SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of SIS, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that SIS has overall better performance. Conclusions: SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of SIS in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.

Effects of a combined aerobic and strength training program in youth patients with acute lymphoblastic leukemia

Cure rates of youth with Acute Lymphoblastic Leukemia (ALL) have increased in the past decades, but survivor's quality of life and physical fitness has become a growing concern. Although previous reports showed that resistance training is feasible and effective, we hypothesized that a more intense exercise program would also be feasible, but more beneficial than low- to moderate-intensity training programs. We aimed to examine the effects of an exercise program combining high-intensity resistance exercises and moderate-intensity aerobic exercises in young patients undergoing treatment for ALL. A quasi-experimental study was conducted. The patients (n = 6; 5-16 years of age) underwent a 12-week intra-hospital training program involving high-intensity strength exercises and aerobic exercise at 70% of the peak oxygen consumption. At baseline and after 12 weeks, we assessed sub-maximal strength (10 repetition-maximum), quality of life and possible adverse effects. A significant improvement was observed in the sub maximal strength for bench press (71%), lat pull down (50%), leg press (73%) and leg extension (64%) as a result of the training (p < 0.01). The parents' evaluations of their children's quality of life revealed an improvement in fatigue and general quality of life, but the children's self-reported quality of life was not changed. No adverse effects occurred. A 12-week in-hospital training program including high-intensity resistance exercises promotes marked strength improvements in patients during the maintenance phase of the treatment for Acute Lymphoblastic Leukemia without side-effects. Parents' evaluations of their children revealed an improvement in the quality of life.

Effectiveness of a multifactorial falls prevention program in community-dwelling older people when compared to usual care: study protocol for a randomised controlled trial (Prevquedas Brazil)

Background Falling in older age is a major public health concern due to its costly and disabling consequences. However very few randomised controlled trials (RCTs) have been conducted in developing countries, in which population ageing is expected to be particularly substantial in coming years. This article describes the design of an RCT to evaluate the effectiveness of a multifactorial falls prevention program in reducing the rate of falls in community-dwelling older people. Methods/design Multicentre parallel-group RCT involving 612 community-dwelling men and women aged 60 years and over, who have fallen at least once in the previous year. Participants will be recruited in multiple settings in Sao Paulo, Brazil and will be randomly allocated to a control group or an intervention group. The usual care control group will undergo a fall risk factor assessment and be referred to their clinicians with the risk assessment report so that individual modifiable risk factors can be managed without any specific guidance. The intervention group will receive a 12-week Multifactorial Falls Prevention Program consisting of: an individualised medical management of modifiable risk factors, a group-based, supervised balance training exercise program plus an unsupervised home-based exercise program, an educational/behavioral intervention. Both groups will receive a leaflet containing general information about fall prevention strategies. Primary outcome measures will be the rate of falls and the proportion of fallers recorded by monthly falls diaries and telephone calls over a 12 month period. Secondary outcomes measures will include risk of falling, fall-related self-efficacy score, measures of balance, mobility and strength, fall-related health services use and independence with daily tasks. Data will be analysed using the intention-to-treat principle.The incidence of falls in the intervention and control groups will be calculated and compared using negative binomial regression analysis. Discussion This study is the first trial to be conducted in Brazil to evaluate the effectiveness of an intervention to prevent falls. If proven to reduce falls this study has the potential to benefit older adults and assist health care practitioners and policy makers to implement and promote effective falls prevention interventions. Trial registration ClinicalTrials.gov (NCT01698580)

Constraint handling rules. Compositional semantics and program transformation

This thesis intends to investigate two aspects of Constraint Handling Rules (CHR). It proposes a compositional semantics and a technique for program transformation. CHR is a concurrent committed-choice constraint logic programming language consisting of guarded rules, which transform multi-sets of atomic formulas (constraints) into simpler ones until exhaustion [Frü06] and it belongs to the declarative languages family. It was initially designed for writing constraint solvers but it has recently also proven to be a general purpose language, being as it is Turing equivalent [SSD05a]. Compositionality is the first CHR aspect to be considered. A trace based compositional semantics for CHR was previously defined in [DGM05]. The reference operational semantics for such a compositional model was the original operational semantics for CHR which, due to the propagation rule, admits trivial non-termination. In this thesis we extend the work of [DGM05] by introducing a more refined trace based compositional semantics which also includes the history. The use of history is a well-known technique in CHR which permits us to trace the application of propagation rules and consequently it permits trivial non-termination avoidance [Abd97, DSGdlBH04]. Naturally, the reference operational semantics, of our new compositional one, uses history to avoid trivial non-termination too. Program transformation is the second CHR aspect to be considered, with particular regard to the unfolding technique. Said technique is an appealing approach which allows us to optimize a given program and in more detail to improve run-time efficiency or spaceconsumption. Essentially it consists of a sequence of syntactic program manipulations which preserve a kind of semantic equivalence called qualified answer [Frü98], between the original program and the transformed ones. The unfolding technique is one of the basic operations which is used by most program transformation systems. It consists in the replacement of a procedure-call by its definition. In CHR every conjunction of constraints can be considered as a procedure-call, every CHR rule can be considered as a procedure and the body of said rule represents the definition of the call. While there is a large body of literature on transformation and unfolding of sequential programs, very few papers have addressed this issue for concurrent languages. We define an unfolding rule, show its correctness and discuss some conditions in which it can be used to delete an unfolded rule while preserving the meaning of the original program. Finally, confluence and termination maintenance between the original and transformed programs are shown. This thesis is organized in the following manner. Chapter 1 gives some general notion about CHR. Section 1.1 outlines the history of programming languages with particular attention to CHR and related languages. Then, Section 1.2 introduces CHR using examples. Section 1.3 gives some preliminaries which will be used during the thesis. Subsequentely, Section 1.4 introduces the syntax and the operational and declarative semantics for the first CHR language proposed. Finally, the methodologies to solve the problem of trivial non-termination related to propagation rules are discussed in Section 1.5. Chapter 2 introduces a compositional semantics for CHR where the propagation rules are considered. In particular, Section 2.1 contains the definition of the semantics. Hence, Section 2.2 presents the compositionality results. Afterwards Section 2.3 expounds upon the correctness results. Chapter 3 presents a particular program transformation known as unfolding. This transformation needs a particular syntax called annotated which is introduced in Section 3.1 and its related modified operational semantics !0t is presented in Section 3.2. Subsequently, Section 3.3 defines the unfolding rule and prove its correctness. Then, in Section 3.4 the problems related to the replacement of a rule by its unfolded version are discussed and this in turn gives a correctness condition which holds for a specific class of rules. Section 3.5 proves that confluence and termination are preserved by the program modifications introduced. Finally, Chapter 4 concludes by discussing related works and directions for future work.

Domain-Specific Program Checking

Lint-like program checkers are popular tools that ensure code quality by verifying compliance with best practices for a particular programming language. The proliferation of internal domain-specific languages and models, however, poses new challenges for such tools. Traditional program checkers produce many false positives and fail to accurately check constraints, best practices, common errors, possible optimizations and portability issues particular to domain-specific languages. We advocate the use of dedicated rules to check domain-specific practices. We demonstrate the implementation of domain-specific rules, the automatic fixing of violations, and their application to two case-studies: (1) Seaside defines several internal DSLs through a creative use of the syntax of the host language; and (2) Magritte adds meta-descriptions to existing code by means of special methods. Our empirical validation demonstrates that domain-specific program checking significantly improves code quality when compared with general purpose program checking.

Developing a smoking cessation program for Turkish-speaking migrants in Switzerland: novel findings and promising effects

Introduction: Recent studies show that smoking prevalence in the Turkish-speaking migrant population in Switzerland is substantially higher than in the general population. A specific group treatment for Turkish-speaking migrants was developed and tested in order to provide the migrant population with equal access to smoking cessation programs and to improve the migration-sensitive quality of such programs by sociocultural targeting. Methods: The evaluation of the program included quantitative (questionnaires t1 and t2 and follow-up by telephone) and qualitative methods (participant observation and semi-structured interviews). Results: The results showed that 37.7% of the 61 participants were smoke free at the 12-month follow-up. The factors of being in a partnership and using nicotine replacement products during the program were positively associated with successful cessation. We also demonstrated the importance of “strong ties” (strong relationships between participants) and the sensitivity of the program to sociocultural (e.g., social aspects of smoking in Turkish culture, which were addressed in relapse prevention), socioeconomic (e.g., low financial resources, which were addressed by providing the course for free), and migration-specific (e.g., underdeveloped access to smoking cessation programs, which was addressed using outreach strategy for recruiting) issues. Conclusions: Overall, the smoking cessation program was successfully tested and is now becoming implemented as a regular service of the Swiss Public Health Program for Tobacco Prevention (by the Swiss Association for Smoking Prevention).

Effectiveness, safety and cost-effectiveness of homeopathy in general practice - summarized health technology assessment

Introduction: The Health Technology Assessment report on effectiveness, cost-effectiveness and appropriateness of homeopathy was compiled on behalf of the Swiss Federal Office for Public Health (BAG) within the framework of the 'Program of Evaluation of Complementary Medicine (PEK)'. Materials and Methods: Databases accessible by Internet were systematically searched, complemented by manual search and contacts with experts, and evaluated according to internal and external validity criteria. Results: Many high-quality investigations of pre-clinical basic research proved homeopathic high-potencies inducing regulative and specific changes in cells or living organisms. 20 of 22 systematic reviews detected at least a trend in favor of homeopathy. In our estimation 5 studies yielded results indicating clear evidence for homeopathic therapy. The evaluation of 29 studies in the domain 'Upper Respiratory Tract Infections/Allergic Reactions' showed a positive overall result in favor of homeopathy. 6 out of 7 controlled studies were at least equivalent to conventional medical interventions. 8 out of 16 placebocontrolled studies were significant in favor of homeopathy. Swiss regulations grant a high degree of safety due to product and training requirements for homeopathic physicians. Applied properly, classical homeopathy has few side-effects and the use of high-potencies is free of toxic effects. A general health-economic statement about homeopathy cannot be made from the available data. Conclusion: Taking internal and external validity criteria into account, effectiveness of homeopathy can be supported by clinical evidence and professional and adequate application be regarded as safe. Reliable statements of cost-effectiveness are not available at the moment. External and model validity will have to be taken more strongly into consideration in future studies.

Substance use disorder treatment programs in Switzerland and the USA: Program characteristics and 1-year outcomes

AIM: This study compared matched samples of substance use disorder (SUD) patients in Swiss and United States (US) residential treatment programs and examined the relationship of program characteristics to patients' substance use and psychosocial functioning at a 1-year follow-up. DESIGN AND SETTING: The study used a prospective, naturalistic design and a sample of 10 public programs in the German-speaking part of Switzerland and 15 US public treatment programs. PARTICIPANTS: A total of 358 male patients in Swiss programs were matched on age, marital status and education with 358 male patients in US programs. A total of 160 Swiss and 329 US patient care staff members also participated. MEASUREMENT: Patients completed comparable inventories at admission, discharge and 1-year follow-up to assess their substance use and psychological functioning and receipt of continuing care. Staff members reported on program characteristics and their beliefs about substance use. FINDINGS: Compared to Swiss patients, US patients had more severe substance use and psychological problems at intake and although they did not differ on abstinence and remission at follow-up, had somewhat poorer outcomes in other areas of functioning. Swiss programs were longer and included more individual treatment sessions; US programs included more group sessions and were more oriented toward a disease model of treatment. Overall, length of program, treatment intensity and 12-step orientation were associated with better 1-year outcomes for patients in both Swiss and US programs. CONCLUSIONS: The sample of Swiss and US programs studied here differed in patient and treatment characteristics; however, in general, there were comparable associations between program characteristics and patients' 1-year outcomes. These findings suggest that associations between treatment processes and patients' outcomes may generalize from one cultural context to another.

Learning styles vary among general surgery residents: analysis of 12 years of data

PURPOSE: Understanding the learning styles of individuals may assist in the tailoring of an educational program to optimize learning. General surgery faculty and residents have been characterized previously as having a tendency toward particular learning styles. We seek to understand better the learning styles of general surgery residents and differences that may exist within the population. METHODS: The Kolb Learning Style Inventory was administered yearly to general surgery residents at the University of Cincinnati from 1994 to 2006. This tool allows characterization of learning styles into 4 groups: converging, accommodating, assimilating, and diverging. The converging learning style involves education by actively solving problems. The accommodating learning style uses emotion and interpersonal relationships. The assimilating learning style learns by abstract logic. The diverging learning style learns best by observation. Chi-square analysis and analysis of variance were performed to determine significance. RESULTS: Surveys from 1994 to 2006 (91 residents, 325 responses) were analyzed. The prevalent learning style was converging (185, 57%), followed by assimilating (58, 18%), accommodating (44, 14%), and diverging (38, 12%). At the PGY 1 and 2 levels, male and female residents differed in learning style, with the accommodating learning style being relatively more frequent in women and assimilating learning style more frequent in men (Table 1, p < or = 0.001, chi-square test). Interestingly, learning style did not seem to change with advancing PGY level within the program, which suggests that individual learning styles may be constant throughout residency training. If a resident's learning style changed, it tended to be to converging. In addition, no relation exists between learning style and participation in dedicated basic science training or performance on the ABSIT/SBSE. CONCLUSIONS: Our data suggests that learning style differs between male and female general surgery residents but not with PGY level or ABSIT/SBSE performance. A greater understanding of individual learning styles may allow more refinement and tailoring of surgical programs.

Postgraduate training program

BACKGROUND: Faculties face the permanent challenge to design training programs with well-balanced educational outcomes, and to offer various organised and individual learning opportunities. AIM: To apply our original model to a postgraduate training program in rheumatology in general, and to various learning experiences in particular, in order to analyse the balance between different educational objectives. METHODS: Learning times of various educational activities were reported by the junior staff as targeted learners. The suitability of different learning experiences to achieve cognitive, affective and psychomotor learning objectives was estimated. Learning points with respect to efficacy were calculated by multiplication of the estimated learning times by the perceived appropriateness of the educational strategies. RESULTS: Out of 780 hours of professional learning per year (17.7 hours/week), 37.7% of the time was spent under individual supervision of senior staff, 24.4% in organised structured learning, 22.6% in self-studies, and 15.3% in organised patient-oriented learning. The balance between the different types of learning objectives was appropriate for the overall program, but not for each particular learning experience. Acquisition of factual knowledge and problem solving was readily aimed for during organised teaching sessions of different formats, and by personal targeted reading. Attitudes, skills and competencies, as well as behavioural and performance changes were mostly learned during caring for patients under interactive supervision by experts. CONCLUSION: We encourage other faculties to apply this approach to any other curriculum of undergraduate education, postgraduate training or continuous professional development in order to foster the development of well-balanced learning experiences.

Periodontal and general health in long-term periodontal maintenance patients treated in a Norwegian private practice: a descriptive report from a compliant and partially compliant survivor population

BACKGROUND There is weak evidence to support the benefit of periodontal maintenance therapy in preventing tooth loss. In addition, the effects of long-term periodontal treatment on general health are unclear. METHODS Patients who were compliant and partially compliant (15 to 25 years' follow-up) in private practice were observed for oral and systemic health changes. RESULTS A total of 219 patients who were compliant (91 males and 128 females) were observed for 19.1 (range 15 to 25; SD ± 2.8) years. Age at reassessment was 64.6 (range: 39 to 84; SD ± 9.0) years. A total of 145 patients were stable (0 to 3 teeth lost), 54 were downhill (4 to 6 teeth lost), and 21 patients extreme downhill (>6 teeth lost); 16 patients developed hypertension, 13 developed type 2 diabetes, and 15 suffered myocardial infarcts (MIs). A minority developed other systemic diseases. Risk factors for MI included overweight (odds ratio [OR]: 9.04; 95% confidence interval [CI]: 2.9 to 27.8; P = 0.000), family history with cardiovascular disease (OR: 3.10; 95% CI: 1.07 to 8.94; P = 0.029), type 1 diabetes at baseline (P = 0.02), and developing type 2 diabetes (OR: 7.9; 95% CI: 2.09 to 29.65; P = 0.000). A total of 25 patients who were partially compliant (17 males and eight females) were observed for 19 years. This group had a higher proportion of downhill and extreme downhill cases and MI. CONCLUSIONS Patients who left the maintenance program in a periodontal specialist practice in Norway had a higher rate of tooth loss than patients who were compliant. Patients who were compliant with maintenance in a specialist practice in Norway have a similar risk of developing type 2 diabetes as the general population. A rate of 0.0037 MIs per patient per year was recorded for this group. Due to the lack of external data, it is difficult to assess how this compares with patients who have periodontal disease and are untreated.

An evaluation of the personal response system program for the elderly in Harris County, Texas

The Personal Response System Program at Huffington Center on Aging, Baylor College of Medicine, provides emergency call systems for elderly people living independently in Houston, Texas. The goal of the project was to complete a formative evaluation of the Personal Response System Program. The specific aims of the evaluation were three-fold. One aim was to evaluate participant health status and level of disability. The second aim was to develop a health care cost estimation strategy. Finally, a preliminary cost-effectiveness analysis was completed to evaluate the program's impact on health care costs and health status among the elderly target population. ^ The evaluation was a longitudinal, randomized experimental design. After the screening of 120 volunteers for eligibility, clients were asked to complete a written questionnaire and a monthly health service contact diary. Volunteers were contacted by telephone interviewers to collect health status information from 100 eligible clients (83%) on three occasions during the six months of follow-up. ^ Initially, volunteers were randomized to two experimental groups. The two groups were found to be comparable at the beginning of the study. No significant differences were detected related to health status, level of disability, or history of physician visits at baseline. However, the group with the Personal Response System (PRS) device had more adverse health events, higher IADL scores, more frequent use of walkers, lower average health status scores, and fewer community volunteers hours than the usual care comparison group. ^ The health care costs were estimated based on an algorithm adapted from the American Medical Association guidelines. Average total health care costs for the group with the PRS device ($912) were greater than the usual care group ($464). However, median health care values for the PRS group ($263) were similar to the usual care comparison group ($234). The preliminary findings indicated that the use of the PRS device was not associated with health care cost savings. ^ In the preliminary cost-effectiveness analysis, use of the personal response system was found to be associated with increased mental health status among elderly clients. The cost-effectiveness evaluation indicated that the associated cost for six months was $710 per unit increase in mental component score when the $150 PRS subscription was included. However, clients with the PRS device were found to have a greater decline in physical health status during the six-month follow-up. The beneficial effect on mental health status was found to be in contrast to negative findings associated with changes in physical health status. The implications for future research relate to the need to identify risk factors among geriatric populations to better target groups that would most likely benefit from PRS Program enrollment. ^

Effects of regional versus general anesthesia on outcomes after total hip arthroplasty: a retrospective propensity-matched cohort study

BACKGROUND Many orthopaedic surgical procedures can be performed with either regional or general anesthesia. We hypothesized that total hip arthroplasty with regional anesthesia is associated with less postoperative morbidity and mortality than total hip arthroplasty with general anesthesia. METHODS This retrospective propensity-matched cohort study utilizing the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) database included patients who had undergone total hip arthroplasty from 2007 through 2011. After matching, logistic regression was used to determine the association between the type of anesthesia and deep surgical site infections, hospital length of stay, thirty-day mortality, and cardiovascular and pulmonary complications. RESULTS Of 12,929 surgical procedures, 5103 (39.5%) were performed with regional anesthesia. The adjusted odds for deep surgical site infections were significantly lower in the regional anesthesia group than in the general anesthesia group (odds ratio [OR] = 0.38; 95% confidence interval [CI] = 0.20 to 0.72; p < 0.01). The hospital length of stay (geometric mean) was decreased by 5% (95% CI = 3% to 7%; p < 0.001) with regional anesthesia, which translates to 0.17 day for each total hip arthroplasty. Regional anesthesia was also associated with a 27% decrease in the odds of prolonged hospitalization (OR = 0.73; 95% CI = 0.68 to 0.89; p < 0.001). The mortality rate was not significantly lower with regional anesthesia (OR = 0.78; 95% CI = 0.43 to 1.42; p > 0.05). The adjusted odds for cardiovascular complications (OR = 0.61; 95% CI = 0.44 to 0.85) and respiratory complications (OR = 0.51; 95% CI = 0.33 to 0.81) were all lower in the regional anesthesia group. CONCLUSIONS Compared with general anesthesia, regional anesthesia for total hip arthroplasty was associated with a reduction in deep surgical site infection rates, hospital length of stay, and rates of postoperative cardiovascular and pulmonary complications. These findings could have an important medical and economic impact on health-care practice.

Addressing Multilevel Program Complexity by Evaluation Design

In this paper, we present the evaluation design for a complex multilevel program recently introduced in Switzerland. The evaluation embraces the federal level, the cantonal program level, and the project level where target groups are directly addressed. We employ Pawson and Tilley’s realist evaluation approach, in order to do justice to the varying context factors that impact the cantonal programs leading to varying effectiveness of the implemented activities. The application of the model to the canton of Uri shows that the numerous vertical and horizontal relations play a crucial role for the program’s effectiveness. As a general learning for the evaluation of complex programs, we state that there is a need to consider all affected levels of a program and that no monocausal effects can be singled out in programs where multiple interventions address the same problem. Moreover, considering all affected levels of a program can mean going beyond the borders of the actual program organization and including factors that do not directly interfere with the policy delivery as such. In particular, we found that the relationship between the cantonal and the federal level was a crucial organizational factor influencing the effectiveness of the cantonal program.

MBA Program Reputation: Objective Rankings for Students, Employers and Program Administrators

Widely publicized reports of fresh MBAs receiving multiple job offers with six-figure annual salaries leave a long-lasting general impression about the high quality of selected business schools. Business Week reports on a regular basis ranking of MBA programs based on subjective surveys of students and employers. This paper ranks MBA programs using objective data from three different points of view students, employers, and MBA program administrators.