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## (1)H, (15)N and (13)C assignments of the Rhipicephalus (Boophilus) microplus anti-microbial peptide microplusin

REZENDE, Carlos A.; SILVA, Fernanda D.; DAFFRE, Sirlei; PIRES, Jose R.
Fonte: SPRINGER Publicador: SPRINGER
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
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Microplusin, a Rhipicephalus (Boophilus) microplus anti-microbial peptide (AMP) is the first member of a new family of cysteine-rich AMPs with histidine-rich regions at the N- and C-termini, which is being fully characterized by biophysical and biochemical methods. Here we report the NMR resonance assignments for (1)H, (15)N, and (13)C nuclei in the backbone and side chains of the microplusin as basis for further studies of structure, backbone dynamics and interactions mapping.; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); CNPq; Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ); FAPERJ; FAPESP; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

## Como as organizações brasileiras identificam pessoas aptas a assumir atribuições e responsabilidades no contexto do processo sucessório: um estudo de caso; How Brazilian organizations identify people ready to take on more complex assignments and responsibilities in the context of the succession process: a case study.

Ohtsuki, Celi Hiromi
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 29/10/2013 PT
Relevância na Pesquisa
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## Gene3D: structural assignments for the biologist and bioinformaticist alike

Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/01/2003 EN
Relevância na Pesquisa
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The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH.

## DSSPcont: continuous secondary structure assignments for proteins

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/07/2003 EN
Relevância na Pesquisa
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The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure.

## Homework assignments, consequences, and classroom performance in social studies and mathematics1

Harris, V. William; Sherman, James A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //1974 EN
Relevância na Pesquisa
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Elementary school students who frequently answered questions incorrectly in class were given daily homework assignments in social studies and math, but they rarely completed the assignments accurately and their classroom performance in social studies and math was only slightly better than when they did not have homework assignments. However, consequences provided for accurate completion of homework assignments increased the number of students completing homework and the accuracy with which homework assignments were completed. Further, assignments of homework with consequences for accuracy were associated with more accurate classroom performance.

## Proton hyperfine resonance assignments using the nuclear Overhauser effect for ferric forms of horse and tuna cytochrome c.

Satterlee, J D; Moench, S
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /07/1987 EN
Relevância na Pesquisa
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Proton hyperfine resonance assignments for cytochromes c from several species are currently being successfully pursued by several laboratories. These efforts focus mostly on the ferrous forms. In contrast to that work, we have pursued assignments of the proton hyperfine shifted resonances for horse and tuna ferricytochromes c. Our results indicate that assignments are nearly identical in those two proteins. Using the pre-steady state nuclear Overhauser effect, several additional assignments have been made for the tuna protein, whereas for the horse protein, the following protons have been assigned: heme 7, alpha CH2; heme 7, beta CH2; histidine 18, beta CH2 and alpha CH; and the methionine 80, beta CH2.

## A simplified formula for quantification of the probability of deterministic assignments in permuted block randomization

Zhao, Wenle; Weng, Yanqiu
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/01/2011 EN
Relevância na Pesquisa
26.93%
Open label and single blinded randomized controlled clinical trials are vulnerable to selection bias when the next treatment assignment is predictable based on the randomization algorithm and the preceding assignment history. While treatment predictability is an issue for all constrained randomization algorithms, deterministic assignments are unique to permuted block randomization. Deterministic assignments may lead to treatment predictability with certainty and selection bias, which could inflate the type I error and hurts the validity of trial results. It is important to accurately evaluate the probability of deterministic assignments in permuted block randomization, so proper protection measures can be implemented. For trials with number of treatment arms T = 2 and a balance block size B = 2m, Matts and Lachin indicated that the probability of deterministic assignment is 1m+1. For more general situations, with T ≥ 2 and a block size B=∑j=1Tmj, Dupin-Spriet provided a formula, which can be written as 1B∑j=1T∑i=1mj∏k=1imj−k+1B−k+1. This formula involves extensive calculation in evaluation. In this paper, we simplified this formula to 1B∑j=1TmjB−mj+1 for general scenarios and 1B−m+1 for trials with a balanced allocation. Through mathematical induction we show the equivalence of the formulas. While the new formula is numerically equivalent to Dupin-Spriet’s formula...

## Assigning Backbone NMR Resonances for Full Length Tau Isoforms: Efficient Compromise between Manual Assignments and Reduced Dimensionality

Harbison, Nicholas W.; Bhattacharya, Shibani; Eliezer, David
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 18/04/2012 EN
Relevância na Pesquisa
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Tau protein is the longest disordered protein for which nearly complete backbone NMR resonance assignments have been reported. Full-length tau protein was initially assigned using a laborious combination of bootstrapping assignments from shorter tau fragments and conventional triple resonance NMR experiments. Subsequently it was reported that assignments of comparable quality could be obtained in a fully automated fashion from data obtained using reduced dimensionality NMR (RDNMR) experiments employing a large number of indirect dimensions. Although the latter strategy offers many advantages, it presents some difficulties if manual intervention, confirmation, or correction of the assignments is desirable, as may often be the case for long disordered and degenerate polypeptide sequences. Here we demonstrate that nearly complete backbone resonance assignments for full-length tau isoforms can be obtained without resorting either to bootstrapping from smaller fragments or to very high dimensionality experiments and automation. Instead, a set of RDNMR triple resonance experiments of modest dimensionality lend themselves readily to efficient and unambiguous manual assignments. An analysis of the backbone chemical shifts obtained in this fashion indicates several regions in full length tau with a notable propensity for helical or strand-like structure that are in good agreement with previous observations.

## EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

Zuiderweg, Erik R.P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /10/2013 EN
Relevância na Pesquisa
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For several of the proteins in the BioMagResBank larger than 200 residues, 60% or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6*10260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al., PLoS Comput Biol. 2009 5 (3): e1000307) and significantly outperformed SAGA (Crippen et al, (2010) J Biomol NMR 46, 281–298), AUTOASSIGN (Zimmerman et al., (1997) J Mol Biol 269:592–610), and IBIS (Hyberts and Wagner (2003) J Biomol NMR 26:335–344). Next...

## NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
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Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure–activity relationship, protein–protein and protein–ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement’s (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB), Berlin, Germany, April 10–13, pp. 176–187. ACM Press, New York, NY. J. Comp. Bio., (2004), 11, pp. 277–298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR, 29, 111–138). Our approach uses NVR’s scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs)...

## A study of promotion and attrition of mid-grade officers in the U.S. Marine Corps: are assignments a key factor?

Morgan, Jerry R.
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
Tipo: Tese de Doutorado Formato: xiv, 75 p. : col. ill.
Relevância na Pesquisa
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Approved for public release, distribution is unlimited; This study analyzes the relationship between selection to major in the Marine Corps, and the survival of midgrade officers to the promotion point of major, by investigating the effects of billet assignments. Specifically, this study looks at the influence of the percentage of time spent in the Fleet Marine Forces (FMF), the percentage of time spent in primary military occupation (PMOS) billet assignments, and the effect of having served in combat, recruiting, security forces, joint, and drill field duties. Models were formulated using groundwork established in previous promotion, retention, and attrition studies. Assignment variables were then introduced to the models. To account for officers' choice for continued service vice forced attrition, the sample was restricted to officers who had attained five years of service. Probit regression was used to find the influence of career assignments on the probability of selection; Heckman's correction was used to control for self-selection bias; and, Cox proportionalhazard regression was used, utilizing the same assignment factors, to find the influence of assignments on the likelihood of attrition. The findings indicated that FMF and PMOS ratios above 60 percent had a negative effect on promotion and retention. Also indicated was that time spent outside the PMOS...

## The effects of military assignments and duties on the marital status of Navy officers

Karacaoglu, Nihat
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
Tipo: Tese de Doutorado Formato: xvi, 155 p. ;
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Approved for public release; distribution is unlimited; This study seeks to determine if military duties and assignments affect the marriage and divorce decisions of United States Navy officers. Previous studies suggest that a stable marriage can have a positive influence on a military member's performance. However, no previous research has looked specifically at how duties and assignments may affect the marital status of Navy officers. This thesis presents an overview of duty types in the Navy and various factors that are believed to affect the marriage and divorce decisions of Navy officers. Based on the literature review, five hypotheses are generated and tested by estimating 32 logit models. The results show that military duties and assignments, gender, and commissioning sources significantly affect the likelihood and timin g of marriage and divorce decisions of Navy officers. The results provide important information that can be used by policy makers to help reduce the adverse effects of duties and assignments on Navy marriages. The study also looks at the relationship bet ween marriage on divorce and the member's decision to leave the Navy. It is recommended that further research be conducted regarding the effects of duties and assignments on divorce for enlisted personnel and members of other US armed forces.; Lieutenant...

## Computer science students' causal attributions for successful and unsuccessful outcomes in programming assignments

Vivian, R.; Falkner, K.; Falkner, N.
Fonte: ACM; Finland Publicador: ACM; Finland
Tipo: Conference paper
Publicado em //2013 EN
Relevância na Pesquisa
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While some students excel in introductory programming courses, others find the course to be significantly challenging and demanding. The way that students reason about the factors that contribute to success or failure may affect their self-efficacy, motivation, future success and whether or not they persist in Computer Science (CS). What factors do students' perceive to cause successful or unsuccessful learning outcomes in first-year programming assignments? Such findings can assist us in identifying causal reasoning that may be detrimental to future success and persistence. We use Attribution Theory (AT) as a framework to explore the "causal attributions" that students apply to explain their causes for success or failure in introductory programming assignments, alluded to in their reflective essays about performance in a course. Our research demonstrates that reflective essays, integrated into learning tasks, can be one effective and efficient way to extract students' casual attributions. Our results indicate that the students raised a number of causal attributions in their essays that were specific to the CS-context and were attributed to both internal and external causes. We highlight problematic areas of casual reasoning and a need to correct misleading reasoning to ensure CS students understand their control over the success of their future programming assignments. This research offers opportunities for future research to develop activities that may encourage students to correctly identify causes of performance outcomes in programming assignments and to determine if such interventions can prevent students from leaving CS.; Rebecca Vivian...

## PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy

Lee, Woonghee; Westler, William M.; Bahrami, Arash; Eghbalnia, Hamid R.; Markley, John L.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
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Summary: PINE-SPARKY supports the rapid, user-friendly and efficient visualization of probabilistic assignments of NMR chemical shifts to specific atoms in the covalent structure of a protein in the context of experimental NMR spectra. PINE-SPARKY is based on the very popular SPARKY package for visualizing multidimensional NMR spectra (T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco). PINE-SPARKY consists of a converter (PINE2SPARKY), which takes the output from an automated PINE-NMR analysis and transforms it into SPARKY input, plus a number of SPARKY extensions. Assignments and their probabilities obtained in the PINE-NMR step are visualized as labels in SPARKY's spectrum view. Three SPARKY extensions (PINE Assigner, PINE Graph Assigner, and Assign the Best by PINE) serve to manipulate the labels that signify the assignments and their probabilities. PINE Assigner lists all possible assignments for a peak selected in the dialog box and enables the user to choose among these. A window in PINE Graph Assigner shows all atoms in a selected residue along with all atoms in its adjacent residues; in addition, it displays a ranked list of PINE-derived connectivity assignments to any selected atom. Assign the Best-by-PINE allows the user to choose a probability threshold and to automatically accept as “fixed” all assignments above that threshold; following this operation...

## AntiPlag: Plagiarism Detection on Electronic Submissions of Text Based Assignments

Jiffriya, M. A. C.; Jahan, M. A. C. Akmal; Ragel, R. G.; Deegalla, S.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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Plagiarism is one of the growing issues in academia and is always a concern in Universities and other academic institutions. The situation is becoming even worse with the availability of ample resources on the web. This paper focuses on creating an effective and fast tool for plagiarism detection for text based electronic assignments. Our plagiarism detection tool named AntiPlag is developed using the tri-gram sequence matching technique. Three sets of text based assignments were tested by AntiPlag and the results were compared against an existing commercial plagiarism detection tool. AntiPlag showed better results in terms of false positives compared to the commercial tool due to the pre-processing steps performed in AntiPlag. In addition, to improve the detection latency, AntiPlag applies a data clustering technique making it four times faster than the commercial tool considered. AntiPlag could be used to isolate plagiarized text based assignments from non-plagiarised assignments easily. Therefore, we present AntiPlag, a fast and effective tool for plagiarism detection on text based electronic assignments.

## The Complexity of Approximately Counting Stable Roommate Assignments

Chebolu, Prasad; Goldberg, Leslie Ann; Martin, Russell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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We investigate the complexity of approximately counting stable roommate assignments in two models: (i) the $k$-attribute model, in which the preference lists are determined by dot products of "preference vectors" with "attribute vectors" and (ii) the $k$-Euclidean model, in which the preference lists are determined by the closeness of the "positions" of the people to their "preferred positions". Exactly counting the number of assignments is #P-complete, since Irving and Leather demonstrated #P-completeness for the special case of the stable marriage problem. We show that counting the number of stable roommate assignments in the $k$-attribute model ($k \geq 4$) and the 3-Euclidean model($k \geq 3$) is interreducible, in an approximation-preserving sense, with counting independent sets (of all sizes) (#IS) in a graph, or counting the number of satisfying assignments of a Boolean formula (#SAT). This means that there can be no FPRAS for any of these problems unless NP=RP. As a consequence, we infer that there is no FPRAS for counting stable roommate assignments (#SR) unless NP=RP. Utilizing previous results by the authors, we give an approximation-preserving reduction from counting the number of independent sets in a bipartite graph (#BIS) to counting the number of stable roommate assignments both in the 3-attribute model and in the 2-Euclidean model. #BIS is complete with respect to approximation-preserving reductions in the logically-defined complexity class $#RH\Pi_1$. Hence...

## Geometric properties of satisfying assignments of random $\epsilon$-1-in-k SAT

Istrate, Gabriel
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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We study the geometric structure of the set of solutions of random $\epsilon$-1-in-k SAT problem. For $l\geq 1$, two satisfying assignments $A$ and $B$ are $l$-connected if there exists a sequence of satisfying assignments connecting them by changing at most $l$ bits at a time. We first prove that w.h.p. two assignments of a random $\epsilon$-1-in-$k$ SAT instance are $O(\log n)$-connected, conditional on being satisfying assignments. Also, there exists $\epsilon_{0}\in (0,\frac{1}{k-2})$ such that w.h.p. no two satisfying assignments at distance at least $\epsilon_{0}\cdot n$ form a "hole" in the set of assignments. We believe that this is true for all $\epsilon >0$, and thus satisfying assignments of a random 1-in-$k$ SAT instance form a single cluster.

## Relevant Explanations: Allowing Disjunctive Assignments

Shimony, Solomon Eyal
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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Relevance-based explanation is a scheme in which partial assignments to Bayesian belief network variables are explanations (abductive conclusions). We allow variables to remain unassigned in explanations as long as they are irrelevant to the explanation, where irrelevance is defined in terms of statistical independence. When multiple-valued variables exist in the system, especially when subsets of values correspond to natural types of events, the over specification problem, alleviated by independence-based explanation, resurfaces. As a solution to that, as well as for addressing the question of explanation specificity, it is desirable to collapse such a subset of values into a single value on the fly. The equivalent method, which is adopted here, is to generalize the notion of assignments to allow disjunctive assignments. We proceed to define generalized independence based explanations as maximum posterior probability independence based generalized assignments (GIB-MAPs). GIB assignments are shown to have certain properties that ease the design of algorithms for computing GIB-MAPs. One such algorithm is discussed here, as well as suggestions for how other algorithms may be adapted to compute GIB-MAPs. GIB-MAP explanations still suffer from instability...

## Belief Updating by Enumerating High-Probability Independence-Based Assignments

Santos Jr., Eugene; Shimony, Solomon Eyal
Tipo: Artigo de Revista Científica