Outcomes of severe traumatic brain injury at time of discharge from tertiary academic hospitals in Bloemfontein.

BACKGROUND: Despite the condition being a major public health concern, limited data are available regarding survival rates and the requirement for post-hospitalisation support of patients with traumatic brain injury (TBI) in South Africa (SA). OBJECTIVES: To describe the clinical profile and in-hospital outcomes of patients with TBI at intensive care units (ICUs) of tertiary referral hospitals in the Free State Province, SA, between 2013 and 2017. METHODS: This retrospective descriptive study of patients with TBI was conducted at Pelonomi Tertiary and Universitas Academic Hospitals. Patients' demographic information and variables such as mechanism and type of injury, Glasgow Coma Scale (GCS) prior to ICU admission, neurosurgical intervention, duration of stay in ICU and hospital, GCS and final outcome at discharge were recorded. RESULTS: The 138 patients included in the final data analysis had a median (range) age of 30.5 (13 - 70) years, with a male predominance of 82.6%. The median lengths of stay in ICU and hospital were 6 and 16 days, respectively. Outcomes data showed that 65.9% of patients survived until discharge from hospital. Of patients whose GCS could be determined at discharge, 52.8% were deceased, 7.9% were in a persistently vegetative state, 11.2% had severe and 13.5% moderate disability, and 14.6% had a good recovery. CONCLUSION: TBI is associated with high mortality and morbidity. The lack of post-hospitalisation rehabilitation, and support for patients and their caregivers, requires urgent redress.

A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

Variable Selection for Qualitative Interactions.

In this article we discuss variable selection for decision making with focus on decisions regarding when to provide treatment and which treatment to provide. Current variable selection techniques were developed for use in a supervised learning setting where the goal is prediction of the response. These techniques often downplay the importance of interaction variables that have small predictive ability but that are critical when the ultimate goal is decision making rather than prediction. We propose two new techniques designed specifically to find variables that aid in decision making. Simulation results are given along with an application of the methods on data from a randomized controlled trial for the treatment of depression.

Cytogenetic analysis of Populus trichocarpa--ribosomal DNA, telomere repeat sequence, and marker-selected BACs.

The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequence assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.

Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.

In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

Modos de pensar y estrategias de la investigación cualitativa / Ways of thinking ans strategies of the quality investigation

Desde un esbozo del fondo histórico de la investigación cualitativa en las ciencias sociales el artículo pone de relieve la “mayor valía” de la investigación cualitativa por describir el perfil de preguntas y su contexto, los cuales demandan una elaboración de esta índole. La pregunta central de la investigación significa el punto de partida y final de cada estudio. Por eso decisiones sobre los métodos siguen más tarde en el proceso de investigación y no deben determinar las metas y condiciones del estudio, si bien este proceso usualmente no avanza linealmente, sino por lazos, o sea repeticiones e iteraciones de varias fases. Como ejemplos de enfoques metodológicos el artículo selecciona el desarrollo de teorías ancladas, la replicación de estudios y la triangulación de métodos. De todas maneras, los métodos cualitativos proporcionan un tamaño enorme de datos (textos, grabaciones de sonido o video, fotos, dibujos, etc.), que se tiene que reducir a su sentido por interpretar el contenido. Se describen detalladamente la codificación, el modo más eficiente de reducir los datos, y el análisis de secuencias de sentido en los datos. Además se recomiendan utilizar ordenadores y programas aptos como herramientas, que ayudan a los investigadores a facilitar sus tareas, mantener una visión sobre sus decisiones y a modificarlas sin dificultad. Al final se mencionan unas tendencias actuales vinculadas con el desarrollo de “métodos mixtos”, es decir no se recomienda un paradigma distinto, sino la selección de métodos conforme a las exigencias de la pregunta de la investigación.

From an outline of the historical background of qualitative research in the social sciences this article underlines the added value of qualitative investigations by describing the profile of typical research questions and their context, which demand qualitative approaches. The central research question defines both the starting point and the goal of every study. Therefore, decisions about methods follow only later in the research process and must not determine goals and conditions of a study, although this process usually does not proceed in a strictly linear way, but with iterations or repetitions of various phases. As examples of methodological approaches the article selects the development of grounded theory, replication of studies, and triangulation. In any case, qualitative methods produce a large amount of data (texts, sound or video recordings, photos, drawings, etc.), which has to be reduced to its meaning by interpreting the content. Coding, the most effective mode of data reduction, and the analysis of sequences of meaning are described in detail. Additionally, it is recommended to use computers and suitable software as tools that contribute to facilitate the researchers’ work, to maintain an overview on their decisions, and to modify them easily. Finally some actual tendencies related to mixed methods are discussed, that is, the article does not recommend to follow a particular paradigm, but to select research methods according to the demands of the research question.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

[Discharge preparation group on a psychiatric ward for acute patients: conception and first experience with the realization]. / Entlassungsgruppe auf akutpsychiatrischer Station: Konzept und erste Erfahrungen mit der Durchführung.

The installation of a discharge preparation group on a psychiatric ward for acutely ill patients shall enable the patient to reflect on their situation of life after the discharge from the hospital, to recognize individual problems and resources and, using multi professional help, to work out suitable ways and means to solve their problems. The participating patients rated this therapeutic offer in the whole as positive, especially because it related to their every-day-lives. This group led to a greater satisfaction of the patients and helped to prepare a more structured way of discharge from the hospital.

Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map.

We report the most complete genetic map to have been constructed for the genus Populus. This map includes 544 markers mapped onto 19 linkage groups, equivalent to the Populus chromosome number, with all markers displaying internally consistent linkage patterns. We estimate the genome length to be between 2,300 and 2,500 cM, based both on the observed number of crossovers in the maternal haplotypes, as well as the total observed map length. Genome coverage was estimated to be greater than 99.9% at 20 cM per marker. We did not detect obvious recombination repression in the maternal tree (a hybrid of Populus trichocarpa Hooker x P. deltoides Marsh.) compared to the paternal tree (pure P. deltoides). Finally, most markers exhibiting segregation distortion were derived from the donor parent in this backcross, and generally occurred in large contiguous blocks on two linkage groups. We hypothesize that divergent selection has occurred on chromosomal scales among the parental species used to create this pedigree, and explore the evolutionary implications of this observation. This genetic linkage map provides the most comprehensive view of the Populus genome reported to date and will prove invaluable for future inquiries into the structural and functional genomics, evolutionary biology, and genetic improvement of this ecologically important model species.

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence.

• In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa, we have mapped two resistance loci, MXC3 and MER, and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations. • We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3. • The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16 kb, respectively. The MXC3 region also contained six disease-resistance candidate genes. • The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker-aided selection.

The development of two flanking SCAR markers linked to a sex determination locus in Salix viminalis L.

Most studies of sex determination systems in plants involve dioecious annuals that have known sex chromosomes. Despite the absence of such structures in the majority of dioecious plants, gender seems to be under relatively strict genetic control in some species. Genetic markers linked to a female sex-determination locus in Salix viminalis L. have been discovered through bulked segregant analysis of three full-sib families using approximately 1,000 arbitrary primers. Two RAPD markers that were present in the common female parent as well as in predominantly female progeny of these families were subsequently sequenced and converted to sequence characterized amplified region (SCAR) markers. The two SCAR markers are correlated with gender in the three full-sib families and are present in 96.4% of the female progeny and 2.2% of the males, providing evidence of linkage to a putative female-specific locus associated with gender determination in S. viminalis. Estimates of recombination suggest that the two markers are flanking a putative sex determination locus, SDL-II, in certain families of S. viminalis.

Demethylation of satellite I DNA during senescence of bovine adrenocortical cells in culture.

Over the finite proliferative life span of cultured bovine adrenocortical cells, satellite I DNA shows a progressive and extensive loss of methylation at CCGG sites. This was shown by Southern blotting after digestion with the methylation-sensitive enzyme HpaII alone, which provides a sensitive indicator of methylation loss, or digestion with the combination of EcoRI and HpaII, which provides a quantitative indication of loss of methylation. Bovine tissues, including adrenal cortex, all showed a much higher level of satellite methylation than cultured adrenocortical cells. After adrenocortical cells are placed in culture, some demethylation of satellite I is seen as early as 10 population doublings. By 80 population doublings, loss of satellite DNA methylation is extensive. The loss does not appear to prevent continued cell division, since an extended life span clone of bovine adrenocortical cells transfected with SV40 T antigen showed a similar pattern of extensive demethylation. Satellite demethylation has been reported in aging in vivo and the present cell culture system may provide an in vitro model for this form of genetic instability.

Translation initiation in Drosophila melanogaster is reduced by mutations upstream of the AUG initiator codon.

The importance to in vivo translation of sequences immediately upstream of the Drosophila alcohol dehydrogenase (Adh) start codon was examined at two developmental stages. Mutations were introduced into the Adh gene in vitro, and the mutant gene was inserted into the genome via germ line transformation. An A-to-T substitution at the -3 position did not affect relative translation rates of the ADH protein at the second-instar larval stage but resulted in a 2.4-fold drop in translation of ADH at the adult stage. A second mutant gene, containing five mutations in the region -1 to -9, was designed to completely block translation initiation. However, transformant lines bearing these mutations still exhibit detectable ADH, albeit at substantially reduced levels. The average fold reduction at the second-instar larval stage was 5.9, while at the adult stage a 12.5-fold reduction was observed.

Characterization of cell surface polypeptides of unfertilized, fertilized, and protease-treated zona-free mouse eggs.

The polypeptide composition of unfertilized, fertilized, and protease-treated zona-free mouse eggs was evaluated in this study. Zona-free eggs were radioiodinated by an Iodogen-catalyzed reaction. Light microscopic autoradiography of egg sections revealed that labeling was restricted to the cell surface. Labeled eggs were solubilized, and cell surface polypeptides were identified by one-dimensional SDS polyacrylamide gel electrophoresis and autoradiography. The unfertilized egg demonstrated 8-10 peptides that incorporated 125I, with major bands observed at approximately 145-150, 94, and 23 kilodaltons (kD). Zona-free eggs fertilized in vitro and then radiolabeled demonstrated several new bands in comparison to unfertilized eggs, with a major band appearing at approximately 36 kD. Treatment of radiolabeled unfertilized eggs with either trypsin or chymotrypsin (1 mg/ml for 5-20 min) caused enzyme-specific modifications in labeled polypeptides. Trypsin (T) treatment resulted in time-dependant modification of the three major peptides at 145-150, 94, and 23 kD. Chymotrypsin (CT) treatment, in contrast, was associated with loss or modification of the 94 kD band, with no apparent effect on either the 145-150 or 23 kD band. Taken together with previous data indicating that T or CT egg treatment interferes with sperm-egg attachment and fusion (Boldt et al.: Biol Reprod 39:19-27, 1988), these results suggest a possible role for the 94 kD protein in sperm-egg interaction.

Carbohydrate involvement in sperm-egg fusion in mice.

The potential involvement of cell-surface carbohydrates in sperm-egg fusion in mice was evaluated in this study. Zona-free mouse eggs were inseminated in the presence of a variety of simple saccharides to determine if certain sugars would act as competitive inhibitors of sperm-egg fusion. Of the sugars tested, L-fucose, galactose, and N-acetylglucosamine caused the greatest inhibition of sperm penetration levels relative to controls. A number of complex saccharides or glycoproteins with differing carbohydrate structures, including fucoidan, ascophyllan, ovomucoid, ovalbumin, fetuin, asialofetuin, and chondroitin sulfate, were also tested as competitive inhibitors of fusion. Only the L-fucose containing saccharides fucoidan and ascophyllan caused significant inhibition of fusion at concentrations of 0.05-1.0 mg/ml and 0.1-5.0 mg/ml, respectively. None of the other compounds tested had any inhibitory effect on fusion when tested at concentrations up to 5 mg/ml. The effect of the inhibitory saccharides was not due to the presence of residual zona material on the surface of the zona-free eggs, since zona-free eggs did not bind an 125I-labeled antibody directed against the ZP3 protein of the mouse zona pellucida. Pretreatment of either sperm or eggs with fucoidan (1 mg/ml) for 60 min prior to insemination caused only small decreases in sperm penetration levels, indicating that fucoidan exerted its major inhibitory effect on fusion only when present during insemination. Treatment of sperm, but not zona-free eggs, with fucosidase prior to insemination caused significant reductions in sperm penetration levels. Other glycosidic enzymes, including glucosidase, galactosidase, and N-acetylglucosaminidase, had no inhibitory effect on the sperm. These data suggest that an L-fucose component of the sperm surface is involved in sperm-egg fusion in the mouse.