A Parallel Solver for Graph Laplacians

Problems from graph drawing, spectral clustering, network flow and graph partitioning can all be expressed in terms of graph Laplacian matrices. There are a variety of practical approaches to solving these problems in serial. However, as problem sizes increase and single core speeds stagnate, parallelism is essential to solve such problems quickly. We present an unsmoothed aggregation multigrid method for solving graph Laplacians in a distributed memory setting. We introduce new parallel aggregation and low degree elimination algorithms targeted specifically at irregular degree graphs. These algorithms are expressed in terms of sparse matrix-vector products using generalized sum and product operations. This formulation is amenable to linear algebra using arbitrary distributions and allows us to operate on a 2D sparse matrix distribution, which is necessary for parallel scalability. Our solver outperforms the natural parallel extension of the current state of the art in an algorithmic comparison. We demonstrate scalability to 576 processes and graphs with up to 1.7 billion edges.Comment: PASC '18, Code: https://github.com/ligmg/ligm

IRRIGATION SCHEDULING FOR SOME SELECTED VEGETABLES CROP AT THE GALMA PILOT IRRIGATION SCHEME

The possibility of improving efficient use of water and energy by applying the right amount of water to cropland at the right time and thereby increasing the extent of irrigation to other areas is not only relevant but calls for urgent attention. The study aims at determining irrigation scheduling for vegetable crops at Galma Pilot Irrigation Scheme of the Ministry of Mater Resources, Zaria Kaduna State. The moisture contents at field capacity and wilting point were obtained from the soil water characteristics software named hydraulic properties calculator (HPC) using the details of the particles size analyses and bulk density obtained from the study area. The crop water requirement for each vegetable crop was estimated based on average of ten years weather data. Water application depth and irrigation interval were calculated based on the initial stage, crop development stage, middle stage and late stage. The irrigation interval for the initial stage for the different crops ranges between 3 – 5 days , crop development stage 4 -6 days, mid season stage 4 – 8 days and 4 -8 days at maturity. The water application depth ranges from 13 -20mm at the initial stage for the different crops, 14 – 22mm at the development stages, 19 -35mm at the middle stage and maturity stage

Examining Sanction Type and Drug Offender Recidivism : A Register-Based Study in Finland

Nordic countries incarcerate offenders at much lower rates in comparison with incarceration rates in the United States, and reincarcerate fewer people per capita. Non-custodial alternatives to sanctions, including fines and community service, are used extensively in Finland to reduce negative effects of institutionalization and subsequent disadvantage caused by incarceration. The nature of drug-involved offenders within the Finnish system is reviewed in light of current research about the effectiveness of incarceration and deterrence-based approaches for drug offenders. Employing a 2014 sample from register data (consisting of official government records) of drug offenders in Finland with a 3-year recidivism period, this study utilizes a genetic matching procedure to compare offenders who received fines, conditional sentences (probation), or incarceration. While recognizing that numerous confounding variables affect incarceration, we compare a matched sample of drug offenders and the sanctions they have received from the Finland judicial system to determine whether offenders who initially receive a fine or a conditional sentence reenter the correctional system at different rates than those who are incarcerated. After matching, results found no significant differences between offenders receiving incarceration sentences or those who received noncustodial sentences (fine, or conditional sentence) for general and drug-related recidivism. These results are presented within the context of the Finnish corrections system in order to inform the criminal justice community about culture, incarceration, and process differences that could positively affect working with drug offenders in other localities.Nordic countries incarcerate offenders at much lower rates in comparison with incarceration rates in the United States, and reincarcerate fewer people per capita. Non-custodial alternatives to sanctions, including fines and community service, are used extensively in Finland to reduce negative effects of institutionalization and subsequent disadvantage caused by incarceration. The nature of drug-involved offenders within the Finnish system is reviewed in light of current research about the effectiveness of incarceration and deterrence-based approaches for drug offenders. Employing a 2014 sample from register data (consisting of official government records) of drug offenders in Finland with a 3-year recidivism period, this study utilizes a genetic matching procedure to compare offenders who received fines, conditional sentences (probation), or incarceration. While recognizing that numerous confounding variables affect incarceration, we compare a matched sample of drug offenders and the sanctions they have received from the Finland judicial system to determine whether offenders who initially receive a fine or a conditional sentence reenter the correctional system at different rates than those who are incarcerated. After matching, results found no significant differences between offenders receiving incarceration sentences or those who received noncustodial sentences (fine, or conditional sentence) for general and drug-related recidivism. These results are presented within the context of the Finnish corrections system in order to inform the criminal justice community about culture, incarceration, and process differences that could positively affect working with drug offenders in other localities.Peer reviewe

Design of dynamic load-balancing tools for parallel applications

The design of general-purpose dynamic load-balancing tools for parallel applications is more challenging than the design of static partitioning tools. Both algorithmic and software engineering issues arise. The authors have addressed many of these issues in the design of the Zoltan dynamic load-balancing library. Zoltan has an object-oriented interface that makes it easy to use and provides separation between the application and the load-balancing algorithms. It contains a suite of dynamic load-balancing algorithms, including both geometric and graph-based algorithms. Its design makes it valuable both as a partitioning tool for a variety of applications and as a research test-bed for new algorithmic development. In this paper, the authors describe Zoltan's design and demonstrate its use in an unstructured-mesh finite element application

Developing and Selecting Auditory Warnings for a Real-Time Behavioral Intervention

Real-time sensing and computing technologies are increasingly used in the delivery of real-time health behavior interventions. Auditory signals play a critical role in many of these interventions, impacting not only behavioral response but also treatment adherence and participant retention. Yet, few behavioral interventions that employ auditory feedback report the characteristics of sounds used and even fewer design signals specifically for their intervention. This paper describes a four-step process used in developing and selecting auditory warnings for a behavioral trial designed to reduce indoor secondhand smoke exposure. In step one, relevant information was gathered from ergonomic and behavioral science literature to assist a panel of research assistants in developing criteria for intervention-specific auditory feedback. In step two, multiple sounds were identified through internet searches and modified in accordance with the developed criteria, and two sounds were selected that best met those criteria. In step three, a survey was conducted among 64 persons from the primary sampling frame of the larger behavioral trial to compare the relative aversiveness of sounds, determine respondents\u27 reported behavioral reactions to those signals, and assess participant’s preference between sounds. In the final step, survey results were used to select the appropriate sound for auditory warnings. Ultimately, a single-tone pulse, 500 milliseconds (ms) in length that repeats every 270 ms for three cycles was chosen for the behavioral trial. The methods described herein represent one example of steps that can be followed to develop and select auditory feedback tailored for a given behavioral intervention

Randomised Controlled Trial of Real-Time Feedback and Brief Coaching to Reduce Indoor Smoking

Background: Previous secondhand smoke (SHS) reduction interventions have provided only delayed feedback on reported smoking behaviour, such as coaching, or presenting results from child cotinine assays or air particle counters. Design: This SHS reduction trial assigned families at random to brief coaching and continuous real-time feedback (intervention) or measurement-only (control) groups. Participants: We enrolled 298 families with a resident tobacco smoker and a child under age 14. Intervention: We installed air particle monitors in all homes. For the intervention homes, immediate light and sound feedback was contingent on elevated indoor particle levels, and up to four coaching sessions used prompts and praise contingent on smoking outdoors. Mean intervention duration was 64 days. Measures: The primary outcome was \u27particle events\u27 (PEs) which were patterns of air particle concentrations indicative of the occurrence of particle-generating behaviours such as smoking cigarettes or burning candles. Other measures included indoor air nicotine concentrations and participant reports of particle-generating behaviour. Results: PEs were significantly correlated with air nicotine levels (r=0.60) and reported indoor cigarette smoking (r=0.51). Interrupted time-series analyses showed an immediate intervention effect, with reduced PEs the day following intervention initiation. The trajectory of daily PEs over the intervention period declined significantly faster in intervention homes than in control homes. Pretest to post-test, air nicotine levels, cigarette smoking and e-cigarette use decreased more in intervention homes than in control homes. Conclusions: Results suggest that real-time particle feedback and coaching contingencies reduced PEs generated by cigarette smoking and other sources

Prediction of individuals at high risk of chronic kidney disease during treatment with lithium for bipolar disorder.

BACKGROUND: Lithium is the most effective treatment in bipolar disorder. Its use is limited by concerns about risk of chronic kidney disease (CKD). We aimed to develop a model to predict risk of CKD following lithium treatment initiation, by identifying individuals with a high-risk trajectory of kidney function. METHODS: We used United Kingdom Clinical Practice Research Datalink (CPRD) electronic health records (EHRs) from 2000 to 2018. CPRD Aurum for prediction model development and CPRD Gold for external validation. We used elastic net regularised regression to generate a prediction model from potential features. We performed discrimination and calibration assessments in an external validation data set. We included all patients aged ≥ 16 with bipolar disorder prescribed lithium. To be included patients had to have ≥ 1 year of follow-up before lithium initiation, ≥ 3 estimated glomerular filtration rate (eGFR) measures after lithium initiation (to be able to determine a trajectory) and a normal (≥ 60 mL/min/1.73 m2) eGFR at lithium initiation (baseline). In the Aurum development cohort, 1609 fulfilled these criteria. The Gold external validation cohort included 934 patients. We included 44 potential baseline features in the prediction model, including sociodemographic, mental and physical health and drug treatment characteristics. We compared a full model with the 3-variable 5-year kidney failure risk equation (KFRE) and a 3-variable elastic net model. We used group-based trajectory modelling to identify latent trajectory groups for eGFR. We were interested in the group with deteriorating kidney function (the high-risk group). RESULTS: The high risk of deteriorating eGFR group included 191 (11.87%) of the Aurum cohort and 137 (14.67%) of the Gold cohort. Of these, 168 (87.96%) and 117 (85.40%) respectively developed CKD 3a or more severe during follow-up. The model, developed in Aurum, had a ROC area of 0.879 (95%CI 0.853-0.904) in the Gold external validation data set. At the empirical optimal cut-point defined in the development dataset, the model had a sensitivity of 0.91 (95%CI 0.84-0.97) and a specificity of 0.74 (95% CI 0.67-0.82). However, a 3-variable elastic net model (including only age, sex and baseline eGFR) performed similarly well (ROC area 0.888; 95%CI 0.864-0.912), as did the KFRE (ROC area 0.870; 95%CI 0.841-0.898). CONCLUSIONS: Individuals at high risk of a poor eGFR trajectory can be identified before initiation of lithium treatment by a simple equation including age, sex and baseline eGFR. Risk was increased in individuals who were younger at commencement of lithium, female and had a lower baseline eGFR. We did not identify strong predicters of eGFR decline specific to lithium-treated patients. Notably, lithium duration and toxicity were not associated with high-risk trajectory

Role of Heterozygous APC Mutation in Niche Succession and Initiation of Colorectal Cancer – A Computational Study

Mutations in the adenomatous polyposis coli (APC) gene are found in most colorectal cancers. They cause constitutive activation of proliferative pathways when both alleles of the gene are mutated. However studies on individuals with familial adenomatous polyposis (FAP) have shown that a single mutated APC allele can also create changes in the precancerous colon crypt, like increased number of stem cells, increased crypt fission, greater variability of DNA methylation patterns, and higher somatic mutation rates. In this paper, using a computational model of colon crypt dynamics, we evolve and investigate a hypothesis on the effect of heterozygous APC mutation that explains these different observations. Based on previous reports and the results from the computational model we propose the hypothesis that heterozygous APC mutation has the effect of increasing the chances for a stem cell to divide symmetrically, producing two stem cell daughters. We incorporate this hypothesis into the model and perform simulation experiments to investigate the consequences of the hypothesis. Simulations show that this hypothesis links together the changes in FAP crypts observed in previous studies. The simulations also show that an APC+/− stem cell gets selective advantages for dominating the crypt and progressing to cancer. This explains why most colon cancers are initiated by APC mutation. The results could have implications for preventing or retarding the onset of colon cancer in people with inherited or acquired mutation of one APC allele. Experimental validation of the hypothesis as well as investigation into the molecular mechanisms of this effect may therefore be worth undertaking

Cancer Stem Cells and Side Population Cells in Breast Cancer and Metastasis

In breast cancer it is never the primary tumour that is fatal; instead it is the development of metastatic disease which is the major cause of cancer related mortality. There is accumulating evidence that suggests that Cancer Stem Cells (CSC) may play a role in breast cancer development and progression. Breast cancer stem cell populations, including side population cells (SP), have been shown to be primitive stem cell-like populations, being long-lived, self-renewing and highly proliferative. SP cells are identified using dual wavelength flow cytometry combined with Hoechst 33342 dye efflux, this ability is due to expression of one or more members of the ABC transporter family. They have increased resistance to chemotherapeutic agents and apoptotic stimuli and have increased migratory potential above that of the bulk tumour cells making them strong candidates for the metastatic spread of breast cancer. Treatment of nearly all cancers usually involves one first-line agent known to be a substrate of an ABC transporter thereby increasing the risk of developing drug resistant tumours. At present there is no marker available to identify SP cells using immunohistochemistry on breast cancer patient samples. If SP cells do play a role in breast cancer progression/Metastatic Breast Cancer (MBC), combining chemotherapy with ABC inhibitors may be able to destroy both the cells making up the bulk tumour and the cancer stem cell population thus preventing the risk of drug resistant disease, recurrence or metastasis