Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE

Trophic classification of Tennessee Valley area reservoirs derived from LANDSAT multispectral scanner data

LANDSAT MSS data from four different dates were extracted from computer tapes using a semiautomated digital data handling and analysis system. Reservoirs were extracted from the surrounding land matrix by using a Band 7 density level slice of 3; and descriptive statistics to include mean, variance, and ratio between bands for each of the four bands were calculated. Significant correlations ( 0.80) were identified between the MSS statistics and many trophic indicators from ground truth water quality data collected at 35 reservoirs in the greater Tennessee Valley region. Regression models were developed which gave significant estimates of each reservoir's trophic state as defined by its trophic state index and explained in all four LANDSAT frames at least 85 percent of the variability in the data. To illustrate the spatial variations within reservoirs as well as the relative variations between reservoirs, a table look up elliptical classification was used in conjunction with each reservoir's trophic state index to classify each reservoir on a pixel by pixel basis and produce color coded thematic representations

Entropy/IP: Uncovering Structure in IPv6 Addresses

In this paper, we introduce Entropy/IP: a system that discovers Internet address structure based on analyses of a subset of IPv6 addresses known to be active, i.e., training data, gleaned by readily available passive and active means. The system is completely automated and employs a combination of information-theoretic and machine learning techniques to probabilistically model IPv6 addresses. We present results showing that our system is effective in exposing structural characteristics of portions of the IPv6 Internet address space populated by active client, service, and router addresses. In addition to visualizing the address structure for exploration, the system uses its models to generate candidate target addresses for scanning. For each of 15 evaluated datasets, we train on 1K addresses and generate 1M candidates for scanning. We achieve some success in 14 datasets, finding up to 40% of the generated addresses to be active. In 11 of these datasets, we find active network identifiers (e.g., /64 prefixes or `subnets') not seen in training. Thus, we provide the first evidence that it is practical to discover subnets and hosts by scanning probabilistically selected areas of the IPv6 address space not known to contain active hosts a priori.Comment: Paper presented at the ACM IMC 2016 in Santa Monica, USA (https://dl.acm.org/citation.cfm?id=2987445). Live Demo site available at http://www.entropy-ip.com

Improved Electroformed Structural Copper and Copper Alloys

Electroforming offers a superior means for fabricating internally cooled heat exchangers and structures subjected to thermal environments. Copper is deposited from many such applications because of the good thermal conductivity. It suffers from mediocre yield strength as a structural material and loses mechanical strength at intermediate temperatures. Mechanical properties similar to those of electroformed nickel are desired. Phase 1 examined innovative means to improve deposited copper structural performance. Yield strengths as high as 483 MPa (70 ksi) were obtained with useful ductility while retaining a high level of purity essential to good thermal conductivity. Phase 2 represents a program to explore new additive combinations in copper electrolytes to produce a more fine, equiaxed grain which can be thermally stabilized by other techniques such as alloying in modest degrees and dispersion strengthening. Evaluation of new technology - such as the codeposition of fullerness (diamond-like) particles were made to enhance thermal conductivity in low alloys. A test fire quality tube-bundle engine was fabricated using these copper property improvement concepts to show the superiority of the new coppers and fabrications methods over competitive technologies such as brazing and plasma deposition

Risk of Suicide Attempt in Adopted and Nonadopted Offspring

OBJECTIVE: We asked whether adoption status represented a risk of suicide attempt for adopted and nonadopted offspring living in the United States. We also examined whether factors known to be associated with suicidal behavior would mediate the relationship between adoption status and suicide attempt. METHODS: Participants were drawn from the Sibling Interaction and Behavior Study, which included 692 adopted and 540 nonadopted offspring and was conducted at the University of Minnesota from 1998 to 2008. Adoptees were systematically ascertained from records of 3 large Minnesota adoption agencies; nonadoptees were ascertained from Minnesota birth records. Outcome measures were attempted suicide, reported by parent or offspring, and factors known to be associated with suicidal behavior including psychiatric disorder symptoms, personality traits, family environment, and academic disengagement. RESULTS: The odds of a reported suicide attempt were ∼4 times greater in adoptees compared with nonadoptees (odds ratio: 4.23). After adjustment for factors associated with suicidal behavior, the odds of reporting a suicide attempt were reduced but remained significantly elevated (odds ratio: 3.70). CONCLUSIONS: The odds for reported suicide attempt are elevated in individuals who are adopted relative to those who are not adopted. The relationship between adoption status and suicide attempt is partially mediated by factors known to be associated with suicidal behavior. Continued study of the risk of suicide attempt in adopted offspring may inform the larger investigation of suicidality in all adolescents and young adults

The Management and Use of Social Network Sites in a Government Department

In this paper we report findings from a study of social network site use in a UK Government department. We have investigated this from a managerial, organisational perspective. We found at the study site that there are already several social network technologies in use, and that these: misalign with and problematize organisational boundaries; blur boundaries between working and social lives; present differing opportunities for control; have different visibilities; have overlapping functionality with each other and with other information technologies; that they evolve and change over time; and that their uptake is conditioned by existing infrastructure and availability. We find the organisational complexity that social technologies are often hoped to cut across is, in reality, something that shapes their uptake and use. We argue the idea of a single, central social network site for supporting cooperative work within an organisation will hit the same problems as any effort of centralisation in organisations. We argue that while there is still plenty of scope for design and innovation in this area, an important challenge now is in supporting organisations in managing what can best be referred to as a social network site 'ecosystem'.Comment: Accepted for publication in JCSCW (The Journal of Computer Supported Cooperative Work

Comparison of X-ray and gamma-ray dose-response curves for pink somatic mutations in Tradescantia clone 02

Microdosimetric data indicate that the mean specific energy,zeta, produced by individual charged particles from X rays and gamma rays is different for the two radiation qualities by nearly a factor of two. In order to test whether this influences the initial, linear component in the dose-effect relations, a comparison was made between dose-response curves for pink somatic mutations inTradescantia clone 02 stamen hairs following X and gamma irradiations. Absorbed doses ranged from 2.66 to 300 rad. The results are in agreement with predictions made on the basis of microdosimetric data. At low doses gamma rays are substantially less effective than X rays. The RBE of gamma rays vs. X rays at low doses was approximately 0.6, a value lower than those usually reported in other experimental systems

Lower urinary tract symptoms that predict microscopic pyuria

INTRODUCTION AND HYPOTHESIS: Urinary dipsticks and culture analyses of a mid-stream urine specimen (MSU) at 10(5) cfu ml(-1) of a known urinary pathogen are considered the gold standard investigations for diagnosing urinary tract infection (UTI). However, the reliability of these tests has been much criticised and they may mislead. It is now widely accepted that pyuria (≥1 WBC μl(-1)) detected by microscopy of a fresh unspun, unstained specimen of urine is the best biological indicator of UTI available. We aimed to scrutinise the greater potential of symptoms analysis in detecting pyuria and UTI. METHODS: Lower urinary tract symptom (LUTS) descriptions were collected from patients with chronic lower urinary tract symptoms referred to a tertiary referral unit. The symptoms informed a 39-question inventory, grouped into storage, voiding, stress incontinence and pain symptoms. All questions sought a binary yes or no response. A bespoke software package was developed to collect the data. The study was powered to a sample of at least 1,990 patients, with sufficient power to analyse 39 symptoms in a linear model with an effect size of Cohen's f(2) = 0.02, type 1 error probability = 0.05; and power (1-β); 95% where β is the probability of type 2 error). The inventory was administered to 2,050 female patients between August 2004 and November 2011. The data were collated and the following properties assessed: internal consistency, test-retest reliability, inter-observer reliability, internal responsiveness, external responsiveness, construct validity analysis and a comparison with the International Consultation on Incontinence Modular Questionnaire for female lower urinary tract symptoms (ICIQ-FLUTS). The dependent variable used as a surrogate marker of UTI was microscopic pyuria. An MSU sample was sent for routine culture. RESULTS: The symptoms proved reliable predictors of microscopic pyuria. In particular, voiding symptoms correlated well with microscopic pyuria (χ(2) = 88, df = 1, p < 0.001). The symptom inventory has significant psychometric characteristics as below: test-retest reliability: Cronbach's alpha was 0.981; inter-observer reliability, Cronbach's alpha was 0.995, internal responsiveness F = 221, p < 0.001, external responsiveness F = 359, df = 5, p < 0.001. The correlation coefficients for the domains of the ICIQ-FLUTS were around R = 0.5, p < 0.001. CONCLUSION: This symptoms score performed well on the standard, psychometric validation. The score changed in response to treatment and in a direction appropriate to the changes in microscopic pyuria. It correlated with measures of quality of life. It would seem to make a good candidate for monitoring treatment progress in ordinary clinical practice