Web Citation Availability: Analysis and Implictions for Scholarship

Five hundred citations to Internet resources from articles published in library and information science journals in 1999 and 2000 were profiled and searched on the Web. The majority contained partial bibliographic information and no date viewed. Most URLs pointed to content pages with edu or org domains and did not include a tilde. More than half (56.4%) were permanent, 81.4 percent were available on the Web, and searching the Internet Archive increased the availability rate to 89.2 percent. Content, domain, and directory depth were associated with availability. Few of the journals provided instruction on citing digital resources. Eight suggestions for improving scholarly communication citation conventions are presented

Web Citation Availability: A Follow-up Study

The researchers report on a study to examine the persistence of Web-based content. In 2002, a sample of 500 citations to Internet resources from articles published in library and information science journals in 1999 and 2000 were analyzed by citation characteristics and searched to determine cited content persistence, availability on the Web, and availability in the Internet Archive. Statistical analyses were conducted to identify citation characteristics associated with availability. The sample URLs were searched again between August 2005 and June 2006 to determine persistence, availability on the Web, and in the Internet Archive. As in the original study, the researchers cross-tabulated the results with URL characteristics and reviewed and analyzed journal instructions to authors on citing content on the Web. Findings included a decrease of 17.4 percent in persistence, and 8.2 percent in availability on the Web. When availability in the Internet Archives was factored in, the overall availability of Web content in the sample dropped from 89.2 percent to 80.6 percent. The statistical analysis confirmed the association between the likelihood that cited content will be found by future researchers and citation characteristics of content, domain, page type, and directory depth. The researchers also found an increase in the number of journals that provide instruction to authors on citing content on the Web

The major human and mouse granzymes are structurally and functionally divergent

Approximately 2% of mammalian genes encode proteases. Comparative genomics reveals that those involved in immunity and reproduction show the most interspecies diversity and evidence of positive selection during evolution. This is particularly true of granzymes, the cytotoxic proteases of natural killer cells and CD8+ T cells. There are 5 granzyme genes in humans and 10 in mice, and it is suggested that granzymes evolve to meet species-specific immune challenge through gene duplication and more subtle alterations to substrate specificity. We show that mouse and human granzyme B have distinct structural and functional characteristics. Specifically, mouse granzyme B is 30 times less cytotoxic than human granzyme B and does not require Bid for killing but regains cytotoxicity on engineering of its active site cleft. We also show that mouse granzyme A is considerably more cytotoxic than human granzyme A. These results demonstrate that even “orthologous” granzymes have species-specific functions, having evolved in distinct environments that pose different challenges

Reference database marine mammal literature

A comprehensive Reference Database has been designed for the marine mammal literature. The system uses INMAGIC programming (Cambridge, MA) to file, store, search, retrieve, and format the data records. The database was organized to be complementary to features developed by William E. Schevill for his library of older cetacean literature, and it uses direct association of species with some 300 indexed subjects, observation dates, locations, etc. Every component and detail of the references and annotations are available for rapid search by a wide variety of simple and complex strategies. In addition, separately indexed fields provide immediate retrieval of author, editor, year, journal, type of publication, language, genus/species (searchable by order/suborder and family as well), major subject, subject, picture, observation date, geographic location (including area name and latitude/longitude), as well as the location and library call numbers of the document referred to. Codes have been adapted for ease in identifying and searching species, subjects, journals, languages, and geographic areas. These codes may be used separately or in connection with the associated terms and texts. It is anticipated that the Reference Database will be a continuing resource for marine mammal research.Support for beginning work on the Database was by The Marine Mammal Commission and by The National Marine Fisheries Servic

Efficient Reionization in a Large Hydrodynamic Galaxy Formation Simulation

Accuracy in the topology and statistics of a simulated Epoch of Reionization (EoR) are vital to draw connections between observations and physical processes. While full radiative transfer models produce the most accurate reionization models, they are highly computationally expensive, and are infeasible for the largest cosmological simulations. Instead, large simulations often include EoR models that are pre-computed via the initial density field, or post-processed where feedback effects are ignored. We introduce Astrid-ES, a resimulation of the Astrid epoch of reionisation $20 > z > 5.5$ which includes an on-the-fly excursion-set reionization algorithm. Astrid-ES produces more accurate reionization histories without significantly impacting the computational time. This model directly utilises the star particles produced in the simulation to calculate the EoR history and includes a UV background which heats the gas particles after their reionization. We contrast the reionization topology and statistics in Astrid-ES with the previously employed parametric reionisation model, finding that in Astrid-ES, ionised regions are more correlated with galaxies, and the 21cm power-spectrum shows an increase in large scale power. We calculate the relation between the size of HII regions and the UV luminosity of the brightest galaxy within them. Prior to the overlap phase, we find a power-law fit of $\mathrm{log} (R) = -0.314 M_\mathrm{UV} - 2.550 \mathrm{log}(1+z) + 7.408$ with a standard deviation $\sigma_R < 0.15 \mathrm{dex}$ across all mass bins. We also examine the properties of halos throughout reionization, finding that while the properties of halos in the simulation are correlated with the redshift of reionisation, they are not greatly affected by reionisation itself.Comment: 12 pages, 11 figures. Accepted for publication in Monthly Notices of the Royal Astronomical Societ

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

Astrometric Microlensing by Primordial Black Holes with The Roman Space Telescope

Primordial Black Holes (PBHs) could explain some fraction of dark matter and shed light on many areas of early-universe physics. Despite over half a century of research interest, a PBH population has so far eluded detection. The most competitive constraints on the fraction of dark matter comprised of PBHs ($f_{\rm DM}$) in the $(10^{-9}-10)M_{\odot}$ mass-ranges come from photometric microlensing and bound $f_{\rm DM}\lesssim10^{-2}-10^{-1}$. With the advent of the Roman Space Telescope with its sub-milliarcsecond (mas) astrometric capabilities and its planned Galactic Bulge Time Domain Survey (GBTDS), detecting astrometric microlensing signatures will become routine. Compared with photometric microlensing, astrometric microlensing signals are sensitive to different lens masses-distance configurations and contains different information, making it a complimentary lensing probe. At sub-mas astrometric precision, astrometric microlensing signals are typically detectable at larger lens-source separations than photometric signals, suggesting a microlensing detection channel of pure astrometric events. We use a Galactic simulation to predict the number of detectable microlensing events during the GBTDS via this pure astrometric microlensing channel. Assuming an absolute astrometric precision floor for bright stars of 0.1 mas for the GBTDS, we find that the number of detectable events peaks at $\approx 10^{3} f_{\rm DM}$ for a population of $1 M_{\odot}$ PBHs and tapers to $\approx 10f_{\rm DM}$ and $\approx 100f_{\rm DM}$ at $10^{-4}M_{\odot}$ and $10^{3}M_{\odot}$, respectively. Accounting for the distinguishability of PBHs from Stellar lenses, we conclude the GBTDS will be sensitive to a PBH population at $f_{\rm DM}$ down to $\approx10^{-1}-10^{-3}$ for $(10^{-1}-10^{2})M_{\odot}$ likely yielding novel PBH constraints.Comment: 21 pages, 11 figures, accepted to AAS Journal

Uncovering a Novel Stone in 27 Patients: Calcium Tartrate Tetrahydrate

Objective To further analyze calcium tartrate tetrahydrate stones after a recent case report described this novel stone. Prior to this, there was only one previously reported occurrence of this stone in a human. This unusual stone composition is not tested for routinely. True prevalence and possible causes of this stone are unknown. Materials/Methods During the previous case report, micro-CT and Fourier-transform infrared spectroscopy were used to identify a calcium tartrate tetrahydrate stone. This information was applied to urinary stones with previously unidentified compositions in the Mayo Metals laboratory database between 2010 and March 2018. Two additional stones were identified at our institution. Three patients had medical records available for analysis. Results Between 2010 and March 2018, 35 calcium tartrate stones in 25 patients were identified in the Mayo database as well as 2 at our institution (37 stones in 27 patients). Thirty stones were pure calcium tartrate with the remainder having elements of more common stones. The average age was 46.3 (±14.7) with a slightly higher incidence in females (17 vs 10). Of the 3 medical records investigated, all 3 were males (average age 48.7), and each reported consumption of an energy supplement (Spark) routinely. Conclusion The true prevalence of this relatively unknown stone remains unclear and additional investigation is warranted. We believe all stone laboratories should have access to the IR spectra for calcium tartrate tetrahydrate. Attention should be paid to possible causes of this stone, particularly with relation to oral supplements, to aid with future prevention and treatment