Recurrence microstates for machine learning classification.

Recurrence microstates are obtained from the cross recurrence of two sequences of values embedded in a time series, being the generalization of the concept of recurrence of a given state in phase space. The probability of occurrence of each microstate constitutes a recurrence quantifier. The set of probabilities of all microstates are capable of detecting even small changes in the data pattern. This creates an ideal tool for generating features in machine learning algorithms. Thanks to the sensitivity of the set of probabilities of occurrence of microstates, it can be used to feed a deep neural network, namely, a microstate multi-layer perceptron (MMLP) to classify parameters of chaotic systems. Additionally, we show that with more microstates, the accuracy of the MMLP increases, showing that the increasing size and number of microstates insert new and independent information into the analysis. We also explore potential applications of the proposed method when adapted to different contexts.

Contralateral Axillary Lymph Node Metastases from Breast Carcinoma: Is it Time to Review TNM Cancer Staging?

BACKGROUND: Contralateral axillary lymph node metastasis (CAM) is an infrequent clinical condition currently considered an M1, stage IV, disease. Due to the absence of shared data on CAM significance and on its therapeutic approach, be it curative or simply palliative, its management is still uncertain and undoubtedly represents a clinical challenge. PATIENTS AND METHODS: Patients with pathologically confirmed metachronous CAM were retrospectively evaluated. All patients had been managed at the European Institute of Oncology, Milan, Italy, from 1997. Patients with distant metastases at the time of CAM were excluded. Possible treatments included surgery, systemic therapy and RT (radiotherapy). Outcomes were evaluated as rates of disease-free survival (DFS) and of overall survival (OS). RESULTS: Forty-seven patients with CAM were included in the study. Metachronous CAM occurred 73 months (range 5-500 months) after diagnosis of the primary tumor. The median follow-up time was 5.4 years (interquartile range 2.9-7.0 years). The estimated OS was 72% at 5 years (95% CI 54-83), and 61% at 8 years (95% CI 43-75). The estimated DFS was 61% at 5 years (95% CI 44-74), and 42% at 8 years (95% CI 25-59). CONCLUSION: These findings, together with those from previous studies, show that CAM outcome, particularly if measured as OS, appear better than at other sites of distant dissemination, when CAM is subjected to surgical and systemic treatments with a curative intent. Therefore, a new clinical scenario is suggested where, in the TNM system, CAM is no longer classified as a stage IV, but as an N3 disease.

Maximum entropy principle in recurrence plot analysis on stochastic and chaotic systems.

The recurrence analysis of dynamic systems has been studied since Poincaré's seminal work. Since then, several approaches have been developed to study recurrence properties in nonlinear dynamical systems. In this work, we study the recently developed entropy of recurrence microstates. We propose a new quantifier, the maximum entropy (Smax). The new concept uses the diversity of microstates of the recurrence plot and is able to set automatically the optimum recurrence neighborhood (ϵ-vicinity), turning the analysis free of the vicinity parameter. In addition, ϵ turns out to be a novel quantifier of dynamical properties itself. We apply Smax and the optimum ϵ to deterministic and stochastic systems. The Smax quantifier has a higher correlation with the Lyapunov exponent and, since it is a parameter-free measure, a more useful recurrence quantifier of time series.

Assessment of a tumor bank: a thirty years experience of the University of Siena (Italy).

Tumor biobank plays a pivotal role in cancer biomedical research. The collection of a high variety of biological samples, including DNA, RNA, tissues, cells, blood, plasma and other body fluids, represents a necessary step to plan new strategies in the improvement of oncological patient care. Since 1985, a consolidated experience in biobanking management has been developed at the University of Siena (Italy). During these years, some information about clinico-pathology, surgery and a high number of human bispecimens have been collected. Herein, we described our experience in sampling management to improve the cancer research and the patient care.

Liver transplantation in defects of cholesterol biosynthesis: the case of lathosterolosis.

We report the outcome of liver transplantation (LT) in the only surviving patient with lathosterolosis, a defect of cholesterol biosynthesis characterized by high lathosterol levels associated with progressive cholestasis, multiple congenital anomalies and mental retardation. From her diagnosis at age 2 she had shown autistic behavior, was unable to walk unaided and her sight was impaired by cataracts. By age 7 she developed end-stage liver disease. After a soul-searching discussion within the transplantation team, she was treated with LT as this represented her only lifesaving option. At 1-year follow-up, her lathosterol levels had returned to normal (0.61 mg/dL from 13.04 ± 2.65) and her nutrition improved. She began exploring her environment and walking by holding onto an adult's hand and then independently. Her brain magnetic resonance imaging (MRI) had shown a normal picture at age 1, whereas a volume reduction of white matter with ex vacuo ventricular dilatation and defective myelinization were observed before transplant. At 5-year follow-up, a complete biochemical recovery, an arrest of mental deterioration and a stable MRI picture were achieved, with a return to her every day life albeit with limitations. Timely liver transplant in defects of cholesterol biosynthesis might arrest the progression of neurological damage.

Phylogeny and micro-habitats utilized by lizards determine the composition of their endoparasites in the semiarid Caatinga of Northeast Brazil.

Trophic networks can have architectonic configurations influenced by historical and ecological factors. The objective of this study was to analyze the architecture of networks between lizards, their endoparasites, diet, and micro-habitat, aiming to understand which factors exert an influence on the composition of the species of parasites. All networks showed a compartmentalized pattern. There was a positive relation between diet and the diversity of endoparasites. Our analyses also demonstrated that phylogeny and the use of micro-habitat influenced the composition of species of endoparasites and diet pattern of lizards. The principal factor that explained the modularity of the network was the foraging strategy, with segregation between the "active foragers" and "sit-and-wait" lizards. Our analyses also demonstrated that historical (phylogeny) and ecological factors (use of micro-habitat by the lizards) influenced the composition of parasite communities. These results corroborate other studies with ectoparasites, which indicate phylogeny and micro-habitat as determinants in the composition of parasitic fauna. The influence of phylogeny can be the result of coevolution between parasites and lizards in the Caatinga, and the influence of micro-habitat should be a result of adaptations of species of parasites to occupy the same categories of micro-habitats as hosts, thus favoring contagion.

Epigenetically silenced miR-34b/c as a novel faecal-based screening marker for colorectal cancer.

BACKGROUND: MicroRNAs are tiny non-coding small endogenous RNAs that regulate gene expression by translational repression, mRNA cleavage and mRNA inhibition. The aim of this study was to investigate the hypermethylation of miR-34b/c and miR-148a in colorectal cancer, and correlate this data to clinicopathological features. We also aimed to evaluate the hypermethylation of miR-34b/c in faeces specimens as a novel non-invasive faecal-DNA-based screening marker. METHODS: The 5-aza-2'-deoxycytidine treatment and methylation-specific PCR were carried out to detect the hypermethylation of miR-34b/c and miR-148a. RESULTS: The miR-34b/c hypermethylation was found in 97.5% (79 out of 82) of primary colorectal tumours, P=0.0110. In 75% (21 out of 28) of faecal specimens we found a hypermethylation of miR-34b/c while only in 16% (2 out of 12) of high-grade dysplasia. In addition, miR-148a was found to be hypermethylated in 65% (51 out of 78) of colorectal tumour tissues with no significant correlation to clinicopathological features. However, a trend with female gender and advanced age was found, P=0.083. We also observed a trend to lower survival rate in patients with miR-148a hypermethylation with 10-year survival probability: 48 vs 65%, P=0.561. CONCLUSIONS: These findings show that aberrant hypermethylation of miR-34b/c could be an ideal class of early screening marker, whereas miR-148a could serve as a disease progression follow-up marker.

Is there a prognostic role for C-reactive protein in ischemic stroke?

OBJECTIVES: We investigated the relationship between C-reactive protein (CRP)-values in the acute phase of stroke and the risk of further fatal and non-fatal ischemic events. MATERIALS AND METHODS: We analysed 462 consecutive incident ischemic strokes. Patients were divided into two subgroups on the basis of a CRP cut-off level of 9 mg/l. Primary end points were any new vascular fatal and non-fatal event recorded during the follow-up period. RESULTS: During a follow-up of 2.27 years, in 132 patients occurred a primary end point. Patients with CRP values > or = 9 mg/l had more frequently primary end point. The hazard ratio (HR) for cardiovascular events was 3.59; 1.93 for cerebrovascular events; 7.43 for vascular deaths and 5.78 for death from any cause. Cox proportional hazard multivariate analysis identified CRP values > or = 9 (HR = 4.19, 95% CI: 1.85-9.50, P = 0.001), the lack of secondary prevention therapy at discharge (HR = 4.35, 95% CI: 1.87-10.1, P = 0.001), age >70 years (HR = 3.09, 95% CI: 1.04-9.24, P = 0.04) as independent predictors of fatal events. CONCLUSIONS: CRP levels > or = 9 mg/l, evaluated in incident ischemic stroke within 24 h, predict a higher risk of further ischemic events and mortality.

Familial gastric cancer and Li-Fraumeni syndrome.

Gastric cancer occurs in some familial diseases with inherited cancer predisposition. Genetic factors have been correlated with the hereditary diffuse gastric cancer and other familial gastric cancer conditions as hereditary non-polyposis colorectal cancer and Li-Fraumeni syndrome. The present study was aimed at searching for germ line mutations of TP53 gene in familial gastric cancer with cluster for Li-Fraumeni syndrome or Li-Fraumeni-like syndrome. Twenty-three pedigrees with characteristics for Li-Fraumeni-like syndrome were identified. DNA of the proband was sequenced using polymerase chain reaction/single-strand conformation polymorphism. Among these 23 cases, no germ line mutation of TP53 was identified, while two single-nucleotide polymorphisms were identified in four patients. In our area, in which a high rate of familial aggregation was demonstrated, the lack of germ line mutation of TP53 together with the infrequency of mutation of E-cadherin gene seem to limit the role of genetic predisposition in the development of gastric cancer.

Immediate breast reconstruction with latissimus dorsi flap for patients with local recurrence of breast cancer.

BACKGROUND: Ipsilateral breast cancer recurrence (IBTR) occurs in about 7% of patients with primary invasive breast tumor. Salvage mastectomy and breast reconstruction are often discussed and latissimus dorsi (LD) flap is frequently proposed. METHODS: We retrospectively investigated 111 consecutive locally relapsing patients who underwent salvage mastectomy and immediate LD reconstruction. All included patients with IBTR previously underwent conserving surgery for BC, and received a postoperative irradiation. Primary endpoints were disease free survival and overall survival. Secondary endpoints were surgical complications and re-interventions. RESULTS: Invasive ductal cancer was the most frequent histotype (60.4%) of breast cancer reappearance. rpT1, rpT2 and rpT3 were observed respectively in 50.5%, 20,7% and 3,6% of the patients. rpTis occurred in 11,7% of cases. Positive axillary nodes were observed in 9,9% of patients at reappearance. Post-operative complication other than seroma occurred in 17,1% of patients, while seroma at the donor site was observed in 61.3% of cases. At 5-year after surgery overall survival was 92% (95% CI: 85%-96%) and disease free survival was 78% (95% CI: 69%-85%). CONCLUSIONS: Immediate latissimus dorsi flap reconstruction in selected patients with isolated breast tumor recurrence, which occurred after breast irradiation, provides an effective treatment with a satisfactory outcome.

The interferon gamma receptor 1 (IFNGR1) -56C/T gene polymorphism is associated with increased risk of early gastric carcinoma.

BACKGROUND AND AIMS: It has been demonstrated that polymorphisms within inflammation-related genes are associated with the risk of gastric carcinoma (GC) in people infected with Helicobacter pylori. Recently, polymorphisms in the gene encoding the interferon gamma receptor 1 (IFNGR1) were found to be associated with increased susceptibility to H pylori infection. We aimed to determine the association between polymorphisms in the IFNGR1 gene and development of chronic gastritis and GC. METHODS: In a case-control study including 733 controls, 213 patients with chronic gastritis and 393 patients with GC, the IFNGR1 -611*G/*A, -56*C/*T, +1004*A/*C and +1400*T/*C polymorphisms were genotyped. A second independent case-control study including 100 controls and 65 patients with GC was used for confirmation of the original results. The effect of the -56*C/*T promoter polymorphism in the level of expression of the IFNGR1 gene was evaluated by an IFNGR1 -56*C/*T allele specific luciferase reporter assay. RESULTS: In patients with early onset GC (defined as being less than 40 years of age at the time of diagnosis) we found a significant over-representation of the IFNGR1 -56*T/*T homozygous genotype with an odds ratio (OR) of 4.1 (95% confidence interval (CI) 1.6 to 10.6). This result was confirmed in a second independent case-control study. In the luciferase reporter assay we observed a 10-fold increase (p<0.001) in luciferase expression associated with the IFNGR1-56*T allele. CONCLUSIONS: Our results indicate that the IFNGR1 -56C/T polymorphism is a relevant host susceptibility factor for GC development. Our data also indicate that this genetic polymorphism is functionally relevant and may be related to the early development of GC.

Standard and controversies in sentinel node in breast cancer patients.

Axillary management in breast cancer is still controversial. Recent clinical trials have clearly demonstrated that in breast-conserving surgery, axillary dissection could be an overtreatment when metastases are present in only 1-2 sentinel lymph nodes. Nonetheless, axillary dissection remains the principal treatment in patients undergoing mastectomy with at least one metastatic sentinel lymph node and in patients eligible for breast conserving surgery with three or more positive sentinel lymph nodes. In this analytical review, we discuss the clinical evidence, taking into account recent guidelines, for axillary management.

Metabonomic analysis of exhaled breath condensate in adults by nuclear magnetic resonance spectroscopy.

Exhaled breath condensate (EBC) is a noninvasive method for the study of airway lining fluid. Nuclear magnetic resonance (NMR) spectroscopy can provide biochemical profiles of metabolites in biological samples. The aim of the present study was to validate the NMR metabonomic analysis of EBC in adults, assessing the role of pre-analytical variables (saliva and disinfectant contamination) and the potential clinical feasibility. In total, 36 paired EBC and saliva samples, obtained from healthy subjects, laryngectomised patients and chronic obstructive pulmonary disease patients, were analysed by means of (1)H-NMR spectroscopy followed by principal component analysis. The effect on EBC of disinfectant, used for reusable parts of the condenser, was assessed after different washing procedures. To evaluate intra-day repeatability, eight subjects were asked to collect EBC and saliva twice within the same day. All NMR saliva spectra were significantly different from corresponding EBC samples. EBC taken from condensers washed with recommended procedures invariably showed spectra perturbed by disinfectant. Each EBC sample clustered with corresponding samples of the same group, while presenting intergroup qualitative and quantitative signal differences (94% of the total variance within the data). In conclusion, the nuclear magnetic resonance metabonomic approach could identify the metabolic fingerprint of exhaled breath condensate in different clinical sets of data. Moreover, metabonomics of exhaled breath condensate in adults can discriminate potential perturbations induced by pre-analytical variables.

Sterol profiling in red blood cell membranes and plasma of newborns receiving total parenteral nutrition.

BACKGROUND AND OBJECTIVES: Total parenteral nutrition (TPN) is a lifesaving therapy in children with intestinal failure, frequently complicated by liver dysfunction. Plant sterols (phytosterols) of lipid emulsions have been supposed to contribute to cholestasis in TPN-treated children. The present study aimed to evaluate the plasma and red blood cell membrane (RBCM) phytosterol levels in newborns after a short period of TPN. PATIENTS AND METHODS: Phytosterols, cholesterol, and other sterol levels were quantified by gas chromatography-mass spectrometry in 15 healthy control infants, 22 patients after TPN, and 11 patients before TPN. Sterols of lipid emulsions were quantified. RESULTS: Plasma and RBCM phytosterol levels were, respectively, on average 56 micromol/L and 83 micromol/g per protein in patients after TPN, 13 micromol/L and 15 micromol/g per protein in patients before TPN, and 9 micromol/L and 13 micromoL/g per protein in control infants (P < 0.05 for differences). The days of TPN and the total amount of infused lipids correlated significantly with RBCM phytosterol (P < 0.05); correlations for plasma were positive but not significant. No correlation was observed with plasma bilirubin, gamma-glutamyltransferase, or alanine transaminase. CONCLUSIONS: Plasma and RBCM phytosterols increase significantly in newborns after a short period of TPN. Higher phytosterol levels were observed in some patients that could have been due to their individual variability in phytosterol metabolism and/or clearance. A greater accumulation of phytosterols in membranes may induce TPN-related cholestasis.

Nipple-sparing mastectomy with different approaches: surgical incisions, complications, and cosmetic results. Preliminary results of 100 consecutive patients at a single center.

Nipple- and areola-sparing mastectomy is a novel surgical approach that preserves the nipple-areolar complex. Patients with moderate and/or severe breast ptosis are usually not eligible for this surgical approach. In this study, we aimed to demonstrate the feasibility of nonconventional surgical approaches for nipple-sparing mastectomy. One hundred consecutive patients diagnosed with primary breast cancer (BC) were enrolled in this study. Clinical and pathological data such as body mass index, smoking status, breast ptosis, complications, and aesthetic satisfaction (Breast-Q test) were collected. According to different types of breast ptosis, surgical procedures were classified as (a) hemi-periareolar, (b) round block, (c) vertical pattern, and (d) wise pattern skin incisions. We performed statistical analysis to assess the correlation with complications, degree of ptosis, and breast-Q scores. Among the 117 surgical procedures performed in 100 patients with BC, no significant associations are verified considering clinical and pathological data, complications, pre- and postsurgery satisfactions, and other parameters. Different surgical approaches represent the evolution of "classic" nipple-sparing mastectomy, thus meeting the cosmetic and oncological results. These procedures are safe and also indicated in cases conventionally considered as not eligible for nipple-areola preservation.

Hereditary diffuse gastric cancer and E-cadherin: description of the first germline mutation in an Italian family.

AIMS: Germline mutation of the E-cadherin gene (CDH1) accounts for the Hereditary Diffuse Gastric Cancer (HDGC) syndrome. Fourteen pedigrees with Diffuse Gastric Cancer that fulfilled the International Gastric Cancer Linkage Consortium (IGCLC) criteria were selected and screened for CDH1 germline mutations. METHODS: The entire coding region of the CDH1 gene and all intron-exon boundaries were analyzed by direct sequencing in the 14 families fulfilling the IGCLC criteria. E-cadherin immunohistochemical expression was evaluated on tumour as well as normal formalin-fixed paraffin embedded tissues. RESULTS: A novel germline missense mutation was found. It was a single C-->T substitution in exon 8, resulting in a transition of CCG-->CTG (C1118T; Pro373Leu) demonstrated in the proband and her brother. At immunohistochemical analysis, the staining intensity was reduced and considered weakly positive (15%). CONCLUSIONS: The first CDH1 germline mutation of an Italian family is herein reported. The present missense mutation has never been described so far.

Development and validation of a LC/MS/MS method for simultaneous quantification of oxcarbazepine and its main metabolites in human serum.

A fast, sensitive and specific LC/MS/MS method for the simultaneous analysis of oxcarbazepine (OXC), 10-hydroxycarbazepine (MHD) and trans-diol-carbazepine (DHD), in human serum, has been developed and validated. Serum drugs were extracted by C8 solid-phase cartridges (SPE) and separated in less than 3 min on a C18 reverse-phase column using an isocratic elution. A tandem mass spectrometer, as detector, was used for quantitative analysis in positive mode by a multiple reaction monitoring. Calibration curves, obtained on two ranges of concentration (0.78-50 mg/L for MHD and 0.078-5.0 mg/L for OXC and DHD), showed correlation coefficients (r) better than 0.997. Within day and between days quality controls imprecision, as CV%, ranged from 0.3 to 4.6% and from 1.9 to 5.8%, respectively. Cyheptamide (CYE) was used as internal standard. No detectable carry-over and no relevant cross-talk and matrix effect occurred. Samples from 24 treated patients were analysed and drug serum concentrations obtained by this method are in agreement with those of other methods and also are well correlated (r=0.88) in comparison to our routine HPLC-UV method. Based on the analytical results and short run time, the method is suitable to support routine analysis of therapeutic drugs monitoring from human serum of treated patients or for pharmacokinetic studies.

Universal temporal characteristics and vanishing of multifractality in Barkhausen avalanches.

Barkhausen effect in ferromagnetic materials provides an excellent area for investigating scaling phenomena found in disordered systems exhibiting crackling noise. The critical dynamics is characterized by random pulses or avalanches with scale-invariant properties, power-law distributions, and universal features. However, the traditional Barkhausen avalanches statistics may not be sufficient to fully characterize the complex temporal correlation of the magnetic domain walls dynamics. Here we focus on the multifractal scenario to quantify the temporal scaling characteristics of Barkhausen avalanches in polycrystalline and amorphous ferromagnetic films with thicknesses from 50 to 1000 nm. We show that the multifractal properties are dependent on film thickness, although they seem to be insensitive to the structural character of the materials. Moreover, we observe for the first time the vanishing of the multifractality in the domain walls dynamics. As the thickness is reduced, the multifractal behavior gives place to a monofractal one over the entire range of time scales. This reorganization in the temporal scaling characteristics of Barkhausen avalanches is understood as a universal restructuring associated to the dimensional crossover, from three- to two-dimensional magnetization dynamics.

A Novel Multi-step Virtual Screening for the Identification of Human and Mouse mPGES-1 Inhibitors.

We present here the development of a novel virtual screening protocol combining Structure-based and Ligand-based drug design approaches for the identification of mouse mPGES-1 inhibitors. We used the existing 3D structural data of the murine enzyme to hypothesize the inhibitors binding mode, which was the starting point for docking simulations, shape screening, and pharmacophore hypothesis screening. The protocol allowed the identification of 16 mouse mPGES-1 inhibitors with low micromolar activity, which, notably, also inhibit the human enzyme in the same concentration range. The inhibitors predicted binding mode is expected to be the base for the rational drug design of new potent dual species inhibitors of human and murine mPGES-1.