238 research outputs found
Unifying Access and Resource Usage Control over Standard Client-Server Interactions
No full textWe propose a novel framework for integrated access and resource usage control over standard clientserver interactions. Historically, access control has been developed without considering resource usage. Resource control has thus developed as an ad hoc server-centric set of mechanisms (e.g., file system quota, network bandwidth quote, etc.). We believe that resource usage control is strongly related to access control and so should be implemented using a unified, global enforcement framework. We introduce such a framework, where services have resource usage constraints and principals have resource usage histories. To access and use a service, a principal must have the appropriate access and sufficient resource usage rights when considering its usage history. Our framework is able to enforce global stateful policies, yet do not require changes to existing message-passing applications. We have built a prototype and used it to specify and enforce an example policy that includes role-based control and delegation. We applied our system to control access and resource usage for three different services, network, DNS, and SMB file systems, to demonstrate its effectiveness and wide applicability.Technical report DCS-TR-67
The Impact Of The Development Of ICT In Several Hungarian Economic Sectors
Full text linkAs the author could not find a reassuring mathematical and
statistical method in the literature for studying the effect of
information communication technology on enterprises, the author
suggested a new research and analysis method that he also used to study the Hungarian economic sectors. The question of what
factors have an effect on their net income is vital for enterprises. At first, the author studied some potential indicators related to economic sectors, then those indicators were compared to the net income of the surveyed enterprises. The resulting data showed that the growing penetration of electronic marketplaces contributed to the change of the net income of enterprises to the greatest extent.
Furthermore, among all the potential indicators, it was the only indicator directly influencing the net income of enterprises.
With the help of the compound indicator and the financial data
of the studied economic sectors, the author made an attempt to find a connection between the development level of ICT and
profitability. Profitability and productivity are influenced by a lot of other factors as well. As the effect of the other factors could not be measured, the results – shown in a coordinate system - are not full but informative.
The highest increment of specific Gross Value Added was
produced by the fields of ‘Manufacturing’, ‘Electricity, gas and water supply’, ‘Transport, storage and communication’ and
‘Financial intermediation’. With the exception of ‘Electricity, gas and water supply’, the other economic sectors belong to the group of underdeveloped branches (below 50 percent).
On the other hand, ‘Construction’, ‘Health and social work’ and
‘Hotels and restaurants’ can be seen as laggards, so they got into the lower left part of the coordinate system.
‘Agriculture, hunting and forestry’ can also be classified as a
laggard economic sector, but as the effect of the compound
indicator on the increment of Gross Value Added was less
significant, it can be found in the upper left part of the coordinate system. Drawing a trend line on the points, it can be made clear that it shows a positive gradient, that is, the higher the usage of ICT devices, the higher improvement can be detected in the specific Gross Value Added
Text-based content search and retrieval in ad hoc P2P communities
No full textWe consider the problem of content search and retrieval in peer-to-peer (P2P) communities. P2P computing is a potentially powerful model for information sharing between ad hoc groups of users because of its low cost of entry and natural model for resource scaling with community size. As P2P communities grow in size, however, locating information distributed across the large number of peers becomes problematic. We present a distributed text-based content search and retrieval algorithm to address this problem. Our algorithm is based on a state-of-the-art text-based document ranking algorithm: the vector-space model, instantiated with the TFxIDF ranking rule. A naive application of TFxIDF would require each peer in a community to collect an inverted index of the entire community. This is costly both in terms of bandwidth and storage. Instead, we show how TFxIDF can be approximated given compact summaries of peers’ local inverted indexes. We make three contributions: (a) we show how the TFxIDF rule can be adapted to use the index summaries, (b) we provide a heuristic for adaptively determining the set of peers that should be contacted for a query, and (c) we show that our algorithm tracks TFxIDF’s performance very closely, regardless of how documents are distributed throughout the community. Furthermore, our algorithm preserves the main flavor of TFxIDF by retrieving close to the same set of documents for any given query.Technical report DCS-TR-48
High diagnostic yield of tuberculosis from screening urine samples from HIV-infected patients with advanced immunodeficiency using the Xpert MTB/RIF assay.
Full text link: ABSTRACT:: We determined the diagnostic yield of the Xpert MTB/RIF assay for tuberculosis (TB) when testing small volumes of urine from ambulatory HIV-infected patients prior to starting antiretroviral therapy (ART) in South Africa. Compared to a gold standard of sputum culture, the sensitivity of urine Xpert among those with CD4 cell counts of <50, 50-100 and >100 cells/?L were 44.4%, 25.0% and 2.7% (P=0.001), respectively. Urine Xpert testing provides a means of rapid TB diagnosis in patients with advanced immunodeficiency and poor prognosis. These data are indicative of high rates of TB dissemination and renal involvement in this clinical population
Robust data partitioning for ad-hoc query processing
No full textThesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 59-62).Data partitioning can significantly improve query performance in distributed database systems. Most proposed data partitioning techniques choose the partitioning based on a particular expected query workload or use a simple upfront scheme, such as uniform range partitioning or hash partitioning on a key. However, these techniques do not adequately address the case where the query workload is ad-hoc and unpredictable, as in many analytic applications. The HYPER-PARTITIONING system aims to ll that gap, by using a novel space-partitioning tree on the space of possible attribute values to dene partitions incorporating all attributes of a dataset. The system creates a robust upfront partitioning tree, designed to benet all possible queries, and then adapts it over time in response to the actual workload. This thesis evaluates the robustness of the upfront hyper-partitioning algorithm, describes the implementation of the overall HYPER-PARTITIONING system, and shows how hyper-partitioning improves the performance of both selection and join queries.by Qui T. Nguyen.M. Eng
PlanetP: Using Gossiping to Build Content Addressable Peer-to-Peer Information Sharing Communities
No full textWe present PlanetP, a peer-to-peer (P2P) content search and retrieval infrastructure targeting communities wishing to share large sets of text documents. P2P computing is an attractive model for information sharing between ad hoc groups of users because of its low cost of entry and explicit model for resource scaling. As communities grow, however, a key challenge becomes finding relevant information. To address this challenge, our design centers around indexing, content search, and retrieval rather than scalable name-based object location, which has been the focus of recent P2P systems. PlanetP takes the novel approach of replicating the global directory and a compact summary index at every peer using gossiping. PlanetP then leverages this information to approximate a state-of-the-art document ranking algorithm to help users locate relevant information within the large communal data set. Using a prototype implementation together with simulation, we show: (i) it is possible to design a gossiping algorithm that reliably maintains a copy of communal state at each peer yet requires only a modest amount of bandwidth, (ii) our content search and retrieval algorithm tracks the performance of the original ranking algorithm very closely, giving P2P communities a search and retrieval algorithm as good as that possible assuming a centralized server, and (iii) PlanetP's gossiping and search and retrieval algorithms both scale well to communities of at least several thousand peersTechnical report DCS-TR-48
PlanetP: Infrastructure Support for P2P Information Sharing
No full textStorage technology trends are providing massive storage in extremely small packages while declining computing costs are resulting in a rising number of devices per person. The confluence of these trends are presenting a new, critical challenge to storage and file system designers: how to enable users to effectively manage, use, and share huge amounts of data stored across a multitude of devices. In this paper, we present a novel middleware storage system, PlanetP, which is designed from first principles as a peer-to-peer (P2P), semantically indexed storage layer. PlanetP makes two novel design choices to meet the above challenge. First, PlanetP concentrates on content-based querying for information retrieval and assumes that the unit of storage is a snippet of XML, allowing it to index arbitrary data for search and retrieval, regardless of the applications used to create and manipulate the data. Second, PlanetP adopts a P2P approach, avoiding centralization of storage and indexing. This makes PlanetP particularly suitable for information sharing among ad hoc groups of users, each of which may have to manage data distributed across multiple devices. PlanetP is targeted for groups of up to 1000 users; results from studying communities of 100-200 peers running on a cluster of PCs indicates that PlanetP should scale well to the 1000-member threshold. Finally, we describe BreezeFS, a semantic file system that we have implemented to validate PlanetP’s utility.Technical report DCS-TR-46
Increased Enrichment and Generation of Isogenic Lines Using a Transient Reporter for Editing Enrichment
No full textabstract: Alzheimer’s disease (AD) affects over 5 million individuals each year in the United States. Furthermore, most cases of AD are sporadic, making it extremely difficult to model and study in vitro. CRISPR/Cas9 and base editing technologies have been of recent interest because of their ability to create single nucleotide edits at nearly any genomic sequence using a Cas9 protein and a guide RNA (sgRNA). Currently, there is no available phenotype to differentiate edited cells from unedited cells. Past research has employed fluorescent proteins bound to Cas9 proteins to attempt to enrich for edited cells, however, these methods are only reporters of transfection (RoT) and are no indicative of actual base-editing occurring. Thus, this study proposes a transient reporter for editing enrichment (TREE) and Cas9-mediated adenosine TREE (CasMasTREE) which use plasmids to co-transfect with CRISPR/Cas9 technologies to serve as an indicator of base-editing. Specifically, TREE features a blue fluorescent protein (BFP) mutant that, upon a C-T conversion, changes the emission spectrum to a green fluorescent protein (GFP). CasMasTREE features a mCherry and GFP protein separated by a stop codon which can be negated using an A-G conversion. By employing a sgRNA that targets one of the TREE plasmids and at least one genomic site, cells can be sorted for GFP(+) cells. Using these methods, base-edited isogenic hiPSC line generation using TREE (BIG-TREE) was created to generate isogenic hiPSC lines with AD-relevant edits. For example, BIG-TREE demonstrates the capability of converting Apolipoprotein E (APOE), a gene associated with AD-risk development, wildtype (3/3) into another isoform, APOE2/2, to create isogenic hiPSC lines. The capabilities of TREE are vast and can be applied to generate various models of diseases with specific genomic edits.Dissertation/ThesisMasters Thesis Biomedical Engineering 202
Distributionally Robust Inverse Covariance Estimation: The Wasserstein Shrinkage Estimator
No full textWe introduce a distributionally robust maximum likelihood estimation model with a Wasserstein ambiguity set to infer the inverse covariance matrix of a p-dimensional Gaussian random vector from n independent samples. The proposed model minimizes the worst case (maximum) of Stein’s loss across all normal reference distributions within a prescribed Wasserstein distance from the normal distribution characterized by the sample mean and the sample covariance matrix. We prove that this estimation problem is equivalent to a semidefinite program that is tractable in theory but beyond the reach of general-purpose solvers for practically relevant problem dimensions p. In the absence of any prior structural information, the estimation problem has an analytical solution that is naturally interpreted as a nonlinear shrinkage estimator. Besides being invertible and well conditioned even for p > n, the new shrinkage estimator is rotation equivariant and preserves the order of the eigenvalues of the sample covariance matrix. These desirable properties are not imposed ad hoc but emerge naturally from the underlying distributionally robust optimization model. Finally, we develop a sequential quadratic approximation algorithm for efficiently solving the general estimation problem subject to conditional independence constraints typically encountered in Gaussian graphical models.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Team Peyman Mohajerin EsfahaniTeam Bart De Schutte
Investigating the roles of microbial immigration in wastewater treatment processes
Full text linkMicrobial communities are groups of microorganisms co-occurring and interacting in an ecosystem. The assembly of a community could be determined by multiple mechanisms, such as competition, niche differentiation, death, birth, and immigration. Among them, microbial immigration describes the process of microorganisms travelling from an upstream to a downstream community. It has been widely observed in natural and engineered ecosystems, such as lakes, rivers, drinking water treatment distribution systems, and wastewater treatment processes. Immigration can play important roles in biological wastewater treatment because different bioreactors are physically connected, and the flux of biomass can be higher than those in natural systems. However, currently available methods do not differentiate active and inactive immigrants, which poses a challenge to accurately quantifying immigration’s contribution to the assembly and function of the downstream community.
In this dissertation, an ecogenomics-based mass balance (EGMB) approach is developed and applied to evaluate microbial activity and quantify the contribution of immigration in wastewater treatment processes. Chapter 1 reviewed the concept of microbial community assembly and the phenomenon of immigration in various ecosystems, including natural environments, engineered environments, and human microbiome. Methods that were commonly used to quantify the roles of immigration were introduced and their limitations were identified. The EGMB approach was briefly introduced and applied to anaerobic digestion (AD) as the model system to study the roles of microbial immigration.
Chapter 2 describes the investigation microbial immigration from one wastewater treatment plant (WWTP), i.e., Stickney Water Reclamation Plant that was one of the largest WWTPs in the world. The results revealed that around 25% of the microbial populations in the Stickney’s AD were inactive immigrants introduced by the feed sludge. They were primarily aerobic microorganisms had negative growth rates, in contrast to native AD populations that were obligate anaerobes and had positive growth rates. The presence of these immigration-resulted residue populations led to the fact that digestion efficiency can never reach 100%.
Chapter 3 expands the investigation of immigration to the global AD microbiome. Fifty- one full-scale municipal WWTPs were sampled and analyzed using 16S rRNA gene sequencing. It was found that feed sludge introduced immigrants were ubiquitously present in AD microbiome, which has been overlooked by previous studies. On the other hand, the abundances of immigrants varied significantly from less than 1% of the total AD populations to over 30%, which was affected by operation conditions such as pretreatment and operation temperature.
In Chapter 4, genomics-guided batch experiments were conducted to shed lights on the activities of immigrants in AD. Metagenomics and metatranscriptomics analyses were used to demonstrate that feed sludge-associated immigrants were capable of anaerobic respiration using nitrate, nitrite, sulfate, and sulfur. When these electron acceptors were added to fresh AD sludge, populations with stimulated growth based on the measurement of rRNA and mRNA abundance were observed to match those identified by metagenomics. Anaerobic respiration was further detected to be prevalent in full-scale ADs but represented a very minor process compared methanogenesis. These microbial populations using electron acceptors were observed with negative growth rates in Chapter 2. With the successful identification of inactive immigrants, it also allows to efficiently pinpoint native AD populations that actively contribute to the digestion process, such as those capable of anaerobic amino acids degradation.
Chapter 5 and Chapter 6 examines the key amino-acid degraders in using continuous enrichment with single amino acids as the substrates and AD sludge as the inoculum. In Chapter 5, a clear community shift between short-term and long-term enrichment was observed along a time course of 18 months. Uncultured populations related to the order Bacteroidales were observed to be predominant (>20% 16S rRNA abundance) in the short-term enrichment, but were competed out (50) that encode peptidase were also highly expressed, suggesting a proteolytic lifestyle compared to cultured amino acids degraders that might rely on monomer substrates. Finally, these proteolytic amino acids degraders were found to be prevalent and active in full-scale anaerobic digesters, indicating their important ecological roles in protein degradation in the native habitats.
Chapter 7 investigates microbial immigration in an industrial wastewater treatment process configured with an upper-flow anaerobic sludge blanket reactor followed by an activated sludge process. Microbial immigrants were shown to have low abundance in the downstream activated sludge, in contrast to most ADs studied in Chapter 2 and Chapter 3. Moreover, a machine learning tool revealed that the change of environmental parameters had weaker impacts on inactive immigrants than on active community members. The observation was consistent with the results that immigrants had negative growth rate and were less active in the downstream environment.
Chapter 8 summarizes the key findings of this dissertation and discusses the implication to ecological theories, environmental researches, and engineering applications. Multiple limitations of the methods are identified and further research directions are discussed. Overall, the findings described in this dissertation demonstrate that the EGMB approach is effective in quantifying microbial activity in a complex ecosystem, and elucidate the roles of immigration in community assembly. In the case of full-scale ADs, the findings in this dissertation, for the first time, reveal that microbial immigrants associated with feed sludge represents a significant portion of the AD microbiome. Majority of them are not actively participating in the digestion process but a small fraction can serve as seed populations and possibly maintain the stability of the AD process. In addition to drawing the attention to the overlooked roles of microbial immigration in wastewater treatment processes, the EGMB approach and the findings can be applied to a variety of environments, where the roles of microbial immigration remain to be further characterized.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2022-08-01The student, Ran Mei, accepted the attached license on 2020-06-08 at 09:29.The student, Ran Mei, submitted this Dissertation for approval on 2020-06-08 at 09:48.This Dissertation was approved for publication on 2020-06-11 at 10:42.DSpace SAF Submission Ingestion Package generated from Vireo submission #15436 on 2020-10-02 at 15:49:10Made available in DSpace on 2020-10-07T22:48:05Z (GMT). No. of bitstreams: 2
MEI-DISSERTATION-2020.pdf: 23653582 bytes, checksum: e228513340dcf99ed9ca544ae8e5d3cc (MD5)
LICENSE.txt: 4204 bytes, checksum: 2b90c416fb415e3e7c5cee3b1bbeafd2 (MD5)
Previous issue date: 2020-06-11Embargo set by: Seth Robbins for item 116286
Lift date: 2022-10-07T22:48:14Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 116286
Lift date: 2022-10-07T22:50:13Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemAuthor requested closed access (OA after 2yrs) in Vireo ETD systemLimite
- …
