Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome.

MOTIVATION: Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance. RESULTS: AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes. AVAILABILITY AND IMPLEMENTATION: AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluation of Nanomechanical Properties of Tomato Root by Atomic Force Microscopy.

Here, different tissue surfaces of tomato root were characterized employing atomic force microscopy on day 7 and day 21 of growth through Young's modulus and plasticity index. These parameters provide quantitative information regarding the mechanical behavior of the tomato root under fresh conditions in different locations of the cross-section of root [cell surface of the epidermis, parenchyma (Pa), and vascular bundles (Vb)]. The results show that the mechanical parameters depend on the indented region, tissue type, and growth time. Thereby, the stiffness increases in the cell surface of epidermal tissue with increasing growth time (from 9.19 ± 0.68 to 13.90 ± 1.68 MPa) and the cell surface of Pa tissue displays the opposite behavior (from 1.74 ± 0.49 to 0.48 ± 0.55); the stiffness of cell surfaces of Vb tissue changes from 10.60 ± 0.58 to 6.37 ± 0.53 MPa, all cases showed a statistical difference (p < 0.05). Viscoelastic behavior dominates the mechanical forces in the tomato root. The current study is a contribution to a better understanding of the cell mechanics behavior of different tomato root tissues during growth.

Consensus document on dog and cat allergy.

The prevalence of sensitization to dogs and cats varies by country, exposure time and predisposition to atopy. It is estimated that 26% of European adults coming to the clinic for suspected allergy to inhalant allergens are sensitized to cats and 27% to dogs. This document is intended to be a useful tool for clinicians involved in the management of people with dog or cat allergy. It was prepared from a consensus process based on the RAND/UCLA method. Following a literature review, it proposes various recommendations concerning the diagnosis and treatment of these patients, grounded in evidence and clinical experience. The diagnosis of dog and cat allergy is based on a medical history and physical examination that are consistent with each other and is confirmed with positive results on specific IgE skin tests. Sometimes, especially in polysensitized patients, molecular diagnosis is strongly recommended. Although the most advisable measure would be to avoid the animal, this is often impossible and associated with a major emotional impact. Furthermore, indirect exposure to allergens occurs in environments in which animals are not present. Immunotherapy is emerging as a potential solution to this problem, although further supporting studies are needed.

Clinical Management and Use of Health Care Resources in the Treatment of Nasal Polyposis in Spanish Allergy Centers: The POLAR Study.

BACKGROUND: Nasal polyposis (NP) is a chronic inflammatory disease that constitutes a major health problem with significant comorbidities and a considerable associated socioeconomic burden. OBJECTIVE: To describe the clinical features and management of patients with NP attending Spanish allergy centers, the use of health care resources, and the degree of compliance with the diagnostic and therapeutic recommendations of the European Position Paper on Rhinosinusitis and Nasal Polyps (EPOS). METHODS: We performed a multicenter, observational, and cross-sectional epidemiologic study of 671 patients consulting for NP in 67 Spanish allergy departments. We used sociodemographic and clinical questionnaires to evaluate clinical characteristics, use of health care resources, diagnostic methods, and treatment administered. RESULTS: NP was closely associated with asthma (66%), allergic rhinitis (45.9%), and hypersensitivity to nonsteroidal anti-inflammatory drugs (NSAIDs) (26%). Atopy was present in the 50% of cases, with Dermatophagoides pteronyssinus as the most frequent sensitizing allergen. Eleven percent of NP patients visited the emergency department during the previous year, and more than 58% used primary care, allergy, or otorhinolaryngology services. The most frequently used diagnostic tests were skin prick tests (93.6%) and anterior rhinoscopy (79.4%). Intranasal corticosteroids were the drug class most frequently prescribed by allergists (74.6%). Specific immunotherapy was prescribed in 21% of patients. CONCLUSIONS: NP is a chronic inflammatory disease that generates considerable use of health care resources. The close association with atopy, asthma, and NSAID hypersensitivity highlights the usefulness of an allergy workup in all patients with NP. Analysis of the clinical management of NP by allergists in Spain revealed a high degree of compliance with EPOS diagnostic and therapeutic recommendations.

Propene epoxidation with O2 or H2-O2 mixtures over silver catalysts: theoretical insights into the role of the particle size.

The adsorption and dissociation of molecular O2 over silver extended surfaces, nanoparticles and clusters of different size, as well as the reaction between adsorbed O2 and H2 to form less nucleophilic hydroperoxide groups have been investigated by means of periodic DFT calculations. Hydroperoxide formation from O2 and H2 is in all systems kinetically favoured over O2 dissociation, which becomes energetically forbidden on small planar clusters. The nature and reactivity towards propene of all oxygen species present on silver, including adsorbed molecular O2, atomic O, and hydroperoxide groups, have been theoretically explored. Formation of the oxametallacycle intermediate involved in propene epoxidation is energetically accessible on subnanometric three-dimensional silver nanoparticles, but competitive pathways leading to hydrogen abstraction and allyl formation always involve lower activation barriers. Theoretical findings have been experimentally confirmed by Raman spectroscopy of O2 adsorption and catalytic testing of planar and three dimensional silver clusters.

Resistance Exercise Program in Cognitively Normal Older Adults: CERT-Based Exercise Protocol of the AGUEDA Randomized Controlled Trial.

OBJECTIVES: To provide a comprehensive CERT (Consensus on Exercise Reporting Template)-based description of the resistance exercise program implemented in the AGUEDA (Active Gains in brain Using Exercise During Aging) study, a randomized controlled trial investigating the effects of a 24-week supervised resistance exercise program on executive function and related brain structure and function in cognitively normal older adults. DESIGN AND PARTICIPANTS: 90 cognitively normal older adults aged 65 to 80 were randomized (1:1) to a: 1) resistance exercise group; or a 2) wait-list control group. Participants in the exercise group (n = 46) performed 180 min/week of resistance exercise (3 supervised sessions per week, 60 min/session) for 24 weeks. INTERVENTION: The exercise program consisted of a combination of upper and lower limb exercises using elastic bands and the participant's own body weight as the main resistance. The load and intensity were based on the resistance of the elastic bands (7 resistances), number of repetitions (individualized), motor complexity of exercises (3 levels), sets and rest (3 sets/60 sec rest), execution time (40-60 sec) and velocity (as fast as possible). SETTINGS: The maximum prescribed-target intensity was 70-80% of the participants' maximum rate of perceived exertion (7-8 RPE). Heart rate, sleep quality and feeling scale were recorded during all exercise sessions. Those in the wait-list control group (n = 44) were asked to maintain their usual lifestyle. The feasibility of AGUEDA project was evaluated by retention, adherence, adverse events and cost estimation on the exercise program. RESULTS AND CONCLUSIONS: This study details the exercise program of the AGUEDA trial, including well-described multi-language manuals and videos, which can be used by public health professionals, or general public who wish to implement a feasible and low-cost resistance exercise program. The AGUEDA exercise program seems to be feasible by the high retention (95.6%) and attendance rate (85.7%), very low serious adverse event (1%) and low economic cost (144.23 € /participant/24 weeks). We predict that a 24-week resistance exercise program will have positive effects on brain health in cognitively normal older adults.

Periodic DFT investigation of the effect of aluminium content on the properties of the acid zeolite H-FER.

Periodic DFT calculations were performed on H-FER models having Si/Al ratios of 71 : 1, 35 : 1 and 8 : 1, in order to investigate the effect of aluminium content on the properties of the zeolite Brønsted acid sites. Relative stability of these sites was found to be dependent on Si/Al ratio, which is the main factor dictating the relative concentration of Brønsted acid sites having different types of local configuration, to the point that some types of acid site are formed only when the aluminium content of the zeolite is relatively high. The number of AlO(4) tetrahedra sharing an oxygen with the SiO(4) tetrahedron involved in the Brønsted acid site determines the Si-O(H)-Al angle, O-H stretching frequency and deprotonation energy (and hence acid strength). For Brønsted acid protons not involved in intra-zeolite H-bonding, a correlation was found between Si-O(H)-Al angle and O-H stretching frequency.

[Clinical outcomes in patients with psoriasis following discontinuation of efalizumab due to suspension of marketing authorization]. / Evolución clínica de los pacientes psoriásicos tratados con efalizumab al suspender el fármaco.

INTRODUCTION: In February 2009, the European Medicines Agency suspended the marketing authorization for efalizumab after 3 confirmed cases of progressive multifocal leukoencephalopathy were reported. To assess the consequences of this decision, we performed a prospective follow-up study of patients in our department who were being treated with efalizumab at the time and compared clinical outcomes with data from the literature. PATIENTS AND METHODS: Thirty-two patients (28 with plaque psoriasis and 4 with palmoplantar psoriasis) were enrolled between February and March 2009. We recorded psoriasis area and severity index (PASI) scores at the moment of efalizumab discontinuation, at 6 weeks post-discontinuation, and at 3-monthly intervals thereafter. PASI scores prior to treatment with efalizumab were also noted. For patients who experienced rebounds with generalized psoriasis, we noted the time that had elapsed since efalizumab discontinuation and the treatment they were receiving. RESULTS: Even though 92.8% of the patients were considered good responders (>75% reduction in PASI score), 25% of the group (8/32) experienced rebound and 15.7% (5/32) experienced relapse. The percentage of patients in whom rebound was observed on transition therapy was 18% (2/11) for cyclosporin, 50% (1/2) for methotrexate, 50% (1/2) for adalimumab, 50% (1/2) for etanercept, and 27% (3/11) for topical treatment. CONCLUSIONS: We observed a very high rate of rebound and generalized inflammation in patients whose disease had previously been well controlled for several years.

Reference values for facilitating the interpretation of the ESPRINT-15 questionnaire (Spanish version).

OBJECTIVE: ESPRINT-15 is a specific, short-form instrument to measure health-related quality of life in adults suffering from allergic rhinitis. The aim of this study was to obtain reference values in order to improve its interpretability. METHODS: ESPRINT-15 was administered to a representative sample of Spanish adults with allergic rhinitis. Means and percentiles were obtained, taking into account the kind of rhinitis (persistent/intermittent) and symptom severity (very mild/mild/moderate/severe). RESULTS: A total of 2756 patients participated in the study. Mean (SD) scores were significantly lower (better) for men than for women (2.2 [1.4] vs 2.4 [1.4], P<.001, effect size [ES] is congruent to 0.15). Patients with intermittent rhinitis showed better scores than patients with persistent rhinitis (2.1 [1.4] vs. 2.5 [1.4], P<.001, ES is congruent to 0.21). Mean (SD) scores were higher (worse) when severity of symptoms increased, ranging from 0.9 (0.9) (very mild) to 3.7 (1.0) (severe) (ES is congruent to 1.0 between each consecutive group of symptom severity). CONCLUSIONS: The magnitude of the differences found among groups of patients reinforces the usefulness of providing reference values stratified by gender, type of allergic rhinitis, and symptom severity. The percentiles obtained can be used in clinical practice to evaluate individual scores, and assign the patient to the corresponding reference group.

Using radio astronomical receivers for molecular spectroscopic characterization in astrochemical laboratory simulations: A proof of concept.

We present a proof of concept on the coupling of radio astronomical receivers and spectrometers with chemical reactors and the performances of the resulting setup for spectroscopy and chemical simulations in laboratory astrophysics. Several experiments including cold plasma generation and UV photochemistry were performed in a 40 cm long gas cell placed in the beam path of the Aries 40 m radio telescope receivers operating in the 41-49 GHz frequency range interfaced with fast Fourier transform spectrometers providing 2 GHz bandwidth and 38 kHz resolution. The impedance matching of the cell windows has been studied using different materials. The choice of the material and its thickness was critical to obtain a sensitivity identical to that of standard radio astronomical observations. Spectroscopic signals arising from very low partial pressures of CH3OH, CH3CH2OH, HCOOH, OCS, CS, SO2 (<10-3 mbar) were detected in a few seconds. Fast data acquisition was achieved allowing for kinetic measurements in fragmentation experiments using electron impact or UV irradiation. Time evolution of chemical reactions involving OCS, O2 and CS2 was also observed demonstrating that reactive species, such as CS, can be maintained with high abundance in the gas phase during these experiments.

Reticular synthesis of porous molecular 1D nanotubes and 3D networks.

Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal-organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of 'reticular synthesis', in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the 'node and strut' principles of reticular synthesis to molecular crystals.

Biliodigestive anastomosis in liver transplantation: review of 13 years.

Hepaticojejunostomy is a good alternative technique for biliary reconstruction in liver transplantation. Among 517 liver transplants performed between March 1992 and July 2005, 33 involved hepaticojejunostomy, namely, 18 men and 12 women of average age: 44.8 years. The main cause for this technique was retransplant (n = 10), secondary biliary cirrhosis (n = 5), alcoholic cirrhosis (n = 5), HCV cirrhosis (n = 2), primary biliary cirrhosis (n = 1), cryptogenic cirrhosis (n = 1), sclerosing cholangitis (n = 3), fulminant liver failure (n = 1), autoimmune cirrhosis (n = 1), and insulinoma metastasis (n = 1). Choledochojejunostomy was performed for all Roux-en-Y loops, with an average cold ischemia time of 361.16 minutes (180-780). The biliary complications were biliary fistula in four cases (13.3%), including two who required surgery; stenosis of the anastomosis in two cases (6.6%) including one diagnosed by HIDA that resolved with medical treatment and the other, diagnosed by cholangio-MRI, requiring a new hepaticojejunostomy; and biliary peritonitis in three cases (10%), all of whom required surgery. The vascular complications were thrombosis of the hepatic artery (n = 1), which required retransplantation, and pseudoaneurysm of hepatic artery (n = 1). No biliary complications occurred. The 6-month patient survival was 80% and the 6-month graft survival was 77%; no patient died due to biliary complications. Hepaticojejunostomy is a technique with higher morbidity than choledocho-choledochostomy, but it is the best alternative when the latter is not possible.

Immune Regulation of the Metastatic Process: Implications for Therapy.

Metastatic disease is the major cause of fatalities in cancer patients, but few therapies are designed to target the metastatic process. Cancer cells must perform a number of steps to successfully establish metastatic foci, including local invasion, intravasation, survival, extravasation, and growth in ectopic tissue. Due to the nonrandom distribution of metastasis, it has long been recognized that the tissue microenvironment must be an important determinant of colonization. More recently it has been established in animal models that immune cells regulate the metastatic process, including a dominant role for monocytes and macrophages, and emerging roles for neutrophils and various lymphocyte populations. While most research has focused on the early dissemination process, patients usually present clinically with disseminated, if not macroscopic, disease. Identifying pathways by which immune cells regulate growth and therapeutic resistance within metastatic sites is therefore key to the development of pharmacological agents that will significantly extend patient survival.

Molecular tracking of coagulase-negative staphylococcal isolates from catheter-related infections.

Three molecular typing methods (pulsed-field electrophoresis, localization of the mecA gene, and probing the vicinity of mec) have been used for the characterization of 40 catheter-related isolates of coagulase-negative staphylococci (CNS) in 14 patients admitted to the same hospital. The 40 isolates yielded 14 different SmaI banding patterns and corresponding unique localizations of mecA, each associated with a unique ClaI mecA polymorph. In 6 of the 14 patients the contaminated skin at the catheter entry site was the source of 4 local infections and 2 cases of bacteremia. A contaminated hub was the origin of 2 local infections and 4 cases of bacteremia in 6 more patients. The remaining 2 patients had positive cultures from both skin and catheter hub. In each bacteremic patient, the CNS recovered from catheter-related sites (tip, skin, and/or hub) and the CNS recovered from blood were identical, but each of these matching isolates was unique to the particular patients, indicating a low rate of cross-infection from patient to patient. Although classical methods for typing CNS (e.g., biotype and antibiotype) are readily available for most hospital laboratories, they have limitations concerning reproducibility and discriminatory power. Molecular epidemiologic techniques can provide powerful support to traditional techniques in determining the etiologic role of CNS in the disease process.

Use of a commercial double-test tablet (Rosco PGUA/indole) for screening of Escherichia coli.

A commercial double-test tablet (Rosco PGUA/indole) for detection of beta-glucuronidase (beta-GUR) activity and indole production was evaluated on a collection of 393 isolates of Enterobacteria. Both beta-GUR and indole were positive on 96.6% of Escherichia coli strains. beta-GUR, only, was also detected in 25 Shigella spp., four Enterobacter cloacae, eight Citrobacter freundii, and five Salmonella enteritidis strains, none of which were indole producers. An additional 261 consecutive clinical isolates of oxidase-negative nonswarming Gram-negative bacilli were studied in a parallel comparative field trial against conventional identification methods. For 200 strains, the standard method and PGUA/indole test were performed from the primary culture plate. The remaining 61 (23.4%) required subculture before testing. Sensitivity, specificity, positive predictive value, and negative predictive value of PGUA/indole test in the screening for E. coli were, respectively, 94.1%, 100%, 100%, and 87.1%. In our experience, PGUA/indole test is a rapid, precise, simple-to-perform, and economical method for screening E. coli. However, the need for a large inoculum may limit its application on primary cultures.

Progesterone metabolism during storage of blood samples from Gyr cattle: effects of anticoagulant, time and temperature of incubation.

Ten Gyr cows with a functional corpus luteum were used to evaluate the effects of time and temperature of incubation of blood samples on progesterone (P4) concentrations detected in plasma or serum. From each cow, a blood sample was collected into a flask containing no anticoagulant, another into an heparinized flask and a third into a flask containing sodium fluoride. The blood from each flask was divided into 46 aliquots. One of them was centrifuged within 5 min of collection. The remaining 45 aliquots were divided into three groups and kept at three different temperatures: 4 degrees C, 17 degrees C, or 37 degrees C. For each anticoagulant, aliquots from every cow and incubation temperature were centrifuged every 30 min for 6 h, and then at 8, 12 and 24 h. Plasma or serum were separated immediately after centrifugation and were kept frozen at -20 degrees C until assayed for progesterone. The mean initial concentration of P4 in serum (8.3 ng/ml) significantly diminished (P<0.05) to 6.7 ng/ml after 5 h of incubation at 4 degrees C, 3 h at 17 degrees C, or 2 h at 37 degrees C. In plasma from heparinized blood the initial concentration (7.8 ng/ml) declined significantly after 6 h of incubation at 4 degrees C, 2 h at 17 degrees C, or 1 h at 37 degrees C. Sodium fluoride used as anticoagulant prevented the degradation of P4 since the initial concentration of P4 (6.7 ng/ml) never declined during incubation at either 4 degrees C or 37 degrees C; the only significant reduction occurred after 24 h of incubation at 17 degrees C.

[Can we increase phosphate removal with conventional hemodialysis?]. / Se puede aumentar la eliminación de fósforo con la hemodiálisis convencional?

BACKGROUND: The aim of the present study was to investigate the effect of different dialysate buffer and glucose concentrations, membrane surface (S) bigger than 2 m2 and increased dialysate flow (Qd) in phosphate (P) removal. METHODS: A. First phase (5 patients): the following variations in dialysate composition were introduced. A: glucose 1.60 g/L, bicarbonate: 39 mEq/L, acetate 4 mEq/L, B: glucose 1.5 g/L bicarbonate 17 mEq/L, acetate 10 mEq/L; C: glucose 0, bicarbonate: 39 mEq/L, acetate 4 mEq/L; and D: glucose 0, bicarbonate 17 mEq/L, acetate 10 mEq/L. B. Second phase (14 patients): variations in S and Qd were: 1. Qd: 500 mL/min + Hemophan 2 m2, 2. Qd: 500 mL/min + Hemophan 2.6 m2, 3. Qd: 750 mL/min + Hemophan 2 m2, 4. Qd: 750 mL/min + Hemophan 2.6 m2. RESULTS: Comparing HDs performed with low bicarbonate (B and D) respect to current buffer formulations (A and C), total P removal was 997.3 (+/- 237.3) vs 882 (+/- 216.1) mg (p NS). No differences were found by grouping the sessions according to glucose concentration. There were no significant differences in total phosphate removal between the two different S or Qd. The most important predictive factor of total P removal was the initial P and 2 hours serum P concentration, and PTH concentration. CONCLUSIONS: i) Removal of P is better predicted by pre-dialysis P serum concentration; ii) P removal was not affected by the changes in bicarbonate and glucose concentration in the dialysate; iii) the increase of the dialyzer area between 2 and 2.6 m2 augments Kt/V, but without influencing P elimination; iv) a higher Qd does not determine significant differences in P removal and v) higher PTH is associated with a higher P elimination.

The effect of orally administered midazolam on children of three age groups during restorative dental care.

PURPOSE: The effects of orally administered midazolam on three groups of preschool children who differed by age only and required dental treatment were studied. Sixty-one children age 24-58 months participated in this institutionally-approved study. METHODS: Selection criteria for the children included: demonstrated disruptive behaviors; healthy (ASA I); required at least one restorative appointment involving a posterior quadrant; no known drug allergies; were between two and five years of age; and had no prior experience with sedative trials. The children were divided into three groups according to age: Group I (24-35 months), Group II (36-47 months), and Group III (47-59 months). Each child received midazolam 0.5 mg/kg orally 15 minutes before treatment. Behavior was evaluated using the Ohio State Behavior Rating Scale (OS). Physiological parameters including heart rate, oxygen saturation, systolic and diastolic blood pressure were also evaluated. Data were analyzed using chi-square, cross tabulation, descriptive statistics, ANOVA, t-tests, and regression and correlation analysis. RESULTS: Results indicated no statistically significant difference in behavior across all age groups as evaluated by the OS. CONCLUSION: No significant differences of clinical significance were noted.