Providing web-based mental health services to at-risk women

<p>Abstract</p> <p>Background</p> <p>We examined the feasibility of providing web-based mental health services, including synchronous internet video conferencing of an evidence-based support/education group, to at-risk women, specifically poor lone mothers. The objectives of this study were to: (i) adapt a face-to-face support/education group intervention to a web-based format for lone mothers, and (ii) evaluate lone mothers' response to web-based services, including an online video conferencing group intervention program.</p> <p>Methods</p> <p>Participating mothers were recruited through advertisements. To adapt the face-to-face intervention to a web-based format, we evaluated participant motivation through focus group/key informant interviews (n = 7), adapted the intervention training manual for a web-based environment and provided a computer training manual. To evaluate response to web-based services, we provided the intervention to two groups of lone mothers (n = 15). Pre-post quantitative evaluation of mood, self-esteem, social support and parenting was done. Post intervention follow up interviews explored responses to the group and to using technology to access a health service. Participants received $20 per occasion of data collection. Interviews were taped, transcribed and content analysis was used to code and interpret the data. Adherence to the intervention protocol was evaluated.</p> <p>Results</p> <p>Mothers participating in this project experienced multiple difficulties, including financial and mood problems. We adapted the intervention training manual for use in a web-based group environment and ensured adherence to the intervention protocol based on viewing videoconferencing group sessions and discussion with the leaders. Participant responses to the group intervention included decreased isolation, and increased knowledge and confidence in themselves and their parenting; the responses closely matched those of mothers who obtained same service in face-to-face groups. Pre-and post-group quantitative evaluations did not show significant improvements on measures, although the study was not powered to detect these.</p> <p>Conclusions</p> <p>We demonstrated that an evidence-based group intervention program for lone mothers developed and evaluated in face-to-face context transferred well to an online video conferencing format both in terms of group process and outcomes.</p

All nonadherence is equal but is some more equal than others? Tuberculosis in the digital era

Adherence to treatment for tuberculosis (TB) has been a concern for many decades, resulting in the World Health Organization's recommendation of the direct observation of treatment in the 1990s. Recent advances in digital adherence technologies (DATs) have renewed discussion on how to best address nonadherence, as well as offering important information on dose-by-dose adherence patterns and their variability between countries and settings. Previous studies have largely focussed on percentage thresholds to delineate sufficient adherence, but this is misleading and limited, given the complex and dynamic nature of adherence over the treatment course. Instead, we apply a standardised taxonomy – as adopted by the international adherence community – to dose-by-dose medication-taking data, which divides missed doses into 1) late/noninitiation (starting treatment later than expected/not starting), 2) discontinuation (ending treatment early), and 3) suboptimal implementation (intermittent missed doses). Using this taxonomy, we can consider the implications of different forms of nonadherence for intervention and regimen design. For example, can treatment regimens be adapted to increase the “forgiveness” of common patterns of suboptimal implementation to protect against treatment failure and the development of drug resistance? Is it reasonable to treat all missed doses of treatment as equally problematic and equally common when deploying DATs? Can DAT data be used to indicate the patients that need enhanced levels of support during their treatment course? Critically, we pinpoint key areas where knowledge regarding treatment adherence is sparse and impeding scientific progress

Local alignment of generalized k-base encoded DNA sequence

<p>Abstract</p> <p>Background</p> <p>DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base individually. The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence.</p> <p>Results</p> <p>Although two-base encoding is currently used in practice, many other encoding schemes are possible, whereby two ore more bases are encoded at a time. A generalized <it>k</it>-base encoding scheme is presented, whereby feasible higher order encodings are better able to differentiate errors in the encoded sequence from true DNA sequence variants. A generalized version of the previous two-base encoding DNA sequence comparison algorithm is used to compare a <it>k</it>-base encoded sequence to a DNA reference sequence. Finally, simulations are performed to evaluate the power, the false positive and false negative SNP discovery rates, and the performance time of <it>k</it>-base encoding compared to previous methods as well as to the standard DNA sequence comparison algorithm.</p> <p>Conclusions</p> <p>The novel generalized <it>k</it>-base encoding scheme and resulting local alignment algorithm permits the development of higher fidelity ligation-based next generation sequencing technology. This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time.</p

FAAST: Flow-space Assisted Alignment Search Tool

<p>Abstract</p> <p>Background</p> <p>High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments.</p> <p>Results</p> <p>We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool).</p> <p>Conclusions</p> <p>We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed.</p> <p>The tool is available at <url>http://www.ifm.liu.se/bioinfo/</url></p

FAAST: Flow-space Assisted Alignment Search Tool

<p>Abstract</p> <p>Background</p> <p>High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments.</p> <p>Results</p> <p>We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool).</p> <p>Conclusions</p> <p>We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed.</p> <p>The tool is available at <url>http://www.ifm.liu.se/bioinfo/</url></p

The role of the RACK1 ortholog Cpc2p in modulating pheromone-induced cell cycle arrest in fission yeast

The detection and amplification of extracellular signals requires the involvement of multiple protein components. In mammalian cells the receptor of activated C kinase (RACK1) is an important scaffolding protein for signal transduction networks. Further, it also performs a critical function in regulating the cell cycle by modulating the G1/S transition. Many eukaryotic cells express RACK1 orthologs, with one example being Cpc2p in the fission yeast Schizosaccharomyces pombe. In contrast to RACK1, Cpc2p has been described to positively regulate, at the ribosomal level, cells entry into M phase. In addition, Cpc2p controls the stress response pathways through an interaction with Msa2p, and sexual development by modulating Ran1p/Pat1p. Here we describe investigations into the role, which Cpc2p performs in controlling the G protein-mediated mating response pathway. Despite structural similarity to Gβ-like subunits, Cpc2p appears not to function at the G protein level. However, upon pheromone stimulation, cells overexpressing Cpc2p display substantial cell morphology defects, disorientation of septum formation and a significantly protracted G1 arrest. Cpc2p has the potential to function at multiple positions within the pheromone response pathway. We provide a mechanistic interpretation of this novel data by linking Cpc2p function, during the mating response, with its previous described interactions with Ran1p/Pat1p. We suggest that overexpressing Cpc2p prolongs the stimulated state of pheromone-induced cells by increasing ste11 gene expression. These data indicate that Cpc2p regulates the pheromone-induced cell cycle arrest in fission yeast by delaying cells entry into S phase

Evolution favors protein mutational robustness in sufficiently large populations

BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. RESULTS: Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by existing mathematical theories, and can be quantitatively related to the way that the proteins occupy their neutral network. CONCLUSIONS: Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon may contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations

Grammar-based distance in progressive multiple sequence alignment

Background: We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algorithm uses a grammar-based distance metric to determine the order in which biological sequences are to be pairwise aligned. The progressive alignment occurs via pairwise aligning new sequences with an ensemble of the sequences previously aligned. Results: The performance of the proposed algorithm is validated via comparison to popular progressive multiple alignment approaches, ClustalW and T-Coffee, and to the more recently developed algorithms MAFFT, MUSCLE, Kalign, and PSAlign using the BAliBASE 3.0 database of amino acid alignment files and a set of longer sequences generated by Rose software. The proposed algorithm has successfully built multiple alignments comparable to other programs with significant improvements in running time. The results are especially striking for large datasets. Conclusion: We introduce a computationally efficient progressive alignment algorithm using a grammar based sequence distance particularly useful in aligning large datasets

Electronic learning can facilitate student performance in undergraduate surgical education: a prospective observational study

BACKGROUND: Our institution recently introduced a novel internet accessible computer aided learning (iCAL) programme to complement existing surgical undergraduate teaching methods. On graduation of the first full cycle of undergraduate students to whom this resource was available we assessed the utility of this new teaching facility. METHOD: The computer programme prospectively records usage of the system on an individual user basis. We evaluated the utilisation of the web-based programme and its impact on class ranking changes from an entry-test evaluation to an exit examination in surgery. RESULTS: 74.4% of students were able to access iCAL from off-campus internet access. The majority of iCAL usage (64.6%) took place during working hours (08:00–18:00) with little usage on the weekend (21.1%). Working hours usage was positively associated with improvement in class rank (P = 0.025, n = 148) but out-of hours usage was not (P = 0.306). Usage during weekdays was associated with improved rank (P = 0.04), whereas weekend usage was not (P = 0.504). There were no significant differences in usage between genders (P = 0.3). Usage of the iCAL system was positively correlated with improvement in class rank from the entry to the exit examination (P = 0.046). Students with lower ranks on entry examination, were found to use the computer system more frequently (P = 0.01). CONCLUSION: Electronic learning complements traditional teaching methods in undergraduate surgical teaching. Its is more frequently used by students achieving lower class ranking with traditional teaching methods, and this usage is associated with improvements in class ranking

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

<p>Abstract</p> <p>Background</p> <p>Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.</p> <p>Results</p> <p>We present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divide and conquer approach is then applied to break the sequences into fragments that can be aligned independently by an external alignment program. These partial alignments are assembled together to form a complete alignment of the original sequences.</p> <p>Conclusions</p> <p>MISHIMA provides improved performance compared to the commonly used multiple alignment methods. As an example, six complete genome sequences of bacteria species <it>Helicobacter pylori </it>(about 1.7 Mb each) were successfully aligned in about 6 hours using a single PC.</p