence. Given a collection of people or other entities with their attributes or behavior, we identify unusually similar pairs, and we pose the question: Are these two people linked, or can their similarity be explained by chance? Computing similarities is a core operation in many domains, but two constraints differentiate our version of the problem. First, the score assigned to a pair should account for the probability of a coincidental match. Second, no training data is provided; we must learn about the system from the unlabeled data and make reasonable assumptions about the linked pairs. This problem has applications to social network analysis, where it can be valuable to identify implicit relationships among people from indicators of coordinated activity. It also arises in situations where we must decide whether two similar observations correspond to two different entities or to the same entity observed twice. This dissertation explores how to assess such ties and, in particular, how the similarity scores should depend on not only the two entities in question but also properties of the entire data set. We develop scoring functions that incorporate both the similarity and rarity of a pair. Then, using these functions, we investigate the statistical power of a data set to reveal (or conceal) such pairs. In the dissertation, we develop generative models of linked pairs and independent entities and use them to derive scoring functions for pairs in three different domains: people with job histories, Gaussian-distributed points in Euclidean space, and people (or entities) in a bipartite affiliation graph. For the first, we present a case study in fraud detection that highlights the potential, as well as the complexities, of using these methods to address real-world problems. In the latter two domains, we develop an inference framework to estimate whether two entities were more likely generated independently or as a pair. In these settings, we analyze how the scoring function works in terms of similarity and rarity; how well it can detect pairs as a function of the data set; and how it differs from existing similarity functions when applied to real data

The Promise of the Dual Prevention Pill: A Framework for Development and Introduction

Women of reproductive age need multipurpose prevention technology (MPT) products to address two overlapping health risks: unintended pregnancy and HIV. Currently, condoms are the only available MPT, however male condoms are not within the control of a woman, and the use of female condoms has been limited by low acceptability and cost. Oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, yet uptake and adherence among women have been low to date. Women globally need more options for HIV and pregnancy prevention. Several MPTs for simultaneous HIV and pregnancy prevention are in various stages of development and clinical testing, although most are many years away from market launch. A dual prevention pill (DPP), a daily oral pill combining oral contraceptives and PrEP, both of which are licensed, approved products in many low- and middle-income countries (LMIC), is likely to be the fastest route to getting an MPT product into the hands of women. The DPP is one option that could enhance method choice, particularly for women who are already using oral contraceptives. By leveraging the oral contraceptive market and reaching women currently using condoms or with an unmet need for contraception, the DPP has the potential to increase the uptake of PrEP. The successful rollout of the DPP will require careful consideration of user-, provider-, and product-centered factors during product development and introduction. Early attention to these interrelated factors can help ensure that the DPP has the ideal characteristics for maximum product acceptability, that effective and quality services are designed and implemented, and that users can make informed choices, demand the product, and use it effectively. The proposed framework outlines key considerations for the effective development and introduction of the DPP, which could also facilitate integration models for future MPTs

Does size matter? A randomized controlled trial to assess the impact of external diameter on adherence to 3 different intravaginal rings among 24 US couples

Background: Intravaginal rings (IVRs) are being developed as multipurpose prevention technologies (MPTs) for simultaneous HIV and pregnancy prevention. However, no empirical data exists to support the current 54-58mm size as ideal. Understanding the impact of IVR size on adherence is critical for developing a product that can be used correctly and consistently. Methods: We conducted a randomized, open-label, 3-way crossover trial comparing adherence, preference, and acceptability of 3 non-medicated silicone IVRs of differing external diameters: 46mm, 56mm and 66mm. 24 couples in Atlanta, GA and Bronx, NY were randomized to the sequence of IVR use, used each continuously for ~30 days. The primary objective was to compare ring adherence, defined as never having the IVR out of the vagina for \u3e 30 minutes in 24h. Women reported occurrence and duration of expulsions and removals via daily text. We summarized the proportion of days the IVR was removed, expelled, or out all day, and the proportion of women adherent to each IVR. We used mixed methods logistic regression models with random intercepts (per participant) to compare the probability of each event happening per day of IVR use, per IVR. Results: 23/24 couples completed the study. 78%, 75% and 59% of participants were adherent to the IVRs of diameter 46mm, 56mm and 66mm respectively (Table 1). The 46mm and 66mm IVR performed similarly, with more expulsions and 24h outages for the 66mm IVR. When adjusting for size and sequence, women had \u3e 15 times the odds of the 66mm IVR being out all day versus the 56mm IVR (15.7, 95% CI: 3.4, 72.6). Conclusions: External diameter of these non-medicated IVRs had a significant impact on frequency of removal and expulsion. Product developers should prioritize IVRs in the range of 46mm-56mm

A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates

While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster ~one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly (or less frequent) booster vaccine, and as a primary vaccine for pediatric use including in infants

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Force of tuberculosis infection among adolescents in a high HIV and TB prevalence community: a cross-sectional observation study

BACKGROUND: Understanding of the transmission dynamics of tuberculosis (TB) in high TB and HIV prevalent settings is required in order to develop effective intervention strategies for TB control. However, there are little data assessing incidence of TB infection in adolescents in these settings. METHODS: We performed a tuberculin skin test (TST) and HIV survey among secondary school learners in a high HIV and TB prevalence community. TST responses to purified protein derivative RT23 were read after 3 days. HIV-infection was assessed using Orasure(R) collection device and ELISA testing. The results of the HIV-uninfected participants were combined with those from previous surveys among primary school learners in the same community, and force of TB infection was calculated by age. RESULTS: The age of 820 secondary school participants ranged from 13 to 22 years. 159 participants had participated in the primary school surveys. At a 10 mm cut-off, prevalence of TB infection among HIV-uninfected and first time participants, was 54% (n = 334/620). HIV prevalence was 5% (n = 40/816). HIV infection was not significantly associated with TST positivity (p = 0.07). In the combined survey dataset, TB prevalence was 45% (n = 645/1451), and was associated with increasing age and male gender. Force of infection increased with age, from 3% to 7.3% in adolescents [greater than or equal to]20 years of age. CONCLUSIONS: We show a high force of infection among adolescents, positively associated with increasing age. We postulate this is due to increased social contact with infectious TB cases. Control of the TB epidemic in this setting will require reducing the force of infection

Innate Immune Responses of Pulmonary Epithelial Cells to Burkholderia pseudomallei Infection

10.1371/journal.pone.0007308PLoS ONE410

Current Challenges for the Early Detection of Alzheimer's Disease: Brain Imaging and CSF Studies

The development of prevention therapies for Alzheimer's disease (AD) would greatly benefit from biomarkers that are sensitive to the subtle brain changes that occur in the preclinical stage of the disease. Reductions in the cerebral metabolic rate of glucose (CMRglc), a measure of neuronal function, have proven to be a promising tool in the early diagnosis of AD. In vivo brain 2-[18F]fluoro-2-Deoxy-D-glucose-positron emission tomography (FDG-PET) imaging demonstrates consistent and progressive CMRglc reductions in AD patients, the extent and topography of which correlate with symptom severity. There is increasing evidence that hypometabolism appears during the preclinical stages of AD and can predict decline years before the onset of symptoms. This review will give an overview of FDG-PET results in individuals at risk for developing dementia, including: presymptomatic individuals carrying mutations responsible for early-onset familial AD; patients with Mild Cognitive Impairment (MCI), often a prodrome to late-onset sporadic AD; non-demented carriers of the Apolipoprotein E (ApoE) ε4 allele, a strong genetic risk factor for late-onset AD; cognitively normal subjects with a family history of AD; subjects with subjective memory complaints; and normal elderly followed longitudinally until they expressed the clinical symptoms and received post-mortem confirmation of AD. Finally, we will discuss the potential to combine different PET tracers and CSF markers of pathology to improve the early detection of AD