gebhart/patrepeval huggingface dataset:
Amyloid Oligomer Conformation in a Group of Natively Folded Proteins (2008)

Recent in vitro and in vivo studies suggest that destabilized proteins with defective folding induce aggregation and toxicity in protein-misfolding diseases. One such unstable protein state is called amyloid oligomer, a precursor of fully aggregated forms of amyloid. Detection of various amyloid oligomers with A11, an anti-amyloid oligomer conformation-specific antibody, revealed that the amyloid oligomer represents a generic conformation and suggested that toxic beta-aggregation processes possess a common mechanism. By using A11 antibody as a probe in combination with mass spectrometric analysis, we identified GroEL in bacterial lysates as a protein that may potentially have an amyloid oligomer conformation. Surprisingly, A11 reacted not only with purified GroEL but also with several purified heat shock proteins, including human Hsp27, 40, 70, 90; yeast Hsp104; and bovine Hsc70. The native folds of A11-reactive proteins in purified samples were characterized by their anti-beta-aggregation activity in terms of both functionality and in contrast to the beta-aggregation promoting activity of misfolded pathogenic amyloid oligomers. The conformation-dependent binding of A11 with natively folded Hsp27 was supported by the concurrent loss of A11 reactivity and anti-beta-aggregation activity of heat-treated Hsp27 samples. Moreover, we observed consistent anti-beta-aggregation activity not only by chaperones containing an amyloid oligomer conformation but also by several A11-immunoreactive non-chaperone proteins. From these results, we suggest that the amyloid oligomer conformation is present in a group of natively folded proteins. The inhibitory effects of A11 antibody on both GroEL/ES-assisted luciferase refolding and Hsp70-mediated decelerated nucleation of Abeta aggregation suggested that the A11-binding sites on these chaperones might be functionally important. Finally, we employed a computational approach to uncover possible A11-binding sites on these targets. Since the beta-sheet edge was a common structural motif having the most similar physicochemical properties in the A11-reactive proteins we analyzed, we propose that the beta-sheet edge in some natively folded amyloid oligomers is designed positively to prevent beta aggregation.
The cytoprotective drug amifostine modifies both expression and activity of the pro-angiogenic factor VEGF-A (2010)

Taken together, our results indicate that amifostine treatment modulates tumour angiogenesis by two apparently opposite mechanisms - the increased VEGF-A expression by tumour cells and the inhibition of EC capacity to respond to VEGF-A stimulation.
Compile-time analyses and run-time support for a higher order, distributed data-structures based, parallel language (1996)

Our thesis provides new compile-time analyses, and new run-time support methods for a statically scoped, distributed data-structures based, parallel dialect of Lisp. The language is formed by embedding first-class tuplespaces in a higher-order subset of Scheme that also supports list data structures and assignments.
The compile-time methods include a control flow analyser called the Pundit, which provides a new basis for the static analysis of parallel programs. The Pundit identifies properties such as lock-freeness, read-only regions, and tuplespace-operation collections in a language setting that includes features such as: parallelism, non-determinism, dynamic task creation, shared content-addressed memories, explicit synchronisation, list data structures, assignments, and higher-order functions.
The thesis provides the first formal model of content-addressing in tuplespaces. Using the model, the thesis provides the first tuplespace analyser that fully resolves static tuplespace partitionings, efficiently.
The thesis provides a new, highly-concurrent kernel for tuplespaces that permits simultaneous reads and writes to a kernel data structure. The kernel relies on atomic reads and writes to memory, the use of spin locks for explicit serialisation, and the use of automatic space management to recycle deleted data. The kernel is optimisable; using the properties proven by the Pundit for a program, the kernel allows certain lock counts in some cases to be reduced to the minimum permissible.
The thesis also provides new methods of generation and specialisation of code for accessing tuplespace objects. The specialisations include: dispatch simplification, dispatch elimination, and specialisation of matching code.
The methods provided by the thesis have been implemented. The effectiveness of the methods is demonstrated by experiments that measure the implementation's performance on a suite of fine-grain coordinated, benchmark programs using a Silicon Graphics, Power Series, cache-coherent multiprocessor. The experiments show that the cost of kernel locks is often dominant in a computation, which, the methods are able to effectively eliminate. The experiments also show that the simplification and elimination of tuplespace dispatches effectively removes the often dominating code-size cost from the object codes of the benchmarks.
Driving modes for designing the cornering response of fully electric vehicles with multiple motors (2015)

Fully electric vehicles with multiple drivetrains allow a significant variation of the steady-state and transient cornering responses through the individual control of the electric motor drives. As a consequence, alternative driving modes can be created that provide the driver the option to select the preferred dynamic vehicle behavior. This article presents a torque-vectoring control structure based on the combination of feedforward and feedback contributions for the continuous control of vehicle yaw rate. The controller is specifically developed to be easily implementable on real-world vehicles. A novel model-based procedure for the definition of the control objectives is described in detail, together with the automated tuning process of the algorithm. The implemented control functions are demonstrated with experimental vehicle tests. The results show the possibilities of torque-vectoring control in designing the vehicle understeer characteristic.
Low-power synchronous oscillator in SiGe technology for UMTS 2000 applications (2002)

The design of a 2 GHz Synchronous Oscillator (SO) dedicated to UMTS 2000 third generation mobile phones is presented. Taking advantage of a 0.35 /spl mu/m non-selective epitaxy growth (NSEG) SiGe technology, this SO is suitable for a low-power double-loop frequency synthesizer. Simulation results highlight the good trade-off obtained between high frequency characteristics and power consumption, which is of strategic importance for portable electronics.
Why a ring? (1981)

In a world increasingly populated with Ethernets and Ethernet-like nets a few sites continue to experiment with rings of active repeaters for local data communication. This paper explores some of the engineering problems involved in designing a ring that has no central control, and then compared the M.I.T.-designed ring with Ethernet on a variety of operational and subtle technical grounds, on each of which the ring may possess important or interesting advantages.
Simultaneous Lightwave Information and Power Transfer: Policies, Techniques, and Future Directions (2019)

Harvesting energy from the surrounding environment is an important and practical solution to prolong the life of the energy-constrained Internet-of-Things (IoT) devices, e.g., wireless sensors. Visible light communications (VLC) has been proved able to provide high-speed data links while meeting the illumination requirement. Thereby, the energy of VLC signals may be harvested by the energy-constrained IoT terminals, such as indoor sensors and portable/wearable devices. This paper presents the concept of simultaneous lightwave information and power transfer (SLIPT) with a particular focus on the design of the receiver and the practical methods to realize SLIPT in the domains of time, signal components, and photoelectric converters. Furthermore, this paper also introduces the applications of SLIPT to various network topologies and communication technologies, e.g., multiple input multiple output, hybrid VLC-radio frequency, and secure communications. Finally, a detailed discussion of future research directions and challenges for the design of SLIPT systems is also presented.
Reactivity of Sulfur-Containing Molecules on Noble Metal Surfaces. 2. tert-Butyl Thioalcohol on Au(110) (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactivity of Sulfur-Containing Molecules on Noble Metal Surfaces. 2. tert-Butyl Thioalcohol on Au(110)Deborah M. Jaffey and Robert J. MadixCite this: J. Am. Chem. Soc. 1994, 116, 7, 3012–3019Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/ja00086a034https://doi.org/10.1021/ja00086a034research-articleACS PublicationsRequest reuse permissionsArticle Views279Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Decision support system for substation operation (2003)

The authors describe a prototype for a hybrid expert system developed to provide advice to station operators in real time. The domain of this expert system is transmission planning as applied to real-time operation. It consists of symbolic and procedural modules that address a variety of electrical concerns at generating stations, including breaker thermal duties, breaker fault duties, and voltage-critical load buses. Once the system is invoked, the prevailing operating state is evaluated for static security-limit violations. If any violations are encouraged, the system searches its knowledge base for plausible plans to alleviate the problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Priority-based wavelength assignment algorithm in WDM networks (2001)

In this paper, a priority-based wavelength assignment algorithm, Dynamic Threshold Method (DTM), is proposed. A set of wavelengths, Preferred Wavelength Set (PWS), is pre-allocated for each priority request. Based on the usage of wavelength in the PWS of a priority request, a threshold is dynamically calculated to decide whether the wavelengths for the higher priority request can be allocated to the lower. By using DTM, the blocking probability of the high priority request is guaranteed to be a lower degree, and at the same time performance of the low priority request is improved. So the network's average blocking probability is minimized. Simulation results of the network performance show that the proposed algorithm performs well in different dynamic traffic load situation.
Clinical assessment and quality of life of postmenopausal women treated with a new intermittent progestogen combination hormone replacement therapy: a placebo-controlled study (2003)

The constant-estrogen, intermittent-progestogen regimen was highly effective in relieving menopausal symptoms and in improving quality of life and was well received by the study participants.
Machine Learning Models for Analysis of Vital Signs Dynamics: A Case for Sepsis Onset Prediction (2019)

The high level of predictive accuracy along with the simplicity and availability of input variables present great potential if applied in ICUs. Variability of a patient's vital signs proves to be a good indicator of one's chance to become septic during ICU stay.
Hybridization of a Flexible Cyclooctatetraene Core and Rigid Aceneimide Wings for Multiluminescent Flapping π Systems (2014)

The hybridization of flexible and rigid π-conjugated frameworks is a potent concept for producing new functional materials. In this article, a series of multifluorescent flapping π systems that combine a flexible cyclooctatetraene (COT) core and rigid aceneimide wings with various π-conjugation lengths has been designed and synthesized, and their structure/properties relationships have been investigated. Whereas these molecules have a V-shaped bent conformation in the ground state, the bent structure changes to a planar conformation in the lowest excited singlet (S1 ) state irrespective of the lengths of the aceneimide wings. However, the fluorescence behavior in solution is distinct between the naphthaleneimide system and the anthraceneimide system. The former has a nonemissive S1 state owing to the significant contribution of the antiaromatic character of the planar COT frontier molecular orbitals, thereby resulting in complete fluorescence quenching in solution. In contrast, the latter anthraceneimide system shows an intense emission, which is ascribed to the planar but distorted S1 state that shows the allowed transition between the π-molecular orbitals delocalized over the COT core and the acene wings. The other characteristic of these π systems is the significantly redshifted fluorescence in the crystalline state relative to their monomer fluorescence. The relationship between the packing structures and the fluorescence properties was investigated by preparing a series of hybrid π systems with different sizes of substituents on the imide moieties, which revealed the effect of the twofold π-stacked structure of the V-shaped molecules on the large bathochromic shift in emission.
The Low Density Lipoprotein Receptor-related Protein Modulates Levels of Matrix Metalloproteinase 9 (MMP-9) by Mediating Its Cellular Catabolism (2001)

Members of the matrix metalloproteinase (MMP) family of enzymes participate in matrix remodeling and share a number of structural and functional features. The activity of this family of proteinases is carefully regulated at the level of zymogen activation and by a family of specific inhibitors termed tissue inhibitors of metalloproteinases (TIMP). It is now becoming clear that levels of certain MMPs are modulated by their association with cellular receptors that mediate their rapid internalization and degradation. In the current investigation we report that the amount of MMP-9 in conditioned cell culture medium is significantly increased when mouse embryonic fibroblasts are grown in the presence of the 39-kDa receptor-associated protein (RAP), an antagonist of ligand binding to low density lipoprotein receptor-related protein (LRP). In vitro assays reveal that the MMP-9.TIMP-1 complex binds to LRP with high affinity and that the binding determinant for LRP appears to reside on MMP-9. Cell lines expressing LRP mediate the internalization of 125I-labeled MMP-9.TIMP-1 complexes, whereas cell lines genetically deficient in LRP show a diminished capacity to mediate the cellular catabolism of MMP-9.TIMP-1 complexes. The results demonstrate that LRP is a functional receptor for MMP-9 and suggest a major role for LRP in modulating remodeling of the extracellular matrix by regulating extracellular proteinase activity.
Efficient Acoustic Echo Cancellation With Reduced-Rank Adaptive Filtering Based on Selective Decimation and Adaptive Interpolation (2008)

This paper presents a new approach to efficient acoustic echo cancellation (AEC) based on reduced-rank adaptive filtering equipped with selective-decimation and adaptive interpolation. We propose a novel structure of an AEC scheme that jointly optimizes an interpolation filter, a decimation unit, and a reduced-rank filter. With a practical choice of parameters in AEC, the total computational complexity of the proposed reduced-rank scheme with the normalized least mean square (NLMS) algorithm is approximately half of that of the full-rank NLMS algorithm. We discuss the convergence properties of the proposed scheme and present a convergence condition. First, we examine the performance of the proposed scheme in a single-talk situation with an error-minimization criterion adopted in the decimation selection. Second, we investigate the potential of the proposed scheme in a double-talk situation by employing an ideal decimation selection. In addition to mean squared error (MSE) and power spectrum analysis of the echo estimation error, subjective assessments based on absolute category rating are performed, and the results demonstrate that the proposed structure provides significant improvements compared to the full-rank NLMS algorithm.
Towards Concept-Based Translation Models Using Search Logs for Query Expansion (2012)

Query logs have been successfully used to improve Web search. One of the directions exploits user clickthrough data to extract related terms to a query to perform query expansion (QE). How-ever, term relations have been created between isolated terms without considering their context, giving rise to the problem of term ambiguity. To solve this problem, we propose several ways to place terms in their contexts. On the one hand, contiguous terms can form a phrase; and on the other hand, terms at proximi-ty can provide less strict but useful contextual constraints mutual-ly. Relations extracted between such more constrained groups of terms are expected to be less noisy than those between single terms. In this paper, the constrained groups of terms are called concepts. We exploit user query logs to build statistical translation models between concepts, which are then used for QE.
Compatibilizing effect of block copolymers added to the polymer/polymer interface (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCompatibilizing effect of block copolymers added to the polymer/polymer interfaceSpiros H. Anastasiadis, Irena Gancarz, and Jeffrey T. KobersteinCite this: Macromolecules 1989, 22, 3, 1449–1453Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://doi.org/10.1021/ma00193a074Request reuse permissionsArticle Views953Altmetric-Citations268LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (698 KB) Get e-Alertsclose Get e-Alerts
Identification of an enhancer/silencer sequence directing the aleurone‐specific expression of a barley chitinase gene (1994)

Chitinases are expressed in various plant tissues where they are thought to play a role in defense against chitin-containing pathogens. Transient gene expression assays have been used in tissues of barley to delineate promoter sequences involved in the regulation of an aleurone-specific chitinase gene (Chi26), and of a vegetatively expressed chitinase gene (Chi33). The assays measured the activities of transcriptional fusions between chitinase 5' upstream sequences and GUS reporter genes after DNA delivery by particle bombardment. Analysis of Chi26 5' and 3' promoter deletions indicated that sequences between -200 and -140 confer developmental and aleurone-specific expression. Deletions/replacements covering this part of the promoter indicated that sequences between -179 and -147 (E-region) direct expression in aleurone cells. The ability of the 33bp E-region of the Chi26 promoter to activate transcription specifically in aleurone was confirmed by constructing and testing two types of chimeric promoters. The first type, which contained two copies of the E-region fused to the CaMV 35S TATA box, conferred aleurone-specific expression of a GUS reporter gene. The second type, which contained a single copy of the E-region inserted into a deleted, inactive Chi33 promoter derivative, was also capable of directing transcription in aleurone but not in leaves. The pattern of expression of this and other Chi26/Chi33 chimeric promoters suggest that the E-region contains cis-acting sequences which activate transcription in aleurone and silence transcription in leaves. DNA sequence motifs implicated in the regulation of Chi26 and Chi33 are described.
A trial of phenome analysis using 4000 <i>Ds</i>‐insertional mutants in gene‐coding regions of Arabidopsis (2006)

Mutant lines covering all Arabidopsis genes allow us to pursue systematic functional genomics. A comprehensive phenotype description, called a phenome, is highly sought after in the profiling of -omics data. We selected 4000 transposon-insertional lines with transposon insertions in their gene-coding regions, and systematically observed the visible phenotype of each line. For the first 3 weeks after germination, plants were grown on agar plates and the juvenile phenotypes were recorded. Then the plants were transferred to soil and their phenotypes were recorded at each growth stage. About 140 lines showed clear and reproducible visible phenotypes, including novel phenotypic mutants as well as previously reported ones. All descriptions of the mutants showing visible phenotypes were classified into eight primary categories (seedling, leaves, flowering and growth, stems, branching, flowers, siliques and seed yield) and 43 secondary categories of morphological phenotypes. Phenotypic images have been entered into a searchable database (http://rarge.gsc.riken.jp/phenome/). One example investigated through the use of plural alleles was a mutant of a novel gene related to glycerolipid biosynthesis, with a unique visible phenotype of sepal opening. Our results suggest that we can find more novel visible phenotypes and their corresponding genes, and that phenotypic mutants of gene knockouts are not exhausted yet. This study provides basic data on large-scale phenotyping of gene knockout lines in plants, and will contribute to the completion of an international effort to develop a phenome database of all the functional genes in Arabidopsis.