Assessing the effect of source code characteristics on changeability

Maintenance is the phase of the software lifecycle that comprises any modification after the delivery of an application. Modifications during this phase include correcting faults, improving internal attributes, as well as adapting the application to different environments. As application knowledge and architectural integrity degrade over time, so does the facility with which changes to the application are introduced. Thus, eliminating source code that presents characteristics that hamper maintenance becomes necessary if the application is to evolve. We group these characteristics under the term Source Code Issues. Even though there is support for detecting Source Code Issues, the extent of their harmfulness for maintenance remains unknown. One of the most studied Source Code Issue is cloning. Clones are duplicated code, usually created as programmers copy, paste, and customize existing source code. However, there is no agreement on the harmfulness of clones. This thesis proposes and follows a novel methodology to assess the effect of clones on the changeability of methods. Changeability is the ease with which a source code entity is modified. It is assessed through metrics calculated from the history of changes of the methods. The impact of clones on the changeability of methods is measured by comparing the metrics of methods that contain clones to those that do not. Source code characteristics are then tested to establish whether they are endemic of methods whose changeability decay increase when cloned. In addition to findings on the harmfulness of cloning, this thesis contributes a methodology that can be applied to assess the harmfulness of other Source Code Issues. The contributions of this thesis are twofold. First, the findings answer the question about the harmfulness of clones on changeability by showing that cloned methods are more likely to change, and that some cloned methods have significantly higher changeability decay when cloned. Furthermore, it offers a characterization of such harmful clones. Second, the methodology provides a guide to analyze the effect of Source Code Characteristics in changeability; and therefore, can be adapted for other Source Code Issues

Phase imaging with intermodulation atomic force microscopy

Intermodulation atomic force microscopy (IMAFM) is a dynamic mode of atomic force microscopy (AFM) with two-tone excitation. The oscillating AFM cantilever in close proximity to a surface experiences the nonlinear tip-sample force which mixes the drive tones and generates new frequency components in the cantilever response known as intermodulation products (IMPs). We present a procedure for extracting the phase at each IMP and demonstrate phase images made by recording this phase while scanning. Amplitude and phase images at intermodulation frequencies exhibit enhanced topographic and material contrast.Comment: 6 pages, 6 page

Prototyping of petalets for the Phase-II Upgrade of the silicon strip tracking detector of the ATLAS Experiment

In the high luminosity era of the Large Hadron Collider, the HL-LHC, the instantaneous luminosity is expected to reach unprecedented values, resulting in about 200 proton-proton interactions in a typical bunch crossing. To cope with the resultant increase in occupancy, bandwidth and radiation damage, the ATLAS Inner Detector will be replaced by an all-silicon system, the Inner Tracker (ITk). The ITk consists of a silicon pixel and a strip detector and exploits the concept of modularity. Prototyping and testing of various strip detector components has been carried out. This paper presents the developments and results obtained with reduced-size structures equivalent to those foreseen to be used in the forward region of the silicon strip detector. Referred to as petalets, these structures are built around a composite sandwich with embedded cooling pipes and electrical tapes for routing the signals and power. Detector modules built using electronic flex boards and silicon strip sensors are glued on both the front and back side surfaces of the carbon structure. Details are given on the assembly, testing and evaluation of several petalets. Measurement results of both mechanical and electrical quantities are shown. Moreover, an outlook is given for improved prototyping plans for large structures.Comment: 22 pages for submission for Journal of Instrumentatio

Predictors of diabetes risk in urban and rural areas in Colombia

Background: Nutritional habits low in fruits and vegetables and sedentary lifestyle are associated with a higher risk of developing Type 2 Diabetes (T2D). However, it is important to assess differences between urban and rural areas. This study aimed to analyze the associations between the risk of developing T2D and setting in the Colombian north coast in 2017. Methods: This cross-sectional study included 1,005 subjects. Data was collected by interviewing self-identified members of an urban community and a rural-indigenous population. The interaction terms were evaluated as well as the confounders. Then, adjusted binary logistic regressions were used to estimate the odds ratio (OR) and 95% Confidence Intervals (CI). Results: subjects with a high risk of T2D are more likely to belong to the urban setting (OR = 1.908; 95%CI = 1.201-2.01) compared with those with lower T2D after adjusting for age, Body Mass Index (BMI), physical activity, history of high levels of glycemia, and diabetes in relatives. Conclusions: Urban communities are more likely to have T2D compared with rural-indigenous populations. These populations have differences from the cultural context, including personal, and lifestyle factors.Peer reviewe

New Evidence on Regucalcin, Body Composition, and Walking Ability Adaptations to Multicomponent Exercise Training in Functionally Limited and Frail Older Adults

Background: Regucalcin, or senescence marker protein-30 (SMP30), is a Ca2+-binding protein with multiple functions reported in the literature. Physical exercise has been shown to improve aging markers; nevertheless, SMP30 in humans has not been extensively researched. Older adults experience a decline in functional capacity and body composition. The purpose of this study was to examine the effects of a multicomponent training (MCT) program on SMP30 and its regulation of walking ability and body composition in functionally limited, frail, and pre-frail older adults. Methods: A total of 34 older adults (aged 80.3 +/- 6.1 years) were divided into an intervention group (IG = 20) and control group (CG = 14). The IG performed a supervised MCT (strength, endurance, balance, coordination, and flexibility) program for 6 months, 3 days per week, whereas the CG continued their normal lives without any specific physical training. SMP30 was analyzed in plasma after 3 and 6 months of MCT, while some physical fitness variables (Timed Up and Go (TUG) and 6-min walk test (6MWT)) and body composition (fat mass and lean mass) were measured at baseline, as well as after 3 months and 6 months of MCT. Results: No significant changes were observed in SPM30 between the IG (877.5 a.u. to 940.5 a.u., respectively) and CG (790.4 a.u. to 763.8 a.u., respectively). Moreover, no SMP30 differences were found between groups after 3 and 6 months of MCT. The IG improved significantly in the 6MWT after 3 months (472.2 +/- 84.2 m) compared to baseline (411.2 +/- 75.2 m). The IG also significantly enhanced their TUG performance after 3 months (7.6 +/- 1.6 s) and 6 months (7.3 +/- 1.8 s) of training compared to baseline (9.3 +/- 3.2 s) (all, p < 0.001). There were no significant differences in body composition between the IG and CG through the 6 months of MCT. Conclusions: The present study suggests that MCT did not change SMP30 levels from 3 to 6 months, where there were changes in neither walking ability nor body composition; however, MCT was effective in improving 6MWT and TUG performance from baseline to 3 months

Chemical pressure effects on the spectroscopic properties of Nd3+-doped gallium nano-garnets

[EN] Nd3+-doped RE3Ga5O12 (RE = Gd, Y, and Lu) nano-crystalline garnets of 40-45 nm in size have been synthesized by a sol-gel method. With the decrease of the RE atom size, the chemical pressure related to the decreasing volumes of the GaO4 tetrahedral, GaO6 octahedral and REO8 dodecahedral units drive the nano-garnets toward a more compacted structure, which is evidenced by the change of the vibrational phonon mode frequencies. The chemical pressure also increases the crystal-field strength felt by the RE3+ ions while decreases the orthorhombic distortion of the REO8 local environment. These effects alter the absorption and emission properties of the Nd3+ ion measured in the near-infrared luminescence range from 0.87 to 1.43 ¿m associated with the 4 F3/2¿4 IJ (J = 9/2, 11/2, 13/2) transitions. The 4 F3/2 luminescence decay curves show non-exponential behavior due to dipole-dipole energy transfer interactions among Nd3+ ions that increases with pressure.Authors are grateful to The Governments of Spain and India for the Indo-Spanish Joint Programme of Bilateral Cooperation in Science and Technology (PRI-PIBIN-2011-1153/DST-INT-Spain-P-38-11). Dr. Venkatramu is grateful to DAE-BRNS, Government of India for the award of DAE Research Award for Young Scientist (No. 2010/20/34/5/BRNS/2223). This work have been partially supported by MINECO under The National Program of Materials (MAT2013-46649-C4-2-P/-3-P/-4-P), The Consolider-Ingenio 2010 Program (MALTA CSD2007-00045), by Fundacion CajaCanarias (ENER-01), and by the EU-FEDER funds. V. Monteseguro wishes to thank MICINN for the FPI grant (BES-2011-044596). Authors also thank Agencia Canaria de Investigacion, Innovacion y Sociedad de la Informacion for the funds given to Universidad de La Laguna, co-financed by The European Social Fund by a percentage of 85%.Monteseguro, V.; Rathaiah, M.; Linganna, K.; Lozano-Gorrin, AD.; Hernandez-Rodriguez, MA.; Martin, IR.; Babu, P.... (2015). Chemical pressure effects on the spectroscopic properties of Nd3+-doped gallium nano-garnets. Optical Materials Express. 5(8):1661-1673. https://doi.org/10.1364/OME.5.001661S1661167358Pollnau, M., Hardman, P. ., Clarkson, W. ., & Hanna, D. . (1998). Upconversion, lifetime quenching, and ground-state bleaching in Nd3+:LiYF4. Optics Communications, 147(1-3), 203-211. doi:10.1016/s0030-4018(97)00524-5Brandle, C. D., & Barns, R. L. (1974). Crystal stoichiometry of Czochralski grown rare-earth gallium garnets. Journal of Crystal Growth, 26(1), 169-170. doi:10.1016/0022-0248(74)90223-1Venkatramu, V., Giarola, M., Mariotto, G., Enzo, S., Polizzi, S., Jayasankar, C. K., … Speghini, A. (2010). Nanocrystalline lanthanide-doped Lu3Ga5O12garnets: interesting materials for light-emitting devices. Nanotechnology, 21(17), 175703. doi:10.1088/0957-4484/21/17/175703Speghini, A., Piccinelli, F., & Bettinelli, M. (2011). Synthesis, characterization and luminescence spectroscopy of oxide nanopowders activated with trivalent lanthanide ions: The garnet family. Optical Materials, 33(3), 247-257. doi:10.1016/j.optmat.2010.10.039Krsmanović, R., Morozov, V. A., Lebedev, O. I., Polizzi, S., Speghini, A., Bettinelli, M., & Tendeloo, G. V. (2007). Structural and luminescence investigation on gadolinium gallium garnet nanocrystalline powders prepared by solution combustion synthesis. Nanotechnology, 18(32), 325604. doi:10.1088/0957-4484/18/32/325604Naccache, R., Vetrone, F., Speghini, A., Bettinelli, M., & Capobianco, J. A. (2008). Cross-Relaxation and Upconversion Processes in Pr3+ Singly Doped and Pr3+/Yb3+ Codoped Nanocrystalline Gd3Ga5O12: The Sensitizer/Activator Relationship. The Journal of Physical Chemistry C, 112(20), 7750-7756. doi:10.1021/jp711494dAntic-Fidancev, E., Hölsä, J., Lastusaari, M., & Lupei, A. (2001). Dopant-host relationships in rare-earth oxides and garnets doped with trivalent rare-earth ions. Physical Review B, 64(19). doi:10.1103/physrevb.64.195108Rodríguez-Carvajal, J. (1993). Recent advances in magnetic structure determination by neutron powder diffraction. Physica B: Condensed Matter, 192(1-2), 55-69. doi:10.1016/0921-4526(93)90108-iMonteseguro, V., Rodríguez-Hernández, P., Ortiz, H. M., Venkatramu, V., Manjón, F. J., Jayasankar, C. K., … Muñoz, A. (2015). Structural, elastic and vibrational properties of nanocrystalline lutetium gallium garnet under high pressure. Physical Chemistry Chemical Physics, 17(14), 9454-9464. doi:10.1039/c4cp05903dRay, S., León-Luis, S. F., Manjón, F. J., Mollar, M. A., Gomis, Ó., Rodríguez-Mendoza, U. R., … Lavín, V. (2014). Broadband, site selective and time resolved photoluminescence spectroscopic studies of finely size-modulated Y2O3:Eu3+ phosphors synthesized by a complex based precursor solution method. Current Applied Physics, 14(1), 72-81. doi:10.1016/j.cap.2013.07.027Nekvasil, V. (1978). The Crystal Field for Nd3+ in Garnets. Physica Status Solidi (b), 87(1), 317-323. doi:10.1002/pssb.2220870137Rodríguez-Mendoza, U. R., León-Luis, S. F., Muñoz-Santiuste, J. E., Jaque, D., & Lavín, V. (2013). Nd3+-doped Ca3Ga2Ge3O12garnet: A new optical pressure sensor. Journal of Applied Physics, 113(21), 213517. doi:10.1063/1.4809217Kaminska, A., Buczko, R., Paszkowicz, W., Przybylińska, H., Werner-Malento, E., Suchocki, A., … Saxena, S. (2011). Merging of the4F3/2level states of Nd3+ions in the photoluminescence spectra of gadolinium-gallium garnets under high pressure. Physical Review B, 84(7). doi:10.1103/physrevb.84.075483Allik, T. H., Stewart, S. A., Sardar, D. K., Quarles, G. J., Powell, R. C., Morrison, C. A., … Pinto, A. A. (1988). Preparation, structure, and spectroscopic properties ofNd3+:{La1−xLux}3[Lu1−yGay]2Ga3O12crystals. Physical Review B, 37(16), 9129-9139. doi:10.1103/physrevb.37.9129Wu, K., Yao, B., Zhang, H., Yu, H., Wang, Z., Wang, J., & Jiang, M. (2010). Growth and properties of Nd:Lu3Ga5O12 laser crystal by floating-zone method. Journal of Crystal Growth, 312(24), 3631-3636. doi:10.1016/j.jcrysgro.2010.09.029Jia, Z., Arcangeli, A., Tao, X., Zhang, J., Dong, C., Jiang, M., … Tonelli, M. (2009). Efficient Nd3+→Yb3+ energy transfer in Nd3+,Yb3+:Gd3Ga5O12 multicenter garnet crystal. Journal of Applied Physics, 105(8), 083113. doi:10.1063/1.3115442Guillot-Noel, O., Bellamy, B., Viana, B., & Gourier, D. (1999). Correlation between rare-earth oscillator strengths and rare-earth–valence-band interactions in neodymium-dopedYMO4(M=V,P, As),Y3Al5O12,andLiYF4matrices. Physical Review B, 60(3), 1668-1677. doi:10.1103/physrevb.60.1668Demidovich, A. A., Shkadarevich, A. P., Danailov, M. B., Apai, P., Gasmi, T., Gribkovskii, V. P., … Batay, L. E. (1998). Comparison of cw laser performance of Nd:KGW, Nd:YAG, Nd:BEL, and Nd:YVO 4 under laser diode pumping. Applied Physics B: Lasers and Optics, 67(1), 11-15. doi:10.1007/s003400050467Inokuti, M., & Hirayama, F. (1965). Influence of Energy Transfer by the Exchange Mechanism on Donor Luminescence. The Journal of Chemical Physics, 43(6), 1978-1989. doi:10.1063/1.1697063Lupei, V., & Lupei, A. (2000). Emission dynamics of the4F3/2level ofNd3+in YAG at low pump intensities. Physical Review B, 61(12), 8087-8098. doi:10.1103/physrevb.61.8087Maeda, K., Wada, N., Umino, M., Abe, M., Takada, Y., Nakano, N., & Kuroda, H. (1984). Concentration Dependence of Fluorescence Lifetime of Nd3+-Doped Gd3Ga5O12Lasers. Japanese Journal of Applied Physics, 23(Part 2, No. 10), L759-L760. doi:10.1143/jjap.23.l759Geusic, J. E., Marcos, H. M., & Van Uitert, L. G. (1964). LASER OSCILLATIONS IN Nd‐DOPED YTTRIUM ALUMINUM, YTTRIUM GALLIUM AND GADOLINIUM GARNETS. Applied Physics Letters, 4(10), 182-184. doi:10.1063/1.1753928Löhring, J., Nicklaus, K., Kujath, N., & Hoffmann, D. (2007). Diode pumped Nd:YGG laser for direct generation of pulsed 935 nm radiation for water vapour measurements. Solid State Lasers XVI: Technology and Devices. doi:10.1117/12.708220Maunier, C., Doualan, J. L., Moncorgé, R., Speghini, A., Bettinelli, M., & Cavalli, E. (2002). Growth, spectroscopic characterization, and laser performance of Nd:LuVO_4, a new infrared laser material that is suitable for diode pumping. Journal of the Optical Society of America B, 19(8), 1794. doi:10.1364/josab.19.00179