ROBUST TECHNIQUES FOR BUILDING FOOTPRINT EXTRACTION IN AERIAL LASER SCANNING 3D POINT CLOUDS

The building footprint is crucial for a volumetric 3D representation of a building that is applied in urban planning, 3D city modeling, cadastral and topographic map generation. Aerial laser scanning (ALS) has been recognized as the most suitable means of large-scale 3D point cloud data (PCD) acquisition. PCD can produce geometric detail of a scanned surface. However, it is almost impossible to get point clouds without noise and outliers. Besides, data incompleteness and occlusions are two common phenomena for PCD. Most of the existing methods for building footprint extraction employ classification, segmentation, voting techniques (e.g., Hough-Transform or RANSAC), or Principal Component Analysis (PCA) based methods. It is known that classical PCA is highly sensitive to outliers, even RANSAC which is known as a robust technique for shape detection is not free from outlier effects. This paper presents a novel algorithm that employs MCMD (maximum consistency within minimum distance), MSAC (a robust variant of RANSAC) and a robust regression to extract reliable building footprints in the presence of outliers, missing points and irregular data distributions. The algorithm is successfully demonstrated through two sets of ALS PCD

Psip1/Ledgf p75 restrains<i>Hox</i>gene expression by recruiting both trithorax and polycomb group proteins

Trithorax and polycomb group proteins are generally thought to antagonize one another. The trithorax familymember MLL (myeloid/lymphoid or mixedlineage leukemia) is presumed to activate Hox expression, counteracting polycomb-mediated repression. PC4 and SF2 interacting protein 1 (PSIP1)/p75, also known as LEDGF, whose PWWP domain binds to H3K36me3, interacts with MLL and tethers MLL fusion proteins toHOXA9 in leukaemias. Here we show, unexpectedly, that Psip1/p75 regulates homeotic genes by recruiting not only MLL complexes, but also the polycomb group protein Bmi1. In Psip1-/- cells binding of Mll1/2, Bmi1 and the co-repressor Ctbp1 at Hox loci are all abrogated and Hoxa and Hoxd mRNA expression increased. Our data not only reveal a potential mechanism of action for Psip1 in the regulation of Hox genes but also suggest an unexpected interplay between proteins usually considered as transcriptional activators and repressors. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Personalized genomic medicine depends on integrated analyses that combine genetic and phenotypic data from individual patients with reference knowledge of the functional and clinical significance of sequence variants. Sources of this reference knowledge include the ClinVar repository of human genetic variants, a community resource that accepts submissions from external groups, and UniProtKB/Swiss-Prot, an expert-curated resource of protein sequences and functional annotation. UniProtKB/Swiss-Prot provides knowledge on the functional impact and clinical significance of over 30 000 human protein-coding sequence variants, curated from peer-reviewed literature reports. Here we present a pilot study that lays the groundwork for the integration of curated knowledge of protein sequence variation from UniProtKB/Swiss-Prot with ClinVar. We show that existing interpretations of variant pathogenicity in UniProtKB/Swiss-Prot and ClinVar are highly concordant, with 88% of variants that are common to the two resources having interpretations of clinical significance that agree. Re-curation of a subset of UniProtKB/Swiss-Prot variants according to American College of Medical Genetics and Genomics (ACMG) guidelines using ClinGen tools further increases this level of agreement, mainly due to the reclassification of supposedly pathogenic variants as benign, based on newly available population frequency data. We have now incorporated ACMG guidelines and ClinGen tools into the UniProt Knowledgebase (UniProtKB) curation workflow and routinely submit variant data from UniProtKB/Swiss-Prot to ClinVar. These efforts will increase the usability and utilization of UniProtKB variant data and will facilitate the continuing (re-)evaluation of clinical variant interpretations as data sets and knowledge evolve

HAMAP in 2015: updates to the protein family classification and annotation system

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorith

Exploring the synergies between cross compliance and certification schemes

This report presents some of the interim results of the project 'Facilitating the CAP reform: Compliance and competitiveness of European agriculture'. It examines the similarities and differences between mandatory cross compliance standards and those set by voluntary certification schemes. There is a potential synergy between cross compliance and certification schemes, not least because both approaches set minimum standards and enforce those standards through inspection systems. Although there are some strong limitations, there is sufficient overlap in the standards set and in approaches to control to warrant further investigation of the potential for the harmonisation of standards and collaborative approaches to control

HAMAP in 2013, new developments in the protein family classification and annotation system

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profile

Compliance with mandatory standards in agriculture : a comparative approach of the EU vis-à-vis the United States, Canada and New Zealand

This report presents some of the interim results of the project 'Facilitating the CAP reform: Compliance and competitiveness of European agriculture'. It summarises and integrates the implementation of cross compliance measures in seven EU countries (France, Germany, Italy, Netherlands, United Kingdom, Spain and Poland), with a particular focus on the degree of compliance and the costs of compliance. Also, the implementation of similar measures is examined in three non-EU countries (Canada, United States and New Zealand)

Time to look for evidence : Results-based approach to biodiversity conservation on farmland in Europe

Increased use of annual payments to land managers for ecological outcomes indicates a growing interest in exploring the potential of this approach. In this viewpoint, we drew on the experiences of all schemes paying for biodiversity outcomes/results on agricultural land operating in the EU and EFTA countries with the aim of reviewing the decisive elements of the schemes' design and implementation as well as the challenges and opportunities of adopting a results-based approach. We analysed the characteristics of results-based schemes using evidence from peer-reviewed literature, technical reports, scheme practitioners and experts in agri-environment-climate policy. We developed a typology of the schemes and explored critical issues influencing the feasibility and performance of results-based schemes. The evidence to date shows that there are at least 11 advantages to the results-based approach not found in management-based schemes with similar objectives, dealing with environmental efficiency, farmers' participation and development of local biodiversity-based projects. Although results-based approaches have specific challenges at every stage of design and implementation, for many of these the existing schemes provide potential solutions. There is also some apprehension about trying a results-based approach in Mediterranean, central and eastern EU Member States. We conclude that there is clear potential to expand the approach in the European Union for the Rural Development programming period for 2021-2028. Nevertheless, evidence is needed about the approach's efficiency in delivering conservation outcomes in the long term, its additionality, impact on the knowledge and attitudes of land managers and society at large, development of ways of rewarding the achievement of actual results, as well as its potential for stimulating innovative grassroots solutions.Peer reviewe