bluuebunny/crossref_metadata_2025 huggingface dataset:
Communication: Rigorous calculation of dissociation energies (D) of the water trimer, (H2O)3 and (D2O)3
Authors: Wang Yimin , Bowman Joel M.
Published: October 2011

Using a recent, full-dimensional, ab initio potential energy surface [Y. Wang, X. Huang, B. C. Shepler, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 134, 094509 (2011)]10.1063/1.3554905 together with rigorous diffusion Monte Carlo calculations of the zero-point energy of the water trimer, we report dissociation energies, D0, to form one monomer plus the water dimer and three monomers. The calculations make use of essentially exact zero-point energies for the water trimer, dimer, and monomer, and benchmark values of the electronic dissociation energies, De, of the water trimer [J. A. Anderson, K. Crager, L. Fedoroff, and G. S. Tschumper, J. Chem. Phys. 121, 11023 (2004)]10.1063/1.1799931. The D0 results are 3855 and 2726 cm−1 for the 3H2O and H2O + (H2O)2 dissociation channels, respectively, and 4206 and 2947 cm−1 for 3D2O and D2O + (D2O)2 dissociation channels, respectively. The results have estimated uncertainties of 20 and 30 cm−1 for the monomer plus dimer and three monomer of dissociation channels, respectively.
Surface passivation of p-type Ge substrate with high-quality GeNx layer formed by electron-cyclotron-resonance plasma nitridation at low temperature
Authors: Fukuda Yukio , Okamoto Hiroshi , Iwasaki Takuro , Otani Yohei , Ono Toshiro
Published: October 2011

We have investigated the effects of the formation temperature and postmetallization annealing (PMA) on the interface properties of GeNx/p-Ge fabricated by the plasma nitridation of Ge substrates using an electron-cyclotron-resonance-generated nitrogen plasma. The nitridation temperature is found to be a critical parameter in improving the finally obtained GeNx/Ge interface properties. The GeNx/Ge formed at room temperature and treated by PMA at 400 °C exhibits the best interface properties with an interface trap density of 1 × 1011 cm−2 eV−1. The GeNx/Ge interface is unpinned and the Fermi level at the Ge surface can move from the valence band edge to the conduction band edge.
Direct solar energy conversion and storage through coupling between photoelectrochemical and ferroelectric effects
Authors: Lo Chi-Wei , Li Chensha , Jiang Hongrui
Published: October 2011

Harvesting and storing solar energy has become more and more important. Current solid-state photovoltaic cells and conventional photoelectrochemical cells are not capable of directly storing the converted energy, which has to be facilitated by connecting to external storing devices. We demonstrate a device architecture that can convert and store solar energy in the electrical form within an intrinsically single structure. Mobile charge is internally stored, based on the coupling between photoelectrochemical and ferroelectric effects. The tested device architecture can be photo-charged under 1000 W/m2 of white light to an open-circuit voltage of 0.47V with a capacity of 37.62 mC/cm2. After removal of the light source, the mobile charge stored lasts more than 8 hours, and the open-circuit output voltage lasts more than 24 hours.
Carbon nanotube plane fastener
Authors: Hirahara Kaori , Ajioka Shoichi , Nakayama Yoshikazu
Published: October 2011

We report a feature of carbon nanotubes (CNTs) that arises when the surfaces of two vertically-aligned CNT brushes are pressed together. Adhesion between the CNTs creates a plane fastener-like device. Observations from scanning electron microscopy and measurements of adhesion properties indicate a device-dependence on CNT density and shape near the tip region. Among other applications, such fasteners have the potential to attach small components onto micron-sized electronic devices.
Ultralow magnetic fields elicit unexplained spin dynamics in water
Authors: Smart Ashley G.
Published: October 2011

Record-sensitive NMR measurements show that we still have more to learn about the most abundant liquid on the planet.
Microfluidic circuits harvest mechanical energy
Authors: Wilson R. Mark
Published: October 2011

Embedded in a pair of shoes, circuits composed of a train of conductive droplets could generate a few watts of power—enough to charge a cell phone from a casual stroll.
3D printing breaks out of its mold
Authors: Matthews Jermey N. A.
Published: October 2011

Medical implants, injection-molding tools, and aircraft custom parts are just a few of the products being manufactured with technology once reserved for prototyping.
Binary black hole mergers
Authors: Baumgarte Thomas W. , Shapiro Stuart L.
Published: October 2011

Solving the equations of general relativity presents unique challenges. Nowadays many of those have been met, and new numerical simulations are revealing surprising astrophysical phenomena.
Political Determinants of Regional Financing: The Case of Spain
Authors: Reino Juan Luis Gómez , Alcalde Ana Herrero
Published: October 2011

We contribute to the literature on the political determinants of regional financing by analyzing the case of Spain, a largely decentralized country. Using a dynamic panel data model, we argue that the rise in relative bargaining power of regional parties in Spain can partly explain the increase in budgetary allocations to regions observed during the period 1986–2006. In particular, our results show that the rise in parliamentary representation of the nationalist Catalonian party, measured by the Banzhaf voting power index, has been a significant factor in ensuring increasing financial resources to regional governments. In addition, the traditional hypotheses of the political economy literature on legislative apportionment are tested for the case of Spain, with no significant results observed. The overall distribution of regional financing in Spain seems to be in general well aligned with the basic economic principles of efficiency and equity recommended for such a system.
Lipid Peptide Core Nanoparticles as Multivalent Vaccine Candidates against Streptococcus pyogenes
Authors: Skwarczynski Mariusz , Parhiz Bibi Hamideh , Soltani Fatemeh , Srinivasan Saranya , Kamaruzaman Khairul A. , Lin I-Chun , Toth Istvan
Published: October 2011

Traditional vaccine approaches for Group A streptococcus (GAS) infection are inadequate owing to the host’s production of cross-reactive antibodies that recognize not only the bacteria but also human tissue. To overcome this problem a peptide subunit-based vaccine was proposed, which would incorporate only minimal non-cross reactive epitopes. However, special delivery systems/adjuvants were required because short peptides are not immunogenic. In this study we have incorporated two epitopes from two different GAS proteins into a lipid core peptide (LCP) self-adjuvanting delivery system to achieve better protection against a wide range of GAS serotypes. Multivalent and monovalent constructs were synthesized with the help of an azide alkyne cycloaddition (click) reaction and their ability to self-assemble under aqueous conditions was examined. The compounds significantly differed in their ability to form small size nanoparticles, which are believed to be most appropriate for peptide-based subunit vaccine delivery. The LCP conjugates possessing two different epitopes, in contrast to monoepitopic constructs, formed small nanoparticles (5–15 nm) presumably owing to a suitable hydrophilic-hydrophobic balance of the molecules.
Reviewing hook degradation to promote ejection after ingestion by marine fish
Authors: McGrath Shane P. , Butcher Paul A. , Broadhurst Matt K. , Cairns Stuart C.
Published: October 2011

A widely recommended strategy for releasing fish that have ingested hooks is to simply cut the line. The utility of this approach is based on the premise that the individual will eventually eject the hook following sufficient oxidation. However, few quantitative data are available describing the mechanisms affecting hook decay. We addressed this issue by testing the independence of various technical factors on the degradation of 828 hooks comprising 23 designs (absolute sizes 227–611 mm2) after protracted submersion in seawater. Twelve replicates of each hook were destructively assessed for compression and tensile strengths (using a force gauge) and 24 replicates were weighed, photographed and submersed in seawater. After submersion for 8 and 28 days, 12 replicate hooks were removed, re-photographed, re-weighed and tested for compression and tensile strengths to provide indices of decay. Hook degradation was mainly affected by the wire material and diameter and could be significantly promoted by choosing carbon steel designs, either with a wire diameter of ≤0.9 mm for the examined sizes or, alternatively, bait-holder barbs (or similar modifications) along the shaft. By rapidly oxidising and weakening after ingestion, such designs could ultimately help to reduce negative impacts of hooks on released fish.
Providing HIV-negative results to low-risk clients by telephone
Authors: Conway Damian P. , Healey Loretta M. , Rauwendaal Evert , Templeton David J. , Davies Stephen C.
Published: October 2011

Background
In Australia, Health Department policies differ on the recommended method of providing HIV results. Traditionally, all results have been provided in person. Our aim was to trial provision of HIV-negative test results by telephone to low-risk clients attending sexual health services and to assess clients’ preferences for delivery method. Methods: During 4 months in 2009 at two sexual health services in Sydney, all clients assessed as low-risk for HIV infection were invited to receive their HIV result by telephone. Non-receipt of results was defined as failure to receive results within 30 days of the test being performed. Results: Of 763 clients tested, 328 (43%) were excluded following risk assessment, 30 (4%) declined to participate and 405 (53%) were enrolled. Among enrolled clients, 86% received their HIV result by telephone within 30 days, 97% were satisfied with delivery of the result by telephone and 93% preferred telephone delivery for their next HIV result. Only one enrolled client returned a positive HIV result. Independent predictors of receiving results within the 30-day timeframe were clinic attendance for sexually transmissible infection screening (P = 0.021), lack of anogenital symptoms (P = 0.015) and not being a sex worker (P = 0.001). Conclusions: In this study of telephone provision of HIV results to low HIV-risk clients, there were no adverse events and clients expressed satisfaction with the process plus a strong preference for telephone delivery of future results. There was a decreased rate of failure to receive HIV results compared with other Australian studies.
Binding of blood proteins to carbon nanotubes reduces cytotoxicity
Authors: Ge Cuicui , Du Jiangfeng , Zhao Lina , Wang Liming , Liu Ying , Li Denghua , Yang Yanlian , Zhou Ruhong , Zhao Yuliang , Chai Zhifang , Chen Chunying
Published: October 2011

With the potential wide uses of nanoparticles such as carbon nanotubes in biomedical applications, and the growing concerns of nanotoxicity of these engineered nanoparticles, the importance of nanoparticle–protein interactions cannot be stressed enough. In this study, we use both experimental and theoretical approaches, including atomic force microscope images, fluorescence spectroscopy, CD, SDS-PAGE, and molecular dynamics simulations, to investigate the interactions of single-wall carbon nanotubes (SWCNTs) with human serum proteins, and find a competitive binding of these proteins with different adsorption capacity and packing modes. The
π
-
π
stacking interactions between SWCNTs and aromatic residues (Trp, Phe, Tyr) are found to play a critical role in determining their adsorption capacity. Additional cellular cytotoxicity assays, with human acute monocytic leukemia cell line and human umbilical vein endothelial cells, reveal that the competitive bindings of blood proteins on the SWCNT surface can greatly alter their cellular interaction pathways and result in much reduced cytotoxicity for these protein-coated SWCNTs, according to their respective adsorption capacity. These findings have shed light toward the design of safe carbon nanotube nanomaterials by comprehensive preconsideration of their interactions with human serum proteins.
Intestinal inflammation allows
Salmonella
to use ethanolamine to compete with the microbiota
Authors: Thiennimitr Parameth , Winter Sebastian E. , Winter Maria G. , Xavier Mariana N. , Tolstikov Vladimir , Huseby Douglas L. , Sterzenbach Torsten , Tsolis Renée M. , Roth John R. , Bäumler Andreas J.
Published: October 2011

Conventional wisdom holds that microbes support their growth in vertebrate hosts by exploiting a large variety of nutrients. We show here that use of a specific nutrient (ethanolamine) confers a marked growth advantage on
Salmonella enterica
serovar Typhimurium (
S.
Typhimurium) in the lumen of the inflamed intestine. In the anaerobic environment of the gut, ethanolamine supports little or no growth by fermentation. However,
S.
Typhimurium is able to use this carbon source by inducing the gut to produce a respiratory electron acceptor (tetrathionate), which supports anaerobic growth on ethanolamine. The gut normally converts ambient hydrogen sulfide to thiosulfate, which it then oxidizes further to tetrathionate during inflammation. Evidence is provided that
S.
Typhimurium's growth advantage in an inflamed gut is because of its ability to respire ethanolamine, which is released from host tissue, but is not utilizable by competing bacteria. By inducing intestinal inflammation,
S.
Typhimurium sidesteps nutritional competition and gains the ability to use an abundant simple substrate, ethanolamine, which is provided by the host.
Mycobacterium tuberculosislipomannan blocks TNF biosynthesis by regulating macrophage MAPK-activated protein kinase 2 (MK2) and microRNA miR-125b
Authors: Rajaram Murugesan V. S. , Ni Bin , Morris Jessica D. , Brooks Michelle N. , Carlson Tracy K. , Bakthavachalu Baskar , Schoenberg Daniel R. , Torrelles Jordi B. , Schlesinger Larry S.
Published: October 2011

Contact ofMycobacterium tuberculosis(M.tb) with the immune system requires interactions between microbial surface molecules and host pattern recognition receptors. MajorM.tb-exposed cell envelope molecules, such as lipomannan (LM), contain subtle structural variations that affect the nature of the immune response. Here we show that LM from virulentM.tb(TB-LM), but not from avirulentMyocobacterium smegmatis(SmegLM), is a potent inhibitor of TNF biosynthesis in human macrophages. This difference in response is not because of variation in Toll-like receptor 2-dependent activation of the signaling kinase MAPK p38. Rather, TB-LM stimulation leads to destabilization of TNF mRNA transcripts and subsequent failure to produce TNF protein. In contrast, SmegLM enhances MAPK-activated protein kinase 2 phosphorylation, which is critical for maintaining TNF mRNA stability in part by contributing microRNAs (miRNAs). In this context, human miRNA miR-125b binds to the 3′ UTR region of TNF mRNA and destabilizes the transcript, whereas miR-155 enhances TNF production by increasing TNF mRNA half-life and limiting expression of SHIP1, a negative regulator of the PI3K/Akt pathway. We show that macrophages incubated with TB-LM and liveM.tbinduce high miR-125b expression and low miR-155 expression with correspondingly low TNF production. In contrast, SmegLM and liveM. smegmatisinduce high miR-155 expression and low miR-125b expression with high TNF production. Thus, we identify a unique cellular mechanism underlying the ability of a majorM.tbcell wall component, TB-LM, to block TNF biosynthesis in human macrophages, thereby allowingM.tbto subvert host immunity and potentially increase its virulence.
The potential for modifying plant volatile composition to enhance resistance to arthropod pests.
Authors: Åhman I. , Glinwood R. , Ninkovic V.
Published: October 2011

Plant volatiles provide herbivorous arthropods with information that allows them to discriminate between host and non-host plants. Volatiles may also indicate plant stress status, and natural enemies can use herbivore-induced plant volatiles as cues for prey location. Neighbouring plants may also make use of volatile cues to prepare for herbivore attack. Since both constitutive and inducible plant volatile emissions can be modified by plant breeding, the possibility exists to improve plant resistance against important pests both directly and indirectly via improved biological control. So far this approach has been tested only in the realm of research, predominantly using transgenic
Arabidopsis
with modified composition of terpenoids or C
6
green leaf compounds. However, several studies have shown that it is indeed possible both to reduce herbivory and to enhance natural enemy attraction simultaneously. If such effects can be translated into increased and more stable yields in important crops, this strategy might be explored by the plant breeding industry and eventually become available to plant growers in the form of resistant cultivars. There are, however, ecological challenges associated with this approach, and the modified plant volatile composition should preferably be inducible specifically by the target pests, or by field application of specific elicitors based on forecasts of pest attack.
Agricultural residues and energy crops as potentially economical and novel substrates for microbial production of butanol (a biofuel).
Authors: Qureshi N.
Published: October 2011

This review describes the production of acetone butanol ethanol (ABE) from a variety of agricultural residues and energy crops employing biochemical or fermentation processes. A number of organisms are available for this bioconversion including
Clostridium beijerinckii
P260,
C. beijerinckii
BA101,
Clostridium acetobutylicum
and
Clostridium saccharobutylicum
P262. Some of these strains (P260 and P262) were used in an industrial setting in South Africa. One of the major limitations of these cultures is that none of them produce greater than 30 g/l total ABE unless integrated with simultaneous product recovery to reduce the toxicity of accumulated products. These cultures can utilize both hexose and pentose sugars derived from lignocellulosic hydrolysates such as maize (corn) fibre, wheat straw (one of the novel substrates), barley straw, maize stover and switchgrass. Substrates such as Jerusalem artichoke, maize, rye, millet, molasses, potato, soya molasses and agricultural wastes can also be used by the cultures listed. Additional carbohydrates that can be used include dextrins, fructose, sucrose and lactose. It is recommended that cultures that can produce greater amounts of ABE per litre of culture broth be developed. In order to economize the process of butanol production by fermentation, process technologies have been developed that integrate lignocellulosic biomass hydrolysis, fermentation and simultaneous product recovery. It should be noted that in continuous process where a product was recovered simultaneously, 461.3 g/l ABE was produced from 1125 g sugar in a 1 litre culture volume.
The interaction between public and private R&D expenditure and national productivity
Authors: Coccia Mario
Published: October 2011

Starting from the epistemological position of the positive interaction between public and private R&D expenditures at country level for maintaining productivity growth, the purpose of this paper is to provide empiricist–positivist arguments of this stance in order to design R&D policy that supports national competitiveness in fast-changing and turbulent markets
Economic Implications of Agricultural Water Use in Eastern India
Authors: Xenarios Stefanos , Amarasinghe Upali , Sharma Bharat
Published: October 2011

The irrigation services are often state-subsidized in agrarian economies for the enhancement of agricultural productivity while they also target poverty alleviation. The agriculture-dependent states of India offer representative examples of undervalued irrigation services mainly sourced by canal networks. However, canal irrigation is nowadays lagging behind private groundwater initiatives but with significant costs which question the concept of low water pricing in agriculture. This paper assesses irrigation water costs in representative backward clusters of Bihar state in eastern India while the effects on different landholding groups are analysed. The results indicate that marginal landholders heavily rely on purchased water from unofficial markets while they pay the highest amount for irrigation. This is due to limited access in the canal network, possession of inefficient pumping systems and cultivation of crops with a high demand for water. However, acute policy reforms could drastically decrease water costs and improve agricultural productivity.
Interaction between FIP5 and SNX18 regulates epithelial lumen formation
Authors: Willenborg Carly , Jing Jian , Wu Christine , Matern Hugo , Schaack Jerome , Burden Jemima , Prekeris Rytis
Published: October 2011

During the morphogenesis of the epithelial lumen, apical proteins are thought to be transported via endocytic compartments to the site of the forming lumen, although the machinery mediating this transport remains to be elucidated. Rab11 GTPase and its binding protein, FIP5, are important regulators of polarized endocytic transport. In this study, we identify sorting nexin 18 as a novel FIP5-interacting protein and characterize the role of FIP5 and SNX18 in epithelial lumen morphogenesis. We show that FIP5 mediates the transport of apical proteins from apical endosomes to the apical plasma membrane and, along with SNX18, is required for the early stages of apical lumen formation. Furthermore, both proteins bind lipids, and FIP5 promotes the capacity of SNX18 to tubulate membranes, which implies a role for FIP5 and SNX18 in endocytic carrier formation and/or scission. In summary, the present findings support the hypothesis that this FIP5-SNX18 complex plays a pivotal role in the polarized transport of apical proteins during apical lumen initiation in epithelial cells.
Pathogens and polymers: Microbe–host interactions illuminate the cytoskeleton
Authors: Haglund Cat M. , Welch Matthew D.
Published: October 2011

Intracellular pathogens subvert the host cell cytoskeleton to promote their own survival, replication, and dissemination. Study of these microbes has led to many discoveries about host cell biology, including the identification of cytoskeletal proteins, regulatory pathways, and mechanisms of cytoskeletal function. Actin is a common target of bacterial pathogens, but recent work also highlights the use of microtubules, cytoskeletal motors, intermediate filaments, and septins. The study of pathogen interactions with the cytoskeleton has illuminated key cellular processes such as phagocytosis, macropinocytosis, membrane trafficking, motility, autophagy, and signal transduction.
A copper-lined magnet coil with maximum field of 700 T for electromagnetic flux compression
Authors: Takeyama Shojiro , Kojima Eiji
Published: October 2011

A copper-lined (CL) primary coil, which is a composite of steel and copper, was devised for the electromagnetic flux compression technique to generate ultrahigh magnetic fields. The newly developed coil was found to be highly efficient for electromagnetic energy transfer and provided stabilization of the liner implosive motion with less influence from the current feeding gap. Dynamical current density distribution of the materials used in a primary coil was evaluated and applied to the design of the CL coil. Fields of up to 730 T were achieved by employing the CL coil with an energy injected from a 4 MJ condenser bank. This value is the highest achieved thus far in an indoor setting. The peak magnetic fields were found to depend significantly on the initial seed magnetic field. The optimum seed fields for obtaining the highest peak magnetic field were determined.
Improved performance of GaN-based light-emitting diodes with high-quality GaN grown on InN islands
Authors: Lee Sang-Jun , Cho Chu-Young , Hong Sang-Hyun , Han Sang-Heon , Yoon Sukho , Park Yongjo , Park Seong-Ju
Published: October 2011

The effect of GaN grown on InN islands on InGaN/GaN multiple quantum wells (MQWs) light-emitting diodes (LEDs) is investigated. The pit density of GaN grown on InN islands is decreased and the photoluminescence intensity of GaN grown on InN islands is increased compared with those of GaN without InN islands. The LEDs fabricated with GaN grown on InN islands show higher optical output power and lower reverse-bias leakage current than the LEDs without InN islands. These enhancements are attributed to the InN islands which reduce the threading dislocations and stress of GaN and MQWs.
Evaluation of Soybean Genotypes for Resistance to Charcoal Rot
Authors: Mengistu Alemu , Arelli P. A. , Bond J. P. , Shannon G. J. , Wrather A. J. , Rupe J. B. , Chen P. , Little C. R. , Canaday C. H. , Newman M. A. , Pantalone V. R.
Published: October 2011

Charcoal rot, caused by Macrophomina phaseolina, significantly reduces yield in soybean more than most other diseases in the midsouthern United States. There are no commercial genotypes marketed as resistant to charcoal rot. Reactions of 27 maturity group (MG) III, 29 Early MG IV, 34 Late MG IV, and 59 MG V genotypes were evaluated for M. phaseolina between 2006 and 2008 in a non-irrigated, no-till field that had been artificially infested for three years. There was significant variation in root colonization among genotypes and years, indicating the value of screening genotypes over multiple years. Based on CFUI there was no genotype that was consistently immune to charcoal rot each year. However, there were a total of six genotypes (one genotype in MG III, one in Late MG IV, and four in MG V) that were identified as moderately resistant. Some of the commercial and public genotypes were resistant to M. phaseolina at levels equal to or greater than the standard DT97-4290, a moderately resistant cultivar. The genotypes identified as having moderate resistance across the three years could be useful as sources for developing resistant soybean genotypes.

Accepted for publication 27 July 2011. Published 26 September 2011.
Diagnostic Workup of Paediatric Patients With Inflammatory Bowel Disease in Europe
Authors: de Bie Charlotte I. , Buderus Stephan , Sandhu Bhupinder K. , de Ridder Lissy , Paerregaard Anders , Veres Gabor , Dias Jorge Amil , Escher Johanna C. ,   EUROKIDS Porto IBD Working Group of ESPGHAN
Published: October 2011

Objective:

In 2005, the Inflammatory Bowel Disease (IBD) Working Group of the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition published consensus guidelines on the diagnostic workup of paediatric IBD, the Porto criteria. According to these guidelines, children suspected of having IBD should undergo an oesophagogastroduodenoscopy (OGD), ileocolonoscopy, and (except in cases of definitive ulcerative colitis) adequate imaging of the small bowel. To audit and evaluate the diagnostic workup of paediatric patients with IBD in Europe, the Working Group created EUROKIDS, a prospective, Web‐based registry of newly diagnosed paediatric patients with IBD.

Methods:

Patients with IBD (ages 0–18 years) were registered in 44 centres in 18 countries. Data on diagnostic workup were analysed according to the year of diagnosis, type of IBD, and centre size. Diagnostic yield of OGD and ileal intubation were evaluated.

Results:

Between 2004 and 2009, 2087 newly diagnosed patients were correctly registered. Both OGD and ileocolonoscopy had been performed in 64% of all of the patients and increased significantly from year 1 (52 %) to 5 (71%, P < 0.001). Small‐bowel follow‐through use decreased during the years (year 1 n = 213, year 5 n = 108; P < 0.001), whereas magnetic resonance imaging use increased (year 1 n = 25, year 5 n = 171; P < 0.001). Patients diagnosed as having Crohn disease (CD, 59%) and ulcerative colitis (58%) were more likely to have had a complete diagnostic workup than patients diagnosed as having IBD unclassified (45%). In CD, the diagnostic yield of OGD was 7.5% and the yield of ileal intubation was 13%.

Conclusions:

The quality of diagnostic workup in paediatric patients with IBD increased steadily between 2004 and 2009. Small‐bowel imaging by magnetic resonance imaging superseded the use of small‐bowel follow‐through. OGD and ileal intubation contributed to a definitive diagnosis of CD.
Midazolam‐Ketamine Combination for Moderate Sedation in Upper GI Endoscopy
Authors: Motamed Farzaneh , Aminpour Yasaman , Hashemian Hesam , Soltani Alireza E. , Najafi Mehri , Farahmand Fatemeh
Published: October 2011

Objectives:

The aim of the study was to compare the quality of sedation with 3 different sedation regimens in upper gastrointestinal endoscopy (UGIE) in pediatric patients.

Methods:

One hundred fifty consecutive children who underwent UGIE were randomly assigned to 1 of the 3 medication regimens. Patients in group A (n = 49) received placebo. Forty‐five minutes after the placebo was given, repeated intravenous (IV) doses of 0.1 mg/kg midazolam were administered titrated to achieve a level of deep sedation. Patients in group B (n = 51) received oral ketamine instead of placebo, and patients in group C (n = 50) received oral fentanyl instead of placebo with the same methodology and sedation endpoint.

Results:

The mean dose of midazolam administered in group B patients was remarkably lower compared with that of groups A and C. Patients in group B showed less distress in IV line placement and separation from parents, higher comfort level, more endoscopist satisfaction, and higher sedation depth compared with groups A and C. The recovery time was significantly shorter in group B. All of the 3 regimens were safe. All of the complications were managed successfully.

Conclusions:

Our data suggest that synergistic sedation with oral ketamine and IV midazolam for UGIE in children is a suitable and safe sedation. The higher rate of vomiting in group B in contrast to previous studies must be caused mainly by the oral route of ketamine administration.
Pulmonary embolism: predicting disease severity
Authors: Burrowes K. S. , Clark A. R. , Marcinkowski A. , Wilsher M. L. , Milne D. G. , Tawhai M. H.
Published: October 2011

Pulmonary embolism (PE) is the most common cause of acute pulmonary hypertension, yet it is commonly undiagnosed, with risk of death if not recognized promptly and managed accordingly. Patients typically present with hypoxemia and hypocapnia, although the presentation varies greatly, being confounded by co-mordidities such as pre-existing cardio-respiratory disease. Previous studies have demonstrated variable patient outcomes in spite of similar extent and distribution of pulmonary vascular occlusion, but the pathophysiological determinants of outcome remain unclear. Computational models enable exact control over many of the compounding factors leading to functional outcomes and therefore provide a useful tool to understand and assess these mechanisms. We review the current state of pulmonary blood flow models. We present a pilot study within 10 patients presenting with acute PE, where patient-derived vascular occlusions are imposed onto an existing model of the pulmonary circulation enabling predictions of resultant haemodynamics after embolus occlusion. Results show that mechanical obstruction alone is not sufficient to cause pulmonary arterial hypertension, even when up to 65 per cent of lung tissue is occluded. Blood flow is found to preferentially redistribute to the gravitationally non-dependent regions. The presence of an additional downstream occlusion is found to significantly increase pressures.
Simulating the physiology of athletes during endurance sports events: modelling human energy conversion and metabolism
Authors: van Beek Johannes H. G. M. , Supandi Farahaniza , Gavai Anand K. , de Graaf Albert A. , Binsl Thomas W. , Hettling Hannes
Published: October 2011

The human physiological system is stressed to its limits during endurance sports competition events. We describe a whole body computational model for energy conversion during bicycle racing. About 23 per cent of the metabolic energy is used for muscle work, the rest is converted to heat. We calculated heat transfer by conduction and blood flow inside the body, and heat transfer from the skin by radiation, convection and sweat evaporation, resulting in temperature changes in 25 body compartments. We simulated a mountain time trial to Alpe d'Huez during the Tour de France. To approach the time realized by Lance Armstrong in 2004, very high oxygen uptake must be sustained by the simulated cyclist. Temperature was predicted to reach 39
°
C in the brain, and 39.7
°
C in leg muscle. In addition to the macroscopic simulation, we analysed the buffering of bursts of high adenosine triphosphate hydrolysis by creatine kinase during cyclical muscle activity at the biochemical pathway level. To investigate the low oxygen to carbohydrate ratio for the brain, which takes up lactate during exercise, we calculated the flux distribution in cerebral energy metabolism. Computational modelling of the human body, describing heat exchange and energy metabolism, makes simulation of endurance sports events feasible.
Nonlinear models of development, amplification and compression in the mammalian cochlea
Authors: Szalai R. , Tsaneva-Atanasova K. , Homer M. E. , Champneys A. R. , Kennedy H. J. , Cooper N. P.
Published: October 2011

This paper reviews current understanding and presents new results on some of the nonlinear processes that underlie the function of the mammalian cochlea. These processes occur within mechano-sensory hair cells that form part of the organ of Corti. After a general overview of cochlear physiology, mathematical modelling results are presented in three parts. First, the dynamic interplay between ion channels within the sensory inner hair cells is used to explain some new electrophysiological recordings from early development. Next, the state of the art is reviewed in modelling the electro-motility present within the outer hair cells (OHCs), including the current debate concerning the role of cell body motility versus active hair bundle dynamics. A simplified model is introduced that combines both effects in order to explain observed amplification and compression in experiments. Finally, new modelling evidence is presented that structural longitudinal coupling between OHCs may be necessary in order to capture all features of the observed mechanical responses.
Image-based multi-scale modelling and validation of radio-frequency ablation in liver tumours
Authors: Payne Stephen , Flanagan Ronan , Pollari Mika , Alhonnoro Tuomas , Bost Claire , O'Neill David , Peng Tingying , Stiegler Philipp
Published: October 2011

The treatment of cancerous tumours in the liver remains clinically challenging, despite the wide range of treatment possibilities, including radio-frequency ablation (RFA), high-intensity focused ultrasound and resection, which are currently available. Each has its own advantages and disadvantages. For non- or minimally invasive modalities, such as RFA, considered here, it is difficult to monitor the treatment
in vivo
. This is particularly problematic in the liver, where large blood vessels act as heat sinks, dissipating delivered heat and shrinking the size of the lesion (the volume damaged by the heat treatment) locally; considerable experience is needed on the part of the clinician to optimize the heat treatment to prevent recurrence. In this paper, we outline our work towards developing a simulation tool kit that could be used both to optimize treatment protocols in advance and to train the less-experienced clinicians for RFA treatment of liver tumours. This tool is based on a comprehensive mathematical model of bio-heat transfer and cell death. We show how simulations of ablations in two pigs, based on individualized imaging data, compare directly with experimentally measured lesion sizes and discuss the likely sources of error and routes towards clinical implementation. This is the first time that such a ‘loop’ of mathematical modelling and experimental validation
in vivo
has been performed in this context, and such validation enables us to make quantitative estimates of error.
Modelling natural and artificial hands with synergies
Authors: Bicchi Antonio , Gabiccini Marco , Santello Marco
Published: October 2011

We report on recent work in modelling the process of grasping and active touch by natural and artificial hands. Starting from observations made in human hands about the correlation of degrees of freedom in patterns of more frequent use (postural synergies), we consider the implications of a geometrical model accounting for such data, which is applicable to the pre-grasping phase occurring when shaping the hand before actual contact with the grasped object. To extend applicability of the synergy model to study force distribution in the actual grasp, we introduce a modified model including the mechanical compliance of the hand's musculotendinous system. Numerical results obtained by this model indicate that the same principal synergies observed from pre-grasp postural data are also fundamental in achieving proper grasp force distribution. To illustrate the concept of synergies in the dual domain of haptic sensing, we provide a review of models of how the complexity and heterogeneity of sensory information from touch can be harnessed in simplified, tractable abstractions. These abstractions are amenable to fast processing to enable quick reflexes as well as elaboration of high-level percepts. Applications of the synergy model to the design and control of artificial hands and tactile sensors are illustrated.
Motor–sensory convergence in object localization: a comparative study in rats and humans
Authors: Horev Guy , Saig Avraham , Knutsen Per Magne , Pietr Maciej , Yu Chunxiu , Ahissar Ehud
Published: October 2011

In order to identify basic aspects in the process of tactile perception, we trained rats and humans in similar object localization tasks and compared the strategies used by the two species. We found that rats integrated temporally related sensory inputs (‘temporal inputs’) from early whisk cycles with spatially related inputs (‘spatial inputs’) to align their whiskers with the objects; their perceptual reports appeared to be based primarily on this spatial alignment. In a similar manner, human subjects also integrated temporal and spatial inputs, but relied mainly on temporal inputs for object localization. These results suggest that during tactile object localization, an iterative motor–sensory process gradually converges on a stable percept of object location in both species.
The neurobiology of Etruscan shrew active touch
Authors: Brecht Michael , Naumann Robert , Anjum Farzana , Wolfe Jason , Munz Martin , Mende Carolin , Roth-Alpermann Claudia
Published: October 2011

The Etruscan shrew,Suncus etruscus, is not only the smallest terrestrial mammal, but also one of the fastest and most tactile hunters described to date. The shrew's skeletal muscle consists entirely of fast-twitch types and lacks slow fibres. Etruscan shrews detect, overwhelm, and kill insect prey in large numbers in darkness. The cricket prey is exquisitely mechanosensitive and fast-moving, and is as big as the shrew itself. Experiments with prey replica show that shape cues are both necessary and sufficient for evoking attacks. Shrew attacks are whisker guided by motion- and size-invariant Gestalt-like prey representations. Shrews often attack their prey prior to any signs of evasive manoeuvres. Shrews whisk at frequencies of approximately 14 Hz and can react with latencies as short as 25–30 ms to prey movement. The speed of attacks suggests that shrews identify and classify prey with a single touch. Large parts of the shrew's brain respond to vibrissal touch, which is represented in at least four cortical areas comprising collectively about a third of the cortical volume. Etruscan shrews can enter a torpid state and reduce their body temperature; we observed that cortical response latencies become two to three times longer when body temperature drops from 36°C to 24°C, suggesting that endothermy contributes to the animal's high-speed sensorimotor performance. We argue that small size, high-speed behaviour and extreme dependence on touch are not coincidental, but reflect an evolutionary strategy, in which the metabolic costs of small body size are outweighed by the advantages of being a short-range high-speed touch and kill predator.
The role of self-touch in somatosensory and body representation disorders after stroke
Authors: van Stralen H. E. , van Zandvoort M. J. E. , Dijkerman H. C.
Published: October 2011

Somatosensory impairments occur in about half of the cases of stroke. These impairments range from primary deficits in tactile detection and the perception of features, to higher order impairments in haptic object recognition and bodily experience. In this paper, we review the influence of active- and self-touch on somatosensory impairments after stroke. Studies have shown that self-touch improves tactile detection in patients with primary tactile deficits. A small number of studies concerned with the effect of self-touch on bodily experience in healthy individuals have demonstrated that self-touch influences the structural representation of one's own body. In order to better understand the effect of self-touch on body representations, we present an informal study of a stroke patient with somatoparaphrenia and misoplegia. The role of self-touch on body ownership was investigated by asking the patient to stroke the impaired left hand and foreign hands. The patient reported ownership and a change in affect over all presented hands through self-touch. The time it took to accomplish ownership varied, based on the resemblance of the foreign hand to the patient's own hand. Our findings suggest that self-touch can modulate impairments in body ownership and affect, perhaps by helping to reinstate the representation of the body.
HVJ Liposomes and HVJ Envelope Vectors
Authors: Kaneda Yasufumi
Published: October 2011

This protocol describes techniques for construction of fusion-mediated vectors based on inactivated HVJ (hemagglutinating virus of Japan; Sendai virus). HVJ liposomes are constructed by fusing liposomes containing DNA with inactivated HVJ. The HVJ envelope vector, a more simplified vector, incorporates DNA into inactivated HVJ particles without liposomes. Both vectors have many advantages. They can be used to introduce proteins, peptides, oligonucleotides (including antisense oligonucleotides, decoy oligonucleotides, and ribozymes), and short interfering RNA (siRNA), as well as plasmid DNA, into cultured cells in vitro and into organs in vivo. Fusion-mediated delivery avoids the degradation of therapeutic molecules before reaching the cytoplasm. Finally, repeated injection of the vector in vivo is not inhibited and even enhances the effects of the delivered molecules. These vectors have been used in many gene therapy experiments in animal models to address problems such as liver cirrhosis, hearing impairment, ischemic brain damage, peripheral arterial diseases, and cancers. This protocol describes methods for the preparation of HVJ liposomes and of HVJ envelope vectors and their use in delivery of plasmid DNA into various cells and tissues.
Immunostaining of Drosophila Testes
Authors: Bonaccorsi Silvia , Giansanti Maria G. , Cenci Giovanni , Gatti Maurizio
Published: October 2011

Fixed Drosophila testis preparations can be immunostained with a variety of antibodies. This article describes a general procedure for immunostaining. The concentration of the primary antibody will vary with both the type of antibody and the type of incubation and should be determined empirically each time.
Cerebellar Craniotomy for In Vivo Calcium Imaging of Astrocytes
Authors: Kuhn Bernd , Hoogland Tycho M. , Wang Samuel S.-H.
Published: October 2011

The cerebellar cortex contains two astrocyte types: the Bergmann glia of the molecular layer and the velate protoplasmic astrocytes of the granule cell layer. In vivo, these cell types generate both subcellular calcium transients and trans-glial calcium waves. It is possible to perform in vivo calcium imaging in cerebellar astrocytes. One method involves injection of a replication-incompetent recombinant adenovirus for gene transfer of a fluorescent calcium indicator protein. A second method uses multicell bolus loading (MCBL) in the molecular layer of the cerebellum with synthetic calcium indicators. This protocol presents a cerebellar craniotomy procedure which can be used to prepare a virus-injected animal for in vivo imaging. It can also be used to prepare an animal for MCBL.
Digital Scanned Laser Light-Sheet Fluorescence Microscopy (DSLM) of Zebrafish and Drosophila Embryonic Development
Authors: Keller Philipp J. , Schmidt Annette D. , Wittbrodt Jochen , Stelzer Ernst H.K.
Published: October 2011

Embryonic development is one of the most complex processes encountered in biology. In vertebrates and higher invertebrates, a single cell transforms into a fully functional organism comprising several tens of thousands of cells, arranged in tissues and organs that perform impressive tasks. In vivo observation of this biological process at high spatiotemporal resolution and over long periods of time is crucial for quantitative developmental biology. Importantly, such recordings must be realized without compromising the physiological development of the specimen. In digital scanned laser light-sheet fluorescence microscopy (DSLM), a specimen is rapidly scanned with a thin sheet of light while fluorescence is recorded perpendicular to the axis of illumination with a camera. Combining light-sheet technology and fast laser scanning, DSLM delivers quantitative data for entire embryos at high spatiotemporal resolution. Compared with confocal and two-photon fluorescence microscopy, DSLM exposes the embryo to at least three orders of magnitude less light energy, but still provides up to 50 times faster imaging speeds and a 10–100-fold higher signal-to-noise ratio. By using automated image processing algorithms, DSLM images of embryogenesis can be converted into a digital representation. These digital embryos permit following cells as a function of time, revealing cell fate as well as cell origin. By means of such analyses, developmental building plans of tissues and organs can be determined in a whole-embryo context. This article presents a sample preparation and imaging protocol for studying the development of whole zebrafish and Drosophila embryos using DSLM.
Imaging of Fixed Ciona Embryos for Creating 3D Digital Replicas
Authors: Robin François B. , Dauga Delphine , Tassy Olivier , Sobral Daniel , Daian Fabrice , Lemaire Patrick
Published: October 2011

During embryonic development, cell behaviors that are tightly coordinated both spatially and temporally integrate at the tissue level and drive embryonic morphogenesis. Over the past 20 years, advances in imaging techniques, in particular, the development of confocal imaging, have opened a new world in biology, not only giving us access to a wealth of information, but also creating new challenges. It is sometimes difficult to make the best use of the recordings of the complex, inherently three-dimensional (3D) processes we now can observe. In particular, these data are often not directly suitable for even simple but conceptually fundamental quantifications. This article presents a method for imaging embryonic development with cellular resolution in fixed ascidian embryos. A large fraction of the ascidian community primarily studies the development of the cosmopolitan ascidian Ciona intestinalis. Because the embryos of this species are insufficiently transparent and show significant autofluorescence, live imaging is difficult. Thus, whole embryos are fixed and optically cleared. They are then stained and imaged on a regular or two-photon confocal microscope. The resulting image stacks can subsequently be digitalized and segmented to produce 3D embryo replicas that can be interfaced to a model organism database and used to quantify cell shapes.