Domain similarity based orthology detection

Background: Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. Results: We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. Conclusion: We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda.<br

The Greater Kansas City Early Care and Education Landscape Study Final Report: Jackson County, Missouri

The report includes data that will allow districts, schools, centers, funders, and supporters to better understand who is accessing early childhood services, what services are being accessed, and who is providing those services. The survey showed that schools, centers, and homes differed with respect to children served, program characteristics, and staff characteristic. Likely as a result of their access to more sources of revenue, school-based programs were more likely to be accredited, to have appropriately educated teachers who receive fair compensation and benefits, to offer services such as transportation and summer school, and to use strategies to engage families compared to centers and homes. The focus on formal learning opportunities varied with respect to program type. School-based programs were most likely to use a curriculum and to assess kindergarten readiness (100% and 71%, respectively), followed by centers (74% and 50%, respectively), then homes (65% and 32%, respectively)

Hässeldala – a key site for Last Termination climate events in northern Europe

The Last Termination (19 000–11 000 a BP) with its rapid and distinct climate shifts provides a perfect laboratory to study the nature and regional impact of climate variability. The sedimentary succession from the ancient lake at Hässeldala Port in southern Sweden with its distinct Lateglacial/early Holocene stratigraphy (&gt;14.1–9.5 cal. ka BP) is one of the few chronologically well‐constrained, multi‐proxy sites in Europe that capture a variety of local and regional climatic and environmental signals. Here we present Hässeldala's multi‐proxy records (lithology, geochemistry, pollen, diatoms, chironomids, biomarkers, hydrogen isotopes) in a refined age model and place the observed changes in lake status, catchment vegetation, summer temperatures and hydroclimate in a wider regional context. Reconstructed mean July temperatures increased between c. 14.1 and c. 13.1 cal. ka BP and subsequently declined. This latter cooling coincided with drier hydroclimatic conditions that were probably associated with a freshening of the Nordic Seas and started a few hundred years before the onset of Greenland Stadial 1 (c. 12.9 cal. ka BP). Our proxies suggest a further shift towards colder and drier conditions as late as c. 12.7 cal. ka BP, which was followed by the establishment of a stadial climate regime (c. 12.5–11.8 cal. ka BP). The onset of warmer and wetter conditions preceded the Holocene warming over Greenland by c. 200 years. Hässeldala's proxies thus highlight the complexity of environmental and hydrological responses across abrupt climate transitions in northern Europe

Statistical analysis plan for the Early Youth Engagement in first episode psychosis (EYE-2) study: a pragmatic cluster randomised controlled trial of implementation, effectiveness and cost-effectiveness of a team-based motivational engagement intervention to improve engagement

Background Early Intervention in Psychosis (EIP) services improve health outcomes for young people with psychosis in the medium-long term, but 25% of young people disengage in the first 12 months with costs to their mental health, families, society and health services. This study will evaluate the effectiveness of a team-based motivational engagement intervention, the Early Youth Engagement (EYE-2) intervention. Methods and design The EYE-2 trial is a cluster randomised controlled trial comparing the EYE-2 intervention plus standardised EIP service to standardised EIP service alone, with randomisation at the clinical team (cluster) level. The study aimed to enrol 950 young people (aged 14–35 years) with first episode psychosis in 10 teams per arm. Results The primary outcome is time to disengagement: days from the date of allocation to care coordinator to date of the last contact following either refusal to engage with an EIP team or lack of response to EIP contact for 3 consecutive months which will be analysed using a shared frailty model. Secondary outcomes are Health of the Nation Outcome Scale (HoNOS), Process of Recovery Questionnaire (QPR), DIALOG (a service user-reported measure of quality of life and treatment satisfaction) and service use outcomes which will be analysed using mixed effects regression models. Discussion This paper is the detailed statistical analysis plan for the EYE-2 trial. Any changes to, or deviations from, this plan will be described and justified in the final trial report. Trial registration ISRCTN 51629746. Prospectively registered on 7 May 2019. Date assigned 10 May 2019

Georgia College & State University Nursing Program

In order to evaluate the effectiveness of the Georgia College & State University (GC&SU) Nursing Program, a non-experimental, survey research study was conducted by senior nursing students in the Nursing Research class. The survey evaluated the teaching and learning strategies used in the program, the students\u27 perceptions of preparedness for nursing after graduation, and the students\u27 perceptions of the strengths and weaknesses of the GC&SU nursing curriculum. Each participant signed an informed consent form. Forty-five out of a possible 142 nursing students responded to the survey. A statistical analysis of the responses was conducted and comparisons of answers were analyzed across the different nursing cohorts. Implications and recommendations for changes for the GC&SU Nursing Program were stated. As demand for registered nurses continues to increase, nursing programs in the United States are rising to meet this need by educating clinically proficient nurses. GC&SU nursing program graduates approximately 80 nursing students per year. In May 2003, 94% of the nursing graduates passed the licensure exam, helping fill the need in healthcare settings. Nursing faculty realize that they must prepare nurses who are adept at performing essential nursing skills including assessment, safe medication administration, nursing care for ill clients and health teaching

Genomic characterization of novel Neisseria species

Abstract: Of the ten human-restricted Neisseria species two, Neisseria meningitidis, and Neisseria gonorrhoeae, cause invasive disease: the other eight are carried asymptomatically in the pharynx, possibly modulating meningococcal and gonococcal infections. Consequently, characterizing their diversity is important for understanding the microbiome in health and disease. Whole genome sequences from 181 Neisseria isolates were examined, including those of three well-defined species (N. meningitidis; N. gonorrhoeae; and Neisseria polysaccharea) and genomes of isolates unassigned to any species (Nspp). Sequence analysis of ribosomal genes, and a set of core (cgMLST) genes were used to infer phylogenetic relationships. Average Nucleotide Identity (ANI) and phenotypic data were used to define species clusters, and morphological and metabolic differences among them. Phylogenetic analyses identified two polyphyletic clusters (N. polysaccharea and Nspp.), while, cgMLST data grouped Nspp isolates into nine clusters and identified at least three N. polysaccharea clusters. ANI results classified Nspp into seven putative species, and also indicated at least three putative N. polysaccharea species. Electron microscopy identified morphological differences among these species. This genomic approach provided a consistent methodology for species characterization using distinct phylogenetic clusters. Seven putative novel Neisseria species were identified, confirming the importance of genomic studies in the characterization of the genus Neisseria