bluuebunny/crossref_metadata_2025 huggingface dataset:
Are there general laws in parasite ecology?
Authors: POULIN R.
Published: January 2007

As a scientific discipline matures, its theoretical underpinnings tend to consolidate around a few general laws that explain a wide range of phenomena, and from which can be derived further testable predictions. It is one of the goals of science to uncover the general principles that produce recurring patterns in nature. Although this has happened in many areas of physics and chemistry, ecology is yet to take this important step. Ecological systems are intrinsically complex, but this does not necessarily mean that everything about them is unpredictable or chaotic. Ecologists, whose grand aim is to understand the interactions that govern the distribution, abundance and diversity of living organisms at different scales, have uncovered several regular patterns, i.e. widely observable statistical tendencies, in the abundance or diversity of organisms in natural ecosystems. Some of these patterns, however, are contingent, i.e. they are only true under particular circumstances; nevertheless, the broad generality of many patterns hints at the existence of universal principles. What about parasite ecology: is it also characterized by recurring patterns and general principles? Evidence for repeatable empirical patterns in parasite ecology is reviewed here, in search of patterns that are consistently detectable across taxa or geographical areas. The coverage ranges from the population level all the way to large-scale patterns of parasite diversity and abundance (or biomass) and patterns in the structure of host-parasite interaction networks. Although general laws seem to apply to these extreme scales of studies, most patterns observed at the intermediate scale, i.e. the parasite community level, appear highly contingent and far from universal. The general laws uncovered to date are proving valuable, as they offer glimpses of the underlying processes shaping parasite ecology and diversity.
Adorno's Schreker: Charting the self-dissolution of the distant sound
Authors: DAUB ADRIAN
Published: January 2007

Franz Schreker's opera Der ferne Klang is usually discussed using the term ‘phantasmagoria’, as a guiding thread. This article argues that this term names not one but two phenomena: as used by Theodor W. Adorno in his analysis of Wagner, the term denotes the repression of musical production in order to create a music without origin. In a lesser-known piece Adorno uses the term slightly differently, in a sense pioneered first by his friend Walter Benjamin. This second sense is interested in the repression not of musical production, but of the acoustic means of production that conspire to create a unified, synaesthetic experience (rather than an aesthetic object). This second sense, the denial of any sense data outside of the one experience to be had in an opera house, is exceedingly fruitful when applied to Der ferne Klang, since its hero is questing for the titular sound which is located in that very space the aural phantasmagoria has to pretend does not exist. Reading Schreker's opera keeping both senses of the term in mind may allow us to overcome Adorno's own somewhat negative assessment of Schreker's modernism and to locate within the opera a certain self-consciousness of phantasmagoric production.
‘A face like music’: Shaping images into sound in The Second Mrs Kong
Authors: BEARD DAVID
Published: January 2007

Premièred at Glyndebourne in October 1994 and subsequently performed in the UK, Austria, Germany and Holland, The Second Mrs Kong was the result of a collaboration between the American writer Russell Hoban and British composer Harrison Birtwistle. The opera's reception has tended to emphasise the disparity between Hoban's diverse and eclectic interests, which emerge not only in the libretto but also in his novels and essays, and Birtwistle's more introspective and linear approach. Possible connections between Hoban's aesthetics and Birtwistle's music have generally been disregarded. I argue, however, that the opera's main aesthetic concerns – namely, the mediation of images through ideas and the workings of image-identification in diverse media – are shaped by a productive exchange between librettist and composer. The clearest expression of this interaction is the love between Kong, who embodies ‘the idea of’ King Kong from the 1933 RKO film, and Pearl, a character drawn from Vermeer's iconic painting Girl with a Pearl Earring. The representation of these visual icons in The Second Mrs Kong is inflected by Birtwistle's own views on images, by his attempts to find musical analogues for visual techniques, as revealed especially in his sketches, and by his lively engagement with Hoban's ideas.
The ‘rival queans’ and the play of identity in Handel's Admeto
Authors: ASPDEN SUZANNE
Published: January 2007

Francesca Cuzzoni and Faustina Bordoni, singers famous for their 1720s London rivalry, were not necessarily the warring protagonists history has made them out to be. While opera historians have long acknowledged the role audience factions played in creating the rivalry, the contribution made by the opera company itself has not been considered. Working from the premise that the Royal Academy shaped its operas around this important aspect of its stars' public personae, I focus on Handel's Admeto (1727) to examine both the way opera was structured to take account of the rivalry and the concomitant play with the singers' identities provided in the work. I argue that, in employing the miniature portrait and female disguise as its two central plot devices, and in the theatricality of its music, Admeto explores notions of authenticity and identity, female mutability, and anxiety and disavowal.
Stabilities and Conformational Transitions of Various Proteases in the Presence of an Organic Solvent
Authors: Ogino Hiroyasu , Gemba Yuichi , Yutori Yoshikazu , Doukyu Noriyuki , Ishimi Kosaku , Ishikawa Haruo
Published: January 2007

The half‐life of the activity of the PST‐01 protease that was secreted by organic solvent‐tolerant Pseudomonas aeruginosa PST‐01 was very long in the presence of methanol as compared to that in the absence of methanol. The conformational transitions of the PST‐01 protease, α‐chymotrypsin, thermolysin, and subtilisin in the presence and absence of methanol were monitored by measuring the CD spectra. The conformational stabilities of the PST‐01 protease and subtilisin in the presence of methanol were higher than those in the absence of methanol. This resulted in high stability of these proteases in the presence of methanol. Furthermore, it was suggested that the organic solvent stabilities of enzymes were closely related to the secondary structure by monitoring the conformational transitions of polyamino acids, which form the particular conformations, in the presence and absence of methanol.
Zonal asymmetry of the Antarctic Oscillation
Authors: Fan Ke
Published: January 2007

In this research, the zonal asymmetry of the southern annular mode, or the Antarctic Oscillation (AAO), is studied. It is indicated that apparent zonal asymmetry exists in the normalized sea level pressure differences between the middle and high latitudes during the boreal summer, among different longitudes, especially between the Western and Eastern Hemispheres. Results show that the Southern Oscillation (SO) is responsible for part of the zonal asymmetry in AAO. The Western Hemisphere and the Eastern Hemisphere parts of AAO are correlated at 0.23 and 0.52 respectively for the period of 1959–1998 before and after the linear regressions on the Southern Oscillation Index (SOI) have been removed from the time series. The paper also discusses the relationship between the precipitation in the East Asia and the AAO before and after removing the linear regressions on SO index (SOI), indicating the stable relationship between the East Asian precipitation and the zonal symmetric component of AAO.
An ozone‐modified refractive index for vertically propagating planetary waves
Authors: Nathan Terrence R. , Cordero Eugene C.
Published: January 2007

An ozone‐modified refractive index (OMRI) is derived for vertically propagating planetary waves using a mechanistic model that couples quasigeostrophic potential vorticity and ozone volume mixing ratio. The OMRI clarifies how wave‐induced heating due to ozone photochemistry, ozone transport, and Newtonian cooling (NC) combine to affect wave propagation, attenuation, and drag on the zonal mean flow. In the photochemically controlled upper stratosphere, the wave‐induced ozone heating (OH) always augments the NC, whereas in the dynamically controlled lower stratosphere, the wave‐induced OH may augment or reduce the NC depending on the detailed nature of the wave vertical structure and zonal mean ozone gradients. For a basic state representative of Northern Hemisphere winter, the wave‐induced OH can increase the planetary wave drag by more than a factor of two in the photochemically controlled upper stratosphere and decrease it by as much as 25% in the dynamically controlled lower stratosphere. Because the zonal mean ozone distribution appears explicitly in the OMRI, the OMRI can be used as a tool for understanding how changes in stratospheric ozone due to solar variability and chemical depletion affect stratosphere‐troposphere communication.
Coupled air‐sea response to solar forcing in the Pacific region during northern winter
Authors: van Loon Harry , Meehl Gerald A. , Shea Dennis J.
Published: January 2007

Observations since the middle of the 19th century show that the decadal solar oscillation at its peaks strengthens the major convergence zones in the tropical Pacific (Intertropical Convergence Zone, ITCZ, and South Pacific Convergence Zone, SPCZ) during northern winter. Through an amplifying set of coupled feedbacks, a set of processes is described that link solar forcing and its response in the tropical Pacific with reductions in precipitation in the northwest United States. The process begins with an increase in solar forcing which results in a strengthening of the major convergence zones in the tropical Pacific. This then increases the precipitation in those regions and increases the southeast trade winds. Stronger trades increase the upwelling of colder water in the eastern equatorial Pacific and extend the cold tongue westward, thus reducing precipitation in the western Pacific. This redistribution of diabatic heating and associated convective heating anomalies thus produces anomalies in the tropical Hadley (north‐south) and Walker (east‐west) circulations. The former weakens as subsidence in equatorial latitudes is enhanced; the latter strengthens and extends westward. Additionally, the resulting anomalous Rossby wave response in the atmosphere, and consequent positive sea level pressure anomalies in the eastern region of the Aleutian low in the North Pacific that extends to western North America, is associated with reductions of precipitation in the northwest United States. The response of the climate system to solar forcing is manifested as a strengthening of the climatological precipitation maxima in the tropics.
The SM protein VPS‐45 is required for RAB‐5‐dependent endocytic transport in Caenorhabditis elegans
Authors: Gengyo‐Ando Keiko , Kuroyanagi Hidehito , Kobayashi Tetsuo , Murate Motohide , Fujimoto Kazushi , Okabe Shigeo , Mitani Shohei
Published: January 2007

Rab5, a small guanosine triphosphatase, is known to regulate the tethering and docking reaction leading to SNARE (soluble NSF attachment protein receptors)‐mediated fusion between endosomes. However, it is uncertain how the signal of the activated Rab5 protein is transduced by its downstream effectors during endosome fusion. Here, we show that the Sec1/Munc18 gene vps‐45 is essential for not only viability and development but also receptor‐mediated and fluid‐phase endocytosis pathways in Caenorhabditis elegans. We found that VPS‐45 interacts with a Rab5 effector, Rabenosyn‐5 (RABS‐5), and the mutants of both vps‐45 and rabs‐5 show similar endocytic phenotypes. In the macrophage‐like cells of vps‐45 and rabs‐5 mutants, aberrantly small endosomes were accumulated, and the endosome fusion stimulated by the mutant RAB‐5 (Q78L) is suppressed by these mutations. Our results indicate that VPS‐45 is a key molecule that functions downstream from RAB‐5, cooperating with RABS‐5, to regulate the dynamics of the endocytic system in multicellular organisms.
Detection of heterozygous nonsense mutations in genes of interest using an Escherichia coli‐based stop codon assay
Authors: Moon Young Joon , Kang Yoonsung , Choi Jee‐Hye , Lee Kwang‐Ho
Published: January 2007

Since nonsense mutations are closely associated with severe conditions of genetic disorders, including familial cancers, rapid and precise detection of those mutations is very important for research purposes and molecular diagnosis. Currently, screening methods such as the FASAY (functional analysis of separated alleles in yeast) and the Y‐SC (stop codon assay in yeast) are used for functional detection of nonsense mutations in genes of interest. But these yeast‐based approaches are time‐consuming, expensive and complicated. In order to circumvent these problems, we, in the present study, devised a novel Escherichia coli‐based screening method, the E‐SC (E. coli stop codon assay) for the detection of heterozygous nonsense mutations in genes of interest. Our strategy was based on the fact that the plasmid replicating with a low copy number in E. coli allows an effective separation of normal and mutant alleles. Moreover, it relies on the expression vector, resulting in the formation of white and blue colonies for mutant and normal alleles through the expression of PCR‐amplified fragment/lacZ fusion protein respectively. To evaluate the applicability of the E‐SC method for the detection of the heterozygous truncating mutation, PCR‐amplified exon 7 of the StAR [steroidogenic acute regulatory protein; causative gene of the CAH (congenital lipoid adrenal hyperplasia)] and RT (reverse transcription)–PCR‐amplified full‐length cDNA of MeCP2 (methyl‐CpG‐binding protein 2; causative gene of Rett syndrome) were used. The E‐SC showed an almost 1:1 ratio of blue/white colonies in all patients examined, whereas the control samples produced blue colonies only. These results demonstrate that the E‐SC system is useful for rapid and precise detection of known and unknown heterozygous truncation mutations in genes that cause genetic disorders and familial cancers.
Production, purification and characterization of recombinant dengue multiepitope protein
Authors: Tripathi Nagesh K. , Shrivastva Ambuj , Pattnaik Priyabrata , Parida Manmohan , Dash Paban K. , Jana Asha M. , Rao P. V. Lakshmana
Published: January 2007

Dengue is an acute mosquito‐borne viral disease of humankind. Dengue fever, dengue haemorrhagic fever and dengue shock syndrome have become global public health problems in recent years. rDME‐G (recombinant dengue multiepitope protein that can specifically detect IgG) was produced in a 5‐litre fermenter in Escherichia coli for use in diagnosis. The culture was induced with 1 mM isopropyl β‐d‐thiogalactoside and cells were further grown for 4 h before harvesting. After fermentation, dry cell weight resulted in approx. 16.2 g/l. The rDME‐G protein was purified from inclusion bodies using affinity chromatography. The final yield of purified rDME‐G protein from fermentation resulted in approx. 168 mg/l of pure biologically active rDME‐G protein. The purity of rDME‐G protein was checked by SDS/PAGE analysis and the reactivity of this protein was further determined by Western blotting. The purified protein was used to develop an in‐house dipstick ELISA and tested using a panel of 60 patient sera characterized using the commercially available tests for detection of dengue antibody. We compared our results with IgG‐capture ELISA (Pan‐Bio, Windsor, QLD, Australia) and rapid IC (immuno‐chromatography) test (Pan‐Bio). By using rDME‐G protein as an antigen, in the dipstick ELISA, the results were in excellent agreement with commercial rapid IC test and IgG capture ELISA. These results show that the product has a promising potential to be used for diagnosis of dengue in both laboratory‐ and field‐based detection systems with minimum cost and a high degree of sensitivity and specificity.
Morphology and ultrastructure of Siberian sturgeon (Acipenser baerii) spermatozoa using scanning and transmission electron microscopy
Authors: Psenicka Martin , Alavi S.M. Hadi , Rodina Marek , Gela David , Nebesarova Jana , Linhart Otomar
Published: January 2007

Background information. Available data concerning the sperm morphology of teleost fishes demonstrate wide variation. In the present study, the spermatozoa of Siberian sturgeon (Acipenser baerii Brandt, 1869), a chondrostean fish, was investigated. In contrast with teleost fish, chondrostean spermatozoa have a head with a distinct acrosome, whereas other structures, such as a midpiece and a single flagellum, are present in spermatozoa of most species.

Results. The average length of the head including the acrosome and the midpiece was 7.01±0.83 μm. Ten posterolateral projections derived from the acrosome were present on a subacrosomal region, with mean lengths of 0.94±0.15 μm and widths of 0.93±0.11 μm. The nucleus consisted of electrodense homogeneous nuclear chromatin. Three intertwining endonuclear canals, bound by membranes, traversed the nucleus longitudinally from the acrosomal end to the basal nuclear fossa region. There were between three and six mitochondria, two types of centrioles (proximal and distal) in the midpiece and two vacuoles composed of lipid droplets. The flagellum (44.75±4.93 μm in length), originating from the centriolar apparatus, had a typical 9+2 eukaryotic flagellar organization. In addition, there was an extracellular cytoplasm canal between the cytoplasmic sheath and the flagellum.

Conclusions. A principal components analysis explained the individual morphological variation fairly well. Of the total accumulated variance, 41.45% was accounted for by parameters related to the head and midpiece of the sperm and the length of the flagellum. Comparing the present study with previous studies of morphology of sturgeon spermatozoa, there were large inter‐ or intra‐specific differences that could be valuable taxonomically.
Phagocytosis by Trichomonas vaginalis: new insights
Authors: Pereira‐Neves Antonio , Benchimol Marlene
Published: January 2007

Background information. The parasitic protozoan Trichomonas vaginalis is the causative agent of trichomoniasis, a sexually transmitted disease. The phagocytic activity of this parasite has not been completely elucidated. In order to better understand the mechanisms of trichomonal phagocytosis, we have studied the in vitro capacity of T. vaginalis to phagocytose and degrade Saccharomyces cerevisiae cells.

Results and conclusions. To analyse the phagocytic ability and capacity, two isolates of T. vaginalis presenting different virulence grades were used. Complementary techniques, such as fluorescence microscopy, computer‐based fluorescence analysis, scanning and transmission electron microscopy and the use of drugs that interfere with the actin microfilaments, were used in order to follow the behaviour of the actin cytoskeleton during phagocytosis of yeast cells by T. vaginalis. It was concluded that: (1) T. vaginalis changes its shape rapidly and engulfs the yeast cells, which are almost as large as the parasite; (2) long‐term and fresh cultures are able to phagocytose, although the low‐virulence strain JT demonstrated a lower activity when compared with the highly virulent T016 isolate; (3) the T016 strain exhibited an amoeboid morphology during the internalization of yeast cells in contrast with the JT strain; (4) attachment of yeast cells to the parasite occurs via the whole cell surface, including both anterior and recurrent flagella; (5) two forms of phagocytosis were observed: a ‘sinking’ process without any apparent participation of plasma membrane extensions and the classical phagocytosis where pseudopodia are extended toward the target cell; (6) the internalized S. cerevisiae are digested in lysosomes; (7) competitor sugars D‐mannose or L‐fucose inhibit the phagocytosis, and inhibition was 1.67 times higher in long‐term cultured JT than that of the parasites from fresh isolate T016; (8) a thick layer of actin microfilaments was present underlying the plasma membrane, and especially in the pseudopodia and around the phagocytosed particles; (9) a dramatic change in the distribution pattern of fibrillar actin occurred during phagocytosis; (10) cytochalasin D depressed the phagocytosis; (11) a non‐specific recognition and phagocytosis of yeast cells by T. vaginalis is mediated by a mannose receptor present on the parasite surface; (12) the phagocytic process may occur simultaneously during mitosis of the parasite.
Comparison of extracellular matrix in skin and saphenous veins from patients with varicose veins: does the skin reflect venous matrix changes?
Authors: Sansilvestri-Morel Patricia , Fioretti Florence , Rupin Alain , Senni Karim , Fabiani Jean Noël , Godeau Gaston , Verbeuren Tony J.
Published: January 2007

Varicose vein disease is a frequently occurring pathology with multifactorial causes and a genetic component. An intense remodelling of the varicose vein wall has been described and could be at the origin of its weakness and altered elasticity. We have described previously a dysregulation of collagen synthesis in cultured smooth muscle cells from saphenous veins and in dermal fibroblasts from the skin of patients with varicose veins, suggesting a systemic defect in their connective tissue. The present study describes comparative morphological and immunohistochemical data in both the skin and saphenous veins of eight control subjects (undergoing coronary bypass surgery) and eight patients with varicose veins. Histological staining of glycoproteins, the elastic fibre network and collagen bundles showed that the remodelling and fragmentation of elastic fibres observed in varicose veins were also present in the skin of the patients. When compared with control subjects, we observed in both the veins and skin of patients with varicose veins (i) an increase in the elastic network, as quantified by image analysis; (ii) an accumulation of collagen type I, fibrillin-1 and laminin; and (iii) an overproduction of MMP (matrix metalloproteinase)-1, MMP-2 and MMP-3, analysed by immunohistochemistry, but normal levels of other MMPs (MMP-7 and MMP-9) and their inhibitors (TIMP-1, TIMP-2 and TIMP-3). An imbalance of extracellular matrix production/degradation was thus observed in veins as well as in the skin of the patients with varicose veins and, taken together, these findings show that remodelling is present in different organs, confirming systemic alterations of connective tissues.
Myotrophin is a more powerful predictor of major adverse cardiac events following acute coronary syndrome than N-terminal pro-B-type natriuretic peptide
Authors: Khan Sohail Q. , Kelly Dominic , Quinn Paulene , Davies Joan E. , Ng Leong L.
Published: January 2007

Myotrophin is a 12 kDa protein initially isolated from hypertrophied hearts of spontaneously hypertensive rats and acts by modulating NF-κB (nuclear factor κB) activity. We have reported previously the presence of myotrophin in patients with human systolic heart failure; however, its role as a predictor of MACE (major adverse cardiac events) in patients with ACS (acute coronary syndrome) is unclear. In the present study, we sought to investigate this and compared myotrophin with NTproBNP (N-terminal pro-B-type natriuretic peptide), a marker of MACE. We studied 356 patients with ACS {276 men; mean age, 63.0±12.8 years; 80.6% STEMI [ST segment elevation MI (myocardial infarction)]; and 19.4% NSTEMI (non-STEMI)}. Blood measurement was made at 25–48 h after the onset of chest pain. The plasma concentration of myotrophin and NTproBNP was determined using in-house non-competitive immunoassays. Patients were followed-up for the combined end point of death, MI or need for urgent revascularization. Over the median follow-up period of 355 (range 0–645) days, there were 28 deaths, 27 non-fatal MIs and 73 patients required urgent revascularization. Myotrophin was raised in patients with MACE compared with survivors [510.7 (116.0–7445.6) fmol/ml compared with 371.5 (51.8–6990.4) fmol/ml respectively; P=0.001; values are medians (range)]. Using a Cox proportional hazards model, myotrophin {HR (hazard ratio), 1.64 [95% CI (confidence interval), 0.97–2.76]; P=0.05} and Killip class above 1 [HR, 1.52 (95% CI, 0.93–2.42); P=0.10] were the only independent predictors of MACE. A Kaplan–Meier survival curve revealed a significantly better clinical outcome in patients with myotrophin below the median compared with those with myotrophin above the median (log rank, 7.63; P=0.006). In conclusion, after an ACS, levels of myotrophin are more informative at predicting MACE than NTproBNP and may be useful to risk stratify patients.
Model-assisted physiological analysis of Phyllo, a rice architectural mutant
Authors: Luquet Delphine , Song You Hong , Elbelt Sonia , This Dominique , Clément-Vidal Anne , Périn Christophe , Fabre Denis , Dingkuhn Michael
Published: January 2007

Studies of phenotype of knockout mutants can provide new insights into physiological, phenological and architectural feedbacks in the plant system. Phyllo, a mutant of Nippon Bare rice (Oryza sativa L.) producing small leaves in rapid succession, was isolated during multiplication of a T-DNA insertion library. Phyllo phenotype was compared with the wild type (WT) during vegetative development in hydroponics culture using a wide range of physiological and biometric measurements. These were integrated with the help of the functional–structural model EcoMeristem, explicitly designed to study interactions between morphogenesis and carbon assimilation. Although the phenotype of the mutant was caused by a single recessive gene, it differed in many ways from the WT, suggesting a pleiotropic effect of this mutation. Phyllochron was 25 (1–4 leaf stage) to 38% (>>4 leaf stage) shorter but showed normal transition from juvenile to adult phase after leaf 4. Leaf size also increased steadily with leaf position as in WT. The mutant had reduced leaf blade length : width and blade : sheath length ratios, particularly during the transition from heterotrophic to autotrophic growth. During the same period, root : shoot dry weight ratio was significantly diminished. Specific leaf area (SLA) was strongly increased in the mutant but showed normal descending patterns with leaf position. Probably related to high SLA, the mutant had much lower light-saturated leaf photosynthetic rates and lower radiation use efficiency (RUE) than the WT. Leaf extension rates were strongly reduced in absolute terms but were high in relative terms (normalised by final leaf length). The application of the EcoMeristem model to these data indicated that the mutant was severely deficient in assimilate, resulting from low RUE and high organ initiation rate causing high assimilate demand. This was particularly pronounced during the heterotrophic–autotrophic transition, probably causing shorter leaf blades relative to sheaths, as well as a temporary reduction of assimilate partitioning to roots. The model accurately simulated the mutant’s high leaf mortality and absence of tillering. The simulated assimilate shortage was supported by observed reductions in starch storage in sheaths. Soluble sugar concentrations differed between mutant and WT in roots but not in shoots. Specifically, the hexose : sucrose ratio was 50% lower in the roots of the mutant, possibly indicating low invertase activity. Furthermore, two OsCIN genes coding for cell wall invertases were not expressed in roots, and others were expressed weakly. This was interpreted as natural silencing via sugar signalling. In summary, the authors attributed the majority of observed allometric and metabolic modifications in the mutant to an extreme assimilate shortage caused by hastened shoot organogenesis and inefficient leaf morphology.
Urocanic acid is a major chemoattractant for the skin-penetrating parasitic nematode
Strongyloides stercoralis
Authors: Safer Daniel , Brenes Mario , Dunipace Seth , Schad Gerhard
Published: January 2007

Host-seeking behavior by parasitic nematodes relies heavily on chemical cues emanating from potential hosts. Nonspecific cues for
Strongyloides stercoralis
, a nematode that infects humans and a few other mammals, include carbon dioxide and sodium chloride; however, the characteristic species specificity of this parasite suggested the existence of other, more specific cues. Here we show that the infective larva of
S. stercoralis
is strongly attracted to an extract of mammalian skin and that the active component in this skin extract is urocanic acid. Urocanic acid, a histidine metabolite, is particularly abundant in mammalian skin and skin secretions, suggesting that it serves as an attractant specific to mammalian hosts. The attractant activity of urocanic acid is suppressed by divalent metal ions, suggesting a possible strategy for preventing infection.
From the Psi to Charm: The Experiments of 1975 and 1976
Authors: Burton Richter
Published: January 2007

Exactly 25 months ago the announcement of the ψ/J particle by Professor Ting's and my groups [1,2] burst on the community of particle physicists. Nothing so strange and completely unexpected had happened in particle physics for many years. Ten days later my group found the second of the ψ's, [3] and the sense of excitement in the community intensified. The long awaited discovery of anything which would give a clue to the proper direction in which to move in understanding the elementary particles loosed a flood of theoretical papers that washed over the journals in the next year.

The experiments that I and my colleagues carried through in the two years after the discovery of ψ the have, I believe, selected from all the competing explanations the one that is probably correct. It is these experiments that I wish to describe. The rapid progress is a consequence of the power of the electron-positron colliding-beam technique, and so I also want to describe this technique and tell something of my involvement in it.
Recent Progress in the Experimental Determination of Magnetization Density Distributions
Authors: J B Forsyth
Published: January 2007

Some recent experimental determinations of the magnetization density distributions in crystalline solids are reviewed. There have been a number of investigations of the magnetic form factors of 3dand 4dparamagnetic metals and the measurements on the ferromagnetic 3delements have been extended to binary substitutional alloys between two 3delements. The review also includes sections devoted to first group transition metal intermetallic compounds, covalency effects and magnetization densities of rare earth and actinide materials. In conclusion, some new contributions to the experimental technique itself are discussed.
Theoretical Momentum Densities
Authors: Peter Lindner
Published: January 2007

This review is primarily concerned with theoretical calculations of momentum densities and Compton cross sections for molecular systems. Qualitative properties of a momentum space representation are given. A comparison between experimental and theoretical cross sections within the impulse approximation is made. Ab initio calculations for small molecules, like the nitrogen and water molecules, are studied. Various approaches to treat large molecules are studied and compared for the formamide and p-benzoquinone molecules. Some comments on calculations for solid state systems are given.
Theoretical Determination and Analysis of Electronic Charge Distributions
Authors: Vedene H Smith Jr
Published: January 2007

The present status of the accurate calculation of molecular and crystalline charge densities is reviewed critically with emphasis on the role of basis sets and electron correlation. The analysis, interpretation and use of the various types of charge densities are considered in some detail.
The Spectrum and Term System of P IV
Authors: Per Olof Zetterberg  , Carl Erik Magnusson
Published: January 2007

The spectrum of triply ionized phosphorus has been studied in the wavelength region 200-9 800 Å by using a sliding spark in vacuum. Some 590 lines are classified, about 530 of which had not been classified before. Most of the terms are new, and the term system has been recalculated. Many intersystem combination lines fix the singlet and triplet systems relative to each other. The ionization energy has been derived by means of a polarization formula applied to terms of the 3snh, 3sniand 3snkseries, yielding the value 414 922.8±1.0 cm-1.
Lifetime and Fission-probability Estimates
Authors: H Hagelund  , A S Jensen
Published: January 2007

Fission lifetime distributions and fission cross sections are investigated using an analytic approximation to the level density containing shell effects and including collective rotational states. The observed particle induced fission probabilities are reasonably well reproduced. The compound nucleus fission is investigated for the reactions oxygen on gold and tungsten. The fission probability and lifetime distribution are estimated and compared with available experimental data. Fission probabilities are sensitive to model parameters, e.g., extrapolated barrier heights. For each energy, the theoretical uncertainty limits include the observed values but the calculated energy dependence is too fast compared to observations. It is found that higher-order fission dominates. The lifetime distribution is fairly insensitive to the model parameters with short lifetimes of less than 10-17 s being dominant. However, in agreement with experiments, a significant contribution from lifetimes longer than 10-17 s is found. The size of the long components is consistent with the lifetime experiments for oxygen on gold and too small for oxygen on natural tungsten.
Symmetry Projection Technique for the LMTO Method
Authors: G Arbman  , J Neve
Published: January 2007

A projection operator technique has been computationally implemented in order to take advantage of symmetry when solving the band problem with the LMTO (linear combination of muffin-tin orbitals) method. The Hamiltonian and overlap matrices are blockdiagonalized using the group of the Hamiltonian. The method described here is completely general and the limitation is set only by the capacity of the particular computer used in the calculation. The advantage gained is twofold: faster diagonalization because of smaller matrices and a clear classification in symmetry directions, both of particular importance for compounds with their large number of bands. The method is applied to EuO.
Baryon Decays and SU(3) Breaking
Authors: G Gustafson  , J Hamilton  , H Nielsen  , G C Oades  , B Tromborg
Published: January 2007

We present a method of studying the strong baryonic decays of resonances (or analogously the couplings of bound states) which places emphasis on the dynamics of the decays. We introduce the idea of a total reduced width and show how broken SU(3) leads to relations and predictions for these reduced widths. We also comment on the implications of this work for the usual type of SU(3) fits, and on the values of various coupling constants.
Multiplicities and Forward-Backward Correlations in p̄p Interactions at 22.4 GeV/c
Authors: E G Boos  , V V Samojlov  , M A Tashimov  , T Temiraliev  , B V Batyunya  , I V Boguslavsky  , N A Buzdavina  , I M Gramenitsky  , V G Ivanov  , R Lednický  , L A Tikhonova  , T Topuriya  , A Valkarova  , V Vrba  , Z Zlatanov  , J Ervanne  , R Orava  , H Villanen  , P Villanen  , J Patocka  , R K Dementiev  , T A Garanina  , E M Leikin  , N A Pozhidaeva  , V I Rud  , M Suk  , J Zacek  , J Cvach  , I Herynek  , P Reimer  , J Sedlak  , V Simak
Published: January 2007

We study forward-backward multiplicity correlations in p̄p-interactions at 22.4 GeV/c and discuss multiplicities in a simple two-component picture. When the charged particle multiplicity distribution is divided into even and odd components the probability to produce an odd state is found to be higher than the probability to produce an even state, which may be interpreted to be due to diffraction dissociation. An application of the two-component picture to the forward-backward and to the overall multiplicities is discussed.
Resonant Wave Interactions in Inhomogeneous Media
Authors: D Anderson
Published: January 2007

Using a simple physical approach the maximum amplification of parametric processes in inhomogeneous plasmas is determined for various cases including arbitrary wave dampings. The analysis is extended to include the pump wave equation assuming heavy damping of one of the decay waves (nonlinear Landau damping). The inhomogeneity in this case decreases the energy transfer between the modes as compared to the homogeneous situation.
Thermodynamic Stability and Critical Point in Simple Fluids and Ferromagnets
Authors: L de Cesare
Published: January 2007

By using a rigorous characterization of a critical point, based on Tisza's thermodynamic theory of phase transitions, we have obtained for simple fluids and ferromagnets, in a unified way and without making additional hypotheses, the usual and new inequalities among critical indices. In contrast to the previous thermodynamic attempts, we have been able to establish when the index relations are valid as strict equalities. Furthermore, we have derived expressions for some critical indices in terms of critical amplitudes; then the possibility of finite cusps and discontinuities for the specific heats at the critical point has been explicitly considered and the precise connection between the static scaling hypotheses and the thermodynamic stability has been established. Finally we have stressed the analogy between fluids and ferromagnets and pointed out some important differences which follow from the slope of the saturation curve being zero for ferromagnets, unlike that for fluids. For ferromagnets it is also proved that, when the Rushbrooke (Griffiths) index relation is valid as a strict equality, it results in 0<β<1, where β is the phase-boundary critical index. Incidentally, the paper gives several results which are in agreement with the experimental evidence obtained within the stability framework.
Inferring phylogeny from whole genomes
Authors: Górecki Paweł , Tiuryn Jerzy
Published: January 2007

Motivation: Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This limitation leads to the problem of transforming unrooted gene tree into a rooted tree, and then reconciling rooted trees. The main questions are ‘What about biological interpretation of choosing rooting?’, ‘Can we find efficiently the optimal rootings?’, ‘Is the optimal rooting unique?’.

Results: In this paper we present a model of reconciling unrooted gene tree with a rooted species tree, which is based on a concept of choosing rooting which has minimal reconciliation cost. Our analysis leads to the surprising property that all the minimal rootings have identical distributions of gene duplications and gene losses in the species tree. It implies, in our opinion, that the concept of an optimal rooting is very robust, and thus biologically meaningful. Also, it has nice computational properties. We present a linear time and space algorithm for computing optimal rooting(s). This algorithm was used in two different ways to reconstruct the optimal species phylogeny of five known yeast genomes from approximately 4700 gene trees. Moreover, we determined locations (history) of all gene duplications and gene losses in the final species tree. It is interesting to notice that the top five species trees are the same for both methods.

Availability: Software and documentation are freely available from

Contact:  gorecki@mimuw.edu.pl
Biological network comparison using graphlet degree distribution
Authors: Pržulj Nataša
Published: January 2007

Motivation: Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally infeasible, and thus heuristics, such as the degree distribution, clustering coefficient, diameter, and relative graphlet frequency distribution have been sought. It is easy to demonstrate that two networks are different by simply showing a short list of properties in which they differ. It is much harder to show that two networks are similar, as it requires demonstrating their similarity in all of their exponentially many properties. Clearly, it is computationally prohibitive to analyze all network properties, but the larger the number of constraints we impose in determining network similarity, the more likely it is that the networks will truly be similar.

Results: We introduce a new systematic measure of a network's local structure that imposes a large number of similarity constraints on networks being compared. In particular, we generalize the degree distribution, which measures the number of nodes ‘touching’ k edges, into distributions measuring the number of nodes ‘touching’ k graphlets, where graphlets are small connected non-isomorphic subgraphs of a large network. Our new measure of network local structure consists of 73 graphlet degree distributions of graphlets with 2–5 nodes, but it is easily extendible to a greater number of constraints (i.e. graphlets), if necessary, and the extensions are limited only by the available CPU. Furthermore, we show a way to combine the 73 graphlet degree distributions into a network ‘agreement’ measure which is a number between 0 and 1, where 1 means that networks have identical distributions and 0 means that they are far apart. Based on this new network agreement measure, we show that almost all of the 14 eukaryotic PPI networks, including human, resulting from various high-throughput experimental techniques, as well as from curated databases, are better modeled by geometric random graphs than by Erdös–Rény, random scale-free, or Barabási–Albert scale-free networks.

Availability: Software executables are available upon request.

Contact:  natasha@ics.uci.edu
Efficient inference on known phylogenetic trees using Poisson regression
Authors: Rosset Saharon
Published: January 2007

Motivation: We suggest the use of Poisson regression for time inference and hypothesis testing on a bifurcating Phylogenetic tree with known topology. This method is computationally simple and naturally accommodates variable substitution rates across different sites, without requiring the estimation of these rates. We identify the assumptions under which this is a maximum-likelihood inference approach and show that in some realistic situations—in particular, when the probability of repeated mutation within each branch of the tree is small—these assumptions hold with high probability.

Results: Our motivating domain is human mitochondrial DNA trees, and we illustrate our method on a problem of estimating the time to most recent common ancestor of all non-African mtDNA, using publicly available data. We test for molecular clock violations using multiple comparisons, and conclude that the global molecular clock hypothesis cannot be rejected based on these data.

Contact:  srosset@us.ibm.com
Similarities and differences of gene expression in yeast stress conditions
Authors: Rokhlenko Oleg , Wexler Ydo , Yakhini Zohar
Published: January 2007

Motivation and Methods: All living organisms and the survival of all cells critically depend on their ability to sense and quickly adapt to changes in the environment and to other stress conditions. We study stress response mechanisms in Saccharomyces cerevisiae by identifying genes that, according to very stringent criteria, have persistent co-expression under a variety of stress conditions. This is enabled through a fast clique search method applied to the intersection of several co-expression graphs calculated over the data of Gasch et al. This method exploits the topological characteristics of these graphs.

Results: We observe cliques in the intersection graphs that are much larger than expected under a null model of changing gene identities for different stress conditions but maintaining the co-expression topology within each one. Persistent cliques are analyzed to identify enriched function as well as enriched regulation by a small number of TFs. These TFs, therefore, characterize a universal and persistent reaction to stress response. We further demonstrate that the vertices (genes) of many cliques in the intersection graphs are co-localized in the yeast genome, to a degree far beyond the random expectation. Co-localization can hypothetically contribute to a quick co-ordinated response. We propose the use of persistent cliques in further study of properties of co-regulation.

Supplementary information:  

Contact:  olegro@cs.technion.ac.il
Tandem repeats over the edit distance
Authors: Sokol Dina , Benson Gary , Tojeira Justin
Published: January 2007

Motivation: A tandem repeat in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence.

Results: In this paper we describe an efficient algorithm for finding all tandem repeats within a sequence, under the edit distance measure. The contributions of this paper are two-fold: theoretical and practical. We present a precise definition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeats.

Availability: The algorithm has been implemented in C++, and the software is available upon request and can be used at . The use of this tool will assist biologists in discovering new ways that tandem repeats affect both the structure and function of DNA and protein molecules.

Contact:  sokol@sci.brooklyn.cuny.edu