University of Colorado Denver

About: University of Colorado Denver is a education organization based out in Denver, Colorado, United States. It is known for research contribution in the topics: Population & Health care. The organization has 27444 authors who have published 57213 publications receiving 2539937 citations. The organization is also known as: CU Denver & UCD.

Evolutionary and biomedical insights from the rhesus macaque genome

Abstract: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

Ceritinib in ALK-Rearranged Non–Small-Cell Lung Cancer

Abstract: BackgroundNon–small-cell lung cancer (NSCLC) harboring the anaplastic lymphoma kinase gene (ALK) rearrangement is sensitive to the ALK inhibitor crizotinib, but resistance invariably develops. Ceritinib (LDK378) is a new ALK inhibitor that has shown greater antitumor potency than crizotinib in preclinical studies. MethodsIn this phase 1 study, we administered oral ceritinib in doses of 50 to 750 mg once daily to patients with advanced cancers harboring genetic alterations in ALK. In an expansion phase of the study, patients received the maximum tolerated dose. Patients were assessed to determine the safety, pharmacokinetic properties, and antitumor activity of ceritinib. Tumor biopsies were performed before ceritinib treatment to identify resistance mutations in ALK in a group of patients with NSCLC who had had disease progression during treatment with crizotinib. ResultsA total of 59 patients were enrolled in the dose-escalation phase. The maximum tolerated dose of ceritinib was 750 mg once daily; dose-l...

Normalization and microbial differential abundance strategies depend upon data characteristics

Abstract: Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets ( 20 samples per group) but also critically the only method tested that has a good control of false discovery rate. These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.

Long-term effects of home visitation on maternal life course and child abuse and neglect : Fifteen-year follow-up of a randomized trial

Abstract: Context. —Home-visitation services have been promoted as a means of improving maternal and child health and functioning. However, long-term effects have not been examined. objective. —To examine the long-term effects of a program of prenatal and early childhood home visitation by nurses on women's life course and child abuse and neglect. Design. —Randomized trial. Setting. —Semirural community in New York. Participants. —Of 400 consecutive pregnant women with no previous live births enrolled, 324 participated in a follow-up study when their children were 15 years old. Intervention. —Families received a mean of 9 home visits during pregnancy and 23 home visits from the child's birth through the second birthday. Data Sources and Measures. —Women's use of welfare and number of subsequent children were based on self-report; their arrests and convictions were based on self-report and archived data from New York State. Verified reports of child abuse and neglect were abstracted from state records. Main Results. —During the 15-year period after the birth of their first child, in contrast to women in the comparison group, women who were visited by nurses during pregnancy and infancy were identified as perpetrators of child abuse and neglect in 0.29 vs 0.54 verified reports ( P P =.02), 65 vs 37 months between the birth of the first and a second child ( P =.001), 60 vs 90 months' receiving Aid to Families With Dependent Children ( P =.005), 0.41 vs 0.73 behavioral impairments due to use of alcohol and other drugs ( P =.03), 0.18 vs 0.58 arrests by self-report ( P P Conclusions. —This program of prenatal and early childhood home visitation by nurses can reduce the number of subsequent pregnancies, the use of welfare, child abuse and neglect, and criminal behavior on the part of low-income, unmarried mothers for up to 15 years after the birth of the first child.

Parks and Peoples: The Social Impact of Protected Areas

Abstract: This review examines the social, economic, and political effects of environmental conservation projects as they are manifested in protected areas. We pay special attention to people living in and displaced from protected areas, analyze the worldwide growth of protected areas over the past 20 years, and offer suggestions for future research trajectories in anthropology. We examine protected areas as a way of seeing, understanding, and producing nature (environment) and culture (society) and as a way of attempting to manage and control the relationship between the two. We focus on social, economic, scientific, and political changes in places where there are protected areas and in the urban centers that control these areas. We also examine violence, conflict, power relations, and governmentality as they are connected to the processes of protection. Finally, we examine discourse and its effects and argue that anthropology needs to move beyond the current examinations of language and power to attend to the ways in which protected areas produce space, place, and peoples.