Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to (...) genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50, which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1, showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED. (shrink)

Interaction is the cornerstone of the online world. Most Americans converse with known and unknown others online every day, on social media sites, blogs, and after stories on news sites. While many...

Interaction is the cornerstone of the online world. Most Americans converse with known and unknown others online every day, on social media sites, blogs, and after stories on news sites. While many...

The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different (...) research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge. (shrink)

Indonesia and Taiwan are two countries that have been affected by the tourism sector, although with different policies to control the COVID-19 pandemic. Taiwan is known as a country with pandemic policies that have been recognized around the world, although it has a high vulnerability to experiencing a high number of infections due to its geographical and political position close to the source of the pandemic. On the other hand, Indonesia is known for its controversial pandemic management and control policies. (...) Indonesia and Taiwan have carried out various public policies to increase tourism activities during the pandemic, such as accelerating vaccination in tourist areas and for tourists, as well as various other stimuli to stimulate tourism. The debate over vaccination raises questions about attitudes toward vaccines in society. The lack of clarity on psychosocial and political conditions creates confusion among the public in perceiving the COVID-19 pandemic and in perceiving the risks of traveling. This can affect people's attitudes toward vaccines, travel anxiety, and travel intentions. This study aims to analyze traveling intention due to the COVID-19 pandemic through COVID-19 Risk Perception, Fear of COVID-19, Risk Perception to Travel, Vaccine Attitude, and Fear to Travel. The research in Indonesia involved 358 respondents while the research in Taiwan involved 283 respondents. The research analysis used multiple regression and simple linear regression to ascertain the role of each association. The results showed that the travel intention of Indonesian tourists was formed from the direct and indirect roles of covid 19 risk perception, fear of covid 19, risk perception to travel, vaccine attitude, and fear to travel. Meanwhile, the travel intention of Taiwanese tourists is not influenced by a fear of covid. The travel intention model of Taiwanese tourists is formed from the direct and indirect roles of covid 19 risk perception, risk perception to travel, vaccine attitude, and fear to travel. This research contributes to tourism risk management in the face of pandemics, particularly in terms of government policies that can reduce tourism anxiety to travel during disasters. (shrink)

_Parallax_ is an international, peer-reviewed journal that aims towards a critical engagement with the production of culture and knowledge. The journal explores a wide range of cultural practices, reconfiguring the production and understanding of culture as well as the relation between theory and practice itself. This text brings together scholars from a number of different theoretical backgrounds to consider the ethical and political processes involved in witnessing, and the possible limits of theory in some situations. Contributors include J.M. Bernstein, Kelly (...) Oliver, Griselda Pollock, Laurence Rickels, Avital Ronell and Hayden White. (shrink)

The Restoration settlement, the political backcloth to Aubrey's essay, proceeded in two stages. The first, in, saw the rehabilitation of the King and the ...

Many have thought that there is a problem with causal commerce between immaterial souls and material bodies. In Physicalism or Something Near Enough, Jaegwon Kim attempts to spell out that problem. Rather than merely posing a question or raising a mystery for defenders of substance dualism to answer or address, he offers a compelling argument for the conclusion that immaterial souls cannot causally interact with material bodies. We offer a reconstruction of that argument that hinges on two premises: Kim’s Dictum (...) and the Nowhere Man principle. Kim’s Dictum says that causation requires a spatial relation. Nowhere Man says that souls can’t be in space. By our lights, both premises can be called into question. We’ll begin our evaluation of the argument by pointing out some consequences of Kim’s Dictum. For some, these will be costs. We will then present two defeaters for Kim’s Dictum and a critical analysis of Kim’s case for Nowhere Man. The upshot is that Kim’s argument against substance dualism fails. (shrink)

Author Aubrey Neal suggests that one of these issues that lingers with us today is scepticism, and in 'How Skeptics do Ethics', he unravels the thread of this philosophy from its origins in enlightenment thinking down to our present age.

Empathy is a form of emotionally charged imaginative perspective‐taking. It is also the unique source of a particular form of understanding, which I will call humane understanding. Humane understanding consists in the direct apprehension of the intelligibility of others’ emotions. This apprehension is an epistemic good whose ethical significance is multifarious. In this paper, I focus on elaborating the sense in which humane understanding of others is non‐instrumentally valuable to its recipients. People have a complex but profound need to be (...) humanely understood. Because we respond to others’ very real need when we pursue this sort of understanding of their emotions, empathy is best understood as itself a way of caring, rather than just a means to promote other caring behavior. (shrink)

The attention paid to the influence of organizational philanthropy on consumer responses has precipitated a shift in the role this practice plays in organizational dynamics—with philanthropy becoming an increasingly strategic marketing tool. The authors develop and test a model predicting that: (1) perceived organizational credibility will mediate the relationship between awareness of philanthropy and the outcomes of advocacy and financial sacrifice; (2) consumer social consciousness will moderate the relationship between awareness of philanthropy and firm credibility, and between credibility and the (...) outcome variables; and (3) these moderated relationships will be mediated by perceived credibility. Data obtained from a sample of professional golf patrons support our assertions. Notably, the findings implicate perceived credibility as a key intervening variable in the hypothesized relationships for the PGA Tour. (shrink)

An accessible guide to the theories of 19 major educational thinkers, the strengths and limitations of their ideas, their relevance today and how they can be used in the classroom and other educational settings.

If the argument of this short study is sound, we have here a point of view which needs to be borne in mind as an aid to the solution of, not only textual and literary problems, but even more those problems which are associated with the attempt to employ such terms as 'polytheism' and 'monotheism' in connexion with Israelite thought, and also those which are inherent in the question of the prophetic psychology or, again, that of revelation. It may also (...) be argued that along this line we gain a new approach to the New Testament extension of Jewish Monotheism in the direction of the later Trinitarianism. . . . At any rate, we can see how it was possible for a Jewish Christian to relate his Messiah so closely with the divine Being as to afford a basis for the later (and Greek) metaphysical formulation of the doctrine of the Trinity. --from the author's conclusions. (shrink)

A sensibility is, on a rough first pass, an emotional orientation to the world. It shapes how things appear to us, evaluatively speaking. By transfiguring things’ evaluative appearances, a change in sensibility can profoundly alter one’s overall experience of the world. I argue that some forms of sensibility change entail (1) risking one’s knowledge of what experiences imbued with one’s prior sensibility were like, and (2) surrendering one’s grasp on the intelligibility of one’s prior emotional apprehensions. These costs have consequences (...) for Laurie Paul’s ‘problem of transformative experience.’ Paul has argued that when we are poised to become someone new, our inexperience generates problems for authentic choice about our own futures. By reckoning with the epistemic losses involved in sensibility change, I show that this problem must not be confined to novel transformations. Prior experience does not guarantee the knowledge or understanding necessary for choosing authentically (in Paul’s sense). If the problem Paul highlights is indeed a problem _at all,_ then, it is a still more pervasive and intractable one than it has been taken to be. (shrink)

Pronouns often convey information about a person’s social identity (e.g., gender). Consequently, pronouns have become a focal point in academic and public debates about whether pronouns should be changed to be more inclusive, such as for people whose identities do not fit current pronoun conventions (e.g., gender non-binary individuals). Here, we make an empirical contribution to these debates by investigating which social identities lay speakers think that pronouns should encode and why. Across four studies, participants were asked to evaluate different (...) types of real and hypothetical pronouns, including binary gender pronouns, race pronouns, and identity-neutral pronouns. We sampled participants from two languages with different pronoun systems: English (N = 1,120) and Turkish (N = 260). English pronouns commonly denote binary gender (e.g., he for men), whereas Turkish pronouns are identity-neutral (e.g., o for anyone). Participants’ reasoning about pronouns reflected both a familiarity preference (i.e., participants preferred the pronoun type used in their language) and—critically—participants’ social ideologies. In both language contexts, participants’ ideological beliefs that social groups are inherently distinct (essentialism) and should be hierarchal (social dominance orientation) predicted relatively greater endorsement of binary gender pronouns and race pronouns. A preregistered experimental study with an English-speaking sample showed that the relationship between ideology and pronoun endorsement is causal: Ideologies shape attitudes toward pronouns. Together, the present research contributes to linguistic and psychological theories concerning how people reason about language and informs policy-relevant questions about whether and how to implement language changes for social purposes. (shrink)

Digital artifacts — humanly-constructed items that inhabit our computers and networks — suffer an unfortunate reputation as being virtual and therefore unreal, and all too easy to reproduce on the cheap. These features together prompt the question of this article: if digital artifacts can be reproduced for free, and if they are unreal, why do they have economic value at all? Using a focal case study of bitcoin — the most unreal digital artifact of them all, and one that has (...) been copied and pasted a thousand times over — I answer the question. Some digital artifacts can't be copied on the cheap, as it turns out, and they are real enough to be useful. (shrink)

Abstract: If anger is the emotion of injustice, and if most injustices have prominent epistemic dimensions, then where is the anger in epistemic injustice? Despite the question my task is not to account for the lack of attention to anger in epistemic injustice discussions. Instead, I argue that a particular texture of transformative anger – a knowing resistant anger – offers marginalized knowers a powerful resource for countering epistemic injustice. I begin by making visible the anger that saturates the silences (...) that epistemic injustices repeatedly manufacture and explain the obvious: silencing practices produce angry experiences. I focus on tone policing and tone vigilance to illustrate the relationship between silencing and angry knowledge management. Next, I use María Lugones’s pluralist account of anger to bring out the epistemic dimensions of knowing resistant anger in a way that also calls attention to their histories and felt textures. The final section draws on feminist scholarship about the transformative power of angry knowledge to suggest how it might serve as a resource for resisting epistemic injustice. (shrink)

There are predicates and subjects. It is thus tempting to think that there are properties on the one hand, and things that have them on the other. I have no quarrel with this thought; it is a fine place to begin a theory of properties and property-having. But in this paper, I argue that one such theory—bare particularism—is false. I pose a dilemma. Either bare particulars instantiate the properties of their host substances or they do not. If they do not, (...) then bare particularism is both unmotivated and false. If they do, then the view faces a problematic—and, I shall argue, false—crowding consequence. (shrink)

Materialists about human persons think that we are material through and through—wholly material beings. Those who endorse materialism more widely think that everything is material through and through. But what is it to be wholly material? In this article, I answer that question. I identify and defend a definition or analysis of ‘wholly material’.

We develop a new puzzle concerning a material being's relationship to the smallest parts of the material world. In particular, we investigate how a being could be responsible for anything if its be...