bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrastructural changes in the myxamoebae of Physarum polycephalum in response to a microcyst-inducing concentration of mannitol
Authors: Williams Lynda M. , Lafontaine Jean-G.
Published: November 2007

The response of axenically cultured Physarum polycephalum myxamoebae to a microcyst-inducing concentration of mannitol (0.5 M) has been studied for both log-phase and maximum-concentration cultures. Results indicate that mannitol alone is not sufficient to induce encystment; a population effect is also necessary. Myxamoebae may continue to divide in the presence of mannitol if this effect is absent. Early ultrastructural changes have been noted indicating that the primary mode of action of mannitol is via the change in osmotic potential of the medium. Nuclear and cytoplasmic ultrastructural changes during the encystment process are documented. Recovery of log-phase cells to undergo mitosis involves definite morphological changes, which are also described. Ruthenium red staining was utilised to emphasize changes in the cell coat and indicate possible sites of accumulation of cell wall material.
Natural intersectional hybridization between North American species of Populus (Salicaceae) in sections Aigeiros and Tacamahaca. II. Taxonomy
Authors: Eckenwalder James E.
Published: November 2007

Five of six possible hybrid combinations of the two native North American species of Populus sect. Aigeiros Duby with the three native species of sect. Tacamahaca Spach have been found in nature. Putative hybrids occur wherever species of the two sections are sympatric and sometimes even beyond the range of one or both parents. Parents of the sixth possible combination are not, however, sympatric and this explains the apparent absence of the corresponding hybrid. Although the five hybrids can easily be recognized as a group, each parentage yields hybrids of unique morphology, all of which have previously been provided with binomials. Variability within each hybrid reflects variation in its parents. These hybrids are morphologically intermediate between their putative parents and have an additive chromatographic profile combining leaf flavonoids of each pair. Trees of P. × generosa (P. deltoides × P. trichocarpa) and P. × jackii (P. deltoides × P. balsamifera) from natural populations closely resemble artificial hybrids between their presumed parents. Three natural hybrids, P. × acuminata (P. deltoides × P. anguslifolia), P. × jackii, and P. × parryi (P. fremontii × P. trichocarpa), are all cultivated as shade trees. Keys distinguish the five hybrids from each other and from their parents; each hybrid is described; its nomenclature is clarified; and its range is mapped in relation to those of its parents.
Evidence of competition for water as a factor in the mechanism of root-bud inhibition in milkweed (Asclepias syriaca)
Authors: Hsiao Andrew I. , McIntyre Gordon I.
Published: November 2007

In experiments with seedlings of milkweed, Asclepias syriaca L., grown in sand culture under controlled conditions, growth of the root buds was significantly increased within 24 h of the excision of the parent shoot. However, only a few of the measured buds continued to grow, the growth of most of the remianing buds being arrested within 48 h of their release from inhibition. At low humidity (approx. 30–50% relative humidity (RH)), the decapitated disbudded stem, bearing only a single pair of leaves, promoted the early growth of the root buds but strongly inhibited their subsequent elongation and emergence as shoots. The mature stem itself, when completely defoliated, also exerted a significant degree of inhibition of root-shoot production. At high humidity (93–100% RH), which reduced transpiration by approximately 50%, this inhibiting effect of mature shoot tissue was either eliminated or greatly reduced, while the rate of emergence and subsequent growth of shoots produced from the root buds following the complete removal of the parent shoot were also significantly increased. The results suggest, as a working hypothesis, that transpiration-induced reduction in water potential (ψ) plays a major role in the mechanism of root-bud inhibition.
RETAILER'S INVENTORY POLICY AND SUPPLIER'S DELIVERY POLICY UNDER TWO-LEVEL TRADE CREDIT STRATEGY
Authors: SU CHIA-HSIEN , OUYANG LIANG-YUH , HO CHIA-HUEI , CHANG CHUN-TAO
Published: November 2007

This paper presents a stylized model to determine the optimal strategy for the integrated supplier-retailer inventory model under the condition that both the supplier and retailer have adopted a trade credit strategy. By analyzing the total channel profit function, we develop an algorithm to simultaneously determine the retailer's optimal order quantity and the number of shipment per production run from the supplier to the retailer. Our results demonstrate that the trade credit strategy is effective to supply chain system performance when customers are sensitive to the credit period length offered by the retailer. Moreover, when customers are sensitive to the credit period, if the retailer conveys partial advantage gained from the trade credit offered by the supplier to customers by suitably adjusting the customer's credit period then the entire system and every channel partner can benefit.
TIME AS A QUANTUM OBSERVABLE
Authors: OLKHOVSKY V. S. , RECAMI E.
Published: November 2007

Some new results are presented and recent developments are reviewed on the study of Time in quantum physics as an observable, canonically conjugate to energy. Operators for the observable Time are investigated in particle and photon quantum theory. In particular, this paper deals with the Hermitian (more precisely, maximal Hermitian, but non-self-adjoint) operator for Time which appears: (i) for particles, in ordinary nonrelativistic quantum mechanics; and (ii) for photons (i.e. in first-quantization quantum electrodynamics). In conclusion, various recent and possible future applications of the time quantum analysis for tunnelling processes, nuclear collisions and systems with (quasi)discrete energy spectra are indicated.
HIGHER GAUGE THEORY AND GRAVITY IN 2+1 DIMENSIONS
Authors: MANN R. B. , POPESCU E. M.
Published: November 2007

Non-Abelian higher gauge theory has recently emerged as a generalization of standard gauge theory to higher-dimensional (two-dimensional in the present context) connection forms, and as such, it has been successfully applied to the non-Abelian generalizations of the Yang–Mills theory and 2-form electrodynamics. (2+1)-dimensional gravity, on the other hand, has been a fertile testing ground for many concepts related to classical and quantum gravity, and it is therefore only natural to investigate whether we can find an application of higher gauge theory in this latter context. In the present paper we investigate the possibility of applying the formalism of higher gauge theory to gravity in 2+1 dimensions, and we show that a nontrivial model of (2+1)-dimensional gravity coupled to scalar and tensorial matter fields — the ΣΦEA model — can be formulated as a higher gauge theory (as well as a standard gauge theory). Since the model has a very rich structure — it admits as solutions black-hole BTZ-like geometries, particle-like geometries as well as Robertson–Friedman–Walker cosmological-like expanding geometries — this opens a wide perspective for higher gauge theory to be tested and understood in a relevant gravitational context. Additionally, it offers the possibility of studying gravity in 2+1 dimensions coupled to matter in an entirely new framework.
HAMILTON–JACOBI ANSATZ TO STUDY THE HAWKING RADIATION OF KERR–NEWMAN–KASUYA BLACK HOLES
Authors: CHEN DEYOU , YANG SHUZHENG
Published: November 2007

Taking the self-gravitation interaction and unfixed background space–time into account, we study the Hawking radiation of Kerr–Newman–Kasuya black holes using Hamilton–Jacobi method. The result shows that the tunneling rate is related to the change of Bekenstein–Hawking entropy and the radiation spectrum deviates from the purely thermal one, which is accordant with that obtained using Parikh and Wilczek's method and gives a correction to the Hawking radiation of the black hole.
Alexander von Humboldt in Russia: the 1829 expedition
Authors: Naumann F.
Published: November 2007

Alexander von Humboldt was one of the most important figures in history in general and particularly in the history of natural sciences. He was one of the last universal scholars and his contributions have been appreciated ever since. Even today people are fascinated by his achievements as a natural scientist, explorer, researcher, adventurer, geologist and humanist. Von Humboldt is widely recognized as the founder of modern regional studies. He explored the then unknown Central American countries, studied the geographical distribution of plants for an entire continent and started the popularization of science. In doing so he anticipated an ecological view of nature and an understanding of the impact of technology on society.

From the beginning, von Humboldt attempted to understand, reflect and explain nature as a whole. Therefore, his famous volume ‘
Kosmos
’ bears the subtitle ‘
Outline of a physical survey of the World
’. If nothing else, this work was the result of his almost unbelievable enthusiasm to devote his life to the study and interpretation of nature regardless of the necessary effort and exertion required.

From his childhood days, von Humboldt felt the urge to travel to faraway regions and countries seldom visited by other Europeans. He wanted to visit and explore Asia, particularly India and then Siberia, and the New World so that he could compare the Andes with the Himalayas, the Venezuelan Llanos with the Siberian steppes. Unfortunately, he was prevented from going to India. But a quarter of a century after finishing his journey to America (1799–1804) he received an offer from the Russian minister of finance, Count Georg of Cancrin, to lead a nine-month expedition through the Russian empire. The expedition started out in April 1829 accompanied by the mineralogist Gustav Rose and the botanist Christian Gottfried Ehrenberg. In late December von Humboldt returned to Germany.

Not only had the team covered a distance of 19 000 kilometres but they had also made a wealth of invaluable scientific discoveries. At the same time, relationships were established with Russia which proved very favourable for subsequent explorers.

Since 1993, the German Association of Graduates and Friends of Moscow Lomonosow University (DAMU) has been active in reviving traditional Russian–German relationships by recalling and acknowledging German explorers and researchers in Russia. To date five excursions following von Humboldt's footsteps into Russia have taken place.
The German geologist Georg Hartung (1821–1891) and the geology of the Azores and Madeira islands
Authors: Pinto M. S. , Bouheiry A.
Published: November 2007

In 1853 and 1854, the German geologist G. Hartung (1821–1891) was living in Funchal, on the Portuguese island of Madeira. During this time Charles Lyell visited the archipelago to carry out the fieldwork that led the famous British geologist to write
On the Geology of Some Parts of Madeira
, published in the
Quarterly Journal
in 1854, and to make abundant references to the geology, morphology, palaeontology and living flora and fauna of the islands in the sixth edition of the
Elements of Geology
(1865) and in the 1868 edition of the
Principles of Geology
. Lyell was accompanied by Hartung during the visit to Madeira and to the Canary Islands. Hartung left on him a deep and lasting influence, so that Lyell wrote that his German colleague had ‘proved a most active fellow-labourer’. Lyell liked to talk to young geologists from whom he felt ‘old stagers’ had much to learn, and that was probably the case with Hartung.

Hartung visited the Azores archipelago in 1857 and in 1860 produced a book (
Die Azoren in ihrer äusseren Erscheinung und nach ihrer geognostischen Natur
) and an atlas with very fine plates of views of the volcanic landscape of S. Miguel Island. In 1864, he published
Geologische Beschreibung der Inseln Madeira und Porto Santo
on the geology of Madeira and Porto Santo that was the result of his ideas and field observations made from 1850 to 1854. Both books have palaeontological sections written by German-speaking authors.
Betrachtungen über Erhebungskrater, ältere und neuere Eruptivmassen nebst einer Schilderung der geologischen Verhältnisse der Insel Gran Canaria
, published in 1862, also refers to Madeira and the Azores.

Hartung's work on these archipelagos was important from both a geological and a historical point of view, and he became involved in the discussion of Leopold von Buch's ‘upheaval’ and Charles Lyell's ‘upbuilding’ theories.
‘Marks of extreme violence': Charles Darwin's geological observations at St Jago (São Tiago), Cape Verde islands
Authors: Pearson P. N. , Nicholas C. J.
Published: November 2007

The first stop on Charles Darwin's famous voyage around the world in HMS
Beagle
was at Porto Praya (Praia), the principal town on the island of St Jago (São Tiago) in the Cape Verde archipelago. From 16 January to 8 February 1832, Darwin enjoyed his first substantive opportunity to study the natural history of an exotic place. Darwin himself regarded this occasion as a significant turning point in his life because, according to his autobiography, it was here that he decided to research and publish a book on the geology of the places visited on the voyage. He also recalled that it was here, the very first port call, that convinced him of the ‘wonderful superiority’ of Charles Lyell's uniformitarian geology over the doctrine of successive cataclysms that he had been taught in England. Later commentators have generally accepted this account, which is significant for understanding the intellectual background to the
Origin of Species
, at face value. In this paper we reconstruct some of Darwin's observations at St Jago based on his contemporaneous notes and diary, and in the light of our own visit made in January 2002. We find little evidence to substantiate the claim that he interpreted the geology in Lyellian terms at the time. Instead, he formulated a theory involving a great cataclysm to explain the dramatic scenery in the island's interior. He speculated that a torrent of water had carved the main valleys of the island, leaving deposits of diluvium in their beds. It is indisputable that Darwin came to embrace gradualist thinking enthusiastically during the voyage. Some of his observations made on St Jago, especially relating to uplift of the coast, were instrumental in this change of view, but the conversion was gradual, not sudden. His later published works make no mention of his original catastrophist interpretations.
Geophysical travellers: the magneticians of the Carnegie Institution of Washington
Authors: Good G. A.
Published: November 2007

Between 1904 and World War II, a group of researchers ranged the world over in an effort to understand the Earth's magnetism. They called themselves ‘magneticians’ and they worked for the Department of Terrestrial Magnetism at the Carnegie Institution of Washington. Directed by Louis Agricola Bauer (1865–1932) and John Adam Fleming (1877–1956), these investigators followed carefully selected routes through Africa, Asia, South America, and other remote regions. They carried with them a heavy complement of instruments, camp gear, and evening wear, for those times when they reached outposts of European civilization.
Geological travellers in Auvergne, 1751–1800
Authors: Taylor K. L.
Published: November 2007

Within the half-century after Guettard's epoch-making journey of 1751, geologists came to see the Auvergne region of France as a place of unusual interest for field investigation. This paper reports on an effort to catalogue instances of scientific travel in Auvergne up to the end of the eighteenth century, before observers during the first decade of the nineteenth century (such as von Buch, d'Aubuisson and Ramond) validated the establishment of Auvergne as an iconic place for geologists. In addition to those who ventured into Auvergne to investigate its geology, a significant number of the eighteenth-century observers were residents of Auvergne; these are tabulated separately from those journeying from elsewhere. Published results of Auvergne observations accomplished by 1800 suggest that the Auvergne geological phenomena were already becoming fixed as part of the geological traveller's canonical itinerary.
Development of an Intergrated System for Electrochemical Detection
Authors: Cardoso Juliana L. , Fontes Marcelo B. , Gongora-Rubio Mário R.
Published: November 2007

There is an increasing interest on research laboratories to employ easy-touse equipments, which should present low fabrication costs. In this work is presented a homemade multipotentiostat that allows the realization of four simultaneous electrochemical analyses. Its sensitivity ranges are: 1 μA/V, 100 μA/V, 10 μA/V, 1 μA/V, and 100 nA/V. The multipotentiostat is portable and uses two nine-volt batteries as power supplies. It was specially designed for voltammetrics analysis (Cyclic Voltammetry, and Differential Pulse Voltammetry), with a user- interface developed in LabVIEWTM v.7.0. The data acquisition and system control are made by a commercial Data Acquisition board (DAC) LabPC+, from National Instruments. Functioning and flexibility were verified using the two voltammetric methods to detect K3Fe(CN)6, a calibration solution. In future works, a self-interface will permit field measurements using PDAs as us er interface.
Design, Simulation, Fabrication and Characterization of a Pressure Sensor arranged in Wheatstone Piezoresistive Bridge
Authors: Camolesi Alessandro , de Souza Pablo R. , Fruett F.
Published: November 2007

In this paper, a Wheatstone piezoresistive bridge was designed, simulated, fabricated and characterized. The Finite Elements Method was used to simulate both: the piezoeffect in a single-resistor and the stress-induced unbalance in a Wheatstone piezoresistive bridge. The process, used to fabricate the Wheatstone piezoresistive bridge sensor, is totally CMOS compatible.
Versatile N-Type Profile Engineering by Controlling Arsenic Surface Segregation in Silicon RPCVD
Authors: Popadić M. , Sarubbi F. , Scholtes T. L. , Nanver L. K.
Published: November 2007

With the purpose of controlling the incorporation of arsenic during RPCVD Si epitaxy, the surface segregation of As during lowtemperature epi growth was investigated. Parameters such as the Si growth rate, As deposition rate and As incorporation rate, which in previous models were either not evaluated or assumed to be constant, were found here to depend on both the As surface coverage and the arsine partial pressure. Knowledge of these dependencies was employed in simultaneous As deposition and Si epi growth to obtain highlycontrollable doping profiles by appropriate variation of the arsine partial pressure.
Rhythmic Constraints on Hippocampal Processing: State and Phase-Related Fluctuations of Synaptic Excitability During Theta and the Slow Oscillation
Authors: Schall Kurt P. , Kerber Jon , Dickson Clayton T.
Published: November 2007

Coordinated patterns of state-dependent synchronized oscillatory activity have been suggested to play differential roles in both the encoding and consolidation phases of hippocampal-dependent memories. Previous studies have concentrated on the mutually exclusive patterns of theta and sharp-wave/ripple activity because these were thought to be the only collective oscillatory patterns expressed in the hippocampus. Recently we (and others) have described a novel rhythmic activity expressed during anesthesia and deep sleep, the hippocampal slow oscillation (SO). In an attempt to describe the differential effects of theta and the SO on processing in the hippocampal circuit, we performed evoked potential analysis of two major pathways (the commissural and perforant) in urethan-anesthetized rats across spontaneously expressed theta and SO states. We show that synaptic excitability was significantly enhanced in all pathways during the SO as compared with theta with the exception of the medial perforant path to the dentate gyrus, which showed greater excitability during theta. Furthermore, within each ongoing rhythm, there was a phase-dependent modulation of synaptic excitability. This occurred across all sites and similarly favored the falling phase (positive to negative) of both theta and the SO. Differential effects on the input, processing, and output circuitries of the hippocampus across mutually exclusive coordinated oscillatory patterns expressed during different states may be relevant for the staging of memory processes in the medial temporal lobe.
Recovery of Gaze Stability During Vestibular Regeneration
Authors: Haque Asim , Zakir Mridha , Dickman J. David
Published: November 2007

Many motion related behaviors, such as gaze stabilization, balance, orientation, and navigation largely depend on a properly functioning vestibular system. After vestibular insult, many of these responses are compromised but can return during the regeneration of vestibular receptors and afferents as is known to occur in birds, reptiles, and amphibians. Here we characterize gaze stability in pigeons to rotational motion during regeneration after complete bilateral vestibular loss via an ototoxic antibiotic. Immediate postlesion effects included severe head oscillations, postural ataxia, and total lack of gaze control. We found that these abnormal behaviors gradually subsided, and gaze stability slowly returned to normal function according to a temporal sequence that lasted several months. We also found that the dynamic recovery of gaze function during regeneration was not homogeneous for all types of motion. Instead high-frequency motion stability was first achieved, followed much later by slow movement stability. In addition, we found that initial gaze stability was established using almost exclusive head-response components with little eye-movement contribution. However, that trend reversed as recovery progressed so that when gaze stability was complete, the eye component had increased and the head response had decreased to levels significantly different from that observed in normal birds. This was true even though the head-fixed VOR response recovered normally. Recovery of gaze stability coincided well with the three stage temporal sequence of morphologic regeneration previously described by our laboratory.
Second-Order SMO Improves SVM Online and Active Learning
Authors: Glasmachers Tobias , Igel Christian
Published: November 2007

Iterative learning algorithms that approximate the solution of support vector machines (SVMs) have two potential advantages. First, they allow online and active learning. Second, for large data sets, computing the exact SVM solution may be too time-consuming, and an efficient approximation can be preferable. The powerful LASVM iteratively approaches the exact SVM solution using sequential minimal optimization (SMO). It allows efficient online and active learning. Here, this algorithm is considerably improved in speed and accuracy by replacing the working set selection in the SMO steps. A second-order working set selection strategy, which greedily aims at maximizing the progress in each single step, is incorporated.
Robust L1 Principal Component Analysis and Its Bayesian Variational Inference
Authors: Gao Junbin
Published: November 2007

We introduce a robust probabilistic L1-PCA model in which the conventional gaussian distribution for the noise in the observed data was replaced by the Laplacian distribution (or L1 distribution). Due to the heavy tail characteristics of the L1 distribution, the proposed model is supposed to be more robust against data outliers. In this letter, we demonstrate how a variational approximation scheme enables effective inference of key parameters in the probabilistic L1-PCA model. As the L1 density can be expanded as a superposition of infinite number of gaussian densities, we express the L1-PCA model as a marginalized model over the superpositions. By doing so, a tractable Bayesian inference can be achieved based on the variational expectation-maximization-type algorithm.
Neural Network Models for Conditional Distribution Under Bayesian Analysis
Authors: Miazhynskaia Tatiana , Frühwirth-Schnatter Sylvia , Dorffner Georg
Published: November 2007

We use neural networks (NN) as a tool for a nonlinear autoregression to predict the second moment of the conditional density of return series. The NN models are compared to the popular econometric GARCH(1,1) model. We estimate the models in a Bayesian framework using Markov chain Monte Carlo posterior simulations. The interlinked aspects of the proposed Bayesian methodology are identification of NN hidden units and treatment of NN complexity based on model evidence. The empirical study includes the application of the designed strategy to market data, where we found a strong support for a nonlinear multilayer perceptron model with two hidden units.
Bayesian Spiking Neurons II: Learning
Authors: Deneve Sophie
Published: November 2007

In the companion letter in this issue (“Bayesian Spiking Neurons I: Inference”), we showed that the dynamics of spiking neurons can be interpreted as a form of Bayesian integration, accumulating evidence over time about events in the external world or the body. We proceed to develop a theory of Bayesian learning in spiking neural networks, where the neurons learn to recognize temporal dynamics of their synaptic inputs. Meanwhile, successive layers of neurons learn hierarchical causal models for the sensory input. The corresponding learning rule is local, spike-time dependent, and highly nonlinear. This approach provides a principled description of spiking and plasticity rules maximizing information transfer, while limiting the number of costly spikes, between successive layers of neurons.
Competitive Assimilation or Strategic Nonassimilation?
Authors: Bloom Stephen
Published: November 2007

This article tests the competitive assimilation and strategic nonassimilation models, using district-level data from Latvia. Unlike the coordination dynamic of the competitive assimilation game, the strategic nonassimilation game highlights the strategic interaction between Russian and Latvian players. Russian parents do not look to other Russian parents when deciding to send their children to Latvian schools; rather, they look to Latvian children. They anticipate whether their children will be accepted or excluded in the Latvian classroom. My chief empirical finding is a significant interactive relationship between the size of Russian population and the strength of Latvian nationalism. In regions with small Russian populations, Latvian nationalism fuels assimilation. In regions with large Russian populations, Latvian nationalism propels nonassimilation.
Administrative Challenge or Ethical Dilemma? Responding Justly When a Student With a Disability Engages in a Violent or Disruptive Act
Authors: Faircloth Susan C. , Ritter Suzanne T. , Wilson Felicia R.
Published: November 2007

This case study involves an 8-year-old American Indian student with a disability, who was videotaped assaulting another student as they exited the school bus. Although acts of school violence are common on campuses across the nation, this incident is particularly complex, given the disability status of the student committing this act. This case provides an opportunity for both practicing and aspiring school leaders to explore a number of administrative and ethical dilemmas related to the discipline of students with disabilities and other special educational needs, utilizing a framework grounded in principles of social justice and equity.
Eradication of disseminated leukemia in a syngeneic murine leukemia model using pretargeted anti-CD45 radioimmunotherapy
Authors: Pagel John M. , Hedin Nathan , Drouet Lacey , Wood Brent L. , Pantelias Anastasia , Lin Yukang , Hamlin Donald K. , Wilbur D. Scott , Gopal Ajay K. , Green Damian , Appelbaum Frederick R. , Press Oliver W.
Published: November 2007

We describe the use of pretargeted radioimmunotherapy (PRIT) using an anti–murine CD45 antibody-streptavidin (SA) conjugate followed by radiobiotin to deliver radiation selectively to murine hematolymphoid tissues, which may potentially augment the efficacy and decrease the toxicity of radioimmunotherapy for disseminated murine leukemia. Biodistribution and therapeutic results demonstrated high target organ to nontarget organ ratios of radioactivity and significant long-term survival in leukemic mice using PRIT. These data suggest that anti-CD45 PRIT using an anti–CD45-SA conjugate in a syngeneic murine model of disseminated leukemia may be more effective and less toxic than directly labeled monoclonal antibodies.
Hematopoietic origin of hepatic stellate cells in the adult liver
Authors: Miyata Eri , Masuya Masahiro , Yoshida Shuro , Nakamura Shiho , Kato Keizo , Sugimoto Yuka , Shibasaki Tetsunori , Yamamura Kentaro , Ohishi Kohshi , Nishii Kazuhiro , Ishikawa Fumihiko , Shiku Hiroshi , Katayama Naoyuki
Published: November 2007

Hepatic stellate cells are believed to play a key role in the development of liver fibrosis. Several studies have reported that bone marrow cells can give rise to hepatic stellate cells. We hypothesized that hepatic stellate cells are derived from hematopoietic stem cells. To test this hypothesis, we generated chimeric mice by transplantation of clonal populations of cells derived from single enhanced green fluorescent protein (EGFP)–marked Lin−Sca-1+c-kit+CD34− cells and examined the histology of liver tissues obtained from the chimeric mice with carbon tetrachloride (CCl4)–induced injury. After 12 weeks of CCl4 treatment, we detected EGFP+ cells in the liver, and some cells contained intracytoplasmic lipid droplets. Immunofluorescence analysis demonstrated that 50% to 60% of the EGFP+ cells were negative for CD45 and positive for vimentin, glial fibrillary acidic protein, ADAMTS13, and α-smooth muscle actin. Moreover, EGFP+ cells isolated from the liver synthesized collagen I in culture. These phenotypes were consistent with those of hepatic stellate cells. The hematopoietic stem cell–derived hepatic stellate cells seen in male-to-male transplants revealed only one Y chromosome. Our findings suggest that hematopoietic stem cells contribute to the generation of hepatic stellate cells after liver injury and that the process does not involve cell fusion.
Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Schriek Sarah , Rückert Christian , Staiger Dorothee , Pistorius Elfriede K , Michel Klaus-Peter
Published: November 2007

Background

So far very limited knowledge exists on L-arginine catabolism in cyanobacteria, although six major L-arginine-degrading pathways have been described for prokaryotes. Thus, we have performed a bioinformatic analysis of possible L-arginine-degrading pathways in cyanobacteria. Further, we chose Synechocystis sp. PCC 6803 for a more detailed bioinformatic analysis and for validation of the bioinformatic predictions on L-arginine catabolism with a transcript analysis.

Results

We have evaluated 24 cyanobacterial genomes of freshwater or marine strains for the presence of putative L-arginine-degrading enzymes. We identified an L-arginine decarboxylase pathway in all 24 strains. In addition, cyanobacteria have one or two further pathways representing either an arginase pathway or L-arginine deiminase pathway or an L-arginine oxidase/dehydrogenase pathway. An L-arginine amidinotransferase pathway as a major L-arginine-degrading pathway is not likely but can not be entirely excluded. A rather unusual finding was that the cyanobacterial L-arginine deiminases are substantially larger than the enzymes in non-photosynthetic bacteria and that they are membrane-bound. A more detailed bioinformatic analysis of Synechocystis sp. PCC 6803 revealed that three different L-arginine-degrading pathways may in principle be functional in this cyanobacterium. These are (i) an L-arginine decarboxylase pathway, (ii) an L-arginine deiminase pathway, and (iii) an L-arginine oxidase/dehydrogenase pathway. A transcript analysis of cells grown either with nitrate or L-arginine as sole N-source and with an illumination of 50 μmol photons m-2 s-1 showed that the transcripts for the first enzyme(s) of all three pathways were present, but that the transcript levels for the L-arginine deiminase and the L-arginine oxidase/dehydrogenase were substantially higher than that of the three isoenzymes of L-arginine decarboxylase.

Conclusion

The evaluation of 24 cyanobacterial genomes revealed that five different L-arginine-degrading pathways are present in the investigated cyanobacterial species. In Synechocystis sp. PCC 6803 an L-arginine deiminase pathway and an L-arginine oxidase/dehydrogenase pathway represent the major pathways, while the L-arginine decarboxylase pathway most likely only functions in polyamine biosynthesis. The transcripts encoding the enzymes of the two major pathways were constitutively expressed with the exception of the transcript for the carbamate kinase, which was substantially up-regulated in cells grown with L-arginine.
The candidate genes TAF5L, TCF7, PDCD1 , IL6 and ICAM1 cannot be excluded from having effects in type 1 diabetes
Authors: Cooper Jason D , Smyth Deborah J , Bailey Rebecca , Payne Felicity , Downes Kate , Godfrey Lisa M , Masters Jennifer , Zeitels Lauren R , Vella Adrian , Walker Neil M , Todd John A
Published: November 2007

Background

As genes associated with immune-mediated diseases have an increased prior probability of being associated with other immune-mediated diseases, we tested three such genes, IL23R , IRF5 and CD40 , for an association with type 1 diabetes. In addition, we tested seven genes, TAF5L , PDCD1, TCF7, IL12B , IL6 , ICAM1 and TBX21 , with published marginal or inconsistent evidence of an association with type 1 diabetes.

Methods

We genotyped reported polymorphisms of the ten genes, nonsynonymous SNPs (nsSNPs) and, for the IL12B and IL6 regions, tag SNPs in up to 7,888 case, 8,858 control and 3,142 parent-child trio samples. In addition, we analysed data from the Wellcome Trust Case Control Consortium genome-wide association study to determine whether there was any further evidence of an association in each gene region.

Results

We found some evidence of associations between type 1 diabetes and TAF5L , PDCD1 , TCF7 and IL6 (ORs = 1.05 – 1.13; P = 0.0291 – 4.16 × 10-4). No evidence of an association was obtained for IL12B , IRF5 , IL23R, ICAM1, TBX21 and CD40 , although there was some evidence of an association (OR = 1.10; P = 0.0257) from the genome-wide association study for the ICAM1 region.

Conclusion

We failed to exclude the possibility of some effect in type 1 diabetes for TAF5L , PDCD1 , TCF7 , IL6 and ICAM1 . Additional studies, of these and other candidate genes, employing much larger sample sizes and analysis of additional polymorphisms in each gene and its flanking region will be required to ascertain their contributions to type 1 diabetes susceptibility.
A comparative study between mixed-type tumours from human salivary and canine mammary glands
Authors: Genelhu Marisa CLS , Cardoso Sérgio V , Gobbi Helenice , Cassali Geovanni D
Published: November 2007

Background

In comparative pathology, canine mammary tumours have special interest because of their similarities with human breast cancer. Mixed tumours are uncommon lesions in the human breast, but they are found most frequently in the mammary gland of the female dogs and in the human salivary glands. The aim of the study was to compare clinical, morphological and immunohistochemical features of human salivary and canine mammary gland mixed tumours, in order to evaluate the latter as an experimental model for salivary gland tumours.

Methods

Ten examples of each mixed tumour type (human pleomorphic adenoma and carcinomas ex-pleomorphic adenomas and canine mixed tumour and metaplastic carcinoma) were evaluated. First, clinical and morphologic aspects of benign and malignant variants were compared between the species. Then, streptavidin-biotin-peroxidase immunohistochemistry was performed to detect the expression of cytokeratins, vimentin, p63 protein, estrogen receptor, β-catenin, and E-cadherin.

Results

After standardization, similar age and site distributions were observed in human and canine tumours. Histological similarities were identified in the comparison of the benign lesions as well. Metaplastic carcinomas also resembled general aspects of carcinomas ex-pleomorphic adenomas in morphological evaluation. Additionally, immunohistochemical staining further presented similar antigenic expression between lesions.

Conclusion

There are many similar features between human salivary and canine mammary gland mixed tumours. This observation is of great relevance for those interested in the study and management of salivary gland tumours, since canine lesions may constitute useful comparative models for their investigations.
General Chemistry: Expanding the Learning Outcomes and Promoting Interdisciplinary Connections through the Use of a Semester-long Project
Authors: Wenzel Thomas J.
Published: November 2007

The laboratory component of a first-semester general chemistry course for science majors is described. The laboratory involves a semester-long project undertaken in a small-group format. Students are asked to examine whether plants grown in soil contaminated with lead take up more lead than those grown in uncontaminated soil. They are also asked to examine whether the acidity of the rainwater affects the amount of lead taken up by the plants. Groups are then given considerable independence in the design and implementation of the experiment. Once the seeds are planted, which takes about 4 wk into the term, several shorter experiments are integrated in before it is time to harvest and analyze the plants. The use of a project and small working groups allows for the development of a broader range of learning outcomes than occurs in a“ traditional” general chemistry laboratory. The nature of these outcomes and some of the student responses to the laboratory experience are described. This particular project also works well at demonstrating the connections among chemistry, biology, geology, and environmental studies.
Development of a Neuroscience-oriented “Methods” Course for Graduate Students of Pharmacology and Toxicology
Authors: Surratt Christopher K. , Witt-Enderby Paula A. , Johnson David A. , Anderson Carl A. , Bricker J. Douglas , Davis Vicki L. , Firestine Steven M. , Meng Wilson S.
Published: November 2007

To provide graduate students in pharmacology/toxicology exposure to, and cross-training in, a variety of relevant laboratory skills, the Duquesne University School of Pharmacy developed a “methods” course as part of the core curriculum. Because some of the participating departmental faculty are neuroscientists, this course often applied cutting-edge techniques to neuroscience-based systems, including experiments with brain G protein–coupled receptors. Techniques covered by the course include animal handling and behavioral testing, bacterial and mammalian cell culture, enzyme-linked immunosorbent assay, western blotting, receptor binding of radioligands, plasmid DNA amplification and purification, reverse transcriptase-polymerase chain reaction, gel electrophoresis, and UV-visible and fluorescence spectroscopy. The course also encompasses research aspects such as experimental design and record keeping, statistical analysis, and scientific writing. Students were evaluated via laboratory reports and examinations, and students in turn evaluated the course using a detailed exit survey. This course introduces the graduate student to many more techniques and approaches than can be provided by the traditional graduate “rotation” format alone and should serve as a template for graduate programs in many basic research disciplines.
Assessing Students' Ability to Trace Matter in Dynamic Systems in Cell Biology
Authors: Wilson Christopher D. , Anderson Charles W. , Heidemann Merle , Merrill John E. , Merritt Brett W. , Richmond Gail , Sibley Duncan F. , Parker Joyce M.
Published: November 2007

College-level biology courses contain many complex processes that are often taught and learned as detailed narratives. These processes can be better understood by perceiving them as dynamic systems that are governed by common fundamental principles. Conservation of matter is such a principle, and thus tracing matter is an essential step in learning to reason about biological processes. We present here multiple-choice questions that measure students' ability and inclination to trace matter through photosynthesis and cellular respiration. Data associated with each question come from students in a large undergraduate biology course that was undergoing a shift in instructional strategy toward making fundamental principles (such as tracing matter) a central theme. We also present findings from interviews with students in the course. Our data indicate that 1) many students are not using tracing matter as a tool to reason about biological processes, 2) students have particular difficulties tracing matter between systems and have a persistent tendency to interconvert matter and energy, and 3) instructional changes seem to be effective in promoting application of the tracing matter principle. Using these items as diagnostic tools allows instructors to be proactive in addressing students' misconceptions and ineffective reasoning.
An Intensive Primary-Literature–based Teaching Program Directly Benefits Undergraduate Science Majors and Facilitates Their Transition to Doctoral Programs
Authors: Kozeracki Carol A. , Carey Michael F. , Colicelli John , Levis-Fitzgerald Marc
Published: November 2007

UCLA's Howard Hughes Undergraduate Research Program (HHURP), a collaboration between the College of Letters and Science and the School of Medicine, trains a group of highly motivated undergraduates through mentored research enhanced by a rigorous seminar course. The course is centered on the presentation and critical analysis of scientific journal articles as well as the students' own research. This article describes the components and objectives of the HHURP and discusses the results of three program assessments: annual student evaluations, interviews with UCLA professors who served as research advisors for HHURP scholars, and a survey of program alumni. Students indicate that the program increased their ability to read and present primary scientific research and to present their own research and enhanced their research experience at UCLA. After graduating, they find their involvement in the HHURP helped them in securing admission to the graduate program of their choice and provided them with an advantage over their peers in the interactive seminars that are the foundation of graduate education. On the basis of the assessment of the program from 1998–1999 to 2004–2005, we conclude that an intensive literature-based training program increases student confidence and scientific literacy during their undergraduate years and facilitates their transition to postgraduate study.
What Good Is a Scientist in the Classroom? Participant Outcomes and Program Design Features for a Short-Duration Science Outreach Intervention in K–12 Classrooms
Authors: Laursen Sandra , Liston Carrie , Thiry Heather , Graf Julie
Published: November 2007

Many short-duration science outreach interventions have important societal goals of raising science literacy and increasing the size and diversity of the science workforce. Yet, these long-term outcomes are inherently challenging to evaluate. We present findings from a qualitative research study of an inquiry-based, life science outreach program to K–12 classrooms that is typical in design and excellent in execution. By considering this program as a best case of a common outreach model, the “scientist in the classroom,” the study examines what benefits may be realized for each participant group and how they are achieved. We find that K–12 students are engaged in authentic, hands-on activities that generate interest in science and new views of science and scientists. Teachers learn new science content and new ways to teach it, and value collegial support of their professional work. Graduate student scientists, who are the program presenters, gain teaching and other skills, greater understanding of education and diversity issues, confidence and intrinsic satisfaction, and career benefits. A few negative outcomes also are described. Program elements that lead to these benefits are identified both from the research findings and from insights of the program developer on program design and implementation choices.
A Simple E-Mail Mechanism To Enhance Reflection, Independence, and Communication in Young Researchers
Authors: Campbell A. Malcolm , Lom Barbara
Published: November 2007

Providing undergraduates with mentored research experiences is a critical component of contemporary undergraduate science education. Although the benefits of undergraduate research experiences are apparent, the methods for mentoring young scientists as they first begin navigating the research lab environment are reinvented in labs all over the world. Students come to research labs with varied skills, motivations, needs, and dispositions, placing each student and mentor in a unique relationship. How can we help students become aware of their own intellectual progress? How can we encourage our students to take initial steps toward independent investigation? When do we need to let setbacks happen? We have developed a simple mechanism to address these common problems. Each week, students in our labs answer a series of five questions by e-mail that improve lab communication and help students develop into mature scientists without taxing an instructor's already busy schedule. Our observations, experiences, and student feedback indicate that this approach is a useful mechanism to help faculty who mentor young scientists in the research lab.
Genome Consortium for Active Teaching: Meeting the Goals of BIO2010
Authors: Campbell A. Malcolm , Ledbetter Mary Lee S. , Hoopes Laura L.M. , Eckdahl Todd T. , Heyer Laurie J. , Rosenwald Anne , Fowlks Edison , Tonidandel Scott , Bucholtz Brooke , Gottfried Gail
Published: November 2007

The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomorrow's life science professionals. GCAT participants have access to affordable microarrays, microarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT's network of supportive colleagues encourages faculty to explore genomics through student research and to learn a new and complex method with their undergraduates. GCAT is meeting important goals of BIO2010 by making research methods accessible to undergraduates, training faculty in genomics and bioinformatics, integrating mathematics into the biology curriculum, and increasing participation by underrepresented minority students.