The State of Sustainable Research Software: Results from the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1)

This article summarizes motivations, organization, and activities of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1) held in Manchester, UK in September 2017. The WSSSPE series promotes sustainable research software by positively impacting principles and best practices, careers, learning, and credit. This article discusses the Code of Conduct, idea papers, position papers, experience papers, demos, and lightning talks presented during the workshop. The main part of the article discusses the speed-blogging groups that formed during the meeting, along with the outputs of those sessions

Simple Models for Turbulent Self-Regulation in Galaxy Disks

We propose that turbulent heating, wave pressure and gas exchanges between different regions of disks play a dominant role in determining the preferred, quasi-equilibrium, self-similar states of gas disks on large-scales. We present simple families of analytic, thermohydrodynamic models for these global states, which include terms for turbulent pressure and Reynolds stresses. Star formation rates, phase balances, and hydrodynamic forces are all tightly coupled and balanced. The models have stratified radial flows, with the cold gas slowly flowing inward in the midplane of the disk, and with the warm/hot phases that surround the midplane flowing outward. The models suggest a number of results that are in accord with observation, as well as some novel predictions, including the following. 1) The large-scale gas density and thermal phase distributions in galaxy disks can be explained as the result of turbulent heating and spatial couplings. 2) The turbulent pressures and stresses that drive radial outflows in the warm gas also allow a reduced circular velocity there. This effect was observed by Swaters, Sancisi and van der Hulst in NGC 891, a particularly turbulent edge-on disk. The models predict that the effect should be universal in such disks. 3) They suggest that a star formation rate like the phenomenological Schmidt Law is the natural result of global thermohydrodynamical balance, and may not obtain in disks far from equilibrium. (Abridged)Comment: 37 pages, 1 gif figure, accepted for publication in the Astrophysical Journa

HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRRF01_AE and CRF02_AG

Background: Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno([coreceptor]) and webPSSM. Methods: Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno([coreceptor]) (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile (R) Enhanced-Sensitivity-Tropism-Assay. Results: The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno([coreceptor]) was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno([coreceptor]) was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno([coreceptor]) and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. Conclusions: Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors

Storm fronts over galaxy discs: Models of how waves generate extraplanar gas and its anomalous kinematics

The existence of partially ionized, diffuse gas and dust clouds at kiloparsec scale distances above the central planes of edge-on, galaxy discs was an unexpected discovery about 20 yrs ago. Subsequent observations showed that this EDIG (extended or extraplanar diffuse interstellar gas) has rotation velocities approximately 10-20% lower than those in the central plane, and have been hard to account for. Here we present results of hydrodynamic models, with radiative cooling and heating from star formation. We find that in models with star formation generated stochastically across the disc an extraplanar gas layer is generated as long as the star formation is sufficiently strong. However, this gas rotates at nearly the same speed as the mid-plane gas. We then studied a range of models with imposed spiral or bar waves in the disc. EDIG layers were also generated in these models, but primarily over the wave regions, not over the entire disc. Because of this partial coverage, the EDIG clouds move radially, as well as vertically, with the result that observed kinematic anomalies are reproduced. The implication is that the kinematic anomalies are the result of three-dimensional motions when the cylindrical symmetry of the disc is broken. Thus, the kinematic anomalies are the result of bars or strong waves, and more face-on galaxies with such waves should have an asymmetric EDIG component. The models also indicate that the EDIG can contain a significant fraction of cool gas, and that some star formation can be triggered at considerable heights above the disc midplane. We expect all of these effects to be more prominent in young, forming discs, to play a role in rapidly smoothing disc asymmetries, and in working to self-regulate disc structure.Comment: 30 pages, 9 figs., accepted for MNRAS with additional referee correction

Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction

BACKGROUND: Replication capacity (RC) of specific HIV isolates is occasionally blamed for unexpected treatment responses. However, the role of viral RC in response to antiretroviral therapy is not yet fully understood. MATERIALS AND METHODS: We developed a method for predicting RC from genotype using support vector machines (SVMs) trained on about 300 genotype-RC pairs. Next, we studied the impact of predicted viral RC (pRC) on the change of viral load (VL) and CD4(+) T-cell count (CD4) during the course of therapy on about 3,000 treatment change episodes (TCEs) extracted from the EuResist integrated database. Specifically, linear regression models using either treatment activity scores (TAS), the drug combination, or pRC or any combination of these covariates were trained to predict change in VL and CD4, respectively. RESULTS: The SVM models achieved a Spearman correlation (rho) of 0.54 between measured RC and pRC. The prediction of change in VL (CD4) was best at 180 (360) days, reaching a correlation of rho = 0.45 (rho = 0.27). In general, pRC was inversely correlated to drug resistance at treatment start (on average rho = -0.38). Inclusion of pRC in the linear regression models significantly improved prediction of virological response to treatment based either on the drug combination or on the TAS (t-test; p-values range from 0.0247 to 4 10(-6)) but not for the model using both TAS and drug combination. For predicting the change in CD4 the improvement derived from inclusion of pRC was not significant. CONCLUSION: Viral RC could be predicted from genotype with moderate accuracy and could slightly improve prediction of virological treatment response. However, the observed improvement could simply be a consequence of the significant correlation between pRC and drug resistance

Kontroversen und Effekte des Diskurses zu sogenannter Clankriminalität: Zur diskursiven Konstruktion von Clans und sozialen Zugehörigkeiten

Innerhalb des Beitrags werden Fremdzuschreibungen, die mit einem als Clan bezeichneten Kollektiv in Verbindung gebracht werden, unter einer Perspektive von (Nicht-)Zugehörigkeit betrachtet. Die empirische Grundlage bilden 52 leitfadengestützte teilstrukturierte Expert:inneninterviews mit 66 Repräsentant:innen verschiedener Professionsgruppen, die mit vermeintlichen Clans respektive dem Phänomen sogenannter Clankriminalität befasst sind. Es deutet sich an, dass die zugeschriebene Zugehörigkeit zu einem diffusen, als Clan bezeichneten Kollektiv – sofern der Begriff affirmativ verwendet wird – vielfach gegenüber anderen Formen der Zugehörigkeit überbetont wird. Die Zuschreibung Clan vereinigt insbesondere Zugehörigkeitsformen von Familie sowie Ethnizität. Dies führt dazu, dass lebensweltliche Erfahrungen, Problemlagen sowie Normbrüche respektive Kriminalität vor allem vor dem Hintergrund einer vermeintlichen Clanzugehörigkeit betrachtet werden

Proliferation of \u3cem\u3eChondrodonta\u3c/em\u3e as a Proxy of Environmental Instability at the Onset of OAE1a: Insights from Shallow-Water Limestones of the Apulia Carbonate Platform

Chondrodonta is an opportunistic, oyster-like bivalve, common in shallow-water carbonates of the Cretaceous Tethyan Realm. Despite its high abundance and widespread geographic distribution, the precise relationship between the early Aptian proliferation and environmental perturbations resulting from the Oceanic Anoxic Event 1a (OAE1a), has not been investigated. Stratigraphic and geochemical analyses of the lower Aptian Chondrodonta bedsets within the inner platform limestones of the Apulia Carbonate Platform (Gargano Promontory, southern Italy) are conducted to assess the environmental controls on the Chondrodonta proliferation and its timing and causal relationship to OAE1a. Chondrodonta occurs with sparse to common individuals within requieniid rudist floatstone–rudstones, forms monospecific biostromes during the early phase of stressed environmental conditions and then rapidly disappears at the peak of OAE1a. It proliferates in dysoxic seawater with relatively increased trophic sources, which correlate to increasing nutrient levels in the nearby pelagic realm. Chondrodonta-rich beds are associated worldwide with the onset of OAE1a and occur in a transitional context between a stable and a strongly stressed environment, where the opportunistic behaviour of Chondrodonta is rather efficient. Increasing nutrient load and unstable environmental conditions right below the peak of OAE1a created an environmental ‘window’ favourable for Chondrodonta to proliferate, outplaying the less tolerant benthos (for example, rudists). The occurrence, duration and position of the environmental window were controlled by local palaeogeographic and hydrodynamic settings (i.e. low energy, decreased seawater oxygenation and circulation). Further increase in inhospitable conditions, leading to OAE1a, constituted an upper threshold for Chondrodonta and allowed mesotrophic taxa like Bacinella–Lithocodium and orbitolinids to dominate the benthic communities. The present study suggests that the proliferation of Chondrodonta in shallow-water platform carbonates can be used as proxy for the initial phase of ecological stress related to OAE1a

Isotopic Characterization of Water Masses in the Southeast Pacific Region: Paleoceanographic Implications

In this study, we used stable isotopes of oxygen (δ18O), deuterium (δD), and dissolved inorganic carbon (δ13CDIC) in combination with temperature, salinity, oxygen, and nutrient concentrations to characterize the coastal (71°–78°W) and an oceanic (82°–98°W) water masses (SAAW—Subantarctic Surface Water; STW—Subtropical Water; ESSW—Equatorial Subsurface water; AAIW—Antarctic Intermediate Water; PDW—Pacific Deep Water) of the Southeast Pacific (SEP). The results show that δ18O and δD can be used to differentiate between SAAW-STW, SAAW-ESSW, and ESSW-AAIW. δ13CDIC signatures can be used to differentiate between STW-ESSW (oceanic section), SAAW-ESSW, ESSW-AAIW, and AAIW-PDW. Compared with the oceanic section, our new coastal section highlights differences in both the chemistry and geometry of water masses above 1,000 m. Previous paleoceanographic studies using marine sediments from the SEP continental margin used the present-day hydrological oceanic transect to compare against, as the coastal section was not sufficiently characterized. We suggest that our new results of the coastal section should be used for past characterizations of the SEP water masses that are usually based on continental margin sediment samples

Interacting Galaxies in the A901/902 Supercluster with STAGES

We present a study of galaxy mergers and the influence of environment in the Abell 901/902 supercluster at z~0.165. We use HST ACS F606W data from the STAGES survey, COMBO-17, Spitzer 24um, and XMM-Newton X-ray data. Our analysis utilizes both a visual classification system, and quantitative CAS parameters to identify systems which show evidence of a recent or ongoing merger of mass ratio >1/10. Our results are: (1) After visual classification and minimizing the contamination from false projection pairs, we find that the merger fraction f_merge is 0.023+/-0.007. The estimated fractions of likely major mergers, likely minor mergers, and ambiguous cases are 0.01+/-0.004, 0.006+/-0.003, and 0.007+/-0.003, respectively. (2) The mergers lie outside the cluster core of radius R < 0.25 Mpc: the lack of mergers in the core is likely due to the large galaxy velocity dispersion in the core. Mergers populate the region (0.25 Mpc < R <= 2 Mpc) between the core and outskirt. In this region, the estimated frequency of mergers is similar to those seen at typical group overdensities. This suggests ongoing growth of the clusters via accretion of group and field galaxies. (3) We compare our observed merger fraction with those reported in other clusters and groups out to z~0.4. Existing data points on the merger fraction for L<= L* galaxies in clusters allow for a range of evolutionary scenarios. (4) The fraction of mergers, which lie on the blue cloud is 80%+/-18% versus 34%+/-7% for non-interacting galaxies, implying that interacting galaxies are preferentially blue. (5) The average SFR, based on UV or UV+IR data, is enhanced by a factor of ~1.5 to 2 in mergers compared to non-interacting galaxies. However, mergers in the clusters contribute only a small fraction (between 10% and 15%) of the total SFR density.(Abridged)Comment: Accepted for publication in ApJ. 34 pages, 16 figures. Version with full resolution figures available at: http://www.as.utexas.edu/~alh/apj/int/ ; updated abridged abstrac

History of Galaxy Interactions and their Impact on Star Formation over the Last 7 Gyr from GEMS

We perform a comprehensive estimate of the frequency of galaxy mergers and their impact on star formation over z~0.24--0.80 (lookback time T_b~3--7 Gyr) using 3698 (M*>=1e9 Msun) galaxies with GEMS HST, COMBO-17, and Spitzer data. Our results are: (1) Among 790 high mass (M*>=2.5e10 Msun) galaxies, the visually-based merger fraction over z~0.24--0.80, ranges from 9%+-5% to 8%+-2%. Lower limits on the major and minor merger fractions over this interval range from 1.1% to 3.5%, and 3.6% to 7.5%, respectively. This is the first approximate empirical estimate of the frequency of minor mergers at z<1. For a visibility timescale of ~0.5 Gyr, it follows that over T_b~3--7 Gyr, ~68% of high mass systems have undergone a merger of mass ratio >1/10, with ~16%, 45%, and 7% of these corresponding respectively to major, minor, and ambiguous `major or minor' mergers. The mean merger rate is a few x 1e-4 Gyr-1 Mpc-3. (2) We compare the empirical merger fraction and rate for high mass galaxies to a suite of Lambda CDM-based models: halo occupation distribution models, semi-analytic models, and hydrodynamic SPH simulations. We find qualitative agreement between observations and models such that the (major+minor) merger fraction or rate from different models bracket the observations, and show a factor of five dispersion. Near-future improvements can now start to rule out certain merger scenarios. (3) Among ~3698 M*>=1e9 Msun galaxies, we find that the mean SFR of visibly merging systems is only modestly enhanced compared to non-interacting galaxies over z~0.24--0.80. Visibly merging systems only account for less than 30% of the cosmic SFR density over T_b~3--7 Gyr. This suggests that the behavior of the cosmic SFR density over the last 7 Gyr is predominantly shaped by non-interacting galaxies.Comment: Accepted for Publication in the Astrophysical Journal. 17 pages of text, 21 figures, 3 tables. Uses emulateapj5.st