gebhart/patrepeval huggingface dataset:
Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data (2010)

Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in modern-day genomic experiments, automated computational methods for protein function prediction are urgently needed. Established methods use sequence or structure similarity to infer functions but those types of data do not suffice to determine the biological context in which proteins act. Current high-throughput biological experiments produce large amounts of data on the interactions between proteins. Such data can be used to infer interaction networks and to predict the biological process that the protein is involved in. Here, we develop a probabilistic approach for protein function prediction using network data, such as protein-protein interaction measurements. We take a Bayesian approach to an existing Markov Random Field method by performing simultaneous estimation of the model parameters and prediction of protein functions. We use an adaptive Markov Chain Monte Carlo algorithm that leads to more accurate parameter estimates and consequently to improved prediction performance compared to the standard Markov Random Fields method. We tested our method using a high quality S. cereviciae validation network with 1622 proteins against 90 Gene Ontology terms of different levels of abstraction. Compared to three other protein function prediction methods, our approach shows very good prediction performance. Our method can be directly applied to protein-protein interaction or coexpression networks, but also can be extended to use multiple data sources. We apply our method to physical protein interaction data from S. cerevisiae and provide novel predictions, using 340 Gene Ontology terms, for 1170 unannotated proteins and we evaluate the predictions using the available literature.
Enhanced efficacy of therapy with antisense BCL-2 oligonucleotides plus anti-CD20 monoclonal antibody in <i>scid</i> mouse/human lymphoma xenografts (2004)

Monoclonal anti-CD20 antibody (rituximab) is active, but not curative, therapy for B-cell non-Hodgkin's lymphoma. BCL-2 is an antiapoptotic protein whose expression is dysregulated in most indolent B-cell malignancies. Antisense oligonucleotides (AS-ODNs) that down-regulate BCL-2 expression induce apoptosis and chemosensitize B-cell lymphoma cells. We hypothesized that BCL-2 down-regulation by AS-ODNs would sensitize cells to rituximab and improve therapeutic results. There is enhanced apoptosis and reduction in cell numbers when DoHH2 cells are treated in vitro with rituximab plus BCL-2 AS-ODNs, compared with either agent alone. There is little in vitro effect on WSU-FSCCL cells by rituximab, AS-ODNs that down-regulate BCL-2 by targeting the immunoglobulin portions of the BCL-2-immunoglobulin fusion molecule, or a combination of the two. The combination is more effective than either agent alone in clearing DoHH2 cells from ascites in scid mice. Combination therapy with AS-BCL-2-ODNs and rituximab significantly prolongs survival in both the DoHH2 and WSU-FSCCL models. With higher and repeated doses, this combination could be curative. We conclude that the combination of rituximab and antisense-mediated down-regulation of BCL-2 has enhanced activity against human lymphoma, prolongs survival, and could cure mice bearing human lymphoma. This merits investigation in clinical trials.
Regulation of the VLA integrin-ligand interactions through the beta 1 subunit. (1992)

Integrins from the very late activation antigen (VLA) subfamily are involved in cellular attachment to extracellular matrix (ECM) proteins and in intercellular adhesions. It is known that the interaction of integrin proteins with their ligands can be regulated during cellular activation. We have investigated the regulation of different VLA-mediated adhesive interactions through the common beta 1 chain. We have found that certain anti-beta 1 antibodies strongly enhance binding of myelomonocytic U-937 cells to fibronectin. This beta 1-mediated regulatory effect involved both VLA-4 and VLA-5 fibronectin receptors. Moreover, anti-beta 1 mAb also induced VLA-4-mediated binding to a recombinant soluble form of its endothelial cell ligand VCAM-1. Non-activated peripheral blood T lymphocytes, unable to mediate VLA-4 interactions with fibronectin or VCAM-1, acquired the ability to bind these ligands in the presence of anti-beta 1 mAb. The anti-beta 1-mediated changes in the affinities of beta 1 integrin for their ligands were comparable to those triggered by different lymphocyte activation agents such as anti-CD3 mAb or phorbol ester. Adhesion of melanoma cells to other ECM proteins such as laminin or collagen as well as that of alpha 2-transfected K-562 cells to collagen, was also strongly enhanced by anti-beta 1 mAb. These beta 1-mediated regulatory effects on different VLA-ligand interactions do not involve changes in cell surface membrane expression of different VLA heterodimers. The anti-beta 1-mediated functional effects required an active metabolism, cytoskeleton integrity and the existence of physiological levels of intracellular calcium as well as a functional Na+/H+ antiporter. Beta 1 antibodies not only increased cell attachment but also promoted spreading and cytoplasmic extension of endothelial cells on plates coated with either fibronectin, collagen, or laminin as well as induced the rapid appearance of microspikes in U-937 cells on fibronectin. Moreover, both beta 1 integrin and the cytoskeletal protein talin colocalized in the anti-beta 1 induced microspikes. These results emphasize the central role of the common beta 1 chain in regulating different adhesive functions mediated by VLA integrins as well as cellular morphology.
Plasma Lipoproteins Support Prothrombinase and Other Procoagulant Enzymatic Complexes (1998)

The prothrombinase complex (factor [F]Xa, FVa, calcium ions, and lipid membrane) converts prothrombin to thrombin (FIIa). To determine whether plasma lipoproteins could provide a physiologically relevant surface, we determined the rates of FIIa production by using purified human coagulation factors, and isolated fasting plasma lipoproteins from healthy donors. In the presence of 5 nmol/L FVa, 5 nmol/L FXa, and 1.4 micromol/L prothrombin, physiological levels of very low density lipoprotein (VLDL) (0.45 to 0.9 mmol/L triglyceride, or 100 to 200 micromol/L phospholipid) yielded rates of 2 to 8 nmol Flla x L(-1) x s(-1) in a donor-dependent manner. Low density lipoprotein (LDL) and high density lipoprotein (HDL) also supported prothrombinase but at much lower rates (< or =1.0 nmol FIIa x L(-1) x s[-1]). For comparison, VLDL at 2 mmol/L triglyceride yielded approximately 50% the activity of 2X10(8) thrombin-activated platelets per milliliter. Although the FIIa production rate was slower on VLDL than on synthetic phosphatidylcholine/phosphatidylsenne vesicles (approximately 50 nmol FIIa x L(-1) x s[-1]), the prothrombin Km values were similar, 0.8 and 0.5 micromol/L, respectively. Extracted VLDL lipids supported rates approaching those of phosphatidylcholine/phosphatidylserine vesicles, indicating the importance of the intact VLDL conformation. However, the presence of VLDL-associated, factor-specific inhibitors was ruled out by titration experiments, suggesting a key role for lipid organization. VLDL also supported FIIa generation in an assay system comprising 0.1 nmol/L FVIIa; 0.55 nmol/L tissue factor; physiological levels of FV, FVIII, FIX, and FX; and prothrombin (3 nmol/L FIIa x L(-1) x s[-1]). These results indicate that isolated human VLDL can support all the components of the extrinsic coagulation pathway, yielding physiologically relevant rates of thrombin generation in a donor-dependent manner. This support is dependent on the intact lipoprotein structure and does not appear to be regulated by specific VLDL-associated inhibitors. Further studies are needed to determine the extent of this activity in vivo.
Basic Study for Next-generation Gene Therapy Products (2003)

Successful gene therapy depends largely on vectors that can efficiently deliver the therapeutic genes into the target tissues and cells. Recombinant adenovirus (Ad) vectors continue to be the preferred vectors for gene therapy because they can easily be grown to high titers and can efficiently transfer genes into both dividing and nondividing cells. However, there are some limitations such as the time-consuming and labor-intensive procedures for vector construction, coxsackievirus-adenovirus receptor (CAR)-dependent gene transfer, immunologic side effects, lack of tissue specificity, lack of regulation of gene expression, etc. In this paper, I review our approach to the development of advanced recombinant Ad vectors. The next generation of Ad vectors have not only become promising vectors for gene therapy but also important tools for gene transfer into mammalian cells.
The <i>PAG</i> gene product, a stress-induced protein with antioxidant properties, is an Abl SH3-binding protein and a physiological inhibitor of c-Abl tyrosine kinase activity (1997)

Biochemical and genetic evidence suggests that the tyrosine kinase activity of c-Abl is tightly regulated in vivo by a cellular factor binding to the Src homology 3 (SH3) domain of Abl. We used the yeast two-hybrid system to identify a gene, PAG, whose protein product (Pag) interacts specifically with the Abl SH3 domain. Pag, also known as macrophage 23-kD stress protein (MSP23), is a member of a novel family of proteins with antioxidant activity implicated in the cellular response to oxidative stress and in control of cell proliferation and differentiation. In a co-expression assay, Pag associates with c-Abl in vivo and inhibits tyrosine phosphorylation induced by overexpression of c-Abl. Inhibition requires the Abl SH3 and kinase domains and is not observed with other Abl SH3-binding proteins. Expression of Pag also inhibits the in vitro kinase activity of c-Abl, but not SH3-mutated Abl or v-Abl. When transfected in NIH-3T3 cells, Pag is localized to nucleus and cytoplasm and rescues the cytostatic effect induced by c-Abl. These observations suggest Pag is a physiological inhibitor of c-Abl in vivo.
Beam Hardening Correction for Middle-Energy Industrial Computerized Tomography (2006)

In this paper, a new beam hardening correction (BHC) method for middle-energy industrial computerized tomography (CT) is presented. Our method is derived from linearization and is straightforward without iteration involved. The linearization is commonly used as a preprocessing method in BHC. Conventionally, only one-material objects can be conveniently corrected by linearization. In industrial CT, two-material objects, especially cylinders with high-Z material outside and low-Z material inside are frequently encountered. Our approach focuses on this kind of objects. The new method works well as long as the two-material object meets the conditions that the thickness of the outer material (usually wall) is thick enough and the second-order item of the Taylor expansion of the linearization is relatively small. We pointed out and proved that there is an approximately constant scaling factor difference between our linearization step and an ideal correction based on prior knowledge of objects. The scaling factor magnifies the attenuation coefficient of the inner material after reconstruction. Therefore, a weighting function is introduced into our algorithm as a restoration. To sum up, there are three steps in our method: 1) correct raw projections by the mapping function of the outer material; 2) reconstruct the cross-section image from the modified projections; 3) scale the image by a weighting function. With this method, the beam hardening artifacts are greatly reduced and the overall attenuation coefficients are accurately obtained. We also presented a compensation step to remove the countercupping artifacts in case that the conditions are not fully met. Our method is well verified in both numerical simulations and practical experiments on a 450-KeV CT system.
D-ary Bounded-Length Huffman Coding (2007)

Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem. Length-limited Huffman coding, useful for many practical applications, is one such variant, in which codes are restricted to the set of codes in which none of the n codewords is longer than a given length, l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> . Binary length-limited coding can be done in O(nl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) time and O(n) space via the widely used Package-Merge algorithm. In this paper the Package-Merge approach is generalized without increasing complexity in order to introduce a minimum codeword length, l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> , to allow for objective functions other than the minimization of expected codeword length, and to be applicable to both binary and nonbinary codes; nonbinary codes were previously addressed using a slower dynamic programming approach. These extensions have various applications - including faster decompression - and can be used to solve the problem of finding an optimal code with bounded fringe, that is, finding the best code among codes with a maximum difference between the longest and shortest codewords. The previously proposed method for solving this problem was nonpolynomial time, whereas solving this using the novel algorithm requires only O(n(l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> - l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) time and O(n) space.
Equilibrium of Iron-Carbon Alloys with Mixtures of CO-CO<sub>2</sub> and CH<sub>4</sub>-H<sub>2</sub> (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEquilibrium of Iron-Carbon Alloys with Mixtures of CO-CO2 and CH4-H2Rodney P. SmithCite this: J. Am. Chem. Soc. 1946, 68, 7, 1163–1175Publication Date (Print):July 1, 1946Publication History Published online1 May 2002Published inissue 1 July 1946https://pubs.acs.org/doi/10.1021/ja01211a010https://doi.org/10.1021/ja01211a010research-articleACS PublicationsRequest reuse permissionsArticle Views446Altmetric-Citations155LEARN 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
Molecular Wires Comprising π-Extended Ethynyl- and Butadiynyl-2,5-Diphenyl-1,3,4-Oxadiazole Derivatives:  Synthesis, Redox, Structural, and Optoelectronic Properties (2006)

2,5-Diphenyl-1,3,4-oxadiazole (OXD) derivatives with terminal ethynyl- (4a,b) and butadiynyl- (8a,b) substituents have been synthesized in high yields. 2-Methyl-3,5-hexadiyn-2-ol has not been exploited previously in the synthesis of terminal butadiynes. Crystals of 8a and 8b are remarkably stable to long-term storage under ambient conditions. The X-ray crystal structure of 8a reveals that the butadiyne moieties are spatially isolated by the aromatic moieties, which explains the high stability. Two series of derived pi-conjugated molecules, Donor-(C[triple bond]C)(n)-OXD (n = 1, 2) and OXD-(C[triple bond]C)(n)-Donor-(C[triple bond]C)(n)-OXD (n = 1) [Donor = tetrathiafulvalene (TTF), bithiophene, 9-(4,5-dimethyl-1,3-dithiol-2-ylidene)fluorene, and triphenylamine], have been synthesized using Sonogashira reactions and characterized by X-ray crystallography, cyclic voltammetry, and optical absorption/emission spectroscopy. The electron-withdrawing effect of the OXD units is manifested by a positive shift of the donor oxidation waves in these systems: the butadiynylene spacer (n = 2) further shifts the first oxidation waves by 40-80 mV compared to analogues n = 1. The absorption spectra of TTF-OXD hybrids 10d and 11 are blue-shifted by 80 nm compared to the bithienyl-bridged derivative 10f and are similar to the butadiynyl-OXD building-block 8a, demonstrating that conjugation is disrupted by a neutral TTF unit. Solutions of the TTF-OXD and 9-(4,5-dimethyl-1,3-dithiol-2-ylidene)fluorene-OXD hybrids, 10d, 10g, 11, and 13, are only very weakly fluorescent due to quenching from the electron-donor moieties. In contrast, the triphenylamine-OXD hybrids 12a, 12b, 14a, and 14b are fluorescent; the PLQYs of the butadiynylene derivatives 14a and 14b are lower than those of the ethynylene-bridged analogues 12a and 12b.
Infusing NLU into Automatic Question Generation (2016)

We present a fresh approach to automatic question generation that significantly increases the percentage of acceptable questions compared to prior state-of-the-art systems. In our evaluation of the top 20 questions, our system generated 71% more acceptable questions by informing the generation process with Natural Language Understanding techniques. The system also introduces our DeconStructure algorithm which creates an intuitive and practical structure for easily accessing sentence functional constituents in NLP applications.
Stability of a composite discharge sustained by static and rf electric fields. II. Mechanism for the stabilizing effect of an rf field on the positive column of a dc discharge (1982)

The stabilizing effect of an rf field on the positive column of a dc discharge has been studied. A theoretical analysis shows that the improved stability of this composite discharge results from the formation of zones near both of the rf electrodes in which the conductivity is substantially higher than that in the plasma column. The theoretical results are illustrated by experimental data.
HgTe/CdTe heterojunctions: A lattice-matched Schottky barrier structure (1982)

HgTe-CdTe lattice-matched heterojunctions were formed by the epitaxial growth of HgTe on CdTe substrates using a low-temperature metal organic chemical vapor deposition technique. These heterojunctions combine features of the Schottky barrier structure, due to the high carrier concentrations found in the semimetallic HgTe, with the structural perfection present in a lattice-matched heterojunction. The measured Schottky barrier height varied from 0.65 to 0.92 eV depending on the details of the heterojunction growth procedure used. This dependence may be due to the formation of an inversion layer in the CdTe at the interface. Presence of such an inversion layer suggests that the valence band discontinuity between HgTe and CdTe is small, in agreement with previous theoretical estimates.
Time Domain Simulation of Nonlinear Response of a Coupled TLP System In Random Seas (1994)

This paper presents a result of an analysis of the nonlinear interaction and response of the coupled ISSC-TLP System to the random seas in the time domain. The environmental load also includes the effect of the concurrent steady winds and currents. The first- and second-order wave-exciting forces are calculated using a robust higher-order boundary element method (HOBEM), while the nonlinear tendon dynamic analysis is performed using the three-dimensional hybrid element method with the upgated Lagrangian formulation. The Morison equation is employed for the wave and current load on slender structures. The analysis is focused on the nonlinear responses due to the nonlinear environmental load and nonlinear interaction between the platform and tendons that includes the offset, setdown, large coupled surge-heave motion in the low frequency and resonant heave/pitch responses with the springing loads in the high frequency.
Design of Class E power amplifier with nonlinear parasitic output capacitance (1999)

The Class E amplifier exploits the output shunt capacitor for charge-storing during the operation cycle. The amplifier works even with a nonlinear output capacitor, but the required component values are different from the values resulting with the linear capacitor. In this paper the equations and component values are solved for the first time for a Class E amplifier having a nonlinear output capacitor with hyperabrupt junction voltage-capacitance characteristics. A hyperabrupt junction capacitor is present especially at the drain-to-bulk junction of practical MOS devices. The results of the analysis are presented in plots providing initial component values for MOS Class E power amplifier design. The procedure is validated with a design example of a single-stage 900 MHz MOS power amplifier operating from a 2-V supply voltage.
Evaluation of Human Papillomavirus Antibodies and Risk of Subsequent Head and Neck Cancer (2013)

HPV16 E6 seropositivity was present more than 10 years before diagnosis of oropharyngeal cancers.
Investigating the distance limit of a metal nanoparticle based spectroscopic ruler (2011)

Conventional Förster resonance energy transfer (FRET) processes involving a pair of fluorophore and organic quencher are restricted to an upper distance limit of ~10 nm. The application of a metal nanoparticle as a quencher can overcome the distance barrier of the traditional FRET technique. However, no standard distance dependence of this resonance energy transfer (RET) process has been firmly established. We have investigated the nonradiative energy transfer process between an organic donor (fluorescein) and gold nanoparticle quencher connected by double stranded (ds) DNA. The quenching efficiency of the gold nanoparticle as a function of distance between the donor and acceptor was determined by time-resolved lifetime analyses of the donor. Our results showed a 1/d(4) distance dependence for the RET process for longer distances (>10 nm) and 1/d(6) distance dependence for shorter distances (<10 nm). Our results clearly indicate the applicability of metal nanoparticle based quenchers for studying systems that exceed the 10 nm FRET barrier.