Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Achieving business and IT alignment from organisational learning perspectives

Business and IT alignment has continued as a top concern for business and IT executives for almost three decades. Many researchers have conducted empirical studies on the relationship between business-IT alignment and performance. Yet, these approaches, lacking a social perspective, have had little impact on sustaining performance and competitive advantage. In addition to the limited alignment literature that explores organisational learning that is represented in shared understanding, communication, cognitive maps and experiences. Hence, this paper proposes an integrated process that enables social and intellectual dimensions through the concept of organisational learning. In particular, the feedback and feed- forward process which provide a value creation across dynamic multilevel of learning. This mechanism enables on-going effectiveness through development of individuals, groups and organisations, which improves the quality of business and IT strategies and drives to performance.

Revising the Program Portfolio: Elevating Academic Program Performance and Strategic Alignment

At many institutions, program review is an underproductive exercise. Review of existing programs is often a check-the-box formality, with inconsistent criteria and little connection to institutional priorities or funding considerations. Decisions about where to concentrate resources across the portfolio can be highly politicized. This report profiles how academic planning exemplars use program review as a strategic tool, integrating data on academic quality, student demand, and resource utilization to improve the economics of challenged programs and prioritize programs for investment and expansion.

Quality of performance of the operation of sugarcane mechanized planting in day and night shifts

The sugarcane mechanized planting is becoming increasingly widespread in Brazil due to a higher operability and better working conditions offered to workers compared to other types of planting. Studies related to this topic are insufficient or scarce in Brazil. In this context, the aim of this study was to evaluate the operation quality of sugarcane mechanized planting in two operation shifts, by means of statistical process control. The mechanized planting was held on March 2012 and statistical design was completely randomized with two treatments, totaling 40 replications for the day shift and 40 replications for the night shift. The variables evaluated were: speed, engine rotation, engine oil pressure, water temperature of the engine, effective field capacity and the time consumption hourly and effective fuel. The use of statistical control charts showed that random intrinsic do not cause this process. The tractor alignment error showed outliers in the day and night shifts operations, indicating a possible delay in receiving the signal. The water temperature of the engine and the effective fuel consumption showed lower variability in nighttime operation with average values of 81°C and 22.66 L ha-1, respectively. The hourly fuel consumption had greater variability and consequently lower quality during the night of the operation, with an average consumption of 25.46 L h-1 while the day shift showed 26.86 L h-1.

Non-water-suppressed proton MR spectroscopy improves spectral quality in the human spinal cord

Magnetic resonance spectroscopy enables insight into the chemical composition of spinal cord tissue. However, spinal cord magnetic resonance spectroscopy has rarely been applied in clinical work due to technical challenges, including strong susceptibility changes in the region and the small cord diameter, which distort the lineshape and limit the attainable signal to noise ratio. Hence, extensive signal averaging is required, which increases the likelihood of static magnetic field changes caused by subject motion (respiration, swallowing), cord motion, and scanner-induced frequency drift. To avoid incoherent signal averaging, it would be ideal to perform frequency alignment of individual free induction decays before averaging. Unfortunately, this is not possible due to the low signal to noise ratio of the metabolite peaks. In this article, frequency alignment of individual free induction decays is demonstrated to improve spectral quality by using the high signal to noise ratio water peak from non-water-suppressed proton magnetic resonance spectroscopy via the metabolite cycling technique. Electrocardiography (ECG)-triggered point resolved spectroscopy (PRESS) localization was used for data acquisition with metabolite cycling or water suppression for comparison. A significant improvement in the signal to noise ratio and decrease of the Cramér Rao lower bounds of all metabolites is attained by using metabolite cycling together with frequency alignment, as compared to water-suppressed spectra, in 13 healthy volunteers.

The effectiveness of laceback ligatures during initial orthodontic alignment: a systematic review and meta-analysis

Lacebacks may be used to limit unwanted incisor proclination during initial orthodontic alignment; however, their use has not met with universal approval. This systematic review aims to appraise the evidence in relation to the effectiveness of lacebacks in controlling incisor position during initial alignment. Electronic database searches of published literature (MEDLINE via Ovid, Cochrane Central Register of Controlled Trials, LILACS, and IBECS) and unpublished literature were performed. Search terms used included randomized controlled trial, controlled clinical trial, random allocation, double blind method, orthodontics, and laceback. Data were extracted using custom forms. Risk of bias assessment was made using the Cochrane Collaboration risk of bias tool. The quality of the evidence was also assessed using GRADE. Mean differences in incisor inclination and antero-posterior changes in incisor and molar position during alignment were calculated. Two studies involving 97 participants were found to be at low risk of bias and were included in the quantitative synthesis. The random effects meta-analysis demonstrated that the use of lacebacks was associated with 0.5 mm greater posterior movement of the incisors during alignment; this finding was of limited clinical importance and statistically non-significant [95 per cent confidence interval (CI): -1.25, 0.25, P = 0.19]. Little difference (0.46 mm) was also found between laceback and non-laceback groups with regards to mesial molar movement (95 per cent CI: -0.33, 1.24, P = 0.26). According to the GRADE assessment, the overall quality of evidence relating to the use of lacebacks was high. There is no evidence to support the use of lacebacks for the control of the sagittal position of the incisors during initial orthodontic alignment.

Next-generation tissue microarray (ngTMA) increases the quality of biomarker studies: an example using CD3, CD8, and CD45RO in the tumor microenvironment of six different solid tumor types

Background Tissue microarray (TMA) technology revolutionized the investigation of potential biomarkers from paraffin-embedded tissues. However, conventional TMA construction is laborious, time-consuming and imprecise. Next-generation tissue microarrays (ngTMA) combine histological expertise with digital pathology and automated tissue microarraying. The aim of this study was to test the feasibility of ngTMA for the investigation of biomarkers within the tumor microenvironment (tumor center and invasion front) of six tumor types, using CD3, CD8 and CD45RO as an example. Methods Ten cases each of malignant melanoma, lung, breast, gastric, prostate and colorectal cancers were reviewed. The most representative H&E slide was scanned and uploaded onto a digital slide management platform. Slides were viewed and seven TMA annotations of 1 mm in diameter were placed directly onto the digital slide. Different colors were used to identify the exact regions in normal tissue (n = 1), tumor center (n = 2), tumor front (n = 2), and tumor microenvironment at invasion front (n = 2) for subsequent punching. Donor blocks were loaded into an automated tissue microarrayer. Images of the donor block were superimposed with annotated digital slides. Exact annotated regions were punched out of each donor block and transferred into a TMA block. 420 tissue cores created two ngTMA blocks. H&E staining and immunohistochemistry for CD3, CD8 and CD45RO were performed. Results All 60 slides were scanned automatically (total time < 10 hours), uploaded and viewed. Annotation time was 1 hour. The 60 donor blocks were loaded into the tissue microarrayer, simultaneously. Alignment of donor block images and digital slides was possible in less than 2 minutes/case. Automated punching of tissue cores and transfer took 12 seconds/core. Total ngTMA construction time was 1.4 hours. Stains for H&E and CD3, CD8 and CD45RO highlighted the precision with which ngTMA could capture regions of tumor-stroma interaction of each cancer and the T-lymphocytic immune reaction within the tumor microenvironment. Conclusion Based on a manual selection criteria, ngTMA is able to precisely capture histological zones or cell types of interest in a precise and accurate way, aiding the pathological study of the tumor microenvironment. This approach would be advantageous for visualizing proteins, DNA, mRNA and microRNAs in specific cell types using in situ hybridization techniques.

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans­membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2/.

Examining the impact of pre-k and kindergarten classroom alignment on school readiness outcomes

This study explored children’s experiences of instructional alignment from prekindergarten to kindergarten and analyzed the impact of those alignment experiences on children’s school readiness outcomes. The study answered the following overarching research question: Does the alignment of children’s learning experiences between prekindergarten and kindergarten impact school readiness outcomes? Three sub-questions drove the research design: (1) How do children’s prekindergarten and kindergarten learning experiences align; (2) To what extent does the alignment of early learning experiences predict children’s school readiness outcomes; and (3) Does the quality of prekindergarten classroom teacher interactions moderate the impact of any PK-K alignment effects? Using cluster analysis and hierarchical linear modeling (HLM) to analyze data from over 1,300 children in the 2009 Head Start Family and Child Experiences Survey (FACES), the study found that children have distinct and definable experiences of PK-K alignment. Results also indicated a disparity in children’s PK-K alignment experiences, with Hispanic/Latino children more likely to attend Head Start programs with poor systems transition practices followed by kindergartens with poor classroom structures. The study found that growth in the use of instructional activity centers from prekindergarten to kindergarten is predictive of better literacy and math outcomes. Findings further suggested that boys, minority students, and children from lower income households are predicted to score lower than girls, white classmates, and higher-income peers across school readiness measures. Findings support the need for equitable transition and alignment practices for children from all racial and ethnic groups. They also argue for an increase in child-directed activity centers in kindergarten. With one exception, the current findings did not support the hypothesis that prekindergarten teacher quality is a moderator of alignment effects on children’s school readiness outcomes. The study presents suggestions for further research.

A total quality management methodology for universities

This research document is motivated by the need for a systemic, efficient quality improvement methodology at universities. There exists no methodology designed for a total quality management (TQM) program in a university. The main objective of this study is to develop a TQM Methodology that enables a university to efficiently develop an integral total quality improvement (TQM) Plan. ^ Current research focuses on the need of improving the quality of universities, the study of the perceived best quality universities, and the measurement of the quality of universities through rankings. There is no evidence of research on how to plan for an integral quality improvement initiative for the university as a whole, which is the main contribution of this study. ^ This research is built on various reference TQM models and criteria provided by ISO 9000, Baldrige and Six Sigma; and educational accreditation criteria found in ABET and SACS. The TQM methodology is proposed by following a seven-step metamethodology. The proposed methodology guides the user to develop a TQM plan in five sequential phases: initiation, assessment, analysis, preparation and acceptance. Each phase defines for the user its purpose, key activities, input requirements, controls, deliverables, and tools to use. The application of quality concepts in education and higher education is particular; since there are unique factors in education which ought to be considered. These factors shape the quality dimensions in a university and are the main inputs to the methodology. ^ The proposed TQM Methodology is used to guide the user to collect and transform appropriate inputs to a holistic TQM Plan, ready to be implemented by the university. Different input data will lead to a unique TQM plan for the specific university at the time. It may not necessarily transform the university into a world-class institution, but aims to strive for stakeholder-oriented improvements, leading to a better alignment with its mission and total quality advancement. ^ The proposed TQM methodology is validated in three steps. First, it is verified by going through a test activity as part of the meta-methodology. Secondly, the methodology is applied to a case university to develop a TQM plan. Lastly, the methodology and the TQM plan both are verified by an expert group consisting of TQM specialists and university administrators. The proposed TQM methodology is applicable to any university at all levels of advancement, regardless of changes in its long-term vision and short-term needs. It helps to assure the quality of a TQM plan, while making the process more systemic, efficient, and cost effective. This research establishes a framework with a solid foundation for extending the proposed TQM methodology into other industries. ^

Talking about quality: exploring how ‘quality’ is conceptualized in European hospitals and healthcare systems

BACKGROUND: Conceptualization of quality of care - in terms of what individuals, groups and organizations include in their meaning of quality, is an unexplored research area. It is important to understand how quality is conceptualised as a means to successfully implement improvement efforts and bridge potential disconnect in language about quality between system levels, professions, and clinical services. The aim is therefore to explore and compare conceptualization of quality among national bodies (macro level), senior hospital managers (meso level), and professional groups within clinical micro systems (micro level) in a cross-national study. METHODS: This cross-national multi-level case study combines analysis of national policy documents and regulations at the macro level with semi-structured interviews (383) and non-participant observation (803 hours) of key meetings and shadowing of staff at the meso and micro levels in ten purposively sampled European hospitals (England, the Netherlands, Portugal, Sweden, and Norway). Fieldwork at the meso and micro levels was undertaken over a 12-month period (2011-2012) and different types of micro systems were included (maternity, oncology, orthopaedics, elderly care, intensive care, and geriatrics). RESULTS: The three quality dimensions clinical effectiveness, patient safety, and patient experience were incorporated in macro level policies in all countries. Senior hospital managers adopted a similar conceptualization, but also included efficiency and costs in their conceptualization of quality. 'Quality' in the forms of measuring indicators and performance management were dominant among senior hospital managers (with clinical and non-clinical background). The differential emphasis on the three quality dimensions was strongly linked to professional roles, personal ideas, and beliefs at the micro level. Clinical effectiveness was dominant among physicians (evidence-based approach), while patient experience was dominant among nurses (patient-centered care, enough time to talk with patients). Conceptualization varied between micro systems depending on the type of services provided. CONCLUSION: The quality conceptualization differed across system levels (macro-meso-micro), among professional groups (nurses, doctors, managers), and between the studied micro systems in our ten sampled European hospitals. This entails a managerial alignment challenge translating macro level quality definitions into different local contexts.

[association Between Physical And Psychosocial Impacts Of Oral Disorders And Quality Of Life Among The Elderly].

This study sought to evaluate the association between the impact of oral disorders in terms of physical/psychosocial dimensions and quality of life among the elderly. It involved a cross-sectional study conducted among the elderly (65-74 years) in 2008/2009. The social impact was assessed using the Oral Health Impact Profile (OHIP 14) and the quality of life using the SF 12 Short-Form Health Survey. Descriptive, univariate and multivariate (logistic regression) analysis was conducted with correction for the design effect, using SPSS(r)18.0 software. Of the 800 individuals approached, 736 elderly individuals participated (TR = 92%), with a mean age of 67.77 years, the majority of whom showed no impact based on the measurement of the prevalence of OHIP. The functional limitation dimension of the OHIP was associated with the physical domain of the SF12, irrespective of the other variables investigated. However, the seriousness of OHIP and its psychological discomfort and disability dimensions was associated with the mental domain of the SF12. The conclusion reached is that some impacts of oral disorders were associated with unsatisfactory quality of life in the physical and mental domains.

Applying The Maternal Near Miss Approach For The Evaluation Of Quality Of Obstetric Care: A Worked Example From A Multicenter Surveillance Study.

To assess quality of care of women with severe maternal morbidity and to identify associated factors. This is a national multicenter cross-sectional study performing surveillance for severe maternal morbidity, using the World Health Organization criteria. The expected number of maternal deaths was calculated with the maternal severity index (MSI) based on the severity of complication, and the standardized mortality ratio (SMR) for each center was estimated. Analyses on the adequacy of care were performed. 17 hospitals were classified as providing adequate and 10 as nonadequate care. Besides almost twofold increase in maternal mortality ratio, the main factors associated with nonadequate performance were geographic difficulty in accessing health services (P < 0.001), delays related to quality of medical care (P = 0.012), absence of blood derivatives (P = 0.013), difficulties of communication between health services (P = 0.004), and any delay during the whole process (P = 0.039). This is an example of how evaluation of the performance of health services is possible, using a benchmarking tool specific to Obstetrics. In this study the MSI was a useful tool for identifying differences in maternal mortality ratios and factors associated with nonadequate performance of care.

[diet Quality And Associated Factors Among The Elderly: A Population-based Study In Campinas, São Paulo State, Brazil].

The aim of this study was to assess the quality of diet among the elderly and associations with socio-demographic variables, health-related behaviors, and diseases. A population-based cross-sectional study was conducted in a representative sample of 1,509 elderly participants in a health survey in Campinas, São Paulo State, Brazil. Food quality was assessed using the Revised Diet Quality Index (DQI-R). Mean index scores were estimated and a multiple regression model was employed for the adjusted analyses. The highest diet quality scores were associated with age 80 years or older, Evangelical religion, diabetes mellitus, and physical activity, while the lowest scores were associated with home environments shared with three or more people, smoking, and consumption of soft drinks and alcoholic beverages. The findings emphasize a general need for diet quality improvements in the elderly, specifically in subgroups with unhealthy behaviors, who should be targeted with comprehensive strategies.

Mastication Movements And Sleep Quality Of Patients With Myofascial Pain: Occlusal Device Therapy Improvements.

Patients with myofascial pain experience impaired mastication, which might also interfere with their sleep quality. The purpose of this study was to evaluate the jaw motion and sleep quality of patients with myofascial pain and the impact of a stabilization device therapy on both parameters. Fifty women diagnosed with myofascial pain by the Research Diagnostic Criteria were enrolled. Pain levels (visual analog scale), jaw movements (kinesiography), and sleep quality (Epworth Sleepiness Scale; Pittsburgh Sleep Quality Index) were evaluated before (control) and after stabilization device use. Range of motion (maximum opening, right and left excursions, and protrusion) and masticatory movements during Optosil mastication (opening, closing, and total cycle time; opening and closing angles; and maximum velocity) also were evaluated. Repeated-measures analysis of variance in a generalized linear mixed models procedure was used for statistical analysis (α=.05). At baseline, participants with myofascial pain showed a reduced range of jaw motion and poorer sleep quality. Treatment with a stabilization device reduced pain (P<.001) and increased both mouth opening (P<.001) and anteroposterior movement (P=.01). Also, after treatment, the maximum opening (P<.001) and closing (P=.04) velocities during mastication increased, and improvements in sleep scores for the Pittsburgh Sleep Quality Index (P<.001) and Epworth Sleepiness Scale (P=.04) were found. Myofascial pain impairs jaw motion and quality of sleep; the reduction of pain after the use of a stabilization device improves the range of motion and sleep parameters.