gebhart/patrepeval huggingface dataset:
Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network (1999)

A major activity of molecular chaperones is to prevent aggregation and refold misfolded proteins. However, when allowed to form, protein aggregates are refolded poorly by most chaperones. We show here that the sequential action of two Escherichia coli chaperone systems, ClpB and DnaK-DnaJ-GrpE, can efficiently solubilize excess amounts of protein aggregates and refold them into active proteins. Measurements of aggregate turbidity, Congo red, and 4,4'-dianilino-1, 1'-binaphthyl-5,5'-disulfonic acid binding, and of the disaggregation/refolding kinetics by using a specific ClpB inhibitor, suggest a mechanism where (i) ClpB directly binds protein aggregates, ATP induces structural changes in ClpB, which (ii) increase hydrophobic exposure of the aggregates and (iii) allow DnaK-DnaJ-GrpE to bind and mediate dissociation and refolding of solubilized polypeptides into native proteins. This efficient mechanism, whereby chaperones can catalytically solubilize and refold a wide variety of large and stable protein aggregates, is a major addition to the molecular arsenal of the cell to cope with protein damage induced by stress or pathological states.
Priority-based smart household power control model (2012)

In the paper, we present the design and implementation of a priority-based Smart Home Simulation (SHS) system. The system architecture as well as particular device types used are described with a detailed presentation of the consumption planning and control mechanism. The SHS system is based on the multi-agent approach, where the global consumption control is driven mostly by the inter-agent communication.
RNAi mechanisms in <i>Caenorhabditis elegans</i> (2005)

RNA interference (RNAi) is a form of gene silencing induced by double stranded RNA (dsRNA) that is processed into short interfering RNAs (siRNAs). RNAi can induce both post-transcriptional and transcriptional gene silencing. In Caenorhabditis elegans, there are several distinct pathways where post-transcriptional or/and transcriptional RNAi mechanisms are involved. RNAi in C. elegans is also systemic and heritable. This review will discuss RNAi related pathways, features of RNAi in C. elegans and possibilities of endogenous gene regulation by RNAi.
Long‐term and cross‐reactive immunogenicity of inactivated trivalent influenza vaccine in the elderly: MF59‐adjuvanted vaccine versus unadjuvanted vaccine (2013)

Elderly people are at great risk for influenza-related serious complications. However, influenza vaccine-induced antibodies are believed to decline more rapidly in the elderly. This study was designed to evaluate the long-term and cross-reactive immunogenicity among those aged ≥65 years for two seasonal trivalent influenza vaccines during the 2009-2010 influenza season. One vaccine had the MF59 adjuvant, while the other did not contain an adjuvant. Serum hemagglutinin inhibition (HI) titers were determined pre-vaccination and at 1 and 6 months post-vaccination. Of the 100 subjects, 95 (95%) were followed-up for 1 month after vaccination, and 76 (76%) were followed-up for 6 months after vaccination. Both vaccines met the European Medicines Agency (EMA) criteria 1 month after vaccination. However, seroprotection for influenza B was not satisfactory, with a rate of 55.3% for the MF59 adjuvant vaccine and 47.9% for the vaccine without adjuvant. At 6 months post-vaccination, the MF59-adjuvanted vaccine showed a higher seroprotection rate than the unadjuvanted vaccine. At this point, the MF59-adjuvanated vaccine still met the criteria of EMA for A/H1N1 (62.5% vs. 55.5%, P = 0.64) and A/H3N2 (72.5% vs. 47.2%, P = 0.04). Both vaccines showed excellent cross-reactive immunogenicity for influenza A/Solomon Island/3/2006 (H1N1) and A/Wisconsin/67/2005 (H3N2), without significant differences. In comparison, cross-reactive immunogenicity was not remarkable for the A/California/7/2009 (H1N1) and A/New Caledonia/20/1999 (H1N1) strains, which have a greater antigenic distance. In conclusion, the MF59-adjuvanted influenza vaccine showed superior long-term immunogenicity in the elderly compared to the unadjuvanted vaccine. However, cross-reactive immunogenicity was not remarkably enhanced with the MF59 adjuvant.
Optimal alignment between groups of sequences and its application to multiple sequence alignment (1993)

Four algorithms, A-D, were developed to align two groups of biological sequences. Algorithm A is equivalent to the conventional dynamic programming method widely used for aligning ordinary sequences, whereas algorithms B-D are designed to evaluate the cost for a deletion/insertion more accurately when internal gaps are present in either or both groups of sequences. Rigorous optimization of the 'sum of pairs' (SP) score is achieved by algorithm D, whose average performance is close to O(MNL2), where M and N are numbers of sequences included in the two groups and L is the mean length of the sequences. Algorithm B uses some approximations to cope with profile-based operations, whereas algorithm C is a simpler variant of algorithm D. These group-to-group alignment algorithms were applied to multiple sequence alignment with two iterative strategies: a progressive method based on a given binary tree and a randomized grouping--realignment method. The advantages and disadvantages of the four algorithms are discussed on the basis of the results of examinations of several protein families.
Role of amino acid hydrophobicity, aromaticity, and molecular volume on IAPP(20–29) amyloid self‐assembly (2011)

Aromatic amino acids strongly promote cross-β amyloid formation; whether the amyloidogenicity of aromatic residues is due to high hydrophobicity and β-sheet propensity or formation of stabilizing π-π interactions has been debated. To clarify the role of aromatic residues on amyloid formation, the islet amyloid polypeptide 20-29 fragment [IAPP(20-29)], which contains a single aromatic residue (Phe 23), was adopted as a model. The side chain of residue 23 does not self-associate in cross-β fibrils of IAPP(20-29) (Nielsen et al., Angew Chem Int Ed 2009;48:2118-2121), allowing investigation of the amyloidogenicity of aromatic amino acids in a context where direct π-π interactions do not occur. We prepared variants of IAPP(20-29) in which Tyr, Leu, Phe, pentafluorophenylalanine (F5-Phe), Trp, cyclohexylalanine (Cha), α-naphthylalanine (1-Nap), or β-naphthylalanine (2-Nap) (in order of increasing peptide hydrophobicity) were incorporated at position 23 (SNNXGAILSS-NH2), and the kinetic and thermodynamic effects of these mutations on cross-β self-assembly were assessed. The Tyr, Leu, and Trp 23 variants failed to readily self-assemble at concentrations up to 1.5 mM, while the Cha 23 mutant fibrillized with attenuated kinetics and similar thermodynamic stability relative to the wild-type Phe 23 peptide. Conversely, the F5-Phe, 1-Nap, and 2-Nap 23 variants self-assembled at enhanced rates, forming fibrils with greater thermodynamic stability than the wild-type peptide. These results indicate that the high amyloidogenicity of aromatic amino acids is a function of hydrophobicity, β-sheet propensity, and planar geometry and not the ability to form stabilizing or directing π-π bonds.
Extracellular proteolytic activation of bacteriolytic peptidoglycan hydrolases of<i>Staphylococcus simulans</i>biovar<i>staphylolyticus</i> (1993)

Staphylococcus simulans biovar staphylolyticus secreted two bacteriolytic peptidoglycan hydrolases as proproteins that were activated as they were processed by an extracellular sulphydryl protease. This processing resulted in the production of multiple molecular-mass forms of each enzyme. Cells from early exponential phase cultures were susceptible to lysis by the mature forms of each of the peptidoglycan hydrolases whereas stationary phase cells were resistant. Thus secretion of these bacteriolytic enzymes during early exponential growth as precursors that are activated later by the protease would provide time for the cells to become resistant.
[Detection of the new tumor marker MUSE 11 antigen in sera of pancreatic cancer patients: a comparison with sialyl SSEA-I antigen]. (1991)

Using sera from patients with pancreatic cancer and chronic pancreatitis, we measured the level of the adenocarcinoma-associated antigen MUSE 11. A comparative study between levels of MUSE 11 and levels of sialyl SSEA-1 antigen (SLX) was also carried out. With respect to the MUSE 11 antigen, positive incidence was found in 17 out of 26 pancreatic cancer patients (65%), and in 1 out of 13 chronic pancreatitis patients (8%). Similar results were obtained from the assay of SLX levels. However, no correlation was found between the two markers. Out of 9 samples which showed MUSE 11 negative, three were positive for SLX. Out of 13 samples showing SLX negative, seven were positive for MUSE 11. Twenty out of 26 (77%) cases showed positive results for either antigen. These data suggest that the MUSE 11 antigen may be useful for the diagnosis of pancreatic cancers.
Factors Influencing Phenotypic Diversity of Human Prostate Carcinoma Cells Metastasizing in Athymic Nude Mice (1985)

Three related human prostate carcinoma cell lines, PC-3, 1-LN-PC-3-1A (1-LN), and 1-LN-PC-3-1A clone 4 (clone 4) were compared in terms of relative metastatic capacity in adult and young male nude mice. Only 1-LN produced lung metastases after intravenous injection into both 6- to 8-week-old and 4-week-old nude mice, as well as in mice injected intraperitoneally. The extent of the phenotypic diversity exhibited by these human prostate tumor lines was influenced by inherent dissemination ability, age of the host, and route of injection. These lines provide a useful system for the analysis of the biology of human tumor metastasis in nude mice.
Heat transfer in rocket combustion chambers (1993)

Complexities of liquid rocket engine heat transfer which involve the injector faceplate and film cooled walls are being investigated by computational analysis. A conjugate heat transfer analysis was used to describe localized heating phenomena associated with particular injector configurations and film coolant flows. These components were analyzed, and the analyses verified when appropriate test data were available. The component analyses are being synthesized into an overall flowfield/heat transfer model. A Navier-Stokes flow solver, the FDNS code, was used to make the analyses. Particular attention was given to the representation of the thermodynamic properties of the fluid streams. Unit flow models of specific coaxial injector elements have been developed and are being used to describe the flame structure near the injector faceplate.
NUTRITION OF ANIMAL CELLS IN TISSUE CULTURE: IX. SYNTHETIC MEDIUM No. 703 (1954)

Previous reports from this laboratory described a synthetic medium, solution 199, that contained 60 ingredients and supported cell life for an average period of four to five weeks. The assays were carried out in roller tubes in which chick embryo mesenchyme tissues were cultivated directly on the glass. More recently, the synthetic media have been improved very considerably, and Earle's replicate culture assay procedures have been adapted for use in testing them. By means of these techniques, it has been possible to make accurate quantitative experiments with new synthetic solutions some of which are capable of yielding, in one week, five- and sixfold increases in the population of replicate cultures prepared from washed suspensions of Earle's L strain mouse cells. This was acommplished by omitting the purines and pyrimidines from solution 199, by adding greatly increased levels of cysteine, ascorbic acid, and glutathione, and by the addition of certain purified coenzymes. In solution 703, which is described in detail, cultures of L strain cells have been maintained in a healthy, active state for over five months, with renewal of the medium twice a week.
Edge behavior of error diffusion (2002)

Error diffusion is an important technique for digital halftoning. One of the most observable artifacts of error diffusion is the inherent edge enhancement. We analyze the edge behavior of error diffusion. We show that error diffusion does not always enhance edges. For some error diffusion weights, it actually blurs the images. We demonstrate that the source for edge enhancement or blurring is the nonuniform distribution of the correction terms. We propose an enhancement index to predict the overall edge behavior for a given set of weights.
Optimum diversity combining with finite-tap decision feedback equalization in digital cellular mobile radio (2002)

This paper analyzes the performance of space diversity structures combined with finite-tap decision-feedback equalization technique in a mobile radio environment with QAM transmission and frequency-selective fading. Two optimum diversity structures, combining-diversity and selection-diversity, are considered in our analysis. By analytic techniques and simulation, we show that for the same number of taps the improvement is always greater with combining-diversity structure. The combining-diversity with a certain finite number of taps can outperform the selection-diversity with infinite taps. The numbers of taps to approach optimum performance (infinite-tap bound) in outage for different mobile environments are also determined. The decision-feedback equalizer not only provides better performance than the linear equalizer, but also needs a smaller number of taps to approach the optimum performance, especially in the combining diversity system or in the severe time-dispersion environment.
Allo‐, Epiallo‐ und Pseudoyohimbane sowie Heteroyohimbane durch Reaktion eines tetracyclischen Aldehyds mit Acetessigester in verschiedenen Lösungsmitteln (1990)

Allo‐, Epiallo‐, and Pseudoyohimbanes as well as Heteroyohimbanes by Reaction of a Tetracyclic Aldehyde with Acetoacetate in Different Solvents The reaction of methyl acetoacetate with 4 in CH 3 OH/ CH 3 ONa leads to 11 and 12 with yohimbane skeleton but bicyclo ring E. In DMF/ t BuOK, the epialloheteroyohimbane 13 is produced in fairly good yield, whereas in THF/NaH the allo‐19‐hydroxyyohimbinone 17 is formed, which undergoes thermal decomposition to the alloyohimb‐18‐enone 19 . Finally, a full description of an early mentioned synthesis of rac ‐de‐plancheine ( 7 ) is given.
Clarifying the Dominant Sources and Mechanisms of Cirrus Cloud Formation (2013)

Formation of cirrus clouds depends on the availability of ice nuclei to begin condensation of atmospheric water vapor. Although it is known that only a small fraction of atmospheric aerosols are efficient ice nuclei, the critical ingredients that make those aerosols so effective have not been established. We have determined in situ the composition of the residual particles within cirrus crystals after the ice was sublimated. Our results demonstrate that mineral dust and metallic particles are the dominant source of residual particles, whereas sulfate and organic particles are underrepresented, and elemental carbon and biological materials are essentially absent. Further, composition analysis combined with relative humidity measurements suggests that heterogeneous freezing was the dominant formation mechanism of these clouds.
A phenomenological particle‐based platelet model for simulating filopodia formation during early activation (2014)

We developed a phenomenological three-dimensional platelet model to characterize the filopodia formation observed during early stage platelet activation. Departing from continuum mechanics based approaches, this coarse-grained molecular dynamics (CGMD) particle-based model can deform to emulate the complex shape change and filopodia formation that platelets undergo during activation. The platelet peripheral zone is modeled with a two-layer homogeneous elastic structure represented by spring-connected particles. The structural zone is represented by a cytoskeletal assembly comprising of a filamentous core and filament bundles supporting the platelet's discoid shape, also modeled by spring-connected particles. The interior organelle zone is modeled by homogeneous cytoplasm particles that facilitate the platelet deformation. Nonbonded interactions among the discrete particles of the membrane, the cytoskeletal assembly, and the cytoplasm are described using the Lennard-Jones potential with empirical constants. By exploring the parameter space of this CGMD model, we have successfully simulated the dynamics of varied filopodia formations. Comparative analyses of length and thickness of filopodia show that our numerical simulations are in agreement with experimental measurements of flow-induced activated platelets. Copyright © 2015 John Wiley & Sons, Ltd.
Hardware Accelerated Sequence Alignment with Traceback (2009)

Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space‐efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.
Quantitative Imaging in Cancer Evolution and Ecology (2013)

Cancer therapy, even when highly targeted, typically fails because of the remarkable capacity of malignant cells to evolve effective adaptations. These evolutionary dynamics are both a cause and a consequence of cancer system heterogeneity at many scales, ranging from genetic properties of individual cells to large-scale imaging features. Tumors of the same organ and cell type can have remarkably diverse appearances in different patients. Furthermore, even within a single tumor, marked variations in imaging features, such as necrosis or contrast enhancement, are common. Similar spatial variations recently have been reported in genetic profiles. Radiologic heterogeneity within tumors is usually governed by variations in blood flow, whereas genetic heterogeneity is typically ascribed to random mutations. However, evolution within tumors, as in all living systems, is subject to Darwinian principles; thus, it is governed by predictable and reproducible interactions between environmental selection forces and cell phenotype (not genotype). This link between regional variations in environmental properties and cellular adaptive strategies may permit clinical imaging to be used to assess and monitor intratumoral evolution in individual patients. This approach is enabled by new methods that extract, report, and analyze quantitative, reproducible, and mineable clinical imaging data. However, most current quantitative metrics lack spatialness, expressing quantitative radiologic features as a single value for a region of interest encompassing the whole tumor. In contrast, spatially explicit image analysis recognizes that tumors are heterogeneous but not well mixed and defines regionally distinct habitats, some of which appear to harbor tumor populations that are more aggressive and less treatable than others. By identifying regional variations in key environmental selection forces and evidence of cellular adaptation, clinical imaging can enable us to define intratumoral Darwinian dynamics before and during therapy. Advances in image analysis will place clinical imaging in an increasingly central role in the development of evolution-based patient-specific cancer therapy.
Mass Spectrometry in Grape and Wine Chemistry (2009)

Preface. Acknowledgments. Introduction. PART I: MASS SPECTROMETRY. 1 Ionization Methods. 1.1. Electrospray Ionization. 1.2. Atmospheric Pressure Chemical Ionization. 1.3. Atmospheric Pressure Photoionization. 1.4. Surface-Activated Chemical Ionization. 1.5. Matrix-Assisted Laser. References. 2 Mass Analyzers and Accurate Mass Measurements. 2.1. Double-Focusing Mass Analyzers. 2.2. Quadrupole Mass Filters. 2.3. Ion Traps. 2.4. Time of Flight. References. 3. MS/MS Methodologies. 3.1. Triple Quadrupole. 3.2. The Q-TOF. 3.3. The MALDI TOF-TOF. References. PART II: APPLICATIONS OF MASS SPECTROMETRY IN GRAPE AND WINE CHEMSITRY. 4 Grape Aroma Compounds: Terpenes, C 13 -Norisopenoids, Benzene Compounds, and 3-Alkyl-2-Methoxypyrazines. 4.1. Introduction. 4.2. The SPE-GC/MS of Terpenes, Norisoprenoids and Benzenoids. 4.3. The SPME-GC/MS of Methoxypyrazines in Juice and Wine. References. 5 Volatile and Aroma Compounds in Wines. 5.1. Higher Alcohols and Esters Formed from Yeasts. 5.2. Volatile Sulfur Compounds in Wines. 5.3. Carbonyl Compounds in Wines and Distillates. 5.4. Ethyl and Vinyl Phenols in Wines. 5.5. 2'-Aminoacetophenone in Wines. References. 6 Grape and Wine Polyphenols. 6.1. Introduction. 6.2. The LC/MS of Non-Anthocyanic Polyphenols of Grape. 6.3. The LC/MS of Non-Anthocyanic Polyphenols of Wine. 6.4. Liquid-Phase MS of Grape Anthocyanins. 6.5. The LC/MS of Anthocynanis Derivatives in Wine. 6.6. The MALDI-TOF of Grape Procyanidins. References. 7 Compounds Released in Wine from Wood. 7.1. Introduction. 7.2. The GC/MS of Wood Volatile Compounds. 7.3. The GC/PICI-MS/MS of Wood Volatile Phenols and Benzene Aldehydes in Wine. References. 8 Compounds Responsible for Wine Defects. 8.1. Ochratoxin A in Grape and Wine. 8.2. The SPME-GC/MS/MS Analysis of TCA and TBA in Wine. 8.3. Geosmin. 8.4. Analysis of 1-Octen-3-one. 8.5. Analysis of 2-Methoxy-3,5-dimethypyrazine in Wine. 8.6. Biogenic Amines in Grape and Wine. 8.7. Ethyl Carbamate in Wine. 8.8. Wine Geranium Taint. 8.9. Mousy Off-Flavor of Wines. References. 9 Pesticides in Grape and Wine. 9.1. Introduction. 9.2. Analytical Methods. 9.3. Isothiocyanates in Wine. References. 10 Peptides and Proteins of Grape and Wine. 10.1. Introduction. 10.2. Analytical Methods. References. Index.
A Generalized Term Dependence Model in Information Retrieval (1983)

The tree dependence model has been used successfully to incorporate dependencies between certain term pairs on the information retrieval process, while the Bahadur Lazarsfeld Expansion (BLE) which specifies dependencies between all subsets of terms has been used to identify productive clusters of items in a clustered data base environment. The successes of these models are unlikely to be accidental; it is of interest therefore to examine the similarities between the two models. The disadvantage of the BLE model is the exponential number of terms appearings in the full expression, while a truncated BLE system may produce negative probability values. The disadvantage of the tree dependence model is the restriction to dependencies between certain term pairs only and the exclusion of higher-order dependencies. A generalized term dependence model is introduced in this study which does not carry the disadvantages of either the tree dependence or the BLE models. Sample evaluation results are included to demonstrate the usefulness of the generalized system.
Advanced mechatronic technology for turbine blades maintenance (1998)

Turbine blades requiring regular and certified repair and maintenance cycles. An advanced maintenance system for turbine blades based on a multi-axis high-speed milling center with reverse engineering devices enables adaptive reshaping of blades with individual geometries due to the functional requirements. In order to perform the repair procedure as automatically as possible, an adaptive milling technique was applied. The principle of the adaptive milling for the repair purpose is to generate a milling path for a turbine blade geometry and modify it for a damaged blade according to the geometrical information provided by the 3D sensors. The RTD work performed to reach these goals are are outlined. The authors discuss the simulation and verification of multi-axis milling processes, 3D shape measurement, and the milling reference model.