Reify Your Collection Queries for Modularity and Speed!

Modularity and efficiency are often contradicting requirements, such that programers have to trade one for the other. We analyze this dilemma in the context of programs operating on collections. Performance-critical code using collections need often to be hand-optimized, leading to non-modular, brittle, and redundant code. In principle, this dilemma could be avoided by automatic collection-specific optimizations, such as fusion of collection traversals, usage of indexing, or reordering of filters. Unfortunately, it is not obvious how to encode such optimizations in terms of ordinary collection APIs, because the program operating on the collections is not reified and hence cannot be analyzed. We propose SQuOpt, the Scala Query Optimizer--a deep embedding of the Scala collections API that allows such analyses and optimizations to be defined and executed within Scala, without relying on external tools or compiler extensions. SQuOpt provides the same "look and feel" (syntax and static typing guarantees) as the standard collections API. We evaluate SQuOpt by re-implementing several code analyses of the Findbugs tool using SQuOpt, show average speedups of 12x with a maximum of 12800x and hence demonstrate that SQuOpt can reconcile modularity and efficiency in real-world applications.Comment: 20 page

Seismic imaging in the Krafla high-temperature geothermal field, NE Iceland, using zero- and far-offset vertical seismic profiling (VSP) data

The research leading to these results has received funding from the European Community's Seventh Framework Program under grant agreement No. 608553 (Project IMAGE). We thank Landsvirkjun, the operator of the Krafla geothermal field, for technical and logistical support during the survey. We also thank the Operational Support Group of the International Continental Scientific Drilling Program (ICDP) for their technical support. We further acknowledge the support from the Research Council of Norway through its Centres of Excellence funding scheme, project 22372 (SP).Peer reviewedPostprin

Core-log-seismic integration in metamorphic rocks and its implication for the regional geology: A case study for the ICDP drilling project COSC-1, Sweden

Continental collision causes deformation in the crust along shear zones. However, the physical and chemical conditions at which these zones operate and the deformation processes that enable up to hundreds of km of tectonic transport are still unclear because of the depth at which they occur and the challenges in imaging them. Ancient exhumed collision zones allow us to investigate these processes much better, for example at the COSC‐1 borehole in the central Scandinavian Caledonides. This study combines data from the COSC‐1 borehole with different seismic measurements to provide constraints on the spatial lithological and textural configuration of the Seve Nappe Complex. This is one of the few studies that shows that core‐log‐seismic integration in metamorphic rocks allows to identify the spatial distribution of major lithological units. Especially gamma ray logs in combination with density data are powerful tools to distinguish between mafic and felsic lithologies in log‐core correlation. Our results indicate that reflections along the borehole are primarily caused by compositional rather than textural changes. Reflections in the Seve Nappe Complex are not as distinct as in greater depths but continuous and several of them can be linked to magmatic intrusions, which have been metamorphically overprinted. Their setting indicates that the Seve Nappe Complex consists of the remnants of a volcanic continental margin. Our results suggest that ductile‐deformed middle crustal reflectivity is primarily a function of pre‐orogenic lithological variations which has to be considered when deciphering mountain building processes

Evaluation of the upper respiratory tract in the horse during treadmill exercise - A review Part ll: Measurement of upper airway flow mechanics

Literature pertaining to the evaluation of the upper respiratory tract of the horse during exercise was reviewed. Articles were found by searching two databases. Videoendoscopy of the upper airways during exercise is presented in part I of this review. Part II describes upper airway pressure and airflow measurements for objective assessement of the prescence of a respiratory limitation. Different measurement techniques and definitions of upper airway pressure as well as airflow measurement techniques are described. Upper airway pressures and flow indices increase linearly with increasing exercise. Airflow resistance as caused by laryngeal hemiplegia grade IV increases negative upper airway pressure and limits inspiratory flow. Dorsal displacement of the soft palate alters both inspiratory and expiratory pressures

Compressed AFM-IR hyperspectral nanoimaging

Infrared (IR) hyperspectral imaging is a powerful approach in the field of materials and life sciences. However, for the extension to modern sub-diffraction nanoimaging it still remains a highly inefficient technique, as it acquires data via inherent sequential schemes. Here, we introduce the mathematical technique of low-rank matrix reconstruction to the sub-diffraction scheme of atomic force microscopy-based infrared spectroscopy (AFM-IR), for efficient hyperspectral IR nanoimaging. To demonstrate its application potential, we chose the trypanosomatid unicellular parasites Leishmania species as a realistic target of biological importance. The mid-IR spectral fingerprint window covering the spectral range from 1300 to 1900 cm−1 was chosen and a distance between the data points of 220 nm was used for nanoimaging of single parasites. The method of k-means cluster analysis was used for extracting the chemically distinct spatial locations. Subsequently, we randomly selected only 10% of an originally gathered data cube of 134 (x) × 50 (y) × 148 (spectral) AFM-IR measurements and completed the full data set by low-rank matrix reconstruction. This approach shows agreement in the cluster regions between full and reconstructed data cubes. Furthermore, we show that the results of the low-rank reconstruction are superior compared to alternative interpolation techniques in terms of error-metrics, cluster quality, and spectral interpretation for various subsampling ratios. We conclude that by using low-rank matrix reconstruction the data acquisition time can be reduced from more than 14 h to 1–2 h. These findings can significantly boost the practical applicability of hyperspectral nanoimaging in both academic and industrial settings involving nano- and bio-materials

A novel gain-of-function mutation of Piezo1 is functionally affirmed in red blood cells by high-throughput patch clamp

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