bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Dairy Bacterium Displays
I
n
V
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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

ABSTRACT

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

ABSTRACT

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.
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.
Cryptographically sound implementations for typed information-flow security
Authors: Fournet Cédric , Rezk Tamara 
Published: August 2010

In language-based security, confidentiality and integrity policies conveniently specify the permitted flows of information between different parts of a program with diverse levels of trust. These policies enable a simple treatment of security, and they can often be verified by typing. However, their enforcement in concrete systems involves delicate compilation issues.
We consider cryptographic enforcement mechanisms for imperative programs with untrusted components. Such programs may represent, for instance, distributed systems connected by some untrusted network. In source programs, security depends on an abstract access-control policy for reading and writing the shared memory. In their implementations, shared memory is unprotected and security depends instead on encryption and signing.
We build a translation from well-typed source programs and policies to cryptographic implementations. To establish its correctness, we develop a type system for the target language. Our typing rules enforce a correct usage of cryptographic primitives against active adversaries; from an information-flow viewpoint, they capture controlled forms of robust declassification and endorsement. We showtype soundness for a variant of the non-interference property, then show that our translation preserves typability.
We rely on concrete primitives and hypotheses for cryptography, stated in terms of probabilistic polynomial-time algorithms and games. We model these primitives as commands in our target language. Thus, we develop a uniform language-based model of security, ranging from computational non-interference for probabilistic programs down to standard cryptographic hypotheses.
Latency-constrained aggregation in sensor networks
Authors: Becchetti LUCA , Marchetti-Spaccamela Alberto , Vitaletti Andrea , Korteweg Peter , Skutella Martin , Stougie Leen 
Published: August 2010

A sensor network consists of sensing devices which may exchange data through wireless communication; sensor networks are highly energy constrained since they are usually battery operated. Data aggregation is a possible way to save energy consumption: nodes may delay data in order to aggregate them into a single packet before forwarding them towards some central node (sink). However, many applications impose constraints on the maximum delay of data; this translates into latency constraints for data arriving at the sink.
We study the problem of data aggregation to minimize maximum energy consumption under latency constraints on sensed data delivery, and we assume unique communication paths that form an intree rooted at the sink. We prove that the offline problem is strongly NP-hard and we design a 2-approximation algorithm. The latter uses a novel rounding technique.
Almost all real-life sensor networks are managed online by simple distributed algorithms in the nodes. In this context we consider both the case in which sensor nodes are synchronized or not. We assess the performance of the algorithm by competitive analysis. We also provide lower bounds for the models we consider, in some cases showing optimality of the algorithms we propose. Most of our results also hold when minimizing the total energy consumption of all nodes.
A relational approach to interprocedural shape analysis
Authors: Jeannet Bertrand , Loginov Alexey , Reps Thomas , Sagiv Mooly 
Published: August 2010

This article addresses the verification of properties of imperative programs with recursive procedure calls, heap-allocated storage, and destructive updating of pointer-valued fields, that is,
interprocedural shape analysis
. The article makes three contributions.

— It introduces a new method for abstracting relations over memory configurations for use in abstract interpretation.
— It shows how this method furnishes the elements needed for a compositional approach to shape analysis. In particular, abstracted relations are used to represent the shape transformation performed by a sequence of operations, and an overapproximation to relational composition can be performed using the meet operation of the domain of abstracted relations.

— It applies these ideas in a new algorithm for context-sensitive interprocedural shape analysis. The algorithm creates procedure summaries using abstracted relations over memory configurations, and the meet-based composition operation provides a way to apply the summary transformer for a procedure
P
at each call site from which
P
is called.

The algorithm has been applied successfully to establish properties of both (i) recursive programs that manipulate lists and (ii) recursive programs that manipulate binary trees.
Novel Models of Myxoid Liposarcoma Xenografts Mimicking the Biological and Pharmacologic Features of Human Tumors
Authors: Frapolli Roberta , Tamborini Elena , Virdis Emanuela , Bello Ezia , Tarantino Eva , Marchini Sergio , Grosso Federica , Sanfilippo Roberta , Gronchi Alessandro , Tercero Juan Carlos , Peloso Gabriella , Casali Paolo , Pilotti Silvana , D'Incalci Maurizio 
Published: August 2010

Abstract
Purpose: Myxoid liposarcoma is a common subtype of liposarcoma. It is associated in more than 90% of cases with the chromosomal translocation t(12;16)(q13;p11) leading to the fusion FUS-CHOP gene that is responsible for the oncogenic transformation of preadipocytes. Recently the marine natural product trabectedin has shown highly selective activity for myxoid liposarcoma, even in the most aggressive round-cell subtype.
Experimental Design: Fragments of 17 sarcomas were transplanted s.c. in female athymic NCr-nu/nu mice. Xenografts were established and characterized by morphology, fluorescence in situ hybridization analysis for the translocation and reverse transcriptase-PCR analysis for fusion transcripts. Trabectedin was injected i.v.
Results: Seven of 17 tumors grew as continuous xenografts, five of them being myxoid liposarcoma of the round-cell subtype. The chromosomal rearrangement and fusion transcripts in different passages were the same as in the human tumors from which they were derived. The responsiveness to trabectedin in type II myxoid liposarcoma xenografts was as high as in patients. The pathologic response was associated with the presence of the FUS-CHOP fusion gene, indicating that the drug does not totally eradicate the disease. Type III myxoid liposarcoma xenografts seemed much less sensitive to trabectedin, confirming previous clinical observations.
Conclusions: This study reports for the first time the characterization of human myxoid liposarcoma xenografts that adequately mimic the biological and pharmacologic features of the human tumor. These models offer a useful tool for investigating the mechanism of selectivity of trabectedin, testing new combinations with this drug and evaluating novel therapies for myxoid liposarcoma. Clin Cancer Res; 16(20); 4958–67. ©2010 AACR.
Dynamic MicroRNA Expression Programs During Cardiac Differentiation of Human Embryonic Stem Cells
Authors: Wilson Kitchener D. , Hu Shijun , Venkatasubrahmanyam Shivkumar , Fu Ji-Dong , Sun Ning , Abilez Oscar J. , Baugh Joshua J.A. , Jia Fangjun , Ghosh Zhumur , Li Ronald A. , Butte Atul J. , Wu Joseph C. 
Published: August 2010

Background—
MicroRNAs (miRNAs) are a newly discovered endogenous class of small, noncoding RNAs that play important posttranscriptional regulatory roles by targeting messenger RNAs for cleavage or translational repression. Human embryonic stem cells are known to express miRNAs that are often undetectable in adult organs, and a growing body of evidence has implicated miRNAs as important arbiters of heart development and disease.

Methods and Results—
To better understand the transition between the human embryonic and cardiac “miRNA-omes,” we report here the first miRNA profiling study of cardiomyocytes derived from human embryonic stem cells. Analyzing 711 unique miRNAs, we have identified several interesting miRNAs, including miR-1, -133, and -208, that have been previously reported to be involved in cardiac development and disease and that show surprising patterns of expression across our samples. We also identified novel miRNAs, such as miR-499, that are strongly associated with cardiac differentiation and that share many predicted targets with miR-208. Overexpression of miR-499 and -1 resulted in upregulation of important cardiac myosin heavy-chain genes in embryoid bodies; miR-499 overexpression also caused upregulation of the cardiac transcription factor MEF2C.

Conclusions—
Taken together, our data give significant insight into the regulatory networks that govern human embryonic stem cell differentiation and highlight the ability of miRNAs to perturb, and even control, the genes that are involved in cardiac specification of human embryonic stem cells.
Assessment of Reanalysis Daily Extreme Temperatures with China’s Homogenized Historical Dataset during 1979–2001 Using Probability Density Functions
Authors: Mao Jiafu , Shi Xiaoying , Ma Lijuan , Kaiser Dale P. , Li Qingxiang , Thornton Peter E. 
Published: August 2010

Abstract
Using a recently homogenized observational daily maximum (TMAX) and minimum temperature (TMIN) dataset for China, the extreme temperatures from the 40-yr ECMWF Re-Analysis (ERA-40), the Japanese 25-year Reanalysis (JRA-25), the NCEP/Department of Energy Global Reanalysis 2 (NCEP-2), and the ECMWF’s ERA-Interim (ERAIn) reanalyses for summer (June–August) and winter (December–February) are assessed by probability density functions for the periods 1979–2001 and 1990–2001. For 1979–2001, no single reanalysis appears to be consistently accurate across eight areas examined over China. The ERA-40 and JRA-25 reanalyses show similar representations and close skill scores over most of the regions of China for both seasons. NCEP-2 generally has lower skill scores, especially over regions with complex topography. The regional and seasonal differences identified are commonly associated with different geographical locations and the methods used to diagnose these quantities. All the selected reanalysis products exhibit better performance for winter compared to summer over most regions of China. The TMAX values from the reanalysis tend to be systematically underestimated, while TMIN is systematically closer to observed values than TMAX. Comparisons of the reanalyses to reproduce the 99.7 percentiles for TMAX and 0.3 percentiles for TMIN show that most reanalyses tend to underestimate the 99.7 percentiles in maximum temperature both in summer and winter. For the 0.3 percentiles in TMIN, NCEP-2 is relatively inaccurate with a −12°C cold bias over the Qinghai–Tibetan Plateau in winter. ERA-40 and JRA-25 generally overestimate the extreme TMIN, and the extreme percentage differences of ERA-40 and JRA-25 are quite similar over all of the regions. The results are generally similar for 1990–2001, but in contrast to the other three reanalysis products the newly released ERAIn is very reasonable, especially for wintertime TMIN, with a skill score greater than 0.83 for each region of China. This demonstrates the great potential of this product for use in future impact assessments on continental scales where those impacts are based on extreme temperatures.
Frontal Scale Air–Sea Interaction in High-Resolution Coupled Climate Models
Authors: Bryan Frank O. , Tomas Robert , Dennis John M. , Chelton Dudley B. , Loeb Norman G. , McClean Julie L. 
Published: August 2010

Abstract
The emerging picture of frontal scale air–sea interaction derived from high-resolution satellite observations of surface winds and sea surface temperature (SST) provides a unique opportunity to test the fidelity of high-resolution coupled climate simulations. Initial analysis of the output of a suite of Community Climate System Model (CCSM) experiments indicates that characteristics of frontal scale ocean–atmosphere interaction, such as the positive correlation between SST and surface wind stress, are realistically captured only when the ocean component is eddy resolving. The strength of the coupling between SST and surface stress is weaker than observed, however, as has been found previously for numerical weather prediction models and other coupled climate models. The results are similar when the atmospheric component model grid resolution is doubled from 0.5° to 0.25°, an indication that shortcomings in the representation of subgrid scale atmospheric planetary boundary layer processes, rather than resolved scale processes, are responsible for the weakness of the coupling. In the coupled model solutions the response to mesoscale SST features is strongest in the atmospheric boundary layer, but there is a deeper reaching response of the atmospheric circulation apparent in free tropospheric clouds. This simulated response is shown to be consistent with satellite estimates of the relationship between mesoscale SST and all-sky albedo.
Surface Ocean Mixing Inferred from Different Multisatellite Altimetry Measurements
Authors: Beron-Vera Francisco J. , Olascoaga María J. , Goni Gustavo J. 
Published: August 2010

Abstract
Two sea surface height (SSH) anomaly fields distributed by Archiving, Validation, and Interpretation of Satellite Oceanographic (AVISO) Altimetry are evaluated in terms of the effects that they produce on mixing. One SSH anomaly field, tagged REF, is constructed using measurements made by two satellite altimeters; the other SSH anomaly field, tagged UPD, is constructed using measurements made by up to four satellite altimeters. Advection is supplied by surface geostrophic currents derived from the total SSH fields resulting from the addition of these SSH anomaly fields to a mean SSH field. Emphasis is placed on the extraction from the currents of Lagrangian coherent structures (LCSs), which, acting as skeletons for patterns formed by passively advected tracers, entirely control mixing. The diagnostic tool employed to detect LCSs is provided by the computation of finite-time Lyapunov exponents. It is found that currents inferred using UPD SSH anomalies support mixing with characteristics similar to those of mixing produced by currents inferred using REF SSH anomalies. This result mainly follows from the fact that, being more easily characterized as chaotic than turbulent, mixing as sustained by currents derived using UPD SSH anomalies is quite insensitive to spatiotemporal truncations of the advection field.
On the Calculation of Available Potential Energy in Internal Wave Fields
Authors: Kang Dujuan , Fringer Oliver 
Published: August 2010

Abstract
A comparison of three common formulations for calculating the available potential energy (APE) in internal wave fields is presented. The formulations are the perturbation APE (APE1), the exact local APE (APE2), and its approximation for linear stratification (APE3). The relationship among these formulations is illustrated through a graphical interpretation and a derivation of the energy conservation laws. Numerical simulations are carried out to quantitatively assess the performance of each APE formulation under the influence of different nonlinear and nonhydrostatic effects. The results show that APE2 is the most attractive in evaluating the local APE, especially for nonlinear internal waves, since use of APE2 introduces the smallest errors when computing the energy conservation laws. Larger errors arise when using APE1 because of the large disparity in magnitude between the kinetic energy and APE1. It is shown that the disparity in the tendency of APE1 is compensated by a large flux arising from the reference pressure and density fields. Because the tendency of the kinetic energy is close to that of APE3, computational errors arise when using APE3 only in the presence of nonlinear stratification, and these errors increase for stronger flow nonlinearity.
Conservative Transport Schemes for Spherical Geodesic Grids: High-Order Reconstructions for Forward-in-Time Schemes
Authors: Skamarock William C. , Menchaca Maximo 
Published: August 2010

Abstract
The finite-volume transport scheme of Miura, for icosahedral–hexagonal meshes on the sphere, is extended by using higher-order reconstructions of the transported scalar within the formulation. The use of second- and fourth-order reconstructions, in contrast to the first-order reconstruction used in the original scheme, results in significantly more accurate solutions at a given mesh density, and better phase and amplitude error characteristics in standard transport tests. The schemes using the higher-order reconstructions also exhibit much less dependence of the solution error on the time step compared to the original formulation.
The original scheme of Miura was only tested using a nondeformational time-independent flow. The deformational time-dependent flow test used to examine 2D planar transport in Blossey and Durran is adapted to the sphere, and the schemes are subjected to this test. The results largely confirm those generated using the simpler tests. The results also indicate that the scheme using the second-order reconstruction is most efficient and its use is recommended over the scheme using the first-order reconstruction. The second-order reconstruction uses the same computational stencil as the first-order reconstruction and thus does not create any additional parallelization issues.