A distributed approach for parameter estimation in Systems Biology models

Due to the lack of experimental measurements, biological variability and experimental errors, the value of many parameters of the systems biology Mathematical models is yet unknown or uncertain. A possible computational solution is the parameter estimation, that is the identification of the parameter values that determine the best model fitting respect to experimental data. We have developed an environment to distribute each run of the parameter estimation algorithm on a different computational resource. The key feature of the implementation is a relational database that allows the user to swap the candidate solutions among the working nodes during the computations. The comparison of the distributed implementation with the parallel one showed that the presented approach enables a faster and better parameter estimation of systems biology models

Synergistic cytotoxicity and pharmacogenetics of gemcitabine and pemetrexed combination in pancreatic cancer cell lines

PURPOSE: Gemcitabine is an inhibitor of ribonucleotide reductase (RR) and DNA synthesis and is an effective agent in the treatment of pancreas cancer. The present study investigates whether the multitargeted antifolate pemetrexed would be synergistic with gemcitabine against MIA PaCa-2, PANC-1, and Capan-1 pancreatic cancer cell lines. EXPERIMENTAL DESIGN: Cells were treated with gemcitabine and pemetrexed, and the type of drug interaction was assessed using the combination index. Cytotoxicity of gemcitabine was examined with inhibitors of (a) deoxycytidine kinase (dCK), which activates gemcitabine by phosphorylation, and (b) 5'-nucleotidase (drug dephosphorylation) and cytidine deaminase (drug deamination), the main inactivating enzymes. The effects of gemcitabine and pemetrexed on cell cycle were analyzed by flow cytometry, and apoptosis was examined by fluorescence microscopy. Finally, quantitative, real-time PCR was used to study the pharmacogenetics of the drug combination. RESULTS: Synergistic cytotoxicity and enhancement of apoptosis was demonstrated, mostly with the sequence pemetrexed-->gemcitabine. Pemetrexed increased cells in S phase, the most sensitive to gemcitabine, and a positive correlation was found between the expression ratio of dCK:RR and gemcitabine sensitivity. Indeed, pemetrexed significantly enhanced dCK gene expression (+227.9, +86.0, and +135.5% in MIA PaCa-2, PANC-1, and Capan-1 cells, respectively), and the crucial role of this enzyme was confirmed by impairment of gemcitabine cytotoxicity after dCK saturation with 2'-deoxycytidine. CONCLUSIONS: These data demonstrate that the gemcitabine and pemetrexed combination displays schedule-dependent synergistic cytotoxic activity, favorably modulates cell cycle, induces apoptosis, and enhances dCK expression in pancreatic cancer cells

Approximating Fractional Time Quantum Evolution

An algorithm is presented for approximating arbitrary powers of a black box unitary operation, $\mathcal{U}^t$, where $t$ is a real number, and $\mathcal{U}$ is a black box implementing an unknown unitary. The complexity of this algorithm is calculated in terms of the number of calls to the black box, the errors in the approximation, and a certain `gap' parameter. For general $\mathcal{U}$ and large $t$, one should apply $\mathcal{U}$ a total of $\lfloor t \rfloor$ times followed by our procedure for approximating the fractional power $\mathcal{U}^{t-\lfloor t \rfloor}$. An example is also given where for large integers $t$ this method is more efficient than direct application of $t$ copies of $\mathcal{U}$. Further applications and related algorithms are also discussed.Comment: 13 pages, 2 figure

SNPRanker: a tool for identification and scoring of SNPs associated to target genes

Summary The identification of genes and SNPs involved in human diseases remains a challenge. Many public resources, databases and applications, collect biological data and perform annotations, increasing the global biological knowledge. The need of SNPs prioritization is emerging with the development of new high-throughput genotyping technologies, which allow to develop customized disease-oriented chips. Therefore, given a list of genes related to a specific biological process or disease as input, a crucial issue is finding the most relevant SNPs to analyse. The selection of these SNPs may rely on the relevant a-priori knowledge of biomolecular features characterising all the annotated SNPs and genes of the provided list. The bioinformatics approach described here allows to retrieve a ranked list of significant SNPs from a set of input genes, such as candidate genes associated with a specific disease. The system enriches the genes set by including other genes, associated to the original ones by ontological similarity evaluation. The proposed method relies on the integration of data from public resources in a vertical perspective (from genomics to systems biology data), the evaluation of features from biomolecular knowledge, the computation of partial scores for SNPs and finally their ranking, relying on their global score. Our approach has been implemented into a web based tool called SNPRanker, which is accessible through at the URL http://www.itb.cnr.it/snpranker. An interesting application of the presented system is the prioritisation of SNPs related to genes involved in specific pathologies, in order to produce custom arrays

A Business Process Reengineering of the Surgical Path through Lean Technique: The Real Case Study of a Midsize Italian Hospital

This period of pandemic has had important consequences on the flow and the entire organization of any hospital. In particular, the number of accesses to the emergency room has increased, with the consequent urgent need to reorgani ze it quickly. The model proposed in this paper allows to respond to these needs by freeing not only shifts of nursing staff but also surgical staff. This workforce can then be relocated in the emergency room or of the intensive care unit who are in fact at the forefront of emergency management. The aim of this study conducted by the authors is to analyze, inside the context of a midsize Italian hospital, the actual organization model, and then to approach it by Business Process Reengineering (BPR) methodology with the goal to propose a KPI management system that evaluates the efficiency of the whole surgical path. The second objective of the study is to verify if the Operating Rooms (ORs) are properly sized to cover the surgical workload or if it would be necessary to build new ORs (answer to this question is the project mandate by Surgical Wards Chiefs). The last objective is to implement a flexible to cope with emergency situations such as a pandemic. The main result is the approximate maintenance of surgical annual activity (8169 vs 7889). The fewer resources required can be reallocated to deal with emergencies such as the current COVID-19 pandemic. In fact, the surgical shifts decreased during the test case from 464 versus 365 (-15,32%). The rooms’ utilization coefficient rose from 41% to over 52%, whereas the surgeons’ utilization coefficient rose to 61% (with values over 68% for parallel shifts). The results achieved demonstrate that improving efficiency of surgical processes is feasible and a systematic approach allows to respond to new global health challenges

The cell cycle DB: a systems biology approach to cell cycle analysis

The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly. The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models

Fetal Doppler changes one week after endoscopic equatorial laser for twin-to-twin transfusion syndrome: a longitudinal study

Objective: To investigate sequential Doppler changes in donors and recipients before and 1 week after endoscopic laser for twin\u2010to\u2010twin transfusion syndrome (TTTS) and to examine factors that may be associated with such changes. Methods: In TTTS pregnancies undergoing laser treatment, we examined fetal Doppler changes before and 1 week postintervention. Intrauterine death rates and preoperative factors were analyzed in relation to Doppler changes. Results: Among 129 (85.4%) donors surviving at 1 week after laser, there was normalization of umbilical artery flow in 26 (72.2%) of 36 cases with preoperative abnormal Dopplers. In the remaining 10 (27.8%) fetuses, abnormal findings persisted. The rate of later intrauterine death was significantly higher in the latter group (6 of 10, 60.0%) compared with fetuses in which Doppler findings normalized (4 of 26, 15.4%; P < .05), with no difference in the rate of severe donor growth restriction between the 2 groups (80.0% vs 65.4%, respectively; P = .688). Conclusions: In about 70% of TTTS donors with preoperative abnormal umbilical artery Doppler, there was normalization 1 week after endoscopic laser. The incidence of fetal growth restriction was not significantly different in donors with persistence of Doppler abnormalities compared with those with normalized findings

Meropenem vs standard of care for treatment of neonatal late onset sepsis (NeoMero1): A randomised controlled trial.

BACKGROUND: The early use of broad-spectrum antibiotics remains the cornerstone for the treatment of neonatal late onset sepsis (LOS). However, which antibiotics should be used is still debatable, as relevant studies were conducted more than 20 years ago, recruited in single centres or countries, evaluated antibiotics not in clinical use anymore and had variable inclusion/exclusion criteria and outcome measures. Moreover, antibiotic-resistant bacteria have become a major problem in many countries worldwide. We hypothesized that efficacy of meropenem as a broad-spectrum antibiotic is superior to standard of care regimens (SOC) in empiric treatment of LOS and aimed to compare meropenem to SOC in infants aged 44 weeks meeting the Goldstein criteria of sepsis, were randomized in a 1:1 ratio to receive meropenem or one of the two SOC regimens (ampicillin+gentamicin or cefotaxime+gentamicin) chosen by each site prior to the start of the study for 8-14 days. The primary outcome was treatment success (survival, no modification of allocated therapy, resolution/improvement of clinical and laboratory markers, no need of additional antibiotics and presumed/confirmed eradication of pathogens) at test-of-cure visit (TOC) in full analysis set. Stool samples were tested at baseline and Day 28 for meropenem-resistant Gram-negative organisms (CRGNO). The primary analysis was performed in all randomised patients and in patients with culture confirmed LOS. Proportions of participants with successful outcome were compared by using a logistic regression model adjusted for the stratification factors. From September 3, 2012 to November 30th 2014, total of 136 patients (instead of planned 275) in each arm were randomized; 140 (52%) were culture positive. Successful outcome at TOC was achieved in 44/136 (32%) in the meropenem arm vs. 31/135 (23%) in the SOC arm (p = 0.087). The respective numbers in patients with positive cultures were 17/63 (27%) vs. 10/77 (13%) (p = 0.022). The main reason of failure was modification of allocated therapy. Treatment emergent adverse events occurred in 72% and serious adverse events in 17% of patients, the Day 28 mortality was 6%. Cumulative acquisition of CRGNO by Day 28 occurred in 4% of patients in the meropenem and 12% in the SOC arm (p = 0.052). CONCLUSIONS: Within this study population, we found no evidence that meropenem was superior to SOC in terms of success at TOC, short term hearing disturbances, safety or mortality were similar in both treatment arms but the study was underpowered to detect the planned effect. Meropenem treatment did not select for colonization with CRGNOs. We suggest that meropenem as broad-spectrum antibiotic should be reserved for neonates who are more likely to have Gram-negative LOS, especially in NICUs where microorganisms producing extended spectrum- and AmpC type beta-lactamases are circulating