63 research outputs found
CiteSee: Augmenting Citations in Scientific Papers with Persistent and Personalized Historical Context
When reading a scholarly article, inline citations help researchers
contextualize the current article and discover relevant prior work. However, it
can be challenging to prioritize and make sense of the hundreds of citations
encountered during literature reviews. This paper introduces CiteSee, a paper
reading tool that leverages a user's publishing, reading, and saving activities
to provide personalized visual augmentations and context around citations.
First, CiteSee connects the current paper to familiar contexts by surfacing
known citations a user had cited or opened. Second, CiteSee helps users
prioritize their exploration by highlighting relevant but unknown citations
based on saving and reading history. We conducted a lab study that suggests
CiteSee is significantly more effective for paper discovery than three
baselines. A field deployment study shows CiteSee helps participants keep track
of their explorations and leads to better situational awareness and increased
paper discovery via inline citation when conducting real-world literature
reviews
Scim: Intelligent Skimming Support for Scientific Papers
Researchers need to keep up with immense literatures, though it is
time-consuming and difficult to do so. In this paper, we investigate the role
that intelligent interfaces can play in helping researchers skim papers, that
is, rapidly reviewing a paper to attain a cursory understanding of its
contents. After conducting formative interviews and a design probe, we suggest
that skimming aids should aim to thread the needle of highlighting content that
is simultaneously diverse, evenly-distributed, and important. We introduce
Scim, a novel intelligent skimming interface that reifies this aim, designed to
support the skimming process by highlighting salient paper contents to direct a
skimmer's focus. Key to the design is that the highlights are faceted by
content type, evenly-distributed across a paper, with a density configurable by
readers at both the global and local level. We evaluate Scim with an in-lab
usability study and deployment study, revealing how skimming aids can support
readers throughout the skimming experience and yielding design considerations
and tensions for the design of future intelligent skimming tools
Beyond Summarization: Designing AI Support for Real-World Expository Writing Tasks
Large language models have introduced exciting new opportunities and
challenges in designing and developing new AI-assisted writing support tools.
Recent work has shown that leveraging this new technology can transform writing
in many scenarios such as ideation during creative writing, editing support,
and summarization. However, AI-supported expository writing--including
real-world tasks like scholars writing literature reviews or doctors writing
progress notes--is relatively understudied. In this position paper, we argue
that developing AI supports for expository writing has unique and exciting
research challenges and can lead to high real-world impacts. We characterize
expository writing as evidence-based and knowledge-generating: it contains
summaries of external documents as well as new information or knowledge. It can
be seen as the product of authors' sensemaking process over a set of source
documents, and the interplay between reading, reflection, and writing opens up
new opportunities for designing AI support. We sketch three components for AI
support design and discuss considerations for future research.Comment: 3 pages, 1 figure, accepted by The Second Workshop on Intelligent and
Interactive Writing Assistant
Transitional cylindrical swirling flow in presence of a flat free surface
This article is devoted to the study of an incompressible viscous flow of a
fluid partly enclosed in a cylindrical container with an open top surface and
driven by the constant rotation of the bottom wall. Such type of flows belongs
to a group of recirculating lid-driven cavity flows with geometrical
axisymmetry and of the prescribed boundary conditions of Dirichlet type --
no-slip on the cavity walls. The top surface of the cylindrical cavity is left
open with an imposed stress-free boundary condition, while a no-slip condition
with a prescribed rotational velocity is imposed on the bottom wall. The
Reynolds regime corresponds to transitional flows with some incursions in the
fully laminar regime. The approach taken here revealed new flow states that
were investigated based on a fully three-dimensional solution of the
Navier--Stokes equations for the free-surface cylindrical swirling flow,
without resorting to any symmetry property unlike all other results available
in the literature. Theses solutions are obtained through direct numerical
simulations based on a Legendre spectral element method.Comment: Computers and Fluids, In Pres
The Semantic Reader Project: Augmenting Scholarly Documents through AI-Powered Interactive Reading Interfaces
Scholarly publications are key to the transfer of knowledge from scholars to
others. However, research papers are information-dense, and as the volume of
the scientific literature grows, the need for new technology to support the
reading process grows. In contrast to the process of finding papers, which has
been transformed by Internet technology, the experience of reading research
papers has changed little in decades. The PDF format for sharing research
papers is widely used due to its portability, but it has significant downsides
including: static content, poor accessibility for low-vision readers, and
difficulty reading on mobile devices. This paper explores the question "Can
recent advances in AI and HCI power intelligent, interactive, and accessible
reading interfaces -- even for legacy PDFs?" We describe the Semantic Reader
Project, a collaborative effort across multiple institutions to explore
automatic creation of dynamic reading interfaces for research papers. Through
this project, we've developed ten research prototype interfaces and conducted
usability studies with more than 300 participants and real-world users showing
improved reading experiences for scholars. We've also released a production
reading interface for research papers that will incorporate the best features
as they mature. We structure this paper around challenges scholars and the
public face when reading research papers -- Discovery, Efficiency,
Comprehension, Synthesis, and Accessibility -- and present an overview of our
progress and remaining open challenges
Retinoic acid regulates avian lung branching through a molecular network
Retinoic acid (RA) is of major importance during vertebrate embryonic development and its levels need to be strictly regulated otherwise congenital malformations will develop. Through the action of specific nuclear receptors, named RAR/RXR, RA regulates the expression of genes that eventually influence proliferation and tissue patterning. RA has been described as crucial for different stages of mammalian lung morphogenesis, and as part of a complex molecular network that contributes to precise organogenesis; nonetheless, nothing is known about its role in avian lung development. The current report characterizes, for the first time, the expression pattern of RA signaling members (stra6, raldh2, raldh3, cyp26a1, rar alpha, and rar beta) and potential RA downstream targets (sox2, sox9, meis1, meis2, tgf beta 2, and id2) by in situ hybridization. In the attempt of unveiling the role of RA in chick lung branching, in vitro lung explants were performed. Supplementation studies revealed that RA stimulates lung branching in a dose-dependent manner. Moreover, the expression levels of cyp26a1, sox2, sox9, rar beta, meis2, hoxb5, tgf beta 2, id2, fgf10, fgfr2, and shh were evaluated after RA treatment to disclose a putative molecular network underlying RA effect. In situ hybridization analysis showed that RA is able to alter cyp26a1, sox9, tgf beta 2, and id2 spatial distribution; to increase rar beta, meis2, and hoxb5 expression levels; and has a very modest effect on sox2, fgf10, fgfr2, and shh expression levels. Overall, these findings support a role for RA in the proximal-distal patterning and branching morphogenesis of the avian lung and reveal intricate molecular interactions that ultimately orchestrate branching morphogenesis.The authors would like to thank Ana Lima
for slide sectioning and Rita Lopes for contributing to the initiation
of this project. This work has been funded by FEDER funds,
through the Competitiveness Factors Operational Programme
(COMPETE), and by National funds, through the Foundation for
Science and Technology (FCT), under the scope of the Project
POCI-01-0145-FEDER-007038; and by the Project NORTE-01-0145-
FEDER-000013, supported by the Northern Portugal Regional Operational
Programme (NORTE 2020), under the Portugal 2020 Partnership
Agreement, through the European Regional Development Fund
(FEDER). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio
The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study
Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to similar to 2.8M SNPs with BMI and WHRadjBMI in four strata (men <= 50y, men > 50y, women <= 50y, women > 50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR< 5%) age-specific effects, of which 11 had larger effects in younger (< 50y) than in older adults (>= 50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may providefurther insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.</p
The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape : A Large-Scale Genome-Wide Interaction Study
Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to similar to 2.8M SNPs with BMI and WHRadjBMI in four strata (men 50y, women 50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR= 50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may providefurther insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.Peer reviewe
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