Thu, 07 Aug 2008 21:27:20 BST CiteULike: Author Cai http://www.citeulike.org/author/Cai CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/tbg/article/3096362 <i>Automatic Face and Gesture Recognition, 2000. Proceedings. Fourth IEEE International Conference on (2000), pp. 422-427.</i><br /><br />In order to incorporate naturalness in the design of human computer interfaces (HCI), it is desirable to develop recognition techniques capable of handling continuous natural gesture and speech inputs. Though many different researchers have reported high recognition rates for gesture recognition using hidden Markov models (HMM), the gestures used are mostly pre-defined and are bound with syntactical and grammatical constraints. But natural gestures do not string together in syntactical bindings. Moreover, strict classification of natural gestures is not feasible. We have examined hand gestures made in a very natural domain, that of a weather person narrating in front of a weather map. The gestures made by the weather person are embedded in a narration. This provides us with abundant data from an uncontrolled environment to study the interaction between speech and gesture in the context of a display. We hypothesize that this domain is very similar to that of a natural human-computer interface. We present an HMM architecture for continuous gesture recognition framework and keyword spotting. To explore the relation between gesture and speech, we conducted a statistical co-occurrence analysis of different gestures with a selected set of spoken keywords. We then demonstrate how this co-occurrence analysis can be exploited to improve the performance of continuous gesture recognition Exploiting speech/gesture co-occurrence for improving continuous gesture recognition in weather narration R Sharma J Cai S Chakravarthy I Poddar Y Sethi doi:10.1109/AFGR.2000.840669 Automatic Face and Gesture Recognition, 2000. Proceedings. Fourth IEEE International Conference on (2000), pp. 422-427. 2008-08-07T16:00:24-00:00 2000 Automatic Face and Gesture Recognition, 2000. Proceedings. Fourth IEEE International Conference on 422 427 no-tag http://www.citeulike.org/user/DigitalPig/article/3091242 <i>Colloids and Surfaces B: Biointerfaces, Vol. 49, No. 1. (15 April 2006), pp. 49-54.</i><br /><br />This study applied TAM air isothermal calorimeter to measure the adsorption enthalpies of DNA on eight colloidal fractions from permanent-charge and variable-charge soils. The adsorption of DNA on soil colloids was also examined by equilibrium adsorption analysis. The data evaluated from isotherms fitted by Langmuirean model revealed that the affinity of DNA for variable-charge soil colloids was higher than that for permanent-charge soil colloids. More tightly bound DNA molecules were observed on coarse clays and inorganic clays than on fine clays and organic clays, respectively. The adsorption enthalpies of DNA on permanent-charge soil colloids were higher than those on variable-charge soil colloids. DNA adsorption on organic clays is endothermic, whereas that on inorganic clays is exothermic. Dehydration and electrostatic repulsion were considered to cause the higher adsorption enthalpies of DNA with organic clays, while hydrogen bonding, ligand exchange and electrostatic attraction result in the lower DNA adsorption enthalpies on inorganic clays. The thermodynamic parameters presented in this study have important implication for providing further insight into mechanisms of the adsorption of DNA on soil particles. Microcalorimetric studies on the adsorption of DNA by soil colloidal particles Peng Cai Qiaoyun Huang Daihua Jiang Xingmin Rong Wei Liang doi:10.1016/j.colsurfb.2006.02.011 Colloids and Surfaces B: Biointerfaces, Vol. 49, No. 1. (15 April 2006), pp. 49-54. 2008-08-06T17:59:23-00:00 2006 Colloids and Surfaces B: Biointerfaces 49 1 49 54 dna isoelectrical-point http://www.citeulike.org/user/bpcusack/article/2837449 <i>Genetics, Vol. 179, No. 1. (May 2008), pp. 487-496.</i><br /><br />Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence. De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae. J Cai R Zhao H Jiang W Wang doi:10.1534/genetics.107.084491 Genetics, Vol. 179, No. 1. (May 2008), pp. 487-496. 2008-05-27T13:07:35-00:00 2008 Genetics 0016-6731 179 1 487 496 wiki http://www.citeulike.org/user/pedjor/article/3084869 <i>Astroparticle Physics, Vol. 29, No. 4. (May 2008), pp. 243-256.</i><br /><br />A method is developed to search for air showers initiated by photons using data recorded by the surface detector of the Auger Observatory. The approach is based on observables sensitive to the longitudinal shower development, the signal risetime and the curvature of the shower front. Applying this method to the data, upper limits on the flux of photons of 3.8×10-3, above , are derived, with corresponding limits on the fraction of photons being 2.0%, 5.1%, and 31% (all limits at 95% c.l.). These photon limits disfavor certain exotic models of sources of cosmic rays. The results also show that the approach adopted by the Auger Observatory to calibrate the shower energy is not strongly biased by a contamination from photons. Upper limit on the cosmic-ray photon flux above 1019 eV using the surface detector of the Pierre Auger Observatory J Abraham P Abreu M Aglietta C Aguirre D Allard I Allekotte J Allen P Allison J Alvarez-Muñiz M Ambrosio L Anchordoqui S Andringa A Anzalone C Aramo S Argirò K Arisaka E Armengaud F Arneodo F Arqueros T Asch H Asorey P Assis BS Atulugama J Aublin M Ave G Avila T Bäcker D Badagnani AF Barbosa D Barnhill SLC Barroso P Bauleo JJ Beatty T Beau BR Becker KH Becker JA Bellido S Benzvi C Berat T Bergmann P Bernardini X Bertou PL Biermann P Billoir O Blanch-Bigas F Blanco P Blasi C Bleve H Blümer M Bohácová C Bonifazi R Bonino M Boratav J Brack P Brogueira WC Brown P Buchholz A Bueno RE Burton NG Busca KS Caballero-Mora B Cai DV Camin L Caramete R Caruso W Carvalho A Castellina O Catalano G Cataldi L Cazon R Cester J Chauvin A Chiavassa JA Chinellato A Chou J Chye PDJ Clark RW Clay E Colombo R Conceição B Connolly F Contreras J Coppens A Cordier U Cotti S Coutu CE Covault A Creusot A Criss J Cronin A Curutiu S Dagoret-Campagne K Daumiller BR Dawson RM de Almeida C De Donato SJ de Jong De La de Mello de Mello I De Mitri V de Souza Del O Deligny A Della Selva C Delle Fratte H Dembinski C Di Giulio JC Diaz C Dobrigkeit JC D'Olivo D Dornic A Dorofeev Dos MT Dova D D'Urso I Dutan MA Duvernois R Engel L Epele M Erdmann CO Escobar A Etchegoyen Facal H Falcke G Farrar AC Fauth N Fazzini F Ferrer S Ferry B Fick A Filevich A Filipcic I Fleck R Fonte CE Fracchiolla W Fulgione B García García D Garcia-Pinto X Garrido H Geenen G Gelmini H Gemmeke PL Ghia M Giller H Glass MS Gold G Golup Gomez Gómez Gómez P Gonçalves Gonçalves D Gonzalez JG Gonzalez M González D Góra A Gorgi P Gouffon V Grassi AF Grillo C Grunfeld Y Guardincerri F Guarino GP Guedes J Gutiérrez JD Hague JC Hamilton P Hansen D Harari S Harmsma JL Harton A Haungs T Hauschildt MD Healy T Hebbeker G Hebrero D Heck C Hojvat VC Holmes P Homola J Hörandel A Horneffer M Horvat M Hrabovský T Huege M Hussain M Iarlori A Insolia F Ionita A Italiano M Kaducak KH Kampert T Karova B Kégl B Keilhauer E Kemp RM Kieckhafer HO Klages M Kleifges J Kleinfeller R Knapik J Knapp DH Koang A Krieger O Krömer D Kuempel N Kunka A Kusenko G La Rosa C Lachaud BL Lago D Lebrun P Lebrun J Lee Leigui A Letessier-Selvon M Leuthold I Lhenry-Yvon R López Lopez Lozano Luna MC Maccarone C Macolino S Maldera G Mancarella ME Manceñido D Mandat P Mantsch AG Mariazzi IC Maris Marquez D Martello J Martínez Martínez HJ Mathes J Matthews JAJ Matthews G Matthiae D Maurizio PO Mazur T Mccauley M Mcewen RR Mcneil MC Medina G Medina-Tanco A Meli D Melo E Menichetti A Menschikov Chr Meurer R Meyhandan MI Micheletti G Miele W Miller S Mollerach M Monasor Monnier F Montanet B Morales C Morello JC Moreno C Morris M Mostafá MA Muller R Mussa G Navarra JL Navarro S Navas P Necesal L Nellen C Newman-Holmes D Newton NT Thao N Nierstenhoefer D Nitz D Nosek L Nozka J Oehlschläger T Ohnuki A Olinto VM Olmos-Gilbaja M Ortiz F Ortolani S Ostapchenko L Otero N Pacheco Pakk M Palatka J Pallotta G Parente E Parizot S Parlati S Pastor M Patel T Paul V Pavlidou K Payet M Pech J Pe¸kala R Pelayo IM Pepe L Perrone S Petrera P Petrinca Y Petrov PN Diep PN Dong PT Nhung A Pichel R Piegaia T Pierog M Pimenta T Pinto V Pirronello O Pisanti M Platino J Pochon P Privitera M Prouza EJ Quel J Rautenberg A Redondo S Reucroft B Revenu FAS Rezende J Ridky S Riggi M Risse C Rivière V Rizi M Roberts C Robledo G Rodriguez MD Rodríguez-Frías Rodriguez Rodriguez I Rodriguez-Cabo G Ros J Rosado M Roth C Roucelle B Rouillé-D'orfeuil E Roulet AC Rovero F Salamida H Salazar G Salina F Sánchez M Santander CE Santo EM Santos F Sarazin S Sarkar R Sato V Scherini H Schieler A Schmidt F Schmidt T Schmidt O Scholten P Schovánek F Schüssler SJ Sciutto M Scuderi A Segreto D Semikoz M Settimo RC Shellard I Sidelnik BB Siffert G Sigl Smetniansky De Grande A Smialkowski R Smída AGK Smith BE Smith GR Snow P Sokolsky P Sommers J Sorokin H Spinka R Squartini E Strazzeri A Stutz F Suarez T Suomijärvi AD Supanitsky MS Sutherland J Swain Z Szadkowski J Takahashi A Tamashiro A Tamburro O Tascau R Tcaciuc D Thomas R Ticona J Tiffenberg C Timmermans W Tkaczyk Todero B Tomé A Tonachini I Torres D Torresi P Travnicek A Tripathi G Tristram D Tscherniakhovski M Tueros V Tunnicliffe R Ulrich M Unger M Urban Valdés I Valiño L Valore AM van den Berg V van Elewyck RA Vázquez D Veberic A Veiga A Velarde T Venters V Verzi M Videla L Villaseñor S Vorobiov L Voyvodic H Wahlberg O Wainberg P Walker D Warner AA Watson S Westerhoff G Wieczorek L Wiencke B Wilczynska H Wilczynski C Wileman MG Winnick H Wu B Wundheiler T Yamamoto P Younk E Zas D Zavrtanik M Zavrtanik A Zech A Zepeda M Ziolkowski doi:10.1016/j.astropartphys.2008.01.003 Astroparticle Physics, Vol. 29, No. 4. (May 2008), pp. 243-256. 2008-08-05T10:40:12-00:00 2008 Astroparticle Physics 29 4 243 256 auger flux photon http://www.citeulike.org/user/yoonk/article/2836840 <i>Genome Res. (15 May 2008), gr.072769.107.</i><br /><br />We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the co-expressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a pre-determined alignment result, GibbsModule iteratively updates the core motif shared by co-expressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared to peer algorithms on a number of synthetic and real datasets. Applying GibbsModule to analyze the binding regions of the Kruppel-like factor (Klf) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published Klf motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. Sox2 motif was found to be a collaborating motif to the Klf motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and non-functional binding sites. All 7 tested binding sites in GibbsModule predicted CRMs had higher ChIP signals as compared to the other 7 tested binding sites located outside of predicted CRMs. GibbsModule is available at http://biocomp.bioen.uiuc.edu/GibbsModule. 10.1101/gr.072769.107 Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells Dan Xie Jun Cai Na-Yu Chia Huck Ng Sheng Zhong doi:10.1101/gr.072769.107 Genome Res. (15 May 2008), gr.072769.107. 2008-05-27T08:52:20-00:00 2008 Genome Res. gr.072769.107 no-tag http://www.citeulike.org/user/MllePapillon/article/3067575 <i>Journal of pharmaceutical and biomedical analysis, Vol. 39, No. 1-2. (1 September 2005), pp. 334-338.</i><br /><br />In this paper, a simple and sensitive fluorimetric method for the determination of tiopronin (N-(2-mercaptopropionyl)-glycine) is proposed. The method is based on the strong inhibitory effect of tiopronin on the multienzyme redox system of hemoglobin, nicotinamide adenine dinucleotide (NADH) and H(2)O(2), in which the intrinsic fluorescence of NADH was employed as the detection signal. The calibration graph is linear in the range 6.13 x 10(-7) to 6.13 x 10(-6) M with a detection limit of 1.65 x 10(-7) M and the relative standard deviation of 2.02%. Kinetics in the pseudo-first-order conditions was investigated by stopped-flow spectrofluorometry and the inhibition mechanism of tiopronin was verified of the competitive type. Fluorometric assay of tiopronin based on inhibition of multienzyme redox system. J Xu R Cai J Wang Z Liu X Wu doi:10.1016/j.jpba.2005.03.004 Journal of pharmaceutical and biomedical analysis, Vol. 39, No. 1-2. (1 September 2005), pp. 334-338. 2008-07-31T20:32:36-00:00 2005 Journal of pharmaceutical and biomedical analysis 0731-7085 39 1-2 334 338 nmpg http://www.citeulike.org/user/newdawn/article/3064812 <i>(2005), pp. 1463-1469.</i> Adaptive testing of software components Kai-Yuan Cai TY Chen Yong-Chao Li Wei-Yi Ning YT Yu doi:10.1145/1066677.1067011 (2005), pp. 1463-1469. 2008-07-31T08:40:05-00:00 2005 1463 1469 ACM adaptive component testing http://www.citeulike.org/user/michaelbussmann/article/3063764 <i>Computer Physics Communications, Vol. In Press, Accepted Manuscript</i> Scalability Analysis of Parallel Particle-In-Cell Codes on Computational Grids Weifeng Tao Dongsheng Cai Xiaoyang Yan Nishikawa Ken-Ichi Bertrand Lembege doi:10.1016/j.cpc.2008.07.004 Computer Physics Communications, Vol. In Press, Accepted Manuscript 2008-07-30T16:41:49-00:00 Computer Physics Communications In Press, Accepted Manuscript algorithm computing grid parallel particle-in-cell pic scaling simulation http://www.citeulike.org/user/DocNero/article/3059250 <i>Affective Computing and Intelligent Interaction (2007), pp. 24-35.</i><br /><br />Facial expression plays an important role in face to face communication in that it conveys nonverbal information and emotional intent beyond speech. In this paper, an approach for facial expression synthesis with an expressive Chinese talking avatar is proposed, where a layered parametric framework is designed to synthesize intermediate facial expressions using PAD emotional parameters [5], which describe the human emotional state with three nearly orthogonal dimensions. Partial Expression Parameter (PEP) is proposed to depict the facial expression movements in specific face regions, which act as the mid-level expression parameters between the low-level Facial Animation Parameters (FAPs) [11] and the high-level PAD emotional parameters. A pseudo facial expression database is established by cloning the real human expression to avatar and the corresponding emotion states for each expression is annotated using PAD score. An emotion-expression mapping model is trained on the database to map the emotion state (PAD) into facial expression configuration (PEP). Perceptual evaluation shows the input PAD value is consistent with that of human perception on synthetic expression, which supports the effectiveness of our approach. Facial Expression Synthesis Using PAD Emotional Parameters for a Chinese Expressive Avatar Shen Zhang Zhiyong Wu Helen Meng Lianhong Cai doi:10.1007/978-3-540-74889-2_3 Affective Computing and Intelligent Interaction (2007), pp. 24-35. 2008-07-30T09:22:34-00:00 2007 Affective Computing and Intelligent Interaction 24 35 emotion expression facial pad http://www.citeulike.org/user/schmoutz/article/3057610 <i>Progress in brain research, Vol. 170 (2008), pp. 53-64.</i><br /><br />Oxytocin (OXT) that is released centrally is believed to be anxiolytic and have stress-attenuating effects. Oxytocin knockout (OXTKO) mice, a genetic model of OXT deficiency, have heightened corticosterone release after acute stress and greater anxiety-related behaviour in an elevated plus maze compared to wild-type (WT) mice. In the present set of experiments, we recorded the rise in body temperature, referred to as stress-induced hyperthermia (SIH), following transfer to a metabolic cage, which triggers both anxiety and corticosterone release in mice. SIH is a marker of activation of the hypothalamic-pituitary-adrenal (HPA) axis and sympathetic nervous system. Because corticosterone release after acute stress is typically greater in OXTKO than in WT mice, we measured SIH as a surrogate marker of corticosterone release. Following transfer to a metabolic cage, both OXTKO and WT mice increased body temperature, but to the same degree. Pregnant mice, which are known to have blunted corticosterone release to acute stress, had attenuated SIH after transfer to a metabolic cage compared to cycling mice, but both genotypes manifested the same degree of attenuation. In addition, we tested the effects of the cannabinoid receptor 1 (CBR1) antagonist/inverse agonist (AM251) upon feeding and SIH in OXTKO versus WT mice. CBR1 antagonists are known to diminish food intake and to enhance corticosterone both basally and following acute stress. Although AM251 blunted food intake, the effect was equivalent in both genotypes. The agent did not affect the SIH response compared to mice treated with vehicle. SIH is excellent for defining anxiolytic or blunted corticosterone responses (such as the stress hyporesponsiveness of pregnancy), but is limited in its ability to detect the heightened corticosterone responses that have been reported in OXTKO mice following exposure to psychogenic stress. Oxytocin knockout mice: a model for studying stress-related and ingestive behaviours. JA Amico JA Miedlar HM Cai RR Vollmer doi:10.1016/S0079-6123(08)00405-6 Progress in brain research, Vol. 170 (2008), pp. 53-64. 2008-07-29T19:14:59-00:00 2008 Progress in brain research 0079-6123 170 53 64 no-tag http://www.citeulike.org/user/fmccown/article/3056916 <i>(2008), pp. 459-466.</i> Exploring traversal strategy for web forum crawling Yida Wang Jiang-Ming Yang Wei Lai Rui Cai Lei Zhang Wei-Ying Ma doi:10.1145/1390334.1390413 (2008), pp. 459-466. 2008-07-29T14:52:14-00:00 2008 459 466 ACM web-crawling http://www.citeulike.org/user/zdai/article/1582188 <i>Curr Protein Pept Sci, Vol. 6, No. 5. (October 2005), pp. 443-449.</i><br /><br />Protein-protein interactions play a central role in numerous processes in cell and are one of the main research fields in current functional proteomics. The increase of finished genomic sequences has greatly stimulated the progress for detecting the functions of the genes and their encoded proteins. As complementary ways to the high through-put experimental methods, various methods of bioinformatics have been developed for the study of the protein-protein interaction. These methods range from the sequence homology-based to the genomic-context based. Recently, it tends to integrate the data from different methods to build the protein-protein interaction network, and to predict the protein function from the analysis of the network structure. Efforts are ongoing to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed. Computational methods for protein-protein interaction and their application. TL Shi YX Li YD Cai KC Chou Curr Protein Pept Sci, Vol. 6, No. 5. (October 2005), pp. 443-449. 2007-08-22T10:05:10-00:00 2005 Curr Protein Pept Sci 1389-2037 6 5 443 449 no-tag http://www.citeulike.org/user/RalfMitschke/article/3050148 <i>SIGSOFT Softw. Eng. Notes, Vol. 32, No. 5. (September 2007), pp. 31-37.</i> Assessment of Contemporary Modularization Techniques - ACoM'07: workshop report Alessandro Garcia Phil Greenwood George Heineman Robert Walker Yuanfang Cai Hong Yang Elisa Baniassad Cristina Lopes Christa Schwanninger Jianjun Zhao doi:10.1145/1290993.1291005 SIGSOFT Softw. Eng. Notes, Vol. 32, No. 5. (September 2007), pp. 31-37. 2008-07-28T13:53:13-00:00 2007 SIGSOFT Softw. Eng. Notes 0163-5948 32 5 31 37 ACM module-decomposition http://www.citeulike.org/user/jyuh/article/722962 <i>Biometrika, Vol. 93, No. 2. (June 2006), pp. 329-342.</i> On the accelerated failure time model for current status and interval censored data Tian Lu Cai Tianxi doi:10.1093/biomet/93.2.329 Biometrika, Vol. 93, No. 2. (June 2006), pp. 329-342. 2006-07-02T09:46:21-00:00 2006 Biometrika 0006-3444 93 2 329 342 Oxford University Press aft interval-censor http://www.citeulike.org/user/middell/article/1897673 <i>Science, Vol. 318, No. 5852. (9 November 2007), pp. 938-943.</i><br /><br />Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrated a correlation between the arrival directions of cosmic rays with energy above 6 x 1019 electron volts and the positions of active galactic nuclei (AGN) lying within [~]75 megaparsecs. We rejected the hypothesis of an isotropic distribution of these cosmic rays with at least a 99% confidence level from a prescribed a priori test. The correlation we observed is compatible with the hypothesis that the highest-energy particles originate from nearby extragalactic sources whose flux has not been substantially reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources. 10.1126/science.1151124 Correlation of the Highest-Energy Cosmic Rays with Nearby Extragalactic Objects The doi:10.1126/science.1151124 Science, Vol. 318, No. 5852. (9 November 2007), pp. 938-943. 2007-11-11T06:39:18-00:00 2007 Science 318 5852 938 943 no-tag http://www.citeulike.org/user/dimka/article/3042969 <i>Medical hypotheses (21 July 2008)</i><br /><br />Parkinson's disease (PD) is one of the most common neurodegenerative disorders and still remains incurable. New targets for potential pharmacological intervention should be explored and evaluated in order to slow down, delay or reverse the progress of this disease, and/or to avoid the serious side effects of levodopa praeparatum. Potassium (K(+)) channels widely express in basal ganglia and play crucial roles in the pathophysiology of PD, thereby raising their therapeutic application. Based on data from some pilot studies, we propose that K(+) channels may provide possible new therapeutic targets for slowing down the progressive loss of dopamine neurons in PD. The most promising targets of K(+) channels, including Kv, K(ATP), Kir, SK, and K2P channels, etc. deserve further pursuit for making comprehensive use of their novel therapeutic potential. Attempts to confirm this hypothesis may lead to new therapeutic strategy of PD. Potassium channels: Possible new therapeutic targets in Parkinson's disease. Yan Wang Peng-Lin Yang Ji-Fei Tang Jia-Feng Lin Xiao-Hong Cai Xiao-Tong Wang Guo-Qing Zheng doi:10.1016/j.mehy.2008.05.021 Medical hypotheses (21 July 2008) 2008-07-25T16:13:53-00:00 2008 Medical hypotheses 0306-9877 desease kir review http://www.citeulike.org/user/mnqf3pkg/article/3039215 <i>Molecular neurobiology, Vol. 36, No. 3. (December 2007), pp. 224-231.</i><br /><br />Autosomal recessive mutations in the ALS2 gene lead to a clinical spectrum of motor dysfunction including juvenile onset amyotrophic lateral sclerosis (ALS2), primary lateral sclerosis, and hereditary spastic paraplegia. The 184-kDa alsin protein, encoded by the full-length ALS2 gene, contains three different guanine-nucleotide-exchange factor-like domains, which may play a role in the etiology of the disease. Multiple in vitro biochemical and cell biology assays suggest that alsin dysfunction affects endosome trafficking through a Rab5 small GTPase family-mediated mechanism. Four ALS2-deficient mouse models have been generated by different groups and used to study the behavioral and pathological impact of alsin deficiency. These mouse models largely fail to recapitulate hallmarks of motor neuron disease, but the subtle deficits that are observed in behavior and pathology have aided in our understanding of the relationship between alsin and motor dysfunction. In this review, we summarize recent clinical and molecular reports regarding alsin and attempt to place these results within the larger context of motor neuron disease. Alsin and the molecular pathways of amyotrophic lateral sclerosis. J Chandran J Ding H Cai doi:10.1007/s12035-007-0034-x Molecular neurobiology, Vol. 36, No. 3. (December 2007), pp. 224-231. 2008-07-24T11:28:52-00:00 2007 Molecular neurobiology 0893-7648 36 3 224 231 alsin mouse mutation structure http://www.citeulike.org/user/rrbarb/article/2031837 <i>Construction Management and Economics, Vol. 25, No. 9. (September 2007), pp. 937-950.</i> Personal constructs affecting interpersonal trust and willingness to share knowledge between architects in project design teams Ding Zhikun Ng Fungfai Cai Qiying doi:10.1080/01446190701468828 Construction Management and Economics, Vol. 25, No. 9. (September 2007), pp. 937-950. 2007-11-30T19:24:11-00:00 2007 Construction Management and Economics 0144-6193 25 9 937 950 Routledge, part of the Taylor & Francis Group knowledge-management sharing http://www.citeulike.org/user/vmsr/article/1852511 <i>Nature, Vol. 427, No. 6973. (29 January 2004), pp. 461-465.</i><br /><br />A sudden increase in permeability of the inner mitochondrial membrane, the so-called mitochondrial permeability transition, is a common feature of apoptosis and is mediated by the mitochondrial permeability transition pore (mtPTP). It is thought that the mtPTP is a protein complex formed by the voltage-dependent anion channel, members of the pro- and anti-apoptotic BAX-BCL2 protein family, cyclophilin D, and the adenine nucleotide (ADP/ATP) translocators (ANTs). The latter exchange mitochondrial ATP for cytosolic ADP and have been implicated in cell death. To investigate the role of the ANTs in the mtPTP, we genetically inactivated the two isoforms of ANT in mouse liver and analysed mtPTP activation in isolated mitochondria and the induction of cell death in hepatocytes. Mitochondria lacking ANT could still be induced to undergo permeability transition, resulting in release of cytochrome c. However, more Ca2+ than usual was required to activate the mtPTP, and the pore could no longer be regulated by ANT ligands. Moreover, hepatocytes without ANT remained competent to respond to various initiators of cell death. Therefore, ANTs are non-essential structural components of the mtPTP, although they do contribute to its regulation. The ADP/ATP translocator is not essential for the mitochondrial permeability transition pore. JE Kokoszka KG Waymire SE Levy JE Sligh J Cai DP Jones GR MacGregor DC Wallace doi:10.1038/nature02229 Nature, Vol. 427, No. 6973. (29 January 2004), pp. 461-465. 2007-11-01T20:06:16-00:00 2004 Nature 1476-4687 427 6973 461 465 vmsr_publications http://www.citeulike.org/user/tnhh/article/3032412 <i>(2007), pp. 1-8.</i> Location anonymity in continuous location-based services Toby Xu Ying Cai doi:10.1145/1341012.1341062 (2007), pp. 1-8. 2008-07-22T09:36:39-00:00 2007 1 8 ACM anonymity location location-based-services privacy http://www.citeulike.org/user/jyuh/article/3022209 <i>Biometrics (20 June 2008)</i><br /><br />In the presence of high-dimensional predictors, it is challenging to develop reliable regression models that can be used to accurately predict future outcomes. Further complications arise when the outcome of interest is an event time, which is often not fully observed due to censoring. In this article, we develop robust prediction models for event time outcomes by regularizing the Gehan's estimator for the accelerated failure time (AFT) model (Tsiatis, 1996, Annals of Statistics18, 305-328) with least absolute shrinkage and selection operator (LASSO) penalty. Unlike existing methods based on the inverse probability weighting and the Buckley and James estimator (Buckley and James, 1979, Biometrika66, 429-436), the proposed approach does not require additional assumptions about the censoring and always yields a solution that is convergent. Furthermore, the proposed estimator leads to a stable regression model for prediction even if the AFT model fails to hold. To facilitate the adaptive selection of the tuning parameter, we detail an efficient numerical algorithm for obtaining the entire regularization path. The proposed procedures are applied to a breast cancer dataset to derive a reliable regression model for predicting patient survival based on a set of clinical prognostic factors and gene signatures. Finite sample performances of the procedures are evaluated through a simulation study. Regularized Estimation for the Accelerated Failure Time Model. T Cai J Huang L Tian doi:10.1111/j.1541-0420.2008.01074.x Biometrics (20 June 2008) 2008-07-20T07:31:27-00:00 2008 Biometrics 1541-0420 aft http://www.citeulike.org/user/austin/article/3015830 <i>PLoS ONE, Vol. 3, No. 7. (2008)</i><br /><br />BACKGROUND: The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. METHODS/PRINCIPAL FINDINGS: By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. CONCLUSIONS/SIGNIFICANCE: Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users. Targeted development of registries of biological parts. J Peccoud MF Blauvelt Y Cai KL Cooper O Crasta EC DeLalla C Evans O Folkerts BM Lyons SP Mane R Shelton MA Sweede SA Waldon doi:10.1371/journal.pone.0002671 PLoS ONE, Vol. 3, No. 7. (2008) 2008-07-17T21:39:45-00:00 2008 PLoS ONE 1932-6203 3 7 no-tag http://www.citeulike.org/user/egozi/article/3014136 <i>Computer Vision and Image Understanding, Vol. 70, No. 2. (May 1998), pp. 142-156.</i><br /><br />Motion of physical objects in the world is, in general, nonrigid. In robotics and computer vision, the motion of nonrigid objects is of growing interest to researchers from a wide spectrum of disciplines. The nonrigid objects being studied may be generally categorized into three groups according to the degree of deformation of body parts: articulated, elastic, and fluid. In articulated motion, individual rigid parts of an object move independently of one another and the motion of the whole object is nonrigid in nature. Elastic motion is nonrigid motion that conforms to a certain degree of continuity or smoothness. Fluid motion violates even the continuity assumption and may involve topological variations and turbulent deformations. This paper presents an overview of existing work on articulated and elastic motion, motivated by problems relating to the motion of the human body and of an animal heart, respectively. We study various approaches for recovering the 3D structure and motion of objects through a sequence of images in a bottom-up fashion, a strategy widely employed by various investigators. These approaches are classified as (1) motion recovery without shape models, and (2) model-based analysis. In the discussion of each algorithm, we also include a description of the complexity of feature and motion constraints, which are highly related to each other. Nonrigid Motion Analysis: Articulated and Elastic Motion, JK Aggarwal Q Cai W Liao B Sabata doi:10.1006/cviu.1997.0620 Computer Vision and Image Understanding, Vol. 70, No. 2. (May 1998), pp. 142-156. 2008-07-17T11:05:33-00:00 1998 Computer Vision and Image Understanding 70 2 142 156 motion-analysis http://www.citeulike.org/user/eme/article/3013855 <i>(16 Jul 2008)</i><br /><br />The Dark Energy Survey collaboration will study cosmic acceleration with a 5000 deg2 griZY survey in the southern sky over 525 nights from 2011-2016. The DES data management (DESDM) system will be used to process and archive these data and the resulting science ready data products. The DESDM system consists of an integrated archive, a processing framework, an ensemble of astronomy codes and a data access framework. We are developing the DESDM system for operation in the high performance computing (HPC) environments at NCSA and Fermilab. Operating the DESDM system in an HPC environment offers both speed and flexibility. We will employ it for our regular nightly processing needs, and for more compute-intensive tasks such as large scale image coaddition campaigns, extraction of weak lensing shear from the full survey dataset, and massive seasonal reprocessing of the DES data. Data products will be available to the Collaboration and later to the public through a virtual-observatory compatible web portal. Our approach leverages investments in publicly available HPC systems, greatly reducing hardware and maintenance costs to the project, which must deploy and maintain only the storage, database platforms and orchestration and web portal nodes that are specific to DESDM. In Fall 2007, we tested the current DESDM system on both simulated and real survey data. We used Teragrid to process 10 simulated DES nights (3TB of raw data), ingesting and calibrating approximately 250 million objects into the DES Archive database. We also used DESDM to process and calibrate over 50 nights of survey data acquired with the Mosaic2 camera. Comparison to truth tables in the case of the simulated data and internal crosschecks in the case of the real data indicate that astrometric and photometric data quality is excellent. The Dark Energy Survey Data Management System Joseph Mohr Wayne Barkhouse Cristina Beldica Emmanuel Bertin Dora Cai Luiz da Costa Anthony Darnell Gregory Daues Michael Jarvis Michelle Gower Huan Lin Leandro Martelli Eric Neilsen Chow-Choong Ngeow Ricardo Ogando Alex Parga Erin Sheldon Douglas Tucker Nikolay Kuropatkin Chris Stoughton (16 Jul 2008) 2008-07-17T08:23:17-00:00 2008 astrophysics cosmology datamanagement des http://www.citeulike.org/user/schmoutz/article/3008937 <i>Neuroscience letters (6 July 2008)</i><br /><br />Both anxiety-related behavior [J.A. Amico, R.C. Mantella, R.R. Vollmer, X. Li, Anxiety and stress responses in female oxytocin deficient mice, J. Neuroendocrinol. 16 (2004) 1-6; R.C. Mantella, R.R. Vollmer, X. Li, J.A. Amico, Female oxytocin-deficient mice display enhanced anxiety-related behavior, Endocrinology 144 (2003) 2291-2296] and the release of corticosterone following a psychogenic stress such as exposure to platform shaker was greater in female [J.A. Amico, R.C. Mantella, R.R. Vollmer, X. Li, Anxiety and stress responses in female oxytocin deficient mice, J. Neuroendocrinol. 16 (2004) 1-6; R.C. Mantella, R.R. Vollmer, L. Rinaman, X. Li, J.A. Amico, Enhanced corticosterone concentrations and attenuated Fos expression in the medial amygdala of female oxytocin knockout mice exposed to psychogenic stress, Am. J. Physiol. Regul. Integr. Comp. Physiol. 287 (2004) R1494-R1504], but not male [R.C. Mantella, R.R. Vollmer, J.A. Amico, Corticosterone release is heightened in food or water deprived oxytocin deficient male mice, Brain Res. 1058 (2005) 56-61], oxytocin gene deletion (OTKO) mice compared to wild type (WT) cohorts. In the present study we exposed OTKO and WT female mice to another psychogenic stress, inserting a rectal probe to record body temperature followed by brief confinement in a metabolic cage, and measured plasma corticosterone following the stress. OTKO mice released more corticosterone than WT mice (P<0.03) following exposure to this stress. In contrast, if OTKO and WT female and male mice were administered insulin-induced hypoglycemia, an acute physical stress, corticosterone release was not different between genotypes. The absence of central OT signaling pathways in female mice heightens the neuroendocrine (e.g., corticosterone) response to psychogenic stress, but not to the physical stress of insulin-induced hypoglycemia. Corticosterone release in oxytocin gene deletion mice following exposure to psychogenic versus non-psychogenic stress. Janet A Amico Hou-Ming Cai Regis R Vollmer doi:10.1016/j.neulet.2008.07.004 Neuroscience letters (6 July 2008) 2008-07-16T16:48:05-00:00 2008 Neuroscience letters 0304-3940 no-tag http://www.citeulike.org/user/egozi/article/3008209 <i>Computer Vision and Image Understanding (March 1999), pp. 428-440.</i><br /><br />Human motion analysis is receiving increasing attention from computer vision researchers. This interest is motivated by a wide spectrum of applications, such as athletic performance analysis, surveillance, man-machine interfaces, content-based image storage and retrieval, and video conferencing. This paper gives an overview of the various tasks involved in motion analysis of the human body. We focus on three major areas related to interpreting human motion: (1) motion analysis involving human body parts, (2) tracking a moving human from a single view or multiple camera perspectives, and (3) recognizing human activities from image sequences. Motion analysis of human body parts involves the low-level segmentation of the human body into segments connected by joints and recovers the 3D structure of the human body using its 2D projections over a sequence of images. Tracking human motion from a single view or multiple perspectives focuses on higher-level processing, in which moving humans are tracked without identifying their body parts. After successfully matching the moving human image from one frame to another in an image sequence, understanding the human movements or activities comes naturally, which leads to our discussion of recognizing human activities. Human Motion Analysis: A Review JK Aggarwal Q Cai doi:10.1006/cviu.1998.0744 Computer Vision and Image Understanding (March 1999), pp. 428-440. 2008-07-16T12:29:03-00:00 1999 Computer Vision and Image Understanding 1077-3142 428 440 Elsevier action_recognition review http://www.citeulike.org/user/jjray/article/553494 <i>Nature, Vol. 440, No. 7082., pp. 358-362.</i> Stochastic protein expression in individual cells at the single molecule level Long Cai Nir Friedman Sunney Xie doi:10.1038/nature04599 Nature, Vol. 440, No. 7082., pp. 358-362. 2006-03-15T23:36:34-00:00 Nature 0028-0836 440 7082 358 362 Nature Publishing Group noise stochastic transcriptional_burst http://www.citeulike.org/user/schwartz/article/2975506 <i>J. Opt. Soc. Am. A, Vol. 25, No. 7. (1 July 2008), pp. 1497-1503.</i><br /><br />The scintillation properties of astigmatic dark hollow beams (DHBs) in weak atmospheric turbulence were investigated in detail. An explicit expression for the on-axis scintillation index of an astigmatic DHB propagating in weak atmospheric turbulence was derived. It was found that the scintillation index value of an astigmatic DHB with suitable astigmatism (i.e., ratio of the beam waist size in the x direction to that in the y direction), dark size, beam waist size, and wavelength can be smaller than that of a stigmatic DHB and that of stigmatic and astigmatic flat-topped, annular, and Gaussian beams in weak atmospheric turbulence particularly at long propagation ranges. Our results will be useful in long-distance free-space optical communications. Scintillation of astigmatic dark hollow beams in weak atmospheric turbulence Yangjian Cai Halil Eyyubo?lu Yahya Baykal J. Opt. Soc. Am. A, Vol. 25, No. 7. (1 July 2008), pp. 1497-1503. 2008-07-09T09:03:22-00:00 2008 J. Opt. Soc. Am. A 25 7 1497 1503 OSA atmosphere dark-hollow mitigation http://www.citeulike.org/user/baikanamako/article/2972574 <i>Neuroscience letters (18 June 2008)</i><br /><br />The mechanism by which a brief episode of sublethal ischemia followed by reperfusion (ischemic preconditioning, IPC) prevents the lethal effects of subsequent periods of prolonged ischemia, are poorly understood. A completely randomized, controlled study was designed to study the effect of IPC using a rabbit model of ischemic spinal cord injury. Twenty-four white adult New England rabbits were randomly assigned to one of 3 groups (n=8 per group); the groups were assigned as follows: Group I: sham-operation group, Group II: ischemic reperfusion (I/R) group, and Group III: ischemic preconditioning group. Spinal cord ischemia was induced by introducing an infra renal aortic cross-clamp for 30min. Following injury, rabbits were subjected to 30min, 2h, or 8h of reperfusion in Group II. In Group III, subjects underwent three cycles, 5min each, of ischemia followed by 5min of reperfusion, before receiving 30min of ischemia. We previously reported that the association between ASK1 (apoptosis signal-regulating kinase 1) and 14-3-3 played an important role in regulating ischemia/reperfusion spinal cord injuries. To evaluate the effect of ischemic preconditioning in injured spinal cords, we examined alterations in spinal tissue morphology, activation of key members of the ASK1-mediated signaling pathway, and the association between ASK1 and 14-3-3. Changes in spinal cord morphology were observed with hematoxylin and eosin (H&E) staining and electron microscopy. The phosphorylation levels of ASK1, JNK, and p38 were assessed by immunoblot analysis. The association between ASK1 and 14-3-3 was analyzed by co-immunoprecipitation experiments. We observed that swelling of the neurocyte bodies and hemorrhage of the spinal cord were dramatically decreased in Group III compared to Group II. In addition, the degree of apoptosis among neurocytes was reduced in Group III compared to Group II. Finally, the phosphorylation of ASK1, JNK, p38 and the dissociation of ASK1 from 14-3-3 were dramatically decreased in Group III compared with Group II. These results indicate that ischemic preconditioning may have a protective affect against ASK1/14-3-3 dissociation-induced spinal cord injuries. Ischemic preconditioning suppresses apoptosis of rabbit spinal neurocytes by inhibiting ASK1-14-3-3 dissociation. Chengwei Yang Yongxin Ren Feng Liu Weihua Cai Ning Zhang David J Nagel Guoyong Yin doi:10.1016/j.neulet.2008.06.037 Neuroscience letters (18 June 2008) 2008-07-08T13:17:32-00:00 2008 Neuroscience letters 0304-3940 neta http://www.citeulike.org/user/jyuh/article/2969088 <i>The British journal of mathematical and statistical psychology (27 June 2008)</i><br /><br />Structural equation models (SEMs) have been widely applied to examine interrelationships among latent and observed variables in social and psychological research. Motivated by the fact that correlated discrete variables are frequently encountered in practical applications, a non-linear SEM that accommodates covariates, and mixed continuous, ordered, and unordered categorical variables is proposed. Maximum likelihood methods for estimation and model comparison are discussed. One real-life data set about cardiovascular disease is used to illustrate the methodologies. Non-linear structural equation models with correlated continuous and discrete data. Sik-Yum Lee Xin-Yuan Song Jing-Heng Cai Wing-Yee So Ching-Wang Ma Chung-Ngor Chan doi:10.1348/000711008X292343 The British journal of mathematical and statistical psychology (27 June 2008) 2008-07-07T09:55:35-00:00 2008 The British journal of mathematical and statistical psychology 0007-1102 sem http://www.citeulike.org/user/qiongcai/article/2967529 <i>(2006), pp. 259-272.</i> Support for High-Frequency Streaming in CMPs Ram Rangan Neil Vachharajani Adam Stoler Guilherme Ottoni David August George Cai doi:10.1109/MICRO.2006.47 (2006), pp. 259-272. 2008-07-06T16:44:34-00:00 2006 259 272 IEEE Computer Society many-core parallel-communications http://www.citeulike.org/user/AlistairSellar/article/2952150 <i>Journal of Climate, Vol. 16, No. 1. (1 January 2003), pp. 144-155.</i><br /><br />This paper proposes a mechanism that explains how coupled dynamics alone can spontaneously give rise to a realistic west–east asymmetric mean state and an ENSO-like interannual variability without requiring the existence of an external preexisting west–east asymmetry in circulation. The essence of the newly proposed mechanism is that the basinwide ocean–atmosphere coupling acts to reduce the effective restoring force. As a result, the coupled oceanic waves travel more and more slowly within the equatorial ocean basin as the coupling strength increases. When the coupling strength reaches a critical value, the zonally leveled thermocline becomes unstable as a result of the weakening of the effective restoring force, at which the theoretical limit of the traveling timescale would be infinite without nonlinearity. Due to nonlinearity in the coupled system, this primary air–sea interaction instability leads to a west–east asymmetric mean state in which the atmosphere has a prevailing easterly and the ocean basin has a deep-in-west–shallow-in-east thermocline with a warm-west–cold-east sea surface temperature. The direction of the west–east asymmetry in the mean state is dictated by a planetary factor of the earth, namely, that the Coriolis parameter changes sign at the equator. As the coupling strength further increases, the asymmetry in the mean state amplifies and the phase speeds of the coupled equatorial oceanic waves begin to decrease gradually toward an asymptotic limit equal to the full speed in the uncoupled situation. Using the coupling coefficient that is consistent with the observation, the fully coupled model can produce a realistic mean state in which the basinwide SST (thermocline depth) difference is 4.2°C (116 m) and the westward wind stress at the central Pacific basin is 0.54 dyn cm–2. The self-sustained oscillation has a primary period of 3.7 yr. The SST in the west (east) oscillates between 27.5° and 28.5°C (between 25.2° and 22.5°C). Formation of the Cold Tongue and ENSO in the Equatorial Pacific Basin Ming Cai doi:10.1175/1520-0442(2003)016<0144:FOTCTA>2.0.CO;2 Journal of Climate, Vol. 16, No. 1. (1 January 2003), pp. 144-155. 2008-07-02T13:04:21-00:00 2003 Journal of Climate 16 1 144 155 climate enso mechanisms http://www.citeulike.org/user/pulsus-morbi/article/2951661 <i>Nuclear Physics A, Vol. 757, No. 1-2. (8 August 2005), pp. 102-183.</i><br /><br />We review the most important experimental results from the first three years of nucleus-nucleus collision studies at RHIC, with emphasis on results from the STAR experiment, and we assess their interpretation and comparison to theory. The theory-experiment comparison suggests that central Au[thin space]+[thin space]Au collisions at RHIC produce dense, rapidly thermalizing matter characterized by: (1) initial energy densities above the critical values predicted by lattice QCD for establishment of a quark-gluon plasma (QGP); (2) nearly ideal fluid flow, marked by constituent interactions of very short mean free path, established most probably at a stage preceding hadron formation; and (3) opacity to jets. Many of the observations are consistent with models incorporating QGP formation in the early collision stages, and have not found ready explanation in a hadronic framework. However, the measurements themselves do not yet establish unequivocal evidence for a transition to this new form of matter. The theoretical treatment of the collision evolution, despite impressive successes, invokes a suite of distinct models, degrees of freedom and assumptions of as yet unknown quantitative consequence. We pose a set of important open questions, and suggest additional measurements, at least some of which should be addressed in order to establish a compelling basis to conclude definitively that thermalized, deconfined quark-gluon matter has been produced at RHIC. Experimental and theoretical challenges in the search for the quark-gluon plasma: The STAR Collaboration's critical assessment of the evidence from RHIC collisions Adams Star-Collaboration doi:10.1016/j.nuclphysa.2005.03.085 Nuclear Physics A, Vol. 757, No. 1-2. (8 August 2005), pp. 102-183. 2008-07-02T09:38:18-00:00 2005 Nuclear Physics A 757 1-2 102 183 experimentalist jet supresssion http://www.citeulike.org/user/claudiacalcagno/article/2949128 <i>Radiology, Vol. 244, No. 1. (July 2007), pp. 64-77.</i><br /><br />"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. The vulnerable, or high-risk, atherosclerotic plaque: noninvasive MR imaging for characterization and assessment. T Saam TS Hatsukami N Takaya B Chu H Underhill WS Kerwin J Cai MS Ferguson C Yuan doi:10.1148/radiol.2441051769 Radiology, Vol. 244, No. 1. (July 2007), pp. 64-77. 2008-07-01T19:29:05-00:00 2007 Radiology 0033-8419 244 1 64 77 atherosclerosis http://www.citeulike.org/user/YoshiY/article/2948439 <i>Journal of Economic Theory, Vol. 92, No. 2. (June 2000), pp. 234-273.</i><br /><br />We study bargaining situations in which one side consists of a group of people, who elect a representative to bargain with another party on their behalf. A two-phase bargaining model is developed in which a principal-agent problem between the constituency and its representative is embedded. With a natural refinement of sequential equilibrium, we characterize the set of equilibria and examine its efficiency properties. We show that agency problems in the delegation relationship rather than asymmetric information between the two bargainers can cause severe bargaining inefficiency (i.e., delay in reaching agreements). Extensions of the model and applications to union-firm bargaining are then discussed briefly. Journal of Economic Literature Classification Numbers: C78, D82, J52. Bargaining on Behalf of a Constituency Hongbin Cai doi:10.1006/jeth.1999.2631 Journal of Economic Theory, Vol. 92, No. 2. (June 2000), pp. 234-273. 2008-07-01T14:17:49-00:00 2000 Journal of Economic Theory 92 2 234 273 bargaining game_theory http://www.citeulike.org/user/dchughes/article/2947358 <i>PLoS biology, Vol. 2, No. 9. (September 2004)</i><br /><br />The vertebrate retina is comprised of seven major cell types that are generated in overlapping but well-defined intervals. To identify genes that might regulate retinal development, gene expression in the developing retina was profiled at multiple time points using serial analysis of gene expression (SAGE). The expression patterns of 1,051 genes that showed developmentally dynamic expression by SAGE were investigated using in situ hybridization. A molecular atlas of gene expression in the developing and mature retina was thereby constructed, along with a taxonomic classification of developmental gene expression patterns. Genes were identified that label both temporal and spatial subsets of mitotic progenitor cells. For each developing and mature major retinal cell type, genes selectively expressed in that cell type were identified. The gene expression profiles of retinal Müller glia and mitotic progenitor cells were found to be highly similar, suggesting that Müller glia might serve to produce multiple retinal cell types under the right conditions. In addition, multiple transcripts that were evolutionarily conserved that did not appear to encode open reading frames of more than 100 amino acids in length ("noncoding RNAs") were found to be dynamically and specifically expressed in developing and mature retinal cell types. Finally, many photoreceptor-enriched genes that mapped to chromosomal intervals containing retinal disease genes were identified. These data serve as a starting point for functional investigations of the roles of these genes in retinal development and physiology. Genomic analysis of mouse retinal development. S Blackshaw S Harpavat J Trimarchi L Cai H Huang WP Kuo G Weber K Lee RE Fraioli SH Cho R Yung E Asch L Ohno-Machado WH Wong CL Cepko doi:10.1371/journal.pbio.0020247 PLoS biology, Vol. 2, No. 9. (September 2004) 2008-07-01T10:16:18-00:00 2004 PLoS biology 1545-7885 2 9 retina http://www.citeulike.org/user/wjfjin/article/2946200 <i>Fuzzy Systems and Knowledge Discovery (2005), pp. 320-323.</i><br /><br />HTTP request exploitations take substantial portion of network-based attacks. This paper presents a novel anomaly detection framework, which uses data mining technologies to build four independent detection models. In the training phase, these models mine specialty of every web program using web server log files as data source, and in the detection phase, each model takes the HTTP requests upon detection as input and calculates at least one anomalous probability as output. All the four models totally generate eight anomalous probabilities, which are weighted and summed up to produce a final probability, and this probability is used to decide whether the request is malicious or not. Experiments prove that our detection framework achieves close to perfect detection rate under very few false positives. Data Mining Methods for Anomaly Detection of HTTP Request Exploitations Xiao-Feng Wang Jing-Li Zhou Sheng-Sheng Yu Long-Zheng Cai doi:10.1007/11540007_39 Fuzzy Systems and Knowledge Discovery (2005), pp. 320-323. 2008-07-01T01:25:14-00:00 2005 Fuzzy Systems and Knowledge Discovery 320 323 anomaly http://www.citeulike.org/user/Neeperando/article/187153 <i>Science, Vol. 298, No. 5591. (4 October 2002), pp. 129-149.</i><br /><br />Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect. The genome sequence of the malaria mosquito Anopheles gambiae. RA Holt GM Subramanian A Halpern GG Sutton R Charlab DR Nusskern P Wincker AG Clark JM Ribeiro R Wides SL Salzberg B Loftus M Yandell WH Majoros DB Rusch Z Lai CL Kraft JF Abril V Anthouard P Arensburger PW Atkinson H Baden V de Berardinis D Baldwin V Benes J Biedler C Blass R Bolanos D Boscus M Barnstead S Cai A Center K Chaturverdi GK Christophides MA Chrystal M Clamp A Cravchik V Curwen A Dana A Delcher I Dew CA Evans M Flanigan A Grundschober-Freimoser L Friedli Z Gu P Guan R Guigo ME Hillenmeyer SL Hladun JR Hogan YS Hong J Hoover O Jaillon Z Ke C Kodira E Kokoza A Koutsos I Letunic A Levitsky Y Liang JJ Lin NF Lobo JR Lopez JA Malek TC McIntosh S Meister J Miller C Mobarry E Mongin SD Murphy DA O'Brochta C Pfannkoch R Qi MA Regier K Remington H Shao MV Sharakhova CD Sitter J Shetty TJ Smith R Strong J Sun D Thomasova LQ Ton P Topalis Z Tu MF Unger B Walenz A Wang J Wang M Wang X Wang KJ Woodford JR Wortman M Wu A Yao EM Zdobnov H Zhang Q Zhao S Zhao SC Zhu I Zhimulev M Coluzzi A della Torre CW Roth C Louis F Kalush RJ Mural EW Myers MD Adams HO Smith S Broder MJ Gardner CM Fraser E Birney P Bork PT Brey JC Venter J Weissenbach FC Kafatos FH Collins SL Hoffman doi:10.1126/science.1076181 Science, Vol. 298, No. 5591. (4 October 2002), pp. 129-149. 2005-05-09T17:13:03-00:00 2002 Science 1095-9203 298 5591 129 149 gambiae genome http://www.citeulike.org/group/5070/article/2942417 <i>The Journal of clinical investigation, Vol. 112, No. 5. (September 2003), pp. 725-735.</i><br /><br />Increased production of reactive oxygen species and loss of endothelial NO bioactivity are key features of vascular disease states such as diabetes mellitus. Tetrahydrobiopterin (BH4) is a required cofactor for eNOS activity; pharmacologic studies suggest that BH4 may mediate some of the adverse effects of diabetes on eNOS function. We have now investigated the importance and mechanisms of BH4 availability in vivo using a novel transgenic mouse model with endothelial-targeted overexpression of the rate-limiting enzyme in BH4 synthesis, guanosine triphosphate-cyclohydrolase I (GTPCH). Transgenic (GCH-Tg) mice demonstrated selective augmentation of endothelial BH4 levels. In WT mice, induction of diabetes with streptozotocin (STZ) increased vascular oxidative stress, resulting in oxidative loss of BH4, forming BH2 and biopterin. Endothelial cell superoxide production in diabetes was increased, and NO-mediated endothelium-dependent vasodilatation was impaired. In diabetic GCH-Tg mice, superoxide production from the endothelium was markedly reduced compared with that of WT mice, endothelial BH4 levels were maintained despite some oxidative loss of BH4, and NO-mediated vasodilatation was preserved. These findings indicate that BH4 is an important mediator of eNOS regulation in diabetes and is a rational therapeutic target to restore NO-mediated endothelial function in diabetes and other vascular disease states. Tetrahydrobiopterin-dependent preservation of nitric oxide-mediated endothelial function in diabetes by targeted transgenic GTP-cyclohydrolase I overexpression. NJ Alp S Mussa J Khoo S Cai T Guzik A Jefferson N Goh KA Rockett KM Channon doi:10.1172/JCI17786 The Journal of clinical investigation, Vol. 112, No. 5. (September 2003), pp. 725-735. 2008-06-30T00:02:35-00:00 2003 The Journal of clinical investigation 0021-9738 112 5 725 735 diabetes endothelial gtpcyclohydrolase tetrahydrobiopterinm http://www.citeulike.org/user/ingedwar/article/2940412 <i>Microelectronics Journal, Vol. 37, No. 11. (November 2006), pp. 1280-1284.</i><br /><br />A MEMS-based energy harvesting device, micro piezoelectric power generator, is designed to convert ambient vibration energy to electrical power via piezoelectric effect. In this work, the generator structure of composite cantilever with nickel metal mass is devised. Micro-electronic-mechanical systems (MEMS) related techniques such as sol-gel, RIE dry etching, wet chemical etching, UV-LIGA are developed to fabricate the device and then its performance is measured on vibration testing setup. The investigation shows that the designed device is expected to resonantly operate in low-frequency environmental vibration through tailoring the structure dimension. Under the resonant operation with frequency of about 608 Hz, a first prototype of the generator result in about 0.89 V AC peak-peak voltage output to overcome germanium diode rectifier toward energy storage, and its power output is in microwatt level of 2.16 [mu]W. Fabrication and performance of MEMS-based piezoelectric power generator for vibration energy harvesting Hua-Bin Fang Jing-Quan Liu Zheng-Yi Xu Lu Dong Li Wang Di Chen Bing-Chu Cai Yue Liu doi:10.1016/j.mejo.2006.07.023 Microelectronics Journal, Vol. 37, No. 11. (November 2006), pp. 1280-1284. 2008-06-28T23:50:05-00:00 2006 Microelectronics Journal 37 11 1280 1284 piezoelectric scavenging vibration http://www.citeulike.org/user/ebalp/article/2073902 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 6. (2007)</i><br /><br />In this paper, we investigate the dynamical properties of electroencephalogram (EEG) signals of humans in sleep. By using a modified random walk method, we demonstrate that scale-invariance is embedded in EEG signals after a detrending procedure is applied. Furthermore, we study the dynamical evolution of the probability density function (PDF) of the detrended EEG signals by nonextensive statistical modeling. It displays a scale-independent property, which is markedly different from the usual scale-dependent PDF evolution and cannot be described by the Fokker-Planck equation. Scale invariance of human electroencephalogram signals in sleep Shi Cai Zhao Jiang Tao Zhou Pei Zhou Hui Yang Bing Wang doi:10.1103/PhysRevE.76.061903 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 6. (2007) 2007-12-07T17:14:35-00:00 2007 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 76 6 APS criticality http://www.citeulike.org/user/thienanh/article/500579 <i>Pattern Recognition, Vol. 39, No. 4. (April 2006), pp. 717-720.</i><br /><br />We study the problem of image retrieval based on semi-supervised learning. Semi-supervised learning has attracted a lot of attention in recent years. Different from traditional supervised learning. Semi-supervised learning makes use of both labeled and unlabeled data. In image retrieval, collecting labeled examples costs human efforts, while vast amounts of unlabeled data are often readily available and offer some additional information. In this paper, based on support vector machine (SVM), we introduce a semi-supervised learning method for image retrieval. The basic consideration of the method is that, if two data points are close to each, they should share the same label. Therefore, it is reasonable to search a projection with maximal margin and locality preserving property. We compare our method to standard SVM and transductive SVM. Experimental results show efficiency and effectiveness of our method. An algorithm for semi-supervised learning in image retrieval Ke Lu Jidong Zhao Deng Cai doi:10.1016/j.patcog.2005.11.009 Pattern Recognition, Vol. 39, No. 4. (April 2006), pp. 717-720. 2006-02-10T13:31:16-00:00 2006 Pattern Recognition 39 4 717 720 no-tag http://www.citeulike.org/user/jago/article/1433429 <i>GeoInformatica, Vol. 11, No. 2. (June 2007), pp. 217-237.</i> Contextualization of Geospatial Database Semantics for HumanGIS Interaction Cai Guoray doi:10.1007/s10707-006-0001-0 GeoInformatica, Vol. 11, No. 2. (June 2007), pp. 217-237. 2007-07-04T16:45:18-00:00 2007 GeoInformatica 1384-6175 11 2 217 237 Springer context-awareness hci ontology http://www.citeulike.org/user/benavides/article/2933192 <i>Journal of Systems and Software, Vol. 81, No. 6. (June 2008), pp. 1051-1058.</i><br /><br />This paper is the first in a new annual series whose goal is to answer the following question: what are the active research focuses within the field of software engineering? We considered 7 top journals and 7 top international conferences in software engineering and examined all the 691 papers published in these journals or presented at these conferences in 2006. Consequently, we have a number of findings. (1) Seventy-three percent of journal papers focus on 20% of subject indexes in software engineering, including Testing and Debugging (D.2.5), Management (D.2.9), and Software/Program Verification (D.2.4). (2) Eighty-nine percent of conference papers focus on 20% of subject indexes in software engineering, including Software/Program Verification (D.2.4), Testing and Debugging (D.2.5), and Design Tools and Techniques (D.2.2). (3) Seventy-seven percent of journal/conference papers focus on 20% of subject indexes in software engineering, including Testing and Debugging (D.2.5), Software/Program Verification (D.2.4), and Management (D.2.9). (4) The average number of references cited by a journal paper is about 33, whereas this number becomes around 24 for a conference paper. An analysis of research topics in software engineering - 2006 Kai-Yuan Cai David Card doi:10.1016/j.jss.2007.08.028 Journal of Systems and Software, Vol. 81, No. 6. (June 2008), pp. 1051-1058. 2008-06-27T09:53:18-00:00 2008 Journal of Systems and Software 81 6 1051 1058 education fundations miphisis http://www.citeulike.org/user/starz1010101/article/781521 <i>Biol Cybern, Vol. 95, No. 2. (August 2006), pp. 113-121.</i><br /><br />Although spike-timing-dependent plasticity (STDP) is well characterized when pre- and postsynaptic spikes are paired with a given time lag, how this generalizes for more complex spike-trains is unclear. Recent experiments demonstrate that contributions to synaptic plasticity from different spike pairs within a spike train do not add linearly. In the visual cortex conditioning with spike triplets shows that the effect of the first spike pair dominates over the second. Using a previously proposed calcium-dependent plasticity model, we show that short-term synaptic dynamics and interaction between successive back-propagating action potentials (BPAP) may jointly account for the nonlinearities observed. Paired-pulse depression and attenuation of BPAPs are incorporated into the model through the use-dependent depletion of pre- and postsynaptic resources, respectively. Simulations suggest that these processes may play critical roles in determining how STDP operates in the context of natural spike-trains. A Biophysical Basis for the Inter-spike Interaction of Spike-timing-dependent Plasticity. NT Shah LC Yeung LN Cooper Y Cai HZ Shouval doi:10.1007/s00422-006-0071-y Biol Cybern, Vol. 95, No. 2. (August 2006), pp. 113-121. 2006-08-01T09:36:45-00:00 2006 Biol Cybern 0340-1200 95 2 113 121 bap computational temporal_code http://www.citeulike.org/user/jyuh/article/2925886 <i>Biometrics (19 June 2008)</i><br /><br />A retrospective dental study was conducted to evaluate the degree to which pulpal involvement affects tooth survival. Due to the clustering of teeth, the survival times within each subject could be correlated and thus the conventional method for the case-control studies cannot be directly applied. In this article, we propose a marginal model approach for this type of correlated case-control within cohort data. Weighted estimating equations are proposed for the estimation of the regression parameters. Different types of weights are also considered for improving the efficiency. Asymptotic properties of the proposed estimators are investigated and their finite sample properties are assessed via simulations studies. The proposed method is applied to the aforementioned dental study. Marginal Hazards Regression for Retrospective Studies within Cohort with Possibly Correlated Failure Time Data. Sangwook Kang Jianwen Cai doi:10.1111/j.1541-0420.2008.01077.x Biometrics (19 June 2008) 2008-06-25T13:11:04-00:00 2008 Biometrics 1541-0420 recurrent http://www.citeulike.org/user/marryrene/article/2925648 <i>(24 Jun 2008)</i><br /><br />A class of dynamical dark energy models, dubbed Spinor Quintom, can be constructed by a spinor field $ψ$ with a nontraditional potential. We find that, if choosing suitable potential, this model is able to allow the equation-of-state to cross the cosmological constant boundary without introducing any ghost fields. In a further investigation, we show that this model is able to mimic a perfect fluid of Chaplygin gas with $p=-c/ρ$ during the evolution, and also realizes the Quintom scenario with its equation-of-state across -1. Dark Energy Model with Spinor Matter and Its Quintom Scenario Yi-Fu Cai Jing Wang (24 Jun 2008) 2008-06-25T10:38:21-00:00 2008 dark energy http://www.citeulike.org/user/cjrosales/article/2925568 <i>Robotics and Automa