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Abstract Background Microarrays are a popular tool used in experiments to measure gene expression levels. Improving the reproducibility of microarray results produced by different chips from various manufacturers is important to create comparable and combinable experimental results. Alternative splicing has been cited as a possible cause of differences in expression measurements across platforms, though no study to this point has been conducted to show its influence in cross-platform differences. Results Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity. Conclusion The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms.

With the growing worldwide refugee crisis, there is a need for evidence-based interventions that specifically deal with the consequences of cumulative trauma-exposure in refugee youth. Refugee children have unique service needs and differ from their non-refugee peers in terms of sociocultural trauma, language, culture, and educational barriers. This article explains the complexities associated with understanding refugee youth and presents a proposal for studying the possible benefits of Tree of Life therapy. At the present time, Tree of Life therapy has no evidence-base because the published studies of Tree of Life with refugee and/or immigrant youth have sample sizes of one, six, eight, and twenty-nine. As a culturally-grounded, strength-based group counseling approach, Tree of Life therapy addresses traumatic experiences, recognizes participants' cultural differences, highlights individual skills, and aids in instilling both confidence and hope for the future. Ncazelo Ncube, the co-founder and main developer of Tree of Life, describes this therapy as a collective narrative practice that considers cultural beliefs and values (2006, 2010, 2018, 2019). The proposed research design is to study the effectiveness of the Tree of Life in Canada, the United States, the United Kingdom, and South Africa. The research plan is to use pragmatic, group-randomized controlled trials in the "real world" settings of schools and agencies in each of the four countries. In addition, the article describes the development of the Roots and Wings Questionnaire for Children and Youth, a culturally relevant, child-friendly questionnaire. The Tree of Life is a readily available therapy with great potential for helping traumatized refugee youth as well as other trauma-impacted young people worldwide., Competing Interests: Conflict of InterestThe authors declare they have no conflict of interest., (© Springer Nature Switzerland AG 2019.)

Background: The 1000 Genomes Project provides a database of genomic variants from whole genome sequencing of 2504 individuals across five continental superpopulations. This database can enrich our background knowledge of worldwide blood group variant geographic distribution and identify novel variants of potential clinical significance., Study Design and Methods: The 1000 Genomes database was analyzed to 1) expand knowledge about continental distributions of known blood group variants, 2) identify novel variants with antigenic potential and their geographic association, and 3) establish a baseline scaffold of chromosomal coordinates to translate next-generation sequencing output files into a predicted red blood cell (RBC) phenotype., Results: Forty-two genes were investigated. A total of 604 known variants were mapped to the GRCh37 assembly; 120 of these were reported by 1000 Genomes in at least one superpopulation. All queried variants, including the ACKR1 promoter silencing mutation, are located within exon pull-down boundaries. The analysis yielded 41 novel population distributions for 34 known variants, as well as 12 novel blood group variants that warrant further validation and study. Four prediction algorithms collectively flagged 79 of 109 (72%) known antigenic or enzymatically detrimental blood group variants, while 4 of 12 variants that do not result in an altered RBC phenotype were flagged as deleterious., Conclusion: Next-generation sequencing has known potential for high-throughput and extended RBC phenotype prediction; a database of GRCh37 and GRCh38 chromosomal coordinates for 120 worldwide blood group variants is provided as a basis for this clinical application., (© 2018 AABB.)

The authors of the above paper noticed an error in publication. In Results section, under sub-section RHD genetic variations, the deletion nomenclature for Sample 1 was incorrectly given as [NC_000001.11(NG_007494.1):c.(1-15149_1-15153)_(148+3154_148+3158)del].

Only two partial deletions longer than 655 nucleotides had been reported for the RHD gene, constrained within the gene and causing DEL phenotypes. Using a combination of quantitative PCR and long-range PCR, we examined three distinct deletions affecting parts of the RHD gene in three blood donors. Their RHD nucleotide sequences and exact boundaries of the breakpoint regions were determined. DEL phenotypes were caused by a novel 18.4 kb deletion and a previously published 5.4 kb deletion of the RHD gene; a D-negative phenotype was caused by a novel 7.6 kb deletion. Examination of the deletion-flanking regions suggested microhomology-mediated end-joining, replication slippage, and non-homologous end-joining, respectively, as the most likely mechanisms for the three distinct deletions. We described two new deletions affecting parts of the RHD gene, much longer than any previously reported partial deletion: one was the first deletion observed at the 5' end of the RHD gene extending into the intergenic region, and the other the second deletion observed at its 3' end. Large deletions present at either end are a mechanism for a much reduced RhD protein expression or its complete loss. Exact molecular characterization of such deletions is instrumental for accurate RHD genotyping.

This review provides a critical assessment of knowledge regarding the determination of organic phosphorus (OP) and organic nitrogen (ON) in aquatic systems, with an emphasis on biogeochemical considerations and analytical challenges. A general background on organic phosphorus and organic nitrogen precedes a discussion of sample collection, extraction, treatment/conditioning and preconcentration of organic phosphorus/nitrogen from sediments, including suspended particulate matter, and waters, including sediment porewaters. This is followed by sections on the determination of organic phosphorus/nitrogen components. Key techniques covered for organic phosphorus components are molecular spectrometry, atomic spectrometry and enzymatic methods. For nitrogen the focus is on the measurement of total organic nitrogen concentrations by carbon hydrogen nitrogen analysis and high temperature combustion, and organic nitrogen components by gas chromatography, high-performance liquid chromatography, gel electrophoresis, mass spectrometry, nuclear magnetic resonance spectrometry, X-ray techniques and enzymatic methods. Finally future trends and needs are discussed and recommendations made.

A review of studies which investigated drawings of the ideal man and the occupational aspirations of boys (ages 11-18 years) from several countries indicated that becoming a professional athlete was a popular but unrealistic aspiration for many adolescent boys. Boys who were athletes and nonathletes from diverse ethnic groups and nationalities dreamed of becoming professional athletes. In two additional studies in the United States of America, adolescents were asked why they thought boys most often selected professional athlete as a possible future occupation. Adolescents perceived professional athletes as rich, famous, and glorified. Enhancement of status and financial gain were ranked as more important than the desire to play sports.

Six hundred young adolescents (11 to 16 years old) from 4 countries (Guatemala, Iceland, Mexico, and the United States) ranked the importance of 10 qualities of the opposite-sex ideal person. Those from the United States responded in an individualistic fashion; they ranked being fun, being sexy, and having considerable money as important for the ideal. Those from Guatemala responded in a collectivistic fashion; they ranked liking children as important, but being fun and good looking as unimportant. Adolescents from Mexico and Iceland reported patterns of values not clearly associated with either collectivism or individualism.

The self-conceptions of 100 girls (11-17 years old) from Sri Lanka and the United States were studied from the traditional Western perspective of identity development as a process in which adolescents become increasingly independent and autonomous. This perspective is based on male development in Western countries and may not adequately describe the experience of girls of non-Western adolescents, for whom relationships with others may be central to identity formation. The participating girls drew self-portraits and either answered the question "How would you describe yourself to yourself?" or completed the sentence "I am..." 20 times. The results indicate that relationships and independence are important themes for the girls from the United States and from Sri Lanka. Older girls differed from younger girls in that greater maturity was associated with greater interest in interpersonal relationships and future lives.

During early adolescence, youth begin to make choices about their future. Sundberg and Tyler (1970) found differences between adolescents in the Netherlands and the United States as to their possibilities for future occupations and leisure activities. Since there have been many changes in both countries over the past twenty-five years, the present study was designed as a replication and expansion of that research. Participants were 522 14- and 15-year-olds in the Netherlands and the United States who filled out the Sundberg and Tyler questionnaire (in the original Dutch and English forms) and drew a picture of the ideal man or woman engaged in an activity. Two-way (country by gender) ANOVAs indicated that the number of occupations listed was greater for adolescents in the Netherlands than in the United States, and that girls listed more occupations than did boys, but considered fewer occupations as actual possibilities for themselves. There was an apparent increase in the number of leisure activities listed by adolescents in the Netherlands. In the U.S., the ideal person was more often drawn as being at work (44.9%) as compared with the Netherlands (20.4%). U.S. students seemed more inclined to glamorize work; popular drawings had themes which linked work and success, achievement and wealth. Dutch students seemed to be interested in quality of life; their drawings depicted sports, relaxation, attractiveness, and humor.

Adolescent girls (N = 118) from diverse social backgrounds in Sri Lanka described their views of womanhood. Qualities of the ideal woman considered most important were kindness and honesty, liking children, intelligence, and having a good job. Although the traditional role of the Sri Lankan woman is that of homemaker, most girls in the study (55%) drew the ideal woman working outside the home, often as a teacher or a doctor. Nevertheless, adolescent girls emphasized traditional qualities of the woman at both work and home as self-sacrificing and serving others.

Soil, silt, and water samples from the Habitant Creek water-shed, Nova Scotia, a tobacco-growing area, have been monitored for organochlorine insecticides. Most samples contain measurable quantities of many persistent pesticides used in farming during the past decade. Sediment levels indicate that residues settle in sluggish parts of the stream. Drainage ditches show highest residual content caused in part by mass transport of soil in runoff. Residue content of water samples is normally one-tenth to one-hundredth that of silt, but is much higher during periods of heavy runoff. Levels vary with the seasons and are highest in the fall, decrease through the spring and summer, and are lowest in the winter. Although samples of well water taken fairly close to the stream showed virtually no residual content, a natural drainage reservior had a pesticide content similar to that in the stream.