bluuebunny/crossref_metadata_2025 huggingface dataset:
Marshall receives Cryosphere Young Investigator Award
Authors: Sturm Matthew , Marshall Hans‐Peter
Published: June 2011

It gives me the greatest pleasure to introduce H. P. Marshall of Boise State University, winner of the 2010 Cryosphere Young Investigator Award. Marshall is currently an assistant professor, but I have known him since he was an undergraduate. Even back then, I might have guessed he would win this award. His research has extraordinary depth and breadth for one so new. He is the acknowledged master of the frequency modulated continuous wave (FMCW) radar for snow in the United States and is pioneering unique partnerings between snow geophysics and snow microstudies through the use of near‐infrared photography and micropenetrometry. He has worked all over the Arctic and the Rocky Mountain west and is perhaps the most capable and pleasant of companions during fieldwork. The data he is collecting now may soon inform us about how snow distributes over large areas, a topic that has eluded quantification up to now. Moreover, if he is successful in developing and fielding an accurate and practical airborne snow radar, his work is likely to revolutionize snow field studies. He is fully deserving of the 2010 Cryosphere Young Investigator Award, and I expect we will continue to see excellence from him in the future.
Research Spotlight: Dual‐dynamic approach improves soil water transport model
Authors: Schultz Colin
Published: June 2011

To simulate perfectly the flow of water through the ground, one would need to know the details of every pore, passage, and air pocket in the soil. To circumvent such daunting requirements, researchers simulate soil moisture transport as if the water were flowing through a series of cylindrical tubes, with the groundwater transport influenced by both gravity and pressure. This simplified representation holds up well when the soil is wet, but the analogy begins to break down when moisture levels drop. At very low moisture levels a dynamic nearly negligible at high flow rates begins to dominate: the adsorption of water onto soil particles. Water creates a thin film around individual grains of soil through molecular, ionicelectrostatic, and other attraction forces, but these interactions, while well known, are generally overlooked in models of soil moisture transport.
Research Spotlight: Aircraft measured oil evaporating from Gulf oil spill
Authors: Tretkoff Ernie
Published: June 2011

Following the Gulf of Mexico oil spill in April 2010, some hydrocarbons dissolved in the ocean, while other leaked hydrocarbons that did not dissolve evaporated into the atmosphere. Ryerson et al. describe airborne in situ measurements of the hydrocarbons in the atmosphere after the oil spill, during initial cleanup operations. By comparing the amounts of chemicals in the atmosphere with those in crude oil, they determined which compounds dissolved in the ocean and which evaporated; by measuring the rate at which the compounds reached the atmosphere, they could estimate that oil and gas were leaking into the Gulf at a rate of at least 32,600–47,700 barrels of fluid per day.
Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria
Authors: Bailey Jake V , Salman Verena , Rouse Gregory W , Schulz-Vogt Heide N , Levin Lisa A , Orphan Victoria J
Published: June 2011

We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.
The significance of nitrogen cost minimization in proteomes of marine microorganisms
Authors: Grzymski Joseph J , Dussaq Alex M
Published: June 2011

Marine microorganisms thrive under low levels of nitrogen (N). N cost minimization is a major selective pressure imprinted on open-ocean microorganism genomes. Here we show that amino-acid sequences from the open ocean are reduced in N, but increased in average mass compared with coastal-ocean microorganisms. Nutrient limitation exerts significant pressure on organisms supporting the trade-off between N cost minimization and increased average mass of amino acids that is a function of increased A+T codon usage. N cost minimization, especially of highly expressed proteins, reduces the total cellular N budget by 2.7–10%; this minimization in combination with reduction in genome size and cell size is an evolutionary adaptation to nutrient limitation. The biogeochemical and evolutionary precedent for these findings suggests that N limitation is a stronger selective force in the ocean than biosynthetic costs and is an important evolutionary strategy in resource-limited ecosystems.
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential
Authors: Klatt Christian G , Wood Jason M , Rusch Douglas B , Bateson Mary M , Hamamura Natsuko , Heidelberg John F , Grossman Arthur R , Bhaya Devaki , Cohan Frederick M , Kühl Michael , Bryant Donald A , Ward David M
Published: June 2011

Phototrophic microbial mat communities from 60 °C and 65 °C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B′, but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness.
Analysis of bacterial core communities in the central Baltic by comparative RNA–DNA-based fingerprinting provides links to structure–function relationships
Authors: Brettar Ingrid , Christen Richard , Höfle Manfred G
Published: June 2011

Understanding structure–function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.
Vitamin D in Adipose Tissue and Serum 25‐Hydroxyvitamin D After Roux‐en‐Y Gastric Bypass
Authors: Pramyothin Pornpoj , Biancuzzo Rachael M. , Lu Zhiren , Hess Donald T. , Apovian Caroline M. , Holick Michael F.
Published: June 2011

Vitamin D is stored in body fat. The purpose of this study was to determine vitamin D concentration in abdominal fat of obese patients who underwent roux‐en‐Y gastric bypass (RYGB), and to describe changes in serum 25‐hydroxyvitamin D (25(OH)D) levels in relation to loss of body fat. Subjects from a single clinic who were scheduled for RYGB were invited into the study. Abdominal subcutaneous, omental, and mesenteric fat were obtained at time of surgery. Adipose vitamin D2 and vitamin D3 concentrations were measured by high‐performance liquid chromatography (HPLC). Weight and serum 25(OH)D were assessed at baseline and every 3 months up to 1 year. Seventeen subjects were included, and fat samples were available from eleven. Total vitamin D content in subcutaneous abdominal fat was 297.2 ± 727.7 ng/g tissue, and a wide range was observed (4–2,470 ng/g). Both vitamin D2 and vitamin D3 were detected in some of the fat samples. At baseline, 25(OH)D was 23.1 ± 12.6 ng/ml. Average weight loss was 54.8 kg at 12 months, of which ∼40 kg was fat mass. Despite daily vitamin D intake of ≥2,500 IU throughout the study, no significant increase in serum 25(OH)D was observed, with mean serum concentration of 25(OH)D at 1 year of 26.2 ± 5.36 ng/ml (P = 0.58). We conclude that vitamin D in adipose tissue does not significantly contribute to serum 25(OH)D despite dramatic loss of fat mass after RYGB.
Longitudinal Associations Between Key Dietary Behaviors and Weight Gain Over Time: Transitions Through the Adolescent Years
Authors: Laska Melissa N. , Murray David M. , Lytle Leslie A. , Harnack Lisa J.
Published: June 2011

Previous studies have yielded inconsistent results when documenting the association between key dietary factors and adolescent weight change over time. The purpose of this study was to examine the extent to which changes in adolescent sugar‐sweetened beverage (SSB), diet soda, breakfast, and fast‐food consumption were associated with changes in BMI and percent body fat (PBF). This study analyzed data from a sample of 693 Minnesota adolescents followed over 2 years. Random coefficient models were used to examine the relationship between dietary intake and BMI and PBF and to separate cross‐sectional and longitudinal associations. Adjusting for total physical activity, total energy intake, puberty, race, socioeconomic status, and age, cross‐sectional findings indicated that for both males and females, breakfast consumption was significantly and inversely associated with BMI and PBF, and diet soda intake was significantly and positively associated with BMI and PBF among females. In longitudinal analyses, however, there were fewer significant associations. Among males there was evidence of a significant longitudinal association between SSB consumption and PBF; after adjustment for energy intake, an increase of one serving of SSB per day was associated with an increase of 0.7 units of PBF among males. This study adds to previous research through its methodological strengths, including adjustment for physical activity and energy intake assessed using state‐of‐the‐art methods (i.e., accelerometers and 24‐h dietary recalls), as well as its evaluation of both BMI and PBF. Additional research is needed to better understand the complex constellation of factors that contribute to adolescent weight gain over time.
A general strategy for the evolution of bond-forming enzymes using yeast display
Authors: Chen Irwin , Dorr Brent M. , Liu David R.
Published: June 2011

The ability to routinely generate efficient protein catalysts of bond-forming reactions chosen by researchers, rather than nature, is a long-standing goal of the molecular life sciences. Here, we describe a directed evolution strategy for enzymes that catalyze, in principle, any bond-forming reaction. The system integrates yeast display, enzyme-mediated bioconjugation, and fluorescence-activated cell sorting to isolate cells expressing proteins that catalyze the coupling of two substrates chosen by the researcher. We validated the system using model screens for
Staphylococcus aureus
sortase A–catalyzed transpeptidation activity, resulting in enrichment factors of 6,000-fold after a single round of screening. We applied the system to evolve sortase A for improved catalytic activity. After eight rounds of screening, we isolated variants of sortase A with up to a 140-fold increase in LPETG-coupling activity compared with the starting wild-type enzyme. An evolved sortase variant enabled much more efficient labeling of LPETG-tagged human CD154 expressed on the surface of HeLa cells compared with wild-type sortase. Because the method developed here does not rely on any particular screenable or selectable property of the substrates or product, it represents a powerful alternative to existing enzyme evolution methods.
Superbanana plateau resonance in the vicinity of the phase space boundary in tokamaks
Authors: Shaing K.C. , Tsai T.H. , Chu M.S. , Sun Y. , Sabbagh S.A.
Published: June 2011

A theory for the superbanana plateau resonance that occurs at the phase space boundary is presented to refine the comprehensive theory for neoclassical toroidal plasma viscosity in tokamaks. The results of the theory reproduce those of the standard superbanana plateau resonance theory when the resonance occurs away from the boundary. It shows that the strength of the superbanana plateau resonance weakens in the vicinity of the phase space boundary. It also indicates that it is important to know the resonance pitch angle parameter when comparing the results of the superbanana plateau resonance with those of the experiments. The theory is used to refine the kernel for the superbanana plateau resonance in the approximate expression for the neoclassical toroidal plasma viscosity.
Potential fluctuation associated with the energetic-particle-induced geodesic acoustic mode in the Large Helical Device
Authors: Ido T. , Shimizu A. , Nishiura M. , Nakamura S. , Kato S. , Nakano H. , Yoshimura Y. , Toi K. , Ida K. , Yoshinuma M. , Satake S. , Watanabe F. , Morita S. , Goto M. , Itoh K. , Kubo S. , Shimozuma T. , Igami H. , Takahashi H. , Yamada I. , Narihara K.
Published: June 2011

Geodesic acoustic modes (GAM) driven by energetic particles are observed in the Large Helical Device (LHD) by a heavy ion beam probe. The GAM localizes near the magnetic axis. It is confirmed that the energetic-particle-induced GAM is accompanied by an electrostatic potential fluctuation and radial electric field fluctuation. The amplitude of the potential fluctuation is several hundred volts, and it is much larger than the potential fluctuation associated with turbulence-induced GAMs observed in the edge region in tokamak plasmas. The energetic-particle-induced GAM modulates the amplitude of the density fluctuation in a high-frequency range. The observed GAM frequency is constant at the predicted GAM frequency in plasmas with reversed magnetic shear. On the other hand, it shifts upwards from the predicted GAM frequency in plasmas with monotonic magnetic shear.
Incorporation of in-plane interconnects to reflow bonding for electrical functionality
Authors: Moğulkoç B , Jansen H V , ter Brake H J M , Elwenspoek M C
Published: June 2011

Incorporation of in-plane electrical interconnects to reflow bonding is studied to provide electrical functionality to lab-on-a-chip or microfluidic devices. Reflow bonding is the packaging technology, in which glass tubes are joined to silicon substrates at elevated temperatures. The tubes are used to interface the silicon-based fluidic devices and are directly compatible with standard Swagelok® connectors. After the bonding, the electrically conductive lines will allow probing into the volume confined by the tube, where the fluidic device operates. Therefore methods for fabricating electrical interconnects that survive the bonding procedure at elevated temperature and do not alter the properties of the bond interface are investigated.
A single-mask thermal displacement sensor in MEMS
Authors: Krijnen B , Hogervorst R P , van Dijk J W , Engelen J B C , Woldering L A , Brouwer D M , Abelmann L , Soemers H M J R
Published: June 2011

This work presents a MEMS displacement sensor based on the conductive heat transfer of a resistively heated silicon structure towards an actuated stage parallel to the structure. This differential sensor can be easily incorporated into a silicon-on-insulator-based process, and fabricated within the same mask as electrostatic actuators and flexure-based stages. We discuss a lumped capacitance model to optimize the sensor sensitivity as a function of the doping concentration, the operating temperature, the heater length and width. We demonstrate various sensor designs. The typical sensor resolution is 2 nm within a bandwidth of 25 Hz at a full scale range of 110 µm.
Golgi localization of ERManI defines spatial separation of the mammalian glycoprotein quality control system
Authors: Pan Shujuan , Wang Shufang , Utama Budi , Huang Lu , Blok Neil , Estes Mary K. , Moremen Kelley W. , Sifers Richard N.
Published: June 2011

The Golgi complex has been implicated as a possible component of endoplasmic reticulum (ER) glycoprotein quality control, although the elucidation of its exact role is lacking. ERManI, a putative ER resident mannosidase, plays a rate-limiting role in generating a signal that targets misfolded N-linked glycoproteins for ER-associated degradation (ERAD). Herein we demonstrate that the endogenous human homologue predominantly resides in the Golgi complex, where it is subjected to O-glycosylation. To distinguish the intracellular site where the glycoprotein ERAD signal is generated, a COPI-binding motif was appended to the N terminus of the recombinant protein to facilitate its retrograde translocation back to the ER. Partial redistribution of the modified ERManI was observed along with an accelerated rate at which N-linked glycans of misfolded α1-antitrypsin variant NHK were trimmed. Despite these observations, the rate of NHK degradation was not accelerated, implicating the Golgi complex as the site for glycoprotein ERAD substrate tagging. Taken together, these data provide a potential mechanistic explanation for the spatial separation by which glycoprotein quality control components operate in mammalian cells.
The spindle checkpoint protein Mad2 regulates APC/C activity during prometaphase and metaphase of meiosis I inSaccharomyces cerevisiae
Authors: Tsuchiya Dai , Gonzalez Claire , Lacefield Soni
Published: June 2011

In many eukaryotes, disruption of the spindle checkpoint protein Mad2 results in an increase in meiosis I nondisjunction, suggesting that Mad2 has a conserved role in ensuring faithful chromosome segregation in meiosis. To characterize the meiotic function of Mad2, we analyzed individual budding yeast cells undergoing meiosis. We find that Mad2 sets the duration of meiosis I by regulating the activity of APCCdc20. In the absence of Mad2, most cells undergo both meiotic divisions, but securin, a substrate of the APC/C, is degraded prematurely, and prometaphase I/metaphase I is accelerated. Some mad2Δ cells have a misregulation of meiotic cell cycle events and undergo a single aberrant division in which sister chromatids separate. In these cells, both APCCdc20and APCAma1are prematurely active, and meiosis I and meiosis II events occur in a single meiotic division. We show that Mad2 indirectly regulates APCAma1activity by decreasing APCCdc20activity. We propose that Mad2 is an important meiotic cell cycle regulator that ensures the timely degradation of APC/C substrates and the proper orchestration of the meiotic divisions.
SEAL: a distributed short read mapping and duplicate removal tool
Authors: Pireddu Luca , Leo Simone , Zanetti Gianluigi
Published: June 2011

Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode.

Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/.

Contact:  luca.pireddu@crs4.it
JSBML: a flexible Java library for working with SBML
Authors: Dräger Andreas , Rodriguez Nicolas , Dumousseau Marine , Dörr Alexander , Wrzodek Clemens , Le Novère Nicolas , Zell Andreas , Hucka Michael
Published: June 2011

Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend.

Availability: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.

Contact:  jsbml-team@sbml.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
GeneNetWeaver:in silicobenchmark generation and performance profiling of network inference methods
Authors: Schaffter Thomas , Marbach Daniel , Floreano Dario
Published: June 2011

Motivation: Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks.

Results: Here, we describe a novel and comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community as an open-source software called GeneNetWeaver (GNW). In addition to the generation of detailed dynamical models of gene regulatory networks to be used as benchmarks, GNW provides a network motif analysis that reveals systematic prediction errors, thereby indicating potential ways of improving inference methods. The accuracy of network inference methods is evaluated using standard metrics such as precision-recall and receiver operating characteristic curves. We show how GNW can be used to assess the performance and identify the strengths and weaknesses of six inference methods. Furthermore, we used GNW to provide the international Dialogue for Reverse Engineering Assessments and Methods (DREAM) competition with three network inference challenges (DREAM3, DREAM4 and DREAM5).

Availability: GNW is available at http://gnw.sourceforge.net along with its Java source code, user manual and supporting data.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  dario.floreano@epfl.ch
Organizing Your Practice to Support Carers
Authors: Simon Chantal
Published: June 2011

Carers are more likely to have seen their GP recently than any other support professional. Therefore, it is vital for GPs within primary care teams to know how to identify and support carers in order to involve them in patient care and maintain the health of the carer, thus preserving the caregiving situation. This article explores ways to organize your practice so that carers can contribute to patient care and be supported in their role.
Human Subthalamic Neuron Spiking Exhibits Subtle Responses to Sedatives
Authors: MacIver M. Bruce , Bronte-Stewart Helen M. , Henderson Jaimie M. , Jaffe Richard A. , Brock-Utne John G.
Published: June 2011

Background

During deep brain stimulation implant surgery, microelectrode recordings are used to map the location of targeted neurons. The effects produced by propofol or remifentanil on discharge activity of subthalamic neurons were studied intraoperatively to determine whether they alter neuronal activity.

Methods

Microelectrode recordings from 11 neurons, each from individual patients, were discriminated and analyzed before and after administration of either propofol or remifentanil. Subthalamic neurons in rat brain slices were recorded in patch-clamp to investigate cellular level effects.

Results

Neurons discharged at 42 ± 9 spikes/s (mean ± SD) and showed a common pattern of inhibition that lasted 4.3 ms. Unique discharge profiles were evident for each neuron, seen using joint-interval analysis. Propofol (intravenous bolus 0.3 mg/kg) produced sedation, with minor effects on discharge activity (less than 2.0% change in frequency). A prolongation of recurrent inhibition was evident from joint-interval analysis, and propofol's effect peaked within 2 min, with recovery evident at 10 min. Subthalamic neurons recorded in rat brain slices exhibited inhibitory synaptic currents that were prolonged by propofol (155%) but appeared to lack tonic inhibitory currents. Propofol did not alter membrane potential, membrane resistance, current-evoked discharge, or holding current during voltage clamp. Remifentanil (0.05 mg/kg) had little effect on overall subthalamic neuron discharge activity and did not prolong recurrent inhibition.

Conclusions

These results help to characterize the circuit properties and feedback inhibition of subthalamic neurons and demonstrate that both propofol and remifentanil produce only minor alterations of subthalamic neuron discharge activity that should not interfere with deep brain stimulation implant surgery.
Effect of Head Elevation on Passive Upper Airway Collapsibility in Normal Subjects during Propofol Anesthesia
Authors: Kobayashi Masato , Ayuse Takao , Hoshino Yuko , Kurata Shinji , Moromugi Shunji , Schneider Hartmut , Kirkness Jason P. , Schwartz Alan R. , Oi Kumiko
Published: June 2011

Background

Head elevation can restore airway patency during anesthesia, although its effect may be offset by concomitant bite opening or accidental neck flexion. The aim of this study is to examine the effect of head elevation on the passive upper airway collapsibility during propofol anesthesia.

Method

Twenty male subjects were studied, randomized to one of two experimental groups: fixed-jaw or free-jaw. Propofol infusion was used for induction and to maintain blood at a constant target concentration between 1.5 and 2.0 μg/ml. Nasal mask pressure (PN) was intermittently reduced to evaluate the upper airway collapsibility (passive PCRIT) and upstream resistance (RUS) at each level of head elevation (0, 3, 6, and 9 cm). The authors measured the Frankfort plane (head flexion) and the mandible plane (jaw opening) angles at each level of head elevation. Analysis of variance was used to determine the effect of head elevation on PCRIT, head flexion, and jaw opening within each group.

Results

In both groups the Frankfort plane and mandible plane angles increased with head elevation (P < 0.05), although the mandible plane angle was smaller in the free-jaw group (i.e., increased jaw opening). In the fixed-jaw group, head elevation decreased upper airway collapsibility (PCRIT ~ -7 cm H₂O at greater than 6 cm elevation) compared with the baseline position (PCRIT ~ -3 cm H₂O at 0 cm elevation; P < 0.05).

Conclusion

: Elevating the head position by 6 cm while ensuring mouth closure (centric occlusion) produces substantial decreases in upper airway collapsibility and maintains upper airway patency during anesthesia.
Long‐term Follow‐up of Children With 6‐Thioguanine‐related Chronic Hepatoxicity Following Treatment for Acute Lymphoblastic Leukaemia
Authors: Rawat Dinesh , Gillett Peter M. , Devadason David , Wilson David C. , McKiernan Patrick J.
Published: June 2011

6‐Thioguanine (6‐TG) therapy in childhood acute lymphoblastic leukaemia results in chronic hepatotoxicity and portal hypertension. We report follow‐up data in a cohort of 10 children with acute lymphoblastic leukaemia and 6‐TG‐related hepatotoxicity described initially in 2006. Clinically significant portal hypertension was present in the majority of patients several years after cessation of 6‐TG treatment. These data reflect the natural history of noncirrhotic portal hypertension and emphasises the need to incorporate ongoing surveillance in the transition arrangement to adult services in this select group of patients.
Optimizing Early Nutritional Support Based on Recent Recommendations in VLBW Infants and Postnatal Growth Restriction
Authors: Senterre Thibault , Rigo Jacques
Published: June 2011

Objective:

The aim of this study was to evaluate postnatal growth up to discharge in very low birth weight infants after optimizing nutritional support based on recent nutritional recommendations.

Patients and Methods:

A prospective, nonrandomized, consecutive, and observational study in infants weighing <1250 g.

Results:

One hundred two infants were included during a 2‐year period (birth weight 1005 ± 157 g, gestational age 28.5 ± 1.9 weeks). First‐day nutritional intake was 38 ± 6 kcal/kg/day with 2.4 ± 0.3 g/kg/day of protein. Mean intake during the first week of life was 80 ± 14 kcal/kg/day with 3.2 ± 0.5 g/kg/day of protein. On average from birth to discharge, 122 ± 10 kcal/kg/day and 3.7 ± 0.2 g/kg/day of protein were administered. Postnatal weight loss was limited to the first 3 days of life, and birth weight was regained after 7 days in average. Catch‐up occurred after the second week in all groups of very low birth weight infants. Small‐for‐gestational age infants demonstrated an earlier and higher weight gain, allowing a rapid catch‐up growth. The same proportion of infants was small‐for‐gestational age at birth and at discharge (20%, P = 0.74).

Conclusions:

This study confirmed that the first week of life is a critical period to promote growth and that early nutrition from the first day of life is essential. Postnatal weight loss may be limited and subsequent growth may be optimized with a dramatic reduction of postnatal growth restriction.
Infection of hepatocytes with 17-D vaccine-strain yellow fever virus induces a strong pro-inflammatory host response
Authors: Woodson Sara E. , Holbrook Michael R.
Published: June 2011

Yellow fever virus (YFV) causes serious disease in endemic areas of South America and Africa, even though a very well tolerated vaccine is available. YFV primarily targets the liver where as many as 80 % of hepatocytes may be involved during infection. The objective of this project was to compare and contrast the cytokine response from hepatocytes infected with either wild-type (Asibi) or vaccine (17-D-204) strains of YFV, with the goal of identifying responses that might be correlated with disease severity or vaccine efficacy. We report here that PH5CH8 hepatocytes support a productive infection with both wild-type and vaccine-strain YFV. Infection with either virus resulted in elevated expression of several pro- and anti-inflammatory cytokines [interleukin (IL)-1β, IL-4, IL-6, IL-8, IL-10 and tumour necrosis factor-α) with a corresponding increase in transcription. Hepatocytes infected with vaccine virus had a more profound response than did cells infected with wild-type virus. Pre-stimulation of hepatocytes with IL-6 resulted in reduced viral titres, elevated concentrations of cytokines released from Asibi virus-infected cells and improved cell viability in cells infected with 17-D virus. Data reported here suggest that 17-D virus stimulates an appropriate antiviral inflammatory response in hepatocytes, while Asibi virus can attenuate the host response. These data identify potential mechanisms that are associated with increased virulence in wild-type virus infections and also provide clues towards potential immune-response limitations that may be associated with vaccine-related adverse events.
Comprehensive linker-scanning mutagenesis of the hepatitis C virus E1 and E2 envelope glycoproteins reveals new structure–function relationships
Authors: Rychłowska Małgorzata , Owsianka Ania M. , Foung Steven K. H. , Dubuisson Jean , Bieńkowska-Szewczyk Krystyna , Patel Arvind H.
Published: June 2011

Despite extensive research, many details about the structure and functions of hepatitis C virus (HCV) glycoproteins E1 and E2 are not fully understood, and their crystal structure remains to be determined. We applied linker-scanning mutagenesis to generate a panel of 34 mutants, each containing an insertion of 5 aa at a random position within the E1E2 sequence. The mutated glycoproteins were analysed by using a range of assays to identify regions critical for maintaining protein conformation, E1E2 complex assembly, CD81 receptor binding, membrane fusion and infectivity. The results, while supporting previously published data, provide several interesting new findings. Firstly, insertion at amino acid 587 or 596 reduced E1E2 heterodimerization without affecting reactivity with some conformation-sensitive mAbs or with CD81, thus implicating these residues in glycoprotein assembly. Secondly, insertions within a conserved region of E2, between amino acid residues 611 and 631, severely disrupted protein conformation and abrogated binding of all conformation-sensitive antibodies, suggesting that the structural integrity of this region is critical for the correct folding of E2. Thirdly, an insertion at Leu-682 specifically affected membrane fusion, providing direct evidence that the membrane-proximal ‘stem’ of E2 is involved in the fusion mechanism. Overall, our results show that the HCV glycoproteins generally do not tolerate insertions and that there are a very limited number of sites that can be changed without dramatic loss of function. Nevertheless, we identified two E2 insertion mutants, at amino acid residues 408 and 577, that were infectious in the murine leukemia virus-based HCV pseudoparticle system.
Elastic wave mode separation for tilted transverse isotropy media
Authors: Yan Jia , Sava Paul
Published: June 2011

Seismic waves propagate through the earth as a superposition of different wave modes. Seismic imaging in areas characterized by complex geology requires techniques based on accurate reconstruction of the seismic wavefields. A crucial component of the methods in this category, collectively known as wave‐equation migration, is the imaging condition that extracts information about the discontinuities of physical properties from the reconstructed wavefields at every location in space. Conventional acoustic migration techniques image a scalar wavefield representing the P‐wave mode, in contrast to elastic migration techniques, which image a vector wavefield representing both the P‐ and S‐waves. For elastic imaging, it is desirable that the reconstructed vector fields are decomposed into pure wave modes, such that the imaging condition produces interpretable images, characterizing, for example, PP or PS reflectivity. In anisotropic media, wave mode separation can be achieved by projection of the reconstructed vector fields on the polarization vectors characterizing various wave modes. For heterogeneous media, because polarization directions change with position, wave mode separation needs to be implemented using space‐domain filters. For transversely isotropic media with a tilted symmetry axis, the polarization vectors depend on the elastic material parameters, including the tilt angles. Using these parameters, we separate the wave modes by constructing nine filters corresponding to the nine Cartesian components of the three polarization directions at every grid point. Since the S polarization vectors in transverse isotropic media are not defined in the singular directions, e.g., along the symmetry axes, we construct these vectors by exploiting the orthogonality between the SV and SH polarization vectors, as well as their orthogonality with the P polarization vector. This procedure allows one to separate all three modes, with better preserved P‐wave amplitudes than S‐wave amplitudes. Realistic synthetic examples show that this wave mode separation is effective for both 2D and 3D models with strong heterogeneity and anisotropy.
Discontinuous Galerkin frequency domain forward modelling for the inversion of electric permittivity in the 2D case
Authors: El Bouajaji Mohamed , Lanteri Stéphane , Yedlin Matthew
Published: June 2011

We have recently developed a discontinuous Galerkin frequency domain modelling algorithm for the solution of the 2D transverse magnetic Maxwell equations. This method is formulated on an unstructured triangular discretization of the computational domain and makes use of a high order polynomial interpolation of the electromagnetic field components within each triangular element. The discontinuous nature of the approximation naturally allows for a local definition of the interpolation order that is, in combination with a possibly non‐conforming local refinement of the mesh, a key ingredient for obtaining a flexible and accurate discretization method. Moreover, heterogeneity of the propagation media is easily dealt with by assuming element‐wise values of the electromagnetic parameters. In this paper, we propose the use of this discontinuous Galerkin frequency domain method as the forward modelling algorithm for solving the inverse problem for the electric permittivity in the 2D case. The inversion process is based on a gradient minimization technique developed by Pratt for seismological applications. Preliminary numerical results are presented for the imaging of a simplified subsurface model with the aim of assessing the performances of the proposed inversion methodology with regards to the number of frequencies, the number of recorded data and the number of sources.
Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information
Authors: Edsgärd D. , Scheel M. , Hansen N. T. , Ralfkiaer U. , Jensen T. S. , Skakkebæk N. E. , Brunak S. , Gupta R. , Rajpert‐De Meyts E. , Ottesen A. M.
Published: June 2011

To search for disease‐related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk‐associated genes among loci targeted by CNVs. The top‐ranked candidate, RLN1, encoding a Relaxin‐H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome‐wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed in both groups (p = 1). Immunohistochemistry for Relaxin‐H1 (RLN1), Relaxin‐H2 (RLN2) and their cognate receptor, RXFP1, detected one, and in some cases both, of the relaxins in Leydig cells, Sertoli cells and a subset of neoplastic germ cells, whereas the receptor was present in Leydig cells and spermatids. Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population‐wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible role of the relaxin peptides in spermatogenesis and warrant further studies.
Foetal exposure to phthalate esters and anogenital distance in male newborns
Authors: Suzuki Y. , Yoshinaga J. , Mizumoto Y. , Serizawa S. , Shiraishi H.
Published: June 2011

Phthalate esters, commonly used as plasticizers, show anti‐androgenic activity and cause male reproductive malformation in experimental animals. However, the effects of prenatal exposure to phthalate esters in humans have not been extensively studied. The purpose of this study was to examine the relationship between prenatal exposure to phthalate esters and the anogenital distance (AGD) as a reproductive endpoint in human male newborns. Spot urine samples were collected from 111 Japanese pregnant women after obtaining their informed consent. Seven urinary phthalate ester metabolites were determined by high performance liquid chromatography–tandem mass spectrometry. Urinary isoflavones concentrations were measured as possible covariates because their oestrogenicities and high exposure levels among Japanese have the potential to affect male genital development. Birth outcomes and AGD, the distance from the centre of the anus to external genitalia, were measured for their male newborns. In a multiple regression model, the log‐transformed mono‐2‐ethylhexyl phthalate concentration (specific gravity‐corrected) was negatively significant, and maternal smoking status was positively significant, in explaining anogenital index (AGI) when potential covariates were controlled for. Urinary isoflavones did not significantly contribute to AGI in any models. Our results suggest that prenatal exposure to di(2‐ethylhexyl) phthalate affects reproductive development in human males.
Mental health problems and medically unexplained physical symptoms in adult survivors of childhood sexual abuse: an integrative literature review
Authors: NELSON S. , BALDWIN N. , TAYLOR J.
Published: June 2011

Accessible summary

People who were sexually abused as children are at higher risk than non‐abused people of suffering symptoms that doctors can't explain (e.g. irritable bowel syndrome), and to have mental ill health (e.g. anxiety and depression).

Relations between themselves and doctors or nurses can often become strained and frustrating, bringing high healthcare costs without relief of their ‘medically unexplained symptoms’. The aim in the literature review was to find an evidence base that might contribute to more helpful treatment or support, to improving relationships with medical staff and revealing gaps in knowledge.

Some theories about why sexual abuse survivors with mental ill health have these unexplained symptoms were found to stigmatize them. Other theories conflicted with each other. This increases the difficulty of identifying helpful interventions. Research focussed on finding out ‘risk factors’ rather than on improving people's health. It rarely involved survivors themselves, or staff who worked closely with them.

Recommendations include consulting survivors themselves about their experiences, and about how doctors and nurses could work more sensitively with them; learning from patients' case histories and medical records; studying sexually abused children's health problems as they grow into adulthood; and supporting neurobiological research.

People sexually abused in childhood are at higher risk than non‐abused people of medically unexplained symptoms such as irritable bowel syndrome or chronic pain, with mental ill health and high healthcare use. Friction and frustration, with high, unproductive healthcare costs, can often develop between these patients and health‐care professionals such as general practitioners and nursing staff. The aim of this integrative literature review was to seek a sound evidence base from which to develop helpful interventions, improve relationships and identify gaps in knowledge. It found some theories about interconnections among childhood sexual abuse mental health and medically unexplained symptoms, such as ‘somatization’ or ‘secondary gain’, were used prejudicially, stigmatizing survivors. Conflicting theories make more difficult the search for effective interventions. Researchers rarely collaborated with sexual abuse specialists. Emphasis on identifying key risk factors, rather than providing support or alleviating distress, and lack of studies where survivors voiced their own experiences, meant very few targeted interventions for this group were proposed. Recommendations to enable effective interventions include making abuse survivors the prime study focus; qualitative research with survivors, to assist doctors and nursing staff with sensitive care; case histories using medical records; prospective studies with sexually abused children; support for the growing field of neurobiological research.
Complex regulation of the global regulatory gene csrA: CsrA‐mediated translational repression, transcription from five promoters by Eσ70 and EσS, and indirect transcriptional activation by CsrA
Authors: Yakhnin Helen , Yakhnin Alexander V. , Baker Carol S. , Sineva Elena , Berezin Igor , Romeo Tony , Babitzke Paul
Published: June 2011

CsrA of Escherichia coli is an RNA‐binding protein that globally regulates gene expression by repressing translation and/or altering the stability of target transcripts. Here we explored mechanisms that control csrA expression. Four CsrA binding sites were predicted upstream of the csrA initiation codon, one of which overlapped its Shine–Dalgarno sequence. Results from gel shift, footprint, toeprint and in vitro translation experiments indicate that CsrA binds to these four sites and represses its own translation by directly competing with 30S ribosomal subunit binding. Experiments were also performed to examine transcription of csrA. Primer extension, in vitro transcription and in vivo expression studies identified two σ70‐dependent (P2 and P5) and two σS‐dependent (P1 and P3) promoters that drive transcription of csrA. Additional primer extension studies identified a fifth csrA promoter (P4). Transcription from P3, which is indirectly activated by CsrA, is primarily responsible for increased csrA expression as cells transition from exponential to stationary‐phase growth. Taken together, our results indicate that regulation of csrA expression occurs by a variety of mechanisms, including transcription from multiple promoters by two sigma factors, indirect activation of its own transcription, as well as direct repression of its own translation.