bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing memory access latency with asymmetric DRAM bank organizations
Authors: Son Young Hoon , Seongil O. , Ro Yuhwan , Lee Jae W. , Ahn Jung Ho 
Published: July 2013

DRAM has been a de facto standard for main memory, and advances in process technology have led to a rapid increase in its capacity and bandwidth. In contrast, its random access latency has remained relatively stagnant, as it is still around 100 CPU clock cycles. Modern computer systems rely on caches or other latency tolerance techniques to lower the average access latency. However, not all applications have ample parallelism or locality that would help hide or reduce the latency. Moreover, applications' demands for memory space continue to grow, while the capacity gap between last-level caches and main memory is unlikely to shrink. Consequently, reducing the main-memory latency is important for application performance. Unfortunately, previous proposals have not adequately addressed this problem, as they have focused only on improving the bandwidth and capacity or reduced the latency at the cost of significant area overhead.
We propose asymmetric DRAM bank organizations to reduce the average main-memory access latency. We first analyze the access and cycle times of a modern DRAM device to identify key delay components for latency reduction. Then we reorganize a subset of DRAM banks to reduce their access and cycle times by half with low area overhead. By synergistically combining these reorganized DRAM banks with support for non-uniform bank accesses, we introduce a novel DRAM bank organization with center high-aspect-ratio mats called CHARM. Experiments on a simulated chip-multiprocessor system show that CHARM improves both the instructions per cycle and system-wide energy-delay product up to 21% and 32%, respectively, with only a 3% increase in die area.
ZSim
Authors: Sanchez Daniel , Kozyrakis Christos 
Published: July 2013

Architectural simulation is time-consuming, and the trend towards hundreds of cores is making sequential simulation even slower. Existing parallel simulation techniques either scale poorly due to excessive synchronization, or sacrifice accuracy by allowing event reordering and using simplistic contention models. As a result, most researchers use sequential simulators and model small-scale systems with 16-32 cores. With 100-core chips already available, developing simulators that scale to thousands of cores is crucial.
We present three novel techniques that, together, make thousand-core simulation practical. First, we speed up detailed core models (including OOO cores) with instruction-driven timing models that leverage dynamic binary translation. Second, we introduce bound-weave, a two-phase parallelization technique that scales parallel simulation on multicore hosts efficiently with minimal loss of accuracy. Third, we implement lightweight user-level virtualization to support complex workloads, including multiprogrammed, client-server, and managed-runtime applications, without the need for full-system simulation, sidestepping the lack of scalable OSs and ISAs that support thousands of cores.
We use these techniques to build zsim, a fast, scalable, and accurate simulator. On a 16-core host, zsim models a 1024-core chip at speeds of up to 1,500 MIPS using simple cores and up to 300 MIPS using detailed OOO cores, 2-3 orders of magnitude faster than existing parallel simulators. Simulator performance scales well with both the number of modeled cores and the number of host cores. We validate zsim against a real Westmere system on a wide variety of workloads, and find performance and microarchitectural events to be within a narrow range of the real system.
Protozoa
Authors: Zhao Hongzhou , Shriraman Arrvindh , Kumar Snehasish , Dwarkadas Sandhya 
Published: July 2013

State-of-the-art multiprocessor cache hierarchies propagate the use of a fixed granularity in the cache organization to the design of the coherence protocol. Unfortunately, the fixed granularity, generally chosen to match average spatial locality across a range of applications, not only results in wasted bandwidth to serve an individual thread's access needs, but also results in unnecessary coherence traffic for shared data. The additional bandwidth has a direct impact on both the scalability of parallel applications and overall energy consumption.
In this paper, we present the design of Protozoa, a family of coherence protocols that eliminate unnecessary coherence traffic and match data movement to an application's spatial locality. Protozoa continues to maintain metadata at a conventional fixed cache line granularity while 1) supporting variable read and write caching granularity so that data transfer matches application spatial granularity, 2) invalidating at the granularity of the write miss request so that readers to disjoint data can co-exist with writers, and 3) potentially supporting multiple non-overlapping writers within the cache line, thereby avoiding the traditional ping-pong effect of both read-write and write-write false sharing. Our evaluation demonstrates that Protozoa consistently reduce miss rate and improve the fraction of transmitted data that is actually utilized.
Design space exploration and optimization of path oblivious RAM in secure processors
Authors: Ren Ling , Yu Xiangyao , Fletcher Christopher W. , van Dijk Marten , Devadas Srinivas 
Published: July 2013

Keeping user data private is a huge problem both in cloud computing and computation outsourcing. One paradigm to achieve data privacy is to use tamper-resistant processors, inside which users' private data is decrypted and computed upon. These processors need to interact with untrusted external memory. Even if we encrypt all data that leaves the trusted processor, however, the address sequence that goes off-chip may still leak information. To prevent this address leakage, the security community has proposed ORAM (Oblivious RAM). ORAM has mainly been explored in server/file settings which assume a vastly different computation model than secure processors. Not surprisingly, naïvely applying ORAM to a secure processor setting incurs large performance overheads.
In this paper, a recent proposal called Path ORAM is studied. We demonstrate techniques to make Path ORAM practical in a secure processor setting. We introduce background eviction schemes to prevent Path ORAM failure and allow for a performance-driven design space exploration. We propose a concept called super blocks to further improve Path ORAM's performance, and also show an efficient integrity verification scheme for Path ORAM. With our optimizations, Path ORAM overhead drops by 41.8%, and SPEC benchmark execution time improves by 52.4% in relation to a baseline configuration. Our work can be used to improve the security level of previous secure processors.
SurfNoC
Authors: Wassel Hassan M. G. , Gao Ying , Oberg Jason K. , Huffmire Ted , Kastner Ryan , Chong Frederic T. , Sherwood Timothy 
Published: July 2013

As multicore processors find increasing adoption in domains such as aerospace and medical devices where failures have the potential to be catastrophic, strong performance isolation and security become first-class design constraints. When cores are used to run separate pieces of the system, strong time and space partitioning can help provide such guarantees. However, as the number of partitions or the asymmetry in partition bandwidth allocations grows, the additional latency incurred by time multiplexing the network can significantly impact performance.
In this paper, we introduce SurfNoC, an on-chip network that significantly reduces the latency incurred by temporal partitioning. By carefully scheduling the network into waves that flow across the interconnect, data from different domains carried by these waves are strictly non-interfering while avoiding the significant overheads associated with cycle-by-cycle time multiplexing. We describe the scheduling policy and router microarchitecture changes required, and evaluate the information-flow security of a synthesizable implementation through gate-level information flow analysis. When comparing our approach for varying numbers of domains and network sizes, we find that in many cases SurfNoC can reduce the latency overhead of implementing cycle-level non-interference by up to 85%.
Molecular Pathways: Targeting MYC-induced Metabolic Reprogramming and Oncogenic Stress in Cancer
Authors: Li Bo , Simon M. Celeste 
Published: July 2013

Abstract
MYC is a multifunctional transcription factor that is deregulated in many human cancers. MYC impacts a collaborative genetic program that orchestrates cell proliferation, metabolism, and stress responses. Although the progression of MYC-amplified tumors shows robust dependence on MYC activity, directly targeting MYC as a therapeutic method has proven to be technically difficult. Therefore, alternative approaches are currently under development with a focus on interference with MYC-mediated downstream effects. To fuel rapid cell growth, MYC reprograms cancer cell metabolism in a way that is substantially different from normal cells. The MYC-induced metabolic signature is characterized by enhanced glucose and glutamine uptake, increased lactate production, and altered amino acid metabolism. Targeting MYC-reprogrammed cancer cell metabolism is considered to be promising based on multiple preclinical studies. In addition, the increased biosynthetic demand of MYC-driven tumors coupled with limited nutrient access within tumor microenvironments create multiple levels of oncogenic stress, which can also be used as tumor-specific targets for pharmacologic intervention. Presumably, the best therapeutic strategy for treating MYC-amplified tumors is combined targeting of multiple MYC-mediated pathways, especially those involved in regulating cell proliferation, metabolism, and oncogenic stress. Clin Cancer Res; 19(21); 5835–41. ©2013 AACR.
Reply to “Comments on ‘Current GCMs' Unrealistic Negative Feedback in the Arctic'”
Authors: Boé Julien , Hall Alex , Qu Xin 
Published: July 2013

Abstract
Pithan and Mauritsen argue that the 2009 results of Boé et al. are not consistent with current understanding of the lapse-rate feedback in the Arctic. They also argue that these results arise to an important extent from self-correlation issues. In this response, the authors argue that their results are not inconsistent with current understanding of lapse-rate feedback and demonstrate that the conclusions remain unchanged when all possibilities of self-correlation are excluded.
How Oceanic Oscillation Drives Soil Moisture Variations over Mainland Australia: An Analysis of 32 Years of Satellite Observations*
Authors: Bauer-Marschallinger Bernhard , Dorigo Wouter A. , Wagner Wolfgang , van Dijk Albert I. J. M. 
Published: July 2013

AbstractAustralia is frequently subject to droughts and floods. Its hydrology is strongly connected to oceanic and atmospheric oscillations (climate modes) such as the El Niño–Southern Oscillation (ENSO), Indian Ocean dipole (IOD), and southern annular mode (SAM). A global 32-yr dataset of remotely sensed surface soil moisture (SSM) was used to examine hydrological variations in mainland Australia for the period 1978–2010. Complex empirical orthogonal function (CEOF) analysis was applied to extract independent signals and to investigate their relationships to climate modes. The annual cycle signal represented 46.3% of the total variance and a low but highly significant connection with SAM was found. Two multiannual signals with a lesser share in total variance (6.3% and 4.2%) were identified. The first one had an unstable period of 2–5 yr and reflected an east–west pattern that can be associated with ENSO and SAM but not with IOD. The second one, a 1- to 5-yr oscillation, formed a dipole pattern between the west and north and can be linked to ENSO and IOD. As expected, relationships with ENSO were found throughout the year and are especially strong during southern spring and summer in the east and north. Somewhat unexpectedly, SAM impacts strongest in the north and east during summer and is proposed as the key driver of the annual SSM signal. The IOD explains SSM variations in the north, east, and southeast during spring and also in the west during winter.
Empirical Localization of Observation Impact in Ensemble Kalman Filters
Authors: Anderson Jeffrey , Lei Lili 
Published: July 2013

Abstract
Localization is a method for reducing the impact of sampling errors in ensemble Kalman filters. Here, the regression coefficient, or gain, relating ensemble increments for observed quantity y to increments for state variable x is multiplied by a real number α defined as a localization. Localization of the impact of observations on model state variables is required for good performance when applying ensemble data assimilation to large atmospheric and oceanic problems. Localization also improves performance in idealized low-order ensemble assimilation applications. An algorithm that computes localization from the output of an ensemble observing system simulation experiment (OSSE) is described. The algorithm produces localizations for sets of pairs of observations and state variables: for instance, all state variables that are between 300- and 400-km horizontal distance from an observation. The algorithm is applied in a low-order model to produce localizations from the output of an OSSE and the computed localizations are then used in a new OSSE. Results are compared to assimilations using tuned localizations that are approximately Gaussian functions of the distance between an observation and a state variable. In most cases, the empirically computed localizations produce the lowest root-mean-square errors in subsequent OSSEs. Localizations derived from OSSE output can provide guidance for localization in real assimilation experiments. Applying the algorithm in large geophysical applications may help to tune localization for improved ensemble filter performance.
Which MJO Events Affect North American Temperatures?
Authors: Schreck Carl J. , Cordeira Jason M. , Margolin David 
Published: July 2013

Abstract
Tropical convection from the Madden–Julian oscillation (MJO) excites and amplifies extratropical Rossby waves around the globe. This forcing is reflected in teleconnection patterns like the Pacific–North American (PNA) pattern, and it can ultimately result in temperature anomalies over North America. Previous studies have not explored whether the extratropical response might vary from one MJO event to another. This study proposes a new index, the multivariate PNA (MVP), to identify variations in the extratropical waveguide over the North Pacific and North America that might affect the response to the MJO. The MVP is the first combined EOF of 20–100-day OLR, 850-hPa streamfunction, and 200-hPa streamfunction over the North Pacific and North America. The North American temperature patterns that follow each phase of the MJO change with the sign of the MVP. For example, real-time multivariate MJO (RMM) phase 5 usually leads to warm anomalies over eastern North America. This relationship was only found when the MVP was negative, and it was not associated with El Niño or La Niña. RMM phase 8, on the other hand, usually leads to cold anomalies. Those anomalies only occur if the MVP is positive, which happens somewhat more frequently during La Niña years. Composite analyses based on combinations of the MJO and the MVP show that variability in the Pacific jet and its associated wave breaking play a key role in determining whether and how the MJO affects North American temperatures.
Tornado Probability of Detection and Lead Time as a Function of Convective Mode and Environmental Parameters
Authors: Brotzge Jerald A. , Nelson Steven E. , Thompson Richard L. , Smith Bryan T. 
Published: July 2013

Abstract
The ability to provide advanced warning on tornadoes can be impacted by variations in storm mode. This research evaluates 2 yr of National Weather Service (NWS) tornado warnings, verification reports, and radar-derived convective modes to appraise the ability of the NWS to warn across a variety of convective modes and environmental conditions. Several specific hypotheses are considered: (i) supercell morphologies are the easiest convective modes to warn for tornadoes and yield the greatest lead times, while tornadoes from more linear, nonsupercell convective modes, such as quasi-linear convective systems, are more difficult to warn for; (ii) parameters such as tornado distance from radar, population density, and tornado intensity (F scale) introduce significant and complex variability into warning statistics as a function of storm mode; and (iii) tornadoes from stronger storms, as measured by their mesocyclone strength (when present), convective available potential energy (CAPE), vertical wind shear, and significant tornado parameter (STP) are easier to warn for than tornadoes from weaker systems. Results confirmed these hypotheses. Supercell morphologies caused 97% of tornado fatalities, 96% of injuries, and 92% of damage during the study period. Tornado warnings for supercells had a statistically higher probability of detection (POD) and lead time than tornado warnings for nonsupercells; among supercell storms, tornadoes from supercells in lines were slightly more difficult to warn for than tornadoes from discrete or clusters of supercells. F-scale intensity and distance from radar had some impact on POD, with less impact on lead times. Higher mesocyclone strength (when applicable), CAPE, wind shear, and STP values were associated with greater tornado POD and lead times.
Ankle Joint Pressure Changes in a Pes Cavovarus Model
Authors: Schmid Timo , Zurbriggen Sebastian , Zderic Ivan , Gueorguiev Boyko , Weber Martin , Krause Fabian G. 
Published: July 2013

Background: A fixed cavovarus foot deformity can be associated with anteromedial ankle arthrosis due to elevated medial joint contact stresses. Supramalleolar valgus osteotomies (SMOT) and lateralizing calcaneal osteotomies (LCOT) are commonly used to treat symptoms by redistributing joint contact forces. In a cavovarus model, the effects of SMOT and LCOT on the lateralization of the center of force (COF) and reduction of the peak pressure in the ankle joint were compared. Methods: A previously published cavovarus model with fixed hindfoot varus was simulated in 10 cadaver specimens. Closing wedge supramalleolar valgus osteotomies 3 cm above the ankle joint level (6 and 11 degrees) and lateral sliding calcaneal osteotomies (5 and 10 mm displacement) were analyzed at 300 N axial static load (half body weight). The COF migration and peak pressure decrease in the ankle were recorded using high-resolution TekScan pressure sensors. Results: A significant lateral COF shift was observed for each osteotomy: 2.1 mm for the 6 degrees ( P = .014) and 2.3 mm for the 11 degrees SMOT ( P = .010). The 5 mm LCOT led to a lateral shift of 2.0 mm ( P = .042) and the 10 mm LCOT to a shift of 3.0 mm ( P = .006). Comparing the different osteotomies among themselves no significant differences were recorded. No significant anteroposterior COF shift was seen. A significant peak pressure reduction was recorded for each osteotomy: The SMOT led to a reduction of 29% ( P = .033) for the 6 degrees and 47% ( P = .003) for the 11 degrees osteotomy, and the LCOT to a reduction of 41% ( P = .003) for the 5 mm and 49% ( P = .002) for the 10 mm osteotomy. Similar to the COF lateralization no significant differences between the osteotomies were seen. Conclusion: LCOT and SMOT significantly reduced anteromedial ankle joint contact stresses in this cavovarus model. The unloading effects of both osteotomies were equivalent. More correction did not lead to significantly more lateralization of the COF or more reduction of peak pressure but a trend was seen. Clinical Relevance: In patients with fixed cavovarus feet, both SMOT and LCOT provided equally good redistribution of elevated ankle joint contact forces. Increasing the amount of displacement did not seem to equally improve the joint pressures. The site of osteotomy could therefore be chosen on the basis of surgeon’s preference, simplicity, or local factors in case of more complex reconstructions.
A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids
Authors: Sturm Sabine , Engelken Johannes , Gruber Ansgar , Vugrinec Sascha , G Kroth Peter , Adamska Iwona , Lavaud Johann 
Published: July 2013

Abstract

Background
Light, the driving force of photosynthesis, can be harmful when present in excess; therefore, any light harvesting system requires photoprotection. Members of the extended light-harvesting complex (LHC) protein superfamily are involved in light harvesting as well as in photoprotection and are found in the red and green plant lineages, with a complex distribution pattern of subfamilies in the different algal lineages.

Results
Here, we demonstrate that the recently discovered “red lineage chlorophyll a/b-binding-like proteins” (RedCAPs) form a monophyletic family within this protein superfamily. The occurrence of RedCAPs was found to be restricted to the red algal lineage, including red algae (with primary plastids) as well as cryptophytes, haptophytes and heterokontophytes (with secondary plastids of red algal origin). Expression of a full-length RedCAP:GFP fusion construct in the diatom Phaeodactylum tricornutum confirmed the predicted plastid localisation of RedCAPs. Furthermore, we observed that similarly to the fucoxanthin chlorophyll a/c-binding light-harvesting antenna proteins also RedCAP transcripts in diatoms were regulated in a diurnal way at standard light conditions and strongly repressed at high light intensities.

Conclusions
The absence of RedCAPs from the green lineage implies that RedCAPs evolved in the red lineage after separation from the the green lineage. During the evolution of secondary plastids, RedCAP genes therefore must have been transferred from the nucleus of the endocytobiotic alga to the nucleus of the host cell, a process that involved complementation with pre-sequences allowing import of the gene product into the secondary plastid bound by four membranes. Based on light-dependent transcription and on localisation data, we propose that RedCAPs might participate in the light (intensity and quality)-dependent structural or functional reorganisation of the light-harvesting antennae of the photosystems upon dark to light shifts as regularly experienced by diatoms in nature. Remarkably, in plastids of the red lineage as well as in green lineage plastids, the phycobilisome based cyanobacterial light harvesting system has been replaced by light harvesting systems that are based on members of the extended LHC protein superfamily, either for one of the photosystems (PS I of red algae) or for both (diatoms). In their proposed function, the RedCAP protein family may thus have played a role in the evolutionary structural remodelling of light-harvesting antennae in the red lineage.