A Grid-based solution for management and analysis of microarrays in distributed experiments

Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip® Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper

Use of a Plasma-Sprayed Titanium-Hydroxyapatite Femoral Stem in Hip Arthroplasty in Patients Older than 70 Years. Is Cementless Fixation a Reliable Option in the Elderly?

Background: Although cementless implants are increasing in popularity, the use of cementless femoral stems for total hip arthroplasty (THA) and hip hemiarthroplasty (HH) in elderly patients remains controversial. The aim of this study was to report the outcomes of a cementless stem used in a large multicentric cohort of elderly patients receiving elective THA and HH for displaced femoral neck fracture. Methods: A total of 293 patients (301 hips) aged 70 years or older (mean age, 78 years; range, 70–93) who received the same cementless plasma-sprayed porous titanium–hydroxyapatite stem were retrospectively evaluated after primary THA and HH to investigate stem survival, complications, and clinical and radiographic results. Results: Cumulative stem survival was 98.5% (95% CI, 96.4–99.4%; 91 hips at risks) with revision due to any reason as the end-point at 10-year follow-up (mean 8.6 years, range 4–12). No stem was revised due to aseptic loosening. The mean Forgotten Joint Score was 98.7. Radiographically, the implants showed complete osseointegration, with slight stress-shieling signs in less than 10% of the hips. Conclusion: The use of cementless stems was proven to be a reliable and versatile option even in elderly patients for elective THA and HH for femoral neck fracture

Subcutaneous Ticks in Wild Carnivores: Any Host-Related Differences?

SIMPLE SUMMARY: Ticks are obligate parasites living part of their life attached on the skin surface of different mammal species. In the last decades, there have been several reports of ticks found dead underneath the skin of foxes, raccoon dogs, golden jackals, domestic dogs, and a human being. The biological reasons behind this phenomenon are still unclear, although most of the reports are in canid species, suggesting that the immunological response of canids might favor it. The aim of this study was to investigate the presence of ticks under the skin of different wild carnivore species in Northwestern Italy, where they have never been described before. Out of 63 wild carnivores, 11 foxes were found infested with 51 dead ticks under the skin of the animals. All the preserved ticks collected underneath the skin of the foxes were identified as Ixodes spp., meaning that this tick species might be more frequently involved in the phenomenon, as already suggested by the scientific community. By contrast, no subcutaneous ticks were found in wolves, the other most prevalent wild canid species in Northwestern Italy, supporting the idea that the immune reaction of wolves may not favor the embedment of ticks underneath the skin. ABSTRACT: Ticks under the skin have been shown in different canid species such as red fox, domestic dog, and raccoon dog. Despite being increasingly reported in Europe in the last decade, the biological mechanisms associated to subcutaneous ticks (SCT), as well as the predisposing factors, are not yet clear. The main goal of this study was to investigate the presence of SCT in wild carnivores in Northwestern Italy. Sixty-three wild carnivores were examined, and SCT were submitted to histological examination or stored in ethanol for morphological and molecular identification. A portion of the cox1 gene and 16S rDNA were amplified, and positive PCR products were sequenced. Fifty-one small brown-coloured nodules of about 2 × 3 mm containing ticks in different decomposition stages were observed in 11 out of 30 foxes. Seven ticks were classified as Ixodes ricinus, while 14 ticks were determined only at the genus level (Ixodes spp.), and in two ticks no morphological key was applicable due to the advanced degradation status. By PCR, the rDNA fragment of six ticks (26.1%, 95% CI: 12.6–46.5%) was amplified, and BLAST analysis revealed a 99–100% nucleotide similarity to I. ricinus. At the histological examination, the inflammatory response varied from a mild to a moderate mixed infiltrate, primarily composed by neutrophils and lymphocytes. The results of this study confirm foxes as the main wild reservoir for SCT. The absence of SCT in other carnivores (badgers and martens) is in accordance with other studies. Ixodes ricinus is the most frequently reported tick species, corroborating the idea that longirostral ticks might be more frequently associated to SC embedment than brevirostral ticks

Case-report: Massive infection by Cysticercus longicollis in a captive Lemur catta from Italy

An adult male ring-tailed lemur (Lemur catta) from a biopark of northern Italy was submitted to necropsy. A multi-organ parasitic infection was macroscopically evident. Abundant sero-hemorrhagic fluid with larval parasites was present in all cavities. The microscopic evaluation of parasites and the molecular characterization revealed the presence of Cysticercus longicollis (the larval stage of Taenia crassiceps). Histology of liver, lungs, intestine and urinary bladder revealed several larval parasites surrounded by a severe lymphocytic infiltrate, fibrous tissue and hemorrhages. This is the first report of a ring-tailed lemur with an infection of C. longicollis in Italy. The source of infection is still not known however, the discovery of this parasite in a captive lemur poses more attention on the control of parasitic diseases implementing monitoring tests and biosecurity measures

Exceptional Response in BRAF p.V600E-Mutant Enteric-Type Adenocarcinoma of the Lung With Cutaneous Spread: A Case Report

Background: Enteric-type adenocarcinoma of the lung (lung-ETAC) is a rare form of lung cancer with histologic similarities to colorectal cancer, with aggressive behavior and unfavorable prognosis. Case presentation: An 81-year-old man presented with discolored skin lesions on the chest and abdomen. After comprehensive evaluation, including skin biopsy and molecular profiling, the patient was diagnosed with having lung-ETAC with a BRAF p.V600E mutation. Treatment with dabrafenib and trametinib initially resulted in positive results, with improvement in skin lesions and overall clinical condition. Nevertheless, approximately 6 months after, the disease had progression with new skin lesions reappearing. Conclusions: We reported a unique case of a patient with BRAF p.V600E-mutant lung-ETAC with metastatic skin lesions achieving complete cutaneous response after targeted treatment with dabrafenib and trametinib, highlighting the potential for targeted therapy in patients with lung-ETAC harboring a BRAF p.V600E mutation

A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data

<p>Abstract</p> <p>Background</p> <p>Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order to analyze microarray data. Two of the most known free analysis software packages are the R-based Bioconductor and dChip. The part of dChip software concerning the calculation and the analysis of gene expression has been modified to permit its execution on both cluster environments (supercomputers) and Grid infrastructures (distributed computing).</p> <p>This work is not aimed at replacing existing tools, but it provides researchers with a method to analyze large datasets without any hardware or software constraints.</p> <p>Results</p> <p>An application able to perform the computation and the analysis of gene expression on large datasets has been developed using algorithms provided by dChip. Different tests have been carried out in order to validate the results and to compare the performances obtained on different infrastructures. Validation tests have been performed using a small dataset related to the comparison of HUVEC (Human Umbilical Vein Endothelial Cells) and Fibroblasts, derived from same donors, treated with IFN-α.</p> <p>Moreover performance tests have been executed just to compare performances on different environments using a large dataset including about 1000 samples related to Breast Cancer patients.</p> <p>Conclusion</p> <p>A Grid-enabled software application for the analysis of large Microarray datasets has been proposed. DChip software has been ported on Linux platform and modified, using appropriate parallelization strategies, to permit its execution on both cluster environments and Grid infrastructures. The added value provided by the use of Grid technologies is the possibility to exploit both computational and data Grid infrastructures to analyze large datasets of distributed data. The software has been validated and performances on cluster and Grid environments have been compared obtaining quite good scalability results.</p

Risk of Hospitalization and Death for COVID-19 in People with Parkinson's Disease or Parkinsonism

The risk of COVID-19 and related death in people with Parkinson's disease or parkinsonism is uncertain. The aim of the study was to assess the risk of hospitalization for COVID-19 and death in a cohort of patients with Parkinson's disease or parkinsonism compared with a control population cohort, during the epidemic bout (March-May 2020) in Bologna, northern Italy

Analysis of the correlations between the severity of lung involvement and olfactory psychophysical scores in coronavirus disease 2019 (COVID-19) patients

Interstitial pneumonia is an important complication of COVID-19 and a reliable negative prognostic factor. This study aimed to analyze the correlation between olfactory psychophysical scores and severity of lung involvement detected by chest computed tomography in COVID-19 patients suspected of having interstitial pneumonia. We also evaluated whether severity of respiratory disease predicted recovery of olfactory dysfunction