CiteULike: Author Chu

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

Jonghwan Kim — 2008-03-20T20:38:46-00:00

Cell, Vol. 132, No. 6. (21 March 2008), pp. 1049-1061.

Summary Much attention has focused on a small set of transcription factors that maintain human or mouse embryonic stem (ES) cells in a pluripotent state. To gain a more complete understanding of the regulatory network that maintains this state, we identified target promoters of nine transcription factors, including somatic cell reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) and others (Nanog, Dax1, Rex1, Zpf281, and Nac1), on a global scale in mouse ES cells. We found that target genes fall into two classes: promoters bound by few factors tend to be inactive or repressed, whereas promoters bound by more than four factors are largely active in the pluripotent state and become repressed upon differentiation. Furthermore, we propose a transcriptional hierarchy for reprogramming factors and broadly distinguish targets of c-Myc versus other factors. Our data provide a resource for exploration of the complex network maintaining pluripotency.

Playful Tray: Adopting Ubicomp and Persuasive Techniques into Play-Based Occupational Therapy for Reducing Poor Eating Behavior in Young Children

Jin-Ling Lo — 2008-07-24T18:56:50-00:00

UbiComp 2007: Ubiquitous Computing (2007), pp. 38-55.

This study has created the Playful Tray that adopts Ubicomp and persuasive techniques into play-based occupational therapy for reducing poor eating behavior in young children after they reached their self-feeding age. The design of the Playful Tray reinforces active participation of children in the activity of eating by integrating digital play with eating. Results of a pilot user study suggest that the Playful Tray may improve child meal completion time and reduce negative power play interactions between parents and children, resulting in an improved family mealtime experience.

Binding Studies of Molecular Linkers to ZnO and MgZnO Nanotip Films

O Taratula — 2008-03-06T17:45:21-00:00

J. Phys. Chem. B, Vol. 110, No. 13. (6 April 2006), pp. 6506-6515.

Abstract: Two bifunctional linkers, a rigid-rod p-ethynyl-isophthalic acid capped with a Ru(II)-polypyridyl complex and 3-mercaptopropionic acid, were covalently bound to ZnO nanotip films grown by metal-organic chemical vapor deposition (MOCVD) technology. This highly vertically aligned, crystalline form of ZnO had not been functionalized before. The binding was studied by Fourier transform (FT) IR and UV spectroscopies and probed, in the case of the Ru complex, by static and dynamic fluorescence quenching. The molecules did bind through the carboxylic acid groups, and the FT-IR attenuated total reflectance spectra are indicative of a bidentate carboxylate binding mode. Other molecules (heptanoic acid, isophthalic acid, and trimethoxy(2-phenylethyl)silane) were also bound to the ZnO nanotips. A comparison was made with epitaxial ZnO films grown by MOCVD and ZnO mesoporous films prepared from colloidal solutions to investigate the effect of the ZnO morphology. The ZnO nanotips were excellent binding substrates, particularly for the rigid-rod linker. Since ZnO films are etched at low pH (<4), novel nanotip films made of ternary MgxZn1-xO, which is formed by alloying ZnO with MgO and is more resistant to acids, were developed. The MgxZn1-xO nanotip films were employed to use linkers with acidic groups and to study the effect of pH pretreatment of the surface on the binding.

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

Xiao-Yong Li — 2008-02-12T14:29:09-00:00

PLoS Biology, Vol. 6, No. 2. (1 February 2008), e27.

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior–posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over 40 well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal–ventral patterning genes, whose expression we show to be quantitatively modulated by anterior–posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.

Comparative regional assessment of factors impacting freshwater fish biodiversity in Canada

C Chu — 2008-07-21T06:48:16-00:00

Canadian Journal of Fisheries and Aquatic Sciences (May 2003), pp. 624-634.

This study presents a broad analysis of freshwater fish species biodiversity in relation to environmental and stress metrics throughout Canada. Species presence–absence data were used to calculate richness and rarity indices by tertiary watershed. Richness is higher in the southern parts of Canada, whereas rarity is concentrated in a "ring of rarity" around the periphery of the country. Environmental and stress indices were developed for each watershed using readily available mapped information. The environmental index was estimated using growing degree-days above 5°C, elevation range (m) within the watershed, mean annual sunshine hours, and mean annual vapour pressure (kPa). The number of crop farms, forestry, waste management, and petroleum refining facilities, road density (km·1000 km–2), dwelling density, and discharge sites (chimneys and laundry outlets) per 1000 km2 described the human stresses in each watershed. Conservation priority rankings were developed for the watersheds using an integrative index of the three indices. Watersheds in southern Ontario and British Columbia were ranked high because they contain the greatest biodiversity and the most stress. This study indicates how regional analyses can guide fisheries and watershed management.Notre étude présente une large analyse de la biodiversité des espèces de poissons sur tout le territoire canadien en relation avec des métriques de l'environnement et du stress. Des données de présence–absence des espèces ont permis de calculer des indices de richesse et de rareté par bassin versant tertiaire. La richesse est plus importante dans les régions du sud du Canada, alors que la rareté se distribue en un « anneau de rareté » à la périphérie du pays. Des indices de l'environnement et du stress ont pu être élaborés pour chaque bassin versant à l'aide de données cartographiées facilement disponibles. L'indice environnemental se base sur le nombre de degrés-jours de croissance au-dessus de 5 °C, l'étendue des altitudes (m) dans le bassin, le nombre moyen annuel d'heures d'ensoleillement et la pression de vapeur moyenne annuelle (kPa). Le nombre de fermes agricoles, d'industries forestières, d'installations de récupération des déchets et de raffineries de pétrole, ainsi que la densité des routes (km·1000 km–2), des habitations et des sites de déversements (cheminées et décharges de blanchisseries) par 1000 km2 ont servi à décrire les stress anthropiques dans chaque bassin. Un classement de priorité de conservation a été élaboré pour les bassins à l'aide d'un indice intégrateur des trois indices. Les bassins de l'Ontario et de la Colombie-Britannique ont reçu des rangs élevés car ils contiennent la plus grande biodiversité et subissent les plus grands stress. Notre étude démontre comment des analyses régionales peuvent orienter la gestion des pêches et l'aménagement des bassins versants.[Traduit par la Rédaction]

Self-Diffusion of an Entangled DNA Molecule by Reptation

Douglas Smith — 2006-08-20T17:39:30-00:00

Physical Review Letters, Vol. 75, No. 22. (27 November 1995), 4146.

Diffusion coefficients ( D ) of fluorescently labeled DNA molecules in entangled DNA solutions were measured by tracking Brownian motion. The measured lifetime of tubelike topological constraints that hinder diffusion was longer than the minimum lifetime assumed in the reptation theory. The scaling of D with polymer length and concentration was close to reptation predictions for the highest concentration and longest chain studied. These observations illustrate reptation at the microscopic level.

Fault recognition method for speed-up and speed-down process of rotating machinery based on independent component analysis and Factorial Hidden Markov Model

Zhinong Li — 2008-07-19T04:40:00-00:00

Journal of Sound and Vibration, Vol. 291, No. 1-2. (21 March 2006), pp. 60-71.

The behavior characteristics of the speed-up and speed-down process of rotating machinery possess the distinct diagnostic value. The abundant information, non-stationarity, poor repeatability and reproducibility in this process lead to the necessity to find the corresponding method of feature extraction and fault recognition. In this paper, combining independent component analysis (ICA) and Factorial Hidden Markov Model (FHMM), a new method of the fault recognition named ICA-FHMM is proposed. In the proposed method, ICA is used for the redundancy reduction and feature extraction of the multi-channel detection, and FHMM as a classifier to recognize the faults of the speed-up and speed-down process in rotating machinery. This method is compared with another recognition method named ICA-HMM, in which ICA is similarly used for the feature extraction, however Hidden Markov Model (HMM) as a classifier. Experimental results show that the proposed method is very effective, and the ICA-FHMM recognition method is superior to the ICA-HMM recognition method.

Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods.

HC Liu — 2008-07-17T13:05:15-00:00

Journal of biomedical informatics, Vol. 41, No. 4. (August 2008), pp. 570-579.

Past experiments of the popular Affymetrix (Affy) microarrays have accumulated a huge amount of public data sets. To apply them for more wide studies, the comparability across generations and experimental environments is an important research topic. This paper particularly investigates the issue of cross-generation/laboratory predictions. That is, whether models built upon data of one generation (laboratory) can differentiate data of another. We consider eight public sets of three cancers. They are from different laboratories and are across various generations of Affy human microarrays. Each cancer has certain subtypes, and we investigate if a model trained from one set correctly differentiates another. We propose a simple rank-based approach to make data from different sources more comparable. Results show that it leads to higher prediction accuracy than using expression values. We further investigate normalization issues in preparing training/testing data. In addition, we discuss some pitfalls in evaluating cross-generation/laboratory predictions. To use data from various sources one must be cautious on some important but easily neglected steps.

The Diet-Aware Dining Table: Observing Dietary Behaviors over a Tabletop Surface

Keng-Hao Chang — 2008-07-17T04:35:59-00:00

Pervasive Computing (2006), pp. 366-382.

We are what we eat. Our everyday food choices affect our long-term and short-term health. In the traditional health care, professionals assess and weigh each individual’s dietary intake using intensive labor at high cost. In this paper, we design and implement a diet-aware dining table that can track what and how much we eat. To enable automated food tracking, the dining table is augmented with two layers of weighing and RFID sensor surfaces. We devise a weight-RFID matching algorithm to detect and distinguish how people eat. To validate our diet-aware dining table, we have performed experiments, including live dining scenarios (afternoon tea and Chinese-style dinner), multiple dining participants, and concurrent activities chosen randomly. Our experimental results have shown encouraging recognition accuracy, around 80%. We believe monitoring the dietary behaviors of individuals potentially contribute to diet-aware healthcare.

Superconductivity up to 37 K in (A1-xSrx)Fe2As2 with A=K and Cs arXiv:0806.1301

K Sasmal — 2008-07-16T13:16:00-00:00

(11 Jun 2008)

A new hight Tc Fe-based compound system, AFe2As2 with A = K, Cs, K/Sr and Cs/Sr has been found. Through electron-doping, Tc of the A = K and Cs compounds rises to ~37 K, and finally enter a spin-density-wave state (SDW) through further electron doping with Sr. The observation demonstrates the crucial role of the (FeAs)-layers in the superconductivity in the Fe-based layered system and the special feature of elemental A-layers in this complex chemical system may provide new avenues to superconductivity at a higher Tc.

Association between genetic variation in transforming growth factors beta1 and beta3 and renal dysfunction in non-diabetic Chinese.

BC Hu — 2008-07-15T15:44:41-00:00

Clinical and experimental hypertension (New York, N.Y. : 1993), Vol. 30, No. 2. (February 2008), pp. 121-131.

Genetic variants of transforming growth factor (TGF) beta1 have been reported to be associated with diabetic nephropathy. Few studies investigated polymorphisms in the TGF-beta1 and TGF-beta3 genes in relation to renal dysfunction in non-diabetic subjects. In all, 601 non-diabetic Chinese were genotyped for the TGF-beta1 T869C and TGF-beta3 IVS3-98G>A polymorphisms by PCR-restriction fragment length polymorphism and real-time allele-specific PCR, respectively. Renal dysfunction was defined as a predicted glomerular filtration rate (GFR) of 60mL/min/1.73m(2) or less. 24-hour urinary albumin excretion was measured by an immunonephelometric assay in 352 hypertensive subjects. Our study sample included 184 (30.6%) women, 396 (65.9%) hypertensive patients (65.9%), and 94 (15.6%) patients with renal dysfunction. In men but not women, the TGF-beta1 TC genotype was significantly (p = 0.0005) overrepresented in patients with renal dysfunction (52.2% vs 36.8% in subjects with normal renal function). Accordingly, in men, with adjustment for age, body mass index, and systolic and diastolic blood pressure, serum creatinine concentration was significantly (p < or = 0.03) higher in the TC heterozygotes than TT and CC homozygotes. Furthermore, in 231 male hypertensive patients, with similar adjustments applied, 24-hour urinary albumin excretion was significantly (p = 0.02) higher in the IVS3-98 AA homozygotes than G allele carriers. In further multivariate regression analysis, only in men, TGF-beta1 and TGF-beta3 genotypes as independent predictors had statistically significant effect on serum creatinine (p = 0.007) and urinary albumin excretion (p = 0.022), respectively. Our study demonstrated the associations of genetic variants in the TGF-beta genes with renal dysfunction and albuminuria in non-diabetic Han Chinese men but not women.

Truncated Nambu-Poisson Bracket and Entropy Formula for Multiple Membranes

Chong-Sun Chu — 2008-07-15T05:14:58-00:00

(14 Jul 2008)

We show that there exists a cut-off version of Nambu-Poisson bracket which defines a finite dimensional Lie 3-algebra. The algebra still satisfies the fundamental identity and thus produces N=8 supersymmetric BLG type equation of motion for multiple M2 branes. By counting the number of the moduli and the degree of freedom, we derive an entropy formula which scales as N^3/2 as expected for the multiple M2 branes.

Knowledge-based query expansion to support scenario-specific retrieval of medical free text

Liu — 2007-03-09T23:29:11-00:00

Information Retrieval, Vol. 10, No. 2. (April 2007), pp. 173-202.

Lansoprazole for the prevention of recurrences of ulcer complications from long-term low-dose aspirin use.

KC Lai — 2008-07-12T03:29:00-00:00

The New England journal of medicine, Vol. 346, No. 26. (27 June 2002), pp. 2033-2038.

BACKGROUND: The role of gastric acid suppression in preventing the recurrence of ulcer complications after the eradication of Helicobacter pylori infection in patients taking long-term low-dose aspirin is uncertain. METHODS: We enrolled 123 patients who had ulcer complications after using low-dose aspirin continuously for more than one month and who had H. pylori infection. After the ulcers had healed and the H. pylori infection was eradicated, the patients were randomly assigned to treatment with 30 mg of lansoprazole daily or placebo, in addition to 100 mg of aspirin daily, for 12 months. The primary end point was the recurrence of ulcer complications. RESULTS: During a median follow-up of 12 months, 9 of the 61 patients in the placebo group (14.8 percent), as compared with 1 of the 62 patients in the lansoprazole group (1.6 percent), had a recurrence of ulcer complications (adjusted hazard ratio, 9.6; 95 percent confidence interval, 1.2 to 76.1). Of these 10 patients, 4 had evidence of a recurrence of H. pylori infection and 2 had taken nonsteroidal antiinflammatory drugs before the onset of complications. Patients in the lansoprazole group were significantly less likely to have a recurrence of ulcer complications than patients in the placebo group (P=0.008). There was no significant difference in mortality between the two groups. CONCLUSIONS: In patients who had ulcer complications related to the long-term use of low-dose aspirin, treatment with lansoprazole in addition to the eradication of H. pylori infection significantly reduced the rate of recurrence of ulcer complications.

Recent advances in the IBM GALE Mandarin transcription system

SM Chu — 2008-07-11T00:21:24-00:00

Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on (2008), pp. 4329-4332.

This paper describes the system and algorithmic developments in the automatic transcription of Mandarin broadcast speech made at IBM in the second year of the DARPA GALE program. Technical advances over our previous system include improved acoustic models using embedded tone modeling, and a new topic-adaptive language model (LM) rescoring technique based on dynamically generated LMs. We present results on three community-defined test sets designed to cover both the broadcast news and the broadcast conversation domain. It is shown that our new baseline system attains a 15.4% relative reduction in character error rate compared with our previous GALE evaluation system. And a further 13.6% improvement over the baseline is achieved with the two described techniques.

Biomarker discovery in microarray gene expression data with Gaussian processes

Wei Chu — 2005-08-20T13:51:42-00:00

Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3385-3393.

Electrically controlled surface plasmon resonance frequency of gold nanorods

KC Chu — 2008-07-09T05:07:06-00:00

Applied Physics Letters, Vol. 89, No. 10. (2006)

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Overexpression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice.

Q Wang — 2008-07-08T08:20:18-00:00

Plant molecular biology, Vol. 67, No. 6. (August 2008), pp. 589-602.

DREB transcription factors play key roles in plant stress signalling transduction pathway, they can specifically bind to DRE/CRT element (G/ACCGAC) and activate the expression of many stress inducible genes. Here, a novel rice DREB transcription factor, OsDREB1F, was cloned and characterised via subtractive suppression hybridisation (SSH) from upland rice. Expression analysis revealed that OsDREB1F gene was induced by salt, drought, cold stresses, and also ABA application, but not by pathogen, wound, and H(2)O(2). Subcellular localization results indicated that OsDREB1F localizes in nucleus. Yeast activity assay demonstrated that OsDREB1F gene encodes a transcription activator, and can specifically bind to DRE/CRT but not to ABRE element. Transgenic plants harbouring OsDREB1F gene led to enhanced tolerance to salt, drought, and low temperature in both rice and Arabidopsis. The further characterisation of OsDREB1F-overexpressing Arabidopsis showed that, besides activating the expression of COR genes which contain DRE/CRT element in their upstream promoter regions, the expression of rd29B and RAB18 genes were also activated, suggested that OsDREB1F may also participate in ABA-dependent pathway.

Comparison of the diuretic effect of furosemide mixed with human albumin or fresh frozen plasma for patients with hypoalbuminemia in the intensive care unit.

CW Hsu — 2008-07-08T08:15:08-00:00

Journal of nephrology, Vol. 19, No. 5. (t 2006), pp. 621-627.

BACKGROUND: Diuretics are commonly used in the intensive care unit (ICU) for patients with fluid over-loading. Hypoalbuminemia is a major cause of diuretic resistance. Albumin mixed with furosemide can promote diuresis and sodium excretion in patients with hypoalbuminemia. The purpose of this study is to compare the diuretic effect of furosemide (FU) mixed with human albumin (HA) or fresh frozen plasma (FFP) in ICU patients with hy-poalbuminemia. METHODS: Patients with fluid overloading and hypoalbuminemia who needed diuretic treatment were enrolled and were divided into 2 groups: the first group having clearance of creatinine (CCr) >20 ml/min, and the second group having CCr < or = 20 ml/min. FU (60 mg) mixed with HA (HA group), 60 mg FU mixed with FFP (FFP group) and water (placebo group) were given intravenously to these patients for 60 minutes in random order on the first, third and fifth day. After drug administration, 8-hour urine was collected, and urine amount and urinary sodium excretion were checked. RESULTS: Both the HA group and the FFP group had significantly higher urinary volume and sodium excretion than the placebo group in the patients with CCr >20 ml/min or CCr < or = 20 ml/min (p < 0.01). In the patients with CCr >20 ml/min, there was no difference in the amount of urine excretion and cumulative urinary sodium excretion between the HA group and FFP group. In the patients with CCr < or =ml;20 ml/min, the HA group had a significantly higher urine output and urinary sodium excretion than the FFP group (p < 0.05). CONCLUSIONS: In ICU patients, 60 mg FU mixed with HA or FFP has a similar diuretic effect in patients with CCr >20 ml/min. FFP is an effective alternative choice for improving diuresis for ICU patients with hypoalbuminemia. In patients with CCr < or = 20 ml/min, albumin mixed with 60 mg FU has a superior diuretic effect compared with FFP mixed with FU.

Challenges and opportunities for photochemists on the verge of solar energy conversion.

CC Chu — 2008-07-07T09:02:13-00:00

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology, Vol. 7, No. 5. (May 2008), pp. 521-530.

Has photochemistry missed the boat on solar energy conversion? Certainly not, but it is time to reach out and make a difference if we do not want to have to choose between feeding our families or our thirst for fuel. Compared to other initiatives, such as biofuels or nuclear fusion, direct conversion of solar energy into electricity or fuels is lagging behind in terms of funding, and this is slowing progress on overcoming critical bottlenecks. This perspective outlines some of the key fundamental issues in solar energy conversion based on organic photovoltaic devices or artificial photosynthesis where being a photochemist can make a difference.

Functional profiling of the Saccharomyces cerevisiae genome.

G Giaever — 2006-01-25T01:50:18-00:00

Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391.

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

A Self-Organizing Storage Cluster for Parallel Data-Intensive Applications

Hong Tang — 2008-04-30T20:15:33-00:00

(2004)

Analysis of quasi-static scheduling techniques in a virtualized reconfigurable machine

Yury Markovskiy — 2008-07-04T16:46:05-00:00

(2002), pp. 196-205.

Corrosion characterization of durable silver coatings by electrochemical impedance spectroscopy and accelerated environmental testing

Chung-Tse Chu — 2008-07-04T16:16:34-00:00

Appl. Opt., Vol. 45, No. 7. (1 March 2006), pp. 1583-1593.

Highly reflective front-surface silver mirrors are needed for many optical applications. While various protective dielectric coating schemes have been developed, the long-term durability of Ag mirrors is still of great concern in the optics community for a variety of applications under harsh environments. The corrosion protection behavior of a SiN x -coated silver-mirror coating scheme was tested with electrochemical impedance spectroscopy (EIS) and accelerated environmental testing, including humidity and salt fog tests. The EIS data obtained were fitted with different equivalent circuit models. The results suggested that the 100Å thick SiN x coating produced by rf magnetron sputtering was porous and acted as a leaky capacitor on the Ag film, whereas the addition of a NiCrN x interlayer as thin as 3Å between SiN x and Ag films resulted in a much denser SiN x coating with a low-frequency impedance value of 2 orders of magnitude higher than that without the interlayer. Humidity and salt fog testing of different silver coatings showed similar results. The 100Å SiN x /3Å-NiCrN x /Ag coating exhibited excellent corrosion resistance against the corrosive environments used in this study.

Stream computations organized for reconfigurable execution

André Dehon — 2008-07-04T13:45:16-00:00

Microprocessors and Microsystems, Vol. 30, No. 6. (4 September 2006), pp. 334-354.

Reconfigurable systems can offer the high spatial parallelism and fine-grained, bit-level resource control traditionally associated with hardware implementations, along with the flexibility and adaptability characteristic of software. While reconfigurable systems create new opportunities for engineering and delivering high-performance programmable systems, the traditional approaches to programming and managing computations used for hardware systems (e.g., Verilog, VHDL) and software systems (e.g., C, Fortran, Java) are inappropriate and inadequate for exploiting reconfigurable platforms. To address this need, we develop a stream-oriented compute model, system architecture, and execution patterns which can capture and exploit the parallelism of spatial computations while simultaneously abstracting software applications from hardware details (e.g., timing, device capacity, and microarchitectural implementation details) and consequently allowing applications to scale to exploit newer, larger, and faster hardware platforms. Further, we describe hardware and software techniques that make this late-bound platform mapping viable and efficient.

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets

Liang Chu — 2008-07-03T09:44:13-00:00

BMC Systems Biology, Vol. 2, No. 1. (2008)

BACKGROUND:Cancer is caused by genetic abnormalities, such as mutations of oncogenes or tumor suppressor genes, which alter downstream signal transduction pathways and protein-protein interactions. Comparisons of the interactions of proteins in cancerous and normal cells can shed light on the mechanisms of carcinogenesis.RESULTS:We constructed initial networks of protein-protein interactions involved in the apoptosis of cancerous and normal cells by use of two human yeast two-hybrid data sets and four online databases. Next, we applied a nonlinear stochastic model, maximum likelihood parameter estimation, and Akaike Information Criteria (AIC) to eliminate false-positive protein-protein interactions in our initial protein interaction networks by use of microarray data. Comparisons of the networks of apoptosis in HeLa (human cervical carcinoma) cells and in normal primary lung fibroblasts provided insight into the mechanism of apoptosis and allowed identification of potential drug targets. The potential targets include BCL2, caspase-3 and TP53. Our comparison of cancerous and normal cells also allowed derivation of several party hubs and date hubs in the human protein-protein interaction networks involved in caspase activation.CONCLUSIONS:Our method allows identification of cancer-perturbed protein-protein interactions involved in apoptosis and identification of potential molecular targets for development of anti-cancer drugs.

A Comparative Analysis of RFID Adoption in Retail and Manufacturing Sectors

Mithu Bhattacharya — 2008-07-02T17:10:10-00:00

RFID, 2008 IEEE International Conference on (2008), pp. 241-249.

Radio Frequency Identification (RFID) technology mandates by large retailers and various government agencies has driven compliance requirements for many organizations to implement the technology. In this paper, we use content analysis methodology and examine open literature, news releases, industry white papers, and published journal and conference articles to identify and compare current implementation status, adoption drivers, potential benefits, supply chain activities, applicable tasks, and challenges of implementing RFID in the retail and manufacturing sectors. Our analysis concluded that whereas RFID applicable tasks for retail and manufacturing sectors are significantly different, the adoption drivers, benefits, supply chain activities, and challenges are similar.

SIP-RLTS: An RFID Location Tracking System Based on SIP

Zang Li — 2008-07-02T17:03:03-00:00

RFID, 2008 IEEE International Conference on (2008), pp. 173-182.

Radio Frequency Identification (RFID) technology has recently being favorably considered as a cost-effective alternative for indoor location tracking. However, most current implementations use active tags and conventional middleware, which are more expensive, complicate to use, and may not work with other pervasive devices such as IP Multimedia systems or cell phones. In this paper, we propose an RFID-enabled location tracking system, SIP-RLTS, based on Session Initiation Protocol (SIP). Our proposed solution can be used for both Push and Pull location tracking modes and can be used with either active or passive tags. The use of SIP infrastructure, coupled with the proposed location-oriented middleware extension, Ontology infrastructure and semantic integration, making SIP-RLTS a more cost-effective solution for the next generation communication services.

The vulnerable, or high-risk, atherosclerotic plaque: noninvasive MR imaging for characterization and assessment.

T Saam — 2008-07-01T19:29:05-00:00

Radiology, Vol. 244, No. 1. (July 2007), pp. 64-77.

"Vulnerable" plaques are atherosclerotic plaques that have a high likelihood to cause thrombotic complications, such as myocardial infarction or stroke. Plaques that tend to progress rapidly are also considered to be vulnerable. Besides luminal stenosis, plaque composition and morphology are key determinants of the likelihood that a plaque will cause cardiovascular events. Noninvasive magnetic resonance (MR) imaging has great potential to enable characterization of atherosclerotic plaque composition and morphology and thus to help assess plaque vulnerability. A classification for clinical, as well as pathologic, evaluation of vulnerable plaques was recently put forward in which five major and five minor criteria to define vulnerable plaques were proposed. The purpose of this review is to summarize the status of MR imaging with regard to depiction of the criteria that define vulnerable plaques by using existing MR techniques. The use of MR imaging in animal models and in human disease in various vascular beds, particularly the carotid arteries, is presented.

Evolution of e-commerce Web sites: A conceptual framework and a longitudinal study

Sung-Chi Chu — 2007-02-23T13:45:50-00:00

Information & Management, Vol. 44, No. 2. (March 2007), pp. 154-164.

Before the 1990s, the digital exchange of information between companies was achieved using electronic data interchange (EDI) and needed agreement between the organizations. The early 1990s saw the commercialization of the Internet and the advent of open computer technology and connectivity became affordable for individuals as well as businesses. The consequence was the World Wide Web. As e-commerce activities extended across businesses, enterprises, and industries, a genre of Web sites emerged allowing the integrative management of business operations. Here, we provide an evolutionary perspective of e-commerce Web sites. We posited that there have been four eras. To chart the evolution of e-commerce Web sites, a conceptual framework was developed to characterize such sites. Based on the framework, we conducted a longitudinal study between 1993 and 2001. The result showed that the proposed four eras were clearly discernible.

A spatio-temporal approach for global validation and analysis of MODIS aerosol products

Charles Ichoku — 2008-07-01T03:55:45-00:00

Geophysical Research Letters, Vol. 29, No. 12. (29 June 2002), 8006.

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

WG Noid — 2008-06-30T22:13:37-00:00

The Journal of Chemical Physics, Vol. 128, No. 24. (2008)

Correlation of metabolic syndrome with residual renal function, solute transport rate and peritoneal solute clearance in chronic peritoneal dialysis patients.

HY Chen — 2008-06-29T03:42:33-00:00

Blood purification, Vol. 26, No. 2. (2008), pp. 138-144.

BACKGROUND: Metabolic syndrome (MetS) and insulin resistance (IR) strongly promote macrovascular complications and endothelial dysfunction. They accelerate the progression of renal dysfunction in chronic kidney disease patients. However, their correlation with residual renal function (RRF) and peritoneal characteristics have never been investigated. METHODS: The inter-relationships of IR (homeostatic model assessment, HOMA(IR)), serum adiponectin level, body mass index (BMI), highly sensitive C-reactive protein (hs-CRP), RRF, peritoneal solute clearance (Kt/V(urea)) and solute transport rate of 104 chronic peritoneal dialysis (PD) patients were examined. RESULTS: Patients with (n = 57) and without (n = 47) clinically diagnosed MetS had the same degree of RRF, peritoneal Kt/V(urea), and solute transport rate. Higher HOMA(IR) (p = 0.011), BMI (p = 0.01) and hs-CRP (p = 0.032), as well as lower adiponectin (p = 0.019), were associated with lower peritoneal Kt/V(urea). Serum adiponectin was negatively associated with solute transport rate (p = 0.02). In multiple regression analysis, higher HOMA(IR) (p = 0.005), BMI (p = 0.021) and hs-CRP (p < 0.001) correlated with lower peritoneal Kt/V(urea). CONCLUSIONS: MetS plays an important role in both macrovascular complications and endothelial dysfunction in chronic PD patients, which correlates with changes in peritoneal solute clearance and solute transport rate but not RRF.

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.

JW Chu — 2005-11-16T17:19:32-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 37. (13 September 2005), pp. 13111-13116.

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbein et al. [Otterbein, L. R., Graceffa, P. & Dominguez, R. (2001) Science 293, 708-711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. & Dominguez, R. (2003) J. Biol. Chem. 278, 34172-34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an alpha-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 microm) and of G-ADP (8.5 microm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.

Feedback Circuit among INK4 Tumor Suppressors Constrains Human Glioblastoma Development

Ruprecht Wiedemeyer — 2008-04-18T20:29:27-00:00

Cancer Cell, Vol. 13, No. 4. (8 April 2008), pp. 355-364.

Summary We have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18INK4C and p16INK4A codeletion. Functional reconstitution of p18INK4C in GBM cells null for both p16INK4A and p18INK4C resulted in impaired cell-cycle progression and tumorigenic potential. Conversely, RNAi-mediated depletion of p18INK4C in p16INK4A-deficient primary astrocytes or established GBM cells enhanced tumorigenicity in vitro and in vivo. Furthermore, acute suppression of p16INK4A in primary astrocytes induced a concomitant increase in p18INK4C. Together, these findings uncover a feedback regulatory circuit in the astrocytic lineage and demonstrate a bona fide tumor suppressor role for p18INK4C in human GBM wherein it functions cooperatively with other INK4 family members to constrain inappropriate proliferation.

Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice

Fang — 2008-04-11T05:44:31-00:00

The Plant Journal, Vol. 54, No. 2. (April 2008), pp. 177-189.

Orientational control is an efficient control mechanism for phase switching in the E. coli fim system.

D Chu — 2008-06-24T12:32:07-00:00

Journal of theoretical biology, Vol. 244, No. 3. (7 February 2007), pp. 541-551.

The fim system in E. coli controls the expression of type-1 fimbriae. These are hair-like structures that can be used to attach to host cells. Fimbriation is controlled by a mechanism called "orientational control." We present two families of models for orientational control to understand the details of how it works. We find that the main benefits of orientational control are that (i) it allows rapid adjustment of fimbriation levels in response to a change of environmental conditions while (ii) keeping the overall frequencies with which a cell switches between the fimbriate state and the afimbriate state low. The main reason for the efficiency of orientational control in regulation of fimbriation levels is that it keeps the system far from its steady state.

Localization of phosphorylated ERK/MAP kinases to mitochondria and autophagosomes in Lewy body diseases.

JH Zhu — 2008-06-19T18:13:33-00:00

Brain pathology (Zurich, Switzerland), Vol. 13, No. 4. (October 2003), pp. 473-481.

We previously found that sustained ERK activation contributes to toxicity elicited by the parkinsonian neurotoxin 6-hydroxydopamine. In addition, substantia nigra neurons from patients with incidental Lewy body disease, Parkinson disease (PD), and diffuse Lewy body dementia (DLB) display abnormal phospho-ERK accumulations in the form of discrete cytoplasmic granules. In this study, we investigated the subcellular localization of phospho-ERK immunoreactive granules using double label confocal microscopy and immuno-electron microscopy. A small percentage of phospho-ERK granules co-localized with the early endosome marker Rab5, but not with cathepsin D, 20S proteasome beta-subunit, or cytochrome P450 reductase. Phospho-ERK immunoreactivity was often associated with mitochondrial proteins (MnSOD, 60 kDa and 110 kDa mitochondrial antigens), and some vesicular-appearing phospho-ERK granules appeared to envelop enlarged mitochondria by confocal laser scanning microscopy. Ultrastructural immuno-gold studies revealed phospho-ERK labeling in mitochondria and in association with bundles of approximately 10 nm fibrils. Heavily labeled mitochondria were observed within autophagosomes. As mitochondrial pathology may play a pivotal role in Parkinson and other related neurodegenerative diseases, these studies suggest a potential interaction between dysfunctional mitochondria, autophagy, and ERK signaling pathways.

Regulation of Autophagy by Extracellular Signal-Regulated Protein Kinases During 1-Methyl-4-Phenylpyridinium-Induced Cell Death

Zhu — 2007-01-27T11:11:36-00:00

American Journal of Pathology, Vol. 170, No. 1. (1 January 2007), pp. 75-86.

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map

Sean Collins — 2007-02-22T10:11:12-00:00

Nature (21 February 2007)

IMG/M: a data management and analysis system for metagenomes.

VM Markowitz — 2008-03-28T03:21:41-00:00

Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m.

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.

EA Winzeler — 2006-01-25T01:43:16-00:00

Science, Vol. 285, No. 5429. (6 August 1999), pp. 901-906.

The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.

Improvement in diabetes control with a monitoring system based on a hand-held, touch-screen electronic diary.

MW Tsang — 2008-06-17T09:46:55-00:00

Journal of telemedicine and telecare, Vol. 7, No. 1. (2001), pp. 47-50.

We conducted a six-month prospective interventional crossover study examining a computerized diabetes monitoring system (DMS) that conveyed dietary information. The objectives were to compare glycaemic control between intervention and control periods, and to assess patients' acceptance of the DMS. Nineteen patients were randomized into two groups, each using the DMS for three months and serving as the control group for another three months. The patients recorded information about their meal portions and blood glucose readings in a hand-held electronic diary. After transmitting the data to the DMS through a telephone modem, the patients received immediate feedback about the carbohydrate, protein and fat content of the meal, as well as the calorie content. A significant improvement in glycaemic control was achieved during intervention compared with control periods (mean HbA1C reduction of 0.825%). The DMS was also highly acceptable: 95% patients found it easy to operate while 63% found it useful. The DMS was thus a feasible model of telemedicine in diabetes care and a larger study is warranted to examine its cost-effectiveness.

The perception of cross-modal simultaneity (or “the Greenwich Observatory Problem” revisited)

Daniel Levitin — 2008-06-16T12:48:59-00:00

COMPUTING ANTICIPATORY SYSTEMS: CASYS'99 - Third International Conference, Vol. 517, No. 1. (2000), pp. 323-329.

The cutting stock problem with mixed objectives: Two heuristics based on dynamic programming

Julien Antonio — 2008-06-14T18:15:44-00:00

European Journal of Operational Research, Vol. 114, No. 2. (16 April 1999), pp. 395-402.

The purpose of this paper is to provide efficient methods for solving a large spectrum of industrial cutting stock problems. We propose two methods. Both are based on dynamic programming. In both methods, we reduce the computation burden by keeping, at each stage of the dynamic programming process, only the states which seem to be the most promising in terms of cost. One of the methods favours the computation time at the expense of the quality of the solution; this method is used in the sale department, where the goal is to propose a "good" solution in less than one minute. The second method favours the quality of the solution. Industrial applications are proposed.

Probing the Steroid Binding Domain-like I (SBDLI) of the Sigma-1 Receptor Binding Site Using N-Substituted Photoaffinity Labels.

Dominique Fontanilla — 2008-06-13T17:46:03-00:00

Biochemistry (12 June 2008)

Radioiodinated photoactivatable photoprobes can provide valuable insights regarding protein structure. Previous work in our laboratory showed that the cocaine derivative and photoprobe 3-[ (125)I]iodo-4-azidococaine ([ (125)I]IACoc) binds to the sigma-1 receptor with 2-3 orders of magnitude higher affinity than cocaine [Kahoun, J. R. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1393-1397]. Using this photoprobe, we demonstrated the insertion site for [ (125)I]IACoc to be Asp188 [Chen, Y. (2007) Biochemistry 46, 3532-3542], which resides in the proposed steroid binding domain-like II (SBDLII) region (amino acids 176-194) [Pal, A. (2007) Mol. Pharmacol. 72, 921-933]. An additional photoprobe based on the sigma-1 receptor ligand fenpropimorph, 1- N-(2-3-[ (125)I]iodophenyl)propane ([ (125)I]IAF), was found to label a peptide in both the SBDLII and steroid binding domain-like I (SBDLI) (amino acids 91-109) [Pal, A. (2007) Mol. Pharmacol. 72, 921-933]. In this report, we describe two novel strategically positioned carrier-free, radioiodinated photoaffinity labels specifically designed to probe the putative "nitrogen interacting region" of sigma-1 receptor ligands. These two novel photoprobes are (-)-methyl 3-(benzoyloxy)-8-2-(4-azido-3-[ (125)I]iodobenzene)-1-ethyl-8-azabicyclo[3.2.1]octane-2-carboxylate ([ (125)I]-N-IACoc) and N-propyl- N-(4-azido-3-iodophenylethyl)-3-(4-fluorophenyl)propylamine ([ (125)I]IAC44). In addition to reporting their binding affinities to the sigma-1 and sigma-2 receptors, we show that both photoaffinity labels specifically and covalently derivatized the pure guinea pig sigma-1 receptor (26.1 kDa) [Ramachandran, S. (2007) Protein Expression Purif. 51, 283-292]. Cleavage of the photolabeled sigma-1 receptor using Endo Lys C and cyanogen bromide (CNBr) revealed that the [ (125)I]-N-IACoc label was located primarily in the N-terminus and SBDLI-containing peptides of the sigma-1 receptor, while [ (125)I]IAC44 was found in peptide fragments consistent with labeling of both SBDLI and SBDLII.

Theoretical analysis of velocity-selective Raman transitions

Kathryn Moler — 2007-11-28T10:44:39-00:00

Physical Review A, Vol. 45, No. 1. (1 January 1992), 342.

This paper analyzes the use of Raman transitions to select a narrow velocity distribution of atoms. We determine the evolution of the atomic wave function comprised of both the internal state and the external momentum of the atom in the presence of two counterpropagating laser beams. The effects of a single π pulse; two separated Ramsey π/2 pulses; and a sequence of four π/2 pulses are analyzed.

Processing of DNA for Nonhomologous End-joining Is Controlled by Kinase Activity and XRCC4/Ligase IV

Joe Budman — 2008-06-12T13:51:15-00:00

J. Biol. Chem., Vol. 282, No. 16. (20 April 2007), pp. 11950-11959.

Nonhomologous end-joining (NHEJ) repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. To repair the broken ends, NHEJ processes noncompatible ends into a ligatable form but suppresses processing of compatible ends. It is not known how NHEJ controls polymerase and nuclease activities to act exclusively on noncompatible ends. Here, we analyzed processing independently of ligation by using a two-stage assay with extracts that recapitulated the properties of NHEJ in vivo. Processing of noncompatible ends required wortmannin-sensitive kinase activity. Since DNA-dependent protein kinase catalytic subunit (DNA-PKcs) brings the ends together before undergoing activation of its kinase, this suggests that processing occurred after synapsis of the ends. Surprisingly, all polymerase and most nuclease activity required XRCC4/Ligase IV. This suggests a mechanism for how NHEJ suppresses processing to optimize the preservation of DNA sequence. 10.1074/jbc.M610058200

Enabling conferencing applications on the internet using an overlay muilticast architecture

Yang Chu — 2008-06-12T12:04:12-00:00

SIGCOMM Comput. Commun. Rev., Vol. 31, No. 4. (October 2001), pp. 55-67.

Linear and nonlinear optical properties of carbon nanotubes from first-principles calculations

GY Guo — 2008-06-10T11:12:06-00:00

Physical Review B, Vol. 69, No. 20. (28 May 2004), 205416.