Search results for "PIP"

panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.

2018

Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…

Comparison of Two Solid-Phase Extraction (SPE) Methods for the Identification and Quantification of Porcine Retinal Protein Markers by LC-MS/MS

2018

Proper sample preparation protocols represent a critical step for liquid chromatography-mass spectrometry (LC-MS)-based proteomic study designs and influence the speed, performance and automation of high-throughput data acquisition. The main objective of this study was to compare two commercial solid-phase extraction (SPE)-based sample preparation protocols (comprising SOLA&micro

Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation

2015

Unwinding DNA and unleasing inflammation Fighting infections often comes with collateral damage, which sometimes can be deadly. For instance, in septic shock, the overwhelming release of inflammatory mediators drives multi-organ failure. Rialdi et al. now report a potential new therapeutic target for controlling excessive inflammation: the DNA unwinding enzyme topoisomerase I (Top1) (see the Perspective by Pope and Medzhitov). Upon infection, Top1 specifically localizes to the promoters of pathogen-induced genes and promotes their transcription by helping to recruit RNA polymerase II. Pharmacological inhibition of Top1 in a therapeutic setting increased survival in several mouse models of s…

Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq

2020

International audience; A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2'-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successfully applied to detect and quantify Nm residues in vari…

2020

Friedreich’s ataxia is the commonest autosomal recessive ataxia among population of European descent. Despite the huge advances performed in the last decades, a cure still remains elusive. One of the most studied hallmarks of the disease is the increased production of oxidative stress markers in patients and models. This feature has been the motivation to develop treatments that aim to counteract such boost of free radicals and to enhance the production of antioxidant defenses. In this work, we present and critically review those “antioxidant” drugs that went beyond the disease’s models and were approved for its application in clinical trials. The evaluation of these trials highlights some …

Numerical Study on the Heading Misalignment and Current Velocity Reduction of a Vessel-Shaped Offshore Fish Farm

2019

Recently, the concept of a vessel-shaped fish farm was proposed for open sea applications. The fish farm comprises a vessel-shaped floater, five fish cages, and a single-point mooring system. Such a system weathervanes, and this feature increases the spread area of fish waste. Still, the downstream cages may experience decreased exchange of water flow when the vessel heading is aligned with the current direction, and fish welfare may be jeopardized. To ameliorate the flow conditions, a dynamic positioning (DP) system may be required, and its power consumption should relate to the heading misalignment. This paper proposes an integrated method for predicting the heading misalignment between t…

Using UAV Based 3D Modelling to Provide Smart Monitoring of Road Pavement Conditions

2020

Road pavements need adequate maintenance to ensure that their conditions are kept in a good state throughout their lifespans. For this to be possible, authorities need efficient and effective databases in place, which have up to date and relevant road condition information. However, obtaining this information can be very difficult and costly and for smart city applications, it is vital. Currently, many authorities make maintenance decisions by assuming road conditions, which leads to poor maintenance plans and strategies. This study explores a pathway to obtain key information on a roadway utilizing drone imagery to replicate the roadway as a 3D model. The study validates this by using stru…

Semi-automated annotation of page-based documents within the Genre and Multimodality framework

2016

This paper describes ongoing work on a tool developed for annotating document images for their multimodal features and compiling this information into a corpus. The tool leverages open source computer vision and natural language processing libraries to describe the content and structure of multimodal documents and to generate multiple layers of XML annotation. The paper introduces the annotation schema, describes the document processing pipeline and concludes with a brief description of future work.

CCDC 754487: Experimental Crystal Structure Determination

2010

Related Article: M.Karna, M.Lahtinen, J.Valkonen|2009|Acta Crystallogr.,Sect.E:Struct.Rep.Online|65|o2952|doi:10.1107/S1600536809045139

CCDC 717659: Experimental Crystal Structure Determination

2009

Related Article: K.Raatikainen, J.Huuskonen, M.Lahtinen, P.Metrangolo, K.Rissanen|2009|Chem.Commun.||2160|doi:10.1039/b901473j