gebhart/patrepeval huggingface dataset:
Antibody response elicited by T-dependent and T-independent antigens in gene targeted κ-deficient mice (1994)

Animal models substantially contribute to the understanding of the pathogenesis of various human diseases, including those associated with genetic defects. Our study investigated the characteristics of antibody responses elicited by T-dependent and T-independent antigens in mice rendered kappa-deficient by targeted deletion of the J kappa C kappa gene segments. It is known that in normal murine species the kappa repertoire dominates the antibody repertoire (kappa/lambda ratio = 95:5). Our results indicate that the kappa gene deletion causes the alternative usage of lambda 1 (93%) and lambda 2 (7%) light chains, confirming previous studies demonstrating that in kappa-deficient mice all B cells express Ig lambda receptors. The anti-trinitrophenylbenzene (TNP) response in K-/- mice was compensated for by lambda 1 and lambda 2 bearing Igs. However, isoelectric focusing analysis of anti-TNP antibodies showed a considerably more restricted pattern of lambda anti-TNP antibodies in K-/- as compared with kappa antibodies in normal mice. No major differences were observed in the affinity for the hapten of kappa or lambda 1 or lambda 2 mAbs obtained from 129/Sv and K-/- mice. Furthermore, lambda 1 and lambda 2 chains can reconstitute the expression of an idiotype (460Id) borne on kappa anti-TNP antibodies. The 460Id was detected both in polyclonal and monoclonal anti-TNP antibodies obtained from K-/- mice. Our results clearly showed that the kappa anti-TNP repertoire is compensated by the lambda repertoire even though the latter is clonally restricted in K-/- mice.
Large complexes of .beta.-poly(L-malate) with DNA polymerase .alpha., histones, and other proteins in nuclei of growing plasmodia of Physarum polycephalum (1995)

Of the various cell types in the life cycle of Physarum polycephalum, only the growing plasmodium contains the unusual polyester beta-poly(L-malate). The nuclei exhibit large complexes of this polymer with nuclear proteins, among them DNA polymerase alpha, histones, and HMG-like proteins. The complexes are indicated by the results of size exclusion chromatography and chemical cross-linking with 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide hydrochloride (EDC). After hydroxylaminolysis of the cross-linked polyester, the proteins are liberated and visualized on Western blots. The complexes of 1200-1400 kDa molecular mass exceed by far the size of free beta-poly(L-malate) and proteins. The observed variation in mass appears to be mainly a function of the kind and stoichiometry of the protein constituents and may explain the relatively high molecular mass in S phase and the low molecular mass during G2 phase of the mitotic cycle. The complexes are considerably stable at moderate ionic strength (100 mM KCl). Also, endogenous beta-poly(L-malate) does not exchange with added beta-[14C]poly(L-malate) during the lysis of the nuclei and the sample preparation. The complexes are dissociated at elevated concentrations of KCl, in the presence of spermine hydrochloride, or by treatment with DEAE/cellulose. Available evidence indicates that beta-poly(L-malate) may be involved in the maintenance of the plasmodial state of P. polycephalum.
Toward device-quality GaAs growth by molecular beam epitaxy on offcut Ge/Si1−xGex/Si substrates (1998)

The epitaxial growth of GaAs on Si substrates through the use of a Ge/graded Si1−xGex/Si buffer layer would allow monolithic integration of GaAs-based opto-electronics with Si microelectronics. As an initial step toward this goal, this study examines factors which influence the quality of GaAs growth by molecular beam epitaxy (MBE) on bulk Ge substrates. Key findings include the need for an epitaxial Ge smoothing cap deposited in the MBE chamber, the significant detrimental effect of As overpressure on the resultant GaAs crystalline quality, and the efficiency of a very thin (∼3 nm) migration enhanced epitaxy (MEE) nucleation layer at suppressing both anti-phase domain (APD) formation and interdiffusion across the GaAs/Ge heterointerface. Using this developed optimized growth process, APD-free GaAs on Ge is obtained which has undetectable Ga and Ge cross-diffusion, and As diffusion into the substrate at ⩽1×1018 cm−3. Preliminary results for growths on Ge/Si1−xGex/Si substrates are also presented.
End-to-End Abstractive Summarization for Meetings. (2020)

With the abundance of automatic meeting transcripts, meeting summarization is of great interest to both participants and other parties. Traditional methods of summarizing meetings depend on complex multi-step pipelines that make joint optimization intractable. Meanwhile, there are a handful of deep neural models for text summarization and dialogue systems. However, the semantic structure and styles of meeting transcripts are quite different from articles and conversations. In this paper, we propose a novel end-to-end abstractive summary network that adapts to the meeting scenario. We design a role vector to depict the difference among speakers and a hierarchical structure to accommodate long meeting transcripts. Empirical results show that our model considerably outperforms previous approaches in both automatic metrics and human evaluation. For example, in the ICSI dataset, the ROUGE-1 score increases from 32.00% to 39.51%.
A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA--promoter DNA complex formation. (1994)

TATA-binding protein (TBP)-associated factors (TAFs) in TFIID are required for activator proteins to stimulate transcription, but the mechanism by which TAFs function is poorly understood. To study how TAFs participate in transcriptional activation by the Epstein-Barr virus activator Zta, we used agarose gel electrophoresis and DNase I footprinting to compare transcription complex assembly in reactions with either TFIID or TBP in the presence and absence of wild-type Zta or a deletion of Zta lacking its activation domain. A stable complex of promoter DNA with Zta, TFIIA, and TFIID rapidly formed on a template with Zta-binding sites. Zta stimulation of stable complex formation required TAFs as well as the Zta activation domain and TFIIA. The Zta activation domain also induced a TAF-dependent DNA-protein interaction near and downstream of the transcription star site. Stable complexes formed within 1 min supported activated transcription when RNA polymerase II and the remaining general transcription factors were subsequently added. This rapid assembly of a stable Zta-TFIIA-TFIID-promoter complex is probably a significant component of the mechanism by which TAFs and the Zta activation domain cooperate to stimulate transcription.
Three-dimensional structure of Gln25-ribonuclease T1 at 1.84-.ANG. resolution: structural variations at the base recognition and catalytic sites (1992)

The structure of the Gln25 variant of ribonuclease T1 (RNase T1) crystallized at pH 7 and at high ionic strength has been solved by molecular replacement using the coordinates of the Lys25-RNase T1/2'-guanylic acid (2'GMP) complex at pH 5 [Arni et al. (1988) J. Biol. Chem. 263, 15358-15368] and refined by energy minimization and stereochemically restrained least-squares minimization to a crystallographic R-factor of 14.4% at 1.84-A resolution. The asymmetric unit contains three molecules, and the final model consists of 2302 protein atoms, 3 sulfates (at the catalytic sites), and 179 solvent water molecules. The estimated root mean square (rms) error in the coordinates is 0.15 A, and the rms deviation from ideality is 0.018 A for bond lengths and 1.8 degrees for bond angles. Significant differences are observed between the three molecules in the asymmetric unit at the base recognition and catalytic sites.
Fast stereo matching using reliability-based dynamic programming and consistency constraints (2003)

A method for solving binocular and multiview stereo matching problems is presented here. A weak consistency constraint is proposed, which expresses the visibility constraint in the image space. It can be proved that the weak consistency constraint holds for scenes that can be represented by a set of 3D points. As well, also proposed is a new reliability measure for dynamic programming techniques, which evaluates the reliability of a given match. A novel reliability-based dynamic programming algorithm is derived accordingly, which can selectively assign disparity values to pixels when the reliabilities of the corresponding matches exceed a given threshold. Consistency constraints and the new reliability-based dynamic programming algorithm can be combined in an iterative approach. The experimental results show that the iterative approach can produce dense (60-90%) and reliable (total error rate of 0.1-1.1%) matching for binocular stereo datasets. It can also generate promising disparity maps for trinocular and multiview stereo datasets.
Distilling the Knowledge in a Neural Network (2015)

A very simple way to improve the performance of almost any machine learning algorithm is to train many different models on the same data and then to average their predictions. Unfortunately, making predictions using a whole ensemble of models is cumbersome and may be too computationally expensive to allow deployment to a large number of users, especially if the individual models are large neural nets. Caruana and his collaborators have shown that it is possible to compress the knowledge in an ensemble into a single model which is much easier to deploy and we develop this approach further using a different compression technique. We achieve some surprising results on MNIST and we show that we can significantly improve the acoustic model of a heavily used commercial system by distilling the knowledge in an ensemble of models into a single model. We also introduce a new type of ensemble composed of one or more full models and many specialist models which learn to distinguish fine-grained classes that the full models confuse. Unlike a mixture of experts, these specialist models can be trained rapidly and in parallel.
Flexible and planar graphene conductive additives for lithium-ion batteries (2010)

Graphene is introduced into a lithium-ion battery (LIB) as a type of novel but powerful planar conductive additive and the flexible graphene-based conducting network is characterized by a novel “plane-to-point” conducting mode with exceptional electron transport properties and unique geometrical nature (a soft and ultrathin planar structure). With a much lower fraction of graphene additives than those of commercial carbon based additives, the graphene-introduced LiFePO4 cathode shows better charge/discharge performance than commercial cases. Graphene also shows a better performance compared to carbon nanotubes, another type of novel conductive additive with similar fractions. These results present us an indication that graphene will possibly find early application as a flexible and planar conductive additive in high performance LIBs, as our further efforts have shown that a graphene-introduced battery is of better performance as compared to real commercial batteries with conventional additives.
On-chip electroporation, membrane repair dynamics and transient in-cell recordings by arrays of gold mushroom-shaped microelectrodes (2012)

This study demonstrates the use of on-chip gold mushroom-shaped microelectrodes (gMμEs) to generate localized electropores in the plasma membrane of adhering cultured neurons and to electrophysiologically monitor the ensuing membrane repair dynamics. Delivery of an alternating voltage pulse (0.5-1 V, 100 Hz, 300 ms) through an extracellularly positioned micrometer-sized gMμE electroporates the patch of plasma membrane facing the microelectrode. The repair dynamics of the electropores were analyzed by continuous monitoring of the neuron transmembrane potential, input resistance (R(in)) and action potential (AP) amplitude with an intracellular microelectrode and a number of neighbouring extracellular gMμEs. Electroporation by a gMμE is associated with local elevation of the free intracellular calcium concentration ([Ca(2+)](i)) around the gMμE. The membrane repair kinetics proceeds as an exponential process interrupted by abrupt recovery steps. These abrupt events are consistent with the "membrane patch model" of membrane repair in which patches of intracellular membrane fuse with the plasma membrane at the site of injury. Membrane electroporation by a single gMμE generates a neuron-gMμE configuration that permits recordings of attenuated intracellular action potentials. We conclude that the use of on-chip cultured neurons via a gMμE configuration provides a unique neuroelectronic interface that enables the selection of individual cells for electroporation, generates a confined electroporated membrane patch, monitors membrane repair dynamics and records attenuated intracellular action potentials.
Welfare Regimes in the Wake of State Socialism (2013)

Abstract This chapter examines the evolution of welfare regimes in contemporary China and Vietnam. Specifically, it examines how the degeneration of state-socialist regimes and the evolution of new political economies in their wake have shaped institutional arrangements governing the provision and payment for education and health services and their stratification effects. It is argued that welfare regimes and stratification in contemporary China and Vietnam may not be understood without appreciating their properties under state-socialism and how these countries’ specific paths of extrication from state-socialism have affected welfare regimes degeneration and subsequent development under a new market-Leninist form of political economy. The subordination of markets to Leninist political institutions (organizational, ideological, and cultural) suggests that Viet nam and China represent a distinctive form of political economy. Alongside areas of convergence, divergence in the two countries’ welfare regimes reflects not only differences in wealth but in the character of distributive politics.
Rapidly in Situ Forming Biodegradable Robust Hydrogels by Combining Stereocomplexation and Photopolymerization (2007)

Our previous studies have shown that stereocomplexed hydrogels can be rapidly formed in vitro as well as in vivo upon mixing aqueous solutions of eight-arm poly(ethylene glycol)-poly(l-lactide) (PEG-PLLA) and poly(ethylene glycol)-poly(d-lactide) (PEG-PDLA) star block copolymers. In this study, stereocomplexation and photopolymerization are combined to yield rapidly in situ forming robust hydrogels. Two types of methacrylate-functionalized PEG-PLLA and PEG-PDLA star block copolymers, PEG-PLLA-MA and PEG-PDLA-MA, which have methacrylate groups at the PLA chain ends and PEG-MA/PLLA and PEG-MA/PDLA, which have methacrylate groups at the PEG chain ends, were designed and prepared. Results showed that stereocomplexed hydrogels could be rapidly formed (within 1-2 min) in a polymer concentration range of 12.5-17.5% (w/v), in which the methacrylate group hardly interfered with the stereocomplexation. When subsequently photopolymerized, these hydrogels showed largely increased storage moduli as compared to the corresponding hydrogels that were cross-linked by stereocomplexation or photopolymerization only. Interestingly, the storage modulus of stereocomplexed-photopolymerized PEG-PLA-MA hydrogels increased linearly with increasing stereocomplexation equilibration time prior to photopolymerization (from ca. 6 to 32 kPa), indicating that stereocomplexation aids in photopolymerization. Importantly, photopolymerization of stereocomplexed hydrogels could take place at very low initiator concentrations (0.003 wt %). Swelling/degradation studies showed that combining stereocomplexation and photopolymerization yielded hydrogels with prolonged degradation times as compared to corresponding hydrogels cross-linked by photopolymerization only (3 vs 1.5 weeks). Stereocomplexed-photopolymerized PEG-MA/PLA hydrogels degraded much slower than corresponding PEG-PLA-MA hydrogels, with degradation times ranging from 7 to more than 16 weeks. Therefore, combining stereocomplexation and photopolymerization is a novel approach to obtain rapidly in situ forming robust hydrogels.
Produtos Naturais em Fase Avançada de Testes Clínicos no Tratamento contra o Câncer (2007)

Atualmente, os produtos naturais representam uma inestimável fonte de substâncias químicas tendo um importante papel no tratamento do câncer. Devido à importância da natureza como fonte de novos candidatos a fármacos no tratamento contra o câncer, o objetivo dessa revisão é enfocar os produtos naturais, que estão em fase avançada de testes clínicos e dentre em breve poderão ser introduzidos no mercado no combate ao câncer.
Rubber-Degrading Enzyme from a Bacterial Culture (1990)

Rubber-degrading activity was found in the extracellular culture medium of Xanthomonas sp. strain 35Y which was grown on natural rubber latex. Natural rubber in the latex state was degraded by the crude enzyme, and two fractions were separately observed by gel permeation chromatography of the reaction products. One fraction was of higher molecular weight (HMW) with a very wide MW distribution from 10 to 10, and the other fraction was of lower molecular weight (LMW) with a MW of a few hundred. H-nuclear magnetic resonance spectra of the partially purified fractions were those expected of cis-1,4-polyisoprene mixtures with the structure OHC-CH(2)-(-CH(2)-C(-CH(3)) = CH-CH(2)-)(n)-CH(2)-C(=O)-CH(3), with average values of n of about 113 and 2 for HMW and LMW fractions, respectively. The LMW fraction consisted mostly of one component in gas-liquid chromatography as well as in gel permeation chromatography, and the main component was identified as 12-oxo-4,8-dimethyl trideca-4,8-diene-1-al (acetonyl diprenyl acetoaldehyde, A(l)P(2)A(t)) by C-nuclear magnetic resonance and gas chromatography-mass spectra. Not only the latices of natural and synthetic isoprene rubber, but also some kinds of low-MW polyisoprene compounds of cis-1,4 type, were degraded by the crude enzyme. The rubber-degrading reaction was found to be at least partly oxygenase catalyzed from the incorporation of O into A(l)P(2)A(t) under an O(2) atmosphere.
Reactions at high pressures. [3+2] Dipolar cycloaddition of nitrones with vinyl ethers (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions at high pressures. [3+2] Dipolar cycloaddition of nitrones with vinyl ethersCarl Michael Dicken and Philip DeShongCite this: J. Org. Chem. 1982, 47, 11, 2047–2051Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://pubs.acs.org/doi/10.1021/jo00132a014https://doi.org/10.1021/jo00132a014research-articleACS PublicationsRequest reuse permissionsArticle Views841Altmetric-Citations56LEARN 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
Multiplexed Detection of Protein−Peptide Interaction and Inhibition Using Capillary Electrophoresis (2006)

High-speed capillary electrophoresis (CE) was employed to detect binding and inhibition of SH2 domain proteins using fluorescently labeled phosphopeptides as affinity probes. Single SH2 protein-phosphopeptide complexes were detected and confirmed by competition and fluorescence anisotropy. The assay was then extended to a multiplexed system involving separation of three SH2 domain proteins: Src, SH2-Bbeta, and Fyn. The selectivity of the separation was improved by altering the charge of the peptide binding partners used, thus demonstrating a convenient way to control resolution for the multiplexed assay. The separation was completed within 6 s, allowing rapidly dissociating complexes to be detected. Two low molecular weight inhibitors were tested for inhibition selectivity and efficacy. One inhibitor interrupted binding interaction of all three proteins, while the other selectively inhibited Src only leaving SH2-Bbeta and Fyn complex barely affected. IC(50) of both selective and nonselective inhibitors were determined and compared for different proteins. The IC(50) of the nonselective inhibitor was 49 +/- 9, 323 +/- 42, and 228 +/- 19 microM (n = 3) for Src, SH2-Bbeta, and Fyn, respectively, indicating different efficacy of the nonselective inhibitor for different SH2 domain protein. It is concluded that high-speed CE has the potential for multiplexed screening of drugs that disrupt protein-protein interactions.
Quantitative NMR measurements of hippocampal atrophy in Alzheimer's disease (1988)

Nuclear magnetic resonance (NMR) imaging was employed to study 10 patients with Alzheimer's disease (AD) and seven healthy elderly control subjects. Coronal sections were used to make volumetric measurements of the hippocampus, ventricles, subarachnoid space, and brain parenchyma. The hippocampal volume (normalized relative to the size of the lenticular nucleus) was reduced by 40% in the AD group compared to the controls, with no overlap between the two groups. Overall measures of brain atrophy and ventricular and sulcal enlargement also showed significantly different group means, although with overlap between the two groups. Hippocampal atrophy did not correlate with either overall brain atrophy or dementia severity, although the degree of brain atrophy was correlated with dementia severity. These results show that NMR is capable of providing in vivo quantification of diminished hippocampal size in AD which is not correlated with overall brain atrophy and which may differentiate AD from normal aging.
An overview of gradient descent optimization algorithms (2016)

Gradient descent optimization algorithms, while increasingly popular, are often used as black-box optimizers, as practical explanations of their strengths and weaknesses are hard to come by. This article aims to provide the reader with intuitions with regard to the behaviour of different algorithms that will allow her to put them to use. In the course of this overview, we look at different variants of gradient descent, summarize challenges, introduce the most common optimization algorithms, review architectures in a parallel and distributed setting, and investigate additional strategies for optimizing gradient descent.