COPIM – Revenue Models for Open Access Monographs 2020

A report by the Community-led Open Publication Infrastructures for Monographs project (COPIM) analysing the open access economic models in use today in scholarly publishing. The report examines academic monograph publishing in the context of today’s challenging monograph publishing environment: from Covid-19 and budget cuts, to print sales, funder mandates, and research evaluation. Launched in 2019, and funded by Arcadia and Research England, the COPIM project is an international partnership of researchers, universities, librarians, open access (OA) book publishers and infrastructure providers. It is fostering community-owned, open systems and infrastructures to enable OA book publishing to flourish. This project report builds on a decade of studies written by OA advocates and consultants around the world, and updates their research to describe the environment and economics of OA publishing in 2020. The report will eventually become one component of a practical ‘toolkit’ that COPIM will produce on how presses might transition to sustainably publishing OA monographs

Introducing Biology Undergraduates to Authentic Research through Grand Challenges in Global Health: Examining Environmental Factors that Influence the Development of Zebrafish Embryos

To increase student excitement and engagement in science, a course-based undergraduate research experience (CURE) has been introduced in the curriculum at IUPUI. In Fall 2013, original research projects investigating prenatal alcohol, nicotine and caffeine exposure effects on development of zebrafish embryos was introduced into the Introductory Biology K102 course. This research project was also a part of a new Themed Learning Community (TLC) at IUPUI called “From Molecules to Medicines” that examined grand challenges in global health. In documenting the developmental effects on zebrafish embryos, and designing new protocols to address student research questions, students gained experience with authentic research methods, laboratory techniques, microscopy, image analyses, statistical analyses, scientific writing and presentation skills. This project, especially in a freshman undergraduate lab setting, requires a new way of problem-solving, but greatly facilitates student excitement and engagement in science through the use of research-based high-impact practices for student success and persistence. To continue an inquiry-based lab on global health issues and to keep IUPUI biology curricula current with the rapid rise of bioinformatics, concepts of bioinformatics were introduced into the Cell Biology Laboratory K325 course in Spring, 2014. Students were allowed to work on their own investigatory projects to analyzed zebrafish microarray data to find genes affected after ethanol exposure. Students used NCBI/ Ensembl databases to retrieve the gene/protein sequences, and various freely available tools (GeneBank, Protein Data Bank, BLAST, ClustalW, ExPasy, Phylogenetic Tree) to investigate the evolutionary conservation of genes/proteins affected after ethanol exposure. Student learnt 3D-protein structure construction and observed how 3D-protein structure could change with single amino acid changes. Preliminary assessment indicates that students are gaining an understanding the web-based databases and tools and enjoying the investigatory nature of the lab exercises

Next generation sequencing sheds light on the natural history of hepatitis C infection in patients that fail treatment

Background and rationale of the study: High rates of sexually-transmitted infection and reinfection with hepatitis C (HCV) have recently been reported in HIV-infected men who have sex with men and reinfection has also been described in monoinfected injecting drug users. The diagnosis of reinfection has traditionally been based on direct Sanger sequencing of samples pre and post-treatment, but not on more sensitive deep sequencing techniques. We studied viral quasispecies dynamics in patients who failed standard of care therapy in a high-risk HIV-infected cohort of patients with early HCV infection to determine whether treatment failure was associated with reinfection or recrudescence of pre-existing infection. Paired sequences (pre- and post- treatment) were analysed. The HCV E2 hypervariable region-1 was amplified using nested RT-PCR with indexed genotype-specific primers and the same products were sequenced using both Sanger and 454 pyrosequencing approaches. Results: Of 99 HIV-infected patients with acute HCV treated with 24-48 weeks of pegylated interferon alpha and ribavirin, 15 failed to achieve a sustained virological response (6 relapsed, 6 had a null response and 3 had a partial response). Using direct sequencing, 10/15 patients (66%) had evidence of a previously undetected strain post-treatment; in many studies, this is interpreted as reinfection. However, pyrosequencing revealed that 15/15 (100%) of patients had evidence of persisting infection. 6/15 (40%) patients had evidence of a previously undetected variant present in the post-treatment sample in addition to a variant that was detected at baseline. This could represent superinfection or a limitation of the sensitivity of pyrosequencing. Conclusion: In this high-risk group, the emergence of new viral strains following treatment failure is most commonly associated with emerging dominance of pre-existing minority variants rather than re-infection. Superinfection may occur in this cohort but reinfection is over-estimated by Sanger sequencing. (Hepatology 2014;

Searching for a link between the magnetic nature and other observed properties of Herbig Ae/Be stars and stars with debris disks

Among the 21 Herbig Ae/Be stars studied, new detections of a magnetic field were achieved in six stars. For three Herbig Ae/Be stars, we confirm previous magnetic field detections. The largest longitudinal magnetic field, = -454+-42G, was detected in the Herbig Ae/Be star HD101412 using hydrogen lines. No field detection at a significance level of 3sigma was achieved in stars with debris disks. Our study does not indicate any correlation of the strength of the longitudinal magnetic field with disk orientation, disk geometry, or the presence of a companion. We also do not see any simple dependence on the mass-accretion rate. However, it is likely that the range of observed field values qualitatively supports the expectations from magnetospheric accretion models giving support for dipole-like field geometries. Both the magnetic field strength and the X-ray emission show hints for a decline with age in the range of ~2-14Myrs probed by our sample supporting a dynamo mechanism that decays with age. However, our study of rotation does not show any obvious trend of the strength of the longitudinal magnetic field with rotation period. Furthermore, the stars seem to obey the universal power-law relation between magnetic flux and X-ray luminosity established for the Sun and main-sequence active dwarf stars.Comment: 21 pages, 16 figures, 7 tables, accepted for publication in A&

High-Contrast NIR Polarization Imaging of MWC480

One of the key predictions of modeling from the IR excess of Herbig Ae stars is that for protoplanetary disks, where significant grain growth and settling has occurred, the dust disk has flattened to the point that it can be partially or largely shadowed by the innermost material at or near the dust sublimation radius. When the self-shadowing has already started, the outer disk is expected to be detected in scattered light only in the exceptional cases that the scale height of the dust disk at the sublimation radius is smaller than usual. High-contrast imaging combined with the IR spectral energy distribution allow us to measure the degree of flattening of the disk, as well as to determine the properties of the outer disk. We present polarimetric differential imaging in $H$ band obtained with Subaru/HiCIAO of one such system, MWC 480. The HiCIAO data were obtained at a historic minimum of the NIR excess. The disk is detected in scattered light from 0\farcs2-1\farcs0 (27.4-137AU). Together with the marginal detection of the disk from 1998 February 24 by HST/NICMOS, our data constrain the opening half angle for the disk to lie between 1.3$\leq\theta\leq 2.2^\circ$. When compared with similar measures in CO for the gas disk from the literature, the dust disk subtends only $\sim$30% of the gas disk scale height (H/R$\sim$0.03). Such a dust disk is a factor of 5-7 flatter than transitional disks, which have structural signatures that giant planets have formed.Comment: 21 pages, 6 figures, 1 table, ApJ accepted 2012-05-0

The CR chondrite clan

The (1) CR chondrites, (2) LEW 85332,(3) Acfer 182,(4) ALH 85085-like chondrites, and (5) Bencubbin-like chondritic breccias are five kinds of chondritic groups which have dramatically different petrographic characteristics, but have mineralogical, bulk chemical, and oxygen and nitrogen isotopic similarities that indicate they are closely related. They are all considered to be members of what we term the CR chondrite clan. Distinguishing characteristics of CR clan chondrites include : (a) reduced, Mg-rich mafic silicates, (b) hydrous matrix and/or dark inclusions (except for Bencubbin-like chondrites), (c) high modal abundances of FeNi metal, (d) FeNi metal having a solar Ni : Co ratio, (e) solar (CI) abundances of refractory and moderately volatile lithophiles, and highly depleted abundances of volatile lithophiles, (f) similar oxygen isotopic compositions of whole rocks, chondrules and matrices, which are on or near the CR mixing line, and (g) anomalously high ^N abundances. CR clan chondrites must have formed in the same local region of the nebula, from closely related reservoirs of materials. The coexistence of anhydrous chondrules with hydrous matrix (and dark inclusions) in the LEW 85332,Acfer 182,and ALH 85085-like chondrites, as well as the widely differing degrees of hydration within and between chondritic samples, implies that hydration of the components was not variable in a single locality, but took place at a variety of locales prior to final lithification of the CR clan chondrites

GASPS observations of Herbig Ae/Be stars with PACS/Herschel. The atomic and molecular content of their protoplanetary discs

We observed a sample of 20 representative Herbig Ae/Be stars and five A-type debris discs with PACS onboard of Herschel. The observations were done in spectroscopic mode, and cover far-IR lines of [OI], [CII], CO, CH+, H2O and OH. We have a [OI]63 micron detection rate of 100% for the Herbig Ae/Be and 0% for the debris discs. [OI]145 micron is only detected in 25%, CO J=18-17 in 45% (and less for higher J transitions) of the Herbig Ae/Be stars and for [CII] 157 micron, we often found spatially variable background contamination. We show the first detection of water in a Herbig Ae disc, HD 163296, which has a settled disc. Hydroxyl is detected as well in this disc. CH+, first seen in HD 100546, is now detected for the second time in a Herbig Ae star, HD 97048. We report fluxes for each line and use the observations as line diagnostics of the gas properties. Furthermore, we look for correlations between the strength of the emission lines and stellar or disc parameters, such as stellar luminosity, UV and X-ray flux, accretion rate, PAH band strength, and flaring. We find that the stellar UV flux is the dominant excitation mechanism of [OI]63 micron, with the highest line fluxes found in those objects with a large amount of flaring and greatest PAH strength. Neither the amount of accretion nor the X-ray luminosity has an influence on the line strength. We find correlations between the line flux of [OI]63 micron and [OI]145 micron, CO J = 18-17 and [OI]6300 \AA, and between the continuum flux at 63 micron and at 1.3 mm, while we find weak correlations between the line flux of [OI]63 micron and the PAH luminosity, the line flux of CO J = 3-2, the continuum flux at 63 micron, the stellar effective temperature and the Brgamma luminosity. (Abbreviated version)Comment: 20 pages, 29 figures, accepted by Astronomy and Astrophysic

Fragment properties at the catastrophic disruption threshold: The effect of the parent body's internal structure

Numerical simulations of asteroid break-ups, including both the fragmentation of the parent body and the gravitational interactions between the fragments, have allowed us to reproduce successfully the main properties of asteroid families formed in different regimes of impact energy, starting from a non-porous parent body. In this paper, using the same approach, we concentrate on a single regime of impact energy, the so-called catastrophic threshold usually designated by Q*D, which results in the escape of half of the target's mass. Thanks to our recent implementation of a model of fragmentation of porous materials, we can characterize Q*D for both porous and non-porous targets with a wide range of diameters. We can then analyze the potential influence of porosity on the value of Q*D, and by computing the gravitational phase of the collision in the gravity regime, we can characterize the collisional outcome in terms of the fragment size and ejection speed distributions, which are the main outcome properties used by collisional models to study the evolutions of the different populations of small bodies. We also check the dependency of Q*D on the impact speed of the projectile. In the strength regime, which corresponds to target sizes below a few hundreds of meters, we find that porous targets are more difficult to disrupt than non-porous ones. In the gravity regime, the outcome is controlled purely by gravity and porosity in the case of porous targets. In the case of non-porous targets, the outcome also depends on strength. We then propose some power-law relationships between Q*D and both target's size and impact speed that can be used in collisional evolution models.Comment: 18 pages, 19 Figures. Accepted for publication in Icaru

Evidence of continued injecting drug use after attaining sustained treatment-induced clearance of the hepatitis C virus: implications for reinfection

Background: People who inject drugs (PWID) are at the greatest risk of hepatitis C virus (HCV) infection, yet are often denied immediate treatment due to fears of on-going risk behaviour. Our principal objective was to examine evidence of continued injecting drug use among PWID following successful treatment for HCV and attainment of a sustained viral response (SVR). Methods: PWID who attained SVR between 1992 and June 2012 were selected from the National Scottish Hepatitis C Clinical Database. Hospitalisation and mortality records were sourced for these patients using record linkage techniques. Our primary outcome variable was any hospitalisation or death, which was indicative of injecting drugs post-SVR. Results: The cohort comprised 1170 PWID (mean age at SVR 39.6y; 76% male). The Kaplan Meier estimate of incurring the primary outcome after three years of SVR was 10.59% (95% CI, 8.75–12.79) After adjusting for confounding, the risk of an injection related hospital episode or death post-SVR was significantly increased with advancing year of SVR: AHR:1.07 per year (95% CI, 1.01–1.14), having a pre-SVR acute alcohol intoxication-related hospital episode: AHR:1.83 (95% CI, 1.29–2.60), and having a pre-SVR opiate or injection-related hospital episode: AHR:2.59 (95% CI, 1.84–3.64). Conclusion: Despite attaining the optimal treatment outcome, these data indicate that an increasing significant minority of PWID continue to inject post-SVR at an intensity which leads to either hospitalisation or death and increased risk of reinfection