Analysing Java Identifier Names

Identifier names are the principal means of recording and communicating ideas in source code and are a significant source of information for software developers and maintainers, and the tools that support their work. This research aims to increase understanding of identifier name content types - words, abbreviations, etc. - and phrasal structures - noun phrases, verb phrases, etc. - by improving techniques for the analysis of identifier names. The techniques and knowledge acquired can be applied to improve program comprehension tools that support internal code quality, concept location, traceability and model extraction. Previous detailed investigations of identifier names have focused on method names, and the content and structure of Java class and reference (field, parameter, and variable) names are less well understood. I developed improved algorithms to tokenise names, and trained part-of-speech tagger models on identifier names to support the analysis of class and reference names in a corpus of 60 open source Java projects. I confirm that developers structure the majority of names according to identifier naming conventions, and use phrasal structures reported in the literature. I also show that developers use a wider variety of content types and phrasal structures than previously understood. Unusually structured class names are largely project-specific naming conventions, but could indicate design issues. Analysis of phrasal reference names showed that developers most often use the phrasal structures described in the literature and used to support the extraction of information from names, but also choose unexpected phrasal structures, and complex, multi-phrasal, names. Using Nominal - software I created to evaluate adherence to naming conventions - I found developers tend to follow naming conventions, but that adherence to published conventions varies between projects because developers also establish new conventions for the use of typography, content types and phrasal structure to support their work: particularly to distinguish the roles of Java field names

Narrative review of primary care point-of-care testing (POCT) and antibacterial use in respiratory tract infection (RTI)

Antimicrobial resistance is a global problem and is being addressed through national strategies to improve diagnostics, develop new antimicrobials and promote antimicrobial stewardship. A narrative review of the literature was undertaken to ascertain the value of C reactive protein (CRP) and procalcitonin, measurements to guide antibacterial prescribing in adult patients presenting to GP practices with symptoms of respiratory tract infection (RTI). Studies that were included were randomised controlled trials,controlled before and after studies, cohort studies and economic evaluations. Many studies demonstrated that the use of CRP tests in patients presenting with RTI symptoms reduces antibiotic prescribing by 23.3% to36.16%. Procalcitonin is not currently available as a point-of-care testing (POCT), but has shown value for patients with RTI admitted to hospital. GPs and patients report a good acceptability for a CRP POCT and economic evaluations show cost-effectiveness of CRP POCT over existing RTI management in primary care. POCTs increase diagnostic precision for GPs in the better management of patients with RTI. CRP POCT can better target antibacterial prescribing by GPs and contribute to national antimicrobial resistance strategies. Health services need to develop ways to ensure funding is transferred in order for POCT to be implemented

Towards precision radial velocity science with SALT’s High-Resolution Spectrograph

We describe efforts to equip the Southern African Large Telescope (SALT) for precision radial velocity (PRV) work. Our current focus is on commissioning the high-stability (HS) mode of the High-Resolution Spectrograph (HRS), the mode intended to support exoplanet science. After replacing the original commercial iodine cell with a custom-built, precisely characterised one and following established best practice in terms of observing strategy and data reduction, this system now delivers 3-4 m/s radial velocity stability on 5th and 6th magnitude stars. Unfortunately, the throughput is compromised by the HRS dichroic split being at 555 nm (i.e. roughly midway through the 100 nm span of the iodine absorption spectrum). Furthermore, SALT’s fixed elevation axis limits the exposure time available for a given target and hence the depth and/or precision achievable with the iodine cell. The HS mode’s simultaneous ThAr option uses the full 370–890 nm passband of the HRS and does not suffer gas cell absorption losses, so it may be more suitable for exoplanet work. The first step was to quantify the internal stability of the spectrograph, which requires simultaneously injecting arc light into the object and calibration fibres. The HS mode’s optical feed was modified accordingly, stability test runs were conducted and the necessary analysis tools were developed. The initial stability test yielded encouraging results and though more testing is still to be done, SAL a laser frequency comb to support the development of HRS PRV capability

Mid-Infrared Extinction Mapping of Infrared Dark Clouds II. The Structure of Massive Starless Cores and Clumps

(abridged) We develop the mid-infrared extinction (MIREX) mapping technique of Butler & Tan (2009, Paper I), presenting a new method to correct for the Galactic foreground emission based on observed saturation in independent cores. Using Spitzer GLIMPSE 8 micron images, this allows us to accurately probe mass surface densities, Sigma, up to ~0.5g/cm^2 with 2" resolution. We then characterize the structure of 42 massive starless and early-stage IRDC cores and their surrounding clumps, measuring Sigma_cl(r) from the core/clump centers. We first assess the properties of the core/clump at a scale where the total enclosed mass as projected on the sky is M_cl=60Msun. We find these objects have a mean radius of R_cl~0.1pc, mean Sigma_cl=0.3g/cm^2 and, if fit by a power law density profile rho_cl ~ r^{-k_{rho,cl}}, a mean value of k_{rho,cl}=1.1. If we assume a core is embedded in each clump and subtract the surrounding clump envelope to derive the core properties, we find a mean core density power law index of k_{rho,c} = 1.6. We repeat this analysis as a function of radius and derive the best-fitting power law plus uniform clump envelope model for each of the 42 core/clumps. The cores have typical masses of M_c~100Msun and mean Sigma_c~0.1g/cm^2, and are embedded in clumps with comparable mass surface densities. We conclude massive starless cores exist and are well-described by singular polytropic spheres. Their relatively low values of Sigma and the fact that they are IR dark may imply that their fragmentation is inhibited by magnetic fields rather than radiative heating. Comparing to massive star-forming cores, there is tentative evidence for an evolution towards higher densities and steeper density profiles as star formation proceeds.Comment: 28 pages, 16 figures, to appear in ApJ, high-resolution version available http://www.astro.ufl.edu/~butler85/Publications.htm

Detection of Planetary and Stellar Companions to Neighboring Stars via a Combination of Radial Velocity and Direct Imaging Techniques

13 pages, 6 figures, 4 tables, accepted for publication in the Astronomical Journal (submitted 25 Feb 2019; accepted 28 April 2019). Machine readable tables and Posteriors from the RadVel fits are available here: http://stephenkane.net/rvfits.tarThe sensitivities of radial velocity (RV) surveys for exoplanet detection are extending to increasingly longer orbital periods, where companions with periods of several years are now being regularly discovered. Companions with orbital periods that exceed the duration of the survey manifest in the data as an incomplete orbit or linear trend, a feature that can either present as the sole detectable companion to the host star, or as an additional signal overlain on the signatures of previously discovered companion(s). A diagnostic that can confirm or constrain scenarios in which the trend is caused by an unseen stellar rather than planetary companion is the use of high-contrast imaging observations. Here, we present RV data from the Anglo-Australian Planet Search (AAPS) for 20 stars that show evidence of orbiting companions. Of these, six companions have resolved orbits, with three that lie in the planetary regime. Two of these (HD 92987b and HD 221420b) are new discoveries. Follow-up observations using the Differential Speckle Survey Instrument (DSSI) on the Gemini South telescope revealed that 5 of the 20 monitored companions are likely stellar in nature. We use the sensitivity of the AAPS and DSSI data to place constraints on the mass of the companions for the remaining systems. Our analysis shows that a planetary-mass companion provides the most likely self-consistent explanation of the data for many of the remaining systems.Peer reviewedFinal Accepted Versio

The Gliese 86 Binary System: A Warm Jupiter Formed in a Disk Truncated at ≈2 au

© 2022. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/Gliese 86 is a nearby K dwarf hosting a giant planet on a ≈16 day orbit and an outer white dwarf companion on a ≈century-long orbit. In this study we combine radial velocity data (including new measurements spanning more than a decade) with high angular resolution imaging and absolute astrometry from Hipparcos and Gaia to measure the current orbits and masses of both companions. We then simulate the evolution of the Gl 86 system to constrain its primordial orbit when both stars were on the main sequence; the closest approach between the two stars was then about 9 au. Such a close separation limited the size of the protoplanetary disk of Gl 86 A and dynamically hindered the formation of the giant planet around it. Our measurements of Gl 86 B and Gl 86 Ab’s orbits reveal Gl 86 as a system in which giant planet formation took place in a disk truncated at ≈2 au. Such a disk would be just big enough to harbor the dust mass and total mass needed to assemble Gl 86 Ab’s core and envelope, assuming a high disk accretion rate and a low viscosity. Inefficient accretion of the disk onto Gl 86 Ab, however, would require a disk massive enough to approach the Toomre stability limit at its outer truncation radius. The orbital architecture of the Gl 86 system shows that giant planets can form even in severely truncated disks and provides an important benchmark for planet formation theory.Peer reviewe

The Gliese 86 Binary System: A Warm Jupiter Formed in a Disk Truncated at approximate to 2 au

Gliese 86 is a nearby K dwarf hosting a giant planet on a ≈16 day orbit and an outer white dwarf companion on a ≈century-long orbit. In this study we combine radial velocity data (including new measurements spanning more than a decade) with high angular resolution imaging and absolute astrometry from Hipparcos and Gaia to measure the current orbits and masses of both companions. We then simulate the evolution of the Gl 86 system to constrain its primordial orbit when both stars were on the main sequence; the closest approach between the two stars was then about 9 au. Such a close separation limited the size of the protoplanetary disk of Gl 86 A and dynamically hindered the formation of the giant planet around it. Our measurements of Gl 86 B and Gl 86 Ab’s orbits reveal Gl 86 as a system in which giant planet formation took place in a disk truncated at ≈2 au. Such a disk would be just big enough to harbor the dust mass and total mass needed to assemble Gl 86 Ab’s core and envelope, assuming a high disk accretion rate and a low viscosity. Inefficient accretion of the disk onto Gl 86 Ab, however, would require a disk massive enough to approach the Toomre stability limit at its outer truncation radius. The orbital architecture of the Gl 86 system shows that giant planets can form even in severely truncated disks and provides an important benchmark for planet formation theory

Brain functional network integrity sustains cognitive function despite atrophy in presymptomatic genetic frontotemporal dementia.

INTRODUCTION: The presymptomatic phase of neurodegenerative disease can last many years, with sustained cognitive function despite progressive atrophy. We investigate this phenomenon in familial frontotemporal dementia (FTD). METHODS: We studied 121 presymptomatic FTD mutation carriers and 134 family members without mutations, using multivariate data-driven approach to link cognitive performance with both structural and functional magnetic resonance imaging. Atrophy and brain network connectivity were compared between groups, in relation to the time from expected symptom onset. RESULTS: There were group differences in brain structure and function, in the absence of differences in cognitive performance. Specifically, we identified behaviorally relevant structural and functional network differences. Structure-function relationships were similar in both groups, but coupling between functional connectivity and cognition was stronger for carriers than for non-carriers, and increased with proximity to the expected onset of disease. DISCUSSION: Our findings suggest that the maintenance of functional network connectivity enables carriers to maintain cognitive performance.K.A.T. is supported by the British Academy Postdoctoral Fellowship (PF160048) and the Guarantors of Brain (101149). J.B.R. is supported by the Wellcome Trust (103838) the Medical Research Council (SUAG/051 G101400) and the Cambridge NIHR Biomedical Research Centre. R. S.-V. is supported by the Instituto de Salud Carlos III and the JPND network PreFrontAls (01ED1512/AC14/0013) and the Fundació Marató de TV3 (20143810). M.M and E.F are supported by the UK Medical Research Council, the Italian Ministry of Health and the Canadian Institutes of Health Research as part of a Centres of Excellence in Neurodegeneration grant, and also a Canadian Institutes of Health Research operating grant (MOP 327387) and funding from the Weston Brain Institute. J.D.R., D.C. and K.M.M. are supported by the NIHR Queen Square Dementia Biomedical Research Unit, the NIHR UCL/H Biomedical Research Centre and the Leonard Wolfson Experimental Neurology Centre (LWENC) Clinical Research Facility. J.D.R. is supported by an MRC Clinician Scientist Fellowship (MR/M008525/1) and has received funding from the NIHR Rare Disease Translational Research Collaboration (BRC149/NS/MH), the MRC UK GENFI grant (MR/ M023664/1) and The Bluefield Project. F.T. is supported by the Italian Ministry of Health (Grant NET-2011-02346784). L.C.J. and J.V.S. are supported by the Association for Frontotemporal Dementias Research Grant 2009, ZonMw Memorabel project number 733050103 and 733050813, and the Bluefield project. R.G. supported by Italian Ministry of Health, Ricerca Corrente. The Swedish contributors C.G., L.O. and C.A. were supported by grants from JPND Prefrontals Swedish Research Council (VR) 529-2014-7504, Swedish Research Council (VR) 2015- 02926, Swedish Research Council (VR) 2018-02754, Swedish FTD Initiative-Schorling Foundation, Swedish Brain Foundation, Swedish Alzheimer Foundation, Stockholm County Council ALF, Karolinska Institutet Doctoral Funding and StratNeuro, Swedish Demensfonden, during the conduct of the study

Brain functional network integrity sustains cognitive function despite atrophy in presymptomatic genetic frontotemporal dementia

Introduction: The presymptomatic phase of neurodegenerative disease can last many years, with sustained cognitive function despite progressive atrophy. We investigate this phenomenon in familial frontotemporal dementia (FTD). Methods: We studied 121 presymptomatic FTD mutation carriers and 134 family members without mutations, using multivariate data-driven approach to link cognitive performance with both structural and functional magnetic resonance imaging. Atrophy and brain network connectivity were compared between groups, in relation to the time from expected symptom onset. Results: There were group differences in brain structure and function, in the absence of differences in cognitive performance. Specifically, we identified behaviorally relevant structural and functional network differences. Structure-function relationships were similar in both groups, but coupling between functional connectivity and cognition was stronger for carriers than for non-carriers, and increased with proximity to the expected onset of disease. Discussion: Our findings suggest that the maintenance of functional network connectivity enables carriers to maintain cognitive performance.K.A.T. is supported by the British Academy Postdoctoral Fellowship (PF160048) and the Guarantors of Brain (101149). J.B.R. is supported by theWellcome Trust (103838), the Medical Research Council (SUAG/051 G101400), and the Cambridge NIHR Biomedical Research Centre. R. S.-V. is supported by the Instituto de Salud Carlos III and the JPND network PreFrontAls (01ED1512/AC14/0013) and the Fundació Marató de TV3 (20143810). M.M and E.F are supported by the UK Medical Research Council, the Italian Ministry of Health, and the Canadian Institutes of Health Research as part of a Centres of Excellence in Neurodegeneration grant, and also a Canadian Institutes of Health Research operating grant (MOP 327387) and funding from the Weston Brain Institute. J.D.R., D.C., and K.M.M. are supported by the NIHR Queen Square Dementia Biomedical Research Unit, the NIHR UCL/H Biomedical Research Centre, and the LeonardWolfson Experimental Neurology Centre (LWENC) Clinical Research Facility. J.D.R. is supported by an MRC Clinician Scientist Fellowship (MR/M008525/1) and has received funding from the NIHR Rare Disease Translational Research Collaboration (BRC149/NS/MH), the MRC UK GENFI grant (MR/ M023664/1), and The Bluefield Project. F.T. is supported by the Italian Ministry of Health (Grant NET-2011-02346784). L.C.J. and J.V.S. are supported by the Association for Frontotemporal Dementias Research Grant 2009, ZonMwMemorabel project number 733050103 and 733050813, and the Bluefield project. R.G. is supported by Italian Ministry of Health, Ricerca Corrente. J.L. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy within the framework of the Munich Cluster for Systems Neurology (EXC 2145; SyNergy - ID 390857198). The Swedish contributors C.G., L.O., and C.A. were supported by grants from JPND Prefrontals Swedish Research Council (VR) 529-2014-7504, JPND GENFI-PROX Swedish Research Council (VR) 2019-02248, Swedish Research Council (VR) 2015- 02926, Swedish Research Council (VR) 2018-02754, Swedish FTD Initiative- Schorling Foundation, Swedish Brain Foundation, Swedish Alzheimer Foundation, Stockholm County Council ALF, Karolinska InstitutetDoctoral Funding, and StratNeuro, Swedish Demensfonden, during the conduct of the study