gebhart/patrepeval huggingface dataset:
Considerations in engineering parallel multiobjective evolutionary algorithms (2003)

Developing multiobjective evolutionary algorithms (MOEAs) involves thoroughly addressing the issues of efficiency and effectiveness. Once convinced of an MOEA's effectiveness the researcher often desires to reduce execution time and/or resource expenditure, which naturally leads to considering the MOEA's parallelization. Parallel MOEAs (pMOEAs) or distributed MOEAs are relatively new developments with few associated publications. pMOEA creation is not a simple task, involving analyzing various parallel paradigms and associated parameters. Thus, a thorough discussion of the major parallelized MOEA paradigms is included in this paper and succinct observations are made regarding an analysis of the current literature. Specifically, a previous MOEA notation is extended into the pMOEA domain to enable precise description and identification of various sets of interest. Innovative concepts for pMOEA migration, replacement and niching schemes are discussed, as well as presenting the first known generic pMOEA formulation. Taken together, this paper's analyses in conjunction with an original pMOEA design serve as a pedagogical framework and example of the necessary process to implement an efficient and effective pMOEA.
Electromechanical effects in carbon nanotubes:Ab initioand analytical tight-binding calculations (2003)

We perform ab initio calculations of charged graphene and single-wall carbon nanotubes (CNTs). A wealth of electromechanical behaviors is obtained. (1) Both nanotubes and graphene expand upon electron injection. (2) Upon hole injection, metallic nanotubes and graphene display a nonmonotonic behavior. Upon increasing hole densities, the lattice constant initially contracts, reaches a minimum, and then starts to expand. The hole densities at minimum lattice constants are 0.3 $|e|/\mathrm{atom}$ for graphene and between 0.1 and $0.3|e|/\mathrm{atom}$ for the metallic nanotubes studied. (3) Semiconducting CNT's with small diameters $(d\ensuremath{\lesssim}20\mathrm{\AA{}})$ always expand upon hole injection. (4) Semiconducting CNT's with large diameters $(d\ensuremath{\gtrsim}20\mathrm{\AA{}})$ display a behavior intermediate between those of metallic and large-gap CNT's. (5) The strain versus extra charge displays a linear plus power-law behavior, with characteristic exponents for graphene, metallic, and semiconducting CNT's. All these features are physically understood within a simple tight-binding total-energy model.
Evolutionarily homologous alpha 2 beta 2 oligomeric structures in beta-ketoadipate succinyl-CoA transferases from Acinetobacter calcoaceticus and Pseudomonas putida. (1981)

Homogeneous beta-ketoadipate succinyl-CoA transferase (EC 2.8.3.6) preparations were obtained from extracts of Acinetobacter calcoaceticus and Pseudomonas putida. Gel filtration indicated that the respective transferases have similar molecular weights of 108,000 and 109,000; each transferase appears to have an alpha 2 beta 2 oligomeric structure formed by association of nonidentical subunits with a molecular weight of about 25,000. The subunits were separated by sodium dodecyl sulfate-gel electrophoresis, and differences in their primary structures were revealed by determination of the NH2-terminal amino acid sequences of the oligomers. The transferases cross-react immunologically and possess similar amino acid compositions. These are remarkably similar to the amino acid compositions of gamma-carboxymuconolactone decarboxylases (EC 4.1.1.44) and beta-ketoadipate enol-lactone hydrolases (EC 3.1.1.24), enzymes that mediate consecutive reactions preceding the transferase step in the beta-ketoadipate pathway.
Inhaled Insulin: An Overview (2001)

In Brief Various methods of insulin administration other than injection have been sought since the discovery of insulin. For the past several years, systems that deliver insulin via the pulmonary route have been developed and evaluated. Based on available data, pulmonary insulin appears to be safe, efficacious, and well accepted by patients. This article describes the technology behind several of these pulmonary administration systems and outlines the most recent data from clinical trials evaluating pulmonary insulin.
Glyphs for visualizing uncertainty in vector fields (1996)

Environmental data have inherent uncertainty which is often ignored in visualization. Meteorological stations and doppler radars, including their time series averages, have a wealth of uncertainty information that traditional vector visualization methods such as meteorological wind barbs and arrow glyphs simply ignore. We have developed a new vector glyph to visualize uncertainty in winds and ocean currents. Our approach is to include uncertainty in direction and magnitude, as well as the mean direction and length, in vector glyph plots. Our glyph shows the variation in uncertainty, and provides fair comparisons of data from instruments, models, and time averages of varying certainty. We also define visualizations that incorporate uncertainty in an unambiguous manner as verity visualization. We use both quantitative and qualitative methods to compare our glyphs to traditional ones. Subjective comparison tests with experts are provided, as well as objective tests, where the information density of our new glyphs and traditional glyphs are compared. The design of the glyph and numerous examples using environmental data are given. We show enhanced visualizations, data together with their uncertainty information, that may improve understanding of environmental vector field data quality.
Primary and Secondary Kinase Genotypes Correlate With the Biological and Clinical Activity of Sunitinib in Imatinib-Resistant Gastrointestinal Stromal Tumor (2008)

The clinical activity of sunitinib after imatinib failure is significantly influenced by both primary and secondary mutations in the predominant pathogenic kinases, which has implications for optimization of the treatment of patients with GIST.
Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein-engineered NADH-preferring xylose reductase from Pichia stipitis (2007)

A recombinant Saccharomyces cerevisiae strain transformed with xylose reductase (XR) and xylitol dehydrogenase (XDH) genes from Pichia stipitis (PsXR and PsXDH, respectively) has the ability to convert xylose to ethanol together with the unfavourable excretion of xylitol, which may be due to intercellular redox imbalance caused by the different coenzyme specificity between NADPH-preferring XR and NAD(+)-dependent XDH. In this study, we focused on the effect(s) of mutated NADH-preferring PsXR in fermentation. The R276H and K270R/N272D mutants were improved 52- and 146-fold, respectively, in the ratio of NADH/NADPH in catalytic efficiency [(k(cat)/K(m) with NADH)/(k(cat)/K(m) with NADPH)] compared with the wild-type (WT), which was due to decrease of k(cat) with NADPH in the R276H mutant and increase of K(m) with NADPH in the K270R/N272D mutant. Furthermore, R276H mutation led to significant thermostabilization in PsXR. The most positive effect on xylose fermentation to ethanol was found by using the Y-R276H strain, expressing PsXR R276H mutant and PsXDH WT: 20 % increase of ethanol production and 52 % decrease of xylitol excretion, compared with the Y-WT strain expressing PsXR WT and PsXDH WT. Measurement of intracellular coenzyme concentrations suggested that maintenance of the of NADPH/NADP(+) and NADH/NAD(+) ratios is important for efficient ethanol fermentation from xylose by recombinant S. cerevisiae.
Inhibition of human α7 nicotinic acetylcholine receptors by open channel blockers of N‐methyl‐D‐aspartate receptors (2003)

1. Human alpha 7 nicotinic acetylcholine (ACh) receptors were expressed in Xenopus oocytes and the effects of the N-methyl-D-aspartate (NMDA) receptor open channel blockers memantine and cerestat on this receptor were examined using two-electrode voltage-clamp recordings and 125I-alpha-bungarotoxin (125I-alpha-bgtx) binding. 2. Memantine and cerestat produced complete inhibition of ACh-induced inward currents with affinities similar to that reported for native NMDA receptors. Cerestat, IC50 1.7 (-1; +2) microm, was more potent than memantine, IC50 5 (-3;+8) microM, and the effects of both drugs were fully and rapidly reversible. 3. Inhibition of alpha 7 receptor function was voltage-independent, and it occurred at concentrations far lower than those needed to inhibit (never completely) binding of 125I-alpha-bgtx to alpha 7 receptors, suggesting that the effects of memantine or cerestat are noncompetitive. 4. These results provide evidence that human alpha 7 receptors are inhibited by memantine and cerestat and suggest that caution should be applied when using these compounds to study systems in which NMDA and nACh receptors co-exist.
The isolation and characterization of a mutant strain of Saccharomyces cerevisiae that requires a long chain base for growth and for synthesis of phosphosphingolipids. (1983)

A mutant of Saccharomyces cerevisiae has been obtained that shows an absolute growth requirement for long chain bases found in sphingolipids. In the absence of a long chain base, the cells are unable to synthesize the phosphoinositol-containing sphingolipids characteristic of yeast. These results suggest that one or more of the yeast sphingolipids plays a vital biological role.
Synthesis and migration insertion polymerization (MIP) of CpFe(CO)2(CH2)6PPh2(FpC6P) for PFpC6P: macromolecule stability, degradability and redox activity (2014)

CpFe(CO)2(CH2)6PPh2 (FpC6P) is synthesized as a monomer for bulk migration insertion polymerization (MIP). Due to the presence of a longer alkyl spacer in FpC6P, intramolecular cyclization reactions, which are observed during the MIP of CpFe(CO)2(CH2)3PPh2 (FpC3P), were completely suppressed under the conditions of the polymerization. The resultant PFpC6P is soluble in common organic solvents and stable enough for GPC analysis. However, the polymer degrades in solution over a few days because the PFpC6P chain is constructed from relatively weak metal coordination bonds. In the presence of an oxidant, e.g. H2O2, degradation of the polymers was accelerated. When the solution was exposed to LED light (wavelength: 400–410 nm), degradation was completed in 20 minutes with CO release first followed by the dissociation of phosphine. DSC analysis indicates that PFpC6P has a Tg of ca. 68 °C, which is lower than that of PFpC3P (ca. 99 °C). TGA analysis reveals that PFpC6P is thermally stable up to 170 °C and leaves a ca. 35.2% char yield at 676 °C after three stages of weight loss. CV data shows that the polymer in DMF has reversible redox activity, with an oxidation peak at 0.74 V and a reduction peak at 0.56 V (relative to a Ag electrode).
Monoclonal antibodies to a 100-kd protein reveal abundant A beta-negative plaques throughout gray matter of Alzheimer's disease brains. (1997)

Here we describe the initial characterization of a 100-kd protein recognized by four new monoclonal antibodies that reveal abundant and unique plaque-like lesions throughout gray matter of Alzheimer's disease brains. This 100-kd protein and these new plaque-like lesions were identified by four monoclonal antibodies raised to immunogens extracted from Alzheimer's disease neurofibrillary abnormalities. However, these antibodies did not recognize hyperphosphorylated tau in Western blots or neurofibrillary lesions by immunohistochemistry. As all of these antibodies displayed similar properties, one, AMY117, was used to characterize the new plaque-like lesions in detail. These studies demonstrated that AMY117-positive plaques were not visualized by amyloid stains and never co-localized with A beta deposits, although AMY117-positive and A beta-positive lesions frequently occurred in the same cortical and subcortical gray matter regions. Abundant AMY117-positive plaques were found in the brains of all 32 sporadic Alzheimer's disease patients and all 6 elderly Down's syndrome subjects. Although AMY117-positive plaques also were seen in the brains of nondemented patients with numerous A beta deposits. AMY117-positive plaques were rare or absent in the brains of other elderly controls and patients with other neurodegenerative or neuropsychiatric disorders. We conclude that the AMY117-positive plaques described here for the first time are major lesions of the Alzheimer's disease brain. Thus, it will be important to elucidate the role played by the 100-kd protein and the AMY117 plaques in the etiology and pathogenesis of Alzheimer's disease.
Simulation of biological cell sorting using a two-dimensional extended Potts model (1992)

We simulate the sorting of a mixture of two types of biological cells using a modified version of the large-Q Potts model with differential adhesivity. We find long-distance cell movement leading to sorting with a logarithmic increase in the length scale of homogeneous clusters. Sorted clusters then round. We find two successive phases: A rapid boundary-driven creation of a low-cohesivity cell monolayer around the aggregate, and a slower boundary-independent internal rearrangement.
Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides. (1992)

Synthesis of mRNA in kinetoplastid protozoa involves the process of trans-splicing, in which an identical 39-41-nucleotide (depending on the species) mini-exon is placed at the 5' end of mature mRNAs. The mini-exon sequence is highly conserved among all members of the Kinetoplastida, nucleotides 1-6 being identical in the four genera so far examined. Prior to trans-splicing, the mini-exon donor RNA is capped by the addition of a (5'-5') triphosphate-linked 7-methylguanosine, followed by modification of the first four transcribed nucleotides. Partial structures have been previously deduced for this cap 4 moiety from Trypanosoma brucei and Leptomonas collosoma. We have purified enough cap 4 from T. brucei and Crithidia fasciculata to allow definitive structural analysis by combined liquid chromatography/mass spectrometry and gas chromatography/mass spectrometry. The results, together with the known mini-exon sequence, show that cap 4 in both species has the structure m7G(5')ppp(5')m6(2)AmpAmpCmpm3Ump. The presence of N6,N6,2'-O-trimethyladenosine and 3,2'-O-dimethyluridine, nucleosides previously unknown in nature, were confirmed by rigorous comparison with synthetic standards. The conservation of cap 4 between these divergent genera suggests that this structure may be common to most if not all Kinetoplastida.
High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. (2011)

Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for Nannochloropsis sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that Nannochloropsis is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology.
Protein sequence and mass spectrometric analyses of tau in the Alzheimer's disease brain. (1992)

Tau with unusually slow mobilities in sodium dodecyl sulfate-polyacrylamide gel electrophoresis was purified from the Sarkosyl-insoluble pellet of Alzheimer's disease brain homogenates. Such species of tau (PHF-tau) are considered to construct the framework of the sodium dodecyl sulfate-soluble form of paired helical filaments (PHF). Detailed comparison of peptide maps of PHF-tau and normal tau before and after dephosphorylation pointed to three anomalously eluted peaks which contained abnormally phosphorylated peptides, residues 191-225, 226-240, 260-267, and 386-438, according to the numbering of the longest tau isoform (Goedert, M., Spillantini, M. G., Jakes, R., Rutherford, D., and Crowther, R. A. (1989) Neuron 3, 519-526). Protein sequence and mass spectrometric analyses localized Thr-231 and Ser-235 as the abnormal phosphorylation sites and further indicated that each tau 1 site (residues 191-225) and the most carboxyl-terminal portion of the protein (residues 386-438) carries more than two abnormal phosphates. Ser-262 was also phosphorylated in a fraction of PHF-tau. Modifications other than phosphorylation, removal of the initiator methionine, and N alpha-acetylation at the amino terminus and deamidation at 2 asparaginyl residues were found in PHF-tau, but these modifications were also present in normal tau.
Exploring the Limits of Language Modeling (2016)

In this work we explore recent advances in Recurrent Neural Networks for large scale Language Modeling, a task central to language understanding. We extend current models to deal with two key challenges present in this task: corpora and vocabulary sizes, and complex, long term structure of language. We perform an exhaustive study on techniques such as character Convolutional Neural Networks or Long-Short Term Memory, on the One Billion Word Benchmark. Our best single model significantly improves state-of-the-art perplexity from 51.3 down to 30.0 (whilst reducing the number of parameters by a factor of 20), while an ensemble of models sets a new record by improving perplexity from 41.0 down to 23.7. We also release these models for the NLP and ML community to study and improve upon.
Real-time pickup method for a three-dimensional image based on integral photography (1997)

We studied integral photography (IP), which creates three-dimensional autostereoscopic images. In particular we studied the possibility of a new method that uses a television camera to shoot directly numerous real images produced by a lens array. Unlike the conventional IP method in which the film is placed immediately behind a lens array, this method employs a television camera, which enables us to shoot moving pictures. Of a number of factors affecting the process of image pickup, we examined some optical factors and compared them with those obtained by the conventional IP method. The results show that with this new direct pickup method that uses a television camera, we can obtain an IP image like those obtained by using the conventional IP method. Further, we conducted an experiment with an high-definition TV camera, confirming the production of an autostereoscopic image by using a display device that combines a liquid-crystal panel and pinholes.
Studies on the removal of some toxic metal ions from aqueous solutions and industrial waste. Part I (Removal of lead and cadmium by hydrous iron and aluminium oxide) (1988)

Abstract The adsorption of two metal ions Pb2+ and Cd2+ has been observed on hydrous aluminium and iron oxide which are prepared and characterized by well known methods. Hydrous ferric oxide exhibits bettwr sorption capacity for the metal ions. The uptake of lead is much higher than cadmiua and follows Langmuir model. Thermodynamic parameters of the process have been estimated by kinetic measurements which also provide mechanistic information.
Dislocation motion in GaN light-emitting devices and its effect on device lifetime (1997)

In this study, dislocation motions in GaN-based materials and devices were quantitatively estimated in order to determine why GaN-based light-emitting diodes have remarkable reliability and longevity in spite of extremely high dislocation density. The dislocation velocity of GaN-based materials was calculated by estimating the activation energy of dislocation, and comparing it with that of GaAs, which are typically used for light-emitting devices. It was estimated that the dislocation mobility of GaN-related materials was lower than that of GaAs by a factor of approximately 10−10–10−16, at room temperature. Furthermore, dislocation velocity under current injection became about 10−20 times lower than that of GaAs, under the assumption that the dislocations in GaN-related materials do not act as nonradiative recombination centers. The possibility of degradation under high current densities and high temperature, as would be found in GaN-based laser diodes, is also discussed.
IL13 Receptor α2 Signaling Requires a Scaffold Protein, FAM120A, to Activate the FAK and PI3K Pathways in Colon Cancer Metastasis (2015)

IL13 signaling through its receptor IL13Rα2 plays a critical role in colon cancer invasion and liver metastasis, but the mechanistic features of this process are obscure. In this study, we identified a scaffold protein, FAM120A (C9ORF10), as a signaling partner in this process. FAM120A was overexpressed in human colon cancer cell lines and 55% of human colon cancer specimens. IL13Rα2-FAM120A coimmunoprecipitation experiments revealed further signaling network associations that could regulate the activity of IL13Rα2, including FAK, SRC, PI3K, G-protein-coupled receptors, and TRAIL receptors. In addition, FAM120A associated with kinesins and motor proteins involved in cargo movement along microtubules. IL13Rα2-triggered activation of the FAK and PI3K/AKT/mTOR pathways was mediated by FAM120A, which also recruited PI3K and functioned as a scaffold protein to enable phosphorylation and activation of PI3K by Src family kinases. FAM120A silencing abolished IL13-induced cell migration, invasion, and survival. Finally, antibody blockade of IL13Rα2 or FAM120A silencing precluded liver colonization in nude mice or metastasis. In conclusion, we identified FAM120A in the IL13/IL13Rα2 signaling pathway as a key mediator of invasion and liver metastasis in colon cancer.
Taxonomic rearrangement of the genus Schizochytrium sensu lato based on morphology, chemotaxonomic characteristics, and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): emendation for Schizochytrium and erection of Aurantiochytrium and Oblongichytrium gen. nov. (2007)

The genus Schizochytrium sensu lato has been characterized by successive binary division of its vegetative cells. However, the molecular phylogeny strongly suggests that this genus is not a natural taxon, because the original and recorded strains that have been identified as Schizochytrium spp. separately form three well-supported monophyletic groups in the 18S rRNA gene tree. These three groups are clearly distinguishable by their combined morphological characteristics and the profiles of the polyunsaturated fatty acids and carotenoid pigments they contain, although these are hard to distinguish using only a single feature. Therefore, three different genera are proposed to accommodate these three groups, i.e., Schizochytrium sensu stricto, Aurantiochytrium, and Oblongichytrium gen. nov.
Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G‐250 and R‐250 (1988)

An improved procedure for staining of proteins following separation in polyacrylamide gels is described which utilizes the colloidal properties of Coomassie Brilliant Blue G-250 and R-250. The new method is based on addition of 20% v/v methanol and higher concentrations of ammonium sulfate to the staining solution previously described. The method combines the advantage of much shorter staining time with high sensitivity, a clear background not requiring destaining, stepwise staining, and stable fixation after staining. The method has been applied to staining of polyacrylamide gels after sodium dodecyl sulfate-electrophoresis and isoelectric focusing in carrier ampholyte-generated pH gradients.