Analogous Examples Research Articles

Zn2+‐linked dimerization of UreG from Helicobacter pylori, a chaperone involved in nickel trafficking and urease activation

The biosynthesis of the active metal-bound form of the nickel-dependent enzyme urease involves the formation of a lysine-carbamate functional group concomitantly with the delivery of two Ni(2+) ions into the precast active site of the apoenzyme and with GTP hydrolysis. In the urease system, this role is performed by UreG, an accessory protein belonging to the group of homologous P-loop GTPases, often required to complete the biosynthesis of nickel-enzymes. This study is focused on UreG from Helicobacter pylori (HpUreG), a bacterium responsible for gastric ulcers and cancer, infecting large part of the human population, and for which urease is a fundamental virulence factor. The soluble HpUreG was expressed in E. coli and purified to homogeneity. On-line size exclusion chromatography and light scattering indicated that apo-HpUreG exists as a monomer in solution. Circular dichroism, which demonstrated the presence of a well-defined secondary structure, and NMR spectroscopy, which revealed a large number of residues that appear structured on the basis of their backbone amide proton chemical shift dispersion, indicated that, at variance with other UreG proteins so far characterized, this protein is significantly folded in solution. The amino acid sequence of HpUreG is 29% identical to that of HypB from Methanocaldococcus jannaschii, a dimeric zinc-binding GTPase involved in the in vivo assembly of [Ni,Fe]-hydrogenase. A homology-based molecular model of HpUreG was calculated, which allowed us to identify structural and functional features of the protein. Isothermal titration microcalorimetry demonstrated that HpUreG specifically binds 0.5 equivalents of Zn(2+) per monomer (K(d) = 0.33 +/- 0.03 microM), whereas it has 20-fold lower affinity for Ni(2+) (K(d) = 10 +/- 1 microM). Zinc ion binding (but not Ni(2+) binding) causes protein dimerization, as confirmed using light scattering measurements. The structural rearrangement occurring upon Zn(2+)-binding and consequent dimerization was evaluated using circular dichroism and fluorescence spectroscopy. Fully conserved histidine and cysteine residues were identified and their role in zinc binding was verified by site-directed mutagenesis and microcalorimetry. The results are analyzed and discussed with respect to analogous examples of GTPases in nickel metabolism.

The first examples of mRNA cap analogs bearing boranophosphate modification

The syntheses of mRNA cap analogs modified with boranophosphate moiety at either the alpha or beta-position of the 5', 5'-triphosphate bridge (m(7)Gppp(BH3)G, m(7)Gpp(BH3)pG and m(7)Gpp(BH3)pm(7)G) are described. The preliminary biological characterization of these compounds revealed that they have high affinity for translational factor eIF4E and high potency to inhibit cap-dependent translation in cell free system. The analogs modified at the beta-position were also found to be resistant to DcpS decapping pyrophosphatase.

Analogies in medicine: valuable for learning, reasoning, remembering and naming

Analogies are important tools in human reasoning and learning, for resolving problems and providing arguments, and are extensively used in medicine. Analogy and similarity involve a structural alignment or mapping between domains. This cognitive mechanism can be used to make inferences and learn new abstractions. Through analogies, we try to explain a knowledge to be achieved (the target), with pieces of information already familiar to the learner (the source), keeping in mind the constraints of similarity, structure and purpose. The purpose of this essay is to examine the use of analogies in medicine. We provide a brief review of the theoretical basis of analogical reasoning. This theoretical background is discussed in the light of actual examples of analogies retrieved from medical literature. In medicine, analogies have long been used to explain several physiologic and pathologic processes. Besides deeper structural relations, superficial attribute similarity is extensively used in many medical specialties. These attribute similarities are important in naming, categorizing and classifying, and play a role as learning and memorizing tools. Analogies also serve as basis for medical nomenclature. The choice of the source of analogies is highly dependent on cultural background, and may derive from ancient or diverse cultures. Learning by analogies may thus require research on culture diversity in order to establish an adequate justification and to comprehend the purpose of an analogy.

ACC/AHA/HRS 2008 Guidelines for Device-Based Therapy of Cardiac Rhythm Abnormalities

ACC/AHA/HRS 2008 Guidelines for Device-Based Therapy of Cardiac Rhythm Abnormalities

Automorphically-invariant ideals satisfying multilinear identities, and group-theoretic applications

Let A be an arbitrary (not necessarily associative or commutative) algebra over a field K. It is proved that if A has an ideal of finite codimension r satisfying a multilinear identity f ≡ 0 , then A also has an ideal satisfying the same identity f ≡ 0 that is invariant under all automorphisms of A and has finite codimension bounded in terms of r and f. The result is stronger in characteristic zero, where f need not be multilinear. As a corollary, it is proved that if a locally nilpotent torsion-free group G has a normal subgroup H satisfying a multilinear commutator identity ϰ ( H ) ≡ 1 with quotient G / H of finite rank r, then G also has a characteristic subgroup C satisfying the same identity ϰ ( C ) ≡ 1 with quotient G / C of finite rank bounded in terms of r and ϰ. An example shows that the main result cannot be extended to algebras not over fields, even to Lie algebras over integers. An analogous example shows that the result on characteristic nilpotent subgroups with quotients of finite rank, which was proved by the authors earlier in torsion-free and periodic cases, cannot be extended to mixed nilpotent groups.

Consequences of No Child Left Behind on evaluation purpose, design, and impact

AbstractAs an outgrowth of No Child Left Behind's narrow definition of scientifically based research, the priority given to certain quantitative evaluation designs has sparked debate among those in the evaluation community. Federal mandates for particular evaluation methodologies run counter to evaluation practice and to the direction of most evaluation theorists, who advocate for flexibility and adaptability in methods choices. The impact of this mandate for randomized clinical trials as the sine qua non of evaluation methods is not yet discernible, but the potential impact is explored through an analogous example involving the World Bank. © Wiley Periodicals, Inc.

Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription

The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host–pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent manner. Our data also suggest the presence of a host cell factor that acts within the virus producer cells. In addition to providing an example of an RNA-mediated cell-type-dependent block to viral replication, our data also provides evidence which help to resolve the dilemma of how HIV-1 genomes with mismatched DIS sequences can recombine to generate chimeric viral RNA genomes.

Is P4P Really FFS?

IT IS COMMON FOR SOCIETAL TRENDS AND PREFERENCES TO be recycled. Men’s neckties have varied from thin to wide and back to thin again. Government policies have favored individual responsibility, then social responsibility, and again individual responsibility. In health care, policy makers have swung between concern about access and concern about cost, attempting to increase or decrease medical care supply in response. Until 1980, there was widespread belief in a fairly severe physician shortage in Canada and the United States. By 1990, it was thought that too many physicians were performing too many services. Now, in the 2000s, physician shortages are again the topic of discussion. In the 1960s and 1970s, health policy makers were concerned about access and institutionalized a system that expanded insurance for patients (thus separating them from the true costs of care) and organized a reimbursement system based on fee for service (FFS) and costs incurred. As access expanded, so did health care expenditures. By the 1980s and early 1990s, health care costs in Canada and the United States were thought to be too high. The view that supply created its own demand was common and best epitomized by Roemer’s law: hospital bed utilization reflects supply. In his article on “protecting the commons,” Hiatt criticized the FFS model as having significant negative externalities for society, providing too much health care at the expense of other social services. A solution was to pay physicians and hospitals a flat amount to provide care through prospective case payments, capitation, or global budgets rather than per service. The 1990s were filled with reforms that used 2 mechanisms to correct the problem of rising health care costs and “protecting the commons”: (1) managed care, the insertion of third-party management tools that included incentives for reducing care and (2) competition between health care systems and “plans” for patients on the basis of cost and quality. Together these ideas were known as “managed competition,” an approach originally proposed by Enthoven. The objectives of managed competition, capitation, and global budgets (supply-side constraints) were to reduce unnecessary care without reducing necessary or appropriate care. In managed care, health care administrators would be able to control which patients received which types of care to increase the proportion of care that was deemed appropriate. Theoretically, managed competition made sense, but it quickly fell out of favor in many circles, particularly among the public, precisely because it was successful at achieving its goal; ie, it effectively reduced the provision of care and kept health care costs from continuing to escalate. Restricting only unnecessary care proved to be quite difficult. The RAND Health Insurance Experiment provided an analogous example of the relationship between (consumer) cost sharing (a demand-side intervention) and appropriateness. Increased patient co-payments reduced all health care service use, not just ineffective or unnecessary utilization. It seems that both supply-side and demand-side attempts to control costs provide financial barriers that limit both necessary and unnecessary treatment. Now, as the pendulum appears poised to swing away from cost concerns and back toward improving access, the Institute of Medicine’s Quality Chasm and Rewarding Performance reports have broadened priorities, also focusing attention on improving quality. To improve both quality and access, a new idea has been promoted: pay for performance (P4P).

Plastidic trnFUUC Pseudogenes in North American Genus Boechera (Brassicaceae): Mechanistic Aspects of Evolution

The origin and maintenance of a plastidic tandem repeat next to the TRNF (UUC) gene were analyzed in the genus BOECHERA in a phylogenetic context and were compared to published analogous examples that emerged in parallel in the Asteraceae and Juncaceae, respectively. Although we identified some features common to these taxonomic groups with respect to structure and origin of the region, obvious differences were encountered, which argue against a specific mechanism or evolutionary principle underlying the parallel origin and maintenance of the TRNF-tandem repeats in those families. In contrast to the situation in the Asteraceae, no reciprocal recombinant repeat types have been observed in the Brassicaceae. Forty copy types, classified into three groups, were isolated from 103 chloroplast haplotypes of BOECHERA and it was demonstrated that they are composed of four subregions of various origins. We discuss various mutation mechanisms such as DNA replication slippage, and inter- and intrachromosomal recombination which were reported to mediate variation in copy numbers and other types of observed sequence length polymorphism. It is shown that the observed molecular structure of the tandem repeat region did not fully fit the particular patterns expected under a scenario of evolution including any of the known mechanisms. Nevertheless, it appeared that intermolecular unequal crossing-over is most likely the driving force in the evolution of this tandem repeat. However, it remains to be explained, why no reciprocal recombinant copy types have been observed. The reconstructed phylogenetic relationships among copies reflected different evolutionary scenarios as follows: (1) A single and ancient origin of copies pre-dates the radiation of BOECHERA. (2) Parallel expansion and shortening of the tandem repeat within different BOECHERA lineages. (3) Conservation of the first copy, as it was the only one present in all chloroplast haplotypes.

Tau-functions, Grassmannians and rank one conditions

In integrable systems, specifically the KP hierarchy, there are functions known as “tau-functions”, closely related to the Schur polynomials in terms of which they are often written. Although they are generally viewed as the solutions to a collection of nonlinear PDEs, in this note they will equivalently be characterized by a quadratic difference equation. Sato's theorem associates tau-functions to the points of a Grassmann manifold. To make that amazing theorem clear to non-experts, we will first show an analogous (but easily understood) example of a linear ODE and its solution from a flow on the xy-plane. In each case the solution is created via a flow generated by a certain linear operator. The question we pose is this: “What other operators could have been used to generate solutions in the same way?” Although the answer is well known in the ODE case, the question in the nonlinear case is the main result of our new paper. We will state the result and discuss its relationship to the “trend” of writing tau-functions in terms of matrices satisfying certain rank one conditions. The elucidation of a geometric interpretation of the Hirota bilinear difference equation (HBDE) is a key feature of the proof and will be briefly described.

Novel Aspects of Corrole Chemistry

Corrole is one of the first examples of porphyrin analogs reported in the literature. This class of compounds has received a great attention, because of their promising exploitation in different fields, ranging from medicine to material chemistry. Among them, corrole can be considered the prototypical example of contracted porphyrins, with one of the meso carbon bridges missing. Although this macrocycle was first reported more than thirty years ago, only recently more attention has been devoted to the chemistry of corrole. The recent availability of efficient and facile syntheses of meso-substituted corroles has probably been the shuttle for the impressive flourishing of corrole-related papers appearing in literature in the last few years. The aim of this review is to highlight the latest reports in the synthetic chemistry of corrole, with special attention to the synthetic strategies and peripheral functionalizations of this macrocycle.

Critical phenomena and breaking drops: Infinite idealizations in physics

Thermodynamics and Statistical Mechanics are related to one another through the so-called “thermodynamic limit” in which, roughly speaking the number of particles becomes infinite. At critical points (places of physical discontinuity) this limit fails to be regular. As a result, the “reduction” of Thermodynamics to Statistical Mechanics fails to hold at such critical phases. This fact is key to understanding an argument due to Craig Callender to the effect that the thermodynamic limit leads to mistakes in Statistical Mechanics. I discuss this argument and argue that the conclusion is misguided. In addition, I discuss an analogous example where a genuine physical discontinuity—the breaking of drops—requires the use of infinite idealizations.

Argument from Roman Law in Current International Law: Occupation and Acquisitive Prescription

In his Private Law Sources and Analogies of International Law (1927), Hersch Lauterpacht claimed that many rules and concepts of international law stemmed from private law. He also showed that it was common practice in international adjudication and arbitration to look for inspiration there. The rules of private law that had found their way to international law were often common to the great municipal law systems. Many had their origins in Roman private law. This article examines whether and how the International Court of Justice has made use of Roman law rules and concepts. Roman law can be thought to fulfil its role as a source of inspiration for international law in three ways. First, it might have served as a direct historical source during the formative period of the modern law of nations. Second, it might have served as an indirect historical source because of its enduring impact on the great municipal law systems afterwards. Thirdly, it might still be considered ratio scripta, the expression of a timeless and universal law. For the purpose of examining which of these roles Roman law plays in the eyes of the ICJ, the analysis is restricted to two examples of private law analogies: occupation of terra nullius and acquisitive prescription.

A renaissance sword from Racibórz

A broken sword was found in Raciborz, in an assumed Ducal grave, dated back to the 1520s. The sword blade can be classified as a variation of the Type XVII (similar to the Type XVIIIb), the pommel belongs to the Type T5 and the crosspiece to the Type 12. As blade types XVII were mainly in use ca. 1350-1450, it cannot be excluded that the blade of the Raciborz sword was re-hilted and provided with a more fashionable pommel and a crosspiece ca. 1500. Several analogous examples of swords are presented in the paper. Concerning archaeometallurgical analysis of the blade, it was made of one piece of iron, carburised and then hardened. In result, a highquality blade with a soft core and hard edges was produced. For the sake of comparison, selected examples of archaeometallurgical analysis of other late medieval blades are provided.

Stories and Analogies in Cognitive Behaviour Therapy: A Clinical Review

The transfer of knowledge occurs most effectively through the stories – the narratives – that we tell others and ourselves about our experiences. Cognitive behaviour therapists may incorporate stories, metaphors and analogies within their daily practice, when assessing suitability for treatment, challenging unhelpful styles of thinking, and addressing maintaining behaviours. The collaborative development of stories can enhance rapport, enable clients to gain a new perspective upon their problems, increase personal impact and clarity of meaning, and reinforce clients' motivation to effect therapeutic change. This paper discusses the use of the story, anecdote, metaphor, analogy, and quotation within cognitive behaviour therapy (CBT). The contribution of other psychotherapies to these forms of therapeutic communication is outlined. Practical examples of stories and analogies that illustrate the main principles of CBT and its application to the treatment of common mental disorders are described. The benefits and limitations of employing individualized analogies and stories within the therapy session are highlighted.

Applying machine learning to programming by demonstration

‘Familiar’ is a tool that helps end-users automate iterative tasks in their applications by showing examples of what they want to do. It observes the user's actions, predicts what they will do next, and then offers to complete their task. Familiar learns in two ways. First, it creates a model, based on data gathered from training tasks, that selects the best prediction from among several candidates. Experiments show that decision trees outperform heuristic methods, and can be further improved by incrementally updating the classifier at task time. Second, it uses decision stumps inferred from analogous examples in the event trace to predict the parameters of conditional rules. Because data is sparse—for most users balk at giving more than a few training examples—permutation tests are used to calculate the statistical significance of each stump, successfully eliminating bias towards attributes with many different values.

Chalcogens as Terminal Ligands to Iron: Synthesis and Structure of Complexes with FeIII−S and FeIII−Se Motifs

Metal complexes with terminal chalcogenido ligands are known for the early transition-metal complexes, yet for the heavier congeners (e.g., sulfido and selenido), there are no analogous examples for the late 3d metal ions. Reported herein is the isolation and characterization of monomeric iron(III) complexes containing sulfido and selenido ligands; isolation was accomplished using the tripodal ligand tris[(N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea]3-). The FeIII-E (E = S2-, Se2-) complexes were prepared from the iron(II) precursor, [FeII(H3buea)]2-, and the elemental forms of the chalogen. The formulation of [FeIIIH3buea(S)]2- and [FeIIIH3buea(Se)]2- as monomeric complexes with Fe-E units is supported by spectroscopic, analytical, and X-ray diffraction studies. For instance, X-band EPR spectra contain well-resolved axial signals, which are consistent with each complex having S = 5/2 ground states. The solid-state molecular structures reveal FeIII-E bond lengths of 2.211(1) and 2.355(1) A for [FeIIIH3buea(S)]2- and [FeIIIH3buea(Se)]2-, respectively. The primary coordination sphere for each complex also contains three deprotonated urea nitrogen atoms from [H3buea]3-; the apical amine nitrogen atom weakly interacts with the iron centers at distances of greater than 2.6 A. The terminal chalcogenido ligands appear to weakly hydrogen-bond with the urea NH groups of the [H3buea]3-; however, open H-bond cavities are observed for [FeIIIH3buea(S)]2- and [FeIIIH3buea(Se)]2-, which may contribute to their observed long-term instability.

Étude d’une transformation non uniformément hyperbolique de l’intervalle $[0,1[$

We give an example of a non uniformly expanding transformations of [0,1[. Analogous examples have been given by different authors. Our method is based on a general spectral theory for a class of operators satisfying weak “Doeblin-Fortet“ conditions (see [1]). This technique makes it possible to estimate the decay of correlations for non Hölder functions.

A C-terminal aldehyde insect kinin analog enhances inhibition of weight gain and induces significant mortality in Helicoverpa zea larvae

The first reported examples of C-terminal aldehyde analogs of an insect neuropeptide are described. They are hexapeptide insect kinin analogs Boc-VFFPWG-H and Fmoc-RFFPWG-H. Activity observed for these modified analogs in an in vitro insect diuretic assay confirms that the C-terminal aldehyde group is tolerated by an insect kinin receptor. The two analogs demonstrate greatly enhanced activity over standard C-terminal amide insect kinins in a larval weight gain inhibition assay in the corn earworm Helicoverpa zea. Treatment with Boc-VFFPWG-H led to significant increases in larval mortality at doses of 500 pm (45%) and 5 nm (67%). Boc-VFFPWG-H represents a lead analog in the development of novel, environmentally friendly pest insect management agents based on the insect kinin class of neuropeptides.

Iron oxide-copper-gold deposits: an Andean view

Iron oxide-copper-gold (IOCG) deposits, defined primarily by their elevated magnetite and/or hematite contents, constitute a broad, ill-defined clan related to a variety of tectono-magmatic settings. The youngest and, therefore, most readily understandable IOCG belt is located in the Coastal Cordillera of northern Chile and southern Peru, where it is part of a volcano-plutonic arc of Jurassic through Early Cretaceous age. The arc is characterised by voluminous tholeiitic to calc-alkaline plutonic complexes of gabbro through granodiorite composition and primitive, mantle-derived parentage. Major arc-parallel fault systems developed in response to extension and transtension induced by subduction roll-back at the retreating convergent margin. The arc crust was attenuated and subjected to high heat flow. IOCG deposits share the arc with massive magnetite deposits, the copper-deficient end-members of the IOCG clan, as well as with manto-type copper and small porphyry copper deposits to create a distinctive metallogenic signature. The IOCG deposits display close relations to the plutonic complexes and broadly coeval fault systems. Based on deposit morphology and dictated in part by lithological and structural parameters, they can be separated into several styles: veins, hydrothermal breccias, replacement mantos, calcic skarns and composite deposits that combine all or many of the preceding types. The vein deposits tend to be hosted by intrusive rocks, especially equigranular gabbrodiorite and diorite, whereas the larger, composite deposits (e.g. Candelaria-Punta del Cobre) occur within volcano-sedimentary sequences up to 2 km from pluton contacts and in intimate association with major orogen-parallel fault systems. Structurally localised IOCG deposits normally share faults and fractures with pre-mineral mafic dykes, many of dioritic composition, thereby further emphasising the close connection with mafic magmatism. The deposits formed in association with sodic, calcic and potassic alteration, either alone or in some combination, reveal evidence of an upward and outward zonation from magnetite-actinolite-apatite to specular hematite-chlorite-sericite and possess a Cu-Au-Co-Ni-As-Mo-U-(LREE) (light rare earth element) signature reminiscent of some calcic iron skarns around diorite intrusions. Scant observations suggest that massive calcite veins and, at shallower palaeodepths, extensive zones of barren pyritic feldspar-destructive alteration may be indicators of concealed IOCG deposits. The balance of evidence strongly supports a genetic connection of the central Andean IOCG deposits with gabbrodiorite to diorite magmas from which the ore fluid may have been channelled by major ductile to brittle fault systems for several kilometres vertically or perhaps even laterally. The large, composite IOCG deposits originated by ingress of the ore fluid to relatively permeable volcano-sedimentary sequences. The mafic magma may form entire plutons or, alternatively, may underplate more felsic intrusions, as witnessed by the ore-related diorite dykes, but in either case the origin of the ore fluid at greater, unobserved depths may be inferred. It is concluded that external 'basinal' fluids were not a requirement for IOCG formation in the central Andes, although metamorphic, seawater, evaporitic or meteoric fluids may have fortuitously contaminated the magmatic ore fluid locally. The proposed linkage of central Andean and probably some other IOCG deposits to oxidised dioritic magmas may be compared with the well-documented dependency of several other magmatic-hydrothermal deposit types on igneous petrochemistry. The affiliation of a spectrum of base-metal poor gold-(Bi-W-Mo) deposit styles to relatively reduced monzogranite-granodiorite intrusions may be considered as a closely analogous example.