Functional clustering of time series gene expression data by Granger causality

Background: A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results: In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions: This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them.

In vitro schistosomicidal effects of the essential oil of Tagetes erecta

The in vitro schistosomicidal effects of the essential oil obtained from Tagetes erecta L. Asteraceae, leaves (TE-EO) collected in Brazil against Schistosoma mansoni worms are reported in this paper. The oil caused a significant decrease in the motor activity at 50 µg/mL as minimal concentration after 24 h. This oil also caused death of all the parasites and the separation of coupled pairs into individual male and female at 100 µg/mL after 24 h. The viability of adult worm groups treated with the TE-EO at 100 µg/mL was similar to that of groups treated with praziquantel (positive control). In addition, the oil promoted the inhibition of eggs development at all the tested concentrations. These data indicate that the TE-EO could be considered as a promising source for the development of new schistosomicidal agents.

Species of Drosophila (Diptera: Drosophilidae) attracted to dung and carrion baited pitfall traps in the Uruguayan Eastern Serranías

This study investigates the species richness and abundance of Drosophila Fallén, 1823 attracted to dung and carrion baited pitfall traps in natural areas with heterogeneous habitats at the Sierra de Minas, Eastern Serranías, southeastern Uruguay. Collecting was carried out on a monthly basis (May 2002 through April 2003). Drosophilids accounted for 0.84% (n = 131) and 3.61% (n = 158) of the Diptera collected from dung (n = 15,630) and carrion (n = 4,382) pitfall traps, respectively. A total of 12 species were identified, 11 of which belong to the subgenus Drosophila (the richest) and one to the subgenus Sophophora Sturtevant, 1939. Over 90% of the Drosophila specimens collected belong to five species of the subgenus Drosophila, namely D. gaucha Jaeger & Salzano, 1953, D. immigrans Sturtevant, 1921, D. mediovittata Frota-Pessoa, 1954, D. aff. nappae Vilela, Valente & Basso-da-Silva, 2004, and D. ornatifrons Duda, 1927. Drosophila cardini Sturtevant, 1916 is recorded for the first time from Uruguay. Drosophila abundance and species richness in the four habitats sampled in the Uruguayan Eastern Serranías, namely woodlands sierra, riparian forest, pine plantation and grazing grassland, were considered to be a function of habitat conservation. Diversity indices were low in all habitats. Different habitats supported particular coprophilous and necrophilous Drosophila species. The woodland sierra represents the most preserved habitat, and contributed with the highest species richness observed. Drosophila ornatifrons was the dominant species, with a restricted habitat distribution. On the other hand, grazed grassland, an environment modified by livestock management, had the lowest species richness: only a few specimens of D. repleta Wollaston, 1858. Regarding species composition, significant differences were found in some pairwise comparisons of groups of Drosophila species that included D. ornatifrons. Fly attraction to dung can be exploited as an alternative and/or complementary collecting method in ecological studies of Drosophila assemblages in natural areas.

Conceptual problem for noncommutative inflation and the new approach for nonrelativistic inflationary equation of state

In a previous paper, we connected the phenomenological noncommutative inflation of Alexander, Brandenberger and Magueijo [ Phys. Rev. D 67 081301 (2003)] and Koh and Brandenberger [ J. Cosmol. Astropart Phys. 2007 21 ()] with the formal representation theory of groups and algebras and analyzed minimal conditions that the deformed dispersion relation should satisfy in order to lead to a successful inflation. In that paper, we showed that elementary tools of algebra allow a group-like procedure in which even Hopf algebras (roughly the symmetries of noncommutative spaces) could lead to the equation of state of inflationary radiation. Nevertheless, in this paper, we show that there exists a conceptual problem with the kind of representation that leads to the fundamental equations of the model. The problem comes from an incompatibility between one of the minimal conditions for successful inflation (the momentum of individual photons being bounded from above) and the Fock-space structure of the representation which leads to the fundamental inflationary equations of state. We show that the Fock structure, although mathematically allowed, would lead to problems with the overall consistency of physics, like leading to a problematic scattering theory, for example. We suggest replacing the Fock space by one of two possible structures that we propose. One of them relates to the general theory of Hopf algebras (here explained at an elementary level) while the other is based on a representation theorem of von Neumann algebras (a generalization of the Clebsch-Gordan coefficients), a proposal already suggested by us to take into account interactions in the inflationary equation of state.

Lipid and glucose profiles of dairy buffaloes during lactation and dry period

The purpose of this study was to analyze the influence of lactation and dry period in the constituents of lipid and glucose metabolism of buffaloes. One hundred forty-seven samples of serum and plasma were collected between November 2009 and July 2010, from properties raising Murrah, Mediterranean and crossbred buffaloes, located in the State of Sao Paulo, Brazil. Biochemical analysis was obtained by determining the contents of serum cholesterol, triglycerides, beta-hydroxybutyrate (β-HBO), non-esterified fatty acids (NEFA) and plasma glucose. Values for arithmetic mean and standard error mean were calculated using the SAS procedure, version 9.2. Tests for normality of residuals and homogeneity of variances were performed using the SAS Guide Data Analysis. Data were analyzed by ANOVA using the SAS procedure Glimmix. The group information (Lactation), Farm and Age were used in the statistical models. Means of groups were compared using Least Square Means (LSMeans) of SAS, where significant difference was observed at P ≤ 0.05. It was possible to conclude that buffaloes during peak lactation need to metabolize body reserves to supplement the lower amounts of bloodstream lipids, when they remain in negative energy balance. In the dry period, there were significant changes in the lipid profile, characterized by decrease of nutritional requirements, with consequent improvement in the general conditions of the animals.

International cooperation in endourology: percutaneous and flexible ureteroscopic treatment of lower pole kidney stones

Introduction Lower pole kidney stones represent at time a challenge for the urologist. The gold standard treatment for intrarenal stones <2 cm is Extracorporeal Shock Wave Lithotripsy (ESWL) while for those >2 cm is Percutaneous Nephrolithotomy (PCNL). The success rate of ESWL, however, decreases when it is employed for lower pole stones, and this is particularly true in the presence of narrow calices or acute infundibular angles. Studies have proved that ureteroscopy (URS) is an efficacious alternative to ESWL for lower pole stones <2 cm, but this is not reflected by either the European or the American guidelines. The aim of this study is to present the results of a large series of flexible ureteroscopies and PCNLs for lower pole kidney stones from high-volume centers, in order to provide more evidences on the potential indications of the flexible ureteroscopy for the treatment of kidney stones. Materials and Methods A database was created and the participating centres retrospectively entered their data relating to the percutaneous and flexible ureteroscopic management of lower pole kidney stones. Patients included were treated between January 2005 and January 2010. Variables analyzed included case load number, preoperative and postoperative imaging, stone burden, anaesthesia (general vs. spinal), type of lithotripter, access location and size, access dilation type, ureteral access sheath use, visual clarity, operative time, stone-free rate, complication rate, hospital stay, analgesic requirement and follow-up time. Stone-free rate was defined as absence of residual fragments or presence of a single fragment <2 mm in size at follow-up imaging. Primary end-point was to test the efficacy and safety of flexible URS for the treatment of lower pole stones; the same descriptive analysis was conducted for the PCNL approach, as considered the gold standard for the treatment of lower pole kidney stones. In this setting, no statistical analysis was conducted owing to the different selection criteria of the patients. Secondary end-point consisted in matching the results of stone-free rates, operative time and complications rate of flexible URS and PCNL in the subgroup of patients harbouring lower pole kidney stones between 1 and 2 cm in the higher diameter. Results A total 246 patients met the criteria for inclusion. There were 117 PCNLs (group 1) and 129 flexible URS (group 2). Ninety-six percent of cases were diagnosed by CT KUB scan. Mean stone burden was 175±160 and 50±62 mm2 for groups 1 and 2, respectively. General anaesthesia was induced in 100 % and 80% of groups 1 and 2, respectively. Pneumo-ultrasonic energy was used in 84% of cases in the PCNL group, and holmium laser in 95% of the cases in the flexible URS group. The mean operative time was 76.9±44 and 63±37 minutes for groups 1 and 2 respectively. There were 12 major complications (11%) in group 1 (mainly Grade II complications according to Clavidien classification) and no major complications in group 2. Mean hospital stay was 5.7 and 2.6 days for groups 1 and 2, respectively. Ninety-five percent of group 1 and 52% of group 2 required analgesia for a period longer than 24 hours. Intraoperative stone-free rate after a single treatment was 88.9% for group 1 and 79.1% for group 2. Overall, 6% of group 1 and 14.7% of group 2 required a second look procedure. At 3 months, stone-free rates were 90.6% and 92.2% for groups 1 and 2, respectively, as documented by follow-up CT KUB (22%) or combination of intra-venous pyelogram, regular KUB and/or kidney ultrasound (78%). In the subanalysis conducted comparing 82 vs 65 patients who underwent PCNL and flexible URS for lower pole stones between 1 and 2 cm, intreoperative stone-free rates were 88% vs 68% (p= 0.03), respectively; anyway, after an auxiliary procedure which was necessary in 6% of the cases in group 1 and 23% in group 2 (p=0.03), stone-free rates at 3 months were not statistically significant (91.5% vs 89.2%; p=0.6). Conversely, the patients undergoing PCNL maintained a higher risk of complications during the procedure, with 9 cases observed in this group versus 0 in the group of patients treated with URS (p=0.01) Conclusions These data highlight the value of flexible URS as a very effective and safe option for the treatment of kidney stones; thanks to the latest generation of flexible devices, this new technical approach seems to be a valid alternative in particular for the treatment of lower pole kidney stones less than 2 cm. In high-volume centres and in the hands of skilled surgeons, this technique can approach the stone-free rates achievable through PCNL in lower pole stones between 1 and 2 cm, with a very low risk of complications. Furthermore, the results confirm the high success rate and relatively low morbidity of modern PCNL for lower pole stones, with no difference detectable between the prone and supine position.

Analysis of the pig genome for the identification of genomic regions affecting production traits

The aim of this work was to identify markers associated with production traits in the pig genome using different approaches. We focused the attention on Italian Large White pig breed using Genome Wide Association Studies (GWAS) and applying a selective genotyping approach to increase the power of the analyses. Furthermore, we searched the pig genome using Next Generation Sequencing (NSG) Ion Torrent Technology to combine selective genotyping approach and deep sequencing for SNP discovery. Other two studies were carried on with a different approach. Allele frequency changes for SNPs affecting candidate genes and at Genome Wide level were analysed to identify selection signatures driven by selection program during the last 20 years. This approach confirmed that a great number of markers may affect production traits and that they are captured by the classical selection programs. GWAS revealed 123 significant or suggestively significant SNP associated with Back Fat Thickenss and 229 associated with Average Daily Gain. 16 Copy Number Variant Regions resulted more frequent in lean or fat pigs and showed that different copies of those region could have a limited impact on fat. These often appear to be involved in food intake and behavior, beside affecting genes involved in metabolic pathways and their expression. By combining NGS sequencing with selective genotyping approach, new variants where discovered and at least 54 are worth to be analysed in association studies. The study of groups of pigs undergone to stringent selection showed that allele frequency of some loci can drastically change if they are close to traits that are interesting for selection schemes. These approaches could be, in future, integrated in genomic selection plans.

Assessment of population structure by single nucleotide polymorphisms (SNPs) in goat breeds

Single nucleotide polymorphisms (SNPs) may be used in biodiversity studies and commercial tasks like traceability, paternity testing and selection for suitable genotypes. Twenty-seven SNPs were characterized and genotyped on 250 individuals belonging to eight Italian goat breeds. Multilocus genotype data were used to infer population structure and assign individuals to populations. To estimate the number of groups (K) to test in population structure analysis we used likelihood values and variance of the bootstrap samples, deriving optimal K from a drop in the likelihood and a rise in the variance plots against K.

Demonstration of coinfection with and recombination by caprine arthritis-encephalitis virus and maedi-visna virus in naturally infected goats

Recombination of different strains and subtypes is a hallmark of lentivirus infections, particularly for human immunodeficiency virus, and contributes significantly to viral diversity and evolution both within individual hosts and within populations. Recombinant viruses are generated in individuals coinfected or superinfected with more than one lentiviral strain or subtype. This, however, has never been described in vivo for the prototype lentivirus maedi-visna virus of sheep and its closely related caprine counterpart, the caprine arthritis-encephalitis virus. Cross-species infections occur in animals living under natural conditions, which suggests that dual infections with small-ruminant lentiviruses (SRLVs) are possible. In this paper we describe the first documented case of coinfection and viral recombination in two naturally infected goats. DNA fragments encompassing a variable region of the envelope glycoprotein were obtained from these two animals by end-limiting dilution PCR of peripheral blood mononuclear cells or infected cocultures. Genetic analyses, including nucleotide sequencing and heteroduplex mobility assays, showed that these goats harbored two distinct populations of SRLVs. Phylogenetic analysis permitted us to assign these sequences to the maedi-visna virus group (SRLV group A) or the caprine arthritis-encephalitis virus group (SRLV group B). SimPlot analysis showed clear evidence of A/B recombination within the env gene segment of a virus detected in one of the two goats. This case provides conclusive evidence that coinfection by different strains of SRLVs of groups A and B can indeed occur and that these viruses actually recombine in vivo.

[Treatment of the aortic valve and ascending aorta. The significance of reconstructive methods on the aortic root]

BACKGROUND AND OBJECTIVE: The standard surgical repair of disease of the aortic valve and the ascending aorta has been combined replacement, which includes the disadvantage of inserting a mechanical valve. We have investigated an individualized approach which preserves the native valve. PATIENTS AND METHODS: Between October 1995 and October 1997, a consecutive total of 101 patients (72 men, 29 women, aged 21-83 years) underwent operations for disease of the ascending aorta: aortic dissection type A in 34 patients, aneurysmal dilatation in 67. Dilatation of the aortic arch was associated with aortic regurgitation in 58 patients. There were 11 patients with aortic valve stenosis or previously implanted aortic valve prosthesis among a total of 46 whose aortic valve was replaced (group II). Supracommissural aortic replacement with a Dacron tube was performed in 16 patients (group I) with normal valve cusps and an aortic root diameter < 3.5 cm. In 28 patients with an aortic root diameter of 3.5-5.0 cm the aortic root was remodelled (group III). Resuspension of the native aortic valve was undertaken in 11 patients with aortic root dilatation of > 5.0 cm (group IV). RESULTS: Operative intervention was electively performed in 72 patients, without any death. Of 29 patients operated as an emergency for acute type A dissection four died (14%). In 55 of the 58 patients with aortic regurgitation in proved possible to preserve native aortic valve (95%). In the early postoperative phase and after an average follow-up time of 11.8 months, transthoracic echocardiography demonstrated good aortic valve function, except in one patient each of groups III and IV who developed aortic regurgitation grades I or II. CONCLUSION: The described individualized approach makes it possible to preserve the native aortic valve in most patients with aortic regurgitation, at a low risk. Follow-up observations so far indicate good results of the reconstruction.

Thoracoabdominal-aortoiliac multidetector-row CT angiography at 80 and 100 kVp: assessment of image quality and radiation dose

OBJECTIVE: To compare image quality and radiation dose of thoracoabdominal computed tomography (CT) angiography at 80 and 100 kVp and to assess the feasibility of reducing contrast medium volume from 60 to 45 mL at 80 kVp. MATERIALS AND METHODS: This retrospective study had institutional review board approval; informed consent was waived. Seventy-five patients who had undergone thoracoabdominal 64-section multidetector-row CT angiography were divided into 3 groups of 25 patients each. Patients of groups A (tube voltage, 100 kVp) and B (tube voltage, 80 kVp) received 60 mL of contrast medium at 4 mL/s. Patients of group C (tube voltage, 80 kVp) received 45 mL of contrast medium at 3 mL/s. Mean aortoiliac attenuation, image noise, and contrast-to-noise ratio were assessed. The measurement of radiation dose was based on the volume CT dose index. Three independent readers assessed the diagnostic image quality. RESULTS: Mean aortoiliac attenuation for group B (621.1 +/- 90.5 HU) was significantly greater than for groups A and C (485.2 +/- 110.5 HU and 483.1 +/- 119.8 HU; respectively) (P < 0.001). Mean image noise was significantly higher for groups B and C than for group A (P < 0.05). The contrast-to-noise ratio did not significantly differ between the groups (group A, 35.0 +/- 13.8; group B, 31.7 +/- 10.1; group C, 27.3 +/- 11.5; P = 0.08). Mean volume CT dose index in groups B and C (5.2 +/- 0.4 mGy and 4.9 +/- 0.3 mGy, respectively) were reduced by 23.5% and 27.9%, respectively, compared with group A (6.8 +/- 0.8 mGy) (P < 0.001). The average overall diagnostic image quality for the 3 groups was graded as good or better. The score for group A was significantly higher than that for group C (P < 0.01), no difference was seen between group A and B (P = 0.92). CONCLUSIONS: Reduction of tube voltage from 100 to 80 kVp for thoracoabdominal CT angiography significantly reduces radiation dose without compromising image quality. Reduction of contrast medium volume to 45 mL at 80 kVp resulted in lower but still diagnostically acceptable image quality.

Phylogeny of Pasteurellaceae

This chapter provides an overview on the DNA based phylogeny of the family Pasteurellaceae and the genetic relatedness between taxa taking into account the various gene targets and approaches applied in the literature. The classical 16S rRNA gene based phylogeny as well as phylogenies based on house-keeping genes are described. Moreover, strength and weakness of the different trees and their topology are discussed based on the phylogenetic groups resolved. The data should help to get a clearer picture on the recent, current and future classification and also provide information to genetic characterization of members of the family. The history of phylogeny applied to the family as well as the phylogenetic history of the family is thereby presented. In this way it is the story of the search for the optimal phylogenetic marker without giving a final conclusive suggestion but it is also a resource for choosing the appropriate gene target(s) for people investigating the phylogeny of groups of Pasteurellaceae.

Prescription patterns of antimicrobials in veterinary practices in Switzerland

OBJECTIVES The objective of this study was to analyse antimicrobial prescriptions by veterinarians and to evaluate the appropriateness of use compared with prudent use guidelines. PRACTICES AND METHODS: Computerized records of prescriptions and treatments from eight mixed veterinary practices were analysed over a period of 2 years. A total of 61 212 antimicrobial treatments were recorded. Treatments were classified according to animal species treated, indication for treatment, route of administration and antimicrobial class used. For each treatment and antimicrobial substance, the prescribed dose was calculated. Dosage, antimicrobial classes and combinations of different classes used for different indications were compared with published recommendations. RESULTS From the total amount of 1590 kg of active antimicrobial substance, sulphonamides (594 kg), tetracyclines (335 kg), and penicillins and cephalosporins (290 kg) were the classes of which the largest quantity was prescribed. Penicillins and cephalosporins were most frequently prescribed (37% of treatments), followed by aminoglycosides (18%), tetracyclines (14%) and sulphonamides (11%). Sixty-one per cent of the amount of antimicrobials prescribed was used for the treatment of groups of animals via feed or water. Antimicrobial classes classified as highest priority for human medicine by an international group of experts were used in 9% of the prescriptions. The dosage corresponded to the manufacturer's recommendation in 45% of the analysed prescriptions. CONCLUSIONS Most prescriptions corresponded well to guidelines on prudent use of antimicrobials. Nevertheless, the large variation of prescriptions among different veterinarians indicates that the usage of critical antimicrobial substances and the amount of antimicrobials used for group medication without a specific indication could be further reduced.

Information Integration Theory and the Construction of Individually Perceived Group Efficacy

According to Bandura (1997) efficacy beliefs are a primary determinant of motivation. Still, very little is known about the processes through which people integrate situational factors to form efficacy beliefs (Myers & Feltz, 2007). The aim of this study was to gain insight into the cognitive construction of subjective group-efficacy beliefs. Only with a sound understanding of those processes is there a sufficient base to derive psychological interventions aimed at group-efficacy beliefs. According to cognitive theories (e.g., Miller, Galanter, & Pribram, 1973) individual group-efficacy beliefs can be seen as the result of a comparison between the demands of a group task and the resources of the performing group. At the center of this comparison are internally represented structures of the group task and plans to perform it. The empirical plausibility of this notion was tested using functional measurement theory (Anderson, 1981). Twenty-three students (M = 23.30 years; SD = 3.39; 35 % females) of the University of Bern repeatedly judged the efficacy of groups in different group tasks. The groups consisted of the subjects and another one to two fictive group members. The latter were manipulated by their value (low, medium, high) in task-relevant abilities. Data obtained from multiple full factorial designs were structured with individuals as second level units and analyzed using mixed linear models. The task-relevant abilities of group members, specified as fixed factors, all had highly significant effects on subjects’ group-efficacy judgments. The effect sizes of the ability factors showed to be dependent on the respective abilities’ importance in a given task. In additive tasks (Steiner, 1972) group resources were integrated in a linear fashion whereas significant interaction between factors was obtained in interdependent tasks. The results also showed that people take into account other group members’ efficacy beliefs when forming their own group-efficacy beliefs. The results support the notion that personal group-efficacy beliefs are obtained by comparing the demands of a task with the performing groups’ resources. Psychological factors such as other team members’ efficacy beliefs are thereby being considered task relevant resources and affect subjective group-efficacy beliefs. This latter finding underlines the adequacy of multidimensional measures. While the validity of collective efficacy measures is usually estimated by how well they predict performances, the results of this study allow for a somewhat internal validity criterion. It is concluded that Information Integration Theory holds potential to further help understand people’s cognitive functioning in sport relevant situations.

Studies of the mechanism of daunorubicin carcinogenesis: Modulation by vitamin E

Daunorubicin (DNR) is an anthracycline antibiotic used as a cancer chemotherapeutic agent. However, it causes mammary adenocarcinomas in female Sprague-Dawley (SD) rats. Vitamin E (E) has been found to reduce DNR carcinogenicity. I investigated the mechanism of DNR carcinogenicity and its interaction with E in SD rats by studying DNR-DNA adduct formation and the influence of E status on DNR clearance and free radical producing and detoxifying enzymes.^ The hypothesis was that DNR exerts its tumorigenic effect via free radicals generated during redox cycling and production of reactive intermediates capable of forming DNA adducts. E was postulated to act as a protective agent through a combination of its antioxidant property, modulation of drug clearance and levels of free radical producing and detoxifying enzymes.^ DNA adduct formation was measured by the nuclease P1 $\sp{32}$P-post labeling assay. In vitro, DNR was activated by rat liver microsomes and either NADPH or cumene hydrogen peroxide (CuOOH). Rat liver DNA incubated with this mixture formed two adducts when the cofactor was NADPH and three adducts when CuOOH was used. In vivo, SD rats were treated with i.v. doses of DNR. No detectable DNR-DNA adducts were formed in liver or mammary DNA in vivo, although there was an intensification of endogenous DNA adducts.^ Groups, 1, 2, 3 and 4 of weanling female SD rats were fed 0, 100, 1,000 and 10,000 mg $\alpha$-tocopheryl acetate/kg diet respectively. A comparison of Groups 1 and 4 showed no effect of E status on clearance of 10 mg tritiated DNR/kg body weight over 72 hours. However, liver cleared DNR at a faster rate than mammary epithelial cells (MEC).^ Xanthine oxidase, which catalyzes DNR redox cycling, was significantly decreased in liver and MEC of rats in group 4 compared to groups 1, 2, and 3. Detoxifying enzymes were not dramatically affected by E supplementation. Quinone reductase in MEC was significantly increased in group 4 compared to other groups. Overall, the liver had higher levels of free radical detoxifying enzymes compared to MEC.^ These data support a role of free radicals in DNR carcinogenicity because (1) endogenous DNA adducts formed due to free radical insult are further intensified by DNR treatment in vivo, (2) MEC, the specific target of DNR carcinogenicity, cannot rapidly clear DNR and have a lower free radical detoxifying capability than liver, (3) E supplementation caused lowering of free radical generating potential via xanthine oxidase, and increased DNR detoxification due to elevation of quinone reductase in MEC. ^