bluuebunny/crossref_metadata_2025 huggingface dataset:
Do Private Patients have Shorter Waiting Times for Elective Surgery? Evidence from New South Wales Public Hospitals*
Authors: Johar Meliyanni , Savage Elizabeth
Published: August 2010

The Productivity Commission (2008) identified waiting times for elective surgery as a measure of governments’ success in providing accessible health care. At the 2007 COAG meeting, the Prime Minister identified reduction of elective surgery waiting times in public hospitals as a major policy priority. To date, the analysis of waiting time data has been limited to summary statistics by medical procedure, doctor specialty and state. In this paper, we look behind the summary statistics and analyse the extent to which private patients are prioritised over comparable public patients in public hospitals. Our empirical evidence is based on waiting list and admission data from public hospitals in NSW for 2004–2005. We find that private patients have substantially shorter waiting times, and tend to be admitted ahead of their listing rank, especially for procedures that have low urgency levels. We also explore the benefits and costs of this preferential treatment on waiting times.
The PhD Conference in Economics and Business Two Decades On*
Authors: Clements Kenneth W.
Published: August 2010

The PhD Conference in Economics and Business is a unique Australian innovation in the training of doctoral students. The conference is an annual event that has been in operation since 1987 and has involved more than 580 students from around Australia and some other countries. This paper provides a brief overview of the workings and history of this activity, as well as some broader perspectives on the development of PhD programs.
Reforming Taxes on Wine and Other Alcoholic Beverage Consumption*
Authors: Anderson Kym
Published: August 2010

As part of a comprehensive review of Australia’s tax system, the taxes on alcoholic beverages recently came under scrutiny. In its initial response to the review in May 2010, the government chose to not change those taxes, even though the review recommended the wine tax switch from an ad valorem to a volumetric basis and that all beverages be taxed to the same extent per litre of alcohol. This paper introduces a mini‐symposium of three other papers aimed at contributing to what will be an on‐going public policy debate on the optimal taxation of alcohol for purposes of covering social costs associated with harmful alcohol consumption, influencing consumer behaviour through altering beverage prices levels and relativities, and raising government revenue.
The Location Decisions of Multinationals and the Cultural Link: Evidence from Spanish Direct Investment Abroad*
Authors: Barrios Salvador , Benito Juan Miguel
Published: August 2010

We examine the way in which differences in language and culture may affect direct investment decisions. We use a discrete choice approach to model the location decisions of multinationals in which cultural links, language differences, distance and market access are accounted for. This model is used to study the determinants of the location decisions of Spanish multinationals over the period 1988–1997. Cultural ties, including language, are found significantly to affect the location decisions of Spanish firms abroad. These ties, also explain the leading position of Spanish multinationals in Latin American countries compared to more advanced home countries such as the United States, Germany and the United Kingdom. The specific advantage of Spanish multinationals together with the rapid economic development of the Spanish economy, which has traditionally been a large FDI‐recipient, tend to corroborate the view that intangible assets such as culture and language proximity do matter in understanding net outward investment patterns.
Dynamic Modelling and Control of Semifree-Piston Motion in a Rotary Diesel Generator Concept
Authors: Dunne J. F.
Published: August 2010

A new semifree-piston rotary generator concept is modelled dynamically and reduced to a single equation for piston stroke motion. This new concept comprises a toroidal-segment piston and cylinder, which orbit on separate generator disks, coupled by a pair of torsion springs to form a balanced mass-elastic system capable of spin. Conventional cyclic combustion takes place in the cylinder causing resonant motion of the disks. A two-part control strategy is proposed and tested by simulation to address the multi-objectives of maximum mechanical power transfer, minimum peak generator torque, and accurate piston top dead center (TDC) position control. A Part I strategy initially assumes that the combustion gas pressure is a function of time only. This produces torque control that follows a stroke velocity feedback law, which maximizes power transfer and implicitly minimizes generator torque, at the same time as power generation. When stroke-dependent gas pressure is introduced, however, the Part I strategy creates an unstable self-excited nonlinear system. The Part II strategy is designed to control piston TDC position and stabilize the response. This uses proportional control of gas pressure rise, assumed possible through fuel injection control and in-cylinder pressure sensing. An ideal-air-standard-dual-combustion two-stroke cycle is then adopted for nonstochastic simulation purposes, excluding the effect of delays and coupled system dynamics. A study is undertaken of a nominal 1.42 l, 200 mm orbit-radius, constant-pressure-scavenged diesel design with three different spring stiffness values. By focusing near the minimum compression ratio for diesel, to give a lower bound on the possible ideal output power, control gains are found that produce stable motion with piston TDC position errors of less than 1%. The power range is from 16 kW to 336 kW, depending mainly on spring stiffness. Since the concept can also store significant kinetic energy, it is potentially attractive as a range-extender for electric vehicles.
Mechatronic Model and Experimental Validation of a Pneumatic Servo-Solenoid Valve
Authors: Sorli Massimo , Figliolini Giorgio , Almondo Andrea
Published: August 2010

This paper deals with a method for static and dynamic modeling of a three-way pneumatic proportional valve actuated by means of a proportional solenoid, which can be applied in robust design, condition monitoring, and development of advanced control strategies. Test-beds for the experimental identification of the main physical parameters of the valve are described along with the proposed experimental methods. A mechatronic dynamic model of the valve is then presented, which considers the servo-solenoid as the electromagnetic subsystem, the moving parts of the valve as the mechanical subsystem, and the fluid parts for flow-rate control as the pneumatic subsystem. Finally, the proposed mechatronic dynamic model is validated by comparing the experimental and simulated diagrams for adsorbed current, spool position, and instantaneous flow-rate.
Akt–RSK–S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases
Authors: Moritz Albrecht , Li Yu , Guo Ailan , Villén Judit , Wang Yi , MacNeill Joan , Kornhauser Jon , Sprott Kam , Zhou Jing , Possemato Anthony , Ren Jian Min , Hornbeck Peter , Cantley Lewis C. , Gygi Steven P. , Rush John , Comb Michael J.
Published: August 2010

A phosphoproteomic analysis of signaling pathways downstream of oncogenic receptor tyrosine kinases identified potential therapeutic targets.
Reversing Your Losses
Authors: Adler Elizabeth M.
Published: August 2010

Antagonizing ActRIIB signaling may provide a therapeutic approach to treating cancer cachexia.
Fungal Defenses
Authors: Mueller Kristen L.
Published: August 2010

A fungal protein binds to a host cell wall component to allow the fungus to escape immune responses.
Antidepressant Action of Ketamine
Authors: Stern Peter R.
Published: August 2010

Ketamine, an anesthetic and recreational drug, rapidly increases synaptic signaling and antidepressant behavioral responses.
Identification and Characterization of Four Azole-Resistant
erg3
Mutants of
Candida albicans
Authors: Martel Claire M. , Parker Josie E. , Bader Oliver , Weig Michael , Gross Uwe , Warrilow Andrew G. S. , Rolley Nicola , Kelly Diane E. , Kelly Steven L.
Published: August 2010

Sterol analysis identified four
Candida albicans erg3
mutants in which ergosta 7,22-dienol, indicative of perturbations in sterol Δ
5,6
-desaturase (Erg3p) activity, comprised >5% of the total sterol fraction. The
erg3
mutants (CA12, CA488, CA490, and CA1008) were all resistant to fluconazole, voriconazole, itraconazole, ketoconazole, and clotrimazole under standard CLSI assay conditions (MIC values, ≥256, 16, 16, 8, and 1 μg ml
−1
, respectively). Importantly, CA12 and CA1008 retained an azole-resistant phenotype even when assayed in the presence of FK506, a multidrug efflux inhibitor. Conversely, CA488, CA490, and three comparator isolates (CA6, CA14, and CA177, in which ergosterol comprised >80% of the total sterol fraction and ergosta 7,22-dienol was undetectable) all displayed azole-sensitive phenotypes under efflux-inhibited assay conditions. Owing to their ergosterol content, CA6, CA14, and CA177 were highly sensitive to amphotericin B (MIC values, <0.25 μg ml
−1
); CA1008, in which ergosterol comprised <2% of the total sterol fraction, was less sensitive (MIC, 1 μg ml
−1
). CA1008 harbored multiple amino acid substitutions in Erg3p but only a single conserved polymorphism (E266D) in sterol 14α-demethylase (Erg11p). CA12 harbored one substitution (W332R) in Erg3p and no residue changes in Erg11p. CA488 and CA490 were found to harbor multiple residue changes in both Erg3p and Erg11p. The results suggest that missense mutations in
ERG3
might arise in
C. albicans
more frequently than currently supposed and that the clinical significance of
erg3
mutants, including those in which additional mechanisms also contribute to resistance, should not be discounted.
Complementation of a
Saccharomyces cerevisiae
ERG11/CYP51 (Sterol 14α-Demethylase) Doxycycline-Regulated Mutant and Screening of the Azole Sensitivity of
Aspergillus fumigatus
Isoenzymes CYP51A and CYP51B
Authors: Martel Claire M. , Parker Josie E. , Warrilow Andrew G. S. , Rolley Nicola J. , Kelly Steven L. , Kelly Diane E.
Published: August 2010

Aspergillus fumigatus
sterol 14α-demethylase isoenzymes CYP51A and CYP51B were heterologously expressed in a
Saccharomyces cerevisiae
mutant (YUG37-
erg11
), wherein native ERG11/CYP51 expression is controlled using a doxycycline-regulatable promoter. When cultured in the presence of doxycycline, recombinant YUG37-p
cyp51A
and YUG37-p
cyp51B
yeasts were able to synthesize ergosterol and grow; a control strain harboring reverse-oriented
cyp51A
could not. YUG37-p
cyp51A
and YUG37-p
cyp51B
constructs showed identical sensitivity to itraconazole, posaconazole, clotrimazole, and voriconazole. Conversely, YUG37-p
cyp51A
withstood 16-fold-higher concentrations of fluconazole than YUG37-p
cyp51B
(8 and 0.5 μg ml
−1
, respectively).
Genotypic Characterization of UL23 Thymidine Kinase and UL30 DNA Polymerase of Clinical Isolates of Herpes Simplex Virus: Natural Polymorphism and Mutations Associated with Resistance to Antivirals
Authors: Burrel Sonia , Deback Claire , Agut Henri , Boutolleau David
Published: August 2010

The molecular mechanisms of herpes simplex virus (HSV) resistance to antiviral drugs interfering with viral DNA synthesis reported so far rely on the presence of mutations within UL23 (thymidine kinase [TK]) and UL30 (DNA polymerase) genes. The interpretation of genotypic antiviral resistance assay results requires the clear distinction between resistance mutations and natural interstrain sequence variations. The objectives of this work were to describe extensively the natural polymorphism of UL23 TK and UL30 DNA polymerase among HSV-1 and HSV-2 strains and the amino acid changes potentially associated with HSV resistance to antivirals. The sequence analysis of the full-length UL23 and UL30 genes was performed. Ninety-four drug-sensitive clinical isolates (43 HSV-1 and 51 HSV-2) and 3 laboratory strains (KOS, gHSV-2, and MS2) were studied for natural polymorphism, and 25 clinical isolates exhibiting phenotypic traits of resistance to antivirals were analyzed for drug resistance mutations. Our results showed that TK and DNA polymerase are highly conserved among HSV strains, with a weaker variability for HSV-2 strains. This study provided a precise map of the natural polymorphism of both viral enzymes among HSV-1 and HSV-2 isolates, with the identification of 15 and 51 polymorphisms never previously described for TK and DNA polymerase, respectively, which will facilitate the interpretation of genotypic antiviral-resistant testing. Moreover, the genotypic characterization of 25 drug-resistant HSV isolates revealed 8 new amino acid changes located in TK and potentially accounting for acyclovir (ACV) resistance.
Mechanisms Involved in the Selection of HIV-1 Reverse Transcriptase Thumb Subdomain Polymorphisms Associated with Nucleoside Analogue Therapy Failure
Authors: Betancor Gilberto , Puertas Maria C. , Nevot María , Garriga César , Martínez Miguel A. , Martinez-Picado Javier , Menéndez-Arias Luis
Published: August 2010

Previous studies showed an increased prevalence of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) thumb subdomain polymorphisms Pro272, Arg277, and Thr286 in patients failing therapy with nucleoside analogue combinations. Interestingly, wild-type HIV-1BH10RT contains Pro272, Arg277, and Thr286. Here, we demonstrate that in the presence of zidovudine, HIV-1BH10RT mutations P272A/R277K/T286A produce a significant reduction of the viral replication capacity in peripheral blood mononuclear cells in both the absence and presence of M41L/T215Y. In studies carried out with recombinant enzymes, we show that RT thumb subdomain mutations decrease primer-unblocking activity on RNA/DNA complexes, but not on DNA/DNA template-primers. These effects were observed with primers terminated with thymidine analogues (i.e., zidovudine and stavudine) and carbovir (the relevant derivative of abacavir) and were more pronounced when mutations were introduced in the wild-type HIV-1BH10RT sequence context. RT thumb subdomain mutations increased by 2-fold the apparent dissociation equilibrium constant (Kd) for RNA/DNA without affecting theKdfor DNA/DNA substrates. RNase H assays carried out with RNA/DNA complexes did not reveal an increase in the reaction rate or in secondary cleavage events that could account for the decreased excision activity. The interaction of Arg277 with the phosphate backbone of the RNA template in HIV-1 RT bound to RNA/DNA and the location of Thr286 close to the RNA strand are consistent with thumb polymorphisms playing a role in decreasing nucleoside RT inhibitor excision activity on RNA/DNA template-primers by affecting interactions with the template-primer duplex without involvement of the RNase H activity of the enzyme.
In Vivo
and
In Vitro
Sensitivity of
Fasciola hepatica
to Triclabendazole Combined with Artesunate, Artemether, or OZ78
Authors: Duthaler Urs , Smith Thomas A. , Keiser Jennifer
Published: August 2010

Triclabendazole resistance is continually documented from livestock, and hence new treatment strategies for
Fasciola hepatica
infections are needed. We investigated the effect of triclabendazole combined with artesunate, artemether, or OZ78 compared to that of monotherapy against adult and juvenile
F. hepatica
in rats.
In vitro
experiments with triclabendazole and its sulfoxide and sulfone metabolites, each in combination with the peroxides, complemented our study.
F. hepatica
-infected rats were subjected to single drugs or drug combinations 3 to 4 weeks (juvenile flukes) and >8 weeks (adult flukes) postinfection. Negative binomial regressions of worm and egg counts were used to analyze dose-response relationships and whether the effects of drug combinations were synergistic or antagonistic. The
in vitro
assays were evaluated by means of viability scales based on fluke motility. Fifty percent effective dose values of 113.0, 77.7, 22.9, and 2.7 mg/kg of body weight were calculated for monotherapy with artesunate, artemether, OZ78, and triclabendazole, respectively, against adult
F. hepatica
. Likelihood ratio tests revealed synergistic interactions (
P
< 0.05) of combinations of triclabendazole (2.5 mg/kg) plus artesunate or artemether on adult worm burden. Antagonistic effects on the adult burden and egg output were observed when a lower triclabendazole dose (1.25 mg/kg) was combined with the artemisinins. No significant interactions (
P
= 0.07) were observed for OZ78 and triclabendazole combinations and between the triclabendazole effect and the effects of the other partner drugs on juvenile worms. Our
in vitro
studies of adult worms agreed with the
in vivo
results, while the
in vitro
analysis of juvenile worms revealed greater interactions than observed
in vivo
. In conclusion, single-agent triclabendazole demonstrated a more potent
in vivo
and
in vitro
fasciocidal activity than the experimental drugs artesunate, artemether, and OZ78. When combined, synergistic but also antagonistic effects depending on the doses administered were observed, which should be elucidated in more detail in future studies.
Stent-assisted coiling of paraclinoid aneurysms: risks and effectiveness
Authors: Ogilvy Christopher S , Natarajan Sabareesh K , Jahshan Shady , Karmon Yuval , Yang Xinyu , Snyder Kenneth V , Hopkins L Nelson , Siddiqui Adnan H , Levy Elad I
Published: August 2010

Background

Stent assistance for treatment of wide-based aneurysms is becoming rapidly accepted.

Methods

Cases of aneurysms arising in the paraclinoid location of the internal carotid artery treated with intracranial stents and/or bare platinum coils were analyzed retrospectively from our prospectively collected database. We identified 70 aneurysms treated with stent assistance (including one stenting-alone case) and 24 aneurysms treated with coiling alone. Stenting-assisted coiling was achieved either as a one-time treatment or as a two-step maneuver with the stent placed several weeks before coiling, or stent-assisted coiling was used as a second maneuver in aneurysms that recanalized after previous coiling.

Results

In aneurysms treated with stent assistance, 60% had ≥95% occlusion at treatment completion, a result comparing favorably with the 54.2% rate of ≥95% occlusion associated with coiling alone. At last follow-up, 60 aneurysms treated with stent assistance had a 66.7% incidence of ≥95% occlusion, with no in-stent stenosis; 75% of patients treated with coiling alone had ≥95% aneurysm occlusion. Thrombus occurred during stent deployment in two patients, one with and one without neurologic sequelae; stent displacement occurred in one patient without neurologic sequelae. At last follow-up, 57 of 62 patients (91.9%) treated with stent-assisted coiling experienced excellent/good outcomes (modified Rankin scale score ≤2). These results compared favorably with those for the coiling-alone group in which 23 of 24 (95.8%) had good outcomes.

Conclusion

Stent-assisted coiling of paraclinoid aneurysms did not add significantly to morbidity; overall effectiveness was comparable to that of bare coiling of paraclinoid aneurysms. These results require confirmation by a prospective controlled trial.
CREDIT RISK AND INCOMPLETE INFORMATION: FILTERING AND EM PARAMETER ESTIMATION
Authors: FONTANA CLAUDIO , RUNGGALDIER WOLFGANG J.
Published: August 2010

We consider a reduced-form credit risk model where default intensities and interest rate are functions of a not fully observable Markovian factor process, thereby introducing an information-driven default contagion effect among defaults of different issuers. We determine arbitrage-free prices of OTC products coherently with information from the financial market, in particular yields and credit spreads and this can be accomplished via a filtering approach coupled with an EM-algorithm for parameter estimation.
INTERACTIVE REGISTRATION OF INTRACELLULAR VOLUMES WITH RADIAL BASIS FUNCTIONS
Authors: YOSHIZAWA SHIN , TAKEMOTO SATOKO , TAKAHASHI MIWA , MUROI MAKOTO , KAZAMI SAYAKA , MIYOSHI HIROMI , YOKOTA HIDEO
Published: August 2010

We propose a novel approach to 3D image registration of intracellular volumes. The approach extends a standard image registration framework to the curved cell geometry. An intracellular volume is mapped onto another intracellular domain by using two pairs of point set surfaces approximating their nuclear and plasma membranes. The mapping function consists of the affine transformation, tetrahedral barycentric interpolation, and least-squares formulation of radial basis functions for extracted cell geometry features. An interactive volume registration system is also developed based on our approach. We demonstrate that our approach is capable of creating cell models containing multiple organelles from observed data of living cells.
X-RAY RADIATION USING POLARIZED LiNbO3 SINGLE CRYSTALS IN A LOW-PRESSURE GAS AMBIENT
Authors: FUKAO SHINJI , NAKANISHI YOSHIKAZU , SATO YUUKI , YOSHIKADO SHINZO , ITO YOSHIAKI
Published: August 2010

In order to develop miniaturized X-ray devices that provide localized X-ray radiation for medical applications, the dependences of the X-ray intensity on the ambient gas pressure and the inner diameter of the case made of stainless steel were investigated for LiNbO 3 single crystals polarized parallel to the c-axis in a N 2 atmosphere. The smallest inner diameter (16 mm) is slightly larger than the diagonal (14 mm) of the square crystal. The X-ray intensity had a local maximum in the pressure range of approximately 3.9 to 5.4 Pa and it decreased with increasing inner diameter of the case in low vacuums. The X-ray intensity had a local maximum at an inner diameter of 21 mm. The X-ray intensity increased with decreasing pressure in high vacuums.
Zyzzyva
Authors: Kotla Ramakrishna , Alvisi Lorenzo , Dahlin Mike , Clement Allen , Wong Edmund
Published: August 2010

We present Zyzzyva, a protocol that uses speculation to reduce the cost and simplify the design of Byzantine fault tolerant state machine replication. In Zyzzyva, replicas respond to a client's request without first running an expensive three-phase commit protocol to reach agreement on the order in which the request must be processed. Instead, they optimistically adopt the order proposed by the primary and respond immediately to the client. Replicas can thus become temporarily inconsistent with one another, but clients detect inconsistencies, help correct replicas converge on a single total ordering of requests, and only rely on responses that are consistent with this total order. This approach allows Zyzzyva to reduce replication overheads to near their theoretical minimal.
TxLinux
Authors: Rossbach Christopher J. , Hofmann Owen S. , Porter Donald E. , Ramadan Hany E. , Aditya Bhandari , Witchel Emmett
Published: August 2010

TxLinux is a variant of Linux that is the first operating system to use hardware transactional memory (HTM) as a synchronization primitive, and the first to manage HTM in the scheduler. This paper describes and measures TxLinux and discusses two innovations in detail: cooperation between locks and transactions, and theintegration of transactions with the OS scheduler. Mixing locks and transactions requires a new primitive, cooperative transactional spinlocks (
cxspinlocks
) that allow locks and transactions to protect the same data while maintaining the advantages of both synchronization primitives. Cxspinlocks allow the system to attemptexecution of critical regions with transactions and automatically roll back to use locking if the region performs I/O. Integrating the scheduler with HTM eliminates priority inversion. On a series ofreal-world benchmarks TxLinux has similar performance to Linux, exposing concurrency with as many as 32 concurrent threads on 32 CPUs in the same critical region.
Dynamo
Authors: DeCandia Giuseppe , Hastorun Deniz , Jampani Madan , Kakulapati Gunavardhan , Lakshman Avinash , Pilchin Alex , Sivasubramanian Swaminathan , Vosshall Peter , Vogels Werner
Published: August 2010

Reliability at massive scale is one of the biggest challenges we face at Amazon.com, one of the largest e-commerce operations in the world; even the slightest outage has significant financial consequences and impacts customer trust. The Amazon.com platform, which provides services for many web sites worldwide, is implemented on top of an infrastructure of tens of thousands of servers and network components located in many datacenters around the world. At this scale, small and large components fail continuously and the way persistent state is managed in the face of these failures drives the reliability and scalability of the software systems.

This paper presents the design and implementation of Dynamo, a highly available key-value storage system that some of Amazon's core services use to provide an "always-on" experience. To achieve this level of availability, Dynamo sacrifices consistency under certain failure scenarios. It makes extensive use of object versioning and application-assisted conflict resolution in a manner that provides a novel interface for developers to use.
DejaView
Authors: Laadan Oren , Baratto Ricardo A. , Phung Dan B. , Potter Shaya , Nieh Jason
Published: August 2010

As users interact with the world and their peers through their computers, it is becoming important to archive and later search the information that they have
viewed
. We present DejaView, a personal virtual computer recorder that provides a complete record of a desktop computing experience that a user can playback, browse, search, and revive seamlessly. DejaView records visual output, checkpoints corresponding application and file system state, and captures displayed text with contextual information to index the record. A user can then browse and search the record for any visual information that has been displayed on the desktop, and revive and interact with the desktop computing state corresponding to any point in the record. DejaView combines display, operating system, and file system virtualization to provide its functionality transparently without any modifications to applications, window systems, or operating system kernels. We have implemented DejaView and evaluated its performance on real-world desktop applications. Our results demonstrate that DejaView can provide continuous low-overhead recording without any user noticeable performance degradation, and allows browsing, search and playback of records fast enough for interactive use.
Improving file system reliability with I/O shepherding
Authors: Gunawi Haryadi S. , Prabhakaran Vijayan , Krishnan Swetha , Arpaci-Dusseau Andrea C. , Arpaci-Dusseau Remzi H.
Published: August 2010

We introduce a new reliability infrastructure for file systems called I/O shepherding. I/O shepherding allows a file system developer to craft nuanced reliability policies to detect and recover from a wide range of storage system failures. We incorporate shepherding into the Linux ext3 file system through a set of changes to the consistency management subsystem, layout engine, disk scheduler, and buffer cache. The resulting file system, CrookFS, enables a broad class of policies to be easily and correctly specified. We implement numerous policies, incorporating data protection techniques such as retry, parity, mirrors, checksums, sanity checks, and data structure repairs; even complex policies can be implemented in less than 100 lines of code, confirming the power and simplicity of the shepherding framework. We also demonstrate that shepherding is properly integrated, adding less than 5% overhead to the I/O path.
Information flow control for standard OS abstractions
Authors: Krohn Maxwell , Yip Alexander , Brodsky Micah , Cliffer Natan , Kaashoek M. Frans , Kohler Eddie , Morris Robert
Published: August 2010

Decentralized Information Flow Control (DIFC) is an approach to security that allows application writers to control how data flows between the pieces of an application and the outside world. As applied to privacy, DIFC allows untrusted software to compute with private data while trusted security code controls the release of that data. As applied to integrity, DIFC allows trusted code to protect untrusted software from unexpected malicious inputs. In either case, only bugs in the trusted code, which tends to be small and isolated, can lead to security violations.

We present
Flume
, a new DIFC model that applies at the granularity of operating system processes and standard OS abstractions (e.g., pipes and file descriptors). Flume was designed for simplicity of mechanism, to ease DIFC's use in existing applications, and to allow safe interaction between conventional and DIFC-aware processes. Flume runs as a user-level reference monitor onLinux. A process confined by Flume cannot perform most system calls directly; instead, an interposition layer replaces system calls with IPCto the reference monitor, which enforces data flowpolicies and performs safe operations on the process's behalf. We ported a complex web application (MoinMoin Wiki) to Flume, changingonly 2% of the original code. Performance measurements show a 43% slowdown on read workloadsand a 34% slowdown on write workloads, which aremostly due to Flume's user-level implementation.
Systems biology, models, and concurrency
Authors: Fontana Walter
Published: August 2010

Models will play a central role in the representation, storage, manipulation, and communication of knowledge in systems biology. Models capable of fulfilling such a role will likely differ from the all familiar styles deployed with great success in the physical sciences. Molecular systems at the basis of cellular decision processes are concurrent and combinatorial. Their behavior is as much constrained by relationships of causality between molecular interactions as it is by chemical kinetics. Understanding how such systems give rise to coherent behavior and designing effective interventions to fight disease will require a notion of model that is akin to the concept of program in computer science. I will discuss recent progress in implementing a platform and tools for formal analysis that bring us closer to this vision. Protein interactions are represented by means of rules expressed in a formal language that captures a very simple, yet effective and biologically meaningful level of abstraction. Models, then, are collections of rules operating on an initial set of agents, in complete analogy to rules of organic chemical reactions. I will describe tools for analyzing and navigating rule collections as well as exploring their dynamics. We draw on concepts familiar to computer science, especially event structures, and adapt them to biological needs with the goal of formalizing the notion of "pathway". The challenges are many, but a road map for the future is discernible. Computer science will play a central role in providing an additional foundational layer, both theoretical and practical, that neither physics nor chemistry can offer on their own in the future definition of the biological sciences.
Formal verification of translation validators
Authors: Tristan Jean-Baptiste , Leroy Xavier
Published: August 2010

Translation validation consists of transforming a program and
a posteriori
validating it in order to detect a modification of itssemantics. This approach can be used in a verified compiler, provided that validation is formally proved to be correct. We present two such validators and their Coq proofs of correctness. The validators are designed for two instruction scheduling optimizations: list scheduling and trace scheduling.
High-level small-step operational semantics for transactions
Authors: Moore Katherine F. , Grossman Dan
Published: August 2010

Software transactions have received significant attention as a way to simplify shared-memory concurrent programming, but insufficient focus has been given to the precise meaning of software transactions or their interaction with other language features. This work begins to rectify that situation by presenting a family of formal languages that model a wide variety of behaviors for software transactions. These languages abstract away implementation details of transactional memory, providing high-level definitions suitable for programming languages. We use small-step semantics in order to represent explicitly the interleaved execution of threads that is necessary to investigate pertinent issues.

We demonstrate the value of our core approach to modeling transactions by investigating two issues in depth. First, we consider parallel nesting, in which parallelism and transactions can nest arbitrarily. Second, we present multiple models for weak isolation, in which nontransactional code can violate the isolation of a transaction. For both, type-and-effect systems let us soundly and statically restrict what computation can occur inside or outside a transaction. We prove some key language-equivalence theorems to confirm that under sufficient static restrictions, in particular that each mutable memory location is used outside transactions or inside transactions (but not both), no program can determine whether the language implementation uses weak isolation or strong isolation.
Enhancing modular OO verification with separation logic
Authors: Chin Wei-Ngan , David Cristina , Nguyen Huu Hai , Qin Shengchao
Published: August 2010

Conventional specifications for object-oriented (OO) programs must adhere to behavioral subtyping in support of class inheritance and method overriding. However, this requirement inherently weakens the specifications of overridden methods in superclasses, leading to imprecision during program reasoning. To address this, we advocate a fresh approach to OO verification that focuses on the distinction and relation between specifications that cater to calls with static dispatching from those for calls with dynamic dispatching. We formulate a novel specification subsumption that can avoid code re-verification, where possible. Using a predicate mechanism, we propose a flexible scheme for supporting class invariant and lossless casting. Our aim is to lay the foundation for a practical verification system that is precise, concise and modular for sequential OO programs. We exploit the separation logic formalism to achieve this.
Cyclic proofs of program termination in separation logic
Authors: Brotherston James , Bornat Richard , Calcagno Cristiano
Published: August 2010

We propose a novel approach to proving the termination of heap-manipulating programs, which combines separation logic with
cyclic proof
within a Hoare-style proof system.Judgements in this system express (guaranteed) termination of the program when started from a given line in the program and in a state satisfying a given precondition, which is expressed as a formula of separation logic. The proof rules of our system are of two types: logical rules that operate on preconditions; and symbolic execution rules that capture the effect of executing program commands.

Our logical preconditions employ inductively defined predicates to describe heap properties, and proofs in our system are cyclic proofs: cyclic derivations in which some inductive predicate is unfolded infinitely often along every infinite path, thus allowing us to discard all infinite paths in the proof by an infinite descent argument. Moreover, the use of this soundness condition enables us to avoid the explicit construction and use of ranking functions for termination. We also give a completeness result for our system, which is relative in that it relies upon completeness of a proof system for logical implications in separation logic. We give examples illustrating our approach, including one example for which thecorresponding ranking function is non-obvious: termination of the classical algorithm for in-place reversal of a (possibly cyclic) linked list.
Lightweight semiformal time complexity analysis for purely functional data structures
Authors: Danielsson Nils Anders
Published: August 2010

Okasaki and others have demonstrated how purely functional data structures that are efficient even in the presence of persistence can be constructed. To achieve good time bounds essential use is often made of laziness. The associated complexity analysis is frequently subtle, requiring careful attention to detail, and hence formalising it is valuable. This paper describes a simple library which can be used to make the analysis of a class of purely functional data structures and algorithms almost fully formal. The basic idea is to use the type system to annotate every function with the time required to compute its result. An annotated monad is used to combine time complexity annotations. The library has been used to analyse some existing data structures, for instance the deque operations of Hinze and Paterson's finger trees.
Automatic inference of stationary fields
Authors: Unkel Christopher , Lam Monica S.
Published: August 2010

Java programmers can document that the relationship between two objects is unchanging by declaring the field that encodes that relationship to be final. This information can be used in program understanding and detection of errors in new code additions. Unfortunately, few fields in programs are actually declared final. Programs often contain fields that could be final, but are not declared so. Moreover, the definition of final has restrictions on initializationthat limit its applicability.

We introduce
stationary
fields as a generalization of final. A field in a program is stationary if, for every object that contains it, all writes to the field occur before all the reads. Unlike the definition of final fields, there can be multiple writes during initialization, and initialization can span multiple methods.

We have developed an efficient algorithm for inferring which fields are stationary in a program, based on the observation that many fields acquire their value very close to object creation. We presume that an object's initialization phase has concluded when its reference is saved in some heap object. We perform precise analysis only regarding recently created objects. Applying our algorithm to real-world Java programs demonstrates that stationary fields are more common than final fields: 44-59% vs. 11-17% respectively in our benchmarks.

These surprising results have several significant implications. First, substantial portions of Java programs appear to be written in a functional style. Second, initialization of these fields occurs very close to object creation, when very good alias information is available. These results open the door for more accurate and efficient pointer alias analysis.
Demand-driven alias analysis for C
Authors: Zheng Xin , Rugina Radu
Published: August 2010

This paper presents a demand-driven, flow-insensitive analysisalgorithm for answering may-alias queries. We formulate thecomputation of alias queries as a CFL-reachability problem, and use this formulation to derive a demand-driven analysis algorithm. The analysis uses a worklist algorithm that gradually explores the program structure and stops as soon as enough evidence is gathered to answer the query. Unlike existing techniques, our approach does not require building or intersecting points-to sets.

Experiments show that our technique is effective at answering alias queries accurately and efficiently in a demand-driven fashion. For a set of alias queries from the SPEC2000 benchmarks, an implementation of our analysis is able to accurately answer 96% of the queries in 0.5 milliseconds per query on average, using only 65 KB of memory. Compared to a demand-driven points-to analysis that constructs and intersects points-to sets on the fly, our alias analysis can achieve better accuracy while running more than 30 times faster. The low run-time cost and low memory demands of the analysis make it a very good candidate not only for compilers, but also for interactive tools, such as program understanding tools or integrated development environments (IDEs).
Generating precise and concise procedure summaries
Authors: Yorsh Greta , Yahav Eran , Chandra Satish
Published: August 2010

We present a framework for generating procedure summaries that are (a) precise - applying the summary in a given context yields the same result as re-analyzing the procedure in that context, and(b) concise - the summary exploits the commonalitiesin the ways the procedure manipulates abstract values, and does not contain superfluous context information.

The use of a precise and concise procedure summary inmodular analyses provides a way to capture infinitely many possible contexts in a finite way; in interprocedural analyses, it provides a compact representation of an explicit input-output summary table without loss of precision.

We define a class of abstract domains and transformers for which precise and concise summaries can be efficiently generated using our framework. Our framework is rich enough to encode a wide range of problems, including all IFDS and IDE problems. In addition, we show how the framework is instantiated to provide novel solutions to two hard problems: modular linear constant propagation and modular typestate verification, both in the presence of aliasing. We implemented a prototype of our framework that computes summaries for the typestate domain, and report on preliminary experimental results.
A theory of contracts for web services
Authors: Castagna Giuseppe , Gesbert Nils , Padovani Luca
Published: August 2010

Contracts are behavioural descriptions of Web services. We devise a theory of contracts that formalises the compatibility of a client to a service, and the safe replacement of a service with another service. The use of contracts statically ensures the successful completion of every possible interaction between compatible clients and services.

The technical device that underlies the theory is the definition of filters, which are explicit coercions that prevent some possible behaviours of services and, in doing so, they make services compatible with different usage scenarios. We show that filters can be seen as proofs of a sound and complete subcontracting deduction system which simultaneously refines and extends Hennessy's classical axiomatisation of the must testing preorder. The relation is decidable and the decision algorithm is obtained via a cut-elimination process that proves the coherence of subcontracting as a logical system.

Despite the richness of the technical development, the resulting approach is based on simple ideas and basic intuitions. Remarkably, its application is mostly independent of the language used to program the services or the clients. We also outline the possible practical impact of such a work and the perspectives of future research it opens.
Imperative self-adjusting computation
Authors: Acar Umut A. , Ahmed Amal , Blume Matthias
Published: August 2010

Self-adjusting computation enables writing programs that can automatically and efficiently respond to changes to their data (e.g., inputs). The idea behind the approach is to store all data that can change over time in modifiable references and to let computations construct traces that can drive change propagation. After changes have occurred, change propagation updates the result of the computation by re-evaluating only those expressions that depend on the changed data. Previous approaches to self-adjusting computation require that modifiable references be written at most once during execution---this makes the model applicable only in a purely functional setting.

In this paper, we present techniques for imperative self-adjusting computation where modifiable references can be written multiple times. We define a language SAIL (Self-Adjusting Imperative Language) and prove consistency, i.e., that change propagation and from-scratch execution are observationally equivalent. Since SAIL programs are imperative, they can create cyclic data structures. To prove equivalence in the presence of cycles in the store, we formulate and use an untyped, step-indexed logical relation, where step indices are used to ensure well-foundedness. We show that SAIL accepts an asymptotically efficient implementation by presenting algorithms and data structures for its implementation. When the number of operations (reads and writes) per modifiable is bounded by a constant, we show that change propagation becomes as efficient as in the non-imperative case. The general case incurs a slowdown that is logarithmic in the maximum number of such operations. We describe a prototype implementation of SAIL as a Standard ML library.
On the computational soundness of cryptographically masked flows
Authors: Laud Peeter
Published: August 2010

To speak about the security of information flow in programs employing cryptographic operations, definitions based on computational indistinguish ability of distributions over program states have to be used. These definitions, as well as the accompanying analysis tools, are complex and error-prone to argue about. Cryptographically masked flows, proposed by Askarov, Hedin and Sabelfeld, are an abstract execution model and security definition that attempt to abstract away the details of computational security. This abstract model is useful because analysis of programs can be conducted using the usual techniques for enforcing non-interference.

In this paper we investigate under which conditions this abstract model is computationally sound, i.e. when does the security of a program in their model imply the computational security of this program. This paper spells out a reasonable set of conditions and then proposes a simpler abstract model that is nevertheless no more restrictive than the cryptographically masked flows together with these conditions for soundness.
From dirt to shovels
Authors: Fisher Kathleen , Walker David , Zhu Kenny Q. , White Peter
Published: August 2010

An
ad hoc data source
is any semistructured data source for which useful data analysis and transformation tools are not readily available. Such data must be queried, transformed and displayed by systems administrators, computational biologists, financial analysts and hosts of others on a regular basis. In this paper, we demonstrate that it is possible to generate a suite of useful data processing tools, including a semi-structured query engine, several format converters, a statistical analyzer and data visualization routines directly from the ad hoc data itself, without any human intervention. The key technical contribution of the work is a multi-phase algorithm that automatically infers the structure of an ad hoc data source and produces a format specification in the PADS data description language. Programmers wishing to implement custom data analysis tools can use such descriptions to generate printing and parsing libraries for the data. Alternatively, our software infrastructure will push these descriptions through the PADS compiler, creating format-dependent modules that, when linked with format-independent algorithms for analysis and transformation, result infully functional tools. We evaluate the performance of our inference algorithm, showing it scales linearlyin the size of the training data - completing in seconds, as opposed to the hours or days it takes to write a description by hand. We also evaluate the correctness of the algorithm, demonstrating that generating accurate descriptions often requires less than 5% of theavailable data.