High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly

Mouse E14 embryonic stem cells (ESCs) are a well-characterized and widespread used ESC line, often employed for genome-wide studies involving next generation sequencing analysis. More than 2×10(9) sequences made on Illumina platform derived from the genome of E14 ESCs were used to build a database of about 2.7×10(6) single nucleotide variants (SNVs). The identified variants are enriched in intergenic regions, but several thousands reside in gene exons and regulatory regions, such as promoters, enhancers, splicing sites and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly reference that increases the number of mapped reads of about 5%. We performed a Reduced Representation Bisulfite Sequencing on E14 ESCs and we obtained an increase of about 120,000 called CpGs and avoided about 20,000 wrong CpG calls with respect to the mm9 genome reference

Coverage and Deployment Analysis of Narrowband Internet of Things in the Wild

Narrowband Internet of Things (NB-IoT) is gaining momentum as a promising technology for massive Machine Type Communication (mMTC). Given that its deployment is rapidly progressing worldwide, measurement campaigns and performance analyses are needed to better understand the system and move toward its enhancement. With this aim, this paper presents a large scale measurement campaign and empirical analysis of NB-IoT on operational networks, and discloses valuable insights in terms of deployment strategies and radio coverage performance. The reported results also serve as examples showing the potential usage of the collected dataset, which we make open-source along with a lightweight data visualization platform.Comment: Accepted for publication in IEEE Communications Magazine (Internet of Things and Sensor Networks Series

Equivalence and Characterizations of Linear Rank-Metric Codes Based on Invariants

We show that the sequence of dimensions of the linear spaces, generated by a given rank-metric code together with itself under several applications of a field automorphism, is an invariant for the whole equivalence class of the code. The same property is proven for the sequence of dimensions of the intersections of itself under several applications of a field automorphism. These invariants give rise to easily computable criteria to check if two codes are inequivalent. We derive some concrete values and bounds for these dimension sequences for some known families of rank-metric codes, namely Gabidulin and (generalized) twisted Gabidulin codes. We then derive conditions on the length of the codes with respect to the field extension degree, such that codes from different families cannot be equivalent. Furthermore, we derive upper and lower bounds on the number of equivalence classes of Gabidulin codes and twisted Gabidulin codes, improving a result of Schmidt and Zhou for a wider range of parameters. In the end we use the aforementioned sequences to determine a characterization result for Gabidulin codes.Comment: 37 pages, 1 figure, 3 tables, extended version of arXiv:1905.1132

A Cross-Layer Location-Based Approach for Mobile-Controlled Connectivity

We investigate into the potentiality of an enhanced Power and Location-based Vertical Handover (PLB-VHO) approach, based on a combination of physical parameters (i.e., location and power attenuation information), for mobile-controlled connectivity across UMTS and WLAN networks. We show that the location information in a multiparameter vertical handover can significantly enhance communication performance. In the presented approach a power attenuation map for the visited area is built and kept updated by exploiting the information sharing of power measurements with other cooperating mobile devices inside the visited networks. Such information is then used for connectivity switching in handover decisions. The analytical model for the proposed technique is first presented and then compared with a traditional Power-Based approach and a simplified Location-Based technique. Simulation results show the effectiveness of PLB-VHO approach, in terms of (i) network performance optimization and (ii) limitation of unnecessary handovers (i.e., mitigation ofping-pong effect)

Significant relationship of combined ACP1/PTPN22 genotype variants with the growth of uterine leiomyomas

Objective: To analyze the interaction between ACP1 and PTPN22 concerning their effects on the growth of the tumor. In previous paper we have shown (i) that ACP1*B/*B genotype of ACP1 is negatively associated with the growth of leiomyomas and (ii) that there is a negative association of *C/*C genotype of PTPN22 with tumor growth. Materials and methods: Two hundred and three White women from the population of Rome with symptomatic leiomyomas were recruited in the University of Rome Tor Vergata. All subjects gave consent for the participation in the study that was approved by the Council of Department. ACP1 and PTPN22 genotypes were determined by DNA analysis. Results: The proportion of women with small leiomyomas decreases with the decrease of the number of protective factors and it is 37.2% in women carrying the joint genotype ACP1*B/*B-PTPN22 *C/*C (two protective factors) and 0% in women carrying no protective factors. Three way contingency table analysis by a log linear model has shown no evidence of epistatic interaction between the two genetic systems but a highly significant cooperative effect on the dimension of leiomyomas. There is a highly significant negative correlation between the number of protective factors and the dimension of leiomyomas with a minimum (cm 4.74) in women carrying the joint genotype ACP1*B/B-PTPN22 *C/*C and a maximum (cm 7.25) in women carrying no protective factors. Conclusion: The present study suggests a cooperative interaction between ACP1 and PTPN22 concerning their effects on the growth of uterine leiomyomas. The determination of the genotype of the two systems may help to evaluate the risk of clinical manifestations of this common benign tumor. Keywords: ACP1, PTPN22, Uterine leiomyoma