Equilibrium and out-of-equilibrium dynamics in a molecular layer of azopolymer floating on water studied by Interfacial Shear Rheology

We report the details of the construction and calibration of an ultra sensitive surface rheometer, inspired by the setup described in [C.F. Brooks et al Langmuir 15, 2450 (1999)], which makes use of high resolution video tracking of the motion of a floating magnetized needle and is capable of measuring the viscoelastic response of a Langmuir monolayer with an accuracy of 10^-5 N/m. This instrument is then employed for the rheological characterization of a Langmuir monolayer of a photosensitive azobenzene polymer, which can be brought out of equilibrium by a suitable photoperturbation. The complex dynamic shear modulus G= G' + i G" is measured as a function of temperature and illumination power and wavelength. The reversible rheological ch anges induced in the film by photo-perturbation are monitored during time, observing a transition from a predominantly elastic (G' > G'') to a viscoelastic (G' \approx G'') regime. These results are confirmed by comparison with independent measurements performed by us using other rheological techniques. Finally a discussion is made, taking into account the results of a recent x-ray photon correlation spectroscopy experiment on the same polymer in equilibrium and out of equilibrium.Comment: Proceedings of the International Discussion Meeting on Relaxation in Complex Systems, Rome, 2009 12 pages, 7 figure

Laparoscopic bilateral hand-assisted nephrectomy: end-stage renal disease from tuberculosis, an unusual indication for nephrectomy before transplantation.

The purpose of the study was to sterilize renal tuberculous foci in a pretransplantation patient with a laparoscopic hand-assisted approach and to verify the feasibility of bilateral nephrectomy for this indication. This case report is the first description of hand-assisted laparoscopic bilateral nephrectomy for this pathologic condition. The 33-year-old patient had end-stage renal disease from renal tuberculosis. A commercially available hand-assistance device was used through a midline 8-cm supraumbilical incision and with four ports. The procedure was successfully completed. The total operative time was 3 hours and 40 minutes. Estimated blood loss was 250 mL. The postoperative course was uneventful, and clinical follow-up at 3 weeks revealed a successful outcome. Hand-assisted bilateral laparoscopic nephrectomy in patients with chronic renal failure from tuberculosis represents a viable option because it is feasible and effective. The hand-assisted approach increases the safety of the procedure while retaining all the advantages of minimally invasive surgery

Diversity in form and function:Vertical distribution of soil fauna mediates multidimensional trait variation

It has been widely recognized that species show extensive variation in form and function. Based on species’ attributes, they can be positioned along major axes of variation, which are often defined by life-history traits, such as number of offspring, age at maturity or generation time. Less emphasis has been given in this respect to tolerance traits, especially to resistance to abiotic stress conditions, which often determine community (dis)assembly and distribution. Soil fauna species distribution is governed to a large extent by environmental conditions that filter communities according to functional traits, such as abiotic stress tolerance, morphology and body size. Trait-based approaches have been successfully used to predict soil biota responses to abiotic stress. It remains unclear, though, how these traits relate to life-history traits that determine individual performance, that is, reproduction and survival. Here, we analyse patterns in multidimensional trait distribution of dominant groups of soil fauna, that is, Isopoda, Gastropoda and Collembola, known to be important to the functioning of ecosystems. We compiled trait information from existing literature, trait databases and supplementary measurements. We looked for common patterns in major axes of trait variation and tested if vertical distribution of species in the soil explained trait variation based on three components of trait diversity (trait richness, evenness and divergence). Our results showed that two to three axes of variation structured the trait space of life-history and tolerance traits in each of the taxonomic groups and that vertical distribution in soil explained the main axis of trait variation. We also found evidence of environmental filtering on soil fauna along the vertical soil distribution, with lower trait richness and trait divergence in soil-dwelling than in surface-living species. Our study was partially limited by the lack of detailed trait measurements for the selected taxonomic groups. In this regard, there is an urgent need for standardized trait databases across invertebrate groups to improve trait-based diversity analysis and fill gaps in the mechanistic understanding behind trait distribution, trait filtering and the link with species fitness and performance

Uncertainties and Systematic Effects on the estimate of stellar masses in high z galaxies

We discuss the uncertainties and the systematic effects that exist in the estimates of the stellar masses of high redshift galaxies, using broad band photometry, and how they affect the deduced galaxy stellar mass function. We use at this purpose the latest version of the GOODS-MUSIC catalog. In particular, we discuss the impact of different synthetic models, of the assumed initial mass function and of the selection band. Using Charlot & Bruzual 2007 and Maraston 2005 models we find masses lower than those obtained from Bruzual & Charlot 2003 models. In addition, we find a slight trend as a function of the mass itself comparing these two mass determinations with that from Bruzual & Charlot 2003 models. As consequence, the derived galaxy stellar mass functions show diverse shapes, and their slope depends on the assumed models. Despite these differences, the overall results and scenario remains unchanged. The masses obtained with the assumption of the Chabrier initial mass function are in average 0.24 dex lower than those from the Salpeter assumption, at all redshifts, causing a shift of galaxy stellar mass function of the same amount. Finally, using a 4.5 um-selected sample instead of a Ks-selected one, we add a new population of highly absorbed, dusty galaxies at z\simeq 2-3 of relatively low masses, yielding stronger constraints on the slope of the galaxy stellar mass function at lower masses.Comment: 5 pages, 4 figures, proceedings of the conference "Probing Stellar Populations out to the Distant Universe", Cefalu (Italy), September 7 - 19, 2008. To be published in the AIP Conf. Proc. Serie

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

Background: Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic scale, are necessary and urgent. In this scenario, the Gene Ontology has provided the means to standardize the annotation classification with a structured vocabulary which can be easily exploited by computational methods.Results: Argot2 is a web-based function prediction tool able to annotate nucleic or protein sequences from small datasets up to entire genomes. It accepts as input a list of sequences in FASTA format, which are processed using BLAST and HMMER searches vs UniProKB and Pfam databases respectively; these sequences are then annotated with GO terms retrieved from the UniProtKB-GOA database and the terms are weighted using the e-values from BLAST and HMMER. The weighted GO terms are processed according to both their semantic similarity relations described by the Gene Ontology and their associated score. The algorithm is based on the original idea developed in a previous tool called Argot. The entire engine has been completely rewritten to improve both accuracy and computational efficiency, thus allowing for the annotation of complete genomes.Conclusions: The revised algorithm has been already employed and successfully tested during in-house genome projects of grape and apple, and has proven to have a high precision and recall in all our benchmark conditions. It has also been successfully compared with Blast2GO, one of the methods most commonly employed for sequence annotation. The server is freely accessible at http://www.medcomp.medicina.unipd.it/Argot2Journal Articleinfo:eu-repo/semantics/publishe

CANDELS Multi-wavelength Catalogs: Source Detection and Photometry in the GOODS-South Field

We present a UV-to-mid infrared multi-wavelength catalog in the CANDELS/GOODS-S field, combining the newly obtained CANDELS HST/WFC3 F105W, F125W, and F160W data with existing public data. The catalog is based on source detection in the WFC3 F160W band. The F160W mosaic includes the data from CANDELS deep and wide observations as well as previous ERS and HUDF09 programs. The mosaic reaches a 5$\sigma$ limiting depth (within an aperture of radius 0.17 arcsec) of 27.4, 28.2, and 29.7 AB for CANDELS wide, deep, and HUDF regions, respectively. The catalog contains 34930 sources with the representative 50% completeness reaching 25.9, 26.6, and 28.1 AB in the F160W band for the three regions. In addition to WFC3 bands, the catalog also includes data from UV (U-band from both CTIO/MOSAIC and VLT/VIMOS), optical (HST/ACS F435W, F606W, F775W, F814W, and F850LP), and infrared (HST/WFC3 F098M, VLT/ISAAC Ks, VLT/HAWK-I Ks, and Spitzer/IRAC 3.6, 4.5, 5.8, 8.0 $\mu$m) observations. The catalog is validated via stellar colors, comparison with other published catalogs, zeropoint offsets determined from the best-fit templates of the spectral energy distribution of spectroscopically observed objects, and the accuracy of photometric redshifts. The catalog is able to detect unreddened star-forming (passive) galaxies with stellar mass of 10^{10}M_\odot at a 50% completeness level to z$\sim$3.4 (2.8), 4.6 (3.2), and 7.0 (4.2) in the three regions. As an example of application, the catalog is used to select both star-forming and passive galaxies at z$\sim$2--4 via the Balmer break. It is also used to study the color--magnitude diagram of galaxies at 0<z<4.Comment: The full resolution article is now published in ApJS (2013, 207, 24). 22 pages, 21 figures, and 5 tables. The catalogue is available on the CANDELS website: http://candels.ucolick.org/data_access/GOODS-S.html MAST: http://archive.stsci.edu/prepds/candels and Rainbow Database: https://arcoiris.ucolick.org/Rainbow_navigator_public and https://rainbowx.fis.ucm.es/Rainbow_navigator_publi

Acinetobacter baumannii in intensive care unit: A novel system to study clonal relationship among the isolates

<p>Abstract</p> <p>Background</p> <p>The nosocomial infections surveillance system must be strongly effective especially in highly critic areas, such as Intensive Care Units (ICU). These areas are frequently an epidemiological epicentre for transmission of multi-resistant pathogens, like <it>Acinetobacter baumannii</it>. As an epidemic outbreak occurs it is very important to confirm or exclude the genetic relationship among the isolates in a short time. There are several molecular typing systems used with this aim. The Repetitive sequence-based PCR (REP-PCR) has been recognized as an effective method and it was recently adapted to an automated format known as the DiversiLab system.</p> <p>Methods</p> <p>In the present study we have evaluated the combination of a newly introduced software package for the control of hospital infection (VIGI@ct) with the DiversiLab system. In order to evaluate the reliability of the DiversiLab its results were also compared with those obtained using f-AFLP.</p> <p>Results</p> <p>The combination of VIGI@ct and DiversiLab enabled an earlier identification of an <it>A. baumannii </it>epidemic cluster, through the confirmation of the genetic relationship among the isolates. This cluster regards 56 multi-drug-resistant <it>A. baumannii </it>isolates from several specimens collected from 13 different patients admitted to the ICU in a ten month period. The <it>A. baumannii </it>isolates were clonally related being their similarity included between 97 and 100%. The results of the DiversiLab were confirmed by f-AFLP analysis.</p> <p>Conclusion</p> <p>The early identification of the outbreak has led to the prompt application of operative procedures and precautions to avoid the spread of pathogen. To date, 6 months after the last <it>A. baumannii </it>isolate, no other related case has been identified.</p

Early diagnosis of bladder cancer through the detection of urinary tyrosine-phosphorylated proteins

BACKGROUND: A noninvasive, highly sensitive and specific urine test is needed for bladder cancer (BC) diagnosis and surveillance in addition to the invasive cystoscopy. We previously described the diagnostic effectiveness of urinary tyrosine-phosphorylated proteins (UPY) and a new assay (UPY-A) for their measurement in a pilot study. The aim of this work was to evaluate the performances of the UPY-A using an independent cohort of 262 subjects. METHODS: Urinary tyrosine-phosphorylated proteins were measured by UPY-A test. The area under ROC curve, cutoff, sensitivity, specificity and predictive values of UPY-A were determined. The association of UPY levels with tumour staging, grading, recurrence and progression risk was analysed by Kruskal–Wallis and Wilcoxon's test. To test the probability to be a case if positive at the UPY-A, a logistic test adjusted for possible confounding factor was used. RESULTS: Results showed a significant difference of UPY levels between patients with BC vs healthy controls. For the best cutoff value, 261.26 Standard Units (SU), the sensitivity of the assay was 80.43% and the specificity was 78.82%. A statistically significant difference was found in the levels of UPY at different BC stages and grades between Ta and T1 and with different risk of recurrence and progression. A statistically significant increased risk for BC at UPY-A ⩾261.26 SU was observed. CONCLUSIONS: The present study supplies important information on the diagnostic characteristics of UPY-A revealing remarkable performances for early stages and allowing its potential use for different applications encompassing the screening of high-risk subjects, primary diagnosis and posttreatment surveillance