U-CHANGE Project: a multidimensional consensus on how clinicians, patients and caregivers may approach together the new urothelial cancer scenario

Introduction

Advanced urothelial carcinoma remains aggressive and very hard to cure, while new treatments will pose a challenge for clinicians and healthcare funding policymakers alike. The U-CHANGE Project aimed to redesign the current model of care for advanced urothelial carcinoma patients to identify limitations ("as is" scenario) and recommend future actions ("to be" scenario).

Methods

Twenty-three subject-matter experts, divided into three groups, analyzed the two scenarios as part of a multidimensional consensus process, developing statements for specific domains of the disease, and a simplified Delphi methodology was used to establish consensus among the experts.

Results

Recommended actions included increasing awareness of the disease, increased training of healthcare professionals, improvement of screening strategies and care pathways, increased support for patients and caregivers and relevant recommendations from molecular tumor boards when comprehensive genomic profiling has to be provided for appropriate patient selection to ad hoc targeted therapies.

Discussion

While the innovative new targeted agents have the potential to significantly alter the clinical approach to this highly aggressive disease, the U-CHANGE Project experience shows that the use of these new agents will require a radical shift in the entire model of care, implementing sustainable changes which anticipate the benefits of future treatments, capable of targeting the right patient with the right agent at different stages of the disease.

Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. An interesting prediction of our model, supported by the experimental data, is that high growth rates are not necessarily accompanied by low growth yields. The resource allocation strategies enabling high-rate, high-yield growth of E. coli lead to a higher saturation of enzymes and ribosomes, and thus to a more efficient utilization of proteomic resources. Our model thus contributes to a fundamental understanding of the quantitative relationship between rate and yield in E. coli and other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.

The national COVID-19 vaccination campaign targeting the extremely vulnerable: the Florence Medical Oncology Unit experience in patients with cancer

BACKGROUND

International and national oncology societies had released recommendations in favor of COVID-19 vaccination in cancer patients. In the context of the national vaccination campaign targeting the so called extremely vulnerable, we aimed to assess the safety and efficacy of the mRNA vaccines in a cohort of 623 patients.

METHODS

Between March 26 and April 04, 2021, the Pfizer and BioNTech BNT162b2 mRNA and the Moderna mRNA-1273 vaccines were given as a two-dose prime-boost regimen. Starting on September 25th 2021 a third dose was offered to patients in whom a suboptimal immunogenicity with COVID-19 vaccination could be expected. Safety assessments were performed by phone call 7 days after each dose. Electronic health records were accessed to review demographic information, disease history, treatment detail, and outcome events of participants patients'.

FINDINGS

No toxicities were reported in 63.7%, 54%, and in 48.7% patients with cancer after each dose. Mild-to-moderate pain at the injection site was the most commonly adverse event. After the second dose, 46% of the 610 patients reported toxicity, with more systemic side-effects observed. Fever was reported in 45% of patients, with a temperature ≥ 38 °C in 21.4% of them. Of the 335 patients receiving a third vaccine dose, 51% reported toxicity, with 13% of patients reporting more than one effect. Logistic regression analysis reported mixed results, with limited variables or categories reporting a significant odd ratio. The type of vaccine reported a significant value at first dose (OR = 0.12; CI 0.52, 0.26; p = 0.00). Thirty-four cases of COVID-19 infection were reported with only one patient requiring a short-term hospitalization for monitoring.

INTERPRETATION

The safety profile of the mRNA vaccines does not raise any specific concerns and support prioritization of vaccination for cancer patients.

Patterns of progression of patients with high-volume metastatic castration-sensitive prostate cancer treated with early docetaxel chemotherapy: The LONGITUDE observational study

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Background: In patients (pts) with high-volume (HV) metastatic castration sensitive prostate cancer (mCSPC) the addition of six cycles of docetaxel (TXT) to androgen deprivation therapy (ADT) in the CHAARTED and STAMPEDE trials prolonged survival by 10-18 months (mo). Aim of our study was to evaluate the principal patterns of relapse after TXT and their clinical and prognostic significance. Methods: We conducted a multicentric (14 Italian Centers), prospective, observational study enrolling HV mCSPC patients treated with ADT plus early TXT. Clinical and pathological features were recorded. Time to castration resistance (TCR) and overall survival (OS) were estimated by the Kaplan-Meier method and compared with the log-rank test. The Chi-Square test, t-test or Wilcoxon-Mann-Whitney test were used to assess difference between the groups as appropriate. Results: We identified 166 de novo mCSPC pts, with a median age of 64 years (range 38-84). The most common metastatic sites at diagnosis were: bone (93%) and lymph nodes (81%); visceral disease (lung and liver) was present in 36% of cases. 87% of pts had good Eastern Cooperative Oncology Group Performance Status (0-1), the median baseline PSA was 359 ng/ml (range 2.64-5800) and 43% experienced cancer pain. 87% of 158 evaluable pts had a Grade Group (GG) ³4. The majority of pts (81%) completed six cycles of TXT. The median time to PSA nadir was 10.2 months (mo), PSA response > 50% was achieved in 96% of pts and the most common best response reported was partial response (58%). At the time of this analysis, 122 pts (67%) had biochemical or radiographic progressive disease (PD) to TXT and 67 of these (60%) developing new metastatic sites (NMS). No differences with respect of main clinical features was found between NMS pts and nonNMS, with the exception of GG (96% of NMS pts had GG 4-5 vs 74% of nonNMS; p = 0.002). In NMS group we found a higher rate of nodal PD (52% vs 22%, p = 0.001) and higher rate of bone PD (73% vs 47%, p = 0.005) compared to nonNMS. No differences in the rate of visceral PD. With a median follow-up of 27.9 mo, the median TCR was 14.3 mo (95%CI 12.8-16.7), without significant differences between NMS and nonNMS groups. About 90% of progressed pts received first-line treatment for mCRPC disease with similar outcomes. The median OS was 41.8 mo for the overall population, with not significant differences between NMS and nonNMS groups (22 mo and 25 mo). Overall, median OS from mCRPC diagnosis was 19.6 mo, similar in NMS and no-NMS pts (10 mo and 12 mo). Conclusions: In progressive mCSPC pts receiving early TXT, we observed more frequently the development of NMS with an elevated GG and a trophism for bone and lymph nodes. However, the NMS progression does not seem to have a prognostic role. An extended follow up and the prospective data will be provided.

Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species

BACKGROUND AND AIMS

Sugar concentration is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this study was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modelling approach.

METHODS

We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of compounds other than sugar and starch, synthesis and hydrolysis of starch, and water dilution) involved in the accumulation of soluble sugars during fruit development.

KEY RESULTS

Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwifruit). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared with all other species.

CONCLUSIONS

Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the co-ordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not greatly affected by ethylene-associated events.

Reducing a model of sugar metabolism in peach to catch different patterns among genotypes

Several studies have been conducted to understand the dynamic of primary metabolisms in fruit by translating them into mathematics models. An ODE kinetic model of sugar metabolism has been developed by Desnoues et al. (2018) to simulate the accumulation of different sugars during peach fruit development. Two major drawbacks of this model are (a) the number of parameters to calibrate and (b) its integration time that can be long due to non-linearity and time-dependent input functions. Together, these issues hamper the use of the model for a large panel of genotypes, for which few data are available. In this paper, we present a model reduction scheme that explicitly addresses the specificity of genetic studies in that: (i) it yields a reduced model that is adapted to the whole expected genetic diversity (ii) it maintains network structure and variable identity, in order to facilitate biological interpretation. The proposed approach is based on the combination and the systematic evaluation of different reduction methods. Thus, we combined multivariate sensitivity analysis, structural simplification and timescale-based approaches to simplify the number and the structure of ordinary differential equations of the model. The original and reduced models were compared based on three criteria, namely the corrected Aikake Information Criterion (AIC_C), the calibration time and the expected error of the reduced model over a progeny of virtual genotypes. The resulting reduced model not only reproduces the predictions of the original one but presents many advantages including a reduced number of parameters to be estimated and shorter calibration time, opening new promising perspectives for genetic studies and virtual breeding. The validity of the reduced model was further evaluated by calibration on 30 additional genotypes of an inter-specific peach progeny for which few data were available.

Organ-wide and ploidy-dependent regulation both contribute to cell-size determination: evidence from a computational model of tomato fruit

The development of a new organ is the result of coordinated events of cell division and expansion, in strong interaction with each other. This study presents a dynamic model of tomato fruit development that includes cell division, endoreduplication, and expansion processes. The model is used to investigate the potential interactions among these developmental processes within the context of the neo-cellular theory. In particular, different control schemes (either cell-autonomous or organ-controlled) are tested and compared to experimental data from two contrasting genotypes. The model shows that a pure cell-autonomous control fails to reproduce the observed cell-size distribution, and that an organ-wide control is required in order to get realistic cell-size variations. The model also supports the role of endoreduplication as an important determinant of the final cell size and suggests that a direct effect of endoreduplication on cell expansion is needed in order to obtain a significant correlation between size and ploidy, as observed in real data.

Leaf Production and Expansion: A Generalized Response to Drought Stresses from Cells to Whole Leaf Biomass-A Case Study in the Tomato Compound Leaf

It is clearly established that there is not a unique response to soil water deficit but that there are as many responses as soil water deficit characteristics: Drought intensity, drought duration, and drought position during plant cycle. For a same soil water deficit, responses can also differ on plant genotype within a same species. In spite of this variability, at least for leaf production and expansion processes, robust tendencies can be extracted from the literature when similar watering regimes are compared. Here, we present response curves and multi-scale dynamics analyses established on tomato plants exposed to different soil water deficit treatments. Results reinforce the trends already observed for other species: Reduction in plant leaf biomass under water stress was due to reduction in individual leaf biomass and areas whereas leaf production and specific leaf area were not affected. The dynamics of leaf expansion was modified both at the leaf and cell scales. Cell division and expansion were reduced by drought treatments as well as the endoreduplication process. Combining response curves analyses together with dynamic analyses of tomato compound leaf growth at different scales not only corroborate results on simple leaf responses to drought but also increases our knowledge on the cellular mechanisms behind leaf growth plasticity.

Are compound leaves more complex than simple ones? A multi-scale analysis

Background and Aims

The question of which cellular mechanisms determine the variation in leaf size has been addressed mainly in plants with simple leaves. It is addressed here in tomato taking into consideration the expected complexity added by the several lateral appendages making up the compound leaf, the leaflets.

Methods

Leaf and leaflet areas, epidermal cell number and areas, and endoreduplication (co-) variations were analysed in Solanum lycopersicum considering heteroblastic series in a wild type (Wva106) and an antisense mutant, the Pro35S:Slccs52AAS line, and upon drought treatments. All plants were grown in an automated phenotyping platform, PHENOPSIS, adapted to host plants grown in 7 L pots.

Key Results

Leaf area, leaflet area and cell number increased with leaf rank until reaching a plateau. In contrast, cell area slightly decreased and endoreduplication did not follow any trend. In the transgenic line, leaf area, leaflet areas and cell number of basal leaves were lower than in the wild type, but higher in upper leaves. Reciprocally, cell area was higher in basal leaves and lower in upper leaves. When scaled up at the whole sympodial unit, all these traits did not differ significantly between the transgenic line and the wild type. In response to drought, leaf area was reduced, with a clear dose effect that was also reported for all size-related traits, including endoreduplication.

Conclusions

These results provide evidence that all leaflets have the same cellular phenotypes as the leaf they belong to. Consistent with results reported for simple leaves, they show that cell number rather than cell size determines the final leaf areas and that endoreduplication can be uncoupled from leaf and cell sizes. Finally, they re-question a whole-plant control of cell division and expansion in leaves when the Wva106 and the Pro35S:Slccs52AAS lines are compared.

A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of a markedly low fructose-to-glucose ratio phenotype

The concentrations of sugars in fruit vary with fruit development, environment and genotype. In general, there were weak correlations between the variations in sugar concentrations and the activities of enzymes directly related with the synthesis or degradation of sugars. This finding suggests that the relationships between enzyme activities and metabolites are often non-linear and are difficult to assess. To simulate the concentrations of sucrose, glucose, fructose and sorbitol during the development of peach fruit, a kinetic model of sugar metabolism was developed by taking advantage of recent profiling data. Cell compartmentation (cytosol and vacuole) was described explicitly, and data-driven enzyme activities were used to parameterize equations. The model correctly accounts for both annual and genotypic variations, which were observed in 10 genotypes derived from an interspecific cross. They provided important information on the mechanisms underlying the specification of phenotypic differences. In particular, the model supports the hypothesis that a difference in fructokinase affinity could be responsible for a low fructose-to-glucose ratio phenotype, which was observed in the studied population.

Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions

Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85%) and decreased its fresh weight (up to 60%), big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16-18% in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which (i) the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and (ii) the high dry matter content in control treatment (C) was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4, and 8. The model was then applied to design ideotypes with high dry matter content in C condition and low fresh mass loss in WD condition. The ideotypes outperformed the RILs especially for large and medium fruit-size genotypes, by combining high pedicel conductance and high active uptake of sugars. Interestingly, five small fruit-size RILs were close to the selected ideotypes, and likely bear interesting traits and alleles for adaptation to WD.

Integrating Physiology and Architecture in Models of Fruit Expansion

Architectural properties of a fruit, such as its shape, vascular patterns, and skin morphology, play a significant role in determining the distributions of water, carbohydrates, and nutrients inside the fruit. Understanding the impact of these properties on fruit quality is difficult because they develop over time and are highly dependent on both genetic and environmental controls. We present a 3D functional-structural fruit model that can be used to investigate effects of the principle architectural properties on fruit quality. We use a three step modeling pipeline in the OpenAlea platform: (1) creating a 3D volumetric mesh representation of the internal and external fruit structure, (2) generating a complex network of vasculature that is embedded within this mesh, and (3) integrating aspects of the fruit's function, such as water and dry matter transport, with the fruit's structure. We restrict our approach to the phase where fruit growth is mostly due to cell expansion and the fruit has already differentiated into different tissue types. We show how fruit shape affects vascular patterns and, as a consequence, the distribution of sugar/water in tomato fruit. Furthermore, we show that strong interaction between tomato fruit shape and vessel density induces, independently of size, an important and contrasted gradient of water supply from the pedicel to the blossom end of the fruit. We also demonstrate how skin morphology related to microcracking distribution affects the distribution of water and sugars inside nectarine fruit. Our results show that such a generic model permits detailed studies of various, unexplored architectural features affecting fruit quality development.

Complete response in metastatic renal cell carcinoma after radiotherapy and everolimus: a clinical case and review of the literature

We report the case of a man affected by renal cell carcinoma with vertebral metastases, who presented a radiological complete response after systemic treatment with everolimus.

Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits

The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.

Safety of eribulin mesylate and concomitant radiotherapy for metastatic breast cancer: a single-center experience

Aim: This study evaluates, for the first time, the safety of eribulin in metastatic breast cancer patients concomitantly treated with palliative radiotherapy (RT). Patients & materials: A total of 17 patients were pretreated for metastatic breast cancer. Patients received eribulin mesylate and bone RT. Results: The most frequent grade 3 hematologic adverse events were neutropenia (56%) and anemia (20%). Mean pain score decreased from 2 (baseline) to 0.7 (end of observation). Analgesic score remained stable (1.8 vs 1.6). Bone pain scores dropped within a few weeks and remained below baseline values throughout the analysis. The overall response rate was 29%, and the clinical benefit rate was 59%. Conclusion: Eribulin is characterized by a manageable safety profile also when combined with palliative RT.

Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development

Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.

Impact of age on cytotoxic-induced ovarian failure in breast cancer treated with adjuvant chemotherapy and triptorelin

AIM

This study analyzes our single-center, retrospective experience on 63 premenopausal breast cancer patients treated with monthly triptorelin and concomitant chemotherapy.

PATIENTS & METHODS

Concomitant chemotherapy and triptorelin were adopted as part of premature ovarian failure prevention strategy.

RESULTS

Age at diagnosis was the main factor influencing fertility preservation (p = 0.002). Compared with patients aged 41-45 years, the probability of menses resumption was almost threefold than for women aged 35-40 years, and significantly higher for women aged <35 years (hazard ratio: 9.0; p = 0.0001). The cumulative proportion among patients who resumed menses was 33.3% at 6 months, 75% at 12 months and 87.5% at 24 months. Seven patients attempted pregnancy, and five (71%) obtained healthy deliveries.

CONCLUSION

We observed an acceptable rate of fertility preservation. Age at diagnosis influences fertility preservation.

Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits

The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.

Cyberknife stereotactic radiotherapy for isolated nodal recurrence of prostate cancer

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Background: We report a preliminary clinical experience in stereotactic body radiation therapy (SBRT) delivered using Cyberknife for isolated nodal metastases from prostate cancer. Methods: Between November 2011 and December 2013, 30 patients (39 lesions) were treated with SRT for recurrent prostate cancer with isolated nodal metastases. Prescribed doses and schedules of fractionation varied according to site of disease, ranging from 24 Gy in 1 fraction to 36 Gy in 3 fractions. Most commonly used schedules were 30 Gy in 3 fractions and 36 in Gy in 3 fractions on alternating days. Biochemical response, acute and late toxicity were analyzed. Results: At a median follow-up of 12 months (range: 2-24.9), reduction of PSA ≥ 50% was observed in 18 cases, reduction < 50% was observed in 7, while PSA was stable in 1 case and raised in 8 cases. At the time of analysis, among the 30 patients treated, 2 were dead for systemic disease; 12 patients experienced a relapse of disease in other sites and were treated with HT and salvage chemotherapy. Sixteen patients were still free of disease. In 24 cases, imaging evaluation three months after treatment was available. No in field recurrence was detected, CR was detected in three cases, PR in 14 and SD in 8 patients. The treatment with Cyberknife was well tolerated: one patient experienced G2 acute genitourinary toxicity. Late toxicity was evaluated in patients with more than 3 months of follow up and only one complained G1 proctitis. We did not observe any acute or late severe toxicity (≥G3). Conclusions: Our experience shows that SRT with Cyberknife for isolated nodal relapse from prostate cancer is a safe treatment, with promising results in terms of efficacy.

Prognostic factors in patients receiving third line targeted therapy for metastatic renal cell carcinoma

PURPOSE

Several prognostic models have been proposed for metastatic renal cell carcinoma but none has been validated in patients who receive third line targeted agents. We evaluated prognostic factors in patients with metastatic renal cell carcinoma who received a third line targeted agent.

MATERIALS AND METHODS

We retrospectively reviewed data on 2,065 patients with clear cell metastatic renal cell carcinoma who were treated with targeted therapy at a total of 23 centers in Italy. Included in final analysis were 281 patients treated with 3 targeted agents. Overall survival was the main outcome. Cox proportional hazards regression followed by bootstrap validation was used to identify independent prognostic factors.

RESULTS

Three clinical characteristics (ECOG performance status greater than 1, metastasis at diagnosis and liver metastasis) and 2 biochemical factors (hemoglobin less than the lower limit of normal and neutrophil count greater than the upper limit of normal, respectively) were prognostic. Patients were classified into 3 risk categories, including low-zero or 1, intermediate-2 and high risk-more than 2 risk factors. Median overall survival was 19.7, 10.1 and 5.5 months, and 1-year overall survival was 71%, 43% and 15%, respectively. The major limitation was the retrospective nature of this study and absent external validation.

CONCLUSIONS

This nomogram included clinical and biochemical prognostic factors. In clinical trials it may be useful to select patients and define the prognosis.

Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios

BACKGROUND

Fruit taste is largely affected by the concentration of soluble sugars and organic acids and non-negligibly by fructose concentration, which is the sweetest-tasting sugar. To date, many studies investigating the sugars in fruit have focused on a specific sugar or enzyme and often on a single variety, but only a few detailed studies addressing sugar metabolism both as a whole and dynamic system are available. In commercial peach fruit, sucrose is the main sugar, followed by fructose and glucose, which have similar levels. Interestingly, low fructose-to-glucose ratios have been observed in wild peach accessions. A cross between wild peach and commercial varieties offers an outstanding possibility to study fruit sugar metabolism.

RESULTS

This work provides a large dataset of sugar composition and the capacities of enzymes that are involved in sugar metabolism during peach fruit development and its genetic diversity. A large fraction of the metabolites and enzymes involved in peach sugar metabolism were assayed within a peach progeny of 106 genotypes, of which one quarter displayed a low fructose-to-glucose ratio. This profiling was performed at six stages of growth using high throughput methods. Our results permit drawing a quasi-exhaustive scheme of sugar metabolism in peach. The use of a large number of genotypes revealed a remarkable robustness of enzymatic capacities across genotypes and years, despite strong variations in sugar composition, in particular the fructose-to-glucose ratio, within the progeny. A poor correlation was also found between the enzymatic capacities and the accumulation rates of metabolites.

CONCLUSIONS

These results invalidate the hypothesis of the straightforward enzymatic control of sugar concentration in peach fruit. Alternative hypotheses concerning the regulation of fructose concentration are discussed based on experimental data. This work lays the foundation for a comprehensive study of the mechanisms involved in sugar metabolism in developing fruit.

Hyperlipidemia and hypothyroidism among metastatic renal cell carcinoma patients taking sunitinib malate. Related or unrelated adverse events?

BACKGROUND

In recent years, new-onset hypothyroidism was extensively reported in patients receiving sunitinib for malignancy. Effects of sunitinib on serum lipids are not described, however a hyperlipidemic state is commonly observed in hypothyroid patients. Here we report about the incidence and severity of hypercholesterolemia and hypertriglyceridemia in a cohort of patients receiving sunitinib for metastatic renal cell carcinoma.

PATIENTS AND METHODS

Thyroid function tests, serum triglycerides, and cholesterol were prospectively evaluated in 39 consecutive metastatic renal cell carcinoma patients, who were receiving sunitinib as a first-line treatment. Incidence of hyperlipidemia, thyroid function impairment, and their possible relationship were investigated.

RESULTS

Thyroid function tests, serum cholesterol, and triglycerides were assessed at baseline and before the beginning of each sunitinib cycle. During treatment, median triglyceride levels increased up to 271.3 mg/dL, and median cholesterol increased up to 234.7 mg/dL (+113% and +22%, respectively). A hyperlipidemic state developed in 27 patients (69.2%) within a mean time of 1.8 six-week cycles (range, 1-5 cycles) and persisted during treatment. Hypothyroidism was observed in 20 patients (51.2%) and usually developed within 2.3 cycles. Because hypothyroidism and hyperlipidemia developed at different time points of treatment and among different patients, our results failed to demonstrate a correlation between these adverse events.

CONCLUSION

New-onset hyperlipidemia was observed in an increased percentage of patients taking sunitinib. The mechanism of this side effect is still unclear. We recommend careful monitoring of serum lipid levels during sunitinib administration to recognize possible consequences, especially on cardiovascular health.

Ecophysiological process-based model to simulate carbon fluxes in plants

Carbon fluxes in plants have been subject to many modeling studies. The conceptual framework of models of carbon acquisition, allocation, and metabolism in plants are first introduced, together with methods to calibrate and evaluate the validity of the resulting models. The possibility to combine different models within an integrated plant-organ system is illustrated. In the last part of the chapter, methods used to measure the carbon flows at the plant scale are discussed.

In-silico analysis of water and carbon relations under stress conditions. A multi-scale perspective centered on fruit

Fruit development, from its early stages, is the result of a complex network of interacting processes, on different scales. These include cell division, cell expansion but also nutrient transport from the plant, and exchanges with the environment. In the presence of nutrient limitation, in particular, the plant reacts as a whole, by modifying its architecture, metabolism, and reproductive strategy, determining the resources available for fruit development, which in turn affects the overall source-sink balance of the system. Here, we present an integrated model of tomato that explicitly accounts for early developmental changes (from cell division to harvest), and use it to investigate the impact of water deficit and carbon limitation on nutrient fluxes and fruit growth, in both dry and fresh mass. Variability in fruit response is analyzed on two different scales: among trusses at plant level, and within cell populations at fruit level. Results show that the effect of stress on individual cells strongly depends on their age, size, and uptake capabilities, and that the timing of stress application, together with the fruit position on the plant, is crucial in determining the final phenotypic outcome. Water deficit and carbon depletion impacted either source size, source activity, or sink strength with contrasted effects on fruit growth. An important prediction of the model is the major role of symplasmic transport of carbon in the early stage of fruit development, as a catalyst for cell and fruit growth.

Lymphopenia and clinical outcome of elderly patients treated with sunitinib for metastatic renal cell cancer

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Background: Lymphopenia is associated with toxicity and outcome in several cancer types. We assessed the association of pre-treatment lymphopenia with toxicity and clinical outcome of elderly patients with metastatic renal cell cancer treated with first-line sunitinib. We evaluated the prognostic factors in these patients. Methods: We reviewed the clinical files of 181 patients aged >70 years with mRCC treated with first-line sunitinib in seventeen Italian Oncology Units from February 2006 to September 2011. Baseline lymphopenia was defined as lymphocyte counts <1,000/µL. Results: Twenty–nine patients (16.0%) had a baseline lymphocyte counts <1,000/µL, and 152 (84%) ≥1,000/µL. No difference between the two groups was reported in overall response rate (p = 0.207), dose reductions (p = 0.740); discontinuations due to adverse events (p = 0.175), overall incidence of grade 3-4 toxicities (p = 0.112) even if more patients in the group with lymphopenia had grade 3-4 neutropenia (p = 0.017), grade 3-4 thrombocytopenia (p = 0.017) and grade 3-4 diarrhea (p = 0.006). In multivariate analysis, performance status and Heng score were predictors of progression-free survival (p = 0.015 and p = 0.0006, respectively), while performance status, Heng score, and lymphopenia were found to be significantly associated with overall survival (p = 0.007, p < 0.0001 and p = 0.023, respectively). Conclusions: Sunitinib appeared safe and active in elderly patients with lymphopenia. Lymphocyte counts is an independent prognostic factor for OS in elderly patients with mRCC treated with first-line sunitinib.

Towards multiscale plant models: integrating cellular networks

One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.

Towards multiscale plant models: integrating cellular networks

One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.

Updated safety result of a large Italian early access program (EAP) with cabazitaxel plus prednisone (CbzP) in metastatic castration-resistant prostate cancer (mCRPC) patients who progressed during or after docetaxel (D) therapy

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Background: A significant percentage of mCRPC pts, who have progressed on D therapy, have a long life expectancy and are candidates for additional treatments. In TROPIC trial pts who progressed during or after D had a statistically significant OS advantage and clinical benefit with CbzP in respect to mitoxantrone plus prednisone (MP). Benefits observed in the TROPIC study supported a global EAP, to allow pts with mCRPC to have an early access to CbzP and provide confirmatory data in daily clinical practice Methods: We report the safety results of the first 90 pts entered into EAP and treated with CbzP, out of 232 pts enrolled by 25 Italian centers between Jan and Aug 2011 Results: Pts characteristics were median age 70 years (≥ 75 years 22.2%); ECOG PS 0-1, 97.8%; median N. of previous D cycles 8 (median cumulative D 675mg/m2); 14.1% received 675 ÷ 900 mg and 40.0% ≥ 900 mg of D. Median time from last D dose to first CbzP dose was 5.29 months including any other chemotherapy treatment.At the time of this analysis 50% of pts had received 4 cycles of CbzP. 33 pts discontinued CbzP mainly due to PD (42.4%), AEs (related/not related, 27.3%), investigator’s (3.0 %) / pts decision (18.2%) and others (9.1%). AEs resulting in CbzP discontinuation (10.0%) are mainly fatigue, pyrexia and haematological disorders. A total of 57 pts were still on treatment. In the 33 discontinued pts, CbzP has been delayed in 24.2% while a dose reduction occurred in 21.2% of pts. AEs of any grade were observed in 81/90 pts. Most common G 3/4 AEs were leukopenia (25.6%), neutropenia (48.9%), anaemia (6.7%), diarrhoea (1.1%), asthenia (3.3%) and fatigue (5.6%). One death occurred during the study period in a heavily pretreated pt who received 33 cycles of D Conclusions: This preliminary safety analysis suggests the good tolerability of cabazitaxel, in terms of haematological as well as non-haematological AEs even in heavily pretreated pts according to the previous experience of Italian Centers in theTROPIC trial. This is remarkable because of the increased similarity of the patient’ populations treated in the EAP and daily clinical practice

Preliminary safety results of an Italian early-access program (EAP) with cabazitaxel plus prednisone (CbzP) in patients with docetaxel-refractory metastatic castration-resistant prostate cancer (mCRPC)

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Background: A significant number of docetaxel (D) refractory mCRPC patients (pts) have a life expectancy of > 15 months and ask for additional efficacious treatments. In the phase 3 TROPIC trial treatment of mCRPC patients with CbzP who progressed during or after docetaxel resulted in a statistically significant overall survival benefit compared with mitoxantrone / prednisone (Lancet 2010). This survival benefit supported establishment of a global early access program (EAP), allowing pts with mCRPC to have access to the drug prior to its commercial availability. Here we describe preliminary safety results from the EAP in Italy.

Methods: We report here the data of the first 16 mCRPC patients (out of the 123 enrolled by 19 Italian centers until Sept 2011 in EAP) treated with Cbz (25mg/m2 Q3W) plus P(10mg bid).

Results: Pts were median age 73.5 years (>75 years 38%), ECOG PS-0 81.3% and had received a median of 7 prior cycles of D (median cumulative D dose 562.5mg). Median time from last D dose to inclusion was 7.1 months. Overall, 62.5% (10 Pts) had 2 or more metastatic sites (bone 94%, regional/distant lymph nodes 25% and 44%, lung 12.5%, other sites 19%). A limited number of relevant adverse events (AE) were observed. All grade AEs were seen in 14/16 pts (81.3%), with 4/16 pts experiencing grade 3/4 leukopenia, 8/16 pts grade 3 - 4 neutropenia, one patient with febrile neutropenia and one with hypertransaminasaemia. Grade 1-2 asthenia and fatigue were experienced respectively by 2 pts. No grade 3 / 4 diarrhea, vomiting or constipation were observed and no AEs results in death. All pts received at least 2 cycles of CbzP (2÷5) and only one patient permanently discontinued treatment (disease progression).

Conclusions: This preliminary analysis of Italian pts enrolled in the EAP provides real world safety data and suggests a good safety profile of cabazitaxel even in heavily pretreated pts, which is in agreement with Italian experience in TROPIC. Results of the entire Italian cohort with a longer follow-up will be presented.

Newly onset hyperlipidemia in metastatic renal cell carcinoma patients treated with sunitinib

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Background: To our knowledge effects of sunitinib on serum lipids metabolism are not described. Here we report about the occurrence of hypercholesterolemia and hypertriglyceridemia in patients receiving sunitinib for metastatic renal cell carcinoma (mRCC).

Methods: Between July 2008 and September 2011, we prospectively evaluated serum triglycerides and cholesterol in 37 patients receiving sunitinib for mRCC according to classic 6-week schedule. On average they received sunitinib for 10.3 cycles. Serum lipids were measured before the beginning of treatment and at the end of each sunitinib ON period as routine laboratory evaluations.

Results: At baseline median triglycerides was 163,83 mg/dl (± 76,6 mg/dl 95% CI) and median cholesterol was 201.6 mg/dl (± 35.5 mg/dl 95% CI). During sunitinib administration 25 patients (67.5 %) presented an elevation of serum lipids as compared to baseline. These abnormalities usually developed within 1.8 cycles (range 1-5 cycles). While on sunitinb median triglycerides was 333,6 mg/dl and median cholesterol was 243.5 mg/dl (+ 103% and + 21% respectively, compared to baseline). Patients who developed hypercholesterolemia presented an increase of both HDL and LDL cholesterol.

Conclusions: Hyperlipidemia develops in an elevate percentage of patients on sunitinib. The mechanism of this event remains unclear. Recently, an interaction between platelet derived growth factor receptor (PDGFR) and lipoprotein receptor (LR) family was described and this is supposed to be an important step towards the internalization of LR itself. Because sunitinib inhibits PDGFR, a lower plasma lipoproteins clearance could be expected, resulting in an increase of serum lipids. It is noteworthy that PDGFR inhibition was associated with delayed atherosclerotic plaque formation, having an anti-atherogenetic effect. Therefore treatment with sunitinib, even if associated to hypertension and hyperlipidemia, may not result in an increase of cardiovascular events.

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli

Gene regulatory networks consist of direct interactions, but also include indirect interactions mediated by metabolism. We investigate to which extent these indirect interactions arising from metabolic coupling influence the dynamics of the system. To this end, we build a qualitative model of the gene regulatory network controlling carbon assimilation in Escherichia coli, and use this model to study the changes in gene expression following a diauxic shift from glucose to acetate. In particular, we compare the relative variation in the steady-state concentrations of enzymes and transcription regulators during growth on glucose and acetate, as well as the dynamic response of gene expression to the exhaustion of glucose and the subsequent assimilation of acetate. We find significant differences between the dynamics of the system in the absence and presence of metabolic coupling. This shows that interactions arising from metabolic coupling cannot be ignored when studying the dynamics of gene regulatory networks.

Sunitinib-induced hyperparathyroidism: a possible mechanism to altered bone homeostasis

BACKGROUND

Sunitinib malate is an orally bioavailable tyrosine kinase inhibitor that is active against many tyrosine kinase receptors involving crucial pathways in both healthy tissues and malignant tissues. Because its use in clinical practice is quite recent, many of its possible side effects remain unknown. In this report, the authors describe the incidence of new-onset hyperparathyroidism in a cohort of patients with metastatic renal cell carcinoma who received treatment with sunitinib.

METHODS

Twenty-six patients who received first-line sunitinib for metastatic renal cell carcinoma were enrolled in this study for a mineral and parathyroid function assessment. Plasma levels of intact parathyroid hormone; serum levels of calcium, phosphorus, 25-hydroxyvitamin D(3), and 1,25-dihydrovitamin D(3); and urinary 24-hour calcium and phosphorus excretion all were measured in each patient. Biochemical evaluations were performed before the beginning of treatment and at the end of each sunitinib treatment period.

RESULTS

Eighteen of 26 patients (69.2%) developed hyperparathyroidism with normal serum calcium levels, and 6 of them developed hypophosphatemia. Patients presented with a mean elevation of parathyroid hormone after 2.2 cycles of sunitinib. The levels of 25-OH vitamin D(3) were stable over the course of treatment, whereas 1,25-OH vitamin D(3) levels were increased in 5 hyperparathyroid patients. Those who presenting with elevated parathyroid hormone levels had low or undetectable urinary calcium levels. Parathyroid hormone elevation usually persisted but did not progress during long-term therapy with sunitinib. Permanent treatment interruption resulted in a resolution of hyperparathyroidism.

CONCLUSIONS

Hyperparathyroidism developed in an high percentage of patients on sunitinib. Therefore, the authors concluded that sunitinib may affect parathyroid function and bone mineral homeostasis, possibly resulting in abnormal bone remodeling.

Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli

The adaptation of the bacterium Escherichia coli to carbon starvation is controlled by a large network of biochemical reactions involving genes, mRNAs, proteins, and signalling molecules. The dynamics of these networks is difficult to analyze, notably due to a lack of quantitative information on parameter values. To overcome these limitations, model reduction approaches based on quasi-steady-state (QSS) and piecewise-linear (PL) approximations have been proposed, resulting in models that are easier to handle mathematically and computationally. These approximations are not supposed to affect the capability of the model to account for essential dynamical properties of the system, but the validity of this assumption has not been systematically tested. In this paper, we carry out such a study by evaluating a large and complex PL model of the carbon starvation response in E. coli using an ensemble approach. The results show that, in comparison with conventional nonlinear models, the PL approximations generally preserve the dynamics of the carbon starvation response network, although with some deviations concerning notably the quantitative precision of the model predictions. This encourages the application of PL models to the qualitative analysis of bacterial regulatory networks, in situations where the reference time scale is that of protein synthesis and degradation.

The impact of sunitinib-induced hypothyroidism on progression-free survival of metastatic renal cancer patients: a prospective single-center study

BACKGROUND

Several studies have reported unexpected rates of hypothyroidism in patients treated with sunitinib. The biochemical basis of this impairment is unknown. A relationship between hypothyroidism and improved outcome has been suggested in some cancer patients. Here we describe the incidence of newly onset hypothyroidism and its relationship with progression-free survival in metastatic renal cell carcinoma patients undergoing sunitinib treatment at our institution.

PATIENTS AND METHODS

Between July 2007 and June 2009, 22 patients received a first line sunitinib for metastatic renal cell carcinoma. Thyroid function tests were prospectively evaluated as routine laboratory assessment in every patient, at baseline and on the first and last day of every ON and OFF sunitinib period.

RESULTS

The median duration of treatment was 39.5 weeks. During sunitinib therapy, 13 patients (59.1%) showed at least one elevated TSH level. No reductions of TSH below normal ranges were observed. L-thyroxine replacement therapy was required in 2 patients. Based on thyroid function, median progression-free survival was 8.55 months for hypothyroid compared with 7.03 months for euthyroid patients (P < 0.05).

CONCLUSION

Patients administered sunitinib have an high incidence of hypothyroidism. The improved outcome of hypothyroid patients suggests an important relationship between sunitinib and this uncommon side effect.

Modeling lymphocyte homing and encounters in lymph nodes

BACKGROUND

The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research.

RESULTS

In this paper, we present a hybrid discrete/continuous model of the lymph node, accounting for differences in cell velocity and chemotactic response, influenced by the spatial compartmentalization of the lymph node and the regulation of cells migration, encounter, and antigen presentation during the inflammation process.

CONCLUSION

Our model reproduces the correct timing of an immune response, including the observed time delay between duplication of T helper cells and duplication of B cells in response to antigen exposure. Furthermore, we investigate the consequences of the absence of dendritic cells at different times during infection, and the dependence of system dynamics on the regulation of lymphocyte exit from lymph nodes. In both cases, the model predicts the emergence of an impaired immune response, i.e., the response is significantly reduced in magnitude. Dendritic cell removal is also shown to delay the response time with respect to normal conditions.

Gemcitabine plus docetaxel as first-line biweekly therapy in locally advanced and/or metastatic urothelial carcinoma: a phase II study

The purpose of the study was to evaluate objective response rate, survival and toxicity of the combination of gemcitabine-docetaxel administered on a biweekly schedule as first-line treatment in advanced/relapsed or metastatic urothelial carcinoma. Treatment consisted of the sequenced administration of gemcitabine 1500 mg/m(2) and docetaxel 60 mg/m(2) (2 h intravenous infusion) on days 1, 14 of a 28-day cycle for 6 months. A total of 33 patients, 22 men and 11 women, were enrolled, aged 41-75 years (median 64 years). The majority of patients had a good performance status (94%; status<2). Thirteen patients had locally advanced disease (39%) and 20 metastasic disease (41%). A total of 178 treatment cycles were administered with a median number of 5.4 cycles for a patients (range 2-8). Toxicity was primarily hematologic with the most frequent grade >2 being neutropenia (11%), with three episodes of febrile neutropenia. Anemia and thrombocytopenia were milder and had a lower incidence. The most frequent nonhematological toxicities were alopecia, followed by asthenia. Cardiac and pulmonary toxicity was minimal. No toxic deaths were recorded during study and follow-up. Overall response rate was 53.1%, including four complete responses (12.5%) and 13 partial responses (40.6%), whereas six patients (18.8%) had disease stabilization. Median time to progression was 10.2 months (95% confidence interval: 5.1-13.7), with a median survival of 14.8 months (95% confidence interval: 9.4-20.2) after an observation of 30 months (range 4-30+). The results of this study suggested that combination therapy with gemcitabine and docetaxel administered twice a week is particularly active and well tolerated as first-line treatment in advanced and/or metastatic urothelial carcinoma. Once data are confirmed in a larger study and longer follow-up, the favorable toxicity profile of this regimen may offer an interesting alternative to the cisplatin-based regimen.

An enhanced agent based model of the immune system response

We describe some recent enhancements introduced in C-ImmSim, a simulator of the immune system response that we have been developing for a number of years along with preliminary results produced by the simulation of the Highly Active Anti-Retroviral Therapy in HIV-1 infected patients.

Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case

The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, and the elasticity parameters of the unzipped strands.

Inference of DNA sequences from mechanical unzipping: an ideal-case study

The performances of Bayesian inference to predict the sequence of DNA molecules from fixed-force unzipping experiments are investigated. We show that the probability of misprediction decreases exponentially with the amount of collected data. The decay rate is calculated as a function of biochemical parameters (binding free energies), the sequence content, the applied force, the elastic properties of a DNA single strand, and time resolution.