bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding sources of inefficiency in general-purpose chips
Authors: Hameed Rehan , Qadeer Wajahat , Wachs Megan , Azizi Omid , Solomatnikov Alex , Lee Benjamin C. , Richardson Stephen , Kozyrakis Christos , Horowitz Mark 
Published: October 2012

Due to their high volume, general-purpose processors, and now chip multiprocessors (CMPs), are much more cost effective than ASICs, but lag significantly in terms of performance and energy efficiency. This paper explores the sources of these performance and energy overheads in general-purpose processing systems by quantifying the overheads of a 720p HD H.264 encoder running on a general-purpose CMP system. It then explores methods to eliminate these overheads by transforming the CPU into a specialized system for H.264 encoding. We evaluate the gains from customizations useful to broad classes of algorithms, such as SIMD units, as well as those specific to particular computation, such as customized storage and functional units.
The ASIC is 500x more energy efficient than our original four-processor CMP. Broadly applicable optimizations improve performance by 10x and energy by 7x. However, the very low energy costs of actual core ops (100s fJ in 90nm) mean that over 90% of the energy used in these solutions is still "overhead". Achieving ASIC-like performance and efficiency requires algorithm-specific optimizations. For each sub-algorithm of H.264, we create a large, specialized functional unit that is capable of executing 100s of operations per instruction. This improves performance and energy by an additional 25x and the final customized CMP matches an ASIC solution's performance within 3x of its energy and within comparable area.
Reducing cache power with low-cost, multi-bit error-correcting codes
Authors: Wilkerson Chris , Alameldeen Alaa R. , Chishti Zeshan , Wu Wei , Somasekhar Dinesh , Lu Shih-lien 
Published: October 2012

Technology advancements have enabled the integration of large on-die embedded DRAM (eDRAM) caches. eDRAM is significantly denser than traditional SRAMs, but must be periodically refreshed to retain data. Like SRAM, eDRAM is susceptible to device variations, which play a role in determining refresh time for eDRAM cells. Refresh power potentially represents a large fraction of overall system power, particularly during low-power states when the CPU is idle. Future designs need to reduce cache power without incurring the high cost of flushing cache data when entering low-power states.
In this paper, we show the significant impact of variations on refresh time and cache power consumption for large eDRAM caches. We propose Hi-ECC, a technique that incorporates multi-bit error-correcting codes to significantly reduce refresh rate. Multi-bit error-correcting codes usually have a complex decoder design and high storage cost. Hi-ECC avoids the decoder complexity by using strong ECC codes to identify and disable sections of the cache with multi-bit failures, while providing efficient single-bit error correction for the common case. Hi-ECC includes additional optimizations that allow us to amortize the storage cost of the code over large data words, providing the benefit of multi-bit correction at same storage cost as a single-bit error-correcting (SECDED) code (2% overhead). Our proposal achieves a 93% reduction in refresh power vs. a baseline eDRAM cache without error correcting capability, and a 66% reduction in refresh power vs. a system using SECDED codes.
An integrated GPU power and performance model
Authors: Hong Sunpyo , Kim Hyesoon 
Published: October 2012

GPU architectures are increasingly important in the multi-core era due to their high number of parallel processors. Performance optimization for multi-core processors has been a challenge for programmers. Furthermore, optimizing for power consumption is even more difficult. Unfortunately, as a result of the high number of processors, the power consumption of many-core processors such as GPUs has increased significantly.
Hence, in this paper, we propose an integrated power and performance (IPP) prediction model for a GPU architecture to predict the optimal number of active processors for a given application. The basic intuition is that when an application reaches the peak memory bandwidth, using more cores does not result in performance improvement.
We develop an empirical power model for the GPU. Unlike most previous models, which require measured execution times, hardware performance counters, or architectural simulations, IPP predicts execution times to calculate dynamic power events. We then use the outcome of IPP to control the number of running cores. We also model the increases in power consumption that resulted from the increases in temperature.
With the predicted optimal number of active cores, we show that we can save up to 22.09%of runtime GPU energy consumption and on average 10.99% of that for the five memory bandwidth-limited benchmarks.
Energy proportional datacenter networks
Authors: Abts Dennis , Marty Michael R. , Wells Philip M. , Klausler Peter , Liu Hong 
Published: October 2012

Numerous studies have shown that datacenter computers rarely operate at full utilization, leading to a number of proposals for creating servers that are
energy proportional
with respect to the computation that they are performing.

In this paper, we show that as servers themselves become more energy proportional, the datacenter network can become a significant fraction (up to 50%) of cluster power. In this paper we propose several ways to design a high-performance datacenter network whose power consumption is more proportional to the amount of traffic it is moving -- that is, we propose
energy proportional datacenter networks
.

We first show that a flattened butterfly topology itself is inherently more power efficient than the other commonly proposed topology for high-performance datacenter networks. We then exploit the characteristics of modern plesiochronous links to adjust their power and performance envelopes dynamically. Using a network simulator, driven by both synthetic workloads and production datacenter traces, we characterize and understand design tradeoffs, and demonstrate an 85% reduction in power --- which approaches the ideal energy-proportionality of the network.
Our results also demonstrate two challenges for the designers of future network switches: 1) We show that there is a significant power advantage to having independent control of each unidirectional channel comprising a network link, since many traffic patterns show very asymmetric use, and 2) system designers should work to optimize the high-speed channel designs to be more energy efficient by choosing optimal data rate and equalization technology. Given these assumptions, we demonstrate that energy proportional datacenter communication is indeed possible.
Infrared fluorescence for vascular barrier breach in vivo – A novel method for quantitation of albumin efflux
Authors: Furlan-Freguia Christian , Mosnier Laurent , Yegneswaran Subramanian , Ruf Wolfram , Griffin John , von Drygalski Annette 
Published: October 2012

SummaryVascular hyperpermeability contributes to morbidity in inflammation. Current methodologies for in vivo assessment of permeability based on extravasation of Evans Blue (EB)-bound albumin are cumbersome and often lack sensitivity. We developed a novel infrared fluorescence (IRF) methodology for measurement of EB-albumin extravasation to quantify vascular permeability in murine models. Vascular permeability induced by endotoxaemia was examined for all solid organs, brain, skin and peritoneum by IRF and the traditional absorbance-based measurement of EB in tissue extracts. Organ IRF increased linearly with increasing concentrations of intravenous EB (2.5–25 mg/kg). Tissue IRF was more sensitive for EB accumulation compared to the absorbance-based method. Accordingly, differences in vascular permeability and organ EB accumulation between lipopolysaccharide-treated and saline-treated mice were often significant when analysed by IRF-based detection but not by absorbance-based detection. EB was detected in all 353 organs analysed with IRF but only in 67% (239/353) of organs analysed by absorbance-based methodology, demonstrating improved sensitivity of EB detection in organs with IRF. In contrast, EB in plasma after EB administration was readily measured by both methods with high correlation between the two methods (n=116, r2=0.86). Quantitation of organ-specific EB-IRF differences due to endotoxin was optimal when IRF was compared between mice matched for weight, gender, and age, and with appropriate corrections for organ weight and EB plasma concentrations. Notably, EB-IRF methodology leaves organs intact for subsequent histopathology. In summary, EB-IRF is a novel, highly sensitive, rapid, and convenient method for the relative quantification of EB in intact organs of treatment versus control mice.
Factor XIII expression within aortic valves and its plasma activity in patients with aortic stenosis: association with severity of disease
Authors: Kapusta Przemyslaw , Wypasek Ewa , Natorska Joanna , Grudzien Grzegorz , Sobczyk Dorota , Sadowski Jerzy , Undas Anetta 
Published: October 2012

SummaryAortic valve stenosis (AS) shares several similarities with atherosclerosis. Factor XIII (FXIII) has been detected within atherosclerotic plaques and may contribute to the development of atherosclerosis via multiple mechanisms. In the current study, we sought to investigate FXIII expression within human stenotic aortic valves and its association with severity of the disease. We prospectively enrolled 91 consecutive patients with AS scheduled for isolated valve replacement. Valvular FXIII subunit A (FXIII-A), fibrin and macrophages expression was evaluated by immunostaining. FXIII-A subunit transcripts and FXIII-A Val34Leu polymorphism was determined by real-time PCR. Plasma FXIII (pFXIII) activity was measured. We demonstrated that the valvular FXIII-A was predominantly expressed on the aortic side of leaflets, colocalized with alternatively activated macrophages (AAM). Areas stained for FXIII-A showed positive correlations with valvular fibrin presence, degree of calcification, pFXIII activity and the severity of AS, reflected by mean and maximum transvalvular gradients (all, p<0.001). The FXIII-A mRNA in the stenotic leaflets was significantly elevated compared to control leaflets. Interestingly, pFXIII activity was also positively correlated with mean (p<0.001) and maximum (p=0.001) transvalvular gradient. The FXIII-A Val34Leu polymorphism did not affect FXIII-A and fibrin expression in AS valves. In conclusion, the study is the first to show abundant expression of FXIII-A at the mRNA and protein levels within human stenotic aortic valves, which is associated with the severity of AS. Our findings might suggest that FXIII in the stenotic valves is presented in AAM and may be involved in the AS progression.
Oral anticoagulation continuation compared with heparin bridging therapy among high risk patients undergoing implantation of cardiac rhythm devices
Authors: Feng Lei , Li Yang , Li Jian , Yu Bo 
Published: October 2012

SummaryIt was the objective of this study to systematically compare the effects of oral anticoagulation (OAC) with heparin bridging therapy among patients at high risk for thromboembolism undergoing implantation of cardiac rhythm devices. A systematic search of PubMed/MEDLINE, Ovid and Elsevier, and the Cochrane Library databases was conducted. Six trials that met our inclusion criteria were identified and included in the present study. The endpoints of this meta-analysis included pocket haematoma, severe haematoma requiring drainage/revision, thromboembolic events, and length of hospital stay. Data were expressed as odds ratios (ORs) and 95% confidence interval (CIs). There was a statistically significant reduction of pocket haematoma (OR 0.29, 95% CI: 0.17 to 0.49, p<0.00001) and haematoma drainage/revision (OR 0.15, 95%CI: 0.04 to 0.54, p=0.004), respectively, in the OAC continuation group versus the heparin bridging group. We did not detect any statistically sig- nificant differences of thromboembolic events (OR 0.48, 95%CI: 0.07 to 3.54, p=0.48) in the two groups. There was a trend that patients in bridging group had longer hospital stays. In conclusion, OAC continu- ation had a better risk-beneficial ratio and shorter length of hospital stay, and was more convenient to implement compared with heparin bridging therapy among patients at high risk for thromboembolism undergoing implantation of cardiac rhythm devices.
An Equilibrator System to Measure Dissolved Oxygen and Its Isotopes
Authors: Rafelski Lauren Elmegreen , Paplawsky Bill , Keeling Ralph F. 
Published: October 2012

Abstract
An equilibrator is presented that is designed to have a sufficient equilibration time even for insoluble gases, and to minimize artifacts associated with not equilibrating to the total gas tension. A gas tension device was used to balance the pressure inside the equilibrator with the total gas tension. The equilibrator has an e-folding time of 7.36 ± 0.74 min for oxygen and oxygen isotopes, allowing changes on hourly time scales to be easily resolved. The equilibrator delivers “equilibrated” air at a flow rate of 3 mL min−1 to an isotope ratio mass spectrometer. The high gas sampling flow rate would allow the equilibrator to be interfaced with many potential devices, but further development may be required for use at sea. This system was tested at the Scripps Institution of Oceanography pier, in La Jolla, California. A mathematical model validated with performance tests was used to assess the sensitivity of the equilibrated air composition to headspace pressure and makeup gas composition. Parameters in this model can be quantified to establish corrections under different operating conditions. For typical observed values, under the operating conditions presented here, the uncertainty in the measurement due to the equilibrator system is 2.2 per mil for δ(O2/N2), 1.5 per mil for δ(O2/Ar), 0.059 per mil for δ18O, and 0.0030 per mil for Δ17O.
Eligibility criteria in randomized phase II and III adjuvant and neoadjuvant breast cancer trials: Not a significant barrier to enrollment
Authors: Filion Myriam , Forget Geneviève , Brochu Olyvia , Provencher Louise , Desbiens Christine , Doyle Catherine , Poirier Brigitte , DuRocher Martin , Camden Stéphanie , Lemieux Julie 
Published: October 2012

Background Clinical trial recruitment can be impeded by eligibility criteria being too numerous or too restrictive. Purpose This study’s principal objective was to determine whether a specific category of eligibility criteria could be identified as a major barrier to patient enrollment. Methods Nine phase II or III clinical trials, opened between June 2004 and July 2008, were selected. A retrospective cohort of women diagnosed with invasive, nonmetastatic breast cancer and potentially eligible for these clinical trials was used. All eligibility criteria were sorted into the following categories: definition of disease, precision, safety, ethical and legal, or administrative. A total of 985 patient-trials were evaluated, defined as the experimental unit since one patient could be eligible to more than one trial. Proportions of cases with ‘not met’ eligibility criteria were assessed for each category in each trial. Results Two clinical trials had a ‘not met’ subcategory criterion of over 20%. ‘Pathology’ and ‘consent’ subcategory criteria were ‘not met’ in 24.2% and 92.7% of cases for the NEOCAN and NCIC CTG MA.27 trials, respectively. NCIC CTG MA.27 had the highest proportion of ‘not met’ subcategory due to an inclusion criterion requiring participation to two companion studies. National Surgical Adjuvant Breast and Bowel Project (NSABP) B-38 had a proportion of 18.8% of cases ‘not meeting’ the receptor status subcategory criterion. All other subcategories of eligibility criteria assessed were ‘not met’ by less than 15% of patients. Overall, few subcategories had over 10% of ineligible patients. Limitations Many eligibility criteria were considered ‘nonevaluable’ because the information evaluated would have required additional procedures not performed as part of the general practice. Conclusion The subjects from the study population are not precluded from entry in a trial because of stringent eligibility criteria. Eligibility criteria should reflect as much as possible the whole population to whom the treatment will be offered, with the exception of drugs targeting a specific receptor or pathway where only a subpopulation is hypothesized to benefit from the therapy. In the breast cancer clinical trials evaluated for the present study, no criterion precluding recruitment was shared by many or all trials and no specific eligibility criterion was consistently the reason for patients’ ineligibility.
Macrolide resistance determinants among Streptococcus pneumoniae isolates from carriers in Central Greece
Authors: Grivea Ioanna N , Sourla Alexia , Ntokou Eleni , Chryssanthopoulou Denise C , Tsantouli Alexandra G , Syrogiannopoulos George A 
Published: October 2012

Abstract

Background
We sought to characterize the temporal trends in nasopharyngeal carriage of macrolide-resistant pneumococci during a period with increased heptavalent pneumococcal conjugate vaccine (PCV7) coverage in Central Greece.

Methods

Streptococcus pneumoniae isolates were recovered from 2649 nasopharyngeal samples obtained from day-care center attendees in Central Greece during 2005–2009. A phenotypic and genotypic analysis of the isolates was performed, including the identification of macrolide resistance genes mef(A), subclasses mef(A) and mef(E), as well as erm(B).

Results
Of the 1105 typeable S. pneumoniae isolates, 265 (24%) were macrolide-resistant; 22% in 2005, 33.3% in 2006, 23.7% in 2007, and 20.5% in 2009 (P=0.398). Among these macrolide-resistant pneumococci, 28.5% possessed erm(B), 24.3% erm(B)+mef(E), 41.8% mef(E), and 5.3% mef(A). A mef gene as the sole resistance determinant was carried by 31% of macrolide-resistant isolates belonging to PCV7 serotypes and 75.8% of the non-PCV7 serotypes. Across the 4 annual surveillances, pneumococci carrying mef(A) gradually disappeared, whereas serotype 19F isolates carrying both erm(B) and mef(E) persisted without significant yearly fluctuations. Among isolates belonging to non-PCV7 serotypes, macrolide-resistance was observed in those of serotypes 6A, 19A, 10A, 15A, 15B/C, 35F, 35A, and 24F. In 2009, ie 5 years after the introduction of PCV7 in our country, 59% of macrolide-resistant pneumococci belonged to non-PCV7 serotypes.

Conclusions
Across the study period, the annual frequency of macrolide-resistant isolates did not change significantly, but in 2009 a marked shift to non-PCV7 serotypes occurred. Overall, more than half of the macrolide-resistant isolates possessed erm(B) either alone or in combination with mef(E). erm(B) dominated among isolates belonging to PCV7 serotypes, but not among those of non-PCV7 serotypes.
Novel synergistic antitumor effects of rapamycin with bortezomib on hepatocellular carcinoma cells and orthotopic tumor model
Authors: Wang Cun , Gao Dongmei , Guo Kun , Kang Xiaonan , Jiang Kai , Sun Chun , Li Yan , Sun Lu , Shu Hong , Jin Guangzhi , Sun Haiyan , Wu Weizhong , Liu Yinkun 
Published: October 2012

Abstract

Background
Despite recent advances in the treatment of hepatocellular carcinoma (HCC), the chemotherapy efficacy against HCC is still unsatisfactory. The mammalian target of rapamycin (mTOR) has been emerged as an important cancer therapeutic target. However, HCC cells often resistant to rapamycin because of the paradoxical activation of Akt by rapamycin. In this study, we investigated whether bortezomib could enhance the antitumor effects of rapamycin.

Methods
The effects of rapamycin and bortezomib on HCC proliferation, apoptosis, migration, and invasiveness in vitro were assessed by CCK-8 analysis, flow cytometry, Hoechst 33342 staining and transwell assays, respectively. Total and phosphorylated protein levels of Akt were detected by Western blotting. The effects of rapamycin and/or bortezomib on the mRNA expression levels of p53, p27, p21 and Bcl-2 family in HCCLM3 cells were evaluated by RT-PCR. The roles of rapamycin and bortezomib on HCC growth and metastasis in xenograft models were evaluated by tumor volumes and fluorescent signals. The effects of rapamycin and bortezomib on cell proliferation and apoptosis in vivo were test by PCNA and TUNEL staining.

Results
Bortezomib synergized with rapamycin to reduce cell growth, induce apoptosis, and inhibit cell mobility in vitro. Further mechanistic studies showed that bortezomib inhibited rapamycin-induced phosphorylated Akt, which in turn enhanced apoptosis of HCC cell lines. The alteration of the mRNA expression of cell cycle inhibitors p53, p27, p21 and apoptosis associated genes Bcl-2, Bax were also involved in the synergistic antitumor effects of rapamycin and bortezomib. P53 inhibitor PFT-α significantly attenuate the effect of rapamycin and bortezomib on cell apoptosis, which indicated that the pro-apoptotic effect of rapamycin and bortezomib may be p53-dependent. Treatment of HCCLM3-R bearing nude mice with rapamycin and bortezomib significantly enhanced tumor growth inhibition (72.4%), comparing with either rapamycin- (54.7%) or bortezomib-treated mice (22.4%). In addition, the lung metastasis was significantly suppressed in mice received the combination treatment (16.6%). The combination treatment of rapamycin and bortezomib significantly inhibited tumor cell proliferation and tumor angiogenesis in vivo.

Conclusion
The combination of rapamycin with bortezomib could be a novel and promising therapeutic approach to the treatment of HCC.