Spontaneous chirality via long-range electrostatic forces

We consider a model for periodic patterns of charges constrained over a cylindrical surface. In particular we focus on patterns of chiral helices, achiral rings or vertical lamellae, with the constraint of global electroneutrality. We study the dependence of the patterns' size and pitch angle on the radius of the cylinder and salt concentration. We obtain a phase diagram by using numerical and analytic techniques. For pure Coulomb interactions, we find a ring phase for small radii and a chiral helical phase for large radii. At a critical salt concentration, the characteristic domain size diverges, resulting in macroscopic phase segregation of the components and restoring chiral symmetry. We discuss possible consequences and generalizations of our model.Comment: Revtex, 4 pages, 4 figure

ITSoneDB: a reliable resource for the investigation of the human mycobiome

Aim: In the last ten years the human microbiome investigation has raised a constantly increasing interest both in the scientific community and in public opinion. The gained evidences have clearly defined how it deeply influences both the physiological and pathological processes. Even if most of the attention was focused on prokaryotes, more recently the survey of fungal communities, the so called mycobiome [1], gained momentum. In this framework, the advent of Next Generation Sequencing (NGS) technologies and the DNA metabarcoding (exploits marker genes to taxonomically classify species) has allowed to rapidly and accurately investigate complex microbiomes. Regarding the mycobiome, the ITS1 (Internal Transcribed Spacer 1) of the eukaryotic ribosomal gene cluster is the most promising marker. The taxonomic annotation of microbial species relies on well-curated databases. In this respect we carried out a benchmark assessment of ITSoneDB [2] and UNITE [3] as reference databases for the investigation of fungal communities. Method: In order to obtain an in-silico fungal mock community we have randomly drawn 1,000 fungal genomes from the Genome NCBI database. The ITS1 regions were in-silico amplified by using primersearch and an in-house developed Python script. Then, Illumina 2x250 paired end ITS1 sequence amplicons have been generated in silico by using the Art-Illumina software. The obtained mock community includes 109 Families, 163 Genera and 73 Species. The sequences have been analysed by using QIIME2 by using both ITSoneDB and UNITE as reference databases. Results: The databases performances in correctly profiling the mycobiome relative abundances have been assessed at Family, Genus and Species ranks by using the Pearson correlation (R2). Both ITSoneDB and UNITE have shown a R2=1 at Family and Genera level. At the Species level ITSoneDB outperformed UNITE by obtaining more accurate results both in terms of classified sequences (Table 1) and relative abundance correlation (Figure 1). Conclusion: UNITE taxonomic assignments were very consistent at Family and Genus levels but not at species rank. Remarkably, as ITSoneDB results are consistent at every taxonomic level it represents a state of the art resource for the metabarcoding-based investigation of fungal microbial communities

A data-driven analysis of the current debate on the linkages between performance and strategy studies

This paper focuses on how the relations between performance management and measurement (PMM) and strategy are considered by scholars. These relations are crucial in building a comprehensive body of knowledge of a complex and multifaceted phenomenon which attracts scholars pertaining to different management disciplines. The results obtained by adopting quantitative methodologies (descriptive statistics and text-mining analysis) on a sample of articles recently published in the most influential international 'business, and management accounting' journals, contribute to extant literature by providing evidence that several connections exist between key-concepts which are usually considered an exclusive heritage of single management disciplines, such as strategy, organisation, management control, and so forth. For that reason, an integration of competences and methodologies is needed to support further research in the field. We also find evidence suggesting that the organisational perspective should be particularly considered when investigating the relations between strategy, management control systems and PMM

HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research

BACKGROUND: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data. RESULTS: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at . CONCLUSION: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation

Histomorphometrical evaluation of cells and tissues in contact with a new anti-wear dental implant surface: Bioloy® coating

Dental implants rehabilitation of edentulous patients is the current accepted treatment to increase prosthetic stabilization. Various implant surface modifications have been tried to enhance osseointegration and to reduce the spread of detrimental metallic ions toward host tissues [1]. The aim of this preliminary study was to investigate in vitro the viability, proliferation and adhesion of a Bioloy® (B®) coating compared to machined and sandblasted surfaces and to assess histologically in vivo the bone response to customized mini-implants coated with B® () placed in the mandible of patients. B® is a titanium niobium nitride coating applied on surface by physical vapor deposition (Permedica Spa). It is a thin ceramic monolayer, extremely hard and with high resistance against wear, scratches and corrosion [2] Viability and adhesion was tested at 24, 48 and 72 hours after seeding of SAOS-2 on customised scaffold. Cell viability (2x104 cells) was evaluated by AlamarBlue® assay [3] and it resulted statistically higher on B® than in the other 2 groups (48 and 72 hours, p-valu

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways with major ecological implications. In aquatic ecosystems, bioinvasions may cause adverse effects on the water quality resulting from changes in biological, chemical and physical properties linked to significant transformations of the microbial taxonomic and functional diversity. Here we used an effective and highly sensitive experimental strategy, bypassing the efficiency bottleneck of the traditional bacterial isolation and culturing method, to identify changes of the planktonic microbial community inhabiting a marine coastal lagoon (Varano, Adriatic Sea) under the influence of an outbreak-forming alien jellyfish species. Water samples were collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m−3; E, up to 0.03 medusae m−3) to conduct a snapshot microbiome analysis by a metagenomic approach. After extraction of the genetic material in the environmental water samples, we deep-sequenced metagenomic amplicons of the V5–V6 region of the 16S rRNA bacterial gene by an Illumina MiSeq platform. Experiments were carried out in triplicates, so six libraries of dual indexed amplicons of 420 bp were successfully sequenced on the MiSeq platform using a 2 × 250 bp paired-end sequencing strategy. Approximately 7.5 million paired-end reads (i.e. 15 million total reads) were generated, with an average of 2.5 million reads (1.25 M pairs) per sample replicate. The sequence data, analyzed through a novel bioinformatics pipeline (BioMaS), showed that the structure of the resident bacterial community was significantly affected by the occurrence of jellyfish outbreaks. Clear qualitative and quantitative differences were found between the western and eastern areas (characterized by many or few jellyfish), with 84 families, 153 genera and 324 species in the W samples, and 104 families, 199 genera and 331 species in the E samples. Significant differences between the two sampling areas were particularly detected in the occurrence of 16 families, 22 genera and 61 species of microbial taxa. This is the first time that a NGS platform has been used to screen the impact of jellyfish bioinvasions on the aquatic microbiome, providing a preliminary assessment of jellyfish-driven changes of the functional and structural microbial biodiversity

heterogeneity of large cell carcinoma of the lung an immunophenotypic and mirna based analysis

Large cell carcinomas (LCCs) of the lung are heterogeneous and may be of different cell lineages. We analyzed 56 surgically resected lung tumors classified as LCC on the basis of pure morphologic grounds, using a panel of immunophenotypic markers (adenocarcinoma [ADC]-specific, thyroid transcription factor-1, cytokeratin 7, and napsin A; squamous cell carcinoma [SQCC]–specific, p63, cytokeratin 5, desmocollin 3, and Δnp63) and the quantitative analysis of microRNA-205 (microRNA sample score [mRSS]). Based on immunoprofiles 19 (34%) of the cases were reclassified as ADC and 14 (25%) as SQCC; 23 (41%) of the cases were unclassifiable. Of these 23 cases, 18 were classified as ADC and 5 as SQCC according to the mRSS. Our data show that an extended panel of immunohistochemical markers can reclassify around 60% of LCCs as ADC or SQCC. However, a relevant percentage of LCCs may escape convincing immunohistochemical classification, and mRSS could be used for further typing, but its clinical relevance needs further confirmation. Large cell carcinoma (LCC) of the lung is 1 of 4 major histopathologic tumor subtypes recognized by current classifications of lung tumors. However, although squamous cell carcinoma (SQCC), adenocarcinoma (ADC), and small cell carcinoma are well-defined entities with typical morphologic, immunophenotypic, and molecular features, LCCs, with the exception of the rare neuroendocrine, rhabdoid, basaloid, and lymphoepithelioma-like subtypes, are defined as poorly differentiated non–small cell tumors lacking features of ADC and SQCC. Therefore, the term LCC has frequently and improperly been used as a synonym of undifferentiated non–small cell lung carcinoma (NSCLC) and has been used as a "wastebasket" for tumors lacking a definite morphologic pattern. Studies show that, by using ancillary techniques, a relevant percentage of LCCs could be reclassified as SQCC or ADC. Gene profiling shows that most LCCs have profiles quite similar to ADC or SQCC. 1-3 Similarly, by using appropriate immunohistochemical stains, almost two thirds of LCCs can be reclassified as poorly differentiated ADC or SQCC. 4,5 These studies have profound clinical relevance because rendering a diagnosis of LCC may represent a challenge for oncologists who need accurate subtyping of lung cancers to provide patients with optimal targeted chemotherapeutic agents, showing different efficacy with specific NSCLC categories (usually effective for ADC and not for others). 6,

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.; Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).; Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.Peer ReviewedPostprint (published version

Marine phycotoxin levels in shellfish-14 years of data gathered along the Italian coast

Along the Italian coasts, toxins of algal origin in wild and cultivated shellfish have been reported since the 1970s. In this study, we used data gathered by the Veterinary Public Health Institutes (IZS) and the Italian Environmental Health Protection Agencies (ARPA) from 2006 to 2019 to investigate toxicity events along the Italian coasts and relate them to the distribution of potentially toxic species. Among the detected toxins (OA and analogs, YTXs, PTXs, STXs, DAs, AZAs), OA and YTX were those most frequently reported. Levels exceeding regulatory limits in the case of OA (≤2,448 μg equivalent kg-1) were associated with high abundances of Dinophysis spp., and in the case of YTXs (≤22 mg equivalent kg-1) with blooms of Gonyaulax spinifera, Lingulodinium polyedra, and Protoceratium reticulatum. Seasonal blooms of Pseudo-nitzschia spp. occur all along the Italian coast, but DA has only occasionally been detected in shellfish at concentrations always below the regulatory limit (≤18 mg kg-1). Alexandrium spp. were recorded in several areas, although STXs (≤13,782 μg equivalent kg-1) rarely and only in few sites exceeded the regulatory limit in shellfish. Azadinium spp. have been sporadically recorded, and AZAs have been sometimes detected but always in low concentrations (≤7 μg equivalent kg-1). Among the emerging toxins, PLTX-like toxins (≤971 μg kg-1 OVTX-a) have often been detected mainly in wild mussels and sea urchins from rocky shores due to the presence of Ostreopsis cf. ovata. Overall, Italian coastal waters harbour a high number of potentially toxic species, with a few HAB hotspots mainly related to DSP toxins. Nevertheless, rare cases of intoxications have occurred so far, reflecting the whole Mediterranean Sea conditions