A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

Modeling of Early SIV/HIV Infection

Although HIV has infected over 20 million people worldwide, it is a rather poorly transmitted virus since less than 1 out of 100 to 1,000 acts of sexual intercourse results in virus transmission. The factors that could potentially explain why the probability of transmission is so small are poorly understood. It is nearly impossible to study HIV replication in the first 2-3 weeks of infection because the virus is undetectable until after that duration. By using stochastic simulations of mathematical models of early virus replication, we investigate how the duration of the eclipse phase prior to virus production (eclipse stage) affects the probability of infection of the host and time to the detectable virus load for simian immunodeficiency virus (SIV) infection of monkeys. The probability of infection strongly depends on the dose of the infectious agent and the viral production mechanism that is used, and there are significant differences in times to infection between the deterministic and stochastic models. We show that our model consistently predicts the time to virus detection in macaques infected with a low dose of SIV. However, the model fails to accurately predict the dependence of the probability of SIV infection on the initial viral dose in monkeys. Our results suggest that additional mechanisms must be considered for understanding early virus dynamics, in particular, spatial distribution and the turnover of CD4+ T cells, which are primary targets for the virus

Constraints on the Progenitor System of the Type Ia Supernova 2014J from Pre-Explosion Hubble Space Telescope Imaging

We constrain the properties of the progenitor system of the highly reddened Type Ia supernova (SN) 2014J in Messier 82 (M82; d ~ 3.5 Mpc). We determine the SN location using Keck-II K-band adaptive optics images, and we find no evidence for flux from a progenitor system in pre-explosion near-ultraviolet through near-infrared Hubble Space Telescope (HST) images. Our upper limits exclude systems having a bright red giant companion, including symbiotic novae with luminosities comparable to that of RS Ophiuchi. While the flux constraints are also inconsistent with predictions for comparatively cool He-donor systems (T < ~35,000 K), we cannot preclude a system similar to V445 Puppis. The progenitor constraints are robust across a wide range of R_V and A_V values, but significantly greater values than those inferred from the SN light curve and spectrum would yield proportionally brighter luminosity limits. The comparatively faint flux expected from a binary progenitor system consisting of white dwarf stars would not have been detected in the pre-explosion HST imaging. Infrared HST exposures yield more stringent constraints on the luminosities of very cool (T < 3000 K) companion stars than was possible in the case of SN Ia 2011fe.Comment: Accepted by ApJ 14 May 2014 with only minor revision

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries

Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results suggest that, in order to appropriately model early HIV/SIV dynamics, additional factors must be considered in the model development. These may include variability in monkey susceptibility to infection, within-host competition between different viruses for target cells at the initial site of virus replication in the mucosa, innate immune response, and possibly the inclusion of several different tissue compartments. The sobering news is that while an increase in model complexity is needed to explain the available experimental data, testing and rejection of more complex models may require more quantitative data than is currently available

Testing GRBs as Standard Candles

Several correlations among Gamma Ray Burst (GRB) observables with available redshifts have been recently identified. Proper evaluation and calibration of these correlations may facilitate the use of GRBs as standard candles constraining the expansion history of the universe up to redshifts of $z>6$. Here we use the 69 GRB dataset recently compiled by Schaefer (astro-ph/0612285) and we test the calibration of five of the above correlations (1:\epkk-E_\gamma, 2:\epkk-L, 3:\tlag-L, $4:V-L$, 5:\trt-L) with respect to two potential sources of systematics: Evolution with redshift and cosmological model used in the calibration. In examining the model dependence we assume flat \lcdm and vary \omm. Our approach avoids the circularity problem of previous studies since we do not fix \omm to find the correlation parameters. Instead we simultaneously minimize $\chi^2$ with respect to both the log-linear correlation parameters $a$, $b$ and the cosmological parameter \omm. We find no statistically significant evidence for redshift dependence of $a$ and $b$ in any of the correlation relations tested. We also find that one of the five correlation relations tested (\epkk-E_\gamma) has a significantly lower intrinsic dispersion compared to the other correlations. For this correlation relation, the maximum likelihood method favors the existence of a cosmological constant while the other four correlation favor a flat matter dominated universe \omm \simeq 1. Finally, a cross-correlation analysis between the GRBs and SnIa data for various values of \omm has shown that the $E_{peak}-E_\gamma$ relation traces well the SnIa redshift regime. However, even the tightest correlation relation ($E_{peak}-E_\gamma$) provides much weaker constraints on \omm than current SnIa data.Comment: 10 pages, 3 figures. Improved statistical analysis. Minor changes in results. Accepted in MNRAS (to appear

Abemaciclib in Combination with Single-Agent Options in Patients with Stage IV Non–Small Cell Lung Cancer: A Phase Ib Study

Purpose: Abemaciclib, a dual inhibitor of cyclin-dependent kinases 4 and 6, has demonstrated preclinical activity in non–small cell lung cancer (NSCLC). A multicenter, nonrandomized, open-label phase Ib study was conducted to test safety, MTD, pharmacokinetics, and preliminary antitumor activity of abemaciclib in combination with other therapies for treatment in patients with metastatic NSCLC. Patients and Methods: An initial dose escalation phase was used to determine the MTD of twice-daily oral abemaciclib (150, 200 mg) plus pemetrexed, gemcitabine, or ramucirumab, followed by an expansion phase for each drug combination. Pemetrexed and gemcitabine were administered according to label. The abemaciclib plus ramucirumab study examined two dosing schedules. Results: The three study parts enrolled 86 patients; all received ≥1 dose of combination therapy. Across arms, the most common treatment-emergent adverse events were fatigue, diarrhea, neutropenia, decreased appetite, and nausea. The trial did not identify an abemaciclib MTD for the combination with pemetrexed or gemcitabine but did so for the combination of abemaciclib with days 1 and 8 ramucirumab (8 mg/kg). Plasma sample analysis showed that abemaciclib did not influence the pharmacokinetics of the combination agents and the combination agents did not affect abemaciclib exposure. The disease control rate was 57% for patients treated with abemaciclib–pemetrexed, 25% for abemaciclib–gemcitabine, and 54% for abemaciclib–ramucirumab. Median progression-free survival was 5.55, 1.58, and 4.83 months, respectively. Conclusions: Abemaciclib demonstrated an acceptable safety profile when dosed on a continuous twice-daily schedule in combination with pemetrexed, gemcitabine, or ramucirumab. Abemaciclib exposures remained consistent with those observed in single-agent studies

How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae)

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Genome-wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of Tolpis succulenta (Asteraceae) on Graciosa island in the Azores. These two known extant populations of T. succulenta on Graciosa have recently evolved self-compatibility. Despite the expectation that selfing would occur at an appreciable rate (self-incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self-incompatible colonists of T. succulenta from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self-compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season

The Forum: Fall 2002

Fall 2002 journal of the Honors Program at the University of North Dakota. The issue includes stories, poems, essays and art by undergraduate students.https://commons.und.edu/und-books/1050/thumbnail.jp

Reconsidering power and distance

A wide range of studies indicate that power and distance affect the production and interpretation of language. However, this paper argues that greater consideration needs to be given to the conceptual nature of these dimensions, and to terminological usage. In the first half of the paper, the need for this consideration is explained. A number of pragmatic studies are examined, and this reveals that authors often use the same terms with different meanings, or different terms with the same meaning, and that the parameters are rarely explicitly defined. Then the paper reviews recent calls for an extra parameter of interlocutor relations to be added: for affect to be separated from distance. In the second half of the paper, relevant social psychological research is reported, and it is concluded that the number of ‘horizontal’ dimensions of interlocutor relations needs to be reconsidered. Power, on the other hand, emerges as a robust and relatively unitary dimension, yet its label has connotations that may not be cross-culturally valid