Clustering of reads with alignment-free measures and quality values

BACKGROUND: The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). RESULTS: In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D(q)-type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html)

Fatigue behavior of as-built L-PBF A357.0 parts

Laser-based powder bed fusion (L-PBF) is nowadays the preeminent additive manufacturing (AM) technique to produce metal parts. Nonetheless, relatively few metal powders are currently available for industrial L-PBF, especially if aluminum-based feedstocks are involved. In order to fill the existing gap, A357.0 (also known as A357 or A13570) powders are here processed by L-PBF and, for the first time, the fatigue behavior is investigated in the as-built state to verify the net-shaping potentiality of AM. Both the low-cycle and high-cycle fatigue areas are analyzed to draw the complete Wohler diagram. The infinite lifetime limit is set to 2 7 106stress cycles and the staircase method is applied to calculate a mean fatigue strength of 60 MPa. This value is slightly lower but still comparable to the published data for AlSi10Mg parts manufactured by L-PBF, even if the A357.0 samples considered here have not received any post-processing treatment

Tracking local magnetic dynamics via high-energy charge excitations in a relativistic Mott insulator

We use time- and energy-resolved optical spectroscopy to investigate the coupling of electron-hole excitations to the magnetic environment in the relativistic Mott insulator Na$_2$IrO$_3$. We show that, on the picosecond timescale, the photoinjected electron-hole pairs delocalize on the hexagons of the Ir lattice via the formation of quasi-molecular orbital (QMO) excitations and the exchange of energy with the short-range-ordered zig-zag magnetic background. The possibility of mapping the magnetic dynamics, which is characterized by typical frequencies in the THz range, onto high-energy (1-2 eV) charge excitations provides a new platform to investigate, and possibly control, the dynamics of magnetic interactions in correlated materials with strong spin-orbit coupling, even in the presence of complex magnetic phases.Comment: 5 pages, 4 figures, supplementary informatio

Development of a New and Improved Guanidine-based Rac1 Inhibitor with in Vivo Activity against Non-Small Cell Lung Cancer

Rac1 (Ras-related C3 botulinum toxin substrate 1), is a member of the family of Rho GTPases involved in the dynamic control of cytoskeleton reorganization and other fundamental cellular functions including growth, motility and survival. Aberrant activity of Rac1 and its regulators is common in human cancer. In particular, deregulated expression/activity of Rac Guanine nucleotide Exchange Factors (GEFs), responsible for Rac activation, has been largely associated to a metastatic phenotype and drug resistance. Thus, the development of novel Rac1-GEF interaction inhibitors is a promising strategy for finding new preclinical candidates. In this work, we have studied structure-activity relationships within a new family of N,N’-disubstituted guanidine as Rac1-GEF protein-protein interaction inhibitors, starting from our first developed member 1A-116. We found that new analogue 1D-142, bearing a pyridine ring instead of benzene ring, presents improved antiproliferative activity in human cancer cell lines and higher potency as Rac1-GEF interaction inhibitor in vitro. In addition, 1D-142 reduces TNFα-induced NF-κB nuclear translocation, a mechanisms mediated by Rac1 during cell proliferation and migration in NSCLC. Notably, 1D-142 was used to show for the first time the application of a Rac1 inhibitor in a lung cancer animal model.Fil: Ciarlantini, Matias Sebastián. Instituto Nacional de Tecnología Industrial; ArgentinaFil: Barquero, Andrea Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Wetzler, Diana Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Bayo Fina, Juan Miguel. Universidad Austral. Facultad de Ciencias Biomédicas; Argentina. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; ArgentinaFil: Dodes Traian, Martín Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Bucci, Hernán Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Fiore, Esteban Juan. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; Argentina. Universidad Austral. Facultad de Ciencias Biomédicas; ArgentinaFil: Gandolfi Donadío, Lucía. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Instituto Nacional de Tecnología Industrial; ArgentinaFil: Defelipe, Lucas Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Ramirez, Javier Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad de Microanálisis y Métodos Físicos en Química Orgánica. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Unidad de Microanálisis y Métodos Físicos en Química Orgánica; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Orgánica; ArgentinaFil: Mazzolini Rizzo, Guillermo Daniel. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; Argentina. Universidad Austral. Hospital Universitario Austral; ArgentinaFil: Comin, Maria Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Instituto Nacional de Tecnología Industrial; Argentin

Quantitative risk assessment of human salmonellosis and listeriosis related to the consumption of raw milk in Italy.

Two quantitative risk assessment (RA) models were developed to describe the risk of salmonellosis and listeriosis linked to consumption of raw milk sold in vending machines in Italy. Exposure assessment considered the official microbiological records monitoring raw milk samples from vending machines performed by the regional veterinary authorities from 2008 to 2011, microbial growth during storage, destruction experiments, consumption frequency of raw milk, serving size, and consumption preference. Two separate RA models were developed: one for the consumption of boiled milk and the other for the consumption of raw milk. The RA models predicted no human listeriosis cases per year either in the best or worst storage conditions and with or without boiling raw milk, whereas the annual estimated cases of salmonellosis depend on the dose-response relationships used in the model, the milk storage conditions, and consumer behavior in relation to boiling raw milk or not. For example, the estimated salmonellosis cases ranged from no expected cases, assuming that the entire population boiled milk before consumption, to a maximum of 980,128 cases, assuming that the entire population drank raw milk without boiling, in the worst milk storage conditions, and with the lowest dose-response model. The findings of this study clearly show how consumer behavior could affect the probability and number of salmonellosis cases and in general, the risk of illness. Hence, the proposed RA models emphasize yet again that boiling milk before drinking is a simple yet effective tool to protect consumers against the risk of illness inherent in the consumption of raw milk. The models may also offer risk managers a useful tool to identify or implement appropriate measures to control the risk of acquiring foodborne pathogens. Quantification of the risks associated with raw milk consumption is necessary from a public health perspective

Four-Year Monitoring of Foodborne Pathogens in Raw Milk Sold by Vending Machines in Italy

Prevalence data were collected from official microbiological records monitoring four selected foodborne pathogens (Salmonella spp., Listeria monocytogenes, Escherichia coli O157:H7 and Campylobacter jejuni) in raw milk sold by self-service vending machines in seven Italian Regions (n. 60907 samples from 1239 vending machines) during the years 2008 to 2011. Data of samples analyzed both by culture-based and real-time PCR methods were collected in one Region. A total of 100 raw milk consumers in four regions were interviewed while purchasing raw milk from vending machines. One hundred and seventy eight samples out of 60907 were positive for one of the four foodborne pathogens investigated; overall, 18 samples were positive for Salmonella spp., 83 for L. monocytogenes, 24 for E. coli O157:H7 and 53 for C. jejuni in the seven Regions investigated. There were no significant differences in prevalence among Regions, but a significant increase in C. jejuni prevalence was observed over the years. A comparison of the two different analysis methods showed that real-time PCR is from 2.71 to 9.40 times more sensitive than culture-based method. Data on consumer habits showed that some behaviors may enhance the risk of infection due to raw milk consumption: 37% of consumers do not boil milk before consumption, 93% never use an insulated bag to transport raw milk home, and raw milk is consumed by children under five years of age. The study emphasizes that end-product controls alone are not sufficient to guarantee an adequate level of consumer protection. The beta distribution of positive samples in this study and the data on raw milk consumer habits are useful and appropriate for the development of a National Quantitative Risk Assessment of Salmonella spp., L. monocytogenes, E. coli O157 and C. jejuni related to raw milk consumption