bluuebunny/crossref_metadata_2025 huggingface dataset:
Streptococcus pneumoniae Serotypes 9 and 14 Circulating in Brazil over a 23-Year Period Prior to Introduction of the 10-Valent Pneumococcal Conjugate Vaccine: Role of International Clones in the Evolution of Antimicrobial Resistance and Description of a Novel Genotype
Authors: Pinto Tatiana C. A. , Kegele Fabíola C. O. , Dias Cícero A. G. , Barros Rosana R. , Peralta José M. , Merquior Vânia L. C. , Carvalho Maria da Gloria , Chochua Sopio , Hawkins Paulina , McGee Lesley , Teixeira Lucia M.
Published: August 2016

Antimicrobial-resistant pneumococcal strains have been detected worldwide since the 1960s. In Brazil, the first penicillin-nonsusceptible pneumococci (PNSP) were reported in the 1980s, and their emergence and dissemination have been mainly attributed to serogroup 9 and serotype 14 strains, especially those highly related to recognized international clones. In the present study, antimicrobial susceptibility testing and multilocus sequence typing were performed on 315 pneumococcal isolates belonging to serogroup 9 (
n
= 99) or serotype 14 (
n
= 216), recovered from patients or asymptomatic carriers between 1988 and 2011 in Brazil, in order to trace changes in antimicrobial resistance and genotypes prior to the full introduction of the pneumococcal conjugate vaccine in the country. Over the 23-year study period, the PNSP levels increased, and four clonal complexes (CC156, CC66, CC15, and CC5401) have played important roles in the evolution and dissemination of pneumococcal isolates belonging to serogroup 9 and serotype 14, as well as in the emergence of antimicrobial resistance, in the pre-pneumococcal-vaccination era. The earliest PNSP strains detected in this study belonged to serotype 9N/ST66 and were single locus variants of the international clone Tennessee
14
-18 ST67 (CC66). The first serotype 14 PNSP isolates were identified in 1990 and were related to the England
14
-9 ST9 (CC15) clone. Serotype 14 PNSP variants of the Spain
9V
-3 ST156 clone with elevated penicillin MICs and nonsusceptibility to other beta-lactams were detected in 1995 and showed an increasing trend over the years. The results also indicated that introduction of ST156 in our region was preceded by the emergence of trimethoprim-sulfamethoxazole resistance and by the dissemination of ST162. In addition to the presence of successful international clones, a novel regional serotype 14 genotype (CC5401) has emerged in 1996.
Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis Patients
Authors: Greipel Leonie , Fischer Sebastian , Klockgether Jens , Dorda Marie , Mielke Samira , Wiehlmann Lutz , Cramer Nina , Tümmler Burkhard
Published: August 2016

The chronic airway infections with
Pseudomonas aeruginosa
in people with cystic fibrosis (CF) are treated with aerosolized antibiotics, oral fluoroquinolones, and/or intravenous combination therapy with aminoglycosides and β-lactam antibiotics. An international strain collection of 361
P. aeruginosa
isolates from 258 CF patients seen at 30 CF clinics was examined for mutations in 17 antimicrobial susceptibility and resistance loci that had been identified as hot spots of mutation by genome sequencing of serial isolates from a single CF clinic. Combinatorial amplicon sequencing of pooled PCR products identified 1,112 sequence variants that were not present in the genomes of representative strains of the 20 most common clones of the global
P. aeruginosa
population. A high frequency of singular coding variants was seen in
spuE
,
mexA
,
gyrA
,
rpoB
,
fusA1
,
mexZ
,
mexY
,
oprD
,
ampD
,
parR
,
parS
, and
envZ
(
amgS
), reflecting the pressure upon
P. aeruginosa
in lungs of CF patients to generate novel protein variants. The proportion of nonneutral amino acid exchanges was high. Of the 17 loci,
mexA
,
mexZ
, and
pagL
were most frequently affected by independent stop mutations. Private and
de novo
mutations seem to play a pivotal role in the response of
P. aeruginosa
populations to the antimicrobial load and the individual CF host.
Antimicrobial Susceptibility of Pseudomonas aeruginosa Isolated from Cystic Fibrosis Patients in Northern Europe
Authors: Mustafa Muhammad-Hariri , Chalhoub Hussein , Denis Olivier , Deplano Ariane , Vergison Anne , Rodriguez-Villalobos Hector , Tunney Michael M. , Elborn J. Stuart , Kahl Barbara C. , Traore Hamidou , Vanderbist Francis , Tulkens Paul M. , Van Bambeke Françoise
Published: August 2016

Pseudomonas aeruginosa
is a major cause of morbidity and mortality in cystic fibrosis patients. This study compared the antimicrobial susceptibilities of 153
P. aeruginosa
isolates from the United Kingdom (UK) (
n =
58), Belgium (
n =
44), and Germany (
n =
51) collected from 118 patients during routine visits over the period from 2006 to 2012. MICs were measured by broth microdilution. Genes encoding extended-spectrum β-lactamases (ESBL), metallo-β-lactamases, and carbapenemases were detected by PCR. Pulsed-field gel electrophoresis and multilocus sequence typing were performed on isolates resistant to ≥3 antibiotic classes among the penicillins/cephalosporins, carbapenems, fluoroquinolones, aminoglycosides, and polymyxins. Based on EUCAST/CLSI breakpoints, susceptibility rates were ≤30%/≤40% (penicillins, ceftazidime, amikacin, and ciprofloxacin), 44 to 48%/48 to 63% (carbapenems), 72%/72% (tobramycin), and 92%/78% (colistin) independent of patient age. Sixty percent of strains were multidrug resistant (MDR; European Centre for Disease Prevention and Control criteria). Genes encoding the most prevalent ESBL (BEL, PER, GES, VEB, CTX-M, TEM, SHV, and OXA), metallo-β-lactamases (VIM, IMP, and NDM), or carbapenemases (OXA-48 and KPC) were not detected. The Liverpool epidemic strain (LES) was prevalent in UK isolates only (75% of MDR isolates). Four MDR sequence type 958 (ST958) isolates were found to be spread over the three countries. The other MDR clones were evidenced in ≤3 isolates and localized in a single country. A new sequence type (ST2254) was discovered in one MDR isolate in Germany. Clonal and nonclonal isolates with different susceptibility profiles were found in 20 patients. Thus, resistance and MDR are highly prevalent in routine isolates from 3 countries, with meropenem, tobramycin, and colistin remaining the most active drugs.
Bayesian Estimation of Tobramycin Exposure in Patients with Cystic Fibrosis
Authors: Barras Michael A. , Serisier David , Hennig Stefanie , Jess Katrina , Norris Ross L. G.
Published: August 2016

Fixed tobramycin (mg/kg) dosing is often inappropriate in patients with cystic fibrosis (CF), as pharmacokinetics are highly variable. The area under the concentration-time curve (AUC) is an exposure metric suited to monitoring in this population. Bayesian strategies to estimate AUC have been available for over 20 years but are not standard practice in the clinical setting. To assess their suitability for use in clinical practice, three AUC estimation methods using limited sampling were compared to measured true exposure by using intensive sampling tobramycin data. Adults prescribed once daily intravenous tobramycin had eight concentrations taken over 24 h. An estimate of true exposure within one dosing interval was calculated using the trapezoidal method and compared to three alternate estimates determined using (i) a two-sample log-linear regression (LLR) method (local hospital practice); (ii) a Bayesian estimate using one concentration (AUC
1
); and (iii) a Bayesian estimate using two concentrations (AUC
2
). Each method was evaluated against the true measured exposure by a Bland-Altman analysis. Twelve patients with a median (range) age and weight of 25 (18 to 36) years and 66.5 (51 to 76) kg, respectively, were recruited. There was good agreement between the true exposure and the three alternate estimates of AUC, with a mean AUC bias of <10 mg/liter · h in each case, i.e., −8.2 (LLR), 3.8 (AUC
1
), and 1.0 (AUC
2
). Bayesian analysis-based and LLR estimation methods of tobramycin AUC are equivalent to true exposure estimation. All three methods may be suitable for use in the clinical setting; however, a one-sample Bayesian method may be most useful in ambulatory patients for which coordinating blood samples is difficult. Suitably powered, randomized clinical trials are required to assess patient outcomes.
Effect of Antifungal Treatment in a Diet-Based Murine Model of Disseminated Candidiasis Acquired via the Gastrointestinal Tract
Authors: Kadosh David , Najvar Laura K. , Bocanegra Rosie , Olivo Marcos , Kirkpatrick William R. , Wiederhold Nathan P. , Patterson Thomas F.
Published: August 2016

Candida albicans
, normally found as a commensal in the gut, is a major human fungal pathogen responsible for both mucosal and systemic infections in a wide variety of immunocompromised individuals, including cancer patients and organ transplant recipients. The gastrointestinal tract represents a major portal of entry for the establishment of disseminated candidiasis in many of these individuals. Here we report the development of a diet-based mouse model for disseminated candidiasis acquired via the gastrointestinal tract. Using this model, as well as an appropriate immunosuppression regimen, we demonstrate that dissemination of
C. albicans
from the gastrointestinal tract can result in mortality within 30 days postinfection. We also show a significant increase in fungal burden in systemic organs, but not gastrointestinal tract organs, upon immunosuppression. Importantly, we demonstrate that the administration of two widely used antifungals, fluconazole and caspofungin, either pre- or postimmunosuppression, significantly reduces fungal burdens. This model should prove to be of significant value for testing the ability of both established and experimental therapeutics to inhibit
C. albicans
dissemination from the gastrointestinal tract in an immunocompromised host as well as the subsequent mortality that can result from disseminated candidiasis.
Characterization of a Novel IncHI2 Plasmid Carrying Tandem Copies of
bla
CTX-M-2
in a
fosA6
-Harboring Escherichia coli Sequence Type 410 Strain
Authors: Guo Qinglan , Ding Baixing , Jové Thomas , Stoesser Nicole , Cooper Vaughn S. , Wang Minggui , Doi Yohei
Published: August 2016

The extended-spectrum β-lactamase gene
bla
CTX-M-2
is mainly associated with IS
CR1
embedded in complex
sul1
-type integrons, but information on the genetic context of plasmids harboring the IS
CR1-bla
CTX-M-2
module remains limited. In this study, a
bla
CTX-M-2
-harboring plasmid (pYD786-1) belonging to the sequence type 2 (ST2)-IncHI2 plasmid type and isolated from an
Escherichia coli
ST410 clinical strain was sequenced and analyzed. pYD786-1 belongs to the APEC-O1-R-type IncHI2 plasmids, which are widely distributed in human, poultry, and livestock strains. It contains a multidrug resistance mosaic region (MRR) consisting of a Tn
21
::In2 transposon backbone augmented by acquisition of duplicate IS
CR1-bla
CTX-M-2
modules. Tn
2411
, a Tn
21
::In2 precursor, likely played a role in the generation of the MRR in pN13-01290_23, the putative progenitor plasmid of pYD786-1, found in a foodborne
Salmonella
strain. Tn
21/
Tn
2411
::In::IS
CR1-bla
CTX-M-2
derivatives, including pYD786-1, have been identified in strains from Europe, South America, and the United States, suggesting potential global dissemination of the
bla
CTX-M-2
modules mediated by this vehicle.
Bioluminescent Reporters for Rapid Mechanism of Action Assessment in Tuberculosis Drug Discovery
Authors: Naran Krupa , Moosa Atica , Barry Clifton E. , Boshoff Helena I. M. , Mizrahi Valerie , Warner Digby F.
Published: August 2016

The tuberculosis (TB) drug discovery pipeline is fueled by compounds identified in whole-cell screens against the causative agent,
Mycobacterium tuberculosis
. Phenotypic screening enables the selection of molecules that inhibit essential cellular functions in live, intact bacilli grown under a chosen
in vitro
condition. However, deducing the mechanism of action (MOA), which is important to avoid promiscuous targets, often requires significant biological resources in a lengthy process that risks decoupling medicinal chemistry and biology efforts. Therefore, there is a need to develop methods enabling rapid MOA assessment of putative “actives” for triage decisions. Here, we describe a modified version of a bioluminescence reporter assay that allows nondestructive detection of compounds targeting either of two macromolecular processes in
M. tuberculosis
: cell wall biosynthesis or maintenance of DNA integrity. Coupling the
luxCDABE
operon from
Photorhabdus luminescens
to mycobacterial promoters driving expression of the
iniBAC
operon (P
iniB
-LUX) or the DNA damage-inducible genes,
recA
(P
recA
-LUX) or
radA
(P
radA
-LUX), provided quantitative detection in real time of compounds triggering expression of any of these promoters over an extended 10- to 12-day incubation. Testing against known anti-TB agents confirmed the specificity of each reporter in registering the MOA of the applied antibiotic in
M. tuberculosis
, independent of bactericidal or bacteriostatic activity. Moreover, profiles obtained for experimental compounds indicated the potential to infer complex MOAs in which multiple cellular processes are disrupted. These results demonstrate the utility of the reporters for early triage of compounds based on the provisional MOA and suggest their application to investigate polypharmacology in known and experimental anti-TB agents.
Cefazolin and Ertapenem, a Synergistic Combination Used To Clear Persistent Staphylococcus aureus Bacteremia
Authors: Sakoulas George , Olson Joshua , Yim Juwon , Singh Niedita B. , Kumaraswamy Monika , Quach Diana T. , Rybak Michael J. , Pogliano Joseph , Nizet Victor
Published: August 2016

Ertapenem and cefazolin were used in combination to successfully clear refractory methicillin-susceptible
Staphylococcus aureus
(MSSA) bacteremia. In addition, recent work has demonstrated activity of combination therapy with beta-lactams from different classes against methicillin-resistant
S. aureus
(MRSA). The ertapenem-plus-cefazolin combination was evaluated for synergy
in vitro
and
in vivo
in a murine skin infection model using an index MSSA bloodstream isolate from a patient in whom persistent bacteremia was cleared with this combination and against a cadre of well-described research strains and clinical strains of MSSA and MRSA. Against the index MSSA bloodstream isolate, ertapenem and cefazolin showed synergy using both checkerboard (fractional inhibitory concentration [FIC] index = 0.375) and time-kill assays. Using a disk diffusion ertapenem potentiation assay, the MSSA isolate showed a cefazolin disk zone increased from 34 to 40 mm.
In vitro
pharmacokinetic/pharmacodynamic modeling at clinically relevant drug concentrations demonstrated bactericidal activity (>3 log
10
-CFU/ml reduction) of the combination but bacteriostatic activity of ether drug alone at 48 h. A disk diffusion potentiation assay showed that ertapenem increased the cefazolin zone of inhibition by >3 mm for 34/35 (97%) MSSA and 10/15 (67%) MRSA strains. A murine skin infection model of MSSA showed enhanced activity of cefazolin plus ertapenem compared to monotherapy with these agents. After successful use in clearance of MSSA bacteremia, the combination of ertapenem and cefazolin showed synergy against MSSA
in vitro
and
in vivo
. This combination may warrant consideration for future clinical study in MSSA bacteremia.
Ehrlichia chaffeensis TRP32 Is a Nucleomodulin That Directly Regulates Expression of Host Genes Governing Differentiation and Proliferation
Authors: Farris Tierra R. , Dunphy Paige S. , Zhu Bing , Kibler Clayton E. , McBride Jere W.
Published: August 2016

Ehrlichia chaffeensisis an obligately intracellular bacterium that reprograms the mononuclear phagocyte through diverse effector-host interactions to modulate numerous host cell processes, including transcription. In a previous study, we reported thatE. chaffeensisTRP32, a type 1 secreted effector, interacts with multiple host nucleus-associated proteins and also autoactivates reporter gene expression in yeast. In this study, we demonstrate that TRP32 is a nucleomodulin that binds host DNA and alters host gene transcription. TRP32 enters the host cell nucleus via a noncanonical translocation mechanism that involves phosphorylation of Y179 located in a C-terminal trityrosine motif. Both genistein and mutation of Y179 inhibited TRP32 nuclear entry. An electromobility shift assay (EMSA) demonstrated TRP32 host DNA binding via its tandem repeat domain. TRP32 DNA-binding and motif preference were further confirmed by supershift assays, as well as competition and mutant probe analyses. Using chromatin immunoprecipitation with next-generation sequencing (ChIP-seq), we determined that TRP32 binds a G-rich motif primarily within ±500 bp of the gene transcription start site. An ontology analysis identified genes involved in processes such as immune cell differentiation, chromatin remodeling, and RNA transcription and processing as primary TRP32 targets. TRP32-bound genes (n= 1,223) were distributed on all chromosomes and included several global regulators of proliferation and inflammation such as those encoding FOS, JUN, AKT3, and NRAS and noncoding RNA genes microRNA 21 (miRNA 21) and miRNA 142. TRP32 target genes were differentially regulated during infection, the majority of which were repressed, and direct repression/activation of these genes by TRP32 was confirmedin vitrowith a cellular luciferase reporter assay.
Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay
Authors: Heussler Gary E. , Miller Jon L. , Price Courtney E. , Collins Alan J. , O'Toole George A.
Published: August 2016

CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished using overexpression of
cas
genes or plasmid loss assays; little work has focused on endogenous CRISPR-acquired immunity from viral predation. Here, we developed a new biofilm-based assay system to enrich for
Pseudomonas aeruginosa
strains with new spacer acquisition. We used this assay to demonstrate that
P. aeruginosa
rapidly acquires spacers protective against DMS3
vir
, an engineered lytic variant of the Mu-like bacteriophage DMS3, through primed CRISPR adaptation from spacers present in the native CRISPR2 array. We found that for the
P. aeruginosa
type I-F system, the
cas1
gene is required for CRISPR adaptation,
recG
contributes to (but is not required for) primed CRISPR adaptation,
recD
is dispensable for primed CRISPR adaptation, and finally, the ability of a putative priming spacer to prime can vary considerably depending on the specific sequences of the spacer.

IMPORTANCE
Our understanding of CRISPR adaptation has expanded largely through experiments in type I CRISPR systems using plasmid loss assays, mutants of
Escherichia coli
, or
cas1-cas2
overexpression systems, but there has been little focus on studying the adaptation of endogenous systems protecting against a lytic bacteriophage. Here we describe a biofilm system that allows
P. aeruginosa
to rapidly gain spacers protective against a lytic bacteriophage. This approach has allowed us to probe the requirements for CRISPR adaptation in the endogenous type I-F system of
P. aeruginosa
. Our data suggest that CRISPR-acquired immunity in a biofilm may be one reason that many
P. aeruginosa
strains maintain a CRISPR-Cas system.
HubP, a Polar Landmark Protein, Regulates Flagellar Number by Assisting in the Proper Polar Localization of FlhG in Vibrio alginolyticus
Authors: Takekawa Norihiro , Kwon Soojin , Nishioka Noriko , Kojima Seiji , Homma Michio
Published: August 2016

The marine bacterium
Vibrio alginolyticus
has a single polar flagellum, the number of which is regulated positively by FlhF and negatively by FlhG. FlhF is intrinsically localized at the cell pole, whereas FlhG is localized there through putative interactions with the polar landmark protein HubP. Here we focused on the role of HubP in the regulation of flagellar number in
V. alginolyticus
. Deletion of
hubP
increased the flagellar number and completely disrupted the polar localization of FlhG. It was thought that the flagellar number is determined primarily by the absolute amount of FlhF localized at the cell pole. Here we found that deletion of
hubP
increased the flagellar number although it did not increase the polar amount of FlhF. We also found that FlhG overproduction did not reduce the polar localization of FlhF. These results show that the absolute amount of FlhF is not always the determinant of flagellar number. We speculate that cytoplasmic FlhG works as a quantitative regulator, controlling the amount of FlhF localized at the pole, and HubP-anchored polar FlhG works as a qualitative regulator, directly inhibiting the activity of polar FlhF. This regulation by FlhF, FlhG, and HubP might contribute to achieving optimal flagellar biogenesis at the cell pole in
V. alginolyticus
.

IMPORTANCE
For regulation of the flagellar number in marine
Vibrio
, two proteins, FlhF and FlhG, work as positive and negative regulators, respectively. In this study, we found that the polar landmark protein HubP is involved in the regulation of flagellar biogenesis. Deletion of
hubP
increased the number of flagella without increasing the amount of pole-localizing FlhF, indicating that the number of flagella is not determined solely by the absolute amount of pole-localizing FlhF, which is inconsistent with the previous model. We propose that cytoplasmic FlhG and HubP-anchored polar FlhG negatively regulate flagellar formation through two independent schemes.
Effect of ischaemic brain injury on sexual function in adult mice
Authors: Tang Yaohui , Yuan Falei , Cai Beibei , Xia Weiliang , Wang Yongting , Yang Guo-Yuan
Published: August 2016

Objective

Priapism refers to a condition with persistent abnormal erection of the penis, which is usually caused by disease or injury in the brain or spinal cord, or obstruction to the outflow of blood through the dorsal vein at the root of the penis, without sexual desires. The effect of cerebral ischaemia on sexual function is unknown. The aim of this study is to explore whether priapism occurs in adult mice. Furthermore, we examined the relationship between priapism and the region of infarct in the brain.

Design

Adult male CD-1 mice who underwent permanent middle cerebral artery occlusion (pMCAO) were closely examined from 2 hours to 14 days postoperation.

Results

We found that priapism occurs in ∼80% of the mice with pMCAO, which could persist up to 14 days. Further study has demonstrated that the occurrence of priapism is related to the infarct region: priapism is found only in mice with ischaemic injury extending to the hypothalamus and the hippocampus regions.

Conclusion

Our result suggested priapism may be used as a deep brain injury marker for evaluating brain injury in mice after pMCAO.
Design method reliability assessment from an extended database of axial load tests on piles driven in sand
Authors: Yang Z.X. , Guo W.B. , Jardine R.J. , Chow F.
Published: August 2016

The accurate prediction of axial capacity remains a challenging task for piles driven in sands. Rigorous database studies have become key tools for assessing the efficacy of design methods. This paper employs the 117 high-quality entries in the recently developed Zhejiang University – Imperial College London (ZJU–ICL) database to check for potential biases between nine prediction procedures, considering a range of factors. The analysis highlights the critical importance of addressing age after driving, open and closed ends, tension versus compression, and concrete compared to steel. It also shows the hierarchy of reliability parameters associated with the alternative approaches. The “full” Imperial College pile (ICP) approach and The University of Western Australia (UWA) approaches are found to have significant advantages in eliminating potential biases. It is also argued that design load and resistance or safety factors should be varied to match the design and site investigation methods applied, as well as the loading uncertainty and degree of load cycling, which often vary between applications. Noting that predictions for base capacities Qbare inherently less reliable than for shaft Qs, especially in rapidly varying ground profiles, credible lower bound parameters (cone resistance, qc) are recommended for Qbassessment. It is also recommended that the potential effects of cycling be addressed carefully in cases that involve substantial environmental loading.
Developing of an instrument for assessing students’ data analysis skills in the undergraduate physics laboratory
Authors: Eshach Haim , Kukliansky Ida
Published: August 2016

This paper describes the development and field test of the Laboratory Data Analysis Instrument (LDAI), aimed at diagnosing first-year students’ understanding of data analysis procedures. The design of this student-centered instrument is based on difficulties related to students’ data analysis skills required in an introductory physics laboratory. Difficulties were determined from previous literature, observations in laboratory classes, and interviews with students. The LDAI is single-context based, consisting of 30 multiple-choice and true/false questions embedded in a real laboratory report from a real laboratory. It was validated by seven experts: three physics professors, one science education lecturer, and three experienced laboratory instructors. Administration to 77 participants resulted in a Cronbach’s alpha of 0.702. The LDAI is a promising step toward having a valid and reliable diagnostic instrument that can be used by laboratory instructors in undergraduate physics laboratories.
Accurate theoretical study on the ground and first-excited states of Na2: potential energy curves, spectroscopic parameters, and vibrational energy levels
Authors: Zhang Lu-Lu , Song Yu-Zhi , Gao Shou-Bao , Xu Ji-Hua , Zhou Yong , Meng Qing-Tian
Published: August 2016

Potential energy curves (PECs) for the ground and first-excited electronic states of Na2 are obtained by fitting the ab initio energies calculated at the MRCI(Q)/aug-cc-pVXZ (X = T, Q, 5) level of theory, which are subsequently extrapolated to the complete basis set limit. The relativistic effect and core–valence correlation are also considered. The PECs are accurate at both short and long internuclear distances with the root-mean-squared deviations being 0.72 cm−1 for Na2 [Formula: see text] and 0.36 cm−1 for Na2 [Formula: see text]. Utilizing the obtained PECs, we calculate the spectroscopic parameters, vibrational energy levels, classical turning points, inertial rotation, and centrifugal distortion constants, which are in good agreement with other theoretical and experimental work.
ASEAN ECONOMIC INTEGRATION COMPARED: WHAT DO THE NUMBERS TELL US?
Authors: CHEN LURONG , CUYVERS LUDO , DE LOMBAERDE PHILIPPE
Published: August 2016

In the comparative literature on regional (economic) integration processes, the ASEAN experience is often contrasted with the European (EU) integration process. More than any other integration process in the world, the ASEAN case is singled out as a counter-model for the EU. The ASEAN model is thereby associated with features such as: low levels of institutionalization, pragmatism, bottom-up or de facto regionalization, regional production platforms, and so on. The positive features of this ‘model’ are often emphasized; however, in recent years there have also been calls for deepening the institutionalization of ASEAN, including from the ADB.

The purpose of our paper is double: On the one hand, we present a long-term meta-analysis of available indicators in order to compare more accurately the ASEAN experience with other integration experiences worldwide, and complement (and test) the mostly qualitative approaches in the comparative literature. This should allow to better identify convergences and divergences between ASEAN and other integration processes. On the other hand, by comparing ASEAN with benchmark cases, we shed new light on the potential for further deepening the economic integration process in Southeast Asia. The latter comparison is complemented with gravity-type model estimations to assess the potential for further developing intra-ASEAN trade.

It is shown that ASEAN’s export space is expanding faster than the world average and that there is still space for ASEAN countries to further develop the role of its intra-regional trade. ASEAN can further improve the region’s competitiveness by reducing the non-tariff barriers and technical barriers, trade facilitation, strengthening regional value chains, facilitating factor mobility and enhancing regional cooperation.
BEYOND THE SECRETARIAT: ADDRESSING GOVERNANCE ISSUES IN ASEAN ECONOMIC COMMUNITY
Authors: PITAKDUMRONGKIT KAEWKAMOL
Published: August 2016

This article investigates interactions between institutional designs and values upheld by states on institutional effectiveness, for the purpose of understanding why particular institutions perform better than the others in extracting compliance and cooperation from countries. I contend that institutional effectiveness — defined as the ability to extract states’ compliance and foster cooperation — is explained by dynamics between institutional functions and actors’ governing principles. The higher the compatibility between these two factors, the higher the degree of institutions’ effectiveness, and vice versa. This argument was validated through cases of non-tariff barrier (NTB) elimination and trade facilitation under the ASEAN Economic Community framework.
Limit Cycle Bifurcation of Infinity and Degenerate Singular Point in Three-Dimensional Vector Field
Authors: Du Chaoxiong , Liu Yirong , Zhang Qi
Published: August 2016

Our work focuses on investigating limit cycle bifurcation for infinity and a degenerate singular point of a fifth degree system in three-dimensional vector field. By using singular value method to compute focal values carefully, we give the expressions of the focal values (Lyapunov constants) at the origin and at infinity. Moreover, we obtain that four limit cycles at most can bifurcate from the origin and three limit cycles can bifurcate from infinity. At the same time, we show the structure of limit cycles from the origin and the infinity. It is interesting for this kind of nonlinear phenomenon that a string of large limit cycles encircle a string of small limit cycles by simultaneous Hopf bifurcation, which is hardly seen for similar published results in three-dimensional vector field, our result is new.
Designing Chaotic Systems by Piecewise Affine Systems
Authors: Wu Tiantian , Li Qingdu , Yang Xiao-Song
Published: August 2016

Based on mathematical analysis, this paper provides a methodology to ensure the existence of homoclinic orbits in a class of three-dimensional piecewise affine systems. In addition, two chaotic generators are provided to illustrate the effectiveness of the method.
When Parallels and Meridians are Limit Cycles for Polynomial Vector Fields on Quadrics of Revolution in the Euclidean 3-Space
Authors: Dias Fabio Scalco , Llibre Jaume , Mello Luis Fernando
Published: August 2016

We study polynomial vector fields of arbitrary degree in [Formula: see text] with an invariant quadric of revolution. We characterize all the possible configurations of invariant meridians and parallels that these vector fields can exhibit. Furthermore, we analyze when these invariant meridians and parallels can be limit cycles.
Asymptotic behavior and blowup for two generalized Ginzburg–Landau type equations with several nonlinear source terms
Authors: Jin Shoubo , Zhang Zufeng , Zhang Qun
Published: August 2016

In this paper, the long-time behavior and blowup of solutions for two generalized Ginzburg–Landau type equations with several nonlinear source terms are investigated. First, the conditions in which the solutions of the two equations are positive are analyzed by using Green’s function. According to the characteristics of nonlinear terms, four different functionals are constructed for solving the problems. Finally, we obtain the long-time behavior and finite-time blowup of solutions for the initial and boundary value problem by using these functionals.
Model Reduction for Flow Analysis and Control
Authors: Rowley Clarence W. , Dawson Scott T.M.
Published: August 2016

Advances in experimental techniques and the ever-increasing fidelity of numerical simulations have led to an abundance of data describing fluid flows. This review discusses a range of techniques for analyzing such data, with the aim of extracting simplified models that capture the essential features of these flows, in order to gain insight into the flow physics, and potentially identify mechanisms for controlling these flows. We review well-developed techniques, such as proper orthogonal decomposition and Galerkin projection, and discuss more recent techniques developed for linear systems, such as balanced truncation and dynamic mode decomposition (DMD). We then discuss some of the methods available for nonlinear systems, with particular attention to the Koopman operator, an infinite-dimensional linear operator that completely characterizes the dynamics of a nonlinear system and provides an extension of DMD to nonlinear systems.
Particle Migration due to Viscoelasticity of the Suspending Liquid and Its Relevance in Microfluidic Devices
Authors: D'Avino Gaetano , Greco Francesco , Maffettone Pier Luca
Published: August 2016

The fast growth of microfluidic applications based on complex fluids is a result of the unique fluid dynamics of these systems, enabling the creation of devices for health care or biological and chemical analysis. Microchannels designed to focus, concentrate, or separate particles suspended in viscoelastic liquids are becoming common. The key fluid dynamical issue on which such devices work is viscoelasticity-induced lateral migration. This phenomenon was discovered in the 1960s in macroscopic channels and has received great attention within the microfluidic community in the past decade. This review presents the current understanding, both from experiments and theoretical analysis, of viscoelasticity-driven cross-flow migration. Examples of promising microfluidic applications show the unprecedented capabilities offered by such technology based on geometrically simple microchannels and rheologically complex liquids.
Marine Hydrokinetic Energy from Western Boundary Currents
Authors: Bane John M. , He Ruoying , Muglia Michael , Lowcher Caroline F. , Gong Yanlin , Haines Sara M.
Published: August 2016

The kinetic energy in ocean currents, or marine hydrokinetic (MHK) energy, is a renewable energy resource that can help meet global energy requirements. An ocean circulation model–based census shows that subtropical surface western boundary currents (WBCs) are the only nearshore, large-scale currents swift enough to drive large electricity-generating ocean turbines envisioned for future use. We review several WBCs in the context of kinetic energy extraction. The power density in the Gulf Stream off North Carolina at times reaches several thousand watts per square meter at 75 m below the surface, and the annual average power is approximately 500–1,000 W m−2. Significant fluctuations occur with periods of 3–20 days (Gulf Stream meanders) and weeks to months (Gulf Stream path shifts). Interannual variations in annual average power occur because of year-to-year changes in these WBC motions. No large-scale turbines presently exist, and the road to establishing MHK facilities in WBCs will encounter challenges that are similar in many aspects to those associated with the development of offshore wind power.
Biogeochemical Transformations in the History of the Ocean
Authors: Lenton Timothy M. , Daines Stuart J.
Published: August 2016

The ocean has undergone several profound biogeochemical transformations in its 4-billion-year history, and these were an integral part of the coevolution of life and the planet. This review focuses on changes in ocean redox state as controlled by changes in biological activity, nutrient concentrations, and atmospheric O2. Motivated by disparate interpretations of available geochemical data, we aim to show how quantitative modeling—spanning microbial mats, shelf seas, and the open ocean—can help constrain past ocean biogeochemical redox states and show what caused transformations between them. We outline key controls on ocean redox structure and review pertinent proxies and their interpretation. We then apply this quantitative framework to three key questions: How did the origin of oxygenic photosynthesis transform ocean biogeochemistry? How did the Great Oxidation transform ocean biogeochemistry? And how was ocean biogeochemistry transformed in the Neoproterozoic-Paleozoic?
Multiple Stressors and the Functioning of Coral Reefs
Authors: Harborne Alastair R. , Rogers Alice , Bozec Yves-Marie , Mumby Peter J.
Published: August 2016

Coral reefs provide critical services to coastal communities, and these services rely on ecosystem functions threatened by stressors. By summarizing the threats to the functioning of reefs from fishing, climate change, and decreasing water quality, we highlight that these stressors have multiple, conflicting effects on functionally similar groups of species and their interactions, and that the overall effects are often uncertain because of a lack of data or variability among taxa. The direct effects of stressors on links among functional groups, such as predator-prey interactions, are particularly uncertain. Using qualitative modeling, we demonstrate that this uncertainty of stressor impacts on functional groups (whether they are positive, negative, or neutral) can have significant effects on models of ecosystem stability, and reducing uncertainty is vital for understanding changes to reef functioning. This review also provides guidance for future models of reef functioning, which should include interactions among functional groups and the cumulative effect of stressors.
Gene Editing: A New Tool for Viral Disease
Authors: Kennedy Edward M. , Cullen Bryan R.
Published: August 2016

The emergence of the CRISPR/Cas system of antiviral adaptive immunity in bacteria as a facile system for gene editing in mammalian cells may well lead to gene editing becoming a novel treatment for a range of human diseases, especially those caused by deleterious germline mutations. Another potential target for gene editing are DNA viruses that cause chronic pathogenic diseases that cannot be cured by using currently available drugs. We review the current state of this field and discuss the potential advantages and problems with using a gene editing approach as a treatment for diseases caused by DNA viruses.
Bats as Viral Reservoirs
Authors: Hayman David T.S.
Published: August 2016

Bats are hosts of a range of viruses, including ebolaviruses, and many important human viral infections, such as measles and mumps, may have their ancestry traced back to bats. Here, I review viruses of all viral families detected in global bat populations. The viral diversity in bats is substantial, and viruses with all known types of genomic structures and replication strategies have been discovered in bats. However, the discovery of viruses is not geographically even, with some apparently undersampled regions, such as South America. Furthermore, some bat families, including those with global or wide distributions such as Emballonuridae and Miniopteridae, are underrepresented on viral databases. Future studies, including those that address these sampling gaps along with those that develop our understanding of viral-host relationships, are highlighted.
Hierarchical Task Planning for Multiarm Robot with Multiconstraint
Authors: Wang Yifan , Sun Hanxu , Chen Gang , Jia Qingxuan , Yu Boyang
Published: August 2016

Multiarm systems become the trends of space robots, for the on-orbit servicing missions are becoming more complex and various. A hierarchical task planning method with multiconstraint for multiarm space robot is presented in this paper. The process of task planning is separated into two hierarchies: mission profile analysis and task node planning. In mission profile analysis, several kinds of primitive tasks and operators are defined. Then, a complex task can be decomposed into a sequence of primitive tasks by using hierarchical task network (HTN) with those primitive tasks and operators. In task node planning,A⁎algorithm is improved to adapt the continuous motion of manipulator. Then, some of the primitive tasks which cannot be executed directly because of constraints are further decomposed into several task nodes by using improvedA⁎algorithm. Finally, manipulators execute the task by moving from one node to another with a simple path plan algorithm. The feasibility and effectiveness of the proposed task planning method are verified by simulation.
A Numerical Method Based on Daubechies Wavelet Basis and B-Spline Patches for Elasticity Problems
Authors: Liu Yanan , Din Keqin
Published: August 2016

The Daubechies (DB) wavelets are used for solving 2D plane elasticity problems. In order to improve the accuracy and stability in computation, the DB wavelet scaling functions in0,+∞)comprising boundary scaling functions are chosen as basis functions for approximation. The B-spline patches used in isogeometry analysis method are constructed to describe the problem domain. Through the isoparametric analysis approach, the function approximation and relevant computation based on DB wavelet functions are implemented on B-spline patches. This work makes an attempt to break the limitation that problems only can be discretized on uniform grids in the traditional wavelet numerical method. Numerical examples of 2D elasticity problems illustrate that this kind of analysis method is effective and stable.
Research of Jiles-Atherton Dynamic Model in Giant Magnetostrictive Actuator
Authors: Liu Yongguang , Gao Xiaohui , Chen Chunxu
Published: August 2016

Due to the existence of multicoupled nonlinear factors in the giant magnetostrictive actuator (GMA), building precise mathematical model is highly important to study GMA’s characteristics and control strategies. Minor hysteresis loops near the bias magnetic field would be often applied because of its relatively good linearity. Load, friction, and disc spring stiffness seriously affect the output characteristics of the GMA in high frequency. Therefore, the current-displacement dynamic minor loops mathematical model coupling of electric-magnetic-machine is established according to Jiles-Atherton (J-A) dynamic model of hysteresis material, GMA structural dynamic equation, Ampere loop circuit law, and nonlinear piezomagnetic equation and demonstrates its correctness and effectiveness in the experiments. Finally, some laws are achieved between key structural parameters and output characteristics of GMA, which provides important theoretical foundation for structural design.
A Monte-Carlo Algorithm for 3D Fibre Detection from Microcomputer Tomography
Authors: Gloeckner Robert , Kolling Stefan , Heiliger Christian
Published: August 2016

A model-based approach to analyze fibre distributions in polymer composites applicable for high fibre content is suggested. The algorithm is a four-step iterative method using Monte-Carlo techniques in order to increase speed and robustness for fibre detection. Samples with up to 20% volume fraction of glass fibres and different matrix polymers (PP, PBT) have been analyzed regarding distributions of orientation and length and thickness of the fibres.
Effect of Codoping Cl Anion and 5-AVA Cation on Performance of Large-Area Perovskite Solar Cells with Double-Mesoporous Layers
Authors: Pei Yaxian , Zou Xiaoping , Guan Yingxiang , Teng Gongqing
Published: August 2016

For the perovskite solar cells (PSCs), the performance of the PSCs has become the focus of the research by improving the quality of the perovskite absorption layer. So far, the performance of the large-area PSCs is lower than that of small-area PSCs. In the paper, the experiments were designed to improve the photovoltaic performance of the large-area PSCs by improved processing technique. Here we investigated the optoelectronic properties of the prototypical CH3NH3PbI3(MAPbI3) further modulated by introducing other extrinsic ions (specifically codoped Cl−and 5-AVA+). Moreover, we used inorganic electron extraction layer to achieve very rapid photogenerated carrier extraction eliminating local structural defects over large areas. Ultimately, we fabricated a best-performing perovskite solar cell based on codoping Cl anion and 5-AVA cation which uses a double layer of mesoporous TiO2and ZrO2as a scaffold infiltrated with perovskite and does not require a hole-conducting layer. The experiment results indicated that an average efficiency of double-mesoporous layer-based devices with codoping Cl anion and 5-AVA cation was obtained with exceeding 50% enhancement, compared to that of pure single-mesoporous layer-based device.
Analysis of Free Pendulum Vibration Absorber Using Flexible Multi-Body Dynamics
Authors: Gumus Emrah , Ertas Atila
Published: August 2016

Structures which are commonly used in our infrastructures are becoming lighter with progress in material science. These structures due to their light weight and low stiffness have shown potential problem of wind-induced vibrations, a direct outcome of which is fatigue failure. In particular, if the structure is long and flexible, failure by fatigue will be inevitable if not designed properly. The main objective of this paper is to perform theoretical analysis for a novel free pendulum device as a passive vibration absorber. In this paper, the beam-tip mass-free pendulum structure is treated as a flexible multibody dynamic system and the ANCF formulation is used to demonstrate the coupled nonlinear dynamics of a large deflection of a beam with an appendage consisting of a mass-ball system. It is also aimed at showing the complete energy transfer between two modes occurring when the beam frequency is twice the ball frequency, which is known as autoparametric vibration absorption. Results are discussed and compared with findings of MSC ADAMS. This novel free pendulum device is practical and feasible passive vibration absorber in the mitigation of large amplitude wind-induced vibrations in traffic signal structures.
Two Improved Cancellation Techniques for Direct-Conversion Receivers
Authors: Hao Xueyuan , Yan Xiaohong
Published: August 2016

To solve the problems of carrier leakage and DC offset in direct-conversion receiver (DCR) system, the paper proposed two kinds of improved technology to overcome the problems in DCR system. One is the RF carrier cancellation technology; the traditional cancellation technology based on lumped parameter filter can be easily influenced by distribution parameters, the improved circuits use a 3 db bridge to realize a 180-degree phase shifter, and the method can adapt to a wider range of RF frequency. Another is DC offset cancellation technique; a novel DC servo loop circuit is proposed to replace the traditional AC-coupled amplifier circuit. It can improve the integrity of the baseband signal and reduces the complexity of the subsequent software algorithm. Experimental results show that two kinds of improved technology can improve the performance of DCR and expand its scope of application.