bluuebunny/crossref_metadata_2025 huggingface dataset:
Homotopy Lie groups
Authors: Møller Jesper M.
Published: January 2008

Homotopy Lie groups, recently invented by W.G. Dwyer and C.W. Wilkerson [13], represent the culmination of a long evolution. The basic philosophy behind the process was formulated almost 25 years ago by Rector [32, 33] in his vision of a homotopy theoretic incarnation of Lie group theory. What was then technically impossible has now become feasible thanks to modern advances such as Miller’s proof of the Sullivan conjecture [25] and Lannes’s division functors [22]. Today, with Dwyer and Wilkerson’s implementation of Rector’s vision, the tantalizing classification theorem seems to be within grasp. Supported by motivating examples and clarifying exercises, this guide quickly leads, without ignoring the context or the proof strategy, from classical finite loop spaces to the important definitions and striking results of this new theory.
Effects of chondrogenic and osteogenic regulatory factors on composite constructs grown using human mesenchymal stem cells, silk scaffolds and bioreactors
Authors: Augst Alexander , Marolt Darja , Freed Lisa E , Vepari Charu , Meinel Lorenz , Farley Michelle , Fajardo Robert , Patel Nipun , Gray Martha , Kaplan David L , Vunjak-Novakovic Gordana
Published: January 2008

Human mesenchymal stem cells (hMSCs) isolated from bone marrow aspirates were cultured on silk scaffolds in rotating bioreactors for three weeks with either chondrogenic or osteogenic medium supplements to engineer cartilage- or bone-like tissue constructs. Osteochondral composites formed from these cartilage and bone constructs were cultured for an additional three weeks in culture medium that was supplemented with chondrogenic factors, supplemented with osteogenic factors or unsupplemented. Progression of cartilage and bone formation and the integration between the two regions were assessed by medical imaging (magnetic resonance imaging and micro-computerized tomography imaging), and by biochemical, histological and mechanical assays. During composite culture (three to six weeks), bone-like tissue formation progressed in all three media to a markedly larger extent than cartilage-like tissue formation. The integration of the constructs was most enhanced in composites cultured in chondrogenic medium. The results suggest that tissue composites with well-mineralized regions and substantially less developed cartilage regions can be generated
in vitro
by culturing hMSCs on silk scaffolds in bioreactors, that hMSCs have markedly higher capacity for producing engineered bone than engineered cartilage, and that chondrogenic factors play major roles at early stages of bone formation by hMSCs and in the integration of the two tissue constructs into a tissue composite.
Female-mediated causes and consequences of status change in a social fish
Authors: Fitzpatrick J.L , Desjardins J.K , Milligan N , Stiver K.A , Montgomerie R , Balshine S
Published: January 2008

In highly social species, dominant individuals often monopolize reproduction, resulting in reproductive investment that is status dependent. Yet, for subordinates, who typically invest less in reproduction, social status can change and opportunities to ascend to dominant social positions are presented suddenly, requiring abrupt changes in behaviour and physiology. In this study, we examined male reproductive anatomy, physiology and behaviour following experimental manipulations of social status in the cooperatively breeding cichlid fish,Neolamprologus pulcher. This unusual fish species lives in permanent social groups composed of a dominant breeding pair and 1–20 subordinates that form a linear social dominance hierarchy. By removing male breeders, we created 18 breeding vacancies and thus provided an opportunity for subordinate males to ascend in status. Dominant females play an important role in regulating status change, as males successfully ascended to breeder status only when they were slightly larger than the female breeder in their social group. Ascending males rapidly assumed behavioural dominance, demonstrated elevated gonadal investment and androgen concentrations compared with males remaining socially subordinate. Interestingly, to increase gonadal investment ascending males appeared to temporarily restrain somatic growth. These results highlight the complex interactions between social status, reproductive physiology and group dynamics, and underscore a convergent pattern of reproductive investment among highly social, cooperative species.
Evolution of protein domain promiscuity in eukaryotes
Authors: Basu Malay Kumar , Carmel Liran , Rogozin Igor B. , Koonin Eugene V.
Published: January 2008

Numerous eukaryotic proteins contain multiple domains. Certain domains show a tendency to occur in diverse domain architectures and can be considered “promiscuous.” These promiscuous domains are, typically, involved in protein–protein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. A systematic comparative-genomic analysis of promiscuous domains in eukaryotes is described. Two quantitative measures of domain promiscuity are introduced and applied to the analysis of 28 genomes of diverse eukaryotes. Altogether, 215 domains are identified as strongly promiscuous. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fast-changing feature of eukaryotic proteins, with few domains remaining promiscuous throughout the evolution of eukaryotes. Some domains appear to have attained promiscuity independently in different lineages, for example, animals and plants. It is proposed that promiscuous domains persist within a relatively small pool of evolutionarily stable domain combinations from which numerous rare architectures emerge during evolution. Domain promiscuity positively correlates with the number of experimentally detected domain interactions and with the strength of purifying selection affecting a domain. Thus, evolution of promiscuous domains seems to be constrained by the diversity of their interaction partners. The set of promiscuous domains is enriched for domains mediating protein–protein interactions that are involved in various forms of signal transduction, especially in the ubiquitin system and in chromatin. Thus, a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks.
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid
Authors: Salsbury Freddie R. , Knutson Stacy T. , Poole Leslie B. , Fetrow Jacquelyn S.
Published: January 2008

Cysteine sulfenic acid (Cys‐SOH), a reversible modification, is a catalytic intermediate at enzyme active sites, a sensor for oxidative stress, a regulator of some transcription factors, and a redox‐signaling intermediate. This post‐translational modification is not random: specific features near the cysteine control its reactivity. To identify features responsible for the propensity of cysteines to be modified to sulfenic acid, a list of 47 proteins (containing 49 known Cys‐SOH sites) was compiled. Modifiable cysteines are found in proteins from most structural classes and many functional classes, but have no propensity for any one type of protein secondary structure. To identify features affecting cysteine reactivity, these sites were analyzed using both functional site profiling and electrostatic analysis. Overall, the solvent exposure of modifiable cysteines is not different from the average cysteine. The combined sequence, structure, and electrostatic approaches reveal mechanistic determinants not obvious from overall sequence comparison, including: (1) pKas of some modifiable cysteines are affected by backbone features only; (2) charged residues are underrepresented in the structure near modifiable sites; (3) threonine and other polar residues can exert a large influence on the cysteine pKa; and (4) hydrogen bonding patterns are suggested to be important. This compilation of Cys‐SOH modification sites and their features provides a quantitative assessment of previous observations and a basis for further analysis and prediction of these sites. Agreement with known experimental data indicates the utility of this combined approach for identifying mechanistic determinants at protein functional sites.
Basic‐helix‐loop‐helix (bHLH) transcription factor DEC2 negatively regulates vascular endothelial growth factor expression
Authors: Sato Fuyuki , Bhawal Ujjal Kumar , Kawamoto Takeshi , Fujimoto Katsumi , Imaizumi Tadaatsu , Imanaka Tadanobu , Kondo Jun , Koyanagi Satoru , Noshiro Mitsuhide , Yoshida Hidemi , Kusumi Tomomi , Kato Yukio , Kijima Hiroshi
Published: January 2008

DEC1 (BHLHB2/Sharp2/Stra13) and DEC2 (BHLHB3/Sharp1) are basic‐helix‐loop‐helix (bHLH) transcription factors, involved in cellular differentiation, responses to hypoxia and circadian rhythms. We recently showed that the expression of DEC1 and DEC2 was up‐regulated by hypoxia; however, the functions of these two factors under hypoxic conditions have not been elucidated in detail. It is well established that the expression of vascular endothelial growth factor (VEGF) is up‐regulated by hypoxia, and the expression of VEGF in response to hypoxia depends on transcriptional activation by a heterodimer comprising hypoxia‐inducible factor 1α (HIF‐1α) and arylhydrocarbon receptor nuclear translocator 1 (ARNT1). In the present study, we showed that DEC2, but not DEC1, suppressed VEGF gene expression under hypoxic conditions. DEC2 protein was co‐immunoprecipitated with HIF‐1α but not with ARNT1. The binding of HIF‐1α to the hypoxia response element (HRE) in the VEGF promoter was decreased by DEC2 over‐expression, and increased by DEC2 knockdown. We also showed that the circadian expression of VEGF showed a reciprocal pattern to that of DEC2 in cartilage. DEC2 had a circadian oscillation in implanted Sarcoma 180 cells. We conclude that DEC2 negatively regulates VEGF expression and plays an important role in the pathological conditions in which VEGF is involved.
Not all ALMT1‐type transporters mediate aluminum‐activated organic acid responses: the case of ZmALMT1 – an anion‐selective transporter
Authors: Piñeros Miguel A. , Cançado Geraldo M. A. , Maron Lyza G. , Lyi Sangbom M. , Menossi Marcelo , Kochian Leon V.
Published: January 2008

The phytotoxic effects of aluminum (Al) on root systems of crop plants constitute a major agricultural problem in many areas of the world. Root exudation of Al‐chelating molecules such as low‐molecular‐weight organic acids has been shown to be an important mechanism of plant Al tolerance/resistance. Differences observed in the physiology and electrophysiology of root function for two maize genotypes with contrasting Al tolerance revealed an association between rates of Al‐activated root organic acid release and Al tolerance. Using these genotypes, we cloned ZmALMT1, a maize gene homologous to the wheat ALMT1 and Arabidopsis AtALMT1 genes that have recently been described as encoding functional, Al‐activated transporters that play a role in tolerance by mediating Al‐activated organic acid exudation in roots. The ZmALMT1 cDNA encodes a 451 amino acid protein containing six transmembrane helices. Transient expression of a ZmALMT1::GFP chimera confirmed that the protein is targeted to the plant cell plasma membrane. We addressed whether ZmALMT1 might underlie the Al‐resistance response (i.e. Al‐activated citrate exudation) observed in the roots of the Al‐tolerant genotype. The physiological, gene expression and functional data from this study confirm that ZmALMT1 is a plasma membrane transporter that is capable of mediating elective anion efflux and influx. However, gene expression data as well as biophysical transport characteristics obtained from Xenopus oocytes expressing ZmALMT1 indicate that this transporter is implicated in the selective transport of anions involved in mineral nutrition and ion homeostasis processes, rather than mediating a specific Al‐activated citrate exudation response at the rhizosphere of maize roots.
Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation
Authors: Yahalom Avital , Kim Tae‐Houn , Roy Bijoyita , Singer Ruth , Von Arnim Albrecht G. , Chamovitz Daniel A.
Published: January 2008

The roles of individual eukaryotic translation initiation factor 3 (eIF3) subunits are largely unclear, although some are essential, while others are thought to have regulatory roles. The ‘e’ subunit, also known as Int‐6/Int6, is a candidate for a regulatory subunit as it is not essential for translation initiation in yeasts. eIF3e associates with the COP9 signalosome, and localizes to the nucleus in certain tissues. To further elucidate the roles of eIF3e, we have taken a genetic approach using Arabidopsis as a model system. Overexpression of eIF3e results in defects similar to mutations in the COP9 signalosome. eIF3e protein, but not transcript, over accumulates in csn mutants, and eIF3e is degraded in a proteasome‐dependent fashion. In vitro and in vivo assays suggest that excess eIF3e inhibits translation. We conclude that the COP9 signalosome maintains a precise regulation of eIF3e levels, which is necessary for normal development in Arabidopsis.
Parvalbumin – the major tropical fish allergen
Authors: Lim Dawn Li‐Chern , Neo Keng Hwee , Yi Fong Cheng , Chua Kaw Yan , Goh Denise Li‐Meng , Shek Lynette Pei‐Chi , Giam Yoke Chin , Van Bever Hugo PS , Lee Bee Wah
Published: January 2008

Fish allergy is common in countries where consumption is high. Asian nations are amongst the world’s largest consumers of fish but the allergen profiles of tropical fish are unknown. This study sought to evaluate the allergenicity of four commonly consumed tropical fish, the threadfin (Polynemus indicus), Indian anchovy (Stolephorus indicus), pomfret (Pampus chinensis) and tengirri (Scomberomorus guttatus). Immunoglobulin E (IgE) cross‐reactivity with parvalbumin of cod fish (Gad c 1), the major fish allergen, was also studied. Detection of tropical fish and cod specific‐IgE was performed by UniCap assay, and skin prick tests were also carried out. The IgE‐binding components of tropical fish were identified using IgE immunoblot techniques, and cross‐reactivity with Gad c 1 was assessed by ELISA inhibition and IgE immunoblot inhibition. Clinically, nine of 10 patients studied were allergic to multiple fish. All patients exhibited detectable specific‐IgE to cod fish (10 of 10 skin prick test positive, eight of 10 UniCap assay positive) despite lack of previous exposure. The major allergen of the four tropical fish was the 12‐kDa parvalbumin. IgE cross‐reactivity of these allergens to Gad c 1 was observed to be moderate to high in the tropical fish studied. Parvalbumins are the major allergens in commonly consumed tropical fish. They are cross‐reactive with each other as well as with Gad c 1. Commercial tests for cod fish appear to be sufficient for the detection of tropical fish specific‐IgE.
Metabolic changes detected by proton magnetic resonance spectroscopy in vivo and in vitro in a murin model of Parkinson’s disease, the MPTP‐intoxicated mouse
Authors: Chassain Carine , Bielicki Guy , Durand Elodie , Lolignier Stéphane , Essafi Fatma , Traoré Amidou , Durif Franck
Published: January 2008

Parkinson’s disease is a neurodegenerative disorder characterized by the progressive loss of the dopaminergic neurons in the substantia nigra pars compacta, which project to the striatum. The aim of this study was to analyze in vivo and in vitro consequences of dopamine depletion on amount of metabolites in a mouse model of Parkinson’s disease using proton 1H magnetic resonance spectroscopy (MRS). The study was performed on control mice (n = 7) and MPTP‐intoxicated mice (n = 7). All the experiments were performed at 9.4 T. For in vivo MRS acquisitions, mice were anesthetized and carefully placed on an animal handling system with the head centered in birdcage coil used for both excitation and signal reception. Spectra were acquired in a voxel (8 μL) centered in the striatum, applying a point‐resolved spectroscopy sequence (TR = 4000 ms, TE = 8.8 ms). After in vivo MRS acquisitions, mice were killed; successful lesion verified by tyrosine hydroxylase immunolabeling on the substantia nigra pars compacta and in vitro MRS acquisitions performed on perchloric extracts of anterior part of mice brains. In vitro spectra were acquired using a standard one‐pulse experiment. The absolute concentrations of metabolites were determined using jmrui (Lyon, France) from 1H spectra obtained in vivo on striatum and in vitro on perchloric extracts. Glutamate (Glu), glutamine (Gln), and GABA concentrations obtained in vivo were significantly increased in striatum of MPTP‐lesioned mice (Glu: 15.5 ± 2.5 vs. 12.9 ± 1.0 mmol/L, p < 0.05; Gln: 2.3 ± 0.9 vs. 1.8 ± 0.6 mmol/L, p < 0.05; GABA: 2.3 ± 0.9 vs. 1.3 ± 0.6 mmol/L, p < 0.05). The in vitro results confirmed these results, Glu (10.9 ± 2.5 vs. 7.9 ± 1.7 μmol/g, p < 0.05), Gln (6.8 ± 2.9 vs. 4.3 ± 1.0 μmol/g, p < 0.05), and GABA (2.9 ± 0.9 vs. 1.5 ± 0.4 μmol/g, p < 0.01). The present study strongly supports a hyperactivity of the glutamatergic cortico‐striatal pathway hypothesis after dopaminergic denervation in association with an increase of striatal GABA levels. It further shows an increased of striatal Gln concentrations, perhaps as a strategy to protect neurons from Glu excitotoxic injury after striatal dopamine depletion.
NMDA receptor‐mediated excitotoxic neuronal apoptosis in vitro and in vivo occurs in an ER stress and PUMA independent manner
Authors: Concannon Caoimhín G. , Ward Manus W. , Bonner Helena P. , Kuroki Katsura , Tuffy Liam P. , Bonner Caroline T. , Woods Ina , Engel Tobias , Henshall David C. , Prehn Jochen H. M.
Published: January 2008

Disruption of endoplasmic reticulum (ER) Ca2+ homeostasis and ER dysfunction have been suggested to contribute to excitotoxic and ischaemic neuronal injury. Previously, we have characterized the neural transcriptome following ER stress and identified the BH3‐only protein, p53 up‐regulated mediator of apoptosis (PUMA), as a central mediator of ER stress toxicity. In this study, we investigated the effects of excitotoxic injury on ER Ca2+ levels and induction of ER stress responses in models of glutamate‐ and NMDA‐induced excitotoxic apoptosis. While exposure to the ER stressor tunicamycin induced an ER stress response in cerebellar granule neurons, transcriptional activation of targets of the ER stress response, including PUMA, were absent following glutamate‐induced apoptosis. Confocal imaging revealed no long‐term changes in the ER Ca2+ level in response to glutamate. Murine cortical neurons and organotypic hippocampal slice cultures from PUMA+/+ and PUMA−/− animals provided no evidence of ER stress and did not differ in their sensitivity to NMDA. Finally, NMDA‐induced excitotoxic apoptosis in vivo was not associated with ER stress, nor did deficiency in PUMA alleviate the injury induced. Our data suggest that NMDA receptor‐mediated excitotoxic apoptosis occurs in vitro and in vivo in an ER stress and PUMA independent manner.
Seawater Mg/Ca controls polymorph mineralogy of microbial CaCO3: A potential proxy for calcite‐aragonite seas in Precambrian time
Authors: RIES J. B. , ANDERSON M. A. , HILL R. T.
Published: January 2008

A previously published hydrothermal brine‐river water mixing model driven by ocean crust production suggests that the molar Mg/Ca ratio of seawater (mMg/Casw) has varied significantly (~1.0–5.2) over Precambrian time, resulting in six intervals of aragonite‐favouring seas (mMg/Casw > 2) and five intervals of calcite‐favouring seas (mMg/Casw < 2) since the Late Archaean. To evaluate the viability of microbial carbonates as mineralogical proxy for Precambrian calcite‐aragonite seas, calcifying microbial marine biofilms were cultured in experimental seawaters formulated over the range of Mg/Ca ratios believed to have characterized Precambrian seawater. Biofilms cultured in experimental aragonite seawater (mMg/Casw = 5.2) precipitated primarily aragonite with lesser amounts of high‐Mg calcite (mMg/Cacalcite = 0.16), while biofilms cultured in experimental calcite seawater (mMg/Casw = 1.5) precipitated exclusively lower magnesian calcite (mMg/Cacalcite = 0.06). Furthermore, Mg/Cacalcite varied proportionally with Mg/Casw. This nearly abiotic mineralogical response of the biofilm CaCO3 to altered Mg/Casw is consistent with the assertion that biofilm calcification proceeds more through the elevation of , via metabolic removal of CO2 and/or H+, than through the elevation of Ca2+, which would alter the Mg/Ca ratio of the biofilm's calcifying fluid causing its pattern of CaCO3 polymorph precipitation (aragonite vs. calcite; Mg‐incorporation in calcite) to deviate from that of abiotic calcification. If previous assertions are correct that the physicochemical properties of Precambrian seawater were such that Mg/Casw was the primary variable influencing CaCO3 polymorph mineralogy, then the observed response of the biofilms’ CaCO3 polymorph mineralogy to variations in Mg/Casw, combined with the ubiquity of such microbial carbonates in Precambrian strata, suggests that the original polymorph mineralogy and Mg/Cacalcite of well‐preserved microbial carbonates may be an archive of calcite‐aragonite seas throughout Precambrian time. These results invite a systematic evaluation of microbial carbonate primary mineralogy to empirically constrain Precambrian seawater Mg/Ca.
Carbon pools and isotopic trends in a hypersaline cyanobacterial mat
Authors: WIELAND A. , PAPE T. , MÖBIUS J. , KLOCK J.–H. , MICHAELIS W.
Published: January 2008

The fine‐scale depth distribution of major carbon pools and their stable carbon isotopic signatures (δ13C) were determined in a cyanobacterial mat (Salin‐de‐Giraud, Camargue, France) to study early diagenetic alterations and the carbon preservation potential in hypersaline mat ecosystems. Particular emphasis was placed on the geochemical role of extracellular polymeric substances (EPS). Total carbon (Ctot), organic carbon (Corg), total nitrogen (Ntot), total hydrolysable amino acids (THAA), carbohydrates, cyanobacteria‐derived hydrocarbons (8‐methylhexadecane, n‐heptadec‐5‐ene, n‐heptadecane) and EPS showed highest concentrations in the top millimetre of the mat and decreased with depth. The hydrocarbons attributed to cyanobacteria showed the strongest decrease in concentration with depth. This correlated well with the depth profiles of oxygenic photosynthesis and oxygen, which were detected in the top 0.6 and 1.05 mm, respectively, at a high down‐welling irradiance (1441 µmol photons m−2 s−1). At depths beneath the surface layer, the Corg was composed mainly of amino acids and carbohydrates. A resistance towards microbial degradation could have resulted from interactions with diverse functional groups present in biopolymers (EPS) and with minerals deposited in the mat. A 13C enrichment with depth for the total carbon pool (Ctot) was observed, with δ13C values ranging from –16.3‰ at the surface to –11.3‰ at 9–10 mm depth. Total lipids depicted a δ13C value of –17.2‰ in the top millimetre and then became depleted in 13C with depth (–21.7 to –23.3‰). The δ13C value of EPS varied only slightly with depth (–16.1 to –17.3‰) and closely followed the δ13C value of Corg at depths beneath 4 mm. The EPS represents an organic carbon pool of preservation potential during early stages of diagenesis in recent cyanobacterial mats as a result of a variety of possible interactions. Their analyses might improve our understanding of fossilized microbial remains from mat ecosystems.
Fossilized microorganisms associated with zeolite–carbonate interfaces in sub‐seafloor hydrothermal environments
Authors: IVARSSON M. , LINDBLOM S. , BROMAN C. , HOLM N. G.
Published: January 2008

In this paper we describe carbon‐rich filamentous structures observed in association with the zeolite mineral phillipsite from sub‐seafloor samples drilled and collected during the Ocean Drilling Program (ODP) Leg 197 at the Emperor Seamounts. The filamentous structures are ~5 µm thick and ~100–200 µm in length. They are found attached to phillipsite surfaces in veins and entombed in vein‐filling carbonates. The carbon content of the filaments ranges between ~10 wt% C and 55 wt% C. They further bind to propidium iodide (PI), which is a dye that binds to damaged cell membranes and remnants of DNA.

Carbon‐rich globular microstructures, 1–2 µm in diameter, are also found associated with the phillipsite surfaces as well as within wedge‐shaped cavities in phillipsite assemblages. The globules have a carbon content that range between ~5 wt% C and 55 wt% C and they bind to PI. Ordinary globular iron oxides found throughout the samples differ in that they contain no carbon and do not bind to the dye PI. The carbon‐rich globules are mostly concentrated to a film‐like structure that is attached to the phillipsite surfaces. This film has a carbon content that ranges between ~25 wt% C and 75 wt% C and partially binds to PI. EDS analyses show that the carbon in all structures described are not associated with calcium and therefore not bound in carbonates. The carbon content and the binding to PI may indicate that the filamentous structures could represent fossilized filamentous microorganisms, the globules could represent fossilized microbial cells and the film‐like structures could represent a microbially produced biofilm.

Our results extend the knowledge of possible habitable niches for a deep biosphere in sub‐seafloor environments and suggests, as phillipsite is one of the most common zeolite mineral in volcanic rocks of the oceanic crust, that it could be a common feature in the oceanic crust elsewhere.
Earliest fossil record of bacterial–cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA)
Authors: TOMESCU A. M. F. , HONEGGER R. , ROTHWELL G. W.
Published: January 2008

Cyanobacteria in terrestrial and aquatic habitats are frequently associated with heterotrophic bacteria, and such associations are most often metabolically interactive. Functionally, the members of such bacterial–cyanobacterial consortia benefit from diverse metabolic capabilities of their associates, thus exceeding the sum of their parts. Such associations may have been just as ubiquitous in the past, but the fossil record has not produced any direct evidence for such associations to date. In this paper, we document fossil bacteria associated with a macrophytic cyanobacterial mat in the early Silurian (Llandovery) Massanutten Sandstone of Virginia, USA. Both the bacterial and the cyanobacterial cells are preserved by mineral replacement (pyrite subsequently replaced by iron oxyhydroxides) within an amorphous carbonaceous matrix which represents the common exopolysaccharide investment of the cyanobacterial colony. The bacteria are rod‐shaped, over 370 nm long and 100 nm in diameter, and occur both as isolated cells and as short filaments. This occurrence represents the oldest fossil evidence for bacterial–cyanobacterial associations, documenting that such consortia were present 440 Ma ago, and revealing the potential for them to be recognized deeper in the fossil record.
Quantification of bird migration by radar – a detection probability problem
Authors: SCHMALJOHANN HEIKO , LIECHTI FELIX , BÄCHLER ERICH , STEURI THOMAS , BRUDERER BRUNO
Published: January 2008

Besides the scientific interest in the quantification of bird migration, there is an increasing need to quantify bird movements for the assessment of bird collision risk with artificial structures. In many environmental impact studies, the radar method is used in an inappropriate manner. The processing of echoes consists often of counting blips within defined screen fields, and the surveyed volume is estimated without reference to the detection probabilities of different ‘target sizes’ (radar cross‐sections). The aim of this paper is to present a procedure to quantify bird migration reliably using radar by stating the theoretical requirements of every single step of this procedure and presenting methodological solutions using our own radar data from extensive field studies. Our methodological solutions can be applied to various radar systems, including widely used ship radar. The procedure presented involves discriminating the echoes of birds and insects and estimating the different detection probabilities of differently ‘sized’ birds (radar cross‐sections). By ignoring the different detection probabilities, density estimations may be wrong by as much as 400%. We fear that quantification of bird migration and predicted bird numbers affected by collisions with artificial structures are in many cases based on unreliable estimates.
Inflation and Welfare: A Search Approach
Authors: CRAIG BEN , ROCHETEAU GUILLAUME
Published: January 2008

This paper uses a search model of monetary exchange to provide new insights for evaluating the welfare costs of inflation. We first show that the search model of money can rationalize the estimates of the welfare cost of inflation based on the “welfare triangle” methodology of Bailey (1956) and Lucas (2000) provided that buyers appropriate the social marginal benefit of their real balances. For other mechanisms, the measure given by the welfare triangle has to be scaled up by a factor that increases with sellers' market power. We introduce capital and endogenous participation decisions and study how the cost of inflation is affected. We provide calibrated examples in which a deviation from the Friedman rule is optimal.
Can Interest‐Bearing Money Circulate? A Small‐Denomination Arkansan Experiment, 1861–63
Authors: BURDEKIN RICHARD C. K. , WEIDENMIER MARC D.
Published: January 2008

Legal restrictions theory suggests that dominance of non‐interest‐bearing currency is possible only because legal impediments prevent financial institutions from offering interest‐bearing alternatives. A viable interest‐bearing medium must be issued in denominations low enough for day‐to‐day use, however, and without historical examples of small‐denomination interest‐bearing issues we cannot properly test whether interest‐bearing currency will circulate as legal restrictions theory predicts. Civil War Arkansas offers a rare instance where large quantities of small‐denomination interest‐bearing money were actually issued, mostly below $5. The results of this Arkansan experiment show that small‐denomination interest‐bearing issues can indeed function as the primary medium of exchange.
Productivity Improvement through Modeling: An Overview of Manufacturing Experience for the Food Industry
Authors: Ivester Robert W.
Published: January 2008

ABSTRACT: Food production and manufacturing of durable goods share common needs for understanding, modeling, and controlling processing conditions in order to obtain desirable product characteristics. This article presents a review of research on manufacturing process modeling, with a focus on historical developments in the metrology and standards infrastructure to improve productivity and competitiveness of machining systems. To remain competitive, manufacturing requires accurate and reliable machines and processes whose characteristics are known and guaranteed for a wide variety of tasks and conditions. Productive, high‐quality manufacturing will increasingly rely on a science‐based understanding and monitoring of the available machining processes and equipment to produce the first part and every subsequent part on time and to specification with no significant time spent on process development or setup.
Prevalence of nonspecific low back pain in schoolchildren aged between 13 and 15 years
Authors: Masiero Stefano , Carraro Elena , Celia Andrea , Sarto Diego , Ermani Mario
Published: January 2008

Aim: To investigate the annual (2005) prevalence of nonspecific low back pain (LBP), defined as lumbago not attributed to recognizable, known specific pathology, in a population of adolescents.

Methods: We investigated 7542 school teenagers with a structured questionnaire consisting of demographic and anthropometric items, psychosocial factors and life style, presence and intensity of LBP, family history of LBP, and questions about whether the teenager had been referred to a physician for this problem. Univariate (t‐test, Mann–Whitney U‐test and chi‐square test) and multivariate analyses (logistic regression) were performed.

Results: A total of 1180 (20.5%) teenagers reported one or more episodes of LBP, of whom 900 (76.3%) had consulted a health provider. A significantly greater percentage of LBP was found in the students who practised aerobics and swimming compared to the other sports. The search for risk factors in the whole population revealed no associations between LBP and the investigated anthropometrics or lifestyle items, whereas a significant association was found for gender (to be female), positive family history of LBP and absence of sports activity.

Conclusions: Our study shows that nonspecific LBP is a frequent event in teenagers, particularly in females, sedentary children and those with a family history of LBP.
Geochemical Quantification of Semiarid Mountain Recharge
Authors: Wahi Arun K. , Hogan James F. , Ekwurzel Brenda , Baillie Matthew N. , Eastoe Christopher J.
Published: January 2008

Analysis of a typical semiarid mountain system recharge (MSR) setting demonstrates that geochemical tracers help resolve the location, rate, and seasonality of recharge as well as ground water flowpaths and residence times. MSR is defined as the recharge at the mountain front that dominates many semiarid basins plus the often‐overlooked recharge through the mountain block that may be a significant ground water resource; thus, geochemical measurements that integrate signals from all flowpaths are advantageous. Ground water fluxes determined from carbon‐14 (14C) age gradients imply MSR rates between 2 × 106 and 9 × 106 m3/year in the Upper San Pedro Basin, Arizona, USA. This estimated range is within an order of magnitude of, but lower than, prior independent estimates. Stable isotopic signatures indicate that MSR has a 65% ± 25% contribution from winter precipitation and a 35% ± 25% contribution from summer precipitation. Chloride and stable isotope results confirm that transpiration is the dominant component of evapotranspiration (ET) in the basin with typical loss of more than 90% of precipitation‐less runoff to ET. Such geochemical constraints can be used to further refine hydrogeologic models in similar high‐elevation relief basins and can provide practical first estimates of MSR rates for basins lacking extensive prior hydrogeologic measurements.
MLR–ANN and RTO Approach to μ‐opioid Receptor‐binding Affinity. Pooling Data from Different Sources
Authors: Ramírez‐Galicia Guillermo , Garduño‐Juárez Ramón , Deeb Omar , Hemmateenejad Bahram
Published: January 2008

One hundred and six morphinan derivatives were taken from the Drug Evaluation Committee reports to propose several quantitative structure–activity relationship models to describe the μ‐receptor‐binding affinity. After several procedures to reduce the descriptor number, 21 descriptors were selected for the descriptor pool by a complete Multiple Linear Regression methodology. In this procedure only three molecules were considered as outliers. Several tests changing the relation between training:predicted sets were considered to find the best relation between these sets. The higher the number of molecules in the predicted set the higher the predictive power was observed. The optimal number of descriptors was established using the Akaike’s information criterion and Kubinyi fitness function parameters. The Artificial Neuron Network methodology was applied to improve the Multiple Linear Regression best result. Finally, the regression through the origin methodology was applied to establish the best model from the Artificial Neuron Network methodology. The best quantitative structure–activity relationship model was proven to be independent of chance correlation.
Impact of primary tumour stage on survival in dogs with solitary lung tumours
Authors: Polton G. A. , Brearley M. J. , Powell S. M. , Burton C. A.
Published: January 2008

Objectives:The objective of this study was to determine simple prognostic criteria for differentiation of canine solitary lung tumour cases into those that will and will not benefit from thoracic surgery.

Methods:This was a retrospective study using the records of cases presented to Davies Veterinary Specialists, Hitchin, UK, from December 1998 to December 2005. Survival analyses were performed using the Kaplan‐Meier and logrank methods. Potentially significant variables were evaluated by multivariate Cox analysis.

Results:Forty‐two patients met the inclusion criteria. Primary tumour stage T1, absence of neoplastic lymph nodes and metastases, and papillary tumour type were statistically significant favourable prognostic indicators on univariate analysis. Multivariate analysis attributed significance to primary tumour stage T1 and papillary type only. Median survival times were 555 days for T1N0M0 tumours of papillary type and 72 days for the remainder.

ClinicalSignificance:Survival time following surgery in dogs with primary lung tumours was poor except in clinical stage T1N0M0 cases. These data support use of clinical techniques to dichotomise cases as T1N0M0 or other, improving decision making in thoracic surgery. These data validate initiation of prospective studies examining the role of chemotherapy in the management of advanced cases.
Offense and defense in landscape‐level invasion control
Authors: Drury Kevin L. S. , Rothlisberger John D.
Published: January 2008

Biological invasions are multi‐stage processes comprising chance demographic events, species interactions, and dispersal. Despite this complexity, simple models can increase understanding of the invasion process. We model the spread of aquatic invasive species through a network of lakes to evaluate the effectiveness of two intervention strategies. The first, which we call offense, contains the invader at sources; the second, which we call defense, protects uninvaded destinations. Deterministic models reveal the effects of these intervention strategies on spread rates. Practical applications involve finite collections of uninvaded lakes, however, and we therefore also present a stochastic model to describe how these strategies affect expected times to important invasion milestones. When the goal is to reduce overall spread rates, both approaches agree that offense is better early in invasions, but that defense is better after 1/2 the lakes are invaded. When the goal is to protect areas of high conservation value, however, defensive site protection always provides lower per site introduction rates. Although we focus on lakes, our results are quite general, and could be applied to any discrete habitat patches including, for example, fragmented terrestrial habitats.
Can punishment maintain sex?
Authors: Rankin Daniel J.
Published: January 2008

Individuals who reproduce asexually have a two‐fold advantage over their sexually‐reproducing counterparts as they are able to reproduce twice as fast. Explaining why sexual reproduction is favoured over asexual reproduction therefore remains an important challenge in evolutionary biology. Various mechanisms involving resistance to parasites, adaptation to novel environments and helping to purge the genome of deleterious mutations have all been proposed as potential mechanisms which could promote the evolution of sex. A recent article has suggested that spiteful males may help to reduce the two‐fold advantage of asexual females. Here I discuss this idea, and further ask whether punishment of asexual females by sexual females could be one way in which sexual reproduction could be maintained in groups of animals; in light of recent research on the repression of competition, it could be possible that asexual females which reproduce faster than their sexual counterparts will be punished for using group resources. It may therefore be possible that the behaviour of sexual individuals towards asexual females could have fitness consequences which could potentially reduce the two‐fold advantage they gain from reproducing parthenogenetically.
Reducing Friction in Tilting-Pad Bearings by the Use of Enclosed Recesses
Authors: Heinrichson Niels , Santos Ilmar Ferreira
Published: January 2008

A three-dimensional thermoelastohydrodynamic model is applied to the analysis of tilting-pad bearings with spherical pivots and equipped with deep recesses in the high-pressure regions. A potential for a 10–20% reduction in the friction loss compared to conventional plain bearing pads is documented. Design suggestions minimizing the power loss are given for various length-to-width ratios. The tilting angle in the sliding direction is more sensitive to correct positioning of the pivot point than conventional bearing pads. Improving the performance by equipping a tilting-pad bearing with a deep recess therefore requires accurate analysis and design of the bearing. Similarly, a high sensitivity perpendicular to the sliding direction suggests that this method of reducing friction is more feasible when using line pivots or spring beds than when using spherical pivots for controlling the tilting angle.
Numerical Modeling of Mixed Lubrication and Flash Temperature in EHL Elliptical Contacts
Authors: Deolalikar Neelesh , Sadeghi Farshid , Marble Sean
Published: January 2008

Highly loaded ball and rolling element bearings are often required to operate in the mixed elastohydrodynamic lubrication regime in which surface asperity contact occurs simultaneously during the lubrication process. Predicting performance (i.e., pressure, temperature) of components operating in this regime is important as the high asperity contact pressures can significantly reduce the fatigue life of the interacting components. In this study, a deterministic mixed lubrication model was developed to determine the pressure and temperature of mixed lubricated circular and elliptic contacts for measured and simulated surfaces operating under pure rolling and rolling/sliding condition. In this model, we simultaneously solve for lubricant and asperity contact pressures. The model allows investigation of the condition and transition from boundary to full-film lubrication. The variation of contact area and load ratios is examined for various velocities and slide-to-roll ratios. The mixed lubricated model is also used to predict the transient flash temperatures occurring in contacts due to asperity contact interactions and friction. In order to significantly reduce the computational efforts associated with surface deformation and temperature calculation, the fast Fourier transform algorithm is implemented.
A realist account of the ontology of impairment
Authors: Vehmas S , Mäkelä P
Published: January 2008

This paper provides a philosophical analysis of the ontology of impairment, in part social and in part not. The analysis is based on the division between two categories of facts concerning the world we live in: “brute” and institutional facts. Brute facts are those that require no human institution for their existence. To state a brute fact requires naturally the institution of language, but the fact stated is not the same as the statement of it. For example, regardless of any human institution or opinion, the presence of an extra chromosome 21 is a brute fact, and despite of people’s constructions or deconstructions, this fact remains. As for the lives of people with extra chromosome 21, the social reality and human institutions enter the picture. The social and moral status of these people is never a matter of brute fact.
On the argument that enhancement is “cheating”
Authors: Schermer M
Published: January 2008

One frequently used argument in the discussion on human enhancement is that enhancement is a form of cheating. This argument is well-known in relation to doping in sports, but recently it has also been used with regard to cognitive enhancement in the context of education and exams. This paper analyses the enhancement-is-cheating argument by comparing sports and education, and by evaluating how the argument can be interpreted in both contexts. If cheating is understood as breaking the rules in order to gain an unfair advantage over others, it can be argued that some enhancements are a form of cheating. This problem of cheating is, however, relatively easy to remedy by either changing the rules, or by instituting controls and sanctions. This does not, therefore, constitute a categorical objection to enhancement. A further analysis of the intuitions behind the enhancement-is-cheating argument, however, shows that if sports and education are understood as “practices”, with their own internal goods and standards of excellence, some potential problems of enhancement can be articulated. These concern the internal goods and standards of excellence that are characteristic of specific practices. Seen from this perspective, the important question is how enhancement technologies might be embedded in specific practices—or how they might corrode them.
Ethics of deliberation, consent and coercion in psychiatry
Authors: Liégeois A , Eneman M
Published: January 2008

In psychiatry, caregivers try to get free and informed consent of patients, but often feel required to restrict freedom and to use coercion. The present article develops ethical advice given by an Ethics Committee for Mental Health Care. The advice recommends an ethical ideal of shared deliberation, consisting of information, motivation, consensus and evaluation. For the exceptional use of coercion, the advice develops three criteria, namely incapacity to deliberate, threat of serious harm and proportionality between harm and coercion.

The article also discusses the viewpoints of the ethical advice and of the European Convention on Human Rights and Biomedicine: is the advice in agreement with the Convention and can the advice refine the guidelines of the Convention for the particular context of psychiatry? Although the Convention emphasises the autonomy of the individual patient, whereas the advice focuses on the relationships between the partners involved, the advice enjoys a complementary and supportive function in the application of the Convention.
THEORY OF RESONANT SPIN HALL EFFECT
Authors: ZHANG FU-CHUN , SHEN SHUN-QING
Published: January 2008

A brief review is presented on the resonant spin Hall effect, where a tiny external electric field induces a saturated spin Hall current in a 2-dimensional electron or hole gas in a perpendicular magnetic field. The phenomenon is attributed to the energy level crossing associated with the spin-orbit coupling and the Zeeman splitting. We summarize recent theoretical development of the effect in various systems and discuss possible experiments to observe the effect.