Neighborhood Counting Measure Metric and Minimum Risk Metric: An empirical comparison

Wang in a PAMI paper proposed Neighborhood Counting Measure (NCM) as a similarity measure for the k-nearest neighbors classification algorithm. In his paper, Wang mentioned Minimum Risk Metric (MRM) an earlier method based on the minimization of the risk of misclassification. However, Wang did not compare NCM with MRM because of its allegedly excessive computational load. In this letter, we empirically compare NCM against MRM on k-NN with k=1, 3, 5, 7 and 11 with decision taken with a voting scheme and k=21 with decision taken with a weighted voting scheme on the same datasets used by Wang. Our results shows that MRM outperforms NCM for most of the k values tested. Moreover, we show that the MRM computation is not so probihibitive as indicated by Wang. ©2009 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE

Total ankle replacement in young patients

High physical demand and younger age are currently considered contraindications for total ankle replacement. The number of Total Ankle Replacements (TAR) is widespread increasing and indications are expanding thanks to a steady improvement in prosthetic designs and better outcome. Commentary of the literature: in 1999 a study of 100 uncemented STAR\u2122 (Waldemar-Link, Hamburg, Germany) prostheses showed a survival rate of 75% at 6.8 years in patients under 50 years old. Other studies (es, Barg et Al.) shows the risk of failure age-related in young patients compared to older group. A report of 780 TAR from the Swedish Ankle Register showed patients with primary or post-traumatic osteoarthritis under  60 years of age to have a 1.8 higher chance of revision compared to older patients. Discussion: ankle replacement has been traditionally reserved for patients older 50 years old and with low physical demand. Contrariwise this belief, TAR have already been used with a wide range of ages, sometimes even patients younger than 30 years old. Most of the "negative" score and results showed before are related to "second-generation" prosthetic designs, while recent studies used a "third-generation" prosthetic design. Conclusions: recent evidences showed better clinical results and higher satisfaction in people under the age of 50 compared to ankle arthrodesis with comparable rate of complications and survivorship. Younger people will have however a higher rate of reoperation but in the meantime, they will prevent progressive degeneration of adjacent joints

New perspectives in vaccination and immunotherapies for HBV infections

AbstractThe woodchuck hepatitis B virus (WHV), the closest genetically related virus of HBV, and its natural host Marmota monax constitute a well recognized animal model. The application of this model for the evaluation of immunogenicity and protection of new formulations of HBV vaccines for human use, for lamivudine-CHO-PreS/S vaccine therapy and WHV particles coupled with HBV derived woodchuck PreS/S antibodies (IC complex) studies, as shown that the PreS/S-CHO vaccine is the first human vaccine able to elicit non sterilizing protection in the woodchuck model. The very early appearance and selection of the domain B FLLA motif resistant mutant not neutralized by the antibodies produced following vaccination, has confirmed that more potent antivirals and/or multiple targeted options with possible inclusion of immune complexes should be considered

Surface and Aerodynamic Parameters Estimation for Urban and Rural Areas

Numerical weather prediction models require an accurate parametrization of the energy budget at the air-ground interface, that can be obtained only through long-term atmospheric boundary layer measurements at different spatial and temporal scales. Despite their importance, such measurements are still scarce even in well-characterized areas. In this paper, a three-year dataset from four micrometeorological stations run by the Regional Agency for Environmental Protection of Lazio was analyzed to estimate albedo, zero-displacement height, roughness length and surface properties over Rome and its suburbs, characterizing differences and interconnections between urban, suburban and rural areas of the same municipality. The integral albedo coefficient at the zenith for the urban station was found to be almost twice that for suburban and rural stations. The zero-displacement height of the urban site was strongly dependent on wind direction, with values varying between 12.0 and 17.8 m, while the roughness length (≈1.5 m) was almost independent of upwind direction, but it was significantly higher than the typical values calculated for rural stations (≈0.4 m). The apparent thermal capacities and thermal conductivity at all the non-urban sites were in fair agreement with each other and typical of soils with relatively low water content, as expected for a relatively dry Mediterranean area like Rome, while the apparent thermal diffusivity reflected the presence of different soil types

Simple peptide quantification approach for MS-based proteomics quality control

Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 mu L of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 mu g as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control

Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.We thank GenProbio srl for the financial support of the Laboratory of Probiogenomics. Part of this research is conducted using the High Performance Computing (HPC) facility of the University of Parma. D.v.S. is a member of The APC Microbiome Institute funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (Grant numbers SFI/12/RC/2273a and SFI/12/RC/2273b). This work was financially supported by a PostDoc fellowship (Bando Ricerca Finalizzata) to G.A. F.T. is funded by Italian Ministry of Health through the Bando Ricerca Finalizzata (Grant Number GR-2018-12365988)

Clinical, anamnestic, and sociodemographic predictors of positive SARS-CoV-2 testing in children: A cross sectional study in a tertiary hospital in Italy

ObjectivesWe aimed to identify clinical, anamnestic, and sociodemographic characteristics associated with a positive swab for SARS-CoV2, and to provide a predictive score to identify at risk population in children aged 2-14 years attending school and tested for clinical symptoms of COVID-19.DesignCross sectional study.SettingOutpatient clinic of the IRCCS Burlo Garofolo, a maternal and child health tertiary care hospital and research centre in Italy.Data collection and analysisData were collected through a predefined form, filled out by parents, and gathered information on sociodemographic characteristics, and specific symptoms, which were analysed to determine their association with a positive SARS-CoV-2 swab. The regression coefficients of the variables included in the multivariate analysis were further used in the calculation of a predictive score of the positive or negative test.ResultsBetween September 20th and December 23rd 2020, from 1484 children included in the study, 127 (8.6%) tested positive. In the multivariate analysis, the variables retained by the model were the presence of contact with a cohabiting, non-cohabiting or unspecified symptomatic case (respectively OR 37.2, 95% CI 20.1-68.7; 5.1, 95% CI 2.7-9.6; 15.6, 95% CI 7.3-33.2); female sex (OR 1.49, 95% CI 1.0-2.3); age (6-10 years old: OR 3.2, 95% CI 1.7-6.1 p<0.001; >10 years old: OR 4.8, 95% CI 2.7-8.8 p<0.001); fever (OR 3.9, 95% CI 2.3-6.4); chills (OR 1.9, 95% CI 1.1-3.3); headache (OR 1.45, 95% CI 0.9-2.4); ageusia (OR 1.3, 95% CI 0.54.0); sore throat (OR 0.48, 95% CI 0.3-0.8); earache (OR 0.4, 95% CI 0.1-1.3); rhinorrhoea (OR 0.8, 95% CI 0.5-1.3); and diarrhoea (OR 0.52, 95% CI 0.2-1.1). The predictive score based on these variables generated 93% sensitivity and 99% negative predictive value.ConclusionsThe timely identification of SARS-CoV2 cases among children is useful to reduce the dissemination of the disease and its related burden. The predictive score may be adopted in a public health perspective to rapidly identify at risk children

Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach

The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings

Genetic strategies for sex-biased persistence of gut microbes across human life

Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.We thank GenProbio Srl for the financial support of the Laboratory of Probiogenomics. Part of this research is conducted using the High- Performance Computing (HPC) facility of the University of Parma. This research has financially been supported by the Programme “FIL-Quota Incentivante” of University of Parma and co-sponsored by Fondazione Cariparma”. D.v.S. is a member of APC Microbiome Ireland funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan (Grant no. SFI/12/RC/2273-P1 and SFI/12/RC/ 2273-P2). G.T. has been supported by “Fondazione Cariparma” in the framework of the project entitled “Parma Microbiota”. LMV has been supported by by “Programma Operativo Nazionale 2014–2020 of the Italian Ministry of University and Research. The funding from Project AGL2017-83653R (Spanish “Ministerio de Ciencia, Innovación y Universidades (MCIU)”, “Agencia Estatal de Investigación (AEI)” and FEDER) is also acknowledged

First Results of the “Carbonaceous Aerosol in Rome and Environs (CARE)” Experiment: Beyond Current Standards for PM10

In February 2017 the “Carbonaceous Aerosol in Rome and Environs (CARE)” experiment was carried out in downtown Rome to address the following specific questions: what is the color, size, composition, and toxicity of the carbonaceous aerosol in the Mediterranean urban background area of Rome? The motivation of this experiment is the lack of understanding of what aerosol types are responsible for the severe risks to human health posed by particulate matter (PM) pollution, and how carbonaceous aerosols influence radiative balance. Physicochemical properties of the carbonaceous aerosol were characterised, and relevant toxicological variables assessed. The aerosol characterisation includes: (i) measurements with high time resolution (min to 1–2 h) at a fixed location of black carbon (eBC), elemental carbon (EC), organic carbon (OC), particle number size distribution (0.008–10 μ m), major non refractory PM1 components, elemental composition, wavelength-dependent optical properties, and atmospheric turbulence; (ii) 24-h measurements of PM10 and PM2.5 mass concentration, water soluble OC and brown carbon (BrC), and levoglucosan; (iii) mobile measurements of eBC and size distribution around the study area, with computational fluid dynamics modeling; (iv) characterisation of road dust emissions and their EC and OC content. The toxicological assessment includes: (i) preliminary evaluation of the potential impact of ultrafine particles on lung epithelia cells (cultured at the air liquid interface and directly exposed to particles); (ii) assessment of the oxidative stress induced by carbonaceous aerosols; (iii) assessment of particle size dependent number doses deposited in different regions of the human body; (iv) PAHs biomonitoring (from the participants into the mobile measurements). The first experimental results of the CARE experiment are presented in this paper. The objective here is to provide baseline levels of carbonaceous aerosols for Rome, and to address future research directions. First, we found that BC and EC mass concentration in Rome are larger than those measured in similar urban areas across Europe (the urban background mass concentration of eBC in Rome in winter being on average 2.6 ± 2.5 μ g · m − 3 , mean eBC at the peak level hour being 5.2 (95% CI = 5.0–5.5) μ g · m − 3 ). Then, we discussed significant variations of carbonaceous aerosol properties occurring with time scales of minutes, and questioned on the data averaging period used in current air quality standard for PM 10 (24-h). Third, we showed that the oxidative potential induced by aerosol depends on particle size and composition, the effects of toxicity being higher with lower mass concentrations and smaller particle size. Albeit this is a preliminary analysis, findings reinforce the need for an urgent update of existing air quality standards for PM 10 and PM 2.5 with regard to particle composition and size distribution, and data averaging period. Our results reinforce existing concerns about the toxicity of carbonaceous aerosols, support the existing evidence indicating that particle size distribution and composition may play a role in the generation of this toxicity, and remark the need to consider a shorter averaging period (<1 h) in these new standards