bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution
Authors: Putnam Christopher D. , Hammel Michal , Hura Greg L. , Tainer John A. 
Published: December 2007

AbstractCrystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 Å to 10 Å resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein–nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.
Singularity-free trajectory planning of platform-type parallel manipulators for minimum actuating effort and reactions
Authors: Chen Chun-Ta , Chi Hua-Wei 
Published: December 2007

SUMMARYDue to the existence of singular configurations within the workspace for a platform- type parallel manipulator (PPM), the actuating force demands increase drastically as the PPM approaches or crosses singular points. Therefore, in this report, a numerical technique is presented to plan a singularity-free trajectory of the PPM for minimum actuating effort and reactions. By using the parametric trajectory representation, the singularity-free trajectory planning problem can be cast to the determination of undetermined control points, after which a particle swarm optimization algorithm is employed to find the optimal control points. This algorithm ensures that the obtained trajectories can avoid singular points within the workspace and that the PPM has the minimum actuating effort and reactions. Simulations and discussions are presented to demonstrate the effectiveness of the algorithm.
Our Brain as Stone Age Computer
Authors: Greiffenstein Manfred F. 
Published: December 2007

Evolutionary Cognitive Neuroscience. 2007. Steven M. Platek, Julian P. Keenan, & Todd K. Shackelford (Eds.). Cambridge, MA: MIT Press, 616 pp., $65.00 (HB)Clinical neuropsychologists are most interested in the ‘what’ of brain function. Neuropsychological assessment requires only a working knowledge of functional localization and the tests best suited to capture that specialization. The ‘why’ of cortical specialization is not necessary for good clinical work. The edited volume Evolutionary Cognitive Neuroscience is entirely devoted to the ‘how’ and ‘why’ of brain specialization based on the fact (not ‘theory’) of natural selection. Editors Steven Platek, Julian Keenan, and Todd Shackelford are well qualified to organize and write this book; they devoted their careers to understanding neuropsychological functions as evolved mechanisms designed to solve recurrent survival and reproduction problems of our evolutionary past. In this view, our brains are Stone Age computers.
Diversity of cutaneous bacteria with antifungal activity isolated from female four-toed salamanders
Authors: Lauer Antje , Simon Mary Alice , Banning Jenifer L , Lam Brianna A , Harris Reid N 
Published: December 2007

Abstract
Among the microbiota of amphibian skin are bacteria that produce antifungal compounds. We isolated cutaneous bacteria from the skins of three populations of the nest-attending plethodontid salamander Hemidactylium scutatum and subsequently tested the bacterial isolates against two different fungi (related to Mariannaea elegans and Rhizomucor variabilis) that were obtained from dead salamander eggs. The culturable antifungal bacteria were phylogenetically characterized based on 16S rRNA phylogeny, and belonged to four phyla, comprising 14 bacterial families, 16 genera and 48 species. We found that about half of the antifungal bacterial genera and families were shared with a related salamander species, but there was virtually no overlap at the species level. The proportion of culturable antifungal bacterial taxa shared between two large populations of H. scutatum was the same as the proportion of taxa shared between H. scutatum and Plethodon cinereus, suggesting that populations within a species have unique antifungal bacterial species. Approximately 30% of individuals from both salamander species carried anti-M. elegans cutaneous bacteria and almost 90% of P. cinereus and 100% of H. scutatum salamanders carried anti-R. variabilis cutaneous bacteria. A culture independent method (PCR/DGGE) revealed a shared resident bacterial community of about 25% of the entire resident bacterial community within and among populations of H. scutatum. Thus, the culturable antifungal microbiota was far more variable on salamander skins than was the bacterial microbiota detected by PCR/DGGE. The resident cutaneous antifungal bacteria may play an important role in amphibians' innate defense against pathogens, including the lethal chytrid fungus Batrachochytrium dendrobatidis.
Thermodynamic constraints on methanogenic crude oil biodegradation
Authors: Dolfing Jan , Larter Stephen R , Head Ian M 
Published: December 2007

Abstract
Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleum reservoirs and anoxic environments contaminated with petroleum. There are several possible routes whereby hydrocarbons may be converted to methane: (i) complete oxidation of alkanes to H2 and CO2, linked to methanogenesis from CO2 reduction; (ii) oxidation of alkanes to acetate and H2, linked to acetoclastic methanogenesis and CO2 reduction; (iii) oxidation of alkanes to acetate and H2, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction; (iv) oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis and (v) oxidation of alkanes to acetate alone, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction. We have developed the concept of a ‘window of opportunity’ to evaluate the range of conditions under which each route is thermodynamically feasible. On this basis the largest window of opportunity is presented by the oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis. This contradicts field-based evidence that indicates that in petroleum rich environments acetoclastic methanogenesis is inhibited and that methanogenic CO2 reduction is the predominant methanogenic process. Our analysis demonstrates that under those biological constraints oxidation of alkanes to acetate and H2, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction offers a greater window of opportunity than complete oxidation of alkanes to H2 and CO2 linked to methanogenic CO2 reduction, and hence is the process most likely to occur.
Sparse inverse covariance estimation with the graphical lasso
Authors: Friedman Jerome , Hastie Trevor , Tibshirani Robert 
Published: December 2007

Abstract
We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm—the graphical lasso—that is remarkably fast: It solves a 1000-node problem (∼500000 parameters) in at most a minute and is 30–4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bühlmann (2006). We illustrate the method on some cell-signaling data from proteomics.
Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic
Authors: Johnson Catherine L. , Leising Andrew W. , Runge Jeffrey A. , Head Erica J. H. , Pepin Pierre , Plourde Stéphane , Durbin Edward G. 
Published: December 2007

Abstract
Johnson, C. L., Leising, A. W., Runge, J. A., Head, E. J. H., Pepin, P., Plourde, S., and Durbin, E. G. 2008. Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic. – ICES Journal of Marine Science, 65: 339–350. Demographic time-series from four fixed stations in the Northwest Atlantic Ocean demonstrate variable timing of entry into and emergence from dormancy in subpopulations of the planktonic copepod Calanus finmarchicus. A proxy for timing of entry was established as the date each year when the proportion of the fifth copepodid stage (CV) in the subpopulation rose to half its overall climatological maximum CV proportion at that station. The proxy for timing of emergence at each station was set as the first date when adults were more than 10% of the total abundance of copepodid stages. An alternate emergence proxy date was determined by back-calculating the spawning dates of the first early copepodid stages appearing in spring, using a stage-structured, individual-based model. No single environmental cue (photoperiod, surface temperature, or average surface-layer chlorophyll a concentration) consistently explained entry or emergence dates across all stations. Among hypotheses put forward to explain dormancy in Calanus species, we cannot eliminate the lipid accumulation window hypothesis for onset of dormancy or a lipid-modulated endogenous timer controlling dormancy duration. The fundamental premise of these hypotheses is that individuals can only enter dormancy if their food and temperature history allows them to accumulate sufficient lipid to endure overwintering, moult, and undergo early stages of gonad maturation.
Seasonal relationships between the copepod community and hydrographic conditions in the southern East China Sea
Authors: Lan Yang-Chi , Lee Ming-An , Chen Wen-Yu , Hsieh Feng-Jen , Pan Jia-Yi , Liu Don-Chung , Su Wei-Cheng 
Published: December 2007

Abstract
Lan, Y-C., Lee, M-A., Chen, W-Y., Hsieh, F-J., Pan, J-Y., Liu, D-C., and Su, W-C. 2008. Seasonal relationships between the copepod community and hydrographic conditions in the southern East China Sea. – ICES Journal of Marine Science, 65: 462–468. We studied the relationship between seasonal variation of the copepod community and hydrographic conditions in the southern East China Sea (ECS). Hydrographic conditions in the southwestern ECS were influenced by the China Coastal Current (CCC) from late autumn to early spring and by the South China Sea Current (SCSC) during the rest of the year, and in the southeastern ECS by the Kuroshio Current (KC) year-round. We identified 141 species of copepods belonging to 54 genera and 27 families. Diversity and evenness of copepods were higher in waters influenced by the KC and the SCSC, and lower in waters with intrusion of the CCC. The CCC transported dominant copepods such as Paracalanus aculeatus, Paracalanus parvus, and Calanus sinicus into the southwestern ECS in late autumn and winter, whereas the SCSC carried Temora discaudata, Oncaea venusta, and P. aculeatus in spring, and Undinula vulgaris, T. discaudata, and P. aculeatus in summer. In the southeastern ECS, the KC brought in tropical copepods having clear seasonal variations throughout the year. We examined the relationships between indicator copepod species and currents and oceanographic conditions, using canonical correlation analysis.
Polyhedral realization of crystal bases for generalized Kac–Moody algebras
Authors: Shin Dong-Uy 
Published: December 2007

AbstractIn this paper, we give a polyhedral realization of the crystal B(∞) of Uq−(𝔤) for the generalized Kac–Moody algebras. As applications, we give explicit descriptions of crystals for the generalized Kac–Moody algebras of rank 2 and 3, and Monster Lie algebras.
Gnotobiotic Mouse Immune Response Induced byBifidobacteriumsp. Strains Isolated from Infants
Authors: Ménard Odile , Butel Marie-José , Gaboriau-Routhiau Valérie , Waligora-Dupriet Anne-Judith 
Published: December 2007

ABSTRACTBifidobacterium, which is a dominant genus in infants’ fecal flora and can be used as a probiotic, has shown beneficial effects in various pathologies, including allergic diseases, but its role in immunity has so far been little known. Numerous studies have shown the crucial role of the initial intestinal colonization in the development of the intestinal immune system, and bifidobacteria could play a major role in this process. For a better understanding of the effect ofBifidobacteriumon the immune system, we aimed at determining the impact ofBifidobacteriumon the T-helper 1 (TH1)/TH2 balance by using gnotobiotic mice. Germfree mice were inoculated withBifidobacterium longumNCC2705, whose genome is sequenced, and with nineBifidobacteriumstrains isolated from infants’ fecal flora. Five days after inoculation, mice were killed. Transforming growth factor β1 (TGF-β1), interleukin-4 (IL-4), IL-10, and gamma interferon (IFN-γ) gene expressions in the ileum and IFN-γ, tumor necrosis factor alpha (TNF-α), IL-10, IL-4, and IL-5 secretions by splenocytes cultivated for 48 h with concanavalin A were quantified. TwoBifidobacteriumspecies had no effect (B. adolescentis) or little effect (B. breve) on the immune system.Bifidobacterium bifidum,Bifidobacterium dentium, and oneB. longumstrain induced TH1 and TH2 cytokines at the systemic and intestinal levels. OneB. longumstrain induced a TH2 orientation with high levels of IL-4 and IL-10, both secreted by splenocytes, and of TGF-β gene expression in the ileum. The other two strains induced TH1 orientations with high levels of IFN-γ and TNF-α splenocyte secretions.Bifidobacterium's capacity to stimulate immunity is species specific, but its influence on the orientation of the immune system is strain specific.
Pentenolide Analogues of Antifungal Butenolides: Strategies Towards 3,6-Disubstituted Pyranones and Unexpected Loss of Biological Effect
Authors: Šnajdr Ivan , Pavlík Jan , Schiller Radan , Kuneš Jiří , Pour Milan 
Published: December 2007

Pentenolide analogues of antifungal 3,5-disubstituted butenolides were prepared by oxidative cyclization of 2-(substituted aryl)hex-5-enoic acids as the key step. Given the limitations of the methodology, another approach to the title compounds based on the Pd-catalyzed carbonylative lactonization of 4-iodo-3-en-1-ols was developed, and the carbonylation conditions were optimized. While the former sequence allows only the introduction of a substituted methyl at C6, pyranones bearing a range of various C-substituents at C6 can be prepared by the latter. Somewhat surprisingly, unlike the corresponding butenolides with the same substitution pattern, the title pentenolides possess no antifungal or cytostatic activity.
The burden of cancer at work: estimation as the first step to prevention
Authors: Rushton L , Hutchings S , Brown T 
Published: December 2007

Objectives:Work-related cancers are largely preventable. The overall aim of this project is to estimate the current burden of cancer in Great Britain attributable to occupational factors, and identify carcinogenic agents, industries and occupations for targeting risk prevention.Methods:Attributable fractions and numbers were estimated for mortality and incidence for bladder, lung, non-melanoma skin, and sinonasal cancers, leukaemia and mesothelioma for agents and occupations classified as International Agency for Research on Cancer (IARC) Group 1 and 2A carcinogens with “strong” or “suggestive” evidence for carcinogenicity at the specific cancer site in humans. Risk estimates were obtained from published literature and national data sources used for estimating proportions exposed.Results:In 2004, 78 237 men and 71 666 women died from cancer in Great Britain. Of these, 7317 (4.9%) deaths (men: 6259 (8%); women: 1058 (1.5%)) were estimated to be attributable to work-related carcinogens for the six cancers assessed. Incidence estimates were 13 338 (4.0%) registrations (men: 11 284 (6.7%); women 2054 (1.2%)). Asbestos contributed over half the occupational attributable deaths, followed by silica, diesel engine exhaust, radon, work as a painter, mineral oils in metal workers and in the printing industry, environmental tobacco smoke (non-smokers), work as a welder and dioxins. Occupational exposure to solar radiation, mineral oils and coal tars/pitches contributed 2557, 1867 and 550 skin cancer registrations, respectively. Industries/occupations with large numbers of deaths and/or registrations include construction, metal working, personal and household services, mining (not metals), land transport and services allied to transport, roofing, road repair/construction, printing, farming, the Armed Forces, some other service industry sectors and manufacture of transport equipment, fabricated metal products, machinery, non-ferrous metals and metal products, and chemicals.Conclusions:Estimates for all but leukaemia are greater than those currently used in UK health and safety strategy planning and contrast with small numbers (200–240 annually) from occupational accidents. Sources of uncertainty in the estimates arise principally from approximate data and methodological issues. On balance, the estimates are likely to be a conservative estimate of the true risk. Long latency means that past high exposures will continue to give substantial numbers in the near future. Although levels of many exposures have reduced, recent measurements of others, such as wood dust and respirable quartz, show continuing high levels.
Platelet functions and clinical effects in acute myelogenous leukemia
Authors: Bruserud Øystein , Foss Brynjar 
Published: December 2007

SummaryPlatelets interact with normal peripheral blood cells via adhesion as well as soluble mediators, and platelet released mediators can affect hematopoietic stem and progenitor cells. Interactions may also be involved between platelets and circulating malignant cells, which is suggested by the effects platelets seem to have on metastasis and the various platelet abnormalities observed in various malignant disorders, including acute myelogenous leukemia (AML) and other leukemias. It is only recently that the interactions between platelets and AML cells have been characterized in detail, and studies show that; i) platelets and AML blasts can affect functional characteristic of each other, ii) chemotherapeutic drugs frequently used in AML therapy can alter several platelet functions, iii) the systemic levels of various cytokines are enhanced during AML chemotherapy, including cytokines known to affect both leukemic blasts and platelet activation, and iv) platelet secretion of growth factors are clearly detected in peripheral blood stem cells autografts. In this review we describe platelet interactions with normal leukocytes, normal hematopoietic and leukemic cells and the possible clinical relevance of these interactions in AML.
Fondaparinux for the treatment of patients with acute heparininduced thrombocytopenia
Authors: Finch Christopher , Howard Amanda , Minhas Sohail , Lobo Bob 
Published: December 2007

SummaryHeparin-induced thrombocytopenia (HIT) is a life-threatening immune response to heparin that is associated with a high risk of thromboembolic complications. We prospectively treated seven subjects with acute HIT with fondaparinux and compared the results to a similar historical control population from the same hospital. Six of the seven fondaparinux-treated subjects were transitioned to warfarin, beginning after platelet count recovery occurred. Ten historical controls were treated with a direct thrombin inhibitor (DTI), eight of which were transitioned to warfarin. The primary study outcome was platelet count recovery which was defined as an increase from baseline by at least 30% of nadir to greater than 100,000/mm3 by day seven. Seven subjects were prospectively treated with fondaparinux for a median of eight days. Six of the seven had HIT with thrombosis at the time of enrollment. All fondaparinux treated subjects had a complete platelet count recovery, and none experienced a new thromboembolic complication, major bleeding or death by week four. One subject underwent limb amputation. Ten historical controls were treated with a DTI for a median duration of eleven days. Platelet count recovery occurred in eight of the ten historical controls. No new thromboembolic complications or major bleeds occurred but limb gangrene occurred in four controls. The development of limb gangrene in the historical controls may have been a result of delayed recognition of HIT and/ or inappropriately early institution of warfarin in the historical controls. This pilot study suggests that fondaparinux may be useful in patients with acute HIT.
High-dose atorvastatin in peripheral arterial disease (PAD): Effect on endothelial function, intima-media-thickness and local progression of PAD
Authors: Simon Roger , Loo Bernd van der , Kovacevic Tamara , Brockes Christiane , Rousson Valentin , Amann-Vesti Beatrice , Spring Silviana , Koppensteiner Renate 
Published: December 2007

SummaryBeneficial effects of aggressive lipid-lowering with high-dose atorvastatin (80 mg/day) have been demonstrated in patients with coronary and cerebrovascular disease. The impact of such a therapy in patients with peripheral arterial disease (PAD) is less known so far. Here we studied the effects of high-dose atorvastatin on brachial artery endothelial function, common carotid intima-media thickness (IMT) and local progression of PAD in these patients. One hundred of 500 patients screened with documented PAD were randomly assigned to receive 80 mg of atorvastatin daily for six months or to continue on conventional medical treatment. Ninety-six percent of patients in the control group were on standard statin treatment. High resolution B-mode ultrasonography was used to study brachial artery flowmediated dilation (FMD), IMT and ankle-brachial index (ABI) at baseline and at six months. FMD and IMT at baseline and at six months were 4.1 (0.06–8.6) versus 5.0 (0.76 vs. 8.1) %, p=0.96, and 0.76 (0.66–0.82) versus 0.73 (0.63–0.81) mm, p=0.41, respectively, in the atorvastatin group, and 2.66 (-1.9 – 6.9) versus 3.65 (0.0–8.6)%, p=0.02, and 0.78 (0.71–0.90) versus 0.77 (0.70–0.90) mm, p=0.48,in the control group. ABI at baseline and at six months was not different in either group. LDL cholesterol was reduced from 2.53 (2.21–3.28) to 1.86 (1.38–2.29) mM (p<0.0001) in the atorvastatin group, whereas levels remained stable in the control group [2.38 (1.94–3.16) vs.2.33 (1.82–2.84) mM, p=0.61]. Major adverse cardiovascular events occurred in 2.1% in the atorvastatin group and 1.9% in the control group (p= 0.61). In conclusion, in this pilot trial aggressive lipid-lowering with 80 mg of atorvastatin daily for six months had no effect on brachial artery FMD in patients with PAD. IMT andABI were also similar in patients with and without high-dose atorvastatin at six months.