PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Deep observation of the NGC1275 region with MAGIC: search of diffuse gamma-ray emission from cosmic rays in the Perseus cluster

Clusters of galaxies are expected to be reservoirs of cosmic rays (CRs) that should produce diffuse γ-ray emission due to their hadronic interactions with the intra-cluster medium. The nearby Perseus cool-core cluster, identified as the most promising target to search for such an emission, has been observed with the MAGIC telescopes at very-high energies (VHE, E ≥ 100 GeV) for a total of 253 hr from 2009 to 2014. The active nuclei of NGC 1275, the central dominant galaxy of the cluster, and IC 310, lying at about 0.6º from the centre, have been detected as point-like VHE γ-ray emitters during the first phase of this campaign. We report an updated measurement of the NGC 1275 spectrum, which is described well by a power law with a photon index Γ = 3.6 ± 0.2_(stat) ± 0.2_(syst) between 90 GeV and 1200 GeV. We do not detect any diffuse γ-ray emission from the cluster and so set stringent constraints on its CR population. To bracket the uncertainties over the CR spatial and spectral distributions, we adopt different spatial templates and power-law spectral indexes α. For α = 2.2, the CR-to-thermal pressure within the cluster virial radius is constrained to be ≤ 1 − 2%, except if CRs can propagate out of the cluster core, generating a flatter radial distribution and releasing the CR-to-thermal pressure constraint to ≤ 20%. Assuming that the observed radio mini-halo of Perseus is generated by secondary electrons from CR hadronic interactions, we can derive lower limits on the central magnetic field, B_(0), that depend on the CR distribution. For α = 2.2, B_(0) ≥ 5 − 8 µG, which is below the ∼25 µG inferred from Faraday rotation measurements, whereas for α ≤ 2.1, the hadronic interpretation of the diffuse radio emission contrasts with our γ-ray flux upper limits independently of the magnetic field strength.

Transmission and Transport of Energy in the Western U.S. and Canada: A Law and Policy Road Map

This collection of short essays arose from the inaugural meeting of the Idaho Symposium on Energy in the West, which was held in November, 2014. The topic for this first Symposium was Transmission and Transport of Energy in the Western U.S. and Canada: A Law and Policy Road Map. The essays in this collection provide a notable introduction to the major energy issues facing the West today. Topics include: building a resilient legal architecture for western energy production; natural gas flaring; transmission planning for wind energy; utilities and rooftop solar; special considerations for western states and the Clean Power Plan; the Clean Power Plan's implications for the western grid; siting renewable energy on public lands; and implications of utility reform in New York and Hawaii for the Northwest.

The Future Direction of Delaware Law (Including a Brief Exegesis on Fee Shifting Bylaws)

Delaware sets the governance standards for most public companies. The ability to attract corporations could not be explained solely by the existence of a favorable statutory regime. Delaware was not invariably the first or the only state to implement management friendly provisions. Given the interpretive gaps in the statute and the critical importance of the common law in the governance process, courts played an outsized role in setting legal standards. The management friendly nature of the Delaware courts contributed significantly to the state’s attraction to public corporations. A current example of a management friendly trend in the case law had seen the recent decisions setting out the board’s authority to adopt bylaws under Section 109 of the Delaware General Corporation Law (DGCL), particularly those involving the shifting of fees in litigation against the corporation or its directors. The DGCL allows bylaws that address “the business of the corporation, the conduct of its affairs, and its rights or powers or the rights or powers of its stockholders, directors, officers or employees.” The broad parameters are, however, subject to limits. Bylaws cannot be inconsistent with the certificate of incorporation or “the law.” Law includes the common law. The Delaware courts have used the limitations imposed by “the law” to severely restrict the reach of shareholder inspired bylaws. The courts have not used the same principles to impose similar restraints on bylaws adopted by the board of directors. This can be seen with respect to bylaws that restrict or even eliminate the right of shareholders to bring actions against management and the corporation. In ATP Tour, Inc. v. Deutscher Tennis Bund the court approved a fee shifting bylaw that had littl relationship to the internal affairs of the corporation. The decision upheld the bylaw as facially valid.The decision ignored a number of obvious legal infirmities. Among other things, the decision did not adequately address the requirement in Section 109(b) that bylaws be consistent with “the law.” The decision obliquely acknowledged that the provisions would “by their nature, deter litigation” but otherwise made no effort to assess the impact of this deterrence on shareholders causes of action. The provision in fact had the practical effect of restricting, if not eliminating, litigation rights granted by the DGCL and the common law. Perhaps most significantly, however, the bylaws significantly limited common law rights of shareholders to bring actions against the corporation and the board. Given the high dismissal rates for these actions, fee shifting bylaws imposed a meaningful risk of liability on plaintiffs. Moreover, because judgments in derivative suits were paid to the corporation, shareholders serving as plaintiffs confronted the risk of liability without any offsetting direct benefit. By preventing suits in this area, the bylaw effectively insulated the behavior of boards from legal challenge. The ATP decision was poorly reasoned and overstepped acceptable boundaries. The management friendly decision threatened the preeminent role of Delaware in the development of corporate law. The decision raised the specter of federal intervention and the potential for meaningful competition from the states. Because the opinion examined the bylaw in the context of non-stock companies, the reasoning may remain applicable only to those entities and never make the leap to for-profit stock corporations. Nonetheless, the analysis reflects a management friendly approach that does not adequately take into account the impact of the provision on the rights of shareholders.

Mineralogical analysis of ceramic tiles by FTIR: A quantitative attempt

A method for quantitative mineralogical analysis by ATR-FTIR has been developed. The method relies on the use of the main band of calcite as a reference for the normalization of the IR spectrum of a mineral sample. In this way, the molar absorptivity coefficient in the Lambert–Beer law and the components of a mixture in mole percentage can be calculated. The GAMS equation modeling environment and the NLP solver CONOPT (©ARKI Consulting and Development) were used to correlate the experimental data in the samples considered. Mixtures of different minerals and gypsum were used in order to measure the minimum band intensity that must be considered for calculations and the detection limit. Accordingly, bands of intensity lower than 0.01 were discarded. The detection limit for gypsum was about 7% (mol/total mole). Good agreement was obtained when this FTIR method was applied to ceramic tiles previously analyzed by X-ray diffraction (XRD) or mineral mixtures prepared in the lab.

Member State BITS after the Treaty of Lisbon: solid foundation or first victims of EU investment policy? Research Paper in Law, 02/2012

[Introduction.] This paper discusses the uncertain future of Member State BITs with third countries in the light of the developing EU investment policy. The question will be examined on the basis of the proposed Regulation establishing transitional arrangements for bilateral investment agreements between Member States and third countries presented by the Commission on 7 July 20101 and the European Parliament’s Position adopted at first reading on 10 May 2011.2 The proposed Regulation and the Commission Communication of the same day are meant to be the “first steps in the development of an EU international investment policy”.3 The first chapters present the legal framework relevant for this question and its evolution to better understand the particular challenges of this transition process. The second chapter examines the relationship of EU law and investment law, with a brief introduction of the notion of investment law and the scope of the EU’s new investment competence. The third chapter outlines the legal framework for the continuation and termination of treaties under international and EU law. The fourth chapter concerns BITs, first covering the particular nature of BITs and then the CJEU’s judgments in the BIT Cases of 2009. The fifth chapter consists of a step by step analysis of the different provisions of the proposed Regulation.

L’Europa sociale e il diritto: il contributo del metodo comparato [Social Europe and the law: the contribution of the comparative method]. WP C.S.D.L.E. "Massimo D'Antona" .INT - 94/2012

The essay explores the evolution of comparative law and the contribution of its more recent methodological results on the process of European social integration through law. The analysis of the comparative method in general glides on a discipline, such a as labour law, traditionally linked to the "nomos" of the nation state and looks at the process of its own supranationalization through the lens which is the comparative method; a method used mainly by the juridical format (national and supranational courts). The analysis focuses on the fixed term contract and on the vexing question of collective social fundamental rights vis a vis fundamental economic freedoms in the EU where national constitutional traditions and supranational principals risk collision due also to the comparative method.

The Case Law of the ECJ concerning the Free Provision of Services : 2000 - 2005. Research Papers in Law, 2/2006

Introduction. The present overview covers the period starting from 2000 until the end of 2005.1 This is the follow-up to our overview covering the 1995-1999 period.2 The first striking feature of the present contribution is that it has to deal with almost 3,5 times as many cases as the previous one. Hence, the ECJ has gone from deciding 40 cases in the five year period between 1995- 1999 to deciding over 140 cases based on Art 49 between 2000-2005. This confirms, beyond any doubt, the tendency already observed in our previous overview, that a “third generation” case law on services is being developed at a very rapid pace by the ECJ. This third generation case law is based on the idea that Article 49 EC is not limited to striking down discriminatory measures but extends to the elimination of all hindrances to the free provision of services. This idea was first expressed in the Tourist Guide cases, the Greek and Dutch TV cases and most importantly in the Säger case.3 It has been confirmed ever since. As was to be expected, this broad brush approach of the Court’s has led to an ever-increasing amount of litigation reaching Luxemburg. It is clear that, if indicators were used to weight the importance of the Court’s case law during the relevant period, services would score much higher than goods, both from a quantitative and from a qualitative perspective.4 Hence, contrary to the previous overview, this one cannot deal in detail with any of the judgments delivered during the reference period. The aim of the present contribution is restricted to presenting the basic trends of the Court’s case law in the field of services Therefore, the analysis follows a fundamentally horizontal approach, fleetingly considering the facts of individual cases, with a view to identifying the conceptual premises of the Court’s approach to the free movement of services. Nonetheless, the substantial solutions adopted by the Court in some key topics, such as concession contracts, healthcare services, posted workers and gambling, are also presented as case studies. In this regard, the analysis is organized in four sections. First we explore the (ever expanding) scope of the freedom to provide services (Section 2), then we go on to identify the nature of the violations and of justifications thereto (Section 3), before carrying out some case studies to concretely illustrate the above (Section 4). Then, for the sake of completeness, we try to deduce the general principles running through the totality of the relevant case law (Section 5). Inevitably, some concluding remarks follow (Section 6).5

The Party of Regions monopolises power in Ukraine. OSW Commentary No. 40, 2010-09-29

Since the Party of Regions took power in Ukraine, the process of strengthening the executive branch of government at the expense of the others, together with the instrumental use of the law, has been progressing steadily. By seeking to restrict criticism of the government, the ruling party is aiming at marginalisation of opposition groups and establishing informal control over the main media (largely by exerting pressure on their owners). The role of the Security Service of Ukraine (SBU) is growing, as it is used increasingly frequently to put pressure on Western-oriented NGOs. The government’s control over the judiciary is expanding. These trends had existed before the Party of Regions’ ascension to power, but they were much weaker, as the previous governments did not enjoy such a strong position or the ability to achieve their ends so efficiently. The Party of Regions is planning to take another step towards total power during the local elections scheduled for October 2010. The party is determined to establish control over the local self-governments; to this end, it has amended the legislation in a way which now undermines local civil initiatives. These changes not only illustrate the interests and political standpoint of the ruling elite; they also result from systemic reasons, and these are deeply rooted in the Soviet past. The present Ukrainian state has evolved through the evolutionary transformation of the Ukrainian Soviet Socialist Republic. As a result, the main features of the previous system have been sustained, including the weakness of the representative bodies and the instrumental use of the law. Twenty years into its independent development, Ukraine has developed a merely formal democracy, which is distant from EU standards.

An analysis of the traffic safety system. 1975. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

An analysis of Blackstone's Commentaries on the laws of England : in a series of questions, to which the student is to frame his own answers, by reading that work /

Mode of access: Internet.

San Antonio Alcohol Safety Action Project - analytic study no. 3: final analysis of enforcement - 1972 through 1974. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Regional economic impacts of nuclear power plants /

"BNL 50562."

An analysis of the domestic electric business of the Hartford electric light company, 1914-1926.

Cover title.

Safety analysis of nuclear concrete containment structure /

"NRC FIN no. B5688."