bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement properties of patient-reported outcome measures (PROMs) used in adult patients with chronic kidney disease: a systematic review protocol
Authors: Aiyegbusi Olalekan Lee , Kyte Derek , Cockwell Paul , Marshall Tom , Keeley Thomas , Gheorghe Adrian , Calvert Melanie 
Published: October 2016

IntroductionChronic kidney disease (CKD) is associated with symptoms that can significantly reduce the quality of life (QoL) of patients. Patient-reported outcome measures (PROMs) may facilitate the assessment of the impact of disease and treatment on the QoL, from a patient perspective. PROMs can be used in research and routine clinical practice.Methods and analysisA systematic review of studies evaluating the measurement properties of PROMs in adults with CKD will be conducted. MEDLINE, EMBASE, PsycINFO and CINAHL Plus will be systematically searched from inception. Hand searching of reference lists and citations of included studies will be carried out. 2 reviewers will independently screen the titles and abstracts of all the studies retrieved during the systematic search to determine their eligibility. The COnsensus-based Standards for the selection of health Measurement Instruments (COSMIN) checklist will be used to appraise the methodological quality of the selected studies following the full-text review. Data on the study population, questionnaire characteristics and measurement properties will be extracted from the selected papers. Finally, a narrative synthesis of extracted data will be undertaken.Ethics and disseminationEthical permissions are not required for this study as data from published research articles will be used. Findings will be disseminated through publication in a peer-reviewed journal and presented at conferences. This systematic review will provide a comprehensive assessment of the measurement properties of PROMs currently available for use in adult patients with CKD and present evidence which may inform the selection of measures for use in research and clinical practice.Trial registration numberCRD42016035554.
Separating the wheat from the chaff: region of interest combined with metal artifact reduction for completion angiography following cerebral aneurysm treatment
Authors: Duckworth Edward A M , Nickele Chris , Schafer Sebastian , Bauer Sebastian , Scholz Bernhard , Elijovich Lucas , Hoit Daniel , Doss Vinodh T , Arthur Adam S 
Published: October 2016

IntroductionFollowing complicated endovascular or microsurgical treatments, assessment of radiographic outcome can be challenging due to device resolution and metallic artifact. Two-dimensional and three-dimensional angiography can reveal information about flow and aneurysm obliteration, but may be limited by beam hardening, overlapping vessels, and image degradation in the region of metallic implants. In this study, we investigated the combination of a collimated volumetric imaging (volume of interest, VOI) protocol followed by metal artifact reduction (MAR) post-processing to evaluate the correct positioning of stents, flow diverters, coils, and clips while limiting the radiation dose to the patient.Methods9 patients undergoing 10 procedures were included in our study. All patients underwent endovascular or surgical treatment of a cerebral aneurysm involving stents, flow diverting stents, coils, and/or clips followed by either immediate or early postoperative evaluation of our protocol.ResultsImage datasets corrected for metallic artifacts (VOI-MAR) were judged to be better—a statistically significant finding—than image datasets only corrected for field of view truncation (VOI alone). Qualitatively, images were more interpretable and informative with regards to device position and apposition to the vessel wall for those cases involving a pipeline, and with regards to encroachment on the parent artery and possible residual aneurysm, in all cases.ConclusionsVOI acquisition combined with MAR post-processing provides for accurate and informative evaluation of cerebral aneurysm treatment while limiting the radiation dose to patients.
Subsidence around oceanic ridges along passive margins: NE Arabian Sea
Authors: Misra Achyuta Ayan , Banerjee Smita , Kundu Nishikanta , Mukherjee Brunti 
Published: October 2016

Abstract

The northern part of the western continental margin of India formed due to the separation of the Seychelles from India at
c.
63 Ma. This produced offshore tectonic elements such as the Gop Rift, the Saurashtra Volcanic Platform (SVP) and the Laxmi Ridge, as well as numerous seamounts, e.g. the Raman and Panikkar seamounts. The Laxmi Ridge and the Laxmi Basin have been studied using high-resolution 2D reflection seismic data and well data. Patch and pinnacle carbonate reefs, indicating shallow waters, are common in the north, whereas large, isolated platforms are usually noted in the south. Palaeo-depth estimates are made from well biostratigraphy. Subsidence studies of the SVP suggest that the burial history is consistent with the anomalously hot Réunion plume. We have performed a subsidence analysis south of the SVP on the Laxmi Ridge and Laxmi Basin. The sediment-unloaded basement depths, estimated using using flexural isostasy with effective elastic thicknesses of 10–40 km have been found to be 2000–4000 m in areas where carbonates exist. These carbonates indicate <200 m bathymetry at
c.
65 Ma, and the subsidence discrepancy is thus due to thermal cooling or anomalous heating due to the Deccan plume. Patch and pinnacle reefs in the north suggests that either the rise in sea-level or the rate of subsidence of the basement were fast. The presence of large platforms in the south indicates otherwise. This is possibly due to a greater influence from the Indus Fan sediments towards the north. In addition, the Laxmi Ridge is a spreading centre that remained emergent near or above sea-level due to plume support, which was also greater in the south due to proximity to the plume. When the plume support discontinued, the ridge subsided quickly to present-day depths, which matches the subsidence expected for 60–70 Myr old oceanic crust.

Supplementary material:
A table is available at
https://doi.org/10.6084/m9.figshare.c.3470751
Earliest microbial trace fossils in Archaean pillow lavas under scrutiny: new micro-X-ray absorption near-edge spectroscopy, metamorphic and morphological constraints
Authors: Grosch Eugene G. , Muñoz Manuel , Mathon Olivier , McLoughlin Nicola 
Published: October 2016

Abstract

Filament-shaped titanite microtextures in early Archaean (
c.
3.47 Ga) metabasalts from the Barberton Greenstone Belt of South Africa have been argued to represent Earth's oldest microbial trace fossils, but petrological data on the environmental conditions that led to the formation of these microtextures are sparse. We present here new metamorphic constraints on the equilibrium mineral assemblage containing the titanite microtextures, together with Fe speciation redox variations in the chlorite matrix surrounding the microtextures and morphospace analysis of the microtextures to test their biogenicity. Thermodynamic phase diagram modelling using a calculated rock microdomain composition indicated that the titanite mineral assemblage is stable at temperature conditions of
T
=240–360°C. The high-resolution quantitative mapping results combined with micro-X-ray absorption near-edge spectroscopy at the Fe
K
-edge in chlorite revealed that the titanite microtextures are located in low-temperature, high XFe
3+
chlorite bands, veins and microdomains, supporting an origin as abiotic, retrograde mineral cooling textures. These new data, combined with a late
c.
2.9 Ga U–Pb date for the titanite, are incompatible with the existing biological model, which invokes microbial micro-tunnel formation followed by titanite ‘infilling’ and preservation in the early Archaean sub-seafloor. The continuum of titanite morphologies reported herein indicates that titanite morphology cannot be used as reliable evidence in support of a biogenic origin in these metavolcanic rocks. It is proposed that the titanite microtextures of purported biogenic origin from other greenstone belts, such as the Pilbara Craton of Western Australia, also deserve to be scrutinized by high-resolution petrological investigations.

Supplementary material:
Representative electron microprobe analyses of retrograde minerals and µXANES spectra and corresponding fitted pre-edge peaks for all spot analyses are available at
https://doi.org/10.6084/m9.figshare.c.3498465
Image-Content-Aware I/O Optimization for Mobile Virtualization
Authors: Chen Renhai , Wang Yi , Hu Jingtong , Liu Duo , Shao Zili , Guan Yong 
Published: October 2016

Mobile virtualization introduces extra layers in software stacks, which leads to performance degradation. Notably, each I/O operation has to pass through several software layers to reach the NAND-flash-based storage systems. This article targets at optimizing I/O for mobile virtualization, since I/O becomes one of major performance bottlenecks that seriously affects the performance of mobile devices. Among all the I/O operations, a large percentage is to update metadata. Frequently updated metadata not only degrade overall I/O performance but also severely reduce flash memory lifetime.
In this article, we propose a novel I/O optimization technique to identify the metadata of a guest file system that is stored in a virtual machine image file and frequently updated. Then, these metadata are stored in a small additional non-volatile memory (NVM), which is faster and more endurable to greatly improve flash memory’s performance and lifetime. To the best of our knowledge, this is the first work to identify the file system metadata from regular data in a guest OS image file with NVM optimization. The proposed scheme is evaluated on a real hardware embedded platform. The experimental results show that the proposed techniques can improve write performance to 45.21% in mobile devices with virtualization.
ISAAC
Authors: Shafiee Ali , Nag Anirban , Muralimanohar Naveen , Balasubramonian Rajeev , Strachan John Paul , Hu Miao , Williams R. Stanley , Srikumar Vivek 
Published: October 2016

A number of recent efforts have attempted to design accelerators for popular machine learning algorithms, such as those involving convolutional and deep neural networks (CNNs and DNNs). These algorithms typically involve a large number of multiply-accumulate (dot-product) operations. A recent project, DaDianNao, adopts a near data processing approach, where a specialized neural functional unit performs all the digital arithmetic operations and receives input weights from adjacent eDRAM banks.
This work explores an in-situ processing approach, where memristor crossbar arrays not only store input weights, but are also used to perform dot-product operations in an analog manner. While the use of crossbar memory as an analog dot-product engine is well known, no prior work has designed or characterized a full-fledged accelerator based on crossbars. In particular, our work makes the following contributions: (i) We design a pipelined architecture, with some crossbars dedicated for each neural network layer, and eDRAM buffers that aggregate data between pipeline stages. (ii) We define new data encoding techniques that are amenable to analog computations and that can reduce the high overheads of analog-to-digital conversion (ADC). (iii) We define the many supporting digital components required in an analog CNN accelerator and carry out a design space exploration to identify the best balance of memristor storage/compute, ADCs, and eDRAM storage on a chip. On a suite of CNN and DNN workloads, the proposed ISAAC architecture yields improvements of 14.8×, 5.5×, and 7.5× in throughput, energy, and computational density (respectively), relative to the state-of-the-art DaDianNao architecture.
ASIC clouds
Authors: Magaki Ikuo , Khazraee Moein , Gutierrez Luis Vega , Taylor Michael Bedford 
Published: October 2016

GPU and FPGA-based clouds have already demonstrated the promise of accelerating computing-intensive workloads with greatly improved power and performance.
In this paper, we examine the design of ASIC Clouds, which are purpose-built datacenters comprised of large arrays of ASIC accelerators, whose purpose is to optimize the total cost of ownership (TCO) of large, high-volume chronic computations, which are becoming increasingly common as more and more services are built around the Cloud model. On the surface, the creation of ASIC clouds may seem highly improbable due to high NREs and the inflexibility of ASICs. Surprisingly, however, large-scale ASIC Clouds have already been deployed by a large number of commercial entities, to implement the distributed Bitcoin cryptocurrency system.
We begin with a case study of Bitcoin mining ASIC Clouds, which are perhaps the largest ASIC Clouds to date. From there, we design three more ASIC Clouds, including a YouTube-style video transcoding ASIC Cloud, a Litecoin ASIC Cloud, and a Convolutional Neural Network ASIC Cloud and show 2-3 orders of magnitude better TCO versus CPU and GPU.
Among our contributions, we present a methodology that given an accelerator design, derives Pareto-optimal ASIC Cloud Servers, by extracting data from place-and-routed circuits and computational fluid dynamic simulations, and then employing clever but brute-force search to find the best jointly-optimized ASIC, DRAM subsystem, motherboard, power delivery system, cooling system, operating voltage, and case design. Moreover, we show how data center parameters determine which of the many Pareto-optimal points is TCO-optimal. Finally we examine when it makes sense to build an ASIC Cloud, and examine the impact of ASIC NRE.
Base-victim compression
Authors: Gaur Jayesh , Alameldeen Alaa R. , Subramoney Sreenivas 
Published: October 2016

The memory wall has motivated many enhancements to cache management policies aimed at reducing misses. Cache compression has been proposed to increase effective cache capacity, which potentially reduces capacity and conflict misses. However, complexity in cache compression implementations could increase cache power and access latency. On the other hand, advanced cache replacement mechanisms use heuristics to reduce misses, leading to significant performance gains. Both cache compression and replacement policies should collaborate to improve performance.
In this paper, we demonstrate that cache compression and replacement policies can interact negatively. In many workloads, performance gains from replacement policies are lost due to the need to alter the replacement policy to accommodate compression. This leads to sub-optimal replacement policies that could lose performance compared to an uncompressed cache. We introduce a novel, opportunistic cache compression mechanism, Base-Victim, based on an efficient cache design. Our compression architecture improves performance on top of advanced cache replacement policies, and guarantees a hit rate at least as high as that of an uncompressed cache. For cache-sensitive applications, Base-Victim achieves an average 7.3% performance gain for single-threaded workloads, and 8.7% gain for four-thread multi-program workload mixes.
Accelerating markov random field inference using molecular optical gibbs sampling units
Authors: Wang Siyang , Zhang Xiangyu , Li Yuxuan , Bashizade Ramin , Yang Song , Dwyer Chris , Lebeck Alvin R. 
Published: October 2016

The increasing use of probabilistic algorithms from statistics and machine learning for data analytics presents new challenges and opportunities for the design of computing systems. One important class of probabilistic machine learning algorithms is Markov Chain Monte Carlo (MCMC) sampling, which can be used on a wide variety of applications in Bayesian Inference. However, this probabilistic iterative algorithm can be inefficient in practice on today's processors, especially for problems with high dimensionality and complex structure. The source of inefficiency is generating samples from parameterized probability distributions.
This paper seeks to address this sampling inefficiency and presents a new approach to support probabilistic computing that leverages the native randomness of Resonance Energy Transfer (RET) networks to construct RET-based sampling units (RSU). Although RSUs can be designed for a variety of applications, we focus on the specific class of probabilistic problems described as Markov Random Field Inference. Our proposed RSU uses a RET network to implement a molecular-scale optical Gibbs sampling unit (RSU-G) that can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator. We experimentally demonstrate the fundamental operation of an RSU using a macro-scale hardware prototype. Emulation-based evaluation of two computer vision applications for HD images reveal that an RSU augmented GPU provides speedups over a GPU of 3 and 16. Analytic evaluation shows a discrete accelerator that is limited by 336 GB/s DRAM produces speedups of 21 and 54 versus the GPU implementations.
Clinically Viable Gene Expression Assays with Potential for Predicting Benefit from MEK Inhibitors
Authors: Brant Roz , Sharpe Alan , Liptrot Tom , Dry Jonathan R. , Harrington Elizabeth A. , Barrett J. Carl , Whalley Nicky , Womack Christopher , Smith Paul , Hodgson Darren R. 
Published: October 2016

Abstract
Purpose: To develop a clinically viable gene expression assay to measure RAS/RAF/MEK/ERK (RAS–ERK) pathway output suitable for hypothesis testing in non–small cell lung cancer (NSCLC) clinical studies.
Experimental Design: A published MEK functional activation signature (MEK signature) that measures RAS–ERK functional output was optimized for NSCLC in silico. NanoString assays were developed for the NSCLC optimized MEK signature and the 147-gene RAS signature. First, platform transfer from Affymetrix to NanoString, and signature modulation following treatment with KRAS siRNA and MEK inhibitor, were investigated in cell lines. Second, the association of the signatures with KRAS mutation status, dynamic range, technical reproducibility, and spatial and temporal variation was investigated in NSCLC formalin-fixed paraffin-embedded tissue (FFPET) samples.
Results: We observed a strong cross-platform correlation and modulation of signatures in vitro. Technical and biological replicates showed consistent signature scores that were robust to variation in input total RNA; conservation of scores between primary and metastatic tumor was statistically significant. There were statistically significant associations between high MEK (P = 0.028) and RAS (P = 0.003) signature scores and KRAS mutation in 50 NSCLC samples. The signatures identify overlapping but distinct candidate patient populations from each other and from KRAS mutation testing.
Conclusions: We developed a technically and biologically robust NanoString gene expression assay of MEK pathway output, compatible with the quantities of FFPET routinely available. The gene signatures identified a different patient population for MEK inhibitor treatment compared with KRAS mutation testing. The predictive power of the MEK signature should be studied further in clinical trials. Clin Cancer Res; 23(6); 1471–80. ©2016 AACR.
See related commentary by Xue and Lito, p. 1365
CREBBPInactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M. 
Published: October 2016

AbstractSomatic mutations in CREBBP occur frequently in B-cell lymphoma. Here, we show that loss of CREBBP facilitates the development of germinal center (GC)–derived lymphomas in mice. In both human and murine lymphomas, CREBBP loss-of-function resulted in focal depletion of enhancer H3K27 acetylation and aberrant transcriptional silencing of genes that regulate B-cell signaling and immune responses, including class II MHC. Mechanistically, CREBBP-regulated enhancers are counter-regulated by the BCL6 transcriptional repressor in a complex with SMRT and HDAC3, which we found to bind extensively to MHC class II loci. HDAC3 loss-of-function rescued repression of these enhancers and corresponding genes, including MHC class II, and more profoundly suppressed CREBBP-mutant lymphomas in vitro and in vivo. Hence, CREBBP loss-of-function contributes to lymphomagenesis by enabling unopposed suppression of enhancers by BCL6/SMRT/HDAC3 complexes, suggesting HDAC3-targeted therapy as a precision approach for CREBBP-mutant lymphomas.Significance: Our findings establish the tumor suppressor function of CREBBP in GC lymphomas in which CREBBP mutations disable acetylation and result in unopposed deacetylation by BCL6/SMRT/HDAC3 complexes at enhancers of B-cell signaling and immune response genes. Hence, inhibition of HDAC3 can restore the enhancer histone acetylation and may serve as a targeted therapy for CREBBP-mutant lymphomas. Cancer Discov; 7(1); 38–53. ©2016 AACR.See related commentary by Höpken, p. 14.This article is highlighted in the In This Issue feature, p. 1
Efficacy of prasugrel administration immediately after percutaneous coronary intervention in ST-elevation myocardial infarction
Authors: Flierl Ulrike , Zauner Florian , Sieweke Jan-Thorben , Berliner Christine , Napp L. Christian , Tillmanns Jochen , Bauersachs Johann , Schäfer Andreas 
Published: October 2016

SummaryPrasugrel, a potent thienopyridine, achieves stronger inhibition of platelet activation than clopidogrel. However, onset of inhibition is significantly delayed in patients with acute ST-elevation myocardial infarction (STEMI), as haemodynamic instability and morphine application seem to exhibit significant influence. Since rapid onset of effect was demonstrated in non-STEMI patients when prasugrel was administered only after percutaneous coronary intervention (PCI) without increasing cardiovascular event rates we assessed the efficacy of prasugrel loading immediately after PCI for STEMI instead of pre-loading before revascu-larisation. We investigated 50 consecutive patients with acute STEMI (mean age 56 ± 10 years) admitted for primary PCI. Prasugrel efficacy was assessed by platelet reactivity index (PRI; VASP assay) before, 1, 2, 4, 6, 12, and 24 hours following an oral loading dose of 60 mg immediately after PCI. High on-treatment platelet reactivity (HTPR) was de-fined as PRI>50 %. Prasugrel significantly and rapidly reduced platelet reactivity in acute STEMI patients (p<0.0001 at each time point vs control). Morphine application resulted in a significantly higher HTPR rate among patients having received morphine less than 1 hour before pra-sugrel loading (p<0.001) while concomitant metoclopramide (MCP) treatment did not significantly affect prasugrel efficacy. In conclusion, in contrast to previous reports describing a significant delay in onset of prasugrel-mediated P2Y12 inhibition in acute STEMI, we observed a rapid onset with low HTPR rates comparable to those observed in stable non-STEMI patients. Prasugrel administered directly after primary PCI might therefore be a useful therapeutic strategy in patients with STEMI to provide strong and effective P2Y12 inhibition.