ON THE COMPUTATIONAL HARDNESS OF THE CODE EQUIVALENCE PROBLEM IN CRYPTOGRAPHY

Code equivalence is a well-known concept in coding theory. Re-cently, literature saw an increased interest in this notion, due to the intro-duction of protocols based on the hardness of finding the equivalence between two linear codes. In this paper, we analyze the security of code equivalence, with a special focus on the hardest instances, in the interest of cryptographic usage. Our work stems from a thorough review of existing literature, identifies the various types of solvers for the problem, and provides a precise complexity analysis, where previously absent. Furthermore, we are able to improve on the state of the art, providing more efficient algorithm variations, for which we include numerical simulation data. In the end, the goal of this paper is to provide a complete, single point of access, which can be used as a tool for designing schemes that rely on the code equivalence problem

Analysis of LINE1 Retrotransposons in Huntington’s Disease

Transposable elements (TEs) are mobile genetic elements that made up about half the human genome. Among them, the autonomous non-LTR retrotransposon long interspersed nuclear element-1 (L1) is the only currently active TE in mammals and covers about 17% of the mammalian genome. L1s exert their function as structural elements in the genome, as transcribed RNAs to influence chromatin structure and as retrotransposed elements to shape genomic variation in somatic cells. L1s activity has been shown altered in several diseases of the nervous system. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by an expansion of a CAG repeat in the HTT gene which leads to a gradual loss of neurons most prominently in the striatum and, to a lesser extent, in cortical brain regions. The length of the expanded CAG tract is related to age at disease onset, with longer repeats leading to earlier onset. Here we carried out bioinformatic analysis of public RNA-seq data of a panel of HD mouse models showing that a decrease of L1 RNA expression recapitulates two hallmarks of the disease: it correlates to CAG repeat length and it occurs in the striatum, the site of neurodegeneration. Results were then experimentally validated in HttQ111 knock-in mice. The expression of L1-encoded proteins was independent from L1 RNA levels and differentially regulated in time and tissues. The pattern of expression L1 RNAs in human HD post-mortem brains showed similarity to mouse models of the disease. This work suggests the need for further study of L1s in HD and adds support to the current hypothesis that dysregulation of TEs may be involved in neurodegenerative diseases

Life-history and diet of two populations of Natrix maura (Reptilia, Colubridae) from contrasted habitats in Sardinia

Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia.Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia.Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia

An Air-well sparging minifermenter system for high-throughput protein production.

BackgroundOver the last few years High-Throughput Protein Production (HTPP) has played a crucial role for functional proteomics. High-quality, high yield and fast recombinant protein production are critical for new HTPP technologies. Escherichia coli is usually the expression system of choice in protein production thanks to its fast growth, ease of handling and high yields of protein produced. Even though shake-flask cultures are widely used, there is an increasing need for easy to handle, lab scale, high throughput systems.ResultsIn this article we described a novel minifermenter system suitable for HTPP. The Air-Well minifermenter system is made by a homogeneous air sparging device that includes an air diffusion system, and a stainless steel 96 needle plate integrated with a 96 deep well plate where cultures take place. This system provides aeration to achieve higher optical density growth compared to classical shaking growth without the decrease in pH value and bacterial viability. Moreover the yield of recombinant protein is up to 3-fold higher with a considerable improvement in the amount of full length proteins.ConclusionsHigh throughput production of hundreds of proteins in parallel can be obtained sparging air in a continuous and controlled manner. The system used is modular and can be easily modified and scaled up to meet the demands for HTPP

Transposable element activation promotes neurodegeneration in a Drosophila model of Huntington's disease

Huntington's disease (HD) is an autosomal dominant disorder with progressive motor dysfunction and cognitive decline. The disease is caused by a CAG repeat expansion in the IT15 gene, which elongates a polyglutamine stretch of the HD protein, Huntingtin. No therapeutic treatments are available, and new pharmacological targets are needed. Retrotransposons are transposable elements (TEs) that represent 40% and 30% of the human and Drosophila genomes and replicate through an RNA intermediate. Mounting evidence suggests that mammalian TEs are active during neurogenesis and may be involved in diseases of the nervous system. Here we show that TE expression and mobilization are increased in a Drosophila melanogaster HD model. By inhibiting TE mobilization with Reverse Transcriptase inhibitors, polyQ-dependent eye neurodegeneration and genome instability in larval brains are rescued and fly lifespan is increased. These results suggest that TE activation may be involved in polyQ-induced neurotoxicity and a potential pharmacological target

Characterization of Contractile Forces Generated by Stretch Marks Fibroblasts: In Vitro Study

Abstract: Authors present a study about the contraction forces observed in striae distensae fibroblasts (SMF) in a collagen scaffold. Collagen lattices were used to study the mechanical behavior of SDF within the collagen matrix compared to the lattices produced using the healthy skin derived fibroblasts (NSF). A Forcebox device was used to measure the contractile forces. Striae Rubrae fibroblast’s contractile force was by 28% greater than that generated by the NSF and striae albae fibroblasts (P<0.05). Anomalies and especially differences in forces generated by SMF were observed through all our experiments. These findings complete and corroborate the results and information published in our previous studies. Level of Evidence V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266

The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)-enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements-enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.-Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

Abrupt changes in the graphene on Ge(001) system at the onset of surface melting

By combining scanning probe microscopy with Raman and x-ray photoelectron spectroscopies, we investigate the evolution of CVD-grown graphene/Ge(001) as a function of the deposition temperature in close proximity to the Ge melting point, highlighting an abrupt change of the graphene's quality, morphology, electronic properties and growth mode at 930 degrees. We attribute this discontinuity to the incomplete surface melting of the Ge substrate and show how incomplete melting explains a variety of diverse and long-debated peculiar features of the graphene/Ge(001), including the characteristic nanostructuring of the Ge substrate induced by graphene overgrowth. We find that the quasi-liquid Ge layer formed close to 930 degrees is fundamental to obtain high-quality graphene, while a temperature decrease of 10 degrees already results in a wrinkled and defective graphene film.Comment: in pres

Striae Distensae: In Vitro Study and Assessment of Combined Treatment With Sodium Ascorbate and Platelet-Rich Plasma on Fibroblasts

Introduction: Striae distensae (SD) appear clinically as parallel striae, lying perpendicular to the tension lines of the skin. SD evolve into two clinical phases, an initial inflammatory phase in which they are called “striae rubrae” (SR) and a chronic phase in which they are called striae albae (SA). Fibroblasts seem to play a key role in the pathogenesis of stretch marks. This study was aimed at describing and analyzing stretch marks-derived fibroblasts (SMF), the differences between SR- and SA-derived fibroblasts (SRF, SAF), testing two treatments in vitro (sodium ascorbate and PrP) on SAF. Material and Methods: To characterize the SMF, the expression of alpha smooth muscle actin (alpha SMA) was investigated. Type I collagen expression was measured in SAF, before and after adding different PrP concentrations and sodium ascorbate in the culture medium. Results were processed through statistical analysis models using the Student’s t-test. Results: A significant increase in alpha SMA (P <0.001) was observed in SRF. SAF treated with PrP and sodium ascorbate showed a resumption of their metabolic activity by an increase in collagen type I production and cell proliferation. After 24 h of incubation with PrP 1% and PrP 5% + sodium ascorbate, cell viability was increased by 140% and 151% and by 156 and 178% after 48 h, respectively, compared to the control. Conclusion: Our study shows that a biologically mediated improvement in SMF metabolic activity is possible. Our promising results require further trials to be able to confirm the reproducibility of this combined treatment, particularly in vivo. No Level Assigned: This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable