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- Ahrer, E., et al.
(author)
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Atmospheric characterization and tighter constraints on the orbital misalignment of WASP-94 A b with HARPS
- 2024
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In: Monthly notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 530:3, s. 2749-2759
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Journal article (peer-reviewed)abstract
- We present high spectral resolution observations of the hot Jupiter WASP-94 A b using the HARPS instrument on ESO’s 3.6-m telescope in La Silla, Chile. We probed for Na absorption in its atmosphere as well as constrained the previously reported misaligned retrograde orbit using the Rossiter–McLaughlin effect. Additionally, we undertook a combined atmospheric retrieval analysis with previously published low-resolution data. We confirm the retrograde orbit as well as constrain the orbital misalignment with our measurement of a projected spin-orbit obliquity of λ = 123.0 ± 3.0°. We find a tentative detection of Na absorption in the atmosphere of WASP-94 A b, independent of the treatment of the Rossiter–McLaughlin effect in our analysis (3.6σ and 4.4σ). We combine our HARPS high-resolution data with low-resolution data from the literature and find that while the posterior distribution of the Na abundance results in a tighter constraint than using a single data set, the detection significance does not improve (3.2σ), which we attribute to degeneracies between the low- and high-resolution data.
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| 3. |
- Clark, Kristen D., et al.
(author)
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State-Level Policy Environments, Discrimination, and Victimization among Sexual and Gender Minority People
- 2022
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In: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 19:16
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Journal article (peer-reviewed)abstract
- Legislation has been passed in some states to reduce discrimination and victimization toward sexual and gender minority people (SGM; people who are not solely heterosexual and/or whose gender identity is not equal to what is socially associated with sex assigned at birth). The purpose of these analyses is to test whether state-level policy environments are associated with past-year discrimination and victimization among SGM people. Cross-sectional data from The Population Research in Identity and Disparities for Equality (PRIDE) Study annual questionnaire (collected 2018–2019), a national study of the health of SGM adults in the USA, were used for these analyses. Measures included related to discrimination, victimization, and demographic characteristics. State-level policy environments were measured using data from the Movement Advancement Project. Logistic regression analyses evaluated state-level policy environment scores and past-year discrimination and victimization among gender identity categories. In this sample, 7044 people (gender minority n = 2530) were included. Cisgender sexual minority (odds ratio [OR] = 1.007, p = 0.041) and the gender expansive subgroup of gender minority people (OR = 1.010, p = 0.047) in states with more protective policy environments had greater odds of discrimination. The gender expansive subgroup was found to have greater odds of victimization in states with more protective policy environments (OR = 1.003, p < 0.05). There was no relationship between state-level policy environments and victimization among any other study groups. SGM people may experience increased risk for discrimination and victimization despite legislative protections, posing continued risks for poor health outcomes and marginalization. Evaluation of factors (e.g., implementation strategies, systems of accountability) that influence the effectiveness of state-level polices on the reported experiences of discrimination and victimization among SGM people is needed.
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| 4. |
- De, Kishalay, et al.
(author)
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The Zwicky Transient Facility Census of the Local Universe. I. Systematic Search for Calcium-rich Gap Transients Reveals Three Related Spectroscopic Subclasses
- 2020
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 905:1
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Journal article (peer-reviewed)abstract
- Using the Zwicky Transient Facility alert stream, we are conducting a large spectroscopic campaign to construct a complete, volume-limited sample of transients brighter than 20 mag, and coincident within 100 '' of galaxies in the Census of the Local Universe catalog. We describe the experiment design and spectroscopic completeness from the first 16 months of operations, which have classified 754 supernovae. We present results from a systematic search for calcium-rich gap transients in the sample of 22 low-luminosity (peak absolute magnitude M > -17), hydrogen-poor events found in the experiment. We report the detection of eight new events, and constrain their volumetric rate to greater than or similar to 15% +/- 5% of the SN Ia rate. Combining this sample with 10 previously known events, we find a likely continuum of spectroscopic properties ranging from events with SN Ia-like features (Ca-Ia objects) to those with SN Ib/c-like features (Ca-Ib/c objects) at peak light. Within the Ca-Ib/c events, we find two populations distinguished by their red (g - r approximate to 1.5 mag) or green (g - r approximate to 0.5 mag) colors at the r-band peak, wherein redder events show strong line blanketing features and slower light curves (similar to Ca-Ia objects), weaker He lines, and lower [Ca II]/[O I] in the nebular phase. We find that all together the spectroscopic continuum, volumetric rates, and striking old environments are consistent with the explosive burning of He shells on low-mass white dwarfs. We suggest that Ca-Ia and red Ca-Ib/c objects arise from the double detonation of He shells, while green Ca-Ib/c objects are consistent with low-efficiency burning scenarios like detonations in low-density shells or deflagrations.
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| 5. |
- Mackay, Donna S, et al.
(author)
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Screening of a Large Cohort of Leber Congenital Amaurosis and Retinitis Pigmentosa Patients Identifies Novel LCA5 Mutations and New Genotype-Phenotype Correlations
- 2013
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In: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 34:11, s. 1537-1546
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Journal article (peer-reviewed)abstract
- This study was undertaken to investigate the prevalence of sequence variants in LCA5 in patients with Leber congenital amaurosis (LCA), early-onset retinal dystrophy (EORD), and autosomal recessive retinitis pigmentosa (arRP); to delineate the ocular phenotypes; and to provide an overview of all published LCA5 variants in an online database. Patients underwent standard ophthalmic evaluations after providing informed consent. In selected patients, optical coherence tomography (OCT) and fundus autofluorescence imaging were possible. DNA samples from 797 unrelated patients with LCA and 211 with the various types of retinitis pigmentosa (RP) were screened by Sanger sequence analysis of all LCA5 exons and intron/exon junctions. Some LCA patients were prescreened by APEX technology or selected based on homozygosity mapping. In silico analyses were performed to assess the pathogenicity of the variants. Segregation analysis was performed where possible. Published and novel LCA5 variants were collected, amended for their correct nomenclature, and listed in a Leiden Open Variation Database (LOVD). Sequence analysis identified 18 new probands with 19 different LCA5 variants. Seventeen of the 19 LCA5 variants were novel. Except for two missense variants and one splice site variant, all variants were protein-truncating mutations. Most patients expressed a severe phenotype, typical of LCA. However, some LCA subjects had better vision and intact inner segment/outer segment (IS/OS) junctions on OCT imaging. In two families with LCA5 variants, the phenotype was more compatible with EORD with affected individuals displaying preserved islands of retinal pigment epithelium. One of the families with a milder phenotype harbored a homozygous splice site mutation; a second family was found to have a combination of a stop mutation and a missense mutation. This is the largest LCA5 study to date. We sequenced 1,008 patients (797 with LCA, 211 with arRP) and identified 18 probands with LCA5 mutations. Mutations in LCA5 are a rare cause of childhood retinal dystrophy accounting for ∼2% of disease in this cohort, and the majority of LCA5 mutations are likely null. The LCA5 protein truncating mutations are predominantly associated with LCA. However, in two families with the milder EORD, the LCA5 gene analysis revealed a homozygous splice site mutation in one and a stop mutation in combination with a missense mutation in a second family, suggesting that this milder phenotype is due to residual function of lebercilin and expanding the currently known phenotypic spectrum to include the milder early onset RP. Some patients have remaining foveal cone structures (intact IS/OS junctions on OCT imaging) and remaining visual acuities, which may bode well for upcoming treatment trials.
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- Replogle, Kirstin, et al.
(author)
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The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
- 2008
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 9:131
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Journal article (peer-reviewed)abstract
- Background: Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. Results: We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA: Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing similar to 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. Conclusion: Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.
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| 8. |
- Vega, Paige N., et al.
(author)
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Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer
- 2022
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In: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 12
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Journal article (peer-reviewed)abstract
- The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1(CreERT2/+);Apc(2lox14/+)) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
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