301 research outputs found
KrakenOnMem: A Memristor-Augmented HW/SW Framework for Taxonomic Profiling
No full textState-of-the-art taxonomic profilers that comprise the first step in larger-context metagenomic studies have proven to be computationally intensive, i.e., while accurate, they come at the cost of high latency and energy consumption. Table Lookup operation is a primary bottleneck of today's profilers. In this paper, we first propose TL-PIM, a hardware accelerator based on the processing-in-memory (PIM) paradigm to accelerate Table Lookup. TL-PIM leverages the in-memory compute capability of emerging memory technologies along with intelligent data mapping. Then, we integrate TL-PIM into Kraken2, a state-of-the-art metagenomic profiler, and build an HW/SW co-designed profiler, called KrakenOnMem. Results from a silicon-based prototype of our emerging memory validate the design and required operations on a smaller scale. Our large-scale calibrated simulations show that KrakenOnMem can provide an average of 61.3% speedup compared to original Kraken2 for end-to-end profiling. Additionally, our design improves the energy consumption by orders of magnitude compared to the original Kraken2 while incurring a negligible area overhead. Computer EngineeringElectrical Engineering, Mathematics and Computer ScienceQuantum & Computer Engineerin
The Shooting Method and Nonhomogeneous Multipoint BVPs of Second-Order ODE
No full text In a recent paper, Sun et al. (2007) studied the existence of positive solutions of nonhomogeneous multipoint boundary value problems for a second-order differential equation. It is the purpose of this paper to show that the shooting method approach proposed in the recent paper by the first author can be extended to treat this more general problem.</p
Compressed indexing and local alignment of DNA
No full textMotivation: Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing very long strings such as the human genome in the main memory. For example, a BWT index for the human genome (with about 3 billion characters) occupies just around 1 G bytes. However, these indexes are designed for exact pattern matching, which is too stringent for biological applications. The demand is often on finding local alignments (pairs of similar substrings with gaps allowed). Without indexing, one can use dynamic programming to find all the local alignments between a text T and a pattern P in O ( T P ) time, but this would be too slow when the text is of genome scale (e.g. aligning a gene with the human genome would take tens to hundreds of hours). In practice, biologists use heuristic-based software such as BLAST, which is very efficient but does not guarantee to find all local alignments. Results: In this article, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments. Experiments reveal that BWT-SW is very efficient (e.g. aligning a pattern of length 3 000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically for a simpler similarity model (with gaps disallowed), and we show that the expected running time is O ( T 0.628 P ) for random strings. As far as we know, BWT-SW is the first practical tool that can find all local alignments. Yet BWT-SW is not meant to be a replacement of BLAST, as BLAST is still several times faster than BWT-SW for long patterns and BLAST is indeed accurate enough in most cases (we have used BWT-SW to check against the accuracy of BLAST and found that only rarely BLAST would miss some significant alignments). © The Author 2008. Published by Oxford University Press. All rights reserved.link_to_subscribed_fulltex
Retinal arterioles narrow with increasing duration of anti-retroviral therapy in HIV infection: a novel estimator of vascular risk in HIV?
No full textOBJECTIVES: HIV infection is associated with an increased risk of age-related morbidity mediated by immune dysfunction, atherosclerosis and inflammation. Changes in retinal vessel calibre may reflect cumulative structural damage arising from these mechanisms. The relationship of retinal vessel calibre with clinical and demographic characteristics was investigated in a population of HIV-infected individuals in South Africa. METHODS: Case-control study of 491 adults ≥30 years, composed of 242 HIV-infected adults and 249 age- and gender-matched HIV-negative controls. Retinal vessel calibre was measured using computer-assisted techniques to determine mean arteriolar and venular diameters of each eye. RESULTS: The median age was 40 years (IQR: 35-48 years). Among HIV-infected adults, 87.1% were receiving highly active antiretroviral therapy (HAART) (median duration, 58 months), their median CD4 count was 468 cells/µL, and 84.3% had undetectable plasma viral load. Unadjusted mean retinal arteriolar diameters were 163.67±17.69 µm in cases and 161.34±17.38 µm in controls (p = 0.15). Unadjusted mean venular diameters were 267.77±18.21 µm in cases and 270.81±18.98 µm in controls (p = 0.07). Age modified the effect of retinal arteriolar and venular diameters in relation to HIV status, with a tendency towards narrower retinal diameters in HIV cases but not in controls. Among cases, retinal arteriolar diameters narrowed with increasing duration of HAART, independently of age (167.83 µm 6 years, p-trend = 0.02), and with a HIV viral load >10,000 copies/mL while on HAART (p = 0.05). HIV-related venular changes were not detected. CONCLUSIONS: Narrowing of retinal arteriolar diameters is associated with HAART duration and viral load, and may reflect heightened inflammatory and pro-atherogenic states of the systemic vasculature. Measurement of retinal vascular calibre could be an innovative non-invasive method of estimating vascular risk in HIV-infected individuals
Work Values of University Students in Chinese Mainland, Taiwan, and Hong Kong
No full textLeuty and Hansen (Journal of Vocational Behavior 79:379-390, 2011) identified six domains of work values in undergraduate students in the West. The review undertaken in this paper suggests that the factor structure of work values of university students in Mainland China, Taiwan and Hong Kong essentially matches these six domains, except for the omission of 'Family Maintenance' and Wang's (Indigenous Psychological Research in Chinese Societies 2:206-250, 1993) 'Instrumental Values.' This suggests some commonality in the work values construct between the East and West, but there are a few subtle differences. It is argued that such differences heighten the need for measurement scales with context-specific and society-specific items when examining work values in different settings. © 2012 The Author(s).link_to_subscribed_fulltex
EU immigration trends and policies: Spain and France as case studies. Jean Monnet/Robert Schuman Paper Series Vol. 13 No. 10, August 2013
No full textFrom the Introduction. The Treaty on European Union, also known as the Treaty of Maastricht or the Maastricht
Treaty, created the European Union (EU) from the existing European Economic Community (EEC.) It was signed by the member states on February 7, 1992, and entered into force on
November 1, 1993.1 Among its many innovations was the creation of European citizenship, which would be granted to any person who was a citizen of an EU member state. Citizenship, however, is intertwined with immigration, which the Treaty also attempted to address. Policy on visas, immigration and asylum was originally placed under Pillar 3 of the EU, which dealt with Justice and Home Affairs. In 1997, however, the Amsterdam Treaty moved these policies from Pillar 3 to Pillar 1, signaling “a shift toward more supranational decision-making in this area,” as
opposed to the intergovernmental method of Pillars 2 and 3.
Consumption of dried fruit of Crataegus pinnatifida (hawthorn) suppresses high-cholesterol diet-induced hypercholesterolemia in rats
No full textAuthor name used in this publication: Mabel Yin-Chun YauAuthor name used in this publication: Peter Hoi-Fu Yu2009-2010 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishedGreen (AAM
Author response image 1.
No full textA molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides.MOE (Min. of Education, S’pore)Published versio
Heterogeneous and tissue-specific regulation of effector T cell responses by IFN-gamma during Plasmodium berghei ANKA infection.
No full textIFN-γ and T cells are both required for the development of experimental cerebral malaria during Plasmodium berghei ANKA infection. Surprisingly, however, the role of IFN-γ in shaping the effector CD4(+) and CD8(+) T cell response during this infection has not been examined in detail. To address this, we have compared the effector T cell responses in wild-type and IFN-γ(-/-) mice during P. berghei ANKA infection. The expansion of splenic CD4(+) and CD8(+) T cells during P. berghei ANKA infection was unaffected by the absence of IFN-γ, but the contraction phase of the T cell response was significantly attenuated. Splenic T cell activation and effector function were essentially normal in IFN-γ(-/-) mice; however, the migration to, and accumulation of, effector CD4(+) and CD8(+) T cells in the lung, liver, and brain was altered in IFN-γ(-/-) mice. Interestingly, activation and accumulation of T cells in various nonlymphoid organs was differently affected by lack of IFN-γ, suggesting that IFN-γ influences T cell effector function to varying levels in different anatomical locations. Importantly, control of splenic T cell numbers during P. berghei ANKA infection depended on active IFN-γ-dependent environmental signals--leading to T cell apoptosis--rather than upon intrinsic alterations in T cell programming. To our knowledge, this is the first study to fully investigate the role of IFN-γ in modulating T cell function during P. berghei ANKA infection and reveals that IFN-γ is required for efficient contraction of the pool of activated T cells
Impulsivity and response inhibition in alcohol dependence and problem gambling
No full textINTRODUCTION: Impulsivity is a central feature of drug addiction and may arise as a result of impaired inhibitory control. The extent to which inhibitory deficits arise as a consequence of drug exposure or relate to pre-existing addiction vulnerability is unknown. MATERIALS AND METHODS: This study compared measures of impulsivity in outpatients with alcohol dependence (n = 23) and problem gambling (n = 21), a putative behavioural addiction where direct effects of drug exposure may be minimal. Healthy controls (n = 27) were also tested, in a cross-sectional design. Subjects completed the stop-signal test as a neurocognitive probe of response inhibition, alongside self-report ratings of impulsivity, adult ADHD and OCD. RESULTS: On the stop-signal test, Go reaction time and stop-signal reaction time were significantly slower in the alcohol-dependent group, compared with healthy controls. Healthy controls slowed their responding after successful and failed stop trials. Slowing after failed stop trials was significantly attenuated in the alcohol-dependent subjects. Go reaction time and post-error slowing were correlated with chronicity and severity, respectively, in the alcohol-dependent subjects. Problem gamblers did not differ significantly from controls on the stop-signal test, despite trait elevations in impulsivity ratings. CONCLUSION: Inhibitory control is impaired in alcohol dependence but occurs in the context of psychomotor slowing. In addition, alcohol-dependent individuals failed to show behavioral adjustment following failed stops. These deficits may represent direct effects of chronic alcohol administration on fronto-striatal circuitry
- …
