Time to Organize the Bioinformatics Resourceome

The initial steps toward a bioinformatics resourceome are clear. First, an overall ontology with the high-level concepts (algorithms, databases, organizations, papers, people, etc.) must be created, with a set of standard attributes and a standard set of relations between these concepts (e.g., people publish papers, papers describe algorithms or databases, organizations house people, etc.). The initial ontology should be compact and built for distributed collaborative extension. Second, a mechanism for people to extend this ontology with subconcepts in order to describe their own resources should be designed. The precise location of a tool within a taxonomy is not critical—the author will place it somewhere based on the location of similar/competing resources or based on a best-informed guess. Others may create links to the resource from other appropriate locations in the taxonomy in order to ensure that competing interpretations of the appropriate conceptual location for the resource are accommodated. Third, the formats for the ontologies and the resource descriptions should be published so enterprising software engineers can create interfaces for surfing, searching, and viewing the resources. The resulting distributed system of resource descriptions would be extensible, robust, and useful to the entire biomedical research community

GoSh: a goat and sheep ESTs database.

Made available in DSpace on 2018-06-07T01:03:16Z (GMT). No. of bitstreams: 1 ID29151124.pdf: 69304 bytes, checksum: 128ac67dd2da790fae9cf4d1ab49e9df (MD5) Previous issue date: 2008-02-16bitstream/item/178254/1/ID-29151-1-2-4.pd

The status of PD-L1 and tumor-infiltrating immune cells predict resistance and poor prognosis in BRAFi-treated melanoma patients harboring mutant BRAFV600

In the present study, we have provided clinical evidence of the predictive and prognostic relevance of tumoral PD-L1 expression and density of immune cell infiltration in BRAFV600-mutated metastatic melanoma patients treated with BRAF inhibitor

Blood ozonization in patients with mild to moderate COVID-19 pneumonia: a single centre experience

The emerging outbreak of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide. We prescribed some promising medication to our patients with mild to moderate pneumonia due to SARS-CoV-2, however such drugs as chloroquine, hydrossichloroquine, azithromycin, antivirals (lopinavir/ritonavir, darunavir/cobicistat) and immunomodulating agents (steroids, tocilizumab) were not confirmed as effective against SARS-CoV2. We, therefore, started to use auto-hemotherapy treated with an oxygen/ozone (O2/O3) gaseous mixture as adjuvant therapy. In Udine University Hospital (Italy) we performed a case\u2013control study involving hospitalized adult patients with confirmed COVID-19 with mild to moderate pneumonia. Clinical presentations are based upon clinical phenotypes identified by the Italian Society of Emergency and Urgency Medicine (SIMEU\u2014Societ\ue0 Italiana di Medicina di Emergenza-Urgenza) and patients that met criteria of phenotypes 2 to 4 were treated with best available therapy (BAT), with or without O3-autohemotherapy. 60 patients were enrolled in the study: 30 patients treated with BAT and O2/O3 mixture, as adjuvant therapy and 30 controls treated with BAT only. In the group treated with O3-autohemotherapy plus BAT, patients were younger but with more severe clinical phenotypes. A decrease of SIMEU clinical phenotypes was observed (2.70 \ub1 0.67 vs. 2.35 \ub1 0.88, p = 0.002) in all patients during hospitalization but this clinical improvement\ua0was statistically significant only in O3-treated patients (2.87 \ub1 0.78 vs. 2.27 \ub1 0.83, p < 0.001), differently to the control group (2.53 \ub1 0.51 vs. 2.43 \ub1 0.93, p = 0.522). No adverse events were observed associated with the application of O2/O3 gaseous mixture. O2/O3 therapy as adjuvant therapy could be useful in mild to moderate pneumonia due to SARS-CoV-2. Randomized prospective study is ongoing [Clinical Trials.gov ID: Z7C2CA5837]

Timing of sentinel node biopsy independently predicts disease-free and overall survival in clinical stage I-II melanoma patients: A multicentre study of the Italian Melanoma Intergroup (IMI)

Background: Sentinel lymph node biopsy (SNB) still remains a key procedure to appropriately stage melanoma patients and to select those who are candidate to novel treatments with immunotherapy and targeted therapy in the adjuvant setting. The impact of timing of SNB on disease-free survival (DFS) and overall survival (OS) is still unclear. Material and methods: The study was conducted at 6 Italian Melanoma Intergroup (IMI) centres and included 8953 consecutive clinical stage I-II melanoma patients who were diagnosed, treated, and followed up between November 1997 and March 2018. All patients were prospectively included in dedicated IMI database. Multivariable Cox regression analyses were performed to investigate how baseline characteristics and time interval until SNB are related to DFS and OS. Results: Considering the whole population, at multivariable analysis, after adjusting for age, gender, Breslow thickness, site, ulceration, and the SNB status, a delay in the timing of SNB was associated with a better DFS (adjusted hazard ratio [aHR, delayed versus early SNB] 0.98, 95% confidence interval [CI] 0.97\u20130.99, p < 0.001) and OS (aHR 0.98, 95% CI 0.97\u20130.99, p = 0.001). Specifically, in patients with a negative SNB status, a beneficial impact of delayed SNB (i.e. at least 32 days after primary excision) was confirmed for DFS (aHR 0.70, 95%CI 0.63\u20130.79, p < 0.001) and OS (aHR 0.69, 95%CI 0.61\u20130.78, p < 0.001), whereas in those with a positive SNB status, DFS (aHR 0.96, 95%CI 0.84\u20131.09, p = 0.534) and OS (aHR 0.94 95%CI 0.81\u20131.08, p = 0.374) were not significantly different in patients with early or delayed SNB. Conclusions: Our study does not support a strict time interval for SNB. These results may be useful for national guidelines, for counselling patients and reducing the number of high urgency referrals

A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway