Hydrologic Terrain Processing Using Parallel Computing

Abstract: Topography in the form of Digital Elevation Models (DEMs), is widely used to derive information for the modeling of hydrologic processes. Hydrologic terrain analysis augments the information content of digital elevation data by removing spurious pits, deriving a structured flow field, and calculating surfaces of hydrologic information derived from the flow field. The increasing availability of large terrain datasets with very small ground sample distance (GSD) poses a challenge for existing algorithms that process terrain data to extract this hydrologic information. This paper will describe a parallel algorithm that has been developed to enhance hydrologic terrain pre-processing so that larger datasets can be more efficiently computed. This paper describes a Message Passing Interface (MPI) parallel implementation for Pit Removal. This key functionality is used within the Terrain Analysis Using Digital Elevation Models (TauDEM) package to remove spurious elevation depressions that are an artifact of the raster representation of the terrain. The parallel algorithm works by decomposing the domain into stripes or tiles where each tile is processed by a separate processor. This method also reduces the memory requirements of each processor so that larger size grids can be processed. The parallel pit removal algorithm is adapted from the method of Planchon and Darboux that starts from a large elevation then iteratively scans the grid, lowering each grid cell to the maximum of the original elevation or the lowest neighbor. The MPI implementation reconcile

Listening to Voices: Understanding and Self-Management of Auditory Verbal Hallucinations in Young Adults

Aims Auditory Verbal Hallucinations (AVH) are a hallmark of psychosis, but affect many other clinical populations. Patients’ understanding and self-management of AVH may differ between diagnostic groups, change over time, and influence clinical outcomes. We aimed to explore patients’ understanding and self-management of AVH in a young adult clinical population. Method 35 participants reporting frequent AVH were purposively sampled from a youth mental health service, to capture experiences across psychosis and non-psychosis diagnoses. Diary and photo-elicitation methodologies were used – participants were asked to complete diaries documenting experiences of AVH, and to take photographs representing these experiences. In-depth, unstructured interviews were held, using participant-produced materials as a topic guide. Conventional content analysis was conducted, deriving results from the data in the form of themes. Result Three themes emerged: (1)Searching for answers, forming identities – voice-hearers sought to explain their experiences, resulting in the construction of identities for voices, and descriptions of relationships with them. These identities were drawn from participants’ life-stories (e.g., reflecting trauma), and belief-systems (e.g., reflecting supernatural beliefs, or mental illness). Some described this process as active / volitional. Participants described re-defining their own identities in relation to those constructed for AVH (e.g. as diseased, 'chosen', or persecuted), others considered AVH explicitly as aspects of, or changes in, their personality. (2)Coping strategies and goals – patients’ self-management strategies were diverse, reflecting the diverse negative experiences of AVH. Strategies were related to a smaller number of goals, e.g. distraction, soothing overwhelming emotions, 'reality-checking', and retaining agency. (3)Outlook – participants formed an overall outlook reflecting their self-efficacy in managing AVH. Resignation and hopelessness in connection with disabling AVH are contrasted with outlooks of “acceptance” or integration, which were described as positive, ideal, or mature. Conclusion Trans-diagnostic commonalities in understanding and self-management of AVH are highlighted - answer-seeking and identity-formation processes; a diversity of coping strategies and goals; and striving to accept the symptom. Descriptions of “voices-as-self”, and dysfunctional relationships with AVH, could represent specific features of voice-hearing in personality disorder, whereas certain supernatural/paranormal identities and explanations were clearly delusional. However, no aspect of identity-formation was completely unique to psychosis or non-psychosis diagnostic groups. The identity-formation process, coping strategies, and outlooks can be seen as a framework both for individual therapies and further research

Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.

BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes. Captured and indexed libraries (QXT Target Enrichment System) prepared for 72 patients were sequenced as a multiplex of 16 samples on an Illumina MiSeq sequencer in 150bp paired-end mode. The cohort comprised 22 positive control DNA samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected AID in whom previous Sanger based genetic screening had been non-diagnostic. RESULTS: VIP was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small INDELS, and somatic mosaicism with allele fraction as low as 3%. Six/50 patients (12%) with unclassified AID had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4). Overall, testing with VIP resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%). CONCLUSIONS: The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected AID

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature0315

Inequality in British Columbia : what role does tax policy play?

In 2001 a new provincial government was elected in the province of British Columbia, the BC Liberal party. During their election campaign they promised that lower personal income taxes would stoke the BC economy. Although personal income taxes were lowered after their election, high income earners were given a much higher proportion of the tax cut (when looked at as a dollar value per person) than middle and lower income earners. Further, since government service fees increased in many areas, it is possible that middle and lower income earners may have found themselves paying more to the government in combined taxes and fees than before the advertised tax cuts. It is thus more realistic to suggest that the burden of taxes has shifted rather than to say that taxes were cut. Social services were also cut dramatically. It is suggested that inequality is likely to increase in the province as a result of these changes. The question of whether the changes to the personal income tax rates will have a positive effect on the BC economy, both in the short, medium and long term is considered. In the short term, it is questionable whether reducing personal income taxes will provide any stimulus to such component parts of the economy as the supply of labour and the supply of capital. It is noted that productivity, a key indicator that the BC Liberals sought to alter through changes to personal income taxes, has not improved. In the long term, a decreased investment in such social services as health and education may have a negative effect on the rate of economic growth in the province

Inequality in British Columbia : what role does tax policy play?

In 2001 a new provincial government was elected in the province of British Columbia, the BC Liberal party. During their election campaign they promised that lower personal income taxes would stoke the BC economy. Although personal income taxes were lowered after their election, high income earners were given a much higher proportion of the tax cut (when looked at as a dollar value per person) than middle and lower income earners. Further, since government service fees increased in many areas, it is possible that middle and lower income earners may have found themselves paying more to the government in combined taxes and fees than before the advertised tax cuts. It is thus more realistic to suggest that the burden of taxes has shifted rather than to say that taxes were cut. Social services were also cut dramatically. It is suggested that inequality is likely to increase in the province as a result of these changes. The question of whether the changes to the personal income tax rates will have a positive effect on the BC economy, both in the short, medium and long term is considered. In the short term, it is questionable whether reducing personal income taxes will provide any stimulus to such component parts of the economy as the supply of labour and the supply of capital. It is noted that productivity, a key indicator that the BC Liberals sought to alter through changes to personal income taxes, has not improved. In the long term, a decreased investment in such social services as health and education may have a negative effect on the rate of economic growth in the province.Law, Peter A. Allard School ofGraduat

Inequality in British Columbia : what role does tax policy play?

In 2001 a new provincial government was elected in the province of British Columbia, the BC Liberal party. During their election campaign they promised that lower personal income taxes would stoke the BC economy. Although personal income taxes were lowered after their election, high income earners were given a much higher proportion of the tax cut (when looked at as a dollar value per person) than middle and lower income earners. Further, since government service fees increased in many areas, it is possible that middle and lower income earners may have found themselves paying more to the government in combined taxes and fees than before the advertised tax cuts. It is thus more realistic to suggest that the burden of taxes has shifted rather than to say that taxes were cut. Social services were also cut dramatically. It is suggested that inequality is likely to increase in the province as a result of these changes. The question of whether the changes to the personal income tax rates will have a positive effect on the BC economy, both in the short, medium and long term is considered. In the short term, it is questionable whether reducing personal income taxes will provide any stimulus to such component parts of the economy as the supply of labour and the supply of capital. It is noted that productivity, a key indicator that the BC Liberals sought to alter through changes to personal income taxes, has not improved. In the long term, a decreased investment in such social services as health and education may have a negative effect on the rate of economic growth in the province

Carbon Offset Opportunities at the Duke University Health System

The Duke Carbon Offsets Initiative (DCOI) is collaborating with the Duke University Health System (DUHS) to obtain carbon offsets that will aid in fulfilling the University’s pledge to be carbon neutral by 2024. This study identified and prioritized financially feasible projects within the DUHS that would lead to carbon offsets. A number of carbon reduction opportunities were identified within the DUHS: medical waste management, renewable energy opportunities, energy efficient kitchen equipment, lighting upgrades, organic waste management, and sustainable tableware. Funding from the DCOI would allow the DUHS to invest in projects beyond what its current budget allows while at the same time generating carbon credits for the University thereby benefitting both parties