Benchmarking some Portuguese S&T system research units: 2nd Edition

The increasing use of productivity and impact metrics for evaluation and comparison, not only of individual researchers but also of institutions, universities and even countries, has prompted the development of bibliometrics. Currently, metrics are becoming widely accepted as an easy and balanced way to assist the peer review and evaluation of scientists and/or research units, provided they have adequate precision and recall. This paper presents a benchmarking study of a selected list of representative Portuguese research units, based on a fairly complete set of parameters: bibliometric parameters, number of competitive projects and number of PhDs produced. The study aimed at collecting productivity and impact data from the selected research units in comparable conditions i.e., using objective metrics based on public information, retrievable on-line and/or from official sources and thus verifiable and repeatable. The study has thus focused on the activity of the 2003-06 period, where such data was available from the latest official evaluation. The main advantage of our study was the application of automatic tools, achieving relevant results at a reduced cost. Moreover, the results over the selected units suggest that this kind of analyses will be very useful to benchmark scientific productivity and impact, and assist peer review.Comment: 26 pages, 20 figures F. Couto, D. Faria, B. Tavares, P. Gon\c{c}alves, and P. Verissimo, Benchmarking some portuguese S\&T system research units: 2nd edition, DI/FCUL TR 13-03, Department of Informatics, University of Lisbon, February 201

The relationship between internal and external loads as a tool to monitor physical fitness status of team sport athletes: a systematic review

The efficiency index (Effindex) combines internal and external loads, and it has been considered a promising tool to evaluate physical fitness status. However, its real applicability and limitations have not been elucidated yet. To examine and discuss the findings from studies that used Effindex as a tool for the evaluation of physical fitness status in team sports. A systematic search was performed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The databases conferred were PubMed, Scopus, Web of Science, SPORTDiscus, MEDLINE and CINAHL. The articles selected were published up to March 2021. Fourteen articles were included after meeting the inclusion criteria. A wide variety of combinations of external and internal loading parameters to calculate Effindex were found. The pooled sample included 349 male participants (23 ± 3years). Fifty-nine percent of the sample were soccer players, 20% rugby players, 10% Australian football players, 7% hurling players, and 4% basketball players. Most Effindex calculations used total distance (TD) divided by heart rate derived parameters. However, recent studies have suggested the use of accelerations as the external load parameter. Effindex is a simple and powerful tool for the evaluation of physical fitness status in team sports athletes. The disparity of external and internal loading parameters used to calculate Effindex may affect its sensitivity to detect changes in fitness status in different team sport settings. More studies with indoor team sports and female athletes are warranted

ProteInOn: A Web Tool for Protein Semantic Similarity

Bioinformatics arose from the need to manage and extract knowledge from the vast amount of sequence data generated by automated Molecular Biology techniques. One important step for this was the development of the Gene Ontology (GO), which provided a unified and structured vocabulary to describe proteins, and also a background to compare them, contributing to the integration of knowledge from the sequence level to the system level. Several approaches have been proposed to measure protein similarity in this context, but there are few tools for this purpose available to the scientific community. We present a new web tool, ProteInOn, focused on calculating GO-based protein semantic similarity. It features a stepwise query selection menu, which together with the possibility of selecting results as input for new queries, makes it flexible and customizable. It also incorporates data on protein interactions, allowing for comparative studies between protein similarity and interactions. The tool implements a preliminary weighting factor which increases the specificity of existing semantic similarity measures, and a score for measuring the representativeness of a GO term within a set of proteins. ProteInOn is available at: http://xldb.fc.ul.pt/biotools/proteinon

Phospholipase C2 Affects MAMP-Triggered Immunity by Modulating ROS Production

The activation of phosphoinositide-specific phospholipase C (PI-PLC) is one of the earliest responses triggered by the recognition of several microbe-associated molecular patterns (MAMPs) in plants. The Arabidopsis (Arabidopsis thaliana) PI-PLC gene family is composed of nine members. Previous studies suggested a role for PLC2 in MAMP-triggered immunity, as it is rapidly phosphorylated in vivo upon treatment with the bacterial MAMP flg22. Here, we analyzed the role of PLC2 in plant immunity using an artificial microRNA to silence PLC2 expression in Arabidopsis. We found that PLC2-silenced plants are more susceptible to the type III secretion system-deficient bacterial strain Pseudomonas syringae pv tomato (Pst) DC3000 hrcC− and to the nonadapted pea (Pisum sativum) powdery mildew Erysiphe pisi. However, PLC2-silenced plants display normal susceptibility to virulent (Pst DC3000) and avirulent (Pst DC3000 AvrRPM1) P. syringae strains, conserving typical hypersensitive response features. In response to flg22, PLC2-silenced plants maintain wild-type mitogen-activated protein kinase activation and PHI1, WRKY33, and FRK1 immune marker gene expression but have reduced reactive oxygen species (ROS)-dependent responses such as callose deposition and stomatal closure. Accordingly, the generation of ROS upon flg22 treatment is compromised in the PLC2-defficient plants, suggesting an effect of PLC2 in a branch of MAMP-triggered immunity and nonhost resistance that involves early ROS-regulated processes. Consistently, PLC2 associates with the NADPH oxidase RBOHD, suggesting its potential regulation by PLC2

Toward systems-informed models for biologics disposition: covariates of the abundance of the neonatal Fc Receptor (FcRn) in human tissues and implications for pharmacokinetic modelling

Biologics are a fast-growing therapeutic class, with intertwined pharmacokinetics and pharmacodynamics, affected by the abundance and function of the FcRn receptor. While many investigators assume adequacy of classical models, such as allometry, for pharmacokinetic characterization of biologics, advocates of physiologically-based pharmacokinetics (PBPK) propose consideration of known systems parameters that affect the fate of biologics to enable a priori predictions, which go beyond allometry. The aim of this study was to deploy a systems-informed modelling approach to predict the disposition of Fc-containing biologics. We used global proteomics to quantify the FcRn receptor [p51 and β2-microglobulin (B2M) subunits] in 167 samples of human tissue (liver, intestine, kidney and skin) and assessed covariates of its expression. FcRn p51 subunit was highest in liver relative to other tissues, and B2M was 1–2 orders of magnitude more abundant than FcRn p51 across all sets. There were no sex-related differences, while higher expression was confirmed in neonate liver compared with adult liver. Trends of expression in liver and kidney indicated a moderate effect of body mass index, which should be confirmed in a larger sample size. Expression of FcRn p51 subunit was approximately 2-fold lower in histologically normal liver tissue adjacent to cancer compared with healthy liver. FcRn mRNA in plasma-derived exosomes correlated moderately with protein abundance in matching liver tissue, opening the possibility of use as a potential clinical tool. Predicted effects of trends in FcRn abundance in healthy and disease (cancer and psoriasis) populations using trastuzumab and efalizumab PBPK models were in line with clinical observations, and global sensitivity analysis revealed endogenous IgG plasma concentration and tissue FcRn abundance as key systems parameters influencing exposure to Fc-conjugated biologics

Metrics for GO based protein semantic similarity: a systematic evaluation

<p>Abstract</p> <p>Background</p> <p>Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best approach to semantic similarity in this context, since there is no conclusive evaluation of the various measures. Another issue, is whether electronic annotations should or not be used in semantic similarity calculations.</p> <p>Results</p> <p>We conducted a systematic evaluation of GO-based semantic similarity measures using the relationship with sequence similarity as a means to quantify their performance, and assessed the influence of electronic annotations by testing the measures in the presence and absence of these annotations. We verified that the relationship between semantic and sequence similarity is not linear, but can be well approximated by a rescaled Normal cumulative distribution function. Given that the majority of the semantic similarity measures capture an identical behaviour, but differ in resolution, we used the latter as the main criterion of evaluation.</p> <p>Conclusions</p> <p>This work has provided a basis for the comparison of several semantic similarity measures, and can aid researchers in choosing the most adequate measure for their work. We have found that the hybrid <it>simGIC</it> was the measure with the best overall performance, followed by Resnik's measure using a best-match average combination approach. We have also found that the average and maximum combination approaches are problematic since both are inherently influenced by the number of terms being combined. We suspect that there may be a direct influence of data circularity in the behaviour of the results including electronic annotations, as a result of functional inference from sequence similarity.</p

Discovery of very high energy gamma rays from PKS 1424+240 and multiwavelength constraints on its redshift

We report the first detection of very-high-energy (VHE) gamma-ray emission above 140 GeV from PKS 1424+240, a BL Lac object with an unknown redshift. The photon spectrum above 140 GeV measured by VERITAS is well described by a power law with a photon index of 3.8 +- 0.5_stat +- 0.3_syst and a flux normalization at 200 GeV of (5.1 +- 0.9_stat +- 0.5_syst) x 10^{-11} TeV^-1 cm^-2 s^-1, where stat and syst denote the statistical and systematical uncertainty, respectively. The VHE flux is steady over the observation period between MJD 54881 and 55003 (2009 February 19 to June 21). Flux variability is also not observed in contemporaneous high energy observations with the Fermi Large Area Telescope (LAT). Contemporaneous X-ray and optical data were also obtained from the Swift XRT and MDM observatory, respectively. The broadband spectral energy distribution (SED) is well described by a one-zone synchrotron self-Compton (SSC) model favoring a redshift of less than 0.1. Using the photon index measured with Fermi in combination with recent extragalactic background light (EBL) absorption models it can be concluded from the VERITAS data that the redshift of PKS 1424+240 is less than 0.66.Comment: accepted for publication, Ap

Effects of carbonated water injection on the pore system of a carbonate rock (coquina)

CO2 injection is a well-known Enhanced Oil Recovery (EOR) technique that has been used for years to improve oil extraction from carbonate rock and other oil reservoirs. Optimal functioning of CO2 injection requires a thorough understanding of how this method affects the petrophysical properties of the rocks. We evaluated pore-scale changes in these properties, notably porosity and absolute permeability, following injection of CO2-saturated water in two coquina outcrop samples from the Morro do Chaves Formation in Brazil. The coquinas are close analogues of Pre-salt oil reservoirs off the coast of southern Brazil. The effects of carbonated water injection were evaluated using a series of experimental and numerical steps before and after coreflooding: cleaning, basic petrophysics, microtomography (microCT) imaging, nuclear magnetic resonance (NMR) analyses, and pore network modeling (PNM). Our study was motivated by an earlier experiment which did not show the development of a wormhole in the center of the sample, with a concomitant increase in permeability of the coquina as often noted in the literature. We instead observed a substantial decrease in the absolute permeability (between 71 and 77%), but with little effect on the porosity and no wormhole formation. While all tests were carried out on both samples, here we present a comprehensive analysis for one of the samples to illustrate changes at the pore network level. Different techniques were used for the pore-scale analyses, including pore network modeling using PoreStudio, and software developed by the authors to enable a statistical analysis of the pore network. Results provided much insight in how injected carbonated water affects the pore network of carbonate rocks

A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation

The establishment of nitrogen-fixing root nodules in legume-rhizobia symbiosis requires an intricate communication between the host plant and its symbiont. We are, however, limited in our understanding of the symbiosis signaling process. In particular, how membrane-localized receptors of legumes activate signal transduction following perception of rhizobial signaling molecules has mostly remained elusive. To address this, we performed a coimmunoprecipitation-based proteomics screen to identify proteins associated with Nod factor receptor 5 (NFR5) in Lotus japonicus. Out of 51 NFR5-associated proteins, we focused on a receptor-like cytoplasmic kinase (RLCK), which we named NFR5-interacting cytoplasmic kinase 4 (NiCK4). NiCK4 associates with heterologously expressed NFR5 in Nicotiana benthamiana, and directly binds and phosphorylates the cytoplasmic domains of NFR5 and NFR1 in vitro. At the cellular level, Nick4 is coexpressed with Nfr5 in root hairs and nodule cells, and the NiCK4 protein relocates to the nucleus in an NFR5/NFR1-dependent manner upon Nod factor treatment. Phenotyping of retrotransposon insertion mutants revealed that NiCK4 promotes nodule organogenesis. Together, these results suggest that the identified RLCK, NiCK4, acts as a component of the Nod factor signaling pathway downstream of NFR5

A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular clusters. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices $(0.7 < \Gamma <1.4)$ and clear evidence for an exponential cut-off in the range 1.0-2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices $(1.0 < \Gamma < 1.7)$, however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600-4700 MSPs in Galactic globular clusters, commensurate with previous estimates. The observation of high-energy gamma-ray emission from a globular cluster thus provides a reliable independent method to assess their millisecond pulsar populations that can be used to make constraints on the original neutron star X-ray binary population, essential for understanding the importance of binary systems in slowing the inevitable core collapse of globular clusters.Comment: Accepted for publication in A&A. Corresponding authors: J. Kn\"odlseder, N. Webb, B. Pancraz