Parallelization of whole genome alignment

With the advent of High performance computing, it is now possible to achieve orders of magnitude performance and computation e ciency gains over conventional computer architectures. This thesis explores the potential of using high performance computing to accelerate whole genome alignment. A parallel technique is applied to an algorithm for whole genome alignment, this technique is explained and some experiments were carried out to test it. This technique is based in a fair usage of the available resource to execute genome alignment and how this can be used in HPC clusters. This work is a rst approximation to whole genome alignment and it shows the advantages of parallelism and some of the drawbacks that our technique has. This work describes the resource limitations of current WGA applications when dealing with large quantities of sequences. It proposes a parallel heuristic to distribute the load and to assure that alignment quality is mantained.

Large-Area Photo-Mosaics Using Global Alignment and Navigation Data

Seafloor imagery is a rich source of data for the study of biological and geological processes. Among several applications, still images of the ocean floor can be used to build image composites referred to as photo-mosaics. Photo-mosaics provide a wide-area visual representation of the benthos, and enable applications as diverse as geological surveys, mapping and detection of temporal changes in the morphology of biodiversity. We present an approach for creating globally aligned photo-mosaics using 3D position estimates provided by navigation sensors available in deep water surveys. Without image registration, such navigation data does not provide enough accuracy to produce useful composite images. Results from a challenging data set of the Lucky Strike vent field at the Mid Atlantic Ridge are reported

A clinical trial for uniform multidrug therapy for leprosy patients in Brazil: rationale and design

Leprosy will continue to be a public health problem for several decades. The World Health Organization (WHO) recommends that, for treatment purposes, leprosy cases be classified as either paucibacillary or multibacillary (MB). A uniform leprosy treatment regimen would simplify treatment and halve the treatment duration for MB patients. The clinical trial for uniform multidrug therapy (U-MDT) for leprosy patients (LPs) in Brazil is a randomised, open-label clinical trial to evaluate if the effectiveness of U-MDT for leprosy equals the regular regimen, to determine the acceptability of the U-MDT regimen and to identify the prognostic factors. This paper details the clinical trial methodology and patient enrolment data. The study enrolled 858 patients at two centres and 78.4% of participants were classified as MB according to the WHO criteria. The main difficulty in evaluating a new leprosy treatment regimen is that no reliable data are available for the current treatment regimen. Relapse, reaction and impaired nerve function rates have never been systematically determined, although reaction and impaired nerve function are the two major causes of nerve damage that lead to impairments and disabilities in LPs. Our study was designed to overcome the need for reliable data about the current treatment and to compare its efficacy with that of a uniform regimen.

Brazilian clinical trial of uniform multidrug therapy for leprosy patients: the correlation between clinical disease types and adverse effects

This study sought to verify the correlation between leprosy types and the adverse effects of treatment drugs. This quantitative, prospective, nested study was developed at the Dona Libânia Dermatology Centre in Fortaleza, Brazil. Data were collected from November 2007-November 2008. During this period, 818 leprosy patients were diagnosed and began treatment. Forty patients with tuberculoid leprosy (TT) were selected. Twenty patients followed a standard therapy of dapsone and rifampicin and 20 were administered dapsone, rifampicin and clofazimine (U-MDT). Twenty patients with borderline lepromatous (BL) and lepromatous leprosy (LL) were also selected and treated with U-MDT. All of the subjects received six doses. With the exception of haemolytic anaemia, there was a low incidence of adverse effects in all the groups. We did not observe any differences in the incidence of haemolytic anaemia or other side effects across groups of patients with TT, BL or LL treated with U-MDT.

Tibial component positioning in total knee arthroplasty: bone coverage and extensor apparatus alignment.

Correct positioning of the tibial component in total knee arthroplasty (TKA) must take into account both an optimal bone coverage (defined by a maximal cortical bearing with posteromedial and anterolateral support) and satisfactory patellofemoral tracking. Consequently, a compromise position must be found by the surgeon during the operation to simultaneously meet these two requirements. Moreover, tibial tray positioning depends upon the tibial torsion, which has been shown to act mainly in the proximal quarter of the tibia. Therefore, the correct application of the tibial tray is also theoretically related to the level of bone resection. In this study, we first quantified the torsional profile given by an optimal bone coverage for a symmetrical tibial tray design and for an asymmetrical one. Then, for the two types of tibial trays, we measured the angle difference between optimal bone coverage and an alignment on the middle of the tibial tubercule. Results showed that the values of the torsional profile given by the symmetrical tray were more scattered than those from the asymmetrical one. However, determination of the mean differential angle between the position providing optimal bone coverage and the one providing the best patellofemoral tracking indicated that the symmetrical prosthetic tray offered the best compromise between these two requirements. Although the tibiofemoral joint is known to be asymmetric in both shape and dimension, the asymmetrical tray chosen in this study was found to fulfill this compromise with more difficulty.

Iowa Uniform Crime Report, Iowa Department of Public Safety, 1997

In 1974, the 65th Iowa General Assembly enacted a provision of Chapter 749 B of the Code of Iowa requiring law enforcement agencies to submit reports of crime and arrests to the Bureau of Criminal Investigation. The following language now is contained in section 692.15 Code of Iowa concerning Uniform Crime Reports: If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Iowa Uniform Crime Report, Iowa Department of Public Safety, 1998

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Iowa Uniform Crime Report, Iowa Department of Public Safety, 1999

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Iowa Uniform Crime Report, Iowa Department of Public Safety, 2000

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Iowa Uniform Crime Report, Iowa Department of Public Safety, 2002

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

1995 Iowa Uniform Crime Report

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Iowa Uniform Crime Report, 2001

If it comes to the attention of a sheriff, police department or other law enforcement agency that a public offense has been committed in its jurisdiction, the law enforcement agency shall report information concerning such a public offense to the department on a form to be furnished by the department not more than thirty-five days from the time the public offense first comes to the attention of the law enforcement agency. The reports shall be used to generate crime statistics. The department shall submit statistics to the governor, the general assembly, and the division of criminal and juvenile justice planning of the department of human rights on a quarterly and yearly basis.

Transcription factor map alignment of promoter regions

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments.

Chroma binary similarity and local alignment applied to cover song identification

We present a new technique for audio signal comparison based on tonal subsequence alignment and its application to detect cover versions (i.e., different performances of the same underlying musical piece). Cover song identification is a task whose popularity has increased in the Music Information Retrieval (MIR) community along in the past, as it provides a direct and objective way to evaluate music similarity algorithms.This article first presents a series of experiments carried outwith two state-of-the-art methods for cover song identification.We have studied several components of these (such as chroma resolution and similarity, transposition, beat tracking or Dynamic Time Warping constraints), in order to discover which characteristics would be desirable for a competitive cover song identifier. After analyzing many cross-validated results, the importance of these characteristics is discussed, and the best-performing ones are finally applied to the newly proposed method. Multipleevaluations of this one confirm a large increase in identificationaccuracy when comparing it with alternative state-of-the-artapproaches.

Improving Transition Outcomes-An Innovative State Alignment Grant for Improving Transition Outcome for Youth with Disabilities Through the Use of Intermediaries, 2004

Iowa Vocational Rehabilitation Services, a Division of the State of Iowa Department of Education, in partnership with six other state agencies, applied for and was awarded funding for “Improving Transition Outcomes for Youth with Disabilities Through the Use of intermediaries.” This Innovative State Alignment Grant is funded by the Department of Labor, Office of Disability Employment Policy. For clarity and brevity, the Iowa team chose to use “Improving Transition Outcomes” as the project name, thus providing the acronym ITO. Grant funding began October 1, 2003 with the possibility of renewal for five years.