Linguistics

Contains report on one research project.National Institute of Mental Health (Grant MH-13390-03

Comet and close-approach asteroid mission study. volume 1- summary report final report

Comet and close-approach asteroid mission stud

Plagiocephaly Perception and Prevention: A Need to Intervene Early to Educate Parents

Background: Plagiocephaly is a condition where the cranium has been malformed because of external forces or premature cranial suture fusion. This study’s objective was to gather and examine data regarding parent and caregiver awareness of plagiocephaly and its potential impact on development as well as to determine their rate of concern for positional flattening. Method: A cross-sectional survey study was conducted. Categorical variables were described by frequency and proportions. The study was conducted across eight outpatient pediatric sites. Approximately 1,100 parents and caregivers were targeted. Inclusion criteria required participants to be willing to answer the questionnaire, to be 18 years of age or older, and to have an infant 12 months of age or younger. Results: There were 404 participants, most of whom were female (89.8%) and 30–39 years of age (61.1%). Nineteen children (4.7%) were reported to have plagiocephaly, torticollis, and/or muscle weakness (PTM). A greater percentage of the participants with a child with PTM knew of positional flattening or plagiocephaly (73.3%) compared to those without (53.8%). The respondents with a child with PTM had a greater concern about plagiocephaly than those without (p = .03). Many of the respondents (65.3%) would use a device designed to prevent plagiocephaly. Conclusion: Many parents and caregivers were unaware of plagiocephaly and its potential impact on facial symmetry. A greater percentage of the participants with a child with PTM knew of positional flattening and also had a greater concern about plagiocephaly than those without

Using audio stimuli in acceptability judgment experiments

In this paper, we argue that moving away from written stimuli in acceptability judgment experiments is necessary to address the systematic exclusion of particular empirical phenomena, languages/varieties, and speakers in psycholinguistics. We provide user‐friendly guidelines for conducting acceptability experiments which use audio stimuli in three platforms: Praat, Qualtrics, and PennController for Ibex. In supplementary materials, we include data and R script from a sample experiment investigating English constituent order using written and audio stimuli. This paper aims not only to increase the types of languages, speakers, and phenomena which are included in experimental syntax, but also to help researchers who are interested in conducting experiments to overcome the initial learning curve. Video Abstract link: https://www.youtube.com/watch?v=GoWYY1O9ugsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156434/2/lnc312377_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156434/1/lnc312377.pd

Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData availability: The assembly and annotation are available at the European Nucleotide Archive project accession: PRJEB47812. Additional data files are provided at https://doi.org/10.5281/zenodo.5731560: purged haplotigs, assembly before manual edits, details of manual edits made to the assembly, and repeat library and functional annotation files. Scripts for genome assembly are available at https://github.com/kumarsaurabh20/DChry2.1 (last accessed 5 October 2021) and scripts for the genome annotation and analysis of introns and exons at https://github.com/RishiDeKayne/Danaus_Dchry2.2_annotation (last accessed 5 October 2021).Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long-read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny but highlights 3 inversion differences. The 3 chromosomes involved were previously found to carry peaks of intraspecific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.Royal SocietySwiss National Science FoundationEuropean Union Horizon 202

Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData availability: The assembly and annotation are available at the European Nucleotide Archive project accession: PRJEB47812. Additional data files are provided at https://doi.org/10.5281/zenodo.5731560: purged haplotigs, assembly before manual edits, details of manual edits made to the assembly, and repeat library and functional annotation files. Scripts for genome assembly are available at https://github.com/kumarsaurabh20/DChry2.1 (last accessed 5 October 2021) and scripts for the genome annotation and analysis of introns and exons at https://github.com/RishiDeKayne/Danaus_Dchry2.2_annotation (last accessed 5 October 2021).Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long-read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny but highlights 3 inversion differences. The 3 chromosomes involved were previously found to carry peaks of intraspecific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.Royal SocietySwiss National Science FoundationEuropean Union Horizon 202

F.A.R.O.G. FORUM, Vol. 3 No. 6

https://digitalcommons.library.umaine.edu/francoamericain_forum/1011/thumbnail.jp

Stepwise evolution of a butterfly supergene via duplication and inversion.

This is the final version. Available from the Royal Society via the DOI in this record. Data accessibility Sequencing reads and assemblies are available at the European Nucleotide Archive project (see the electronic supplementary material, table S1 for accession numbers [48]). Assemblies are available in the European Nucleotide Archive project accession PRJEB52180. Additional data files are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.xwdbrv1g0 [49], including genome assemblies and annotations, repeat library and windowed repeat content, whole-genome alignments, VCF and genotype files, window-based diversity and divergence measures and read depth, sequence alignments for genes and phylogenetic trees. Scripts for assembly polishing, the analysis of repeat content, genome annotation and phylogenetic tree construction are available at https://github.com/RishiDeKayne/Danaus_supergene_structure. Scripts for genome alignment and synteny block inference, ancestry painting and divergence analyses, and read depth and copy number analyses are available at https://github.com/simonhmartin/Danaus_supergene_structure.Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.Royal SocietyRoyal SocietySwiss National Science Foundation (SNSF)National Geographic Societ

Relationship Between Sexual Activity, Contraceptive Utilization and Biopsychosocial Characteristics Among Homeless Shelter Adolescents.

Objective: To determine whether biopsychosocial factors are associated with sexual activity and contraceptive utilization among homeless shelter adolescents. Methods: A retrospective study of 440 adolescents at a shelter in Pennsylvania between February 2015 and September 2019 was conducted. The cohort was evaluated to determine what relationship age, gender identity, substance use, and trauma history have with sexual activity and contraceptive utilization. Results: Sexual activity was significantly related to age (mean 15.8+1.4 years in sexually active vs. 14.7+1.6 years in abstinent youth, p\u3c0.001); remote history of self-harm behavior (relative risk ratio (RR) 1.23 [95% CI 1.03-1.46]; p=0.02), history of aggressive behavior (RR 1.21 [95% CI 1.01-1.46]; p=0.04), history of trauma (RR 1.24 [95% CI 1.04-1.48]; p=0.03), and substance use (RR 2.27 [95%CI 1.86-2.77]; p\u3c0.001). There were 55.7% sexually active females vs. 42.50% males reporting contraception use (p=0.01). After adjustment, older age and substance use remained significantly associated with sexual activity (adjusted odds ratio (AOR) 1.58 [95% CI 1.36-1.83]; p\u3c0.001 and AOR 5.18 [95% CI 3.28-8.18]; p\u3c0.001, respectively). Conclusions: Females self-reported sexual activity using contraception more than males. After adjustment, older age and substance use were associated with sexual activity. By better understanding the impact these factors can have on contraceptive utilization, informed policy and practice interventions can be developed and implemented to help increase safe sex practices in spaces where homeless adolescents access healthcare