Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Maximally genuine multipartite entangled mixed X-states of N-qubits

For every possible spectrum of 2(N)-dimensional density operators, we construct an N-qubit X-state of the same spectrum and maximal genuine multipartite (GM-) concurrence, hence characterizing a global unitary transformation that -constrained to output X-states-maximizes the GM-concurrence of an arbitrary input mixed state of N qubits. We also apply semidefinite programming methods to obtain N-qubit X-states with maximal GM-concurrence for a given purity and to provide an alternative proof of optimality of a recently proposed set of density matrices for the purpose, the so-called X-MEMS. Furthermore, we introduce a numerical strategy to tailor a quantum operation that converts between any two given density matrices using a relatively small number of Kraus operators. We apply our strategy to design short operator-sum representations for the transformation between any given N-qubit mixed state and a corresponding X-MEMS of the same purity.

Induced fractional valley number in graphene with topological defects

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Baryon and meson density of states

In a finite size bag like picture consisting of quarks (2 flavour) and gluons with SU(3) colour singlet restriction on the partition function and the chemical potential μ ≠ 0 with the constraint that the baryon number b = 0 and b = 1 for mesons and baryons, respectively we find a very good agreement with baryon density of states upto 2 GeV and with mesonic ones upto 1.3 GeV. Similar to a hadron-scale string theory our calculation also suggests that beyond 1.3 GeV there should exist exotic mesons.

A Survery of Western United States Instream Flow Programs and The Policies that Protect a River's Ecosystem

The Western United States can best be described as a vast, varying land, with the high plains to the east and the jagged horizons of Rockies to the west. However there is one common trait shared by these states: the lack of water resources. With the continued development of this land, the fact that water is scarce is becoming more real. This issue became more difficult to handle as the public became more aware that many competing uses existed for the finite resource, and those different uses were degrading the natural environments of the surface waters. With this realization instream flow policies provides a comprehensive account of the policy framework a selected number of western states have established in order to protect instream flows and the overall health of a river's ecosystem. Also included is the identification of key policies that should be promoted or removed from a state's instream flow program. Ultimately, this thesis continues to add the the ever-evolving process of modernizing water law frameworks.

SCWDS BRIEFS: Volume 21, Number 3 (October 2005)

H5N1 Influenza Virus in Wild Birds: A Fact Sheet Highly Pathogenic Avian Influenza Virus H5N1 and Wild Birds What are avian influenza viruses? What is a Highly Pathogenic Avian Influenza virus? What is “Bird Flu” and what is “HPAI H5N1”? What do we know about avian influenza viruses in wild birds? Do we have HPAI H5N1 in North America? Is there currently a public health risk associated with HPAI H5N1 in wild birds? Is there a domestic animal health risk associated with HPAI in wild birds? What is the possibility of HPAI H5N1 entering North America via migratory wild birds? What is the possibility of this virus being maintained in wild bird populations? Do we have surveillance for HPAI H5N1 in the United States? Additional information on HPAI can be found at these websites: The recognized geographic and species distribution of chronic wasting disease (CWD) has expanded since early September 2005 to include Hampshire County in the eastern panhandle of West Virginia National Fish and Wildlife Health Initiative Guiding Principles Eastern Equine Encephalitis (EEE) virus was isolated from seven white-tailed deer in southwestern Michigan during September 2005 During the past summer, more than 500 head of livestock in North Dakota and South Dakota were lost to one of the largest recorded anthrax outbreaks in U.S. history. Most of the losses were in cattle, but horses, bison, and farm-reared elk also were affected. Dr. John Fischer, Director of SCWDS, has received this year’s Special Recognition Award from the International Association of Fish and Wildlife Agencies (IAFWA). Dr. William Randolph Davidson is retiring in November 2005.

SCWDS BRIEFS: Volume 20, Number 2 (July 2004)

National Veterinary Services Laboratories in Ames, Iowa, confirmed vesicular stomatitis (VS) in horses at one premises in Texas. As of July 21, 2004, infected animals were identified on a total of 45 premises in Colorado (11), New Mexico (21), and Texas (13). These are the first reports of VS in livestock in the United States since the 1998 epizootic. SCWDS VS Studies Chronic Wasting Disease Developments: nearly 118,000 wild white-tailed deer, mule deer, and elk were tested in the United States from October 2002 to September 2003, with 592 animals testing positive for the CWD prion. More than $38,000,000 was spent by federal and state wildlife and animal health agencies on CWD-related activities during this same period. The Second International Chronic Wasting Disease Symposium, hosted by the Wisconsin Department of Natural Resources, will be held in Madison, Wisconsin, July 12-14, 2005. Crow Decoys Used in West Nile Virus Study Although Lyme disease caused by a spirochete bacterium, Borrelia burgdorferi, is relatively rare in the southeastern United States, a Lyme disease-like infection referred to as Southern Tick-Associated Rash Illness (STARI) and thought to be caused by Borrelia lonestari, has been recognized in people in this region. The Ohio Division of Wildlife joined SCWDS as an associate member beginning July 1, 2004. The Final Report of the 2003 Hemorrhagic Disease (HD) Surveillance project has been completed and distributed to all cooperators. New of Caroline Duffie, Robbie Edalgo and wife Jen, Clay George, Darrell Kavanaugh, Lynn Lewis-Weiss’s husband, Dr. Kevin Weiss, and Nate Mechlin. New SCWDS staff include Brian Chandler, Jay Cumbee, Ginger Goekjian, Bill Hamrick, Sabrina McGraw, Kerri Pedersen, and Ben Wilcox. Recent SCWDS Publications Available

SCWDS BRIEFS: Volume 18, Number 3 (October 2002)

• Chronic Wasting Disease Update: Wisconsin, Minnesota, South Dakota, Colorado; National CWD Management – USDA & USDI National Plan for Assisting States, Federal Agencies, and Tribes in Managing Chronic Wasting Disease in Free-ranging and Captive Cervids • West Nile virus (WNV) reaches the Pacific coast • West Nile Virus in Blue Jays • Idaho Brucellosis Linked to Wildlife: All of the epidemiological and laboratory information clearly indicates that brucellosis-infected elk transmitted the disease to the cattle herd. • Tularemia caused a die-off of captured wild prairie dogs this summer at a Texas commercial exotic animal facility that distributes the animals for sale as pets. • Raptors can acquire avian vacuolar myelinopathy (AVM) via ingestion of other affected birds. • House Finch Mycoplasmosis: bacterial eye disease of house finches • Raccoon Rabies report • Toxoplasmosis – The newest finding regarding sea otters in California is the importance of toxoplasmosis as a mortality factor. Toxoplasma gondii is a protozoan parasite that can invade visceral organs and the central nervous system to cause acute, disseminated tissue necrosis and fatal meningoencephalitis in susceptible animals. In recent years, 36% of dead sea otters examined have been infected. Another tissue-invading protozoan, Sarcocystis neurona, also was found in 4% of the otters. • Recovery of remnant populations of the endangered black-footed ferret have been hampered by sylvatic plague, which is caused by the bacterium Yersinia pestis. • Dr. Samantha Gibbs received the Wildlife Disease Association’s Student Research Recognition Award. Dr. Cynthia Tate was selected by the American Association of Veterinary Parasitologists to receive the Best Student Presentation Award. Dr. Andrea Varela won second place in the Student Presentation Award for her presentation at the meeting of the American Association Veterinary Parasitologists. Mr. Michael Yabsley received the Wildlife Disease Association Student Scholarship and the S.A. Ewing Vectorborne Parasitology Award from the University of Georgia’s College of Veterinary Medicine.

On estimating the basic reproduction number in distinct stages of a contagious disease spreading

In epidemiology, the basic reproduction number R-0 is usually defined as the average number of new infections caused by a single infective individual introduced into a completely susceptible population. According to this definition. R-0 is related to the initial stage of the spreading of a contagious disease. However, from epidemiological models based on ordinary differential equations (ODE), R-0 is commonly derived from a linear stability analysis and interpreted as a bifurcation parameter: typically, when R-0 >1, the contagious disease tends to persist in the population because the endemic stationary solution is asymptotically stable: when R-0 <1, the corresponding pathogen tends to naturally disappear because the disease-free stationary solution is asymptotically stable. Here we intend to answer the following question: Do these two different approaches for calculating R-0 give the same numerical values? In other words, is the number of secondary infections caused by a unique sick individual equal to the threshold obtained from stability analysis of steady states of ODE? For finding the answer, we use a susceptibleinfective-recovered (SIR) model described in terms of ODE and also in terms of a probabilistic cellular automaton (PCA), where each individual (corresponding to a cell of the PCA lattice) is connected to others by a random network favoring local contacts. The values of R-0 obtained from both approaches are compared, showing good agreement. (C) 2012 Elsevier B.V. All rights reserved.

Number of recent sexual partners among blood donors in Brazil: associations with donor demographics, donation characteristics, and infectious disease markers

BACKGROUND: Brazilian blood centers ask candidate blood donors about the number of sexual partners in the past 12 months. Candidates who report a number over the limit are deferred. We studied the implications of this practice on blood safety. STUDY DESIGN AND METHODS: We analyzed demographic characteristics, number of heterosexual partners, and disease marker rates among 689,868 donations from three Brazilian centers between July 2007 and December 2009. Donors were grouped based on maximum number of partners allowed in the past 12 months for each center. Chi-square and logistic regression analysis were conducted to examine associations between demographic characteristics, number of sex partners, and individual and overall positive markers rates for human immunodeficiency virus (HIV), human T-lymphotropic virus Types 1 and 2, hepatitis B virus, hepatitis C virus, and syphilis. RESULTS: First-time, younger, and more educated donors were associated with a higher number of recent sexual partners, as was male sex in Sao Paulo and Recife (p < 0.001). Serologic markers for HIV and syphilis and overall were associated with multiple partners in Sao Paulo and Recife (p < 0.001), but not in Belo Horizonte (p = 0.05, p = 0.94, and p = 0.75, respectively). In logistic regression analysis, number of recent sexual partners was associated with positive serologic markers (adjusted odds ratio [AOR], 1.2-1.5), especially HIV (AOR, 1.9-4.4). CONCLUSIONS: Number of recent heterosexual partners was associated with HIV positivity and overall rates of serologic markers of sexually transmitted infections. The association was not consistent across centers, making it difficult to define the best cutoff value. These findings suggest the use of recent heterosexual contacts as a potentially important deferral criterion to improve blood safety in Brazil.

Does anti-obsessional pharmacotherapy treat so-called comorbid depressive and anxiety states?

Background: Obsessive-compulsive disorder (OCD) is a chronic condition that normally presents high rates of psychiatric comorbidity. Depression, tic disorders and other anxiety disorders are among the most common comorbidities in OCD adult patients. There is evidence that the higher the number of psychiatric comorbidities, the worse the OCD treatment response. However, little is known about the impact of OCD treatment on the outcome of the psychiatric comorbidities usually present in OCD patients. The aim of this study was to investigate the impact of exclusive, conventional treatments for OCD on the outcome of additional psychiatric disorders of OCD patients, detected at baseline. Methods: Seventy-six patients with primary OCD admitted to the treatment protocols of the Obsessive-Compulsive Spectrum Disorders Program between July 2007 and December 2009 were evaluated at pre-treatment and after 12 months. Data were analyzed to verify possible associations between,OCD treatment response and the outcome of psychiatric comorbidities. Results: Results showed a significant association between OCD treatment response and improvement of major depression and dysthymia (p-value = 0.002), other anxiety disorders (generalized anxiety disorder, social phobia, specific phobia, posttraumatic stress disorder, panic disorder, agoraphobia and anxiety disorder not otherwise specified) (p-value = 0.054) and tic disorders (p-value = 0.043). Limitations: This is an open, non-blinded study, without rating scales for comorbid conditions. Further research is necessary focusing on the possible mechanisms by which OCD treatment could improve these specific disorders. Conclusions: Our results suggest that certain comorbid disorders may benefit from OCD-targeted treatment. (C) 2012 Elsevier B.V. All rights reserved.

The radical SeCl: A theoretical contribution to the characterization of its low-lying electronic states

All doublet and quartet electronic states correlating with the first dissociation channel of SeCl and some Rydberg states are investigated theoretically at the CASSCF/MRCI level of theory using extended basis sets, including the contribution of spin-orbit effects. The similarity of the potential energy curves with those of SeF suggests that spectroscopic constants for the ground (X (2)Pi) and the first excited quartet (a(4)Sigma) of SeCl could also be determined via an emission resulting from the reaction of selenium with atomic chlorine. The coupling constant of the ground state at R-e is estimated as -1610 cm (1). The potential energy curves calculated and the derived spectroscopic constants do not support the interpretation and assignment of the scarce transitions recorded experimentally as due to (2)Pi-(2)Pi emissions. That the few observed lines might arise from transitions from the state b(4)Sigma(-)(1/2) to a very high vibrational level of the state a(4)Sigma(-)(1/2) is an open possibility, however, the number of vibrational states and the calculated Delta G(1/2) differ significantly from the reported ones. (C) 2012 Elsevier B. V. All rights reserved.

On reducing test length for FSMs with extra states

A long-standing problem when testing from a deterministic finite state machine is to guarantee full fault coverage even if the faults introduce extra states in the implementations. It is well known that such tests should include the sequences in a traversal set which contains all input sequences of length defined by the number of extra states. This paper suggests the SPY method, which helps reduce the length of tests by distributing sequences of the traversal set and reducing test branching. It is also demonstrated that an additional assumption about the implementation under test relaxes the requirement of the complete traversal set. The results of the experimental comparison of the proposed method with an existing method indicate that the resulting reduction can reach 40%. Experimental results suggest that the additional assumption about the implementation can help in further reducing the test suite length. Copyright (C) 2011 John Wiley & Sons, Ltd.

Deviation from quark number scaling of the anisotropy parameter v(2) of pions, kaons, and protons in Au+Au collisions at root s(NN)=200 GeV

Measurements of the anisotropy parameter v(2) of identified hadrons (pions, kaons, and protons) as a function of centrality, transverse momentum p(T), and transverse kinetic energy KET at midrapidity (vertical bar eta vertical bar < 0.35) in Au + Au collisions at root s(N N) = 200 GeV are presented. Pions and protons are identified up to p(T) = 6 GeV/c, and kaons up to p(T) = 4 GeV/c, by combining information from time-of-flight and aerogel Cerenkov detectors in the PHENIX Experiment. The scaling of v(2) with the number of valence quarks (n(q)) has been studied in different centrality bins as a function of transverse momentum and transverse kinetic energy. A deviation from previously observed quark-number scaling is observed at large values of KET/n(q) in noncentral Au + Au collisions (20-60%), but this scaling remains valid in central collisions (0-10%).

Phylogenetic relation among bovine rabies cases from Minas Gerais and Sao Paulo States, Brazil: a possible common origin

Acknowledgements: CAPES, FAPESP process number 2011/06236-0