bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
rv1184c
Locus Encodes Chp2, an Acyltransferase in Mycobacterium tuberculosis Polyacyltrehalose Lipid Biosynthesis
Authors: Touchette Megan H. , Holsclaw Cynthia M. , Previti Mary L. , Solomon Viven C. , Leary Julie A. , Bertozzi Carolyn R. , Seeliger Jessica C. 
Published: October 2014

ABSTRACT

Trehalose glycolipids are found in many bacteria in the suborder
Corynebacterineae
, but methyl-branched acyltrehaloses are exclusive to virulent species such as the human pathogen
Mycobacterium tuberculosis
. In
M. tuberculosis
, the acyltransferase PapA3 catalyzes the formation of diacyltrehalose (DAT), but the enzymes responsible for downstream reactions leading to the final product, polyacyltrehalose (PAT), have not been identified. The PAT biosynthetic gene locus is similar to that of another trehalose glycolipid, sulfolipid 1. Recently, Chp1 was characterized as the terminal acyltransferase in sulfolipid 1 biosynthesis. Here we provide evidence that the homologue Chp2 (Rv1184c) is essential for the final steps of PAT biosynthesis. Disruption of
chp2
led to the loss of PAT and a novel tetraacyltrehalose species, TetraAT, as well as the accumulation of DAT, implicating Chp2 as an acyltransferase downstream of PapA3. Disruption of the putative lipid transporter MmpL10 resulted in a similar phenotype. Chp2 activity thus appears to be regulated by MmpL10 in a relationship similar to that between Chp1 and MmpL8 in sulfolipid 1 biosynthesis. Chp2 is localized to the cell envelope fraction, consistent with its role in DAT modification and possible regulatory interactions with MmpL10. Labeling of purified Chp2 by an activity-based probe was dependent on the presence of the predicted catalytic residue Ser141 and was inhibited by the lipase inhibitor tetrahydrolipstatin (THL). THL treatment of
M. tuberculosis
resulted in selective inhibition of Chp2 over PapA3, confirming Chp2 as a member of the serine hydrolase superfamily. Efforts to produce
in vitro
reconstitution of acyltransferase activity using straight-chain analogues were unsuccessful, suggesting that Chp2 has specificity for native methyl-branched substrates.
Where To Begin? Mapping Transcription Start Sites Genome-Wide in Escherichia coli
Authors: Wade Joseph T. 
Published: October 2014

ABSTRACT

Recent genome-wide studies of bacterial transcription have revealed large numbers of promoters located inside genes. In this issue of the
Journal of Bacteriology
,
Thomason and colleagues
(J. Bacteriol. 197:18–28, 2015, doi:
10.1128/JB.02096-14
) map transcription start sites in
Escherichia coli
on an unprecedented scale. This work provides important insights into the regulation of transcripts that initiate inside genes and sources of variability between studies aimed at identifying these RNAs.
A novel method of adverse event detection can accurately identify venous thromboembolisms (VTEs) from narrative electronic health record data
Authors: Rochefort Christian M , Verma Aman D , Eguale Tewodros , Lee Todd C , Buckeridge David L 
Published: October 2014

Abstract
Background Venous thromboembolisms (VTEs), which include deep vein thrombosis (DVT) and pulmonary embolism (PE), are associated with significant mortality, morbidity, and cost in hospitalized patients. To evaluate the success of preventive measures, accurate and efficient methods for monitoring VTE rates are needed. Therefore, we sought to determine the accuracy of statistical natural language processing (NLP) for identifying DVT and PE from electronic health record data.
Methods We randomly sampled 2000 narrative radiology reports from patients with a suspected DVT/PE in Montreal (Canada) between 2008 and 2012. We manually identified DVT/PE within each report, which served as our reference standard. Using a bag-of-words approach, we trained 10 alternative support vector machine (SVM) models predicting DVT, and 10 predicting PE. SVM training and testing was performed with nested 10-fold cross-validation, and the average accuracy of each model was measured and compared.
Results On manual review, 324 (16.2%) reports were DVT-positive and 154 (7.7%) were PE-positive. The best DVT model achieved an average sensitivity of 0.80 (95% CI 0.76 to 0.85), specificity of 0.98 (98% CI 0.97 to 0.99), positive predictive value (PPV) of 0.89 (95% CI 0.85 to 0.93), and an area under the curve (AUC) of 0.98 (95% CI 0.97 to 0.99). The best PE model achieved sensitivity of 0.79 (95% CI 0.73 to 0.85), specificity of 0.99 (95% CI 0.98 to 0.99), PPV of 0.84 (95% CI 0.75 to 0.92), and AUC of 0.99 (95% CI 0.98 to 1.00).
Conclusions Statistical NLP can accurately identify VTE from narrative radiology reports.
The long term results of vertebral artery ostium stenting in a single center
Authors: Sun Xuan , Ma Ning , Wang Bo , Mo Dapeng , Gao Feng , Xu Xiaotong , Liu Lian , Song Ligang , Miao Zhongrong 
Published: October 2014

Background and purposeThe long term results of vertebral artery ostium (VAO) stenting remain uncertain. We sought to evaluate the incidence and risk factors for recurrent ischemic events on long term follow-up in patients who have undergone VAO stenting.Methods190 consecutive patients who had undergone a total of 202 stenting procedures for symptomatic atherosclerotic VAO stenosis between January 2011 and December 2012 were screened. Baseline demographics of the patients and morphological features of VAO were recorded. The primary outcome events analyzed included recurrent transient ischemic attack (TIA), stroke, and vascular related mortality. Risk factors for these recurrent events were identified. Other outcome events analyzed included in-stent restenosis (ISR) ≥50% and stent fracture noted on follow-up.ResultsOf the 188 patients with available follow-up data (mean follow-up period 16.7 months), 34 patients suffered recurrent TIAs (18.1%); none had stroke or death. 40 patients were found to have ISR (21.2%) and nine patients had stent fracture (4.7%). Patients with recurrent events were significantly more likely to have ISR, stent fracture, vessel tortuosity, and hyperlipidemia than patients without recurrent events.ConclusionsStenting for VAO stenosis seems to be safe and efficacious. The majority of recurrent events were TIAs, which may be related to ISR, stent fracture, vessel tortuosity, and hyperlipidemia.
Mesenchymal stem cells: mechanisms and role in bone regeneration
Authors: Qin Yunhao , Guan Junjie , Zhang Changqing 
Published: October 2014

Abstract
Stimulating bone growth and regeneration, especially in patients with delayed union or non-union of bone, is a challenge for orthopaedic surgeons. Treatments employed for bone regeneration are based on the use of cells, biomaterials and factors. Among these therapies, cell treatment with mesenchymal stem cells (MSCs) has a number of advantages as MSCs: (1) are multipotent cells that can migrate to sites of injury; (2) are capable of suppressing the local immune response; and (3) are available in large quantities from the patients themselves. MSC therapies have been used for stimulating bone regeneration in animal models and in patients. Methods of application range from direct MSC injection, seeding MSCs on synthetic scaffolds, the use of gene-modified MSCs, and hetero-MSCs application. However, only a small number of these cell-based strategies are in clinical use, and none of these treatments has become the gold standard treatment for delayed or non-union of bone.
Fast Compressed Tries through Path Decompositions
Authors: Grossi Roberto , Ottaviano Giuseppe 
Published: October 2014

Tries are popular data structures for storing a set of strings, where common prefixes are represented by common root-to-node paths. More than 50 years of usage have produced many variants and implementations to overcome some of their limitations. We explore new succinct representations of path-decomposed tries and experimentally evaluate the corresponding reduction in space usage and memory latency, comparing with the state of the art. We study the following applications: compressed string dictionary and monotone minimal perfect hash for strings.
In compressed string dictionary, we obtain data structures that outperform other state-of-the-art compressed dictionaries in space efficiency while obtaining predictable query times that are competitive with data structures preferred by the practitioners. On real-world datasets, our compressed tries obtain the smallest space (except for one case) and have the fastest lookup times, whereas access times are within 20% slower than the best-known solutions.
In monotone minimal perfect hash for strings, our compressed tries perform several times faster than other trie-based monotone perfect hash functions while occupying nearly the same space. On real-world datasets, our tries are approximately 2 to 5 times faster than previous solutions, with a space occupancy less than 10% larger.
SCORPIO
Authors: Daya Bhavya K. , Chen Chia-Hsin Owen , Subramanian Suvinay , Kwon Woo-Cheol , Park Sunghyun , Krishna Tushar , Holt Jim , Chandrakasan Anantha P. , Peh Li-Shiuan 
Published: October 2014

In the many-core era, scalable coherence and on-chip interconnects are crucial for shared memory processors. While snoopy coherence is common in small multicore systems, directory-based coherence is the de facto choice for scalability to many cores, as snoopy relies on ordered interconnects which do not scale. However, directory-based coherence does not scale beyond tens of cores due to excessive directory area overhead or inaccurate sharer tracking. Prior techniques supporting ordering on arbitrary unordered networks are impractical for full multicore chip designs
We present SCORPIO, an ordered mesh Network-on-Chip (NoC) architecture with a separate fixed-latency, bufferless network to achieve distributed global ordering. Message delivery is decoupled from the ordering, allowing messages to arrivein any order and at any time, and still be correctly ordered. The architecture is designed to plug-and-play with existing multicore IP and with practicality, timing, area, and power as top concerns. Full-system 36 and 64-core simulations on SPLASH-2 and PARSEC benchmarks show an average application runtime reduction of 24.1% and 12.9%, in comparison to distributed directory and AMD HyperTransport coherence protocols, respectively
The SCORPIO architecture is incorporated in an 11 mm-by-13mm chip prototype, fabricated in IBM 45nm SOI technology, comprising 36 Freescale e200 Power ArchitectureTMcores with private L1 and L2 caches interfacing with the NoC via ARM AMBA, along with two Cadence on-chip DDR2 controllers. The chip prototype achieves a post synthesis operating frequency of 1 GHz (833MHz post-layout) with an estimated power of 28.8W (768mW per tile), while the network consumes only 10% of tile area and 19 % of tile power.
Avoiding core's DUE & SDC via acoustic wave detectors and tailored error containment and recovery
Authors: Upasani Gaurang , Vera Xavier , González Antonio 
Published: October 2014

The trend of downsizing transistors and operating voltage scaling has made the processor chip more sensitive against radiation phenomena making soft errors an important challenge. New reliability techniques for handling soft errors in the logic and memories that allow meeting the desired failures-in-time (FIT) target are key to keep harnessing the benefits of Moore's law. The failure to scale the soft error rate caused by particle strikes, may soon limit the total number of cores that one may have running at the same time
This paper proposes a light-weight and scalable architecture to eliminate silent data corruption errors (SDC) and detected unrecoverable errors (DUE) of a core. The architecture uses acoustic wave detectors for error detection. We propose to recover by confining the errors in the cache hierarchy, allowing us to deal with the relatively long detection latencies. Our results show that the proposed mechanism protects the whole core (logic, latches and memory arrays) incurring performance overhead as low as 0.60%
SleepScale
Authors: Liu Yanpei , Draper Stark C. , Kim Nam Sung 
Published: October 2014

Power consumption in data centers has been growing significantly in recent years. To reduce power, servers are beingequipped with increasingly sophisticated power management mechanisms. Different mechanisms offer dramatically different trade-offs between power savings and performance penalties. Considering the complexity, variety, and temporallyvarying nature of the applications hosted in a typical data center, intelligently determining which power management policy to use and when is a complicated task.
In this paper we analyze a system model featuring both performance scaling and low-power states. We reveal the interplay between performance scaling and low-power states via intensive simulation and analytic verification. Based on the observations, we present SleepScale, a runtime power management tool designed to efficiently exploit existing power control mechanisms. At run time, SleepScale characterizes power consumption and quality-of-service (QoS) for each lowpower state and frequency setting, and selects the best policy for a given QoS constraint. We evaluate SleepScale using workload traces from data centers and achieve significant power savings relative to conventional power management strategies
Row-buffer decoupling
Authors: O Seongil , Son Young Hoon , Kim Nam Sung , Ahn Jung Ho 
Published: October 2014

Modern DRAM devices for the main memory are structured to have multiple banks to satisfy ever-increasing throughput, energy-efficiency, and capacity demands. Due to tight cost constraints, only one row can be buffered (opened) per bank and actively service requests at a time, while the row must be deactivated (closed) before a new row is stored into the row buffers. Hasty deactivation unnecessarily re-opens rows for otherwise row-buffer hits while hindsight accompanies the deactivation process on the critical path of accessing data for row-buffer misses. The time to (de)activate a row is comparable to the time to read an open row while applications are often sensitive to DRAM latency. Hence, it is critical to make the right decision on when to close a row. However, the increasing number of banks per DRAM device over generations reduces the number of requests per bank. This forces a memory controller to frequently predict when to close a row due to a lack of information on future requests, while the dynamic nature of memory access patterns limits the prediction accuracy
In this paper, we propose a novel DRAM microarchitecture that can eliminate the need for any prediction. First, we identify that precharging the bitlines dominates the deactivate time, while sense amplifiers that work as a row buffer are physically coupled with the bitlines such that a single command precharges both bitlines and sense amplifiers simultaneously. By decoupling the bitlines from the row buffers using isolation transistors, the bitlines can be precharged right after a row becomes activated. Therefore, only the sense amplifiers need to be precharged for a miss in most cases, taking an order of magnitude shorter time than the conventional deactivation process. Second, we show that this row-buffer decoupling enables internal DRAM ?-operations to be separated and recombined, which can be exploited by memory controllers to make the main memory system more energy efficient. Our experiments demonstrate that row-buffer decoupling improves the geometric mean of the instructions per cycle and MIPS2/W by 14% and 29%, respectively, for memory-intensive SPEC CPU2006 applications
OmniOrder
Authors: Qian Xuehai , Sahelices Benjamin , Torrellas Josep 
Published: October 2014

Effective execution of atomic blocks of instructions (also called transactions) can enhance the performance and programmability of multiprocessors. Atomic blocks can be demarcated in software as in Transactional Memory (TM) or dynamically generated by the hardware as in aggressive implementations of strict memory consistency. In most current designs, when two atomic blocks conflict, one is squashed -- a performance loss that is often unnecessary.
To avoid this waste, this paper presents OmniOrder, the first design that efficiently executes conflicting atomic blocks concurrently in a directory-based coherence environment. The idea is to keep only non-speculative data in the caches and, when the cache coherence protocol transfers a line, include in the message the history of speculative updates to the line. The coherence protocol transitions are unmodified. We evaluate OmniOrder with 64-core simulations. In a TM environment, OmniOrder reduces the execution time of the STAMP applications by an average of 18.4% over a scheme that squashes on conflict. In an environment with SC enforcement with speculation, we run 11 programs that implement concurrent algorithms. OmniOrder reduces the programs' execution time by an average of 15.3% relative to a scheme that squashes on conflict. Finally, OmniOrder's communication overhead of transferring the history of speculative updates is negligible
EOLE
Authors: Perais Arthur , Seznec André 
Published: October 2014

Even in the multicore era, there is a continuous demand to increase the performance of single-threaded applications. However, the conventional path of increasing both issue width and instruction window size inevitably leads to the power wall. Value prediction (VP) was proposed in the mid 90's as an alternative path to further enhance the performance of wide-issue superscalar processors. Still, it was considered up to recently that a performance-effective implementation of Value Prediction would add tremendous complexity and power consumption in almost every stage of the pipeline
Nonetheless, recent work in the field of VP has shown that given an efficient confidence estimation mechanism, prediction validation could be removed from the out-of-order engine and delayed until commit time. As a result, recovering from mispredictions via selective replay can be avoided and a much simpler mechanism -- pipeline squashing -- can be used, while the out-of-order engine remains mostly unmodified.
Yet, VP and validation at commit time entails strong constraints on the Physical Register File. Write ports are needed to write predicted results and read ports are needed in order to validate them at commit time, potentially rendering the overall number of ports unbearable. Fortunately, VP also implies that many single-cycle ALU instructions have their operands predicted in the front-end and can be executed in-place, in-order. Similarly, the execution of single-cycle instructions whose result has been predicted can be delayed until commit time since predictions are validated at commit time
Consequently, a significant number of instructions -- 10% to 60% in our experiments -- can bypass the out-of-order engine, allowing the reduction of the issue width, which is a major contributor to both out-of-order engine complexity and register file port requirement. This reduction paves the way for a truly practical implementation of Value Prediction. Furthermore, since Value Prediction in itself usually increases performance, our resulting {Early | Out-of-Order | Late} Execution architecture, EOLE, is often more efficient than a baseline VP-augmented 6-issue superscalar while having a significantly narrower 4-issue out-of-order engine
Implementation of a Pilot Accountable Care Organization Payment Model and the Use of Discretionary and Nondiscretionary Cardiovascular Care
Authors: Colla Carrie H. , Goodney Philip P. , Lewis Valerie A. , Nallamothu Brahmajee K. , Gottlieb Daniel J. , Meara Ellen 
Published: October 2014

Background—
Accountable care organizations (ACOs) seek to reduce growth in healthcare spending while ensuring high-quality care. We hypothesized that accountable care organization implementation would selectively limit the use of discretionary cardiovascular care (defined as care occurring in the absence of indications such as myocardial infarction or stroke), while maintaining high-quality care, such as nondiscretionary cardiovascular imaging and procedures.

Methods and Results—

The intervention group was composed of fee-for-service Medicare patients (n=819 779) from 10 groups participating in a Medicare pilot accountable care organization, the Physician Group Practice Demonstration (PGPD). Matched controls were patients (n=934 621) from nonparticipating groups in the same regions. We compared use of cardiovascular care before (2002–2004) and after (2005–2009) PGPD implementation, studying both discretionary and nondiscretionary carotid and coronary imaging and procedures. Our main outcome measure was the difference in the proportion of patients treated with imaging and procedures among patients of PGPD practices compared with patients in control practices, before and after PGPD implementation (difference-in-difference). For discretionary imaging, the difference-in-difference between PGPD practices and controls was not statistically significant for discretionary carotid imaging (0.17%; 95% confidence interval, –0.51% to 0.85%;
P
=0.595) or discretionary coronary imaging (–0.19%; 95% confidence interval, –0.73% to 0.35%;
P
=0.468). Similarly, the difference-in-difference was also minimal for discretionary carotid revascularization (0.003%; 95% confidence interval, –0.008% to 0.002%;
P
=0.705) and coronary revascularization (–0.02%; 95% confidence interval, –0.11% to 0.07%;
P
=0.06). The difference-in-difference associated with PGPD implementation was also essentially 0 for nondiscretionary cardiovascular imaging or procedures.

Conclusion—
Implementation of a pilot accountable care organization did not limit the use of discretionary or nondiscretionary cardiovascular care in 10 large health systems.
Trends in the Clinical and Pathological Characteristics of Cardiac Rupture in Patients With Acute Myocardial Infarction Over 35 Years
Authors: Honda Satoshi , Asaumi Yasuhide , Yamane Takafumi , Nagai Toshiyuki , Miyagi Tadayoshi , Noguchi Teruo , Anzai Toshihisa , Goto Yoichi , Ishihara Masaharu , Nishimura Kunihiro , Ogawa Hisao , Ishibashi‐Ueda Hatsue , Yasuda Satoshi 
Published: October 2014

Background

There is little known about whether the clinical and pathological characteristics and incidence of cardiac rupture (
CR
) in patients with acute myocardial infarction (
AMI
) have changed over the years.

Methods and Results

The incidence and clinical characteristics of
CR
were investigated in patients with
AMI
, who were divided into 3 cohorts: 1977–1989, 1990–2000, and 2001–2011. Of a total of 5699 patients, 144 were diagnosed with
CR
and 45 survived. Over the years, the incidence of
CR
decreased (1977–1989, 3.3%; 1990–2000, 2.8%; 2001–2011, 1.7%;
P
=0.002) in association with the widespread adoption of reperfusion therapy. The mortality rate of
CR
decreased (1977–1989, 90%; 1990–2000, 56%; 2001–2011, 50%;
P
=0.002) in association with an increase in the rate of emergent surgery. In multivariable analysis, first myocardial infarction, anterior infarct, female sex, hypertension, and age >70 years were significant risk factors for
CR
, whereas impact of hypertension on
CR
was weaker from 2001 to 2011. Primary percutaneous coronary intervention (
PPCI
) was a significant protective factor against
CR
. In 64 autopsy cases with
CR
, myocardial hemorrhage occurred more frequently in those who underwent
PPCI
or fibrinolysis than those who did not receive reperfusion therapy (no reperfusion therapy, 18.0%; fibrinolysis, 71.4%;
PPCI
, 83.3%;
P
=0.001).

Conclusions

With the development of medical treatment, the incidence and mortality rate of
CR
have decreased. However, first myocardial infarction, anterior infarct, female sex, and old age remain important risk factors for
CR
. Adjunctive cardioprotection against reperfusion‐induced myocardial hemorrhage is emerging in the current
PPCI
era.