117 research outputs found
Lab-on-a-chip workshop activities for secondary school students
The ability to engage and inspire younger generations in novel areas of science is important for bringing new researchers into a burgeoning field, such as lab-on-a-chip. We recently held a lab-on-a-chip workshop for secondary school students, for which we developed a number of hands-on activities that explained various aspects of microfluidic technology, including fabrication (milling and moulding of microfluidic devices, and wax printing of microfluidic paper-based analytical devices, so-called μPADs), flow regimes (gradient formation via diffusive mixing), and applications (tissue analysis and μPADs). Questionnaires completed by the students indicated that they found the workshop both interesting and informative, with all activities proving successful, while providing feedback that could be incorporated into later iterations of the event
Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries.
Melioidosis was first identified in Myanmar in 1911 but for the last century it has remained largely unreported there. Burkholderia pseudomallei was first isolated from the environment of Myanmar in 2016, confirming continuing endemicity. Recent genomic studies showed that B. pseudomallei originated in Australia and spread to Asia, with phylogenetic evidence of repeated reintroduction of B. pseudomallei across countries bordered by the Mekong River and the Malay Peninsula. We present the first whole-genome sequences of B. pseudomallei isolates from Myanmar: nine clinical and seven environmental isolates. We used large-scale comparative genomics to assess the genetic diversity, phylogeography and potential origins of B. pseudomallei in Myanmar. Global phylogenetics demonstrated that Myanmar isolates group in two distantly related clades that reside in a more ancestral Asian clade with high amounts of genetic diversity. The diversity of B. pseudomallei from Myanmar and divergence within our global phylogeny suggest that the original introduction of B. pseudomallei to Myanmar was not a recent event. Our study provides new insights into global patterns of B. pseudomallei dissemination, most notably the dynamic nature of movement of B. pseudomallei within densely populated Southeast Asia. The role of anthropogenic influences in both ancient and more recent dissemination of B. pseudomallei to Myanmar and elsewhere in Southeast Asia and globally requires further study
The TESS-Keck Survey: Science Goals and Target Selection
Space-based transit missions such as Kepler and TESS have demonstrated that
planets are ubiquitous. However, the success of these missions heavily depends
on ground-based radial velocity (RV) surveys, which combined with transit
photometry can yield bulk densities and orbital properties. While most Kepler
host stars are too faint for detailed follow-up observations, TESS is detecting
planets orbiting nearby bright stars that are more amenable to RV
characterization. Here we introduce the TESS-Keck Survey (TKS), an RV program
using ~100 nights on Keck/HIRES to study exoplanets identified by TESS. The
primary survey aims are investigating the link between stellar properties and
the compositions of small planets; studying how the diversity of system
architectures depends on dynamical configurations or planet multiplicity;
identifying prime candidates for atmospheric studies with JWST; and
understanding the role of stellar evolution in shaping planetary systems. We
present a fully-automated target selection algorithm, which yielded 103 planets
in 86 systems for the final TKS sample. Most TKS hosts are inactive,
solar-like, main-sequence stars (4500 K < Teff < 6000 K) at a wide range of
metallicities. The selected TKS sample contains 71 small planets (Rp < 4 Re),
11 systems with multiple transiting candidates, 6 sub-day period planets and 3
planets that are in or near the habitable zone of their host star. The target
selection described here will facilitate the comparison of measured planet
masses, densities, and eccentricities to predictions from planet population
models. Our target selection software is publicly available (at
https://github.com/ashleychontos/sort-a-survey) and can be adapted for any
survey which requires a balance of multiple science interests within a given
telescope allocation.Comment: 23 pages, 10 figures, 5 table
The TESS-Keck Survey. XV. Precise Properties of 108 TESS Planets and Their Host Stars
We present the stellar and planetary properties for 85 TESS Objects of
Interest (TOIs) hosting 108 planet candidates which comprise the TESS-Keck
Survey (TKS) sample. We combine photometry, high-resolution spectroscopy, and
Gaia parallaxes to measure precise and accurate stellar properties. We then use
these parameters as inputs to a lightcurve processing pipeline to recover
planetary signals and homogeneously fit their transit properties. Among these
transit fits, we detect significant transit-timing variations among at least
three multi-planet systems (TOI-1136, TOI-1246, TOI-1339) and at least one
single-planet system (TOI-1279). We also reduce the uncertainties on
planet-to-star radius ratios across our sample, from a median
fractional uncertainty of 8.8 among the original TOI Catalog values to
3.0 among our updated results. With this improvement, we are able to
recover the Radius Gap among small TKS planets and find that the topology of
the Radius Gap among our sample is broadly consistent with that measured among
Kepler planets. The stellar and planetary properties presented here will
facilitate follow-up investigations of both individual TOIs and broader trends
in planet properties, system dynamics, and the evolution of planetary systems.Comment: Accepted at The Astronomical Journal; 21 pages, 9 figure
Physical Parameters of the Multiplanet Systems HD 106315 and GJ 9827
HD 106315 and GJ 9827 are two bright, nearby stars that host multiple super-Earths and sub-Neptunes discovered by K2 that are well suited for atmospheric characterization. We refined the planets' ephemerides through Spitzer transits, enabling accurate transit prediction required for future atmospheric characterization through transmission spectroscopy. Through a multiyear high-cadence observing campaign with Keck/High Resolution Echelle Spectrometer and Magellan/Planet Finder Spectrograph, we improved the planets' mass measurements in anticipation of Hubble Space Telescope transmission spectroscopy. For GJ 9827, we modeled activity-induced radial velocity signals with a Gaussian process informed by the Calcium II H&K lines in order to more accurately model the effect of stellar noise on our data. We measured planet masses of M_b = 4.87 ± 0.37 M_⊕, M_c = 1.92 ± 0.49 M_⊕, and M_d = 3.42 ± 0.62 M_⊕. For HD 106315, we found that such activity radial velocity decorrelation was not effective due to the reduced presence of spots and speculate that this may extend to other hot stars as well (T_(eff) > 6200 K). We measured planet masses of M_b = 10.5 ± 3.1 M_⊕ and M_c = 12.0 ± 3.8 M_⊕. We investigated all of the planets' compositions through comparison of their masses and radii to a range of interior models. GJ 9827 b and GJ 9827 c are both consistent with a 50/50 rock-iron composition, GJ 9827 d and HD 106315 b both require additional volatiles and are consistent with moderate amounts of water or hydrogen/helium, and HD 106315 c is consistent with a ~10% hydrogen/helium envelope surrounding an Earth-like rock and iron core
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
- …