Comprehensive digital preservation repositories: gaps, and what do we mean by “repository” anyway?

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Plant species and habitat structure in a sand dune field in the brazilian Caatinga: a homogeneous habitat harbouring an endemic biota

One dune habitat in the semi-arid Caatinga Biome, rich in endemisms, is described based on plant species composition, woody plant density, mean height and phenology and a multivariate analysis of the micro-habitats generated by variables associated to plants and topography. The local flora is composed mainly by typically sand-dweller species of Caatinga, suggesting the existence of a phytogeographic unity related to the sandy areas in the Caatinga biome, which seems to be corroborated by faunal distribution. Moreover, some species are probably endemic from the dunes, a pattern also found in vertebrates. The plant distribution is patchy, there is no conspicuous herbaceous layer and almost 50% of the ground represents exposed sand. Phenology is not synchronized among species, occurring leaves budding and shedding, flowers development and anthesis, fruits production and dispersion both in rainy and dry seasons. Leaf shedding is low compared to the level usually observed in Caatinga areas and about 50% of the woody individuals were producing leaves in both seasons. Spectrum of dispersal syndromes shows an unexpected higher proportion of zoochorous species among the phanerophytes, accounting for 31.3% of the species, 78.7% of the total frequency and 78.6% of the total density. The habitat of the dunes is very simple and homogeneous in structure and most of environmental variance in the area is explained by one gradient of woody plants density and another of increase of Bromelia antiacantha Bertol. (Bromeliaceae) and Tacinga inamoena (K. Schum.) N.P. Taylor & Stuppy (Cactaceae) toward valleys, which seem to determine two kinds of protected micro-habitats for the small cursorial fauna.

Predicting the range of inbreeding depression of inbred lines in cross-pollinated populations

The objectives of this paper were to derive the genetic variance of inbreeding depression ( ) and to predict the range of inbreeding depression (RID) in cross-pollinated populations. The variance of inbreeding depression is a function of the genetic variances related to dominance effects (, D2, and ), and of the inbreeding coefficients of the two generations in which inbreeding depression is measured (Ft and Fg). The results showed that the higher the level of dominance of a trait, the higher the variance of inbreeding depression. The magnitudes of were expected to be lower in improved (mean gene frequencies = > 0.6) and in unimproved ( < 0.4) populations, than in composite populations ( » 0.5). Data from a maize population used to illustrate the study showed that the range of inbreeding depression in the S¥ generation of selfing was from 48.7% to 85.3% for grain yield, and from 13.9% to 24.5% for plant height. A mating design outlined to estimate the genetic variance of inbreeding depression, the range of inbreeding depression, and of the range of inbred lines is presented.

Estimates of genetic and phenotypic parameters in a segregant population of rice irrigated by continuous flooding

Estimates of genetic and phenotypic parameters were obtained by using data from families of a recurrent selection program in rice. An experiment using population CNA-IRAT 4ME/1/1 was conducted at two locations (Lambari and Cambuquira) in the State of Minas Gerais, Brazil. At Lambari, families S0:2 and S0:3 were assessed during crop seasons 1992/1993 and 1993/1994, respectively. In the Cambuquira trial, only S0:3 families were tested in 1993/1994. The experimental design was a 10 x 10 lattice with three replications. The following traits were assessed: grain yield (GY), mean number of days to flowering (FL), plant height (PH), and the incidence of neck blast (NB) caused by Pyricularia grisea and grain staining (GS) caused by Drechslera oryzae. This population proved to be promising for recurrent selection, as it had high average yield and genetic variability. Heritability estimates obtained using variance components were generally greater than estimates of realized heritability, and heritability obtained by parent-offspring regression

Predicting variety composite means without diallel crossing

Prediction of variety composite means was shown to be feasible without diallel crossing the parental varieties. Thus, the predicted mean for a quantitative trait of a composite is given by: Yk = a1 sigmaVj + a2sigmaTj + a3 - a4, with coefficients a1 = (n - 2k)/k²(n - 2); a2 = 2n(k - 1)/k²(n - 2); a3 = n(k - 1)/k(n - 1)(n - 2); and a4 = n²(k - 1)/k(n - 1)(n - 2); summation is for j = 1 to k, where k is the size of the composite (number of parental varieties of a particular composite) and n is the total number of parent varieties. Vj is the mean of varieties and Tj is the mean of topcrosses (pool of varieties as tester), and and are the respective average values in the whole set. Yield data from a 7 x 7 variety diallel cross were used for the variety means and for the "simulated" topcross means to illustrate the proposed procedure. The proposed prediction procedure was as effective as the prediction based on Yk = - ( -)/k, where and refer to the mean of hybrids (F1) and parental varieties, respectively, in a variety diallel cross. It was also shown in the analysis of variance that the total sum of squares due to treatments (varieties and topcrosses) can be orthogonally partitioned following the reduced model Yjj’ = mu + ½(v j + v j’) + + h j+ h j’, thus making possible an F test for varieties, average heterosis and variety heterosis. Least square estimates of these effects are also given

Absence of linkage between MHC and a gene involved in susceptibility to human schistosomiasis

Six hundred million people are at risk of infection by Schistosoma mansoni. MHC haplotypes have been reported to segregate with susceptibility to schistosomiasis in murine models. In humans, a major gene related to susceptibility/resistance to infection by S. mansoni (SM1) and displaying the mean fecal egg count as phenotype was detected by segregation analysis. This gene displayed a codominant mode of inheritance with an estimated frequency of 0.20-0.25 for the deleterious allele and accounted for more than 50% of the variance of infection levels. To determine if the SM1 gene segregates with the human MHC chromosomal region, we performed a linkage study by the lod score method. We typed for HLA-A, B, C, DR and DQ antigens in 11 informative families from an endemic area for schistosomiasis in Bahia, Brazil, by the microlymphocytotoxicity technique. HLA-DR typing by the polymerase chain reaction with sequence-specific primers (PCR-SSP) and HLA-DQ were confirmed by PCR-sequence-specific oligonucleotide probes (PCR-SSOP). The lod scores for the different q values obtained clearly indicate that there is no physical linkage between HLA and SM1 genes. Thus, susceptibility or resistance to schistosomiasis, as defined by mean fecal egg count, is not primarily dependent on the host's HLA profile. However, if the HLA molecule plays an important role in specific immune responses to S. mansoni, this may involve the development of the different clinical aspects of the disease such as granuloma formation and development of hepatosplenomegaly.

Comparison of AutoSetä and polysomnography for the detection of apnea-hypopnea events

The use of the flow vs time relationship obtained with the nasal prongs of the AutoSetä (AS) system (diagnosis mode) has been proposed to detect apneas and hypopneas in patients with reasonable nasal patency. Our aim was to compare the accuracy of AS to that of a computerized polysomnographic (PSG) system. The study was conducted on 56 individuals (45 men) with clinical characteristics of obstructive sleep apnea (OSA). Their mean (± SD) age was 44.6 ± 12 years and their body mass index was 31.3 ± 7 kg/m2. Data were submitted to parametric analysis to determine the agreement between methods and the intraclass correlation coefficient was calculated. The Student t-test and Bland and Altman plots were also used. Twelve patients had an apnea-hypopnea index (AHI) <10 in bed and 20 had values >40. The mean (± SD) AHI PSG index of 37.6 (28.8) was significantly lower (P = 0.0003) than AHI AS (41.8 (25.3)), but there was a high intraclass correlation coefficient (0.93), with 0.016 variance. For a threshold of AHI of 20, AS showed 73.0% accuracy, 97% sensitivity and 60% specificity, with positive and negative predictive values of 78% and 93%, respectively. Sensitivity, specificity and negative predictive values increased in parallel to the increase in AHI threshold for detecting OSA. However, when the differences of AHI PSG-AS were plotted against their means, the limits of agreement between the methods (95% of the differences) were +13 and -22, showing the discrepancy between the AHI values obtained with PSG and AS. Finally, cubic regression analysis was used to better predict the result of AHI PSG as a function of the method proposed, i.e., AHI AS. We conclude that, despite these differences, AHI measured by AutoSetä can be useful for the assessment of patients with high pre-test clinical probability of OSA, for whom standard PSG is not possible as an initial step in diagnosis.

Simulation of the Interaction Mean Free Path between Neutrons and TRISO Particles

The interaction mean free path between neutrons and TRISO particles is simulated using scripts written in MATLAB to solve the increasing error present with an increase in the packing factor in the reactor physics code Serpent. Their movement is tracked both in an unbounded and in a bounded space. Their track is calculated, depending on the program, linearly directly using the position vectors of the neutrons and the surface equations of all the fuel particles; by dividing the space in multiple subspaces, each of which contain a fraction of the total number of particles, and choosing the particles from those subspaces through which the neutron passes through; or by choosing the particles that lie within an infinite cylinder formed on the movement axis of the neutron. The estimate from the current analytical model, based on an exponential distribution, for the mean free path, utilized by Serpent, is used as a reference result. The results from the implicit model in Serpent imply a too long mean free path with high packing factors. The received results support this observation by producing, with a packing factor of 17 %, approximately 2.46 % shorter mean free path compared to the reference model. This is supported by the packing factor experienced by the neutron, the simulation of which resulted in a 17.29 % packing factor. It was also observed that the neutrons leaving from the surfaces of the fuel particles, in contrast to those starting inside the moderator, do not follow the exponential distribution. The current model, as it is, is thus not valid in the determination of the free path lengths of the neutrons.

Statistical segmentation methods and color variance analysis of retinal images

In this research, the effectiveness of Naive Bayes and Gaussian Mixture Models classifiers on segmenting exudates in retinal images is studied and the results are evaluated with metrics commonly used in medical imaging. Also, a color variation analysis of retinal images is carried out to find how effectively can retinal images be segmented using only the color information of the pixels.

Cytokine profile and nitric oxide levels in sera from patients with brucellosis

The aims of this study were to investigate the serum levels of some cytokines [tumor necrosis factor-alpha (TNF-alpha), interleukin 1ß (IL-1ß), IL-2R, IL-6, and IL-8] and nitric oxide (NO) levels in patients with untreated brucellosis and to test the correlation of these parameters with each other. The study was conducted on 67 subjects, 37 patients with brucellosis and 30 healthy individuals with no history of Brucella infection. Brucellosis was identified by a positive blood culture and/or increased Brucella antibodies in serological tests in addition to compatible clinical symptoms. Cytokine profile analysis was performed by the immulite chemiluminescent enzyme immunometric assay whose inter- and intra-assay coefficients of variance were 2.6-3.6 and 4.4-8.5%, respectively. The levels of nitrites/nitrates, which are representative of NO levels, were measured by the Griess method. Patients with brucellosis had significantly elevated serum levels of nitrites/nitrates, IL-2R, IL-6 and IL-8 (mean ± SD, 102.8 ± 23.8 µmol/l, 806.1 ± 58.5 U/ml, 21.1 ± 2.3 pg/ml, and 8.8 ± 1.6 pg/ml, respectively) compared to healthy controls, whereas TNF-alpha and IL-1ß levels were unchanged. No statistically significant correlation was detected between any of the studied cytokine levels and nitrate/nitrite concentrations according to Pearson's linear correlation test. We conclude that only IL-6, IL-8 and IL-2R are elevated in brucellosis and the extent of elevation depends on the severity and clinical pattern of the disease. Moderate elevation in serum NO was comparable to that observed in previous studies. This explains the absence or very rare occurrence of septic shock in brucellosis.

Category fluency test: effects of age, gender and education on total scores, clustering and switching in Brazilian Portuguese-speaking subjects

Verbal fluency tests are used as a measure of executive functions and language, and can also be used to evaluate semantic memory. We analyzed the influence of education, gender and age on scores in a verbal fluency test using the animal category, and on number of categories, clustering and switching. We examined 257 healthy participants (152 females and 105 males) with a mean age of 49.42 years (SD = 15.75) and having a mean educational level of 5.58 (SD = 4.25) years. We asked them to name as many animals as they could. Analysis of variance was performed to determine the effect of demographic variables. No significant effect of gender was observed for any of the measures. However, age seemed to influence the number of category changes, as expected for a sensitive frontal measure, after being controlled for the effect of education. Educational level had a statistically significant effect on all measures, except for clustering. Subject performance (mean number of animals named) according to schooling was: illiterates, 12.1; 1 to 4 years, 12.3; 5 to 8 years, 14.0; 9 to 11 years, 16.7, and more than 11 years, 17.8. We observed a decrease in performance in these five educational groups over time (more items recalled during the first 15 s, followed by a progressive reduction until the fourth interval). We conclude that education had the greatest effect on the category fluency test in this Brazilian sample. Therefore, we must take care in evaluating performance in lower educational subjects.

The use of light-emitting diodes to stimulate mitochondrial function and liver regeneration of partially hepatectomized rats

The biostimulating effect of laser radiation has been observed in many areas of Medicine. However, there are still several questions to be answered, among them the importance of light coherence in the stimulatory process. In the present study, we used light-emitting diodes (LED) to promote the stimulation of liver regeneration after partial hepatectomy in rats. Fourteen male Wistar rats weighing 200-250 g were submitted to partial hepatectomy (70%) followed by LED light irradiation (630 nm) of the remaining part of the liver at two doses, i.e., 10 (N = 7) and 140 (N = 7) J/cm². A group irradiated with laser, 590 nm (N = 7, 15 J/cm²) was performed for the study of proliferating cell nuclear antigen-labeling index. Data are reported as mean ± SEM. Statistical comparisons of the groups were performed by analysis of variance for parametric measurements followed by the Bonferroni post-test, with the level of significance set at P < 0.05. Respiratory mitochondrial activity was increased in the irradiated groups (states 3 and 4; P < 0.05), with better results for the group exposed to the lower LED dose (10 J/cm²). The proliferating cell nuclear antigen-labeling index, by immunohistochemical staining, was similar for both LED-exposed groups (P > 0.05) and higher than for the control group (P < 0.05). The cell proliferation index obtained with LED and laser were similar (P > 0.05). In conclusion, the present results suggest that LED irradiation promotes biological stimulatory effects during the early stage of liver regeneration and that LED is as effective as laser light, independent of the coherence, divergence and cromaticity.

Muscle strength but not functional capacity is associated with plasma interleukin-6 levels of community-dwelling elderly women

The association of plasma interleukin-6 (IL-6) levels, muscle strength and functional capacity was investigated in a cross-sectional study of community-dwelling elderly women from Belo Horizonte, Brazil. Elderly people who present controlled chronic diseases with no negative impact on physical, psychosocial and mental functionality are considered to be community-dwelling. Psychological and social stress due to unsuccessfully aging can represent a risk for immune system disfunctions. IL-6 levels, isokinetic muscle strength of knee flexion/extension, and functional tests to determine time required to rise from a chair and gait velocity were measured in 57 participants (71.21 ± 7.38 years). Serum levels of IL-6 were measured in duplicate and were performed within one single assay (mouse monoclonal antibody against IL-6; High-Sensitivity, Quantikine®, R & D Systems, USA; intra-assay coefficient of variance = 6.9-7.4%; interassay coefficient of variance = 9.6-6.5%; sensitivity = 0.016-0.110 pg/mL; mean = 0.039 pg/mL). Muscle strength was assessed with the isokinetic dynamometer Biodex System 3 Pro®. After the Shapiro-Wilk normality test was applied, correlations were investigated using Spearman and Kruskal-Wallis tests. Post hoc analysis was performed using the Dunn test. A significant negative correlation was observed between plasma IL-6 levels (1.95 ± 1.77 pg/mL) and muscle strength for knee flexion (70.70 ± 21.14%; r = -0.265; P = 0.047) and extension (271.84 ± 67.85%; r = -0.315; P = 0.017). No significant correlation was observed between IL-6 levels and the functional tests (time to rise from a chair = 14.65 ± 2.82 s and gait velocity = 0.95 ± 0.14 m/s). These results suggest that IL-6 is associated with reduced muscle strength.

An improved strategy for evaluating the extent of chronic arterial baroreceptor denervation in conscious rats

There is no index or criterion of aortic barodenervation, nor can we differentiate among rats that have suffered chronic sham, aortic or sino-aortic denervation. The objective of this study was to develop a procedure to generate at least one quantitative, reproducible and validated index that precisely evaluates the extent of chronic arterial barodenervation performed in conscious rats. Data from 79 conscious male Wistar rats of about 65-70 days of age with diverse extents of chronic arterial barodenervation and used in previous experiments were reanalyzed. The mean arterial pressure (MAP) and the heart rate (HR) of all rats were measured systematically before (over 1 h) and after three consecutive iv bolus injections of phenylephrine (PHE) and sodium nitroprusside (SNP). Four expressions of the effectiveness of barodenervation (MAP lability, PHE ratio, SNP ratio, and SNP-PHE slope) were assessed with linear fixed models, three-level average variance, average separation among levels, outlier box plot analysis, and overlapping graphic analysis. The analysis indicated that a) neither MAP lability nor SNP-PHE slope was affected by the level of chronic sodium intake; b) even though the Box-Cox transformations of both MAP lability [transformed lability index (TLI)] and SNP-PHE slope [transformed general sensitivity index (TGSI), {((3-(ΔHRSNP-ΔHRPHE/ΔMAPSNP-ΔMAPPHE))-0.4-1)/-0.04597}] could be two promising indexes, TGSI proved to be the best index; c) TLI and TGSI were not freely interchangeable indexes for this purpose. TGSI ranges that permit differentiation between sham (10.09 to 11.46), aortic (8.40 to 9.94) and sino-aortic (7.68 to 8.24) barodenervated conscious rats were defined.

Computed tomography assessment of lung structure in patients undergoing cardiac surgery with cardiopulmonary bypass

Hypoxemia is a frequent complication after coronary artery bypass graft (CABG) with cardiopulmonary bypass (CPB), usually attributed to atelectasis. Using computed tomography (CT), we investigated postoperative pulmonary alterations and their impact on blood oxygenation. Eighteen non-hypoxemic patients (15 men and 3 women) with normal cardiac function scheduled for CABG under CPB were studied. Hemodynamic measurements and blood samples were obtained before surgery, after intubation, after CPB, at admission to the intensive care unit, and 12, 24, and 48 h after surgery. Pre- and postoperative volumetric thoracic CT scans were acquired under apnea conditions after a spontaneous expiration. Data were analyzed by the paired Student t-test and one-way repeated measures analysis of variance. Mean age was 63 ± 9 years. The PaO2/FiO2 ratio was significantly reduced after anesthesia induction, reaching its nadir after CPB and partially improving 12 h after surgery. Compared to preoperative CT, there was a 31% postoperative reduction in pulmonary gas volume (P < 0.001) while tissue volume increased by 19% (P < 0.001). Non-aerated lung increased by 253 ± 97 g (P < 0.001), from 3 to 27%, after surgery and poorly aerated lung by 72 ± 68 g (P < 0.001), from 24 to 27%, while normally aerated lung was reduced by 147 ± 119 g (P < 0.001), from 72 to 46%. No correlations (Pearson) were observed between PaO2/FiO2 ratio or shunt fraction at 24 h postoperatively and postoperative lung alterations. The data show that lung structure is profoundly modified after CABG with CPB. Taken together, multiple changes occurring in the lungs contribute to postoperative hypoxemia rather than atelectasis alone.