bluuebunny/crossref_metadata_2025 huggingface dataset:
Body‐Colour Genes in Drosophila.
Authors: Waddington C. H.
Published: August 2010

1. The darkening of the puparium in Drosophila probably involves a tanning reaction similar to that described for Calliphora. It is reduced in ebony, black, and straw‐3, and changed in nature, so as to give a yellower tint, in yellow and yellow‐2. It is somewhat increased in speck, particularly in the region of the anus, where there may be a sharply marked dark band.

2. The pigmentation of the wild‐type adult is due to two processes, a browning which is probably a tanning, and a blackening which is probably a deposition of melanin. The browning is more apparent in the earliest stages of pigmentation, and first affects the chsetse, the darkening of the cuticle becoming stronger at a later stage, chiefly after emergence.

3. In yellow the browning is changed into a yellowing, and the blackening much reduced. The change in the character of the tanning occurs earlier in yellow than in yellow‐2, so that in the latter the bristles are pigmented normally.

4. Straw‐3 reduces both phases of pigmentation, while ebony, and to a less extent speck, increases both phases. Black intensifies the blackening more strongly than the browning.

5. In compounds of black and ebony with straw, the early stages of pigmentation (of chætæ) proceed as in straw, while the later ones (of cuticle) proceed as in black or ebony. It is argued that this indicates that black and ebony act earlier in the reaction sequence than does straw.

6. It is clear that ebony affects not only the quantities of pigments formed, but also the time at which they make their appearance, since it reduces the tanning of the puparium and increases that of the adult. It is suggested that this may provide an explanation of the behaviour of ebony as an antimorph.
Facet Mutants of Drosophila.
Authors: Pilkington R. W.
Published: August 2010

1. The structure of the compound eye of Drosophila melanogaster is described in detail.

2. The development of the normal eye is traced from the late larval to the adult stage. The chief features of the development are as follows:–

(i.) The optic disc differentiates into three layers. This process is affected by Glued.

(ii.) The middle layer of the three. penetrates the outer layer regularly. This process is affected by split and Glued.

(iii.) The middle layer cells next divide to form the cells of the pseudocone. Thisjprocess is affected by split and Glued.

(iv.) The cone cells further divide to form the retinulse. This process is affected by Glued.

(v.) The retinulse are excluded from the cone‐cup formed by the outer layer of the disc.

(vi.) The cone cells and retinulse develop and secrete the pseudocone and rhabdome. Bough causes this process to be irregular, and the amount of secretion is influenced by split and Glued.

3. The structure and development of the facet‐mutants rough, split, and Glued are analysed in detail, and a table is given comparing their structure and development with the wild‐type eye.

4. The nature and origin of fused, flat, and erupted facets is described. The fused facets of rough are different in origin from those of split and Glued. Two varieties of flat facets are found, one of which is present in rough arid the other in Glued, whilst both are found in split. The “cupless” flat facets of rough and split though similar in nature are different in origin.

5. Two rules governing the relationship between the retinulse and cone cells, and the retinulse and the shape of the facets, are stated. The wild type and split adhere to both rules, whilst rough adheres to one rule up to th? end of the second pupal day and Glved does not adhere to either.

6. The structure of the periopticon in the wild and mutant types is described, and the origin of the periopticon in the optic stalk is confirmed by experiments.
THE GENERA OF ARENICOLIDAE (POLYCHAETA)
Authors: WELLS G. P.
Published: August 2010

It is argued that the species currently grouped as Arenicola Lamarck should be distributed between Arenicola, Arenicolides Mesnil and Abarenicola gen. nov.

Formal diagnoses of the family and its constituent genera are given, and suggestions are made as to the most convenient characters for referring arenicolid worms to their genera.
OBSERVATIONS ON THE LAYING AND HATCHING OF OCTOPUS EGGS IN THE SOCIETY'S AQUARIUM
Authors: VEVERS H. G.
Published: August 2010

Three different individuals of Octopus vulgaris laid eggs in the Society's Aquarium in September 1957, May 1960 and August 1960 respectively. Mating was observed in the first instance. The eggs were brooded for a period of thirty‐nine to forty‐two days. The larvae hatched successfully, but did not feed, although offered a variety of foods, and survived for an average of eight days. In each case the mother died immediately or shortly after the hatching of the last larvae. The behaviour of the female during brooding is described.
LARVAL DEVELOPMENT IN THE GENUS CHONOPELTIS (CRUSTACEA: BRANCHIURA)
Authors: FRYER GEOFFREY
Published: August 2010

A description is given of the larval development of Chonopeltis brevis and of a species of which the adult is not yet known. All stages of development are parasitic on fishes, and different hosts are employed by larvae and adults. Attachment is described and host transfer is discussed.
NEW SPECIES OF OCNERODRILINAE (OLIGCOCHAETA)
Authors: JAMIESON B. G. M.
Published: August 2010

The new speciesGordiodrilus nilotiaushas been established to receive the specimens from Tongo on the White Nile (Sudan) referred toG. dominicensisBeddard 1892 by Michaelsen in 1914; and specimens from Siwa Oasis (Egypt) described asGordiodrilussp. by Michaelsen in 1938 have been made the types of a new species,G. siwaensis.Specimens from Lake Baringo (Tanganyika) have been considered to merit establishing a third new species of the genus,G. worthingtoni.All three species belong to an “elegans‐group”, within the genus, which has been defined.

A new monotypic genus from Argentina,Gatesiaand its type speciesGatesia unicahave been described.

Quechuona michaelsenisp.n. from the banks of the Yabebiri River (N. Argentina) has been added to the formerly monotypic genusQuechuona.

The types are in the British Museum (Natural History) with the exception of those ofGordiodrilus niloticuswhich are in the Zoological Museum, Hamburg.
OBSERVATIONS ON THE FEEDING OF THE HEDGEHOG (ERINACEUS EUROPAEUS L.)
Authors: DIMELOW E. J.
Published: August 2010

The feeding of the hedgehog in captivity is described and the degree to which this seems to be affected by hibernation.

Altogether 167 food preference tests were performed by nine hedgehogs and the results seem to indicate that though hedgehogs will eat most of the small invertebrates that they find in their natural habitat, they consistently select some rather than others.
ALIMENTARY AND REPRODUCTIVE SYSTEMS OFOXYCHILUS CELLARIUS(MÜLLER) (STYLOMMATOPHORA)
Authors: RIGBY JOYCE E.
Published: August 2010

Detailed study of the life cycle and the anatomy, histology and functioning of the alimentary and reproductive systems ofOxychilua cellariua(Müller) lead one to regard this snail as a typical and relatively unspecialized member of the Stylommatophora.

Feeding currents within the oesophagus and staomach have been examined during dissection of fresh specimens and the form of the stomach region has been homologized with that of more primitive gastropods.

Histochemical methods have been used to determine the nature of cell contents and secretions along the reproductive tract and the possible part played by these substances during copulation and egg‐laying has been investigated. The path used by sperm prior to, and following, copulation has been traced.

Comparison is made with members of the higher Basommatophora, the Hygrophila. Much greater structural and functional differences become apparent between members of the Stylommatophora and the Basommatophora than have hitherto been suspected.
THE FOOD OF MALLARD ANAS PLATYRHYNCHOS PLATYEHYNCHOS COLLECTED FROM COASTAL AND ESTUARINE AREAS
Authors: OLNEY P. J. S.
Published: August 2010

The food of 177 mallard dnas platyrhynchoa platyrliyncha L. collected from coastal ancl estuarine areas during t.he shooting seasons of 1957‐60 is clescribetl. This sanrplo is subdivided into 1 15 birch obtained froin various localities scatteretl around the coast, antl sixty‐two birds collected from one locality, the Greenhorough and Milfordhope Islands in the River Medway, Kent.

From observations and viscera. analyses it was apparent that the coastal marshes aro used as roosting and to a lesser extent, as feeding grouncln. Much of the food of the hirtls shot over coastal marshas had been obtained from nesrhy hrackish‐watnr was, antl at tho beginning of the season from inland stubble‐fields.

Plant seeds formed the main bulk of the food antl occurred more frequently than any other item.

Mallard feeding in saltmarshes were found to be taking mainly the seeds of Salicornin spp., Atriples spp., antl Suneda rncrritima. The most frequently taken animal materials were the mollusc Snhannecr uvne antl tlie crustaceans Cnrcircts innrnrt, Crnngov wrlgaris and Corophium spp.

In brackish‐water areas, xnallarct were fonnr to the feeding mainly on the seeds of Scirpw maritimw, S . tahernaemonnni, Poanrogeon, lectinahis, Riippin spp. and Cerabphylluni subniersum. Tho nio11usr Hdrohia jenkin.oi and the crustacean Palaemonetes vnriana were the niost frequently nrrurring animal foods. At the heginning of the shooting season anti mainly in Septenihei, barley (Hordeurn spp.) was eaten ancl often in conxiderahle quantities.

It was fonnd that the sixty‐two hirds collertetl from the m e loralitp of the Metlway islands had been feeding on similar speries to tllose hirds rollerted fivnn a numher of different localities.

The differences in diet from year to year and as the season progressed a described A general survey of the literaturr is given and the impnrtance of Scirpus maritimus emphasized.

It. is suggested that mallartl feeding ill thr intertitlal muds are taking hivalves (e.g. Macoma balthica and Scrohiculnrin plana) and Crustarea (e.g. Corophiwrn dctfaov). Phew are a number of saltniaii plant species (e . g. Sprrrtinn toulnaradii agg., Hrrineionr prtulacoidrs) which are not eatan to any great extent, even though tliey may be rommoii constitucmts of the marsh. There in probably littie liinitation in rhoire of food itenis (lue to hardness, though there may be Home limitation by the size and berausr of the rnethod of feeding, by the mobility of the food speries.

The pomihle management, of saltmarsh and twarkish‐water areas to inrretwe the food supply is discussed.
Increased caspase activation and decreased TDP‐43 solubility in progranulin knockout cortical cultures
Authors: Kleinberger Gernot , Wils Hans , Ponsaerts Peter , Joris Geert , Timmermans Jean‐Pierre , Van Broeckhoven Christine , Kumar‐Singh Samir
Published: August 2010

J. Neurochem. (2010) 115, 735–747.

Null mutations in progranulin (GRN) are associated with frontotemporal lobar degeneration characterized by intraneuronal accumulation of TAR DNA‐binding protein‐43 (TDP‐43). However, the mechanism by which GRN deficiency leads to neurodegeneration remains largely unknown. In primary cortical neurons derived from Grn knockout (Grn−/−) mice, we found that Grn‐deficiency causes significantly reduced neuronal survival and increased caspase‐mediated apoptosis, which was not observed in primary mouse embryonic fibroblasts derived from Grn−/− mice. Also, neurons derived from Grn−/− mice showed an increased amount of pTDP‐43 accumulations. Furthermore, proteasomal inhibition with MG132 caused increased caspase‐mediated TDP‐43 fragmentation and accumulation of detergent‐insoluble 35‐ and 25‐kDa C‐terminal fragments in Grn−/− neurons and mouse embryonic fibroblasts. Interestingly, full‐length TDP‐43 also accumulated in the detergent‐insoluble fraction, and caspase‐inhibition prevented MG132‐induced generation of TDP‐43 C‐terminal fragments but did not block the pathological conversion of full‐length TDP‐43 from soluble to insoluble species. These data suggest that GRN functions as a survival factor for cortical neurons and GRN‐deficiency causes increased susceptibility to cellular stress. This leads to increased aggregation and accumulation of full‐length TDP‐43 along with its C‐terminal derivatives by both caspase‐dependent and independent mechanisms.
Parameter Uncertainty Modeling Using the Multidimensional Principal Curves
Authors: Sepasi M. , Sassani F. , Nagamune R.
Published: August 2010

This paper proposes a technique to model uncertainties associated with linear time-invariant systems. It is assumed that the uncertainties are only due to parametric variations caused by independent uncertain variables. By assuming that a set of a finite number of rational transfer functions of a fixed order is given, as well as the number of independent uncertain variables that affect the parametric uncertainties, the proposed technique seeks an optimal parametric uncertainty model as a function of uncertain variables that explains the set of transfer functions. Finding such an optimal parametric uncertainty model is formulated as a noncovex optimization problem, which is then solved by a combination of a linear matrix inequality and a nonlinear optimization technique. To find an initial condition for solving this nonconvex problem, the nonlinear principal component analysis based on the multidimensional principal curve is employed. The effectiveness of the proposed technique is verified through both illustrative and practical examples.
Polynomial Chaos Based Design of Robust Input Shapers
Authors: Singh Tarunraj , Singla Puneet , Konda Umamaheswara
Published: August 2010

A probabilistic approach, which exploits the domain and distribution of the uncertain model parameters, has been developed for the design of robust input shapers. Polynomial chaos expansions are used to approximate uncertain system states and cost functions in the stochastic space. Residual energy of the system is used as the cost function to design robust input shapers for precise rest-to-rest maneuvers. An optimization problem, which minimizes any moment or combination of moments of the distribution function of the residual energy is formulated. Numerical examples are used to illustrate the benefit of using the polynomial chaos based probabilistic approach for the determination of robust input shapers for uncertain linear systems. The solution of polynomial chaos based approach is compared with the minimax optimization based robust input shaper design approach, which emulates a Monte Carlo process.
Robust Stochastic Design of Linear Controlled Systems for Performance Optimization
Authors: Taflanidis Alexandros A. , Scruggs Jeffrey T. , Beck James L.
Published: August 2010

This study discusses a robust controller synthesis methodology for linear, time invariant systems, under probabilistic parameter uncertainty. Optimization of probabilistic performance robustness for H2 and multi-objective H2 measures is investigated, as well as for performance measures based on first-passage system reliability. The control optimization approaches proposed here exploit recent advances in stochastic simulation techniques. The approach is illustrated for vibration response suppression of a civil structure. The results illustrate that, for problems with probabilistic uncertainty, the explicit optimization of probabilistic performance robustness can result in markedly different optimal feedback laws, as well as enhanced performance robustness, when compared to traditional “worst-case” notions of robust optimal control.
Robust Impedance Control of Manipulators Carrying a Heavy Payload
Authors: Aghili Farhad
Published: August 2010

A heavy payload attached to the wrist force/moment (F/M) sensor of a manipulator can cause the conventional impedance controller to fail in establishing the desired impedance due to the noncontact components of the force measurement, i.e., the inertial and gravitational forces of the payload. This paper proposes an impedance control scheme for such a manipulator to accurately shape its force-response without needing any acceleration measurement. Therefore, no wrist accelerometer or a dynamic estimator for compensating the inertial load forces is required. The impedance controller is further developed using an inner/outer loop feedback approach that not only overcomes the robot dynamics uncertainty, but also allows the specification of the target impedance model in a general form, e.g., a nonlinear model. The stability and convergence of the impedance controller are analytically investigated, and the results show that the control input remains bounded provided that the desired inertia is selected to be different from the payload inertia. Experimental results demonstrate that the proposed impedance controller is able to accurately shape the impedance of a manipulator carrying a relatively heavy load according to the desired impedance model.
Self-Induced Patched Receptor Down-Regulation Modulates Cell Sensitivity to the Hedgehog Morphogen Gradient
Authors: Casali Andreu
Published: August 2010

A self-regulating receptor allows cells to maintain the appropriate balance of ligand-bound and unbound receptors.
Reducing Auxin Transport
Authors: VanHook Annalisa M.
Published: August 2010

Strigolactones inhibit branching by modulating auxin transport in
Arabidopsis
.
Science Signaling
Podcast: 24 August 2010
Authors: Comb Michael J. , VanHook Annalisa M.
Published: August 2010

A phosphoproteomic approach identifies potential targets for developing combination therapies to treat cancer.
Therapeutic Drug Monitoring of Linezolid: a Retrospective Monocentric Analysis
Authors: Pea Federico , Furlanut Mario , Cojutti Piergiorgio , Cristini Francesco , Zamparini Eleonora , Franceschi Loretta , Viale Pierluigi
Published: August 2010

The objective of the present retrospective observational study carried out in patients receiving a standard dosage of linezolid and undergoing routine therapeutic drug monitoring (TDM) was to assess the interindividual variability in plasma exposure, to identify the prevalence of attainment of optimal pharmacodynamics, and to define if an intensive program of TDM may be warranted in some categories of patients. Linezolid plasma concentrations (trough [
C
min
] and peak [
C
max
] levels) were analyzed by means of a high-performance liquid chromatography (HPLC) method, and daily drug exposure was estimated (daily area under the plasma concentration-time curve [AUC
24
]). The final database included 280
C
min
and 223
C
max
measurements performed in 92 patients who were treated with the fixed 600-mg dose every 12 h (q12h) intravenously (
n
= 58) or orally (
n
= 34). A wide variability was observed (median values [interquartile range]: 3.80 mg/liter [1.75 to 7.53 mg/liter] for
C
min
, 14.70 mg/liter [10.57 to 19.64] for
C
max
, and 196.08 mg·h/liter [144.02 to 312.10 mg·h/liter] for estimated AUC
24
). Linezolid
C
min
was linearly correlated with estimated AUC
24
(
r
2
= 0.85). Optimal pharmacodynamic target attainment (defined as
C
min
of ≥2 mg/liter and/or AUC
24
/MIC
90
ratio of >80) was obtained in about 60 to 70% of cases, but potential overexposure (defined as
C
min
of ≥10 mg/liter and/or AUC
24
of ≥400 mg·h/liter) was documented in about 12% of cases. A significantly higher proportion of cases with potential overexposure received cotreatment with omeprazole, amiodarone, or amlodipine. Our study suggests that the application of TDM might be especially worthwhile in about 30% of cases with the intent of avoiding either the risk of dose-dependent toxicity or that of treatment failure.
The ADP-Ribosylation Domain of
Pseudomonas aeruginosa
ExoS Is Required for Membrane Bleb Niche Formation and Bacterial Survival within Epithelial Cells
Authors: Angus Annette A. , Evans David J. , Barbieri Joseph T. , Fleiszig Suzanne M. J.
Published: August 2010

Pseudomonas aeruginosa
can establish a niche within the plasma membrane of epithelial cells (bleb niches) within which bacteria can survive, replicate, and swim at speeds detectable by real-time phase-contrast imaging. This novel virulence strategy is dependent on the bacterial type three secretion system (T3SS), since mutants lacking the T3SS needle or known T3SS effectors localize to perinuclear vacuoles and fail to replicate. Here, we determined which of the three effectors (ExoS, ExoT, or ExoY) were required for bleb niche formation and intracellular replication. PAO1 strains with mutations in
exoS
, e
xoT
,
exoY
, or combinations thereof were compared to wild-type and complemented strains.
P. aeruginosa exoS
mutants, but not
exoT
or
exoY
mutants, lost the capacity for bleb niche formation and intracellular replication. Complementation with
exoS
rescued both phenotypes, either in the background of an
exoS
mutant or in a mutant lacking all three known effectors. Complementation with activity domain mutants of
exoS
revealed that the ADP-ribosyltransferase (ADP-r) activity of ExoS, but not the Rho-GAP activity nor the membrane localization domain (MLD) of ExoS, was required to elicit this phenotype. Membrane bleb niches that contained
P. aeruginosa
also bound annexin V-enhanced green fluorescent protein (EGFP), a marker of early apoptosis. These data show that
P. aeruginosa
bleb niches and intracellular survival involve ExoS ADP-r activity and implicate a connection between bleb niche formation and the known role(s) of ExoS-mediated apoptosis and/or Rab GTPase inactivation.
Involvement of Inflammatory Chemokines in Survival of Human Monocytes Fed with Malarial Pigment
Authors: Giribaldi Giuliana , Prato Mauro , Ulliers Daniela , Gallo Valentina , Schwarzer Evelin , Akide-Ndunge Oskar B. , Valente Elena , Saviozzi Silvia , Calogero Raffaele A. , Arese Paolo
Published: August 2010

Hemozoin (HZ)-fed monocytes are exposed to strong oxidative stress, releasing large amounts of peroxidation derivatives with subsequent impairment of numerous functions and overproduction of proinflammatory cytokines. However, the histopathology at autopsy of tissues from patients with severe malaria showed abundant HZ in Kupffer cells and other tissue macrophages, suggesting that functional impairment and cytokine production are not accompanied by cell death. The aim of the present study was to clarify the role of HZ in cell survival, focusing on the qualitative and temporal expression patterns of proinflammatory and antiapoptotic molecules. Immunocytochemical and flow cytometric analyses showed that the long-term viability of human monocytes was unaffected by HZ. Short-term analysis by macroarray of a complete panel of cytokines and real-time reverse transcription (RT)-PCR experiments showed that HZ immediately induced interleukin-1β (IL-1β) gene expression, followed by transcription of eight additional chemokines (IL-8, epithelial cell-derived neutrophil-activating peptide 78 [ENA-78], growth-regulated oncogene α [GROα], GROβ, GROγ, macrophage inflammatory protein 1α [MIP-1α], MIP-1β, and monocyte chemoattractant protein 1 [MCP-1]), two cytokines (tumor necrosis factor alpha [TNF-α] and IL-1receptor antagonist [IL-1RA]), and the cytokine/chemokine-related proteolytic enzyme matrix metalloproteinase 9 (MMP-9). Furthermore, real-time RT-PCR showed that 15-HETE, a potent lipoperoxidation derivative generated by HZ through heme catalysis, recapitulated the effects of HZ on the expression of four of the chemokines. Intermediate-term investigation by Western blotting showed that HZ increased expression of HSP27, a chemokine-related protein with antiapoptotic properties. Taken together, the present data suggest that apoptosis of HZ-fed monocytes is prevented through a cascade involving 15-HETE-mediated upregulation of IL-1β transcription, rapidly sustained by chemokine, TNF-α, MMP-9, and IL-1RA transcription and upregulation of HSP27 protein expression.
A Dairy Bacterium Displays
I
n
V
itro
Probiotic Properties for the Pharyngeal Mucosa by Antagonizing Group A Streptococci and Modulating the Immune Response
Authors: Guglielmetti Simone , Taverniti Valentina , Minuzzo Mario , Arioli Stefania , Zanoni Ivan , Stuknyte Milda , Granucci Francesca , Karp Matti , Mora Diego
Published: August 2010

The probiotic approach represents an alternative strategy in the prevention and treatment of infectious diseases, not only at the intestinal level but also at other sites of the body where the microbiota plays a role in the maintenance of physiological homeostasis. In this context, we evaluated
in vitro
the potential abilities of probiotic and dairy bacteria in controlling
Streptococcus pyogenes
infections at the pharyngeal level. Initially, we analyzed bacterial adhesion to FaDu hypopharyngeal carcinoma cells and the ability to antagonize
S. pyogenes
on FaDu cell layers and HaCat keratinocytes. Due to its promising adhesive and antagonistic features, we studied the dairy strain
Lactobacillus helveticus
MIMLh5, also through
in vitro
immunological experiments. First, we performed quantification of several cytokines and measurement of NF-κB activation in FaDu cells. MIMLh5 efficiently reduced the induction of interleukin-6 (IL-6), IL-8, and tumor necrosis factor alpha (TNF-α), in a dose-dependent manner. After stimulation of cells with IL-1β, active NF-κB was still markedly lowered. Nevertheless, we observed an increased secretion of IL-6, gamma interferon (IFN-γ), and granulocyte-macrophage colony-stimulating factor (GM-CSF) under these conditions. These effects were associated with the ability of MIMLh5 to enhance the expression of the heat shock protein coding gene
hsp70
. In addition, MIMLh5 increased the GM-CSF/G-CSF ratio. This is compatible with a switch of the immune response toward a TH1 pathway, as supported by our observation that MIMLh5, once in contact with bone marrow-derived dendritic cells, triggered the secretion of TNF-α and IL-2. In conclusion, we propose MIMLh5 as a potential probiotic bacterium for the human pharynx, with promising antagonistic and immunomodulatory properties.
Allelic Diversity and Naturally Acquired Allele-Specific Antibody Responses to
Plasmodium falciparum
Apical Membrane Antigen 1 in Kenya
Authors: Osier Faith H. A. , Weedall Gareth D. , Verra Federica , Murungi Linda , Tetteh Kevin K. A. , Bull Pete , Faber Bart W. , Remarque Ed , Thomas Alan , Marsh Kevin , Conway David J.
Published: August 2010

Although
Plasmodium falciparum
apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate, extensive allelic diversity may compromise its vaccine potential. We have previously shown that naturally acquired antibodies to AMA1 were associated with protection from clinical malaria in this Kenyan population. To assess the impact of allelic diversity on naturally acquired immunity, we first sequenced the ectodomain-encoding region of
P. falciparum ama1
from subjects with asymptomatic, mild, and severe malaria and measured allele frequency distributions. We then measured antibodies to three allelic AMA1 proteins (AMA1_3D7, AMA1_FVO, and AMA1_HB3) and used competition enzyme-linked immunosorbent assays (ELISAs) to analyze allele-specific antibodies. Seventy-eight unique haplotypes were identified from 129 alleles sampled. No clustering of allelic haplotypes with disease severity or year of sampling was observed. Differences in nucleotide frequencies in clinical (severe plus mild malaria) versus asymptomatic infections were observed at 16 polymorphic positions. Allele frequency distributions were indicative of balancing selection, with the strongest signature being identified in domain III (Tajima's
D
= 2.51;
P
< 0.05). Antibody reactivities to each of the three allelic AMA1 proteins were highly correlated (
P
< 0.001 for all pairwise comparisons). Although antibodies to conserved epitopes were abundant, 48% of selected children with anti-AMA1 IgG (
n
= 106) had detectable reactivity to allele-specific epitopes as determined by a competition ELISA. Antibodies to both conserved and allele-specific epitopes in AMA1 may contribute to clinical protection.
PRICING AND HEDGING BARRIER OPTIONS IN A HYPER-EXPONENTIAL ADDITIVE MODEL
Authors: JEANNIN MARC , PISTORIUS MARTIJN
Published: August 2010

In this paper, we develop an algorithm to calculate the prices and Greeks of barrier options in a hyper-exponential additive model with piecewise constant parameters. We obtain an explicit semi-analytical expression for the first-passage probability. The solution rests on a randomization and an explicit matrix Wiener-Hopf factorization. Employing this result we derive explicit expressions for the Laplace-Fourier transforms of the prices and Greeks of barrier options. As a numerical illustration, the prices and Greeks of down-and-in digital and down-and-in call options are calculated for a set of parameters obtained by a simultaneous calibration to Stoxx50E call options across strikes and four different maturities. By comparing the results with Monte-Carlo simulations, we show that the method is fast, accurate, and stable.
PRICING AND DELTAS OF DISCRETELY-MONITORED BARRIER OPTIONS USING STRATIFIED SAMPLING ON THE HITTING-TIMES TO THE BARRIER
Authors: JOSHI MARK , TANG ROBERT
Published: August 2010

We develop new Monte Carlo techniques based on stratifying the stock's hitting-times to the barrier for the pricing and Delta calculations of discretely-monitored barrier options using the Black-Scholes model. We include a new algorithm for sampling an Inverse Gaussian random variable such that the sampling is restricted to a subset of the sample space. We compare our new methods to existing Monte Carlo methods and find that they can substantially improve convergence speeds.
COMPUTATION OF VOLATILITY IN STOCHASTIC VOLATILITY MODELS WITH HIGH FREQUENCY DATA
Authors: BARUCCI EMILIO , MANCINO MARIA ELVIRA
Published: August 2010

We consider general stochastic volatility models driven by continuous Brownian semimartingales, we show that the volatility of the variance and the leverage component (covariance between the asset price and the variance) can be reconstructed pathwise by exploiting Fourier analysis from the observation of the asset price. Specifying parametrically the asset price model we show that the method allows us to compute the parameters of the model. We provide a Monte Carlo experiment to recover the volatility and correlation parameters of the Heston model.
CLIMATE POLICY AND THE OPTIMAL BALANCE BETWEEN MITIGATION, ADAPTATION AND UNAVOIDED DAMAGE
Authors: BOSELLO FRANCESCO , CARRARO CARLO , DE CIAN ENRICA
Published: August 2010

It has become commonly accepted that a successful climate strategy should compound mitigation and adaptation. The accurate combination between adaptation and mitigation that can best address climate change is still an open question. This paper proposes a framework that integrates mitigation, adaptation, and climate change residual damages into an optimisation model. This set-up is used to provide some insights on the welfare maximising resource allocation between mitigation and adaptation, on their optimal timing, and on their marginal contribution to reducing vulnerability to climate change. The optimal mix between three different adaptation modes (reactive adaptation, anticipatory adaptation, and investment in innovation for adaptation purposes) within the adaptation bundle is also identified. Results suggest that the joint implementation of mitigation and adaptation is welfare improving. Mitigation should start immediately, whereas adaptation somewhat later. It is also shown that in a world where the probability of climate-related catastrophic events is small and where decision makers have a high discount rate, adaptation is unambiguously the preferred option. Adaptation needs, both in developed and developing countries, will be massive, especially during the second half of the century. Most of the adaptation burden will be on developing countries. International cooperation is thus required to equally distribute the costs of adaptation.
SHORT-TERM CO2ABATEMENT IN THE EUROPEAN POWER SECTOR: 2005–2006
Authors: DELARUE ERIK D. , ELLERMAN A. DENNY , D'HAESELEER WILLIAM D.
Published: August 2010

This paper provides an estimate of short-term abatement of CO2emissions through fuel switching in the European power sector in response to the CO2price imposed by the EU Emissions Trading Scheme (EU ETS) in 2005 and 2006. The estimate is based on the use of a highly detailed simulation model of the European power sector in which abatement is the difference between simulations of actual conditions with and without the observed CO2price. We estimate that the cumulative abatement over this period was about 53 million metric tons. The paper also explains the complex relationship between abatement and daily, weekly, and seasonal variations in load, relative fuel prices, and the price of CO2allowances.
Low-overhead byzantine fault-tolerant storage
Authors: Hendricks James , Ganger Gregory R. , Reiter Michael K.
Published: August 2010

This paper presents an erasure-coded Byzantine fault-tolerant block storage protocol that is nearly as efficient as protocols that tolerate only crashes. Previous Byzantine fault-tolerant block storage protocols have either relied upon replication, which is inefficient for large blocks of data when tolerating multiple faults, or a combination of additional servers, extra computation, and versioned storage. To avoid these expensive techniques, our protocol employs novel mechanisms to optimize for the common case when faults and concurrency are rare. In the common case, a write operation completes in two rounds of communication and a read completes in one round. The protocol requires a short checksum comprised of cryptographic hashes and homomorphic fingerprints. It achieves throughput within 10% of the crash-tolerant protocol for writes and reads in failure-free runs when configured to tolerate up to 6 faulty servers and any number of faulty clients.
Bouncer
Authors: Costa Manuel , Castro Miguel , Zhou Lidong , Zhang Lintao , Peinado Marcus
Published: August 2010

Attackers exploit software vulnerabilities to control or crash programs. Bouncer uses existing software instrumentation techniques to detect attacks and it generates filters automatically to block exploits of the target vulnerabilities. The filters are deployed automatically by instrumenting system calls to drop exploit messages. These filters introduce low overhead and they allow programs to keep running correctly under attack. Previous work computes filters using symbolic execution along the path taken by a sample exploit, but attackers can bypass these filters by generating exploits that follow a different execution path. Bouncer introduces three techniques to generalize filters so that they are harder to bypass: a new form of program slicing that uses a combination of static and dynamic analysis to remove unnecessary conditions from the filter; symbolic summaries for common library functions that characterize their behavior succinctly as a set of conditions on the input; and generation of alternative exploits guided by symbolic execution. Bouncer filters have low overhead, they do not have false positives by design, and our results show that Bouncer can generate filters that block all exploits of some real-world vulnerabilities.
Triage
Authors: Tucek Joseph , Lu Shan , Huang Chengdu , Xanthos Spiros , Zhou Yuanyuan
Published: August 2010

Diagnosing production run failures is a challenging yet importanttask. Most previous work focuses on offsite diagnosis, i.e.development site diagnosis with the programmers present. This is insufficient for production-run failures as: (1) it is difficult to reproduce failures offsite for diagnosis; (2) offsite diagnosis cannot provide timely guidance for recovery or security purposes; (3)it is infeasible to provide a programmer to diagnose every production run failure; and (4) privacy concerns limit the release of information(e.g. coredumps) to programmers.

To address production-run failures, we propose a system, called
Triage
, that automatically performs onsite software failure diagnosis at the very moment of failure. It provides a detailed diagnosis report, including the failure nature, triggering conditions, related code and variables, the fault propagation chain, and potential fixes. Triage achieves this by leveraging lightweight reexecution support to efficiently capture the failure environment and repeatedly replay the moment of failure, and dynamically--using different diagnosis techniques--analyze an occurring failure. Triage employs afailure diagnosis protocol that mimics the steps a human takes in debugging. This extensible protocol provides a framework to enable the use of various existing and new diagnosis techniques. We also propose a new failure diagnosis technique,
delta analysis
, to identify failure related conditions, code, and variables.

We evaluate these ideas in real system experiments with 10 real software failures from 9 open source applications including four servers. Triage accurately diagnoses the evaluated failures, providing likely root causes and even the fault propagation chain, while keeping normal-run overhead to under 5%. Finally, our user study of the diagnosis and repair of real bugs shows that Triagesaves time (99.99% confidence), reducing the total time to fix by almost half.
Staged deployment in mirage, an integrated software upgrade testing and distribution system
Authors: Crameri Olivier , Knezevic Nikola , Kostic Dejan , Bianchini Ricardo , Zwaenepoel Willy
Published: August 2010

Despite major advances in the engineering of maintainable and robust software over the years, upgrading software remains a primitive and error-prone activity. In this paper, we argue that several problems with upgrading software are caused by a poor integration between upgrade deployment, user-machine testing, and problem reporting. To support this argument, we present a characterization of softwareupgrades resulting from a survey we conducted of 50 system administrators. Motivated by the survey results, we present Mirage, a distributed framework for integrating upgrade deployment, user-machine testing, and problem reporting into the overall upgrade development process. Our evaluation focuses on the most novel aspect of Mirage, namely its staged upgrade deployment based on the clustering of usermachines according to their environments and configurations. Our results suggest that Mirage's staged deployment is effective for real upgrade problems.
AutoBash
Authors: Su Ya-Yunn , Attariyan Mona , Flinn Jason
Published: August 2010

AutoBash is a set of interactive tools that helps users and system administrators manage configurations. AutoBash leverages causal tracking support implemented within our modified Linux kernel to understand the inputs (causal dependencies) and outputs (causal effects) of configuration actions. It uses OS-level speculative execution to try possible actions, examine their effects, and roll them back when necessary. AutoBash automates many of the tedious parts of trying to fix a misconfiguration, including searching through possible solutions, testing whether a particular solution fixes a problem, and undoing changes to persistent and transient state when a solution fails. Our results show that AutoBash correctly identifies the solution to several CVS, gcc cross-compiler, and Apache configuration errors. We also show that causal analysis reduces AutoBash's search time by an average of 35% and solution verification time by an average of 70%.
Integrating concurrency control and energy management in device drivers
Authors: Klues Kevin , Handziski Vlado , Lu Chenyang , Wolisz Adam , Culler David , Gay David , Levis Philip
Published: August 2010

Energy management is a critical concern in wireless sensornets. Despite its importance, sensor network operating systems today provide minimal energy management support, requiring applications to explicitly manage system power states. To address this problem, we present ICEM, a device driver architecture that enables simple, energy efficient wireless sensornet applications. The key insight behind ICEMis that the most valuable information an application can give the OS for energy management is its concurrency. Using ICEM, a low-rate sensing application requires only a single line of energy management code and has an efficiency within 1.6% of a hand-tuned implementation. ICEM's effectiveness questions the assumption that sensornet applications must be responsible for all power management and sensornets cannot have a standardized OS with a simple API.
Generalized file system dependencies
Authors: Frost Christopher , Mammarella Mike , Kohler Eddie , de los Reyes Andrew , Hovsepian Shant , Matsuoka Andrew , Zhang Lei
Published: August 2010

Reliable storage systems depend in part on "write-before" relationships where some changes to stable storage are delayed until other changes commit. A journaled file system, for example, must commit a journal transaction before applying that transaction's changes, and soft updates and other consistency enforcement mechanisms have similar constraints, implemented in each case in system-dependent ways. We present a general abstraction, the patch, that makes write-before relationships explicit and file system agnostic. A patch-based file system implementation expresses dependencies among writes, leaving lower system layers to determine write orders that satisfy those dependencies. Storage system modules can examine and modify the dependency structure, and generalized file system dependencies are naturally exportable to user level. Our patch-based storage system, Feather stitch, includes several important optimizations that reduce patch overheads by orders of magnitude. Our ext2 prototype runs in the Linux kernel and supports a synchronous writes, soft updates-like dependencies, and journaling. It outperforms similarly reliable ext2 and ext3 configurations on some, but not all, benchmarks. It also supports unusual configurations, such as correct dependency enforcement within a loopback file system, and lets applications define consistency requirements without micromanaging how those requirements are satisfied.
Engineering formal metatheory
Authors: Aydemir Brian , Charguéraud Arthur , Pierce Benjamin C. , Pollack Randy , Weirich Stephanie
Published: August 2010

Machine-checked proofs of properties of programming languages have become acritical need, both for increased confidence in large and complex designsand as a foundation for technologies such as proof-carrying code. However, constructing these proofs remains a black art, involving many choices in the formulation of definitions and theorems that make a huge cumulative difference in the difficulty of carrying out large formal developments. There presentation and manipulation of terms with variable binding is a key issue.

We propose a novel style for formalizing metatheory, combining
locally nameless
representation of terms and cofinite quantification of free variable names in inductivedefinitions of relations on terms (typing, reduction, ...). The key technical insight is that our use of cofinite quantification obviates the need for reasoning about equivariance (the fact that free names can be renamed in derivations); in particular, the structural induction principles of relations defined using cofinite quantification are strong enough for metatheoretic reasoning, and need not be explicitly strengthened. Strong inversion principles follow (automatically, in Coq) from the induction principles. Although many of the underlying ingredients of our technique have been used before, their combination here yields a significant improvement over other methodologies using first-order representations, leading to developments that are faithful to informal practice, yet require noexternal tool support and little infrastructure within the proof assistant.

We have carried out several large developments in this style using the Coq proof assistant and have made them publicly available. Our developments include type soundness for System
F
sub; and core ML (with references, exceptions, datatypes, recursion, and patterns) and subject reduction for the Calculus of Constructions. Not only do these developments demonstrate the comprehensiveness of our approach; they have also been optimized for clarity and robustness, making them good templates for future extension.
Contextual effects for version-consistent dynamic software updating and safe concurrent programming
Authors: Neamtiu Iulian , Hicks Michael , Foster Jeffrey S. , Pratikakis Polyvios
Published: August 2010

This paper presents a generalization of standard effect systems that we call
contextual effects
. A traditional effect system computes the effect of an expression
e
. Our system additionally computes the effects of the computational context in which
e
occurs. More specifically, we computethe effect of the computation that has already occurred(the
prior effect
) and the effect of the computation yet to take place (the
future effect
).

Contextual effects are useful when the past or future computation of the program is relevant at various program points. We present two substantial examples. First, we show how prior and future effects can be used to enforce
transactional version consistency
(TVC), a novel correctness property for dynamic software updates. TV Censures that programmer-designated transactional code blocks appear to execute entirely at the same code version, even if a dynamic update occurs in the middle of the block. Second, we show how future effects can be used in the analysis of multi-threaded programs to find thread-shared locations. This is an essential step in applications such as data race detection.
Separation logic, abstraction and inheritance
Authors: Parkinson Matthew J. , Bierman Gavin M.
Published: August 2010

Inheritance is a fundamental concept in object-oriented programming, allowing new classes to be defined in terms of old classes. When used with care, inheritance is an essential tool for object-oriented programmers. Thus, for those interested in developing formal verification techniques, the treatment of inheritance is of paramount importance. Unfortunately, inheritance comes in a number of guises, all requiring subtle techniques.

To address these subtleties, most existing verification methodologies typically adopt one of two restrictions to handle inheritance: either (1) they prevent a derived class from restricting the behaviour of its base class (typically by syntactic means) to trivialize the proof obligations; or (2) they allow a derived class to restrict the behaviour of its base class, but require that every inherited method must be reverified. Unfortunately, this means that typical inheritance-rich code either cannot be verified or results in an unreasonable number of proof obligations.

In this paper, we develop a separation logic for a core object-oriented language. It allows derived classes which override the behaviour of their base class, yet supports the inheritance of methods without reverification where this is safe. For each method, we require two specifications: a
static
specification that is used to verify the implementation and direct method calls (in Java this would be with a super call); and a
dynamic
specification that is used for calls that are dynamically dispatched; along with a simple relationship between the two specifications. Only the dynamic specification is involved with behavioural subtyping. This simple separation of concerns leads to a powerful system that supports all forms of inheritance with low proof-obligation overheads. We both formalize our methodology and demonstrate its power with a series of inheritance examples.
Subcubic algorithms for recursive state machines
Authors: Chaudhuri Swarat
Published: August 2010

We show that the reachability problem for recursive state machines (or equivalently, pushdown systems), believed for long to have cubic worst-case complexity, can be solved in slightly subcubic time. All that is necessary for the new bound is a simple adaptation of a known technique. We also show that a better algorithm exists if the input machine does not have infinite recursive loops.