Do the Fix Ingredients Already Exist? An Empirical Inquiry into the Redundancy Assumptions of Program Repair Approaches

Much initial research on automatic program repair has focused on experimental results to probe their potential to find patches and reduce development effort. Relatively less effort has been put into understanding the hows and whys of such approaches. For example, a critical assumption of the GenProg technique is that certain bugs can be fixed by copying and re-arranging existing code. In other words, GenProg assumes that the fix ingredients already exist elsewhere in the code. In this paper, we formalize these assumptions around the concept of ''temporal redundancy''. A temporally redundant commit is only composed of what has already existed in previous commits. Our experiments show that a large proportion of commits that add existing code are temporally redundant. This validates the fundamental redundancy assumption of GenProg.Comment: ICSE - 36th IEEE International Conference on Software Engineering (2014

Optical air data systems and methods

Systems and methods for sensing air outside a moving aircraft are presented. In one embodiment, a system includes a laser for generating laser energy. The system also includes one or more transceivers for projecting the laser energy as laser radiation to the air. Subsequently, each transceiver receives laser energy as it is backscattered from the air. A computer processes signals from the transceivers to distinguish molecular scattered laser radiation from aerosol scattered laser radiation and determines one or more air parameters based on the scattered laser radiation. Such air parameters may include air speed, air pressure, air temperature and aircraft orientation angle, such as yaw, angle of attack and sideslip

Optical air data systems and methods

Systems and methods for sensing air outside a moving aircraft are presented. In one embodiment, a system includes a laser for generating laser energy. The system also includes one or more transceivers for projecting the laser energy as laser radiation to the air. Subsequently, each transceiver receives laser energy as it is backscattered from the air. A computer processes signals from the transceivers to distinguish molecular scattered laser radiation from aerosol scattered laser radiation and determines one or more air parameters based on the scattered laser radiation. Such air parameters may include air speed, air pressure, air temperature and aircraft orientation angle, such as yaw, angle of attack and sideslip

Alfalfa: Crop for the Future

Alfalfa use by dairy cattle has decreased in recent years because of excessive nonprotein nitrogen and low fiber digestibility. Ideal attributes for plant modification of alfalfa may include those that increase milk potential per acre and/or per ton, enhance digestible NDF, improve protein content and amino acid balance, improve agronomic traits for insect protection (safer forage supply), herbicide tolerance, virus resistance, drought tolerance, cold tolerance, improved mineral availability and enhanced yield. Progress in attaining these attributes will accelerate with the use of biotechnology. Livestock and hay enterprises will benefit from alfalfa that is less prone to contain mycotoxins or toxic weeds, or to induce bloat; have improved nutrient utilization for milk and meat production; and produce less animal wastes resulting in improved efficiency, profitability, and a better environment. Value-added traits of alfalfa are needed to provide farmers new high value profitable products. Processing alfalfa to obtain value added products includes three different fractionation methods: 1) wet fractionation; separation into juice fraction and a fiber fraction, 2) dry fractionation; separation into leaves and stems, and 3) fractionation by passage of the whole herbage through the digestive systems of ruminant animals, leaving a high fiber residue. Phytase from transgenic alfalfa has been tested in poultry and swine rations. Alfalfa hay can be fractionated to yield stems and leaf meal. Alfalfa leaf meal has been shown to be acceptable supplement to replace a portion of alfalfa hay and soybean meal in diets of lactating dairy cattle, replace protein supplement in beef cow diets, finishing steer diets and diets of growing turkeys. The fiber portion of alfalfa can produce lactic acid, ethanol or a bioadhesives for use in plywood

EU pesticides regulation: how public support can be rebuilt

The regulation of pesticides in the EU has become increasingly controversial. But what are the views of EU citizens and how would proposed reforms affect public support for EU pesticides regulation? Jonathan Zeitlin, Maria Weimer, David van der Duin, Theresa Kuhn and Martin Dybdahl Jensen outline findings from a survey experiment conducted in six EU member states

Atomic layer deposited oxide films as protective interface layers for integrated graphene transfer

The transfer of chemical vapour deposited (CVD) graphene from its parent growth catalyst has become a bottleneck for many of its emerging applications. The sacrificial polymer layers that are typically deposited onto graphene for mechanical support during transfer are challenging to fully remove and hence leave graphene and subsequent device interfaces contaminated. Here, we report on the use of atomic layer deposited (ALD) oxide films as protective interface and support layers during graphene transfer. The method avoids any direct contact of the graphene with polymers and through the use of thicker ALD layers (≥100nm), polymers can be eliminated from the transfer-process altogether. The ALD film can be kept as a functional device layer, facilitating integrated device manufacturing. We demonstrate back-gated field effect devices based on single-layer graphene transferred with a protective Al2O3 film onto SiO2 that show significantly reduced charge trap and residual carrier densities. We critically discuss the advantages and challenges of processing graphene/ALD bilayer structures.We acknowledge funding from EPSRC (Grant No. EP/K016636/1, GRAPHTED) and ERC (Grant No. 279342, InsituNANO). ACV acknowledges the Conacyt Cambridge Scholarship and Roberto Rocca Fellowship. JAA-W acknowledges the support of his Research Fellowships from the Royal Commission for the Exhibition of 1851 and Churchill College, Cambridge. RSW acknowledges a Research Fellowship from St. John's College, Cambridge and a Marie Skłodowska-Curie Individual Fellowship (Global) under grant ARTIST (no. 656870) from the European Union's Horizon 2020 research and innovation programme

Microbial biodiversity of Great Salt Lake, Utah

Microbial biodiversity is difficult to measure in extreme environments due to the inability to culture many of the species, especially from hypersaline environments. Great Salt Lake (GSL), Utah, USA offers a unique ecology to study microbial diversity across a salt gradient. GSL has increasing salt from South to North that varies from marine salt concentrations to saturation, respectively. We used three methods to examine the biodiversity of the GSL-traditional cultivation on solid media, 16s rRNA gene sequencing, multiplexed 16s rRNA gene hybridization to the phylochip, and DNA hybridization to the Geochip for metabolic diversity estimates. Over 40 isolates from the North Arm were obtained, while six were selected for identification. Isolates included gammaproteobacteria, bacilli, and actinobacteria. Sequencing the 16S rRNA genes for identification yielded 350 clones. Refraction curves indicated that this did not represent the bacterial diversity of the GSL, while estimation of the diversity with the Affymetrix phylochip produced over 1000 different genera in 31 different families. Estimation of the metabolic diversity found that genes for each activity were present in all three locations. The gene abundance was similar in all locations, except for metal use where the gene abundance declined as the salt gradient declined. This study provides the first evidence of the large microbial diversity supported by GSL to provide a large metabolic potential independent of the salt concentration

Interaction-driven (quasi-) insulating ground states of gapped electron-doped bilayer graphene

Bernal bilayer graphene has recently been discovered to exhibit a wide range of unique ordered phases resulting from interaction-driven effects and encompassing spin and valley magnetism, correlated insulators, correlated metals, and superconductivity. This letter reports on a novel family of correlated phases characterized by spin and valley ordering, observed in electron-doped bilayer graphene. The novel correlated phases demonstrate an intriguing non-linear current-bias behavior at ultralow currents that is sensitive to the onset of the phases and is accompanied by an insulating temperature dependence, providing strong evidence for the presence of unconventional charge carrying degrees of freedom originating from ordering. These characteristics cannot be solely attributed to any of the previously reported phases, and are qualitatively different from the behavior seen previously on the hole-doped side. Instead, our observations align with the presence of charge- or spin-density-waves state that open a gap on a portion of the Fermi surface or fully gapped Wigner crystals. The resulting new phases, quasi-insulators in which part of the Fermi surface remains intact or valley-polarized and valley-unpolarized Wigner crystals, coexist with previously known Stoner phases, resulting in an exceptionally intricate phase diagram

HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data

BACKGROUND: The human leukocyte antigen (HLA) system is a genomic region involved in regulating the human immune system by encoding cell membrane major histocompatibility complex (MHC) proteins that are responsible for self-recognition. Understanding the variation in this region provides important insights into autoimmune disorders, disease susceptibility, oncological immunotherapy, regenerative medicine, transplant rejection, and toxicogenomics. Traditional approaches to HLA typing are low throughput, target only a few genes, are labor intensive and costly, or require specialized protocols. RNA sequencing promises a relatively inexpensive, high-throughput solution for HLA calling across all genes, with the bonus of complete transcriptome information and widespread availability of historical data. Existing tools have been limited in their ability to accurately and comprehensively call HLA genes from RNA-seq data. RESULTS: We created HLAProfiler ( https://github.com/ExpressionAnalysis/HLAProfiler ), a k-mer profile-based method for HLA calling in RNA-seq data which can identify rare and common HLA alleles with > 99% accuracy at two-field precision in both biological and simulated data. For 68% of novel alleles not present in the reference database, HLAProfiler can correctly identify the two-field precision or exact coding sequence, a significant advance over existing algorithms. CONCLUSIONS: HLAProfiler allows for accurate HLA calls in RNA-seq data, reliably expanding the utility of these data in HLA-related research and enabling advances across a broad range of disciplines. Additionally, by using the observed data to identify potential novel alleles and update partial alleles, HLAProfiler will facilitate further improvements to the existing database of reference HLA alleles. HLAProfiler is available at https://expressionanalysis.github.io/HLAProfiler/