On GPU’s viability as a middleware accelerator

Today Graphics Processing Units (GPUs) are a largely underexploited resource on existing desktops and a possible cost-effective enhancement to high-performance systems. To date, most applications that exploit GPUs are specialized scientific applications. Little attention has been paid to harnessing these highly-parallel devices to support more generic functionality at the operating system or middleware level. This study starts from the hypothesis that generic middleware-level techniques that improve distributed system reliability or performance (such as content addressing, erasure coding, or data similarity detection) can be significantly accelerated using GPU support. We take a first step towards validating this hypothesis and we design StoreGPU, a library that accelerates a number of hashing-based middleware primitives popular in distributed storage system implementations. Our evaluation shows that StoreGPU enables up twenty five fold performance gains on synthetic benchmarks as well as on a high-level application: the online similarity detection between large data files.

重症患者急救插管预氧合的临床研究

目的:观察预氧合在ICU重症患者急救插管中的效果并探讨预氧合的最佳方式。方法:选择ICU内低氧血症成年危重患者28例,按入ICU顺序随机分为3组:A组(对照组,n=10),B组(气囊-面罩预氧合组,n=9)和C组(麻醉机-面罩预氧合组,n=9)。A组入室后即行快速气管插管,B组气囊-面罩预氧合5 min后行气管插管,氧流量为15 L/min。C组麻醉机-面罩预氧合5 min后行气管插管,氧流量为4 L/min。观察指标:持续脉搏血氧饱和度(SpO2),动脉血气分析及相关并发症。结果:三组在预氧合之前,各项基本指标比较无统计学差异。在预氧合后,B、C组的SpO2明显高于A组(P0.05);在插管后即刻,B、C组的SpO2也显著高于A组(P0.05),同时C组SpO2高于B组(P0.05)。血气分析中,预氧合后,C组的PaO2和SaO2均高于A、B组(P0.05);在插管后即刻,C组PaO2和SaO2高于A组,同时C组SaO2高于B组(P0.05)。并发症的比较上,C组的腹胀发生率明显低于B组(P0.05)。结论:ICU内急救插管前的预氧合能显著提高患者的血氧水平,效果明显好于直接气管插管;在预氧合的方式中,麻醉机-面罩的预氧合效果要优于常规使用的气囊-面罩,且并发症也较少。     

Focus: Personalized Medicine: The Sociology of the Deceased Harvard Medical Unit at Boston City Hospital

Many graduates of the Harvard Medical Unit (HMU) at Boston City Hospital, in either the clinical training/residency program or the research program at the Thorndike Memorial Laboratory, contributed in major ways to the HMU and constantly relived their HMU experiences. The HMU staff physicians, descending from founder and mentor physicians Francis W. Peabody, Soma Weiss, and George R. Minot, were dedicated to the teaching, development, and leadership of its clinical and research trainees, whose confidence and dedication to patient care as a result of their mentorship led many to lifelong achievements as clinicians, teachers, and mentors. Their experience also led to a lifelong love of the HMU (despite its loss), camaraderie, happiness, and intense friendships with their associates.     

医用供应装置的风险分析及应对策略

医用供应装置的医疗事故时有发生。从气体、电气和机械结构等方面,深入分析和评估医用供应装置的风险,提出加强医用供应装置安全性和避免事故发生的应对措施,并介绍ISO国际标准关于医用供应装置的完整标准体系。     

GPU机群系统上加速EMAN(英文)

近年来,高质量的三维重构对计算机系统的计算能力提出越来越高的需求。EMAN是对冷冻电子显微镜拍摄出来的图像进行单颗粒三维重构的流行软件包。由于GPU显示出优于CPU的性能水平,在GPU机群系统上对EMAN进行加速将有可能取得较好的效果。首先,有必要调查EMAN在计算方面的特点,包括计算密度,访存情况和并行潜力。结果显示其在GPU体系结构上有获得较高性能的潜力。然后,根据此特点完成一款并行EMAN软件,使用CUDA和MPI对EMAN实施不同粒度的并行处理。在一个拥有16颗Intel6核处理器的机群系统上,用8颗FermiGPU加速后的EMAN(CUDA-EMAN)相比于仅使用CPU的并行EMAN程序获得了2.5倍的加速比,也就是1颗FermiGPU相比一个Intel6核处理器可对EMAN加速5倍。     

Temperature field reconstruction for minimally invasive cryosurgery with application to wireless implantable temperature sensors and/or medical imaging

There is an undisputed need for temperature-field reconstruction during minimally invasive cryosurgery. The current line of research focuses on developing miniature, wireless, implantable, temperature sensors to enable temperature-field reconstruction in real time. This project combines two parallel efforts: (i) to develop the hardware necessary for implantable sensors, and (ii) to develop mathematical techniques for temperature-field reconstruction in real time—the subject matter of the current study. In particular, this study proposes an approach for temperature-field reconstruction combining data obtained from medical imaging, cryoprobe-embedded sensors, and miniature, wireless, implantable sensors, the development of which is currently underway. This study discusses possible strategies for laying out implantable sensors and approaches for data integration. In particular, prostate cryosurgery is presented as a developmental model and a two-dimensional proof-of-concept is discussed. It is demonstrated that the lethal temperature can be predicted to a significant degree of certainty with implantable sensors and the technique proposed in the current study, a capability that is yet unavailable.     

Combined MRI–PET dissects dynamic changes in plant structures and functions

Unravelling the factors determining the allocation of carbon to various plant organs is one of the great challenges of modern plant biology. Studying allocation under close to natural conditions requires non-invasive methods, which are now becoming available for measuring plants on a par with those developed for humans. By combining magnetic resonance imaging (MRI) and positron emission tomography (PET), we investigated three contrasting root/shoot systems growing in sand or soil, with respect to their structures, transport routes and the translocation dynamics of recently fixed photoassimilates labelled with the short-lived radioactive carbon isotope ¹¹C. Storage organs of sugar beet ( Beta vulgaris ) and radish plants ( Raphanus sativus ) were assessed using MRI, providing images of the internal structures of the organs with high spatial resolution, and while species-specific transport sectoralities, properties of assimilate allocation and unloading characteristics were measured using PET. Growth and carbon allocation within complex root systems were monitored in maize plants ( Zea mays ), and the results may be used to identify factors affecting root growth in natural substrates or in competition with roots of other plants. MRI–PET co-registration opens the door for non-invasive analysis of plant structures and transport processes that may change in response to genomic, developmental or environmental challenges. It is our aim to make the methods applicable for quantitative analyses of plant traits in phenotyping as well as in understanding the dynamics of key processes that are essential to plant performance.     

二十三种药用种子(或果实)中油的化学组成

本文报道了二十三种药用种子(或果实)的含油率和油的化学组成成分,它们分属于二十个科二十二个属中。本文所发表的大部分资料尚未见国内外文献的报道。     

Multimodality imaging of nitric oxide and nitric oxide synthases

Nitric oxide (NO) and NO synthases (NOSs) are crucial factors in many pathophysiological processes such as inflammation, vascular/neurological function, and many types of cancer. Noninvasive imaging of NO or NOS can provide new insights in understanding these diseases and facilitate the development of novel therapeutic strategies. In this review, we will summarize the current state-of-the-art multimodality imaging in detecting NO and NOSs, including optical (fluorescence, chemiluminescence, and bioluminescence), electron paramagnetic resonance (EPR), magnetic resonance (MR), and positron emission tomography (PET). With continued effort over the last several years, these noninvasive imaging techniques can now reveal the biodistribution of NO or NOS in living subjects with high fidelity which will greatly facilitate scientists/clinicians in the development of new drugs and/or patient management. Lastly, we will also discuss future directions/applications of NO/NOS imaging. Successful development of novel NO/NOS imaging agents with optimal in vivo stability and desirable pharmacokinetics for clinical translation will enable the maximum benefit in patient management.     

Biosynthetic processing of the oligosaccharide chains of cellular fibronectin

We have examined the maturation or processing of the oligosaccharides of cellular fibronectin in cultured chick embryo fibroblasts. Fibronectin was pulse-labeled with [2-³H]mannose or [³⁵S]methionine, and the turnover rates of carbohydrate and polypeptide portions of immunoprecipitated fibronectin were compared. The oligosaccharides on fibronectin were analyzed by gel electrophoresis for alterations in sensitivity to the enzyme endo-β-N-acetylglucosaminidase H, which specifically cleaves the ‘high-mannose’ class of asparagine-linked oligosaccharide. Incorporated mannose was removed only at early time points, suggesting that the structure of fibronectin oligosaccharides was altered due to processing.This possibility was confirmed by the analysis of glycopeptides generated by exhaustive pronase digestion. Two major glycopeptide structures were detected; their properties correspond to a ‘high-mannose’ oligosaccharide precursor and a ‘complex’ carbohydrate product. The precursor-product relationship of these two forms of oligosaccharide chains was demonstrated by pulse-chase labeling experiments. The precursor glycopeptide had an apparent size (M_r 2100) comparable to (Man)₉GlcNAc (M_r 2080), and was sensitive to endo-β-N-acetylglucosaminidase H; nearly all of the labeled mannose incorporated in a 10 min pulse was released from fibronectin glycopeptides by this enzyme. During a 90 min chase period, the glycopeptides became larger and increasingly resistent to endo-β-N-acetylglucosaminadase H cleavage. The final ‘complex’ or processed oligosaccharide structure contained approximately two-thirds less associated with the mature glycoprotein. They also indicate that the ‘complex’ structure is synthesized as a ‘high-mannose’ intermediate which is processed by the removal of mannose.     

Consideration of sample motion in cryo-tomography based on alignment residual interpolation

Recently, it has been shown that the resolution in cryo-tomography could be improved by considering the sample motion in tilt-series alignment and reconstruction, where a set of quadratic polynomials were used to model this motion. One requirement of this polynomial method is the optimization of a large number of parameters, which may limit its practical applicability. In this work, we propose an alternative method for modeling the sample motion. Starting from the standard fiducial-based tilt-series alignment, the method uses the alignment residual as local estimates of the sample motion at the 3D fiducial positions. Then, a scattered data interpolation technique characterized by its smoothness and a closed-form solution is applied to model the sample motion. The motion model is then integrated in the tomographic reconstruction. The new method improves the tomogram quality similar to the polynomial one, with the important advantage that the determination of the motion model is greatly simplified, thereby overcoming one of the major limitations of the polynomial model. Therefore, the new method is expected to make the beam-induced motion correction methodology more accessible to the cryoET community.     

Alternative Substrate Kinetics of Escherichia coli Ribonuclease P: DETERMINATION OF RELATIVE RATE CONSTANTS BY INTERNAL COMPETITION*

A single enzyme, ribonuclease P (RNase P), processes the 5′ ends of tRNA precursors (ptRNA) in cells and organelles that carry out tRNA biosynthesis. This substrate population includes over 80 different competing ptRNAs in Escherichia coli. Although the reaction kinetics and molecular recognition of a few individual model substrates of bacterial RNase P have been well described, the competitive substrate kinetics of the enzyme are comparatively unexplored. To understand the factors that determine how different ptRNA substrates compete for processing by E. coli RNase P, we compared the steady state reaction kinetics of two ptRNAs that differ at sequences that are contacted by the enzyme. For both ptRNAs, substrate cleavage is fast relative to dissociation. As a consequence, V/K, the rate constant for the reaction at limiting substrate concentrations, reflects the substrate association step for both ptRNAs. Reactions containing two or more ptRNAs follow simple competitive alternative substrate kinetics in which the relative rates of processing are determined by ptRNA concentration and their V/K. The relative V/K values for eight different ptRNAs, which were selected to represent the range of structure variation at sites contacted by RNase P, were determined by internal competition in reactions in which all eight substrates were present simultaneously. The results reveal a relatively narrow range of V/K values, suggesting that rates of ptRNA processing by RNase P are tuned for uniform specificity and consequently optimal coupling to precursor biosynthesis.     

高海拔地区肺结核影像表现65例回顾分析

目的：探讨总结高海拔地区肺结核的影像特点,更好的指导临床早期诊断。方法：回顾分析65例西藏高原肺结核的影像特点,总结分析其征象及价值。结果：原发型肺结核3例（5％）,影像表现边缘清楚、密度均匀的致密影,伴有淋巴结增大;侵润型结核31例（48％）,影像表现成分混杂的致密影,可见钙化及卫星灶;血行播散型结核27例（42％）,影像表现两肺弥漫分布的结节影;纤维空洞肺结核4例（5％）,影像表现空洞、纤维化、支气管播散三大特征。结论：高原地区肺结核以侵润型和血行播散型为主,有特定的影像特点,可以用来进行诊断。     

Cytoplasmic granule formation in mouse pancreatic acinar cells. Evidence for formation of immature granules (condensing vacuoles) by aggregation and fusion of progranules of unit size,and for reductions in membrane surface area and immature granule volume during granule maturation

We used a computer-assisted morphometry approach to analyze quantitatively the process of cytoplasmic granule formation in mouse pancreatic acinar cells stimulated with pilocarpine to induce secretion. Our findings suggest that each condensing vacuole/immature granule of pancreatic acinar cells is formed by the progressive aggregation of 106 to 128 unit progranules of narrowly fixed volume, define a range of 7.7 to 9.2 for the factor of volume condensation between the largest immature granules and the mature unit granule, and predict that the formation of a single mature unit granule by the aggregation and fusion of unit progranules involves a net reduction of at least 95% in the amount of membrane surface area associated with these structures.