bluuebunny/crossref_metadata_2025 huggingface dataset:
Instrument performance study on the short and long pulse options of the second Spallation Neutron Source target station
Authors: Zhao J. K. , Herwig Kenneth W. , Robertson J. L. , Gallmeier Franz X. , Riemer Bernard W.
Published: October 2013

The Spallation Neutron Source (SNS) facility at the Oak Ridge National Laboratory is designed with an upgrade option for a future low repetition rate, long wavelength second target station. This second target station is intended to complement the scientific capabilities of the 1.4 MW, 60 Hz high power first target station. Two upgrade possibilities have been considered, the short and the long pulse options. In the short pulse mode, proton extraction occurs after the pulse compression in the accumulator ring. The proton pulse structure is thus the same as that for the first target station with a pulse width of ∼0.7 μs. In the long pulse mode, protons are extracted as they are produced by the linac, with no compression in the accumulator ring. The time width of the uncompressed proton pulse is ∼1 ms. This difference in proton pulse structure means that neutron pulses will also be different. Neutron scattering instruments thus have to be designed and optimized very differently for these two source options which will directly impact the overall scientific capabilities of the SNS facility. In order to assess the merits of the short and long pulse target stations, we investigated a representative suit of neutron scattering instruments and evaluated their performance under each option. Our results indicate that the short pulse option will offer significantly better performance for the instruments and is the preferred choice for the SNS facility.
One-point statistics for turbulent wall-bounded flows at Reynolds numbers up to δ+ ≈ 2000
Authors: Sillero Juan A. , Jiménez Javier , Moser Robert D.
Published: October 2013

One-point statistics are presented for new direct simulations of the zero-pressure-gradient turbulent boundary layer in the range Reθ = 2780–6680, matching channels and pipes at δ+ ≈ 1000–2000. For tripped boundary layers, it is found that the eddy-turnover length is a better criterion than the Reynolds number for the recovery of the largest flow scales after an artificial inflow. Beyond that limit, the integral parameters, mean velocities, Reynolds stresses, and pressure fluctuations of the new simulations agree very well with the available numerical and experimental data, but show clear differences with internal flows when expressed in wall units at the same wall distance and Reynolds number. Those differences are largest in the outer layer, independent of the Reynolds number, and apply to the three velocity components. The logarithmic increase with the Reynolds number of the maximum of the streamwise velocity and pressure fluctuations is confirmed to apply to experimental and numerical internal and external flows. The new simulations also extend to a wider range of Reynolds numbers, and to more than a decade in wall distance, the evidence for logarithmic intensity profiles of the spanwise velocity and of the pressure intensities. Streamwise velocity fluctuations appear to require higher Reynolds numbers to develop a clear logarithmic profile, but it is argued that the comparison of the available near-wall data with fluctuation profiles experimentally obtained by other groups at higher Reynolds numbers can only be explained by assuming the existence of a mesolayer for the fluctuations. The statistics of the new simulation are available in our website.
Increased surface flashover voltage in microfabricated devices
Authors: Sterling R. C. , Hughes M. D. , Mellor C. J. , Hensinger W. K.
Published: October 2013

With the demand for improved performance in microfabricated devices, the necessity to apply greater electric fields and voltages becomes evident. When operating in vacuum, the voltage is typically limited by surface flashover forming along the surface of a dielectric. By modifying the fabrication process, we have discovered it is possible to more than double the flashover voltage. Our finding has significant impact on the realization of next-generation micro- and nano-fabricated devices and for the fabrication of on-chip ion trap arrays for the realization of scalable ion quantum technology.
A barometric pressure sensor based on the air-gap scale effect in a cantilever
Authors: Minh-Dung Nguyen , Takahashi Hidetoshi , Uchiyama Takeshi , Matsumoto Kiyoshi , Shimoyama Isao
Published: October 2013

The most common structure for a conventional barometric pressure sensor consists of a vacuum-sealed cavity and a diaphragm. However, we hypothesize that a simple structure with an unsealed cavity and an ultra-thin cantilever can provide more sensitive measurements. We produced a 300-nm-thick cantilever with a small spring constant, which made the cantilever sensitive to low pressures. We demonstrated that miniaturizing the air-gap of the cantilever enables the sensor to measure barometric pressure changes at a low pressure change rate with a high resolution, which was 1 Pa at 0.05 Hz, and for a gap size of 1.7 μm.
Charge doping of graphene in metal/graphene/dielectric sandwich structures evaluated by C-1s core level photoemission spectroscopy
Authors: Dahal Arjun , Addou Rafik , Coy-Diaz Horacio , Lallo James , Batzill Matthias
Published: October 2013

We show that for metal/graphene/dielectric sandwich structures, charge doping in graphene depends on both the work functions of the metal and the dielectric. Using C-1s core level photoemission spectroscopy we determine the charge doping in graphene for one-sided metal contacts as well as for sandwich structures that are commonly used in graphene devices. The measured Fermi-level shifts are in good agreement with a model that predicts that the difference in charge doping for graphene on a metal compared to graphene sandwiched between a metal and dielectric is given by ΔEF ≈ 0.44 × √(Φmetal − Φdielectric).
Electro-mechanical coupling of semiconductor film grown on stainless steel by oxidation
Authors: Lin M. C. , Wang G. , Guo L. Q. , Qiao L. J. , Volinsky Alex A.
Published: October 2013

Electro-mechanical coupling phenomenon in oxidation film on stainless steel has been discovered by using current-sensing atomic force microscopy, along with the I-V curves measurements. The oxidation films exhibit either ohmic, n-type, or p-type semiconductor properties, according to the obtained I-V curves. This technique allows characterizing oxidation films with high spatial resolution. Semiconductor properties of oxidation films must be considered as additional stress corrosion cracking mechanisms.
Fabrication method for self-aligned bottom-gate oxide thin-film transistors by utilizing backside excimer-laser irradiation through substrate
Authors: Nakata Mitsuru , Tsuji Hiroshi , Fujisaki Yoshihide , Sato Hiroto , Nakajima Yoshiki , Takei Tatsuya , Yamamoto Toshihiro , Kurita Taiichiro
Published: October 2013

A method for fabricating self-aligned bottom-gate InGaZnO (IGZO) thin-film transistors (TFTs) with low parasitic capacitance by utilizing backside excimer-laser irradiation through a substrate is proposed and experimentally validated. Irradiation from the backside of the glass substrate using gate electrode as a mask reduces resistance of the IGZO film selectively for their application as source/drain regions in bottom-gate IGZO-TFTs. This method offers a wide process margin with respect to laser energy density and is applicable to large-area processing.
Localized parametric generation of spin waves in a longitudinally magnetized Ni81Fe19 waveguide
Authors: Brächer T. , Pirro P. , Serga A. A. , Hillebrands B.
Published: October 2013

We demonstrate that in a longitudinally magnetized Ni81Fe19 waveguide spin waves can be generated via parallel parametric generation by a microstrip antenna. By employing microfocus Brillouin light scattering spectroscopy, we show that this method provides an efficient excitation source for backward volume spin waves. We analyze the spatial distribution of the generated spin waves, proving that odd and even waveguide modes can be excited. Furthermore, we study the spin-wave propagation along the Ni81Fe19 waveguide, revealing that the generation process takes place underneath the antenna due to its threshold nature.
In situ doping of catalyst-free InAs nanowires with Si: Growth, polytypism, and local vibrational modes of Si
Authors: Dimakis Emmanouil , Ramsteiner Manfred , Huang Chang-Ning , Trampert Achim , Davydok Anton , Biermanns Andreas , Pietsch Ullrich , Riechert Henning , Geelhaar Lutz
Published: October 2013

Growth and structural aspects of the in situ doping of InAs nanowires with Si have been investigated. The nanowires were grown catalyst-free on Si(111) substrates by molecular beam epitaxy. The supply of Si influenced the growth kinetics, affecting the nanowire dimensions, but not the degree of structural polytypism, which was always pronounced. As determined by Raman spectroscopy, Si was incorporated as substitutional impurity exclusively on In sites, which makes it a donor. Previously unknown Si-related Raman peaks at 355 and 360 cm−1 were identified, based on their symmetry properties in polarization-dependent measurements, as the two local vibrational modes of an isolated Si impurity on In site along and perpendicular, respectively, to the c-axis of the wurtzite InAs crystal.
High order harmonic generation for study of atomic and molecular dynamics
Authors: Dao L. V. , Dinh K. B. , Hannaford P.
Published: October 2013

We present a pump-probe experiment based on the use of a second electrical field to modulate the intensity and the spatial profile of the phase-matched high-order harmonics radiation generated by the first strong driving field. The modification is caused by the variation of the phase-matching condition, e.g., change of electron trajectory and the effect of field gradient forces on the electron that reflect the dynamics of atomic and molecular gases. Atomic argon and molecular oxygen gases are used to demonstrate the feasibility of the technique.
Atomic layer deposition of ZrO2 as gate dielectrics for AlGaN/GaN metal-insulator-semiconductor high electron mobility transistors on silicon
Authors: Ye G. , Wang H. , Arulkumaran S. , Ng G. I. , Hofstetter R. , Li Y. , Anand M. J. , Ang K. S. , Maung Y. K. T. , Foo S. C.
Published: October 2013

In this Letter, the device performance of AlGaN/GaN metal-insulator-semiconductor high electron mobility transistors (MISHEMTs) on silicon substrate using 10-nm-thick atomic-layer-deposited ZrO2 as gate dielectrics is reported. The ZrO2 AlGaN/GaN MISHEMTs showed improved maximum drain current density (Idmax) with high peak transconductance (gmmax) as comparison to Schottky-barrier-gate HEMTs (SB-HEMTs). Also compared to SB-HEMTs, reverse gate leakage current was four orders of magnitude lower and forward gate bias extended to +7.4 V. At energy from −0.29 eV to −0.36 eV, low interface trap state density evaluated by AC conductance and “Hi-Lo frequency” methods indicates good quality of atomic-layer-deposited ZrO2 dielectric layer.
Photosynthetic impairment caused by manganese toxicity and associated antioxidative responses in perennial ryegrass
Authors: Ribera Alejandra E. , Reyes-Díaz Marjorie M. , Alberdi Miren R. , Alvarez-Cortez Daniela A. , Rengel Zed , Mora María de la Luz
Published: October 2013

Manganese (Mn) toxicity can induce oxidative stress and impair photosynthesis in plants. The activity of antioxidant enzymes such as superoxide dismutase (SOD) is increased in Lolium perenne (perennial ryegrass) in response to Mn toxicity (mainly in tolerant cultivars), but it remains unclear whether non-enzymatic antioxidant compounds may have a role in Mn tolerance. Seedlings of perennial ryegrass cv. Nui (Mn-sensitive) and cv. Kingston (Mn-tolerant) were grown in a greenhouse in nutrient solution at increasing Mn doses over 21 days. Even though both cultivars showed similar Mn uptake, dry weight decreases and lipid peroxidation caused by excess Mn were higher in cv. Nui than in Mn-tolerant Kingston. Maximum quantum yield of photosystem II (PSII) (Fv/Fm) declined only in cv. Nui at the highest Mn dose. Effective quantum yield (Ф PSII), electron transport rate, CO2 assimilation, and total chlorophyll concentration in leaves decreased under excess Mn, particularly in the sensitive cultivar. Interestingly, chlorophyll a/b ratio increased (indicating relatively lower concentration of light-harvesting chlorophyll proteins as an adaptive defence mechanism) with an increase in Mn supply only in cv. Kingston, which partially explained its greater Mn tolerance compared with Nui. Concentration of carotenoids was not directly associated with non-photochemical quenching values, suggesting that ryegrass did not dissipate an excess of absorbed energy under Mn toxicity by this mechanism. At increasing excess Mn, both enzymatic (SOD activity) and non-enzymatic antioxidant responses (radical scavenging ability and phenolic concentration) were enhanced, mainly in Kingston. The enhanced antioxidant response in this cultivar suggests the hypothesis of increased capacity to control Mn-triggered oxidative stress as reflected in the reduced lipid peroxidation.
Herbicide efficacy for control of annual ryegrass (Lolium rigidum Gaud.) is influenced more by wheat seeding rate than row spacing
Authors: Lemerle Deirdre , Lockley Peter , Koetz Eric , Diffey Simon
Published: October 2013

Conservation cropping systems with no-till and stubble retention improve soil condition and water conservation. However, tillage is replaced by herbicides for weed control in these systems, increasing the threat of herbicide resistance. In the medium to high rainfall zones of the southern wheatbelt of Australia and under irrigation, wider row spacing is used to enable seeding into heavy stubble loads and to avoid stubble burning. Some evidence suggests that wider rows lead to reduced crop competitive ability and crop yields, greater herbicide dependence, and increased spread of resistance. Our aim was to test the hypothesis that increasing seeding rate compensated for reduced competitive ability at wider row spacings, especially when herbicide performance was suboptimal. We examined the impact of two wheat row spacings (18 and 36 cm) and five seeding rates (resulting in a range of densities of ~80–700 plants/m2) on control of Lolium rigidum with five rates of post-emergence application of diclofop-methyl (Hoegrass®), ranging from label rate to lower rates, over two growing seasons. In the presence of L. rigidum, wheat grain yield was unaffected by row spacing but was significantly reduced at low seeding rates, especially at lower herbicide rates. Lolium rigidum was suppressed at higher crop densities but was also unaffected by row spacing. Grain yield was maximised when post-emergence herbicide was applied at 60–100% of the recommended dose at wheat densities >~300 plants/m2. Significant levels of the weed remained in the crop at anthesis in all treatments. Weed dry matter ranged from 525 g/m2 at low crop densities and with no herbicide to 150 g/m2 with the recommended rate of herbicide and high wheat densities. The implications of manipulating crop competitive ability to improve weed control are discussed, especially in conditions where herbicide performance is unreliable due to weeds developing herbicide resistance or adverse environmental conditions.
Understanding the transmission of H5N1.
Authors: Bourouiba L.
Published: October 2013

H5N1 influenza virus is now endemic in many regions of the world. Outbreaks continue to occur with devastating impact to local economies and threatening human health. The transmission of the virus involves a complex interplay between the spatio-temporal dynamics of the potential avian hosts, the ecology of the virus and poultry farming and trade. Despite increased monitoring of wild bird populations and poultry trade, control measures remain insufficient to mitigate the spread of the virus. Here, we focus on the influence of seasonality of migration and breeding in the transmission of H5N1. We also review recent findings on the interaction between migratory birds and poultry in the pattern of recurrence of H5N1 outbreaks. Finally, impacts of vaccination and co-circulation of avian influenza strains are discussed in the context of re-emergence and silent spreading of the disease.
Sleep quantity and quality in elite youth soccer players: A pilot study
Authors: Robey Elisa , Dawson Brian , Halson Shona , Gregson Warren , Goodman Carmel , Eastwood Peter
Published: October 2013

This study examined the effect of early evening high‐intensity training on the sleep of elite male youth soccer players (n = 12) using wrist actigraphy. High‐intensity training (TRAIN) nights were compared with a home environment (HOME) condition, created by averaging sleep variables on the night before and after TRAIN nights. Additionally, after TRAIN athletes alternately used cold water immersion (TRAIN+CWI) or none, to assess whether cold water immersion (CWI) had any impact on sleep quality and quantity. Ratings of perceived exertion, fatigue and recovery were recorded after training. Actigraphy sleep measures were bedtime, wake time, sleep duration, sleep onset latency, sleep efficiency and wake after sleep onset. Self‐rated scores of sleepiness at bedtime and wake, plus overall sleep quality were also recorded. Only fatigue ratings were higher in TRAIN compared to TRAIN+CWI at bedtime, there were no other differences in training data. Both TRAIN and TRAIN+CWI conditions had significant later (07:45 ± 1:09 h p < 0.01 and 07:34 ± 1:20 h p = 0.01) wake times than HOME (06:44 ± 0:41 h). The TRAIN condition had a significantly higher (7 ± 2; p < 0.01) rating of sleepiness at bedtime compared to HOME (6 ± 1), but no further differences were found in any of the sleep (actigraphy and self‐reported) measures. Across all conditions, time spent asleep was ∼7:30 (±0:52) h:min and sleep efficiency was ∼89% (±6.1). In conclusion, early evening high‐intensity training had no impact on subsequent sleep quality and quantity, nor was there any effect on sleep after performing CWI post‐training.
Subtlex-UK: A New and Improved Word Frequency Database for British English
Authors: van Heuven Walter J. B. , Mandera Pawel , Keuleers Emmanuel , Brysbaert Marc
Published: October 2013

We present word frequencies based on subtitles of British television programmes. We show that the SUBTLEX-UK word frequencies explain more of the variance in the lexical decision times of the British Lexicon Project than the word frequencies based on the British National Corpus and the SUBTLEX-US frequencies. In addition to the word form frequencies, we also present measures of contextual diversity part-of-speech specific word frequencies, word frequencies in children programmes, and word bigram frequencies, giving researchers of British English access to the full range of norms recently made available for other languages. Finally, we introduce a new measure of word frequency, the Zipf scale, which we hope will stop the current misunderstandings of the word frequency effect.
Using Behavioral Economics to Design More Effective Food Policies to Address Obesity
Authors: Liu Peggy J. , Wisdom Jessica , Roberto Christina A. , Liu Linda J. , Ubel Peter A.
Published: October 2013

Many policy interventions that address rising obesity levels in the United States have been designed to provide consumers with more nutrition information, with the goal of encouraging consumers to decrease their caloric intake. We discuss existing information‐provision measures and suggest that they are likely to have little‐to‐modest impact on encouraging lower caloric intake, because making use of such information requires understanding and/or motivation, which many consumers lack, as well as self‐control, which is a limited resource. We highlight several phenomena from the behavioral economics literature (present‐biased preferences, visceral factors, and status quo bias) and explain how awareness of these behavioral phenomena can inform both more effective information‐provision policies and additional policies for regulating restaurants and public school cafeterias that move beyond information to nudge people towards healthier food choices.
Development and Evaluation of a Near‐Infrared Instrument for Single‐Seed Compositional Measurement of Wheat Kernels
Authors: Armstrong Paul R.
Published: October 2013

A single‐kernel, near‐infrared reflectance instrument was designed, built, and tested for its ability to measure composition and traits in wheat kernels. The major objective of the work was targeted at improving an existing design concept of an instrument used for larger seeds such as soybeans and corn but in this case designed for small seeds. Increases in throughput were sought by using a vacuum to convey seeds without compromising measurement accuracy. Instrument performance was evaluated by examining measurement accuracy of wheat kernel moisture, protein content, and kernel mass. Spectral measurements were obtained on individual wheat kernels as they were conveyed by air through an illuminated tube. Partial least squares (PLS) prediction models for these constituents were then developed and evaluated. PLS single‐kernel moisture predictions had a root mean square error of prediction (RMSEP) around 0.5% MC wet basis; protein prediction models had an RMSEP near 0.70%. Prediction of mass was not as good but still provided a reasonable estimate of single‐kernel mass, with RMSEP values of 2.8–4 mg. Data showed that kernel mass and protein content were not correlated, in contrast to some previous research. Overall, results showed the instrument performed comparably to other single‐seed instruments or methods based on accuracy but with an increased throughput at a rate of at least 4 seeds/s.
First Report of Wood Canker Caused by Botryosphaeria dothidea, Diplodia seriata, Neofusicoccum parvum, and Lasiodiplodia theobromae on Grapevine in Turkey
Authors: Akgul D. S. , Savas N. G. , Eskalen A.
Published: October 2013

The Aegean region (western Turkey) is the center of table, raisin, and wine grape cultivation. During the 2012 growing season, wood canker symptoms were observed in vineyards in Manisa city. Symptoms adjacent to pruning wounds, including shoot dieback and wedge-shaped wood discolorations observed in cross section, were among the most prevalent symptoms of the vines. To identify the causal agents, symptomatic woody tissues were surface disinfested with 95% ethanol and flame-sterilized and the discolored outer bark was cut away. The internal tissues (0.5 cm2) were excised from cankers of vines and plated onto potato dextrose agar amended with tetracycline (0.01%) (PDA-tet). The most frequently isolated fungi, based on general growth pattern, speed of growth, and colony color, resembled species in the Botryosphaeriaceae family. According to morphological characteristics, four different groups have been identified based on visual discrimination. After DNA extraction, ribosomal DNA fragments (ITS1-5.8S-ITS2) (2) amplified with ITS4 and ITS5 primers were sequenced and sequences were compared with those deposited in NCBI GenBank database. Four different Botryosphaeriaceae isolates were identified, including Botryosphaeria dothidea (MBAi25AG), Diplodia seriata (MBAi23AG), Lasiodiplodia theobromae (MBAi28AG), and Neofusicoccum parvum (MBAi27AG) (Accession Nos. KF182329, KF182328, KF182331, and KF182330, respectively) with species nomenclature based on Crous et al. (1). Pathogenicity tests were conducted under greenhouse conditions (24°C, 16/8-h day/night, 70% RH) on 1-year-old own rooted grapevine (Vitis vinifera) cv. Sultana Seedless seedlings using one isolate from each of the Botryosphaeriaceae species specified above. Stems of grapevine seedlings were wounded by removing bark with 4-mm cork borer and fresh mycelial plugs were inoculated into the holes and covered with Parafilm. Sterile PDA plugs were placed into the wounds of control seedlings. Five vines were inoculated per isolate. The experiment was repeated twice. After 4 months of incubation, grapevine seedlings were examined for the extent of vascular discoloration and recovery of fungal isolates. Mean lesion lengths on wood tissues were 85.3, 17.2, 13.9, and 13.1 mm for N. parvum, B. dothidea, L. theobromae, and D. seriata, and 6.3 mm for control. Each fungal isolate was successfully re-isolated from inoculated seedlings to fulfill Koch's postulates. To our knowledge, this is the first report of multiple species in the Botryosphaeriaceae causing wood canker and dieback on grapevine in Turkey. These results are significant because Botryosphaeriaceae species are known causal agents of grapevine trunk disease worldwide (3).

References: (1) P. W. Crous et al. Stud. Mycol. 55:235, 2006. (2) B. Slippers et al. Mycologia 96:83, 2004. (3) J. R. Urbez-Torres. Phytopathol. Mediterr. 50:S5, 2011.
Population Structures of ‘Candidatus Liberibacter asiaticus’ in Southern China
Authors: Ma W. , Liang M. , Guan L. , Xu M. , Wen X. , Deng X. , Chen J.
Published: October 2013

Huanglongbing (HLB) is a highly detrimental citrus disease associated with ‘Candidatus Liberibacter asiaticus’, a nonculturable alpha-proteobacterium. Characterization of the bacterial populations is important for development of disease management strategies. In this study, the ‘Ca. L. asiaticus’ populations in eight provinces in southern China where HLB is endemic were analyzed based on tandem repeat number (TRN) variations in a previously characterized genomic locus CLIBASIA_01645. Of the 224 HLB samples collected, 175 (78.3%) samples yielded single polymerase chain reaction (PCR) amplicons (the single amplicon group, SAG) and 49 (21.7%) samples produced multiple PCR amplicons (the multiple amplicon group, MAG). Variations in SAG are summarized by Nei's diversity index (H) and ratio of TRN ≤ 10/TRN > 10 genotypes (R10). Variations in the MAG are described by the percentage of occurrence (PMAG). At an orchard-level comparison, the ‘Ca. L. asiaticus’ population from a Guangdong orchard (n = 24) showed H = 0.50, R10 = 23, and PMAG = 0, significantly different from that of the non-Guangdong orchards in Yunnan (n = 23), H = 0.83, R10 = 2.3, and PMAG = 11.5, and in Hainan (n = 35), H = 0.88, R10 = 1.5, and PMAG = 16.7. In a region-level consideration, the Guangdong ‘Ca. L. asiaticus’ population (n = 78) was H = 0.77, R10 = 25, and PMAG = 1.3, whereas the non-Guangdong population (n = 84) was H = 0.91, R10 = 1.6, and PMAG = 26.9. Overall, significant differences were observed between the ‘Ca. L. asiaticus’ population from Guangdong Province and those from the other provinces. A strong aggregation of TRN = 6, 7, and 8 genotypes is characteristic to the ‘Ca. L. asiaticus’ population in Guangdong. Referenced to genome annotation, we propose that rearrangement of tandem repeats at locus CLIBASIA_01645 could be associated with bacterial environmental adaptation.
A national quality assurance survey of Neisseria gonorrhoeae testing
Authors: Trembizki Ella , Lahra Monica , Stevens Kerrie , Freeman Kevin , Hogan Tiffany , Hogg Geoff , Lawrence Andrew , Limnios Athena , Pearson Julie , Smith Helen , Nissen Michael , Sloots Theo , Whiley David ,   on behalf of ‘GRAND’ study investigators
Published: October 2013

The aims of this study were to (1) conduct a national survey ofNeisseria gonorrhoeaeidentification by National Neisseria Network (NNN) reference laboratories contributing data to the Australian Gonococcal Surveillance Programme and (2) determine the prevalence in Australia of strains ofN. gonorrhoeaelacking gene sequences commonly targeted by in-house PCR assays for confirmation of gonococcal nucleic acid amplification tests. Gonococcal clinical isolates referred to NNN laboratories for the first half of 2012 were screened using in-house real-time PCR assays targeting multicopyopa,porApseudogene andcppBgenes. There were 2455 clinical gonococcal isolates received in the study period; 98.6 % (2420/2455) of isolates harboured all three gene targets, 0.12 % (3/2455) wereporA-negative, 0.04 % (1/2455)opa-negative and 1.14 % (28/2455)cppB-negative by PCR. Notably, no isolates were simultaneously negative for two targets. However, three isolates failed to be amplified by all three PCR methods, one isolate of which was shown to be a commensalNeisseriastrain by 16S rRNA sequencing. Using PCR as the reference standard the results showed that (1) identification ofN. gonorrhoeaeisolates by NNN laboratories was highly specific (99.96 %) and (2) strains ofN. gonorrhoeaelacking gene sequences commonly targeted by in-house PCR assays are present but not widespread throughout Australia at this point in time.
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
Authors: Battle Alexis , Mostafavi Sara , Zhu Xiaowei , Potash James B. , Weissman Myrna M. , McCormick Courtney , Haudenschild Christian D. , Beckman Kenneth B. , Shi Jianxin , Mei Rui , Urban Alexander E. , Montgomery Stephen B. , Levinson Douglas F. , Koller Daphne
Published: October 2013

Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequences of genetic variation by sequencing RNA from 922 genotyped individuals. We present a comprehensive description of the distribution of regulatory variation—by the specific expression phenotypes altered, the properties of affected genes, and the genomic characteristics of regulatory variants. We detect variants influencing expression of over ten thousand genes, and through the enhanced resolution offered by RNA-sequencing, for the first time we identify thousands of variants associated with specific phenotypes including splicing and allelic expression. Evaluating the effects of both long-range intra-chromosomal andtrans(cross-chromosomal) regulation, we observe modularity in the regulatory network, with three-dimensional chromosomal configuration playing a particular role in regulatory modules within each chromosome. We also observe a significant depletion of regulatory variants affecting central and critical genes, along with a trend of reduced effect sizes as variant frequency increases, providing evidence that purifying selection and buffering have limited the deleterious impact of regulatory variation on the cell. Further, generalizing beyond observed variants, we have analyzed the genomic properties of variants associated with expression and splicing and developed a Bayesian model to predict regulatory consequences of genetic variants, applicable to the interpretation of individual genomes and disease studies. Together, these results represent a critical step toward characterizing the complete landscape of human regulatory variation.
Supramolecular architectures ofN-acetyl-L-proline monohydrate andN-benzyl-L-proline
Authors: Rajalakshmi P. , Srinivasan N. , Krishnakumar R. V. , Razak Ibrahim Abdul , Rosli Mohd Mustaqim
Published: October 2013

The title compounds,N-acetyl-L-proline monohydrate, C7H11NO3·H2O, (I), andN-benzyl-L-proline, C12H15NO2, (II), crystallize in the monoclinic space groupP21withZ′ = 1 andZ′ = 2, respectively. The conformation of Cγwith respect to the carboxylic acid group in (I) is Cγ-exoor UP pucker, with the pyrrolidine ring twisted, while in (II), it is Cγ-endoor DOWN, with the pyrrolidine ring assuming an envelope conformation. The crystal packing interactions in (I) are composed of two substructures, one characterized by anR66(24) motif through O—H...O hydrogen bonds and the other by anR44(23) ring through C—H...O interactions. In (II), the crystal packing interactions consist of N—H...O and C—H...O hydrogen bonds. Proline (Pro) exists in its neutral form in (I) and is zwitterionic in (II). This difference in the ionization states of Pro is manifested through the absence of N—H...O and presence of O—H...O interactions in (I), and the presence of N—H...O and absence of O—H...O hydrogen bonds in (II). While C—H...O interactions are present in both (I) and (II), the geometry of the synthons formed by them and their mode of participation in intermolecular interactions is different. Though the title compounds differ significantly in terms of modifications in the Pro skeleton, the differences in their supramolecular structures may also be viewed as a result of the molecular recognition facilitated by the presence of a solvent water molecule in (I) and the zwitterionic state of the amino acid in (II).
The organic–inorganic hybrid material 1-cyclohexylpiperazine-1,4-diium tetrachloridozincate
Authors: Soudani Sarra , Aubert Emmanuel , Jelsch Christian , Ben Nasr Cherif
Published: October 2013

In the crystal structure of the title organic–inorganic hybrid material, (C10H22N2)[ZnCl4], the tetrachloridozincate anions and 1-cyclohexylpiperazine-1,4-diium dications are interconnectedviaN—H...Cl and C—H...Cl hydrogen bonds to form layers parallel to the (001) plane. The cyclohexyl groups from adjacent chains interdigitate, thus building the three-dimensional structure. The piperazinium and cyclohexyl rings exhibit regular spatial chair conformations. The title salt was also characterized by FT–IR and Raman spectroscopic analyses.
Distribution rules of systematic absences on the Conway topograph and their application to powder auto-indexing
Authors: Oishi-Tomiyasu R.
Published: October 2013

This paper presents several general properties of systematic absences that are available before unit-cell parameters and the space group have been determined. The properties are given in the form of distribution rules of Miller indices corresponding to systematic absences on atopograph. A topograph is a graph whose edges are associated with a set of four lattice vectors satisfying Ito's equation 2(|l1*|2+ |l2*|2) = |l1*+l2*|2+ |l1*−l2*|2. It is possible to integrate global information about extinct reflections by using topographs. As an example of the application of these rules, a new powder auto-indexing algorithm is introduced, focusing on its theoretical aspects.
SCEDS: protein fragments for molecular replacement inPhaser
Authors: McCoy Airlie J. , Nicholls Robert A. , Schneider Thomas R.
Published: October 2013

A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of Cαatoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lowerRfactor after ten cycles of all-atom refinement withREFMAC5 than the original template structure. The method has been implemented in the softwarePhaser.
4-Nitroanilinium 3-carboxy-4-hydroxybenzenesulfonate monohydrate
Authors: Sivakumar P. K. , Kumar M. Krishna , Chakkaravarthi G. , Kumar R. Mohan , Kanagadurai R.
Published: October 2013

In the title hydrated salt, C6H7N2O2+·C7H5O6S−·H2O, the benzene ring of the cation makes a dihedral angle of 1.32 (19)° with the attached nitro group. In the anion, an intramolecular O—H...O hydrogen bond with anS(6) ring motif is formed between the carboxyl and hydroxy groups; the dihedral angle between the carboxyl group and the benzene ring is 8.76 (8)°. The crystal structure exhibits intermolecular N—H...O, O—H...O, C—H...O, and π–π [centroid–centroid distances = 3.6634 (9) and 3.7426 (9) Å] interactions to form a three-dimensional network.
Bis(μ-L-arginine-κ3N2,O:O′)bis(L-arginine-κ2N2,O)tetra-μ-chlorido-tetrachloridotetracopper(II)
Authors: Arularasan P. , B.Sivakumar  , Chakkaravarthi G. , Mohan R.
Published: October 2013

The title compound, [Cu4Cl8(C6H14N4O2)4], contains four molecules in the asymmetric unit. In the molecular structure, each of the four Cu2+ions binds to three Cl atoms, one N atom and one O atom, resulting in distorted square-pyramidal coordination environments. The molecular structure is stabilized by weak C—H...O and N—H...Cl hydrogen bonds. The crystal structure exhibit weak intermolecular N—H...O, C—H...O and N—H...Cl interactions, generating a three-dimensional network.
Tris(cyclohexylammonium)cis-dichloridobis(oxalato-κ2O1,O2)stannate(IV) chloride monohydrate
Authors: Sarr Modou , Diallo Waly , Diasse-Sarr Aminata , Plasseraud Laurent , Cattey Hélène
Published: October 2013

The crystal structure of the title compound, (C6H14N)3[Sn(C2O4)2Cl2]Cl·H2O, contains three cyclohexylammonium cations, one stannate(IV) dianion, one isolated chloride anion and one lattice water molecule. The cyclohexylammonium cations adopt chair conformations. In the complex anion, two bidentate oxalate ligands and two chloride anions incispositions coordinate octahedrally to the central SnIVatom. The cohesion of the molecular entities is ensured by the formation of N—H...O, O—H...O, O—H...Cl and N—H...Cl interactions involving cations, anions and the lattice water molecule, giving rise to a layer-like arrangement parallel to (010).
Bis[(5-bromopyridin-2-yl)methanolato-κ2N,O]copper(II) monohydrate
Authors: Hamaguchi Tomohiko , Kawahara Issei , Ando Isao
Published: October 2013

In the title compound, [Cu(C6H5BrNO)2]·H2O, the CuIIion has a square-planer N2O2coordination environment. Slipped π–π stackings [centroid-centroid distances: 3.625 (3), 3.767 (3), 3.935 (3) and 4.255 (3) Å] between pyridine rings and Cu...π interactions (centroid-to-CuIIdistance: 3.56 Å) between Cu2+ions and pyridine rings lead to a layered arrangement parallel to (010). Intermolecular Br...O interactions [Br...O distances: 2.904 (3) and 3.042 (3) Å] and O—H...O hydrogen bonds form a three-dimensional network structure.
1-(5,5-Dimethoxypentyl)-3-methylimidazolium-2-carboxylate
Authors: Walter Olaf
Published: October 2013

The title compound, C12H20N2O4, represents one example of a zwitterionic imidazolium salt with a carboxylate group at the 2-position of the imidazolium ring. The dihedral angle between the heterocyclic ring and the carboxylate group is 31.3 (1)°. The side chain linking the N atom of the ring and the methine C atom has agauche–anti–anticonformation [torsion angles = −60.3 (2), −175.7 (2) and 178.7 (2)°, respectively]. In the crystal, molecules are linked by short C—H...O hydrogen bonds involving the C—H groups in the aromatic ring to generate (001) sheets.
2-Aminobenzoic acid–4-[2-(pyridin-4-yl)ethyl]pyridine (2/1)
Authors: Arman Hadi D. , Tiekink Edward R. T.
Published: October 2013

The asymmetric unit of the title co-crystal, C12H12N2·2C7H7NO2, comprises a centrosymmetric 4-[2-(pyridin-4-yl)ethyl]pyridine molecule and a 2-aminobenzoic acid molecule in a general position. The acid has a small twist between the carboxylic acid residue and the ring [dihedral angle = 7.13 (6)°] despite the presence of an intramolecular N—H...O(carbonyl) hydrogen bond. Three-molecule aggregates are formedviaO—H...N(pyridyl) hydrogen bonds, and these are connected into supramolecular layers in thebcplane by N—H...O(carbonyl) hydrogen bonds and π–π interactions between pyridine and benzene rings [inter-centroid distance = 3.6332 (9) Å]. Layers are connected along theaaxis by weak π–π interactions between benzene rings [3.9577 (10) Å].
‘Bongo Bongo’ and reconfiguring the ‘other’ (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Flynn Alex
Published: October 2013

Fear of immigration has brought about a shift in UK politics. In this new climate, diversity is no longer welcome and the Home Office's message is clear: ‘go home or face arrest’. This editorial addresses the overlap between legal and ethnic categories in this politics of alterity and argues that what is at stake in these debates is nothing less than the reconfiguration of a fit‐and‐proper UK citizen.
The Khat ban in the UK: What about the ‘scientific’ evidence? (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Klein Axel
Published: October 2013

Since the 1920s certain psychoactive substances have been controlled by specially created international agencies. More recently, governments have committed themselves to using evidence in policy‐making. Yet, as the ban on khat in the UK and other countries shows, the assessment process is a perfunctory rather than a decisive component. The Home Secretary set aside scientific advice and bases the decision to ban on considerations outside the health risk ratio, including crime control and counter‐terrorism. However, experience shows that prohibiting substances when demand remains strong is inherently criminogenic. Indeed, the khat ban would appear to play into the hands of radical Islamist organizations. In this article, Axel Klein discusses how political calculations overrule evidence and how this is facilitated by international drug control agencies. Using the term ‘social system’ to explain the relentless extension of bureaucratic remit, he argues that control would now appear inevitable for any substance defined as a drug, regardless of evidence and consequence. As this has implications for other culture‐bound peculiar substances or ‘genussmittel’ he suggests ditching the term ‘drug’ altogether.
Representing financial inclusion: The CGAP microfinance photo contest (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Schwittay Anke
Published: October 2013

This article examines representations of financial inclusion through the lens of the CGAP microfinance photo contest. It situates the contest's winning images within current contestations surrounding global financial inclusion strategies, to show how these photos construct particular representations of microfinance that legitimize CGAP's minimalist, commercially‐driven model. The production of the need for large‐scale financial inclusion is key to this model, which is depicted through gendered representations of microfinance beneficiaries. On the one hand, the CGAP photos present a shift from stereotypical images of female micro‐entrepreneurs in traditional contexts to more complex images that disrupt such stereotypes while at the same time reinforcing other assumptions about microfinance. On the other, they bring men back into the picture as worthy microfinance recipients. While contributing to pluralist representations that valorize photography in developing countries, the CGAP microfinance photo contest is ultimately unable to portray the complexities and contradictions of financial inclusion interventions.
Gender for the 99 per cent (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Lindisfarne Nancy , Neale Jonathan
Published: October 2013

This article looks at the ways elite actors – men and women – try to reinforce gender inequality in order to justify class inequality. In class societies, elites try to naturalize inequality. They often use race or religion, but they always use gender. Gender buttresses class inequality so well because of the way it is embodied – it brings inequality into the most intimate, treasured and loving parts of our lives.
Ruins of hope in a Kyrgyz post‐industrial wasteland (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Pelkmans Mathijs
Published: October 2013

When people find themselves in dire situations, they use their imagination to transcend space and time. Forward‐projected hope and backward‐looking nostalgia are usually juxtaposed for their different temporal orientations and their different roles in social action. This article examines how this plays out in a former mining town in post‐Soviet Kyrgyzstan, whose inhabitants treasure the memories of Soviet modernity while dreaming of a future of economic abundance. Here, the sentiments of nostalgia and hope converge in their resonance with the ruins of empire, while their effects depend upon concealing the fragility of utopian visions.
A thousand Nagdis (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Gold Ann Grodzins , Gujar Bhoju Ram
Published: October 2013

A tributary of the Banas, the Nagdi River flows through the old market town of Jahazpur in Bhilwara District, Rajasthan. Unlike India's major sacred waterways such as the Ganga and the Yamuna which have the status of goddesses, the Nagdi was never deified. However, it figures in Jahazpur's origin legend, reaching back to the epic Mahabharata. Due to a complex convergence of conditions unique to this place but resonant with ecological tragedies the world over, the Nagdi's flow has dwindled and its waters are badly polluted. Everyone in Jahazpur with whom the authors spoke during fieldwork in 2010–11 mourned the end of their river. Once proud of the Nagdi's beauty and miraculous properties, Jahazpur residents were aware of having lost an important part of their environmental and cultural heritage. This article explores the complex causalities of the Nagdi's deterioration and emergent possibilities for its restoration.
Structure and dynamic behavior of Toll‐like receptor 2 subfamily triggered by malarial glycosylphosphatidylinositols of Plasmodium falciparum
Authors: Durai Prasannavenkatesh , Govindaraj Rajiv Gandhi , Choi Sangdun
Published: October 2013

Proinflammatory responses by Toll‐like receptors (TLRs) to malaria infection are considered to be a significant factor in suppressing pathogen growth and in disease control. The key protozoan parasite Plasmodium falciparum causes malaria through glycosylphosphatidylinositols (GPIs), which induce the host immune response mainly via TLR2 signalling. Experimental studies have suggested that malarial GPIs from P. falciparum are recognized by the TLR2 subfamily. However, the interaction site and their involvement in the activation mechanism are still unknown. A better understanding of the detailed structure of the TLR–GPI interaction is important for the design of more effective anti‐malarial therapeutics. We used a molecular docking method to predict the binding regions of malarial GPIs with the TLR2 subfamily members. We also employed molecular dynamics simulations and principal component analysis to understand ligand‐induced conformational changes of the TLR2 subfamily. We observed the expected structural changes upon ligand binding, and significant movements were found in loop regions located in the ligand‐binding site of the TLR2 subfamily. We further propose that the binding modes of malarial GPIs are similar to lipopeptides, and that the lipid portions of the ligands could play an essential role in selective dimerization of the TLR2 subfamily.
Reading Literary Fiction Improves Theory of Mind
Authors: Kidd David Comer , Castano Emanuele
Published: October 2013

A Good Read

Theory of Mind is the human capacity to comprehend that other people hold beliefs and desires and that these may differ from one's own beliefs and desires. The currently predominant view is that literary fiction—often described as narratives that focus on in-depth portrayals of subjects' inner feelings and thoughts—can be linked to theory of mind processes, especially those that are involved in the understanding or simulation of the affective characteristics of the subjects.
Kidd and Castano
(p.
377
, published online 3 October) provide experimental evidence that reading passages of literary fiction, in comparison to nonfiction or popular fiction, does indeed enhance the reader's performance on theory of mind tasks.