OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software

Mathematical Model of Forest Fire Soil-thrower Movement

The design of a forest fire soil-thrower made to prevent and eliminate ground forest fires is presented. A mathematical model of machine movement has been developed, which enables to study the laws of the interaction process of the design with the soil. It is accepted that the machine has two degrees of freedom. The mathematical model has been obtained using the Lagrange equations of the second kind. The design and technological parameters of the forest fire soil-throwing machine, affecting the efficiency of its work, including mass and width of the grip of the ripper casing, mass, radius and frequency of rotation of the milling tool, the number and geometric parameters of the blades are taken into account. Mathematical model enables to determine the effect of these parameters on the characteristics of the movement of ripper casing and milling working body. A mathematical model is needed to synchronize the translational motion of the unit and the rotational motion of the rotor. Formulas have been obtained for the steady motion of the forest fire soil-thrower, that determine the hauling power of tractor and torque that ensures the operation of milling tools

LEGAL PROGRESS IN THE CONDITIONS OF TRANSITION STATE: HISTORICAL AND LAW-CULTURAL MEASUREMENT

The article examines the essential aspects of legal progress in a transitional state in particular. The author identifies and reveals the features of legal progress in the context of political, legal and social instability, when various kinds of institutional transformations, perceptions, changes in the content and principles of the legal regulation mechanism arise and go through the national state and legal space. The paper draws attention to the theoretical feasibility and practical significance of a rigorous analysis of the nature of legal progress, highlighting its criteria in a typologically uncertain legal system, in conditions of a transitional state, which, for example, is important for understanding and evaluating the course of reforms in Russia at the turn of the XX-XXI centuries

Birds and Mammals of the Lena Delta Nature Reserve, Siberia

The Lena Delta is the largest arctic delta covered entirely by tundra. Protected since 1986, it is one of the richest areas in the Arctic north of 71° N for both species diversity and breeding densities. Between 6 June and 17 August 1997, 16 mammal species and 76 bird species were recorded in the Lena Delta Nature Reserve and the surrounding buffer zone. Several species are new to the region: far-eastern curlew, fieldfare, redwing, arctic warbler, red-breasted flycatcher, and common rat. New breeders are merlin and arctic warbler. These 1997 records, combined with those from earlier studies, give a total of 122 bird species for the region. Of these, 67 have been found breeding at least once. Densities ranging from 245 to 641 birds per km² were recorded in two restricted study areas. Such densities are unusually high north of 70° N for non-colonial breeding birds. Lapland longspur (100-300 individuals/km²), red phalarope (up to 200 ind./km²), and several Calidris species were the most common. Ruddy turnstone and dunlin had densities higher than those previously reported from the Lena Delta and other Siberian sites. Among the shorebirds, spotted redshank, pintail snipe, grey plover, dunlin, and curlew sandpiper may have extended their breeding range or increased in population during the last 15 years. But further evidence is still needed to confirm the westward extension of spectacled eider, long-billed dowitcher, and sharp-tailed sandpiper.Le delta de la Lena est le plus grand delta arctique totalement recouvert de toundra. Protégé depuis 1986, il est l'une des zones les plus riches de l'Arctique au nord du 71° de latitude N., tant par la richesse spécifique que par les densités d'oiseaux nicheurs. Seize espèces de mammifères et 76 espèces d'oiseaux ont été observées dans la Réserve naturelle du delta de la Lena et sa zone périphérique entre le 6 juin et le 17 août 1997. Plusieurs espèces sont nouvelles pour la région: courlis de Sibérie, grive litorne, grive mauvis, pouillot boréal, gobemouche nain et rat surmulot. Les nouvelles espèces nicheuses sont le faucon émerillon et le pouillot boréal. Combinés à ceux d'études plus anciennes, nos résultats portent à 122 le nombre total d'espèces d'oiseaux recensés dans cette région et à 67 celui des espèces s'y étant reproduit au moins une fois. Des densités comprises entre 245 et 641 individus au km² ont été trouvées sur deux zones d'étude restreintes, densités exceptionnelles au nord du 70° de latitude N. pour des espèces non coloniales. Les espèces les mieux représentées sont le bruant lapon (100-300 ind./km²), le phalarope à bec large (jusqu'à 200 ind./km²) et plusieurs espèces de Calidris. Le tournepierre à collier et le bécasseau variable avaient des densités plus fortes que celles précédemment rapportées pour le delta de la Lena et d'autres sites sibériens. Le chevalier arlequin, la bécassine à queue pointue, le pluvier argenté, le bécasseau variable et le bécasseau cocorli font partie des limicoles qui semblent avoir étendu leur aire de distribution ou augmenté leur population durant les 15 dernières années, mais d'autres travaux seront nécessaires avant de confirmer l'extension occidentale de l'eider à lunettes, du limnodrome à long bec et du bécasseau à queue pointue

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

ATLAS Run 1 searches for direct pair production of third-generation squarks at the Large Hadron Collider

This paper reviews and extends searches for the direct pair production of the scalar supersymmetric partners of the top and bottom quarks in proton-proton collisions collected by the ATLAS collaboration during the LHC Run 1. Most of the analyses use 20 fb$^{-1}$ of collisions at a centre-of-mass energy of $\sqrt{s}$ = 8 TeV, although in some case an additional 4.7 fb$^{-1}$ of collision data at $\sqrt{s}$ = 7 TeV are used. New analyses are introduced to improve the sensitivity to specific regions of the model parameter space. Since no evidence of third-generation squarks is found, exclusion limits are derived by combining several analyses and are presented in both a simplified model framework, assuming simple decay chains, as well as within the context of more elaborate phenomenological supersymmetric models