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

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

Improving Summarization with Human Edits

Recent work has shown the promise of learning with human feedback paradigms to produce human-determined high-quality text. Existing works use human feedback to train large language models (LLMs) in general domain abstractive summarization and have obtained summary quality exceeding traditional likelihood training. In this paper, we focus on a less explored form of human feedback -- Human Edits. We propose Sequence Alignment (un)Likelihood Training (SALT), a novel technique to use both the human-edited and model-generated data together in the training loop. In addition, we demonstrate simulating Human Edits with ground truth summaries coming from existing training data -- Imitation edits, along with the model-generated summaries obtained after the training, to reduce the need for expensive human-edit data. In our experiments, we extend human feedback exploration from general domain summarization to medical domain summarization. Our results demonstrate the effectiveness of SALT in improving the summary quality with Human and Imitation Edits. Through additional experiments, we show that SALT outperforms the conventional RLHF method (designed for human preferences) -- DPO, when applied to human-edit data. We hope the evidence in our paper prompts researchers to explore, collect, and better use different human feedback approaches scalably.Comment: To appear in proceedings of the Main Conference on Empirical Methods in Natural Language Processing (EMNLP) 202

A System for Series Magnetic Measurements of the LHC Main Quadrupoles

More than 400 twin aperture lattice quadrupoles are needed for the Large Hadron Collider (LHC) which is under construction at CERN. The main quadrupole is assembled with correction magnets in a common cryostat called the Short Straight Section (SSS). We plan to measure all SSS's in cold conditions with an unprecedented accuracy: integrated gradient of the field within 150 ppm, harmonics in a range of 1 to 5 ppm, magnetic axis of all elements within 0.1 mm and their field direction within 0.2 mrad. In this paper we describe the automatic measurement system that we have designed, built and calibrated. Based on the results obtained on the two first prototypes of the SSS's (SSS3 and SSS4) we show that this system meets all above requirements

Potential net primary productivity in South America: application of a global model

We use a mechanistically based ecosystem simulation model to describe and analyze the spatial and temporal patterns of terrestrial net primary productivity (NPP) in South America. The Terrestrial Ecosystem Model (TEM) is designed to predict major carbon and nitrogen fluxes and pool sizes in terrestrial ecosystems at continental to global scales. Information from intensively studies field sites is used in combination with continental—scale information on climate, soils, and vegetation to estimate NPP in each of 5888 non—wetland, 0.5° latitude °0.5° longitude grid cells in South America, at monthly time steps. Preliminary analyses are presented for the scenario of natural vegetation throughout the continent, as a prelude to evaluating human impacts on terrestrial NPP. The potential annual NPP of South America is estimated to be 12.5 Pg/yr of carbon (26.3 Pg/yr of organic matter) in a non—wetland area of 17.0 ° 106 km2. More than 50% of this production occurs in the tropical and subtropical evergreen forest region. Six independent model runs, each based on an independently derived set of model parameters, generated mean annual NPP estimates for the tropical evergreen forest region ranging from 900 to 1510 g°m—2°yr—1 of carbon, with an overall mean of 1170 g°m—2°yr—1. Coefficients of variation in estimated annual NPP averaged 20% for any specific location in the evergreen forests, which is probably within the confidence limits of extant NPP measurements. Predicted rates of mean annual NPP in other types of vegetation ranged from 95 g°m—2°yr—1 in arid shrublands to 930 g°m@?yr—1 in savannas, and were within the ranges measured in empirical studies. The spatial distribution of predicted NPP was directly compared with estimates made using the Miami mode of Lieth (1975). Overall, TEM predictions were °10% lower than those of the Miami model, but the two models agreed closely on the spatial patterns of NPP in south America. Unlike previous models, however, TEM estimates NPP monthly, allowing for the evaluation of seasonal phenomena. This is an important step toward integration of ecosystem models with remotely sensed information, global climate models, and atmospheric transport models, all of which are evaluated at comparable spatial and temporal scales. Seasonal patterns of NPP in South America are correlated with moisture availability in most vegetation types, but are strongly influenced by seasonal differences in cloudiness in the tropical evergreen forests. On an annual basis, moisture availability was the factor that was correlated most strongly with annual NPP in South America, but differences were again observed among vegetation types. These results allow for the investigation and analysis of climatic controls over NPP at continental scales, within and among vegetation types, and within years. Further model validation is needed. Nevertheless, the ability to investigate NPP—environment interactions with a high spatial and temporal resolution at continental scales should prove useful if not essential for rigorous analysis of the potential effects of global climate changes on terrestrial ecosystems

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden

Abstract Background A growing body of evidence indicates that the gut microbiome plays a role in the development of colorectal cancer (CRC). Patients with CRC harbor gut microbiomes that are structurally distinct from those of healthy individuals; however, without the ability to track individuals during disease progression, it has not been possible to observe changes in the microbiome over the course of tumorigenesis. Mouse models have demonstrated that these changes can further promote colonic tumorigenesis. However, these models have relied upon mouse-adapted bacterial populations and so it remains unclear which human-adapted bacterial populations are responsible for modulating tumorigenesis. Results We transplanted fecal microbiota from three CRC patients and three healthy individuals into germ-free mice, resulting in six structurally distinct microbial communities. Subjecting these mice to a chemically induced model of CRC resulted in different levels of tumorigenesis between mice. Differences in the number of tumors were strongly associated with the baseline microbiome structure in mice, but not with the cancer status of the human donors. Partitioning of baseline communities into enterotypes by Dirichlet multinomial mixture modeling resulted in three enterotypes that corresponded with tumor burden. The taxa most strongly positively correlated with increased tumor burden were members of the Bacteroides, Parabacteroides, Alistipes, and Akkermansia, all of which are Gram-negative. Members of the Gram-positive Clostridiales, including multiple members of Clostridium Group XIVa, were strongly negatively correlated with tumors. Analysis of the inferred metagenome of each community revealed a negative correlation between tumor count and the potential for butyrate production, and a positive correlation between tumor count and the capacity for host glycan degradation. Despite harboring distinct gut communities, all mice underwent conserved structural changes over the course of the model. The extent of these changes was also correlated with tumor incidence. Conclusion Our results suggest that the initial structure of the microbiome determines susceptibility to colonic tumorigenesis. There appear to be opposing roles for certain Gram-negative (Bacteroidales and Verrucomicrobia) and Gram-positive (Clostridiales) bacteria in tumor susceptibility. Thus, the impact of community structure is potentially mediated by the balance between protective, butyrate-producing populations and inflammatory, mucin-degrading populations.http://deepblue.lib.umich.edu/bitstream/2027.42/109448/1/40168_2014_Article_48.pd

Twin Rotating Coils for Cold Magnetic Measurements of 15 m Long LHC Dipoles

We describe here a new harmonic coil system for the field measurement of the superconducting, twin aperture LHC dipoles and the associated corrector magnets. Besides field measurements the system can be used as an antenna to localize the quench origin. The main component is a 16 m long rotating shaft, made up of 13 ceramic segments, each carrying two tangential coils plus a central radial coil, all working in parallel. The segments are connected with flexible Ti-alloy bellows, allowing the piecewise straight shaft to follow the curvature of the dipole while maintaining high torsional rigidity. At each interconnection the structure is supported by rollers and ball bearings, necessary for the axial movement for installation and for the rotation of the coil during measurement. Two such shafts are simultaneously driven by a twin-rotating unit, thus measuring both apertures of a dipole at the same time. This arrangement allows very short measurement times (typically 10 s) and is essential to perform cold magnetic measurements of all dipoles. The coil surface and direction are calibrated using a reference dipole. In this paper we describe the twin rotating coil system and its calibration facility, and we give the typical resolution and accuracy achieved with the first commissioned unit