bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Bacterial Heat Shock Response to Photodynamic Therapy‐mediated Oxidative Stress
Authors: St. Denis Tyler G. , Huang Liyi , Dai Tianhong , Hamblin Michael R. 
Published: January 2011

AbstractAntimicrobial photodynamic therapy (PDT) has recently emerged as an effective modality for the selective destruction of bacteria and other pathogenic microorganisms. We investigated whether PDT induced protective responses such as heat shock proteins (HSPs) in bacteria. Using the photosensitizer Toluidine Blue O (TBO) at sublethal PDT conditions, a seven‐fold increase in bacterial HSP GroEL and a three‐fold increase in HSP DnaK were observed in Escherichia coli post PDT. Pretreatment with 50°C heat for 30 min reduced PDT killing in both E. coli and in Enterococcus faecalis, with the most pronounced inhibition occurring at 50 μm TBO with 5 J cm−2 635 nm light, where E. coli killing was reduced by 2 log10 and E. faecalis killing was reduced by 4 log10. Finally, inhibition of the highly conserved chaperone DnaK using a small molecule benzylidene lactam HSP inhibitor potentiated (but not significantly) the effect of PDT at a TBO concentration of 2.5 μm in E. faecalis; however, this effect was not observed in E. coli presumably because inhibitor could not gain access due to Gram‐negative permeability barrier. Induction of HSPs may be a mechanism whereby bacteria could become resistant to PDT and warrants the need for further study in the application of dual PDT‐HSP‐inhibition therapies.
Ejecta–megaregolith accumulation on planetesimals and large asteroids
Authors: WARREN Paul H. 
Published: January 2011

Abstract–Megaregolith accumulation can have important thermal consequences for bodies that lose heat by conduction, as vacuous porosity of the kind observed in the lunar megaregolith lowers thermal conductivity by a factor of 10. I have modeled global average ejecta accumulation as a function of the largest impact size, with no explicit modeling of time. In conjunction with an assumed cratering size‐distribution exponent b, the largest crater constrains the sizes of all other craters that significantly contribute to a megaregolith. The largest impactor mass ratio is a major fraction of the catastrophic‐disruption mass ratio, and in general the largest crater’s diameter is close to the target’s diameter. Total accumulation is roughly 1–5% of (and proportional to) the target’s radius. Global accumulations estimated by this approach are higher than in the classic Housen et al. (1979) study by a factor of roughly 10. This revision is caused mainly by higher (typical) largest crater size. For b ∼ 2, the single largest crater typically contributes close to 50% of the total of new (nonrecycled) ejecta. Megaregolith can be destroyed by sintering, a process whose pressure sensitivity makes it effective at lower temperature on larger bodies. Planetesimals ∼100 km in diameter may be surprisingly well suited (about as well suited as bodies two to three times larger in diameter) for attaining temperatures conducive to widespread melting. A water‐rich composition may be a significant disadvantage in terms of planetesimal heating, as the shallow interior may be densified by aqueous metamorphism, and will have a low sintering temperature.
Primitive olivine‐phyric shergottite NWA 5789: Petrography, mineral chemistry, and cooling history imply a magma similar to Yamato‐980459
Authors: GROSS Juliane , TREIMAN Allan H. , FILIBERTO Justin , HERD Christopher D. K. 
Published: January 2011

Abstract–Knowledge of Martian igneous basaltic compositions is crucial for constraining mantle evolution, including early differentiation and mantle convection. Primitive magmas provide direct information about their mantle source regions, but most Martian meteorites either contain cumulate olivine or crystallized from fractionated melts. The recently discovered Martian meteorite Northwest Africa (NWA) 5789 is an olivine‐phyric shergottite. NWA 5789 has special significance among the Martian meteorites because it appears to represent one of the most magnesian Martian magmas known, other than Yamato (Y) 980459. Its most magnesian olivine cores (Fo85) are in Mg‐Fe equilibrium with a magma of the bulk rock composition, suggesting that the bulk represents a magma composition. Based on the Al/Ti ratio of its pyroxenes, we infer that the rock began to crystallize at a high pressure consistent with conditions in Mars’ lower crust/upper mantle. It continued and completed its crystallization closer to the surface, where cooling was rapid and produced a mesostasis of radiating sprays of plagioclase and pyroxene. The mineralogy, petrology, mineral chemistry, and bulk rock composition of NWA 5789 are very similar to those of Y‐980459. The similarities between the two meteorites suggest that NWA 5789 (like Y‐980459) represents a primitive, mantle‐derived magma composition. They also suggest the possibility that NWA 5789 and Y‐980459 formed in the same lava flow. However, based on the mineralogy and texture of its mesostasis, NWA 5789 must have cooled more slowly than Y‐980459. NWA 5789 will help elucidate the igneous geology and geochemistry of Mars.
Cholesterol Is Not an Essential Source of Nutrition for
Mycobacterium tuberculosis
during Infection
Authors: Yang Xinxin , Gao Jin , Smith Issar , Dubnau Eugenie , Sampson Nicole S. 
Published: January 2011

ABSTRACT

Rv1106c (
hsd
; 3β-hydroxysteroid dehydrogenase) is required by
Mycobacterium tuberculosis
for growth on cholesterol as a sole carbon source, whereas Rv3409c is not. Mutation of Rv1106c does not reduce
Mycobacterium tuberculosis
growth in infected macrophages or guinea pigs. We conclude that cholesterol is not required as a nutritional source during infection.
Linguistic and semantic passage retrieval strategies for question answering
Authors: Bilotti Matthew W. 
Published: January 2011

Question Answering (QA) is the task of searching a large text collection for specific answers to questions posed in natural language. Though they often have access to rich linguistic and semantic analyses of their input questions, QA systems often rely on off-theshelf bag-of-words Information Retrieval (IR) solutions to retrieve passages matching a set of terms extracted from the question.
There is a fundamental disconnect between the capabilities of the bag-of-words retrieval model and the retrieval needs of the QA system. Bag-of-words IR retrieves documents matching a query, but the QA system really needs documents that contain answers. Through question analysis, the QA system has compiled a sophisticated information need representation for what constitutes an answer to the question. This representation is composed of a set of linguistic and semantic constraints satisfied by answer-bearing passages. Unfortunately, off-the-shelf IR libraries commonly used in QA systems can not, in general, check these types of constraints at query-time. Poor quality retrieval can cause a QA system to fail if no answer-bearing text is retrieved, if it is not ranked highly enough, or if it is outranked or overwhelmed by false positives, text that matches the query well, yet supports a wrong answer.
This thesis proposes two linguistic and semantic passage retrieval methods for QA, one based on structured retrieval and the other on rank-learning techniques. In addition, a methodology is proposed for mapping annotated text consisting of labeled spans and typed relations between them into an annotation graph representation. The annotation graph supports query-time linguistic and semantic constraint-checking, and serves as a unifying formalism for the QA system's information need and for retrieved passages. The proposed methods rely only on the relatively weak assumption that the QA system's information need can be represented as an annotation graph. The two approaches are shown to retrieve more answer-bearing text, more highly ranked, compared to a bag-of-words baseline for two different QA tasks. Linguistic and semantic passage retrieval methods are also shown to improve end-to-end QA system accuracy and answer MRR.
Available online at: http://www.cs.cmu.edu/~mbilotti/thesis.pdf.
Personalised video retrieval
Authors: Hopfgartner Frank 
Published: January 2011

A challenging problem in the user profiling domain is to create profiles of users of retrieval systems. This problem even exacerbates in the multimedia domain. Due to the Semantic Gap, the difference between low-level data representation of videos and the higher concepts users associate with videos, it is not trivial to understand the content of multimedia documents and to find other documents that the users might be interested in. A promising approach to ease this problem is to set multimedia documents into their semantic contexts. The semantic context can lead to a better understanding of the personal interests. Knowing the context of a video is useful for recommending users videos that match their information need. By exploiting these contexts, videos can also be linked to other, contextually related videos. From a user profiling point of view, these links can be of high value to recommend semantically related videos, hence creating a semantic-based user profile. This thesis introduces a semantic user profiling approach for news video retrieval, which exploits a generic ontology to put news stories into its context.
Major challenges which inhibit the creation of such semantic user profiles are the identification of user's long-term interests and the adaptation of retrieval results based on these personal interests. Most personalisation services rely on users explicitly specifying preferences, a common approach in the text retrieval domain. By giving explicit feedback, users are forced to update their need, which can be problematic when their information need is vague. Furthermore, users tend not to provide enough feedback on which to base an adaptive retrieval algorithm. Deviating from the method of explicitly asking the user to rate the relevance of retrieval results, the use of implicit feedback techniques helps by learning user interests unobtrusively. The main advantage is that users are relieved from providing feedback. A disadvantage is that information gathered using implicit techniques is less accurate than information based on explicit feedback.
Scalability of findability
Authors: Ke Weimao 
Published: January 2011

Amid the rapid growth of information today is the increasing challenge for people to survive and navigate its magnitude. Dynamics and heterogeneity of large information spaces such as the Web challenge information retrieval in these environments. Collection of information in advance and centralization of IR operations are hardly possible because systems are dynamic and information is distributed.
While monolithic search systems continue to struggle with scalability problems of today, the future of search likely requires a decentralized architecture where many information systems can participate. As individual systems interconnect to form a global structure, finding relevant information in distributed environments transforms into a problem concerning not only information retrieval but also complex networks. Understanding network connectivity will provide guidance on how decentralized search and retrieval methods can function in these information spaces.
The dissertation studies one aspect of scalability challenges facing classic information retrieval models and presents a decentralized, organic view of information systems pertaining to search in large scale networks. It focuses on the impact of network structure on search performance and investigates a phenomenon we refer to as the Clustering Paradox, in which the topology of interconnected systems imposes a scalability limit. Experiments involving large scale benchmark collections provide evidence on the Clustering Paradox in the IR context. In an increasingly large, distributed environment, decentralized searches for relevant information can continue to function well only when systems interconnect in certain ways. Relying on partial indexes of distributed systems, some level of network clustering enables very efficient and effective discovery of relevant information in large scale networks. Increasing or reducing network clustering degrades search performances. Given this specific level of network clustering, search time is well explained by a poly-logarithmic relation to network size, indicating a high scalability potential for searching in a continuously growing information space.
A framework for supporting user-centric collaborative information seeking
Authors: Shah Chirag 
Published: January 2011

Collaboration is often required or encouraged for activities that are too complex or difficult to deal with for an individual. Many situations involving information seeking also call for people working together. Despite its natural appeal and situational necessity, collaboration in information seeking is an understudied domain. The nature of the available information and its role in our lives have changed significantly, but the methods and tools that are used to access and share that information in collaboration have remained largely unaltered. This dissertation is an attempt to develop a new framework for collaborative information seeking (CIS) with a focus on user-centric system designs. To develop this framework, existing practices for doing collaboration, along with motivations and methods, are studied. This initial investigation and a review of literature are followed by a series of carefully created design studies, helping us develop a prototype CIS system, Coagmento. This system is then used for a large-scale laboratory experiment with a focus on studying the role and the impact of awareness in CIS projects. Through this study, it is shown that appropriate support for group awareness can help collaborators be more productive, engaged, and aware in collaboration without burdening them with additional load. Using the lessons derived from the literature as well as the set of studies presented in this dissertation, a novel framework for CIS is proposed. Such a framework could help us develop, study, and evaluate CIS systems with a more comprehensive understanding of various CIS processes, and the users of these systems.
Dissertation available online at: http://comminfo.rutgers.edu/~chirags/papers/Shah_Dissertation.pdf.
Using virtualization and live migration in a scalable mobile wireless testbed
Authors: Hahn Dongwoon , Lee Ginnah , Walker Brenton , Beecher Matt , Mundur Padma 
Published: January 2011

Laboratory-based mobile wireless testbeds such as MeshTest and the CMU Wireless Emulator are powerful platforms that allow users to perform controlled, repeatable, mobile wireless experiments in the lab. Unfortunately such systems can only accommodate 10-20 nodes in an experiment. We have designed and built a prototype of a system that uses software virtualization and live migration to facilitate experiments involving intermittently connected networks with many multiples of the number of physical nodes available on such a testbed.
Building a system like this presents many technical and research challenges. In this paper, we will describe the physical construction and software architecture of the system while providing a discussion on the research issues that we are currently addressing.
Practical affine types
Authors: Tov Jesse A. , Pucella Riccardo 
Published: January 2011

Alms is a general-purpose programming language that supports practical affine types. To offer the expressiveness of Girard's linear logic while keeping the type system light and convenient, Alms uses expressive kinds that minimize notation while maximizing polymorphism between affine and unlimited types.
A key feature of Alms is the ability to introduce abstract affine types via ML-style signature ascription. In Alms, an interface can impose stiffer resource usage restrictions than the principal usage restrictions of its implementation. This form of sealing allows the type system to naturally and directly express a variety of resource management protocols from special-purpose type systems.
We present two pieces of evidence to demonstrate the validity of our design goals. First, we introduce a prototype implementation of Alms and discuss our experience programming in the language. Second, we establish the soundness of the core language. We also use the core model to prove a principal kinding theorem.
Laws of order
Authors: Attiya Hagit , Guerraoui Rachid , Hendler Danny , Kuznetsov Petr , Michael Maged M. , Vechev Martin 
Published: January 2011

Building correct and efficient concurrent algorithms is known to be a difficult problem of fundamental importance. To achieve efficiency, designers try to remove unnecessary and costly synchronization. However, not only is this manual trial-and-error process ad-hoc, time consuming and error-prone, but it often leaves designers pondering the question of: is it inherently impossible to eliminate certain synchronization, or is it that I was unable to eliminate it on this attempt and I should keep trying?
In this paper we respond to this question. We prove that it is impossible to build concurrent implementations of classic and ubiquitous specifications such as sets, queues, stacks, mutual exclusion and read-modify-write operations, that completely eliminate the use of expensive synchronization.
We prove that one cannot avoid the use of either: i) read-after-write (RAW), where a write to shared variable A is followed by a read to a different shared variable B without a write to B in between, or ii) atomic write-after-read (AWAR), where an atomic operation reads and then writes to shared locations. Unfortunately, enforcing RAW or AWAR is expensive on all current mainstream processors. To enforce RAW, memory ordering--also called fence or barrier--instructions must be used. To enforce AWAR, atomic instructions such as compare-and-swap are required. However, these instructions are typically substantially slower than regular instructions.
Although algorithm designers frequently struggle to avoid RAW and AWAR, their attempts are often futile. Our result characterizes the cases where avoiding RAW and AWAR is impossible. On the flip side, our result can be used to guide designers towards new algorithms where RAW and AWAR can be eliminated.
EigenCFA
Authors: Prabhu Tarun , Ramalingam Shreyas , Might Matthew , Hall Mary 
Published: January 2011

We describe, implement and benchmark EigenCFA, an algorithm for accelerating higher-order control-flow analysis (specifically, 0CFA) with a GPU. Ultimately, our program transformations, reductions and optimizations achieve a factor of 72 speedup over an optimized CPU implementation.
We began our investigation with the view that GPUs accelerate high-arithmetic, data-parallel computations with a poor tolerance for branching. Taking that perspective to its limit, we reduced Shivers's abstract-interpretive 0CFA to an algorithm synthesized from linear-algebra operations. Central to this reduction were "abstract" Church encodings, and encodings of the syntax tree and abstract domains as vectors and matrices.
A straightforward (dense-matrix) implementation of EigenCFA performed slower than a fast CPU implementation. Ultimately, sparse-matrix data structures and operations turned out to be the critical accelerants. Because control-flow graphs are sparse in practice (up to 96% empty), our control-flow matrices are also sparse, giving the sparse matrix operations an overwhelming space and speed advantage.
We also achieved speedups by carefully permitting data races. The monotonicity of 0CFA makes it sound to perform analysis operations in parallel, possibly using stale or even partially-updated data.
Tool release
Authors: Halperin Daniel , Hu Wenjun , Sheth Anmol , Wetherall David 
Published: January 2011

We are pleased to announce the release of a tool that records detailed measurements of the wireless channel along with received 802.11 packet traces. It runs on a commodity 802.11n NIC, and records Channel State Information (CSI) based on the 802.11 standard. Unlike Receive Signal Strength Indicator (RSSI) values, which merely capture the total power received at the listener, the CSI contains information about the channel between sender and receiver at the level of individual data subcarriers, for each pair of transmit and receive antennas.
Our toolkit uses the Intel WiFi Link 5300 wireless NIC with 3 antennas. It works on up-to-date Linux operating systems: in our testbed we use Ubuntu 10.04 LTS with the 2.6.36 kernel. The measurement setup comprises our customized versions of Intel's close-source firmware and open-source iwlwifi wireless driver, userspace tools to enable these measurements, access point functionality for controlling both ends of the link, and Matlab (or Octave) scripts for data analysis. We are releasing the binary of the modified firmware, and the source code to all the other components.
Topology-aware resource allocation for data-intensive workloads
Authors: Lee Gunho , Tolia Niraj , Ranganathan Parthasarathy , Katz Randy H. 
Published: January 2011

This paper proposes an architecture for optimized resource allocation in Infrastructure-as-a-Service (IaaS)-based cloud systems. Current IaaS systems are usually unaware of the hosted application's requirements and therefore allocate resources independently of its needs, which can significantly impact performance for distributed data-intensive applications.
To address this resource allocation problem, we propose an architecture that adopts a what if methodology to guide allocation decisions taken by the IaaS. The architecture uses a prediction engine with a lightweight simulator to estimate the performance of a given resource allocation and a genetic algorithm to find an optimized solution in the large search space. We have built a prototype for Topology-Aware Resource Allocation (TARA) and evaluated it on a 80 server cluster with two representative MapReduce-based benchmarks. Our results show that TARA reduces the job completion time of these applications by up to 59% when compared to application-independent allocation policies.
Accelerating SSL with GPUs
Authors: Jang Keon , Han Sangjin , Han Seungyeop , Moon Sue , Park KyoungSoo 
Published: January 2011

SSL/TLS is a standard protocol for secure Internet communication. Despite its great success, today's SSL deployment is largely limited to security-critical domains. The low adoption rate of SSL is mainly due to high computation overhead on the server side.
In this paper, we propose Graphics Processing Units (GPUs) as a new source of computing power to reduce the server-side overhead. We have designed and implemented an SSL proxy that opportunistically offloads cryptographic operations to GPUs. The evaluation results show that our GPU implementation of cryptographic operations, RSA, AES, and HMAC-SHA1, achieves high throughput while keeping the latency low. The SSL proxy significantly boosts the throughput of SSL transactions, handling 21.5K SSL transactions per second, and has comparable response time even when overloaded.