Estimating the number of channels in patch recordings

The estimation of the number of channels in a patch was assumed to be equivalent to the estimation of the binomial parameter n. Seven estimators were evaluated, using data sets simulated for a range of parameters appropriate for single channel recording experiments. No single estimator was best for all parameters; a combination of estimators is a possible option to avoid the biases of individual estimators. All estimators were highly accurate in estimating n in the case that n = 1. For n ≤ 4 the simplest estimator, the maximum number of simultaneously open channels, was the best, For larger values of n the best estimators were Bayesian.     

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m + n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms.     

Paracrine interleukin-8 affects mesenchymal stem cells through the Akt pathway and enhances human umbilical vein endothelial cell proliferation and migration

Interleukin-8 (IL-8) promotes cell homing and angiogenesis, but its effects on activating human bone marrow mesenchymal stem cells (BMSCs) and promoting angiogenesis are unclear. We used bioinformatics to predict these processes. In vitro, BMSCs were stimulated in a high-glucose (HG) environment with 50 or 100 μg/ml IL-8 was used as the IL-8 group. A total of 5 μmol/l Triciribine was added to the two IL-8 groups as the Akt inhibitor group. Cultured human umbilical vein endothelial cells (HUVECs) were cultured in BMSCs conditioned medium (CM). The changes in proliferation, apoptosis, migration ability and levels of VEGF and IL-6 in HUVECs were observed in each group. Seventy processes and 26 pathways were involved in vascular development, through which IL-8 affected BMSCs. Compared with the HG control group, HUVEC proliferation absorbance value (A value), Gap closure rate, and Transwell cell migration rate in the IL-8 50 and IL-8 100 CM groups were significantly increased (P<0.01, n=30). However, HUVEC apoptosis was significantly decreased (P<0.01, n=30). Akt and phospho-Akt (P-Akt) protein contents in lysates of BMSCs treated with IL-8, as well as VEGF and IL-6 protein contents in the supernatant of BMSCs treated with IL-8, were all highly expressed (P<0.01, n=15). These analyses confirmed that IL-8 promoted the expression of 41 core proteins in BMSCs through the PI3K Akt pathway, which could promote the proliferation and migration of vascular endothelial cells. Therefore, in an HG environment, IL-8 activated the Akt signaling pathway, promoted paracrine mechanisms of BMSCs, and improved the proliferation and migration of HUVECs.     

How to Rank Journals

There are now many methods available to assess the relative citation performance of peer-reviewed journals. Regardless of their individual faults and advantages, citation-based metrics are used by researchers to maximize the citation potential of their articles, and by employers to rank academic track records. The absolute value of any particular index is arguably meaningless unless compared to other journals, and different metrics result in divergent rankings. To provide a simple yet more objective way to rank journals within and among disciplines, we developed a κ-resampled composite journal rank incorporating five popular citation indices: Impact Factor, Immediacy Index, Source-Normalized Impact Per Paper, SCImago Journal Rank and Google 5-year h-index; this approach provides an index of relative rank uncertainty. We applied the approach to six sample sets of scientific journals from Ecology (n = 100 journals), Medicine (n = 100), Multidisciplinary (n = 50); Ecology + Multidisciplinary (n = 25), Obstetrics & Gynaecology (n = 25) and Marine Biology & Fisheries (n = 25). We then cross-compared the κ-resampled ranking for the Ecology + Multidisciplinary journal set to the results of a survey of 188 publishing ecologists who were asked to rank the same journals, and found a 0.68–0.84 Spearman’s ρ correlation between the two rankings datasets. Our composite index approach therefore approximates relative journal reputation, at least for that discipline. Agglomerative and divisive clustering and multi-dimensional scaling techniques applied to the Ecology + Multidisciplinary journal set identified specific clusters of similarly ranked journals, with only Nature & Science separating out from the others. When comparing a selection of journals within or among disciplines, we recommend collecting multiple citation-based metrics for a sample of relevant and realistic journals to calculate the composite rankings and their relative uncertainty windows.     

Effect of early shearing during gestation on the productive and reproductive behavior of female sheep offspring in their first 18 months of age

The research has shown the interesting contributions of shearing in mid-gestation on the performance of lambs from birth to weaning. Other studies have reported that shearing at early pregnancy influences the development of the placenta and lamb live weight at birth. However, there was a lack of information on the effect of early-prepartum shearing on the behavior of the offspring from weaning onward. This study evaluated the effect of shearing ewes at 50 days of gestation on the growth, reproductive behavior and response to a gastrointestinal parasite challenge in the female offspring from weaning to 18 months old. Fifty-seven Polwarth female lambs were used, 22 being singles and 35 twins born to ewes either shorn at 50 days of pregnancy (PS, n = 23) or shorn at 62 days postpartum (U, control, n = 34) resulting in four subgroups: single lambs born to PS ewes (n = 8), born to U ewes (n = 14), twin lambs born to PS ewes (n = 15) or born to U ewes (n = 20). All progeny were managed together under improved pasture with a minimum forage allowance of 6% live weight on dry basis. Body weight, body condition score and fecal eggs count were recorded every 14 days from weaning to 18 months of age. Concentrations of progesterone were measured weekly (from 4 to 10 months of age and from 14 to 18 months of age) to establish the onset of puberty. Ovulation rate at an induced and a natural heat (545 ± 1.0 and 562 ± 1.0 day old) was recorded. Prepartum shearing did not affect the age at puberty or the ovulation rate of female offspring, but those born as singles were more precocious ( P = 0.03) and heavier ( P = 0.02) at puberty than twin born lambs. Both the average value of parasite egg count ( P = 0.0 7) and the Famacha index ( P = 0.02) for the entire study period were lower in lambs born to prepartum shorn ewes than those born to postpartum shorn ewes. In conclusion, shearing at 50 days of gestation did not affect the growth or the reproductive behavior of female offspring. However, female lambs born from ewe shorn during gestation showed a better response to the parasitic challenge, and further research is required to confirm this.     

The pH dependence of the affinity,kinetics and cooperativity of ligand binding to the root effect haemoglobin of the goldfish Carassius auratus

• 1.1. The binding of O₂ to goldfish haemoglobin showed a strong pH dependence P₅₀=5.5 mmHg; n = 2.4 at pH 8.0 and P₅₀ = 170 mmHg; n = 1.0 at pH 5.5 such that the protein is only 50% saturated in a solution of air equilibrated buffer at pH 5.5.
• 2.2. The binding of CO is cooperative at high pH (n = 2.8; L = 1000; K_R = 0.1 μM; K_T = 4 μM) and non-cooperative (n = 1) at pH 5.5.
• 3.3. The rate of O₂ dissociation is extremely fast and pH dependent; being 30 sec⁻¹ at pH 8.0 and 400 sec⁻¹ at pH 6.0 at 1°C. At 23°C the rate of this process is too fast to obtain accurate data using stopped-flow techniques.
• 4.4. Partial photolysis of the oxyhaemoglobin species leads to homogeneous recombination kinetics at pH 8.0 with an associated rate constant of 4.7 × 10⁷ M⁻¹ sec⁻¹. At pH < 7.5 the recombination process occurs in two steps. One rate is equal to that observed at pH 8.0. The slower process is favoured at low pH.
• 5.5. Photolysis of the CO haemoglobin complex indicates that, at high pH, combination of CO with deoxyhaemoglobin is cooperative, whilst recombination with Hb(CO)₃ is non-cooperative and occurs at a rate of 1.2 × 10⁶ M⁻¹ sec⁻¹.
• 6.6. At neutral pH recombination of CO with partially linganded haemoglobin occurs in a two-step process. The proportion contributed by each of these two steps in pH dependent.
• 7.7. The functioning of this Root effect haemoglobin is discussed in terms of the two state-model of cooperativity in which the αβ chain heterogeneity is minimal

     

Cortisol and cortisone levels in umbilical cord plasma and maternal plasma of normal pregnancies

A method for assaying cortisol and cortisone using chromatography on either paper or Sephadex LH-20 columns for isolation, followed by competitive protein binding, has been applied to umbilical cord and maternal plasma samples. In mixed cord plasma the mean cortisol concentration was 6.0 ± 0.8 μg/100 ml (n = 9) and the mean cortisone concentration was 13.5 ± 2.9 μg/100 ml (n = 9). In cord arterial plasma the mean cortisol concentration was 6.3 ± 2.9 μg/100 ml (n = 6) and the mean cortisone level was 10.1 ± 2.5 μg/100 ml (n = 6). For cord venous plasma, the mean level of cortisol was 5.6 ± 1.5 μg/100 ml (n = 6) and of cortisone was 13.5 ± 2.4 μg/100 ml (n = 6). Maternal plasma gave a mean value of cortisol of 42.3 ± 4.5 μg/100 ml (n = 6) and of cortisone of 6.2 ± 0.9 μg/100 ml. The results of this study suggest that the fetus at term-gestation produces cortisol. The significance of this production compared with placental transfer of maternal cortisol into the fetal circulation however is uncertain.     

Measuring the sero-prevalence of Leishmania donovani induced cutaneous leishmaniasis: A method comparison study

An in-house enzyme-linked immunosorbent assay (ELISA) based on crude antigen of Leishmania reported a high sero-prevalence (82.0%) in Leishmania donovani induced cutaneous leishmaniasis (CL) in Sri Lanka. ELISA was further compared with established serological tools to identify a suitable point of care diagnostic tool. Sero-prevalence of 100 CL samples were analyzed using in-house ELISA, Indian dipstick test and rK39 strip test. Results obtained were further compared with direct agglutination test (DAT) for 40 CL. Test performance was evaluated using Kappa index value. Clinico-epidemiological characteristics of patients were analyzed using SPSSv25.0. Cost analysis of tests was carried out. ELISA showed a high sero-positivity of 81.0% (n = 81/100) while DAT (57.5%,n = 23/40), Indian dipstick test (22.0%,n = 22/100) and rK39 test (15.0%,n = 15/100) showed a comparatively less sero-positivity. According to Kappa index values, there were no perfect agreement between tests. Among ELISA positive patients (n = 81/100), DAT, Indian dipstick test and rK39 demonstrated sero-positivity rates of 61.3% (n = 19/31), 25.9% (n = 21/81) and 16.0% (n = 13/81) respectively. Among ELISA negative patients (n = 19/100), three assays demonstrated sero-positivity rates of 44.4% (n = 4/9), 5.3% (n = 1/9) and 10.5% (n = 2/19) respectively. DAT can be used as an alternative test when ELISA is not available or negative. Clinico-epidemiological profiles of patients that showed sero-positivity by each assay were different. Cost per patient was approximately 5.5 USD for DAT and 3.0 USD for each other tests. Established serological tests demonstrated different and relatively lower detection rates. Species, strain and antigen heterogeneity, inconsistency in amount of used antigens, sera, antibody expression patterns and testing methodologies could be responsible. This study highlighted the importance of designing an in-house serological assay based on local parasite.     

Cytogenetics of Brazilian monkeys

Karyotypic studies were carried out on some species belonging to the family Cebidae. The chromosome complements have been studied in blood cultures in vitro in the following species: Alouatta fusca clamitans (2n = 50); Aotes trivirgatus (2n = 52); Cebus albifrons (2n = 52); Cebus sp. (2n = 54); Ateles paniscus paniscus (2n = 34); Lagothrix lagotricha (2n = 62). Comparison between the present results and the karyotypes of the Cebidae described in the literature reveal intraspecific and interspecific variability in number and structure of the chromosomes.     

Species richness and beta diversity of aquatic macrophytes in a large subtropical reservoir (Itaipu Reservoir, Brazil): the influence of limnology and morphometry

Assessment of the environmental factors that control species richness (S) is a central issue in ecology. In this study, aquatic macrophyte S was estimated in 235 sampling sites distributed in 8 arms of a large (1350 km²) subtropical reservoir (Itaipu Reservoir, Brazil). Morphometric variables (area, shoreline development and length of shoreline, all measured for each arm; n= 8) and environmental variables measured at each sampling site (extinction coefficient of light (k), electrical conductivity, fetch, distance from the main reservoir body; n = 235) were used to predict aquatic macrophyte S at two spatial scales. At arm scale, linear regression analysis indicated that length of shoreline was a better predictor of S than area. At sampling site scale, multiple regression analysis indicated that S was significantly predicted by electrical conductivity, fetch and distance from the main body. However, other relationships with predictive interest was demonstrated by using non-traditional regression approaches. This analysis started by the visual inspection of scatter plots. The bivariate relationship between S and fetch, for example, showed an envelope or a `left triangle' pattern. The relationship between the number of submerged species and k showed an asymmetrical left triangle pattern. Using randomization procedures, it was demonstrated that these patterns were not generated by chance alone. Beta diversity (estimated within the arms) was significantly and positively correlated with spatial environmental variability. Overall, these results indicate that the prediction of aquatic macrophytes assemblage variables in large waterbodies, specially S, is more complex than previous studies have suggested.     

Inherent errors of the fixed-frame counting method for corneal endothelial cell density in eye banks

The aim of this work was to analyze the magnitude of inherent errors associated with the fixed-frame counting method for corneal endothelial cell density (ECD) measurements. This technique is common among most eye banks worldwide. Three types of mosaics were used: regular and irregular tessellated mosaics (eight increasing densities ranging from 800 to 3,600 cells/mm² by steps of 400 cells/mm²) generated by a computer, and real mosaics (four specimens) obtained from human corneal endothelium flat mounted and stained with Alizarin red. On the three mosaics, the fixed-frame counting method was applied using a computer program. The ECD was calculated for 3,000 successive random positions from calibrated grids which area ranged from 50 × 50 to 300 × 300 μm² (incremental steps of 25 μm). For each grid, the ECD was expressed either as a single count, a mean of five or a mean of 10 measures. The fixed-frame count was constantly associated with an inherent variability but repeatability increased with larger grid size and ECD. The mean calculated out of 10 measures was the most reliable, but still, we noted ±5 % of residual variability from the real ECD. The 100 × 100 μm² grid manual counts, performed in many eye banks, should be abandoned and upgraded to at least 200 × 200 μm² grid counts. Digital image analysis with a variable frame counting method would be the best alternative.     

Structural-functional study of glycine-and-proline-containing peptides (Glyprolines) as potential neuroprotectors

A synthetic scheme for preparation of (Gly-Pro) _n , (Pro-Gly) _n (n = 2, 3), and (Pro-Gly-Pro) _n (n = 1, 2) peptides was elaborated. The effect of the synthesized peptides and the Gly-Pro and Pro-Gly dipeptides on survival of cultured cells of PC12 rat pheochromocytoma was studied under the conditions of oxidative stress induced by brief incubation of the cells with hydrogen peroxide. Peptides of the general formula (Gly-Pro) _n and the Pro-Gly-Pro peptide at a concentration of 0.2–100 μM were shown to decrease the number of damaged cells. The Gly-Pro peptide was the most active and decreased the number of damaged cells by 49% on average at a concentration of 100 μM.     

The Inbreeding Effective Population Number and the Expected Homozygosity for an X-Linked Locus

Assuming random mating and discrete nonoverlapping generations, the inbreeding effective population number, (see PDF), is calculated for an X-linked locus. For large populations, the result agrees with the variance effective population number. As an application, the maintenance of genetic variability by the joint action of mutation and random drift is investigated. It is shown that, if every allele mutates at rate u to new types, then the probabilities of identity in state (and hence the expected homozygosity of females) converge to the approximate value (see PDF) at the approximate asymptotic rate (see PDF).     

LCN2 and TIMP1 as Potential Serum Markers for the Early Detection of Familial Pancreatic Cancer

High-risk individuals of familial pancreatic cancer (FPC) families are considered to be good candidates for screening programs to detect early PC or its high-grade precursor lesions, especially pancreatic intraepithelial neoplasia (PanIN) 2/3 lesions. There is a definite need for diagnostic markers as neither reliable imaging methods nor biomarkers are available to detect these lesions. On the basis of a literature search, the potential serum markers neutrophil gelatinase-associated lipocalin (LCN2), metallopeptidase inhibitor 1 (TIMP1), chemokine (C-X-C motif) ligand 16 (CXCL16), IGFBP4, and iC3a, which were first tested in transgenic KrasLSL.^G12D/+;p53^R172H/+;Pdx1-Cre mice, were identified. ELISA analyses of LCN2, TIMP1, and CXCL16 revealed significantly higher levels in mice with PanIN2/3 lesions or PC compared to mice with normal pancreata or PanIN1 lesions. Analysis of preoperative human serum samples from patients with sporadic PC (n = 61), hereditary PC (n = 24), chronic pancreatitis (n = 28), pancreatic neuroendocrine tumors (n = 11), and FPC patients with histologically proven multifocal PanIN2/3 lesions (n = 3), as well as healthy control subjects (n = 20), confirmed significantly higher serum levels of LCN2 and TIMP1 in patients with PC and multifocal PanIN2/3 lesions. The combination of LCN2 and TIMP1 as a diagnostic test for the detection of PC had a sensitivity, specificity, and positive predictive value of 100% each. Although this preliminary finding needs to be validated in a large series of individuals at high risk for FPC, serum measurement of LCN2 and TIMP1 might be a promising screening tool.     

Prediction of the digestible crude protein and protein digestibility of feed ingredients for rabbits from chemical analysis

Ninety-five data of individual feedstuffs, for which information on chemical analyses and crude protein digestibility (CPD) was available, were subject to sequential multiple linear regression analysis employing CPD and digestible crude protein (DCP) as dependent variables and chemical analysis as independent variables. The feedstuffs were classed separately into dry forages (n=26), cereals and cereal by-products (n=29), protein concentrates (n=18) and by-products (n=22) groups. The procedure followed in each of the groups was to utilize: (1) the feedstuffs in which the Van Soest fiber and the Weende analysis were simultaneously available, and (2) all feedstuffs with data of the variables selected in the first step. The CP content was the best single predictor of the DCP content of feeds, the best equation in terms of R² was obtained in the total group: DCP (g kg⁻¹)=−34.67+0.876×CP (g kg⁻¹), R²=0.948, RSD=7.36, n=93. The addition of the ash content to sequential analysis improved the accuracy of DCP prediction, increasing the R² up to 0.960. Acid detergent fiber was the second independent variable selected in the cereals and by-products groups, the R² obtained was, respectively, higher (0.969) and lower (0.895) than that of general equation. The correlations among the independent variables employed and CPD were low. Only when in the total group the nitrogen linked to acid detergent fiber (N–ADF) measurement was included as independent variable (n=11) a high R² (0.905) was obtained. The N–ADF content that included the heat-damaged protein and the nitrogen associated with lignin could be adequate to estimate the indigestible protein content of feeds. However, more data points would be necessary to confirm its accuracy, taking into account the non-uniformity in the distribution of current data.     

Hormone concentrations temporally associated with contralateral and ipsilateral relationships between the CL and preovulatory follicle during the third follicular wave in heifers

Concentrations of circulating hormones after Day 14 (Day 0 = ovulation) were determined daily in 87 interovulatory intervals (IOIs) in heifers. The IOIs were grouped into four permutations according to an ipsilateral (Ipsi) or contralateral (Contra) relationship between the CL and the preovulatory follicle and two (2W) or three (3W) follicular waves per IOI. The number of IOIs per group differed (P < 0.005) from equality among the Ipsi-2W (n = 27), Contra-2W (n = 31), Ipsi-3W (n = 9), and Contra-3W (n = 20) groups. A continuous decrease in progesterone (luteolysis) began later (P < 0.05) in the Contra-3W group (Day 18.0 ± 0.4) than in each of the Ipsi-2W (15.4 ± 0.2), Contra-2W (15.6 ± 0.2), and Ipsi-3W (16.2 ± 0.5) groups. Concentrations of LH and estradiol began to increase near the beginning of luteolysis in each group. A minor FSH surge that did not stimulate a major follicular wave developed in about 50% of the IOIs in each group, except that none were detected in the Ipsi-3W group. The minor FSH surge reached a peak about 4 days before ovulation and several days after wave 3 had emerged. The hypothesis that luteolysis begins earliest in two-wave IOIs, intermediate in three-wave IOIs with an ipsilateral CL/follicle relationship, and latest in three-wave IOIs with a contralateral relationship was supported. The hypothesis that a minor FSH surge occurs most frequently in association with three follicular waves was not supported.     

Effect of Physical Parameters on the In Situ Survival of Escherichia coli MC-6 in an Estuarine Environment

Survival of Escherichia coli MC-6 of fecal origin in an estuarine environment as affected by time, water temperature, dissolved oxygen, salinity, and montmorillonite in diffusion chambers has been elucidated. Several in situ physical parameters were recorded simultaneously, and viable cell numbers were estimated. The survival of the bacteria varied seasonally. Montmorillonite addition extended the time needed for a 50% reduction of the viable cell population (t_½) of cells by 40% over the t_½ of cells in Rhode River water alone. The effect of this clay was not significantly greater between 50- to 1,000-μg/ml montmorillonite concentrations. In all experiments, the relationships among pairs of variables were studied by regression and correlation analysis. The slope between viable cell numbers and water temperatures increased about 50% for each 10 C increment in temperature and gave a correlation coefficient r = 0.617, significant at 95% confidence level. A similar correlation coefficient, r = 0.670, was obtained between water temperature and t_½ of the initial cell population. In all experiments regressions were performed considering all variables after bacteria had been in the Rhode River environment for 3 days. Coefficient of multiple determinaton was estimated as R² = 0.756. Approximately 75.6% of the variance of viable cell numbers can be explained by variation in water temperature, dissolved oxygen, and salinity. Simple correlation coefficients within the regression steps were also computed. Survival of bacteria was closely and negatively correlated with increasing water temperature (r = -0.717). It is suggested that water temperature is the most important factor in predicting fecal coliform survival from point and nonpoint sources in assessing water quality in an estuarine ecosystem.     

Revelation of genomic breed composition in a crossbred cattle of India with the help of Bovine50K BeadChip

The aim of the present study was to assess the population structure and admixture levels in the Vrindavani composite population in India by using Bovine50KSNP BeadChip data. Genotypic data were generated for randomly selected animals (n = 72) of Vrindavani population and the data for parental breeds i.e., Hariana (n = 10), Holstein-Friesian (n = 63), Jersey (n = 28) and Brown Swiss (n = 22) were retrieved from a public repository. The indices of population structure were calculated using PLINK software and R-program. The merged dataset was analysed for assessing admixture levels and population stratification using three different approaches i.e., principal component analysis (PCA), multi-dimensional scaling (MDS) approach and the model-based approach in STRUCTURE software. The average minor allele frequency (MAF) value for Vrindavani population was estimated to be 0.235. Vrindavani population was found to possess an average ancestry of 39.5, 22.9, 26.9, and 10.7% inheritance levels from Holstein Friesian, Jersey, Hariana and Brown Swiss cattle breeds, respectively.