A Quantitative Study of Java Software Buildability

Researchers, students and practitioners often encounter a situation when the build process of a third-party software system fails. In this paper, we aim to confirm this observation present mainly as anecdotal evidence so far. Using a virtual environment simulating a programmer's one, we try to fully automatically build target archives from the source code of over 7,200 open source Java projects. We found that more than 38% of builds ended in failure. Build log analysis reveals the largest portion of errors are dependency-related. We also conduct an association study of factors affecting build success

Infrared Spectroscopy of Trapped Gases in Metal-Organic Frameworks

There are a range of environmental and industrial applications to capturing carbon dioxide from gas mixtures. Currently, materials being used in these applications bind carbon dioxide too strongly for practical purposes, such that they require large amounts of energy to be regenerated for reuse. Highly porous materials called metal-organic frameworks (MOFs) could serve much more effectively as carbon-capturing materials, as they suck up large amounts of carbon dioxide gas at pressures and temperatures that are nearly ideal for carbon-capture applications. Moreover, they require much less energy than current materials to release the carbon dioxide and be regenerated. Additionally, many different structures can be created fairly easily, so scientists are on the hunt for the ideal carbon-capturing MOF. In this thesis we study Mg-MOF-74, a particularly promising metal-organic framework material for separating carbon dioxide from gas mixtures. We use infrared spectroscopy to probe the interactions between the Mg-MOF-74 host and both carbon dioxide and methane. By shining infrared radiation on Mg-MOF-74 with gases trapped in it and looking at which frequencies of radiation are absorbed by the bound gases, we can learn about the binding nature of the framework. This in turn helps us to better understand the properties are are preferable in metal organic frameworks, and will aid chemists in fabricating new structures that are ideal for carbon-capture and other applications

Infrared Spectroscopy of Trapped Gases in Metal-Organic Frameworks

There are a range of environmental and industrial applications to capturing carbon dioxide from gas mixtures. Currently, materials being used in these applications bind carbon dioxide too strongly for practical purposes, such that they require large amounts of energy to be regenerated for reuse. Highly porous materials called metal-organic frameworks (MOFs) could serve much more effectively as carbon-capturing materials, as they suck up large amounts of carbon dioxide gas at pressures and temperatures that are nearly ideal for carbon-capture applications. Moreover, they require much less energy than current materials to release the carbon dioxide and be regenerated. Additionally, many different structures can be created fairly easily, so scientists are on the hunt for the ideal carbon-capturing MOF. In this thesis we study Mg-MOF-74, a particularly promising metal-organic framework material for separating carbon dioxide from gas mixtures. We use infrared spectroscopy to probe the interactions between the Mg-MOF-74 host and both carbon dioxide and methane. By shining infrared radiation on Mg-MOF-74 with gases trapped in it and looking at which frequencies of radiation are absorbed by the bound gases, we can learn about the binding nature of the framework. This in turn helps us to better understand the properties are are preferable in metal organic frameworks, and will aid chemists in fabricating new structures that are ideal for carbon-capture and other applications

Receipt from Israel M. Schloss

https://digitalcommons.salve.edu/goelet-new-york/1174/thumbnail.jp

Receipt from Israel M. Schloss, duplicate

https://digitalcommons.salve.edu/goelet-new-york/1175/thumbnail.jp

Diversity of O Antigens within the Genus Cronobacter: from Disorder to Order

Cronobacter species are Gram-negative opportunistic pathogens that can cause serious infections in neonates. The lipopolysaccharides (LPSs) that form part of the outer membrane of such bacteria are possibly related to the virulence of particular bacterial strains. However, currently there is no clear overview of O-antigen diversity within the various Cronobacter strains and links with virulence. In this study, we tested a total of 82 strains, covering each of the Cronobacter species. The nucleotide variability of the O-antigen gene cluster was determined by restriction fragment length polymorphism (RFLP) analysis. As a result, the 82 strains were distributed into 11 previously published serotypes and 6 new serotypes, each defined by its characteristic restriction profile. These new serotypes were confirmed using genomic analysis of strains available in public databases: GenBank and PubMLST Cronobacter. Laboratory strains were then tested using the current serotype-specific PCR probes. The results show that the current PCR probes did not always correspond to genomic O-antigen gene cluster variation. In addition, we analyzed the LPS phenotype of the reference strains of all distinguishable serotypes. The identified serotypes were compared with data from the literature and the MLST database (www.pubmlst.org/cronobacter/). Based on the findings, we systematically classified a total of 24 serotypes for the Cronobacter genus. Moreover, we evaluated the clinical history of these strains and show that Cronobacter sakazakii O2, O1, and O4, C. turicensis O1, and C. malonaticus O2 serotypes are particularly predominant in clinical cases

Interactions between carbon and nitrogen dynamics in estimating net primary productivity for potential vegetation in North America

We use the terrestrial ecosystem model (TEM), a process-based model, to investigate how interactions between carbon (C) and nitrogen (N) dynamics affect predictions of net primary productivity (NPP) for potential vegetation in North America. Data on pool sizes and fluxes of C and N from intensively studied field sites are used to calibrate the model for each of 17 non-wetland vegetation types. We use information on climate, soils, and vegetation to make estimates for each of 11,299 non-wetland, 0.5° latitude × 0.5° longitude, grid cells in North America. The potential annual NPP and net N mineralization (NETNMIN) of North America are estimated to be 7.032 × 1015 g C yr−1 and 104.6 × 1012 g N yr−1, respectively. Both NPP and NETNMIN increase along gradients of increasing temperature and moisture in northern and temperate regions of the continent, respectively. Nitrogen limitation of productivity is weak in tropical forests, increasingly stronger in temperate and boreal forests, and very strong in tundra ecosystems. The degree to which productivity is limited by the availability of N also varies within ecosystems. Thus spatial resolution in estimating exchanges of C between the atmosphere and the terrestrial biosphere is improved by modeling the linkage between C and N dynamics. We also perform a factorial experiment with TEM on temperate mixed forest in North America to evaluate the importance of considering interactions between C and N dynamics in the response of NPP to an elevated temperature of 2°C. With the C cycle uncoupled from the N cycle, NPP decreases primarily because of higher plant respiration. However, with the C and N cycles coupled, NPP increases because productivity that is due to increased N availability more than offsets the higher costs of plant respiration. Thus, to investigate how global change will affect biosphere-atmosphere interactions, process-based models need to consider linkages between the C and N cycles

A Fast Sextupole Probe for Snapback Measurement in the LHC Dipoles

In superconducting particle accelerators a fast change of the magnetic field occurs during the first few seconds after the start of an energy ramp. Standard magnetic measurements using a coil rotating at 1 Hz do not have the time resolution required to completely resolve this phase, usually called snapback. For this reason we have developed a new and fast system dedicated to sextupole measurements. The basic component consists of three Hall plates mounted on a ring. In an ideal case this arrangement compensates the main dipole field and produces a signal proportional to the sextupole only. Mechanical tolerances and differences in the sensitivity of the Hall plates are compensated by instrumentation amplifiers and an in situ fine adjustment of the probe orientation. Using this hybrid compensation technique we have measured sextupole variations in an LHC dipole prototype during snapback at a rate of 5 Hz. In this paper we present details on the device and the results of our measurements

TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.)