bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption, diffusion, dewetting, and entrapment of acetone on Ni(111), surface-modified silicon, and amorphous solid water studied by time-of-flight secondary ion mass spectrometry and temperature programmed desorption
Authors: Souda Ryutaro
Published: October 2011

Interactions of acetone with the silicon surfaces terminated with hydrogen, hydroxyl, and perfluorocarbon are investigated; results are compared to those on amorphous solid water (ASW) to gain insights into the roles of hydrogen bonds in surface diffusion and hydration of acetone adspecies. The surface mobility of acetone occurs at ∼60 K irrespective of the surface functional groups. Cooperative diffusion of adspecies results in a 2D liquid phase on the H- and perfluorocarbon-terminated surfaces, whereas cooperativity tends to be quenched via hydrogen bonding on the OH-terminated surface, thereby forming residues that diffuse slowly on the surface after evaporation of the physisorbed species (i.e., 2D liquid). The interaction of acetone adspecies on the non-porous ASW surface resembles that on the OH-terminated Si surface, but the acetone molecules tend to be hydrated on the porous ASW film, as evidenced by their desorption during the glass-liquid transition and crystallization of water. The roles of micropores in hydration of acetone molecules are discussed from comparison with the results using mesoporous Si substrates.
Ag-Au nanoclusters: Structure and phase segregation
Authors: Belić D. , Chantry R. L. , Li Z. Y. , Brown S. A.
Published: October 2011

We present a systematic survey of unprotected Ag-Au nanoclusters prepared by inert gas aggregation. The clusters are initially fully and homogeneously alloyed, exhibiting icosahedral and decahedral structural motifs. Imaging using scanning transmission electron microscopy indicates that over a period of up to 2 yr, the nanoclusters undergo structural transitions into phase-segregated core-shell and Janus particles with Ag-Au cores and AgxO shells. Larger Janus particles undergo a ripening process which results in division into separate Ag-Au-rich and Ag2O-rich particles. We propose that oxidation of the Ag component and subsequent diffusion of AgxO are responsible for the observed phenomena.
Photo-induced charge transport in ZnS nanocrystals decorated single walled carbon nanotube field-effect transistor
Authors: Rajesh  , Sarkar Tapan , Mulchandani Ashok
Published: October 2011

We describe a photoresponse measurement study on a pyrene linked ZnS nanoparticles decorated single walled carbon nanotube (SWNT) field-effect transistor (FET). We observed that the photocurrent response in the system is based on the semiconducting property of the SWNT. It was found that both the organic molecule linker, pyrene, together with ZnS nanocrystals contributed to the total photoresponse of the ZnS-pyrene/SWNT hybrid device. We demonstrated by FET characteristic studies that the majority charge carriers in the ZnS-pyrene/SWNT device upon UV illumination are positively charged photo-induced holes near the p-type SWNT channel.
High-power blue-violet AlGaN-cladding-free m-plane InGaN/GaN laser diodes
Authors: Farrell R. M. , Haeger D. A. , Hsu P. S. , Schmidt M. C. , Fujito K. , Feezell D. F. , DenBaars S. P. , Speck J. S. , Nakamura S.
Published: October 2011

We demonstrate AlGaN-cladding-free (ACF) m-plane InGaN/GaN laser diodes (LDs) with peak output powers and estimated front facet optical power densities that are comparable to the state-of-the-art single-stripe emitter c-plane LDs. The threshold current density, slope efficiency, and peak output power were 4.66 kA/cm2, 1.29 W/A, and 1.6 W, respectively, after facet coating and under pulsed conditions. Catastrophic optical mirror damage was not observed up to an estimated optical power density of 51.2 MW/cm2 at the front mirror facet, indicating the potential for using ACF m-plane InGaN/GaN LDs in high-power LD applications.
Synthesis and Pharmacological Evaluation of Novel Homocamptothecin-Dihydropyridine Derivative Conjugates as Potent Topoisomerase I Inhibitors
Authors: Zhu Ling-Jian , Zhuang Chun-Lin , Lei Ning , Sheng Chun-Quan , Guo Wei , Miao Zhen-Yuan , Liu Wen-Feng , Yao Jian-Zhong , Zhang Wan-Nian
Published: October 2011

Homocamptothecins (hCPT) represent a new generation of antitumour agents targeting DNA topoisomerase I. The expanded seven-membered lactone E-ring that characterizes hCPT enhances the plasma stability of the drug and reinforces the inhibition of topoisomerase I (Topo I) compared with conventional six-membered CPT. In an attempt to improve the antitumour activity of hCP, a series of novel hCPT derivatives conjugating with dihydropyridine derivates were designed and synthesized based on a synthetic route that couples 7-formylhomocamptothecin with different dihydropyridine derivates. Most of the synthesized compounds exhibited good cytotoxic activity on tumour cell line A549, MDA-MB-435, and HCT116. Furthermore, this class of compounds showed superior Topo I inhibition activity comparable to or higher than CPT.
Rhodium dihydride (RhH2) with high volumetric hydrogen density
Authors: Li Bing , Ding Yang , Kim Duck Young , Ahuja Rajeev , Zou Guangtian , Mao Ho-Kwang
Published: October 2011

Materials with very high hydrogen density have attracted considerable interest due to a range of motivations, including the search for chemically precompressed metallic hydrogen and hydrogen storage applications. Using high-pressure synchrotron X-ray diffraction technique and theoretical calculations, we have discovered a new rhodium dihydride (RhH2) with high volumetric hydrogen density (163.7 g/L). Compressing rhodium in fluid hydrogen at ambient temperature, the fcc rhodium metal absorbs hydrogen and expands unit-cell volume by two discrete steps to form NaCl-typed fcc rhodium monohydride at 4 GPa and fluorite-typed fcc RhH2at 8 GPa. RhH2is the first dihydride discovered in the platinum group metals under high pressure. Our low-temperature experiments show that RhH2is recoverable after releasing pressure cryogenically to 1 bar and is capable of retaining hydrogen up to 150 K for minutes and 77 K for an indefinite length of time.
Sport injuries as the main cause of sport career termination among Finnish top‐level athletes
Authors: Ristolainen Leena , Kettunen Jyrki A. , Kujala Urho M. , Heinonen Ari
Published: October 2011

Injuries are common among athletes, and are sometimes so severe that they affect an athlete's career in sport. As studies on sport career termination are few, we conducted a study to investigate the role of injuries as a reason for ending a sport career. The study group consisted of 574 male and female top‐level cross‐country skiers, swimmers, long‐distance runners and soccer players who responded to a retrospective postal questionnaire in 2006. Twenty‐seven athletes (4.9%, 27/548) reported ending their sport career because of injury. A follow‐up interview was conducted by telephone in 2007 (n=20 volunteered to be interviewed) to confirm sport career termination and the reasons for this. Fifteen of the interviewed athletes terminated and five continued their sport on the same level as earlier. Female athletes (12/15) terminated their sport career more frequently than male athletes (3/15). Athletes who reported terminating their sport career because of injury were on average two and a half years older (24.1 years vs. 21.6 years, P=0.006) than athletes who continued the sport. All the swimmers (n=5) who were interviewed terminated their career because of a shoulder injury. All the soccer players who ended their career (n=4) were female and had a severe knee injury, such as anterior cruciate ligament injury. Most of the athletes who terminated their sport career (70.4%, 19/27) reported that the injury caused them mild or moderate permanent disability. We found that sports injuries play a significant role in terminating a career in sport, and in some sports events injuries may commonly be the main reason for sport career termination. Injury prevention and adequate treatment and rehabilitation of injuries are thus essential to avoid the long‐term consequences of severe sport injuries.
Contact electrification of insulating materials
Authors: Lacks Daniel J , Mohan Sankaran R
Published: October 2011

The electrostatic charge that is generated when two materials are contacted or rubbed and then separated is a well-known physical process that has been studied for more than 2500 years. Contact electrification occurs in many contexts, both natural and technological. For example, in dust storms the collisions between particles lead to electrostatic charging and in extreme cases, extraordinary lightning displays. In electrophotography, toner particles are intentionally charged to guide their deposition in well-defined patterns. Despite such a long history and so many important consequences, a fundamental understanding of the mechanism behind contact electrification remains elusive. An open question is what type of species are transferred between the surfaces to generate charge—experiments suggest various species ranging from electrons to ions to nanoscopic bits of material, and theoretical work suggests that non-equilibrium states may play an important role. Another open question is the contact electrification that occurs when two insulating materials with identical physical properties touch—since there is no apparent driving force, it is not clear why charge transfer occurs. A third open question involves granular systems—models and experiments have shown that a particle-size dependence for the charging often exists. In this review, we discuss the fundamental aspects of contact electrification and highlight recent research efforts aimed at understanding these open questions.
Electrical properties of modulation-doped rf-sputtered polycrystalline MgZnO/ZnO heterostructures
Authors: Chin H-A , Cheng I-C , Li C-K , Wu Y-R , Chen J Z , Lu W-S , Lee W-L
Published: October 2011

Modulation doping effect is studied in large-area rf-sputtered polycrystalline MgZnO/ZnO heterostructures. Both polarization effect at the MgZnO/ZnO interface and carrier transferring from the modulation doping layer contribute to the improvement of electrical conductivity of the heterostructure. Modulation doping provides greater enhancement in electrical properties when Mg content in the barrier layer is lower. Temperature-independent carrier concentration is observed in low-temperature Hall measurement, indicating the existence of two-dimensional electron gas in the modulation-doped polycrystalline MgZnO/ZnO structure. The slight drop in mobility at low temperatures is caused mainly by the roughness scattering and impurity scattering.
Mitosis futures: the past is prologue
Authors: McIntosh J. Richard
Published: October 2011

The mechanisms by which cells organize and segregate their chromosomes have been under close scrutiny for years, and significant progress has been made in understanding how mitosis works. Modern cell biology has identified most of the molecules that underlie mitotic spindle function, but the ways in which they are organized and controlled to make an effective and accurate cellular machine are exciting subjects for future study.
Science stories: flies, planes, worms, and lasers
Authors: Rolls Melissa
Published: October 2011

“Tell a story,” my mother instructs her graduate students as they prepare their talks. I will make use of her advice here, and will tell several short stories. The themes revolve around the practice of science—what motivates us to go into science and how we choose questions once we get there. I also touch on progress in scientific tools, teaching, good mentors, and good colleagues, all of which contribute to making a career in science constantly compelling.
Give chance a chance
Authors: Nachury Maxence V.
Published: October 2011

How did I get to become a cell biologist? Or, more generally, why do things happen the way they do? The answer provided by the philosopher Democritus and later adopted by Jacques Monod is “everything existing in the universe is the fruit of chance and necessity.” While I read Monod's book Chance and Necessity as an undergraduate student, little did I appreciate the accuracy of this citation and how much of my scientific trajectory would be guided by chance.
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
Authors: Zhao Yongan , Tang Haixu , Ye Yuzhen
Published: October 2011

Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved a ~20–90-fold speedup relative to BLAST while still achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however, requires a substantial memory footprint to identify alignment seeds, due to its use of a suffix array data structure. Here we present RAPSearch2, a new memory-efficient implementation of the RAPSearch algorithm that uses a collision-free hash table to index a similarity search database. The utilization of an optimized data structure further speeds up the similarity search—another 2–3 times. We also implemented multi-threading in RAPSearch2, and the multi-thread modes achieve significant acceleration (e.g. 3.5X for 4-thread mode). RAPSearch2 requires up to 2G memory when running in single thread mode, or up to 3.5G memory when running in 4-thread mode.

Availability and implementation: Implemented in C++, the source code is freely available for download at the RAPSearch2 website: http://omics.informatics.indiana.edu/mg/RAPSearch2/.

Contact:  yye@indiana.edu

Supplementary information: Available at the RAPSearch2 website.
Comments on ‘An empirical comparison of several recent epistatic interaction detection methods’
Authors: Wan Xiang , Yang Can , Yu Weichuan
Published: October 2011

Contact:  eeyu@ust.hk
Buprenorphine Metabolites, Buprenorphine-3-glucuronide and Norbuprenorphine-3-glucuronide, Are Biologically Active
Authors: Brown Sarah M. , Holtzman Michael , Kim Thomas , Kharasch Evan D.
Published: October 2011

Background

The long-lasting high-affinity opioid buprenorphine has complex pharmacology, including ceiling effects with respect to analgesia and respiratory depression. Plasma concentrations of the major buprenorphine metabolites norbuprenorphine, buprenorphine-3-glucuronide, and norbuprenorphine-3-glucuronide approximate or exceed those of the parent drug. Buprenorphine glucuronide metabolites pharmacology is undefined. This investigation determined binding and pharmacologic activity of the two glucuronide metabolites, and in comparison with buprenorphine and norbuprenorphine.

Methods

Competitive inhibition of radioligand binding to human μ, κ, and δ opioid and nociceptin receptors was used to determine glucuronide binding affinities for these receptors. Common opiate effects were assessed in vivo in SwissWebster mice. Antinociception was assessed using a tail-flick assay, respiratory effects were measured using unrestrained whole-body plethysmography, and sedation was assessed by inhibition of locomotion measured by open-field testing.

Results

Buprenorphine-3-glucuronide had high affinity for human μ (Ki [inhibition constant] = 4.9 ± 2.7 pM), δ (Ki = 270 ± 0.4 nM), and nociceptin (Ki = 36 ± 0.3 μM) but not κ receptors. Norbuprenorphine-3-glucuronide had affinity for human κ (Ki = 300 ± 0.5 nM) and nociceptin (Ki = 18 ± 0.2 μM) but not μ or δ receptors. At the dose tested, buprenorphine-3-glucuronide had a small antinociceptive effect. Neither glucuronide had significant effects on respiratory rate, but norbuprenorphine-3-glucuronide decreased tidal volume. Norbuprenorphine-3-glucuronide also caused sedation.

Conclusions

Both glucuronide metabolites of buprenorphine are biologically active at doses relevant to metabolite exposures, which occur after buprenorphine. Activity of the glucuronides may contribute to the overall pharmacology of buprenorphine.
Perioperative Pharmacokinetics of Methadone in Adolescents
Authors: Sharma Anshuman , Tallchief Danielle , Blood Jane , Kim Thomas , London Amy , Kharasch Evan D.
Published: October 2011

Background

Methadone is frequently administered to adults experiencing anesthesia and receiving pain treatment. Methadone pharmacokinetics in adults are well characterized, including the perioperative period. Methadone is also used in children. There is, however, no information on methadone pharmacokinetics in children of any age. The purpose of this investigation was to determine the pharmacokinetics of intravenous methadone in children undergoing surgery. Perioperative opioid-sparing effects were also assessed.

Methods

Eligible subjects were children 5-18 yr undergoing general anesthesia and surgery, with an anticipated postoperative inpatient stay exceeding 3 days. Three groups of 10 to 11 patients each received intravenous methadone hydrochloride after anesthetic induction in ascending dose groups of 0.1, 0.2, and 0.3 mg/kg (up to 20 mg). Anesthetic care was not otherwise changed. Venous blood was obtained for 4 days, for stereoselective determination of methadone and metabolites. Pain assessments were made each morning. Daily and total opioid consumption was determined. Perioperative opioid consumption and pain was determined in a second cohort, which was matched to age, sex, race, ethnicity, surgical procedure, and length of stay, but not receiving methadone.

Results

The final methadone study cohort was 31 adolescents (14 ± 2 yr, range 10-18) undergoing major spine surgery for a diagnosis of scoliosis. Methadone pharmacokinetics were linear over the dose range 0.1-0.3 mg/kg. Disposition was stereoselective. Methadone administration did not dose-dependently affect postoperative pain scores, and did not dose-dependently decrease daily or total postoperative opioid consumption in spinal fusion patients.

Conclusions

Methadone enantiomer disposition in adolescents undergoing surgery was similar to that in healthy adults.
Ultrasound-Guided, Video-Assisted Transdiaphragmatic Radiofrequency Ablation for Primary Liver Malignancy or Metastatic Nodules
Authors: Nesher Nahum , Haim Mendi Ben , Pevni Demitry , Kessler Ada , Paz Yosef
Published: October 2011

Objective

Percutaneous radiofrequency ablation (RFA) is among the best options in the treatment of primary liver malignancy and metastases because it is a highly effective and minimally invasive alternative to resection in small, nonresectable tumors or in poor surgical candidates and is associated with low morbidity and mortality. We evaluated the clinical feasibility and safety of thoracoscopic, ultrasound (US)-guided RFA of subdiaphragmatic liver malignancies in advanced cirrhotic patients awaiting transplantation.

Methods

Two patients (one female and one male) with end-stage cirrhosis who developed hepatocellular carcinoma were treated thoracoscopically by US-guided RFA. An endoscopic US probe was inserted into the right pleural space through a 10-mm working channel. An RF-operating needle applicator was inserted through a second 10-mm working port after identification of the lesion, penetrating the diaphragm toward the lesion. The procedure duration, applied energy, and generator output were recorded during the intervention. The treatment result and procedure-related complications were analyzed.

Results

The procedure duration was 74 and 92 minutes, respectively. A mean energy deposition of 353 joules resulted in a mean coagulation volume of 115 cm. Tumor ablation was achieved as determined by the postinterventional lack of contrast enhancement in the target region at the follow-up computed tomographic scans performed after 4 months.

Conclusions

RFA offers definite possibilities in the management of small-sized tumors. Thoracoscopic, US-guided transdiaphragmatic RFA has proven to be clinically feasible and safe and can be an effective modality for treating subdiaphragmatic liver lesions. Its minimally invasive nature is the most important advantage compared with surgical resection, especially for patients with high operative risk.
Investigating Perioperative Heart Migration during Robot-Assisted Coronary Artery Bypass Grafting Interventions
Authors: Linte Cristian A. , Cho Daniel S. , Wedlake Chris , Moore John , Chen Elvis , Bainbridge Daniel , Patel Rajni , Peters Terry , Kiaii Bob B.
Published: October 2011

Objective

For robot-assisted coronary artery bypass graft interventions, surgeons typically use a preoperative thoracic computed tomography scan of the patient to plan the procedure. However, the cardiac anatomy is prone to changes induced perioperatively in the effort to access the heart and surgical targets, which, in turn, may invalidate the initial plan. This article presents a method to estimate the perioperative heart migration, information which can be further exploited to refine the preoperative surgical plan.

Methods

Tracked transesophageal ultrasound images of four patients’ hearts were acquired at each stage in the procedure: before lung deflation, after lung deflation, and after both lung deflation and CO2 thoracic insufflation. Anatomic features of interest—the mitral and aortic valves—were identified from each dataset, and their movement between the different procedure stages was recorded and used to estimate the global heart displacement. Moreover, the local morphology of the features of interest was investigated to provide insight on the extent of the deformation the heart has undergone during the workflow.

Results

The study suggested that the heart does undergo substantial displacement—on the order of 10 to 15 mm in each direction (axial, coronal, and sagittal) after lung deflation and CO2 thoracic insufflation. However, no significant differences (P > 0.1) were observed in the morphologic characteristics of the features of interest across the multiple workflow stages, suggesting that local deformations occur at a much smaller scale compared with the global migration.

Conclusions

The quantification of the perioperatively induced changes is critical to track the displacement of the heart and surgical targets. The recorded migration patterns should not be ignored but rather be used to update the surgical plan to better suit the intraoperative environment.
Clinical Advances in Diaphragm Pacing
Authors: Ducko Christopher T.
Published: October 2011

Diaphragmatic pacing is a valuable tool that can significantly benefit certain patients with respiratory insufficiency provided they have an intact phrenic nerve and a functional diaphragm. Careful patient selection is critical to successful long-term results. The main populations that derive benefit from pacing include those with congenital or acquired central hypoventilation syndrome and more commonly those with a high cervical spinal cord injury, where the phrenic nerves remain intact. The pacing electrode of most phrenic nerve pacemakers is implanted directly on the phrenic nerve. A newer device relies on intramuscular implantation of the electrode on the diaphragm at the phrenic nerve motor point. Most patients can be successfully weaned from mechanical ventilation for a substantial time each day, if not completely. This has significant impact on quality of life and implications for healthcare costs. The potential exists for application of this technology to patients with other types of respiratory failure as investigative experience emerges. These include the chronic progressive disease, amyotrophic lateral sclerosis, or temporary scenarios in difficult-to-wean intensive care unit patients. This enabling technology should hold a place in the thoracic surgeon's armamentarium.
Brevibacillus nitrificans sp. nov., a nitrifying bacterium isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks
Authors: Takebe Fumihiko , Hirota Kikue , Nodasaka Yoshinobu , Yumoto Isao
Published: October 2011

A heterotrophic nitrifying bacterium, designated strain DA2T, was isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks. Cells of strain DA2T were Gram-positive, facultatively anaerobic, sporulating rods that were motile by means of peritrichous flagella; they were able to grow at pH 5–8. The major isoprenoid quinone of strain DA2T was menaquinone-7 (MK-7) and its cellular fatty acid profile consisted mainly of iso-C15 : 0 (18.6 %) and anteiso-C15 : 0 (69.1 %). The DNA G+C content was 54.1 mol%. 16S rRNA gene sequence phylogeny suggested that strain DA2T is a member of the genus

Brevibacillus

, with highest sequence similarities (in parentheses) to the type strains of

Brevibacillus choshinensis

(99.7 %),

B. formosus

(99.4 %),

B. brevis

(99.4 %),

B. agri

(99.0 %),

B. reuszeri

(98.8 %),

B. parabrevis

(98.7 %),

B. centrosporus

(98.6 %),

B. limnophilus

(97.4 %),

B. panacihumi

(97.3 %) and

B. invocatus

(97.3 %). DNA–DNA hybridization showed less than 60 % relatedness between strain DA2T and type strains of the most closely related species given above. Given the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA sequence and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Brevibacillus nitrificans is proposed; the type strain of this species is DA2T ( = JCM 15774T = NCIMB 14531T).
Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil
Authors: Gao Zhao-Ming , Xiao Jing , Wang Xing-Na , Ruan Ling-Wei , Chen Xiu-Lan , Zhang Yu-Zhong
Published: October 2011

A taxonomic study was carried out on a cellulase-producing bacterium, strain G21T, isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15–40 °C and in 0.5–10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21T belonged to the genus

Vibrio

and formed a clade with

Vibrio furnissii

ATCC 350116T (97.4 % sequence similarity),

V. fluvialis

LMG 7894T (97.1 %) and

V. ponticus

CECT 5869T (96.1 %). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA–DNA hybridization experiments indicated that the strain was distinct from the closest related

Vibrio

species. Additionally, strain G21T could be differentiated from them phenotypically by the ability to grow in 10 % NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA–DNA hybridization analysis, it is concluded that strain G21T represents a novel species of the genus

Vibrio

, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21T ( = DSM 22851T  = CGMCC 1.10228T).
Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site
Authors: Anand Shailly , Bala Kiran , Saxena Anjali , Schumann Peter , Lal Rup
Published: October 2011

A Gram-staining-positive, heterotrophic, aerobic, non-motile, non-endospore-forming, yellow-coloured rod, designated strain N5T, was isolated from a soil sample collected at an industrial waste site in Noida, on the outskirts of Delhi, India. In phylogenetic analyses based on 16S rRNA gene sequences, strain N5T was most closely related to members of established species in the genus

Microbacterium

(with sequence similarities of approximately 94.0–97.6 %), particularly

Microbacterium indicum

LMG 23459T (97.59 %) and

Microbacterium gubbeenense

LMG 19263T (97.18 %). In DNA–DNA hybridization studies, however, none of the DNA–DNA relatedness values between strain N5T and members of the genus

Microbacterium

exceeded 11.3 %. The genomic DNA G+C content of the novel strain was 68 mol%. The chemotaxonomic characteristics of strain N5T, which had MK-11 and MK-10 as its major menaquinones and anteiso-C15 : 0 (45 %), anteiso-C17 : 0 (37 %), iso-C16 : 0 (8.5 %) and C16 : 0 (4.5 %) as its predominant fatty acids, were consistent with classification in the genus

Microbacterium

. Peptidoglycan in the novel strain, which contained ornithine, alanine, glycine, homoserine, glutamic acid, 3-hydroxyglutamic acid, muramic acid and traces of N-glycolyl residues, was of type B2β. The polar lipid profile of strain N5T comprised diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The novel strain’s major cell-wall sugars were glucose and galactose. Based on the phylogenetic, DNA–DNA hybridization, chemotaxonomic and phenotypic data, strain N5T represents a novel species within the genus

Microbacterium

for which the name Microbacterium amylolyticum sp. nov. is proposed; the type strain is N5T ( = DSM 24221T = CCM 7881T).
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
Authors: Rogers Matthew B. , Hilley James D. , Dickens Nicholas J. , Wilkes Jon , Bates Paul A. , Depledge Daniel P. , Harris David , Her Yerim , Herzyk Pawel , Imamura Hideo , Otto Thomas D. , Sanders Mandy , Seeger Kathy , Dujardin Jean-Claude , Berriman Matthew , Smith Deborah F. , Hertz-Fowler Christiane , Mottram Jeremy C.
Published: October 2011

Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy numbers, identifying large copy number variations between species, with 200 tandem gene arrays in L. major and 132 in L. mexicana. Chromosome copy number also varied significantly between species, with nine supernumerary chromosomes in L. infantum, four in L. mexicana, two in L. braziliensis, and one in L. major. A significant bias against gene arrays on supernumerary chromosomes was shown to exist, indicating that duplication events occur more frequently on disomic chromosomes. Taken together, our data demonstrate that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism.
Proteomic Analysis of a Sea-Ice Diatom: Salinity Acclimation Provides New Insight into the Dimethylsulfoniopropionate Production Pathway
Authors: Lyon Barbara R. , Lee Peter A. , Bennett Jennifer M. , DiTullio Giacomo R. , Janech Michael G.
Published: October 2011

Dimethylsulfoniopropionate (DMSP) plays important roles in oceanic carbon and sulfur cycling and may significantly impact climate. It is a biomolecule synthesized from the methionine (Met) pathway and proposed to serve various physiological functions to aid in environmental stress adaptation through its compatible solute, cryoprotectant, and antioxidant properties. Yet, the enzymes and mechanisms regulating DMSP production are poorly understood. This study utilized a proteomics approach to investigate protein changes associated with salinity-induced DMSP increases in the model sea-ice diatom Fragilariopsis cylindrus (CCMP 1102). We hypothesized proteins associated with the Met-DMSP biosynthesis pathway would increase in relative abundance when challenged with elevated salinity. To test this hypothesis axenic log-phase cultures initially grown at a salinity of 35 were gradually shifted to a final salinity of 70 over a 24-h period. Intracellular DMSP was measured and two-dimensional gel electrophoresis was used to identify protein changes at 48 h after the shift. Intracellular DMSP increased by approximately 85% in the hypersaline cultures. One-third of the proteins increased under high salinity were associated with amino acid pathways. Three protein isoforms of S-adenosylhomo-cysteine hydrolase, which synthesizes a Met precursor, increased 1.8- to 2.1-fold, two isoforms of S-adenosyl Met synthetase increased 1.9- to 2.5-fold, and S-adenosyl Met methyltransferase increased by 2.8-fold, suggesting active methyl cycle proteins are recruited in the synthesis of DMSP. Proteins from the four enzyme classes of the proposed algal Met transaminase DMSP pathway were among the elevated proteins, supporting our hypothesis and providing candidate genes for future characterization studies.
Laser Microdissection Unravels Cell-Type-Specific Transcription in Arbuscular Mycorrhizal Roots, Including CAAT-Box Transcription Factor Gene Expression Correlating with Fungal Contact and Spread
Authors: Hogekamp Claudia , Arndt Damaris , Pereira Patrícia A. , Becker Jörg D. , Hohnjec Natalija , Küster Helge
Published: October 2011

Arbuscular mycorrhizae (AM) are the most widespread symbioses on Earth, promoting nutrient supply of most terrestrial plant species. To unravel gene expression in defined stages of Medicago truncatula root colonization by AM fungi, we here combined genome-wide transcriptome profiling based on whole mycorrhizal roots with real-time reverse transcription-PCR experiments that relied on characteristic cell types obtained via laser microdissection. Our genome-wide approach delivered a core set of 512 genes significantly activated by the two mycorrhizal fungi Glomus intraradices and Glomus mossae. Focusing on 62 of these genes being related to membrane transport, signaling, and transcriptional regulation, we distinguished whether they are activated in arbuscule-containing or the neighboring cortical cells harboring fungal hyphae. In addition, cortical cells from nonmycorrhizal roots served as a reference for gene expression under noncolonized conditions. Our analysis identified 25 novel arbuscule-specific genes and 37 genes expressed both in the arbuscule-containing and the adjacent cortical cells colonized by fungal hyphae. Among the AM-induced genes specifying transcriptional regulators were two members encoding CAAT-box binding transcription factors (CBFs), designated MtCbf1 and MtCbf2. Promoter analyses demonstrated that both genes were already activated by the first physical contact between the symbionts. Subsequently, and corresponding to our cell-type expression patterns, they were progressively up-regulated in those cortical areas colonized by fungal hyphae, including the arbuscule-containing cells. The encoded CBFs thus represent excellent candidates for regulators that mediate a sequential reprogramming of root tissues during the establishment of an AM symbiosis.
Strigolactone Biosynthesis in Medicago truncatula and Rice Requires the Symbiotic GRAS-Type Transcription Factors NSP1 and NSP2
Authors: Liu Wei , Kohlen Wouter , Lillo Alessandra , Op den Camp Rik , Ivanov Sergey , Hartog Marijke , Limpens Erik , Jamil Muhammad , Smaczniak Cezary , Kaufmann Kerstin , Yang Wei-Cai , Hooiveld Guido J.E.J. , Charnikhova Tatsiana , Bouwmeester Harro J. , Bisseling Ton , Geurts René
Published: October 2011

Legume GRAS (GAI, RGA, SCR)-type transcription factors NODULATION SIGNALING PATHWAY1 (NSP1) and NSP2 are essential for rhizobium Nod factor-induced nodulation. Both proteins are considered to be Nod factor response factors regulating gene expression after symbiotic signaling. However, legume NSP1 and NSP2 can be functionally replaced by nonlegume orthologs, including rice (Oryza sativa) NSP1 and NSP2, indicating that both proteins are functionally conserved in higher plants. Here, we show that NSP1 and NSP2 are indispensable for strigolactone (SL) biosynthesis in the legume Medicago truncatula and in rice. Mutant nsp1 plants do not produce SLs, whereas in M. truncatula, NSP2 is essential for conversion of orobanchol into didehydro-orobanchol, which is the main SL produced by this species. The disturbed SL biosynthesis in nsp1 nsp2 mutant backgrounds correlates with reduced expression of DWARF27, a gene essential for SL biosynthesis. Rice and M. truncatula represent distinct phylogenetic lineages that split approximately 150 million years ago. Therefore, we conclude that regulation of SL biosynthesis by NSP1 and NSP2 is an ancestral function conserved in higher plants. NSP1 and NSP2 are single-copy genes in legumes, which implies that both proteins fulfill dual regulatory functions to control downstream targets after rhizobium-induced signaling as well as SL biosynthesis in nonsymbiotic conditions.
iotbx.cif: a comprehensive CIF toolbox
Authors: Gildea Richard J. , Bourhis Luc J. , Dolomanov Oleg V. , Grosse-Kunstleve Ralf W. , Puschmann Horst , Adams Paul D. , Howard Judith A. K.
Published: October 2011

iotbx.cifis a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-levelcctbx[Grosse-Kunstleve, Sauter, Moriarty & Adams (2002).J. Appl. Cryst.35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.
Performance enhancement of real‐time computing for small unmanned helicopter autopilot
Authors: Kodirov Nodir , Kim Doo‐Hyun , Kim Junyeong , Song Seunghwa , Moon Changjoo
Published: October 2011

Purpose

The purpose of this paper is to make performance improvements and timely critical execution enhancements for operational flight program (OFP). The OFP is core software of autonomous control system of small unmanned helicopter.

Design/methodology/approach

In order to meet the time constraints and enhance control application performance, two major improvements were done at real‐time operating system (RTOS) kernel. They are thread scheduling algorithm and lock‐free thread message communication mechanism. Both of them have a direct relationship with system efficiency and indirect relationship with helicopter control application execution stability through improved deadline keeping characteristics.

Findings

In this paper, the suitability of earliest deadline first (EDF) scheduling algorithm and non‐blocking buffer (NBB) mechanism are illustrated with experimental and practical applications. Results of this work show that EDF contributes around 15 per cent finer‐timely execution and NBB enhances kernel's responsiveness around 35 per cent with respect to the number of thread context switch and CPU utilization. These apply for OFP implemented over embedded configurable operating system (eCos) RTOS on x86 architecture‐based board.

Practical implications

This paper illustrates an applicability of deadline‐based real‐time scheduling algorithm and lock‐free kernel communication mechanism for performance enhancement and timely critical execution of autonomous unmanned aerial vehicle control system.

Originality/value

This paper illustrates a novel approach to extend RTOS kernel modules based on unmanned aerial vehicle control application execution scenario. Lock‐free thread communication mechanism is implemented, and tested for applicability at RTOS. Relationship between UAV physical and computation modules are clearly illustrated via an appropriate unified modelling language (UML) collaboration and state diagrams. As experimental tests are conducted not only for a particular application, but also for various producer/consumer scenarios, these adequately demonstrate the applicability of extended kernel modules for general use.
H∞ robust controller for autonomous helicopter hovering control
Authors: Tijani Ismaila B. , Akmeliawati Rini , Legowo Ari , Budiyono Agus , Abdul Muthalif A.G.
Published: October 2011

Purpose

The purpose of this paper is to present the synthesis of a robust controller for autonomous small‐scale helicopter hovering control using extended H∞ loop shaping design techniques.

Design/methodology/approach

This work presents the development of a robust controller for smooth hovering operation required for many autonomous helicopter operations using H∞ loop shaping technique incorporating the Vinnicombe‐gap (v‐gap) metric for validation of robustness to uncertainties due to parameter variation in the system model. Simulation study was conducted to evaluate the performance of the designed controller for robust stability to uncertainty, disturbance rejection, and time‐domain response in line with ADS‐33E level 1 requirements.

Findings

The proposed techniques for a robust controller exhibit an effective performance for both nominal plant and 20 percent variation in the nominal parameters in terms of robustness to uncertainty, disturbance wind gust attenuation up to 95 percent, and transient performance in compliance with ADS‐33E level 1 specifications.

Research limitations/implications

The controller is limited to hovering and low‐speed flight envelope.

Practical implications

This is expected to provide efficient hovering/low‐speed autonomous helicopter flight control required in many civilian unmanned aerial vehicles applications. Also, the technique can be used to simplify the number of robust gain‐scheduled linear controllers required for wide‐envelope flight.

Social implications

The research will facilitate the deployment of low cost, small‐scale autonomous helicopters in various civilian applications.

Originality/value

The research addresses the challenges of parametric variation inherent in helicopter hovering/low‐speed control using an extended H∞ loop shaping technique with v‐gap metric.
Fresh fruit and vegetables and the added value of antioxidants
Authors: Bartels Jos , van den Berg Isabelle
Published: October 2011

Purpose

This study aims to focus on how to capitalise on the natural and logical alliance of nutrients in the marketing of fresh fruit and vegetables.

Design/methodology/approach

A Dutch survey study was carried out among a representative sample of the Dutch population (n=492). Respondents filled out a questionnaire on: perceptions of fresh fruit and vegetables; interest in, knowledge of, and trust in, antioxidants and fresh fruit and vegetables; domain‐specific innovativeness and social identification; means of communication; and information‐seeking and buying behaviour.

Findings

Based on consumption patterns, respondents were divided into non‐, light and heavy organic food users. Results show that there are significant differences between the three consumer groups on domain specific innovativeness, social identification and attitudes towards antioxidants in fresh fruit and vegetables.

Practical implications

Non‐users of organic food are difficult to reach with communication regarding nutrients and organic produce, in contrast to light and heavy users. Light users could be triggered by more peripheral message cues, while heavy users are more sensitive to the content of the message. Differentiated strategies for light and heavy users of organic food should be developed in order to effectively communicate the added value of nutrients in fresh fruit and vegetables.

Originality/value

This study is the first to examine the role of domain specific innovativeness and social identification in attitudes towards antioxidants in fresh fruit and vegetables. The empirical findings from this study are expected to benefit the continued development on health communication messages.
The influence of health‐related information on variety‐seeking behavior
Authors: Lin Chien‐Huang , Lin Hung‐Chou , Lee Sheng‐Hsien
Published: October 2011

Purpose

This paper seeks to explore the effect of mood states and gender on the relationship between health‐related information and variety seeking (VS) behavior among food products.

Design/methodology/approach

Two experiments were conducted to examine the moderating effects of mood states and gender on the relationship between health‐related information and VS.

Findings

The results indicate that sad people incorporate more VS than happy people when health warnings and nutritional labeling are absent, but sad and happy people tend to converge to similar levels of VS when health warnings and nutritional labeling are present. Moreover, males incorporate less VS than females when health warnings are present, while females incorporate less VS than males when nutritional labeling is present.

Practical implications

In the absence of health warnings and nutritional labeling, it is a wiser way for leading brands to cultivate positive consumer moods by utilization of humorous ads, so that they do not search for varied products. For less well‐known brands, inducing negative consumer moods is a better way to encourage brand switching. Further, providing nutritional labeling will strengthen consumer brand loyalty by reducing their VS, especially for females. As the health warnings reduce the VS for males, marketers may take advantage of this effect by associating brand names with health warnings.

Originality/value

As VS is found to be related to over‐consumption, it is important to investigate the effects of health‐related information on VS. However, little empirical evidence has been found on the effect of health‐related information on VS behavior. Further, this study takes into consideration moderating factors as it is important for marketers to realize how health‐related information interacts with the consumer's VS behavior under different mood states and gender. The findings demonstrate that the relationship between health‐related information and VS is moderated by mood states and gender differences, an important contribution to the research on VS behavior.