bluuebunny/crossref_metadata_2025 huggingface dataset:
Room temperature spin filtering effect in GaNAs: Role of hydrogen
Authors: Puttisong Y. , Dagnelund D. , Buyanova I. A. , Tu C. W. , Polimeni A. , Capizzi M. , Chen W. M.
Published: October 2011

Effects of hydrogen on the recently discovered defect-engineered spin filtering in GaNAs are investigated by optical spin orientation and optically detected magnetic resonance. Post-growth hydrogen treatments are shown to lead to nearly complete quenching of the room-temperature spin-filtering effect in both GaNAs epilayers and GaNAs/GaAs multiple quantum wells, accompanied by a reduction in concentrations of Gai interstitial defects. Our finding provides strong evidence for efficient hydrogen passivation of these spin-filtering defects, likely via formation of complexes between Gai defects and hydrogen, as being responsible for the observed strong suppression of the spin-filtering effect after the hydrogen treatments.
Temperature dependent transport studies in InN quantum dots grown by droplet epitaxy on silicon nitride/Si substrate
Authors: Kumar Mahesh , Roul Basanta , Shetty Arjun , Rajpalke Mohana K. , Bhat Thirumaleshwara N. , Kalghatgi A. T. , Krupanidhi S. B.
Published: October 2011

InN quantum dots (QDs) were fabricated on silicon nitride/Si (111) substrate by droplet epitaxy. Single-crystalline structure of InN QDs was verified by transmission electron microscopy, and the chemical bonding configurations of InN QDs were examined by x-ray photoelectron spectroscopy. Photoluminescence measurement shows a slight blue shift compared to the bulk InN, arising from size dependent quantum confinement effect. The interdigitated electrode pattern was created and current–voltage (I–V) characteristics of InN QDs were studied in a metal–semiconductor–metal configuration in the temperature range of 80–300 K. The I–V characteristics of lateral grown InN QDs were explained by using the trap model.
Switch-on dynamics of nanocavity laser devices
Authors: Lorke M. , Nielsen T. R. , Mørk J.
Published: October 2011

Theoretical investigations of the switch-on behavior of semiconductor quantum dot based nanocavity laser devices are presented. From a microscopic treatment of the carrier-carrier and carrier-photon interaction, we find a fast switch-on of the laser device that is enabled by ultrafast carrier dynamics and heavily damped relaxation oscillations. We show that the timescales of the dynamics within the continuum states and the quantum dot states are strongly coupled and investigate the time dependence of the non-equilibrium scattering rates in detail.
Epitaxial oxide growth on polar (111) surfaces
Authors: Blok J. L. , Wan X. , Koster G. , Blank D. H. A. , Rijnders G.
Published: October 2011

Obtaining atomically smooth surfaces and interfaces of perovskite oxide materials on polar (111) surfaces presents a particular challenge as these surfaces and interfaces will reconstruct. Here, the effect of the use of screening buffer layers on the epitaxial growth on such polar surfaces is investigated. Both transmission electron microscopy and in situ reflective high energy electron diffraction data imply that the buffer layers, SrRuO3 or LaAlO3, restore a near bulk-like termination at growth temperature, allowing for coherent growth of BiFeO3 and CaTiO3 for all deposited unit cell layers of the film material.
Temperature dependence of the gain peak in p-doped InAs quantum dot lasers
Authors: Hutchings M. , O’Driscoll I. , Smowton P. M. , Blood P.
Published: October 2011

Gain peak shifts with injection in undoped and p-doped InAs quantum dot laser structures between 200 K and 350 K are measured. The blue-shift with increasing injection, due to state-filling of the inhomogeneous distribution, is temperature independent for a fixed peak gain in the undoped sample, but temperature dependent in the doped sample. This is due to the wide electron state distribution and lowering of the electron quasi Fermi level by p-doping relative to the undoped device. While p-doping reduces the temperature dependence of the threshold current, it comes at the expense of increasing the temperature sensitivity of the wavelength.
Gate control and amplification of magnetoresistance in a three-terminal device
Authors: Kum Hyun , Jahangir Shafat , Basu Debashish , Saha Dipankar , Bhattacharya Pallab
Published: October 2011

Gate control and amplification of magnetoresistance are demonstrated at room temperature in a fully epitaxial three-terminal GaAs-based device. In addition to the two ferromagnetic spin injector and detector electrodes of a MnAs/AlAs/GaAs:Mn/AlAs/MnAs vertical spin valve, a third non-magnetic gate electrode (Ti/Au) is placed directly on top of the heavily p-doped GaAs channel layer. The magnetoresistance of the device can be amplified to reach values as high as 500% at room temperature with the application of a bias to the gate terminal, which modulates the spin selectivity of the tunnel barriers. The experimental results are modeled by solving spin drift-diffusion and tunneling equations self consistently.
Conformal coating of particles in microchannels by magnetic forcing
Authors: Tsai Scott S. H. , Wexler Jason S. , Wan Jiandi , Stone Howard A.
Published: October 2011

We present a co-flow microfluidic method to coat paramagnetic beads with a thin layer of fluid as the beads are pulled across a liquid-liquid interface by an external magnetic field. We show that the coating thickness can be controlled by the magnitude of the flow speed. Also, the number of beads aggregated within a single coating can be adjusted by varying the strength of the magnetic field or the liquid-liquid interfacial tension.
Upper limit of two-dimensional electron density in enhancement-mode Si/SiGe heterostructure field-effect transistors
Authors: Lu T. M. , Lee C.-H. , Huang S.-H. , Tsui D. C. , Liu C. W.
Published: October 2011

In this paper, we present our study of the maximum electron density, nmax, accessible via low-temperature transport experiments in enhancement-mode Si/Si1−xGex heterostructure field-effect transistors. Experimentally, we find that nmax is much higher than the value obtained from self-consistent Schrödinger-Poisson simulations and that nmax can be changed only by changing the Ge concentration in the Si1−xGex barrier layer, not by varying the barrier layer thickness. The discrepancy between experiments and simulations is explained by a non-thermal-equilibrium tunneling-limited model.
Communication: Partial polarization transfer for single-scan spectroscopy and imaging
Authors: Norton Valerie A. , Weitekamp Daniel P.
Published: October 2011

A method is presented to partially transfer nuclear spin polarization from one isotope S to another isotope I by the way of heteronuclear spin couplings, while minimizing the loss of spin order to other degrees of freedom. The desired I spin polarization to be detected is a design parameter, while the sequence of pulses at the two Larmor frequencies is optimized to store the greatest unused S spin longitudinal polarization for subsequent use. The unitary evolution for the case of INS spin systems illustrates the potentially ideal efficiency of this strategy, which is of particular interest when the spin-lattice relaxation time of S greatly exceeds that of I. Explicit timing and pulses are tabulated for the cases for which M ⩽ 10 partial transfers each result in equal final polarization of 1/M or more compared to the final I polarization expected in a single transfer for N = 1, 2, or 3 I spins. Advantages for the ratiometric study of reacting molecules and hyperpolarized initial conditions are outlined.
Electro-absorption modulation in horizontal metal-insulator-silicon-insulator-metal nanoplasmonic slot waveguides
Authors: Zhu Shiyang , Lo G. Q. , Kwong D. L.
Published: October 2011

An ultracompact, broadband, and fully complementary metal-oxide-semiconductor (CMOS) compatible Si nanoplasmonic electro-absorption modulator is proposed based on the recently developed horizontal metal-insulator-silicon-insulator-metal nanoplasmonic slot waveguide. The modulation relies on a highly accumulated electron layer at the insulator/Si interface induced by an applied voltage. Proof-of-concept devices are fabricated using standard Si CMOS technology. A 3-dB modulation around 1550 nm is measured under ∼6.5 V bias for a device with total length of only 4 μm. The design suggests that larger modulation could be achieved by using high-κ dielectrics as the insulator, thinning down the insulator thickness, and narrowing the Si core of the nanoplasmonic waveguide.
Effect of stimulated emission on the transport characteristics of terahertz quantum-cascade lasers
Authors: Sharma R. , Schrottke L. , Wienold M. , Biermann K. , Hey R. , Grahn H. T.
Published: October 2011

We investigate the effect of stimulated emission on the transport characteristics of terahertz quantum-cascade lasers operating in a frequency range between 4.3 and 4.6 THz. The impact of stimulated emission is varied by changing the mirror losses via damaging one or two facets. In the case of voltage-driven measurements, a reduction in the current density near the onset of stimulated emission is observed for the facet-damaged lasers as compared to the original one. The measurements are in qualitative agreement with results of numerical simulations including the effect of stimulated emission.
Communication: State-to-state quantum dynamics study of the OH + CO → H + CO2 reaction in full dimensions (J = 0)
Authors: Liu Shu , Xu Xin , Zhang Dong H.
Published: October 2011

A full dimensional state-to-state quantum dynamics study is carried out for the prototypical complex-formation OH + CO → H + CO2 reaction in the ground rovibrational initial state on the Lakin-Troya-Schatz-Harding potential energy surface by using the reactant-product decoupling method. With three heavy atoms and deep wells on the reaction path, the reaction represents a huge challenge for accurate quantum dynamics study. This state-to-state calculation is the first such a study on a four-atom reaction other than the H2 + OH ↔ H2O + H and its isotope analogies. The product CO2 vibrational and rotational state distributions, and product energy partitioning information are presented for ground initial rovibrational state with the total angular momentum J = 0.
Communication: Lateral phase separation of mixed polymer brushes physisorbed on planar substrates
Authors: Van Lehn Reid C. , Alexander-Katz Alfredo
Published: October 2011

Here, we present a new method to model lateral phase separation in mixed polymer brushes physisorbed to a planar surface with mobile grafting points. The model is based on a local mean field theory that combines a Flory-Huggins approximation for interaction enthalpies with an Alexander-de Gennes brush entropy contribution. Using Monte Carlo sampling, the application of these two interactions to a lattice model yields a range of phase behavior consistent with previous theoretical and experimental work. This model will be useful for predicting mixed polymer brush morphologies on planar surfaces and in principle can be extended to other geometries (e.g., spheres) and polymer systems.
Subtype and pathway specific responses to anticancer compounds in breast cancer
Authors: Heiser Laura M. , Sadanandam Anguraj , Kuo Wen-Lin , Benz Stephen C. , Goldstein Theodore C. , Ng Sam , Gibb William J. , Wang Nicholas J. , Ziyad Safiyyah , Tong Frances , Bayani Nora , Hu Zhi , Billig Jessica I. , Dueregger Andrea , Lewis Sophia , Jakkula Lakshmi , Korkola James E. , Durinck Steffen , Pepin François , Guan Yinghui , Purdom Elizabeth , Neuvial Pierre , Bengtsson Henrik , Wood Kenneth W. , Smith Peter G. , Vassilev Lyubomir T. , Hennessy Bryan T. , Greshock Joel , Bachman Kurtis E. , Hardwicke Mary Ann , Park John W. , Marton Laurence J. , Wolf Denise M. , Collisson Eric A. , Neve Richard M. , Mills Gordon B. , Speed Terence P. , Feiler Heidi S. , Wooster Richard F. , Haussler David , Stuart Joshua M. , Gray Joe W. , Spellman Paul T.
Published: October 2011

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.
Frustration in protein–DNA binding influences conformational switching and target search kinetics
Authors: Marcovitz Amir , Levy Yaakov
Published: October 2011

Rapid recognition of DNA target sites involves facilitated diffusion through which alternative sites are searched on genomic DNA. A key mechanism facilitating the localization of the target by a DNA-binding protein (DBP) is one-dimensional diffusion (sliding) in which electrostatic forces attract the protein to the DNA. As the protein reaches its target DNA site, it switches from purely electrostatic binding to a specific set of interactions with the DNA bases that also involves hydrogen bonding and van der Waals forces. High overlap between the DBP patches used for nonspecific and specific interactions with DNA may enable an immediate transition between the two binding modes following target site localization. By contrast, an imperfect overlap may result in greater frustration between the two potentially competing binding modes and consequently slower switching between them. A structural analysis of 125 DBPs indicates frustration between the two binding modes that results in a large difference between the orientations of the protein to the DNA when it slides compared to when it specifically interacts with DNA. Coarse-grained molecular dynamics simulations of in silico designed peptides comprising the full range of frustrations between the two interfaces show slower transition from nonspecific to specific DNA binding as the overlap between the patches involved in the two binding modes decreases. The complex search kinetics may regulate the search by eliminating trapping of the protein in semispecific sites while sliding.
PCNA binding domains in all three subunits of yeast DNA polymerase δ modulate its function in DNA replication
Authors: Acharya Narottam , Klassen Roland , Johnson Robert E. , Prakash Louise , Prakash Satya
Published: October 2011

DNA polymerase δ (Polδ) plays an essential role in replication from yeast to humans. Polδ in
Saccharomyces cerevisiae
is comprised of three subunits, the catalytic subunit Pol3 and the accessory subunits Pol31 and Pol32. Yeast Polδ exhibits a very high processivity in synthesizing DNA with the proliferating cell nuclear antigen (PCNA) sliding clamp; however, it has remained unclear how Polδ binds PCNA to achieve its high processivity. Here we show that PCNA interacting protein (PIP) motifs in all three subunits contribute to PCNA-stimulated DNA synthesis by Polδ, and mutational inactivation of all three PIP motifs abrogates its ability to synthesize DNA with PCNA. Genetic analyses of mutations in these PIPs have revealed that in the absence of functional Pol32 PIP domain, PCNA binding by both the Pol3 and Pol31 subunits becomes essential for cell viability. Based on our biochemical and genetic studies we infer that yeast Polδ can simultaneously utilize all three PIP motifs during PCNA-dependent DNA synthesis, and suggest that Polδ binds the PCNA homotrimer via its three subunits. We consider the implications of these observations for Polδ’s role in DNA replication.
Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants
Authors: Park Ju-Hyun , Gail Mitchell H. , Weinberg Clarice R. , Carroll Raymond J. , Chung Charles C. , Wang Zhaoming , Chanock Stephen J. , Fraumeni Joseph F. , Chatterjee Nilanjan
Published: October 2011

Recent discoveries of hundreds of common susceptibility SNPs from genome-wide association studies provide a unique opportunity to examine population genetic models for complex traits. In this report, we investigate distributions of various population genetic parameters and their interrelationships using estimates of allele frequencies and effect-size parameters for about 400 susceptibility SNPs across a spectrum of qualitative and quantitative traits. We calibrate our analysis by statistical power for detection of SNPs to account for overrepresentation of variants with larger effect sizes in currently known SNPs that are expected due to statistical power for discovery. Across all qualitative disease traits, minor alleles conferred “risk” more often than “protection.” Across all traits, an inverse relationship existed between “regression effects” and allele frequencies. Both of these trends were remarkably strong for type I diabetes, a trait that is most likely to be influenced by selection, but were modest for other traits such as human height or late-onset diseases such as type II diabetes and cancers. Across all traits, the estimated effect-size distribution suggested the existence of increasingly large numbers of susceptibility SNPs with decreasingly small effects. For most traits, the set of SNPs with intermediate minor allele frequencies (5–20%) contained an unusually small number of susceptibility loci and explained a relatively small fraction of heritability compared with what would be expected from the distribution of SNPs in the general population. These trends could have several implications for future studies of common and uncommon variants.
Fast scaffolding with small independent mixed integer programs
Authors: Salmela Leena , Mäkinen Veli , Välimäki Niko , Ylinen Johannes , Ukkonen Esko
Published: October 2011

Motivation: Assembling genomes from short read data has become increasingly popular, but the problem remains computationally challenging especially for larger genomes. We study the scaffolding phase of sequence assembly where preassembled contigs are ordered based on mate pair data.

Results: We present MIP Scaffolder that divides the scaffolding problem into smaller subproblems and solves these with mixed integer programming. The scaffolding problem can be represented as a graph and the biconnected components of this graph can be solved independently. We present a technique for restricting the size of these subproblems so that they can be solved accurately with mixed integer programming. We compare MIP Scaffolder to two state of the art methods, SOPRA and SSPACE. MIP Scaffolder is fast and produces better or as good scaffolds as its competitors on large genomes.

Availability: The source code of MIP Scaffolder is freely available at http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/.

Contact:  leena.salmela@cs.helsinki.fi
An assessment of substitution scores for protein profile–profile comparison
Authors: Ye Xugang , Wang Guoli , Altschul Stephen F.
Published: October 2011

Motivation: Pairwise protein sequence alignments are generally evaluated using scores defined as the sum of substitution scores for aligning amino acids to one another, and gap scores for aligning runs of amino acids in one sequence to null characters inserted into the other. Protein profiles may be abstracted from multiple alignments of protein sequences, and substitution and gap scores have been generalized to the alignment of such profiles either to single sequences or to other profiles. Although there is widespread agreement on the general form substitution scores should take for profile-sequence alignment, little consensus has been reached on how best to construct profile–profile substitution scores, and a large number of these scoring systems have been proposed. Here, we assess a variety of such substitution scores. For this evaluation, given a gold standard set of multiple alignments, we calculate the probability that a profile column yields a higher substitution score when aligned to a related than to an unrelated column. We also generalize this measure to sets of two or three adjacent columns. This simple approach has the advantages that it does not depend primarily upon the gold-standard alignment columns with the weakest empirical support, and that it does not need to fit gap and offset costs for use with each substitution score studied.

Results: A simple symmetrization of mean profile-sequence scores usually performed the best. These were followed closely by several specific scoring systems constructed using a variety of rationales.

Contact:  altschul@ncbi.nlm.nih.gov

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Authors: Névéol Aurélie , Wilbur W. John , Lu Zhiyong
Published: October 2011

Motivation: Research in the biomedical domain can have a major impact through open sharing of the data produced. For this reason, it is important to be able to identify instances of data production and deposition for potential re-use. Herein, we report on the automatic identification of data deposition statements in research articles.

Results: We apply machine learning algorithms to sentences extracted from full-text articles in PubMed Central in order to automatically determine whether a given article contains a data deposition statement, and retrieve the specific statements. With an Support Vector Machine classifier using conditional random field determined deposition features, articles containing deposition statements are correctly identified with 81% F-measure. An error analysis shows that almost half of the articles classified as containing a deposition statement by our method but not by the gold standard do indeed contain a deposition statement. In addition, our system was used to process articles in PubMed Central, predicting that a total of 52 932 articles report data deposition, many of which are not currently included in the Secondary Source Identifier [si] field for MEDLINE citations.

Availability: All annotated datasets described in this study are freely available from the NLM/NCBI website at http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Neveol/DepositionDataSets.zip

Contact:  aurelie.neveol@nih.gov; john.wilbur@nih.gov; zhiyong.lu@nih.gov

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
Authors: Wainreb Gilad , Wolf Lior , Ashkenazy Haim , Dehouck Yves , Ben-Tal Nir
Published: October 2011

Motivation: Accurate prediction of protein stability is important for understanding the molecular underpinnings of diseases and for the design of new proteins. We introduce a novel approach for the prediction of changes in protein stability that arise from a single-site amino acid substitution; the approach uses available data on mutations occurring in the same position and in other positions. Our algorithm, named Pro-Maya (Protein Mutant stAbilitY Analyzer), combines a collaborative filtering baseline model, Random Forests regression and a diverse set of features. Pro-Maya predicts the stability free energy difference of mutant versus wild type, denoted as ΔΔG.

Results: We evaluated our algorithm extensively using cross-validation on two previously utilized datasets of single amino acid mutations and a (third) validation set. The results indicate that using known ΔΔG values of mutations at the query position improves the accuracy of ΔΔG predictions for other mutations in that position. The accuracy of our predictions in such cases significantly surpasses that of similar methods, achieving, e.g. a Pearson's correlation coefficient of 0.79 and a root mean square error of 0.96 on the validation set. Because Pro-Maya uses a diverse set of features, including predictions using two other methods, it also performs slightly better than other methods in the absence of additional experimental data on the query positions.

Availability: Pro-Maya is freely available via web server at http://bental.tau.ac.il/ProMaya.

Contact:  nirb@tauex.tau.ac.il; wolf@cs.tau.ac.il

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Alcohol: Preventing Harmful Drinking
Authors: Gee Matthew David
Published: October 2011

Alcohol is more harmful than any other drug overall, when physical, psychological and social harm are taken into account. There were 8664 alcohol-related deaths in the UK in 2009. Every GP is estimated to see around 364 heavy drinkers every year and will see more who are drinking less heavily but whose alcohol consumption is still putting their health at risk. GPs are therefore in an ideal position to prevent the significant mortality and morbidity associated with high alcohol consumption. This can be done by early identification of those who are drinking more than is healthy and by providing brief interventions before drinking becomes harmful.
Use of Enteral Nutrition for the Control of Intestinal Inflammation in Pediatric Crohn Disease
Authors: Critch Jeff , Day Andrew S. , Otley Anthony , King‐Moore Cynthia , Teitelbaum Jonathan E. , Shashidhar Harohalli ,   NASPGHAN IBD Committee
Published: October 2011

Exclusive enteral nutrition is an effective yet often underused therapy for the induction of remission in pediatric Crohn disease. The North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition formed the Enteral Nutrition Working Group to review the use of enteral nutrition therapy in pediatric Crohn disease. The group was composed of 5 pediatric gastroenterologists and 1 pediatric nutritionist, all with an interest and/or expertise in exclusive enteral nutrition. Specific attention was placed upon review of the evidence for efficacy of therapy, assessment of the variations in care, identification of barriers to its widespread use, and compilation of the necessary components for a successful program. The present guideline is intended to aid physicians in developing an enteral nutrition therapy program and potentially promote its use.
No Advantage for Antibiotic Treatment Over Placebo in Blastocystis hominis–positive Children With Recurrent Abdominal Pain
Authors: Heyland Klaas , Friedt Michael , Buehr Patrick , Braegger Christian P.
Published: October 2011

Objective:

The aim of the study was to investigate whether recurrent abdominal pain (RAP) in Blastocystis hominis–positive children can be treated successfully with trimethoprim‐sulfamethoxazole (TMP/SMX).

Methods:

From October 2004 to December 2008, all of the patients referred to the Division of Gastroenterology and Nutrition of the University Children's Hospital Zurich because of RAP and detection of B hominis in stool samples as the only pathological finding after a standard workup were offered to participate in the study. Patients were randomly assigned into 2 groups. TMP/SMX or placebo was given for 7 days in a double‐blind, placebo‐controlled manner. Pain index (PI) was measured with a visual analogue scale. Two weeks after completion of treatment, 3 stool samples were collected and patients were followed clinically. If B hominis was still present, metronidazole was given for 7 days.

Results:

Forty patients were included; 37 finished the study (TMP/SMX n = 20, placebo n = 17). Mean PI declined from 7.1 to 3.6 for all of the patients, with a decrease from 6.9 to 4.1 in the TMP/SMX and 7.4 to 3.0 in the placebo group, irrespective of detection of B hominis after treatment. There was no statistically significant difference in PI reduction between the 2 groups. Metronidazole treatment led to a further PI decline from 3.7 to 1.9. Eradication rates were 35% (TMP/SMX) and 44% (metronidazole), compared with spontaneous clearance of 29% in the placebo group.

Conclusions:

There is no advantage for TPM/SMX over placebo in the treatment of RAP in B hominis–positive children.
Stool Pattern Changes in Toddlers Consuming a Follow‐on Formula Supplemented With Polydextrose and Galactooligosaccharides
Authors: Ribeiro Tereza C.M. , Costa‐Ribeiro Hugo , Almeida Patricia S. , Pontes Mariana V. , Leite Maria E.Q. , Filadelfo Lais R. , Khoury Jane C. , Bean Judy A. , Mitmesser Susan H. , Vanderhoof Jon A. , Scalabrin Deolinda M.F.
Published: October 2011

Healthy 9‐ to 48‐month‐old children (n = 133) were randomized to receive a cow's‐milk–based follow‐on formula (control) or the same formula with polydextrose and galactooligosaccharides (PDX/GOS) for 108 days. Pediatricians assessed diarrheal disease, stool pattern, acute respiratory infection, systemic antibiotic use, and growth. The 2 groups had similar weight‐for‐length/height z score and similar odds of having diarrheal disease, acute respiratory infection, and systemic antibiotic use; however, PDX/GOS had greater odds of increased defecation than control (P ≤ 0.01). Addition of PDX and GOS to a follow‐on formula was well tolerated and induced a pattern of more frequent and softer stools in toddlers.
Marinobacter xestospongiae sp. nov., isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea
Authors: Lee On On , Lai Pok Yui , Wu Hui-xian , Zhou Xiao-jian , Miao Li , Wang Hao , Qian Pei-Yuan
Published: October 2011

A Gram-negative, catalase- and oxidase-positive, non-sporulating, rod-shaped and slightly halophilic bacterial strain, designated UST090418-1611T, was isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea coast of Saudi Arabia. Phylogenetic trees based on the 16S rRNA gene sequence placed strain UST090418-1611T in the family

Alteromonadaceae

with the closest relationship to the genus

Marinobacter

. The 16S rRNA gene sequence similarity between the strain and the type strains of recognized

Marinobacter

species ranged from 92.9 to 98.3 %. Although strain UST090418-1611T shared high 16S rRNA gene sequence similarity with

Marinobacter mobilis

CN46T,

M. zhejiangensis

CN74T and

M. sediminum

R65T (98.3, 97.4 and 97.3 %, respectively), the relatedness of the strain to these three strains in DNA–DNA hybridization was only 58, 56 and 33 %, respectively, supporting the novelty of the strain. In contrast to most strains in the genus

Marinobacter

, strain UST090418-1611T tolerated only 6 % (w/v) NaCl, and optimal growth occurred at 2.0 % (w/v) NaCl, pH 7.0–8.0 and 28–36 °C. The predominant cellular fatty acids were C12 : 0 3-OH, C16 : 0, C12 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The genomic DNA G+C content was 57.1 mol%. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we suggest that the strain represents a novel species in the genus

Marinobacter

, for which the name Marinobacter xestospongiae sp. nov. is proposed, with UST090418-1611T ( = JCM 17469T  = NRRL B-59512T) as the type strain.
Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter , Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terricola , Pedobacter glucosidilyticus and Pedobacter lentus
Authors: Zhou Zhichao , Jiang Fan , Wang Shaohua , Peng Fang , Dai Jun , Li Wenxin , Fang Chengxiang
Published: October 2011

A Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12T, was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4–25 °C (optimum, 18 °C), 0–2 % (optimum, 0 %) and pH 6–9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genusPedobacterand showed highest sequence similarity (94.4 %) toPedobacter daechungensisKCTC 12637T. The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising C16 : 1ω7cand/or C16 : 1ω6c), iso-C15 : 0and iso-C17 : 03-OH as major fatty acids supported the allocation of strain A12Tto the genusPedobacteras a representative of a novel species, for which the namePedobacterarcticussp. nov. is proposed. The type strain is A12T( = CCTCC AB 2010223T = NRRL B-59457T). Emended descriptions of the genusPedobacterand ofPedobacter heparinus,Pedobacter daechungensis,Pedobacter terricola,Pedobacter glucosidilyticusandPedobacter lentusare also given.
Alishewanella tabrizica sp. nov., isolated from Qurugöl Lake
Authors: Tarhriz Vahideh , Nematzadeh Ghorbanali , Zununi Vahed Sepideh , Hejazi Mohammad Amin , Hejazi Mohammad Saeid
Published: October 2011

A novel Gram-negative, aerobic, motile and rod-shaped bacterium was isolated from Qurugöl Lake located in a mountainous region near Tabriz city in the north-west of Iran. Growth occurred at pH 6–10 (optimum, pH 7±0.5) and at 10–40 °C (optimum, 30 °C). Strain RCRI4T was able to grow in the absence and presence of NaCl to 3 % (w/v). The major fatty acids were C17 : 0, C16 : 1ω7c/C15 iso3-OH, C17 : 1ω8c and C16 : 0. The G+C content of genomic DNA was 45.3 mol%. Based on the 16S rRNA and gyrB gene sequences, phylogenetic analyses indicated that strain RCRI4T associated with the genus

Alishewanella

, and closely related type strains include

Alishewanella agri

BLO6T (97.8 %),

Alishewanella aestuarii

B11T (97.7 %),

Rheinheimera perlucida

BA131T (97.5 %),

Alishewanella fetalis

CCUG 30811T (97.3 %) and

Alishewanella jeotgali

MS1T (97.1 %). The level of DNA–DNA relatedness between strain RCRI4T and phylogenetically the closest related strains,

A. agri

BLO6T and

R. perlucida

BA131T, was 9 and 14 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic results, it is suggested that strain RCRI4T represents a novel species of the genus

Alishewanella

, for which the name Alishewanella tabrizica sp. nov. is proposed. The type strain is RCRI4T ( = LMG 26473T = JCM 17275T = KCTC 23723T).
Cohnella cellulosilytica sp. nov., isolated from buffalo faeces
Authors: Khianngam Saowapar , Tanasupawat Somboon , Akaracharanya Ancharida , Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: October 2011

A cellulose-degrading bacterium, strain FCN3-3T, was isolated from buffalo faeces collected in Nakhonnayok province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain FCN3-3T was a Gram-positive, aerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in cell-wall peptidoglycan. The major menaquinone was MK-7. Anteiso-C15 : 0 (52.5 %), iso-C16 : 0 (18.9 %) and C16 : 0 (9.1 %) were the predominant cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major phospholipids. The DNA G+C content was 58.0 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain FCN3-3T was affiliated to the genus

Cohnella

and was closely related to

Cohnella phaseoli

GSPC1T,

Cohnella luojiensis

HY-22RT and

Cohnella hongkongensis

HKU3T, with 97.2, 96.8 and 96.3 % sequence similarity, respectively. Strain FCN3-3T could be clearly distinguished from all known species of the genus

Cohnella

by its physiological and biochemical characteristics as well as its phylogenetic position and level of DNA–DNA relatedness. Therefore, the strain represents a novel species of the genus

Cohnella

, for which the name Cohnella cellulosilytica sp. nov. is proposed; the type strain is FCN3-3T ( = KCTC 13645T = TISTR 1996T = PCU 323T).
Aquimarina mytili sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of

Aquimarina macrocephali
Authors: Park Seong Chan , Choe Han Na , Baik Keun Sik , Seong Chi Nam
Published: October 2011

An orange, rod-shaped, gliding bacterium, designated strain PSC33T, was isolated from the gut microflora of a mussel collected from Gwangyang Bay, South Sea (Republic of Korea). Cells were Gram-reaction-negative, strictly aerobic, and catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C15 : 0 3-OH and iso-C17 : 1ω9c. The only isoprenoid quinone was menaquinone-6 (MK-6). The DNA G+C content of strain PSC33T was 37.9 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain PSC33T formed an evolutionary lineage within the radiation encompassing members of the genus

Aquimarina

with

Aquimarina macrocephali

JAMB N27T as its nearest neighbour (96.3 % sequence similarity). A number of phenotypic characteristics distinguished strain PSC33T from recognized members of the genus

Aquimarina

. On the basis of the data presented in this study, strain PSC33T is considered to represent a novel species of the genus

Aquimarina

, for which the name Aquimarina mytili sp. nov. is proposed. The type strain is PSC33T ( = KCTC 23302T = JCM 17454T). An emended description of

A. macrocephali

is also provided.
Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake
Authors: Fukuda Wakao , Yamada Kozo , Miyoshi Yuki , Okuno Hirokazu , Atomi Haruyuki , Imanaka Tadayuki
Published: October 2011

A Gram-stain-negative, non-spore-forming, non-motile, irregularly circular, aerobic/microaerobic appendaged bacterium (strain 120-1T) was isolated from Naga-ike, one of the freshwater lakes in the Skarvsnes ice-free area of Antarctica. Strain 120-1Tgrew between 5 and 35 °C, with optimum growth at 30 °C. The pH range for growth was between 6.0 and 9.0 (optimum of approximately pH 7.0). The range of NaCl concentration allowing growth of strain 120-1Twas between 0 and 5.0 %, with an optimum of 0.5–1.0 %. Strain 120-1Twas able to utilize organic compounds such as glucose, arabinose, gluconate, adipate and malate. Red colonies were formed on plate medium and the carotenoids were present in the cells. Ubiquinones Q-9 and Q-10 were the major respiratory quinones. The major cellular fatty acids were C16 : 0, C18 : 1ω9cand C18 : 1ω7c. The G+C content of the genomic DNA was 61.1 mol%. Comparative analyses of 16S rRNA gene sequences and physiological characteristics of strain 120-1Tindicate that strain 120-1Tis a phylogenetically novel bacterium, and that it represents a novel species in a new genus,Rhodoligotrophosgen. nov., in the orderRhizobiales, familyRhodobiaceae.The nameRhodoligotrophos appendicifergen. nov. sp. nov. is proposed as the type species of this new genus, with 120-1T( = JCM 16873T = ATCC BAA-2115T) as the type strain.
Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules
Authors: Zhang Yan Ming , Li Ying , Chen Wen Feng , Wang En Tao , Sui Xin Hua , Li Qin Qin , Zhang Yun Zeng , Zhou Yu Guang , Chen Wen Xin
Published: October 2011

In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of

Bradyrhizobium

. They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S–23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94 % similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus

Bradyrhizobium

, which was consistent with the results of DNA–DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of

Bradyrhizobium japonicum

,

Bradyrhizobium liaoningense

and ‘Bradyrhizobium daqingense’ originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related

Bradyrhizobium

species, demonstrating that the novel group is distinct phenotypically from other

Bradyrhizobium

species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303T ( = LMG 26136T  = CGMCC 1.10948T  = HAMBI 3180T) as the type strain. The DNA G+C content of strain CCBAU 23303T is 61.5 mol% (T
m).
Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost
Authors: Mykytczuk Nadia C. S. , Wilhelm Roland C. , Whyte Lyle G.
Published: October 2011

A novel aerobic, Gram-positive, motile, coccoid bacterial strain, designated Or1T, was isolated from permafrost active-layer soil collected from the Canadian high Arctic. Strain Or1T was capable of growth over a broad temperature range, including sub-zero growth (below −10 to 37 °C), and at high salinity (0–19 % NaCl), growing optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % NaCl. Its taxonomic and phylogenetic position was determined by using a polyphasic approach, which indicated that strain Or1T was a member of the genus

Planococcus

. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Or1T belonged to the genus

Planococcus

, differing by 0.4–3.6 % from the type strains of all recognized

Planococcus

species, and was related most closely to

Planococcus antarcticus

CMS 26orT (98.8 % similarity) and

Planococcus donghaensis

JH1T (99.6 %). However, DNA–DNA hybridization experiments showed that strain Or1T had low genomic relatedness to

Planococcus antarcticus

CMS 26orT (18 %) and

Planococcus donghaensis

JH1T (46 %). The major menaquinones of strain Or1T were MK-7 (55 %), MK-8 (36 %) and MK-6 (9 %) and the major fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol and anteiso-C17 : 0. The DNA G+C content of strain Or1T was 40.5 mol%. Differential phenotypic, phylogenetic and genomic data suggest that strain Or1T represents a novel species of the genus

Planococcus

, for which the name Planococcus halocryophilus sp. nov. is proposed. The type strain is Or1T ( = DSM 24743T = JCM 17719T).
Halopenitus persicus gen. nov., sp. nov., an archaeon from an inland salt lake
Authors: Amoozegar Mohammad Ali , Makhdoumi-Kakhki Ali , Shahzadeh Fazeli Seyed Abolhassan , Azarbaijani Reza , Ventosa Antonio
Published: October 2011

A novel pale pink-pigmented halophilic archaeon, strain DC30T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain DC30T were non-motile and pleomorphic, from rods to triangular or disc-shaped. Strain DC30T required at least 1.7 M NaCl and 0.05 M MgCl2 for growth (optimum, 3 M NaCl and 0.1 M MgCl2). The optimum pH and temperature for growth of strain DC30T were pH 7.5 and 40 °C, respectively, although it was capable of growth over pH and temperature ranges of 6.5–8.5 and 25–50 °C, respectively. Analysis of the 16S rRNA gene sequence showed that strain DC30T was a member of the family

Halobacteriaceae

. However, it had low 16S rRNA gene sequence similarities of 92.4 %, 89.4 % and 89.1 % to the most closely related haloarchaeal taxa, the type species of the genera

Halorubrum

,

Halogranum

and

Haloplanus

, respectively. The DNA G+C content was 66.0 mol%. Phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, were present. Three minor phospholipids and one unidentified glycolipid were also observed. The only quinone present was MK-8(II-H2). The physiological, biochemical and phylogenetic differences between strain DC30T and other previously described genera of extremely halophilic archaea suggest that strain DC30T represents a novel species in a new genus within the family

Halobacteriaceae

, for which the name Halopenitus persicus gen. nov., sp. nov. is proposed. The type strain of Halopenitus persicus is DC30T ( = IBRC 10041T = KCTC 4046T).
YUCCAGenes Are Expressed in Response to Leaf Adaxial-Abaxial Juxtaposition and Are Required for Leaf Margin Development
Authors: Wang Wei , Xu Ben , Wang Hua , Li Jiqin , Huang Hai , Xu Lin
Published: October 2011

During leaf development, the formation of leaf adaxial-abaxial polarity at the primordium stage is crucial for subsequent leaf expansion. However, little is known about the genetic control from polarity establishment to blade outgrowth. The leaf margin, comprising elongated margin cells and hydathodes, is thought to affect leaf expansion. Here, we show that mutants with defective leaf polarity or with loss of function in the multiple auxin-biosynthetic YUCCA (YUC) genes exhibited a similar abnormal leaf margin and less-expanded leaves. Leaf margins of these mutants contained fewer hydathodes and an increased number of cell patches in which the patterns of epidermal cells resembled those of hydathodes. The previously characterized leaf-abaxialized asymmetric leaves2 (as2) revoluta (rev) and leaf-adaxialized kanadi1 (kan1) kan2 double mutants both produce finger-shaped, hydathode-like protrusions on adaxial and abaxial leaf surfaces, respectively. YUCs are required for formation of the protrusions, as those produced by as2 rev and kan1 kan2 were absent in the yuc1 yuc2 yuc4 triple mutant background. Expressions of YUC1, YUC2, and YUC4 were spatially regulated in the leaf, being associated with hydathodes in wild-type leaves and protrusions on as2 rev and kan1 kan2 leaves. In addition, inhibition of auxin transport by treatment of seedlings with N-(1-naphtyl) phtalamic acid or disruption of the auxin gradient by transforming plants with the 35S:YUC1 construct also blocked leaf margin development. Collectively, our data show that expressions of YUCs in the leaf respond to the adaxial-abaxial juxtaposition, and that the activities of auxin mediate leaf margin development, which subsequently promotes blade outgrowth.
Auxin-Dependent Cell Cycle Reactivation through Transcriptional Regulation ofArabidopsis E2Faby Lateral Organ Boundary Proteins
Authors: Berckmans Barbara , Vassileva Valya , Schmid Stephan P.C. , Maes Sara , Parizot Boris , Naramoto Satoshi , Magyar Zoltan , Kamei Claire Lessa Alvim , Koncz Csaba , Bögre Laszlo , Persiau Geert , De Jaeger Geert , Friml Jiří , Simon Rüdiger , Beeckman Tom , De Veylder Lieven
Published: October 2011

Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture.