julilili42/papers huggingface dataset:
Assays of Proteasome-Dependent Cleavage Products
2005-05-25

The degradation of misfolded, aged, or no longer needed cytosolic proteins depends largely on the ubiquitin-proteasome system. Proteasomes degrade their substrates into fragments of 3-20 amino acids. Human 20S proteasomes can be purified from human erythrocytes by batch adsorption to DEAE-cellulose, ammonium sulfate precipitation, anion-exchange fast protein liquid chromatography (FPLC), and glycerol density gradient ultracentrifugation. 20S proteasomes purified by this method are suitable for the in vitro digestion of synthetic peptides as well as full-length proteins. The degradation products produced by proteasomes are separated by reversed-phase HPLC using an acetonitrile gradient. The obtained fractions are further analyzed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and Edman degradation, which allows a quantitative analysis of the digestion products.
Index
2005-05-25

ABAQUS 61 acceleration sensors 12, 119 f, 301 torque 457 accelerometers 93, 253, 269 ff acceptors 465 accuracy 21, 82 -accelerometers 283 -chemical sensors 504 -crankle angle sensors 419 -electric current sensors 529 -evaluation circuits 263 -high pressure sensors 338 -platinum sensors 350 -pressure sensors 317 -surface micromachining 123 -tire pressure sensors 539 activation 170 active body control (ABC) 428, active front & rear steering (AFS) 429, 444 active pixel sensor (APS) 392 active wheel speed sensors 404 AD converter (ADC) 348, 430 adaptive cruise control (ACC) 2, 16 -radar sensors 372, 379, 382 -steering-angle sensors 428 -stop&go 382, 401 -video sensors 386 adhesion 145 adhesive bonding 84 adhesives, fluorine-based 326 adjustable sources, TCS/TCO 261 ADXL 50 269 aftertreatment 482, 501 Agilent's advanced design system (ADS) 59, 69 aging 496 air bridges 241 air conditioner 314 air flow metering 360 ff air quality sensors (AQS) 509-515 air/fuel (A/F) ratio control 480-500 airbag passenger protection 2-9, 269, 383 airgap deflection, wheel speed 415 Al 2 Au phase 137 ALGOR 61 alignment tolerances 95 alkyline solution 285 allowed tolerance band (ATB) 50 alumina 165 aluminum 154, 347, 354 ammonia 507 Ampere law 29 amperometric limiting current oxygen sensor 491 amplifiers -crankle angle sensors 421 -evaluation circuits 247, 260 ff -force sensors 451 -mass-flow sensors 366 -wheel speed sensors 406 f -yaw rate sensors 302 analog evaluation circuit 259 analog hardware description language (AHDL) 59 analog output air flow meter 366 f analog signal processing 259, 461 analog steering-angle sensors 429 analytical modeling 46 anchoring 94 f, 97 f, 105 angle hysteresis, wheel speed sensors 414 angle sensors -AMR 177 f -GMR 184 -market 15 angular displacement, torque sensors 453 angular momentum conservation 46 angular rate sensors 45, 51, 297-314 -market 13 -packaging 203 -rotationally vibrating 43 -surface micromachining 119 angular response, light sensors 467, 471 anisotropic etching 74, 103, 110 -pressure sensors 320 anisotropic magnetoresistive effect (AMR) 173 ff, 438, 454, 533 annealing 98, 109, 126, 150 anodic bonding 82, 324 anomalies 233 Ansoff's HFFS 61, 69 ANSYS 61 antenna 539 antiblooming 389 antilock braking system (ABS) -magnetic field sensors 172 -market 2, 12 -steering-angle sensors 428, 444 -wheel speed sensors 403 antistiction coating 99 Sensors for Automotive Applications.
Front Matter
2005-05-25

For each of the volumes in the set the prelims comprise the following Half-title page Upcoming Volumes of Sensors Applications, Related Wiley-VCH Titles Title page Copyright page Preface to the Series Preface to the Volume / Foreword Contents List of Contributors List of Abbreviations
Controllable plasma energy bands in a one-dimensional crystal of fractional Josephson vortices
2005-05-26

We consider a 1D chain of fractional vortices in a long Josephson junction\\nwith alternating phase discontinuities. Since each vortex has its\\nown eigenfrequency, the inter-vortex coupling results in eigenmode splitting\\nand in the formation of an oscillatory energy band for plasma waves. The band\\nstructure can be controlled at the design time by choosing the distance between\\nvortices or \\\\emph{during experiment} by varying the topological charge of\\nvortices or the bias current. Thus one can construct an artificial vortex\\ncrystal with controllable energy bands for plasmons.\\n
The Annotation of Temporal Information in Natural Language Sentences
2005-05-26

Abstract In interpreting narratives the most essential information to be extracted is who did what where, when, and why, the classic journalistic imperatives. The ‘who’ and ‘what’ information is usually expressed overtly, and this has made it possible to apply stochastic techniques to problems in this domain (such as word-sense classification and argument structure mapping). The ‘when’ and ‘where’ information is, however, often left implicit, or, at least, only partially specified. The ‘why’ information is rarely explicit. Formal semantic theories of temporal interpretation (e.g. Kamp and Reyle 1993, Ogihara 1996, Abusch 1997) have been quite successful at specifying the contribution that such overt markers as tenses and temporal adverbials make to the meaning of a sentence or discourse.
Loss of the CONSTITUTIVE PHOTOMORPHOGENIC9 Signalosome Subunit 5 Is Sufficient to Cause the cop/det/fus Mutant Phenotype in Arabidopsis
2005-05-27

The COP9 signalosome (CSN) was originally identified based on the constitutively photomorphogenic/de-etiolated/fusca (cop/det/fus) mutants from Arabidopsis thaliana. CSN is evolutionary conserved, and its subunit 5 (CSN5) mediates the deconjugation of NEDD8 from the cullin subunit of E3 ubiquitin ligases (deneddylation). Here, we report on Arabidopsis mutants deficient in CSN5 function. We show that these mutants are phenotypically indistinguishable from the previously described cop/det/fus mutants of other CSN subunits. However, we also show that these mutants retain the CSN complex (lacking CSN5), and this finding is in contrast with the previously described CSN subunit mutants, which lack the CSN complex. We therefore conclude that loss of CSN5 as part of CSN is sufficient to cause the cop/det/fus mutant phenotype. Furthermore, we show that mutants defective in CSN5 as well as mutants defective in CSN are unable to deneddylate the Arabidopsis cullins AtCUL1, AtCUL3A, and AtCUL4. Because these are representative cullin subunits of the three cullin-containing E3 families present in Arabidopsis, we postulate that the cop/det/fus mutant phenotype may be the result of the defects caused by impaired CSN5-dependent deneddylation of cullin-containing E3s.
Reversible Lithium Intercalation into the Three‐Dimensional Cluster Network Structure of Ta6Cl15
2005-05-27

Abstract A crystalline powder of Ta 6 Cl 15 was synthesized through solid state reaction of Ta powder, and TaCl 5 at 700 °C. The structure contains [Ta 6 Cl 12 ] 3+ clusters which are three‐dimensionally interconnected by Cl bridges, leaving cavities which are shown to be suitable for lithium insertion. Reversible lithium intercalation into Ta 6 Cl 15 involves 1 mol of lithium per formula unit under equilibrium conditions, when cells are discharged between 3 and 1.8 V, leading to the upper composition LiTa 6 Cl 15 . Although capacity values within this reversible voltage range are small (ca. 25 Ah·kg −1 ), the cycle life of such Li/Ta 6 Cl 15 cells is excellent, and the initial capacity value is maintained over 1500 cycles. On the other hand, a maximum of 15 moles of lithium can be reacted with one mole Ta 6 Cl 15 when lithium cells were deep‐discharged. This process is likely due to the complete and irreversible reduction of the parent by lithium.
Palmitoylation is a sorting determinant for transport to the myelin membrane
2005-05-28

Myelin is a specialized membrane enriched in glycosphingolipids and cholesterol that contains a restricted set of proteins. The mechanisms by which oligodendrocytes target myelin components to myelin are not known. To identify the sorting determinants for protein transport to myelin, we used a primary oligodendrocyte culture system in which terminal differentiation is synchronized and there is excessive deposition of myelin-like membranes (MLMs). Because several myelin proteins are palmitoylated, we explored the role of acylation in protein transport to MLMs. We found that palmitoylation-deficient mutants of a major myelin protein, proteolipid protein (PLP/DM20), were less efficiently targeted to MLMs. The N-terminal 13 amino acids of PLP/DM20, which are palmitoylated at three sites, were sufficient to direct a fluorescent fusion protein to MLMs. Mutagenesis of the N-terminal palmitoylation motif abolished the transport of the fusion protein to MLMs, indicating that palmitoylation is required for sorting to myelin. Similar results were obtained in myelinating co-cultures of oligodendrocytes and neurons. Furthermore, the combined farnesylation/palmitoylation signals from c-Ha-Ras and the N-terminal consensus sequence for dual palmitoylation from neuromodulin were sufficient for the transport of fluorescent fusion proteins to MLMs. Thus, we conclude that palmitoylation is a sorting determinant for transport to the myelin membrane.
The AGE/RAGE/NF-κB Pathway May Contribute to the Pathogenesis of Polyneuropathy in Impaired Glucose Tolerance (IGT)
2005-05-30

Binding of ligands to the receptor for advanced glycation end products (RAGE) results in activation of the transcription factor nuclear factor kappa B (NF-(kappa)B) and subsequent expression of NF-(kappa)B-regulated cytokines. This has been shown to be a relevant pathomechanism in diabetic polyneuropathies (PNP). To determine whether this pathway may contribute to the pathogenesis of PNP due to impaired glucose tolerance (IGT) we performed a pilot study to demonstrate the presence of the RAGE ligand N (epsilon)-(Carboxymethyl)lysine (CML), the receptor itself and N-(kappa)B in sural nerve biopsies of 4 patients with IGT-related PNP. Biopsies of either 4 patients with diabetic PNP and with Charcot-Marie-Tooth disease (CMT) I and II served as positive and negative controls, respectively. In IGT-related PNP and diabetic PNP, CML, RAGE, and NF-(kappa)B was found in the perineurium, epineurial vessels and in part in endoneurial vessels. CMT patients showed, if any, only weak staining for one or the other antigen. These data suggest that activation of the RAGE pathway may be one of the first steps in the pathogenesis of PNP even before chronic hyperglycemia occurs.
Genetic Determinants of Insulin Action in Polycystic Ovary Syndrome
2005-05-30

We found a higher prevalence of the T45 G polymorphism in the adiponectin gene in women with PCOS compared to controls. This was not associated with a more insulin resistant phenotype in PCOS, however. Other frequent polymorphisms in genes related to insulin resistance and type 2 diabetes showed no association with PCOS.
Computer-supported collaborative learning in higher education: scripts for argumentative knowledge construction in distributed groups
2005-05-30

Learners rarely know how to construct knowledge together in argumentation. This experimental study analyzes two computer-supported collaboration scripts, which should facilitate processes and outcomes of argumentative knowledge construction. One script aims to support the construction of single arguments and the other script aims to support the construction of argumentation sequences. Both scripts were varied independently in a 2x2-factorial design. 120 students of Educational Science participated in the study in groups of three. Results show that the computer-supported scripts facilitate specific processes and outcomes of argumentative knowledge construction. Learners with scripts argued better and acquired more knowledge on argumentation than learners without scripts without impeding acquisition of domain specific knowledge.
Why member portraits can undermine participation
2005-05-30

One possible way to support social awareness in virtual collaborative environments is to provide member portraits. Based on the SIDE-Model (Social Identity Model of Deindividuation Effect) it is argued that these portraits can have ambivalent effects for people who act according to the mode of personal identity and for people who act according to the mode of social identity. An experiment providing an information-exchange dilemma task confirmed these expectations.
NOA‐03 trial of high‐dose methotrexate in primary central nervous system lymphoma: Final report
2005-05-31

Abstract The NOA‐03 trial explored high‐dose methotrexate alone in 37 patients with primary central nervous system lymphoma. The overall median survival was 25 months. After 4 years, the rate of leukoencephalopathy in patients surviving more than 12 months was 58% with and 10% without whole‐brain radiotherapy given at relapse ( p = 0.11). Attention deficits were found in all six tested patients, and memory deficits in four patients. Two patients had normal, three had moderately restricted, and one had markedly restricted quality of life. Thus, high‐dose methotrexate with deferred radiotherapy had only moderate efficacy and was associated with significant neurotoxicity in long‐term surviving patients. Ann Neurol 2005;57:843–847
A Novel Route Towards the Synthesis of Stereospecific N-Substituted Chiral Morpholines
2005-05-31

In this communication a convenient and novel method for the synthesis of chiral N-substituted- (arabinopyrano)[3,4-b]morpholines of pharmacological interest from anhydro sugars is described. Keywords: stereospecific synthesis, morpholines, anhydro sugars
HLA-E Protects Glioma Cells from NKG2D-Mediated Immune Responses In Vitro: Implications for Immune Escape In Vivo
2005-06-01

The nonclassical MHC class I molecule HLA-E is the only known ligand for CD94/NKG2A and CD94/NKG2C expressed on NK and CD8+ alphabeta and gammadelta T cells. HLA-E may transmit either activating signals via CD94/NKG2C or inhibitory signals mediated by CD94/NKG2A. Here we show that HLA-E is expressed at mRNA and protein level in human long-term glioma cell lines, primary ex vivo polyclonal glioblastoma cell cultures and surgical glioblastoma specimens. Furthermore, immunohistochemistry revealed an enhanced in vivo expression of HLA-E in gliomas of lower grades and a massive overexpression in grade IV glioblastomas compared with normal CNS tissue. An immune-inhibitory effect of HLA-E on tumor-specific CTL has already been described. We show that siRNA-mediated silencing of HLA-E or blocking of CD94/NKG2A enables NKG2D-mediated lysis of 51Cr-labeled tumor cells by NK cells. Thus, our study provides the first evidence that expression and interaction of HLA-E on cancer cells with CD94/NKG2A expressed on lymphocytes compromises innate anti-tumor immune responses.
How can opposition support authoritarianism? Lessons from Egypt
2005-06-01

While many observers of politics in the Arab world hold that the emergence of political opposition would be a harbinger of democratization, this article argues that opposition can contribute to the stability and resilience of authoritarian regimes. Based on an empirical analysis of contemporary Egyptian politics, it is shown that, despite the repressive nature of the Egyptian state, political opposition has emerged in various societal contexts: political parties, human rights associations and a popular Islamist current. In order to understand this development, it is important to investigate authoritarian survival strategies 'beyond coercion'. While militant resistance from radical Islamists has been successfully oppressed during the 1990s, the Egyptian incumbents reacted to the challenge of societal dissent by co-opting opposition forces. As a consequence, political opposition in Egypt serves functions entirely different from those in liberal democracies. It contributes to the legitimacy of the Egyptian state. Moreover, by tolerating controlled opposition, societal dissent can be better observed, channelled and moderated. From a more general perspective, political dissent exists in various settings: it prevails not only among opposition, but also within the political elite leading to a delicate juggling act of competing ideas and interests performed at the helm of the polity.
Neuronal mechanisms underlying control of a brain–computer interface
2005-06-01

Abstract Brain–computer interfaces (BCIs) enable humans or animals to communicate or control external devices without muscle activity using electric brain signals. The BCI used here is based on self‐regulation of slow cortical potentials (SCPs), a skill that most people and paralyzed patients can acquire with training periods of several hours up to months. The neurophysiological mechanisms and anatomical sources of SCPs and other event‐related brain potentials have been described but the neural mechanisms underlying the self‐regulation skill for the use of a BCI are unknown. To uncover the relevant areas of brain activation during regulation of SCPs, the BCI was combined with functional magnetic resonance imaging. The electroencephalogram was recorded inside the magnetic resonance imaging scanner in 12 healthy participants who learned to regulate their SCP with feedback and reinforcement. The results demonstrate activation of specific brain areas during execution of the brain regulation skill allowing a person to activate an external device; a successful positive SCP shift compared with a negative shift was closely related to an increase of the blood oxygen level‐dependent response in the basal ganglia. Successful negativity was related to an increased blood oxygen level‐dependent response in the thalamus compared with successful positivity. These results may indicate learned regulation of a cortico‐striatal‐thalamic loop modulating local excitation thresholds of cortical assemblies. The data support the assumption that human subjects learn the regulation of cortical excitation thresholds of large neuronal assemblies as a prerequisite for direct brain communication using an SCP‐driven BCI. This skill depends critically on an intact and flexible interaction between the cortico‐basal ganglia‐thalamic circuits.
Conditional Mutagenesis of the Murine Serum Response Factor Gene Blocks Cardiogenesis and the Transcription of Downstream Gene Targets
2005-06-01

Serum response factor (SRF) homozygous-null embryos from our backcross of SRF(LacZ/)(+) "knock-in" mice failed to gastrulate and form mesoderm, similar to the findings of an earlier study (Arsenian, S., Weinhold, B., Oelgeschlager, M., Ruther, U., and Nordheim, A. (1998) EMBO J. 17, 6289-6299). Our use of embryonic stem cells provided a model system that could be used to investigate the specification of multiple embryonic lineages, including cardiac myocytes. We observed the absence of myogenic alpha-actins, SM22alpha, and myocardin expression and the failure to form beating cardiac myocytes in aggregated SRF null embryonic stem cells, whereas the appearance of transcription factors Nkx2-5 and GATA4 were unaffected. To study the role of SRF during heart organogenesis, we then performed cardiac-specific ablation of SRF by crossing the transgenic alpha-myosin heavy chain Cre recombinase line with SRF LoxP-engineered mice. Cardiac-specific ablation of SRF resulted in embryonic lethality due to cardiac insufficiency during chamber maturation. Conditional ablation of SRF also reduced cell survival concomitant with increased apoptosis and reduced cellularity. Significant reductions in SRF (> or =95%), atrial naturetic factor (> or =80%), and cardiac (> or =60%), skeletal (> or =90%), and smooth muscle (> or =75%) alpha-actin transcripts were also observed in the cardiac-conditional knock-out heart. This was consistent with the idea that SRF directs de novo cardiac and smooth muscle gene activities. Finally, quantitation of the knock-in LacZ reporter gene transcripts in the hearts of cardiac-conditional knock-out embryos revealed an approximately 30% reduction in gene activity, indicating SRF gene autoregulation during cardiogenesis.
Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and o -Xylene in Sediment-Free Iron-Reducing Enrichment Cultures
2005-06-01

ABSTRACT Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and xylene (BTEX) are widespread contaminants in groundwater. We examined the anaerobic degradation of BTEX compounds with amorphous ferric oxide as electron acceptor. Successful enrichment cultures were obtained for all BTEX substrates both in the presence and absence of AQDS (9,10-anthraquinone-2,6-disulfonic acid). The electron balances showed a complete anaerobic oxidation of the aromatic compounds to CO 2 . This is the first report on the anaerobic degradation of o -xylene and ethylbenzene in sediment-free iron-reducing enrichment cultures.
The Role of Sphingosine 1‐Phosphate Receptors in the Trafficking of Hematopoietic Progenitor Cells
2005-06-01

A bstract : Sphingosine 1‐phosphate (S1P) is an ubiquitously present extracellular lipid mediator that is released by several cell types, particularly by activated platelets. The effects of S1P are mediated by a specific family of G protein‐coupled sphingosine 1‐phosphate receptors (S1P1‐S1P5). We demonstrate that S1P acts on hematopoietic progenitor cells as a chemotactic factor, attracting peripheral blood CD34 + cells in vitro . Furthermore, constant activation of S1P receptors augments CXCR4‐mediated signal transduction induced by stromal cell‐derived factor 1 (SDF‐1). These effects are most likely mediated by the S1P1 receptor consistently expressed in both primitive and committed CD34 + hematopoietic progenitor cells (HPCs). In vivo , sustained activation of S1P1 by a receptor agonist during the homing process resulted in increased engraftment. Given the fact that activated platelets represent a major source of extracellular S1P, SDF‐1‐mediated stem cell homing may occur at sites of tissue injury in addition to the bone marrow. This could explain the previously observed contribution of primary hematopoietic stem cells to tissue repair in myocardial infarction and other diseases.
Aquaporins from pathogenic protozoan parasites: structure, function and potential for chemotherapy
2005-06-01

Infectious diseases, caused by protozoa, such as malaria, sleeping sickness, Chagas' disease or leishmaniasis, are a global threat. The increase in the number of affected individuals and the rapid spread of drug‐resistant strains call for specific novel strategies to combat human pathogenic parasites. In the search for novel drug targets, transport proteins for nutrients and metabolites of the parasite—host interface are getting into focus. The present review summarizes and discusses the currently available results on protozoan aquaporins. Various genes coding for aquaporin water and solute channels have been identified in the protozoan genomes and they are probable elements of the parasite's cell membrane. Phylogenetic analysis reveals that individual aquaporin genes are of bacterial or plant origin. So far, six protozoan aquaporins have been cloned and functionally characterized. Typically, these are bifunctional channels and pass water at intermediate to high rates as well as uncharged solutes. In the present review, amino acid compositions of the individual pore entries are compared and permeability properties are attributed to specific protein features. Furthermore, possible physiological roles in osmotic protection and metabolism are discussed. Finally, the potential of protozoan aquaporins for use as a target or entry pathway for chemotherapeutic compounds is reviewed.