bluuebunny/crossref_metadata_2025 huggingface dataset:
Femtosecond polarization resolved spectroscopy: A tool for determination of the three-dimensional orientation of electronic transition dipole moments and identification of configurational isomers
Authors: Theisen Moritz , Linke Martin , Kerbs Max , Fidder Henk , Madjet Mohamed El-Amine , Zacarias Angelica , Heyne Karsten
Published: September 2009

A method is presented that combines femtosecond polarization resolved UV/visible pump–IR probe spectroscopy and density functional theory calculations in determining the three-dimensional orientation of an electronic transition dipole moment (tdm) within the molecular structure. The method is demonstrated on the approximately planar molecule coumarin 314 (C314) dissolved in acetonitrile, which can exist in two ground state configurations: the E- and the Z-isomer. Based on an exhaustive search analysis on polarization resolved measurement data for four different vibrational modes, it is concluded that C314 in acetonitrile is the E-isomer. The electronic tdm vector for the electronic S0→S1 transition is determined and the analysis shows that performing the procedure for four vibrational modes instead of the minimally required three reduces the 1σ probability area from 2.34% to 2.24% of the solution space. Moreover, the fastest rotational correlation time τc for the C314 E-isomer is determined to be 26±2 ps.
Tilted bulk heterojunction organic photovoltaic cells grown by oblique angle deposition
Authors: Li Ning , Forrest Stephen R.
Published: September 2009

We demonstrate small molecule bulk heterojunction organic photovoltaic cells using oblique angle vacuum deposition. Obliquely deposited donor chloroaluminum phthalocyanine (ClAlPc) films on indium tin oxide have surface feature sizes of ∼30 nm, resulting in ClAlPc/C60 donor-acceptor heterojunctions (HJs) with approximately twice the interface area of HJs grown at normal incidence. This results in nearly twice the external quantum efficiency in the ClAlPc absorption band compared with analogous, planar HJs. The efficiency increase is attributed to the increased surface area presented by the donor-acceptor junction to the incident illumination by ClAlPc protrusions lying obliquely to the substrate plane formed during deposition. The power conversion efficiency improves from (2.0±0.1)% to (2.8±0.1)% under 1 sun, AM 1.5G simulated solar illumination. Similarly, the power efficiency of copper phthalocyanine/C60 organic photovoltaic cells is increased from (1.3±0.1)% to (1.7±0.1)%.
A multistate local coupled cluster CC2 response method based on the Laplace transform
Authors: Kats Danylo , Schütz Martin
Published: September 2009

A new Laplace transform based multistate local CC2 response method for calculating excitation energies of extended molecular systems is presented. By virtue of the Laplace transform trick, the eigenvalue problem involving the local CC2 Jacobian is partitioned along the doubles-doubles block (which is diagonal in the parental canonical method) without losing the sparsity in the integral, amplitude, and amplitude response supermatrices. Hence, only an effective eigenvalue problem involving singles vectors has to be solved, while the doubles part can be computed on-the-fly. Within this framework, a multistate treatment of excited states with state specific and adaptive local approximations imposed on the doubles part is straightforwardly possible. Furthermore, in the context of the density fitting approximation of the two-electron integrals, a procedure to specify the local approximation, i.e., the restricted pair lists and domains, on the basis of an analysis of the object to be approximated itself is proposed. Performance and accuracy of the new Laplace transformed density fitted local CC2 (LT-DF-LCC2) response method are tested for set of different test molecules and states. It turns out that LT-DF-LCC2 response is much more robust than the earlier local CC2 response method proposed before, which failed to find some excited states in difficult cases.
Combined temperature-programmed reaction and in situ x-ray scattering studies of size-selected silver clusters under realistic reaction conditions in the epoxidation of propene
Authors: Vajda Stefan , Lee Sungsik , Sell Kristian , Barke Ingo , Kleibert Armin , von Oeynhausen Viola , Meiwes-Broer Karl-Heinz , Rodríguez Arantxa Fraile , Elam Jeffrey W. , Pellin Michael M. , Lee Byeongdu , Seifert Sönke , Winans Randall E.
Published: September 2009

The catalytic activity and dynamical shape changes in size-selected nanoclusters at work are studied under realistic reaction conditions by using a combination of simultaneous temperature-programmed reaction with in situ grazing-incidence small angle x-ray scattering. This approach allows drawing a direct correlation between nanocatalyst size, composition, shape, and its function under realistic reaction conditions for the first time. The approach is illustrated in a chemical industry highly relevant selective partial oxidation of propene on a monodisperse silver nanocatalyst. The shape of the catalyst undergoes rapid change already at room temperature upon the exposure to the reactants, followed by a complex evolution of shape with increasing temperature. Acrolein formation is observed around 50 °C while the formation of the propylene oxide exhibits a sharp onset at 80 °C and is leveling off at 150 °C. At lower temperatures acrolein is produced preferentially to propylene oxide; at temperatures above 100 °C propylene oxide is favored.
Large 1/f noise of unipolar resistance switching and its percolating nature
Authors: Lee S. B. , Park S. , Lee J. S. , Chae S. C. , Chang S. H. , Jung M. H. , Jo Y. , Kahng B. , Kang B. S. , Lee M.-J. , Noh T. W.
Published: September 2009

We investigated the 1/f noise of Pt/NiO/Pt capacitors that show unipolar resistance switching. When they were switched from the low to high resistance states, the power spectral density of the voltage fluctuation was increased by approximately five orders of magnitude. At 100 K, the relative resistance fluctuation SR/R2 in the low resistance state displayed a power law dependence on the resistance R: i.e., SR/R2∝Rw, where w=1.6±0.2. This behavior can be explained by percolation theory; however, at higher temperatures or near the switching voltage, SR/R2 becomes enhanced further. This large 1/f noise can be therefore an important problem in the development of resistance random access memory devices.
Stabilization and destabilization of second-order solitons against perturbations in the nonlinear Schrödinger equation
Authors: Yanay Hilla , Khaykovich Lev , Malomed Boris A.
Published: September 2009

We consider splitting and stabilization of second-order solitons (2-soliton breathers) in a model based on the nonlinear Schrödinger equation, which includes a small quintic term, and weak resonant nonlinearity management (NLM), i.e., time-periodic modulation of the cubic coefficient, at the frequency close to that of shape oscillations of the 2-soliton. The model applies to the light propagation in media with cubic-quintic optical nonlinearities and periodic alternation of linear loss and gain and to Bose–Einstein condensates, with the self-focusing quintic term accounting for the weak deviation of the dynamics from one dimensionality, while the NLM can be induced by means of the Feshbach resonance. We propose an explanation to the effect of the resonant splitting of the 2-soliton under the action of the NLM. Then, using systematic simulations and an analytical approach, we conclude that the weak quintic nonlinearity with the self-focusing sign stabilizes the 2-soliton, while the self-defocusing quintic nonlinearity accelerates its splitting. It is also shown that the quintic term with the self-defocusing/focusing sign makes the resonant response of the 2-soliton to the NLM essentially broader in terms of the frequency.
Carbon nanotube volatile organic liquid sensor
Authors: Song Youngsik , Choi Jaewu
Published: September 2009

Volatile organic liquid sensors with two distinct configurations are developed for a future biosensor using laterally grown carbon nanotubes (CNTs) from two isolated metal electrodes. In the first configuration, the CNTs grown from each electrode weakly contact each other, and the charge transport between them is based on tunneling. In the second configuration, the CNTs in the array are covered with a silicone composite paste and strongly contact each other; Ohmic transport behavior is observed. The signal modulation amplitude with exposure to the volatile organic liquid is higher than two orders in magnitude. The sensing mechanism is based on the capillary force between CNTs and the swelling property of the silicone paste induced by the organic liquids.
Effect of the interfacial area on the equilibrium properties of Lennard-Jones fluid
Authors: Janeček Jiří
Published: September 2009

The influence of the system size on the interfacial and equilibrium properties of the Lennard-Jones fluid obtained using the inhomogeneous Monte Carlo simulations is studied for temperatures covering the vapor-liquid coexistence region. The values of the surface tension, coexistence densities, as well as the pressure of saturated vapor are affected by the varying area of the interface. Moreover the loss of isotropy of the fluid structure is observed as a consequence of using the periodic boundary conditions in molecular simulations. The equilibrium properties are evaluated also in simulation boxes of the shape of hexangular prism and compared to the results of simulations performed in the commonly used quadrangular parallelepiped. Both sets seem to be affected by the finite-size effects in similar extent.
The molecular mean-field approach for correlated relativistic calculations
Authors: Sikkema Jetze , Visscher Lucas , Saue Trond , Iliaš Miroslav
Published: September 2009

A new approach for relativistic correlated electron structure calculations is proposed by which a transformation to a two-spinor basis is carried out after solving the four-component relativistic Hartree–Fock equations. The method is shown to be more accurate than approaches that apply an a priori transformation to a two-spinor basis. We also demonstrate how the two-component relativistic calculations with properly transformed two-electron interaction can be simulated at the four-component level by projection techniques, thus allowing an assessment of errors introduced by more approximate schemes.
Assessing the monitoring of sooty shearwater (Puffinus griseus) abundance in southern New Zealand
Authors: McKechnie Sam , Bragg Corey , Newman Jamie , Scott Darren , Fletcher David , Moller Henrik
Published: September 2009

Recent declines of many seabird populations have placed increased emphasis on determining the status of potentially threatened species. However, the burrow-nesting habits and inter-annual fluctuation in breeding numbers of some species make trend detection difficult, and so knowledge of their population dynamics often remains coarse. Here we report observed fluctuations, and assess the efficacy of monitoring of sooty shearwaters (Puffinus griseus), on three islands in southern New Zealand between the breeding seasons of 1996–97 and 2004–05. Apart from a steady increase in burrow-occupant density at one island, few significant trends in abundance measures were detected. Considerable variation among individual sites within islands led to high uncertainty in island-wide trend estimates. Simulations showed that the measurements of occupant density have a limited ability of detecting all but very pronounced trends, whereas changes in burrow-entrance density are more likely to be detected. Annual fluctuations in the proportion of occupied burrows at individual sampling sites were highly synchronous within islands and reasonably synchronous between two of the islands, suggesting that breeding numbers are at least partly determined by broad-scale factors. The large declines in the abundance of sooty shearwaters reported from the late 1980s to mid-1990s appear not to have continued through our monitoring period. Lack of adequate within- and among-island replication, and short time series of data may severely reduce our ability reliably to detect population trends in many studies of burrowing Procellariiformes.
Do utility corridors affect movements of small terrestrial fauna?
Authors: Carthew Susan M. , Horner Briony , Jones Katherine M. W.
Published: September 2009

Linear forest clearings created by utility corridors have the potential to fragment landscapes, create edge effects and isolate populations of plants and animals. Here, we investigated the impact of utility corridors on small terrestrial fauna inhabiting Nangwarry Native Forest Reserve, south of Penola in south-eastern South Australia. Twelve sites straddling linear clearings of two widths (1.5 and 4.2 m) were surveyed over 2 years with 53 traps arranged as five transects at each site. This resulted in a total of 933 captures of 18 vertebrate species, including four amphibians, eight reptiles and six mammals. Propensity for capture near edges v. interiors, distances moved between recaptures and willingness to cross linear clearings varied among species, and was not related to taxa groups. For example, the small skink Bassiana duperreyi was extremely mobile and crossed tracks regularly. At the other extreme, the frog Neobatrachus pictus was more likely to be caught on interior transects and was never recorded moving between captures. The small dasyurid Antechinus flavipes was the most regularly caught species, and made both short- (<50 m) and long-distance (>1500 m) movements, with longer moves made by dispersing juveniles. Movements by this species often involved clearing crossings, although these were more likely when time between recaptures was longer, particularly for females. However, the overall rate of crossings for this species was not different from that expected if movements were random. In conclusion, the relatively narrow utility corridors studied here did not appear to affect the mobility of the majority of vertebrates significantly, with approximately half of the 85 movements recorded being of animals crossing a clearing, and no significant difference between the proportion crossing the wider (4.2 m) and the narrower (1.5 m) clearings. The present study is one of only a handful investigating movement patterns in reptiles and amphibians, particularly in relation to disturbances. However, sample sizes were small for some species, and future work should focus on those species that look to be either particularly mobile or sedentary, and encompass responses to the wider (up to 15 m) permanent tracks in the region.
Predicting the ecological impact of cane toads (Bufo marinus) on threatened camaenid land snails in north-western Australia
Authors: Pearson David , Greenlees Matthew , Ward-Fear Georgia , Shine Richard
Published: September 2009

The spread of cane toads (Bufo marinus) through north-western Australia may threaten populations of endemic camaenid land snails because these snails exhibit restricted geographic distributions, low vagility and ‘slow’ life-histories. We conducted laboratory trials to determine whether toads would consume camaenids if they encountered them, and conducted field surveys to evaluate the likelihood of such encounters (on the basis of habitat overlap). In laboratory trials with 13 camaenid species, cane toads were more likely to consume camaenids than were two species of native frogs that we tested (Cyclorana australis, Litoria caerulea). However, field surveys suggested that many camaenids are active on vertical surfaces in limestone outcrops, and cane toads rarely venture into these habitats. Although the preferred habitats and activity patterns of camaenids thus reduce their vulnerability to cane toads, we recommend regular surveys of toad and snail numbers to monitor toad impacts. Given the restricted distributions of threatened saxicoline camaenid species in the Kimberley, localised management of grazing stock and fire is feasible to maintain vine-thicket vegetation cover and snail populations, as well as reducing open habitats favoured by toads.
Neural computations underlying action-based decision making in the human brain
Authors: Wunderlich Klaus , Rangel Antonio , O'Doherty John P.
Published: September 2009

Action-based decision making involves choices between different physical actions to obtain rewards. To make such decisions the brain needs to assign a value to each action and then compare them to make a choice. Using fMRI in human subjects, we found evidence for action-value signals in supplementary motor cortex. Separate brain regions, most prominently ventromedial prefrontal cortex, were involved in encoding the expected value of the action that was ultimately taken. These findings differentiate two main forms of value signals in the human brain: those relating to the value of each available action, likely reflecting signals that are a precursor of choice, and those corresponding to the expected value of the action that is subsequently chosen, and therefore reflecting the consequence of the decision process. Furthermore, we also found signals in the dorsomedial frontal cortex that resemble the output of a decision comparator, which implicates this region in the computation of the decision itself.
Life and death during the Great Depression
Authors: Tapia Granados José A. , Diez Roux Ana V.
Published: September 2009

Recent events highlight the importance of examining the impact of economic downturns on population health. The Great Depression of the 1930s was the most important economic downturn in the U.S. in the twentieth century. We used historical life expectancy and mortality data to examine associations of economic growth with population health for the period 1920–1940. We conducted descriptive analyses of trends and examined associations between annual changes in health indicators and annual changes in economic activity using correlations and regression models. Population health did not decline and indeed generally improved during the 4 years of the Great Depression, 1930–1933, with mortality decreasing for almost all ages, and life expectancy increasing by several years in males, females, whites, and nonwhites. For most age groups, mortality tended to peak during years of strong economic expansion (such as 1923, 1926, 1929, and 1936–1937). In contrast, the recessions of 1921, 1930–1933, and 1938 coincided with declines in mortality and gains in life expectancy. The only exception was suicide mortality which increased during the Great Depression, but accounted for less than 2% of deaths. Correlation and regression analyses confirmed a significant negative effect of economic expansions on health gains. The evolution of population health during the years 1920–1940 confirms the counterintuitive hypothesis that, as in other historical periods and market economies, population health tends to evolve better during recessions than in expansions.
Myosins pull together—separately
Authors: Leslie Mitch
Published: September 2009

Study suggests that asynchronous molecular motors can integrate their actions.
Transforming growth factor β is dispensable for the molecular orchestration of Th17 cell differentiation
Authors: Das Jyoti , Ren Guangwen , Zhang Liying , Roberts Arthur I. , Zhao Xin , Bothwell Alfred L.M. , Van Kaer Luc , Shi Yufang , Das Gobardhan
Published: September 2009

Interleukin (IL)-17–producing T helper (Th17) cells play a critical role in the pathophysiology of several autoimmune disorders. The differentiation of Th17 cells requires the simultaneous presence of an unusual combination of cytokines: IL-6, a proinflammatory cytokine, and transforming growth factor (TGF) β, an antiinflammatory cytokine. However, the molecular mechanisms by which TGF-β exerts its effects on Th17 cell differentiation remain elusive. We report that TGF-β does not directly promote Th17 cell differentiation but instead acts indirectly by blocking expression of the transcription factors signal transducer and activator of transcription (STAT) 4 and GATA-3, thus preventing Th1 and Th2 cell differentiation. In contrast, TGF-β had no effect on the expression of retinoic acid receptor–related orphan nuclear receptor γt, a Th17-specific transcription factor. Interestingly, in Stat-6−/−T-bet−/− mice, which are unable to generate Th1 and Th2 cells, IL-6 alone was sufficient to induce robust differentiation of Th17 cells, whereas TGF-β had no effect, suggesting that TGF-β is dispensable for Th17 cell development. Consequently, BALB/c Stat-6−/−T-bet−/− mice, but not wild-type BALB/c mice, were highly susceptible to the development of experimental autoimmune encephalomyelitis, which could be blocked by anti–IL-17 antibodies but not by anti–TGF-β antibodies. Collectively, these data provide evidence that TGF-β is not directly required for the molecular orchestration of Th17 cell differentiation.
Dendritic cells are crucial for maintenance of tertiary lymphoid structures in the lung of influenza virus–infected mice
Authors: GeurtsvanKessel Corine H. , Willart Monique A.M. , Bergen Ingrid M. , van Rijt Leonie S. , Muskens Femke , Elewaut Dirk , Osterhaus Albert D.M.E. , Hendriks Rudi , Rimmelzwaan Guus F. , Lambrecht Bart N.
Published: September 2009

Tertiary lymphoid organs (TLOs) are organized aggregates of B and T cells formed in postembryonic life in response to chronic immune responses to infectious agents or self-antigens. Although CD11c+ dendritic cells (DCs) are consistently found in regions of TLO, their contribution to TLO organization has not been studied in detail. We found that CD11chi DCs are essential for the maintenance of inducible bronchus-associated lymphoid tissue (iBALT), a form of TLO induced in the lungs after influenza virus infection. Elimination of DCs after the virus had been cleared from the lung resulted in iBALT disintegration and reduction in germinal center (GC) reactions, which led to significantly reduced numbers of class-switched plasma cells in the lung and bone marrow and reduction in protective antiviral serum immunoglobulins. Mechanistically, DCs isolated from the lungs of mice with iBALT no longer presented viral antigens to T cells but were a source of lymphotoxin (LT) β and homeostatic chemokines (CXCL-12 and -13 and CCL-19 and -21) known to contribute to TLO organization. Like depletion of DCs, blockade of LTβ receptor signaling after virus clearance led to disintegration of iBALT and GC reactions. Together, our data reveal a previously unappreciated function of lung DCs in iBALT homeostasis and humoral immunity to influenza virus.
Mickie Bhatia: Embryonic stem cells come of age
Authors: Maxmen Amy
Published: September 2009

Mickie Bhatia wants to tap into the therapeutic potential of human stem cells, and he's finding ways to overcome the obstacles that stand in his way.
Antimicrobial Susceptibility of Bacteria Isolated from Urine Samples Obtained from Nursing Home Residents
Authors: Das Rituparna , Perrelli Eleanor , Towle Virginia , Van Ness Peter H. , Juthani-Mehta Manisha
Published: September 2009

In our study of nursing home residents with clinically suspected urinary tract infection who did not require the use of an indwelling catheter, we identified bacteria isolated from urine samples, the resistance patterns of these isolated bacteria, and the antibiotic therapy prescribed to the residents. Escherichia coli, the predominant organism isolated, frequently was resistant to commonly prescribed oral antibiotics. Trimethoprim-sulfamethoxazole remains the best empiric antimicrobial therapy for a urinary tract infection, but nitrofurantoin should be considered if E. coli is identified.
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
Authors: Agarwal Shashank , Yu Hong
Published: September 2009

Biomedical texts can be typically represented by four rhetorical categories: Introduction, Methods, Results and Discussion (IMRAD). Classifying sentences into these categories can benefit many other text-mining tasks. Although many studies have applied different approaches for automatically classifying sentences in MEDLINE abstracts into the IMRAD categories, few have explored the classification of sentences that appear in full-text biomedical articles. We first evaluated whether sentences in full-text biomedical articles could be reliably annotated into the IMRAD format and then explored different approaches for automatically classifying these sentences into the IMRAD categories. Our results show an overall annotation agreement of 82.14% with a Kappa score of 0.756. The best classification system is a multinomial naïve Bayes classifier trained on manually annotated data that achieved 91.95% accuracy and an average F-score of 91.55%, which is significantly higher than baseline systems. A web version of this system is available online at—http://wood.ims.uwm.edu/full_text_classifier/.

Contact:  hongyu@uwm.edu
Automatic assignment of reaction operators to enzymatic reactions
Authors: Leber Markus , Egelhofer Volker , Schomburg Ida , Schomburg Dietmar
Published: September 2009

Background: Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis. Frequently rearrangements and deletions of enzymes and sub-subclasses are necessary.

Results: We use the Dugundji–Ugi model for coding of biochemical reactions which is based on electron shift patterns occurring during reactions. Changes of the bonds or of non-bonded valence electrons are expressed by reaction matrices. Our program calculates reaction matrices automatically on the sole basis of substrate and product chemical structures based on a new strategy for maximal common substructure determination, which allows an accurate atom mapping of the substrate and product atoms. The system has been tested for a large set of enzymatic reactions including all sub-subclasses of the EC classification system. Altogether 147 different representative reaction operators were found in the classified enzymes, 121 of which are unique with respect to an EC sub-subclass. The other 26 comprise groups of enzymes with very similar reactions, being identical with respect to the bonds formed and broken.

Conclusion: The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji–Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions.

Availability: The program to generate reaction matrix descriptors is available upon request.

Contact:  d.schomburg@tu-bs.de
Cleavage of protease-activated receptors on an immortalized oral epithelial cell line by Porphyromonas gingivalis gingipains
Authors: Giacaman Rodrigo A. , Asrani Anil C. , Ross Karen F. , Herzberg Mark C.
Published: September 2009

Porphyromonas gingivalisactivates protease-activated receptors (PARs) on oral keratinocytes, resulting in downstream signalling for an innate immune response. Activation depends onP. gingivalisgingipains, but could be confounded by lipopolysaccharide signalling through Toll-like receptors. We therefore hypothesized thatP. gingivaliscleaves oral keratinocyte PARs in an Arg- (Rgp) or Lys- (Kgp) gingipain-specific manner to upregulate pro-inflammatory cytokines. Immortalized human oral keratinocytes (TERT-2) were incubated with wild-typeP. gingivalis(ATCC 33277) or strains from a panel of isogenic gingipain deletion mutants: Kgp-deficient (KDP 129); Rgp-deficient (KDP 133); or Kgp- and Rgp-deficient (KDP 136). After incubation withP. gingivalis, keratinocytes were probed with specific antibodies against the N-terminus of PAR-1 and PAR-2. Using flow cytometry and immunofluorescence, receptor cleavage was marked by loss of specific antibody binding to the respective PARs. TERT-2 cells constitutively expressed high levels of PAR-1 and PAR-2, and lower levels of PAR-3.P. gingivalisATCC 33277 cleaved PAR-1 and PAR-2 in a dose-dependent manner, while the receptors were unaffected by the protease-negative double mutant (KDP 136) at all m.o.i. tested. The single Kgp-negative mutant preferentially cleaved PAR-1, whereas the Rgp-negative mutant cleaved PAR-2. Wild-type or Kgp-negative mutant cleavage of PAR-1 upregulated expression of IL-1α, IL-1β, IL-6 and TNF-α; the Rgp-negative mutant did not modulate these cytokines. Selective cleavage of PAR-1 on oral epithelial cells byP. gingivalisRgp therefore upregulates expression of pro-inflammatory cytokines.
Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis
Authors: Dunn M. F. , Ramírez-Trujillo J. A. , Hernández-Lucas I.
Published: September 2009

The glyoxylate cycle is an anaplerotic pathway of the tricarboxylic acid (TCA) cycle that allows growth on C2 compounds by bypassing the CO2-generating steps of the TCA cycle. The unique enzymes of this route are isocitrate lyase (ICL) and malate synthase (MS). ICL cleaves isocitrate to glyoxylate and succinate, and MS converts glyoxylate and acetyl-CoA to malate. The end products of the bypass can be used for gluconeogenesis and other biosynthetic processes. The glyoxylate cycle occurs in Eukarya, Bacteria and Archaea. Recent studies of ICL- and MS-deficient strains as well as proteomic and transcriptional analyses show that these enzymes are often important in human, animal and plant pathogenesis. These studies have extended our understanding of the metabolic pathways essential for the survival of pathogens inside the host and provide a more complete picture of the physiology of pathogenic micro-organisms. Hopefully, the recent knowledge generated about the role of the glyoxylate cycle in virulence can be used for the development of new vaccines, or specific inhibitors to combat bacterial and fungal diseases.
Genealogical typing of Neisseria meningitidis
Authors: Didelot Xavier , Urwin Rachel , Maiden Martin C. J. , Falush Daniel
Published: September 2009

Despite the increasing popularity of multilocus sequence typing (MLST), the most appropriate method for characterizing bacterial variation and facilitating epidemiological investigations remains a matter of debate. Here, we propose that different typing schemes should be compared on the basis of their power to infer clonal relationships and investigate the utility of sequence data for genealogical reconstruction by exploiting new statistical tools and data from 20 housekeeping loci for 93 isolates of the bacterial pathogenNeisseria meningitidis. Our analysis demonstrated that all but one of the hyperinvasive isolates established by multilocus enzyme electrophoresis and MLST were grouped into one of six genealogical lineages, each of which contained substantial variation. Due to the confounding effect of recombination, evolutionary relationships among these lineages remained unclear, even using 20 loci. Analyses of the seven loci in the standard MLST scheme using the same methods reproduced this classification, but were unable to support finer inferences concerning the relationships between the members within each complex.
Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa
Authors: Mackey Robin L. , Page Bruce R. , Grobler Douw , Slotow Rob
Published: September 2009

Re‐introduced African elephant (Loxodonta africanaBlumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.
The stem cells of small intestinal crypts: where are they?
Authors: Potten C. S. , Gandara R. , Mahida Y. R. , Loeffler M. , Wright N. A.
Published: September 2009

Recently, there has been resurgence of interest in the question of small intestinal stem cells, their precise location and numbers in the crypts. In this article, we attempt to re‐assess the data, including historical information often omitted in recent studies on the subject. The conclusion we draw is that the evidence supports the concept that active murine small intestinal stem cells in steady state are few in number and are proliferative. There are two evolving, but divergent views on their location (which may be more related to scope of capability and reversibility than to location) several lineage labelling and stem cell self‐renewing studies (based on Lgr5 expression) suggest a location intercalated between the Paneth cells (crypt base columnar cells (CBCCs)), or classical cell kinetic, label‐retention and radiobiological evidence plus other recent studies, pointing to a location four cell positions luminally from the base of the crypt The latter is supported by recent lineage labelling of Bmi‐1‐expressing cells and by studies on expression of Wip‐1 phosphatase. The situation in the human small intestine remains unclear, but recent mtDNA mutation studies suggest that the stem cells in humans are also located above the Paneth cell zone. There could be a distinct and as yet undiscovered relationship between these observed traits, with stem cell properties both in cells of the crypt base and those at cell position 4.
Bony remodelling in unilateral dermatomal cavernous haemangiomatosis of the arm
Authors: Kraus A. , Richards P. J. , Tan B. B.
Published: September 2009

We report a case of a massive unilateral dermatomal cavernous haemangioma (UDCH) affecting the left arm and adjacent neck in the region of the C4–C8 dermatomes, with associated bony remodelling. To our knowledge, this is the first report of the rare condition UDCH with bony abnormalities.
The effect of regular exercise on penile nitric oxide synthase expression in rats
Authors: Ozbek Emin , Tasci Ali Ihsan , Ilbey Yusuf Ozlem , Simsek Abdulmuttalip , Somay Adnan , Metin Gokhan
Published: September 2009

Erectile dysfunction (ED) is a major public health problem that seriously affects the quality of life of patients and their partners and its prevalence increases significantly with ageing. In this study, we tested the hypothesis that age‐associated decrease in penile endothelial (eNOS) and neuronal nitric oxide synthase (nNOS) activity in aged rats may be increased by regular exercise. A total of 28 young (4 m) and aged (24 m) male rats were divided into four equal groups: group 1 – young control; group 2 – young trained; group 3 – old control and group 4 – old trained group. Groups 2 and 4 rats were trained to swim for 30 min a day and 5 days a week, which lasted 8 weeks. At the end of 8 weeks, rats were sacrificed and penile tissues evaluated for eNOS and nNOS activities. eNOS and nNOS activities were evaluated by immunohistochemistry in paraffinized penile tissues and results assessed semiquantitatively. Results also were compared with healthy age‐matched and adult (4 m) controls. Serum level of testosterone (T) was determined using ELISA kits (Beckman Coulter, Fullerton, CA, USA). In penile tissues of aged control rats, eNOS and nNOS staining were weakly positive; however in trained groups, eNOS and nNOS immunoreactivity were increased. In young control group, eNOS and nNOS activities were more intense than aged control. eNOS and nNOS activities were higher in adult trained group than control. Serum T concentrations were significantly higher in young and aged trained group than in control groups. We can suggest that regular exercise upregulates eNOS and nNOS expressions in the aged and young rat penis. Regular exercise may improve penile erection by increasing penile neurotransmitter in both young and aged rats.
Elevated mtDNA diversity in introduced populations of Cynotilapia afra (Günther 1894) in Lake Malawi National Park is evidence for multiple source populations and hybridization
Authors: ZIDANA HASTINGS , TURNER GEORGE F. , Van OOSTERHOUT COCK , HÄNFLING BERND
Published: September 2009

Genetic variation in many invasive species shows little or no signs of a founder event, suggesting that high genetic diversity may facilitate establishment success. The rocky‐shore, plankton‐feeding cichlid fish Cynotilapia afra is endemic to Lake Malawi, but naturally absent from many suitable sites. In the 1960s, this species was introduced to the southern areas of the lake, presumably as a result of the aquarium fish trade. It has now become established on a number of rocky areas within the Lake Malawi National Park. Here, we analysed DNA sequence variation in the mitochondrial control region of six native and four introduced populations of C. afra, and three populations of the closely‐related and hybridizing Pseudotropheus zebra. In contrast to previous studies of Lake Malawi rock dwelling cichlids, network analyses suggested that native populations of C. afra showed high levels of lineage sorting in mtDNA. Introduced populations showed higher sequence and haplotype diversity than their native counterparts. Our analyses suggested that the elevated gene diversity was largely attributed to the fact that the introduced C. afra populations were derived from several genetically distinct and geographically separate populations, and to a lesser extent because of introgressive hybridization with native P. zebra. The establishment and spread of C. afra may be partly because of its ability to occupy a vacant ecological niche, but it may also have been facilitated by its enhanced genetic diversity.
The first evidence that a single cellulase can be essential for cellulose degradation in a cellulolytic microorganism
Authors: Wilson David B.
Published: September 2009

Cellulose is the most abundant carbon source in nature but it is very difficult to degrade because of its insolubility, quasi‐crystalline structure and its presence in plant cell walls in a matrix with other polymers that limit access to the cellulose surface. Most cellulose in soils is degraded by cellulolytic microorganisms that use a number of different approaches to overcome the recalcitrance of cellulose in plant cell walls. All of these approaches involve multiple cellulases and, since cellulose is insoluble and microorganisms cannot ingest particles, the cellulases are present outside of the cell although they can be attached to its outer surface. An impressive article by Tolonen et al. in this issue of Molecular Microbiology shows that deletion of the single family 9 cellulase gene in Clostridium phytofermentans prevents growth on cellulose although the mutant strain grows perfectly well on glucose and its other cellulase genes are transcribed normally. These results show for the first time that a single cellulase can be essential for cellulose degradation by an organism despite the presence of several other cellulases. It will be interesting to learn the detailed mechanism that C. phytofermentans uses to degrade cellulose.
Residential proximity to main roads during pregnancy and the risk of allergic disorders in Japanese infants: The Osaka Maternal and Child Health Study
Authors: Miyake Yoshihiro , Tanaka Keiko , Fujiwara Hiroshi , Mitani Yasuhiro , Ikemi Hiroaki , Sasaki Satoshi , Ohya Yukihiro , Hirota Yoshio
Published: September 2009

Miyake Y, Tanaka K, Fujiwara H, Mitani Y, Ikemi H, Sasaki S, Ohya Y, Hirota Y. Residential proximity to main roads during pregnancy and the risk of allergic disorders in Japanese infants: The Osaka Maternal and Child Health Study. Pediatr Allergy Immunol 2010: 21: 22–28. © 2009 John Wiley & Sons A/S

The role of traffic‐related air pollution in the initiation of allergic disorders in children is still not clearly understood. The present prospective study examined the relation between proximity of the home during pregnancy to the nearest main road, which was used as a surrogate for traffic‐related air pollutants, and the risk of allergic disorders in Japanese infants in an urban area. Subjects were 756 mother–child pairs. Distance of each subject’s home during pregnancy from the center line of all of the 235 main roads in Osaka Prefecture was computed using geographical information system software. The first survey during pregnancy and the second survey between 2 and 9 months post‐partum collected information on potential confounding factors. In the third survey, which was from 16 to 24 months post‐partum, a self‐administered questionnaire included questions on allergic disorders. In the third survey, 22.1% and 18.7% of infants became positive for wheeze and atopic eczema based on criteria of the International Study of Asthma and Allergies in Childhood (ISAAC), respectively. The risk of doctor‐diagnosed asthma and doctor‐diagnosed atopic eczema was 4.4% and 8.9%, respectively. A shorter distance of the residence during pregnancy from the nearest main road was associated with an increased risk of doctor‐diagnosed asthma and atopic eczema (adjusted odds ratios for comparison of <50 m with 200 m or more = 4.01 and 2.26, 95% confidence intervals: 1.44–11.24 and 1.08–4.59, p for trend = 0.02 and 0.03, respectively). No evident relationships were observed between the distance of the residence during pregnancy from the nearest main road and the risk of wheeze or atopic eczema based on the ISAAC criteria. It was difficult to distinguish the effect of the pre‐natal from the post‐natal exposure because most subjects lived at the same home address both before and after childbirth. Our results are likely to support the hypothesis that intrauterine exposure to traffic‐related air pollutants and/or such exposure after birth may increase the risk of more extreme manifestations of allergic disorders in infants.
Executive summary
Authors: Hering Bernhard J. , Cooper David K. C. , Cozzi Emanuele , Schuurman Henk‐Jan , Korbutt Gregory S. , Denner Joachim , O’Connell Philip J. , Vanderpool Harold Y. , Pierson III Richard N.
Published: September 2009

Abstract:  The International Xenotransplantation Association islet xenotransplantation consensus statement describes the conditions for undertaking clinical trials of porcine islet products in type 1 diabetes. Chapter 1 reviews the key ethical requirements and progress toward the definition of an international regulatory framework for clinical trials of xenotransplantation. Chapters 2 to 7 provide in depth and agreed‐upon recommendations on source pigs, pig islet product manufacturing and release testing, preclinical efficacy and complication data required to justify a clinical trial, strategies to prevent transmission of porcine endogenous retrovirus, patient selection for clinical trials, and informed consent. It is planned to update this initial consensus statement in a year's time in light of progress in research, changes in the regulatory framework, and comments submitted after publication.
Chapter 6: Patient selection for pilot clinical trials of islet xenotransplantation
Authors: O’Connell Philip J.
Published: September 2009

Abstract:  Several clinical scenarios would justify trials of islet xenotransplantation, including islet after kidney (IAK) transplantation and islet xenotransplantation for hypoglycemia unawareness. In selecting a patient cohort, several factors unique to xenotransplant trials must be considered, including the potential for unique infective complications, the risks of immunosuppression, and the requirement for life‐long monitoring. These factors need to be balanced against the benefits of improved glycemic control and ability to deliver large numbers of high‐quality islets, something more difficult to achieve in islet allotransplantation. The importance of these risks varies depending on the patient cohort selected and proposed therapy to be undertaken. In islet xenotransplantation for hypoglycemia unawareness, immunosuppressive risks, and problems with life‐long monitoring need special attention in trial design. Whereas in IAK xenotransplantation, consideration must be given to ensure that the procedure does not impact on renal allograft outcomes and patient co‐morbidity, which is already significant in renal transplant recipients. This review outlines the rationale for undertaking islet xenotransplantation in highly select patients with type 1diabetes and addresses some of the unique challenges. At present, no clear consensus exists as to the most appropriate patient group for the first trials of islet xenotransplantation. Rather, this will depend on the type of treatment being proposed, the potential infective risks and the overall burden of immunosuppression.

Table of Contents

Introduction

Selecting a patient cohort with hypoglycemia unawareness for a trial of clinical islet xenotransplantation

Selecting a patient cohort for a trial of xeno‐islet/renal allotransplantation

Conclusion
Strategic Localization of Toll‐like Receptor 4 in the Digestive Tract of Blunt Snout Bream (Megalobrama amblycephala)
Authors: Zhang G. Y. , Wang Y. , Peng K. M. , Wang C. , Tian G. , Liu H. Z.
Published: September 2009

This study was performed to determine the localization strategies of Toll‐like Receptor 4 (TLR4) in digestive tract (oesophagus, bulbodium, foregut, midgut and hindgut) of Blunt snout bream (Megalobrama amblycephala) using immunohistochemical staining method. TLR4 positive cells were observed throughout the digestive tract. In the oesophagus, some positive reactions in lamina propria were found around small blood vessels and there were also some positive cells within the stratified squamous epithelium. Lots of positive cells were observed in the muscular layer of the oesophagus. In bulbodium, foregut and hindgut, the expression of TLR4 was mainly restricted to the apical surface of epithelial cells located at the bottom of the mucosal folds and the mesenchymal cells in lamina propria. It was very interesting that epithelial cells in the midgut, but none in other parts, had many TLR4 positive cytoplasmic granular structures which were also periodic acid Schiff positive. These findings suggested that TLR4 was expressed in a compartmentalized manner in the Blunt snout bream (M. amblycephala) digestive tract and provided novel information about the in vivo localization of pattern recognition receptors.
Histological Structure and Distribution of Carbonic Anhydrase Isozymes (CA‐I, II, III and VI) in Major Salivary Glands in Koalas
Authors: Mizuno T. , McKinnon A. , Ichihara N. , Amasaki T. , Asari M. , Nishita T. , Oishi M. , Soeta S. , Amasaki H.
Published: September 2009

While the mandibular glands usually consist of only mucous acinar cells or a combination of mucous and serous cells in other species of mammals, those of koalas were serous glands. Rabbit mono‐specific polyclonal anti‐canine CA‐I, II, III or VI antiserum showed cross‐reactivity against corresponding koala carbonic anhydrase (CA) isozymes. Although immunohistochemical reactions to CA‐I, II and VI in ductal cells were moderate to strong in the tested salivary glands, no reaction or only slight reactions were observed against CA‐III. In the sublingual glands, moderate immunohistochemical reactions to CA‐I, II and VI were also evident in serous acinar cells and serous demilunes. However, no reactions to the tested isozymes were observed in mucous acinar cells in these glands. With the exception of the histological structure of the mandibular glands, histological features and the distributional profile of CA isozymes of the salivary glands in koalas are relatively close to results obtained from horses.