bluuebunny/crossref_metadata_2025 huggingface dataset:
Cardioprotection against ischaemia/reperfusion by vitamins C and E plus n−3 fatty acids: molecular mechanisms and potential clinical applications
Authors: Rodrigo Ramón , Prieto Juan C. , Castillo Rodrigo
Published: September 2012

The role of oxidative stress in ischaemic heart disease has been thoroughly investigated in humans. Increased levels of ROS (reactive oxygen species) and RNS (reactive nitrogen species) have been demonstrated during ischaemia and post-ischaemic reperfusion in humans. Depending on their concentrations, these reactive species can act either as benevolent molecules that promote cell survival (at low-to-moderate concentrations) or can induce irreversible cellular damage and death (at high concentrations). Although high ROS levels can induce NF-κB (nuclear factor κB) activation, inflammation, apoptosis or necrosis, low-to-moderate levels can enhance the antioxidant response, via Nrf2 (nuclear factor-erythroid 2-related factor 2) activation. However, a clear definition of these concentration thresholds remains to be established. Although a number of experimental studies have demonstrated that oxidative stress plays a major role in heart ischaemia/reperfusion pathophysiology, controlled clinical trials have failed to prove the efficacy of antioxidants in acute or long-term treatments of ischaemic heart disease. Oral doses of vitamin C are not sufficient to promote ROS scavenging and only down-regulate their production via NADPH oxidase, a biological effect shared by vitamin E to abrogate oxidative stress. However, infusion of vitamin C at doses high enough to achieve plasma levels of 10 mmol/l should prevent superoxide production and the pathophysiological cascade of deleterious heart effects. In turn, n−3 PUFA (polyunsaturated fatty acid) exposure leads to enhanced activity of antioxidant enzymes. In the present review, we present evidence to support the molecular basis for a novel pharmacological strategy using these antioxidant vitamins plus n−3 PUFAs for cardioprotection in clinical settings, such as post-operative atrial fibrillation, percutaneous coronary intervention following acute myocardial infarction and other events that are associated with ischaemia/reperfusion.
Role of GLP-1 and DPP-4 in diabetic nephropathy and cardiovascular disease
Authors: Panchapakesan Usha , Mather Amanda , Pollock Carol
Published: September 2012

Although there have been major advances in the understanding of the molecular mechanisms that contribute to the development of diabetic nephropathy, current best practice still leaves a significant treatment gap. The incidence of diabetes and associated nephropathy is increasing, with the main cause of mortality being related to cardiovascular causes. Novel therapies which are both ‘cardio-renal’-protective seem the logical way forward. In the present review, we discuss the GLP-1 (glucagon-like peptide-1) receptor agonists and DPP-4 (dipeptidyl peptidase-4) inhibitors (incretin-based therapies), which are novel antidiabetic agents used in clinical practice and their role in diabetic nephropathy with specific focus on renoprotection and surrogate markers of cardiovascular disease. We discuss the pleiotropic effects of the incretin-based therapies apart from glucose-lowering and highlight the non-GLP-1 effects of DPP (dipeptidyl peptidase) inhibition. Large-scale clinical studies with cardiovascular end points are underway; however, studies with renal end points are lacking but much needed.
Measurements and simulations of a channel flow powered by plasma actuators
Authors: Riherd Mark , Roy Subrata
Published: September 2012

Experimental measurements and numerical simulations of a dielectric barrier discharge driven flow inside a finite length channel have been performed. Plasma actuators have been used to impart momentum to the flow in the near wall region, which diffuses throughout the height of the channel as it convects downstream. This momentum addition is found to be of sufficient magnitude to create an unsteady channel flow with exit velocities on the order of 1–3 m/s. Pressure and velocity measurements have been taken in order to quantify the effects of varying the number of symmetrically placed pairs of plasma actuators in the channel and the operating voltage applied to the actuators, showing a monotonic increase with respect to both parameters. Power law relationships have been determined for these measurements with respect to the operating voltage, with exponents of 2.0 for the exit velocity and of 5.6 for the maximum pressure differential. The pressure measurements also suggest that the pressure increase due to each actuator is independent of the bulk flow inside the channel. Numerical predictions also agree with the measured pressure and velocity distributions across the channel. The bulk velocity and pressure measurements allow for efficiency calculations of the plasma channel, which are shown to also fit into a power law relationship with respect to the operating voltage. The data collected show that the efficiency of these devices is low, less than 0.1%, but that it increases with a power law exponent of 4.09 to 4.35 indicating the possibility of using such channel for pumping small flows.
Characterization of dark current in Ge-on-Si photodiodes
Authors: DiLello N. A. , Johnstone D. K. , Hoyt J. L.
Published: September 2012

Ge-on-Si photodiodes were fabricated from germanium films grown using low-pressure chemical vapor deposition. The mechanisms responsible for the dark current in these devices are studied using geometric analysis, temperature-dependent current-voltage characterization, deep level transient spectroscopy, and device modeling. It is found that an important source of leakage current is associated with the surface depletion region, which is impacted by the nature of the fixed charge at the Ge/dielectric interface. This source of leakage especially affects devices with smaller area, on the order of 10 × 10 μm2. Through a post-metallization anneal (PMA), the dark current of these devices can be reduced by ∼1000X. A similar reduction can be obtained by intentionally doping the top of the germanium film p-type. After the PMA, it is found that the dark current density of large devices is ∼1 mA/cm2, due mainly to generation of minority carriers in the depletion region of the device. The effect of reducing the threading dislocation density is also discussed.
First-principles prediction of a new class of photovoltaic materials: I-III-IV2-V4 phosphides
Authors: Ma Jiahong , Lin Shiyuan , Fan Guanghan , Yao Guangrui , Zhao Yu-Jun
Published: September 2012

A new class of quaternary I-III-IV2-V4, including CuAlGe2P4, CuGaGe2P4, CuAlSn2P4, and CuGaSn2P4 are studied by density functional theory and beyond for potential photovoltaic application. We found that CuAlGe2P4 and CuGaGe2P4 have a ground state of kesterite (KS) structure, while CuAlSn2P4 and CuGaSn2P4 are nearly energetically degenerated for KS and stannite structures. Interestingly, the band gaps of all the studied quaternary compounds are predicted to be in the range of 1.1–1.7 eV by the hybrid functional calculation and Δ-sol approach [M. K.Y. Chan and G. Ceder, Phys. Rev. Lett. 105, 196403 (2010)]. In particular, CuAlSn2P4 in KS structure is predicted to be a potential high-efficiency photovoltaic material since it contains no rare or toxic elements with a direct gap around 1.52 eV.
Advanced modeling of the effective minority carrier lifetime of passivated crystalline silicon wafers
Authors: Ma Fa-Jun , Samudra Ganesh G. , Peters Marius , Aberle Armin G. , Werner Florian , Schmidt Jan , Hoex Bram
Published: September 2012

A strong injection level dependence of the effective minority carrier lifetime (τeff) is typically measured at low injection levels for undiffused crystalline silicon (c-Si) wafers symmetrically passivated by a highly charged dielectric film. However, this phenomenon is not yet well understood. In this work, we concentrate on two of those possible physical mechanisms to reproduce measured τeff data of c-Si wafers symmetrically passivated by atomic layer deposited Al2O3. The first assumes the existence of a defective region close to the c-Si surface. The second assumes asymmetric electron and hole lifetimes in the bulk. Both explanations result in an adequate reproduction of the injection dependent τeff found for both n- and p-type c-Si wafers. However, modeling also predicts a distinctly different injection dependence of τeff for the two suggested mechanisms if the polarity of the effective surface charge is inverted. We test this prediction by experimentally inverting the polarity of the effective surface charge using corona charges. From the experiments and simulations, it is concluded that surface damage is the most likely cause of the significant reduction of τeff  at low injection levels.
New beam line for time-of-flight medium energy ion scattering with large area position sensitive detector
Authors: Linnarsson M. K. , Hallén A. , Åström J. , Primetzhofer D. , Legendre S. , Possnert G.
Published: September 2012

A new beam line for medium energy ion mass scattering (MEIS) has been designed and set up at the Ångström laboratory, Uppsala University, Sweden. This MEIS system is based on a time-of-flight (ToF) concept and the electronics for beam chopping relies on a 4 MHz function generator. Repetition rates can be varied between 1 MHz and 63 kHz and pulse widths below 1 ns are typically obtained by including beam bunching. A 6-axis goniometer is used at the target station. Scattering angle and energy of backscattered ions are extracted from a time-resolved and position-sensitive detector. Examples of the performance are given for three kinds of probing ions, 1H+, 4He+, and 11B+. Depth resolution is in the nanometer range and 1 and 2 nm thick Pt layers can easily be resolved. Mass resolution between nearby isotopes can be obtained as illustrated by Ga isotopes in GaAs. Taking advantage of the large size detector, a direct imaging (blocking pattern) of crystal channels are shown for hexagonal, 4H-SiC. The ToF-MEIS system described in this paper is intended for use in semiconductor and thin film areas. For example, depth profiling in the sub nanometer range for device development of contacts and dielectric interfaces. In addition to applied projects, fundamental studies of stopping cross sections in this medium energy range will also be conducted.
Doubling of rocking resonance frequency of an adhesive microparticle vibrating on a surface
Authors: Saeedi Vahdat Armin , Azizi Saber , Cetinkaya Cetin
Published: September 2012

For some spherical micro-particles on a vibrating flat substrate, in addition to their predicted rocking resonance frequencies, other resonance peaks at their doubles are observed. Here, a mathematical model and experimental results are presented for explaining this observation. It is determined that the frequency doubling is caused by nonlinear coupling between the out-of-plane and rocking modes of motion, and whirling-like motion that must be present for the presence of doubling effect. It is also found that the work-of-adhesion values extracted from the experimental resonance frequencies of a set of particles using the developed model are in good agreement with those reported in the literature.
Strong atomic ordering in Gd-doped GaN
Authors: Ishimaru Manabu , Higashi Kotaro , Hasegawa Shigehiko , Asahi Hajime , Sato Kazuhisa , Konno Toyohiko J.
Published: September 2012

Gd-doped GaN (Ga1−xGdxN) thin films were grown on a GaN(001) template by radio frequency plasma-assisted molecular beam epitaxy and characterized by means of x-ray diffraction (XRD) and transmission electron microscopy (TEM). Three samples with a different Gd composition were prepared in this study: x = 0.02, 0.05, and 0.08. XRD and TEM results revealed that the low Gd concentration GaN possesses the wurtzite structure. On the other hand, it was found that an ordered phase with a quadruple-periodicity along the [001] direction in the wurtzite structure is formed throughout the film with x = 0.08. We proposed the atomistic model for the superlattice structure observed here.
Observation of spin-polarized electron transport in Alq3 by using a low work function metal
Authors: Jang Hyuk-Jae , Pernstich Kurt P. , Gundlach David J. , Jurchescu Oana D. , Richter Curt. A.
Published: September 2012

We present the observation of magnetoresistance in Co/Ca/Alq3/Ca/NiFe spin-valve devices. Thin Ca layers contacting 150 nm thick Alq3 enable the injection of spin-polarized electrons into Alq3 due to the engineering of the band alignment. The devices exhibit symmetric current-voltage (I–V) characteristics indicating identical metal contacts on Alq3, and up to 4% of positive magnetoresistance was observed at 4.5 K. In contrast, simultaneously fabricated Co/Alq3/NiFe devices displayed asymmetric I–V curves due to the different metal electrodes, and spin-valve effects were not observed.
Electromagnetically induced transparency in a Λ-type molecular system with permanent dipole moments revisited
Authors: Singh Niharika , Lawande Q. V. , D’Souza R. , Jagatap B. N.
Published: September 2012

Electromagnetically induced transparency (EIT) in a molecular three-level Λ system with permanent dipole moments and undergoing m- and n-photon transitions by pump and probe lasers is investigated. Analytical expressions are derived for probe absorption spectrum and dispersion for a medium of stationary as well as thermal molecules. Contrary to the earlier study by Zhou et al. [J. Chem. Phys. 131, 034105 (2009)10.1063/1.3176018], we observe no amplification in 2 + 2 photon process when the sign of the difference of the permanent moments of the excited and the ground levels is reversed. Reasons for these contrasting observations are discussed. Our study shows that the permanent moments essentially damp the laser-molecule Rabi frequency to result in narrower EIT line width and larger group velocity index. These effects are further enhanced when the order of the multi-photon process is increased. The importance of the virtual mechanism is discussed by considering the special case of 2 + 1 photon EIT.
Formation and control of wrinkles in graphene by the wedging transfer method
Authors: Calado V. E. , Schneider G. F. , Theulings A. M. M. G. , Dekker C. , Vandersypen L. M. K.
Published: September 2012

We study the formation of wrinkles in graphene upon wet transfer onto a hydrophilic target substrate, whereby draining of water appears to play an important role. We are able to control the orientation of the wrinkles by tuning the surface morphology. Wrinkles are absent in flakes transferred to strongly hydrophobic substrates, a further indication of the role of the interaction of water with the substrate in wrinkle formation. The electrical and structural integrity of the graphene is not affected by the wrinkles, as inferred from Raman measurements and electrical conductivity measurements.
Positive and negative exchange bias effects in the simple perovskite manganite NdMnO3
Authors: Hong Fang , Cheng Zhenxiang , Wang Jianli , Wang Xiaolin , Dou Shixue
Published: September 2012

Exchange bias effects were studied in the simple perovskite NdMnO3. Nd3+ ordering is induced by the Mn3+ ferromagnetic component, and they are antiferromagnetically coupled with each other. At 30 K, both negative and positive exchange bias effects are found, which are dependent on the cooling field. The exchange bias fields are around −2400 Oe and 1800 Oe, respectively. Positive and negative exchange bias effects were also observed at 8 K, but the exchange bias fields are only 130 Oe and −120 Oe. The coupling intensity between Nd3+ ordering and Mn3+ ordering, and their initial states determine the polarity of the exchange bias fields.
Structural properties and band offset determination of p-channel mixed As/Sb type-II staggered gap tunnel field-effect transistor structure
Authors: Zhu Y. , Jain N. , Mohata D. K. , Datta S. , Lubyshev D. , Fastenau J. M. , Liu A. K. , Hudait M. K.
Published: September 2012

The structural properties and band offset determination of p-channel staggered gap In0.7Ga0.3As/GaAs0.35Sb0.65 heterostructure tunnel field-effect transistor (TFET) grown by molecular beam epitaxy (MBE) were investigated. High resolution x-ray diffraction revealed that the active layers are strained with respect to “virtual substrate.” Dynamic secondary ion mass spectrometry confirmed an abrupt junction profile at the In0.7Ga0.3As/GaAs0.35Sb0.65 heterointerface and minimal level of intermixing between As and Sb atoms. The valence band offset of 0.37 ± 0.05 eV was extracted from x-ray photoelectron spectroscopy. A staggered band lineup was confirmed at the heterointerface with an effective tunneling barrier height of 0.13 eV. Thus, MBE-grown staggered gap In0.7Ga0.3As/GaAs0.35Sb0.65 TFET structures are a promising p-channel option to provide critical guidance for the future design of mixed As/Sb type-II based complementary logic and low power devices.
Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths
Authors: Gu Quanli , Trindle Carl , Knee J. L.
Published: September 2012

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.
Dye-assisted dispersion of single-walled carbon nanotubes for solution fabrication of NO2 sensors
Authors: Ramli M. M. , Zhang W. , Silva S. R. P. , Henley S. J.
Published: September 2012

Direct golden orange dye molecules were used as a dispersing agent to produce suspensions of single-walled carbon nanotubes (SWCNTs) in water. Uniform, thin film networks were fabricated by vacuum filtration using different concentrations of SWCNT and transferred subsequently to glass substrates. The dispersion efficiency was compared to other surfactants. Measurement of the sheet resistance as a function of SWCNT concentration showed a transition from 2D percolation to 3D conduction behaviour when the concentration of SWCNTs exceeded 0.001 mg/mL. The electrical response to NO2 gas exposure was investigated as a function of temperature and an optimum response was observed at 200°C.
Probing the RAFT Process Using a Model Reaction between Alkoxyamine and Dithioester
Authors: Li Changxi , He Junpo , Liu Ying , Zhou Yanwu , Yang Yuliang
Published: September 2012

A small-molecular model reaction was designed to probe the reversible addition–fragmentation chain transfer (RAFT) process. In this reaction, alkoxyamine releases radicals that react in situ with dithioester through the RAFT process, generating new radicals through the fragmentation of the intermediate radical. The new radicals can be trapped by free 2,2,6,6-tetramethyl-piperidinyl-N-oxyl radicals (TEMPO) from homolysis of alkoxyamine. The overall reaction is the crossover of the leaving groups between alkoxyamine and dithioester. The advantage of this model as a probe of the RAFT process is that it does not involve polymerization-related elementary reactions such as initiation, propagation, and chain length dependent termination. The kinetics of the model reaction were measured using high-performance liquid chromatography, and then fitted by Monte Carlo simulation to estimate rate coefficients. The obtained rate coefficients of addition for various dithioesters fell into a narrow range of 107–108 L mol–1 s–1, whereas the rate coefficient of fragmentation was model-dependent. It was also found that a significant fraction of the dithioester was consumed by an unspecified additional mechanism. A tentative explanation is proposed in which the intermediate radical undergoes a secondary RAFT reaction with dithioesters, forming a secondary intermediate that serves as a radical reservoir.
Star Polymers of Sodium Styrenesulfonate Prepared by One-Pot TEMPO-Controlled SFRP
Authors: Ding Jianfu , Holdcroft Steven
Published: September 2012

Star polymers of sodium styrenesulfonate with controlled arm length were prepared in a one-pot polymerization. Sodium styrenesulfonate was first polymerized with controlled molecular weight and narrow polydispersity by stable free radical polymerization. Poly(sodium styrenesulfonate) was terminated with divinyl benzene and star polymers prepared via stable free radical coupling of vinylic terminal groups. Star polymers based on arms of 20 and 32 repeat units possessed ~33 and ~41 arms per star respectively. Formation of star polymers with much longer arms was limited by poor coupling kinetics.
Synthesis, Structure, and Properties of a Chiral Zinc(II) Metal-Organic Framework Featuring Linear Trinuclear Secondary Building Blocks
Authors: Chen Zilu , Zhang Chuanbing , Liu Xianlin , Zhang Zhong , Liang Fupei
Published: September 2012

A chiral metal-organic framework formulated as [Zn3(L-TMTA)2(4,4′-bpy)4]·24H2O (1) was prepared from the reaction of Zn(NO3)2·6H2O with trimesoyltri(L-alanine) (L-TMTAH3) in the presence of 4,4′-bipyridine (4,4′-bpy). Compound 1 features linear trinuclear secondary building blocks [Zn3(syn-syn-COO)2(μ2,η3-COO)2]2+. Each linear trinuclear secondary building block is further linked to another eight ones around it by four L-TMTA3– ligands and eight 4,4′-bpy ligands, leading to the construction of a uninodal three-dimensional framework with triangular prism-like one-dimensional channels. Dehydrated compound 1 displays remarkable adsorption selectivity on CO2 and water vapour over N2 gas.
Photocatalytic Hydrogen Evolution Using 9-Phenyl-10-methyl-acridinium Ion Derivatives as Efficient Electron Mediators and Ru-Based Catalysts
Authors: Yamada Yusuke , Yano Kentaro , Fukuzumi Shunichi
Published: September 2012

Photocatalytic hydrogen evolution has been performed by photoirradiation (λ > 420 nm) of a mixed solution of a phthalate buffer and acetonitrile (MeCN) (1 : 1 (v/v)) containing EDTA disodium salt (EDTA), [RuII(bpy)3]2+ (bpy = 2,2′-bipyiridine), 9-phenyl-10-methylacridinium ion (Ph–Acr+–Me), and Pt nanoparticles (PtNPs) as a sacrificial electron donor, a photosensitiser, an electron mediator, and a hydrogen-evolution catalyst, respectively. The hydrogen-evolution rate of the reaction system employing Ph–Acr+–Me as an electron mediator was more than 10 times higher than that employing a conventional electron mediator of methyl viologen. In this reaction system, ruthenium nanoparticles (RuNPs) also act as a hydrogen-evolution catalyst as well as the PtNPs. The immobilization of the efficient electron mediator on the surface of a hydrogen-evolution catalyst is expected to enhance the hydrogen-evolution rate. The methyl group of Ph–Acr+–Me was chemically modified with a carboxy group (Ph–Acr+–CH2COOH) to interact with metal oxide surfaces. In the photocatalytic hydrogen-evolution system using Ph–Acr+–CH2COOH and Pt-loaded ruthenium oxide nanoparticles (Pt/RuO2NPs) as electron donor and hydrogen-evolution catalyst, respectively, the hydrogen-evolution rate was 1.5–2 times faster than the reaction system using Ph–Acr+–Me as an electron mediator. On the other hand, no enhancement in the hydrogen-evolution rate was observed in the reaction system using Ph–Acr+–CH2COOH with PtNPs. Thus, the enhancement of hydrogen-evolution rate originated from the favourable interaction between Ph–Acr+–CH2COOH and RuO2NPs. These results suggest that the use of Ph–Acr+–Me as an electron mediator enables the photocatalytic hydrogen evolution using PtNPs and RuNPs as hydrogen-evolution catalysts, and the chemical modification of Ph–Acr+–Me with a carboxy group paves the way to utilise a supporting catalyst, Pt loaded on a metal oxide, as a hydrogen-evolution catalyst.
Phonological similarity judgments in ASL
Authors: Hall Matthew L. , Ferreira Victor S. , Mayberry Rachel I.
Published: September 2012

We created a novel paradigm to investigate phonological processing in sign and asked how age of acquisition (AoA) may affect it. Participants indicated which of two signs was more phonologically similar to a target, and estimated the strength of the resemblance with a mouse click along a continuous scale. We manipulated AoA by testing deaf native and non-native signers, and hearing L2 signers and sign-naïve participants. Consistent with previous research, judgments by the native and L2 signers reflected similarity based on shared phonological features between signs. By contrast, judgments by the non-native signers and sign-naïve participants were influenced by other (potentially visual or somatosensory) properties of signs that native and L2 signers ignored. These results suggest that early exposure to language helps a learner discern which aspects of a linguistic signal are most likely to matter for language learning, even if that language belongs to a different modality.
An Outbreak of Scabies in Multiple Linked Healthcare Settings in the Netherlands
Authors: Ladbury Georgia , Morroy Gabriella , Hoeven-Dekkers Sandra van , Botermans Corine , Veelenturf Cees , Bastiaens Maarten , Abeelen Cees van , Wijkmans Clementine
Published: September 2012

We report a large scabies outbreak occurring in Tilburg, Netherlands, which affected several different healthcare settings that provide care to the elderly and the mentally disabled. The outbreak demonstrated how the complex system of care provision to vulnerable groups facilitated extensive scabies transmission among multiple linked healthcare settings and the community.

Infect Control Hosp Epidemiol 2012;33(10): 1047-1050
Outbreak of Carbapenem-Resistant Enterobacteriaceae at a Long-Term Acute Care Hospital: Sustained Reductions in Transmission through Active Surveillance and Targeted Interventions
Authors: Chitnis Amit S. , Caruthers Pam S. , Rao Agam K. , Lamb JoAnne , Lurvey Robert , De Rochars Valery Beau , Kitchel Brandon , Cancio Margarita , Török Thomas J. , Guh Alice Y. , Gould Carolyn V. , Wise Matthew E.
Published: September 2012

Objective.

To describe a Klebsiella pneumoniae carbapenemase (KPC)–producing carbapenem-resistant Enterobacteriaceae (CRE) outbreak and interventions to prevent transmission.

Design, Setting, and Patients.

Epidemiologic investigation of a CRE outbreak among patients at a long-term acute care hospital (LTACH).

Methods.

Microbiology records at LTACH A from March 2009 through February 2011 were reviewed to identify CRE transmission cases and cases admitted with CRE. CRE bacteremia episodes were identified during March 2009–July 2011. Biweekly CRE prevalence surveys were conducted during July 2010–July 2011, and interventions to prevent transmission were implemented, including education and auditin? of staff and isolation and cohorting of CRE patients with dedicated nursing staff and shared medical equipment. Trends were evaluated using weighted linear or Poisson regression. CRE transmission cases were included in a case-control study to evaluate risk factors for acquisition. A real-time polymerase chain reaction assay was used to detect the blaKPC gene, and pulsed-field gel electrophoresis was performed to assess the genetic relatedness of isolates.

Results.

Ninety-nine CRE transmission cases, 16 admission cases (from 7 acute care hospitals), and 29 CRE bacteremia episodes were identified. Significant reductions were observed in CRE prevalence (49% vs 8%), percentage of patients screened with newly detected CRE (44% vs 0%), and CRE bacteremia episodes (2.5 vs 0.0 per 1,000 patient-days). Cases were more likely to have received β-lactams, have diabetes, and require mechanical ventilation. All tested isolates were KPC-producing K. pneumoniae, and nearly all isolates were genetically related.

Conclusion.

CRE transmission can be reduced in LTACHs through surveillance testing and targeted interventions. Sustainable reductions within and across healthcare facilities may require a regional public health approach.

Infect Control Hosp Epidemiol 2012;33(10):984-992
Surveillance Definitions of Infections in Long-Term Care Facilities: Revisiting the McGeer Criteria
Authors: Stone Nimalie D. , Ashraf Muhammad S. , Calder Jennifer , Crnich Christopher J. , Crossley Kent , Drinka Paul J. , Gould Carolyn V. , Juthani-Mehta Manisha , Lautenbach Ebbing , Loeb Mark , MacCannell Taranisia , Malani Preeti N. , Mody Lona , Mylotte Joseph M. , Nicolle Lindsay E. , Roghmann Mary-Claire , Schweon Steven J. , Simor Andrew E. , Smith Philip W. , Stevenson Kurt B. , Bradley Suzanne F. ,   Society for Healthcare Epidemiology Long-Term Care Special Interest Group
Published: September 2012

Infection surveillance definitions for long-term care facilities (ie, the McGeer Criteria) have not been updated since 1991. An expert consensus panel modified these definitions on the basis of a structured review of the literature. Significant changes were made to the criteria defining urinary tract and respiratory tract infections. New definitions were added for norovirus gastroenteritis and Clostridum difficile infections.

Infect Control Hosp Epidemiol 2012;33(10):965-977
A conformal integral invariant on Riemannian foliations
Authors: Wang Guofang , Zhang Yongbing
Published: September 2012

Let

M
M

be a closed manifold which admits a foliation structure

F

\mathcal {F}

of codimension

q
≥
2

q\geq 2

and a bundle-like metric

g
0

g_0

. Let

[

g
0

]
B

[g_0]_B

be the space of bundle-like metrics which differ from

g
0

g_0

only along the horizontal directions by a multiple of a positive basic function. Assume

Y
Y

is a transverse conformal vector field and the mean curvature of the leaves of

(
M
,

F

,

g
0

)

(M,\mathcal {F},g_0)

vanishes. We show that the integral

∫
M

Y
(

R

g
T

T

)
d

μ
g

\int _MY(R^T_{g^T})d\mu _g

is independent of the choice of

g
∈
[

g
0

]
B

g\in [g_0]_B

, where

g
T

g^T

is the transverse metric induced by

g
g

and

R
T

R^T

is the transverse scalar curvature. Moreover if

q
≥
3

q\geq 3

, we have

∫
M

Y
(

R

g
T

T

)
d

μ
g

=
0

\int _MY(R^T_{g^T})d\mu _g=0

for any

g
∈
[

g
0

]
B

g\in [g_0]_B

. However there exist codimension

2
2

minimal Riemannian foliations

(
M
,

F

,
g
)

(M,\mathcal {F},g)

and transverse conformal vector fields

Y
Y

such that

∫
M

Y
(

R

g
T

T

)
d

μ
g

≠
0

\int _MY(R^T_{g^T})d\mu _g\neq 0

. Therefore,

∫
M

Y
(

R

g
T

T

)
d

μ
g

\int _MY(R^T_{g^T})d\mu _g

is a nontrivial obstruction for the transverse Yamabe problem on minimal Riemannian foliation of codimension

2
2

.
From conjugacy classes in the Weyl group to unipotent classes, III
Authors: Lusztig G.
Published: September 2012

LetGGbe an affine algebraic group over an algebraically closed field whose identity componentG0G^{0}is reductive. LetWWbe the Weyl group ofGGand letDDbe a connected component ofGGwhose image inG/G0G/G^{0}is unipotent. In this paper we define a map from the set of “twisted conjugacy classes” inWWto the set of unipotentG0G^{0}-conjugacy classes inDDgeneralizing an earlier construction which applied whenGGis connected.
Identifying functional modules in interaction networks through overlapping Markov clustering
Authors: Shih Yu-Keng , Parthasarathy Srinivasan
Published: September 2012

Motivation: In recent years, Markov clustering (MCL) has emerged as an effective algorithm for clustering biological networks—for instance clustering protein–protein interaction (PPI) networks to identify functional modules. However, a limitation of MCL and its variants (e.g. regularized MCL) is that it only supports hard clustering often leading to an impedance mismatch given that there is often a significant overlap of proteins across functional modules.

Results: In this article, we seek to redress this limitation. We propose a soft variation of Regularized MCL (R-MCL) based on the idea of iteratively (re-)executing R-MCL while ensuring that multiple executions do not always converge to the same clustering result thus allowing for highly overlapped clusters. The resulting algorithm, denoted soft regularized Markov clustering, is shown to outperform a range of extant state-of-the-art approaches in terms of accuracy of identifying functional modules on three real PPI networks.

Availability: All data and codes are freely available upon request.

Contact:  srini@cse.ohio-state.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Techniques to cope with missing data in host–pathogen protein interaction prediction
Authors: Kshirsagar Meghana , Carbonell Jaime , Klein-Seetharaman Judith
Published: September 2012

Motivation: Approaches that use supervised machine learning techniques for protein–protein interaction (PPI) prediction typically use features obtained by integrating several sources of data. Often certain attributes of the data are not available, resulting in missing values. In particular, our host–pathogen PPI datasets have a large fraction, in the range of 58–85% of missing values, which makes it challenging to apply machine learning algorithms.

Results: We show that specialized techniques for missing value imputation can improve the performance of the models significantly. We use cross species information in combination with machine learning techniques like Group lasso with ℓ1/ℓ2 regularization. We demonstrate the benefits of our approach on two PPI prediction problems. In our first example of Salmonella–human PPI prediction, we are able to obtain high prediction accuracies with 77.6% precision and 84% recall. Comparison with various other techniques shows an improvement of 9 in F1 score over the next best technique. We also apply our method to Yersinia–human PPI prediction successfully, demonstrating the generality of our approach.

Availability: Predicted interactions, datasets, features are available at: http://www.cs.cmu.edu/~mkshirsa/eccb2012_paper46.html.

Contact:  judithks@cs.cmu.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees
Authors: Mahmud Md Pavel , Wiedenhoeft John , Schliep Alexander
Published: September 2012

Motivation: Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics.

Results: For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L1 distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L1 distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants.

Availability and implementation: TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net.

Contact:  pavelm@cs.rutgers.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks
Authors: Larhlimi Abdelhalim , Basler Georg , Grimbs Sergio , Selbig Joachim , Nikoloski Zoran
Published: September 2012

Motivation: Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions. The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases.

Results: We consider the alternative of designing synthetic strategies which can be used not only to characterize the maximum theoretically possible product yield but also to engineer networks with optimal conversion capability by using a suitable biochemically feasible reaction called ‘stoichiometric capacitance’. In addition, we provide a theoretical solution for decomposing a given stoichiometric capacitance over a set of known enzymatic reactions. We determine the stoichiometric capacitance for genome-scale metabolic networks of 10 organisms from different kingdoms of life and examine its implications for the alterations in flux variability patterns. Our empirical findings suggest that the theoretical capacity of metabolic networks comes at a cost of dramatic system's changes.

Contact:  larhlimi@mpimp-golm.mpg.de, or nikoloski@mpimp-golm.mpg.de

Supplementary Information:  Supplementary tables are available at Bioinformatics online.
Hybrid spatial Gillespie and particle tracking simulation
Authors: Klann Michael , Ganguly Arnab , Koeppl Heinz
Published: September 2012

Motivation: Cellular signal transduction involves spatial–temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.

Results: The proposed simulation allows an interactive or automated switching for regions or species of interest in the cell. Especially we see an application if for instance receptor clustering at the membrane is modeled in detail and the transport through the cytoplasm is included as well. The results show the increase in performance of the overall simulation, and the limits of the approach if crowding is included. Future work will include the development of a GUI to improve control of the simulation.

Availability of Implementation:  www.bison.ethz.ch/research/spatial_simulations.

Contact:  mklann@ee.ethz.ch or koeppl@ethz.ch

Supplementary/Information:  Supplementary data are available at Bioinformatics online.
Decoding properties of tRNA leave a detectable signal in codon usage bias
Authors: Roth Alexander C.
Published: September 2012

Motivation: The standard genetic code translates 61 codons into 20 amino acids using fewer than 61 transfer RNAs (tRNAs). This is possible because of the tRNA's ability to ‘wobble’ at the third base to decode more than one codon. Although the anticodon–codon mapping of tRNA to mRNA is a prerequisite for certain codon usage indices and can contribute to the understanding of the evolution of alternative genetic codes, it is usually not determined experimentally because such assays are prohibitively expensive and elaborate. Instead, the codon reading is approximated from theoretical inferences of nucleotide binding, the wobble rules. Unfortunately, these rules fail to capture all of the nuances of codon reading. This study addresses the codon reading properties of tRNAs and their evolutionary impact on codon usage bias.

Results: Using three different computational methods, the signal of tRNA decoding in codon usage bias is identified. The predictions by the methods generally agree with each other and compare well with experimental evidence of codon reading. This analysis suggests a revised codon reading for cytosolic tRNA in the yeast genome (Saccharomyces cerevisiae) that is more accurate than the common assignment by wobble rules. The results confirm the earlier observation that the wobble rules are not sufficient for a complete description of codon reading, because they depend on genome-specific factors. The computational methods presented here are applicable to any fully sequenced genome.

Availability: By request from the author.

Contact:  alexander.roth@isb-sib.ch
Event extraction across multiple levels of biological organization
Authors: Pyysalo Sampo , Ohta Tomoko , Miwa Makoto , Cho Han-Cheol , Tsujii Jun'ichi , Ananiadou Sophia
Published: September 2012

Motivation: Event extraction using expressive structured representations has been a significant focus of recent efforts in biomedical information extraction. However, event extraction resources and methods have so far focused almost exclusively on molecular-level entities and processes, limiting their applicability.

Results: We extend the event extraction approach to biomedical information extraction to encompass all levels of biological organization from the molecular to the whole organism. We present the ontological foundations, target types and guidelines for entity and event annotation and introduce the new multi-level event extraction (MLEE) corpus, manually annotated using a structured representation for event extraction. We further adapt and evaluate named entity and event extraction methods for the new task, demonstrating that both can be achieved with performance broadly comparable with that for established molecular entity and event extraction tasks.

Availability: The resources and methods introduced in this study are available from http://nactem.ac.uk/MLEE/.

Contact:  pyysalos@cs.man.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs
Authors: Wang Hua , Nie Feiping , Huang Heng , Yan Jingwen , Kim Sungeun , Nho Kwangsik , Risacher Shannon L. , Saykin Andrew J. , Shen Li ,   for the Alzheimer's Disease Neuroimaging Initiative
Published: September 2012

Motivation: Imaging genetic studies typically focus on identifying single-nucleotide polymorphism (SNP) markers associated with imaging phenotypes. Few studies perform regression of SNP values on phenotypic measures for examining how the SNP values change when phenotypic measures are varied. This alternative approach may have a potential to help us discover important imaging genetic associations from a different perspective. In addition, the imaging markers are often measured over time, and this longitudinal profile may provide increased power for differentiating genotype groups. How to identify the longitudinal phenotypic markers associated to disease sensitive SNPs is an important and challenging research topic.

Results: Taking into account the temporal structure of the longitudinal imaging data and the interrelatedness among the SNPs, we propose a novel ‘task-correlated longitudinal sparse regression’ model to study the association between the phenotypic imaging markers and the genotypes encoded by SNPs. In our new association model, we extend the widely used ℓ2,1-norm for matrices to tensors to jointly select imaging markers that have common effects across all the regression tasks and time points, and meanwhile impose the trace-norm regularization onto the unfolded coefficient tensor to achieve low rank such that the interrelationship among SNPs can be addressed. The effectiveness of our method is demonstrated by both clearly improved prediction performance in empirical evaluations and a compact set of selected imaging predictors relevant to disease sensitive SNPs.

Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/Longitudinal/

Contact:  heng@uta.edu or shenli@inpui.edu
Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers
Authors: Tabei Yasuo , Pauwels Edouard , Stoven Véronique , Takemoto Kazuhiro , Yamanishi Yoshihiro
Published: September 2012

Motivation: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug–target interactions is crucial in the drug design process.

Results: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug–target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L1 regularized classifiers over the tensor product space of possible drug–target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug–target interactions and the extracted features are biologically meaningful. The extracted substructure–domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families.

Availability: Softwares are available at the supplemental website.

Contact:  yamanishi@bioreg.kyushu-u.ac.jp

Supplementary Information: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/ .
Multiple instance learning of Calmodulin binding sites
Authors: Minhas Fayyaz ul Amir Afsar , Ben-Hur Asa
Published: September 2012

Motivation: Calmodulin (CaM) is a ubiquitously conserved protein that acts as a calcium sensor, and interacts with a large number of proteins. Detection of CaM binding proteins and their interaction sites experimentally requires a significant effort, so accurate methods for their prediction are important.

Results: We present a novel algorithm (MI-1 SVM) for binding site prediction and evaluate its performance on a set of CaM-binding proteins extracted from the Calmodulin Target Database. Our approach directly models the problem of binding site prediction as a large-margin classification problem, and is able to take into account uncertainty in binding site location. We show that the proposed algorithm performs better than the standard SVM formulation, and illustrate its ability to recover known CaM binding motifs. A highly accurate cascaded classification approach using the proposed binding site prediction method to predict CaM binding proteins in Arabidopsis thaliana is also presented.

Availability: Matlab code for training MI-1 SVM and the cascaded classification approach is available on request.

Contact:  fayyazafsar@gmail.com or asa@cs.colostate.edu