Citations for Software: Providing Identification, Access and Recognition for Research Software

Software plays a significant role in modern academic research, yet lacks a similarly significant presence in the scholarly record. With increasing interest in promoting reproducible research, curating software as a scholarly resource not only promotes access to these tools, but also provides recognition for the intellectual efforts that go into their development. This work reviews existing standards for identifying, promoting discovery of, and providing credit for software development work. In addition, it shows how these guidelines have been integrated into existing tools and community cultures, and provides recommendations for future software curation efforts.

Multi-institution analysis of racial disparity among African- American men eligible for prostate cancer active surveillance

There is a significant controversy on whether race should be a factor in considering active surveillance for low-risk prostate cancer. To address this question, we analyzed a multi-institution database to assess racial disparity between African-American and White-American men with low risk prostate cancer who were eligible for active surveillance but underwent radical prostatectomy. A retrospective analysis of prospectively collected clinical, pathologic and oncologic outcomes of men with low-risk prostate cancer from seven tertiary care institutions that underwent radical prostatectomy from 2003–2014 were used to assess potential racial disparity. Of the 333 (14.8%) African-American and 1923 (85.2%) White-American men meeting active surveillance criteria, African-American men were found to be slightly younger (57.5 vs 58.5 years old; p = 0.01) and have higher BMI (29.3 v 27.9; p \u3c 0.01), pre-op PSA (5.2 v 4.7; p \u3c 0.01), and maximum percentage cancer on biopsy (15.1% v 13.6%; p \u3c 0.01) compared to White-American men. Univariate and multivariate analysis demonstrated similar rates of upgrading, upstaging, positive surgical margin, and biochemical recurrence between races. These results suggest that single institution studies recommending more stringent AS enrollment criteria for AA men with a low-risk prostate cancer may not capture the complete oncologic landscape due to institutional variability in cancer outcomes. Since all seven institutions demonstrated no significant racial disparity, current active surveillance eligibility should not be modified based upon race until a prospective study has been completed. © Dinizo et al

Computer-based tools for assessing micro-longitudinal patterns of cognitive function in older adults

Patterns of cognitive change over micro-longitudinal timescales (i.e., ranging from hours to days) are associated with a wide range of age-related health and functional outcomes. However, practical issues with conducting high-frequency assessments make investigations of micro-longitudinal cognition costly and burdensome to run. One way of addressing this is to develop cognitive assessments that can be performed by older adults, in their own homes, without a researcher being present. Here, we address the question of whether reliable and valid cognitive data can be collected over micro-longitudinal timescales using unsupervised cognitive tests.In study 1, 48 older adults completed two touchscreen cognitive tests, on three occasions, in controlled conditions, alongside a battery of standard tests of cognitive functions. In study 2, 40 older adults completed the same two computerized tasks on multiple occasions, over three separate week-long periods, in their own homes, without a researcher present. Here, the tasks were incorporated into a wider touchscreen system (Novel Assessment of Nutrition and Ageing (NANA)) developed to assess multiple domains of health and behavior. Standard tests of cognitive function were also administered prior to participants using the NANA system.Performance on the two “NANA” cognitive tasks showed convergent validity with, and similar levels of reliability to, the standard cognitive battery in both studies. Completion and accuracy rates were also very high. These results show that reliable and valid cognitive data can be collected from older adults using unsupervised computerized tests, thus affording new opportunities for the investigation of cognitive function

The X-ray spectra and spectral variability of intermediate type Seyfert galaxies: ASCA observations of NGC 4388 and ESO 103-G35

The X-ray spectra of two intermediate type Seyfert galaxies are investigated using ASCA observations separated by more than a year. Both NGC 4388 and ESO 103-G35 exhibit strong, narrow Fe K alpha line emission and absorption by cold neutral gas with a column density ~ 10^23 cm^-2, characteristic of the X-ray spectra of type 2 Seyfert galaxies. The power law continuum flux has changed by a factor of 2 over a time-scale of ~ 2 years for both objects, declining in the case of NGC 4388 and rising in ESO 103-G35. No variation was observed in the equivalent width of the Fe K alpha line in the spectra of NGC 4388, implying that the line flux declined with the continuum. We find that the strength of the line cannot be accounted for by fluorescence in line-of-sight material with the measured column density unless a `leaky-absorber' model of the type favored for IRAS 04575-7537 is employed. The equivalent width of the Fe K alpha emission line is seen to decrease between the observations of ESO 103-G35 while the continuum flux increased. The 1996 observation of ESO 103-G35 can also be fitted with an absorption edge at 7.4 $\pm$ 0.2 keV due to partially ionized iron, and when an ionized absorber model is fitted to the data it is found that the equivalent column of neutral hydrogen rises to 3.5 x 10^23 cm^-2. The Fe K alpha line flux can be accounted by fluorescence in this material alone and this model is also a good representation of the 1988 and 1991 Ginga observations. There is then no requirement for a reflection component in the ASCA spectra of ESO 103-G35 or NGC 4388.Comment: 45 pages, 5 tables, 11 figures. Accepted for publication in the Astrophysical Journa

Humanin: A Novel Central Regulator of Peripheral Insulin Action

Decline in insulin action is a metabolic feature of aging and is involved in the development of age-related diseases including Type 2 Diabetes Mellitus (T2DM) and Alzheimer's disease (AD). A novel mitochondria-associated peptide, Humanin (HN), has a neuroprotective role against AD-related neurotoxicity. Considering the association between insulin resistance and AD, we investigated if HN influences insulin sensitivity.Using state of the art clamp technology, we examined the role of central and peripheral HN on insulin action. Continuous infusion of HN intra-cerebro-ventricularly significantly improved overall insulin sensitivity. The central effects of HN on insulin action were associated with activation of hypothalamic STAT-3 signaling; effects that were negated by co-inhibition of hypothalamic STAT-3. Peripheral intravenous infusions of novel and potent HN derivatives reproduced the insulin-sensitizing effects of central HN. Inhibition of hypothalamic STAT-3 completely negated the effects of IV HN analog on liver, suggesting that the hepatic actions of HN are centrally mediated. This is consistent with the lack of a direct effect of HN on primary hepatocytes. Furthermore, single treatment with a highly-potent HN analog significantly lowered blood glucose in Zucker diabetic fatty rats. Based upon the link of HN with two age-related diseases, we examined if there were age associated changes in HN levels. Indeed, the amount of detectable HN in hypothalamus, skeletal muscle, and cortex was decreased with age in rodents, and circulating levels of HN were decreased with age in humans and mice.We conclude that the decline in HN with age could play a role in the pathogenesis of age-related diseases including AD and T2DM. HN represents a novel link between T2DM and neurodegeneration and along with its analogues offers a potential therapeutic tool to improve insulin action and treat T2DM

East London’s Homeless: a retrospective review of an eye clinic for homeless people

Background There is very little published work on the visual needs of homeless people. This paper is the first study to investigate the visual needs of homeless people in the UK. Although similar work has been done in other countries, this study is unique because the United Kingdom is the only country with a National Health Service which provides free healthcare at the point of access. This study analysed the refractive status of the sample used, determined the demographics of homeless people seeking eye care and established if there is a need for community eye health with access to free spectacle correction in East London. Methods This retrospective case study analysed the clinical records of 1,141 homeless people using the Vision Care for Homeless People services at one of their clinics in East London. All eye examinations were carried out by qualified optometrists and, where appropriate, spectacles were dispensed to patients. Data captured included age, gender, ethnicity and refractive error. Results were analysed using two-sample t-tests with Excel and Minitab. Results Demographics of age, gender and ethnicity are described. Spherical equivalents (SE) were calculated from prescription data available for 841 clinic users. Emmetropia was defined as SE–0.50DS to +1DS, myopia as SE  +1DS. The majority of clinic users were male (79.2 %, n = 923). Approximately 80 % (n = 583) of clinic users were white, 10 % (n = 72) were ‘black’, 4 % (n = 29) ‘Asian’ and the remaining 5.6 % (n = 40) were of ‘mixed ethnicity’ and ‘other’ groups. The mean age of females attending the clinic was significantly lower than that of males (45.9 years, SD = 13.8 vs’ 48.4 years, SD = 11.8) when analysed using a two-sample t-test (t (317) = 2.44, p = 0.02). One third of service users were aged between 50–59 years. Myopia and hyperopia prevalence rates were 37.0 % and 21.0 % respectively. A total of 34.8 % of homeless people were found to have uncorrected refractive error, and required spectacle correction. Conclusions This study has identified a high proportion of uncorrected refractive error in this sample and therefore a need for regular eye examinations and provision of refractive correction for homeless people

Cosmological perturbations through a simple bounce

We present a detailed study of a simple scalar field model that yields non-singular cosmological solutions. We study both the qualitative dynamics of the homogeneous and isotropic background and the evolution of inhomogeneous linear perturbations. We calculate the spectrum of perturbations generated on super-Hubble scales during the collapse phase from initial vacuum fluctuations on small scales and then evolve these numerically through the bounce. We show there is a gauge in which perturbations remain well-defined and small throughout the bounce, even though perturbations in other commonly used gauges become large or ill-defined. We show that the comoving curvature perturbation calculated during the collapse phase provides a good estimate of the resulting large scale adiabatic perturbation in the expanding phase while the Bardeen metric potential is dominated by what becomes a decaying mode after the bounce. We show that a power-law collapse phase with scale factor proportional to $(-t)^{2/3}$ can yield a scale-invariant spectrum of adiabatic scalar perturbations in the expanding phase, but the amplitude of tensor perturbations places important constraints on the allowed initial conditions.Comment: 25 pages, 15 figures, latex with revtex. v2: missing factor of 2 included in tensor-scalar ratio, other minor changes and references added. v3: version to appear in PR

Surface composition and structure of Co\u3csub\u3e3\u3c/sub\u3eO\u3csub\u3e4\u3c/sub\u3e(110) and the effect of impurity segregation

The Co3O4 (110) single crystal surface has been characterized by low energy electron diffraction (LEED), Auger electron spectroscopy, and x-ray photoelectron spectroscopy (XPS). LEED analysis of the clean Co3O4 (110) spinel surface shows a well-ordered pattern with sharp diffraction features. The XPS spectra are consistent with stoichiometric Co3O4 as determined by the concentration ratio of oxygen to cobalt (CO /CCo) and spectral peak shape. In particular, the cobalt 2p XPS spectra are characteristic of the spinel structure with Co3+ occupying octahedral sites and Co2+ in tetrahedral sites within the lattice. During prolonged heating at 630 K, bulk impurities of K, Ca, Na, and Cu segregated to the surface. Sodium desorbed from the surface as NaOH at 825 K, potassium and calcium were only removed by sputtering since no desorption from the surface was detected for temperatures up to 1000 K. Copper also disappeared upon heating above 700 K, most likely by desorbing although the possibility of diffusion back into the bulk could not be eliminated. The appearance of copper impurities correlated with Co3O4 (110) surface reduction to CoO, and the surface could not be fully reoxidized even upon extended oxygen annealing as long as the copper impurity remained on the surface. Upon removal of the Cu from the near-surface region, the surface was easily reoxidized to Co3O4 by O2

Challenges in quantifying changes in the global water cycle

Human influences have likely already impacted the large-scale water cycle but natural variability and observational uncertainty are substantial. It is essential to maintain and improve observational capabilities to better characterize changes. Understanding observed changes to the global water cycle is key to predicting future climate changes and their impacts. While many datasets document crucial variables such as precipitation, ocean salinity, runoff, and humidity, most are uncertain for determining long-term changes. In situ networks provide long time-series over land but are sparse in many regions, particularly the tropics. Satellite and reanalysis datasets provide global coverage, but their long-term stability is lacking. However, comparisons of changes among related variables can give insights into the robustness of observed changes. For example, ocean salinity, interpreted with an understanding of ocean processes, can help cross-validate precipitation. Observational evidence for human influences on the water cycle is emerging, but uncertainties resulting from internal variability and observational errors are too large to determine whether the observed and simulated changes are consistent. Improvements to the in situ and satellite observing networks that monitor the changing water cycle are required, yet continued data coverage is threatened by funding reductions. Uncertainty both in the role of anthropogenic aerosols, and due to large climate variability presently limits confidence in attribution of observed changes