搜索结果：read-only

Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely Escherichia coli , Klebsiella pneumoniae , Pseudomonas aeruginosa and Staphylococcus aureus , and nine genetically diverse E. coli bloodstream infection-associated isolates from different phylogroups and sequence types, both with and without BSA. These sequences were de novo assembled and compared against Illumina-corrected reference genomes. In this small evaluation of 13 isolates we found that nanopore long-read-only R10.4.1/kit 14 assemblies with updated basecallers trained using bacterial methylated DNA produce accurate assemblies with ≥40×depth, sufficient to be cost-effective compared with hybrid ONT/Illumina sequencing in our setting.

In recent years, prompt tuning has proven effective in adapting pre-trained vision-language models to downstream tasks. These methods aim to adapt the pre-trained models by introducing learnable prompts while keeping pretrained weights frozen. However, learnable prompts can affect the internal representation within the self-attention module, which may negatively impact performance variance and generalization, especially in data-deficient settings. To address these issues, we propose a novel approach, Read-only Prompt Optimization (RPO). RPO leverages masked attention to prevent the internal representation shift in the pre-trained model. Further, to facilitate the optimization of RPO, the read-only prompts are initialized based on special tokens of the pre-trained model. Our extensive experiments demonstrate that RPO outperforms CLIP and CoCoOp in base-to-new generalization and domain generalization while displaying better robustness. Also, the proposed method achieves better generalization on extremely data-deficient settings, while improving parameter efficiency and computational overhead. Code is available at https://github.com/mlvlab/RPO.

Internet users increasingly rely on publicly available data for everything from software installation to investment decisions. Unfortunately, the vast majority of public content on the Internet comes with no integrity or authenticity guarantees. This paper presents the self-certifying read-only file system, a content distribution system providing secure, scalable access to public, read-only data.The read-only file system makes the security of published content independent from that of the distribution infrastructure. In a secure area (perhaps off-line), a publisher creates a digitally signed database out of a file system's contents. The publisher then replicates the database on untrusted content-distribution servers, allowing for high availability.The read-only file system avoids performing any cryptographic operations on servers and keeps the overhead of cryptography low on clients, allowing servers to scale to a large number of clients. Measurements of an implementation show that an individual server running on a 550-Mhz Pentium III with FreeBSD can support 1,012 connections per second and 300 concurrent clients compiling a large software package.

Typical concurrency control protocols for atomic actions, such as two-phase locking, perform poorly for long read-only actions. We present four new concurrency control protocols that eliminate all interference between read-only actions and update actions, and thus offer significantly improved performance for read-only actions. The protocols work by maintaining multiple versions of the system state; read-only actions read old versions, while update actions manipulate the most recent version. We focus on the problem of managing the storage required for old versions in a distributed system. One of the protocols uses relatively little space, but has a potentially significant communication cost. The other protocols use more space, but may be cheaper in terms of communication.

Scalable storage systems where data is sharded across many machines are now the norm for Web services as their data has grown beyond what a single machine can handle. Consistently reading data across different shards requires transactional isolation for the reads. Yet a Web service may read from its data store hundreds or thousands of times for a single page load and must minimize read latency to keep response times low. Examining the read-only transaction algorithms for many recent academic and industrial scalable storage systems suggests there is a tradeoff between their power--expressed as the consistency they provide and their compatibility with other types of transactions--and their latency.We show that this tradeoff is fundamental by proving the SNOW Theorem, an impossibility result that states that no read-only transaction algorithm can provide both the lowest latency and the highest power. We then use the tight boundary from the theorem to guide the design of new read-only transaction algorithms for two scalable storage systems, COPS and Rococo. We implement our new algorithms and then evaluate them to demonstrate they provide lower latency for read-only transactions and to understand their impact on overall throughput.

Multiple versions of data are used in database systems to increase concurrency. The higher concurrency results since read-only transactions can be executed without any concurrency control overhead and, therefore, read-only transactions do not interfere with the execution of update transactions. Availability of data in a distributed environment is improved by data replication. We propose a protocol for managing data in a replicated multiversion environment, where execution of read-only transactions or queries becomes completely independent of the underlying concurrency control and replica control mechanisms, and the data availability for read-only transactions increases significantly since they can be executed as long as any one copy of the object is available in the system. In order to validate the feasibility of our approach, we developed a simple prototype to measure the performance improvement in the response times of queries. The results clearly establish the viability of the approach as a useful paradigm for the design of efficient and fault-tolerant distributed database systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Snapshot Isolation (SI), is a multi-version concurrency control algorithm introduced in [BBGMOO95] and later implemented by Oracle. SI avoids many concurrency errors, and it never delays read-only transactions. However it does not guarantee serializability. It has been widely assumed that, under SI, read-only transactions always execute serializably provided the concurrent update transactions are serializable. The reason for this is that all SI reads return values from a single instant of time when all committed transactions have completed their writes and no writes of non-committed transactions are visible. This seems to imply that read-only transactions will not read anomalous results so long as the update transactions with which they execute do not write such results. In the current note, however, we exhibit an example contradicting these assumptions: it is possible for an SI history to be non-serializable while the sub-history containing all update transactions is serializable.

The establishment of an online community is widely held as the most important prerequisite for successful course completion and depends on an interaction between a peer group and a facilitator. Beaudoin reasoned that online students sometimes engage and learn even when not taking part in online discussions. The context of this study was an online course on web-based education for a Masters degree in computer-integrated education at the University of Pretoria. We used a mixed methodology approach to investigate how online activity and discussion postings relate to learning and course completion. We also investigated how student collaborative behaviour and integration into the community related to success. Although the quantitative indices measured showed highly significant differences between the stratifications of student performance, there were notable exceptions unexplained by the trends. The class harboured a well-functioning online learning community. We also uncovered the discontent students in the learning community felt for invisible students who were absent without reason from group assignments or who made shallow and insufficient contributions. Student online visibility and participation can take many forms, like read-only participants who skim over or deliberately harvest others' discussions. Other students can be highly visible without contributing. Students who anticipate limited access due to poor connectivity, high costs or other reasons can manage their log-in time effectively and gain maximum benefit. Absent and seldom contributing students risk forsaking the benefits of the virtual learning community. High quality contributions rather than quantity builds trust among mature students. We suggest how to avoid read-only-participation: communicate the required number of online classroom postings; encourage submission of high quality, thoughtful postings; grade discussions and give formative feedback; award individual grades for group projects and rotate members of groups; augment facilitator communication with Internet-independent media to convey important information. Read-only-participants disrupt the formation of a virtual community of learners and compromise learning.

We present efficient and flexible methods which permit read-only transactions that do not mind reading a possibly slightly old, but still consistent, version of the data base to execute without acquiring locks. This approach avoids the undesirable interferences between such queries and the typically shorter update transactions that cause unnecessary and costly delays. Indexed access by such queries is also supported, unlike by the earlier methods. Old versions of records are maintained only in a transient fashion. Our methods are characterized by their flexibility (number of versions maintained and the timing of version switches, supporting partial rollbacks, and different recovery and buffering methods) and their efficiency (logging, garbage collection, version selection, and incremental, record-level versioning). Distributed data base environments are also supported, including commit protocols with the read-only optimization. We also describe efficient methods for garbage collecting unneeded older versions.

This paper presents an efficient scheme for eliminating conflicts between distributed read-only transactions and distributed update transactions, thereby reducing synchronization delays. The scheme makes use of a multiversion mechanism in order to guarantee that distributed read-only transactions see semantically consistent snap-shots of the database, that they never have to be rolled-back due to their late arrival at retrieval sites, and that they inflict minimal synchronization delays on concurrent update transactions. Proof that the presented scheme guarantees semantic consistency is provided. Two important by-products of this scheme are that the recovery from transaction and system failures is greatly simplified and the taking of database dumps also can be accommodated while leaving the database on-line.

BACKGROUND: The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing. RESULTS: Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome. CONCLUSIONS: Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem. Video Abstract.

Recently, push-based delivery has attracted considerable attention as a means of disseminating information to large client populations in both wired and wireless settings. We address the problem of ensuring the consistency and currency of client read-only transactions in the presence of updates. To this end, additional control information is broadcast. A suite of methods is proposed that vary in the complexity and volume of the control information transmitted and subsequently differ in response times, degrees of concurrency, and space and processing overheads. The proposed methods are combined with caching to improve query latency. The relative advantages of each method are demonstrated through both simulation results and qualitative arguments. Read-only transactions are processed locally at the client without contacting the server and thus the proposed approaches are scalable, i.e., their performance is independent of the number of clients.

暂无摘要（点击查看原文获取完整内容）

In this paper, we investigate the approach of using separate algorithms to process read-only transactions in real-time systems. A read-only transaction (ROT) is a transaction that only reads, but does not update any data item. Since there is a significant proportion of ROTs in several real-time systems, it is important to investigate how to process ROTs effectively. Using an algorithm to process ROTs separately from update transactions may reduce the interference between ROTs and update transactions. This reduced interference alleviates the impact of concurrency control on real-time priority-driven scheduling and improves the timeliness of the system. Moreover, we explore the different consistency requirements of ROTs. Particularly, we define a weaker form of consistency, view consistency, which allows ROTs to perceive different serialization order of update transactions. While view consistency permits non-serializability, ROTs are still ensured to see consistent data. We propose two robust algorithms for different consistency requirements of ROTs. The two algorithms are robust in the sense that they can be used in a compatible way so that a real-time system can provide different consistent data for different applications. The performance of two algorithms was examined through a series of simulation studies. The simulation results show that the two algorithms outperform the high-priority two-phase locking protocol.

Multilevel run-length-limited (ML-RLL) recording technology is employed to increase the capacity of the read-only disc with no change on optical or mechanical units. 4L-RLL recording on read-only disc has been implemented with minimum recorded mark length same as that in conventional digital versatile disc (DVD). The capacity of a double layer DVD disc with 4L-RLL (2, 10) modulation reaches 15 GB. Experimental results show that the ratio of the standard deviation of noise to the dynamic range of readout signal amplitude is lower than 4.53%, which means that the requirement of signal detection for 4L-RLL can be satisfied.

The history of read-only memories in telephone and digital-computer systems is briefly surveyed and their similarity to logic circuits demonstrated by reference to the diode matrix. A description is given of the principles of operation and important characteristics of the following types of read-only memory: capacitor matrix, mutual-inductance matrix, transformer (Dimond ring) type, square-loop ferrite-core matrix, permanent-magnet twistor matrix, flying-spot store and electroluminescent matrix. These memories are briefly compared.

A model for exposing and developing photoresist using the reaction mechanism of physics and the chemistry of resist is built, and the micropatterns of recording marks on a stamper are calculated. Compared with our experimental results, the deviation of pit width in simulation is less than 8%. When the width of recording marks is varied by modulating laser power during exposure, a multilevel (ML) read-only disk can be achieved as a result of the corresponding readout signal. Experimental results show that an 8-level read-only optical disk can be realized. The model of mastering serves well for the development of novel ML disks in which the integration of conventional run-length deviations technologies can greatly increase recording density.

A method for designing the read-only memories (ROM's) needed for multiplication using logarithms is developed. By defining the word length of the multiplicand, multiplier, and product as n bits and the word length of -the rounded logarithms as m bits, design curves are given that allow various values of n and m to be selected for a given multiplier accuracy. Then a table is used to determine, which combination results in an implementation with the least number of bits.

Coherent interlayer cross talk and stray-light intensity of multilayer read-only-memory (ROM) optical disks are investigated. From results of scalar diffraction analyses, we conclude that layer separations above 10 microm are preferred in a system using a 0.85 numerical aperture objective lens in terms of signal quality and stability in focusing control. Disk structures are optimized to prevent signal deterioration resulting from multiple reflections, and appropriate detectors are determined to maintain acceptable stray-light intensity. In the experiment, quadrilayer and octalayer high-density ROM disks are prepared by stacking UV-curable films onto polycarbonate substrates. Data-to-clock jitters of < or = 7% demonstrate the feasibility of multilayer disk storage up to 200 Gbytes.