Enumeration of RNA structures by Matrix Models

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed. We analyze the distribution of the genus of pseudoknots as a function of the total number of nucleotides along the phosphate-sugar backbone.Comment: RevTeX, 4 pages, 2 figure

Mathematical modelling of the loss of tissue compression responsiveness and its role in solid tumour development

This paper presents a mathematical model of normal and abnormal tissue growth. The modelling focuses on the potential role that stress responsiveness may play in causing proliferative disorders which are at the basis of the development of avascular tumours. In particular, we study how an incorrect sensing of its compression state by a cell population can represent a clonal advantage and can generate hyperplasia and tumour growth with well known characteristics such as compression of the tissue, structural changes in the extracellular matrix, change in the percentage of cell type (normal or abnormal), extracellular matrix and extracellular liquid. A spatially independent description of the phenomenon is given initially by a system of nonlinear ordinary dierential equations which is explicitly solved in some cases of biological interest showing a rst phase in which some abnormal cells simply replace the normal ones, a second phase in which the hyper-proliferation of the abnormal cells causes a progressive compression within the tissue itself, and a third phase in which the tissue reaches a compressed state, which presses on the surrounding environment. A travelling wave analysis is also performed which gives an estimate of the velocity of the growing mass

Spontaneous chirality via long-range electrostatic forces

We consider a model for periodic patterns of charges constrained over a cylindrical surface. In particular we focus on patterns of chiral helices, achiral rings or vertical lamellae, with the constraint of global electroneutrality. We study the dependence of the patterns' size and pitch angle on the radius of the cylinder and salt concentration. We obtain a phase diagram by using numerical and analytic techniques. For pure Coulomb interactions, we find a ring phase for small radii and a chiral helical phase for large radii. At a critical salt concentration, the characteristic domain size diverges, resulting in macroscopic phase segregation of the components and restoring chiral symmetry. We discuss possible consequences and generalizations of our model.Comment: Revtex, 4 pages, 4 figure

Slab cracking influence in the fatigue assessment of continuous composite decks

The paper analyzes the influence of the slab cracking in the fatigue assessment of continuous composite decks by considering the effects of slab casting sequences and the shrinkage components (thermal, endogenous and drying). A numerical procedure for the stress calculation accounting for the tension stiffening of the slab longitudinal rebars is presented. The long term effects of casting sequences and concrete shrinkage are analysed with a simplified procedure based on the application of the modular ratio method. With reference to a realistic continuous twin girder composite deck the fatigue verification of the longitudinal girders is carried out by considering three different casting modalities. The obtained results show the important role of the slab casting sequences in the stress range calculation and the remarkable influence of the slab cracking in the fatigue assessment

Enabling Design and Simulation of Massive Parallel Nanoarchitectures

A common element in emerging nanotechnologies is the increasing complex- ity of the problems to face when attempting the design phase, because issues related to technology, specific application and architecture must be evalu- ated simultaneously. In several cases faced problems are known, but require a fresh re-think on the basis of different constraints not enforced by standard design tools. Among the emerging nanotechnologies, the two-dimensional structures based on nanowire arrays is promising in particular for massively parallel architec- tures. Several studies have been proposed on the exploration of the space of architectural solutions, but only a few derived high-level information from the results of an extended and reliable characterization of low-level structures. The tool we present is of aid in the design of circuits based on nanotech- nologies, here discussed in the specific case of nanowire arrays, as best candi- date for massively parallel architectures. It enables the designer to start from a standard High-level Description Languages (HDL), inherits constraints at physical level and applies them when organizing the physical implementation of the circuit elements and of their connections. It provides a complete simu- lation environment with two levels of refinement. One for DC analysis using a fast engine based on a simple switch level model. The other for obtaining transient performance based on automatic extraction of circuit parasitics, on detailed device (nanowire-FET) information derived by experiments or by existing accurate models, and on spice-level modeling of the nanoarray. Re- sults about the method used for the design and simulation of circuits based on nanowire-FET and nanoarray will be presente

Prevalence of PNPLA1 Gene Mutation in 48 Breeding Golden Retriever Dogs

A non-epidermolytic ichthyosis has been identified in Golden Retrievers due to a variant in the PNPLA1 gene, and a genetic test is available to detect wild-type, heterozygous and homozygous dogs. The aims of this study were to investigate the prevalence of the PNPLA1 gene variant in Golden Retrievers used for breeding and to provide more information to breeders in order to restrict the spread of this disease. Clinical examination and assessment of the PNPLA1 genotype using PCR testing of oral swabs were performed in 48 breeding Golden Retrievers. Wild-type, heterozygous or homozygous variants of the PNPLA1 gene were demonstrated in 10 (21%), 23 (48%), and 15 (31%) of the 48 dogs, respectively. In only 3 of the 48 dogs were clinical signs suggestive of ichthyosis identified. Data collected agreed with data reported in the literature. The high prevalence of homozygous and heterozygous variants makes the exclusion of mutated dogs from breeding impractical. Furthermore, the reliability of the PNPLA1 mutation in prediction of clinical signs of ichthyosis is unclear. Additional studies are needed to investigate if PNPLA1 is the only gene involved or if other genes and environmental factors have a role in the development of ichthyosis in Golden Retrievers

<b><i>Topoisomerase 1</i></b> Promoter Variants and Benefit from Irinotecan in Metastatic Colorectal Cancer Patients

Objective: Topoisomerase 1 (topo-1) is an important target for the treatment of metastatic colorectal cancer (CRC). The aim of the present study was to evaluate the correlation between topo-1 single-nucleotide polymorphisms (SNPs) and clinical outcome in metastatic CRC (mCRC) patients. Methods: With the use of specific software (PROMO 3.0), we performed an in silico analysis of topo-1 promoter SNPs; the rs6072249 and rs34282819 SNPs were included in the study. DNA was extracted from 105 mCRC patients treated with FOLFIRI ± bevacizumab in the first line. SNP genotyping was performed by real-time PCR. Genotypes were correlated with clinical parameters (objective response rate, progression-free survival, and overall survival). Results: No single genotype was significantly associated with clinical variables. The G allelic variant of rs6072249 topo-1 SNP is responsible for GC factor and X-box-binding protein transcription factor binding. The same allelic variant showed a nonsignificant trend toward a shorter progression-free survival (GG, 7.5 months; other genotypes, 9.3 months; HR 1.823, 95% CI 0.8904-3.734; p = 0.1). Conclusion: Further analyses are needed to confirm that the topo-1 SNP rs6072249 and transcription factor interaction could be a part of tools to predict clinical outcome in mCRC patients treated with irinotecan-based regimens

Expanding the neurological phenotype of ring chromosome 10 syndrome: A case report and review of the literature

Ring chromosome 10 [r(10)] syndrome is a rare genetic condition, currently described in the medical literature in a small number of case report studies. Typical clinical features include microcephaly, short stature, facial dysmorphisms, ophthalmologic abnormalities and genitourinary malformations. We report a novel case of r(10) syndrome and review the neurological and neuro-radiological phenotypes of the previously described cases. Our patient, a 3 year old Italian girl, represents the 20th case of r(10) syndrome described to date. Intellectual disability/developmental delay (ID/DD), microcephaly, strabismus, hypotonia, stereotyped/aggressive behaviors and elec-troencephalographic abnormalities were identified in our patient, and in a series of previous cases. A brain MRI disclosed a complex malformation involving both the vermis and cerebellar hemispheres; in the literature, posterior cranial fossa abnormalities were documented by CT scan in another case. Two genes deleted in our case (ZMYND11 in 10p and EBF3 in 10q) are involved in autosomal dominant neurodevelopmental disorders, characterized by different expressions of brain and posterior cranial fossa abnormalities, ID/DD, hypotonia and behavioral problems. Our case expands the neurological and neuroradiological phenotype of r(10) syndrome. Although r(10) syndrome represents an extremely rare condition, with a clinical characterization limited to case reports, the recurrence of specific neurological and neuroradiological features suggests the need for specific genotype-phenotype studies

Autologous fibrin sealant (Vivostat®) in the neurosurgical practice: Part I: Intracranial surgical procedure

Background: Hemorrhages, cerebrospinal fluid (CSF) fistula and infections are the most challenging postoperative complications in Neurosurgery. In this study, we report our preliminary results using a fully autologous fibrin sealant agent, the Vivostat® system, in achieving hemostasis and CSF leakage repair during cranio-cerebral procedures. Methods: From January 2012 to March 2014, 77 patients were studied prospectively and data were collected and analyzed. Autologous fibrin sealant, taken from patient's blood, was prepared with the Vivostat® system and applied on the resection bed or above the dura mater to achieve hemostasis and dural sealing. The surgical technique, time to bleeding control and associated complications were recorded. Results: A total of 79 neurosurgical procedures have been performed on 77 patients. In the majority of cases (98%) the same autologous fbrin glue provided rapid hemostasis and dural sealing. No patient developed allergic reactions or systemic complications in association with its application. There were no cases of cerebral hematoma, swelling, infection, or epileptic seizures after surgery whether in the immediate or in late period follow-up. Conclusions: In this preliminary study, the easy and direct application of autologous fibrin sealant agent helped in controlling cerebral bleeding and in providing prompt and efficient dural sealing with resolution of CSF leaks. Although the use of autologous fibrin glue seems to be safe, easy, and effective, further investigations are strongly recommended to quantify real advantages and potential limitations