gebhart/patrepeval huggingface dataset:
Three-Dimensional Plasmonic Nanoclusters (2013)

Assembling nanoparticles into well-defined structures is an important way to create and tailor the optical properties of materials. Most advances in metamaterials research to date have been based on structures fabricated in two-dimensional planar geometries. Here, we show an efficient method for assembling noble metal nanoparticles into stable, three-dimensional (3-D) clusters, whose optical properties can be highly sensitive or remarkably independent of cluster orientation, depending on particle number and cluster geometry. Some of the clusters, such as tetrahedra and icosahedra, could serve as the optical kernels for metafluids, imparting metamaterial optical properties into disordered media such as liquids, glasses, or plastics, free from the requirement of nanostructure orientation.
Beyond genetic markers (1994)

From the Section of Molecular Genetics, Whitaker Cardiovascular Institute, Boston University Center of Advanced Biomedical Research, Boston, Massachusetts, USA.
Evaluation of global synchronization for iterative algebra algorithms on many-core (2015)

Massively parallel computing is applied extensively in various scientific and engineering domains. With the growing interest in many-core architectures and due to the lack of explicit support for inter-block synchronization specifically in GPUs, synchronization becomes necessary to minimize inter-block communication time. In this paper, we have proposed two new inter-block synchronization techniques: 1) Relaxed Synchronization, and 2) Block-Query Synchronization. These schemes are used in implementing numerical iterative solvers where computation/communication overlapping is one used optimization to enhance application performance. We have evaluated and analyzed the performance of the proposed synchronization techniques using Jacobi Iterative Solver in comparison to the state of the art inter-block lock-free synchronization techniques. We have achieved about 1–8% performance improvement in terms of execution time over lock-free synchronization depending on the problem size and the number of thread blocks. We have also evaluated the proposed algorithm on GPU and MIC architectures and obtained about 8–26% performance improvement over the barrier synchronization available in OpenMP programming environment depending on the problem size and number of cores used.
Distributed computing (1992)

A distributed computing system consists of a collection autonomous computers connected by a communication network. The motivation for such a distributed system includes resource and load sharing, reduced costs in computation and communication, higher performance and throughput, and increased reliability and availability.
Discrete copper(ii)-formate complexes as catalytic precursors for photo-induced reversible deactivation polymerization (2015)

Traditional copper-mediated reversible deactivation polymerization techniques (RDRP) employ various components mixed<italic>in situ</italic>(<italic>e.g.</italic>ligand, metal salt, additional deactivation species<italic>etc</italic>.) in order to achieve good control over the molecular weight distributions.
Interaction Of The Human Prion PrP(106−126) Sequence With Copper(II), Manganese(II), And Zinc(II):  NMR and EPR Studies (2004)

The synthetic peptide encompassing residues 106-126 (PrP106-126, KTNMKHMAGAAAAGAVVGGLG) of the human prion protein was considered for its binding properties toward copper(II), manganese(II) and zinc(II) at pH 5.7. 1H and 13C 1D spectra, 1H spin-lattice relaxation rates, and 1H-15N and 1H-13C HSQC 2D experiments were obtained in the absence and in the presence of metal ions. While Zn(II) was found to yield negligible effects upon any NMR parameter, metal-peptide association was demonstrated by the paramagnetic effects of Cu(II) and Mn(II) upon 1D and 2D spectra. Delineation of structures of metal complexes was sought by interpreting the paramagnetic effect on 1H spin-lattice relaxation rates. Exchange of peptide molecules from the metal coordination sphere was shown to provide sizable contribution to the observed relaxation rates. Such contribution was calculated in the case of Cu(II); whereas the faster paramagnetic rates of peptide molecules bound to Mn(II) were determining spin-lattice relaxation rates almost exclusively dominated by exchange. Proton-metal distances were therefore evaluated in the case of the Cu(II) complex only and used as restraints in molecular dynamics calculations where from the structure of the complex was obtained. The peptide was shown to bind copper through the imidazole nitrogen and the ionized amide nitrogen of His-111 and the amino-terminal group with the terminal carboxyl stabilizing the coordination sphere through ionic interactions. The data were interpreted as to demonstrate that the hydrophobic C-terminal region was not affecting the copper-binding properties of the peptide and that this hydrophobic tail is left free to interact with other target molecules. As for the complex with Mn(II), qualitative information was obtained on carbonyl oxygens of Gly-124 and Leu-125, beyond the terminal Gly-126 carboxyl, being at close distance from the metal ion, that also interacts, most likely, through a hydrogen bond of metal-bound water, with the imidazole ring of His-111.
Was cDNA Sequences Modulate Transgene Expression of Was Promoter-Driven Lentiviral Vectors (2009)

Abstract The development of vectors that express a therapeutic transgene efficiently and specifically in hematopoietic cells (HCs) is an important goal for gene therapy of hematological disorders. We have previously shown that a 500-bp fragment from the proximal Was gene promoter in a lentiviral vector (LV) was sufficient to achieve more than 100-fold higher levels of Wiskott-Aldrich syndrome protein in HCs than in nonhematopoietic cells (non-HCs). We show now that this differential was reduced up to 10 times when the enhanced green fluorescent protein gene (eGFP) was expressed instead of Was in the same LV backbone. Insertion of Was cDNA sequences downstream of eGFP in these LVs had a negative effect on transgene expression. This effect varied in different cell types but, overall, Was cDNA sequences increased the hematopoietic specificity of Was promoter-driven LV. We have characterized the minimal fragment required to increase hematopoietic specificity and have demonstrated that the mechanism involves Was promoter regulation and RNA processing. In addition, we have shown that Was cDNA sequences interfere with the enhancer activity of the woodchuck posttranscriptional regulatory element. These results represent the first data showing the role of Was intragenic sequences in gene regulation.
Stress corrosion parameters for glass with different edge finishing (2013)

The influence of stress corrosion on the edge strength becomes important when designing structural glass elements. As the load duration of the design wind load (600 s) or the design temperature load is larger than the common load duration during testing the glass edge, a strength model must be used to take into account the load duration properly. In such a model, both short term parameters (i.e. the flaw geometry and depth) and stress corrosion parameters are involved. The stress corrosion parameters strongly depend upon the environment, especially the temperature and the humidity. In this study, the latter two are kept constant, for the testing at high stress rate (50 MPa/s), to determine the short term parameters as well as for the testing at low stress rate (2 MPa/s), to determine the stress corrosion parameters. The geometry factor and the stress corrosion parameters were determined for arrised and ground edges.
OXIDATION OF SECONDARY PHOSPHINES TO SECONDARY PHOSPHINE OXIDES (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOXIDATION OF SECONDARY PHOSPHINES TO SECONDARY PHOSPHINE OXIDESM. M. Rauhut, I. Hechenbleikner, Helen A. Currier, and V. P. WystrachCite this: J. Am. Chem. Soc. 1958, 80, 24, 6690–6691Publication Date (Print):December 1, 1958Publication History Published online1 May 2002Published inissue 1 December 1958https://pubs.acs.org/doi/10.1021/ja01557a062https://doi.org/10.1021/ja01557a062research-articleACS PublicationsRequest reuse permissionsArticle Views320Altmetric-Citations7LEARN 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
Cellular Trafficking and Photochemical Internalization of Cell Penetrating Peptide Linked Cargo Proteins: A Dual Fluorescent Labeling Study (2011)

Initial cellular uptake of cell penetrating peptide (CPP) linked macromolecules is usually endosomal, with passage from endosome to cytosol a major limitation to efficient delivery. To gain a better understanding of the passage of the CPP-linked proteins, we studied the uptake and localization of CPP-linked proteins that contained two different forms of fluorescent markers, GFP protein and chemically conjugated tetramethylrhodamine, in living cells. Rhodamine labeled TAT-GFP was internalized in multiple cell lines including HEK293, N18-RE-105, hippocampal slices, and human neural progenitor cells and showed predominantly endosomal localization of both fluorescent markers. Cytosolic localization of some rhodamine label was detected to suggest that some of the GFP label had exited from the endosome. However, quantification of the distribution of the rhodamine and GFP label indicated that the protein location was primarily endosomal and that the distribution of TAT-GFP was not significantly different than that of an exclusively endosomal localized exogenous protein (tetanus toxin fragment C - TTC). As a result, photochemical internalization (PCI) was evaluated and caused a significant quantitative redistribution of cellular fluorescence of rhodamine and GFP labels to demonstrate increased cytosolic delivery of GFP. While rhodamine-labeled TAT-GFP showed cytosolic delivery with exposure to specific wavelengths of fluorescent illumination, a similarly labeled GFP fusion protein containing the membrane binding domain of TTC did not mediate PCI in N18-RE-105 cells.
Additional Remarks on Designing Category-Level Attributes for Discriminative Visual Recognition (2013)

This is the supplementary material for Designing Category-Level Attributes for Discriminative Visual Recognition. We first provide an overview of the proposed approach in Section 1. The proof of the theorem is shown in Section 2. Additional remarks of the proposed attribute design algorithm are provided in Section 3. We show additional experiments and applications of the designed attributes for zero-shot learning and video event modeling in Section 4. Finally, we discuss the semantic aspects of automatic attribute design in Section 5. All the figures in this technical report are best viewed in color.
SoftCast (2010)

The focus of this demonstration is the performance of streaming video over the mobile wireless channel. We compare two schemes: the standard approach to video which transmits H.264/AVC-encoded stream over 802.11-like PHY, and SoftCast -- a clean-slate design for wireless video where the source transmits one video stream that each receiver decodes to a video quality commensurate with its specific instantaneous channel quality.
The effect of bucket size tuning in the dynamic hybrid GRACE hash join method (1989)

In this paper, we show detailed analysis and performance evaluation of the Dynamic Hybrid GRACE Hash Join Method (DHGH Method) when the tuple distribution in buckets is unbalanced. The conventional Hash Join Methods specify the tuple distribution in buckets statically. However it may differ from estimation since join operations are applied with selection operations. When the tuple distribution in buckets is unbalanced, the processing cost of join operation becomes more costly than the ideal case when you use Hybrid Hash Join Method (HH Method). On the other hand, when you use the DHGH Method, the destaging buckets are selected dynamically, gives the same performance as the ideal case even if the tuple distribution in buckets is unbalanced such as Zipf-like distributions. We analyze the total I/O cost of a join operation at various number of buckets. The result shows that we have to determine the number of buckets baaed on the tuple distribution in buckets rather than the size of the source relation. It is shown that we had better partition the source relation using a large number of small buckets instead of the smaller number of buckets almost filling the whole main memory adopted in the HH Method.
GROUPING OF -HAEMOLYTIC STREPTOCOCCI BY ENZYME-LINKED IMMUNOSORBENT ASSAY (1980)

A method of grouping beta-haemolytic streptococci serologically by enzyme-linked immunosorbent assay is described. A comparison of this method with double diffusion in agar gel showed complete correlation of results when highly absorbed grouping sera were used.
On the Origin of Regioselectivity in Palladium‐Catalyzed Oxidation of Glucosides (2020)

Abstract The palladium‐catalyzed oxidation of glucopyranosides has been investigated using relativistic density functional theory (DFT) at ZORA‐BLYP−D3(BJ)/TZ2P. The complete Gibbs free energy profiles for the oxidation of secondary hydroxy groups at C2, C3, and C4 were computed for methyl β‐glucoside and methyl carba‐β‐glucoside. Both computations and oxidation experiments on carba‐glucosides demonstrate the crucial role of the ring oxygen in the C3 regioselectivity observed during the oxidation of glucosides. Analysis of the model systems for oxidized methyl β‐glucoside shows that the C3 oxidation product is intrinsically favored in the presence of the ring oxygen. Subsequent energy decomposition analysis (EDA) and Hirschfeld charge analysis reveal the role of the ring oxygen: it positively polarizes C1/C5 by inductive effects and disfavors any subsequent buildup of positive charge at neighboring carbon atoms, rendering C3 the most favored site for the β‐hydride elimination.
ChemInform Abstract: α‐Oxosulfines Part 1: Reactivity of α‐Oxosulfines Obtained from Retro Diels‐Alder Reaction of 1,4‐Oxathiin‐S‐oxides. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Diarylmethylene-tetracyanoethylene cycloadditions (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiarylmethylene-tetracyanoethylene cycloadditionsJohn E. Baldwin and Richard E. PeavyCite this: J. Org. Chem. 1971, 36, 10, 1441–1443Publication Date (Print):May 1, 1971Publication History Published online1 May 2002Published inissue 1 May 1971https://pubs.acs.org/doi/10.1021/jo00809a029https://doi.org/10.1021/jo00809a029research-articleACS PublicationsRequest reuse permissionsArticle Views175Altmetric-Citations6LEARN 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
Spatial conservation areas for water yield hydrological ecosystem services with their economic values effects under climate change: a case study of Teshio watershed located in northernmost of Japan (2019)

Abstract Water resources prioritization conservation planners are increasingly becoming aware of the economic value of water supply ecosystem services (ESs) under climate changes. Here we assessed how the water yield ES framework is implemented in the current spatial prioritization conservation of the water resources under climate change across the Teshio River watershed. We applied the systematic conservation model to optimize the area for water resources which satisfied the protection targets with and without considering economic values of the water yield provision service. The model indicated that the areas of spatial optimal ES protection for water yield with considering economic values were totally different from those without considering economic values of water resources. The optimal priority conservation areas were concentrated in southwestern, southeastern, and some northern areas of this watershed. These places could guarantee water resources sustainability from both environmental protection and socio-economic development standpoints. Moreover, the spatial priority conservation areas for water yield with economic value from hydro-power electricity production were traded off against the areas for water yield with economic values from resident water-use and irrigation for rice. Therefore, the systematic conservation planning of water yield with economic values under climate changes may provide a useful argument to promote the conservation of water resources.
Emotion Recognition in Speech Using Multi-classification SVM (2015)

In order to improve the accuracy of emotion recognition in speech effectively, this paper proposes an emotion recognition algorithm based on SVM classification algorithm. Firstly, we use the SVM multi-class classification algorithm to optimize the parameters of penalty factor and kernel function. Then we use the optimized parameters to realize emotion recognition. Finally we obtain the accuracy of each kind of emotion using the Chinese emotional data set, using a variety of multi classification algorithm based on SVM. The emotion recognition can reach the highest rate of 96.00%.
Supplemental Figure 6 from Identification of TRIML2, a Novel p53 Target, that Enhances p53 SUMOylation and Regulates the Transactivation of Proapoptotic Genes (2023)

&lt;p&gt;Figure S6. TRIML2 does not affect SUMO1- or Ubiquitin modification of p53; TRIML2 is the only TRIM protein differentially regulated by codon 72 polymorphism of p53.&lt;/p&gt;
Supplementary Figures 1 - 7 from A Surprising Cross-Species Conservation in the Genomic Landscape of Mouse and Human Oral Cancer Identifies a Transcriptional Signature Predicting Metastatic Disease (2023)

&lt;p&gt;PDF file - 486KB, Figure S1 (A) Average statistics for depth of coverage at 20X, 30X and 40X of all MOC lines. Robust reads were obtained in all samples with a range of 97-98 percent for 20X, 93-95 percent for 30X and 88-92 percent for 40X. (B) Putative SNVs, nsSNVs (Table S1 and S2) and Indels (Table S4) of all MOC lines. Figure S2 Oncoprints from cBio of AKAP9, MED12L, THSD7A, MUC5B, MYH6, LAMA1, LRP2, and 3 RAS (Table S6) genes representing other candidate tumor promoters as compared to the 3 RAS genes. Note that for AKAPs and MED components, we found 9 AKAP family member mutations in 20.4 percent of tumors, with AKAP9 changes in 7 percent (Fig. 1D). Six components of the mediator complex were mutated in 14.7% of cases, with MED12L changes in 5% (Fig. 1E). Figure S3 Number of nsSNV's per node negative (N0) and node positive (N+) tumor in (A) all TCGA OSCC (note that patient TCGA-D6-6516 (N0) with 1463 mutations is not included in this graph) and (B) TCGA OSCC patients who had smoking history reported. There was no significant difference in the average number of mutations between N0 (3272 nsSNVs) and N+ (3097 nsSNVs) patients regardless of smoking status (Tables S8, S9). This analysis showed 17 genes commonly mutated in mouse indolent and human N0 tumors and 55 common genes mutated in mouse aggressive and human N+ tumors (Supplementary Table S10). However, none of these common genes were mutated at high frequency in the human N0 or N+ datasets (Supplementary Table S11 and 12). Finally, comparing N0 and N+ tumors from human TCGA data also showed that specific mutations occur infrequently in both the metastatic and non-metastatic tumors (data not shown). Figure S4 SAM plotsheet of MOC line microarray data with estimated miss rates for delta=4.68 Figure S5 (A) GSEA data of OCAMP-A on UW/FHCRC data with (B) first condensation of enriched genes. (C) GSEA data of OCAMP-A on MDA data with (D) first condensation of enriched genes. (E) GSEA data of OCAMP-A on TCGA data with (F) first condensation of enriched genes. Figure S6 (A) Disease specific survival (DSS) after weighted voting classification of OCAMP-B signature on the MD Anderson dataset shows worse outcome for those with aggressive classification (p=0.028). Figure S7 (A) Disease specific survival (DSS) and (B) overall survival (OS) after weighted voting classification of OCAMP-B signature on the UW/FHCRC dataset shows worse outcome for those with aggressive classification (p&lt;0.01).&lt;/p&gt;
Modeling of Absorption (2012)

Absorption takes place when a compound enters an organism, which occurs as soon as the molecules enter the first cellular bilayer(s) in the tissue(s) to which is it exposed. At that point, the compound is no longer part of the environment (which includes the alimentary canal for oral exposure), but has become part of the organism. If absorption is prevented or limited, then toxicological effects are also prevented or limited. Thus, modeling absorption is the first step in simulating/predicting potential toxicological effects. Simulation software used to model absorption of compounds of various types has advanced considerably over the past 15 years. There can be strong interactions between absorption and pharmacokinetics (PK), requiring state-of-the-art simulation computer programs that combine absorption with either compartmental pharmacokinetics (PK) or physiologically based pharmacokinetics (PBPK). Pharmacodynamic (PD) models for therapeutic and adverse effects are also often linked to the absorption and PK simulations, providing PK/PD or PBPK/PD capabilities in a single package. These programs simulate the interactions among a variety of factors including the physicochemical properties of the molecule of interest, the physiologies of the organisms, and in some cases, environmental factors, to produce estimates of the time course of absorption and disposition of both toxic and nontoxic substances, as well as their pharmacodynamic effects.