bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
Authors: Kaneko Takakazu , Maita Hiroko , Hirakawa Hideki , Uchiike Nobukazu , Minamisawa Kiwamu , Watanabe Akiko , Sato Shusei
Published: October 2011

The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
Skyline Query Processing in Sensor Network Based on Data Centric Storage
Authors: Song Seokil , Kwak Yunsik , Lee Seokhee
Published: October 2011

Data centric storages for sensor networks have been proposed to efficiently process multi-dimensional range queries as well as exact matches. Usually, a sensor network does not process only one type of the query, but processes various types of queries such as range queries, exact matches and skyline queries. Therefore, a sensor network based on a data centric storage for range queries and exact matches should process skyline queries efficiently. However, existing algorithms for skyline queries have not considered the features of data centric storages. Some of the data centric storages store similar data in sensor nodes that are placed on geographically similar locations. Consequently, all data are ordered in a sensor network. In this paper, we propose a new skyline query processing algorithm that exploits the above features of data centric storages.
Partial defoliation and hydraulic integration in Ocimum basilicum (Lamiaceae): Testing a model for sectored xylem flow using 15 N labeling
Authors: Thorn Alexandra M. , Orians Colin M.
Published: October 2011

• Premise of the study: Xylem sectoriality limits nutrient translocation throughout the plant, which may constrain growth following partial defoliation by herbivores. To date, the implications for nutrient allocation have not been assessed, and sectoriality studies lack a modeling framework for relating intersector transport to the hydraulic properties of the stem.

• Methods: We present an Ohm's law model for sectoriality of xylem transport in basil (Ocimum basilicum), which we parameterized and tested using hydroponically grown split‐root basil, pruned to two branches. To evaluate xylem resistance, we forced KCl solution through excised stems along either direct or indirect pathways. To examine the effect of partial defoliation on nutrient allocation, we applied 15N‐NO3 to one half of the root system after one of three defoliation treatments: uniform, orthostichous to label, or opposite the label.

• Key results: In support of our model, we found a tight correlation between total water uptake and total leaf area and between the actual and predicted proportions of water taken up from the labeled container. Significantly more 15N accumulated in orthostichous than in opposite sector leaves for the uniform and opposite defoliation treatments, but not for the orthostichous defoliation treatment. Across individuals, 15N distribution varied as predicted by the model, but there was generally 10% more 15N crossover than predicted.

• Conclusions: These results support our model and suggest high potential integration for O. basilicum. The fact that our model consistently underestimated the rate of crossover suggests that other mechanisms are also in play. Future research should evaluate possible mechanisms for this mixing, including the role of transporters in specialized transfer cells.
Annular Pancreas Intra Operatively Discovered: A Case Report
Authors: Mzoughi Zeineb , Sadri Ben Abid , Nizar Miloudi , Hassen Hentati , Nafaa Arfa , Taher Khalfallah
Published: October 2011

Annular pancreas is a rare congenital abnormality. This entity can rarely be symptomatic. Patients can present with gastrointestinal obstruction or acute pancreatitis. We report a case with a rich iconography, of an annular pancreas discovered intraoperatively. A 46- year-old woman was operated with the diagnosis of acute cholecystitis with common bile duct stones. At operation, a strip of pancreatic tissue (2 cm) completely encircled the second duodenum. Open cholecytectomy with choledocotomy and stones extractionwas done. Postoperatively, she developed an acute pancreatitis. The post-operative cholangiography showed the annular duct surrounding the second duodenum. Annular pancreas is rare. Symptoms may occur in newborn children. In adults, annular pancreas discovering is radiological or intra operatively.
Comparison of vaginal hysterectomy and tension-free vaginal mesh surgery for pelvic organ prolapsus: review of the first 20 operations performed by a first-time surgeon
Authors: Kanasaki Haruhiko , Oride Aki , Miyazaki Kohji
Published: October 2011

Objective. To review and compare the first 20 cases of vaginal hysterectomy (VH) and tension-free vaginal mesh (TVM) surgery for pelvic organ prolapsus (POP) performed by a first-time surgeon. Method. Operation time, anesthesia time, intraoperative bleeding volume and number of postoperative days in hospital were compared among the first 20 patients who underwent VH surgery or TVM surgery. Results. Operation time was 113.65±29.44 min in the VH group and 88.70±22.65 min in the TVM group, with the latter being significantly shorter. Anesthesia time was also significantly shorter in the TVM group. Intraoperative bleeding volume was ≤30 mL in 1 patient in the VH group, while the mean of the remaining 19 patients was 133.68±83.81 mL. In the TVM group, 14 patients had bleeding volumes of ≤30 mL, with the mean among the remaining 6 patients being 44.67±24.67 mL. The mean number of postoperative days in hospital was 13.3±3.6 days in the VH group and 5.6±2.64 days in the TVM group. When the first 20 patients treated by each surgical technique were divided into the first 10 and second 10 cases, operation and anesthesia times were significantly shortened in the second 10 cases compared with the first 10 cases in the VH group, but no significant differences were observed in the TVM group. Conclusion. TVM surgery should be considered as a first-line treatment for patients with POP since it is relatively easy to perform compared with conventional operations. Surgeons intending to perform TVM surgery, however, should have a full understanding of pelvic anatomy and POP status and receive instruction from experienced surgeons before progressing to practical training.
Obstetric fistula repair: a guide to patient selection
Authors: Umoiyoho Aniefiok J. , Inyang-Etoh Emmanuel C.
Published: October 2011

Objective. The World Health Organization has advocated for the classification of obstetric fistula into simple and complex cases. This study set out to design a guide to patient selection to facilitate the attainment of this goal. Materials and Methods. Associated risk factors were identified and analyzed among a cross section of women who had complex obstetric vesicovaginal fistulas. Results. The risk factors that were identified to affect significantly the prospect of cure following repair were large size of the fistula greater than 4 cm, associated urethral loss and adherence of the fistula to the pubic bone. Others were three or more previous attempts at repair, moderate to severe degree of scarring at the fistula margin, combined vesicovaginal and rectovaginal fistulas and the proximity of the fistula margin to the ureter. Each identified risk factor was allocated a score ranging from 0 to 4 depending on the adjudged capacity of the factor to affect the prospect of cure following repair.  Conclusions. Any case of vesicovaginal fistula with a total score of 4 or less using the proposed prognostic scoring system was adjudged suitable for repair by gynaecological or general surgeons, who have been trained on fistula repair with a significant prospect of success.
Numerical Continuation of Resonances and Bound States in Coupled Channel Schrödinger Equations
Authors: Kłosiewicz Przemysław , Broeckhove Jan , Vanroose Wim
Published: October 2011

In this contribution, we introduce numerical continuation methods and bifurcation theory, techniques which find their roots in the study of dynamical systems, to the problem of tracing the parameter dependence of bound and resonant states of the quantum mechanical Schrödinger equation. We extend previous work on the subject [1] to systems of coupled equations.

Bound and resonant states of the Schrödinger equation can be determined through the poles of the S-matrix, a quantity that can be derived from the asymptotic form of the wave function. We introduce a regularization procedure that essentially transforms the S-matrix into its inverse and improves its smoothness properties, thus making it amenable to numerical continuation. This allows us to automate the process of tracking bound and resonant states when parameters in the Schrödinger equation are varied. We have applied this approach to a number of model problems with satisfying results.
A Low Frequency Model for Acoustic Propagation in a 2D Flow Duct: Numerical Computation
Authors: Joubert Lauris , Joly Patrick
Published: October 2011

In this paper we study a low frequency model for acoustic propagation in a 2D flow duct. For some Mach profile flow, we are able to give a well-posedness theorem. Its proof relies on a quasi-explicit expression of the solution which provides us an efficient numerical method. We give and comment numerical results for particular linear, tangent and quadratic profiles. Finally, we give a numerical validation of our asymptotic model.
TE Mode Mixing Dynamics in Curved Multimode Optical Waveguides
Authors: Perrey-Debain Emmanuel , Abrahams I. David
Published: October 2011

Propagation of light through curved graded index optical waveguides supporting an arbitrary high number of modes is investigated. The discussion is restricted to optical wave fields which are well confined within the core region and losses through radiation are neglected. Using coupled mode theory formalism, two new forms for the propagation kernel for the transverse electric (TE) wave as it travels along a curved two-dimensional waveguide are presented. One form, involving the notion of “bend” modes, is shown to be attractive from a computational point of view as it allows an efficient numerical evaluation of the optical field for sharply bent waveguides.
Asymptotics for Helmholtz and Maxwell Solutions in 3-D Open Waveguides
Authors: Jerez-Hanckes Carlos , Nédélec Jean-Claude
Published: October 2011

We extend classic Sommerfeld and Silver-Müller radiation conditions for bounded scatterers to acoustic and electromagnetic fields propagating over three isotropic homogeneous layers in three dimensions. If X= (x1,x2,x3)ϵℝ3, with x3 denoting the direction orthogonal to the layers, standard conditions only hold for the outer layers in the region ∣x3∣ > ∣∣x∣γ, for γϵ(1/4,1/2) and x large. For ∣x3∣ < ∣∣x∣∣γ and inside the slab, asymptotic behavior depends on the presence of surface or guided modes given by the discrete spectrum of the associated operator.
Bleaching of the giant barrel sponge Xestospongia muta in the Florida Keys
Authors: McMurray Steven E. , Blum James E. , Leichter James J. , Pawlik Joseph R.
Published: October 2011

The giant barrel sponge Xestospongia muta is now the dominant habitat‐forming organism on many Caribbean coral reefs and has been observed to undergo cycles of bleaching similar to those seen for reef‐building corals. We examined bleaching of X. muta at 15‐m, 20‐m, and 30‐m depths over 2000–2005 on Conch Reef, Key Largo, Florida, to determine the spatial and temporal patterns of bleaching, whether bleaching affected sponge mortality, and whether there was a relationship between bleaching and seawater temperatures. Bleaching increased significantly with depth and was greater in autumn than spring, but the response was not uniform across the sponge population. Bleaching of X. muta did not result in sponge mortality, corroborating the conclusion that cyanobacterial symbionts of the sponge provide little or no benefit to the host. There was greater sponge bleaching with higher minimum daily seawater temperature anomalies within 30 d of surveys in the spring. For both the spring and autumn, there was greater bleaching with a higher number of positive 0.5°C daily anomalies within 14 d before surveys. Anomalously warm seawater temperatures fail to completely explain the variability of the observed bleaching response, however, and additional work would be required to conclusively determine whether a causal relationship between bleaching and temperature exists. As has been described for corals, bleaching of X. muta is likely a complex response that may be affected by multiple factors, including light availability and differences in bleaching susceptibility among Synechococcus symbionts.
Fluvial dynamics of dissolved and particulate organic carbon during periodic discharge events in a steep tropical rainforest catchment
Authors: Bass Adrian M. , Bird Michael I. , Liddell Michael J. , Nelson Paul N.
Published: October 2011

In small catchments with rapid flood pulses, detailed temporal data are essential because high‐discharge events can be measured in hours and days, rather than weeks and months. Using high‐resolution (15 min) sampling, we studied the dynamics of aquatic dissolved and particulate organic carbon (DOC and POC) export through episodic discharge events in a small pristine rainforest catchment in northeast Australia between November 2009 and March 2010. High temporal resolution using this instrumentation requires extensive calibration with concurrent field sampling. The concentration of DOC and POC peaked during times of high stream discharge, reflecting an increased mobilization of soil‐water carbon stocks. DOC was the major form of organic carbon in the stream (< 70% of the total carbon export). The majority of total organic carbon exported from the catchment (84%) occurred during significant discharge events (discharge > 50 L s−1), which occurred only 9% of the time. Export of DOC and POC totaled 195 and 68 kg km−2 month−1, respectively, with a DOC : POC ratio of 2.9 ± 0.9. If this subcatchment was sampled at weekly intervals the lateral export of carbon would have been underestimated by between 49% and 78% for DOC and POC, respectively. Preliminary δ13C and molar C : N values of the dissolved and particulate matter suggest that during discharge events, less microbially processed material from the upper soil layers dominated organic matter export, with the opposite being true in nonflood conditions. Not only will the quantities of organic matter exported change in different discharge conditions, but the source and quality may also shift. This study reveals that a field‐portable instrument for DOC and POC quantification can yield robust, high‐temporal‐resolution carbon budget estimates, though detailed, site‐specific calibration is essential.
Crenarchaeol tracks winter blooms of ammonia‐oxidizing Thaumarchaeota in the coastal North Sea
Authors: Pitcher Angela , Wuchter Cornelia , Siedenberg Kathi , Schouten Stefan , Sinninghe Damsté Jaap S.
Published: October 2011

We followed the abundance and distribution of ammonia‐oxidizing Archaea (AOA) in the North Sea from April 2003 to February 2005 and from October 2007 to March 2008 by quantification of archaeal genes and core glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids in suspended particulate matter, to determine whether their abundance in the North Sea is seasonal. GDGT and gene abundance increased during winters and was low during the summer. Crenarchaeol—a GDGT specific to AOA—was a major fraction of the GDGTs and varied in concert with AOA gene abundance, indicating that AOA are the predominant source of crenarchaeol. The presence of crenarchaeol‐based intact polar lipids (IPLs) confirmed that the GDGTs recovered were derived from living AOA, as IPLs are rapidly degraded upon cell senescence and thus their occurrence represents living biomass more robustly than their fossil (i.e., core GDGT) counterparts. Dark incubations of North Sea water sampled during the 2007–2008 seasonal cycle with 13C‐labeled bicarbonate revealed incorporation of inorganic carbon into IPL‐derived GDGTs, directly showing autotrophic production of Thaumarchaeota biomass during the winter. Inhibition of 13C uptake by nitrification inhibitors confirmed that ammonia oxidation was the main source of energy for carbon fixation. Winter blooms of planktonic AOA in the North Sea were recurrent and predictable, occurring annually between November and February, emphasizing the potential importance of AOA in nitrogen cycling in the North Sea.
The land‐use legacy effect: Adding temporal context to lake chemistry
Authors: Martin Sherry L. , Hayes Daniel B. , Rutledge Daniel T. , Hyndman David W.
Published: October 2011

We investigated land use and land cover (LULC) effects, i.e., effects that perpetuate beyond an expected or perceived temporal endpoint, on the chemistry of 35 lakes in the Huron River Watershed, Michigan. Temporal changes in five time steps of LULC were represented by principal components, which were entered hierarchically into a multiple regression to predict water chemistry. We compared model fit using Akaike weights, and model predictive ability using R2, for models representing LULC from a single time up to models that included LULC from all five time steps. The regressions using only the most recent LULC provided the best fit for phosphorus species, but legacy models provided a better fit for all nine other lake water characteristics. Models for all species of nitrogen, calcium, silica, and sulfate showed an intermediate legacy effect and incorporated some historic LULC. Models for conservative ions showed the longest legacy effect, incorporating all five time steps, and had the highest explanatory power of all water chemistry characteristics in our study. Legacy timescales are likely influenced by biological reactivity: highly reactive elements had relatively short legacy timescales and conservative ions had the longest legacy timescales.
The Morning NO x maximum in the forest atmosphere boundary layer
Authors: Alaghmand M. , Shepson P. B. , Starn T. K. , Jobson B. T. , Wallace H. W. , Carroll M. A. , Bertman S. B. , Lamb B. , Edburg S. L. , Zhou X. , Apel E. , Riemer D. , Stevens P. , Keutsch F.
Published: October 2011

Abstract. During the 1998, 2000, 2001, 2008, and 2009 summer intensives of the Program for Research on Oxidants: PHotochemistry, Emissions and Transport (PROPHET), ambient measurement of nitrogen oxides (NO + NO2 = NOx) were conducted. NO and NOx mole fractions displayed a diurnal pattern with NOx frequently highest in early morning. This pattern has often been observed in other rural areas. In this paper, we discuss the potential sources and contributing factors of the frequently observed morning pulse of NOx. Of the possible potential contributing factors to the observed morning pulse of NO and NOx, we find that surface-layer transport and slow upward mixing from soil emissions, related to the thermodynamic stability in the nocturnal boundary layer (NBL) before its morning breakup are the largest contributors. The morning NOx peak can significantly impact boundary layer chemistry, e.g. through production of HONO on surfaces, and by increasing the importance of NO3 chemistry in the morning boundary layer.
Monitoring of inorganic ions, carbonaceous matter and mass in ambient aerosol particles with online and offline methods
Authors: Timonen H. , Aurela M. , Saarnio K. , Frey A. , Saarikoski S. , Teinilä K. , Kulmala M. , Hillamo R.
Published: October 2011

Abstract. Year-long high timeresolution measurements of major chemical components in atmospheric sub-micrometer particles were conducted at an urban background station in Finland 2006–2007. Ions were analyzed using a particle-into-liquid sampler combined with an ion chromatograph (PILS-IC), organic and elemental carbon (OC and EC) by using a semicontinuos OC/EC aerosol carbon analyzer (RT-OCEC), and PM2.5 mass with a tapered element oscillating microbalance (TEOM). Long time series provides information on differences between the used measurement techniques as well as information about the diurnal and seasonal changes. Chemical mass closure was constructed by comparing the identified aerosol mass with the measured PM2.5. The sum of all components measured online (ions, particulate organic matter (POM), EC) represented only 65% of the total PM2.5 mass. The difference can be explained by the difference in cutoff sizes (PM1 for online measurements, PM2.5 for total mass) and by evaporation of the semivolatile/volatile components. In general, some differences in results were observed when the results of the continuous/semicontinuous instruments were compared with those of the conventional filter samplings. For non-volatile compounds, like sulfate and potassium, correlation between the filter samples and the PILS was good but greater differences were observed for the semivolatile compounds like nitrate and ammonium. For OC the results of the RT-OCEC were on average 10% larger than those of the filters. When compared to filter measurements, high resolution measurements provide important data on short pollution plumes as well as on diurnal changes. Clear seasonal and diurnal cycles were observed for nitrate and EC.
Suprathermal electron acceleration during reconnection onset in the magnetotail
Authors: Vaivads A. , Retinò A. , Khotyaintsev Yu. V. , André M.
Published: October 2011

Abstract. We study one event of reconnection onset associated to a small substorm on 27 September 2006 by using Cluster observations at inter-spacecraft separation of about 10 000 km. We focus on the acceleration of suprathermal electrons during different stages of reconnection. We show that several distinct stages of acceleration occur: (1) moderate acceleration during reconnection of pre-existing plasma sheet flux tubes, (2) stronger acceleration during reconnection of lobe flux tubes, (3) production of the most energetic electrons within dipolarization fronts (magnetic pile-up regions). The strongest acceleration is reached at the location of Bz maxima inside the magnetic pile-up region where the reconnection jet stops. Very strong localized dawn-dusk electric field are observed within the magnetic pile-up regions and are associated to most of the magnetic flux transport.
Daily CO2 partial pressure and CO2 outgassing in the upper Yangtze River basin: a case study of Longchuanjiang, China
Authors: Li S. Y. , Lu X. X. , He M. , Zhou Y. , Li L. , Ziegler A. D.
Published: October 2011

Abstract. Rivers have been under sampled to establish them as sinks or sources of the atmospheric carbon oxide (CO2). Such poor coverage is well known for tropical and sub-tropical, particularly monsoon driven rivers. An unprecedented high-temporal-resolution (daily) sampling during July 2008–August 2009 were conducted from the Longchuanjiang River of the upper Yangtze basin, a subtropical monsoon river in China to reveal the daily-to-seasonal dynamics of the partial pressure of CO2 (pCO2) and CO2 degassing flux from the river. The pCO2 levels were supersaturated in CO2 with respect to atmospheric equilibrium (380 μatm) during the entire survey period with obvious daily and seasonal variations, ranging from 450 to 63 000 μatm with an average of 3900 μatm. pCO2 values in the surface water in the wet season were relatively low, except flooding period in November, due to a dilution effect by heavy rainfall. However, both daily and monthly minimal and maximal pCO2 also occurred in this period. In contrast, the pCO2 levels in the dry season were much higher, mainly resulted from lower pH by anthropogenic activities. Net CO2 flux and pCO2 were strongly correlated with pH, but weakly with water temperature, dissolved inorganic carbon and water discharge, and uncorrelated with particulate nutrients and biogenic elements. The estimated water-to-air CO2 degassing flux in the Longchuanjiang River was about 110 mol m−2 yr−1, with the upper limit of 460 mol m−2 yr−1. Our study also indicated that among the total organic carbon remobilized through soil erosion, around 17% (11 400 t C yr−1) of was emitted to the atmosphere, 52% (35 000 t C yr−1) deposited in the river-reservoirs system and 31% (21 000 t C yr−1) exported further downstream. High spatial and temporal resolution of estimates of CO2 emission from the world large rivers is required due to that catchment characteristics and anthropogenic activities are extremely heterogeneous in space and time.
Failure of elastic‐plastic core–shell microcapsules under compression
Authors: Mercadé‐Prieto Ruben , Allen Rachael , Zhang Zhibing , York David , Preece Jon A. , Goodwin Ted E.
Published: October 2011

Characterization of the failure behavior of microcapsules is extremely important to control the release of their core actives by mechanical forces. The strain and stress of elastic‐plastic uninflated core–shell microcapsules at failure (rupture or bursting) has been determined using finite element modeling (FEM) and micromanipulation compression experiments. The ductile failure of polymeric microcapsules at high deformations is considered to occur when the maximum strain in the shell exceeds a critical strain, resulting in their rupture. FEM has been used to determine the maximum strains present in the capsule wall at different deformations for three types of shell material: elastic, elastic—perfectly plastic and elastic—perfectly plastic with strain hardening at large strains. The results obtained were used to determine the failure strain and stress of melamine‐formaldehyde microcapsules, with average population values of ∼0.48 and ∼350 MPa, respectively. Thus, the elastic‐plastic stress–strain relationship has been determined for the core–shell microcapsules tested. © 2011 American Institute of Chemical Engineers AIChE J, 2012
Inequity aversion in relation to effort and relationship quality in long‐tailed Macaques (Macaca fascicularis)
Authors: MASSEN JORG J. M. , VAN DEN BERG LISETTE M. , SPRUIJT BERRY M. , STERCK ELISABETH H. M.
Published: October 2011

Social animals may employ evolved implicit rules to maintain a balance between cooperation and competition. Inequity aversion (IA), the aversive reaction to an unequal distribution of resources, is considered such a rule to avoid exploitation between cooperating individuals. Recent studies have revealed the presence of IA in several nonhuman species. In addition, it has been shown that an effort is crucial for this behavior to occur in animals. Moreover, IA may well depend on the partner's identity. Although dominant individuals typically monopolize food, subordinate individuals obtain less preferred food and usually do not protest. Furthermore, “friends” may pay less attention to equity than “nonfriends.” We tested whether long‐tailed macaques show IA with different cost–benefit ratios. In addition, we determined whether IA depends on relationship quality (RQ). Dominant subjects expressed IA only when a small effort was required. At a very large effort, however, long‐tailed macaques did not show IA, possibly owing to bottom effects on the number of rewards they aim to receive. Moreover, and contrary to our predictions, an individual's inequity response was similar when tested with a “friend” or a “nonfriend.” Therefore, we conclude that long‐tailed macaques show IA only in conditions of moderate effort, yet that IA seems independent of RQ. Furthermore, IA may not be domain specific. Altogether, IA may be a trait present in all species that habitually cooperate, independent of their social organization.
Biologie‐orientierte Synthese (BIOS)
Authors: Wetzel Stefan , Bon Robin S. , Kumar Kamal , Waldmann Herbert
Published: October 2011

Welche Substanzklassen eignen sich am besten als Werkzeuge für chemisch‐biologische Forschung und als Inspiration für medizinalchemische Projekte? Der chemische Strukturraum ist riesig und kann durch Synthese von Verbindungen nicht vollständig exploriert werden. Daher werden Methoden benötigt, mit deren Hilfe die biologisch relevanten Anteile des chemischen Strukturraums identifiziert und kartiert werden können. Die mit diesen Methoden erzeugten Hypothesen inspirieren dann Syntheseprogramme, um die biologisch relevanten Teile des Strukturraumes mit realen Verbindungen zu füllen. Die Biologie‐orientierte Synthese baut darauf auf, dass die Evolution von Proteinen und Naturstoffen sich auf bestimmte Strukturklassen beschränkt. Sie nutzt eine hierarchische Klassifikation bioaktiver Substanzen, die auf Substrukturbeziehungen und der Art der biologischen Aktivität beruht. Mit dieser Methode werden Gerüststrukturen biologisch aktiver Substanzklassen ausgewählt und als Startpunkte für die Synthese von Substanzkollektionen mit fokussierter Diversität genutzt. Scaffold Hunter, ein intuitiv zugängliches und hochgradig interaktives Computerprogramm, ermöglicht die Navigation im chemischen Strukturraum. In Bibliotheken niedermolekularer Substanzen, die nach dem BIOS‐Konzept synthetisiert wurden, ist biologische Aktivität oft angereichert. Sie ermöglichen die Untersuchung komplexer biologischer Phänomene durch direkte Perturbation und können darüber hinaus auch als Inspiration in der Medikamentenentwicklung dienen.
LiClO4 salt concentration effect on the properties of PVC‐modified low molecular weight LENR50‐based solid polymer electrolyte
Authors: Rahman M. Y. A. , Ahmad A. , Lee T. K. , Farina Y. , Dahlan H. M.
Published: October 2011

A work was carried out on a solid polymeric electrolyte system comprising blends of poly (vinyl chloride) and liquid 50% epoxidized natural rubber (LENR50) as a polymer host with LiClO4 as a salt and prepared by solution casting technique. In this paper, the main study was the effect of LiClO4 salt concentration on the electrolyte properties. The effect of the salt on the electrolyte properties was characterized and analyzed with impedance spectroscopy (EIS), X‐ray diffraction (XRD), differential scanning calorimeter (DSC), and scanning electron microscopy (SEM). The EIS result showed that highest ionic conductivity was obtained at 30 wt % salt with a value of 2.3 × 10−8 S cm−1. The XRD results revealed that the LiClO4 salt was fully complexed within the polymer host as no sharp peaks were observed. However, above 30 wt % of salt, some sharp peaks were observed. This phenomenon was caused by the association of ions. Meanwhile, DSC analysis showed that Tg increased as the salt content increased. This implied that LiClO4 salt had interaction with polymer host by forming coordination bond. The morphologies' studies showed that good homogeneity and compatibility of the electrolyte were achieved. Upon the addition of the salt, formation of micropores occurred. It was noted that micropores which aid in mobility of ions in the electrolyte system has increased the ionic conductivity. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Effect of phenol functionalization of carbon nanotubes on properties of natural rubber nanocomposites
Authors: Thomas P. Selvin , Abdullateef Adedigba A. , Al‐Harthi Mamdouh A. , Basfar A. A. , Bandyopadhyay Sri , Atieh Muataz A. , De S. K.
Published: October 2011

This paper reports the results of studies on the effect of phenol functionalization of carbon nanotubes (CNTs) on the mechanical and dynamic mechanical properties of natural rubber (NR) composites. Fourier transform infrared spectrometry (FTIR) indicates characteristic peaks for ether and aromatic rings in the case of phenol functionalized CNT. Although differential scanning calorimetric (DSC) studies show no changes in the glass‐rubber transition temperature (Tg) of NR in the nanocomposites due to surface modification of CNT, dynamic mechanical studies show marginal shifting of Tg to higher temperature, the effect being pronounced in the case of functionalized CNT. Stress‐strain plots suggest an optimum loading of 5 phr CNT in NR formulations and the phenolic functionalization of CNT does not affect significantly the stress‐strain properties of the NR nanocomposites. The storage moduli register an increase in the presence of CNT and this increase is greater in the case of functionalized CNT. Loss tangent showed a decrease in the presence of CNT, and the effect is more pronounced in the case of phenol functionalized CNT. Transmission electron microscopy (TEM) reveals that phenol functionalization causes improvement in dispersion of CNT in NR matrix. This is corroborated by the increase in electrical resistivity in the case of phenol functionalized CNT/NR composites. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Synthesis of full and semi Interpenetrating hydrogel from polyvinyl alcohol and poly (acrylic acid‐co‐hydroxyethylmethacrylate) copolymer: Study of swelling behavior, network parameters, and dye uptake properties
Authors: Mandal Bidyadhar , Ray Samit Kumar , Bhattacharyya Ruma
Published: October 2011

Semi and full interpenetrating network (IPN) hydrogels were synthesized by allowing free radical copolymerization of acrylic acid (AA) and hydroxyethyl methacrylate (HEMA) in the matrix of polyvinyl alcohol (PVOH). Accordingly, four different semi IPN hydrogels were prepared with PVOH: copolymer mass ratio of 1 : 1, 1 : 0.75, 1 : 0.5, and 1 : 0.25. These hydrogels were designated as SEMIIPN1, SEMIIPN2, SEMIIPN3, and SEMIIPN4, respectively. In all of these SEMIIPN, after polymerization PVOH was crosslinked with 2 mass % glutaraldehyde to form the semi IPN structure. In a similar way, sequential full IPN were prepared from PVOH and copolymer of AA and HEMA (designated as PAAHEMA) with same composition except in this case apart from crosslinking of PVOH by 2 mass % glutaraldehyde the PAAHEMA copolymer was further crosslinked with N,N′‐methylenebisacrylamide (NMBA) to produce four full IPN hydrogels designated as FULLIPN1, FULLIPN2, FULLIPN3, and FULLIPN4. All of these semi and full IPN type hydrogels were characterized by carboxylic %, FTIR, UV, DTA‐TGA, XRD, SEM, and mechanical properties. The network parameters, swelling and diffusion characteristics of these hydrogels were also studied. The performance of these semi and full IPNs were compared in terms of their relative abilities for removing varied concentration of rhodamine B (RB) and methyl Violet (MV) dyes from water. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Mild Synthetic Approach to Novel Indole‐1‐Carbinols and Preliminary Evaluation of Their Cytotoxicity in Hepatocarcinoma Cells
Authors: Zedda Gloria , Simbula Gabriella , Begala Michela , Pibiri Monica , Floris Costantino , Casu Mariano , Casu Laura , Tocco Graziella
Published: October 2011

A mild and versatile method for the synthesis of some novel indole‐1‐carbinols has been developed via one‐pot reaction of indoles and paraformaldehyde in the presence of an excess of CaO, MgO, ZnO or TiO2. The solvent‐free reaction provided all the indole derivatives in moderate to good yields and short reaction times. Moreover, the effect of some selected indole‐1‐carbinols on cell proliferation of the hepatoma cell line FaO was evaluated.
Using structural information and citation evidence to detect significant plagiarism cases in scientific publications
Authors: Alzahrani Salha , Palade Vasile , Salim Naomie , Abraham Ajith
Published: October 2011

In plagiarism detection (PD) systems, two important problems should be considered: the problem of retrieving candidate documents that are globally similar to a document q under investigation, and the problem of side‐by‐side comparison of q and its candidates to pinpoint plagiarized fragments in detail. In this article, the authors investigate the usage of structural information of scientific publications in both problems, and the consideration of citation evidence in the second problem. Three statistical measures namely Inverse Generic Class Frequency, Spread, and Depth are introduced to assign a degree of importance (i.e., weight) to structural components in scientific articles. A term‐weighting scheme is adjusted to incorporate component‐weight factors, which is used to improve the retrieval of potential sources of plagiarism. A plagiarism screening process is applied based on a measure of resemblance, in which component‐weight factors are exploited to ignore less or nonsignificant plagiarism cases. Using the notion of citation evidence, parts with proper citation evidence are excluded, and remaining cases are suspected and used to calculate the similarity index. The authors compare their approach to two flat‐based baselines, TF‐IDF weighting with a Cosine coefficient, and shingling with a Jaccard coefficient. In both baselines, they use different comparison units with overlapping measures for plagiarism screening. They conducted extensive experiments using a dataset of 15,412 documents divided into 8,657 source publications and 6,755 suspicious queries, which included 18,147 plagiarism cases inserted automatically. Component‐weight factors are assessed using precision, recall, and F‐measure averaged over a 10‐fold cross‐validation and compared using the ANOVA statistical test. Results from structural‐based candidate retrieval and plagiarism detection are evaluated statistically against the flat baselines using paired‐t tests on 10‐fold cross‐validation runs, which demonstrate the efficacy achieved by the proposed framework. An empirical study on the system's response shows that structural information, unlike existing plagiarism detectors, helps to flag significant plagiarism cases, improve the similarity index, and provide human‐like plagiarism screening results.
Spectral classification of Pleiades brown dwarf candidates
Authors: Seeiger M. , Neuhäuser R. , Eisenbeiss T.
Published: October 2011

We report on the results of the spectroscopy of 10 objects previously classified as brown dwarf candidates via RIJHK colors by Eisenbeiss et al. (2009), who performed deep imaging observations on a ∼0.4 sq.deg. field at the edge of the Pleiades. We describe and judge on classification techniques in the region of M‐type stars. To classify and characterise the objects, visual and near infrared spectra have been obtained with VLT FORS and ISAAC. The spectral classification was performed using the shape of the spectra as well as spectral indices that are sensitive to the spectral type and luminosity class of M‐type stars and late M‐type brown dwarfs. Furthermore a spectrophotometric distance was calculated and compared the distance of the Pleiades to investigate the membership probability. As a second argument we analyzed the proper motion. The brown dwarf candidates were found not to be brown dwarfs, but late‐K to mid‐M‐type dwarf stars. Based on the obtained distance and tabulated proper motions we conclude that all objects are background dwarf stars (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Matrix Training for Generative Spelling in Children with Autism Spectrum Disorder
Authors: Tanji Takayuki , Noro Fumiyuki
Published: October 2011

Children with autism often have difficulty in generative learning. Effective training program for generative learning in these children is needed. In this study, we examined the effectiveness of matrix training for generative spelling in two children with autism spectrum disorder (ASD). Matrix training is a procedure in which stimuli used in teaching are arranged with overlapping within‐syllable units. After training with a Constructed‐Response Matching to Sample (CRMTS) with matrix training, both participants' generative spelling was assessed by CRMTS test using untrained combinations of characters. In this study, spoken syllables (auditory stimuli) are presented as the sample stimulus, and written characters (visual stimuli) are presented as comparison stimuli in CRMTS task. As a result, both participants showed generative spelling by matrix training, however, one of the two participants needed additional matrix training. The results discussed the effectiveness of matrix training as a procedure for teaching generative spelling and some issues to be conducted in applying this procedure for Japanese reading and spelling in children with ASD. Copyright © 2011 John Wiley & Sons, Ltd.
Sensitive spectrofluorimetric determination of tizanidine in pharmaceutical preparations, human plasma and urine through derivatization with dansyl chloride
Authors: Ulu Sevgi Tatar
Published: October 2011

A sensitive spectrofluorimetric method was developed for the determination of tizanidine in human plasma, urine and pharmaceutical preparations. The method is based on reaction of tizanidine with 1‐dimethylaminonaphthalene‐5‐sulphonyl chloride (dansyl chloride) in an alkaline medium to form a highly fluorescent derivative that was measured at 511 nm after excitation at 383 nm. The different experimental parameters affecting the fluorescence intensity of tizanidine was carefully studied and optimized. The fluorescence–concentration plots were rectilinear over the ranges 50–500 and 20–300 ng/mL for plasma and urine, respectively, detection limits of 1.81 and 0.54 ng/mL and quantification limits of 5.43 and 1.62 ng/mL for plasma and urine, respectively. The method presents good performance in terms of linearity, detection and quantification limits, precision, accuracy and specificity. The proposed method was successfully applied for the determination of tizanidine in pharmaceutical preparations. The results obtained were compared with a reference method, using t‐ and F‐tests. Copyright © 2011 John Wiley & Sons, Ltd.
Inulin stimulates phagocytosis of PMA‐treated THP‐1 macrophages by involvement of PI3‐kinases and MAP kinases
Authors: Nagahara Yukitoshi , Nagamori Taome , Tamegai Hidekazu , Hitokuwada Mami , Yoshimi Yoji , Ikekita Masahiko , Shinomiya Takahisa
Published: October 2011

Inulin is a polysaccharide that enhances various immune responses, mainly to T and B cells, natural killer cells, and macrophages in vivo and in vitro. Previous reports describe that inulin activates macrophages indirectly by affecting the alternative complement pathway. In this study, we examined the direct effect of inulin on PMA‐treated THP‐1 macrophages. Inulin treatment did not stimulate the proliferation of THP‐1 macrophages at all. However, inulin treatment significantly increased phagocytosis of the polystyrene beads without the influence of serum. Doses of around 1 mg/mL had the maximal effect, and significant progression of phagocytosis occurred at times treated over 6 h. Inulin augmented phagocytosis not only with polystyrene beads but also with apoptotic cancer cells. The inulin‐induced phagocytosis uptake was suppressed in Toll‐like receptor (TLR) 4 mutated C3H/HeJ mice peritoneal macrophages. Moreover, inulin‐induced THP‐1 macrophage TNF‐α secretion was inhibited using a blocking antibody specific to TLR4, suggesting that TLR4 is involved in the binding of inulin to macrophages. Furthermore, we used specific kinase inhibitors to assess the involvement of inulin‐induced phagocytosis and revealed that phosphoinositide 3‐kinase and mitogen‐activated protein kinase, especially p38, participated in phagocytosis. These results suggest that inulin affects macrophages directly by involving the TLR4 signaling pathway and stimulating phagocytosis for enhancing immunomodulation.
Compound toxicity screening and structure–activity relationship modeling in Escherichia coli
Authors: Planson Anne‐Gaëlle , Carbonell Pablo , Paillard Elodie , Pollet Nicolas , Faulon Jean‐Loup
Published: October 2011

Synthetic biology and metabolic engineering are used to develop new strategies for producing valuable compounds ranging from therapeutics to biofuels in engineered microorganisms. When developing methods for high‐titer production cells, toxicity is an important element to consider. Indeed the production rate can be limited due to toxic intermediates or accumulation of byproducts of the heterologous biosynthetic pathway of interest. Conversely, highly toxic molecules are desired when designing antimicrobials. Compound toxicity in bacteria plays a major role in metabolic engineering as well as in the development of new antibacterial agents. Here, we screened a diversified chemical library of 166 compounds for toxicity in Escherichia coli. The dataset was built using a clustering algorithm maximizing the chemical diversity in the library. The resulting assay data was used to develop a toxicity predictor that we used to assess the toxicity of metabolites throughout the metabolome. This new tool for predicting toxicity can thus be used for fine‐tuning heterologous expression and can be integrated in a computational‐framework for metabolic pathway design. Many structure–activity relationship tools have been developed for toxicology studies in eukaryotes [Valerio (2009), Toxicol Appl Pharmacol, 241(3): 356–370], however, to the best of our knowledge we present here the first E. coli toxicity prediction web server based on QSAR models (EcoliTox server: http://www.issb.genopole.fr/∼faulon/EcoliTox.php). Biotechnol. Bioeng. 2012; 109:846–850. © 2011 Wiley Periodicals, Inc.
The incorporation of the A2 protein to produce novel Qβ virus‐like particles using cell‐free protein synthesis
Authors: Smith Mark T. , Varner Chad T. , Bush Derek B. , Bundy Bradley C.
Published: October 2011

Virus‐like particles (VLPs) have been employed for a number of nanometric applications because they self‐assemble, exhibit a high degree of symmetry, and can be genetically and chemically modified. However, high symmetry does not allow for a single unique modification site on the VLP. Here, we demonstrate the co‐expression of the cytotoxic A2 protein and the coat protein of the bacteriophage Qβ to form a nearly monodispersed population of novel VLPs. Cell‐free protein synthesis allows for direct access and optimization of protein‐synthesis and VLP‐assembly. The A2 is shown to be incorporated at high efficiency, approaching a theoretical maximum of one A2 per VLP. This work demonstrates de novo production of a novel VLP, which contains a unique site that has the potential for future nanometric engineering applications. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2012
The right inferior phrenic artery: Path of its ascending branch at the vena caval foramen
Authors: Townend R.E. , McConnell P.
Published: October 2011

The ascending branch of the right inferior phrenic artery is generally understood to pass to the lateral side of the vena caval foramen, on the inferior surface of the diaphragm. A study of 16 cadavers shows that the artery may pass through the vena caval foramen to run on the superior surface of the diaphragm, before returning to the inferior surface by passing through the muscle of the diaphragm. Clin. Anat. 25:656–658, 2012. © 2011 Wiley Periodicals, Inc.