Analyzing P300 Distractors for Target Reconstruction

P300-based brain-computer interfaces (BCIs) are often trained per-user and per-application space. Training such models requires ground truth knowledge of target and non-target stimulus categories during model training, which imparts bias into the model. Additionally, not all non-targets are created equal; some may contain visual features that resemble targets or may otherwise be visually salient. Current research has indicated that non-target distractors may elicit attenuated P300 responses based on the perceptual similarity of these distractors to the target category. To minimize this bias, and enable a more nuanced analysis, we use a generalized BCI approach that is fit to neither user nor task. We do not seek to improve the overall accuracy of the BCI with our generalized approach; we instead demonstrate the utility of our approach for identifying target-related image features. When combined with other intelligent agents, such as computer vision systems, the performance of the generalized model equals that of the user-specific models, without any user specific data.Comment: 4 pages, 3 figure

Assembly of Highly Asymmetric Genetically-Encoded Amphiphiles for Thermally Targeted Delivery of Therapeutics

<p>Traditional small molecule chemotherapeutics show limited effectiveness in the clinic as their poor pharmacokinetics lead to rapid clearance from circulation and their exposure to off-target tissues results in dose-limiting toxicity. The objective of this dissertation is to exploit a class of recombinant chimeric polypeptides (CPs) to actively target drugs to tumors as conjugation to macromolecular carriers has demonstrated improved efficacy by increasing plasma retention time, reducing uptake by healthy tissues, and enhancing tumor accumulation by exploiting the leaky vasculature and impaired lymphatic drainage characteristic of solid tumors. CPs consist of two principal components: (1) a thermally responsive elastin-like polypeptide (ELP) that displays a soluble-to-aggregate phase transition above a characteristic transition temperature (Tt); and (2) a cysteine-rich peptide fused to one end of the ELP to which small molecule therapeutics can be covalently attached (the conjugation domain). This work describes the development of CP drug-loaded nanoparticles that can be targeted to solid tumors by the external application of mild regional hyperthermia (39-43°C). </p><p>Highly repetitive ELP polymers were assembled by Plasmid Reconstruction Recursive Directional Ligation (PRe-RDL), in which two halves of a parent plasmid, each containing a copy of an oligomer, were ligated together to dimerize the oligomer and reconstitute the functional plasmid. Chimeric polypeptides were constructed by fusing the ELP sequence to a (CGG)8 conjugation domain, expressed in Escherichia coli, and loaded with small molecule hydrophobes through site specific attachment to the conjugation domain. Drug attachment induced the assembly of nanoparticles that retained the thermal responsiveness of the parent ELP in that they experienced a phase transition from soluble nanoparticles to an aggregated phase above their Tt. Importantly, the Tt of these nanoparticles was near-independent of the CP concentration and the structure of the conjugated molecule as long as it displayed an octanol-water distribution coefficient (LogD) > 1.5. </p><p>A series of CP nanoparticles with varying ratios of alanine and valine in the guest residue position was used to develop a quantitative model that described the CP transition temperature in terms of three variables - sequence, chain length, and concentration - and the model was used to identify CPs of varying molecular weights that displayed transition temperatures between 39°C and 43°C. A murine dorsal skin fold window chamber model using a human tumor xenograft was used to validate that only the thermoresponsive CP nanoparticles (and not the controls) exhibited a micelle-to-aggregate phase transition between 39-43°C in vivo. Furthermore, quantitative analysis of the biodistribution profile demonstrated that accumulation of these thermoresponsive CP nanoparticles was significantly enhanced by applying heat in a cyclical manner. It is hoped that this work will provide a helpful resource for the use of thermoresponsive CP nanoparticles in a variety of biomedical applications.</p>Dissertatio

Decoding Neural Activity to Assess Individual Latent State in Ecologically Valid Contexts

There exist very few ways to isolate cognitive processes, historically defined via highly controlled laboratory studies, in more ecologically valid contexts. Specifically, it remains unclear as to what extent patterns of neural activity observed under such constraints actually manifest outside the laboratory in a manner that can be used to make an accurate inference about the latent state, associated cognitive process, or proximal behavior of the individual. Improving our understanding of when and how specific patterns of neural activity manifest in ecologically valid scenarios would provide validation for laboratory-based approaches that study similar neural phenomena in isolation and meaningful insight into the latent states that occur during complex tasks. We argue that domain generalization methods from the brain-computer interface community have the potential to address this challenge. We previously used such an approach to decode phasic neural responses associated with visual target discrimination. Here, we extend that work to more tonic phenomena such as internal latent states. We use data from two highly controlled laboratory paradigms to train two separate domain-generalized models. We apply the trained models to an ecologically valid paradigm in which participants performed multiple, concurrent driving-related tasks. Using the pretrained models, we derive estimates of the underlying latent state and associated patterns of neural activity. Importantly, as the patterns of neural activity change along the axis defined by the original training data, we find changes in behavior and task performance consistent with the observations from the original, laboratory paradigms. We argue that these results lend ecological validity to those experimental designs and provide a methodology for understanding the relationship between observed neural activity and behavior during complex tasks

Collaborative Brain-Computer Interface for Human Interest Detection in Complex and Dynamic Settings

Humans can fluidly adapt their interest in complex environments in ways that machines cannot. Here, we lay the groundwork for a real-world system that passively monitors and merges neural correlates of visual interest across team members via Collaborative Brain Computer Interface (cBCI). When group interest is detected and co-registered in time and space, it can be used to model the task relevance of items in a dynamic, natural environment. Previous work in cBCIs focuses on static stimuli, stimulus- or response- locked analyses, and often within-subject and experiment model training. The contributions of this work are twofold. First, we test the utility of cBCI on a scenario that more closely resembles natural conditions, where subjects visually scanned a video for target items in a virtual environment. Second, we use an experiment-agnostic deep learning model to account for the real-world use case where no training set exists that exactly matches the end-users task and circumstances. With our approach we show improved performance as the number of subjects in the cBCI ensemble grows, and the potential to reconstruct ground-truth target occurrence in an otherwise noisy and complex environment.Comment: 6 pages, 6 figure

Publisher Correction: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Longitudinal landscapes of serum antibody repertoires after influenza infection and vaccination

Vaccination is the most effective means of infectious disease prevention. Despite its success, however, we still lack a clear understanding of vaccine responses in humans. For example, influenza vaccines still leave a large fraction of population vulnerable. Over the past decade, single B-cell analysis and next-generation sequencing (NGS) technologies have become invaluable tools for studying the antibody repertoire to influenza. Such studies have led to discoveries of broadly-neutralizing antibodies (bNAbs), which can neutralize across multiple strains of influenza virus, promoting the notion of designing a universal vaccine that will elicit such antibodies. One of such isolated bNAbs, called FI6, showed remarkable ability to neutralize all of the influenza A virus strains through targeting the conserved epitope in the stem of hemagglutinin (HA). However, it remains unclear whether such bNAbs actually play a role in conferring protection against influenza since antibody proteins (not B-cells) need to circulate at physiologically relevant concentrations in serum to have implications in protection. Using high-resolution proteomics coupled with NGS, we quantitatively determined the serological antibody repertoire to CA09 HA (H1) at the individual clonotype-level in a donor (whom FI6 was isolated from) following influenza infection (in 2010 with pandemic CA09) and vaccination across five years (2010-2014 with seasonal flu vaccine). We analyzed the temporal changes of head-targeting and stem-binding antibodies, illustrating the gradual increase of stem-targeting antibodies following repeated exposures to CA09 HA. Following vaccination in 2014, \u3e60% of the repertoire consisted of one single clonotype of stem-binding antibody that was present at very low abundance in 2010. Our data demonstrate that the repetitive exposure to influenza skews the serological repertoire toward antibodies that target conserved epitopes, and these antibodies continue to be boosted every time the same epitopes are encountered. Once elicited, stem-binding antibodies displayed a tendency to persist in serum across multiple years while head-specific antibodies decayed quicker. The differential longevity of stem-binding and head-specific antibodies presented here has direct implications for the design of the future universal vaccine

Persistent antibody clonotypes dominate the serum response to influenza following repeated vaccination over multiple years

We used Ig-Seq, a liquid chromatography tandem mass spectrometry (LC-MS/MS)–based serum antibody proteomics methodology, to determine the clonal composition and dynamics of the H1N1 California/7/2009 (CA09) hemagglutinin (HA)-reactive antibody repertoire over 5 years in a well-characterized donor from whom a large number of homosubtypic and heterosubtypic neutralizing monoclonal antibodies had been previously isolated by B cell analysis. The donor was infected with the CA09 strain in 2009 and immunized annually for the next five years with seasonal influenza vaccine which contained the CA09 strain. We find that the serological repertoire in this donor was highly static, with a modest number (24) of persistent antibody clonotypes, detected in serum for at least 4 out of 5 years, accounting on average for 72.6 ± 10.0% of the repertoire to the CA09 HA. These persistent antibodies: (i) displayed a higher degree of somatic hypermutation relative to antibodies that could be detected in the serum transiently (i.e. lasted less than 1 year in serum); (ii) comprised a significant fraction that also bound to HA from a phylogenetically distant H5N1 A/Vietnam/1203/2004 (VT04) strain, a hallmark of stem-binding antibodies due to the lack of homology between CA09 and VT04 in the head region of HA and (iii) perhaps most strikingly, but consistent with the wealth of heterosubtypic neutralizing antibodies that had previously been identified from this donor, some of the most abundant persistent antibody clonotypes, including the dominant clone that accounted on average for 18.6 ± 12.3% of the serum titer across 5 years, neutralized both the CA09 and VT04 influenza strains. Our analysis highlights the magnitude of ‘serological imprinting’ in the donor’s serum response to CA09, indicates that seasonal vaccination can further reinforce a stable serological memory and finally suggests that once elicited, antibodies cross-reactive between CA09 and VT04 with heterosubtypic neutralization activity, thus likely to bind to HA-stem, can persist for many years, which is a fundamental goal of universal influenza vaccines

Molecular understanding of the serum antibody repertoires after seasonal influenza vaccination among different age cohorts

Numerous influenza vaccination studies based on bulk serology have indicated that the antibody responses to the vaccine markedly decrease in the elderly. However, whether such decline results from the changes in the overall quantity or the quality of the circulating antibodies in serum remains unknown. Utilizing novel antibody repertoire profiling technologies, combining tandem mass spectrometry (LC-MS/MS) and high-throughput sequencing, we investigated the influenza-specific serological repertoires of 10 donors ranging from 26 to 70 years old vaccinated with Fluzone® 2013-2014 and/or 2014-2015. In particular, we determined the serum antibodies that are specific to the H1 or H3 component of the vaccine or cross-reactive between the two (H1+H3) and examined their relative quantitative distributions. Our data indicate that the proportion of H1+H3 antibodies significantly increases in the elderly and that the somatic hypermutation rates of the influenza-specific antibodies are higher in the elderly. These results suggest that the repeated exposure to the different virus subtypes could have led to the prolonged selection of H1+H3 antibodies targeting highly conserved epitopes. To evaluate the potency of the antibodies circulating in different age groups, we recombinantly expressed a number of representative monoclonal antibodies isolated from the donors in different age groups for further characterizations. Overall, our analysis suggests that the influenza-specific repertoire in the elderly may converge toward shared epitopes but the quality of the antibodies can be superior in terms of cross-reactivity. However, because the antibody repertoire “shrinks” as we age while targeting more conserved epitopes across different influenza subtypes, it is possible that the elderly is particularly susceptible to significantly altered strains. Collectively, profiling vaccine induced serological repertoires among different age cohorts can provide unprecedented insights regarding humoral immunity associated with age and a potential explanation for the vulnerability of the elderly

The Possibility Principle And The Truthmakers For Modal Truths

A necessary part of David Armstrong’s account of truthmakers for modal truths is his Possibility principle: any truthmaker for a contingent truth is also a truthmaker for the possibility of the complement of that contingent truth (if T makes p true and p is contingent, then T makes }*p true). I criticize Armstrong’s Possibility principle for two reasons. First, his argument for the Possibility principle both relies on an unwarranted generalization and vitiates his desire for relevant truthmakers. His argument undercuts relevant truthmakers by entailing that each contingent being is a truthmaker for all modal truths. Second, even if the argument seems successful, the Possibility principle is subject to counterexamples. Armstrong’s being composed of more than fifty atoms makes it true that something composed of more than fifty atoms exists and that truth is contingent, but his being composed of more than fifty atoms does not make it true that it is possible that it is not the case that something composed of more than fifty atoms exists

Control of aggregation temperatures in mixed and blended cytocompatible thermoresponsive block co-polymer nanoparticles

A small library of thermoresponsive amphiphilic copolymers based on polylactide-block-poly((2-(2-methoxyethoxy)ethyl methacrylate)-co-(oligoethylene glycol methacrylate)) (PLA-b-P(DEGMA)-co-(OEGMA)), was synthesised by copper-mediated controlled radical polymerisation (CRP) with increasing ratios of OEGMA:DEGMA. These polymers were combined in two ways to form nanoparticles with controllable thermal transition temperatures as measured by particle aggregation. The first technique involved the blending of two (PLA-b-P(DEGMA)-co-(OEGMA)) polymers together prior to assembling NPs. The second method involved mixing pre-formed nanoparticles of single (PLA-b-P(DEGMA)-co-(OEGMA)) polymers. The observed critical aggregation temperature Tt did not change in a linear relationship with the ratios of each copolymer either in the nanoparticles blended from different copolymers or in the mitures of pre-formed nanoparticles. However, where co-polymer mixtures were based on (OEG)9MA ratios within 5-10 mole% , a linear relationship between (OEG)9MA composition in the blends and Tt was obtained. The data suggest that OEGMA-based copolymers are tunable over a wide temperature range given suitable co-monomer content in the linear polymers or nanoparticles. Moreover, the thermal transitions of the nanoparticles were reversible and repeatable, with the cloud point curves being essentially invariant across at least three heating and cooling cycles, and a selected nanoparticle formulation was found to be readily endocytosed in representative cancer cells and fibroblasts